diff --git a/.DS_Store b/.DS_Store
index 529f8f6..f625838 100644
Binary files a/.DS_Store and b/.DS_Store differ
diff --git a/.vscode/launch.json b/.vscode/launch.json
new file mode 100644
index 0000000..f6b35a0
--- /dev/null
+++ b/.vscode/launch.json
@@ -0,0 +1,15 @@
+{
+ // Use IntelliSense to learn about possible attributes.
+ // Hover to view descriptions of existing attributes.
+ // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+ "version": "0.2.0",
+ "configurations": [
+ {
+ "type": "chrome",
+ "request": "launch",
+ "name": "Launch Chrome against localhost",
+ "url": "http://localhost:3000",
+ "webRoot": "${workspaceFolder}"
+ }
+ ]
+}
\ No newline at end of file
diff --git a/package-lock.json b/package-lock.json
index 8009ce5..4f06c3b 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -11,49 +11,67 @@
"@material-ui/core": "^4.9.12",
"@material-ui/icons": "^4.9.1",
"@material-ui/lab": "^4.0.0-alpha.60",
- "@popperjs/core": "^2.10.2",
"@testing-library/jest-dom": "^4.2.4",
"@testing-library/react": "^9.5.0",
"@testing-library/user-event": "^7.2.1",
"array-move": "^2.2.1",
"bootstrap": "^4.5.0",
+ "browserify": "^17.0.0",
"d3": "^3.5.17",
"d3-boxplot": "^0.7.5",
"d3v5": "npm:d3@^5.16.0",
"dom-to-image": "^2.6.0",
- "evergreen-ui": "^4.28.1",
+ "evergreen-ui": "^2.0.1",
"html2canvas": "^1.3.2",
"jquery": "^3.5.1",
"jspdf": "^2.3.1",
"lodash": "^4.17.21",
- "neat-csv": "^5.2.0",
"phylotree": "github:mwittep/phylotree.js",
"popper.js": "^1.16.1",
- "puppeteer": "^3.3.0",
"react": "^16.13.1",
"react-bootstrap": "^1.0.1",
"react-color": "^2.18.1",
"react-dom": "^16.13.1",
"react-draggable": "^4.4.3",
"react-loading-overlay": "^1.0.1",
- "react-scripts": "3.4.1",
+ "react-scripts": "^4.*.*",
"react-select": "^2.4.4",
"react-sortable-hoc": "^1.11.0",
"react-virtualized": "^9.21.2",
"styled-components": "^5.1.0"
},
"devDependencies": {
- "body-parser": "^1.19.0",
- "express": "^4.17.1",
- "express-pino-logger": "^4.0.0",
"formidable": "^1.2.2",
"nodemon": "^2.0.3",
"npm-run-all": "^4.1.5",
- "pino-colada": "^1.6.1",
"prop-types": "^15.7.2",
"yargs-parser": "^18.1.3"
}
},
+ "node_modules/@ampproject/remapping": {
+ "version": "2.2.0",
+ "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.0.tgz",
+ "integrity": "sha512-qRmjj8nj9qmLTQXXmaR1cck3UXSRMPrbsLJAasZpF+t3riI71BXed5ebIOYwQntykeZuhjsdweEc9BxH5Jc26w==",
+ "dependencies": {
+ "@jridgewell/gen-mapping": "^0.1.0",
+ "@jridgewell/trace-mapping": "^0.3.9"
+ },
+ "engines": {
+ "node": ">=6.0.0"
+ }
+ },
+ "node_modules/@ampproject/remapping/node_modules/@jridgewell/gen-mapping": {
+ "version": "0.1.1",
+ "resolved": "https://registry.npmjs.org/@jridgewell/gen-mapping/-/gen-mapping-0.1.1.tgz",
+ "integrity": "sha512-sQXCasFk+U8lWYEe66WxRDOE9PjVz4vSM51fTu3Hw+ClTpUSQb718772vH3pyS5pShp6lvQM7SxgIDXXXmOX7w==",
+ "dependencies": {
+ "@jridgewell/set-array": "^1.0.0",
+ "@jridgewell/sourcemap-codec": "^1.4.10"
+ },
+ "engines": {
+ "node": ">=6.0.0"
+ }
+ },
"node_modules/@babel/code-frame": {
"version": "7.15.8",
"resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.15.8.tgz",
@@ -66,33 +84,33 @@
}
},
"node_modules/@babel/compat-data": {
- "version": "7.15.0",
- "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.15.0.tgz",
- "integrity": "sha512-0NqAC1IJE0S0+lL1SWFMxMkz1pKCNCjI4tr2Zx4LJSXxCLAdr6KyArnY+sno5m3yH9g737ygOyPABDsnXkpxiA==",
+ "version": "7.19.4",
+ "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.19.4.tgz",
+ "integrity": "sha512-CHIGpJcUQ5lU9KrPHTjBMhVwQG6CQjxfg36fGXl3qk/Gik1WwWachaXFuo0uCWJT/mStOKtcbFJCaVLihC1CMw==",
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/core": {
- "version": "7.15.8",
- "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.15.8.tgz",
- "integrity": "sha512-3UG9dsxvYBMYwRv+gS41WKHno4K60/9GPy1CJaH6xy3Elq8CTtvtjT5R5jmNhXfCYLX2mTw+7/aq5ak/gOE0og==",
- "dependencies": {
- "@babel/code-frame": "^7.15.8",
- "@babel/generator": "^7.15.8",
- "@babel/helper-compilation-targets": "^7.15.4",
- "@babel/helper-module-transforms": "^7.15.8",
- "@babel/helpers": "^7.15.4",
- "@babel/parser": "^7.15.8",
- "@babel/template": "^7.15.4",
- "@babel/traverse": "^7.15.4",
- "@babel/types": "^7.15.6",
+ "version": "7.19.3",
+ "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.19.3.tgz",
+ "integrity": "sha512-WneDJxdsjEvyKtXKsaBGbDeiyOjR5vYq4HcShxnIbG0qixpoHjI3MqeZM9NDvsojNCEBItQE4juOo/bU6e72gQ==",
+ "dependencies": {
+ "@ampproject/remapping": "^2.1.0",
+ "@babel/code-frame": "^7.18.6",
+ "@babel/generator": "^7.19.3",
+ "@babel/helper-compilation-targets": "^7.19.3",
+ "@babel/helper-module-transforms": "^7.19.0",
+ "@babel/helpers": "^7.19.0",
+ "@babel/parser": "^7.19.3",
+ "@babel/template": "^7.18.10",
+ "@babel/traverse": "^7.19.3",
+ "@babel/types": "^7.19.3",
"convert-source-map": "^1.7.0",
"debug": "^4.1.0",
"gensync": "^1.0.0-beta.2",
- "json5": "^2.1.2",
- "semver": "^6.3.0",
- "source-map": "^0.5.0"
+ "json5": "^2.2.1",
+ "semver": "^6.3.0"
},
"engines": {
"node": ">=6.9.0"
@@ -102,6 +120,17 @@
"url": "https://opencollective.com/babel"
}
},
+ "node_modules/@babel/core/node_modules/@babel/code-frame": {
+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.18.6.tgz",
+ "integrity": "sha512-TDCmlK5eOvH+eH7cdAFlNXeVJqWIQ7gW9tY1GJIpUtFb6CmjVyq2VM3u71bOyR8CRihcCgMUYoDNyLXao3+70Q==",
+ "dependencies": {
+ "@babel/highlight": "^7.18.6"
+ },
+ "engines": {
+ "node": ">=6.9.0"
+ }
+ },
"node_modules/@babel/core/node_modules/debug": {
"version": "4.3.2",
"resolved": "https://registry.npmjs.org/debug/-/debug-4.3.2.tgz",
@@ -131,66 +160,50 @@
"semver": "bin/semver.js"
}
},
- "node_modules/@babel/core/node_modules/source-map": {
- "version": "0.5.7",
- "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.5.7.tgz",
- "integrity": "sha1-igOdLRAh0i0eoUyA2OpGi6LvP8w=",
- "engines": {
- "node": ">=0.10.0"
- }
- },
"node_modules/@babel/generator": {
- "version": "7.15.8",
- "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.15.8.tgz",
- "integrity": "sha512-ECmAKstXbp1cvpTTZciZCgfOt6iN64lR0d+euv3UZisU5awfRawOvg07Utn/qBGuH4bRIEZKrA/4LzZyXhZr8g==",
+ "version": "7.19.5",
+ "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.19.5.tgz",
+ "integrity": "sha512-DxbNz9Lz4aMZ99qPpO1raTbcrI1ZeYh+9NR9qhfkQIbFtVEqotHojEBxHzmxhVONkGt6VyrqVQcgpefMy9pqcg==",
"dependencies": {
- "@babel/types": "^7.15.6",
- "jsesc": "^2.5.1",
- "source-map": "^0.5.0"
+ "@babel/types": "^7.19.4",
+ "@jridgewell/gen-mapping": "^0.3.2",
+ "jsesc": "^2.5.1"
},
"engines": {
"node": ">=6.9.0"
}
},
- "node_modules/@babel/generator/node_modules/source-map": {
- "version": "0.5.7",
- "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.5.7.tgz",
- "integrity": "sha1-igOdLRAh0i0eoUyA2OpGi6LvP8w=",
- "engines": {
- "node": ">=0.10.0"
- }
- },
"node_modules/@babel/helper-annotate-as-pure": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.15.4.tgz",
- "integrity": "sha512-QwrtdNvUNsPCj2lfNQacsGSQvGX8ee1ttrBrcozUP2Sv/jylewBP/8QFe6ZkBsC8T/GYWonNAWJV4aRR9AL2DA==",
+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.18.6.tgz",
+ "integrity": "sha512-duORpUiYrEpzKIop6iNbjnwKLAKnJ47csTyRACyEmWj0QdUrm5aqNJGHSSEQSUAvNW0ojX0dOmK9dZduvkfeXA==",
"dependencies": {
- "@babel/types": "^7.15.4"
+ "@babel/types": "^7.18.6"
},
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/helper-builder-binary-assignment-operator-visitor": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-builder-binary-assignment-operator-visitor/-/helper-builder-binary-assignment-operator-visitor-7.15.4.tgz",
- "integrity": "sha512-P8o7JP2Mzi0SdC6eWr1zF+AEYvrsZa7GSY1lTayjF5XJhVH0kjLYUZPvTMflP7tBgZoe9gIhTa60QwFpqh/E0Q==",
+ "version": "7.18.9",
+ "resolved": "https://registry.npmjs.org/@babel/helper-builder-binary-assignment-operator-visitor/-/helper-builder-binary-assignment-operator-visitor-7.18.9.tgz",
+ "integrity": "sha512-yFQ0YCHoIqarl8BCRwBL8ulYUaZpz3bNsA7oFepAzee+8/+ImtADXNOmO5vJvsPff3qi+hvpkY/NYBTrBQgdNw==",
"dependencies": {
- "@babel/helper-explode-assignable-expression": "^7.15.4",
- "@babel/types": "^7.15.4"
+ "@babel/helper-explode-assignable-expression": "^7.18.6",
+ "@babel/types": "^7.18.9"
},
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/helper-compilation-targets": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.15.4.tgz",
- "integrity": "sha512-rMWPCirulnPSe4d+gwdWXLfAXTTBj8M3guAf5xFQJ0nvFY7tfNAFnWdqaHegHlgDZOCT4qvhF3BYlSJag8yhqQ==",
+ "version": "7.19.3",
+ "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.19.3.tgz",
+ "integrity": "sha512-65ESqLGyGmLvgR0mst5AdW1FkNlj9rQsCKduzEoEPhBCDFGXvz2jW6bXFG6i0/MrV2s7hhXjjb2yAzcPuQlLwg==",
"dependencies": {
- "@babel/compat-data": "^7.15.0",
- "@babel/helper-validator-option": "^7.14.5",
- "browserslist": "^4.16.6",
+ "@babel/compat-data": "^7.19.3",
+ "@babel/helper-validator-option": "^7.18.6",
+ "browserslist": "^4.21.3",
"semver": "^6.3.0"
},
"engines": {
@@ -209,16 +222,17 @@
}
},
"node_modules/@babel/helper-create-class-features-plugin": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.15.4.tgz",
- "integrity": "sha512-7ZmzFi+DwJx6A7mHRwbuucEYpyBwmh2Ca0RvI6z2+WLZYCqV0JOaLb+u0zbtmDicebgKBZgqbYfLaKNqSgv5Pw==",
+ "version": "7.19.0",
+ "resolved": "https://registry.npmjs.org/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.19.0.tgz",
+ "integrity": "sha512-NRz8DwF4jT3UfrmUoZjd0Uph9HQnP30t7Ash+weACcyNkiYTywpIjDBgReJMKgr+n86sn2nPVVmJ28Dm053Kqw==",
"dependencies": {
- "@babel/helper-annotate-as-pure": "^7.15.4",
- "@babel/helper-function-name": "^7.15.4",
- "@babel/helper-member-expression-to-functions": "^7.15.4",
- "@babel/helper-optimise-call-expression": "^7.15.4",
- "@babel/helper-replace-supers": "^7.15.4",
- "@babel/helper-split-export-declaration": "^7.15.4"
+ "@babel/helper-annotate-as-pure": "^7.18.6",
+ "@babel/helper-environment-visitor": "^7.18.9",
+ "@babel/helper-function-name": "^7.19.0",
+ "@babel/helper-member-expression-to-functions": "^7.18.9",
+ "@babel/helper-optimise-call-expression": "^7.18.6",
+ "@babel/helper-replace-supers": "^7.18.9",
+ "@babel/helper-split-export-declaration": "^7.18.6"
},
"engines": {
"node": ">=6.9.0"
@@ -228,12 +242,12 @@
}
},
"node_modules/@babel/helper-create-regexp-features-plugin": {
- "version": "7.14.5",
- "resolved": "https://registry.npmjs.org/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.14.5.tgz",
- "integrity": "sha512-TLawwqpOErY2HhWbGJ2nZT5wSkR192QpN+nBg1THfBfftrlvOh+WbhrxXCH4q4xJ9Gl16BGPR/48JA+Ryiho/A==",
+ "version": "7.19.0",
+ "resolved": "https://registry.npmjs.org/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.19.0.tgz",
+ "integrity": "sha512-htnV+mHX32DF81amCDrwIDr8nrp1PTm+3wfBN9/v8QJOLEioOCOG7qNyq0nHeFiWbT3Eb7gsPwEmV64UCQ1jzw==",
"dependencies": {
- "@babel/helper-annotate-as-pure": "^7.14.5",
- "regexpu-core": "^4.7.1"
+ "@babel/helper-annotate-as-pure": "^7.18.6",
+ "regexpu-core": "^5.1.0"
},
"engines": {
"node": ">=6.9.0"
@@ -243,14 +257,12 @@
}
},
"node_modules/@babel/helper-define-polyfill-provider": {
- "version": "0.2.3",
- "resolved": "https://registry.npmjs.org/@babel/helper-define-polyfill-provider/-/helper-define-polyfill-provider-0.2.3.tgz",
- "integrity": "sha512-RH3QDAfRMzj7+0Nqu5oqgO5q9mFtQEVvCRsi8qCEfzLR9p2BHfn5FzhSB2oj1fF7I2+DcTORkYaQ6aTR9Cofew==",
+ "version": "0.3.3",
+ "resolved": "https://registry.npmjs.org/@babel/helper-define-polyfill-provider/-/helper-define-polyfill-provider-0.3.3.tgz",
+ "integrity": "sha512-z5aQKU4IzbqCC1XH0nAqfsFLMVSo22SBKUc0BxGrLkolTdPTructy0ToNnlO2zA4j9Q/7pjMZf0DSY+DSTYzww==",
"dependencies": {
- "@babel/helper-compilation-targets": "^7.13.0",
- "@babel/helper-module-imports": "^7.12.13",
- "@babel/helper-plugin-utils": "^7.13.0",
- "@babel/traverse": "^7.13.0",
+ "@babel/helper-compilation-targets": "^7.17.7",
+ "@babel/helper-plugin-utils": "^7.16.7",
"debug": "^4.1.1",
"lodash.debounce": "^4.0.8",
"resolve": "^1.14.2",
@@ -261,9 +273,9 @@
}
},
"node_modules/@babel/helper-define-polyfill-provider/node_modules/debug": {
- "version": "4.3.2",
- "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.2.tgz",
- "integrity": "sha512-mOp8wKcvj7XxC78zLgw/ZA+6TSgkoE2C/ienthhRD298T7UNwAg9diBpLRxC0mOezLl4B0xV7M0cCO6P/O0Xhw==",
+ "version": "4.3.4",
+ "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.4.tgz",
+ "integrity": "sha512-PRWFHuSU3eDtQJPvnNY7Jcket1j0t5OuOsFzPPzsekD52Zl8qUfFIPEiswXqIvHWGVHOgX+7G/vCNNhehwxfkQ==",
"dependencies": {
"ms": "2.1.2"
},
@@ -289,220 +301,229 @@
"semver": "bin/semver.js"
}
},
- "node_modules/@babel/helper-explode-assignable-expression": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-explode-assignable-expression/-/helper-explode-assignable-expression-7.15.4.tgz",
- "integrity": "sha512-J14f/vq8+hdC2KoWLIQSsGrC9EFBKE4NFts8pfMpymfApds+fPqR30AOUWc4tyr56h9l/GA1Sxv2q3dLZWbQ/g==",
- "dependencies": {
- "@babel/types": "^7.15.4"
- },
+ "node_modules/@babel/helper-environment-visitor": {
+ "version": "7.18.9",
+ "resolved": "https://registry.npmjs.org/@babel/helper-environment-visitor/-/helper-environment-visitor-7.18.9.tgz",
+ "integrity": "sha512-3r/aACDJ3fhQ/EVgFy0hpj8oHyHpQc+LPtJoY9SzTThAsStm4Ptegq92vqKoE3vD706ZVFWITnMnxucw+S9Ipg==",
"engines": {
"node": ">=6.9.0"
}
},
- "node_modules/@babel/helper-function-name": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-function-name/-/helper-function-name-7.15.4.tgz",
- "integrity": "sha512-Z91cOMM4DseLIGOnog+Z8OI6YseR9bua+HpvLAQ2XayUGU+neTtX+97caALaLdyu53I/fjhbeCnWnRH1O3jFOw==",
+ "node_modules/@babel/helper-explode-assignable-expression": {
+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/helper-explode-assignable-expression/-/helper-explode-assignable-expression-7.18.6.tgz",
+ "integrity": "sha512-eyAYAsQmB80jNfg4baAtLeWAQHfHFiR483rzFK+BhETlGZaQC9bsfrugfXDCbRHLQbIA7U5NxhhOxN7p/dWIcg==",
"dependencies": {
- "@babel/helper-get-function-arity": "^7.15.4",
- "@babel/template": "^7.15.4",
- "@babel/types": "^7.15.4"
+ "@babel/types": "^7.18.6"
},
"engines": {
"node": ">=6.9.0"
}
},
- "node_modules/@babel/helper-get-function-arity": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-get-function-arity/-/helper-get-function-arity-7.15.4.tgz",
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+ "node_modules/@babel/helper-function-name": {
+ "version": "7.19.0",
+ "resolved": "https://registry.npmjs.org/@babel/helper-function-name/-/helper-function-name-7.19.0.tgz",
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"dependencies": {
- "@babel/types": "^7.15.4"
+ "@babel/template": "^7.18.10",
+ "@babel/types": "^7.19.0"
},
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/helper-hoist-variables": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-hoist-variables/-/helper-hoist-variables-7.15.4.tgz",
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+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/helper-hoist-variables/-/helper-hoist-variables-7.18.6.tgz",
+ "integrity": "sha512-UlJQPkFqFULIcyW5sbzgbkxn2FKRgwWiRexcuaR8RNJRy8+LLveqPjwZV/bwrLZCN0eUHD/x8D0heK1ozuoo6Q==",
"dependencies": {
- "@babel/types": "^7.15.4"
+ "@babel/types": "^7.18.6"
},
"engines": {
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}
},
"node_modules/@babel/helper-member-expression-to-functions": {
- "version": "7.15.4",
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},
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}
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-dynamic-import/-/plugin-proposal-dynamic-import-7.18.6.tgz",
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},
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@@ -669,11 +710,11 @@
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-export-namespace-from/-/plugin-proposal-export-namespace-from-7.18.9.tgz",
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-json-strings/-/plugin-proposal-json-strings-7.18.6.tgz",
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+ "@babel/helper-plugin-utils": "^7.18.6",
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@@ -699,11 +740,11 @@
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+ "version": "7.18.9",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-logical-assignment-operators/-/plugin-proposal-logical-assignment-operators-7.18.9.tgz",
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+ "@babel/helper-plugin-utils": "^7.18.9",
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},
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+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-nullish-coalescing-operator/-/plugin-proposal-nullish-coalescing-operator-7.18.6.tgz",
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+ "@babel/helper-plugin-utils": "^7.18.6",
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},
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@@ -729,11 +770,11 @@
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+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-numeric-separator/-/plugin-proposal-numeric-separator-7.18.6.tgz",
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+ "@babel/helper-plugin-utils": "^7.18.6",
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},
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@@ -744,15 +785,15 @@
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+ "version": "7.19.4",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-object-rest-spread/-/plugin-proposal-object-rest-spread-7.19.4.tgz",
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},
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@@ -762,11 +803,11 @@
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+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-optional-catch-binding/-/plugin-proposal-optional-catch-binding-7.18.6.tgz",
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+ "@babel/helper-plugin-utils": "^7.18.6",
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},
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@@ -777,12 +818,12 @@
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+ "version": "7.18.9",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-optional-chaining/-/plugin-proposal-optional-chaining-7.18.9.tgz",
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@@ -793,12 +834,12 @@
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+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-private-methods/-/plugin-proposal-private-methods-7.18.6.tgz",
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+ "@babel/helper-create-class-features-plugin": "^7.18.6",
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@@ -808,13 +849,13 @@
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+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-private-property-in-object/-/plugin-proposal-private-property-in-object-7.18.6.tgz",
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- "@babel/helper-plugin-utils": "^7.14.5",
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@@ -825,12 +866,12 @@
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+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-unicode-property-regex/-/plugin-proposal-unicode-property-regex-7.18.6.tgz",
+ "integrity": "sha512-2BShG/d5yoZyXZfVePH91urL5wTG6ASZU9M4o03lKK8u8UW1y08OMttBSOADTcJrnPMpvDXRG3G8fyLh4ovs8w==",
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+ "@babel/helper-create-regexp-features-plugin": "^7.18.6",
+ "@babel/helper-plugin-utils": "^7.18.6"
},
"engines": {
"node": ">=4"
@@ -850,6 +891,17 @@
"@babel/core": "^7.0.0-0"
}
},
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+ "version": "7.8.3",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-bigint/-/plugin-syntax-bigint-7.8.3.tgz",
+ "integrity": "sha512-wnTnFlG+YxQm3vDxpGE57Pj0srRU4sHE/mDkt1qv2YJJSeUAec2ma4WLUnUPeKjyrfntVwe/N6dCXpU+zL3Npg==",
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"resolved": "https://registry.npmjs.org/@babel/plugin-syntax-class-properties/-/plugin-syntax-class-properties-7.12.13.tgz",
@@ -876,11 +928,11 @@
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+ "version": "7.19.0",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-decorators/-/plugin-syntax-decorators-7.19.0.tgz",
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+ "@babel/helper-plugin-utils": "^7.19.0"
},
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@@ -912,11 +964,25 @@
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+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-flow/-/plugin-syntax-flow-7.18.6.tgz",
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+ "@babel/helper-plugin-utils": "^7.18.6"
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-import-assertions/-/plugin-syntax-import-assertions-7.18.6.tgz",
+ "integrity": "sha512-/DU3RXad9+bZwrgWJQKbr39gYbJpLJHezqEzRzi/BHRlJ9zsQb4CK2CA/5apllXNomwA1qHwzvHl+AdEmC5krQ==",
+ "dependencies": {
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},
"engines": {
"node": ">=6.9.0"
@@ -925,6 +991,17 @@
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}
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-import-meta/-/plugin-syntax-import-meta-7.10.4.tgz",
+ "integrity": "sha512-Yqfm+XDx0+Prh3VSeEQCPU81yC+JWZ2pDPFSS4ZdpfZhp4MkFMaDC1UqseovEKwSUpnIL7+vK+Clp7bfh0iD7g==",
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"resolved": "https://registry.npmjs.org/@babel/plugin-syntax-json-strings/-/plugin-syntax-json-strings-7.8.3.tgz",
@@ -937,11 +1014,11 @@
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+ "version": "7.18.6",
+ "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-jsx/-/plugin-syntax-jsx-7.18.6.tgz",
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+ "@babel/helper-plugin-utils": "^7.18.6"
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@@ -1045,11 +1122,11 @@
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-typescript/-/plugin-syntax-typescript-7.18.6.tgz",
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@@ -1059,11 +1136,11 @@
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+ "resolved": "https://registry.npmjs.org/@babel/plugin-transform-regenerator/-/plugin-transform-regenerator-7.18.6.tgz",
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}
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@@ -8492,6 +9234,17 @@
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"resolved": "https://registry.npmjs.org/entities/-/entities-2.2.0.tgz",
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}
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- "resolved": "https://registry.npmjs.org/es-abstract/-/es-abstract-1.19.1.tgz",
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"node": ">= 0.4"
@@ -8552,6 +9317,19 @@
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}
},
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+ "resolved": "https://registry.npmjs.org/es-shim-unscopables/-/es-shim-unscopables-1.0.0.tgz",
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"resolved": "https://registry.npmjs.org/es-to-primitive/-/es-to-primitive-1.2.1.tgz",
@@ -8569,19 +9347,23 @@
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+ "es6-symbol": "^3.1.3",
+ "next-tick": "^1.1.0"
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}
},
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"resolved": "https://registry.npmjs.org/es6-iterator/-/es6-iterator-2.0.3.tgz",
- "integrity": "sha1-p96IkUGgWpSwhUQDstCg+/qY87c=",
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@@ -8617,7 +9399,7 @@
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"resolved": "https://registry.npmjs.org/escape-html/-/escape-html-1.0.3.tgz",
- "integrity": "sha1-Aljq5NPQwJdN4cFpGI7wBR0dGYg="
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},
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+ "resolved": "https://registry.npmjs.org/escodegen/-/escodegen-2.0.0.tgz",
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- "estraverse": "^4.2.0",
+ "estraverse": "^5.2.0",
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},
@@ -8642,52 +9424,110 @@
"esgenerate": "bin/esgenerate.js"
},
"engines": {
- "node": ">=4.0"
+ "node": ">=6.0"
},
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}
},
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+ "resolved": "https://registry.npmjs.org/estraverse/-/estraverse-5.3.0.tgz",
+ "integrity": "sha512-MMdARuVEQziNTeJD8DgMqmhwR11BRQ/cBP+pLtYdSTnf3MIO8fFeiINEbX36ZdNlfU/7A9f3gUw49B3oQsvwBA==",
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+ "node_modules/escodegen/node_modules/levn": {
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+ "resolved": "https://registry.npmjs.org/levn/-/levn-0.3.0.tgz",
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+ "engines": {
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+ "node_modules/escodegen/node_modules/optionator": {
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+ "resolved": "https://registry.npmjs.org/optionator/-/optionator-0.8.3.tgz",
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- "mkdirp": "^0.5.1",
"natural-compare": "^1.4.0",
- "optionator": "^0.8.3",
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- "regexpp": "^2.0.1",
- "semver": "^6.1.2",
- "strip-ansi": "^5.2.0",
- "strip-json-comments": "^3.0.1",
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+ "strip-json-comments": "^3.1.0",
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@@ -8695,29 +9535,42 @@
"eslint": "bin/eslint.js"
},
"engines": {
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+ "node": "^10.12.0 || >=12.0.0"
},
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}
},
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+ "resolved": "https://registry.npmjs.org/eslint-config-react-app/-/eslint-config-react-app-6.0.0.tgz",
+ "integrity": "sha512-bpoAAC+YRfzq0dsTk+6v9aHm/uqnDwayNAXleMypGl6CpxI9oXXscVHo4fk3eJPIn+rsbtNetB4r/ZIidFIE8A==",
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+ "confusing-browser-globals": "^1.0.10"
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+ "engines": {
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},
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- "eslint-plugin-jsx-a11y": "6.x",
- "eslint-plugin-react": "7.x",
- "eslint-plugin-react-hooks": "1.x || 2.x"
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+ "eslint-plugin-react-hooks": "^4.0.8",
+ "eslint-plugin-testing-library": "^3.9.0"
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+ },
+ "eslint-plugin-testing-library": {
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}
},
"node_modules/eslint-import-resolver-node": {
@@ -8742,37 +9595,20 @@
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},
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+ "integrity": "sha512-j4GT+rqzCoRKHwURX7pddtIPGySnX9Si/cgMI5ztrcqOPtk5dDEeZ34CQVPphnqkJytlc97Vuk05Um2mJ3gEQA==",
"dependencies": {
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- "find-up": "^2.1.0",
- "pkg-dir": "^2.0.0"
+ "debug": "^3.2.7"
},
"engines": {
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+ },
+ "peerDependenciesMeta": {
+ "eslint": {
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+ }
}
},
"node_modules/eslint-module-utils/node_modules/debug": {
@@ -8783,180 +9619,181 @@
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+ "string-natural-compare": "^3.0.1"
},
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+ "funding": {
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@@ -19111,18 +19390,21 @@
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},
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+ },
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"type": "tidelift",
"url": "https://tidelift.com/funding/github/npm/browserslist"
@@ -19144,16 +19426,11 @@
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- "integrity": "sha1-G2HAViGQqN/2rjuyzwIAyhMLhtQ=",
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"resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.3.tgz",
- "integrity": "sha1-p9BVi9icQveV3UIyj3QIMcpTvCU="
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@@ -19180,14 +19457,6 @@
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+ "resolved": "https://registry.npmjs.org/globby/-/globby-11.0.1.tgz",
+ "integrity": "sha512-iH9RmgwCmUJHi2z5o2l3eTtGBtXek1OYlHrbcxOYugyHLmAsZrPj43OtHThd62Buh/Vv6VyCBD2bdyWcGNQqoQ==",
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},
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+ "funding": {
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}
},
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},
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}
},
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@@ -19413,9 +19648,9 @@
}
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},
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"version": "0.5.10",
@@ -19543,75 +19778,90 @@
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}
},
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+ "resolved": "https://registry.npmjs.org/react-refresh/-/react-refresh-0.8.3.tgz",
+ "integrity": "sha512-X8jZHc7nCMjaCqoU+V2I0cOhNW+QMBwSUkeXnTi8IPe6zaRWfn60ZzvFDZqWPfmSJfjub7dDW1SP0jaHWLu/hg==",
+ "engines": {
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+ }
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- "@typescript-eslint/parser": "^2.10.0",
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+ "version": "4.0.3",
+ "resolved": "https://registry.npmjs.org/react-scripts/-/react-scripts-4.0.3.tgz",
+ "integrity": "sha512-S5eO4vjUzUisvkIPB7jVsKtuH2HhWcASREYWHAQ1FP5HyCv3xgn+wpILAEWkmy+A+tTNbSZClhxjT3qz6g4L1A==",
+ "dependencies": {
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- "babel-preset-react-app": "^9.1.2",
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+ "bfj": "^7.0.2",
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- "css-loader": "3.4.2",
+ "css-loader": "4.3.0",
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- "file-loader": "4.3.0",
- "fs-extra": "^8.1.0",
- "html-webpack-plugin": "4.0.0-beta.11",
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+ "eslint-plugin-import": "^2.22.1",
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+ "eslint-plugin-testing-library": "^3.9.2",
+ "eslint-webpack-plugin": "^2.5.2",
+ "file-loader": "6.1.1",
+ "fs-extra": "^9.0.1",
+ "html-webpack-plugin": "4.5.0",
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- "mini-css-extract-plugin": "0.9.0",
- "optimize-css-assets-webpack-plugin": "5.0.3",
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+ "jest-circus": "26.6.0",
+ "jest-resolve": "26.6.0",
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+ "mini-css-extract-plugin": "0.11.3",
+ "optimize-css-assets-webpack-plugin": "5.0.4",
"pnp-webpack-plugin": "1.6.4",
- "postcss-flexbugs-fixes": "4.1.0",
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"postcss-loader": "3.0.0",
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- "ts-pnp": "1.1.6",
- "url-loader": "2.3.0",
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+ "postcss-safe-parser": "5.0.2",
+ "prompts": "2.4.0",
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+ "react-dev-utils": "^11.0.3",
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+ "sass-loader": "^10.0.5",
+ "semver": "7.3.2",
+ "style-loader": "1.3.0",
+ "terser-webpack-plugin": "4.2.3",
+ "ts-pnp": "1.2.0",
+ "url-loader": "4.1.1",
+ "webpack": "4.44.2",
+ "webpack-dev-server": "3.11.1",
"webpack-manifest-plugin": "2.2.0",
- "workbox-webpack-plugin": "4.3.1"
+ "workbox-webpack-plugin": "5.1.4"
},
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"react-scripts": "bin/react-scripts.js"
},
"engines": {
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+ "node": "^10.12.0 || >=12.0.0"
},
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+ "fsevents": "^2.1.3"
},
"peerDependencies": {
- "typescript": "^3.2.1"
+ "react": ">= 16",
+ "typescript": "^3.2.1 || ^4"
},
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"typescript": {
@@ -19620,23 +19870,23 @@
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- "@babel/parser": "^7.9.0",
- "@babel/template": "^7.8.6",
- "@babel/traverse": "^7.9.0",
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+ "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.12.3.tgz",
+ "integrity": "sha512-0qXcZYKZp3/6N2jKYVxZv0aNCsxTSVCiK72DTiTYZAu7sjg73W0/aynWjMbiGd87EQL4WyA8reiJVh92AVla9g==",
+ "dependencies": {
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"debug": "^4.1.0",
"gensync": "^1.0.0-beta.1",
"json5": "^2.1.2",
- "lodash": "^4.17.13",
+ "lodash": "^4.17.19",
"resolve": "^1.3.2",
"semver": "^5.4.1",
"source-map": "^0.5.0"
@@ -19657,10 +19907,21 @@
"semver": "bin/semver"
}
},
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+ "version": "6.3.0",
+ "resolved": "https://registry.npmjs.org/camelcase/-/camelcase-6.3.0.tgz",
+ "integrity": "sha512-Gmy6FhYlCY7uOElZUSbxo2UCDH8owEk996gkbrpsgGtrJLM3J7jGxl9Ic7Qwwj4ivOE5AWZWRMecDdF7hqGjFA==",
+ "engines": {
+ "node": ">=10"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/sindresorhus"
+ }
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"node_modules/react-scripts/node_modules/debug": {
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- "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.2.tgz",
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+ "version": "4.3.4",
+ "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.4.tgz",
+ "integrity": "sha512-PRWFHuSU3eDtQJPvnNY7Jcket1j0t5OuOsFzPPzsekD52Zl8qUfFIPEiswXqIvHWGVHOgX+7G/vCNNhehwxfkQ==",
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@@ -19673,30 +19934,17 @@
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- "deprecated": "\"Please update to latest v2.3 or v2.2\"",
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@@ -20144,6 +20384,17 @@
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"resolved": "https://registry.npmjs.org/requires-port/-/requires-port-1.0.0.tgz",
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- "integrity": "sha1-AKn3OHVW4nA46uIyyqNypqWbZlo=",
+ "version": "3.0.0",
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},
"engines": {
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- "resolved": "https://registry.npmjs.org/resolve-from/-/resolve-from-3.0.0.tgz",
- "integrity": "sha1-six699nWiBvItuZTM17rywoYh0g=",
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"engines": {
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- "integrity": "sha1-TapNnbAPmBmIDHn6RXrlsJof04k=",
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- "integrity": "sha1-tdRU3CGZriJWmfNGfloH87lVuv0=",
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+ "resolved": "https://registry.npmjs.org/postcss/-/postcss-7.0.36.tgz",
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"source-map": "^0.6.1",
@@ -20612,6 +20802,10 @@
},
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"node": ">=6.0.0"
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+ "type": "opencollective",
+ "url": "https://opencollective.com/postcss/"
}
},
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"resolved": "https://registry.npmjs.org/retry/-/retry-0.12.0.tgz",
- "integrity": "sha1-G0KmJmoh8HQh0bC1S33BZ7AcATs=",
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"engines": {
"node": ">= 4"
}
},
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+ "resolved": "https://registry.npmjs.org/reusify/-/reusify-1.0.4.tgz",
+ "integrity": "sha512-U9nH88a3fc/ekCF1l0/UP1IosiuIjyTh7hBvXVMHYgVcfGvt897Xguj2UOLDeI5BG2m7/uwyaLVT6fbtCwTyzw==",
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"version": "1.0.1",
"resolved": "https://registry.npmjs.org/rework/-/rework-1.0.1.tgz",
- "integrity": "sha1-MIBqhBNCtUUQqkEQhQzUhTQUSqc=",
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"resolved": "https://registry.npmjs.org/rework-visit/-/rework-visit-1.0.0.tgz",
- "integrity": "sha1-mUWygD8hni96ygCtuLyfZA+ELJo="
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- "integrity": "sha1-8dgClQr33SYxof6+BZZVDIarMZA="
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"resolved": "https://registry.npmjs.org/rgb-regex/-/rgb-regex-1.0.1.tgz",
- "integrity": "sha1-wODWiC3w4jviVKR16O3UGRX+rrE="
+ "integrity": "sha512-gDK5mkALDFER2YLqH6imYvK6g02gpNGM4ILDZ472EwWfXZnC2ZEpoB2ECXTyOVUKuk/bPJZMzwQPBYICzP+D3w=="
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"resolved": "https://registry.npmjs.org/rgba-regex/-/rgba-regex-1.0.0.tgz",
- "integrity": "sha1-QzdOLiyglosO8VI0YLfXMP8i7rM="
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},
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@@ -20723,6 +20914,100 @@
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}
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+ "resolved": "https://registry.npmjs.org/rollup/-/rollup-1.32.1.tgz",
+ "integrity": "sha512-/2HA0Ec70TvQnXdzynFffkjA6XN+1e2pEv/uKS5Ulca40g2L7KuOE3riasHoNVHOsFD5KKZgDsMk1CP3Tw9s+A==",
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+ "resolved": "https://registry.npmjs.org/rollup-plugin-babel/-/rollup-plugin-babel-4.4.0.tgz",
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+ "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-3.0.0.tgz",
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@@ -21050,10 +21413,18 @@
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@@ -21779,6 +22046,11 @@
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"engines": {
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@@ -22301,6 +22611,14 @@
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@@ -22312,6 +22630,29 @@
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@@ -23110,6 +23541,21 @@
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@@ -23405,10 +23880,40 @@
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@@ -23505,12 +24010,11 @@
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- "deprecated": "Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See https://v8.dev/blog/math-random for details.",
+ "version": "8.3.2",
+ "resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
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"bin": {
- "uuid": "bin/uuid"
+ "uuid": "dist/bin/uuid"
}
},
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},
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+ "resolved": "https://registry.npmjs.org/v8-to-istanbul/-/v8-to-istanbul-7.1.2.tgz",
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+ },
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+ "node_modules/v8-to-istanbul/node_modules/source-map": {
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+ "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.7.4.tgz",
+ "integrity": "sha512-l3BikUxvPOcn5E74dZiq5BGsTb5yEwhaTSzccU6t4sDOH8NWJCstKO5QT2CvtFoK6F0saL7p9xHAqHOlCPJygA==",
+ "engines": {
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"version": "3.0.4",
"resolved": "https://registry.npmjs.org/validate-npm-package-license/-/validate-npm-package-license-3.0.4.tgz",
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"resolved": "https://registry.npmjs.org/vary/-/vary-1.1.2.tgz",
- "integrity": "sha1-IpnwLG3tMNSllhsLn3RSShj2NPw=",
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@@ -23544,19 +24069,6 @@
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}
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+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/w3c-xmlserializer/-/w3c-xmlserializer-2.0.0.tgz",
+ "integrity": "sha512-4tzD0mF8iSiMiNs30BiLO3EpfGLZUT2MSX/G+o7ZywDzliWQ3OPtTZ0PTC3B3ca1UAf4cJMHB+2Bf56EriJuRA==",
"dependencies": {
- "domexception": "^1.0.1",
- "webidl-conversions": "^4.0.2",
"xml-name-validator": "^3.0.0"
+ },
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+ "node": ">=10"
}
},
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@@ -23846,37 +24359,40 @@
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+ "version": "6.1.0",
+ "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-6.1.0.tgz",
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+ "engines": {
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- "resolved": "https://registry.npmjs.org/webpack/-/webpack-4.42.0.tgz",
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- "@webassemblyjs/wasm-edit": "1.8.5",
- "@webassemblyjs/wasm-parser": "1.8.5",
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"ajv": "^6.10.2",
"ajv-keywords": "^3.4.1",
"chrome-trace-event": "^1.0.2",
- "enhanced-resolve": "^4.1.0",
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"loader-runner": "^2.4.0",
"loader-utils": "^1.2.3",
"memory-fs": "^0.4.1",
"micromatch": "^3.1.10",
- "mkdirp": "^0.5.1",
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"schema-utils": "^1.0.0",
"tapable": "^1.1.3",
"terser-webpack-plugin": "^1.4.3",
- "watchpack": "^1.6.0",
+ "watchpack": "^1.7.4",
"webpack-sources": "^1.4.1"
},
"bin": {
@@ -23888,6 +24404,14 @@
"funding": {
"type": "opencollective",
"url": "https://opencollective.com/webpack"
+ },
+ "peerDependenciesMeta": {
+ "webpack-cli": {
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+ "webpack-command": {
+ "optional": true
+ }
}
},
"node_modules/webpack-dev-middleware": {
@@ -23909,9 +24433,9 @@
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+ "version": "3.11.1",
+ "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-3.11.1.tgz",
+ "integrity": "sha512-u4R3mRzZkbxQVa+MBWi2uVpB5W59H3ekZAJsQlKUTdl7Elcah2EhygTPLmeFXybQkf9i2+L0kn7ik9SnXa6ihQ==",
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@@ -23921,31 +24445,31 @@
"debug": "^4.1.1",
"del": "^4.1.1",
"express": "^4.17.1",
- "html-entities": "^1.2.1",
+ "html-entities": "^1.3.1",
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"internal-ip": "^4.3.0",
"ip": "^1.1.5",
"is-absolute-url": "^3.0.3",
"killable": "^1.0.1",
- "loglevel": "^1.6.6",
+ "loglevel": "^1.6.8",
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"p-retry": "^3.0.1",
- "portfinder": "^1.0.25",
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"schema-utils": "^1.0.0",
- "selfsigned": "^1.10.7",
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"serve-index": "^1.9.1",
- "sockjs": "0.3.19",
- "sockjs-client": "1.4.0",
- "spdy": "^4.0.1",
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+ "sockjs-client": "^1.5.0",
+ "spdy": "^4.0.2",
"strip-ansi": "^3.0.1",
"supports-color": "^6.1.0",
"url": "^0.11.0",
"webpack-dev-middleware": "^3.7.2",
"webpack-log": "^2.0.0",
"ws": "^6.2.1",
- "yargs": "12.0.5"
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"bin": {
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@@ -23965,11 +24489,22 @@
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- "integrity": "sha1-w7M6te42DYbg5ijwRorn7yfWVN8=",
+ "integrity": "sha512-TIGnTpdo+E3+pCyAluZvtED5p5wCqLdezCyhPZzKPcxvFplEt4i+W7OONCKgeZFT3+y5NZZfOOS/Bdcanm1MYA==",
"engines": {
"node": ">=0.10.0"
}
},
+ "node_modules/webpack-dev-server/node_modules/ansi-styles": {
+ "version": "3.2.1",
+ "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-3.2.1.tgz",
+ "integrity": "sha512-VT0ZI6kZRdTh8YyJw3SMbYm/u+NqfsAxEpWO0Pf9sq8/e94WxxOpPKx9FR1FlyCtOVDNOQ+8ntlqFxiRc+r5qA==",
+ "dependencies": {
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+ },
+ "engines": {
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"node_modules/webpack-dev-server/node_modules/anymatch": {
"version": "2.0.0",
"resolved": "https://registry.npmjs.org/anymatch/-/anymatch-2.0.0.tgz",
@@ -23982,7 +24517,7 @@
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- "integrity": "sha1-GrKLVW4Zg2Oowab35vogE3/mrtk=",
+ "integrity": "sha512-3pKJwH184Xo/lnH6oyP1q2pMd7HcypqqmRs91/6/i2CGtWwIKGCkOOMTm/zXbgTEWHw1uNpNi/igc3ePOYHb6w==",
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@@ -24022,7 +24557,7 @@
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- "deprecated": "Chokidar 2 will break on node v14+. Upgrade to chokidar 3 with 15x less dependencies.",
+ "deprecated": "Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies",
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@@ -24041,38 +24576,51 @@
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- "integrity": "sha1-tdRU3CGZriJWmfNGfloH87lVuv0=",
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- "integrity": "sha1-dfFmQrSA8YenEcgUFh/TpKdlWJg=",
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- "integrity": "sha1-YrEQ4omkcUGOPsNqYX1HLjAd/Ik=",
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},
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+ "resolved": "https://registry.npmjs.org/pkg-dir/-/pkg-dir-3.0.0.tgz",
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- "integrity": "sha1-l/cXtp1IeE9fUmpsWqj/3aBVpNE="
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+ "resolved": "https://registry.npmjs.org/resolve-cwd/-/resolve-cwd-2.0.0.tgz",
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+ "node_modules/webpack-dev-server/node_modules/resolve-from": {
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- "integrity": "sha1-7QMXwyIGT3lGbAKWa922Bas32Zg=",
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"engines": {
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- "integrity": "sha1-qEeQIusaw2iocTibY1JixQXuNo8=",
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- "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
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@@ -24328,39 +24917,35 @@
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- "integrity": "sha1-2Pw9KE3QV5T+hJc8rs3Rz4JP3YU=",
+ "version": "5.1.0",
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- "integrity": "sha1-754xOG8DGn8NZDr4L95QxFfvAMs=",
- "dependencies": {
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- },
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+ "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-4.1.1.tgz",
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- "integrity": "sha1-EYvfW4zcUaKn5w0hHgfisLmxB9M=",
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+ "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-5.2.0.tgz",
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"dependencies": {
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@@ -24372,28 +24957,26 @@
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+ "version": "13.3.2",
+ "resolved": "https://registry.npmjs.org/yargs/-/yargs-13.3.2.tgz",
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"dependencies": {
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- "decamelize": "^1.2.0",
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+ "version": "13.1.2",
+ "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-13.1.2.tgz",
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@@ -24411,6 +24994,23 @@
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@@ -26489,223 +27251,239 @@
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- "integrity": "sha1-2BNVwVYS04bGH53dOSLUMEgipUY=",
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- "integrity": "sha1-7ToIKZ8h11dBsg87gfGU7UnMFQ8="
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- "integrity": "sha1-wOTKB/U4a7F+xeUiULT1lhNlFW0="
+ "integrity": "sha512-JPMZ1TSMRUPVIqEalIBNoBtAYbi8okvcFns4O0YIhcdGebeYZK7dMyHJiQ6GqNBA9kE0Hym4Aqym5rPdsV/4Cw=="
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+ }
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@@ -33613,6 +34915,11 @@
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- "integrity": "sha1-wc56MWjIxmFAM6S194d/OyJfnDg="
+ "integrity": "sha512-7Wn5GMLuHBjZCb2bTmnDOycho0p/7UVaAeqXZGbHrBCl6Yd/xDhQJAXe6Ga9AXJH2I5zY1dEdYw2u1UptnSBJA=="
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@@ -33724,6 +35034,11 @@
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@@ -33780,6 +35088,39 @@
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@@ -40688,84 +41181,95 @@
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"requires": {
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+ "version": "0.15.0",
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@@ -41207,17 +41723,18 @@
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+ "version": "2.2.11",
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+ "version": "1.4.3",
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"resolved": "https://registry.npmjs.org/rework/-/rework-1.0.1.tgz",
- "integrity": "sha1-MIBqhBNCtUUQqkEQhQzUhTQUSqc=",
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@@ -41620,15 +42086,96 @@
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@@ -41869,10 +42464,15 @@
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- "integrity": "sha1-iQN8vJLFarGJJua6TLsgDhVnKmo="
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- "integrity": "sha1-qLE/1r/SSJUZZ0zN5VujaTtwbQk=",
+ "version": "2.1.0",
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@@ -43381,15 +43971,41 @@
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+ "version": "1.2.0",
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+ "minimist": "^1.2.6",
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+ "requires": {
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+ "loader-utils": "^2.0.0",
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+ "integrity": "sha512-Z0DbgELS9/L/75wZbro8xAnT50pBVFQZ+hUEueGDU5FN51YSCYM+jdxsfCiHjwNP/4LCDD0i/graKpeBnOXKRA=="
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- "integrity": "sha1-n5VxD1CiZ5R7LMwSR0HBAoQn5xM="
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+ "resolved": "https://registry.npmjs.org/v8-to-istanbul/-/v8-to-istanbul-7.1.2.tgz",
+ "integrity": "sha512-TxNb7YEUwkLXCQYeudi6lgQ/SZrzNO4kMdlqVxaZPUIUjCv6iSSypUQX70kNBSERpQ8fk48+d61FXk+tgqcWow==",
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}
},
@@ -44139,37 +44801,37 @@
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+ "version": "6.1.0",
+ "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-6.1.0.tgz",
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- "@webassemblyjs/wasm-edit": "1.8.5",
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+ "resolved": "https://registry.npmjs.org/webpack/-/webpack-4.44.2.tgz",
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"ajv-keywords": "^3.4.1",
"chrome-trace-event": "^1.0.2",
- "enhanced-resolve": "^4.1.0",
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"json-parse-better-errors": "^1.0.2",
"loader-runner": "^2.4.0",
"loader-utils": "^1.2.3",
"memory-fs": "^0.4.1",
"micromatch": "^3.1.10",
- "mkdirp": "^0.5.1",
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"node-libs-browser": "^2.2.1",
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"tapable": "^1.1.3",
"terser-webpack-plugin": "^1.4.3",
- "watchpack": "^1.6.0",
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},
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@@ -44274,9 +44936,9 @@
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+ "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-3.11.1.tgz",
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@@ -44286,37 +44948,45 @@
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"del": "^4.1.1",
"express": "^4.17.1",
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"internal-ip": "^4.3.0",
"ip": "^1.1.5",
"is-absolute-url": "^3.0.3",
"killable": "^1.0.1",
- "loglevel": "^1.6.6",
+ "loglevel": "^1.6.8",
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"p-retry": "^3.0.1",
- "portfinder": "^1.0.25",
+ "portfinder": "^1.0.26",
"schema-utils": "^1.0.0",
- "selfsigned": "^1.10.7",
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"semver": "^6.3.0",
"serve-index": "^1.9.1",
- "sockjs": "0.3.19",
- "sockjs-client": "1.4.0",
- "spdy": "^4.0.1",
+ "sockjs": "^0.3.21",
+ "sockjs-client": "^1.5.0",
+ "spdy": "^4.0.2",
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"supports-color": "^6.1.0",
"url": "^0.11.0",
"webpack-dev-middleware": "^3.7.2",
"webpack-log": "^2.0.0",
"ws": "^6.2.1",
- "yargs": "12.0.5"
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"resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-2.1.1.tgz",
- "integrity": "sha1-w7M6te42DYbg5ijwRorn7yfWVN8="
+ "integrity": "sha512-TIGnTpdo+E3+pCyAluZvtED5p5wCqLdezCyhPZzKPcxvFplEt4i+W7OONCKgeZFT3+y5NZZfOOS/Bdcanm1MYA=="
+ },
+ "ansi-styles": {
+ "version": "3.2.1",
+ "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-3.2.1.tgz",
+ "integrity": "sha512-VT0ZI6kZRdTh8YyJw3SMbYm/u+NqfsAxEpWO0Pf9sq8/e94WxxOpPKx9FR1FlyCtOVDNOQ+8ntlqFxiRc+r5qA==",
+ "requires": {
+ "color-convert": "^1.9.0"
+ }
},
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@@ -44330,7 +45000,7 @@
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- "integrity": "sha1-GrKLVW4Zg2Oowab35vogE3/mrtk=",
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}
@@ -44379,42 +45049,60 @@
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- "integrity": "sha512-4FG+RSG9DL7uEwRUZXZn3SS34DiDPfzP0VOiEwtUWlE+AR2EIg+hSyvrIgUUfhdgR/UkAeW2QHgeP+hWrXs7jQ==",
+ "version": "5.0.0",
+ "resolved": "https://registry.npmjs.org/cliui/-/cliui-5.0.0.tgz",
+ "integrity": "sha512-PYeGSEmmHM6zvoef2w8TPzlrnNpXIjTipYK780YswmIP9vjxmd6Y2a3CB2Ks6/AU8NHjZugXvo8w3oWM2qnwXA==",
"requires": {
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- "strip-ansi": "^4.0.0",
- "wrap-ansi": "^2.0.0"
+ "string-width": "^3.1.0",
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- "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-3.0.0.tgz",
- "integrity": "sha1-7QMXwyIGT3lGbAKWa922Bas32Zg="
+ "version": "4.1.1",
+ "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-4.1.1.tgz",
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- "integrity": "sha1-qEeQIusaw2iocTibY1JixQXuNo8=",
+ "version": "5.2.0",
+ "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-5.2.0.tgz",
+ "integrity": "sha512-DuRs1gKbBqsMKIZlrffwlug8MHkcnpjs5VPmL1PAh+mA30U0DTotfDZ0d2UUsXpPmPmMMJ6W773MaA3J+lbiWA==",
"requires": {
- "ansi-regex": "^3.0.0"
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}
}
}
},
+ "color-convert": {
+ "version": "1.9.3",
+ "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-1.9.3.tgz",
+ "integrity": "sha512-QfAUtd+vFdAtFQcC8CCyYt1fYWxSqAiK2cSD6zDB8N3cpsEBAvRxp9zOGg6G/SHHJYAT88/az/IuDGALsNVbGg==",
+ "requires": {
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+ "color-name": {
+ "version": "1.1.3",
+ "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.3.tgz",
+ "integrity": "sha512-72fSenhMw2HZMTVHeCA9KCmpEIbzWiQsjN+BHcBbS9vr1mtt+vJjPdksIBNUmKAW8TFUDPJK5SUU3QhE9NEXDw=="
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"debug": {
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+ "version": "4.3.4",
+ "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.4.tgz",
+ "integrity": "sha512-PRWFHuSU3eDtQJPvnNY7Jcket1j0t5OuOsFzPPzsekD52Zl8qUfFIPEiswXqIvHWGVHOgX+7G/vCNNhehwxfkQ==",
"requires": {
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}
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+ "version": "7.0.3",
+ "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-7.0.3.tgz",
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"extend-shallow": {
"version": "2.0.1",
"resolved": "https://registry.npmjs.org/extend-shallow/-/extend-shallow-2.0.1.tgz",
- "integrity": "sha1-Ua99YUrZqfYQ6huvu5idaxxWiQ8=",
+ "integrity": "sha512-zCnTtlxNoAiDc3gqY2aYAWFx7XWWiasuF2K8Me5WbN8otHKTUKBwjPtNpRs/rbUZm7KxWAaNj7P1a/p52GbVug==",
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@@ -44422,7 +45110,7 @@
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"resolved": "https://registry.npmjs.org/fill-range/-/fill-range-4.0.0.tgz",
- "integrity": "sha1-1USBHUKPmOsGpj3EAtJAPDKMOPc=",
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@@ -44440,15 +45128,10 @@
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- "integrity": "sha1-nmr2KZ2NO9K9QEMIMr0RPfkGxa4=",
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@@ -44457,7 +45140,7 @@
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"resolved": "https://registry.npmjs.org/is-glob/-/is-glob-3.1.0.tgz",
- "integrity": "sha1-e6WuJCF4BKxwcHuWkiVnSGzD6Eo=",
+ "integrity": "sha512-UFpDDrPgM6qpnFNI+rh/p3bUaq9hKLZN8bMUWzxmcnZVS3omf4IPK+BrewlnWjO1WmUsMYuSjKh4UJuV4+Lqmw==",
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@@ -44467,7 +45150,16 @@
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"resolved": "https://registry.npmjs.org/has-flag/-/has-flag-3.0.0.tgz",
- "integrity": "sha1-tdRU3CGZriJWmfNGfloH87lVuv0="
+ "integrity": "sha512-sKJf1+ceQBr4SMkvQnBDNDtf4TXpVhVGateu0t918bl30FnbE2m4vNLX+VWe/dpjlb+HugGYzW7uQXH98HPEYw=="
+ },
+ "import-local": {
+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/import-local/-/import-local-2.0.0.tgz",
+ "integrity": "sha512-b6s04m3O+s3CGSbqDIyP4R6aAwAeYlVq9+WUWep6iHa8ETRf9yei1U48C5MmfJmV9AiLYYBKPMq/W+/WRpQmCQ==",
+ "requires": {
+ "pkg-dir": "^3.0.0",
+ "resolve-cwd": "^2.0.0"
+ }
},
"is-absolute-url": {
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@@ -44477,7 +45169,7 @@
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- "integrity": "sha1-dfFmQrSA8YenEcgUFh/TpKdlWJg=",
+ "integrity": "sha512-9fRVlXc0uCxEDj1nQzaWONSpbTfx0FmJfzHF7pwlI8DkWGoHBBea4Pg5Ky0ojwwxQmnSifgbKkI06Qv0Ljgj+Q==",
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@@ -44485,18 +45177,26 @@
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"resolved": "https://registry.npmjs.org/is-extendable/-/is-extendable-0.1.1.tgz",
- "integrity": "sha1-YrEQ4omkcUGOPsNqYX1HLjAd/Ik="
+ "integrity": "sha512-5BMULNob1vgFX6EjQw5izWDxrecWK9AM72rugNr0TFldMOi0fj6Jk+zeKIt0xGj4cEfQIJth4w3OKWOJ4f+AFw=="
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- "integrity": "sha1-o7MKXE8ZkYMWeqq5O+764937ZU8="
+ "integrity": "sha512-VHskAKYM8RfSFXwee5t5cbN5PZeq1Wrh6qd5bkyiXIf6UQcN6w/A0eXM9r6t8d+GYOh+o6ZhiEnb88LN/Y8m2w=="
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},
+ "pkg-dir": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/pkg-dir/-/pkg-dir-3.0.0.tgz",
+ "integrity": "sha512-/E57AYkoeQ25qkxMj5PBOVgF8Kiu/h7cYS30Z5+R7WaiCCBfLq58ZI/dSeaEKb9WVJV5n/03QwrN3IeWIFllvw==",
+ "requires": {
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+ }
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"readable-stream": {
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"resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-2.3.7.tgz",
@@ -44521,10 +45221,18 @@
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- "integrity": "sha1-l/cXtp1IeE9fUmpsWqj/3aBVpNE="
+ "resolve-cwd": {
+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/resolve-cwd/-/resolve-cwd-2.0.0.tgz",
+ "integrity": "sha512-ccu8zQTrzVr954472aUVPLEcB3YpKSYR3cg/3lo1okzobPBM+1INXBbBZlDbnI/hbEocnf8j0QVo43hQKrbchg==",
+ "requires": {
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+ }
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+ "resolve-from": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/resolve-from/-/resolve-from-3.0.0.tgz",
+ "integrity": "sha512-GnlH6vxLymXJNMBo7XP1fJIzBFbdYt49CuTwmB/6N53t+kMPRMFKz783LlQ4tv28XoQfMWinAJX6WCGf2IlaIw=="
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@@ -44550,25 +45258,26 @@
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+ "version": "3.1.0",
+ "resolved": "https://registry.npmjs.org/string-width/-/string-width-3.1.0.tgz",
+ "integrity": "sha512-vafcv6KjVZKSgz06oM/H6GDBrAtz8vdhQakGjFIvNrHA6y3HCF1CInLy+QLq8dTJPQ1b+KDUqDFctkdRW44e1w==",
"requires": {
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"is-fullwidth-code-point": "^2.0.0",
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- "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-3.0.0.tgz",
- "integrity": "sha1-7QMXwyIGT3lGbAKWa922Bas32Zg="
+ "version": "4.1.1",
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- "integrity": "sha1-qEeQIusaw2iocTibY1JixQXuNo8=",
+ "version": "5.2.0",
+ "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-5.2.0.tgz",
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"requires": {
- "ansi-regex": "^3.0.0"
+ "ansi-regex": "^4.1.0"
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}
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@@ -44576,7 +45285,7 @@
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"resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
- "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
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@@ -44592,37 +45301,33 @@
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- "integrity": "sha1-fIDBe53+vlmeJzZ+DU3VWQFB2zg=",
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+ "workbox-routing": "^5.1.4"
}
},
"workbox-streams": {
- "version": "4.3.1",
- "resolved": "https://registry.npmjs.org/workbox-streams/-/workbox-streams-4.3.1.tgz",
- "integrity": "sha512-4Kisis1f/y0ihf4l3u/+ndMkJkIT4/6UOacU3A4BwZSAC9pQ9vSvJpIi/WFGQRH/uPXvuVjF5c2RfIPQFSS2uA==",
+ "version": "5.1.4",
+ "resolved": "https://registry.npmjs.org/workbox-streams/-/workbox-streams-5.1.4.tgz",
+ "integrity": "sha512-xU8yuF1hI/XcVhJUAfbQLa1guQUhdLMPQJkdT0kn6HP5CwiPOGiXnSFq80rAG4b1kJUChQQIGPrq439FQUNVrw==",
"requires": {
- "workbox-core": "^4.3.1"
+ "workbox-core": "^5.1.4",
+ "workbox-routing": "^5.1.4"
}
},
"workbox-sw": {
- "version": "4.3.1",
- "resolved": "https://registry.npmjs.org/workbox-sw/-/workbox-sw-4.3.1.tgz",
- "integrity": "sha512-0jXdusCL2uC5gM3yYFT6QMBzKfBr2XTk0g5TPAV4y8IZDyVNDyj1a8uSXy3/XrvkVTmQvLN4O5k3JawGReXr9w=="
+ "version": "5.1.4",
+ "resolved": "https://registry.npmjs.org/workbox-sw/-/workbox-sw-5.1.4.tgz",
+ "integrity": "sha512-9xKnKw95aXwSNc8kk8gki4HU0g0W6KXu+xks7wFuC7h0sembFnTrKtckqZxbSod41TDaGh+gWUA5IRXrL0ECRA=="
},
"workbox-webpack-plugin": {
- "version": "4.3.1",
- "resolved": "https://registry.npmjs.org/workbox-webpack-plugin/-/workbox-webpack-plugin-4.3.1.tgz",
- "integrity": "sha512-gJ9jd8Mb8wHLbRz9ZvGN57IAmknOipD3W4XNE/Lk/4lqs5Htw4WOQgakQy/o/4CoXQlMCYldaqUg+EJ35l9MEQ==",
+ "version": "5.1.4",
+ "resolved": "https://registry.npmjs.org/workbox-webpack-plugin/-/workbox-webpack-plugin-5.1.4.tgz",
+ "integrity": "sha512-PZafF4HpugZndqISi3rZ4ZK4A4DxO8rAqt2FwRptgsDx7NF8TVKP86/huHquUsRjMGQllsNdn4FNl8CD/UvKmQ==",
"requires": {
- "@babel/runtime": "^7.0.0",
- "json-stable-stringify": "^1.0.1",
- "workbox-build": "^4.3.1"
+ "@babel/runtime": "^7.5.5",
+ "fast-json-stable-stringify": "^2.0.0",
+ "source-map-url": "^0.4.0",
+ "upath": "^1.1.2",
+ "webpack-sources": "^1.3.0",
+ "workbox-build": "^5.1.4"
}
},
"workbox-window": {
- "version": "4.3.1",
- "resolved": "https://registry.npmjs.org/workbox-window/-/workbox-window-4.3.1.tgz",
- "integrity": "sha512-C5gWKh6I58w3GeSc0wp2Ne+rqVw8qwcmZnQGpjiek8A2wpbxSJb1FdCoQVO+jDJs35bFgo/WETgl1fqgsxN0Hg==",
+ "version": "5.1.4",
+ "resolved": "https://registry.npmjs.org/workbox-window/-/workbox-window-5.1.4.tgz",
+ "integrity": "sha512-vXQtgTeMCUq/4pBWMfQX8Ee7N2wVC4Q7XYFqLnfbXJ2hqew/cU1uMTD2KqGEgEpE4/30luxIxgE+LkIa8glBYw==",
"requires": {
- "workbox-core": "^4.3.1"
+ "workbox-core": "^5.1.4"
}
},
"worker-farm": {
@@ -44974,17 +45725,6 @@
"ansi-styles": "^4.0.0",
"string-width": "^4.1.0",
"strip-ansi": "^6.0.0"
- },
- "dependencies": {
- "strip-ansi": {
- "version": "6.0.1",
- "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz",
- "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==",
- "dev": true,
- "requires": {
- "ansi-regex": "^5.0.1"
- }
- }
}
},
"wrappy": {
@@ -44992,22 +45732,15 @@
"resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz",
"integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8="
},
- "write": {
- "version": "1.0.3",
- "resolved": "https://registry.npmjs.org/write/-/write-1.0.3.tgz",
- "integrity": "sha512-/lg70HAjtkUgWPVZhZcm+T4hkL8Zbtp1nFNOn3lRrxnlv50SRBv7cR7RqR+GMsd3hUXy9hWBo4CHTbFTcOYwig==",
- "requires": {
- "mkdirp": "^0.5.1"
- }
- },
"write-file-atomic": {
- "version": "2.4.1",
- "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-2.4.1.tgz",
- "integrity": "sha512-TGHFeZEZMnv+gBFRfjAcxL5bPHrsGKtnb4qsFAws7/vlh+QfwAaySIw4AXP9ZskTTh5GWu3FLuJhsWVdiJPGvg==",
+ "version": "3.0.3",
+ "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-3.0.3.tgz",
+ "integrity": "sha512-AvHcyZ5JnSfq3ioSyjrBkH9yW4m7Ayk8/9My/DD9onKeu/94fwrMocemO2QAJFAlnnDN+ZDS+ZjAR5ua1/PV/Q==",
"requires": {
- "graceful-fs": "^4.1.11",
"imurmurhash": "^0.1.4",
- "signal-exit": "^3.0.2"
+ "is-typedarray": "^1.0.0",
+ "signal-exit": "^3.0.2",
+ "typedarray-to-buffer": "^3.1.5"
}
},
"ws": {
@@ -45046,14 +45779,6 @@
"resolved": "https://registry.npmjs.org/xmlchars/-/xmlchars-2.2.0.tgz",
"integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw=="
},
- "xregexp": {
- "version": "4.4.1",
- "resolved": "https://registry.npmjs.org/xregexp/-/xregexp-4.4.1.tgz",
- "integrity": "sha512-2u9HwfadaJaY9zHtRRnH6BY6CQVNQKkYm3oLtC9gJXXzfsbACg5X5e4EZZGVAH+YIfa+QA9lsFQTTe3HURF3ag==",
- "requires": {
- "@babel/runtime-corejs3": "^7.12.1"
- }
- },
"xtend": {
"version": "4.0.2",
"resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz",
@@ -45075,45 +45800,52 @@
"integrity": "sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg=="
},
"yargs": {
- "version": "13.3.2",
- "resolved": "https://registry.npmjs.org/yargs/-/yargs-13.3.2.tgz",
- "integrity": "sha512-AX3Zw5iPruN5ie6xGRIDgqkT+ZhnRlZMLMHAs8tg7nRruy2Nb+i5o9bwghAogtM08q1dpr2LVoS8KSTMYpWXUw==",
+ "version": "15.4.1",
+ "resolved": "https://registry.npmjs.org/yargs/-/yargs-15.4.1.tgz",
+ "integrity": "sha512-aePbxDmcYW++PaqBsJ+HYUFwCdv4LVvdnhBy78E57PIor8/OVvhMrADFFEDh8DHDFRv/O9i3lPhsENjO7QX0+A==",
"requires": {
- "cliui": "^5.0.0",
- "find-up": "^3.0.0",
+ "cliui": "^6.0.0",
+ "decamelize": "^1.2.0",
+ "find-up": "^4.1.0",
"get-caller-file": "^2.0.1",
"require-directory": "^2.1.1",
"require-main-filename": "^2.0.0",
"set-blocking": "^2.0.0",
- "string-width": "^3.0.0",
+ "string-width": "^4.2.0",
"which-module": "^2.0.0",
"y18n": "^4.0.0",
- "yargs-parser": "^13.1.2"
+ "yargs-parser": "^18.1.2"
},
"dependencies": {
- "is-fullwidth-code-point": {
- "version": "2.0.0",
- "resolved": "https://registry.npmjs.org/is-fullwidth-code-point/-/is-fullwidth-code-point-2.0.0.tgz",
- "integrity": "sha1-o7MKXE8ZkYMWeqq5O+764937ZU8="
+ "find-up": {
+ "version": "4.1.0",
+ "resolved": "https://registry.npmjs.org/find-up/-/find-up-4.1.0.tgz",
+ "integrity": "sha512-PpOwAdQ/YlXQ2vj8a3h8IipDuYRi3wceVQQGYWxNINccq40Anw7BlsEXCMbt1Zt+OLA6Fq9suIpIWD0OsnISlw==",
+ "requires": {
+ "locate-path": "^5.0.0",
+ "path-exists": "^4.0.0"
+ }
},
- "string-width": {
- "version": "3.1.0",
- "resolved": "https://registry.npmjs.org/string-width/-/string-width-3.1.0.tgz",
- "integrity": "sha512-vafcv6KjVZKSgz06oM/H6GDBrAtz8vdhQakGjFIvNrHA6y3HCF1CInLy+QLq8dTJPQ1b+KDUqDFctkdRW44e1w==",
+ "locate-path": {
+ "version": "5.0.0",
+ "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-5.0.0.tgz",
+ "integrity": "sha512-t7hw9pI+WvuwNJXwk5zVHpyhIqzg2qTlklJOf0mVxGSbe3Fp2VieZcduNYjaLDoy6p9uGpQEGWG87WpMKlNq8g==",
"requires": {
- "emoji-regex": "^7.0.1",
- "is-fullwidth-code-point": "^2.0.0",
- "strip-ansi": "^5.1.0"
+ "p-locate": "^4.1.0"
}
},
- "yargs-parser": {
- "version": "13.1.2",
- "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-13.1.2.tgz",
- "integrity": "sha512-3lbsNRf/j+A4QuSZfDRA7HRSfWrzO0YjqTJd5kjAq37Zep1CEgaYmrH9Q3GwPiB9cHyd1Y1UwggGhJGoxipbzg==",
+ "p-locate": {
+ "version": "4.1.0",
+ "resolved": "https://registry.npmjs.org/p-locate/-/p-locate-4.1.0.tgz",
+ "integrity": "sha512-R79ZZ/0wAxKGu3oYMlz8jy/kbhsNrS7SKZ7PxEHBgJ5+F2mtFW2fK2cOtBh1cHYkQsbzFV7I+EoRKe6Yt0oK7A==",
"requires": {
- "camelcase": "^5.0.0",
- "decamelize": "^1.2.0"
+ "p-limit": "^2.2.0"
}
+ },
+ "path-exists": {
+ "version": "4.0.0",
+ "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-4.0.0.tgz",
+ "integrity": "sha512-ak9Qy5Q7jYb2Wwcey5Fpvg2KoAc/ZIhLSLOSBmRmygPsGwkVVt0fZa0qrtMz+m6tJTAHfZQ8FnmB4MG4LWy7/w=="
}
}
},
@@ -45121,20 +45853,15 @@
"version": "18.1.3",
"resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-18.1.3.tgz",
"integrity": "sha512-o50j0JeToy/4K6OZcaQmW6lyXXKhq7csREXcDwk2omFPJEwUNOVtJKvmDr9EI1fAJZUyZcRF7kxGBWmRXudrCQ==",
- "dev": true,
"requires": {
"camelcase": "^5.0.0",
"decamelize": "^1.2.0"
}
},
- "yauzl": {
- "version": "2.10.0",
- "resolved": "https://registry.npmjs.org/yauzl/-/yauzl-2.10.0.tgz",
- "integrity": "sha1-x+sXyT4RLLEIb6bY5R+wZnt5pfk=",
- "requires": {
- "buffer-crc32": "~0.2.3",
- "fd-slicer": "~1.1.0"
- }
+ "yocto-queue": {
+ "version": "0.1.0",
+ "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
+ "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q=="
}
}
}
diff --git a/package.json b/package.json
index 535f7f3..31741bd 100644
--- a/package.json
+++ b/package.json
@@ -9,7 +9,6 @@
"@testing-library/jest-dom": "^4.2.4",
"@testing-library/react": "^9.5.0",
"@testing-library/user-event": "^7.2.1",
- "popper.js": "^1.16.1",
"array-move": "^2.2.1",
"bootstrap": "^4.5.0",
"browserify": "^17.0.0",
@@ -20,9 +19,10 @@
"evergreen-ui": "^2.0.1",
"html2canvas": "^1.3.2",
"jquery": "^3.5.1",
- "lodash": "^4.17.21",
"jspdf": "^2.3.1",
+ "lodash": "^4.17.21",
"phylotree": "github:mwittep/phylotree.js",
+ "popper.js": "^1.16.1",
"react": "^16.13.1",
"react-bootstrap": "^1.0.1",
"react-color": "^2.18.1",
diff --git a/server/.DS_Store b/server/.DS_Store
index 8a6b06e..710c67f 100644
Binary files a/server/.DS_Store and b/server/.DS_Store differ
diff --git a/server/backend_prepare_data.py b/server/backend_prepare_data.py
index 980119f..a602cb9 100644
--- a/server/backend_prepare_data.py
+++ b/server/backend_prepare_data.py
@@ -162,7 +162,7 @@ def call_classico(tmpdir, nwk, snp):
fp_nwk.flush()
fp_snp.flush()
env = dict(os.environ)
- subprocess.run(["java", "-jar", ScriptDir + "/classico.jar", fp_snp.name,
+ subprocess.run(["java", "-jar", "-Xms4G", ScriptDir + "/classico.jar", fp_snp.name,
fp_nwk.name, tmpdir], env=env)
diff --git a/server/data/go-basic.obo b/server/data/go-basic.obo
index 4cc4c0d..43263fe 100644
--- a/server/data/go-basic.obo
+++ b/server/data/go-basic.obo
@@ -1,5 +1,5 @@
format-version: 1.2
-data-version: releases/2021-12-15
+data-version: releases/2023-04-01
subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3."
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
@@ -17,6 +17,7 @@ subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_pombe "Fission yeast GO slim"
subsetdef: goslim_synapse "synapse GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
+subsetdef: prokaryote_subset "GO subset for prokaryotes"
synonymtypedef: syngo_official_label "label approved by the SynGO project"
synonymtypedef: systematic_synonym "Systematic synonym" EXACT
default-namespace: gene_ontology
@@ -100,7 +101,6 @@ name: alpha-1,6-mannosyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->6) linkage." [GOC:mcc, PMID:2644248]
synonym: "1,6-alpha-mannosyltransferase activity" EXACT []
-xref: EC:2.4.1.232
xref: Reactome:R-HSA-449718 "Addition of a third mannose to the N-glycan precursor by ALG2"
is_a: GO:0000030 ! mannosyltransferase activity
@@ -108,8 +108,16 @@ is_a: GO:0000030 ! mannosyltransferase activity
id: GO:0000010
name: trans-hexaprenyltranstransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: all-trans-hexaprenyl diphosphate + isopentenyl diphosphate = all-trans-heptaprenyl diphosphate + diphosphate." [PMID:9708911, RHEA:20836]
-xref: RHEA:20836
+alt_id: GO:0036422
+def: "Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate." [PMID:9708911, RHEA:27794]
+synonym: "all-trans-heptaprenyl-diphosphate synthase activity" RELATED [EC:2.5.1.30]
+synonym: "HepPP synthase activity" RELATED [EC:2.5.1.30]
+synonym: "heptaprenyl diphosphate synthase activity" RELATED []
+synonym: "heptaprenyl pyrophosphate synthase activity" RELATED [EC:2.5.1.30]
+synonym: "heptaprenyl pyrophosphate synthetase activity" RELATED [EC:2.5.1.30]
+xref: EC:2.5.1.30
+xref: MetaCyc:TRANS-HEXAPRENYLTRANSTRANSFERASE-RXN
+xref: RHEA:27794
is_a: GO:0004659 ! prenyltransferase activity
[Term]
@@ -134,7 +142,7 @@ namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks." [GOC:mah]
synonym: "single-stranded DNA specific endodeoxyribonuclease activity" RELATED []
synonym: "ssDNA-specific endodeoxyribonuclease activity" RELATED [GOC:mah]
-is_a: GO:0004520 ! endodeoxyribonuclease activity
+is_a: GO:0004520 ! DNA endonuclease activity
[Term]
id: GO:0000015
@@ -151,7 +159,6 @@ id: GO:0000016
name: lactase activity
namespace: molecular_function
def: "Catalysis of the reaction: lactose + H2O = D-glucose + D-galactose." [PMID:12023280]
-synonym: "lactase-phlorizin hydrolase activity" BROAD []
synonym: "lactose galactohydrolase activity" EXACT []
xref: EC:3.2.1.108
xref: MetaCyc:LACTASE-RXN
@@ -262,10 +269,10 @@ is_a: GO:0000030 ! mannosyltransferase activity
id: GO:0000027
name: ribosomal large subunit assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit." [GOC:jl]
+def: "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit." [GOC:jl, PMID:30467428]
synonym: "50S ribosomal subunit assembly" NARROW [GOC:mah]
synonym: "60S ribosomal subunit assembly" NARROW [GOC:mah]
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0042255 ! ribosome assembly
relationship: part_of GO:0042273 ! ribosomal large subunit biogenesis
@@ -273,10 +280,10 @@ relationship: part_of GO:0042273 ! ribosomal large subunit biogenesis
id: GO:0000028
name: ribosomal small subunit assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the small ribosomal subunit." [GOC:jl]
+def: "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the small ribosomal subunit." [GOC:jl, PMID:30467428]
synonym: "30S ribosomal subunit assembly" NARROW [GOC:mah]
synonym: "40S ribosomal subunit assembly" NARROW [GOC:mah]
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0042255 ! ribosome assembly
relationship: part_of GO:0042274 ! ribosomal small subunit biogenesis
@@ -357,7 +364,7 @@ is_a: GO:0140414 ! phosphopantetheine-dependent carrier activity
id: GO:0000038
name: very long-chain fatty acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a fatty acid which has a chain length greater than C22." [GOC:hjd]
+def: "The chemical reactions and pathways involving a very long chain fatty acid, a fatty acid with an aliphatic tail of 22 or more carbons." [GOC:hjd]
synonym: "very long chain fatty acid metabolic process" EXACT [GOC:bf]
synonym: "very-long-chain fatty acid metabolic process" EXACT []
synonym: "very-long-chain fatty acid metabolism" EXACT []
@@ -583,8 +590,6 @@ def: "Enables the transfer of L-ornithine from one side of a membrane to the oth
synonym: "histidine/arginine/lysine/ornithine porter activity" RELATED []
synonym: "L-ornithine transporter activity" BROAD []
xref: Reactome:R-HSA-70634 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic)"
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
[Term]
@@ -727,7 +732,7 @@ id: GO:0000083
name: regulation of transcription involved in G1/S transition of mitotic cell cycle
namespace: biological_process
def: "Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle." [GOC:mtg_cell_cycle]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
is_a: GO:1903047 ! mitotic cell cycle process
relationship: part_of GO:0000082 ! G1/S transition of mitotic cell cycle
@@ -869,8 +874,8 @@ def: "The chemical reactions and pathways involving amino acids containing sulfu
synonym: "sulfur amino acid metabolism" EXACT []
synonym: "sulphur amino acid metabolic process" EXACT []
synonym: "sulphur amino acid metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0006790 ! sulfur compound metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
@@ -885,8 +890,8 @@ synonym: "sulfur amino acid synthesis" EXACT []
synonym: "sulphur amino acid biosynthesis" EXACT []
synonym: "sulphur amino acid biosynthetic process" EXACT []
is_a: GO:0000096 ! sulfur amino acid metabolic process
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0044272 ! sulfur compound biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:1901566 ! organonitrogen compound biosynthetic process
[Term]
@@ -900,8 +905,8 @@ synonym: "sulfur amino acid degradation" EXACT []
synonym: "sulphur amino acid catabolic process" EXACT []
synonym: "sulphur amino acid catabolism" EXACT []
is_a: GO:0000096 ! sulfur amino acid metabolic process
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
[Term]
@@ -943,7 +948,6 @@ def: "Enables the transfer of L-methionine from one side of a membrane to the ot
synonym: "L-methionine porter activity" RELATED []
is_a: GO:0005294 ! neutral L-amino acid secondary active transmembrane transporter activity
is_a: GO:0015191 ! L-methionine transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:1901680 ! sulfur-containing amino acid secondary active transmembrane transporter activity
[Term]
@@ -988,13 +992,13 @@ synonym: "histidine formation" EXACT []
synonym: "histidine synthesis" EXACT []
xref: MetaCyc:HISTSYN-PWY
is_a: GO:0006547 ! histidine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
+is_a: GO:0008652 ! amino acid biosynthetic process
[Term]
id: GO:0000107
name: imidazoleglycerol-phosphate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phosphoribulosylformimino-AICAR-P + L-glutamine = D-erythro-imidazole-glycerol-phosphate + aminoimidazole carboxamide ribonucleotide + L-glutamate + 2 H(+)." [RHEA:24793]
+def: "Catalysis of the reaction: phosphoribulosylformimino-AICAR-P + L-glutamine = D-erythro-imidazole-glycerol-phosphate + aminoimidazole carboxamide ribonucleotide + L-glutamate + 2 H+." [RHEA:24793]
synonym: "glutamine amidotransferase:cyclase activity" BROAD []
synonym: "imidazole glycerol phosphate synthase activity" EXACT []
synonym: "imidazole-glycerol-phosphate synthase activity" RELATED []
@@ -1023,7 +1027,6 @@ subset: goslim_pir
synonym: "UvrB-UvrC complex" NARROW [PMID:12145219]
synonym: "UvrBC complex" NARROW [GOC:bhm, PMID:12145219]
is_a: GO:0140513 ! nuclear protein-containing complex
-is_a: GO:1990391 ! DNA repair complex
[Term]
id: GO:0000110
@@ -1110,7 +1113,7 @@ namespace: biological_process
def: "Any process that regulates transcription such that the target genes are transcribed as part of the G2/M transition of the mitotic cell cycle." [GOC:mtg_cell_cycle]
synonym: "G2/M-specific transcription in mitotic cell cycle" RELATED []
synonym: "regulation of transcription from RNA polymerase II promoter during G2/M transition of mitotic cell cycle" RELATED []
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
is_a: GO:1903047 ! mitotic cell cycle process
relationship: part_of GO:0000086 ! G2/M transition of mitotic cell cycle
@@ -1172,7 +1175,7 @@ synonym: "negative regulation of transcription from Pol II promoter" EXACT []
synonym: "negative regulation of transcription from RNA polymerase II promoter" EXACT []
synonym: "negative regulation of transcription from RNA polymerase II promoter, global" RELATED []
is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
relationship: negatively_regulates GO:0006366 ! transcription by RNA polymerase II
[Term]
@@ -1180,11 +1183,10 @@ id: GO:0000123
name: histone acetyltransferase complex
namespace: cellular_component
def: "A protein complex that possesses histone acetyltransferase activity." [GOC:mah]
-comment: Note that this term represents a location, not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function of this complex is represented by the molecular function term 'histone acetyltransferase activity ; GO:0004402'.
+comment: Note that this term represents a protein complex, not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function of this complex is represented by the molecular function term 'histone acetyltransferase activity ; GO:0004402'.
synonym: "histone acetylase complex" EXACT []
is_a: GO:0031248 ! protein acetyltransferase complex
-is_a: GO:0140513 ! nuclear protein-containing complex
-relationship: part_of GO:0005654 ! nucleoplasm
+relationship: part_of GO:0000785 ! chromatin
[Term]
id: GO:0000124
@@ -1282,7 +1284,7 @@ synonym: "alpha-1,6-mannosyltransferase complex" EXACT []
is_a: GO:0031501 ! mannosyltransferase complex
is_a: GO:0098796 ! membrane protein complex
relationship: part_of GO:0000137 ! Golgi cis cisterna
-relationship: part_of GO:0030173 ! integral component of Golgi membrane
+relationship: part_of GO:0000139 ! Golgi membrane
[Term]
id: GO:0000137
@@ -1311,7 +1313,7 @@ relationship: part_of GO:0005794 ! Golgi apparatus
id: GO:0000140
name: acylglycerone-phosphate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-palmitoylglycerol-3-phosphate + NADP+ = palmitoylglycerone phosphate + NADPH + H(+)." [EC:1.1.1.101]
+def: "Catalysis of the reaction: 1-palmitoylglycerol-3-phosphate + NADP+ = palmitoylglycerone phosphate + NADPH + H+." [EC:1.1.1.101]
synonym: "1-acyldihydroxyacetone-phosphate reductase activity" EXACT []
synonym: "1-palmitoylglycerol-3-phosphate:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.101]
synonym: "acyldihydroxyacetone phosphate reductase activity" RELATED [EC:1.1.1.101]
@@ -1385,7 +1387,7 @@ is_a: GO:0044396 ! actin cortical patch organization
id: GO:0000148
name: 1,3-beta-D-glucan synthase complex
namespace: cellular_component
-def: "A protein complex that catalyzes the transfer of a glucose group from UDP-glucose to a (1->3)-beta-D-glucan chain." [EC:2.4.1.34]
+def: "A protein complex that catalyzes the transfer of a glucose group from UDP-glucose to a (1->3)-beta-D-glucan chain." [PMID:7983071]
synonym: "(1->3)-beta-glucan synthase complex" EXACT [GOC:tb]
synonym: "1,3-beta-glucan synthase complex" EXACT [GOC:tb]
is_a: GO:0098797 ! plasma membrane protein complex
@@ -1496,7 +1498,7 @@ synonym: "PP2A complex" EXACT []
synonym: "PP2A-pi" NARROW []
synonym: "PP2a-protector" NARROW []
synonym: "protein phosphatase 2 complex" RELATED [GOC:dph, GOC:rl]
-is_a: GO:0005963 ! magnesium-dependent protein serine/threonine phosphatase complex
+is_a: GO:0008287 ! protein serine/threonine phosphatase complex
[Term]
id: GO:0000160
@@ -1516,7 +1518,7 @@ alt_id: GO:0000168
alt_id: GO:0000169
alt_id: GO:0000173
alt_id: GO:0007233
-def: "A series of molecular signals in which a stress-activated protein kinase (SAPK) cascade relays one or more of the signals, containing at least a Hog1/Sty1 family MAPK, a Pbs2/Wis1 family MAPKK and a Ssk2/Win1 family MAP3K." [PMID:17604854, PMID:9561267]
+def: "The series of molecular signals in which a stress-activated protein kinase (SAPK) cascade relays a signal, containing at least a Hog1/Sty1 family MAPK, a Pbs2/Wis1 family MAPKK and a Ssk2/Win1 family MAP3K." [PMID:17604854, PMID:9561267]
synonym: "activation of MAPK activity involved in osmosensory signaling pathway" NARROW []
synonym: "activation of MAPKK activity during osmolarity sensing" NARROW []
synonym: "activation of MAPKK activity involved in osmosensory signaling pathway" NARROW []
@@ -1613,7 +1615,7 @@ namespace: molecular_function
def: "Catalysis of the site-specific cleavage of RNA by a catalytic RNA-mediated mechanism; substrates include the A3 site in the ITS1 of pre-rRNA." [PMID:17881380]
synonym: "RNase MRP" EXACT []
xref: Wikipedia:RNase_MRP
-is_a: GO:0004521 ! endoribonuclease activity
+is_a: GO:0004521 ! RNA endonuclease activity
[Term]
id: GO:0000172
@@ -1637,10 +1639,11 @@ replaced_by: GO:0000750
[Term]
id: GO:0000175
-name: 3'-5'-exoribonuclease activity
+name: 3'-5'-RNA exonuclease activity
namespace: molecular_function
def: "Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule." [GOC:mah, ISBN:0198547684]
synonym: "3'-5' exoribonuclease activity" EXACT []
+synonym: "3'-5'-exoribonuclease activity" EXACT []
xref: EC:3.1.13.-
xref: Reactome:R-HSA-430028 "Exosome Complex hydrolyzes mRNA by 3' to 5' exoribonuclease digestion"
xref: Reactome:R-HSA-6791222 "21S pre-rRNA is nucleolytically processed at site E (site2a) to yield 18SE pre-rRNA"
@@ -1648,7 +1651,7 @@ xref: Reactome:R-HSA-6791227 "47S pre-rRNA is nucleolytically processed at A' (0
xref: Reactome:R-HSA-9682603 "nsp14 acts as a 3'-to-5' exonuclease to remove misincorporated nucleotides from nascent RNA"
xref: Reactome:R-HSA-9694632 "nsp14 acts as a 3'-to-5' exonuclease to remove misincorporated nucleotides from nascent RNA"
is_a: GO:0008408 ! 3'-5' exonuclease activity
-is_a: GO:0016896 ! exoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016896 ! RNA exonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0000176
@@ -1729,14 +1732,15 @@ is_a: GO:1990837 ! sequence-specific double-stranded DNA binding
[Term]
id: GO:0000183
-name: rDNA heterochromatin assembly
+name: rDNA heterochromatin formation
namespace: biological_process
-def: "The assembly of chromatin characterized by the modified histone H3K9me3, into heterochromatin, resulting in the repression of transcription of rDNA." [PMID:10219245]
+def: "The formation of heterochromatin at ribosomal DNA, characterized by the modified histone H3K9me3." [PMID:10219245]
synonym: "chromatin silencing at rDNA" RELATED []
synonym: "chromatin silencing at ribosomal DNA" BROAD []
synonym: "heterochromatic silencing at rDNA" BROAD []
synonym: "rDNA chromatin silencing" BROAD [GOC:mah]
-is_a: GO:0140718 ! facultative heterochromatin assembly
+synonym: "rDNA heterochromatin assembly" EXACT []
+is_a: GO:0140718 ! facultative heterochromatin formation
relationship: part_of GO:1990700 ! nucleolar chromatin organization
[Term]
@@ -2042,19 +2046,18 @@ is_a: GO:0016567 ! protein ubiquitination
id: GO:0000210
name: NAD+ diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD+ + H2O = AMP + NMN." [EC:3.6.1.22]
-synonym: "NAD diphosphatase activity" EXACT []
-synonym: "NAD pyrophosphatase activity" EXACT []
-synonym: "NAD(+) pyrophosphatase activity" RELATED [EC:3.6.1.22]
-synonym: "NAD+ phosphohydrolase activity" RELATED [EC:3.6.1.22]
-synonym: "NAD+ pyrophosphatase activity" RELATED [EC:3.6.1.22]
-synonym: "NADH pyrophosphatase activity" BROAD [EC:3.6.1.22]
-synonym: "NADP pyrophosphatase activity" BROAD [EC:3.6.1.22]
+def: "Catalysis of the reaction: NAD+ + H2O = AMP + NMN." [RHEA:11800]
+synonym: "NAD diphosphatase activity" BROAD []
+synonym: "NAD pyrophosphatase activity" BROAD []
+synonym: "NAD(+) pyrophosphatase activity" EXACT []
+synonym: "NAD+ phosphohydrolase activity" EXACT []
+synonym: "NAD+ pyrophosphatase activity" EXACT []
+synonym: "NADP pyrophosphatase activity" RELATED [EC:3.6.1.22]
synonym: "nicotinamide adenine dinucleotide pyrophosphatase activity" RELATED [EC:3.6.1.22]
xref: EC:3.6.1.22
xref: MetaCyc:NADPYROPHOSPHAT-RXN
xref: RHEA:11800
-is_a: GO:0004551 ! nucleotide diphosphatase activity
+is_a: GO:0004551 ! dinucleotide phosphatase activity
[Term]
id: GO:0000211
@@ -2084,18 +2087,13 @@ is_a: GO:1903046 ! meiotic cell cycle process
id: GO:0000213
name: tRNA-intron endonuclease activity
namespace: molecular_function
-def: "Catalysis of the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron." [EC:3.1.27.9]
-synonym: "splicing endonuclease activity" RELATED [EC:3.1.27.9]
-synonym: "transfer ribonucleate intron endoribonuclease activity" RELATED [EC:3.1.27.9]
-synonym: "transfer splicing endonuclease activity" RELATED [EC:3.1.27.9]
-synonym: "tRNA splicing endonuclease activity" RELATED [EC:3.1.27.9]
+def: "Catalysis of the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron." [EC:4.6.1.16]
+synonym: "tRNA splicing endonuclease activity" RELATED [EC:4.6.1.16]
synonym: "tRNA-intron endoribonuclease activity" EXACT []
-synonym: "tRNA-splicing endonuclease activity" RELATED [EC:3.1.27.9]
-synonym: "tRNATRPintron endonuclease activity" RELATED [EC:3.1.27.9]
-xref: EC:3.1.27.9
+xref: EC:4.6.1.16
xref: MetaCyc:3.1.27.9-RXN
is_a: GO:0004549 ! tRNA-specific ribonuclease activity
-is_a: GO:0016892 ! endoribonuclease activity, producing 3'-phosphomonoesters
+is_a: GO:0016892 ! RNA endonuclease activity, producing 3'-phosphomonoesters
[Term]
id: GO:0000214
@@ -2181,7 +2179,6 @@ def: "The V0 domain of a proton-transporting V-type ATPase found in the plasma m
synonym: "plasma membrane hydrogen ion-transporting ATPase V0 domain" EXACT []
is_a: GO:0033179 ! proton-transporting V-type ATPase, V0 domain
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
relationship: part_of GO:0033181 ! plasma membrane proton-transporting V-type ATPase complex
[Term]
@@ -2192,7 +2189,6 @@ def: "The V1 domain of a proton-transporting V-type ATPase found in the plasma m
synonym: "plasma membrane hydrogen ion-transporting ATPase V1 domain" EXACT []
is_a: GO:0033180 ! proton-transporting V-type ATPase, V1 domain
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
relationship: part_of GO:0033181 ! plasma membrane proton-transporting V-type ATPase complex
[Term]
@@ -2242,7 +2238,6 @@ def: "A process that is carried out at the cellular level which results in the a
subset: goslim_pombe
synonym: "microtubule cytoskeleton organisation" EXACT [GOC:mah]
synonym: "microtubule cytoskeleton organization and biogenesis" RELATED [GOC:mah]
-synonym: "microtubule dynamics" EXACT [GOC:dph, GOC:tb]
is_a: GO:0007010 ! cytoskeleton organization
is_a: GO:0007017 ! microtubule-based process
@@ -2254,7 +2249,6 @@ def: "Enables the transfer of oxaloacetate from one side of a membrane to the ot
synonym: "oxaloacetate carrier activity" RELATED []
is_a: GO:0015131 ! oxaloacetate transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0000228
@@ -2347,7 +2341,7 @@ namespace: biological_process
def: "The cell cycle phase in higher eukaryotes which follows mitotic prophase and during which the nuclear envelope is disrupted and breaks into membrane vesicles, and the spindle microtubules enter the nuclear region. Kinetochores mature on each centromere and attach to some of the spindle microtubules. Kinetochore microtubules begin the process of aligning chromosomes in one plane halfway between the poles." [GOC:mtg_cell_cycle]
comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
subset: gocheck_do_not_annotate
-is_a: GO:0098763 ! mitotic cell cycle phase
+is_a: GO:0000087 ! mitotic M phase
[Term]
id: GO:0000237
@@ -2449,14 +2443,14 @@ name: spliceosomal complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions." [PMID:9476892]
synonym: "spliceosome assembly" BROAD []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0000398 ! mRNA splicing, via spliceosome
[Term]
id: GO:0000246
name: delta24(24-1) sterol reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ergosterol + NADP(+) = ergosta-5,7,22,24(24(1))-tetraen-3beta-ol + H(+) + NADPH." [EC:1.3.1.71, RHEA:18501]
+def: "Catalysis of the reaction: ergosterol + NADP+ = ergosta-5,7,22,24(24(1))-tetraen-3beta-ol + H+ + NADPH." [EC:1.3.1.71, RHEA:18501]
synonym: "C-24(28) sterol reductase activity" RELATED [EC:1.3.1.71]
synonym: "D24(24-1)-sterol reductase activity" EXACT []
synonym: "delta24(241)-sterol reductase activity" RELATED [EC:1.3.1.71]
@@ -2551,7 +2545,7 @@ id: GO:0000253
name: 3-keto sterol reductase activity
namespace: molecular_function
alt_id: GO:0050576
-def: "Catalysis of the reaction: a 3-beta-hydroxyl sterol + NADP+ = a 3-keto sterol + NADPH + H(+)." [EC:1.1.1.270, GOC:mah, MetaCyc:1.1.1.270-RXN, MetaCyc:RXN3O-4110, MetaCyc:RXN66-19, MetaCyc:RXN66-24, MetaCyc:RXN66-314, MetaCyc:RXN66-319, PMID:9811880]
+def: "Catalysis of the reaction: a 3-beta-hydroxyl sterol + NADP+ = a 3-keto sterol + NADPH + H+." [EC:1.1.1.270, GOC:mah, PMID:9811880]
comment: Note that zymosterol is cholesta-8,24-dien-3-ol.
synonym: "3-keto-steroid reductase activity" EXACT []
synonym: "3-KSR activity" RELATED [EC:1.1.1.270]
@@ -2572,19 +2566,17 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0000254
name: C-4 methylsterol oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4,4-dimethyl-5-alpha-cholesta-8,24-dien-3-beta-ol + NAD(P)H + H(+) + O2 = 4-beta-hydroxymethyl-4-alpha-methyl-5-alpha-cholesta-8,24-dien-3-beta-ol + NAD(P)+ + H2O." [EC:1.14.18.9, PMID:9811880]
+def: "Catalysis of the reaction: 4,4-dimethyl-5-alpha-cholesta-8,24-dien-3-beta-ol + 6 Fe(II)-[cytochrome b5] + 5 H+ + 3 O2 = 4-beta-hydroxymethyl-4-alpha-methyl-5-alpha-cholesta-8,24-dien-3-beta-ol + 6 Fe(III)-[cytochrome b5] + 4 H2O." [PMID:9811880, RHEA:55220]
comment: Note that zymosterol is cholesta-8,24-dien-3-ol.
-synonym: "4,4-dimethyl-5alpha-cholest-7-en-3beta-ol,hydrogen-donor:oxygen oxidoreductase (hydroxylating)" RELATED [EC:1.14.18.9]
-synonym: "4,4-dimethyl-5alpha-cholest-7-en-3beta-ol,NAD(P)H:oxygen oxidoreductase (hydroxylating)" RELATED [EC:1.14.18.9]
-synonym: "4-methylsterol oxidase activity" EXACT []
-synonym: "methylsterol hydroxylase activity" RELATED []
-synonym: "methylsterol monooxygenase activity" RELATED []
+synonym: "4-methylsterol oxidase activity" EXACT [EC:1.14.18.9]
+synonym: "methylsterol hydroxylase activity" RELATED [EC:1.14.18.9]
+synonym: "methylsterol monooxygenase activity" RELATED [EC:1.14.18.9]
xref: EC:1.14.18.9
xref: MetaCyc:1.14.13.72-RXN
xref: Reactome:R-HSA-194641 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol"
xref: Reactome:R-HSA-194669 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol"
xref: RHEA:55220
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+is_a: GO:0016716 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0000255
@@ -2592,7 +2584,7 @@ name: allantoin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving allantoin, (2,5-dioxo-4-imidazolidinyl)urea, an intermediate or end product of purine catabolism." [GOC:mah, ISBN:0198547684]
synonym: "allantoin metabolism" EXACT []
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
@@ -2606,7 +2598,7 @@ synonym: "allantoin breakdown" EXACT []
synonym: "allantoin catabolism" EXACT []
synonym: "allantoin degradation" EXACT []
is_a: GO:0000255 ! allantoin metabolic process
-is_a: GO:0043605 ! cellular amide catabolic process
+is_a: GO:0043605 ! amide catabolic process
is_a: GO:0046700 ! heterocycle catabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
@@ -2653,7 +2645,7 @@ consider: GO:0005622
id: GO:0000260
name: obsolete hydrogen-translocating V-type ATPase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: ATP + H2O + H(+)(in) = ADP + phosphate + H+(out). Found in vacuoles of eukaryotes and in bacteria." [TC:3.A.2.2.1, TC:3.A.2.2.3]
+def: "OBSOLETE. Catalysis of the reaction: ATP + H2O + H+(in) = ADP + phosphate + H+(out). Found in vacuoles of eukaryotes and in bacteria." [TC:3.A.2.2.1, TC:3.A.2.2.3]
comment: This term was made obsolete because it represents a gene product.
synonym: "hydrogen-translocating V-type ATPase activity" EXACT []
is_obsolete: true
@@ -2911,7 +2903,7 @@ replaced_by: GO:0000753
id: GO:0000285
name: 1-phosphatidylinositol-3-phosphate 5-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + ADP + 2 H(+)." [EC:2.7.1.150, RHEA:13609]
+def: "Catalysis of the reaction: a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + ADP + 2 H+." [EC:2.7.1.150, RHEA:13609]
synonym: "ATP:1-phosphatidyl-1D-myo-inositol-3-phosphate 5-phosphotransferase activity" RELATED [EC:2.7.1.150]
synonym: "phosphatidylinositol 3-phosphate 5-kinase activity" RELATED [EC:2.7.1.150]
synonym: "phosphatidylinositol-3-phosphate 5-kinase activity" EXACT []
@@ -2930,7 +2922,7 @@ is_a: GO:0016307 ! phosphatidylinositol phosphate kinase activity
id: GO:0000286
name: alanine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-alanine + H2O + NAD+ = pyruvate + NH3 + NADH + H(+)." [EC:1.4.1.1]
+def: "Catalysis of the reaction: L-alanine + H2O + NAD+ = pyruvate + NH3 + NADH + H+." [EC:1.4.1.1]
synonym: "AlaDH" RELATED [EC:1.4.1.1]
synonym: "alanine oxidoreductase activity" RELATED [EC:1.4.1.1]
synonym: "alpha-alanine dehydrogenase activity" RELATED [EC:1.4.1.1]
@@ -3025,15 +3017,11 @@ is_a: GO:0016722 ! oxidoreductase activity, acting on metal ions
[Term]
id: GO:0000294
-name: nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay
-namespace: biological_process
-def: "A minor degradation pathway nuclear-transcribed mRNAs that begins with an endonucleolytic cleavage to generate unprotected ends." [GOC:krc]
-synonym: "endonucleolytic mRNA decay" EXACT []
-synonym: "mRNA breakdown, endonucleolytic cleavage-dependent decay" EXACT []
-synonym: "mRNA catabolic process, endonucleolytic" EXACT []
-synonym: "mRNA catabolism, endonucleolytic" EXACT []
-synonym: "mRNA degradation, endonucleolytic cleavage-dependent decay" EXACT []
+name: nuclear-transcribed mRNA catabolic process, RNase MRP-dependent
+namespace: biological_process
+def: "A minor MRP-dependent nuclear-transcribed mRNA degradation pathway that begins with an endonucleolytic cleavage to generate unprotected ends." [PMID:14729943]
synonym: "nuclear mRNA catabolic process, endonucleolytic cleavage-dependent decay" EXACT []
+synonym: "nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay" RELATED []
is_a: GO:0000956 ! nuclear-transcribed mRNA catabolic process
[Term]
@@ -3049,7 +3037,6 @@ id: GO:0000296
name: spermine transport
namespace: biological_process
def: "The directed movement of spermine, N,N-bis(3-aminopropyl)-1,4-diaminobutane, a polyamine formed by the transfer of a propylamine group from decarboxylated S-adenosylmethionine to spermidine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc, ISBN:0198506732]
-is_a: GO:0006812 ! cation transport
is_a: GO:0015846 ! polyamine transport
[Term]
@@ -3057,7 +3044,6 @@ id: GO:0000297
name: spermine transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of spermine from one side of a membrane to the other. Spermine is a polybasic amine found in human sperm, in ribosomes and in some viruses, which is involved in nucleic acid packaging. Synthesis is regulated by ornithine decarboxylase which plays a key role in control of DNA replication." [GOC:ai]
-is_a: GO:0008324 ! cation transmembrane transporter activity
is_a: GO:0015203 ! polyamine transmembrane transporter activity
[Term]
@@ -3083,7 +3069,6 @@ def: "OBSOLETE. Integral to that fraction of cells, prepared by disruptive bioch
comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component.
synonym: "integral to membrane of membrane fraction" EXACT []
is_obsolete: true
-consider: GO:0016021
[Term]
id: GO:0000300
@@ -3142,12 +3127,13 @@ is_a: GO:0010035 ! response to inorganic substance
[Term]
id: GO:0000306
-name: extrinsic component of vacuolar membrane
+name: obsolete extrinsic component of vacuolar membrane
namespace: cellular_component
-def: "The component of a vacuolar membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:dos, GOC:jl, GOC:mah]
+def: "OBSOLETE. The component of a vacuolar membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:dos, GOC:jl, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "extrinsic to vacuolar membrane" EXACT []
-is_a: GO:0031312 ! extrinsic component of organelle membrane
-relationship: part_of GO:0005774 ! vacuolar membrane
+is_obsolete: true
+consider: GO:0005774
[Term]
id: GO:0000307
@@ -3266,6 +3252,7 @@ def: "Enables the transfer of sulfite ions from one side of a membrane to the ot
synonym: "sulphite transporter activity" EXACT []
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0000320
@@ -3393,7 +3380,7 @@ is_a: GO:0061695 ! transferase complex, transferring phosphorus-containing group
id: GO:0000334
name: 3-hydroxyanthranilate 3,4-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxyanthranilate + O(2) = cis,cis-2-amino-3-(3-oxoprop-1-enyl)but-2-enedioate + H(+)." [EC:1.13.11.6, RHEA:17953]
+def: "Catalysis of the reaction: 3-hydroxyanthranilate + O2 = cis,cis-2-amino-3-(3-oxoprop-1-enyl)but-2-enedioate + H+." [EC:1.13.11.6, RHEA:17953]
synonym: "3-hydroxyanthranilate oxygenase activity" RELATED [EC:1.13.11.6]
synonym: "3-hydroxyanthranilate:oxygen 3,4-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.6]
synonym: "3-hydroxyanthranilic acid dioxygenase activity" RELATED [EC:1.13.11.6]
@@ -3410,44 +3397,42 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
[Term]
id: GO:0000335
-name: negative regulation of transposition, DNA-mediated
+name: obsolete negative regulation of transposition, DNA-mediated
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA transposition." [GOC:dph, GOC:krc, GOC:tb]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of DNA transposition." [GOC:dph, GOC:krc, GOC:tb]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "down regulation of DNA transposition" EXACT []
synonym: "down-regulation of DNA transposition" EXACT []
synonym: "downregulation of DNA transposition" EXACT []
synonym: "inhibition of DNA transposition" NARROW []
synonym: "negative regulation of DNA transposition" EXACT [GOC:dph]
-is_a: GO:0000337 ! regulation of transposition, DNA-mediated
-is_a: GO:0010529 ! negative regulation of transposition
-is_a: GO:0045910 ! negative regulation of DNA recombination
-relationship: negatively_regulates GO:0006313 ! transposition, DNA-mediated
+is_obsolete: true
+consider: GO:0006313
[Term]
id: GO:0000336
-name: positive regulation of transposition, DNA-mediated
+name: obsolete positive regulation of transposition, DNA-mediated
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of DNA transposition." [GOC:dph, GOC:krc]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of DNA transposition." [GOC:dph, GOC:krc]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "activation of DNA transposition" NARROW []
synonym: "positive regulation of DNA transposition" EXACT [GOC:dph]
synonym: "stimulation of DNA transposition" NARROW []
synonym: "up regulation of DNA transposition" EXACT []
synonym: "up-regulation of DNA transposition" EXACT []
synonym: "upregulation of DNA transposition" EXACT []
-is_a: GO:0000337 ! regulation of transposition, DNA-mediated
-is_a: GO:0010530 ! positive regulation of transposition
-is_a: GO:0045911 ! positive regulation of DNA recombination
-relationship: positively_regulates GO:0006313 ! transposition, DNA-mediated
+is_obsolete: true
+consider: GO:0006313
[Term]
id: GO:0000337
-name: regulation of transposition, DNA-mediated
+name: obsolete regulation of transposition, DNA-mediated
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of DNA transposition, the process of transposing (moving to a different location) a segment of a chromosome or a piece of a DNA molecule." [GOC:dph, GOC:krc]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of DNA transposition, the process of transposing (moving to a different location) a segment of a chromosome or a piece of a DNA molecule." [GOC:dph, GOC:krc]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "regulation of DNA transposition" EXACT [GOC:dph]
-is_a: GO:0000018 ! regulation of DNA recombination
-is_a: GO:0010528 ! regulation of transposition
-relationship: regulates GO:0006313 ! transposition, DNA-mediated
+is_obsolete: true
+consider: GO:0006313
[Term]
id: GO:0000338
@@ -3547,7 +3532,7 @@ synonym: "spliceosomal B complex biosynthesis" NARROW []
synonym: "spliceosomal B complex formation" NARROW []
synonym: "U12-type nuclear mRNA branch site recognition" NARROW []
synonym: "U2-type nuclear mRNA branch site recognition" NARROW []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0000245 ! spliceosomal complex assembly
[Term]
@@ -3566,7 +3551,7 @@ synonym: "spliceosomal C1 complex biosynthesis" NARROW []
synonym: "spliceosomal C1 complex formation" NARROW []
synonym: "U12-type catalytic spliceosome formation for first transesterification step" NARROW []
synonym: "U2-type catalytic spliceosome formation for first transesterification step" NARROW []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0000393 ! spliceosomal conformational changes to generate catalytic conformation
[Term]
@@ -3588,7 +3573,7 @@ synonym: "spliceosomal A2-3 complex biosynthesis" NARROW []
synonym: "spliceosomal A2-3 complex formation" NARROW []
synonym: "spliceosomal C2 complex biosynthesis" NARROW []
synonym: "spliceosomal C2 complex formation" NARROW []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0000393 ! spliceosomal conformational changes to generate catalytic conformation
[Term]
@@ -3597,7 +3582,7 @@ name: trans assembly of SL-containing precatalytic spliceosome
namespace: biological_process
def: "Assembly of a spliceosomal complex containing the SL RNA and the pre-mRNA to be joined, as well as all the spliceosomal snRNPs involved in trans leader splicing. Formation of the trans leader spliceosome brings together the quadruple SL/U4/U5/U6 snRNP and the complex of the U2 snRNP with the splice site of the pre-mRNA." [GOC:krc, GOC:mtg_mpo, ISBN:0879695897]
synonym: "trans assembly of spliced leader-containing precatalytic spliceosome" EXACT []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0000245 ! spliceosomal complex assembly
relationship: part_of GO:0045291 ! mRNA trans splicing, SL addition
@@ -3607,7 +3592,7 @@ name: formation of quadruple SL/U4/U5/U6 snRNP
namespace: biological_process
def: "Formation of a quadruple snRNP complex composed of the spliced leader (SL) RNA along with the U4/U6-U5 tri-snRNP complex. Interactions that may facilitate this include a duplex between the SL and U6 RNAs and interactions between the U5 RNA and the exon sequence at the 5' splice site within the SL RNA." [GOC:krc, ISBN:0879695897]
comment: Note that this step is analogous to 5' splice site selection in cis-splicing.
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0045291 ! mRNA trans splicing, SL addition
[Term]
@@ -3626,7 +3611,7 @@ synonym: "spliceosomal A2-1 complex biosynthesis" NARROW []
synonym: "spliceosomal A2-1 complex formation" NARROW []
synonym: "spliceosomal B1 complex biosynthesis" NARROW []
synonym: "spliceosomal B1 complex formation" NARROW []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0000245 ! spliceosomal complex assembly
relationship: part_of GO:0045292 ! mRNA cis splicing, via spliceosome
@@ -3763,7 +3748,7 @@ id: GO:0000379
name: tRNA-type intron splice site recognition and cleavage
namespace: biological_process
def: "RNA processing that begins when the tertiary structure of a tRNA type intron is recognized, and ends when the endonucleolytic cleavage of the RNA at both the 5' and 3' splice sites occurs." [GOC:krc, GOC:mah, ISBN:0879695897]
-is_a: GO:0006396 ! RNA processing
+is_a: GO:0034470 ! ncRNA processing
relationship: part_of GO:0006388 ! tRNA splicing, via endonucleolytic cleavage and ligation
[Term]
@@ -3790,7 +3775,7 @@ relationship: regulates GO:0000380 ! alternative mRNA splicing, via spliceosome
id: GO:0000384
name: first spliceosomal transesterification activity
namespace: molecular_function
-def: "Catalysis of the first transesterification reaction of spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, while it is still joined to the 3' exon." [GOC:krc, ISBN:0879695897]
+def: "Catalysis of the first transesterification reaction of spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, while it is still joined to the 3' exon." [GOC:krc, ISBN:0879695897, PMID:19239890]
synonym: "lariat formation, 5'-splice site cleavage" RELATED []
is_a: GO:0140098 ! catalytic activity, acting on RNA
@@ -3798,9 +3783,10 @@ is_a: GO:0140098 ! catalytic activity, acting on RNA
id: GO:0000386
name: second spliceosomal transesterification activity
namespace: molecular_function
-def: "Catalysis of the second transesterification reaction of spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure." [GOC:krc, ISBN:0879695897]
+def: "Catalysis of the second transesterification reaction of spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure." [GOC:krc, ISBN:0879695897, PMID:19239890]
synonym: "3'-splice site cleavage, exon ligation" BROAD []
synonym: "lariat formation, 5'-splice site cleavage" RELATED []
+xref: Reactome:R-HSA-9770236 "Formation of the Spliceosomal P complex and exon ligation (new)"
is_a: GO:0140098 ! catalytic activity, acting on RNA
[Term]
@@ -3809,7 +3795,7 @@ name: spliceosomal snRNP assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome." [GOC:krc, GOC:mah, ISBN:0879695897]
synonym: "spliceosomal snRNP biogenesis" RELATED [GOC:mah]
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0000398 ! mRNA splicing, via spliceosome
[Term]
@@ -3827,7 +3813,7 @@ synonym: "spliceosomal B2 complex biosynthesis" NARROW []
synonym: "spliceosomal B2 complex formation" NARROW []
synonym: "U12-type spliceosome conformational change to release U4atac and U11" NARROW []
synonym: "U2-type spliceosome conformational change to release U4 and U1" NARROW []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0000393 ! spliceosomal conformational changes to generate catalytic conformation
[Term]
@@ -3840,7 +3826,7 @@ def: "Recognition of the intron 3'-splice site by components of the assembling U
synonym: "nuclear mRNA 3'-splice site recognition" EXACT [GOC:vw]
synonym: "U12-type nuclear mRNA 3'-splice site recognition" NARROW []
synonym: "U2-type nuclear mRNA 3'-splice site recognition" NARROW []
-is_a: GO:0006376 ! mRNA splice site selection
+is_a: GO:0006376 ! mRNA splice site recognition
[Term]
id: GO:0000390
@@ -3853,7 +3839,7 @@ synonym: "spliceosome complex disassembly" EXACT []
synonym: "spliceosome disassembly" BROAD []
synonym: "U12-type spliceosome disassembly" NARROW []
synonym: "U2-type spliceosome disassembly" NARROW []
-is_a: GO:0032988 ! ribonucleoprotein complex disassembly
+is_a: GO:0032988 ! protein-RNA complex disassembly
relationship: part_of GO:0000398 ! mRNA splicing, via spliceosome
[Term]
@@ -3862,7 +3848,7 @@ name: spliceosomal conformational changes to generate catalytic conformation
namespace: biological_process
def: "Structural rearrangements of the spliceosome complex, containing RNA to be spliced, to generate a catalytic conformation." [GOC:krc]
synonym: "3'-splice site cleavage, exon ligation" BROAD []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0000398 ! mRNA splicing, via spliceosome
[Term]
@@ -3894,7 +3880,7 @@ synonym: "U12-type nuclear mRNA 5' splice site recognition" NARROW []
synonym: "U12-type nuclear mRNA 5'-splice site recognition" NARROW []
synonym: "U2-type nuclear mRNA 5' splice site recognition" NARROW []
synonym: "U2-type nuclear mRNA 5'-splice site recognition" NARROW []
-is_a: GO:0006376 ! mRNA splice site selection
+is_a: GO:0006376 ! mRNA splice site recognition
relationship: part_of GO:0045292 ! mRNA cis splicing, via spliceosome
[Term]
@@ -4010,7 +3996,7 @@ id: GO:0000409
name: regulation of transcription by galactose
namespace: biological_process
def: "Any process involving galactose that modulates the frequency, rate or extent or transcription." [GOC:go_curators]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
[Term]
id: GO:0000410
@@ -4056,38 +4042,39 @@ is_a: GO:0018208 ! peptidyl-proline modification
[Term]
id: GO:0000414
-name: regulation of histone H3-K36 methylation
+name: obsolete regulation of histone H3-K36 methylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3." [GOC:krc]
-is_a: GO:0031060 ! regulation of histone methylation
-relationship: regulates GO:0010452 ! histone H3-K36 methylation
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3." [GOC:krc]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0140673
[Term]
id: GO:0000415
-name: negative regulation of histone H3-K36 methylation
+name: obsolete negative regulation of histone H3-K36 methylation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3." [GOC:krc]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3." [GOC:krc]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of histone H3-K36 methylation" EXACT []
synonym: "down-regulation of histone H3-K36 methylation" EXACT []
synonym: "downregulation of histone H3-K36 methylation" EXACT []
synonym: "inhibition of histone H3-K36 methylation" NARROW []
-is_a: GO:0000414 ! regulation of histone H3-K36 methylation
-is_a: GO:0031061 ! negative regulation of histone methylation
-relationship: negatively_regulates GO:0010452 ! histone H3-K36 methylation
+is_obsolete: true
+consider: GO:0006338
[Term]
id: GO:0000416
-name: positive regulation of histone H3-K36 methylation
+name: obsolete positive regulation of histone H3-K36 methylation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3." [GOC:krc]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3." [GOC:krc]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of histone H3-K36 methylation" NARROW []
synonym: "stimulation of histone H3-K36 methylation" NARROW []
synonym: "up regulation of histone H3-K36 methylation" EXACT []
synonym: "up-regulation of histone H3-K36 methylation" EXACT []
synonym: "upregulation of histone H3-K36 methylation" EXACT []
-is_a: GO:0000414 ! regulation of histone H3-K36 methylation
-is_a: GO:0031062 ! positive regulation of histone methylation
-relationship: positively_regulates GO:0010452 ! histone H3-K36 methylation
+is_obsolete: true
+consider: GO:0046975
[Term]
id: GO:0000417
@@ -4323,10 +4310,14 @@ relationship: part_of GO:0000112 ! nucleotide-excision repair factor 3 complex
id: GO:0000444
name: MIS12/MIND type complex
namespace: cellular_component
+alt_id: GO:0000818
def: "A multiprotein kinetochore subcomplex that binds to centromeric chromatin and forms part of the inner kinetochore. It helps to recruit outer kinetochore subunits that will bind to microtubules. In humans, it consists of MIS12, DSN1, NSL1 and PMF1." [GOC:krc, PMID:14633972, PMID:16585270]
+synonym: "MIND complex" EXACT []
synonym: "Mis12 complex" NARROW []
+synonym: "Mtw1p Including Nnf1p-Nsl1p-Dsn1p complex" RELATED []
+synonym: "nuclear MIS12/MIND complex" RELATED []
is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0000776 ! kinetochore
+relationship: part_of GO:0000939 ! inner kinetochore
[Term]
id: GO:0000445
@@ -4398,10 +4389,12 @@ is_a: GO:0000451 ! rRNA 2'-O-methylation
[Term]
id: GO:0000453
-name: enzyme-directed rRNA 2'-O-methylation
+name: obsolete enzyme-directed rRNA 2'-O-methylation
namespace: biological_process
-def: "The addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis where the methylase specifies the site that becomes methylated without using a guide RNA." [GOC:curators, ISBN:1555811337]
-is_a: GO:0000451 ! rRNA 2'-O-methylation
+def: "OBSOLETE. The addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis where the methylase specifies the site that becomes methylated without using a guide RNA." [GOC:curators, ISBN:1555811337]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0006364
[Term]
id: GO:0000454
@@ -4701,7 +4694,7 @@ name: small nucleolar ribonucleoprotein complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins and a snoRNA to form a small nucleolar ribonucleoprotein (snoRNP) complex." [GOC:krc]
synonym: "snoRNP assembly" EXACT []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
[Term]
id: GO:0000492
@@ -4795,6 +4788,70 @@ is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
is_a: GO:1990234 ! transferase complex
relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
+[Term]
+id: GO:0000510
+name: H3-H4 histone complex chaperone activity
+namespace: molecular_function
+def: "A histone chaperone that carries a H3-H4 histone complex." [PMID:28053344]
+comment: Mammalian cells have seven known sequence variants of histone H3. These are denoted as Histone H3.1, Histone H3.2, Histone H3.3, Histone H3.4 (H3T), Histone H3.5, Histone H3.X and Histone H3.Y (https://en.wikipedia.org/wiki/Histone_H3).
+synonym: "H3-H4 histone carrier activity" EXACT []
+synonym: "H3.1-H4 histone complex chaperone activity" NARROW []
+synonym: "H3.2-H4 histone complex chaperone activity" NARROW []
+synonym: "H3.3-H4 histone complex chaperone activity" NARROW []
+is_a: GO:0140713 ! histone chaperone activity
+
+[Term]
+id: GO:0000511
+name: H2A-H2B histone complex chaperone activity
+namespace: molecular_function
+def: "A histone chaperone that carries a H2A-H2B histone complex." [PMID:28053344]
+synonym: "H2A-H2B histone carrier activity" EXACT []
+is_a: GO:0140713 ! histone chaperone activity
+
+[Term]
+id: GO:0000512
+name: lncRNA-mediated post-transcriptional gene silencing
+namespace: biological_process
+def: "A post-transcriptional gene silencing pathway in which regulatory long noncoding RNAs (lncRNAs) elicit silencing of specific target genes, often miRNAs or mRNAs." [PMID:34454184, PMID:35055152]
+comment: This term should be applied to lncRNAs and proteins associated with this process and not to the target (miRNAs or mRNAs) of the process.
+synonym: "lncRNA-mediated gene silencing" BROAD []
+is_a: GO:0035194 ! ncRNA-mediated post-transcriptional gene silencing
+
+[Term]
+id: GO:0000513
+name: actin severing activator activity
+namespace: molecular_function
+def: "Binds to and increases the activity of a actin severing protein." [PMID:25451933]
+is_a: GO:0140677 ! molecular function activator activity
+
+[Term]
+id: GO:0000514
+name: 3-sulfino-L-alanine: proton, glutamate antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: 3-sulfino-L-alanine (cysteinesulfinate) (out) + H+(in) + L-glutamate(in) = 3-sulfino-L-alanine(in) + H+(out) + L-glutamate(out)." [PMID:11566871, RHEA:70967]
+xref: RHEA:70967
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
+is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
+is_a: GO:0042887 ! amide transmembrane transporter activity
+is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
+is_a: GO:0140848 ! amino acid:monoatomic cation antiporter activity
+is_a: GO:1901680 ! sulfur-containing amino acid secondary active transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
+
+[Term]
+id: GO:0000515
+name: aspartate:glutamate, proton antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + L-aspartate(in) + L-glutamate(out) = H+(in) + L-aspartate(out) + L-glutamate(in)." [PMID:11566871, RHEA:70783]
+xref: RHEA:70783
+is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015556 ! C4-dicarboxylate transmembrane transporter activity
+is_a: GO:0042887 ! amide transmembrane transporter activity
+is_a: GO:0140848 ! amino acid:monoatomic cation antiporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
+
[Term]
id: GO:0000578
name: embryonic axis specification
@@ -4922,7 +4979,7 @@ def: "The cleavage and rejoining of intermediates, such as Holliday junctions, f
synonym: "resolution of meiotic joint molecules as recombinants" NARROW [GOC:elh, GOC:mah]
is_a: GO:0061982 ! meiosis I cell cycle process
relationship: part_of GO:0007131 ! reciprocal meiotic recombination
-relationship: part_of GO:0051307 ! meiotic chromosome separation
+relationship: part_of GO:0045132 ! meiotic chromosome segregation
[Term]
id: GO:0000713
@@ -4999,7 +5056,7 @@ is_a: GO:0006290 ! pyrimidine dimer repair
id: GO:0000721
name: (R,R)-butanediol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reversible reaction: (R,R)-butane-2,3-diol + NAD+ = (R)-acetoin + NADH + H(+)." [EC:1.1.1.4]
+def: "Catalysis of the reversible reaction: (R,R)-butane-2,3-diol + NAD+ = (R)-acetoin + NADH + H+." [EC:1.1.1.4]
synonym: "(R)-2,3-butanediol dehydrogenase activity" RELATED [EC:1.1.1.4]
synonym: "(R)-diacetyl reductase activity" RELATED [EC:1.1.1.4]
synonym: "1-amino-2-propanol dehydrogenase activity" RELATED [EC:1.1.1.4]
@@ -5143,26 +5200,28 @@ relationship: part_of GO:0045002 ! double-strand break repair via single-strand
[Term]
id: GO:0000737
-name: DNA catabolic process, endonucleolytic
+name: obsolete DNA catabolic process, endonucleolytic
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides." [GOC:elh, GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides." [GOC:elh, GOC:mah]
+comment: The reason is that these terms represent Molecular functions in the Biological Process ontology.
synonym: "DNA breakdown, endonucleolytic" EXACT []
synonym: "DNA degradation, endonucleolytic" EXACT []
synonym: "endonucleolytic degradation of DNA" EXACT []
synonym: "endonucleolytic DNA catabolism" EXACT []
-is_a: GO:0006308 ! DNA catabolic process
-is_a: GO:0090305 ! nucleic acid phosphodiester bond hydrolysis
+is_obsolete: true
+replaced_by: GO:0006308
[Term]
id: GO:0000738
-name: DNA catabolic process, exonucleolytic
+name: obsolete DNA catabolic process, exonucleolytic
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides." [GOC:elh, GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides." [GOC:elh, GOC:mah]
+comment: The reason is that these terms represent Molecular functions in the Biological Process ontology.
synonym: "DNA breakdown, exonucleolytic" EXACT []
synonym: "DNA degradation, exonucleolytic" EXACT []
synonym: "exonucleolytic degradation of DNA" EXACT []
-is_a: GO:0006308 ! DNA catabolic process
-is_a: GO:0090305 ! nucleic acid phosphodiester bond hydrolysis
+is_obsolete: true
+replaced_by: GO:0006308
[Term]
id: GO:0000739
@@ -5224,6 +5283,7 @@ namespace: biological_process
def: "During sexual reproduction, the creation of a single nucleus from two nuclei as a result of fusing the nuclear envelopes that surround each nuclei. This takes place following the mutual exchange of one of the two nuclei produced by the mitosis that follows the second meiotic nuclear division. This occurs in ciliated protozoans such as Tetrahymena." [GOC:mah, GOC:pg]
synonym: "karyogamy involved in conjugation without cellular fusion" EXACT [GOC:dph, GOC:tb]
is_a: GO:0000741 ! karyogamy
+is_a: GO:0022414 ! reproductive process
relationship: part_of GO:0000748 ! conjugation with mutual genetic exchange
[Term]
@@ -5234,19 +5294,17 @@ def: "The net movement of nuclei towards one another, leading to the bilateral t
synonym: "nuclear exchange during conjugation without cellular fusion" RELATED []
synonym: "nuclear migration involved in conjugation without cellular fusion" EXACT [GOC:dph, GOC:tb]
is_a: GO:0007097 ! nuclear migration
+is_a: GO:0022414 ! reproductive process
relationship: part_of GO:0000744 ! karyogamy involved in conjugation with mutual genetic exchange
[Term]
id: GO:0000746
-name: conjugation
+name: obsolete conjugation
namespace: biological_process
-def: "The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms." [GOC:elh]
-subset: goslim_aspergillus
-subset: goslim_candida
-subset: goslim_pir
-subset: goslim_yeast
+def: "OBSOLETE. The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms." [GOC:elh]
+comment: This term was obsoleted because it is an unnecessary grouping class.
xref: Wikipedia:Conjugation
-is_a: GO:0044764 ! multi-organism cellular process
+is_obsolete: true
[Term]
id: GO:0000747
@@ -5257,20 +5315,22 @@ alt_id: GO:0007333
alt_id: GO:0030461
alt_id: GO:0030477
def: "A conjugation process that results in the union of cellular and genetic information from compatible mating types. An example of this process is found in Saccharomyces cerevisiae." [GOC:elh]
+subset: goslim_candida
+subset: goslim_pir
subset: goslim_pombe
+subset: goslim_yeast
synonym: "cell fusion" RELATED []
synonym: "mating" RELATED []
-is_a: GO:0000746 ! conjugation
+xref: Wikipedia:Conjugation
is_a: GO:0019953 ! sexual reproduction
-is_a: GO:0140253 ! cell-cell fusion
[Term]
id: GO:0000748
name: conjugation with mutual genetic exchange
namespace: biological_process
-def: "A conjugation process that results in the mutual exchange and union of only genetic information between compatible mating types. Conjugation without cellular fusion requires direct cellular contact between the organisms without plasma membrane fusion. The organisms involved in conjugation without cellular fusion separate after nuclear exchange." [GOC:elh]
+def: "A conjugation process that results in the mutual exchange and union of only genetic information between compatible mating types. Conjugation without cellular fusion requires direct cellular contact between the organisms without plasma membrane fusion. The organisms involved in conjugation without cellular fusion separate after nuclear exchange." [GOC:elh, PMID:22444146]
synonym: "conjugation without cellular fusion" EXACT []
-is_a: GO:0000746 ! conjugation
+is_a: GO:0019953 ! sexual reproduction
[Term]
id: GO:0000749
@@ -5313,8 +5373,9 @@ def: "The aggregation or adhesion of compatible mating types via complementary c
synonym: "agglutination" BROAD []
synonym: "cell-cell adhesion during conjugation with cellular fusion" EXACT []
synonym: "cell-cell adhesion during mating" EXACT []
-is_a: GO:0000771 ! agglutination involved in conjugation
is_a: GO:0022414 ! reproductive process
+is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms
+is_a: GO:0098609 ! cell-cell adhesion
relationship: part_of GO:0000747 ! conjugation with cellular fusion
relationship: part_of GO:0000749 ! response to pheromone triggering conjugation with cellular fusion
@@ -5326,7 +5387,7 @@ alt_id: GO:0007332
def: "The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types in organisms that undergo conjugation cellular fusion." [GOC:clt]
synonym: "shmoo orientation" NARROW []
synonym: "shmooing" NARROW []
-is_a: GO:0000767 ! cell morphogenesis involved in conjugation
+is_a: GO:0000902 ! cell morphogenesis
is_a: GO:0003006 ! developmental process involved in reproduction
relationship: part_of GO:0000747 ! conjugation with cellular fusion
@@ -5380,7 +5441,8 @@ namespace: biological_process
def: "The aggregation or adhesion of compatible mating types via complementary cell-cell interactions during conjugation without cellular fusion of a unicellular organism." [GOC:elh]
synonym: "agglutination involved in conjugation without cellular fusion" EXACT [GOC:dph, GOC:tb]
synonym: "sexual flocculation" EXACT []
-is_a: GO:0000771 ! agglutination involved in conjugation
+is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms
+is_a: GO:0098609 ! cell-cell adhesion
relationship: part_of GO:0000756 ! response to pheromone regulating conjugation with mutual genetic exchange
[Term]
@@ -5401,21 +5463,21 @@ synonym: "adaptation to pheromone involved conjugation without cellular fusion"
synonym: "desensitization to pheromone during conjugation without cellular fusion" EXACT []
is_a: GO:0000756 ! response to pheromone regulating conjugation with mutual genetic exchange
is_a: GO:0022401 ! negative adaptation of signaling pathway
-is_a: GO:0046999 ! regulation of conjugation
[Term]
id: GO:0000761
name: conjugant formation
namespace: biological_process
def: "During conjugation without cellular fusion, the process that results in pairing complementary mating types. Localized morphological, cytological, and cytoskeletal changes connect the mating types without cytoplasmic mixing." [GOC:elh]
-is_a: GO:0000771 ! agglutination involved in conjugation
+is_a: GO:0022414 ! reproductive process
+is_a: GO:0098610 ! adhesion between unicellular organisms
relationship: part_of GO:0000748 ! conjugation with mutual genetic exchange
[Term]
id: GO:0000762
name: pheromone-induced unidirectional conjugation
namespace: biological_process
-def: "The process of unidirectional (polarized) transfer of genetic information in response to a pheromone. It involves direct cellular contact between a donor and recipient cell; the contact is followed by the formation of a cellular bridge that physically connects the cells; some or all of the chromosome(s) of one cell ('male') is then transferred into the other cell ('female'); unidirectional conjugation occurs between cells of different mating types." [GOC:elh]
+def: "Unidirectional transfer of genetic information triggered by to a pheromone signal." [GOC:elh, PMID:17360276, PMID:27021562, PMID:31191478]
is_a: GO:0009291 ! unidirectional conjugation
[Term]
@@ -5459,11 +5521,11 @@ relationship: part_of GO:0000765 ! response to pheromone regulating pheromone-in
[Term]
id: GO:0000767
-name: cell morphogenesis involved in conjugation
+name: obsolete cell morphogenesis involved in conjugation
namespace: biological_process
-def: "The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types." [GOC:elh]
-is_a: GO:0000902 ! cell morphogenesis
-relationship: part_of GO:0000746 ! conjugation
+def: "OBSOLETE. The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types." [GOC:elh]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
[Term]
id: GO:0000768
@@ -5489,17 +5551,15 @@ namespace: biological_process
alt_id: GO:0007325
def: "The directed movement of a peptide pheromone out of a cell by a secretion or export pathway used solely for the export of peptide pheromones." [GOC:elh]
synonym: "a-factor export" NARROW []
-is_a: GO:0009914 ! hormone transport
is_a: GO:0015833 ! peptide transport
[Term]
id: GO:0000771
-name: agglutination involved in conjugation
+name: obsolete agglutination involved in conjugation
namespace: biological_process
-def: "The aggregation or adhesion of compatible mating types via complementary cell-cell interactions prior to the formation of irreversible cellular contacts during conjugation." [GOC:elh]
-is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms
-is_a: GO:0098610 ! adhesion between unicellular organisms
-relationship: part_of GO:0000746 ! conjugation
+def: "OBSOLETE. The aggregation or adhesion of compatible mating types via complementary cell-cell interactions prior to the formation of irreversible cellular contacts during conjugation." [GOC:elh]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
[Term]
id: GO:0000772
@@ -5557,11 +5617,13 @@ namespace: cellular_component
alt_id: GO:0000777
alt_id: GO:0000778
alt_id: GO:0005699
+alt_id: GO:0031617
def: "A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules." [GOC:elh]
comment: Note that the kinetochore overlaps the centromeric DNA, but centromeric DNA is not part of the kinetochore.
subset: goslim_pir
synonym: "condensed chromosome kinetochore" EXACT []
synonym: "condensed nuclear chromosome kinetochore" EXACT []
+synonym: "NMS complex" NARROW []
xref: Wikipedia:Kinetochore
is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
is_a: GO:0099080 ! supramolecular complex
@@ -5626,7 +5688,7 @@ synonym: "chromosome scaffold" RELATED []
synonym: "cytoplasmic chromatin" NARROW []
synonym: "nuclear chromatin" NARROW []
xref: NIF_Subcellular:sao1615953555
-is_a: GO:0110165 ! cellular anatomical entity
+is_a: GO:0032993 ! protein-DNA complex
relationship: part_of GO:0005694 ! chromosome
[Term]
@@ -5642,7 +5704,6 @@ synonym: "cytoplasmic nucleosome" NARROW []
synonym: "nuclear nucleosome" NARROW []
xref: Wikipedia:Nucleosome
is_a: GO:0032993 ! protein-DNA complex
-is_a: GO:0044815 ! DNA packaging complex
relationship: part_of GO:0000785 ! chromatin
[Term]
@@ -5699,7 +5760,7 @@ id: GO:0000795
name: synaptonemal complex
namespace: cellular_component
alt_id: GO:0005716
-def: "A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element." [DOI:10.5772/29752, GOC:elh]
+def: "A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element." [DOI:10.5772/29752, GOC:elh]
xref: Wikipedia:Synaptonemal_complex
is_a: GO:0099086 ! synaptonemal structure
@@ -5722,25 +5783,15 @@ synonym: "condensin I complex" NARROW []
synonym: "nuclear condensin complex" NARROW []
synonym: "SMC complex" RELATED []
synonym: "Smc2-Smc4 complex" NARROW []
-is_a: GO:0044815 ! DNA packaging complex
+is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0005694 ! chromosome
-[Term]
-id: GO:0000798
-name: nuclear cohesin complex
-namespace: cellular_component
-def: "A cohesin complex required for cohesion between sister chromatids that remain in the nucleus." [GOC:elh]
-comment: Note that this term and its children should be used to annotate gene products found in cohesin complexes in organisms that undergo closed mitosis (i.e. where the nuclear envelope does not break down, as in fungi). For organisms in which the nuclear envelope breaks down during mitosis, the parent should be used.
-is_a: GO:0008278 ! cohesin complex
-is_a: GO:0140513 ! nuclear protein-containing complex
-relationship: part_of GO:0000794 ! condensed nuclear chromosome
-
[Term]
id: GO:0000800
name: lateral element
namespace: cellular_component
def: "A proteinaceous core found between sister chromatids during meiotic prophase." [GOC:elh]
-comment: In species that have a synaptonemal complex, the lateral elements are part of this complex. S.pombe is an example of a species that lacks a (canonical) synaptonemal complex, but still has lateral elements.
+comment: In species that have a synaptonemal complex, the lateral elements are part of this complex. S.pombe is an example of a species that lacks a (canonical) synaptonemal complex, but still has lateral elements.
synonym: "axial element" EXACT [GOC:ascb_2009, GOC:dph, GOC:tb]
is_a: GO:0110165 ! cellular anatomical entity
relationship: part_of GO:0000795 ! synaptonemal complex
@@ -5826,11 +5877,11 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0000810
name: diacylglycerol diphosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 1,2-diacyl-sn-glycerol 3-diphosphate + H2O = a 1,2-diacyl-sn-glycerol 3-phosphate + phosphate." [GOC:kad, PMID:8567632, PMID:9452443]
+def: "Catalysis of the reaction: a 1,2-diacyl-sn-glycerol 3-diphosphate + H2O = a 1,2-diacyl-sn-glycerol 3-phosphate + phosphate." [GOC:kad, PMID:8567632, PMID:9452443, RHEA:27449]
synonym: "DGPP phosphatase activity" EXACT []
synonym: "DGPP phosphohydrolase activity" EXACT []
synonym: "diacylglycerol pyrophosphate phosphatase activity" EXACT []
-xref: EC:3.1.3.81
+xref: EC:3.6.1.75
xref: MetaCyc:RXN-11277
xref: RHEA:27449
is_a: GO:0016462 ! pyrophosphatase activity
@@ -5894,16 +5945,6 @@ is_a: GO:0140513 ! nuclear protein-containing complex
relationship: part_of GO:0000228 ! nuclear chromosome
relationship: part_of GO:0000776 ! kinetochore
-[Term]
-id: GO:0000818
-name: nuclear MIS12/MIND complex
-namespace: cellular_component
-def: "A multiprotein kinetochore subcomplex that binds to centromeric chromatin and forms part of the inner kinetochore of a chromosome in the nucleus. It helps to recruit outer kinetochore subunits that will bind to microtubules. Nuclear localization arises in some organisms because the nuclear envelope is not broken down during mitosis. In S. cerevisiae, it consists of at least four proteins: Mtw1p, Nnf1p, Nsl1p, and Dsn1." [GOC:krc, GOC:se, PMID:14633972]
-synonym: "MIND complex" EXACT []
-synonym: "Mtw1p Including Nnf1p-Nsl1p-Dsn1p complex" EXACT []
-is_a: GO:0000444 ! MIS12/MIND type complex
-is_a: GO:0140513 ! nuclear protein-containing complex
-
[Term]
id: GO:0000819
name: sister chromatid segregation
@@ -5944,7 +5985,7 @@ is_a: GO:0043178 ! alcohol binding
id: GO:0000823
name: inositol-1,4,5-trisphosphate 6-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-myo-inositol 1,4,5-trisphosphate + ATP = D-myo-inositol 1,4,5,6-tetrakisphosphate + ADP + 2 H(+)." [MetaCyc:2.7.1.151-RXN]
+def: "Catalysis of the reaction: D-myo-inositol 1,4,5-trisphosphate + ATP = D-myo-inositol 1,4,5,6-tetrakisphosphate + ADP + 2 H+." [MetaCyc:2.7.1.151-RXN]
synonym: "ATP:1D-myo-inositol-1,4,5-trisphosphate 6-phosphotransferase activity" EXACT []
synonym: "inositol polyphosphate multikinase activity" BROAD []
synonym: "inositol trisphosphate 6-kinase activity" BROAD []
@@ -5988,7 +6029,6 @@ comment: This term was made obsolete because it is incorrectly defined; 'inosito
synonym: "inositol diphosphate synthase activity" EXACT []
synonym: "inositol pyrophosphate synthase activity" EXACT []
is_obsolete: true
-consider: GO:0052746
[Term]
id: GO:0000827
@@ -6006,6 +6046,7 @@ id: GO:0000828
name: inositol hexakisphosphate kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + 1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate = ADP + diphospho-1D-myo-inositol-pentakisphosphate. The isomeric configuration of diphospho-1D-myo-inositol-pentakisphosphate (PP-IP5) is unknown." [GOC:elh, GOC:vw, PMID:16429326]
+synonym: "IP6 kinase" EXACT []
xref: Reactome:R-HSA-1855207 "IP6 is phosphorylated to 5-PP-IP5 by IP6K1/2 in the nucleus"
xref: Reactome:R-HSA-1855216 "IP6 is phosphorylated to 1-PP-IP5 by PPIP5K1/2 in the cytosol"
xref: Reactome:R-HSA-1855227 "IP6 is phosphorylated to 5-PP-IP5 by IP6K1/3 in the cytosol"
@@ -6107,9 +6148,10 @@ is_a: GO:0000836 ! Hrd1p ubiquitin ligase complex
[Term]
id: GO:0000900
-name: translation repressor activity, mRNA regulatory element binding
+name: mRNA regulatory element binding translation repressor activity
namespace: molecular_function
def: "Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid." [GOC:clt, GOC:vw, PMID:29061112, PMID:7523370]
+synonym: "translation repressor activity, mRNA regulatory element binding" EXACT []
synonym: "translation repressor activity, nucleic acid binding" BROAD []
is_a: GO:0030371 ! translation repressor activity
is_a: GO:0090079 ! translation regulator activity, nucleic acid binding
@@ -6194,7 +6236,7 @@ is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
id: GO:0000908
name: taurine dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + O(2) + taurine = aminoacetaldehyde + CO(2) + succinate + sulfite." [EC:1.14.11.17, RHEA:15909]
+def: "Catalysis of the reaction: 2-oxoglutarate + O2 + taurine = aminoacetaldehyde + CO2 + succinate + sulfite." [EC:1.14.11.17, RHEA:15909]
synonym: "2-aminoethanesulfonate dioxygenase activity" RELATED [EC:1.14.11.17]
synonym: "alpha-ketoglutarate-dependent taurine dioxygenase activity" RELATED [EC:1.14.11.17]
synonym: "taurine, 2-oxoglutarate:O2 oxidoreductase (sulfite-forming)" RELATED [EC:1.14.11.17]
@@ -6224,12 +6266,12 @@ alt_id: GO:0007104
alt_id: GO:0016288
alt_id: GO:0033205
def: "The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells." [GOC:mtg_cell_cycle]
-comment: Note that this term should not be used for direct annotation. When annotating eukaryotic species, mitotic or meiotic cytokinesis should always be specified for manual annotation and for prokaryotic species use 'FtsZ-dependent cytokinesis ; GO:0043093' or Cdv-dependent cytokinesis ; GO:0061639. Also, note that cytokinesis does not necessarily result in physical separation and detachment of the two daughter cells from each other.
+comment: Note that this term should not be used for direct annotation. When annotating eukaryotic species, mitotic or meiotic cytokinesis should always be specified for manual annotation and for prokaryotic species use 'FtsZ-dependent cytokinesis ; GO:0043093' or Cdv-dependent cytokinesis ; GO:0061639. Also, note that cytokinesis does not necessarily result in physical separation and detachment of the two daughter cells from each other.
subset: gocheck_do_not_manually_annotate
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_generic
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "cell cycle cytokinesis" EXACT []
synonym: "cytokinesis involved in cell cycle" EXACT [GOC:dph, GOC:tb]
xref: Wikipedia:Cytokinesis
@@ -6279,6 +6321,7 @@ id: GO:0000915
name: actomyosin contractile ring assembly
namespace: biological_process
alt_id: GO:0045573
+alt_id: GO:2000708
def: "The process of assembly of a ring composed of actin, myosin, and associated proteins that will function in cytokinesis." [GOC:clt, GOC:dph, GOC:tb]
synonym: "constriction ring assembly" NARROW []
synonym: "contractile ring assembly" EXACT [GOC:ascb_2009, GOC:dph, GOC:tb]
@@ -6287,6 +6330,10 @@ synonym: "cytokinesis, actomyosin contractile ring formation" RELATED [GOC:ascb_
synonym: "cytokinesis, actomyosin ring biosynthesis" RELATED []
synonym: "cytokinesis, actomyosin ring formation" RELATED []
synonym: "cytokinesis, contractile ring assembly" RELATED [GOC:mah]
+synonym: "myosin filament organisation involved in cytokinetic actomyosin contractile ring assembly" RELATED [GOC:mah]
+synonym: "myosin filament organization involved in cytokinetic actomyosin contractile ring assembly" RELATED []
+synonym: "myosin filament organization of constriction ring assembly" RELATED [GOC:obol]
+synonym: "myosin filament organization of contractile ring assembly" RELATED [GOC:obol]
is_a: GO:0000912 ! assembly of actomyosin apparatus involved in cytokinesis
is_a: GO:0044837 ! actomyosin contractile ring organization
@@ -6406,7 +6453,7 @@ relationship: part_of GO:0005815 ! microtubule organizing center
[Term]
id: GO:0000931
-name: gamma-tubulin large complex
+name: gamma-tubulin ring complex
namespace: cellular_component
alt_id: GO:0000924
alt_id: GO:0000925
@@ -6418,6 +6465,7 @@ alt_id: GO:0055032
alt_id: GO:0055033
alt_id: GO:0061494
def: "A complex of gamma tubulin and associated proteins thought to be formed by multimerization of gamma-tubulin small complexes. An example of this structure is found in Schizosaccharomyces pombe." [GOC:mtg_sensu, PMID:12134075, PMID:17021256]
+synonym: "gamma-tubulin large complex" RELATED []
synonym: "gamma-tubulin large complex, centrosomal" NARROW []
synonym: "gamma-tubulin large complex, eMTOC" NARROW []
synonym: "gamma-tubulin large complex, equatorial microtubule organizing center" NARROW []
@@ -6427,8 +6475,8 @@ synonym: "gamma-tubulin large complex, interphase microtubule organizing center"
synonym: "gamma-tubulin large complex, interphase microtubule organizing centre" NARROW []
synonym: "gamma-tubulin large complex, mitotic spindle pole body" NARROW []
synonym: "gamma-tubulin large complex, spindle pole body" NARROW []
-synonym: "gamma-tubulin ring complex" NARROW []
synonym: "gamma-tubulin ring complex, centrosomal" NARROW []
+synonym: "gamma-TuRC" EXACT []
is_a: GO:0000930 ! gamma-tubulin complex
[Term]
@@ -6502,7 +6550,7 @@ id: GO:0000939
name: inner kinetochore
namespace: cellular_component
alt_id: GO:0000941
-def: "The region of a kinetochore closest to centromeric DNA; in mammals the CREST antigens (CENP proteins) are found in this layer; this layer may help define underlying centromeric chromatin structure and position of the kinetochore on the chromosome." [GOC:clt, PMID:10619130, PMID:11483983]
+def: "The region of a kinetochore closest to centromeric DNA which contains many CENP proteins organized in various subcomplexes including CENP-C, CENP-LN, CENP-HIKM, CENP-OPQUR and CENP-TWSX, but excluding the CENP-A containing heterochromatin." [GOC:clt, PMID:10619130, PMID:11483983, PMID:32516549]
synonym: "condensed chromosome inner kinetochore" EXACT []
synonym: "condensed nuclear chromosome inner kinetochore" EXACT []
synonym: "inner centromere core complex" RELATED []
@@ -6611,7 +6659,7 @@ id: GO:0000955
name: amino acid catabolic process via Ehrlich pathway
namespace: biological_process
def: "The chemical reactions and pathways involving the catabolism of amino acids to produce alcohols or carboxylic acids containing one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives, sometimes referred to as fusel acids, may be produced instead of alcohols." [GOC:krc, PMID:18281432]
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
[Term]
id: GO:0000956
@@ -6756,9 +6804,10 @@ is_a: GO:0051276 ! chromosome organization
[Term]
id: GO:0000973
-name: posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery
+name: post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery
namespace: biological_process
def: "The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery even after transcription has been repressed." [GOC:krc, PMID:17373856, PMID:18614049]
+synonym: "posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery" EXACT []
is_a: GO:0000972 ! transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery
[Term]
@@ -6961,7 +7010,7 @@ id: GO:0000995
name: RNA polymerase III general transcription initiation factor activity
namespace: molecular_function
alt_id: GO:0001034
-def: "A general transcription initiation factor activity that contributes to transcription start site selection and transcription initiation of genes transcribed by RNA polymerase III. Factors required for RNA polymerase III transcription initiation include TFIIIA, TFIIIB and TFIIIC. A general transcription initiation factor activity that contributes to transcription start site selection and transcription initiation of genes transcribed by RNA polymerase III. Factors required for RNA polymerase III transcription initiation include TFIIIA, TFIIIB and TFIIIC. RNA polymerase III transcribes genes encoding short RNAs, including tRNAs, 5S rRNA, U6 snRNA, the short ncRNA component of RNases P, the mitochondrial RNA processing (MRP) RNA, the signal recognition particle SRP RNA, and in higher eukaryotes a number of micro and other small RNAs, though there is some variability across species as to whether a given small noncoding RNA is transcribed by RNA polymerase II or RNA polymerase III." [GOC:txnOH-2018, PMID:12381659, PMID:17977614, PMID:20413673, PMID:27068803, Wikipedia:RNA_polymerase_III]
+def: "A general transcription initiation factor activity that contributes to transcription start site selection and transcription initiation of genes transcribed by RNA polymerase III. Factors required for RNA polymerase III transcription initiation include TFIIIA, TFIIIB and TFIIIC. RNA polymerase III transcribes genes encoding short RNAs, including tRNAs, 5S rRNA, U6 snRNA, the short ncRNA component of RNases P, the mitochondrial RNA processing (MRP) RNA, the signal recognition particle SRP RNA, and in higher eukaryotes a number of micro and other small RNAs, though there is some variability across species as to whether a given small noncoding RNA is transcribed by RNA polymerase II or RNA polymerase III." [GOC:txnOH-2018, PMID:12381659, PMID:17977614, PMID:20413673, PMID:27068803, Wikipedia:RNA_polymerase_III]
synonym: "core RNA polymerase III binding transcription factor activity" NARROW []
synonym: "RNA polymerase III general initiation factor activity" EXACT []
synonym: "RNA polymerase III transcription factor activity, sequence-specific DNA binding" NARROW []
@@ -7306,7 +7355,7 @@ namespace: biological_process
def: "The synthesis of RNA from a DNA template by RNA polymerase IV, originating at a Pol IV-specific promoter." [GOC:txnOH, PMID:19110459]
synonym: "transcription from RNA pol IV promoter" EXACT []
synonym: "transcription from RNA polymerase IV promoter" EXACT []
-is_a: GO:0006351 ! transcription, DNA-templated
+is_a: GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0001060
@@ -7315,7 +7364,7 @@ namespace: biological_process
def: "The synthesis of RNA from a DNA template by RNA polymerase V, originating at a Pol V-specific promoter." [GOC:txnOH, PMID:19110459]
synonym: "transcription from RNA pol V promoter" EXACT []
synonym: "transcription from RNA polymerase V promoter" EXACT []
-is_a: GO:0006351 ! transcription, DNA-templated
+is_a: GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0001061
@@ -7660,22 +7709,25 @@ synonym: "promoter clearance during DNA-dependent transcription" EXACT [GOC:txnO
synonym: "promoter clearance from bacterial-type RNA polymerase promoter" NARROW []
synonym: "promoter escape" BROAD []
is_a: GO:0032774 ! RNA biosynthetic process
-relationship: part_of GO:0006351 ! transcription, DNA-templated
+relationship: part_of GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0001110
-name: promoter clearance from RNA polymerase III promoter
+name: RNA polymerase III promoter clearance
namespace: biological_process
-def: "Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase III, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase." [GOC:txnOH]
+def: "A process that mediates the transition from the initiation to the elongation phases of transcription by RNA polymerase III, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase." [GOC:txnOH]
+synonym: "promoter clearance from RNA polymerase III promoter" EXACT []
is_a: GO:0001109 ! promoter clearance during DNA-templated transcription
relationship: part_of GO:0006383 ! transcription by RNA polymerase III
[Term]
id: GO:0001111
-name: promoter clearance from RNA polymerase II promoter
+name: RNA polymerase II promoter clearance
namespace: biological_process
-def: "Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase II, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH, PMID:15020047]
+def: "A process that mediates the transition from the initiation to the elongation phases of transcription by RNA polymerase II, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH, PMID:15020047, PMID:22982364, PMID:31628251]
+synonym: "promoter clearance from RNA polymerase II promoter" EXACT []
synonym: "promoter escape from RNA polymerase II promoter" EXACT []
+synonym: "promoter-paused RNA polymerase II release" EXACT []
is_a: GO:0001109 ! promoter clearance during DNA-templated transcription
relationship: part_of GO:0006366 ! transcription by RNA polymerase II
@@ -7691,7 +7743,7 @@ synonym: "promoter melting" BROAD []
synonym: "transcription open complex formation at bacterial-type RNA polymerase promoter" NARROW []
synonym: "transcriptional open complex formation at bacterial-type RNA polymerase promoter" NARROW []
is_a: GO:0001120 ! protein-DNA complex remodeling
-relationship: part_of GO:0006352 ! DNA-templated transcription, initiation
+relationship: part_of GO:0006352 ! DNA-templated transcription initiation
[Term]
id: GO:0001113
@@ -7701,7 +7753,7 @@ def: "Any process involved in the melting of the DNA hybrid of the core promoter
synonym: "RNA polymerase II promoter melting" EXACT []
synonym: "transcriptional open complex formation at RNA polymerase II promoter" EXACT []
is_a: GO:0001112 ! DNA-templated transcription open complex formation
-relationship: part_of GO:0006367 ! transcription initiation from RNA polymerase II promoter
+relationship: part_of GO:0006367 ! transcription initiation at RNA polymerase II promoter
[Term]
id: GO:0001114
@@ -7712,7 +7764,7 @@ is_a: GO:0032991 ! protein-containing complex
[Term]
id: GO:0001115
-name: protein-DNA-RNA complex subunit organization
+name: protein-DNA-RNA complex organization
namespace: biological_process
def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA-RNA complex." [GOC:txnOH]
synonym: "protein-DNA-RNA complex subunit organisation" EXACT [GOC:mah]
@@ -7723,7 +7775,7 @@ id: GO:0001116
name: protein-DNA-RNA complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins, DNA, and RNA molecules to form a protein-DNA-RNA complex." [GOC:txnOH]
-is_a: GO:0001115 ! protein-DNA-RNA complex subunit organization
+is_a: GO:0001115 ! protein-DNA-RNA complex organization
is_a: GO:0065003 ! protein-containing complex assembly
[Term]
@@ -7731,7 +7783,7 @@ id: GO:0001117
name: protein-DNA-RNA complex disassembly
namespace: biological_process
def: "The disaggregation of a protein-DNA-RNA complex into its constituent components." [GOC:txnOH]
-is_a: GO:0001115 ! protein-DNA-RNA complex subunit organization
+is_a: GO:0001115 ! protein-DNA-RNA complex organization
is_a: GO:0032984 ! protein-containing complex disassembly
[Term]
@@ -7741,14 +7793,14 @@ namespace: biological_process
def: "The disaggregation of a transcription ternary complex, composed of RNA polymerase, template DNA, and an RNA transcript, into its constituent components." [GOC:txnOH]
synonym: "transcription protein-DNA-RNA complex disassembly" EXACT []
is_a: GO:0001117 ! protein-DNA-RNA complex disassembly
-relationship: part_of GO:0006353 ! DNA-templated transcription, termination
+relationship: part_of GO:0006353 ! DNA-templated transcription termination
[Term]
id: GO:0001119
name: protein-DNA-RNA complex remodeling
namespace: biological_process
def: "The acquisition, loss, or modification of macromolecules within a protein-DNA-RNA complex, resulting in the alteration of an existing complex." [GOC:txnOH]
-is_a: GO:0001115 ! protein-DNA-RNA complex subunit organization
+is_a: GO:0001115 ! protein-DNA-RNA complex organization
is_a: GO:0034367 ! protein-containing complex remodeling
[Term]
@@ -7757,7 +7809,7 @@ name: protein-DNA complex remodeling
namespace: biological_process
def: "The acquisition, loss, or modification of macromolecules within a protein-DNA complex, resulting in the alteration of an existing complex." [GOC:txnOH]
is_a: GO:0034367 ! protein-containing complex remodeling
-is_a: GO:0071824 ! protein-DNA complex subunit organization
+is_a: GO:0071824 ! protein-DNA complex organization
[Term]
id: GO:0001128
@@ -7830,6 +7882,7 @@ def: "Binding to an RNA polymerase II (Pol II) complex, typically composed of tw
synonym: "core RNA polymerase II recruiting transcription factor activity" EXACT []
synonym: "transcription factor activity, core RNA polymerase II recruiting" RELATED []
is_a: GO:0000993 ! RNA polymerase II complex binding
+is_a: GO:0030674 ! protein-macromolecule adaptor activity
[Term]
id: GO:0001147
@@ -7993,14 +8046,15 @@ name: reverse transcription
namespace: biological_process
def: "A DNA synthesis process that uses RNA as the initial template for synthesis of DNA, but which also includes an RNase activity to remove the RNA strand of an RNA-DNA heteroduplex produced by the RNA-dependent synthesis step and use of the initial DNA strand as a template for DNA synthesis." [GOC:txnOH, PMID:20358252]
xref: Wikipedia:Reverse_transcription
-is_a: GO:0006278 ! RNA-dependent DNA biosynthetic process
+is_a: GO:0006278 ! RNA-templated DNA biosynthetic process
[Term]
id: GO:0001172
-name: transcription, RNA-templated
+name: RNA-templated transcription
namespace: biological_process
-def: "The cellular synthesis of RNA on a template of RNA." [GOC:txnOH]
+def: "The synthesis of an RNA transcript from an RNA template." [GOC:txnOH]
synonym: "transcription, RNA-dependent" EXACT [GOC:txnOH]
+synonym: "transcription, RNA-templated" EXACT []
is_a: GO:0097659 ! nucleic acid-templated transcription
[Term]
@@ -8012,7 +8066,7 @@ def: "Any process involved in the selection of the specific location within the
synonym: "DNA-dependent transcriptional start site selection" EXACT [GOC:txnOH]
synonym: "transcriptional start site selection at bacterial-type RNA polymerase promoter" NARROW []
is_a: GO:0032774 ! RNA biosynthetic process
-relationship: part_of GO:0006352 ! DNA-templated transcription, initiation
+relationship: part_of GO:0006352 ! DNA-templated transcription initiation
[Term]
id: GO:0001174
@@ -8020,7 +8074,7 @@ name: transcriptional start site selection at RNA polymerase II promoter
namespace: biological_process
def: "Any process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH, PMID:16826228, PMID:18846104]
is_a: GO:0001173 ! DNA-templated transcriptional start site selection
-relationship: part_of GO:0006367 ! transcription initiation from RNA polymerase II promoter
+relationship: part_of GO:0006367 ! transcription initiation at RNA polymerase II promoter
[Term]
id: GO:0001175
@@ -8028,7 +8082,7 @@ name: transcriptional start site selection at RNA polymerase III promoter
namespace: biological_process
def: "Any process involved in the selection of the specific location within the template strand of an RNA polymerase III promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH]
is_a: GO:0001173 ! DNA-templated transcriptional start site selection
-relationship: part_of GO:0006384 ! transcription initiation from RNA polymerase III promoter
+relationship: part_of GO:0006384 ! transcription initiation at RNA polymerase III promoter
[Term]
id: GO:0001177
@@ -8045,7 +8099,7 @@ name: regulation of transcriptional start site selection at RNA polymerase II pr
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of a process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH]
synonym: "regulation of transcription start site selection at RNA polymerase II promoter" EXACT []
-is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter
+is_a: GO:0060260 ! regulation of transcription initiation by RNA polymerase II
relationship: regulates GO:0001174 ! transcriptional start site selection at RNA polymerase II promoter
[Term]
@@ -8069,28 +8123,16 @@ is_a: GO:0140223 ! general transcription initiation factor activity
[Term]
id: GO:0001182
-name: promoter clearance from RNA polymerase I promoter
+name: RNA polymerase I promoter clearance
namespace: biological_process
-def: "Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase I, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH]
+alt_id: GO:0001184
+def: "A process that mediates the transition from the initiation to the elongation phases of transcription by RNA polymerase I, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH, PMID:18559419]
+synonym: "promoter clearance from RNA polymerase I promoter" EXACT []
+synonym: "promoter clearance from RNA polymerase I promoter for nuclear large rRNA transcript" RELATED []
+synonym: "RNA polymerase I promoter escape" EXACT []
is_a: GO:0001109 ! promoter clearance during DNA-templated transcription
relationship: part_of GO:0006360 ! transcription by RNA polymerase I
-[Term]
-id: GO:0001183
-name: transcription elongation from RNA polymerase I promoter for nuclear large rRNA transcript
-namespace: biological_process
-def: "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I promoter for the nuclear large ribosomal RNA (rRNA) transcript by the addition of ribonucleotides catalyzed by RNA polymerase I." [GOC:txnOH]
-is_a: GO:0006362 ! transcription elongation from RNA polymerase I promoter
-relationship: part_of GO:0042790 ! nucleolar large rRNA transcription by RNA polymerase I
-
-[Term]
-id: GO:0001184
-name: promoter clearance from RNA polymerase I promoter for nuclear large rRNA transcript
-namespace: biological_process
-def: "Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase I at a promoter for the nuclear large ribosomal RNA (rRNA) transcript, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH]
-is_a: GO:0001182 ! promoter clearance from RNA polymerase I promoter
-relationship: part_of GO:0042790 ! nucleolar large rRNA transcription by RNA polymerase I
-
[Term]
id: GO:0001186
name: obsolete RNA polymerase I transcription regulator recruiting activity
@@ -8113,7 +8155,7 @@ synonym: "RNA polymerase I transcriptional preinitiation complex assembly" EXACT
synonym: "RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript" NARROW []
synonym: "RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nucleolar primary rRNA transcript" NARROW []
is_a: GO:0070897 ! transcription preinitiation complex assembly
-relationship: part_of GO:0006361 ! transcription initiation from RNA polymerase I promoter
+relationship: part_of GO:0006361 ! transcription initiation at RNA polymerase I promoter
[Term]
id: GO:0001190
@@ -8142,66 +8184,69 @@ consider: GO:0061629
[Term]
id: GO:0001192
-name: maintenance of transcriptional fidelity during DNA-templated transcription elongation
+name: maintenance of transcriptional fidelity during transcription elongation
namespace: biological_process
alt_id: GO:0001194
def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation on a DNA template." [GOC:txnOH]
synonym: "maintenance of transcriptional fidelity during DNA-dependent transcription elongation" EXACT [GOC:txnOH]
synonym: "maintenance of transcriptional fidelity during DNA-dependent transcription elongation from bacterial-type RNA polymerase promoter" EXACT [GOC:txnOH]
+synonym: "maintenance of transcriptional fidelity during DNA-templated transcription elongation" EXACT []
synonym: "maintenance of transcriptional fidelity during DNA-templated transcription elongation from bacterial-type RNA polymerase promoter" NARROW []
is_a: GO:0032774 ! RNA biosynthetic process
-relationship: part_of GO:0006354 ! DNA-templated transcription, elongation
+relationship: part_of GO:0006354 ! DNA-templated transcription elongation
[Term]
id: GO:0001193
-name: maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter
+name: maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II
namespace: biological_process
def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from an RNA polymerase II promoter." [GOC:txnOH, PMID:14531857, PMID:16492753, PMID:17535246]
synonym: "maintenance of transcriptional fidelity during DNA-dependent transcription elongation from RNA polymerase II promoter" EXACT [GOC:txnOH]
-is_a: GO:0001192 ! maintenance of transcriptional fidelity during DNA-templated transcription elongation
-relationship: part_of GO:0006368 ! transcription elongation from RNA polymerase II promoter
+synonym: "maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter" EXACT []
+is_a: GO:0001192 ! maintenance of transcriptional fidelity during transcription elongation
+relationship: part_of GO:0006368 ! transcription elongation by RNA polymerase II
[Term]
id: GO:0001195
-name: maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase III promoter
+name: maintenance of transcriptional fidelity during transcription elongation by RNA polymerase III
namespace: biological_process
def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from a RNA polymerase III promoter." [GOC:txnOH]
synonym: "maintenance of transcriptional fidelity during DNA-dependent transcription elongation from RNA polymerase III promoter" EXACT [GOC:txnOH]
-is_a: GO:0001192 ! maintenance of transcriptional fidelity during DNA-templated transcription elongation
-relationship: part_of GO:0006385 ! transcription elongation from RNA polymerase III promoter
+synonym: "maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase III promoter" EXACT []
+is_a: GO:0001192 ! maintenance of transcriptional fidelity during transcription elongation
+relationship: part_of GO:0006385 ! transcription elongation by RNA polymerase III
[Term]
id: GO:0001196
-name: regulation of mating-type specific transcription from RNA polymerase II promoter
+name: obsolete regulation of mating-type specific transcription from RNA polymerase II promoter
namespace: biological_process
-def: "Any mating-type specific process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:txnOH]
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-is_a: GO:0007532 ! regulation of mating-type specific transcription, DNA-templated
+def: "OBSOLETE. Any mating-type specific process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:txnOH]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0001197
-name: positive regulation of mating-type specific transcription from RNA polymerase II promoter
+name: obsolete positive regulation of mating-type specific transcription from RNA polymerase II promoter
namespace: biological_process
-def: "Any mating-type specific process that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:txnOH]
+def: "OBSOLETE. Any mating-type specific process that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:txnOH]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "activation of transcription from an RNA polymerase II promoter, mating-type specific" NARROW []
synonym: "stimulation of transcription from an RNA polymerase II promoter, mating-type specific" NARROW []
synonym: "up regulation of transcription from an RNA polymerase II promoter, mating-type specific" EXACT []
synonym: "up-regulation of transcription from an RNA polymerase II promoter, mating-type specific" EXACT []
synonym: "upregulation of transcription from an RNA polymerase II promoter, mating-type specific" EXACT []
-is_a: GO:0001196 ! regulation of mating-type specific transcription from RNA polymerase II promoter
-is_a: GO:0045895 ! positive regulation of mating-type specific transcription, DNA-templated
+is_obsolete: true
[Term]
id: GO:0001198
-name: negative regulation of mating-type specific transcription from RNA polymerase II promoter
+name: obsolete negative regulation of mating-type specific transcription from RNA polymerase II promoter
namespace: biological_process
-def: "Any mating-type specific process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:txnOH]
+def: "OBSOLETE. Any mating-type specific process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:txnOH]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "down regulation of RNA polymerase II transcription, mating-type specific" EXACT []
synonym: "down-regulation of RNA polymerase II transcription, mating-type specific" EXACT []
synonym: "downregulation of RNA polymerase II transcription, mating-type specific" EXACT []
synonym: "inhibition of RNA polymerase II transcription, mating-type specific" NARROW []
-is_a: GO:0001196 ! regulation of mating-type specific transcription from RNA polymerase II promoter
-is_a: GO:0045894 ! negative regulation of mating-type specific transcription, DNA-templated
+is_obsolete: true
[Term]
id: GO:0001207
@@ -8366,14 +8411,14 @@ consider: GO:0090398
[Term]
id: GO:0001301
-name: progressive alteration of chromatin involved in cell aging
+name: obsolete progressive alteration of chromatin involved in cell aging
namespace: biological_process
-def: "Any chromatin organization process that occurs during the lifespan of the cell that results in changes in chromatin structure. Such changes may lead to gene dysregulation and ultimately to a loss in cell homeostasis, bringing about an aging phenotype." [GOC:jh, GOC:vw, PMID:12044938]
+def: "OBSOLETE. Any chromatin organization process that occurs during the lifespan of the cell that results in changes in chromatin structure. Such changes may lead to gene dysregulation and ultimately to a loss in cell homeostasis, bringing about an aging phenotype." [GOC:jh, GOC:vw, PMID:12044938]
+comment: This term was obsoleted because it represents a phenotype.
synonym: "age-dependent accumulation of genetic damage" RELATED []
synonym: "progressive alteration of chromatin during cell ageing" EXACT []
synonym: "progressive alteration of chromatin during cell aging" RELATED [GOC:dph, GOC:tb]
-is_a: GO:0006325 ! chromatin organization
-relationship: part_of GO:0007569 ! cell aging
+is_obsolete: true
[Term]
id: GO:0001302
@@ -8419,11 +8464,12 @@ consider: GO:0090398
[Term]
id: GO:0001306
-name: age-dependent response to oxidative stress
+name: obsolete age-dependent response to oxidative stress
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, where the change varies according to the age of the cell or organism." [GOC:jh, PMID:12044938]
-is_a: GO:0006979 ! response to oxidative stress
-relationship: part_of GO:0007571 ! age-dependent general metabolic decline
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, where the change varies according to the age of the cell or organism." [GOC:jh, PMID:12044938]
+comment: This term was obsoleted because it represents a phenotype.
+is_obsolete: true
+consider: GO:0034599
[Term]
id: GO:0001307
@@ -8512,17 +8558,18 @@ is_obsolete: true
[Term]
id: GO:0001315
-name: age-dependent response to reactive oxygen species
+name: obsolete age-dependent response to reactive oxygen species
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of reactive oxygen species, where the change varies according to the age of the cell or organism." [GOC:jh, PMID:12044938]
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of reactive oxygen species, where the change varies according to the age of the cell or organism." [GOC:jh, PMID:12044938]
+comment: This term was obsoleted because it represents a phenotype.
synonym: "age-dependent response to active oxygen species" EXACT []
synonym: "age-dependent response to AOS" EXACT []
synonym: "age-dependent response to reactive oxidative species" EXACT []
synonym: "age-dependent response to reactive oxygen intermediate" EXACT []
synonym: "age-dependent response to ROI" EXACT []
synonym: "age-dependent response to ROS" EXACT []
-is_a: GO:0000302 ! response to reactive oxygen species
-is_a: GO:0001306 ! age-dependent response to oxidative stress
+is_obsolete: true
+consider: GO:0034599
[Term]
id: GO:0001316
@@ -8645,8 +8692,8 @@ is_a: GO:0022607 ! cellular component assembly
id: GO:0001326
name: replication of extrachromosomal circular DNA
namespace: biological_process
-def: "Replication of circular DNA following excision from the chromosome; replication of extrachromosomal circular DNA generally occurs independently of chromosomal replication." [GOC:jh]
-is_a: GO:0006260 ! DNA replication
+def: "Replication of circular DNA following excision from the chromosome; replication of extrachromosomal circular DNA generally occurs independently of chromosomal replication." [GOC:jh, PMID:33867825]
+is_a: GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:0001400
@@ -8727,7 +8774,7 @@ namespace: biological_process
def: "The process in which a glycerophosphodiester is transported across a membrane. Glycerophosphodiesters are small molecules composed of glycerol-3-phosphate and an alcohol, for example, glycerophosphoinositol." [GOC:mcc, PMID:12912892]
is_a: GO:0015711 ! organic anion transport
is_a: GO:0015748 ! organophosphate ester transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0001408
@@ -8888,8 +8935,8 @@ namespace: molecular_function
def: "Catalysis of the reaction: 1-(beta-D-ribofuranosyl)-1,4-dihydronicotinamide + a quinone = 1-(beta-D-ribofuranosyl)nicotinamide + a hydroquinone." [RHEA:12364]
comment: Formerly EC:1.10.99.2.
synonym: "N-ribosyldihydronicotinamide dehydrogenase (quinone) activity" RELATED [EC:1.10.5.1]
-synonym: "NQO(2) activity" RELATED [EC:1.10.5.1]
synonym: "NQO2" RELATED [EC:1.10.5.1]
+synonym: "NQO2 activity" RELATED [EC:1.10.5.1]
synonym: "NRH:quinone oxidoreductase 2 activity" NARROW [EC:1.10.5.1]
synonym: "QR2 activity" RELATED [EC:1.10.5.1]
synonym: "quinone reductase 2 activity" RELATED [EC:1.10.5.1]
@@ -8951,7 +8998,6 @@ synonym: "voltage-sensitive sodium channel complex" EXACT []
xref: NIF_Subcellular:sao785001660
is_a: GO:0034706 ! sodium channel complex
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0001519
@@ -9149,7 +9195,8 @@ name: ovarian follicle development
namespace: biological_process
def: "The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure." [https://www.ncbi.nlm.nih.gov/books/NBK279054/]
synonym: "follicular phase" RELATED []
-is_a: GO:0048608 ! reproductive structure development
+is_a: GO:0003006 ! developmental process involved in reproduction
+is_a: GO:0048856 ! anatomical structure development
relationship: part_of GO:0008585 ! female gonad development
[Term]
@@ -9183,7 +9230,7 @@ name: primary ovarian follicle growth
namespace: biological_process
def: "Increase in size of primary follicles including oocyte growth and granulosa and/or theca cell proliferation until more than one layer of granulosa cells is present (preantral follicle)." [GOC:mtg_mpo, https://www.ncbi.nlm.nih.gov/books/NBK279054/]
is_a: GO:0022602 ! ovulation cycle process
-is_a: GO:0040007 ! growth
+is_a: GO:0048589 ! developmental growth
relationship: part_of GO:0001541 ! ovarian follicle development
[Term]
@@ -9192,7 +9239,7 @@ name: preantral ovarian follicle growth
namespace: biological_process
def: "Increase in size of follicles surrounded by two or more layers of granulosa cells up to the onset of antrum formation." [https://www.ncbi.nlm.nih.gov/books/NBK279054/]
is_a: GO:0022602 ! ovulation cycle process
-is_a: GO:0040007 ! growth
+is_a: GO:0048589 ! developmental growth
relationship: part_of GO:0001541 ! ovarian follicle development
relationship: part_of GO:0048162 ! multi-layer follicle stage
@@ -9236,7 +9283,7 @@ namespace: biological_process
def: "Increase in size of the cumulus surrounding the oocyte including change in morphology due to proliferation and dispersion of cumulus cells." [PMID:30010832]
synonym: "ovarian cumulus growth" RELATED []
is_a: GO:0022602 ! ovulation cycle process
-is_a: GO:0040007 ! growth
+is_a: GO:0048589 ! developmental growth
relationship: part_of GO:0001547 ! antral ovarian follicle growth
relationship: part_of GO:0048165 ! fused antrum stage
@@ -9405,7 +9452,7 @@ is_a: GO:0001565 ! phorbol ester receptor activity
id: GO:0001567
name: cholesterol 25-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + cholesterol + O(2) = 25-hydroxycholesterol + A + H(2)O." [EC:1.14.99.38, RHEA:21104]
+def: "Catalysis of the reaction: AH(2) + cholesterol + O2 = 25-hydroxycholesterol + A + H2O." [EC:1.14.99.38, RHEA:21104]
synonym: "cholesterol 25-monooxygenase activity" RELATED [EC:1.14.99.38]
synonym: "cholesterol,hydrogen-donor:oxygen oxidoreductase (25-hydroxylating) activity" RELATED [EC:1.14.99.38]
xref: EC:1.14.99.38
@@ -9530,9 +9577,8 @@ is_a: GO:0000226 ! microtubule cytoskeleton organization
id: GO:0001579
name: medium-chain fatty acid transport
namespace: biological_process
-def: "The directed movement of medium-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A medium-chain fatty acid is a fatty acid with a chain length of between C6 and C12." [GOC:ai]
-is_a: GO:0006869 ! lipid transport
-is_a: GO:0015718 ! monocarboxylic acid transport
+def: "The directed movement of a medium-chain fatty acid into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A medium-chain fatty acid is a fatty acid with an aliphatic tail of 6 to 12 carbons." [GOC:ai]
+is_a: GO:0015908 ! fatty acid transport
[Term]
id: GO:0001580
@@ -9835,6 +9881,7 @@ name: virus receptor activity
namespace: molecular_function
def: "Combining with a virus component and mediating entry of the virus into the cell." [GOC:bf, GOC:dph, PMID:7621403, UniProtKB-KW:KW-1183]
subset: goslim_chembl
+subset: goslim_generic
synonym: "viral receptor activity" EXACT []
is_a: GO:0140272 ! exogenous protein binding
@@ -9872,6 +9919,7 @@ synonym: "ORPH receptor" EXACT []
synonym: "orphanin-FQ receptor activity" EXACT [GOC:bf]
synonym: "X-opioid receptor activity" RELATED [GOC:bf]
is_a: GO:0004985 ! G protein-coupled opioid receptor activity
+is_a: GO:0008528 ! G protein-coupled peptide receptor activity
[Term]
id: GO:0001627
@@ -9984,7 +10032,7 @@ def: "Combining with a chemoattractant and transmitting the signal across the me
synonym: "G protein chemoattractant receptor activity" EXACT []
synonym: "G-protein chemoattractant receptor activity" EXACT [GOC:bf]
synonym: "G-protein coupled chemoattractant receptor activity" EXACT []
-is_a: GO:0008528 ! G protein-coupled peptide receptor activity
+is_a: GO:0004930 ! G protein-coupled receptor activity
[Term]
id: GO:0001639
@@ -10049,9 +10097,11 @@ is_a: GO:0009884 ! cytokinin receptor activity
[Term]
id: GO:0001648
-name: proteinase activated receptor activity
+name: proteinase-activated receptor activity
namespace: molecular_function
-def: "A G protein-coupled peptide receptor activity that is initiated by cleavage of the N terminus of the receptor by a serine protease, resulting in the generation of a new tethered ligand that interacts with the receptor." [GOC:mah, PMID:11356985]
+def: "A G protein-coupled receptor activity that is activated by cleavage by a serine protease, exposing a tethered ligand corresponding to the new N-terminus, which binds to the receptor and activates it." [GOC:mah, PMID:11356985, PMID:33742547]
+synonym: "protease-activated receptor activity" EXACT []
+synonym: "proteinase activated receptor activity" EXACT []
is_a: GO:0008528 ! G protein-coupled peptide receptor activity
[Term]
@@ -10148,7 +10198,7 @@ namespace: biological_process
def: "A homeostatic process in which an organism modulates its internal body temperature." [GOC:jl]
synonym: "thermoregulation" EXACT [GOC:dph, GOC:tb]
xref: Wikipedia:Thermoregulation
-is_a: GO:0048871 ! multicellular organismal homeostasis
+is_a: GO:0048871 ! multicellular organismal-level homeostasis
[Term]
id: GO:0001660
@@ -10247,16 +10297,7 @@ def: "Binds to and increases the activity of an ATP hydrolysis activity." [GOC:a
synonym: "ATPase stimulator activity" EXACT []
xref: Reactome:R-HSA-5251955 "HSP40s activate intrinsic ATPase activity of HSP70s in the nucleoplasm"
xref: Reactome:R-HSA-5251959 "HSP40s activate intrinsic ATPase activity of HSP70s in the cytosol"
-is_a: GO:0140677 ! molecular function activator activity
-
-[Term]
-id: GO:0001672
-name: regulation of chromatin assembly or disassembly
-namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of chromatin assembly or disassembly." [GOC:go_curators]
-synonym: "regulation of chromatin assembly/disassembly" EXACT []
-is_a: GO:1902275 ! regulation of chromatin organization
-relationship: regulates GO:0006333 ! chromatin assembly or disassembly
+is_a: GO:0060590 ! ATPase regulator activity
[Term]
id: GO:0001673
@@ -10293,7 +10334,7 @@ relationship: part_of GO:0007286 ! spermatid development
id: GO:0001676
name: long-chain fatty acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving long-chain fatty acids, A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [GOC:ajp]
+def: "The chemical reactions and pathways involving a long-chain fatty acid, a fatty acid with an aliphatic tail of 13 to 21 carbons." [GOC:ajp]
synonym: "long-chain fatty acid metabolism" EXACT []
is_a: GO:0006631 ! fatty acid metabolic process
@@ -10303,48 +10344,24 @@ name: formation of translation initiation ternary complex
namespace: biological_process
def: "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator)." [GOC:hjd]
synonym: "translation initiation ternary complex assembly" EXACT []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0006413 ! translational initiation
[Term]
id: GO:0001678
-name: cellular glucose homeostasis
+name: intracellular glucose homeostasis
namespace: biological_process
-def: "A cellular homeostatic process involved in the maintenance of an internal steady state of glucose within a cell or between a cell and its external environment." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "A homeostatic process involved in the maintenance of a steady state level of glucose within a cell." [GOC:dph, GOC:go_curators, GOC:tb]
synonym: "cell glucose homeostasis" EXACT [GOC:dph, GOC:tb]
+synonym: "cellular glucose homeostasis" EXACT []
is_a: GO:0042593 ! glucose homeostasis
-is_a: GO:0055082 ! cellular chemical homeostasis
+is_a: GO:0055082 ! intracellular chemical homeostasis
[Term]
id: GO:0001680
name: tRNA 3'-terminal CCA addition
namespace: biological_process
-def: "Post-transcriptional addition of the terminal 3' CCA sequence to a tRNA which does not encode this sequence within the primary transcript. CCA addition proceeds by the sequential addition of CTP, CTP, and then ATP to the 3' end of the tRNA, yielding a diphosphate with each nucleotide addition." [EC:2.7.7.72, GOC:go_curators]
-synonym: "-C-C-A pyrophosphorylase activity" RELATED [EC:2.7.7.72]
-synonym: "ATP(CTP)-tRNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72]
-synonym: "ATP(CTP):tRNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72]
-synonym: "CCA tRNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72]
-synonym: "CCA-adding enzyme activity" RELATED [EC:2.7.7.72]
-synonym: "CCA-adding enzyme, tRNA adenylyltransferase, tRNA cytidylyltransferase, tRNA CCA-pyrophosphorylase activity" RELATED [EC:2.7.7.72]
-synonym: "CTP(ATP):tRNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72]
-synonym: "CTP:tRNA cytidylyltransferase activity" NARROW [EC:2.7.7.72]
-synonym: "ribonucleic cytidylic cytidylic adenylic pyrophosphorylase activity" RELATED [EC:2.7.7.72]
-synonym: "ribonucleic cytidylyltransferase activity" NARROW [EC:2.7.7.72]
-synonym: "transfer ribonucleate adenyltransferase activity" NARROW [EC:2.7.7.72]
-synonym: "transfer ribonucleate adenylyltransferase activity" NARROW [EC:2.7.7.72]
-synonym: "transfer ribonucleate cytidylyltransferase activity" NARROW [EC:2.7.7.72]
-synonym: "transfer ribonucleate nucleotidyltransferase activity" BROAD [EC:2.7.7.72]
-synonym: "transfer ribonucleic acid nucleotidyl transferase activity" BROAD [EC:2.7.7.72]
-synonym: "transfer ribonucleic adenylyl (cytidylyl) transferase activity" RELATED [EC:2.7.7.72]
-synonym: "transfer ribonucleic-terminal trinucleotide nucleotidyltransferase activity" BROAD [EC:2.7.7.72]
-synonym: "transfer RNA adenylyltransferase activity" NARROW [EC:2.7.7.72]
-synonym: "transfer-RNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72]
-synonym: "tRNA adenylyl(cytidylyl)transferase activity" BROAD [EC:2.7.7.72]
-synonym: "tRNA CCA-diphosphorylase activity" RELATED [EC:2.7.7.72]
-synonym: "tRNA cytidylyltransferase activity" NARROW [EC:2.7.7.72]
-synonym: "tRNA-nucleotidyltransferase activity" BROAD [EC:2.7.7.72]
-xref: KEGG_REACTION:R09382
-xref: MetaCyc:TRNA-CYTIDYLYLTRANSFERASE-RXN
+def: "Post-transcriptional addition of the terminal 3' CCA sequence to a tRNA which does not encode this sequence within the primary transcript. CCA addition proceeds by the sequential addition of CTP, CTP, and then ATP to the 3' end of the tRNA, yielding a diphosphate with each nucleotide addition." [GOC:go_curators, PMID:2247609]
is_a: GO:0042780 ! tRNA 3'-end processing
[Term]
@@ -10460,7 +10477,8 @@ name: histamine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." [GOC:jl, ISBN:0395825172]
synonym: "histamine metabolism" EXACT []
-is_a: GO:0006576 ! cellular biogenic amine metabolic process
+is_a: GO:0006576 ! biogenic amine metabolic process
+is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0052803 ! imidazole-containing compound metabolic process
is_a: GO:0097164 ! ammonium ion metabolic process
@@ -10477,7 +10495,7 @@ synonym: "histamine synthesis" EXACT []
is_a: GO:0001692 ! histamine metabolic process
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0019438 ! aromatic compound biosynthetic process
-is_a: GO:0042401 ! cellular biogenic amine biosynthetic process
+is_a: GO:0042401 ! biogenic amine biosynthetic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
[Term]
@@ -10593,7 +10611,7 @@ relationship: part_of GO:0048332 ! mesoderm morphogenesis
id: GO:0001708
name: cell fate specification
namespace: biological_process
-def: "The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment." [GOC:go_curators]
+def: "The cellular developmental process involved in cell fate commitment in which the cell is designated to follow a developmental path, unless they receive extrinsic cues that direct an alternative fate." [GOC:go_curators]
is_a: GO:0048869 ! cellular developmental process
relationship: part_of GO:0045165 ! cell fate commitment
@@ -10601,7 +10619,7 @@ relationship: part_of GO:0045165 ! cell fate commitment
id: GO:0001709
name: cell fate determination
namespace: biological_process
-def: "A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment." [ISBN:0878932437]
+def: "The cellular developmental process involved in cell fate commitment that occurs after cell fate specification, in which a cell is irreversibly committed to a cellular developmental fate which is heritable on cell division." [ISBN:0878932437]
xref: Wikipedia:Cell_fate_determination
is_a: GO:0048869 ! cellular developmental process
relationship: part_of GO:0045165 ! cell fate commitment
@@ -10672,7 +10690,7 @@ xref: EC:1.4.3.2
xref: MetaCyc:L-AMINO-ACID-OXIDASE-RXN
xref: Reactome:R-HSA-2160492 "IL4I1:FAD oxidises L-Phe to kPPV"
xref: RHEA:13781
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+is_a: GO:0008131 ! primary amine oxidase activity
[Term]
id: GO:0001717
@@ -10794,25 +10812,25 @@ def: "The joining of the small ribosomal subunit, ternary complex, and mRNA." [G
comment: See also the cellular component terms 'eukaryotic 43S preinitiation complex ; GO:0016282', 'eukaryotic 48S initiation complex ; GO:0033290', and their children.
synonym: "formation of translation pre-initiation complex" EXACT []
synonym: "translation preinitiation complex assembly" EXACT []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0002183 ! cytoplasmic translational initiation
[Term]
id: GO:0001732
name: formation of cytoplasmic translation initiation complex
namespace: biological_process
-def: "Joining of the large subunit, with release of IF2/eIF2 and IF3/eIF3. This leaves the functional ribosome at the AUG, with the methionyl/formyl-methionyl-tRNA positioned at the P site." [GOC:hjd]
+def: "Joining of the large ribosomal subunit with the translation preinitiation complex, with release of IF2/eIF2 and IF3/eIF3 or IF5B/eIF5B. This leaves the functional ribosome at the AUG, with the methionyl/formyl-methionyl-tRNA positioned at the P site." [GOC:hjd, PMID:29735639]
synonym: "cytoplasmic translation initiation complex assembly" EXACT []
synonym: "formation of translation initiation complex" BROAD []
synonym: "translation initiation complex assembly" BROAD []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0002183 ! cytoplasmic translational initiation
[Term]
id: GO:0001733
name: galactosylceramide sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + a galactosylceramide = adenosine 3',5'-bisphosphate + a galactosylceramidesulfate." [EC:2.8.2.11, PMID:10727929, RHEA:43304]
+def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + a galactosylceramide = adenosine 3',5'-bisphosphate + a galactosylceramidesulfate." [EC:2.8.2.11, PMID:10727929, RHEA:20613]
synonym: "3'-phosphoadenosine-5'-phosphosulfate-cerebroside sulfotransferase activity" RELATED [EC:2.8.2.11]
synonym: "3'-phosphoadenylyl-sulfate:galactosylceramide 3'-sulfotransferase activity" RELATED [EC:2.8.2.11]
synonym: "cerebroside sulfotransferase activity" EXACT []
@@ -10824,7 +10842,7 @@ synonym: "glycosphingolipid sulfotransferase activity" RELATED [EC:2.8.2.11]
synonym: "GSase" RELATED [EC:2.8.2.11]
xref: EC:2.8.2.11
xref: MetaCyc:GALACTOSYLCERAMIDE-SULFOTRANSFERASE-RXN
-xref: RHEA:43304
+xref: RHEA:20613
is_a: GO:0050694 ! galactose 3-O-sulfotransferase activity
[Term]
@@ -11003,7 +11021,7 @@ id: GO:0001755
name: neural crest cell migration
namespace: biological_process
def: "The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo." [GOC:ascb_2009, GOC:dph, GOC:tb, ISBN:0878932437]
-is_a: GO:0001667 ! ameboidal-type cell migration
+is_a: GO:0090497 ! mesenchymal cell migration
relationship: part_of GO:0014032 ! neural crest cell development
[Term]
@@ -11057,7 +11075,7 @@ relationship: positively_regulates GO:0010092 ! specification of animal organ id
id: GO:0001760
name: aminocarboxymuconate-semialdehyde decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-amino-3-carboxymuconate 6-semialdehyde + H(+) = 2-aminomuconate 6-semialdehyde + CO(2)." [EC:4.1.1.45, RHEA:16557]
+def: "Catalysis of the reaction: 2-amino-3-carboxymuconate 6-semialdehyde + H+ = 2-aminomuconate 6-semialdehyde + CO2." [EC:4.1.1.45, RHEA:16557]
synonym: "2-amino-3-(3-oxoprop-1-en-1-yl)but-2-enedioate carboxy-lyase (2-aminomuconate-semialdehyde-forming)" RELATED [EC:4.1.1.45]
synonym: "2-amino-3-(3-oxoprop-1-en-1-yl)but-2-enedioate carboxy-lyase activity" RELATED [EC:4.1.1.45]
synonym: "2-amino-3-(3-oxoprop-2-enyl)but-2-enedioate carboxy-lyase activity" RELATED [EC:4.1.1.45]
@@ -11078,8 +11096,7 @@ name: beta-alanine transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of beta-alanine from one side of a membrane to the other. Beta-alanine is 3-aminopropanoic acid." [GOC:hjd]
synonym: "beta-alanine transporter activity" BROAD []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
[Term]
id: GO:0001762
@@ -11087,7 +11104,6 @@ name: beta-alanine transport
namespace: biological_process
def: "The directed movement of beta-alanine, 3-aminopropanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:hjd]
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0001763
@@ -11212,15 +11228,18 @@ id: GO:0001774
name: microglial cell activation
namespace: biological_process
def: "The change in morphology and behavior of a microglial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, PMID:10626665, PMID:10695728, PMID:12580336, PMID:9893949]
+is_a: GO:0002269 ! leukocyte activation involved in inflammatory response
is_a: GO:0042116 ! macrophage activation
+is_a: GO:0061900 ! glial cell activation
[Term]
id: GO:0001775
name: cell activation
namespace: biological_process
-def: "A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:mgi_curators]
+def: "A multicellular organismal process by which exposure to an activating factor such as a cellular or soluble ligand results in a change in the morphology or behavior of a cell." [GOC:mgi_curators]
subset: goslim_pir
is_a: GO:0009987 ! cellular process
+is_a: GO:0032501 ! multicellular organismal process
[Term]
id: GO:0001776
@@ -12429,7 +12448,6 @@ def: "The process whose specific outcome is the progression of the placenta over
synonym: "placental development" EXACT []
synonym: "placentation" EXACT [GOC:dph, GOC:tb]
is_a: GO:0048513 ! animal organ development
-is_a: GO:0048608 ! reproductive structure development
[Term]
id: GO:0001891
@@ -12445,7 +12463,6 @@ name: embryonic placenta development
namespace: biological_process
def: "The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin." [GOC:add, ISBN:068340007X]
synonym: "fetal placenta development" EXACT [GOC:dph]
-is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048568 ! embryonic organ development
relationship: part_of GO:0001701 ! in utero embryonic development
relationship: part_of GO:0001890 ! placenta development
@@ -12468,7 +12485,7 @@ namespace: biological_process
def: "A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function." [GOC:add, GOC:isa_complete]
synonym: "tissue maintenance" NARROW [GOC:add]
is_a: GO:0060249 ! anatomical structure homeostasis
-relationship: part_of GO:0048871 ! multicellular organismal homeostasis
+relationship: part_of GO:0048871 ! multicellular organismal-level homeostasis
[Term]
id: GO:0001895
@@ -12496,41 +12513,41 @@ is_a: GO:0001907 ! killing by symbiont of host cells
[Term]
id: GO:0001898
-name: regulation of cytolysis by symbiont of host cells
+name: obsolete regulation of cytolysis by symbiont of host cells
namespace: biological_process
-def: "Any process in which an organism modulates the frequency, rate or extent of the cytolysis by that organism of cells in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add, GOC:dph, GOC:tb]
+def: "OBSOLETE. Any process in which an organism modulates the frequency, rate or extent of the cytolysis by that organism of cells in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add, GOC:dph, GOC:tb]
+comment: This term was obsoleted because it has been used inconsistently.
synonym: "regulation by symbiont of cytolysis of host cells" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0043903 ! regulation of biological process involved in symbiotic interaction
-relationship: regulates GO:0001897 ! cytolysis by symbiont of host cells
+is_obsolete: true
+consider: GO:0031640
[Term]
id: GO:0001899
-name: negative regulation of cytolysis by symbiont of host cells
+name: obsolete negative regulation of cytolysis by symbiont of host cells
namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of cytolysis by that organism of cells in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add, GOC:dph, GOC:tb]
+def: "OBSOLETE. Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of cytolysis by that organism of cells in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add, GOC:dph, GOC:tb]
+comment: This term was obsoleted because it has been used inconsistently.
synonym: "down regulation by symbiont of cytolysis of host cells" EXACT []
synonym: "down-regulation by symbiont of cytolysis of host cells" EXACT []
synonym: "downregulation by symbiont of cytolysis of host cells" EXACT []
synonym: "inhibition by symbiont of cytolysis of host cells" NARROW []
synonym: "negative regulation by symbiont of cytolysis of host cells" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0001898 ! regulation of cytolysis by symbiont of host cells
-is_a: GO:0048519 ! negative regulation of biological process
-relationship: negatively_regulates GO:0001897 ! cytolysis by symbiont of host cells
+is_obsolete: true
[Term]
id: GO:0001900
-name: positive regulation of cytolysis by symbiont of host cells
+name: obsolete positive regulation of cytolysis by symbiont of host cells
namespace: biological_process
-def: "Any process in which an organism activates or increases the frequency, rate or extent of cytolysis by that organism of cells in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add, GOC:dph, GOC:tb]
+def: "OBSOLETE. Any process in which an organism activates or increases the frequency, rate or extent of cytolysis by that organism of cells in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add, GOC:dph, GOC:tb]
+comment: This term was obsoleted because it has been used inconsistently.
synonym: "activation by symbiont of cytolysis of host cells" NARROW []
synonym: "positive regulation by symbiont of cytolysis of host cells" EXACT [GOC:dph, GOC:tb]
synonym: "stimulation by symbiont of cytolysis of host cells" NARROW []
synonym: "up regulation by symbiont of cytolysis of host cells" EXACT []
synonym: "up-regulation by symbiont of cytolysis of host cells" EXACT []
synonym: "upregulation by symbiont of cytolysis of host cells" EXACT []
-is_a: GO:0001898 ! regulation of cytolysis by symbiont of host cells
-is_a: GO:0048518 ! positive regulation of biological process
-relationship: positively_regulates GO:0001897 ! cytolysis by symbiont of host cells
+is_obsolete: true
+consider: GO:0001907
[Term]
id: GO:0001905
@@ -12734,7 +12751,6 @@ name: regulation of receptor recycling
namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of receptor recycling." [GOC:add]
is_a: GO:0023051 ! regulation of signaling
-is_a: GO:0031323 ! regulation of cellular metabolic process
is_a: GO:0060255 ! regulation of macromolecule metabolic process
relationship: regulates GO:0001881 ! receptor recycling
@@ -12750,7 +12766,6 @@ synonym: "inhibition of receptor recycling" NARROW []
is_a: GO:0001919 ! regulation of receptor recycling
is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
is_a: GO:0023057 ! negative regulation of signaling
-is_a: GO:0031324 ! negative regulation of cellular metabolic process
relationship: negatively_regulates GO:0001881 ! receptor recycling
[Term]
@@ -12766,7 +12781,6 @@ synonym: "upregulation of receptor recycling" EXACT []
is_a: GO:0001919 ! regulation of receptor recycling
is_a: GO:0010604 ! positive regulation of macromolecule metabolic process
is_a: GO:0023056 ! positive regulation of signaling
-is_a: GO:0031325 ! positive regulation of cellular metabolic process
relationship: positively_regulates GO:0001881 ! receptor recycling
[Term]
@@ -13243,11 +13257,11 @@ is_a: GO:0005515 ! protein binding
id: GO:0001966
name: thigmotaxis
namespace: biological_process
-def: "The directed movement of a motile cell or organism in response to touch." [GOC:dph]
+def: "The directed movement of an animal in response to touch." [GOC:dph]
synonym: "stereotaxis" EXACT []
synonym: "taxis in response to mechanical stimulus" BROAD []
synonym: "taxis in response to touch stimulus" EXACT []
-is_a: GO:0042330 ! taxis
+is_a: GO:0007610 ! behavior
[Term]
id: GO:0001967
@@ -13331,7 +13345,6 @@ namespace: molecular_function
def: "Binding to retinoic acid, 3,7-dimethyl-9-(2,6,-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid." [GOC:hjd]
is_a: GO:0005501 ! retinoid binding
is_a: GO:0033293 ! monocarboxylic acid binding
-is_a: GO:0043177 ! organic acid binding
[Term]
id: GO:0001973
@@ -13375,6 +13388,7 @@ id: GO:0001977
name: renal system process involved in regulation of blood volume
namespace: biological_process
def: "A slow mechanism of blood pressure regulation that responds to changes in pressure resulting from fluid and salt intake by modulating the quantity of blood in the circulatory system." [GOC:dph, GOC:tb, ISBN:0721643949]
+subset: gocheck_do_not_annotate
synonym: "renal blood volume control of blood pressure" RELATED []
synonym: "renal regulation of blood volume" RELATED [GOC:dph, GOC:tb]
is_a: GO:0003071 ! renal system process involved in regulation of systemic arterial blood pressure
@@ -13968,7 +13982,6 @@ synonym: "regulation of L-glutamate import" BROAD []
synonym: "regulation of L-glutamate transport" BROAD []
synonym: "regulation of L-glutamate uptake" EXACT [GOC:TermGenie]
is_a: GO:0010958 ! regulation of amino acid import across plasma membrane
-is_a: GO:1903959 ! regulation of anion transmembrane transport
relationship: regulates GO:0098712 ! L-glutamate import across plasma membrane
[Term]
@@ -13994,8 +14007,8 @@ synonym: "negative regulation of L-glutamate transport" BROAD []
synonym: "negative regulation of L-glutamate uptake" RELATED [GOC:TermGenie]
synonym: "regulation of L-glutamate import" BROAD []
is_a: GO:0002036 ! regulation of L-glutamate import across plasma membrane
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:0051956 ! negative regulation of amino acid transport
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
relationship: negatively_regulates GO:0098712 ! L-glutamate import across plasma membrane
[Term]
@@ -14021,8 +14034,8 @@ synonym: "upregulation of L-glutamate import" EXACT [GOC:TermGenie]
synonym: "upregulation of L-glutamate transport" BROAD []
synonym: "upregulation of L-glutamate uptake" RELATED [GOC:TermGenie]
is_a: GO:0002036 ! regulation of L-glutamate import across plasma membrane
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:0051957 ! positive regulation of amino acid transport
-is_a: GO:1903961 ! positive regulation of anion transmembrane transport
relationship: positively_regulates GO:0098712 ! L-glutamate import across plasma membrane
[Term]
@@ -14121,16 +14134,21 @@ id: GO:0002049
name: pyoverdine biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of the siderochrome pyoverdine." [PMID:15317763]
-is_a: GO:0002048 ! pyoverdine metabolic process
+is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0019290 ! siderophore biosynthetic process
+is_a: GO:0019438 ! aromatic compound biosynthetic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
[Term]
id: GO:0002050
name: pyoverdine catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of the siderochrome pyoverdine." [PMID:15317763]
-is_a: GO:0002048 ! pyoverdine metabolic process
+is_a: GO:0019439 ! aromatic compound catabolic process
+is_a: GO:0043171 ! peptide catabolic process
is_a: GO:0046215 ! siderophore catabolic process
+is_a: GO:0046700 ! heterocycle catabolic process
+is_a: GO:1901361 ! organic cyclic compound catabolic process
[Term]
id: GO:0002051
@@ -14351,7 +14369,7 @@ name: acrosome matrix dispersal
namespace: biological_process
def: "The proteolytic digestion of components in the acrosomal matrix that occurs as part of the acrosome reaction. The process can occur either in the cumulus oophorous facilitating the penetration of it by the sperm, or at the zona pellucida allowing the sperm to reach the plasma membrane of the egg where the inner acrosomal membrane of the sperm can interact with the egg plasma membrane." [GOC:dph, PMID:3886029]
is_a: GO:0022414 ! reproductive process
-is_a: GO:0051603 ! proteolysis involved in cellular protein catabolic process
+is_a: GO:0051603 ! proteolysis involved in protein catabolic process
relationship: part_of GO:0007340 ! acrosome reaction
[Term]
@@ -14396,7 +14414,6 @@ name: regulation of oxidative phosphorylation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis." [GOC:dph]
synonym: "OXPHOS" EXACT []
-is_a: GO:1903578 ! regulation of ATP metabolic process
is_a: GO:1903715 ! regulation of aerobic respiration
relationship: regulates GO:0006119 ! oxidative phosphorylation
@@ -14477,9 +14494,7 @@ id: GO:0002090
name: regulation of receptor internalization
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of receptor internalization." [GOC:hjd]
-is_a: GO:0031323 ! regulation of cellular metabolic process
is_a: GO:0048259 ! regulation of receptor-mediated endocytosis
-is_a: GO:0060255 ! regulation of macromolecule metabolic process
relationship: regulates GO:0031623 ! receptor internalization
[Term]
@@ -14492,8 +14507,6 @@ synonym: "down-regulation of receptor internalization" EXACT []
synonym: "downregulation of receptor internalization" EXACT []
synonym: "inhibition of receptor internalization" NARROW []
is_a: GO:0002090 ! regulation of receptor internalization
-is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
-is_a: GO:0031324 ! negative regulation of cellular metabolic process
is_a: GO:0048261 ! negative regulation of receptor-mediated endocytosis
relationship: negatively_regulates GO:0031623 ! receptor internalization
@@ -14508,8 +14521,6 @@ synonym: "up regulation of receptor internalization" EXACT []
synonym: "up-regulation of receptor internalization" EXACT []
synonym: "upregulation of receptor internalization" EXACT []
is_a: GO:0002090 ! regulation of receptor internalization
-is_a: GO:0010604 ! positive regulation of macromolecule metabolic process
-is_a: GO:0031325 ! positive regulation of cellular metabolic process
is_a: GO:0048260 ! positive regulation of receptor-mediated endocytosis
relationship: positively_regulates GO:0031623 ! receptor internalization
@@ -14923,14 +14934,15 @@ namespace: cellular_component
def: "A complex of two proteins involved in the thiolation of uridine 34 (U34) of tRNAs decoding two-family box triplets." [PMID:17062623, PMID:18391219]
synonym: "Cut1-Cut2 complex" NARROW []
synonym: "tRNA thiouridylase" BROAD []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005829 ! cytosol
[Term]
id: GO:0002145
name: 4-amino-5-hydroxymethyl-2-methylpyrimidine diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate + H2O = hydroxymethylpyrimidine phosphate + phosphate + H(+)." [MetaCyc:RXN0-3543]
+def: "Catalysis of the reaction: 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate + H2O = hydroxymethylpyrimidine phosphate + phosphate + H+." [MetaCyc:RXN0-3543]
synonym: "HMP-PP diphosphatase" EXACT []
synonym: "HMP-PP pyrophosphatase" EXACT []
xref: MetaCyc:RXN0-3543
@@ -15029,7 +15041,7 @@ is_a: GO:0003727 ! single-stranded RNA binding
id: GO:0002154
name: thyroid hormone mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of a thyroid hormone." [GOC:hjd]
+def: "The series of molecular signals mediated by the detection of a thyroid hormone." [GOC:hjd]
synonym: "thyroid hormone mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0009755 ! hormone-mediated signaling pathway
is_a: GO:0030522 ! intracellular receptor signaling pathway
@@ -15197,7 +15209,6 @@ name: protein localization to paranode region of axon
namespace: biological_process
def: "A cellular protein localization process in which a protein is transported to, or maintained at, the paranode region of an axon." [PMID:18803321]
synonym: "protein localisation to paranode region of axon" EXACT [GOC:mah]
-is_a: GO:0034613 ! cellular protein localization
is_a: GO:0099612 ! protein localization to axon
[Term]
@@ -15228,7 +15239,7 @@ name: homodimeric serine palmitoyltransferase complex
namespace: cellular_component
def: "A homodimeric complex which transfers a palmitoyl group onto serine, forming 3-dehydro-D-sphinganine." [GOC:hjd]
comment: This complex occurs primarily in bacteria.
-is_a: GO:0017059 ! serine C-palmitoyltransferase complex
+is_a: GO:0002178 ! palmitoyltransferase complex
[Term]
id: GO:0002180
@@ -15543,28 +15554,27 @@ is_a: GO:0045089 ! positive regulation of innate immune response
id: GO:0002220
name: innate immune response activating cell surface receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals leading to activation of the innate immune response generated as a consequence of binding to a cell surface receptor." [GOC:add, ISBN:0781735149, PMID:15199967]
+def: "The series of molecular signals initiated by a ligand binding to a cell surface receptor that leads to the activation of an innate immune response." [GOC:add, ISBN:0781735149, PMID:15199967]
synonym: "activation of innate immune response by cell surface receptor signaling pathway" EXACT []
synonym: "innate immune response activating cell surface receptor signalling pathway" EXACT []
is_a: GO:0002429 ! immune response-activating cell surface receptor signaling pathway
-is_a: GO:0002758 ! innate immune response-activating signal transduction
+is_a: GO:0002758 ! innate immune response-activating signaling pathway
[Term]
id: GO:0002221
name: pattern recognition receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of a pattern recognition receptor (PRR) binding to one of its physiological ligands. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species, or damage-associated molecular pattern (DAMPs), endogenous molecules released from damaged cells." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967]
-synonym: "PAMP receptor signaling pathway" EXACT [ISBN:0781735149, PMID:15199967, PMID:15728447]
+def: "The series of molecular signals initiated by a ligand binding to a pattern recognition receptor (PRR), and ending with the regulation of a downstream cellular process, e.g. transcription. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species, or damage-associated molecular pattern (DAMPs), endogenous molecules released from damaged cells." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967]
synonym: "pathogen receptor signaling pathway" EXACT [ISBN:0781735149, PMID:15199967, PMID:15728447]
synonym: "pathogen receptor signalling pathway" EXACT [ISBN:0781735149, PMID:15199967, PMID:15728447]
synonym: "PRR signaling pathway" EXACT [ISBN:0781735149, PMID:15199967, PMID:15728447]
-is_a: GO:0002764 ! immune response-regulating signaling pathway
+is_a: GO:0002758 ! innate immune response-activating signaling pathway
[Term]
id: GO:0002222
name: stimulatory killer cell immunoglobulin-like receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a killer cell immunoglobulin-like receptor capable of cellular activation." [GO_REF:0000022, GOC:add, ISBN:0781735149]
+def: "The series of molecular signals initiated by a ligand binding to a killer cell immunoglobulin-like receptor capable of cellular activation." [GO_REF:0000022, GOC:add, ISBN:0781735149]
synonym: "stimulatory killer cell immunoglobulin-like receptor signalling pathway" EXACT []
synonym: "stimulatory KIR signaling pathway" EXACT [ISBN:0781735149]
is_a: GO:0002220 ! innate immune response activating cell surface receptor signaling pathway
@@ -15573,7 +15583,7 @@ is_a: GO:0002220 ! innate immune response activating cell surface receptor signa
id: GO:0002223
name: stimulatory C-type lectin receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation." [GO_REF:0000022, GOC:add, ISBN:0781735149]
+def: "The series of molecular signals initiated by the binding of C-type lectin to its receptor on the surface of a target cell, and resulting in cellular activation." [GO_REF:0000022, GOC:add, ISBN:0781735149]
synonym: "stimulatory C-type lectin receptor signalling pathway" EXACT []
synonym: "stimulatory Ly49 family receptor signaling pathway" NARROW [ISBN:0781735149]
is_a: GO:0002220 ! innate immune response activating cell surface receptor signaling pathway
@@ -15583,7 +15593,7 @@ is_a: GO:1990858 ! cellular response to lectin
id: GO:0002224
name: toll-like receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response." [GO_REF:0000022, GOC:add, ISBN:0781735149, PMID:12467241, PMID:12524386, PMID:12855817, PMID:15585605, PMID:15728447]
+def: "The series of molecular signals initiated by a ligand binding to a toll-like receptor of a target cell. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate an innate immune response." [GO_REF:0000022, GOC:add, ISBN:0781735149, PMID:12467241, PMID:12524386, PMID:12855817, PMID:15585605, PMID:15728447]
comment: Note that the vertebrate toll-like receptors, unlike the Drosophila Toll molecule, directly bind their ligands. The Drosophila Toll molecule requires the Sptzle factor to bind microbial ligands and then the receptor in order to initiate innate immune responses.
synonym: "TLR signaling pathway" EXACT [ISBN:0781735149]
synonym: "toll-like receptor signalling pathway" EXACT []
@@ -15793,9 +15803,10 @@ relationship: part_of GO:0002246 ! wound healing involved in inflammatory respon
id: GO:0002248
name: connective tissue replacement involved in inflammatory response wound healing
namespace: biological_process
-def: "The series of events leading to growth of connective tissue when loss of tissues that are incapable of regeneration occurs, or when fibrinous exudate cannot be adequately cleared that contribute to an inflammatory response." [GOC:jal, ISBN:0721601871]
+def: "The series of events leading to growth of connective tissue when loss of tissues that are incapable of regeneration occurs, or when fibrinous exudate cannot be adequately cleared, as part of an inflammatory response." [GOC:jal, PMID:9639571]
synonym: "connective tissue replacement during inflammatory response" RELATED [GOC:dph]
synonym: "fibrosis during inflammatory response" NARROW [ISBN:0721601871]
+synonym: "tissue fibrosis development" NARROW []
is_a: GO:0097709 ! connective tissue replacement
relationship: part_of GO:0002246 ! wound healing involved in inflammatory response
@@ -15810,7 +15821,7 @@ is_a: GO:0002507 ! tolerance induction
id: GO:0002250
name: adaptive immune response
namespace: biological_process
-def: "An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory)." [GO_REF:0000022, GOC:add, ISBN:0781735149]
+def: "An immune response mediated by cells expressing specific receptors for antigens produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory)." [GO_REF:0000022, GOC:add, ISBN:0781735149]
synonym: "acquired immune response" EXACT [ISBN:068340007X]
synonym: "immune memory response" EXACT [GOC:add]
xref: Wikipedia:Adaptive_immune_system
@@ -16654,7 +16665,7 @@ is_a: GO:0002327 ! immature B cell differentiation
id: GO:0002330
name: pre-B cell receptor expression
namespace: biological_process
-def: "The process leading up to expression of the pre-B cell receptor on the surface of pre-B cells, starting with the recombination of an immunuglobulin heavy chain locus, including expression of the surrogate light chain, the association of the surrogate light chain with the heavy chain, and expression of the complete pre-B cell receptor on the cell surface. pre-B cell receptor expression is a key checkpoint in the transition of pro-B cell to pre-B cell." [GOC:add, GOC:jal, PMID:15263090, PMID:22949502, PMID:9834086]
+def: "The process leading up to expression of the pre-B cell receptor on the surface of pre-B cells, starting with the recombination of an immunuglobulin heavy chain locus, including expression of the surrogate light chain, the association of the surrogate light chain with the heavy chain, and expression of the complete pre-B cell receptor on the cell surface. pre-B cell receptor expression is a key checkpoint in the transition of pro-B cell to pre-B cell." [GOC:add, GOC:jal, PMID:15263090, PMID:22949502, PMID:9834086]
is_a: GO:0048869 ! cellular developmental process
relationship: part_of GO:0002329 ! pre-B cell differentiation
@@ -16794,6 +16805,7 @@ synonym: "central B lymphocyte deletion" EXACT []
synonym: "central B-cell deletion" EXACT []
synonym: "central B-lymphocyte deletion" EXACT []
is_a: GO:0002516 ! B cell deletion
+is_a: GO:0010623 ! programmed cell death involved in cell development
relationship: part_of GO:0002340 ! central B cell selection
relationship: part_of GO:0002510 ! central B cell tolerance induction
@@ -17558,17 +17570,17 @@ is_a: GO:0048002 ! antigen processing and presentation of peptide antigen
id: GO:0002429
name: immune response-activating cell surface receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of a cell capable of activating or perpetuating an immune response." [GO_REF:0000022, GOC:add, ISBN:0781735149]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of a cell, leading to the activation or perpetuation of an immune response." [GO_REF:0000022, GOC:add, ISBN:0781735149]
synonym: "activation of immune response by cell surface receptor signaling pathway" EXACT []
synonym: "immune response-activating cell surface receptor signalling pathway" EXACT []
-is_a: GO:0002757 ! immune response-activating signal transduction
+is_a: GO:0002757 ! immune response-activating signaling pathway
is_a: GO:0002768 ! immune response-regulating cell surface receptor signaling pathway
[Term]
id: GO:0002430
name: complement receptor mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of a component of the complement pathway binding to a complement receptor. Such components include both whole complement proteins and fragments of complement proteins generated through the activity of the complement pathway." [GO_REF:0000022, GOC:add, ISBN:0781735149]
+def: "The series of molecular signals generated as a consequence of a component of the complement pathway binding to a complement receptor. Such components include both whole complement proteins and fragments of complement proteins generated through the activity of the complement pathway." [GO_REF:0000022, GOC:add, ISBN:0781735149]
synonym: "complement receptor mediated signalling pathway" EXACT []
synonym: "immune response-regulating cell surface receptor signalling pathway" BROAD []
is_a: GO:0002429 ! immune response-activating cell surface receptor signaling pathway
@@ -17577,7 +17589,7 @@ is_a: GO:0002429 ! immune response-activating cell surface receptor signaling pa
id: GO:0002431
name: Fc receptor mediated stimulatory signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of a the binding of the Fc portion of an immunoglobulin by an Fc receptor capable of activating or perpetuating an immune response. The Fc portion of an immunoglobulin is its C-terminal constant region." [GO_REF:0000022, GOC:add, ISBN:0781735149]
+def: "The series of molecular signals generated as a consequence of a the binding of the Fc portion of an immunoglobulin by an Fc receptor capable of activating or perpetuating an immune response. The Fc portion of an immunoglobulin is its C-terminal constant region." [GO_REF:0000022, GOC:add, ISBN:0781735149]
synonym: "Fc receptor mediated stimulatory signalling pathway" EXACT []
synonym: "Fc-receptor mediated stimulatory signaling pathway" EXACT []
is_a: GO:0002429 ! immune response-activating cell surface receptor signaling pathway
@@ -18171,7 +18183,7 @@ id: GO:0002496
name: proteolysis associated with antigen processing and presentation
namespace: biological_process
def: "The hydrolysis of a peptide bond or bonds within a protein contributing to antigen processing and presentation." [GOC:add, ISBN:0781735149, PMID:15224092, PMID:15771591]
-is_a: GO:0051603 ! proteolysis involved in cellular protein catabolic process
+is_a: GO:0051603 ! proteolysis involved in protein catabolic process
relationship: part_of GO:0048002 ! antigen processing and presentation of peptide antigen
[Term]
@@ -19549,7 +19561,7 @@ id: GO:0002628
name: regulation of proteolysis associated with antigen processing and presentation
namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of proteolysis associated with antigen processing and presentation." [GOC:add]
-is_a: GO:1903050 ! regulation of proteolysis involved in cellular protein catabolic process
+is_a: GO:1903050 ! regulation of proteolysis involved in protein catabolic process
relationship: regulates GO:0002496 ! proteolysis associated with antigen processing and presentation
[Term]
@@ -19563,7 +19575,9 @@ synonym: "downregulation of proteolysis associated with antigen processing and p
synonym: "inhibition of proteolysis associated with antigen processing and presentation" NARROW []
is_a: GO:0002584 ! negative regulation of antigen processing and presentation of peptide antigen
is_a: GO:0002628 ! regulation of proteolysis associated with antigen processing and presentation
-is_a: GO:1903051 ! negative regulation of proteolysis involved in cellular protein catabolic process
+is_a: GO:0031330 ! negative regulation of cellular catabolic process
+is_a: GO:0042177 ! negative regulation of protein catabolic process
+is_a: GO:1903051 ! negative regulation of proteolysis involved in protein catabolic process
relationship: negatively_regulates GO:0002496 ! proteolysis associated with antigen processing and presentation
[Term]
@@ -19578,7 +19592,9 @@ synonym: "up-regulation of proteolysis associated with antigen processing and pr
synonym: "upregulation of proteolysis associated with antigen processing and presentation" EXACT []
is_a: GO:0002585 ! positive regulation of antigen processing and presentation of peptide antigen
is_a: GO:0002628 ! regulation of proteolysis associated with antigen processing and presentation
-is_a: GO:1903052 ! positive regulation of proteolysis involved in cellular protein catabolic process
+is_a: GO:0031331 ! positive regulation of cellular catabolic process
+is_a: GO:0045732 ! positive regulation of protein catabolic process
+is_a: GO:1903052 ! positive regulation of proteolysis involved in protein catabolic process
relationship: positively_regulates GO:0002496 ! proteolysis associated with antigen processing and presentation
[Term]
@@ -21056,7 +21072,7 @@ is_a: GO:0002745 ! antigen processing and presentation initiated by receptor med
id: GO:0002752
name: cell surface pattern recognition receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of a cell surface pattern recognition receptor (PRR) binding to one of its physiological ligands. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967]
+def: "The series of molecular signals initiated by a ligand binding to a cell surface pattern recognition receptor (PRR). PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967]
synonym: "cell surface PAMP receptor signaling pathway" EXACT []
synonym: "cell surface pathogen receptor signaling pathway" EXACT []
synonym: "cell surface pattern recognition receptor signalling pathway" EXACT []
@@ -21066,35 +21082,41 @@ is_a: GO:0002221 ! pattern recognition receptor signaling pathway
[Term]
id: GO:0002753
-name: cytoplasmic pattern recognition receptor signaling pathway
+name: cytosolic pattern recognition receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of a cytoplasmic pattern recognition receptor (PRR) binding to one of its physiological ligands. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967]
+alt_id: GO:0039528
+def: "The series of molecular signals initiated by the binding of a ligand from another organism to a cytosolic pattern recognition receptor (PRR). PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967, PMID:17328678, PMID:18272355, PMID:19531363, PMID:21187438]
+comment: This term should be used for annotation when it is not known which cytoplasmic pattern recognition receptor (PRR) has been activated. If the PRR is known, consider instead the child terms. The RIG-like family is composed of at least RIG-I (retinoic acid inducible gene I; also known as DDX58), melanoma differentiation-associated gene 5 (MDA5; also known as helicard or IFIH1) and LGP2.
+synonym: "cytoplasmic caspase-recruiting domain (CARD) helicase signaling pathway" NARROW [PMID:17328678]
synonym: "cytoplasmic PAMP receptor signaling pathway" EXACT []
synonym: "cytoplasmic pathogen receptor signaling pathway" EXACT []
+synonym: "cytoplasmic pattern recognition receptor signaling pathway" EXACT []
+synonym: "cytoplasmic pattern recognition receptor signaling pathway in response to virus" NARROW []
synonym: "cytoplasmic pattern recognition receptor signalling pathway" EXACT []
+synonym: "cytoplasmic pattern recognition receptor signalling pathway in response to virus" NARROW [GOC:mah]
synonym: "cytoplasmic PRR signaling pathway" EXACT []
+synonym: "virus-induced cytoplasmic pattern recognition receptor signaling pathway" NARROW [GOC:bf]
is_a: GO:0002221 ! pattern recognition receptor signaling pathway
is_a: GO:0030522 ! intracellular receptor signaling pathway
-is_a: GO:0035556 ! intracellular signal transduction
[Term]
id: GO:0002754
-name: intracellular endosomal pattern recognition receptor signaling pathway
+name: endosomal pattern recognition receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of an intracellular vesicle pattern recognition receptor (PRR) binding to one of its physiological ligands. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967]
+def: "The series of molecular signals initiated by the binding of a ligand to an intracellular vesicle pattern recognition receptor (PRR). PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967]
+synonym: "intracellular endosomal pattern recognition receptor signaling pathway" EXACT []
synonym: "intracellular vesicle PAMP receptor signaling pathway" RELATED []
synonym: "intracellular vesicle pathogen receptor signaling pathway" RELATED []
synonym: "intracellular vesicle pattern recognition receptor signaling pathway" RELATED []
synonym: "intracellular vesicle pattern recognition receptor signalling pathway" RELATED []
synonym: "intracellular vesicle PRR signaling pathway" RELATED []
-is_a: GO:0002221 ! pattern recognition receptor signaling pathway
-is_a: GO:0030522 ! intracellular receptor signaling pathway
+is_a: GO:0002753 ! cytosolic pattern recognition receptor signaling pathway
[Term]
id: GO:0002755
name: MyD88-dependent toll-like receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the MyD88 adaptor molecule mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response." [GOC:add, ISBN:0781735149, PMID:12467241, PMID:12524386, PMID:12855817, PMID:15585605, PMID:15728447]
+def: "A toll-like receptor signaling pathway in which the MyD88 adaptor molecule mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate an innate immune response." [GOC:add, ISBN:0781735149, PMID:12467241, PMID:12524386, PMID:12855817, PMID:15585605, PMID:15728447]
synonym: "MyD88-dependent TLR signaling pathway" EXACT []
synonym: "MyD88-dependent toll-like receptor signalling pathway" EXACT []
is_a: GO:0002224 ! toll-like receptor signaling pathway
@@ -21103,26 +21125,27 @@ is_a: GO:0002224 ! toll-like receptor signaling pathway
id: GO:0002756
name: MyD88-independent toll-like receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a toll-like receptor not relying on the MyD88 adaptor molecule. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response." [GOC:add, ISBN:0781735149, PMID:12467241, PMID:12524386, PMID:12855817, PMID:15585605, PMID:15728447]
+def: "A toll-like receptor signaling pathway not relying on the MyD88 adaptor molecule. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate an immune response." [GOC:add, ISBN:0781735149, PMID:12467241, PMID:12524386, PMID:12855817, PMID:15585605, PMID:15728447]
synonym: "MyD88-independent TLR signaling pathway" EXACT []
synonym: "MyD88-independent toll-like receptor signalling pathway" EXACT []
is_a: GO:0002224 ! toll-like receptor signaling pathway
[Term]
id: GO:0002757
-name: immune response-activating signal transduction
+name: immune response-activating signaling pathway
namespace: biological_process
-def: "The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately leading to activation or perpetuation of an immune response." [GOC:add]
+def: "The series of molecular signals generated by a ligand binding to its receptor that lead to the activation or perpetuation of an immune response." [GOC:add]
+synonym: "immune response-activating signal transduction" EXACT []
is_a: GO:0002253 ! activation of immune response
is_a: GO:0002764 ! immune response-regulating signaling pathway
[Term]
id: GO:0002758
-name: innate immune response-activating signal transduction
+name: innate immune response-activating signaling pathway
namespace: biological_process
alt_id: GO:0009870
alt_id: GO:0010204
-def: "A series of molecular signals generated as a consequence of a pathogen or microbial effector binding to a plant 'resistance-gene' receptor to activate a plant immune response, usually plant-type hypersensitive response." [GOC:jy, GOC:mah, PMID:11418339, PMID:28105028]
+def: "The series of molecular signals generated by a ligand binding to its receptor that lead to the activation or perpetuation of an innate immune response." [GOC:jy, GOC:mah, PMID:11418339, PMID:28105028]
synonym: "defence response signaling pathway, resistance gene-dependent" RELATED []
synonym: "defence response signaling pathway, resistance gene-independent" RELATED []
synonym: "defence response signalling pathway, resistance gene-dependent" RELATED []
@@ -21134,7 +21157,7 @@ synonym: "effector triggered immunity" BROAD []
synonym: "effector-triggered immune signaling" RELATED []
synonym: "effector-triggered immunity" BROAD []
is_a: GO:0002218 ! activation of innate immune response
-is_a: GO:0002757 ! immune response-activating signal transduction
+is_a: GO:0002757 ! immune response-activating signaling pathway
[Term]
id: GO:0002759
@@ -21143,6 +21166,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of an antimicrobial humoral response." [GOC:add]
is_a: GO:0002831 ! regulation of response to biotic stimulus
is_a: GO:0002920 ! regulation of humoral immune response
+is_a: GO:0031347 ! regulation of defense response
is_a: GO:0032101 ! regulation of response to external stimulus
relationship: regulates GO:0019730 ! antimicrobial humoral response
@@ -21159,6 +21183,7 @@ synonym: "upregulation of antimicrobial humoral response" EXACT []
is_a: GO:0002759 ! regulation of antimicrobial humoral response
is_a: GO:0002833 ! positive regulation of response to biotic stimulus
is_a: GO:0002922 ! positive regulation of humoral immune response
+is_a: GO:0031349 ! positive regulation of defense response
is_a: GO:0032103 ! positive regulation of response to external stimulus
relationship: positively_regulates GO:0019730 ! antimicrobial humoral response
@@ -21227,7 +21252,7 @@ is_a: GO:0002765 ! immune response-inhibiting signal transduction
id: GO:0002767
name: immune response-inhibiting cell surface receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell capable of inhibiting an immune response." [GOC:add, ISBN:0781735149, PMID:15771571]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of the target cell capable of inhibiting an immune response." [GOC:add, ISBN:0781735149, PMID:15771571]
synonym: "immune response-inhibiting cell surface receptor signalling pathway" EXACT []
is_a: GO:0002765 ! immune response-inhibiting signal transduction
is_a: GO:0002768 ! immune response-regulating cell surface receptor signaling pathway
@@ -21236,7 +21261,7 @@ is_a: GO:0002768 ! immune response-regulating cell surface receptor signaling pa
id: GO:0002768
name: immune response-regulating cell surface receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell capable of activating, perpetuating, or inhibiting an immune response." [GOC:add, ISBN:0781735149, PMID:15771571]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of the target cell capable of activating, perpetuating, or inhibiting an immune response." [GOC:add, ISBN:0781735149, PMID:15771571]
synonym: "immune response-regulating cell surface receptor signalling pathway" EXACT []
is_a: GO:0002764 ! immune response-regulating signaling pathway
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -21245,7 +21270,7 @@ is_a: GO:0007166 ! cell surface receptor signaling pathway
id: GO:0002769
name: natural killer cell inhibitory signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of a natural killer cell capable of inhibiting an immune effector process contributing to an immune response." [GOC:add, ISBN:0781735149, PMID:15771571]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of a natural killer cell capable of inhibiting an immune effector process contributing to an immune response." [GOC:add, ISBN:0781735149, PMID:15771571]
synonym: "inhibitory KIR signaling pathway" NARROW []
synonym: "killer cell inhibitory receptor signaling pathway" NARROW []
synonym: "Ly49 inhibitory receptor signaling pathway" RELATED []
@@ -21257,7 +21282,7 @@ is_a: GO:0002767 ! immune response-inhibiting cell surface receptor signaling pa
id: GO:0002770
name: T cell inhibitory signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of a T cell capable of inhibiting an immune effector process contributing to an immune response." [GOC:add, PMID:15258309]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of a T cell capable of inhibiting an immune effector process contributing to an immune response." [GOC:add, PMID:15258309]
synonym: "T cell inhibitory signalling pathway" EXACT []
synonym: "T lymphocyte inhibitory signaling pathway" EXACT []
synonym: "T-cell inhibitory signaling pathway" EXACT []
@@ -21268,7 +21293,7 @@ is_a: GO:0002767 ! immune response-inhibiting cell surface receptor signaling pa
id: GO:0002771
name: inhibitory killer cell immunoglobulin-like receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a inhibitory killer cell immunoglobulin-like receptor capable of inhibiting an immune effector process contributing to an immune response." [GOC:add, ISBN:0781735149, PMID:15771571]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a inhibitory killer cell immunoglobulin-like receptor capable of inhibiting an immune effector process contributing to an immune response." [GOC:add, ISBN:0781735149, PMID:15771571]
synonym: "inhibitory killer cell immunoglobulin-like receptor signalling pathway" EXACT []
synonym: "killer cell inhibitory receptor signaling pathway" EXACT []
synonym: "KIR signaling pathway" EXACT []
@@ -21278,7 +21303,7 @@ is_a: GO:0002767 ! immune response-inhibiting cell surface receptor signaling pa
id: GO:0002772
name: inhibitory C-type lectin receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to an inhibitory C-type lectin receptor capable of inhibiting an immune effector process contributing to an immune response." [GOC:add, ISBN:0781735149, PMID:15771571]
+def: "The series of molecular signals initiated by an extracellular ligand binding to an inhibitory C-type lectin receptor capable of inhibiting an immune effector process contributing to an immune response." [GOC:add, ISBN:0781735149, PMID:15771571]
synonym: "inhibitory C-type lectin receptor signalling pathway" EXACT []
synonym: "Ly49 inhibitory receptor signaling pathway" RELATED []
is_a: GO:0002767 ! immune response-inhibiting cell surface receptor signaling pathway
@@ -21287,7 +21312,7 @@ is_a: GO:0002767 ! immune response-inhibiting cell surface receptor signaling pa
id: GO:0002773
name: B cell inhibitory signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of a B cell capable of inhibiting an immune effector process contributing to an immune response." [GOC:add, PMID:16413920]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of a B cell capable of inhibiting an immune effector process contributing to an immune response." [GOC:add, PMID:16413920]
synonym: "B cell inhibitory signalling pathway" EXACT []
synonym: "B lymphocyte inhibitory signaling pathwayBT-lymphocyte inhibitory signaling pathway" EXACT []
synonym: "B-cell inhibitory signaling pathway" EXACT []
@@ -21297,7 +21322,7 @@ is_a: GO:0002767 ! immune response-inhibiting cell surface receptor signaling pa
id: GO:0002774
name: Fc receptor mediated inhibitory signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of the binding of the Fc portion of an immunoglobulin by an Fc receptor capable of inhibiting an immune effector process contributing to an immune response. The Fc portion of an immunoglobulin is its C-terminal constant region." [GOC:add, ISBN:0781735149]
+def: "The series of molecular signals generated as a consequence of the binding of the Fc portion of an immunoglobulin by an Fc receptor capable of inhibiting an immune effector process contributing to an immune response. The Fc portion of an immunoglobulin is its C-terminal constant region." [GOC:add, ISBN:0781735149]
synonym: "Fc receptor mediated inhibitory signalling pathway" EXACT []
synonym: "Fc-receptor mediated inhibitory signaling pathway" EXACT []
is_a: GO:0002767 ! immune response-inhibiting cell surface receptor signaling pathway
@@ -21445,7 +21470,6 @@ synonym: "downregulation of antifungal peptide production" EXACT []
synonym: "inhibition of antifungal peptide production" NARROW []
is_a: GO:0002785 ! negative regulation of antimicrobial peptide production
is_a: GO:0002788 ! regulation of antifungal peptide production
-is_a: GO:0031348 ! negative regulation of defense response
relationship: negatively_regulates GO:0002781 ! antifungal peptide production
[Term]
@@ -21633,7 +21657,6 @@ synonym: "up-regulation of antifungal peptide production" EXACT []
synonym: "upregulation of antifungal peptide production" EXACT []
is_a: GO:0002225 ! positive regulation of antimicrobial peptide production
is_a: GO:0002788 ! regulation of antifungal peptide production
-is_a: GO:0031349 ! positive regulation of defense response
relationship: positively_regulates GO:0002781 ! antifungal peptide production
[Term]
@@ -21643,7 +21666,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of antimicrobial peptide biosynthesis." [GOC:add]
is_a: GO:0002784 ! regulation of antimicrobial peptide production
is_a: GO:0031326 ! regulation of cellular biosynthetic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
relationship: regulates GO:0002777 ! antimicrobial peptide biosynthetic process
[Term]
@@ -21658,7 +21681,7 @@ synonym: "inhibition of antimicrobial peptide biosynthetic process" NARROW []
is_a: GO:0002785 ! negative regulation of antimicrobial peptide production
is_a: GO:0002805 ! regulation of antimicrobial peptide biosynthetic process
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
relationship: negatively_regulates GO:0002777 ! antimicrobial peptide biosynthetic process
[Term]
@@ -21674,7 +21697,7 @@ synonym: "upregulation of antimicrobial peptide biosynthetic process" EXACT []
is_a: GO:0002225 ! positive regulation of antimicrobial peptide production
is_a: GO:0002805 ! regulation of antimicrobial peptide biosynthetic process
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
relationship: positively_regulates GO:0002777 ! antimicrobial peptide biosynthetic process
[Term]
@@ -23178,7 +23201,7 @@ relationship: positively_regulates GO:0002455 ! humoral immune response mediated
id: GO:0002926
name: tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation
namespace: biological_process
-def: "The process whereby a wobble base uridine residue in a tRNA is modified to 5-methoxycarbonylmethyl-2-thiouridine." [GOC:hjd, UniPathway:UPA00988]
+def: "The process whereby a wobble base uridine residue in a tRNA is modified to 5-methoxycarbonylmethyl-2-thiouridine." [GOC:hjd, PMID:22768388]
synonym: "mcm5 modification" EXACT []
synonym: "mcm5s2U34 biosynthesis" EXACT []
synonym: "tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridine biosynthesis" EXACT []
@@ -23188,7 +23211,7 @@ is_a: GO:0002098 ! tRNA wobble uridine modification
id: GO:0002927
name: archaeosine-tRNA biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways involved in the biosynthesis of archaeosine, an archaea-specific modified base found at position 15 in the D-loop of certain archaeal tRNAs." [GOC:hjd, UniPathway:UPA00393]
+def: "The chemical reactions and pathways involved in the biosynthesis of archaeosine, an archaea-specific modified base found at position 15 in the D-loop of certain archaeal tRNAs." [GOC:hjd, PMID:20129918]
comment: Archaeosine (7-formamidino-7-deazaguanosine) is a structural variant of the hypermodified nucleoside 7-deazaguanosine. The biosynthesis pathway starts with archaeosine tRNA-guanine transglycosylase (ArcTGT) which catalyzes the exchange of guanine at position 15 in the D-loop of archaeal tRNAs with a free 7-cyano-7-deazaguanine.
is_a: GO:0006400 ! tRNA modification
is_a: GO:0009058 ! biosynthetic process
@@ -23290,8 +23313,8 @@ is_a: GO:0030488 ! tRNA methylation
id: GO:0002941
name: synoviocyte proliferation
namespace: biological_process
-def: "The multiplication or reproduction of synoviocytes by cell division, resulting in the expansion of their population. A synoviocyte is a fibroblast-like cell found in synovial tissues." [CL:0000214, PMID:9546370]
-is_a: GO:0008283 ! cell population proliferation
+def: "The multiplication or reproduction of type B synoviocytes by cell division, resulting in the expansion of their population. A type B synoviocyte is a fibroblast-like cell found in synovial tissues." [PMID:10770586, PMID:9546370]
+is_a: GO:0050673 ! epithelial cell proliferation
[Term]
id: GO:0002942
@@ -23374,6 +23397,7 @@ id: GO:0002950
name: ceramide phosphoethanolamine synthase activity
namespace: molecular_function
def: "Catalysis of the reaction: CDP-ethanolamine + a ceramide = CMP + a ceramide phosphoethanolamine." [EC:2.7.8.n3, PMID:25667419]
+xref: EC:2.7.8.n3
xref: Reactome:R-HSA-8959462 "SAMD8 transforms PE and CERA to CPE"
is_a: GO:0016780 ! phosphotransferase activity, for other substituted phosphate groups
@@ -23381,9 +23405,11 @@ is_a: GO:0016780 ! phosphotransferase activity, for other substituted phosphate
id: GO:0002951
name: leukotriene-C(4) hydrolase
namespace: molecular_function
-def: "Catalysis of the reaction Leukotriene C(4) + H(2)O= leukotriene D(4) + L-glutamate." [EC:3.4.19.14, PMID:9774450]
+def: "Catalysis of the reaction leukotriene C(4) + H2O= leukotriene D(4) + L-glutamate." [PMID:9774450, RHEA:31563]
comment: The mouse enzyme is specific for leukotriene C(4), while the human enzyme also has considerable activity toward glutathione and oxidized glutathione (cf. EC:3.4.19.13). PMID:9774450 cites that the mouse form of this enzyme failed to measure activity towards glutathione.
-is_a: GO:0070122 ! isopeptidase activity
+xref: EC:3.4.19.14
+xref: RHEA:31563
+is_a: GO:0008242 ! omega peptidase activity
[Term]
id: GO:0002952
@@ -23414,7 +23440,6 @@ is_obsolete: true
consider: GO:0007267
consider: GO:0010496
consider: GO:0023061
-consider: GO:0031130
[Term]
id: GO:0003002
@@ -24240,7 +24265,7 @@ namespace: biological_process
def: "Renal process involved in the maintenance of an internal steady state of water in the body." [GOC:mtg_cardio]
synonym: "water homeostasis by the renal system" EXACT []
is_a: GO:0003014 ! renal system process
-is_a: GO:0050891 ! multicellular organismal water homeostasis
+is_a: GO:0050891 ! multicellular organismal-level water homeostasis
[Term]
id: GO:0003092
@@ -24546,7 +24571,7 @@ relationship: positively_regulates GO:0003128 ! heart field specification
id: GO:0003130
name: BMP signaling pathway involved in heart induction
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to heart induction." [GOC:mtg_heart]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to heart induction." [GOC:mtg_heart]
synonym: "BMP signalling pathway involved in heart induction" EXACT [GOC:mah]
is_a: GO:0030509 ! BMP signaling pathway
is_a: GO:1905114 ! cell surface receptor signaling pathway involved in cell-cell signaling
@@ -24767,7 +24792,7 @@ relationship: part_of GO:0003145 ! embryonic heart tube formation via epithelial
id: GO:0003154
name: BMP signaling pathway involved in determination of left/right symmetry
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the determination of left/right symmetry." [GOC:mtg_heart, GOC:signaling]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the determination of left/right symmetry." [GOC:mtg_heart, GOC:signaling]
synonym: "BMP signaling pathway involved in determination of left/right asymmetry" EXACT [GOC:dph]
synonym: "BMP signalling pathway involved in determination of left/right symmetry" EXACT [GOC:mah]
is_a: GO:0030509 ! BMP signaling pathway
@@ -24777,7 +24802,7 @@ relationship: part_of GO:0007368 ! determination of left/right symmetry
id: GO:0003155
name: BMP signaling pathway involved in determination of lateral mesoderm left/right asymmetry
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that contributes to the determination of lateral mesoderm left/right asymmetry." [GOC:mtg_heart]
+def: "The series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that contributes to the determination of lateral mesoderm left/right asymmetry." [GOC:mtg_heart]
synonym: "BMP signaling pathway involved in lateral mesoderm left/right asymmetry determination" EXACT []
synonym: "BMP signalling pathway involved in determination of lateral mesoderm left/right asymmetry" EXACT [GOC:mah]
is_a: GO:0003154 ! BMP signaling pathway involved in determination of left/right symmetry
@@ -24848,7 +24873,7 @@ def: "The process whose specific outcome is the progression of the sinoatrial (S
synonym: "SA node development" EXACT [GOC:mtg_heart]
synonym: "SAN development" EXACT [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
synonym: "sinus node development" NARROW [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
-is_a: GO:0048738 ! cardiac muscle tissue development
+is_a: GO:0003228 ! atrial cardiac muscle tissue development
relationship: part_of GO:0003161 ! cardiac conduction system development
[Term]
@@ -25378,7 +25403,7 @@ name: atrial cardiac muscle tissue development
namespace: biological_process
def: "The process whose specific outcome is the progression of cardiac muscle of the atrium over time, from its formation to the mature structure." [GOC:mtg_heart]
synonym: "atrial myocardium development" EXACT [GOC:mtg_heart]
-is_a: GO:0048856 ! anatomical structure development
+is_a: GO:0048738 ! cardiac muscle tissue development
[Term]
id: GO:0003229
@@ -25592,7 +25617,6 @@ namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of membrane depolarization. Membrane depolarization is the process in which membrane potential changes in the depolarizing direction from the resting potential, usually from negative to positive." [GOC:dph, GOC:tb]
is_a: GO:0042391 ! regulation of membrane potential
is_a: GO:0050794 ! regulation of cellular process
-is_a: GO:0050801 ! ion homeostasis
relationship: regulates GO:0051899 ! membrane depolarization
[Term]
@@ -25604,27 +25628,27 @@ is_a: GO:0010002 ! cardioblast differentiation
[Term]
id: GO:0003256
-name: regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation
+name: obsolete regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the differentiation of a myocardial precursor cell." [GOC:mtg_heart]
-is_a: GO:1901213 ! regulation of transcription from RNA polymerase II promoter involved in heart development
-relationship: part_of GO:0060379 ! cardiac muscle cell myoblast differentiation
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the differentiation of a myocardial precursor cell." [GOC:mtg_heart]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0003257
-name: positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation
+name: obsolete positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the differentiation of a myocardial precursor cell." [GOC:mtg_heart]
-is_a: GO:0003256 ! regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation
-is_a: GO:1901228 ! positive regulation of transcription from RNA polymerase II promoter involved in heart development
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the differentiation of a myocardial precursor cell." [GOC:mtg_heart]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0003258
-name: regulation of transcription from RNA polymerase II promoter involved in endocardial precursor cell differentiation
+name: obsolete regulation of transcription from RNA polymerase II promoter involved in endocardial precursor cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the differentiation of an endocardial precursor cell." [GOC:mtg_heart]
-is_a: GO:1901213 ! regulation of transcription from RNA polymerase II promoter involved in heart development
-relationship: part_of GO:0003255 ! endocardial precursor cell differentiation
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the differentiation of an endocardial precursor cell." [GOC:mtg_heart]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0003259
@@ -25718,7 +25742,7 @@ relationship: part_of GO:0003266 ! regulation of secondary heart field cardiobla
id: GO:0003269
name: BMP signaling pathway involved in regulation of secondary heart field cardioblast proliferation
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the modulation of the frequency, rate or extent of cardioblast proliferation in the secondary heart field. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:mtg_heart]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the modulation of the frequency, rate or extent of cardioblast proliferation in the secondary heart field. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:mtg_heart]
synonym: "BMP signaling pathway involved in regulation of second heart field cardioblast proliferation" EXACT [GOC:dph]
synonym: "BMP signalling pathway involved in regulation of secondary heart field cardioblast proliferation" EXACT [GOC:mah]
is_a: GO:0061312 ! BMP signaling pathway involved in heart development
@@ -25986,7 +26010,7 @@ relationship: part_of GO:0055017 ! cardiac muscle tissue growth
id: GO:0003302
name: transforming growth factor beta receptor signaling pathway involved in heart jogging
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, which contributes to the process of heart jogging." [GOC:mtg_heart, GOC:signaling]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a transforming growth factor beta receptor on the surface of a target cell, which contributes to the process of heart jogging." [GOC:mtg_heart, GOC:signaling]
synonym: "transforming growth factor beta receptor signalling pathway involved in heart jogging" EXACT [GOC:mah]
is_a: GO:0035463 ! transforming growth factor beta receptor signaling pathway involved in determination of left/right asymmetry
is_a: GO:1905313 ! transforming growth factor beta receptor signaling pathway involved in heart development
@@ -25996,7 +26020,7 @@ relationship: part_of GO:0003146 ! heart jogging
id: GO:0003303
name: BMP signaling pathway involved in heart jogging
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the process of heart jogging." [GOC:mtg_heart]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the process of heart jogging." [GOC:mtg_heart]
synonym: "BMP signalling pathway involved in heart jogging" EXACT [GOC:mah]
is_a: GO:0003154 ! BMP signaling pathway involved in determination of left/right symmetry
is_a: GO:0061312 ! BMP signaling pathway involved in heart development
@@ -26455,7 +26479,7 @@ synonym: "positive regulation of flagellar movement" RELATED [GOC:TermGenie]
synonym: "positive regulation of flagellum movement" RELATED []
synonym: "positive regulation of microtubule-based flagellum movement" EXACT []
is_a: GO:0003352 ! regulation of cilium movement
-is_a: GO:0051272 ! positive regulation of cellular component movement
+is_a: GO:0048522 ! positive regulation of cellular process
relationship: positively_regulates GO:0003341 ! cilium movement
[Term]
@@ -26468,7 +26492,7 @@ comment: Note that we deem cilium and microtubule-based flagellum to be equivale
synonym: "negative regulation of flagellum movement" RELATED []
synonym: "negative regulation of microtubule-based flagellum movement" EXACT []
is_a: GO:0003352 ! regulation of cilium movement
-is_a: GO:0051271 ! negative regulation of cellular component movement
+is_a: GO:0048523 ! negative regulation of cellular process
relationship: negatively_regulates GO:0003341 ! cilium movement
[Term]
@@ -26649,7 +26673,7 @@ id: GO:0003376
name: sphingosine-1-phosphate receptor signaling pathway
namespace: biological_process
alt_id: GO:0001789
-def: "A series of molecular signals initiated by the sphingolipid sphingosine-1-phosphate (S1P) binding to a receptor on the surface of the cell, and which proceeds with the activated receptor transmitting the signal by promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:ascb_2009, GOC:signaling, PMID:14592418, PMID:22001186, Reactome:R-HSA-419428]
+def: "A G protein-coupled receptor signaling pathway initiated by sphingosine-1-phosphate binding to its receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:ascb_2009, GOC:signaling, PMID:14592418, PMID:22001186, Reactome:R-HSA-419428]
synonym: "S1P receptor signaling pathway" EXACT [GOC:bf]
synonym: "S1P signaling pathway" RELATED [GOC:bf]
synonym: "S1P-activated G-protein coupled receptor signaling pathway" EXACT [GOC:bf]
@@ -26854,7 +26878,6 @@ namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of the addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat." [GOC:ascb_2009, GOC:dph, GOC:jp, GOC:tb]
is_a: GO:0033043 ! regulation of organelle organization
is_a: GO:0043254 ! regulation of protein-containing complex assembly
-is_a: GO:0090113 ! regulation of ER to Golgi vesicle-mediated transport by GTP hydrolysis
relationship: regulates GO:0048208 ! COPII vesicle coating
[Term]
@@ -27140,7 +27163,7 @@ relationship: part_of GO:0003413 ! chondrocyte differentiation involved in endoc
id: GO:0003434
name: BMP signaling pathway involved in growth plate cartilage chondrocyte development
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the progression of a growth plate cartilage chondrocyte over time." [GOC:ascb_2009, GOC:dph, GOC:tb]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the progression of a growth plate cartilage chondrocyte over time." [GOC:ascb_2009, GOC:dph, GOC:tb]
synonym: "BMP signalling pathway involved in growth plate cartilage chondrocyte development" EXACT [GOC:mah]
is_a: GO:0030509 ! BMP signaling pathway
relationship: part_of GO:0003431 ! growth plate cartilage chondrocyte development
@@ -27186,9 +27209,8 @@ id: GO:0003674
name: molecular_function
namespace: molecular_function
alt_id: GO:0005554
-def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." [GOC:pdt]
+def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt]
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
@@ -27227,7 +27249,6 @@ namespace: molecular_function
alt_id: GO:0043566
def: "Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid)." [GOC:dph, GOC:jl, GOC:tb, GOC:vw]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -27236,6 +27257,7 @@ subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "microtubule/chromatin interaction" RELATED []
synonym: "plasmid binding" NARROW []
synonym: "structure specific DNA binding" RELATED []
@@ -27248,9 +27270,8 @@ name: DNA helicase activity
namespace: molecular_function
alt_id: GO:0003679
alt_id: GO:0004003
-def: "Unwinding of a DNA helix, driven by ATP hydrolysis." [EC:3.6.4.12, GOC:jl]
+def: "Unwinding of a DNA helix, driven by ATP hydrolysis." [GOC:jl]
synonym: "ATP-dependent DNA helicase activity" EXACT []
-xref: EC:3.6.4.12
xref: Reactome:R-HSA-5693589 "D-loop dissociation and strand annealing"
is_a: GO:0004386 ! helicase activity
is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
@@ -27285,7 +27306,7 @@ subset: goslim_yeast
synonym: "lamin/chromatin binding" NARROW []
synonym: "microtubule/chromatin interaction" NARROW []
synonym: "nuclear membrane vesicle binding to chromatin" NARROW []
-is_a: GO:0005488 ! binding
+is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0003683
@@ -27444,7 +27465,6 @@ alt_id: GO:0001204
def: "A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons." [GOC:txnOH-2018]
comment: Usage guidance: Most DNA-binding transcription factors do not have enzymatic activity. The presence of specific DNA-binding domains known to be present in DNA-binding transcription factors (HOX, GATA etc) should be used to help decide whether a protein is a DNA binding transcription factor or a coregulator. If a protein has an enzymatic activity (for example, ubiquitin ligase, histone acetyl transferase) and no known DNA binding domain, consider annotating to GO:0003712 transcription coregulator activity. Special care should be taken with proteins containing zinc fingers, Myb/SANT and ARID domains, since only a subset of proteins containing these domains directly and selectively bind to regulatory DNA motifs in cis-regulatory regions.
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -27517,10 +27537,10 @@ consider: GO:0030374
[Term]
id: GO:0003707
-name: steroid hormone receptor activity
+name: nuclear steroid receptor activity
namespace: molecular_function
def: "Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function." [GOC:signaling, PMID:14708019]
-comment: Some steroid hormone receptors reside in the plasma membrane and signal through second messengers or other intracellular signal transduction pathways. For steroid hormone receptors that act in the nucleus to regulate transcription, consider also annotating to the terms: nuclear receptor activity ; GO:0004879' or nuclear receptor transcription coactivator activity ; GO:0030374'.
+synonym: "steroid hormone receptor activity" BROAD []
is_a: GO:0038023 ! signaling receptor activity
[Term]
@@ -27536,12 +27556,12 @@ consider: GO:0006383
[Term]
id: GO:0003711
-name: transcription elongation regulator activity
+name: transcription elongation factor activity
namespace: molecular_function
-def: "A molecular function that regulates transcriptional elongation by enabling the transition from transcription initiation to elongation or by altering the elongation properties of the enzyme during the elongation phase of transcription." [GOC:txnOH-2018, PMID:23878398, PMID:28892040]
+def: "A molecular function that stimulates the elongation properties of the RNA polymerase during the elongation phase of transcription. A subclass of transcription elongation factors enable the transition from transcription initiation to elongation, while another class rescue stalled RNA polymerases." [GOC:txnOH-2018, PMID:23878398, PMID:28892040]
comment: Restored term from obsolete.
-synonym: "transcription elongation factor activity" EXACT []
-synonym: "transcriptional elongation regulator activity" EXACT []
+synonym: "transcription elongation regulator activity" RELATED []
+synonym: "transcriptional elongation regulator activity" RELATED []
is_a: GO:0140110 ! transcription regulator activity
[Term]
@@ -27663,7 +27683,6 @@ alt_id: GO:0000498
alt_id: GO:0044822
def: "Binding to an RNA molecule or a portion thereof." [GOC:jl, GOC:mah]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -27672,6 +27691,7 @@ subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "base pairing with RNA" NARROW []
synonym: "poly(A) RNA binding" RELATED []
synonym: "poly(A)-RNA binding" RELATED []
@@ -27689,6 +27709,11 @@ synonym: "ATP-dependent RNA helicase activity" EXACT []
xref: EC:3.6.4.13
xref: MetaCyc:ADENOSINETRIPHOSPHATASE-RXN
xref: Reactome:R-HSA-72647 "Cap-bound mRNA is activated by helicases"
+xref: Reactome:R-HSA-9770129 "Formation of the Spliceosomal A complex (update)"
+xref: Reactome:R-HSA-9770131 "Formation of the Spliceosomal B* complex (new)"
+xref: Reactome:R-HSA-9770141 "Formation of the Spliceosomal C* complex (update)"
+xref: Reactome:R-HSA-9770142 "Formation of the Spliceosomal B complex (new)"
+xref: Reactome:R-HSA-9770145 "Formation of the Spliceosomal Bact complex (new)"
is_a: GO:0004386 ! helicase activity
is_a: GO:0008186 ! ATP-dependent activity, acting on RNA
is_a: GO:0140098 ! catalytic activity, acting on RNA
@@ -27706,10 +27731,12 @@ id: GO:0003726
name: double-stranded RNA adenosine deaminase activity
namespace: molecular_function
alt_id: GO:0003971
-def: "Catalysis of the reaction: adenosine + H2O = inosine + NH3, in a double-stranded RNA molecule." [GOC:mah]
+def: "Catalysis of the reaction: adenosine + H2O = inosine + NH3, in a double-stranded RNA molecule." [GOC:mah, RHEA:10120]
synonym: "double-stranded RNA specific editase activity" RELATED []
+xref: EC:3.5.4.37
xref: Reactome:R-HSA-77614 "Deamination at C6 position of adenosine in Editosome (ADAR1)"
xref: Reactome:R-HSA-77615 "Deamination at C6 position of adenosine in Editosome (ADAR2)"
+xref: RHEA:10120
is_a: GO:0004000 ! adenosine deaminase activity
[Term]
@@ -27896,11 +27923,9 @@ name: protein disulfide isomerase activity
namespace: molecular_function
alt_id: GO:0006467
def: "Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins." [EC:5.3.4.1, GOC:vw, Wikipedia:Protein_disulfide-isomerase#Function]
-synonym: "disulphide bond biosynthesis" EXACT []
synonym: "disulphide bond formation" EXACT []
synonym: "protein cysteine-thiol oxidation" RELATED []
-synonym: "protein disulfide-isomerase" BROAD [EC:5.3.4.1]
-synonym: "protein disulfide-isomerase reaction" RELATED [EC:5.3.4.1]
+synonym: "protein disulfide-isomerase" EXACT [EC:5.3.4.1]
synonym: "protein disulphide isomerase activity" EXACT []
synonym: "protein thiol-disulfide exchange" EXACT []
synonym: "protein thiol-disulphide exchange" EXACT []
@@ -27934,13 +27959,8 @@ comment: This term was made obsolete because it represents a class of gene produ
synonym: "histone-specific chaperone activity" EXACT []
synonym: "nucleosome assembly chaperone" EXACT []
is_obsolete: true
-consider: GO:0006333
consider: GO:0006334
-consider: GO:0034728
consider: GO:0042393
-consider: GO:0043486
-consider: GO:0044183
-consider: GO:0051082
[Term]
id: GO:0003763
@@ -28001,11 +28021,11 @@ id: GO:0003774
name: cytoskeletal motor activity
namespace: molecular_function
def: "Generation of force resulting in movement, for example along a microfilament or microtubule, or in torque resulting in membrane scission or rotation of a flagellum. The energy required is obtained either from the hydrolysis of a nucleoside triphosphate or by an electrochemical proton gradient (proton-motive force)." [GOC:mah, GOC:vw, PMID:11242086, PMID:29716949]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
+subset: prokaryote_subset
synonym: "motor activity" BROAD []
xref: Reactome:R-HSA-1861595 "Extension of pseudopodia by myosin-X in a PI3K dependent manner"
is_a: GO:0003674 ! molecular_function
@@ -28159,13 +28179,11 @@ replaced_by: GO:0042989
[Term]
id: GO:0003789
-name: obsolete actin filament severing activity
+name: actin filament severing activity
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:ai]
-comment: This term was made obsolete because it describes a biological process.
-synonym: "actin filament severing activity" EXACT []
-is_obsolete: true
-replaced_by: GO:0051014
+def: "Binding to an actin subunit and promoting its dissociation from an actin filament by a local change in actin subunit conformation and orientation, and severing of filaments." [PMID:11812157, PMID:23395798, PMID:23727096]
+synonym: "actin depolymerizing activity" EXACT []
+is_a: GO:0140776 ! protein-containing complex destabilizing activity
[Term]
id: GO:0003790
@@ -28660,6 +28678,7 @@ def: "Catalysis of a biochemical reaction at physiological temperatures. In biol
subset: goslim_agr
subset: goslim_chembl
subset: goslim_flybase_ribbon
+subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
@@ -28700,7 +28719,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0003827
name: alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R + UDP-N-acetyl-alpha-D-glucosamine = 3-(2-[N-acetyl-beta-D-glucosaminyl]-alpha-D-mannosyl)-beta-D-mannosyl-R + H(+) + UDP." [EC:2.4.1.101, RHEA:11456]
+def: "Catalysis of the reaction: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R + UDP-N-acetyl-alpha-D-glucosamine = 3-(2-[N-acetyl-beta-D-glucosaminyl]-alpha-D-mannosyl)-beta-D-mannosyl-R + H+ + UDP." [EC:2.4.1.101, RHEA:11456]
synonym: "alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.101]
synonym: "alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.101]
synonym: "alpha-1,3-mannosylglycoprotein beta-1,2-N-acetylglucosaminyltransferase activity" EXACT []
@@ -28829,7 +28848,7 @@ is_a: GO:0016787 ! hydrolase activity
id: GO:0003833
name: beta-alanyl amine synthase activity
namespace: molecular_function
-def: "Catalysis of the synthesis of beta-alanyl amine conjugate from a precursor biogenetic amine, such as dopamine or histamine." [GOC:bf, ISBN:0198506732, PMID:12900414, PMID:12957543, PMID:25229196]
+def: "Catalysis of the synthesis of beta-alanyl amine conjugate from a precursor biogenic amine, such as dopamine or histamine." [GOC:bf, ISBN:0198506732, PMID:12900414, PMID:12957543, PMID:25229196]
synonym: "beta-alanyl-dopamine synthase activity" RELATED []
synonym: "N-beta-alanyl dopamine synthetase activity" EXACT []
synonym: "NBAD transferase activity" EXACT []
@@ -28863,8 +28882,7 @@ xref: EC:2.4.99.1
xref: MetaCyc:2.4.99.1-RXN
xref: Reactome:R-HSA-4085033 "ST6GAL1,2 transfer Neu5Ac to terminal Gal (alpha-2,6 link)"
xref: Reactome:R-HSA-975902 "ST6GAL1 transfers Neu5Ac to terminal Gal of N-glycans"
-xref: Reactome:R-HSA-977071 "Sialyltransferase I can add sialic acid to the Tn antigen at the alpha 6 position"
-xref: Reactome:R-HSA-977228 "Sialyltransferase I can add sialic acid to the T antigen at the alpha 6 position"
+xref: Reactome:R-HSA-977071 "ST6GAL1 transfers sialic acid to Tn antigens to form sTn antigens"
xref: RHEA:11836
is_a: GO:0008373 ! sialyltransferase activity
@@ -28884,7 +28902,7 @@ xref: Reactome:R-HSA-3656258 "Defective ST3GAL3 does not transfer SA to keratan"
xref: Reactome:R-HSA-4084984 "ST3GAL1-6 transfer Neu5Ac to terminal Gal (alpha-2,3 link)"
xref: Reactome:R-HSA-9603987 "ST3GAL3 transfers Neu5Ac to Type 1 chain to form Type 1 MSGG"
xref: Reactome:R-HSA-9605600 "ST3GAL3,4,6 transfer Neu5Ac to Type 2 chain to form Type 2 MSGG"
-xref: Reactome:R-HSA-981497 "ST3GAL1-4 can add a sialic acid to the T antigen at the alpha 3 position"
+xref: Reactome:R-HSA-981497 "ST3GAL1-4 transfers sialic acid to the T antigen at the alpha 3 position"
xref: RHEA:21616
is_a: GO:0008373 ! sialyltransferase activity
@@ -29003,9 +29021,9 @@ is_a: GO:0042171 ! lysophosphatidic acid acyltransferase activity
id: GO:0003842
name: 1-pyrroline-5-carboxylate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-pyrroline-5-carboxylate + NAD+ + H2O = L-glutamate + NADH + H(+)." [EC:1.2.1.88]
+def: "H2O + L-glutamate 5-semialdehyde + NAD+ = 2 H+ + L-glutamate + NADH." [RHEA:30235]
synonym: "1-pyrroline dehydrogenase" BROAD []
-synonym: "1-pyrroline-5-carboxylate:NAD+ oxidoreductase activity" RELATED [EC:1.5.1.12]
+synonym: "1-pyrroline-5-carboxylate:NAD+ oxidoreductase activity" RELATED []
synonym: "delta1-pyrroline-5-carboxylate dehydrogenase activity" RELATED [EC:1.2.1.88]
synonym: "L-pyrroline-5-carboxylate-NAD+ oxidoreductase activity" RELATED []
synonym: "pyrroline-5-carboxylate dehydrogenase activity" RELATED [EC:1.2.1.88]
@@ -29015,7 +29033,12 @@ xref: MetaCyc:PYRROLINECARBDEHYDROG-RXN
xref: Reactome:R-HSA-6784399 "ALDH4A1 dimer dehydrogenates 4-OH-L-glutamate semialdehyde to 4-OH-L-glutamate"
xref: Reactome:R-HSA-70679 "ALDH4A1 oxidises L-GluSS to Glu"
xref: RHEA:16417
-is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
+xref: RHEA:24882
+xref: RHEA:24943
+xref: RHEA:28234
+xref: RHEA:30235
+xref: RHEA:31155
+is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
[Term]
id: GO:0003843
@@ -29080,7 +29103,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0003845
name: 11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity
namespace: molecular_function
-def: "Catalysis of the reaction: an 11-beta-hydroxysteroid + NAD(P)+ = an 11-oxosteroid + NAD(P)H + H(+)." [PMID:15761036]
+def: "Catalysis of the reaction: an 11-beta-hydroxysteroid + NAD(P)+ = an 11-oxosteroid + NAD(P)H + H+." [PMID:15761036]
subset: gocheck_do_not_annotate
synonym: "11beta-hydroxy steroid dehydrogenase" RELATED []
synonym: "11beta-hydroxysteroid dehydrogenase" RELATED []
@@ -29096,7 +29119,7 @@ is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of
id: GO:0003846
name: 2-acylglycerol O-acyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + 2-acylglycerol = CoA + diacylglycerol." [PMID:4016575]
+def: "Catalysis of the reaction: acyl-CoA + 2-acylglycerol = CoA + diacylglycerol." [PMID:4016575, RHEA:16741]
synonym: "acyl coenzyme A-monoglyceride acyltransferase activity" RELATED [EC:2.3.1.22]
synonym: "acyl-CoA:2-acylglycerol O-acyltransferase activity" RELATED [EC:2.3.1.22]
synonym: "acylglycerol palmitoyltransferase activity" RELATED [EC:2.3.1.22]
@@ -29136,7 +29159,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0003848
name: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine + ATP = (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate + AMP + 2 H(+)." [EC:2.7.6.3, RHEA:11412]
+def: "Catalysis of the reaction: 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine + ATP = (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate + AMP + 2 H+." [EC:2.7.6.3, RHEA:11412]
subset: goslim_chembl
synonym: "2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase activity" EXACT []
synonym: "6-hydroxymethyl-7,8-dihydropterin diphosphokinase activity" RELATED [EC:2.7.6.3]
@@ -29158,7 +29181,7 @@ is_a: GO:0016778 ! diphosphotransferase activity
id: GO:0003849
name: 3-deoxy-7-phosphoheptulonate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-erythrose 4-phosphate + H(2)O + phosphoenolpyruvate = 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate." [EC:2.5.1.54, RHEA:14717]
+def: "Catalysis of the reaction: D-erythrose 4-phosphate + H2O + phosphoenolpyruvate = 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate." [EC:2.5.1.54, RHEA:14717]
comment: Note that this function was formerly EC:4.1.2.15.
synonym: "2-dehydro-3-deoxy-phosphoheptonate aldolase activity" RELATED [EC:2.5.1.54]
synonym: "2-dehydro-3-deoxyphosphoheptonate aldolase activity" EXACT []
@@ -29226,7 +29249,7 @@ is_a: GO:0035250 ! UDP-galactosyltransferase activity
id: GO:0003852
name: 2-isopropylmalate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-methyl-2-oxobutanoate + acetyl-CoA + H(2)O = (2S)-2-isopropylmalate + CoA + H(+)." [EC:2.3.3.13, RHEA:21524]
+def: "Catalysis of the reaction: 3-methyl-2-oxobutanoate + acetyl-CoA + H2O = (2S)-2-isopropylmalate + CoA + H+." [RHEA:21524]
comment: Note that this function was formerly EC:4.1.3.12.
synonym: "3-carboxy-3-hydroxy-4-methylpentanoate 3-methyl-2-oxobutanoate-lyase (CoA-acetylating) activity" RELATED [EC:2.3.3.13]
synonym: "acetyl-CoA:3-methyl-2-oxobutanoate C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming)" RELATED [EC:2.3.3.13]
@@ -29240,27 +29263,29 @@ xref: EC:2.3.3.13
xref: KEGG_REACTION:R01213
xref: MetaCyc:2-ISOPROPYLMALATESYN-RXN
xref: RHEA:21524
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0003853
name: 2-methylacyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-methylbutanoyl-CoA + acceptor = 2-methylbut-2-enoyl-CoA + reduced acceptor." [EC:1.3.99.12]
-synonym: "2-methyl branched chain acyl-CoA dehydrogenase activity" RELATED [EC:1.3.99.12]
-synonym: "2-methylbutanoyl-CoA:(acceptor) oxidoreductase activity" RELATED [EC:1.3.99.12]
-synonym: "2-methylbutanoyl-CoA:acceptor oxidoreductase activity" RELATED [EC:1.3.99.12]
-synonym: "branched-chain acyl-CoA dehydrogenase activity" RELATED [EC:1.3.99.12]
-xref: EC:1.3.99.12
+alt_id: GO:0047119
+def: "Catalysis of the reaction: 2-methylbutanoyl-CoA + H+ + oxidized [electron-transfer flavoprotein] = (2E)-2-methylbut-2-enoyl-CoA + reduced [electron-transfer flavoprotein]." [PMID:10989435, PMID:6401712, RHEA:43780]
+synonym: "2-methyl branched chain acyl-CoA dehydrogenase activity" RELATED [EC:1.3.8.5]
+synonym: "2-methyl-branched-chain-enoyl-CoA reductase activity" RELATED []
+synonym: "branched-chain acyl-CoA dehydrogenase activity" RELATED [EC:1.3.8.5]
+xref: EC:1.3.8.5
+xref: KEGG_REACTION:R03169
+xref: MetaCyc:1.3.1.52-RXN
xref: MetaCyc:2-METHYLACYL-COA-DEHYDROGENASE-RXN
-xref: RHEA:13261
+xref: RHEA:43780
is_a: GO:0003995 ! acyl-CoA dehydrogenase activity
[Term]
id: GO:0003854
name: 3-beta-hydroxy-delta5-steroid dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 3-beta-hydroxy-delta(5)-steroid + NAD+ = a 3-oxo-delta(5)-steroid + NADH + H(+)." [EC:1.1.1.145]
+def: "Catalysis of the reaction: a 3-beta-hydroxy-delta(5)-steroid + NAD+ = a 3-oxo-delta(5)-steroid + NADH + H+." [EC:1.1.1.145]
synonym: "3-beta-hydroxy-5-ene steroid dehydrogenase activity" RELATED [EC:1.1.1.145]
synonym: "3-beta-hydroxy-D5-steroid dehydrogenase activity" EXACT []
synonym: "3beta-HSDH" RELATED [EC:1.1.1.145]
@@ -29290,7 +29315,7 @@ is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of
id: GO:0003855
name: 3-dehydroquinate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O." [EC:4.2.1.10, RHEA:21096]
+def: "Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H2O." [EC:4.2.1.10, RHEA:21096]
synonym: "3-dehydroquinase activity" RELATED [EC:4.2.1.10]
synonym: "3-dehydroquinate hydro-lyase (3-dehydroshikimate-forming)" RELATED [EC:4.2.1.10]
synonym: "3-dehydroquinate hydro-lyase activity" RELATED [EC:4.2.1.10]
@@ -29322,7 +29347,7 @@ is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
id: GO:0003857
name: 3-hydroxyacyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH + H(+)." [EC:1.1.1.35]
+def: "Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH + H+." [EC:1.1.1.35]
comment: See also 'long-chain-3-hydroxyacyl-CoA dehydrogenase activity ; GO:0016509'.
synonym: "3-oxoacyl-thioester reductase activity" RELATED [PMID:19685079]
synonym: "beta-hydroxyacyl dehydrogenase activity" RELATED [EC:1.1.1.35]
@@ -29357,7 +29382,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0003858
name: 3-hydroxybutyrate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-3-hydroxybutanoate + NAD(+) = acetoacetate + H(+) + NADH." [EC:1.1.1.30, RHEA:20521]
+def: "Catalysis of the reaction: (R)-3-hydroxybutanoate + NAD+ = acetoacetate + H+ + NADH." [EC:1.1.1.30, RHEA:20521]
synonym: "D-beta-hydroxybutyrate dehydrogenase activity" RELATED [EC:1.1.1.30]
xref: EC:1.1.1.30
xref: KEGG_REACTION:R01361
@@ -29370,20 +29395,19 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
[Term]
id: GO:0003859
-name: 3-hydroxybutyryl-CoA dehydratase activity
+name: obsolete (3R)-3-hydroxybutyryl-CoA dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-3-hydroxybutanoyl-CoA = crotonoyl-CoA + H(2)O." [EC:4.2.1.55, RHEA:17849]
+def: "OBSOLETE. Catalysis of the reaction: (3R)-3-hydroxybutanoyl-CoA = (2E)-butenoyl-CoA + H2O." [EC:4.2.1.55, RHEA:17849]
+comment: This term was obsoleted because it represents a specific substrate of 3-hydroxyacyl-CoA dehydratase activity ; GO:0018812.
synonym: "(3R)-3-hydroxybutanoyl-CoA hydro-lyase (crotonoyl-CoA-forming)" RELATED [EC:4.2.1.55]
synonym: "(3R)-3-hydroxybutanoyl-CoA hydro-lyase activity" RELATED [EC:4.2.1.55]
+synonym: "3-hydroxybutyryl-CoA dehydratase activity" BROAD []
synonym: "crotonase activity" RELATED [EC:4.2.1.55]
synonym: "D-3-hydroxybutyryl coenzyme A dehydratase activity" RELATED [EC:4.2.1.55]
synonym: "D-3-hydroxybutyryl-CoA dehydratase activity" RELATED [EC:4.2.1.55]
synonym: "enoyl coenzyme A hydrase (D)" BROAD [EC:4.2.1.55]
-xref: EC:4.2.1.55
-xref: KEGG_REACTION:R03027
-xref: MetaCyc:3-HYDROXBUTYRYL-COA-DEHYDRATASE-RXN
-xref: RHEA:17849
-is_a: GO:0016836 ! hydro-lyase activity
+is_obsolete: true
+replaced_by: GO:0018812
[Term]
id: GO:0003860
@@ -29580,7 +29604,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0003870
name: 5-aminolevulinate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycine + H(+) + succinyl-CoA = 5-aminolevulinate + CO(2) + CoA." [EC:2.3.1.37, RHEA:12921]
+def: "Catalysis of the reaction: glycine + H+ + succinyl-CoA = 5-aminolevulinate + CO2 + CoA." [EC:2.3.1.37, RHEA:12921]
synonym: "5-aminolevulinate synthetase activity" RELATED [EC:2.3.1.37]
synonym: "5-aminolevulinic acid synthase activity" RELATED [EC:2.3.1.37]
synonym: "5-aminolevulinic acid synthetase activity" RELATED [EC:2.3.1.37]
@@ -29656,7 +29680,7 @@ is_a: GO:0008443 ! phosphofructokinase activity
id: GO:0003873
name: 6-phosphofructo-2-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: beta-D-fructose 6-phosphate + ATP = beta-D-fructose 2,6-bisphosphate + ADP + 2 H(+)." [EC:2.7.1.105, RHEA:15653]
+def: "Catalysis of the reaction: beta-D-fructose 6-phosphate + ATP = beta-D-fructose 2,6-bisphosphate + ADP + 2 H+." [EC:2.7.1.105, RHEA:15653]
synonym: "6-phosphofructo-2-kinase (phosphorylating)" RELATED [EC:2.7.1.105]
synonym: "6-phosphofructose 2-kinase activity" RELATED [EC:2.7.1.105]
synonym: "ATP:beta-D-fructose-6-phosphate 2-phosphotransferase activity" RELATED [EC:2.7.1.105]
@@ -29674,7 +29698,7 @@ is_a: GO:0008443 ! phosphofructokinase activity
id: GO:0003874
name: 6-pyruvoyltetrahydropterin synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7,8-dihydroneopterin 3'-triphosphate = 6-pyruvoyl-5,6,7,8-tetrahydropterin + H(+) + triphosphate." [EC:4.2.3.12, RHEA:22048]
+def: "Catalysis of the reaction: 7,8-dihydroneopterin 3'-triphosphate = 6-pyruvoyl-5,6,7,8-tetrahydropterin + H+ + triphosphate." [EC:4.2.3.12, RHEA:22048]
synonym: "2-amino-4-oxo-6-[(1S,2R)-1,2-dihydroxy-3-triphosphooxypropyl]-7,8-dihydroxypteridine triphosphate lyase activity" RELATED [EC:4.2.3.12]
synonym: "2-amino-4-oxo-6-[(1S,2R)-1,2-dihydroxy-3-triphosphooxypropyl]-7,8-dihydroxypteridine triphosphate-lyase (6-pyruvoyl-5,6,7,8-tetrahydropterin-forming)" RELATED [EC:4.2.3.12]
synonym: "6-pyruvoyl tetrahydrobiopterin synthase activity" RELATED [EC:4.2.3.12]
@@ -29756,7 +29780,7 @@ id: GO:0003878
name: ATP citrate synthase activity
namespace: molecular_function
alt_id: GO:0046913
-def: "Catalysis of the reaction: acetyl-CoA + ADP + H(+) + oxaloacetate + phosphate = ATP + citrate + CoA." [RHEA:21160]
+def: "Catalysis of the reaction: acetyl-CoA + ADP + H+ + oxaloacetate + phosphate = ATP + citrate + CoA." [RHEA:21160]
comment: Note that this function was formerly EC:4.1.3.8. Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "acetyl-CoA:oxaloacetate acetyltransferase (isomerizing; ADP- phosphorylating) activity" RELATED [EC:2.3.3.8]
synonym: "acetyl-CoA:oxaloacetate acetyltransferase (isomerizing; ADP-phosphorylating)" RELATED [EC:2.3.3.8]
@@ -29777,7 +29801,7 @@ xref: MetaCyc:ATP-CITRATE-PRO-S--LYASE-RXN
xref: MetaCyc:PWY-5172
xref: Reactome:R-HSA-75848 "ACLY tetramer transforms CIT to Ac-CoA"
xref: RHEA:21160
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0003879
@@ -29811,7 +29835,7 @@ is_a: GO:0051998 ! protein carboxyl O-methyltransferase activity
id: GO:0003881
name: CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: myo-inositol + CDP-diacylglycerol = 1-phosphatidyl-1D-myo-inositol + CMP + H(+)." [EC:2.7.8.11, RHEA:11580]
+def: "Catalysis of the reaction: myo-inositol + CDP-diacylglycerol = 1-phosphatidyl-1D-myo-inositol + CMP + H+." [EC:2.7.8.11, RHEA:11580]
synonym: "CDP diglyceride-inositol phosphatidyltransferase activity" RELATED [EC:2.7.8.11]
synonym: "CDP-DG:inositol transferase activity" RELATED [EC:2.7.8.11]
synonym: "CDP-diacylglycerol--inositol phosphatidyltransferase activity" RELATED [EC:2.7.8.11]
@@ -29860,7 +29884,7 @@ is_a: GO:0017169 ! CDP-alcohol phosphatidyltransferase activity
id: GO:0003883
name: CTP synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + UTP + NH3 = ADP + phosphate + CTP." [EC:6.3.4.2]
+def: "Catalysis of the reaction: ATP + UTP + glutamine + H20= ADP + phosphate + CTP + glutamate." [PMID:12354108, RHEA:26426]
synonym: "CTP synthetase activity" RELATED [EC:6.3.4.2]
synonym: "cytidine 5'-triphosphate synthetase activity" RELATED [EC:6.3.4.2]
synonym: "cytidine triphosphate synthetase activity" RELATED [EC:6.3.4.2]
@@ -29871,7 +29895,7 @@ xref: EC:6.3.4.2
xref: MetaCyc:CTPSYN-RXN
xref: Reactome:R-HSA-504054 "UTP + glutamine + ATP + H2O => CTP + glutamate + ADP + orthophosphate [CTPS2]"
xref: Reactome:R-HSA-73647 "UTP + glutamine + ATP + H2O => CTP + glutamate + ADP + orthophosphate [CTPS]"
-xref: RHEA:16597
+xref: RHEA:26426
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
[Term]
@@ -29886,13 +29910,13 @@ xref: EC:1.4.3.3
xref: MetaCyc:D-AMINO-ACID-OXIDASE-RXN
xref: Reactome:R-HSA-389821 "glycine + O2 => glyoxylate + H2O2 + NH4+"
xref: RHEA:21816
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+is_a: GO:0008131 ! primary amine oxidase activity
[Term]
id: GO:0003885
name: D-arabinono-1,4-lactone oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-arabinono-1,4-lactone + O(2) = dehydro-D-arabinono-1,4-lactone + H(2)O(2) + H(+)." [EC:1.1.3.37, RHEA:23756]
+def: "Catalysis of the reaction: D-arabinono-1,4-lactone + O2 = dehydro-D-arabinono-1,4-lactone + H2O2 + H+." [EC:1.1.3.37, RHEA:23756]
synonym: "D-arabinono-1,4-lactone:oxygen oxidoreductase activity" RELATED [EC:1.1.3.37]
xref: EC:1.1.3.37
xref: KEGG_REACTION:R02715
@@ -30016,6 +30040,7 @@ xref: Reactome:R-HSA-6786166 "Translesion synthesis across unhooked ICL by POLN"
xref: Reactome:R-HSA-68950 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer at the origin"
xref: Reactome:R-HSA-69116 "Formation of Okazaki fragments"
xref: Reactome:R-HSA-73932 "Resynthesis of excised residue by POLB"
+xref: Reactome:R-HSA-9710480 "Decitabine triphosphate incorporates into DNA"
is_a: GO:0034061 ! DNA polymerase activity
[Term]
@@ -30257,7 +30282,7 @@ synonym: "DNA ligase (NAD)" RELATED [EC:6.5.1.2]
synonym: "DNA repair enzyme activity" RELATED [EC:6.5.1.2]
synonym: "DNA-joining enzyme" RELATED [EC:6.5.1.2]
synonym: "poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming, NMN-forming)" RELATED [EC:6.5.1.2]
-synonym: "Polydeoxyribonucleotide synthase (NAD(+)) activity" RELATED [EC:6.5.1.2]
+synonym: "polydeoxyribonucleotide synthase (NAD(+)) activity" RELATED [EC:6.5.1.2]
synonym: "polydeoxyribonucleotide synthase (NAD)" RELATED [EC:6.5.1.2]
synonym: "polydeoxyribonucleotide synthase (NAD+) activity" RELATED [EC:6.5.1.2]
synonym: "polynucleotide ligase" BROAD [EC:6.5.1.2]
@@ -30316,7 +30341,6 @@ name: DNA topoisomerase activity
namespace: molecular_function
alt_id: GO:0009387
def: "Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA." [GOC:mah, PMID:8811192]
-xref: EC:5.6.2.-
is_a: GO:0016853 ! isomerase activity
is_a: GO:0140097 ! catalytic activity, acting on DNA
@@ -30388,7 +30412,7 @@ is_a: GO:0070566 ! adenylyltransferase activity
id: GO:0003920
name: GMP reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: IMP + NADP(+) + NH(4)(+) = GMP + 2 H(+) + NADPH." [EC:1.7.1.7, RHEA:17185]
+def: "Catalysis of the reaction: IMP + NADP+ + NH4 = GMP + 2 H+ + NADPH." [EC:1.7.1.7, RHEA:17185]
comment: Note that this function was formerly EC:1.6.6.8.
synonym: "guanosine 5'-monophosphate oxidoreductase activity" RELATED [EC:1.7.1.7]
synonym: "guanosine 5'-monophosphate reductase activity" RELATED [EC:1.7.1.7]
@@ -30404,13 +30428,13 @@ xref: KEGG_REACTION:R01134
xref: MetaCyc:GMP-REDUCT-RXN
xref: Reactome:R-HSA-514604 "GMP + NADPH + H+ => IMP + NADP+ + NH4+ (GMPR,GMPR2)"
xref: RHEA:17185
-is_a: GO:0016657 ! oxidoreductase activity, acting on NAD(P)H, nitrogenous group as acceptor
+is_a: GO:0046857 ! oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor
[Term]
id: GO:0003921
name: GMP synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + XMP + NH4(+) = AMP + diphosphate + GMP + 2H(+)." [RHEA:18301]
+def: "Catalysis of the reaction: ATP + XMP + NH4(+) = AMP + diphosphate + GMP + 2H+." [RHEA:18301]
xref: MetaCyc:GMP-SYN-NH3-RXN
xref: RHEA:18301
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
@@ -30420,7 +30444,7 @@ relationship: part_of GO:0003922 ! GMP synthase (glutamine-hydrolyzing) activity
id: GO:0003922
name: GMP synthase (glutamine-hydrolyzing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + XMP + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate + 2H(+)." [RHEA:11680]
+def: "Catalysis of the reaction: ATP + XMP + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate + 2H+." [RHEA:11680]
synonym: "glutamine amidotransferase activity" RELATED [EC:6.3.5.2]
synonym: "GMP synthase (glutamine-hydrolysing)" RELATED [EC:6.3.5.2]
synonym: "GMP synthetase (glutamine-hydrolysing)" RELATED [EC:6.3.5.2]
@@ -30433,6 +30457,7 @@ synonym: "xanthosine-5'-phosphate:L-glutamine amido-ligase (AMP-forming)" RELATE
xref: EC:6.3.5.2
xref: MetaCyc:GMP-SYN-GLUT-RXN
xref: Reactome:R-HSA-73792 "XMP + L-Glutamine + ATP + H2O => GMP + L-Glutamate + AMP + pyrophosphate"
+xref: Reactome:R-HSA-9748957 "GMPS dimer transforms 6TXMP to 6TGMP"
xref: RHEA:11680
xref: Wikipedia:GMP_synthase_(glutamine-hydrolysing)
is_a: GO:0016884 ! carbon-nitrogen ligase activity, with glutamine as amido-N-donor
@@ -30450,11 +30475,12 @@ id: GO:0003924
name: GTPase activity
namespace: molecular_function
alt_id: GO:0061745
-def: "Catalysis of the reaction: GTP + H2O = GDP + phosphate." [ISBN:0198547684, PMID:26832457, PMID:27218782]
+def: "Catalysis of the reaction: GTP + H2O = GDP + H+ + phosphate." [PMID:26832457, PMID:27218782]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "ARF small monomeric GTPase activity" NARROW []
synonym: "dynamin GTPase activity" NARROW []
synonym: "GTPase activity, coupled" RELATED []
@@ -30525,12 +30551,14 @@ xref: Reactome:R-HSA-8981353 "RASA1 stimulates RAS GTPase activity"
xref: Reactome:R-HSA-8982020 "G alpha (i)i1/i2/i3 in G (i):RGS complex is inactivated"
xref: Reactome:R-HSA-8982021 "G alpha (z) in G alpha (z):RGS complex is inactivated"
xref: Reactome:R-HSA-8982025 "G alpha (q) in G (q):RGS complex is inactivated"
+xref: Reactome:R-HSA-9018814 "RHOT1 hydrolyzes GTP"
+xref: Reactome:R-HSA-9018826 "RHOT2 hydrolyzes GTP"
xref: Reactome:R-HSA-9640195 "RRAGA,B hydrolyzes GTP"
xref: Reactome:R-HSA-9645598 "RRAGC,D hydrolyzes GTP"
xref: Reactome:R-HSA-9649736 "RAS intrinsic GTPase activity hydrolyzes GTP to GDP"
xref: Reactome:R-HSA-983422 "Disassembly of COPII coated vesicle"
xref: RHEA:19669
-is_a: GO:0017111 ! nucleoside-triphosphatase activity
+is_a: GO:0017111 ! ribonucleoside triphosphate phosphatase activity
[Term]
id: GO:0003925
@@ -30541,15 +30569,17 @@ def: "A molecular function regulator that cycles between active GTP-bound and in
synonym: "heterotrimeric G-protein GTPase activity" NARROW []
synonym: "large G-protein activity" NARROW []
synonym: "large G-protein GTPase activity" NARROW []
+synonym: "Ras superfamily protein" NARROW []
synonym: "signaling G protein activity" EXACT []
+synonym: "small G-protein" NARROW []
+synonym: "small GTPase" NARROW []
+synonym: "small GTPase activity" NARROW []
synonym: "small monomeric G protein activity" NARROW []
synonym: "small monomeric GTPase activity" NARROW []
-xref: EC:3.6.5.1
-xref: EC:3.6.5.2
xref: MetaCyc:3.6.1.46-RXN
xref: MetaCyc:3.6.1.47-RXN
is_a: GO:0003924 ! GTPase activity
-is_a: GO:0098772 ! molecular function regulator
+is_a: GO:0098772 ! molecular function regulator activity
[Term]
id: GO:0003926
@@ -30647,7 +30677,7 @@ is_a: GO:0003933 ! GTP cyclohydrolase activity
id: GO:0003935
name: GTP cyclohydrolase II activity
namespace: molecular_function
-def: "Catalysis of the reaction: GTP + 3 H(2)O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + diphosphate + formate + 3 H(+)." [EC:3.5.4.25, RHEA:23704]
+def: "Catalysis of the reaction: GTP + 3 H2O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + diphosphate + formate + 3 H+." [EC:3.5.4.25, RHEA:23704]
synonym: "GTP 7,8-8,9-dihydrolase (diphosphate-forming)" RELATED [EC:3.5.4.25]
synonym: "GTP-8-formylhydrolase activity" RELATED [EC:3.5.4.25]
synonym: "guanosine triphosphate cyclohydrolase II" RELATED [EC:3.5.4.25]
@@ -30702,6 +30732,7 @@ synonym: "inosinic acid dehydrogenase activity" RELATED [EC:1.1.1.205]
xref: EC:1.1.1.205
xref: MetaCyc:IMP-DEHYDROG-RXN
xref: Reactome:R-HSA-73794 "IMP + H2O + NAD+ => XMP + NADH + H+ [IMPDH1,2]"
+xref: Reactome:R-HSA-9748945 "IMPDH tetramers dehydrogenate 6TIMP to 6TXMP"
xref: RHEA:11708
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -30879,7 +30910,7 @@ is_a: GO:0008376 ! acetylgalactosaminyltransferase activity
id: GO:0003948
name: N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(4)-(beta-N-acetyl-D-glucosaminyl)-L-asparagine + H(2)O = N-acetyl-beta-D-glucosaminylamine + L-aspartate + H(+)." [EC:3.5.1.26, RHEA:11544]
+def: "Catalysis of the reaction: N(4)-(beta-N-acetyl-D-glucosaminyl)-L-asparagine + H2O = N-acetyl-beta-D-glucosaminylamine + L-aspartate + H+." [EC:3.5.1.26, RHEA:11544]
synonym: "4-N-(beta-N-acetyl-D-glucosaminyl)-L-asparagine amidohydrolase activity" RELATED [EC:3.5.1.26]
synonym: "aspartylglucosaminidase activity" RELATED [EC:3.5.1.26]
synonym: "aspartylglucosylaminase activity" RELATED [EC:3.5.1.26]
@@ -30936,14 +30967,14 @@ xref: Reactome:R-HSA-5688276 "SIRT4 transfers ADPRib to GLUD"
xref: Reactome:R-HSA-8938073 "PARPs transfer ADP-D-ribose to proteins (poly(ADP-ribosyl)ation)"
xref: Reactome:R-HSA-8948800 "TNKS and TNKS2 PARylate PTEN"
xref: Reactome:R-HSA-9686061 "Nucleoprotein is ADP-ribosylated"
-xref: Reactome:R-HSA-9694773 "Nucleoprotein is ADP-ribosylated"
+xref: Reactome:R-HSA-9729279 "Nucleoprotein is ADP-ribosylated"
is_a: GO:0016763 ! pentosyltransferase activity
[Term]
id: GO:0003951
name: NAD+ kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + NAD(+) = ADP + 2 H(+) + NADP(+)." [EC:2.7.1.23, RHEA:18629]
+def: "Catalysis of the reaction: ATP + NAD+ = ADP + 2 H+ + NADP+." [EC:2.7.1.23, RHEA:18629]
synonym: "ATP:NAD+ 2'-phosphotransferase activity" RELATED [EC:2.7.1.23]
synonym: "DPN kinase activity" RELATED [EC:2.7.1.23]
synonym: "NAD kinase activity" EXACT []
@@ -31057,28 +31088,6 @@ xref: MetaCyc:NQOR-RXN
xref: UM-BBD_reactionID:r0227
is_a: GO:0016655 ! oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
-[Term]
-id: GO:0003956
-name: NAD(P)+-protein-arginine ADP-ribosyltransferase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: NAD(P)+ + L-arginine = nicotinamide + N2-(ADP-D-ribosyl)-L-arginine." [EC:2.4.2.31]
-synonym: "ADP-ribosyltransferase activity" BROAD [EC:2.4.2.31]
-synonym: "mono(ADP-ribosyl)transferase activity" BROAD [EC:2.4.2.31]
-synonym: "mono(ADPribosyl)transferase activity" BROAD [EC:2.4.2.31]
-synonym: "NAD(+):L-arginine ADP-D-ribosyltransferase activity" RELATED [EC:2.4.2.31]
-synonym: "NAD(P)(+)--arginine ADP-ribosyltransferase activity" RELATED [EC:2.4.2.31]
-synonym: "NAD(P)+-arginine ADP-ribosyltransferase activity" EXACT []
-synonym: "NAD(P)+:L-arginine ADP-D-ribosyltransferase activity" RELATED [EC:2.4.2.31]
-synonym: "NAD(P)+:protein-L-arginine ADP-D-ribosyltransferase activity" RELATED [EC:2.4.2.31]
-synonym: "NAD(P)-arginine ADP-ribosyltransferase activity" EXACT []
-synonym: "NAD+:L-arginine ADP-D-ribosyltransferase activity" RELATED [EC:2.4.2.31]
-synonym: "peptidyl-arginine ADP-ribosylation activity" EXACT []
-synonym: "protein-arginine ADP-ribosyltransferase activity" EXACT []
-xref: EC:2.4.2.31
-xref: MetaCyc:2.4.2.31-RXN
-xref: Reactome:R-HSA-1972385 "ADP-Ribosylation of HNP-1"
-is_a: GO:0016763 ! pentosyltransferase activity
-
[Term]
id: GO:0003957
name: NAD(P)+ transhydrogenase (B-specific) activity
@@ -31299,30 +31308,17 @@ replaced_by: GO:0003964
[Term]
id: GO:0003968
-name: RNA-directed 5'-3' RNA polymerase activity
+name: RNA-dependent RNA polymerase activity
namespace: molecular_function
def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time." [EC:2.7.7.48, GOC:mah, GOC:pf]
-synonym: "3D polymerase activity" RELATED [EC:2.7.7.48]
-synonym: "nucleoside-triphosphate:RNA nucleotidyltransferase (RNA-directed)" RELATED [EC:2.7.7.48]
-synonym: "PB1 proteins" RELATED [EC:2.7.7.48]
-synonym: "PB2 proteins" RELATED [EC:2.7.7.48]
-synonym: "phage f2 replicase" NARROW [EC:2.7.7.48]
-synonym: "polymerase L" RELATED [EC:2.7.7.48]
-synonym: "Q-beta replicase activity" RELATED [EC:2.7.7.48]
-synonym: "RDRP" RELATED [EC:2.7.7.48]
-synonym: "ribonucleic acid replicase activity" RELATED [EC:2.7.7.48]
-synonym: "ribonucleic acid-dependent ribonucleate nucleotidyltransferase activity" RELATED [EC:2.7.7.48]
-synonym: "ribonucleic acid-dependent ribonucleic acid polymerase activity" RELATED [EC:2.7.7.48]
-synonym: "ribonucleic replicase activity" RELATED [EC:2.7.7.48]
-synonym: "ribonucleic synthetase activity" RELATED [EC:2.7.7.48]
-synonym: "RNA nucleotidyltransferase (RNA-directed) activity" RELATED [EC:2.7.7.48]
-synonym: "RNA replicase activity" RELATED [EC:2.7.7.48]
-synonym: "RNA synthetase activity" RELATED [EC:2.7.7.48]
-synonym: "RNA-dependent ribonucleate nucleotidyltransferase activity" RELATED [EC:2.7.7.48]
-synonym: "RNA-dependent RNA polymerase activity" RELATED [EC:2.7.7.48]
-synonym: "RNA-dependent RNA replicase activity" RELATED [EC:2.7.7.48]
-synonym: "RNA-directed RNA polymerase activity" BROAD []
-synonym: "transcriptase" BROAD [EC:2.7.7.48]
+synonym: "RdRP activity" EXACT []
+synonym: "RNA nucleotidyltransferase (RNA-directed) activity" EXACT []
+synonym: "RNA replicase activity" RELATED []
+synonym: "RNA synthetase activity" RELATED []
+synonym: "RNA-dependent RNA replicase activity" EXACT []
+synonym: "RNA-directed 5'-3' RNA polymerase activity" EXACT []
+synonym: "RNA-directed RNA polymerase activity" EXACT []
+synonym: "transcriptase" BROAD []
xref: EC:2.7.7.48
xref: MetaCyc:RNA-DIRECTED-RNA-POLYMERASE-RXN
xref: Reactome:R-HSA-168280 "Priming and Initiation of Transcription"
@@ -31506,7 +31502,7 @@ is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and
id: GO:0003979
name: UDP-glucose 6-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + 2 NAD(+) + UDP-alpha-D-glucose = 3 H(+) + 2 NADH + UDP-alpha-D-glucuronate." [EC:1.1.1.22, RHEA:23596]
+def: "Catalysis of the reaction: H2O + 2 NAD+ + UDP-alpha-D-glucose = 3 H+ + 2 NADH + UDP-alpha-D-glucuronate." [EC:1.1.1.22, RHEA:23596]
xref: EC:1.1.1.22
xref: KEGG_REACTION:R00286
xref: MetaCyc:UGD-RXN
@@ -31596,7 +31592,7 @@ is_a: GO:0016453 ! C-acetyltransferase activity
id: GO:0003986
name: acetyl-CoA hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + H(2)O = acetate + CoA + H(+)." [EC:3.1.2.1, RHEA:20289]
+def: "Catalysis of the reaction: acetyl-CoA + H2O = acetate + CoA + H+." [EC:3.1.2.1, RHEA:20289]
synonym: "acetyl coenzyme A acylase activity" RELATED [EC:3.1.2.1]
synonym: "acetyl coenzyme A deacylase activity" RELATED [EC:3.1.2.1]
synonym: "acetyl coenzyme A hydrolase activity" RELATED [EC:3.1.2.1]
@@ -31804,21 +31800,14 @@ id: GO:0003995
name: acyl-CoA dehydrogenase activity
namespace: molecular_function
alt_id: GO:0019109
-def: "Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor." [EC:1.3.99.3]
-synonym: "acyl CoA dehydrogenase activity" RELATED [EC:1.3.99.3]
-synonym: "acyl coenzyme A dehydrogenase activity" RELATED [EC:1.3.99.3]
-synonym: "acyl dehydrogenase activity" RELATED [EC:1.3.99.3]
-synonym: "acyl-CoA reductase activity" EXACT [GOC:mah]
-synonym: "acyl-CoA:(acceptor) 2,3-oxidoreductase activity" RELATED [EC:1.3.99.3]
-synonym: "acyl-CoA:acceptor 2,3-oxidoreductase activity" RELATED [EC:1.3.99.3]
-synonym: "fatty acyl coenzyme A dehydrogenase activity" RELATED [EC:1.3.99.3]
-synonym: "fatty-acyl-CoA dehydrogenase activity" RELATED [EC:1.3.99.3]
-synonym: "general acyl CoA dehydrogenase activity" RELATED [EC:1.3.99.3]
-synonym: "long-chain acyl coenzyme A dehydrogenase activity" RELATED [EC:1.3.99.3]
-synonym: "long-chain acyl-CoA dehydrogenase activity" RELATED [EC:1.3.99.3]
-synonym: "medium-chain acyl-CoA dehydrogenase activity" NARROW [EC:1.3.99.3]
-synonym: "medium-chain acyl-coenzyme A dehydrogenase activity" RELATED [EC:1.3.99.3]
-xref: EC:1.3.99.3
+def: "Catalysis of the reaction: acyl-CoA + oxidized [electron-transfer flavoprotein]= 2,3-dehydroacyl-CoA + reduced [electron-transfer flavoprotein] + H+." [GOC:curators]
+synonym: "acyl CoA dehydrogenase activity" EXACT []
+synonym: "acyl coenzyme A dehydrogenase activity" EXACT []
+synonym: "acyl-CoA reductase activity" EXACT []
+synonym: "fatty acyl coenzyme A dehydrogenase activity" RELATED []
+synonym: "fatty-acyl-CoA dehydrogenase activity" RELATED []
+synonym: "general acyl CoA dehydrogenase activity" RELATED []
+xref: EC:1.3.-.-
xref: MetaCyc:ACYLCOADEHYDROG-RXN
xref: MetaCyc:LONG-CHAIN-FATTY-ACYL-COA-REDUCTASE-RXN
xref: Reactome:R-HSA-109341 "dehydrogenation of 4-cis-decenoyl-CoA to form 2-trans-4-cis-decadienoyl-CoA"
@@ -31833,7 +31822,7 @@ xref: Reactome:R-HSA-77319 "Butanoyl-CoA+FAD<=>Crotonoyl-CoA+FADH2"
xref: Reactome:R-HSA-77327 "Hexanoyl-CoA+FAD<=>trans-Hex-2-enoyl-CoA+FADH2"
xref: Reactome:R-HSA-77338 "Octanoyl-CoA+FAD<=>trans-Oct-2-enoyl-CoA+FADH2"
xref: Reactome:R-HSA-77345 "Decanoyl-CoA+FAD<=>trans-Dec-2-enoyl-CoA+FADH2"
-is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
+is_a: GO:0052890 ! oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor
[Term]
id: GO:0003997
@@ -31867,7 +31856,7 @@ synonym: "Ho 1-3" RELATED [EC:3.6.1.7]
xref: EC:3.6.1.7
xref: MetaCyc:ACYLPHOSPHATASE-RXN
xref: RHEA:14965
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+is_a: GO:0016462 ! pyrophosphatase activity
[Term]
id: GO:0003999
@@ -31886,7 +31875,8 @@ synonym: "APRT activity" RELATED [EC:2.4.2.7]
synonym: "transphosphoribosidase activity" RELATED [EC:2.4.2.7]
xref: EC:2.4.2.7
xref: MetaCyc:ADENPRIBOSYLTRAN-RXN
-xref: Reactome:R-HSA-74213 "Adenine + PRPP => AMP + PPi"
+xref: Reactome:R-HSA-74213 "APRT catalyzes the conversion of adenine to AMP"
+xref: Reactome:R-HSA-9734193 "Defective APRT does not convert adenine to AMP"
xref: RHEA:16609
is_a: GO:0106130 ! purine phosphoribosyltransferase activity
@@ -31899,10 +31889,7 @@ synonym: "adenosine aminohydrolase activity" RELATED [EC:3.5.4.4]
synonym: "adenosine deaminase reaction" EXACT []
xref: EC:3.5.4.4
xref: MetaCyc:ADENODEAMIN-RXN
-xref: Reactome:R-HSA-2161187 "N6-methyl-AMP + H2O => IMP + methylamine"
-xref: Reactome:R-HSA-2161195 "abacavir monophosphate + H2O => carbovir monophosphate + cyclopropylamine"
xref: Reactome:R-HSA-5693346 "CECRI deaminates Ade-Rib to Ino"
-xref: Reactome:R-HSA-74241 "(2'-deoxy)adenosine + H2O => (2'-deoxy)inosine + NH4+ (ADA)"
xref: RHEA:24408
is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
is_a: GO:0019239 ! deaminase activity
@@ -31918,6 +31905,7 @@ synonym: "ATP:adenosine 5'-phosphotransferase activity" RELATED [EC:2.7.1.20]
xref: EC:2.7.1.20
xref: MetaCyc:ADENOSINE-KINASE-RXN
xref: Reactome:R-HSA-109624 "(2'-deoxy)adenosine + ATP => (d)AMP + ADP (ADK)"
+xref: Reactome:R-HSA-9754974 "ADK phosphorylates RBV"
xref: RHEA:20824
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
is_a: GO:0019206 ! nucleoside kinase activity
@@ -31958,27 +31946,27 @@ consider: GO:0043190
id: GO:0004013
name: adenosylhomocysteinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-homocysteine + H2O = adenosine + L-homocysteine." [EC:3.3.1.1]
+def: "Catalysis of the reaction: S-adenosyl-L-homocysteine + H2O = adenosine + L-homocysteine." [RHEA:21708]
subset: goslim_chembl
-synonym: "adenosylhomocysteine hydrolase activity" RELATED [EC:3.3.1.1]
-synonym: "AdoHcyase activity" RELATED [EC:3.3.1.1]
-synonym: "S-adenosyl-L-homocysteine hydrolase activity" RELATED [EC:3.3.1.1]
-synonym: "S-adenosylhomocysteinase activity" RELATED [EC:3.3.1.1]
-synonym: "S-adenosylhomocysteine hydrolase activity" BROAD [EC:3.3.1.1]
-synonym: "S-adenosylhomocysteine synthase activity" RELATED [EC:3.3.1.1]
-synonym: "SAHase activity" RELATED [EC:3.3.1.1]
-xref: EC:3.3.1.1
+synonym: "adenosylhomocysteine hydrolase activity" RELATED []
+synonym: "AdoHcyase activity" RELATED []
+synonym: "S-adenosyl-L-homocysteine hydrolase activity" RELATED []
+synonym: "S-adenosylhomocysteinase activity" RELATED []
+synonym: "S-adenosylhomocysteine hydrolase activity" BROAD []
+synonym: "S-adenosylhomocysteine synthase activity" RELATED []
+synonym: "SAHase activity" RELATED []
+xref: EC:3.13.2.1
xref: MetaCyc:ADENOSYLHOMOCYSTEINASE-RXN
xref: Reactome:R-HSA-174401 "AHCY:NAD+ tetramer hydrolyses AdoHcy"
xref: Reactome:R-HSA-5579084 "Defective AHCY does not hydrolyse AdoHcy"
xref: RHEA:21708
-is_a: GO:0016802 ! trialkylsulfonium hydrolase activity
+is_a: GO:0046508 ! hydrolase activity, acting on carbon-sulfur bonds
[Term]
id: GO:0004014
name: adenosylmethionine decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + H(+) = S-adenosylmethioninamine + CO(2)." [EC:4.1.1.50, RHEA:15981]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + H+ = S-adenosylmethioninamine + CO2." [EC:4.1.1.50, RHEA:15981]
synonym: "adenosyl methionine decarboxylase activity" EXACT []
synonym: "S-adenosyl-L-methionine carboxy-lyase [(5-deoxy-5-adenosyl)(3-aminopropyl)-methylsulfonium-salt-forming]" RELATED [EC:4.1.1.50]
synonym: "S-adenosyl-L-methionine carboxy-lyase activity" RELATED [EC:4.1.1.50]
@@ -32037,6 +32025,7 @@ xref: Reactome:R-HSA-381607 "Activated Adenylyl cyclase synthesizes cyclic AMP"
xref: Reactome:R-HSA-392129 "Adenylate cyclase converts ATP to 3',5'-cyclic AMP (cAMP) and pyrophosphate"
xref: Reactome:R-HSA-5211224 "Anthrax cya catalyzes the conversion of ATP to cAMP"
xref: Reactome:R-HSA-5610727 "GPR161 promotes cAMP production in a G alpha(s)-dependent manner"
+xref: Reactome:R-HSA-9712183 "ADCY3:GNAL:GTP converts ATP to cAMP"
xref: RHEA:15389
is_a: GO:0009975 ! cyclase activity
is_a: GO:0016849 ! phosphorus-oxygen lyase activity
@@ -32073,8 +32062,6 @@ synonym: "succino AMP-lyase activity" BROAD [EC:4.3.2.2, GOC:mah]
xref: EC:4.3.2.2
xref: KEGG_REACTION:R01083
xref: MetaCyc:AMPSYN-RXN
-xref: Reactome:R-HSA-73800 "SAICAR => AICAR + Fumarate"
-xref: Reactome:R-HSA-73828 "adenylosuccinate => adenosine 5'-monophosphate + fumarate"
xref: RHEA:16853
is_a: GO:0016842 ! amidine-lyase activity
@@ -32082,7 +32069,7 @@ is_a: GO:0016842 ! amidine-lyase activity
id: GO:0004019
name: adenylosuccinate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-aspartate + GTP + IMP = N(6)-(1,2-dicarboxyethyl)-AMP + GDP + 3 H(+) + phosphate." [EC:6.3.4.4, RHEA:15753]
+def: "Catalysis of the reaction: L-aspartate + GTP + IMP = N(6)-(1,2-dicarboxyethyl)-AMP + GDP + 3 H+ + phosphate." [EC:6.3.4.4, RHEA:15753]
synonym: "adenylosuccinate synthetase activity" RELATED [EC:6.3.4.4]
synonym: "IMP--aspartate ligase activity" RELATED [EC:6.3.4.4]
synonym: "IMP:L-aspartate ligase (GDP-forming)" RELATED [EC:6.3.4.4]
@@ -32248,7 +32235,6 @@ id: GO:0004028
name: 3-chloroallyl aldehyde dehydrogenase activity
namespace: molecular_function
def: "Catalysis of the reaction: 3-chloroallyl aldehyde + H2O = 2 H+ + 2 e- + 3-chloroacrylic acid." [UM-BBD_enzymeID:e0432]
-xref: Reactome:R-HSA-71260 "ALDH9A1 tetramer dehydrogenates TEABL to form TEABT"
xref: UM-BBD_enzymeID:e0432
is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
@@ -32300,11 +32286,15 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0004031
name: aldehyde oxidase activity
namespace: molecular_function
+alt_id: GO:0050250
def: "Catalysis of the reaction: an aldehyde + H2O + O2 = a carboxylic acid + hydrogen peroxide." [EC:1.2.3.1]
synonym: "aldehyde:oxygen oxidoreductase activity" RELATED [EC:1.2.3.1]
synonym: "quinoline oxidase activity" RELATED [EC:1.2.3.1]
+synonym: "retinal oxidase activity" NARROW []
xref: EC:1.2.3.1
xref: MetaCyc:ALDEHYDE-OXIDASE-RXN
+xref: MetaCyc:RXN-8093
+xref: MetaCyc:RXN-8094
xref: Reactome:R-HSA-3204311 "AOX1 oxidises PXL to PDXate"
xref: RHEA:16829
is_a: GO:0016623 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, oxygen as acceptor
@@ -32389,7 +32379,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0004037
name: allantoicase activity
namespace: molecular_function
-def: "Catalysis of the reaction: allantoate + H(2)O = (S)-ureidoglycolate + urea." [EC:3.5.3.4, RHEA:11016]
+def: "Catalysis of the reaction: allantoate + H2O = (S)-ureidoglycolate + urea." [EC:3.5.3.4, RHEA:11016]
synonym: "allantoate amidinohydrolase activity" RELATED [EC:3.5.3.4]
synonym: "allantoine amidinohydrolase activity" EXACT []
xref: EC:3.5.3.4
@@ -32413,7 +32403,7 @@ is_a: GO:0016812 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0004039
name: allophanate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + 3 H(+) + urea-1-carboxylate = 2 CO(2) + 2 NH(4)(+)." [EC:3.5.1.54, RHEA:19029]
+def: "Catalysis of the reaction: H2O + 3 H+ + urea-1-carboxylate = 2 CO2 + 2 NH4." [EC:3.5.1.54, RHEA:19029]
synonym: "allophanate lyase activity" RELATED [EC:3.5.1.54]
synonym: "urea-1-carboxylate amidohydrolase activity" RELATED [EC:3.5.1.54]
xref: EC:3.5.1.54
@@ -32445,7 +32435,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0004042
name: acetyl-CoA:L-glutamate N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-glutamate + acetyl-CoA = N-acetyl-L-glutamate + CoA + H(+)." [EC:2.3.1.1, RHEA:24292]
+def: "Catalysis of the reaction: L-glutamate + acetyl-CoA = N-acetyl-L-glutamate + CoA + H+." [EC:2.3.1.1, RHEA:24292]
synonym: "acetylglutamate acetylglutamate synthetase activity" RELATED [EC:2.3.1.1]
synonym: "AGAS" RELATED [EC:2.3.1.1]
synonym: "amino acid acetyltransferase activity" RELATED [EC:2.3.1.1]
@@ -32484,7 +32474,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0004044
name: amidophosphoribosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-phospho-beta-D-ribosylamine + L-glutamate + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + L-glutamine + H(2)O." [EC:2.4.2.14, RHEA:14905]
+def: "Catalysis of the reaction: 5-phospho-beta-D-ribosylamine + L-glutamate + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + L-glutamine + H2O." [EC:2.4.2.14, RHEA:14905]
synonym: "5'-phosphoribosylpyrophosphate amidotransferase activity" RELATED [EC:2.4.2.14]
synonym: "5-phosphoribosyl-1-pyrophosphate amidotransferase activity" RELATED [EC:2.4.2.14]
synonym: "5-phosphoribosylamine:diphosphate phospho-alpha-D-ribosyltransferase (glutamate-amidating)" RELATED [EC:2.4.2.14]
@@ -32547,6 +32537,7 @@ xref: MetaCyc:AMINOACYLASE-RXN
xref: Reactome:R-HSA-5433074 "ACY1:Zn2+ dimer hydrolyses mercapturic acids"
xref: Reactome:R-HSA-5579081 "Defective ACY1 does not hydrolyse mercapturic acids"
xref: Reactome:R-HSA-9638046 "ACY3:Zn2+ dimer hydrolyses mercapturic acids"
+xref: Reactome:R-HSA-9753944 "ACY1:Zn2+ dimer deacetylates NAC to L-Cys"
xref: RHEA:15565
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
@@ -32566,7 +32557,7 @@ xref: EC:2.1.2.10
xref: MetaCyc:GCVT-RXN
xref: Reactome:R-HSA-5693977 "AMT transfers NH2CH2 from GCSH:SAMDLL to THF"
xref: RHEA:16945
-is_a: GO:0008168 ! methyltransferase activity
+is_a: GO:0016742 ! hydroxymethyl-, formyl- and related transferase activity
[Term]
id: GO:0004048
@@ -32661,7 +32652,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0004052
name: arachidonate 12(S)-lipoxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: arachidonate + O(2) = (5Z,8Z,10E,12S,14Z)-12-hydroperoxyicosa-5,8,10,14-tetraenoate." [EC:1.13.11.31, RHEA:10428]
+def: "Catalysis of the reaction: arachidonate + O2 = (5Z,8Z,10E,12S,14Z)-12-hydroperoxyicosa-5,8,10,14-tetraenoate." [EC:1.13.11.31, RHEA:10428]
synonym: "12-lipoxygenase activity" RELATED [EC:1.13.11.31]
synonym: "12Delta-lipoxygenase activity" RELATED [EC:1.13.11.31]
synonym: "12S-lipoxygenase activity" RELATED [EC:1.13.11.31]
@@ -32704,7 +32695,7 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0004054
name: arginine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arginine + ATP = N(omega)-phospho-L-arginine + ADP + 2 H(+)." [EC:2.7.3.3, RHEA:22940]
+def: "Catalysis of the reaction: L-arginine + ATP = N(omega)-phospho-L-arginine + ADP + 2 H+." [EC:2.7.3.3, RHEA:22940]
synonym: "adenosine 5'-triphosphate-arginine phosphotransferase activity" RELATED [EC:2.7.3.3]
synonym: "adenosine 5'-triphosphate:L-arginine" RELATED [EC:2.7.3.3]
synonym: "arginine phosphokinase activity" RELATED [EC:2.7.3.3]
@@ -32825,6 +32816,7 @@ xref: EC:2.3.1.5
xref: MetaCyc:ARYLAMINE-N-ACETYLTRANSFERASE-RXN
xref: Reactome:R-HSA-174963 "NAT1 acetylation"
xref: Reactome:R-HSA-174967 "NAT2 acetylation"
+xref: Reactome:R-HSA-9753676 "NAT1,2 acetylate APAP-Cys to APAP-Mer"
xref: RHEA:16613
xref: UM-BBD_enzymeID:e0341
is_a: GO:0008080 ! N-acetyltransferase activity
@@ -33034,9 +33026,9 @@ xref: EC:2.6.1.1
xref: KEGG_REACTION:R00355
xref: MetaCyc:ASPAMINOTRANS-RXN
xref: Reactome:R-HSA-70581 "oxaloacetate + glutamate <=> aspartate + alpha-ketoglutarate [GOT1]"
-xref: Reactome:R-HSA-70592 "PXLP-K259-GOT1 dimer deaminates L-Asp"
+xref: Reactome:R-HSA-70592 "PXLP-K259-GOT1 transaminates alpha-ketoglutarate and aspartate"
xref: Reactome:R-HSA-70596 "GOT2 dimer deaminates L-Asp"
-xref: Reactome:R-HSA-70613 "oxaloacetate + glutamate <=> aspartate + alpha-ketoglutarate [GOT2]"
+xref: Reactome:R-HSA-70613 "GOT2 transaminates oxaloacetate and glutamate"
xref: RHEA:21824
is_a: GO:0008483 ! transaminase activity
@@ -33044,7 +33036,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0004070
name: aspartate carbamoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-aspartate + carbamoyl phosphate = N-carbamoyl-L-aspartate + H(+) + phosphate." [EC:2.1.3.2, RHEA:20013]
+def: "Catalysis of the reaction: L-aspartate + carbamoyl phosphate = N-carbamoyl-L-aspartate + H+ + phosphate." [EC:2.1.3.2, RHEA:20013]
synonym: "aspartate carbamyltransferase activity" RELATED [EC:2.1.3.2]
synonym: "aspartate transcarbamoylase activity" RELATED [EC:2.1.3.2]
synonym: "aspartate transcarbamylase activity" RELATED [EC:2.1.3.2]
@@ -33060,7 +33052,7 @@ synonym: "L-aspartate transcarbamylase activity" RELATED [EC:2.1.3.2]
xref: EC:2.1.3.2
xref: KEGG_REACTION:R01397
xref: MetaCyc:ASPCARBTRANS-RXN
-xref: Reactome:R-HSA-73573 "carbamoyl phosphate + L-aspartate <=> N-carbamoyl L-aspartate + orthophosphate"
+xref: Reactome:R-HSA-73573 "CAD hexamer transforms CAP to N-carb-L-Asp"
xref: RHEA:20013
is_a: GO:0016743 ! carboxyl- or carbamoyltransferase activity
@@ -33081,7 +33073,7 @@ is_a: GO:0016211 ! ammonia ligase activity
id: GO:0004072
name: aspartate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-aspartate + ATP = 4-phospho-L-aspartate + ADP + H(+)." [EC:2.7.2.4, RHEA:23776]
+def: "Catalysis of the reaction: L-aspartate + ATP = 4-phospho-L-aspartate + ADP + H+." [EC:2.7.2.4, RHEA:23776]
synonym: "aspartic kinase activity" RELATED [EC:2.7.2.4]
synonym: "aspartokinase activity" RELATED [EC:2.7.2.4]
synonym: "ATP:L-aspartate 4-phosphotransferase activity" RELATED [EC:2.7.2.4]
@@ -33097,7 +33089,7 @@ is_a: GO:0019202 ! amino acid kinase activity
id: GO:0004073
name: aspartate-semialdehyde dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-aspartate 4-semialdehyde + NADP(+) + phosphate = 4-phospho-L-aspartate + H(+) + NADPH." [EC:1.2.1.11, RHEA:24284]
+def: "Catalysis of the reaction: L-aspartate 4-semialdehyde + NADP+ + phosphate = 4-phospho-L-aspartate + H+ + NADPH." [EC:1.2.1.11, RHEA:24284]
synonym: "ASA dehydrogenase activity" RELATED [EC:1.2.1.11]
synonym: "aspartate semialdehyde dehydrogenase activity" RELATED [EC:1.2.1.11]
synonym: "aspartic beta-semialdehyde dehydrogenase activity" RELATED [EC:1.2.1.11]
@@ -33138,7 +33130,7 @@ is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
id: GO:0004076
name: biotin synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + dethiobiotin + S(2-) = 2 5'-deoxyadenosine + 2 L-methionine + biotin + H(+)." [EC:2.8.1.6, RHEA:22060]
+def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + dethiobiotin + S(2-) = 2 5'-deoxyadenosine + 2 L-methionine + biotin + H+." [EC:2.8.1.6, RHEA:22060]
synonym: "biotin synthetase activity" RELATED [EC:2.8.1.6]
synonym: "dethiobiotin:sulfur sulfurtransferase activity" RELATED [EC:2.8.1.6]
xref: EC:2.8.1.6
@@ -33281,14 +33273,11 @@ is_a: GO:0016868 ! intramolecular transferase activity, phosphotransferases
[Term]
id: GO:0004083
-name: bisphosphoglycerate 2-phosphatase activity
+name: obsolete bisphosphoglycerate 2-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,3-bisphospho-D-glycerate + H(2)O = 3-phospho-D-glycerate + phosphate." [RHEA:21904]
-synonym: "2,3-bisphospho-D-glycerate 2-phosphohydrolase activity" BROAD []
-xref: KEGG_REACTION:R01516
-xref: MetaCyc:BISPHOSPHOGLYCERATE-PHOSPHATASE-RXN
-xref: RHEA:21904
-is_a: GO:0034416 ! bisphosphoglycerate phosphatase activity
+def: "OBSOLETE. Catalysis of the reaction: 2,3-bisphospho-D-glycerate + H2O = 3-phospho-D-glycerate + phosphate." [PMID:8567632, PMID:9452443]
+comment: This term was deprecated because there is no evidence that this reaction exists.
+is_obsolete: true
[Term]
id: GO:0004084
@@ -33329,8 +33318,9 @@ synonym: "unsaturated acyl-CoA reductase activity" RELATED [EC:1.3.8.1]
xref: EC:1.3.8.1
xref: KEGG_REACTION:R01178
xref: MetaCyc:BUTYRYL-COA-DEHYDROGENASE-RXN
+xref: RHEA:24004
xref: UM-BBD_reactionID:r0013
-is_a: GO:0052890 ! oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor
+is_a: GO:0016937 ! short-chain-acyl-CoA dehydrogenase activity
[Term]
id: GO:0004086
@@ -33348,7 +33338,7 @@ consider: GO:0004088
id: GO:0004087
name: carbamoyl-phosphate synthase (ammonia) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 ATP + CO(2) + H(2)O + NH(4)(+) = 2 ADP + carbamoyl phosphate + 5 H(+) + phosphate." [EC:6.3.4.16, RHEA:10624]
+def: "Catalysis of the reaction: 2 ATP + hydrogencarbonate + NH4+ = 2 ADP + carbamoyl phosphate + 2 H+ + phosphate." [EC:6.3.4.16, RHEA:18029]
synonym: "carbamoyl phosphate synthase (ammonia) activity" EXACT []
synonym: "carbamoyl-phosphate synthetase (ammonia) activity" RELATED [EC:6.3.4.16]
synonym: "carbamoyl-phosphate synthetase I activity" RELATED [EC:6.3.4.16]
@@ -33365,7 +33355,7 @@ xref: EC:6.3.4.16
xref: KEGG_REACTION:R00149
xref: MetaCyc:6.3.4.16-RXN
xref: Reactome:R-HSA-70555 "2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate [mitochondrial]"
-xref: RHEA:10624
+xref: RHEA:18029
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
[Term]
@@ -33388,7 +33378,7 @@ synonym: "glutamine-dependent carbamyl phosphate synthetase activity" RELATED [E
synonym: "hydrogen-carbonate:L-glutamine amido-ligase (ADP-forming, carbamate-phosphorylating) activity" RELATED [EC:6.3.5.5]
xref: EC:6.3.5.5
xref: MetaCyc:CARBPSYN-RXN
-xref: Reactome:R-HSA-73577 "L-glutamine + 2 ATP + HCO3- + H2O => carbamoyl phosphate + L-glutamate + 2 ADP + orthophosphate"
+xref: Reactome:R-HSA-73577 "CAD hexamer transforms L-Gln to CAP"
xref: RHEA:18633
is_a: GO:0016884 ! carbon-nitrogen ligase activity, with glutamine as amido-N-donor
@@ -33409,8 +33399,8 @@ synonym: "carboxyanhydrase activity" RELATED [EC:4.2.1.1]
xref: EC:4.2.1.1
xref: MetaCyc:CARBODEHYDRAT-RXN
xref: Reactome:R-HSA-1237045 "Carbonic Anhydrase VI hydrates carbon dioxide to bicarbonate and a proton"
-xref: Reactome:R-HSA-1237047 "Carbonic anhydrase IV hydrates carbon dioxide to bicarbonate and a proton"
-xref: Reactome:R-HSA-1237059 "Carbonic anhydrase IV dehydrates bicarbonate to water and carbon dioxide"
+xref: Reactome:R-HSA-1237047 "CA4:Zn2+ hydrates CO2 to HCO3-"
+xref: Reactome:R-HSA-1237059 "CA4:Zn2+ dehydrates HCO3- to CO2"
xref: Reactome:R-HSA-1237081 "Carbonic anhydrase VI dehydrates bicarbonate to water and carbon dioxide"
xref: Reactome:R-HSA-1475017 "Carbonic anhydrase dehydrates bicarbonate (plasma membrane)"
xref: Reactome:R-HSA-1475022 "Carbonic anhydrase dehydrates bicarbonate (cytosol)"
@@ -33418,8 +33408,8 @@ xref: Reactome:R-HSA-1475025 "Carbonic anhydrase hydrates carbon dioxide (plasma
xref: Reactome:R-HSA-1475026 "Carbonic anhydrase hydrates carbon dioxide (cytosol)"
xref: Reactome:R-HSA-1475028 "Carbonic anhydrase dehydrates bicarbonate (mitochondria)"
xref: Reactome:R-HSA-1475032 "Carbonic anhydrase hydrates carbon dioxide (mitochondria)"
-xref: Reactome:R-HSA-1475435 "Carbonic anhydrase I/II hydrates carbon dioxide"
-xref: Reactome:R-HSA-1475436 "Carbonic anhydrase I/II dehydrates bicarbonate"
+xref: Reactome:R-HSA-1475435 "CA1:Zn2+,CA2:Zn2+ hydrate CO2 to HCO3-"
+xref: Reactome:R-HSA-1475436 "CA1:Zn2+,CA2:Zn2+ dehydrate HCO3- to CO2"
xref: RHEA:10748
is_a: GO:0016836 ! hydro-lyase activity
@@ -33614,7 +33604,7 @@ is_a: GO:0016413 ! O-acetyltransferase activity
id: GO:0004103
name: choline kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + choline = ADP + choline phosphate + 2 H(+)." [EC:2.7.1.32, RHEA:12837]
+def: "Catalysis of the reaction: ATP + choline = ADP + choline phosphate + 2 H+." [EC:2.7.1.32, RHEA:12837]
synonym: "ATP:choline phosphotransferase activity" RELATED []
synonym: "choline kinase (phosphorylating)" RELATED []
synonym: "choline phosphokinase activity" RELATED []
@@ -33703,7 +33693,7 @@ is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
id: GO:0004108
name: citrate (Si)-synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA, where the acetyl group is added to the si-face of oxaloacetate; acetyl-CoA thus provides the two carbon atoms of the pro-S carboxymethyl group." [EC:2.3.3.1, ISBN:0121227073]
+def: "Catalysis of the reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA, where the acetyl group is added to the si-face of oxaloacetate; acetyl-CoA thus provides the two carbon atoms of the pro-S carboxymethyl group." [EC:2.3.3.1]
comment: Note that this function was formerly EC:4.1.3.7.
synonym: "(R)-citric synthase activity" RELATED [EC:2.3.3.1]
synonym: "acetyl-CoA:oxaloacetate C-acetyltransferase [thioester-hydrolysing, (pro-S)-carboxymethyl forming]" RELATED [EC:2.3.3.1]
@@ -33729,7 +33719,7 @@ is_a: GO:0036440 ! citrate synthase activity
id: GO:0004109
name: coproporphyrinogen oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: coproporphyrinogen III + 2 H(+) + O(2) = 2 CO(2) + 2 H(2)O + protoporphyrinogen IX." [EC:1.3.3.3, RHEA:18257]
+def: "Catalysis of the reaction: coproporphyrinogen III + 2 H+ + O2 = 2 CO2 + 2 H2O + protoporphyrinogen IX." [EC:1.3.3.3, RHEA:18257]
synonym: "coprogen oxidase activity" EXACT []
synonym: "coproporphyrinogen-III oxidase activity" EXACT []
synonym: "coproporphyrinogen:oxygen oxidoreductase (decarboxylating)" RELATED [EC:1.3.3.3]
@@ -33758,7 +33748,7 @@ is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldos
id: GO:0004111
name: creatine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+)." [EC:2.7.3.2, RHEA:17157]
+def: "Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H+." [EC:2.7.3.2, RHEA:17157]
synonym: "adenosine triphosphate-creatine transphosphorylase activity" RELATED [EC:2.7.3.2]
synonym: "ATP:creatine N-phosphotransferase activity" RELATED [EC:2.7.3.2]
synonym: "ATP:creatine phosphotransferase activity" RELATED [EC:2.7.3.2]
@@ -33817,7 +33807,7 @@ is_a: GO:0004112 ! cyclic-nucleotide phosphodiesterase activity
id: GO:0004114
name: 3',5'-cyclic-nucleotide phosphodiesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate." [EC:3.1.4.17]
+def: "Catalysis of the reaction: a nucleoside 3',5'-cyclic phosphate + H2O = a nucleoside 5'-phosphate." [RHEA:14653]
synonym: "3', 5'-cyclic nucleoside monophosphate phosphodiesterase activity" RELATED [EC:3.1.4.17]
synonym: "3',5' cyclic-nucleotide phosphodiesterase activity" EXACT []
synonym: "3',5'-cyclic-nucleotide 5'-nucleotidohydrolase activity" RELATED [EC:3.1.4.17]
@@ -33845,7 +33835,7 @@ is_a: GO:0004112 ! cyclic-nucleotide phosphodiesterase activity
id: GO:0004115
name: 3',5'-cyclic-AMP phosphodiesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate." [GOC:ai, RHEA:25277]
+def: "Catalysis of the reaction: 3',5'-cyclic AMP + H2O = AMP + H+." [GOC:ai, RHEA:25277]
synonym: "3',5' cAMP-specific phosphodiesterase activity" EXACT []
synonym: "3',5'-cAMP-specific phosphodiesterase activity" EXACT []
synonym: "3',5'-cyclic-AMP-specific phosphodiesterase activity" EXACT []
@@ -33859,16 +33849,20 @@ xref: Reactome:R-HSA-418553 "cAMP degradation by Phosphodiesterases"
xref: Reactome:R-HSA-9629675 "PDE3A hydrolyses cAMP to AMP"
xref: Reactome:R-HSA-9644869 "p-S54-PDE4B hydrolyses cAMP"
xref: Reactome:R-HSA-9705507 "PDE3B hydrolyses cAMP to AMP"
+xref: Reactome:R-HSA-9708261 "PDE4A hydrolyses cAMP to AMP"
xref: RHEA:25277
is_a: GO:0004114 ! 3',5'-cyclic-nucleotide phosphodiesterase activity
[Term]
id: GO:0004117
-name: calmodulin-dependent cyclic-nucleotide phosphodiesterase activity
+name: calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate; catalytic activity is regulated by calmodulin." [GOC:mah]
+def: "Catalysis of the reactions: 3',5'-cyclic AMP + H2O = AMP + H+ and 3',5'-cyclic GMP + H2O = GMP + H+; this activity is activated by binding to calcium-bound calmodulin." [PMID:8557689, PMID:9419816]
+synonym: "calmodulin-activated cyclic-nucleotide dual specificity phosphodiesterase activity" RELATED []
+synonym: "calmodulin-dependent cyclic-nucleotide phosphodiesterase activity" BROAD []
xref: Reactome:R-HSA-111955 "cAMP hydrolysis by Cam-PDE 1"
-is_a: GO:0004114 ! 3',5'-cyclic-nucleotide phosphodiesterase activity
+is_a: GO:0004115 ! 3',5'-cyclic-AMP phosphodiesterase activity
+is_a: GO:0047555 ! 3',5'-cyclic-GMP phosphodiesterase activity
[Term]
id: GO:0004118
@@ -34071,7 +34065,7 @@ is_a: GO:0009055 ! electron transfer activity
is_a: GO:0015078 ! proton transmembrane transporter activity
is_a: GO:0015453 ! oxidoreduction-driven active transmembrane transporter activity
is_a: GO:0016675 ! oxidoreductase activity, acting on a heme group of donors
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0004130
@@ -34150,7 +34144,6 @@ xref: MetaCyc:AMYLOMALT-RXN
xref: MetaCyc:RXN-1828
xref: MetaCyc:RXN-9023
xref: Reactome:R-HSA-71552 "limit dextrin-glycogenin => ((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl) glycogenin"
-is_a: GO:0004133 ! glycogen debranching enzyme activity
is_a: GO:0016758 ! hexosyltransferase activity
[Term]
@@ -34166,14 +34159,13 @@ synonym: "glycogen phosphorylase-limit dextrin alpha-1,6-glucohydrolase activity
xref: EC:3.2.1.33
xref: MetaCyc:3.2.1.33-RXN
xref: Reactome:R-HSA-71593 "((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin => poly{(1,4)-alpha-glucosyl} glycogenin + alpha-D-glucose"
-is_a: GO:0004133 ! glycogen debranching enzyme activity
is_a: GO:0090599 ! alpha-glucosidase activity
[Term]
id: GO:0004136
name: deoxyadenosine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2'-deoxyadenosine + ATP = ADP + dAMP + 2 H(+)." [EC:2.7.1.76, RHEA:23452]
+def: "Catalysis of the reaction: 2'-deoxyadenosine + ATP = ADP + dAMP + 2 H+." [EC:2.7.1.76, RHEA:23452]
synonym: "ATP:deoxyadenosine 5'-phosphotransferase activity" RELATED [EC:2.7.1.76]
synonym: "deoxyadenosine kinase (phosphorylating)" RELATED [EC:2.7.1.76]
synonym: "purine-deoxyribonucleoside kinase activity" RELATED [EC:2.7.1.76]
@@ -34203,7 +34195,7 @@ is_a: GO:0019136 ! deoxynucleoside kinase activity
id: GO:0004138
name: deoxyguanosine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2'-deoxyguanosine + ATP = ADP + dGMP + 2 H(+)." [EC:2.7.1.113, RHEA:19201]
+def: "Catalysis of the reaction: 2'-deoxyguanosine + ATP = ADP + dGMP + 2 H+." [EC:2.7.1.113, RHEA:19201]
synonym: "(dihydroxypropoxymethyl)guanine kinase activity" RELATED [EC:2.7.1.113]
synonym: "2'-deoxyguanosine kinase activity" RELATED [EC:2.7.1.113]
synonym: "ATP:deoxyguanosine 5'-phosphotransferase activity" RELATED [EC:2.7.1.113]
@@ -34237,7 +34229,7 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0004140
name: dephospho-CoA kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-dephospho-CoA + ATP = ADP + CoA + 2 H(+)." [EC:2.7.1.24, RHEA:18245]
+def: "Catalysis of the reaction: 3'-dephospho-CoA + ATP = ADP + CoA + 2 H+." [EC:2.7.1.24, RHEA:18245]
synonym: "3'-dephospho-CoA kinase activity" RELATED [EC:2.7.1.24]
synonym: "ATP:dephospho-CoA 3'-phosphotransferase activity" RELATED [EC:2.7.1.24]
synonym: "dephosphocoenzyme A kinase (phosphorylating)" RELATED [EC:2.7.1.24]
@@ -34254,7 +34246,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0004141
name: dethiobiotin synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7,8-diaminononanoate + ATP + CO(2) = ADP + dethiobiotin + 4 H(+) + phosphate." [EC:6.3.3.3, RHEA:15805]
+def: "Catalysis of the reaction: 7,8-diaminononanoate + ATP + CO2 = ADP + dethiobiotin + 4 H+ + phosphate." [EC:6.3.3.3, RHEA:15805]
synonym: "7,8-diaminononanoate:carbon-dioxide cyclo-ligase (ADP-forming)" RELATED [EC:6.3.3.3]
synonym: "desthiobiotin synthase activity" RELATED [EC:6.3.3.3]
synonym: "DTB synthetase activity" RELATED [EC:6.3.3.3]
@@ -34311,7 +34303,7 @@ xref: EC:2.7.1.107
xref: MetaCyc:DIACYLGLYKIN-RXN
xref: Reactome:R-HSA-426240 "DAG kinase produces phosphatidic acid from DAG"
xref: RHEA:10272
-is_a: GO:0016301 ! kinase activity
+is_a: GO:0001727 ! lipid kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
[Term]
@@ -34384,14 +34376,6 @@ xref: Reactome:R-HSA-1497794 "Salvage - BH2 is reduced to BH4 by DHFR"
xref: RHEA:15009
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
-[Term]
-id: GO:0004147
-name: dihydrolipoamide branched chain acyltransferase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + dihydrolipoamide = CoA + S-acyldihydrolipoamide, where the acyl group is a branched chain." [GOC:mah]
-synonym: "dihydrolipoamide branched chain transacylase activity" EXACT []
-is_a: GO:0030523 ! dihydrolipoamide S-acyltransferase activity
-
[Term]
id: GO:0004148
name: dihydrolipoyl dehydrogenase activity
@@ -34466,7 +34450,7 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0004151
name: dihydroorotase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-dihydroorotate + H(2)O = N-carbamoyl-L-aspartate + H(+)." [EC:3.5.2.3, RHEA:24296]
+def: "Catalysis of the reaction: (S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate + H+." [EC:3.5.2.3, RHEA:24296]
synonym: "(S)-dihydroorotate amidohydrolase activity" RELATED [EC:3.5.2.3]
synonym: "carbamoylaspartic dehydrase activity" RELATED [EC:3.5.2.3]
synonym: "DHOase activity" RELATED [EC:3.5.2.3]
@@ -34474,7 +34458,7 @@ synonym: "dihydroorotate hydrolase activity" RELATED [EC:3.5.2.3]
xref: EC:3.5.2.3
xref: KEGG_REACTION:R01993
xref: MetaCyc:DIHYDROOROT-RXN
-xref: Reactome:R-HSA-73571 "N-carbamoyl L-aspartate + H+ <=> (S)-dihydroorotate + H2O"
+xref: Reactome:R-HSA-73571 "CAD hexamer dehydrates N-carb-L-Asp to (S)-DHO"
xref: RHEA:24296
is_a: GO:0016812 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
@@ -34482,24 +34466,19 @@ is_a: GO:0016812 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0004152
name: dihydroorotate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-dihydroorotate + A = AH(2) + orotate." [EC:1.3.5.2, RHEA:18073]
-synonym: "(DHO) dehydrogenase activity" RELATED [EC:1.3.5.2]
-synonym: "(S)-dihydroorotate:quinone oxidoreductase activity" EXACT systematic_synonym [EC:1.3.5.2]
-synonym: "DHOdehase activity" RELATED [EC:1.3.5.2]
-synonym: "dihydoorotic acid dehydrogenase activity" RELATED [EC:1.3.5.2]
-synonym: "dihydroorotate:ubiquinone oxidoreductase activity" NARROW [EC:1.3.5.2]
-xref: EC:1.3.5.2
+def: "Catalysis of the reaction: (S)-dihydroorotate + A = AH(2) + orotate." [RHEA:18073]
xref: KEGG_REACTION:R01868
xref: MetaCyc:DIHYDROOROTATE-DEHYDROGENASE-RXN
-xref: Reactome:R-HSA-73569 "(S)-dihydroorotate + ubiquinone => orotate + ubiquinol"
+xref: Reactome:R-HSA-73569 "DHODH:FMN oxidises (S)-DHO to orotate"
xref: RHEA:18073
-is_a: GO:0016635 ! oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor
+is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
[Term]
id: GO:0004153
name: dihydropterin deaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: 7,8-dihydropterin + H2O = 7,8-dihydrolumazine + NH3." [GOC:jl, PMID:19567870]
+is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
is_a: GO:0019239 ! deaminase activity
[Term]
@@ -34573,14 +34552,13 @@ is_a: GO:0016812 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
[Term]
id: GO:0004158
-name: dihydroorotate oxidase activity
+name: obsolete dihydroorotate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-dihydroorotate + O(2) = H(2)O(2) + orotate." [RHEA:15441]
+def: "OBSOLETE. Catalysis of the reaction: (S)-dihydroorotate + O2 = H2O2 + orotate." [GOC:curators]
+comment: There appears to be no evidence for this reaction. The orginal EC used for this reaction was not appropriate.
synonym: "(S)-dihydroorotate:oxygen oxidoreductase activity" RELATED []
synonym: "4,5-L-dihydroorotate:oxygen oxidoreductase activity" RELATED []
-xref: RHEA:15441
-is_a: GO:0004152 ! dihydroorotate dehydrogenase activity
-is_a: GO:0016634 ! oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor
+is_obsolete: true
[Term]
id: GO:0004159
@@ -34633,7 +34611,8 @@ synonym: "geranyl-diphosphate synthase activity" RELATED [EC:2.5.1.1]
synonym: "trans-farnesyl pyrophosphate synthetase activity" RELATED [EC:2.5.1.1]
xref: EC:2.5.1.1
xref: MetaCyc:GPPSYN-RXN
-xref: Reactome:R-HSA-191322 "Addition of isopentenyl pyrophosphate to DMAPP"
+xref: Reactome:R-HSA-191322 "FDPS dimer transfers IPPP to DMAPP"
+xref: Reactome:R-HSA-9717834 "GGPS1 hexamer transfers IPPP to DMAPP"
xref: RHEA:22408
is_a: GO:0004659 ! prenyltransferase activity
@@ -34649,7 +34628,7 @@ is_a: GO:0032451 ! demethylase activity
id: GO:0004163
name: diphosphomevalonate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-5-diphosphomevalonate + ATP = ADP + CO(2) + H(+) + isopentenyl diphosphate + phosphate." [EC:4.1.1.33, RHEA:23732]
+def: "Catalysis of the reaction: (R)-5-diphosphomevalonate + ATP = ADP + CO2 + H+ + isopentenyl diphosphate + phosphate." [EC:4.1.1.33, RHEA:23732]
synonym: "5-pyrophosphomevalonate decarboxylase activity" RELATED [EC:4.1.1.33]
synonym: "ATP:(R)-5-diphosphomevalonate carboxy-lyase (adding ATP; isopentenyl-diphosphate-forming)" RELATED [EC:4.1.1.33]
synonym: "ATP:(R)-5-diphosphomevalonate carboxy-lyase (dehydrating)" RELATED [EC:4.1.1.33]
@@ -34682,25 +34661,26 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
[Term]
id: GO:0004165
-name: dodecenoyl-CoA delta-isomerase activity
+name: delta(3)-delta(2)-enoyl-CoA isomerase activity
namespace: molecular_function
alt_id: GO:0008461
-def: "Catalysis of the reaction: 3-cis-dodecenoyl-CoA = 2-trans-dodecenoyl-CoA." [EC:5.3.3.8]
+def: "Catalysis of the reactions: a (3Z)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA or a (3E)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA." [RHEA:45900]
synonym: "3,2-trans-enoyl-CoA isomerase activity" RELATED [EC:5.3.3.8]
synonym: "acetylene-allene isomerase activity" RELATED [EC:5.3.3.8]
-synonym: "delta(3),Delta(2)-enoyl-CoA isomerase activity" RELATED [EC:5.3.3.8]
-synonym: "delta(3)-cis-Delta(2)-trans-enoyl-CoA isomerase activity" RELATED [EC:5.3.3.8]
-synonym: "delta3,Delta2-enoyl-CoA isomerase activity" RELATED [EC:5.3.3.8]
-synonym: "delta3-cis-delta2-trans-enoyl-CoA isomerase" BROAD [EC:5.3.3.8]
-synonym: "dodecenoyl-CoA (3Z)-(2E)-isomerase activity" RELATED [EC:5.3.3.8]
-synonym: "dodecenoyl-CoA D-isomerase activity" EXACT []
-synonym: "dodecenoyl-CoA delta3-cis-delta2-trans-isomerase activity" RELATED [EC:5.3.3.8]
+synonym: "delta(3),delta(2)-enoyl-CoA isomerase activity" RELATED [EC:5.3.3.8]
+synonym: "delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase activity" RELATED [EC:5.3.3.8]
+synonym: "delta3,delta2-enoyl-CoA isomerase activity" RELATED [EC:5.3.3.8]
+synonym: "delta3-cis-delta2-trans-enoyl-CoA isomerase" EXACT [EC:5.3.3.8]
+synonym: "delta3-delta2 enoyl-CoA isomerase activity" EXACT []
+synonym: "dodecenoyl-CoA (3Z)-(2E)-isomerase activity" NARROW [EC:5.3.3.8]
+synonym: "dodecenoyl-CoA D-isomerase activity" NARROW []
+synonym: "dodecenoyl-CoA delta-isomerase activity" NARROW []
+synonym: "dodecenoyl-CoA delta3-cis-delta2-trans-isomerase activity" NARROW [EC:5.3.3.8]
synonym: "dodecenoyl-CoA isomerase activity" RELATED [EC:5.3.3.8]
xref: EC:5.3.3.8
-xref: MetaCyc:ENOYL-COA-DELTA-ISOM-RXN
xref: Reactome:R-HSA-109338 "Isomerization of cis,cis-3,6-Dodecadienoyl-CoA to form trans,cis-Lauro-2,6-dienoyl-CoA"
xref: Reactome:R-HSA-6809808 "ECI2 isomerizes 3Z-enoyl-CoA to 2E-enoyl-CoA"
-xref: RHEA:23716
+xref: RHEA:45900
is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds
[Term]
@@ -34793,7 +34773,7 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
id: GO:0004170
name: dUTP diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dUTP + H2O = dUMP + diphosphate." [RHEA:10248]
+def: "Catalysis of the reaction: dUTP + H2O = dUMP + H+ + diphosphate." [RHEA:10248]
subset: goslim_chembl
synonym: "deoxyuridine-triphosphatase activity" RELATED [EC:3.6.1.23]
synonym: "desoxyuridine 5'-triphosphatase activity" RELATED [EC:3.6.1.23]
@@ -34806,7 +34786,7 @@ xref: KEGG_REACTION:R02100
xref: MetaCyc:DUTP-PYROP-RXN
xref: Reactome:R-HSA-73666 "dUTP + H2O => dUMP + pyrophosphate"
xref: RHEA:10248
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0004171
@@ -34937,6 +34917,7 @@ xref: Reactome:R-HSA-8854044 "Proteasome degrades AURKA ubiquitinated by SCF-FBX
xref: Reactome:R-HSA-8854071 "Proteasome-mediated degradation of PolyUb-FBXL7"
xref: Reactome:R-HSA-8866553 "misfolded CFTR is degraded by the 26S proteasome"
xref: Reactome:R-HSA-8866858 "CFTR F508del is degraded by the 26S proteasome"
+xref: Reactome:R-HSA-8932355 "26S proteasome degrades Ub-NFE2L2"
xref: Reactome:R-HSA-8934819 "Cytoplasmic proteases cleave Profilaggrin producing Filaggrin"
xref: Reactome:R-HSA-8939801 "26S proteasome degrades PolyUb-RUNX2"
xref: Reactome:R-HSA-8952408 "Polyubiquitinated RUNX3 is degraded by the proteasome"
@@ -34948,6 +34929,9 @@ xref: Reactome:R-HSA-9010096 "Gamma-secretase cleaves APP(672-770) to APP(672-71
xref: Reactome:R-HSA-9011313 "Proteasome degrades ubiquitinated ROBO3.1"
xref: Reactome:R-HSA-9604642 "Proteasome degrades ubiquitinated NICD4"
xref: Reactome:R-HSA-9614271 "Autocleavage of ADGRG6"
+xref: Reactome:R-HSA-9755303 "26S proteasome degrades HIFalpha"
+xref: Reactome:R-HSA-9755306 "ub UBXN7 is degraded by the 26S proteasome"
+xref: Reactome:R-HSA-9762096 "Ub,pS335,S338,T NFE2L2 is degraded"
xref: Reactome:R-HSA-983150 "Proteasomal cleavage of substrate"
xref: Reactome:R-HSA-983158 "Trimming of peptides in ER"
is_a: GO:0008233 ! peptidase activity
@@ -35034,6 +35018,7 @@ name: carboxypeptidase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of a single C-terminal amino acid residue from a polypeptide chain." [https://www.ebi.ac.uk/merops/about/glossary.shtml#CARBOXYPEPTIDASE]
xref: Reactome:R-HSA-1247910 "CNDP2:2Mn2+ dimer hydrolyses CysGly"
+xref: Reactome:R-HSA-9753632 "CNDP2:2Mn2+ dimer hydrolyses APAP-CysGly"
xref: RHEA:28783
is_a: GO:0008238 ! exopeptidase activity
@@ -35049,7 +35034,7 @@ xref: Reactome:R-HSA-2028294 "Mast Cell Carboxypeptidase hydrolyzes Angiotensin-
xref: Reactome:R-HSA-8852809 "CPN, CPB2 cleave C3a, C5a"
xref: Reactome:R-HSA-8866105 "CCPs deglutamylate tubulin"
xref: Reactome:R-HSA-8955712 "SVBP:VASH1,VASH2 hydrolyzes the terminal L-Tyr residue from alphaY-beta tubulin dimer"
-xref: Reactome:R-HSA-9023159 "Carboxypeptidase E cleaves C-peptide (Insulin(57-89)) to yield C-peptide (Insulin(57-87))"
+xref: Reactome:R-HSA-9023159 "Carboxypeptidase E hydrolyzes Insulin(57-89) to yield C-peptide (Insulin(57-87))"
xref: Reactome:R-HSA-9023163 "Carboxypeptidase E cleaves Insulin(25-56) to yield Insulin(25-54)"
is_a: GO:0004180 ! carboxypeptidase activity
is_a: GO:0008235 ! metalloexopeptidase activity
@@ -35397,6 +35382,8 @@ xref: Reactome:R-HSA-9012556 "IL37:2x(CASP1(120-197):CASP1(317-404)) cleaves IL3
xref: Reactome:R-HSA-9013895 "Caspase-8 processing within TLR3 complex"
xref: Reactome:R-HSA-933532 "Processing of caspases"
xref: Reactome:R-HSA-9603534 "Unknown caspase cleaves NTRK3"
+xref: Reactome:R-HSA-9647632 "CASP3 cleaves GSDME"
+xref: Reactome:R-HSA-9647680 "CASP1 cleaves GSDMD"
xref: Reactome:R-HSA-9647999 "RCE1 cleaves S-Farn proRAS proteins"
xref: Reactome:R-HSA-9684273 "3CLp cleaves pp1a"
xref: Reactome:R-HSA-9684309 "3CLp cleaves nsp6-11"
@@ -35405,6 +35392,7 @@ xref: Reactome:R-HSA-9684336 "nsp1-4 cleaves itself"
xref: Reactome:R-HSA-9684340 "3CLp cleaves pp1ab"
xref: Reactome:R-HSA-9684351 "pp1a cleaves itself"
xref: Reactome:R-HSA-9684352 "nsp3-4 cleaves itself"
+xref: Reactome:R-HSA-9686088 "CASP3 cleaves GSDMD"
xref: Reactome:R-HSA-9686930 "RIPK3 is cleaved by CASP8"
xref: Reactome:R-HSA-9693929 "RIPK1 variant is not cleaved by CASP8"
xref: Reactome:R-HSA-9694338 "nsp1-4 cleaves itself"
@@ -35415,6 +35403,10 @@ xref: Reactome:R-HSA-9694601 "nsp3-4 cleaves itself"
xref: Reactome:R-HSA-9694625 "nsp3 cleaves nsp1-4"
xref: Reactome:R-HSA-9694732 "3CLp cleaves pp1ab"
xref: Reactome:R-HSA-9697750 "RIPK1 is cleaved by CASP8:FLIP(L)"
+xref: Reactome:R-HSA-9710101 "CASP4, CASP5 cleave GSDMD"
+xref: Reactome:R-HSA-9729704 "SARS-CoV-2 3CLpro dimer cleaves TAB1"
+xref: Reactome:R-HSA-9729730 "SARS-CoV-2 nsp3 cleaves IRF3"
+xref: Reactome:R-HSA-9729741 "SARS-CoV-2 3CLpro dimer cleaves NLRP12"
is_a: GO:0004175 ! endopeptidase activity
is_a: GO:0008234 ! cysteine-type peptidase activity
@@ -35748,7 +35740,7 @@ xref: Reactome:R-HSA-2534240 "HSPG2 (perlecan) degradation by MMP14, MMP15"
xref: Reactome:R-HSA-2534248 "DCN (decorin) degradation by MMP2, MMP3, MMP7"
xref: Reactome:R-HSA-2537499 "Gelatin degradation by MMP19"
xref: Reactome:R-HSA-264758 "BMP1-3:Zn2+ cleaves pro-APOA1 to APOA1"
-xref: Reactome:R-HSA-3371385 "TNF-alpha is cleaved by ADAM17 (TACE)"
+xref: Reactome:R-HSA-3371385 "TNF- is cleaved by ADAM17 (TACE)"
xref: Reactome:R-HSA-3788075 "Brevican degradation by ADAMTS4, ADAMTS5"
xref: Reactome:R-HSA-3791149 "Brevican degradation by MMP1, 2, 3, 7,8,10,13,19"
xref: Reactome:R-HSA-3791155 "Laminin-322 degradation by MMP14"
@@ -35989,21 +35981,17 @@ replaced_by: GO:0004222
[Term]
id: GO:0004239
-name: obsolete methionyl aminopeptidase activity
+name: initiator methionyl aminopeptidase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the release of N-terminal amino acids, preferentially methionine, from peptides and arylamides." [EC:3.4.11.18]
-comment: This term was made obsolete because it represents a gene product.
+def: "Catalysis of the release of N-terminal initiator methionine from peptides." [EC:3.4.11.18]
+comment: This term was reinstated from obsolete
synonym: "L-methionine aminopeptidase activity" RELATED [EC:3.4.11.18]
synonym: "MAP" RELATED [EC:3.4.11.18]
synonym: "methionine aminopeptidase activity" RELATED [EC:3.4.11.18]
-synonym: "methionyl aminopeptidase activity" EXACT []
synonym: "peptidase M activity" RELATED [EC:3.4.11.18]
xref: EC:3.4.11.18
xref: MetaCyc:3.4.11.18-RXN
-is_obsolete: true
-consider: GO:0004177
-consider: GO:0008235
-consider: GO:0070084
+is_a: GO:0004177 ! aminopeptidase activity
[Term]
id: GO:0004240
@@ -36221,7 +36209,7 @@ subset: goslim_chembl
synonym: "blood coagulation factor activity" RELATED []
synonym: "serine elastase activity" RELATED [GOC:krc]
xref: EC:3.4.21.-
-xref: Reactome:R-HSA-114697 "Thrombin-mediated activation of Proteinase-activated receptors"
+xref: Reactome:R-HSA-114697 "Activated thrombin (factor IIa) cleaves PAR3,4, activating them"
xref: Reactome:R-HSA-1181152 "Cleavage of NODAL proprotein"
xref: Reactome:R-HSA-139893 "Granzyme-B activates BID by cleavage"
xref: Reactome:R-HSA-140599 "factor XIII -> factor XIII cleaved tetramer + 2 factor XIII A activation peptides"
@@ -36292,7 +36280,7 @@ xref: Reactome:R-HSA-1655842 "S1P hydrolyzes SREBP1A,1C,2"
xref: Reactome:R-HSA-166753 "Conversion of C4 into C4a and C4b"
xref: Reactome:R-HSA-166792 "Conversion of C2 into C2a and C2b"
xref: Reactome:R-HSA-166817 "Cleavage of C3 by C3 convertases"
-xref: Reactome:R-HSA-170844 "Latent TGF-beta-1 is cleaved by furin"
+xref: Reactome:R-HSA-170844 "Latent TGF-beta-1 is cleaved by FURIN"
xref: Reactome:R-HSA-171288 "Cleavage of the viral Env gp160 precursor polyprotein"
xref: Reactome:R-HSA-173626 "Activation of C1r"
xref: Reactome:R-HSA-173631 "Activation of C1s"
@@ -36386,8 +36374,14 @@ xref: Reactome:R-HSA-9686710 "Cleavage of S protein into S1:S2"
xref: Reactome:R-HSA-9686731 "TMPRSS2 Mediated SARS-CoV-1 Spike Protein Cleavage and Endocytosis"
xref: Reactome:R-HSA-9694287 "Cleavage of S protein into S1:S2"
xref: Reactome:R-HSA-9694661 "TMPRSS2 Mediated SARS-CoV-2 Spike Protein Cleavage and Endocytosis"
+xref: Reactome:R-HSA-9698988 "Direct Host Cell Membrane Membrane Fusion and Release of SARS-CoV-2 Nucleocapsid"
xref: Reactome:R-HSA-9699007 "FURIN Mediated SARS-CoV-2 Spike Protein Cleavage and Endocytosis"
+xref: Reactome:R-HSA-9708859 "Activated thrombin (factor IIa) cleaves F2R (PAR1), activating it"
+xref: Reactome:R-HSA-9710106 "ELANE cleaves GSDMD"
+xref: Reactome:R-HSA-9710263 "GZMB cleaves GSDME"
xref: Reactome:R-HSA-976743 "Factor I inactivates plasma Factor H-bound C3b"
+xref: Reactome:R-HSA-9769949 "FURIN Mediated SARS-CoV-2 Spike Protein Cleavage"
+xref: Reactome:R-HSA-9770187 "S2 Cleavage by TMPRSS2 Exposes S2' Initiating Cell-Cell Fusion"
xref: Reactome:R-HSA-977371 "Factor I inactivates Factor H-boundC3b"
xref: Reactome:R-HSA-977615 "Factor I inactivates MCP/CR1-bound C4b/C3b"
is_a: GO:0004175 ! endopeptidase activity
@@ -36857,25 +36851,18 @@ id: GO:0004300
name: enoyl-CoA hydratase activity
namespace: molecular_function
alt_id: GO:0016510
-def: "Catalysis of the reaction: (3S)-3-hydroxyacyl-CoA = trans-2-enoyl-CoA + H2O." [EC:4.2.1.17]
-synonym: "(3S)-3-hydroxyacyl-CoA hydro-lyase activity" RELATED [EC:4.2.1.17]
-synonym: "2-enoyl-CoA hydratase activity" RELATED [EC:4.2.1.17]
-synonym: "2-octenoyl coenzyme A hydrase activity" RELATED [EC:4.2.1.17]
-synonym: "acyl coenzyme A hydrase activity" RELATED [EC:4.2.1.17]
-synonym: "beta-hydroxyacid dehydrase activity" RELATED [EC:4.2.1.17]
-synonym: "beta-hydroxyacyl-CoA dehydrase activity" RELATED [EC:4.2.1.17]
-synonym: "crotonyl hydrase activity" RELATED [EC:4.2.1.17]
-synonym: "D-3-hydroxyacyl-CoA dehydratase" BROAD [EC:4.2.1.17]
-synonym: "ECH" RELATED [EC:4.2.1.17]
+def: "Catalysis of the reaction: a 3-hydroxy-fatty acyl-CoA = a enoyl-CoA + H2O. This reaction usually occurs in the reverse direction, leading to the reduction of the double bound of enoyl-CoA in position 2 or 3. Specific reactions catalyzed include: a 4-saturated-(3S)-3-hydroxyacyl-CoA = a (3E)-enoyl-CoA + H2O and a (3S)-3-hydroxyacyl-CoA = a (2E)-enoyl-CoA + H2O." [EC:4.2.1.17]
+synonym: "(3S)-3-hydroxyacyl-CoA hydro-lyase activity" RELATED []
+synonym: "2-enoyl-CoA hydratase activity" RELATED []
+synonym: "2-octenoyl coenzyme A hydrase activity" RELATED []
+synonym: "3-hydroxy-fatty acyl-CoA dehydratase" EXACT []
+synonym: "3-hydroxyacyl-CoA dehydratase" EXACT []
+synonym: "acyl coenzyme A hydrase activity" RELATED []
+synonym: "beta-hydroxyacid dehydrase activity" RELATED []
+synonym: "beta-hydroxyacyl-CoA dehydrase activity" RELATED []
synonym: "enol-CoA hydratase activity" RELATED [EC:4.2.1.17]
-synonym: "enoyl coenzyme A hydrase (D)" BROAD [EC:4.2.1.17]
-synonym: "enoyl coenzyme A hydrase (L)" RELATED [EC:4.2.1.17]
-synonym: "enoyl coenzyme A hydratase activity" RELATED [EC:4.2.1.17]
synonym: "enoyl hydrase activity" RELATED [EC:4.2.1.17]
-synonym: "hydratase, enoyl coenzyme A" RELATED [EC:4.2.1.17]
-synonym: "short chain enoyl coenzyme A hydratase activity" RELATED [EC:4.2.1.17]
synonym: "short-chain enoyl-CoA hydratase activity" EXACT []
-synonym: "trans-2-enoyl-CoA hydratase activity" RELATED [EC:4.2.1.17]
synonym: "unsaturated acyl-CoA hydratase activity" RELATED [EC:4.2.1.17]
xref: EC:4.2.1.17
xref: MetaCyc:ENOYL-COA-HYDRAT-RXN
@@ -36888,7 +36875,6 @@ xref: Reactome:R-HSA-77314 "Crotonoyl-CoA+H2O<=>(S)-3-Hydroxybutanoyl-CoA"
xref: Reactome:R-HSA-77325 "trans-Hex-2-enoyl-CoA+H2O<=>(S)-Hydroxyhexanoyl-CoA"
xref: Reactome:R-HSA-77333 "trans-Oct-2-enoyl-CoA+H2O<=>(S)-Hydroxyoctanoyl-CoA"
xref: Reactome:R-HSA-77344 "trans-Dec-2-enoyl-CoA+H2O<=>(S)-Hydroxydecanoyl-CoA"
-xref: RHEA:16105
xref: UM-BBD_enzymeID:e0014
is_a: GO:0016836 ! hydro-lyase activity
@@ -36928,9 +36914,9 @@ is_a: GO:0016803 ! ether hydrolase activity
[Term]
id: GO:0004303
-name: estradiol 17-beta-dehydrogenase activity
+name: estradiol 17-beta-dehydrogenase [NAD(P)] activity
namespace: molecular_function
-def: "Catalysis of the reaction: estradiol-17-beta + NADP+ = estrone + NADPH + H+." [EC:1.1.1.62]
+def: "Catalysis of the reaction: estradiol-17-beta + NAD(P)+ = estrone + NAD(P)H + H+. The activity can use NAD+ or NADP+ as the acceptor." [EC:1.1.1.62]
synonym: "17-beta-estradiol dehydrogenase activity" RELATED [EC:1.1.1.62]
synonym: "17-beta-HSD activity" BROAD [EC:1.1.1.62]
synonym: "17-beta-hydroxysteroid dehydrogenase activity" BROAD [EC:1.1.1.62]
@@ -36939,10 +36925,12 @@ synonym: "17beta-estradiol dehydrogenase activity" RELATED [EC:1.1.1.62]
synonym: "17beta-HSD" RELATED [EC:1.1.1.62]
synonym: "17beta-hydroxysteroid dehydrogenase activity" RELATED [EC:1.1.1.62]
synonym: "20alpha-hydroxysteroid dehydrogenase" BROAD [EC:1.1.1.62]
+synonym: "estradiol 17-beta-dehydrogenase activity" RELATED []
synonym: "estradiol 17beta-dehydrogenase activity" RELATED [EC:1.1.1.62]
synonym: "estradiol dehydrogenase activity" RELATED [EC:1.1.1.62]
synonym: "estradiol-17beta:NAD(P)+ 17-oxidoreductase activity" RELATED [EC:1.1.1.62]
synonym: "estrogen 17-oxidoreductase activity" RELATED [EC:1.1.1.62]
+synonym: "https://github.com/geneontology/go-ontology/issues/21791" RELATED []
xref: EC:1.1.1.62
xref: MetaCyc:ESTRADIOL-17-BETA-DEHYDROGENASE-RXN
xref: Reactome:R-HSA-5693390 "HSD17B11 dehydrogenates EST17b to E1"
@@ -36974,7 +36962,7 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0004305
name: ethanolamine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + ethanolamine = ADP + 2 H(+) + phosphoethanolamine." [EC:2.7.1.82, RHEA:13069]
+def: "Catalysis of the reaction: ATP + ethanolamine = ADP + 2 H+ + phosphoethanolamine." [EC:2.7.1.82, RHEA:13069]
synonym: "ATP:ethanolamine O-phosphotransferase activity" RELATED [EC:2.7.1.82]
synonym: "ethanolamine kinase (phosphorylating)" RELATED [EC:2.7.1.82]
synonym: "ethanolamine phosphokinase activity" RELATED [EC:2.7.1.82]
@@ -37079,7 +37067,7 @@ id: GO:0004311
name: farnesyltranstransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate." [EC:2.5.1.29, RHEA:17653]
-comment: The catalyzed reaction forms (free) geranylgeranyl diphosphate. There is no relationship between this activity and protein farnesyltransferase activity, GO:0004660, where the catalyzed reaction transfers a farnesyl group from farnesyl diphosphate to a target protein.
+comment: The catalyzed reaction forms (free) geranylgeranyl diphosphate. There is no relationship between this activity and protein farnesyltransferase activity, GO:0004660, where the catalyzed reaction transfers a farnesyl group from farnesyl diphosphate to a target protein.
synonym: "farnesyltransferase activity" BROAD [EC:2.5.1.29]
synonym: "geranylgeranyl pyrophosphate synthase activity" RELATED [EC:2.5.1.29]
synonym: "geranylgeranyl pyrophosphate synthetase activity" RELATED [EC:2.5.1.29]
@@ -37219,26 +37207,21 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
[Term]
id: GO:0004317
-name: 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity
+name: (3R)-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (3R)-3-hydroxypalmitoyl-[acyl-carrier protein] = 2-hexadecenoyl-[acyl-carrier protein] + H2O." [PMID:8088535, RHEA:41908]
-synonym: "(3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] hydro-lyase activity" RELATED [EC:4.2.1.59]
+def: "Catalysis of the reaction: (3R)-hydroxypalmitoyl-[acyl-carrier protein] = 2-hexadecenoyl-[acyl-carrier protein] + H2O." [PMID:8088535, RHEA:41908]
+synonym: "(3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] hydro-lyase activity" RELATED []
synonym: "(3R)-3-hydroxypalmitoyl-acyl-carrier-protein hydro-lyase (hexadec-2-enoyl-acyl-carrier protein-forming)" EXACT []
synonym: "(3R)-3-hydroxypalmitoyl-acyl-carrier-protein hydro-lyase activity" EXACT []
synonym: "3-hydroxypalmitoyl-[acyl-carrier protein] dehydratase activity" EXACT []
+synonym: "3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity" RELATED []
synonym: "3-hydroxypalmitoyl-ACP dehydratase activity" EXACT []
synonym: "3-hydroxypalmitoyl-acyl-carrier-protein dehydratase activity" EXACT []
-synonym: "beta-hydroxypalmitoyl thioester dehydratase activity" RELATED [EC:4.2.1.59]
-synonym: "beta-hydroxypalmitoyl-acyl carrier protein dehydrase activity" RELATED [EC:4.2.1.59]
-synonym: "beta-hydroxypalmityl-ACP dehydrase activity" RELATED [EC:4.2.1.59]
-synonym: "D-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity" RELATED [EC:4.2.1.59]
-synonym: "D-3-hydroxypalmitoyl-acyl-carrier-protein dehydratase activity" RELATED [EC:4.2.1.59]
-xref: EC:4.2.1.59
xref: KEGG_REACTION:R04462
xref: MetaCyc:4.2.1.61-RXN
xref: RHEA:41908
is_a: GO:0004312 ! fatty acid synthase activity
-is_a: GO:0019171 ! 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity
+is_a: GO:0019171 ! (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity
[Term]
id: GO:0004318
@@ -37368,15 +37351,15 @@ is_a: GO:0008937 ! ferredoxin-NAD(P) reductase activity
id: GO:0004325
name: ferrochelatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: protoheme = Fe(2+) + protoporphyrin IX." [EC:4.99.1.1, RHEA:22584]
-synonym: "ferro-protoporphyrin chelatase activity" RELATED [EC:4.99.1.1]
-synonym: "heme synthase activity" RELATED [EC:4.99.1.1]
-synonym: "heme synthetase activity" RELATED [EC:4.99.1.1]
-synonym: "iron chelatase activity" RELATED [EC:4.99.1.1]
-synonym: "protoheme ferro-lyase (protoporphyrin-forming)" RELATED [EC:4.99.1.1]
-synonym: "protoheme ferro-lyase activity" RELATED [EC:4.99.1.1]
-synonym: "protoheme ferrolyase activity" RELATED [EC:4.99.1.1]
-xref: EC:4.99.1.1
+def: "Catalysis of the reaction: heme B (protoheme) + H+ = Fe(2+) + protoporphyrin IX." [RHEA:22584]
+synonym: "ferro-protoporphyrin chelatase activity" EXACT []
+synonym: "heme synthase activity" BROAD []
+synonym: "heme synthetase activity" BROAD [EC:4.98.1.1]
+synonym: "iron chelatase activity" BROAD [EC:4.98.1.1]
+synonym: "protoheme ferro-lyase (protoporphyrin-forming)" EXACT []
+synonym: "protoheme ferro-lyase activity" EXACT [EC:4.98.1.1]
+synonym: "protoheme ferrolyase activity" EXACT []
+xref: EC:4.98.1.1
xref: KEGG_REACTION:R00310
xref: MetaCyc:PROTOHEMEFERROCHELAT-RXN
xref: Reactome:R-HSA-189465 "FECH binds Fe2+ to PRIN9 to form heme"
@@ -37405,9 +37388,9 @@ synonym: "tetrahydrofolyl-[gamma-Glu]n:L-glutamate gamma-ligase (ADP-forming)" R
synonym: "tetrahydropteroyl-[gamma-polyglutamate]:L-glutamate gamma-ligase (ADP-forming)" RELATED [EC:6.3.2.17]
xref: EC:6.3.2.17
xref: MetaCyc:FOLYLPOLYGLUTAMATESYNTH-RXN
-xref: Reactome:R-HSA-197958 "Conversion of cytosolic THF to THF-polyglutamate"
-xref: Reactome:R-HSA-200681 "Conversion of cytosolic 5-methyltetrahydrofolate (5-methylTHF) to 5-methylTHF-polyglutamate"
-xref: Reactome:R-HSA-200682 "Conversion of mitochondrial THF to THF-polyglutamate"
+xref: Reactome:R-HSA-197958 "FPGS-2 transforms THF to THFPG"
+xref: Reactome:R-HSA-200681 "FPGS-2 transforms 5-methyl-THF to 5-methyl-THFPG"
+xref: Reactome:R-HSA-200682 "Mitochondrial FPGS-1 transforms THF to THFPG"
xref: RHEA:10580
is_a: GO:0016881 ! acid-amino acid ligase activity
@@ -37427,7 +37410,7 @@ id: GO:0004328
name: formamidase activity
namespace: molecular_function
alt_id: GO:0034566
-def: "Catalysis of the reaction: formamide + H(2)O = formate + NH(4)(+)." [EC:3.5.1.49, RHEA:21948]
+def: "Catalysis of the reaction: formamide + H2O = formate + NH4." [EC:3.5.1.49, RHEA:21948]
synonym: "formamide amidohydrolase activity" RELATED [EC:3.5.1.49]
synonym: "formamide hydrolase activity" EXACT []
xref: EC:3.5.1.49
@@ -37450,8 +37433,8 @@ synonym: "tetrahydrofolate formylase activity" RELATED [EC:6.3.4.3]
synonym: "tetrahydrofolic formylase activity" RELATED [EC:6.3.4.3]
xref: EC:6.3.4.3
xref: MetaCyc:FORMATETHFLIG-RXN
-xref: Reactome:R-HSA-200711 "THF polyglutamate + formate + ATP => 10-formylTHF polyglutamate + ADP + orthophosphate"
-xref: Reactome:R-HSA-5696839 "MTHFD1L ligates HCOOH to THF to form 10-formyl-THF"
+xref: Reactome:R-HSA-200711 "MTHFD1 dimer ligates HCOOH to THFPG to form 10-formyl-THFPG"
+xref: Reactome:R-HSA-5696839 "MTHFD1L dimer ligates HCOOH to THF to form 10-formyl-THF"
xref: Reactome:R-HSA-6801456 "MTHFD1L transforms 10-formyl-THF to HCOOH and THF"
xref: RHEA:20221
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
@@ -37494,7 +37477,7 @@ synonym: "SMALDO" RELATED [EC:4.1.2.13]
synonym: "zymohexase activity" RELATED [EC:4.1.2.13]
xref: EC:4.1.2.13
xref: MetaCyc:F16ALDOLASE-RXN
-xref: Reactome:R-HSA-71495 "dihydroxyacetone phosphate + D-glyceraldehyde 3-phosphate <=> D-fructose 1,6-bisphosphate"
+xref: Reactome:R-HSA-71495 "Aldolase tetramers convert GA3P and DHAP to F1,6PP"
xref: Reactome:R-HSA-71496 "D-fructose 1,6-bisphosphate <=> dihydroxyacetone phosphate + D-glyceraldehyde 3-phosphate"
xref: RHEA:14729
is_a: GO:0016832 ! aldehyde-lyase activity
@@ -37503,7 +37486,7 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0004333
name: fumarate hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-malate = fumarate + H(2)O." [EC:4.2.1.2, RHEA:12460]
+def: "Catalysis of the reaction: (S)-malate = fumarate + H2O." [EC:4.2.1.2, RHEA:12460]
synonym: "(S)-malate hydro-lyase (fumarate-forming)" RELATED [EC:4.2.1.2]
synonym: "(S)-malate hydro-lyase activity" RELATED [EC:4.2.1.2]
synonym: "fumarase activity" RELATED [EC:4.2.1.2]
@@ -37520,7 +37503,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0004334
name: fumarylacetoacetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-fumarylacetoacetate + H(2)O = acetoacetate + fumarate + H(+)." [EC:3.7.1.2, RHEA:10244]
+def: "Catalysis of the reaction: 4-fumarylacetoacetate + H2O = acetoacetate + fumarate + H+." [EC:3.7.1.2, RHEA:10244]
synonym: "4-fumarylacetoacetate fumarylhydrolase activity" RELATED [EC:3.7.1.2]
synonym: "beta-diketonase activity" RELATED [EC:3.7.1.2]
synonym: "fumarylacetoacetate hydrolase activity" RELATED [EC:3.7.1.2]
@@ -37536,7 +37519,7 @@ is_a: GO:0016823 ! hydrolase activity, acting on acid carbon-carbon bonds, in ke
id: GO:0004335
name: galactokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-galactose + ATP = alpha-D-galactose 1-phosphate + ADP + 2 H(+)." [EC:2.7.1.6, RHEA:13553]
+def: "Catalysis of the reaction: D-galactose + ATP = alpha-D-galactose 1-phosphate + ADP + 2 H+." [EC:2.7.1.6, RHEA:13553]
synonym: "ATP:D-galactose 1-phosphotransferase activity" RELATED [EC:2.7.1.6]
synonym: "ATP:D-galactose-1-phosphotransferase activity" RELATED [EC:2.7.1.6]
synonym: "galactokinase (phosphorylating)" RELATED [EC:2.7.1.6]
@@ -37593,8 +37576,9 @@ synonym: "geranyltransferase activity" RELATED [EC:2.5.1.10]
xref: EC:2.5.1.10
xref: KEGG_REACTION:R02003
xref: MetaCyc:FPPSYN-RXN
-xref: Reactome:R-HSA-191303 "Another isopentenyl pyrophosphate is added to geranyl pyrophosphate"
+xref: Reactome:R-HSA-191303 "FDPS dimer transfers IPPP to GPP"
xref: Reactome:R-HSA-8870469 "RGGT geranylgeranylates RAB proteins"
+xref: Reactome:R-HSA-9717830 "GGPS1 hexamer transfers IPPP to GPP"
xref: RHEA:19361
is_a: GO:0004659 ! prenyltransferase activity
@@ -37671,7 +37655,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0004342
name: glucosamine-6-phosphate deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glucosamine 6-phosphate + H(2)O = beta-D-fructose 6-phosphate + NH(4)(+)." [EC:3.5.99.6, RHEA:12172]
+def: "Catalysis of the reaction: D-glucosamine 6-phosphate + H2O = beta-D-fructose 6-phosphate + NH4." [EC:3.5.99.6, RHEA:12172]
comment: Note that this function was formerly EC:5.3.1.10.
synonym: "2-amino-2-deoxy-D-glucose-6-phosphate aminohydrolase (ketol isomerizing)" RELATED [EC:3.5.99.6]
synonym: "aminodeoxyglucosephosphate isomerase activity" RELATED [EC:3.5.99.6]
@@ -37686,14 +37670,13 @@ xref: KEGG_REACTION:R00765
xref: MetaCyc:GLUCOSAMINE-6-P-DEAMIN-RXN
xref: Reactome:R-HSA-6799604 "GNPDA1,2 hexamers deaminate GlcN6P to Fru(6)P"
xref: RHEA:12172
-is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldoses and ketoses
is_a: GO:0019239 ! deaminase activity
[Term]
id: GO:0004343
name: glucosamine 6-phosphate N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glucosamine 6-phosphate + acetyl-CoA = N-acetyl-D-glucosamine 6-phosphate + CoA + H(+)." [EC:2.3.1.4, RHEA:10292]
+def: "Catalysis of the reaction: D-glucosamine 6-phosphate + acetyl-CoA = N-acetyl-D-glucosamine 6-phosphate + CoA + H+." [EC:2.3.1.4, RHEA:10292]
synonym: "acetyl-CoA:D-glucosamine-6-phosphate N-acetyltransferase activity" RELATED [EC:2.3.1.4]
synonym: "aminodeoxyglucosephosphate acetyltransferase activity" RELATED [EC:2.3.1.4]
synonym: "D-glucosamine-6-P N-acetyltransferase activity" RELATED [EC:2.3.1.4]
@@ -37717,14 +37700,9 @@ name: glucose dehydrogenase activity
namespace: molecular_function
alt_id: GO:0008708
def: "Catalysis of the reaction: D-glucose + acceptor = D-glucono-1,5-lactone + reduced acceptor." [PMID:22027299]
-synonym: "D-glucose:(acceptor) 1-oxidoreductase" RELATED [EC:1.1.99.10]
-synonym: "D-glucose:acceptor 1-oxidoreductase" RELATED [EC:1.1.5.2]
synonym: "glucose dehydrogenase (acceptor) activity" EXACT []
-synonym: "glucose dehydrogenase (Aspergillus) activity" NARROW [EC:1.1.99.10]
-synonym: "glucose dehydrogenase (decarboxylating)" RELATED [EC:1.1.99.10]
-xref: EC:1.1.99.10
-xref: KEGG_REACTION:R00305
-xref: MetaCyc:GLUCOSE-DEHYDROGENASE-ACCEPTOR-RXN
+synonym: "soluble glucose dehydrogenase" EXACT [EC:1.1.99.35]
+xref: EC:1.1.99.35
xref: RHEA:24540
is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
@@ -37762,11 +37740,11 @@ synonym: "glucose 6-phosphate phosphatase activity" RELATED [EC:3.1.3.9]
xref: EC:3.1.3.9
xref: KEGG_REACTION:R00303
xref: MetaCyc:GLUCOSE-6-PHOSPHATASE-RXN
-xref: Reactome:R-HSA-3262512 "G6PC3 hydrolyzes glucose 6-phosphate to form glucose and orthophosphate (ubiquitous)"
-xref: Reactome:R-HSA-3266566 "G6PC2 hydrolyzes glucose 6-phosphate to form glucose and orthophosphate (islet)"
+xref: Reactome:R-HSA-3262512 "G6PC3 hydrolyzes G6P to form Glc and Pi (ubiquitous)"
+xref: Reactome:R-HSA-3266566 "G6PC2 hydrolyzes G6P to form Glc and Pi (islet)"
xref: Reactome:R-HSA-3274540 "Defective G6PC does not hydrolyze glucose 6-phosphate"
xref: Reactome:R-HSA-3282876 "Defective G6PC3 does not hydrolyze glucose 6-phosphate"
-xref: Reactome:R-HSA-71825 "G6PC hydrolyzes glucose 6-phosphate to form glucose and orthophosphate (liver)"
+xref: Reactome:R-HSA-71825 "G6PC hydrolyzes G6P to Glc and Pi (liver)"
xref: RHEA:16689
is_a: GO:0050309 ! sugar-terminal-phosphatase activity
@@ -37791,7 +37769,7 @@ synonym: "phosphosaccharomutase activity" BROAD [EC:5.3.1.9]
xref: EC:5.3.1.9
xref: MetaCyc:PGLUCISOM-RXN
xref: Reactome:R-HSA-70471 "alpha-D-glucose 6-phosphate <=> D-fructose 6-phosphate"
-xref: Reactome:R-HSA-70475 "D-fructose 6-phosphate <=> alpha-D-Glucose 6-phosphate"
+xref: Reactome:R-HSA-70475 "GPI dimer isomerizes Fru(6)P to G6P"
xref: RHEA:11816
is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldoses and ketoses
@@ -37825,7 +37803,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0004349
name: glutamate 5-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-glutamate + ATP = L-glutamyl 5-phosphate + ADP + H(+)." [EC:2.7.2.11, RHEA:14877]
+def: "Catalysis of the reaction: L-glutamate + ATP = L-glutamyl 5-phosphate + ADP + H+." [EC:2.7.2.11, RHEA:14877]
synonym: "ATP-L-glutamate 5-phosphotransferase activity" RELATED [EC:2.7.2.11]
synonym: "ATP:gamma-L-glutamate phosphotransferase activity" RELATED [EC:2.7.2.11]
synonym: "ATP:L-glutamate 5-phosphotransferase activity" RELATED [EC:2.7.2.11]
@@ -37844,7 +37822,7 @@ id: GO:0004350
name: glutamate-5-semialdehyde dehydrogenase activity
namespace: molecular_function
alt_id: GO:0001513
-def: "Catalysis of the reaction: L-glutamate 5-semialdehyde + NADP(+) + phosphate = L-glutamyl 5-phosphate + H(+) + NADPH." [EC:1.2.1.41, RHEA:19541]
+def: "Catalysis of the reaction: L-glutamate 5-semialdehyde + NADP+ + phosphate = L-glutamyl 5-phosphate + H+ + NADPH." [EC:1.2.1.41, RHEA:19541]
synonym: "beta-glutamylphosphate reductase activity" RELATED [EC:1.2.1.41]
synonym: "gamma-glutamyl phosphate reductase activity" RELATED [EC:1.2.1.41]
synonym: "gamma-glutamylphosphate reductase activity" RELATED [EC:1.2.1.41]
@@ -37947,7 +37925,7 @@ is_a: GO:0004353 ! glutamate dehydrogenase [NAD(P)+] activity
id: GO:0004355
name: glutamate synthase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 L-glutamate + NADP(+) = 2-oxoglutarate + L-glutamine + H(+) + NADPH. This is a two-step reaction: (a) L-glutamate + NH3 = L-glutamine + H2O, (b) L-glutamate + NADP+ + H2O = NH3 + 2-oxoglutarate + NADPH + H+." [EC:1.4.1.13, RHEA:15501]
+def: "Catalysis of the reaction: 2 L-glutamate + NADP+ = 2-oxoglutarate + L-glutamine + H+ + NADPH. This is a two-step reaction: (a) L-glutamate + NH3 = L-glutamine + H2O, (b) L-glutamate + NADP+ + H2O = NH3 + 2-oxoglutarate + NADPH + H+." [EC:1.4.1.13, RHEA:15501]
comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "glutamate (reduced nicotinamide adenine dinucleotide phosphate) synthase activity" RELATED [EC:1.4.1.13]
synonym: "glutamate synthetase (NADP) activity" RELATED [EC:1.4.1.13]
@@ -37974,7 +37952,7 @@ is_a: GO:0045181 ! glutamate synthase activity, NAD(P)H as acceptor
id: GO:0004356
name: glutamate-ammonia ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-glutamate + ATP + NH(3) = L-glutamine + ADP + 2 H(+) + phosphate." [EC:6.3.1.2, RHEA:16169]
+def: "Catalysis of the reaction: L-glutamate + ATP + NH3 = L-glutamine + ADP + 2 H+ + phosphate." [EC:6.3.1.2, RHEA:16169]
synonym: "glutamine synthetase activity" EXACT []
synonym: "glutamylhydroxamic synthetase activity" RELATED [EC:6.3.1.2]
synonym: "L-glutamate:ammonia ligase (ADP-forming)" RELATED [EC:6.3.1.2]
@@ -37990,7 +37968,7 @@ is_a: GO:0016211 ! ammonia ligase activity
id: GO:0004357
name: glutamate-cysteine ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-cysteine + L-glutamate + ATP = L-gamma-glutamyl-L-cysteine + ADP + 2 H(+) + phosphate." [EC:6.3.2.2, RHEA:13285]
+def: "Catalysis of the reaction: L-cysteine + L-glutamate + ATP = L-gamma-glutamyl-L-cysteine + ADP + 2 H+ + phosphate." [EC:6.3.2.2, RHEA:13285]
synonym: "gamma-glutamyl-L-cysteine synthetase activity" RELATED [EC:6.3.2.2]
synonym: "gamma-glutamylcysteine synthetase activity" RELATED [EC:6.3.2.2]
synonym: "gamma-glutamylcysteinyl synthetase activity" RELATED [EC:6.3.2.2]
@@ -38071,10 +38049,8 @@ is_a: GO:0070548 ! L-glutamine aminotransferase activity
id: GO:0004361
name: glutaryl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glutaryl-CoA + acceptor = crotonoyl-CoA + CO2 + reduced acceptor." [EC:1.3.8.6]
+def: "3-methylbutanoyl-CoA + H+ + oxidized [electron-transfer flavoprotein] = 3-methyl-(2E)-butenoyl-CoA + reduced [electron-transfer flavoprotein]." [RHEA:13389]
synonym: "glutaryl coenzyme A dehydrogenase activity" RELATED [EC:1.3.8.6]
-synonym: "glutaryl-CoA:(acceptor) 2,3-oxidoreductase (decarboxylating)" RELATED [EC:1.3.8.6]
-synonym: "glutaryl-CoA:acceptor 2,3-oxidoreductase (decarboxylating)" RELATED [EC:1.3.8.6]
xref: EC:1.3.8.6
xref: MetaCyc:GLUTARYL-COA-DEHYDROGENASE-RXN
xref: Reactome:R-HSA-71046 "glutaryl-CoA + FAD => crotonyl-CoA + FADH2 + CO2"
@@ -38112,7 +38088,7 @@ is_a: GO:0047134 ! protein-disulfide reductase (NAD(P)) activity
id: GO:0004363
name: glutathione synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-gamma-glutamyl-L-cysteine + ATP + glycine = ADP + glutathione + 2 H(+) + phosphate." [EC:6.3.2.3, RHEA:13557]
+def: "Catalysis of the reaction: L-gamma-glutamyl-L-cysteine + ATP + glycine = ADP + glutathione + 2 H+ + phosphate." [EC:6.3.2.3, RHEA:13557]
synonym: "gamma-L-glutamyl-L-cysteine:glycine ligase (ADP-forming)" RELATED [EC:6.3.2.3]
synonym: "glutathione synthetase activity" RELATED [EC:6.3.2.3]
synonym: "GSH synthetase activity" RELATED [EC:6.3.2.3]
@@ -38123,6 +38099,7 @@ xref: Reactome:R-HSA-174394 "GSS:Mg2+ dimer synthesizes GSH"
xref: Reactome:R-HSA-5602901 "Defective GSS does not synthesize GSH"
xref: RHEA:13557
is_a: GO:0016881 ! acid-amino acid ligase activity
+is_a: GO:1904091 ! non-ribosomal peptide synthetase activity
[Term]
id: GO:0004364
@@ -38147,6 +38124,8 @@ xref: Reactome:R-HSA-9026777 "GSTM4 dimer transfers GSH to 13(S),14(S)-epoxy-DHA
xref: Reactome:R-HSA-9026780 "LTC4S trimer transfers GSH to 13(S),14(S)-epoxy-DHA to form MCTR1"
xref: Reactome:R-HSA-9026901 "GGT transfers GSH to 16S,17S-epoxy-DHA to form PCTR1"
xref: Reactome:R-HSA-9026911 "LTC4S trimer transfers GSH to 7S(8)-epoxy-17(S)-HDHA to form RCTR1"
+xref: Reactome:R-HSA-9748996 "GST dimers cleave AZA to 6MP"
+xref: Reactome:R-HSA-9753280 "GSTs transfer GSH to NAPQI to form APAP-SG"
is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups
[Term]
@@ -38168,7 +38147,7 @@ synonym: "triosephosphate dehydrogenase activity" BROAD [EC:1.2.1.12]
xref: EC:1.2.1.12
xref: MetaCyc:GAPOXNPHOSPHN-RXN
xref: Reactome:R-HSA-70449 "D-glyceraldehyde 3-phosphate + orthophosphate + NAD+ <=> 1,3-bisphospho-D-glycerate + NADH + H+"
-xref: Reactome:R-HSA-70482 "1,3-bisphospho-D-glycerate + NADH + H+ <=> D-glyceraldehyde 3-phosphate + Orthophosphate + NAD+"
+xref: Reactome:R-HSA-70482 "GAPDH tetramers reduce 1,3BPG to GA3P"
xref: RHEA:10300
is_a: GO:0043891 ! glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity
@@ -38196,35 +38175,6 @@ xref: Reactome:R-HSA-75886 "glycerol 3-phosphate + acyl-CoA => 1-acylglycerol 3-
xref: RHEA:15325
is_a: GO:0008374 ! O-acyltransferase activity
-[Term]
-id: GO:0004367
-name: glycerol-3-phosphate dehydrogenase [NAD+] activity
-namespace: molecular_function
-def: "Catalysis of the reaction: sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH + H+." [EC:1.1.1.8, RHEA:11092]
-synonym: "alpha-glycerol phosphate dehydrogenase (NAD) activity" RELATED [EC:1.1.1.8]
-synonym: "alpha-glycerophosphate dehydrogenase (NAD) activity" RELATED [EC:1.1.1.8]
-synonym: "glycerol 1-phosphate dehydrogenase activity" RELATED [EC:1.1.1.8]
-synonym: "glycerol phosphate dehydrogenase (NAD) activity" RELATED [EC:1.1.1.8]
-synonym: "glycerol-3-phosphate dehydrogenase (NAD) activity" RELATED [EC:1.1.1.8]
-synonym: "glycerophosphate dehydrogenase (NAD) activity" RELATED [EC:1.1.1.8]
-synonym: "hydroglycerophosphate dehydrogenase activity" BROAD [EC:1.1.1.8]
-synonym: "L-alpha-glycerol phosphate dehydrogenase activity" BROAD [EC:1.1.1.8]
-synonym: "L-alpha-glycerophosphate dehydrogenase activity" BROAD [EC:1.1.1.8]
-synonym: "L-glycerol phosphate dehydrogenase activity" BROAD [EC:1.1.1.8]
-synonym: "L-glycerophosphate dehydrogenase activity" BROAD [EC:1.1.1.8]
-synonym: "NAD-alpha-glycerophosphate dehydrogenase activity" RELATED [EC:1.1.1.8]
-synonym: "NAD-dependent glycerol phosphate dehydrogenase activity" RELATED [EC:1.1.1.8]
-synonym: "NAD-dependent glycerol-3-phosphate dehydrogenase activity" RELATED [EC:1.1.1.8]
-synonym: "NAD-L-glycerol-3-phosphate dehydrogenase activity" RELATED [EC:1.1.1.8]
-synonym: "NAD-linked glycerol 3-phosphate dehydrogenase activity" RELATED [EC:1.1.1.8]
-synonym: "NADH-dihydroxyacetone phosphate reductase activity" RELATED [EC:1.1.1.8]
-xref: EC:1.1.1.8
-xref: KEGG_REACTION:R00842
-xref: MetaCyc:1.1.1.8-RXN
-xref: Reactome:R-HSA-75889 "DHAP is converted to G3P by GPD1/GPD1L"
-xref: RHEA:11092
-is_a: GO:0047952 ! glycerol-3-phosphate dehydrogenase [NAD(P)+] activity
-
[Term]
id: GO:0004368
name: glycerol-3-phosphate dehydrogenase (quinone) activity
@@ -38249,7 +38199,7 @@ is_a: GO:0016901 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0004369
name: glycerol-3-phosphate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: sn-glycerol 3-phosphate + O(2) = glycerone phosphate + H(2)O(2)." [EC:1.1.3.21, RHEA:18369]
+def: "Catalysis of the reaction: sn-glycerol 3-phosphate + O2 = glycerone phosphate + H2O2." [EC:1.1.3.21, RHEA:18369]
synonym: "alpha-glycerophosphate oxidase activity" RELATED [EC:1.1.3.21]
synonym: "glycerol phosphate oxidase activity" RELATED [EC:1.1.3.21]
synonym: "glycerol-1-phosphate oxidase activity" RELATED [EC:1.1.3.21]
@@ -38266,7 +38216,7 @@ is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0004370
name: glycerol kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H(+)." [EC:2.7.1.30, RHEA:21644]
+def: "Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H+." [EC:2.7.1.30, RHEA:21644]
synonym: "ATP:glycerol 3-phosphotransferase activity" RELATED [EC:2.7.1.30]
synonym: "ATP:glycerol-3-phosphotransferase activity" RELATED [EC:2.7.1.30]
synonym: "GK" RELATED [EC:2.7.1.30]
@@ -38285,7 +38235,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0004371
name: glycerone kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + glycerone = ADP + glycerone phosphate + 2 H(+)." [EC:2.7.1.29, RHEA:15773]
+def: "Catalysis of the reaction: ATP + glycerone = ADP + glycerone phosphate + 2 H+." [EC:2.7.1.29, RHEA:15773]
synonym: "acetol kinase (phosphorylating)" RELATED [EC:2.7.1.29]
synonym: "acetol kinase activity" RELATED [EC:2.7.1.29]
synonym: "ATP:glycerone phosphotransferase activity" RELATED [EC:2.7.1.29]
@@ -38311,10 +38261,7 @@ synonym: "serine hydroxymethyltransferase activity" RELATED [EC:2.1.2.1]
synonym: "serine transhydroxymethylase activity" RELATED [EC:2.1.2.1]
xref: EC:2.1.2.1
xref: MetaCyc:GLYOHMETRANS-RXN
-xref: Reactome:R-HSA-200651 "5,10-methyleneTHF polyglutamate + glycine <=> tetrahydrofolate polyglutamate (THF polyglutamate) + serine"
-xref: Reactome:R-HSA-200735 "Tetrahydrofolate polyglutamate (THF polyglutamate) + serine <=> 5,10-methyleneTHF polyglutamate + glycine"
-xref: Reactome:R-HSA-5694137 "PXLP-K280-SHMT2 tetramer transfers CH2OH group from 5,10MTHF to glycine"
-xref: Reactome:R-HSA-71249 "SHMT1 tetramer cleaves HTMLYS to yield TEABL and Gly"
+xref: Reactome:R-HSA-5694137 "PXLP-K280-SHMT2 tetramer transfers CH2OH group to Gly to form L-Ser"
xref: RHEA:15481
is_a: GO:0016742 ! hydroxymethyl-, formyl- and related transferase activity
@@ -38494,17 +38441,19 @@ is_a: GO:0035250 ! UDP-galactosyltransferase activity
[Term]
id: GO:0004382
-name: guanosine-diphosphatase activity
+name: GDP phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GDP + H2O = GMP + phosphate." [EC:3.6.1.42, PMID:2989286, RHEA:22156]
+def: "Catalysis of the reaction: GDP + H2O = GMP + phosphate." [PMID:2989286, RHEA:22156]
+synonym: "GDP diphosphatase activity" RELATED []
synonym: "GDP phosphohydrolase activity" RELATED [EC:3.6.1.42]
synonym: "GDPase activity" RELATED [EC:3.6.1.42]
synonym: "guanosine 5'-diphosphatase activity" RELATED [EC:3.6.1.6]
synonym: "guanosine diphosphatase activity" EXACT []
+synonym: "guanosine-diphosphatase activity" EXACT []
xref: EC:3.6.1.42
xref: MetaCyc:GUANOSINE-DIPHOSPHATASE-RXN
xref: RHEA:22156
-is_a: GO:0017110 ! nucleoside-diphosphatase activity
+is_a: GO:0017110 ! nucleoside diphosphate phosphatase activity
[Term]
id: GO:0004383
@@ -38536,7 +38485,6 @@ is_obsolete: true
consider: GO:0004385
consider: GO:0005102
consider: GO:0007155
-consider: GO:0016021
consider: GO:0050839
[Term]
@@ -38555,6 +38503,8 @@ xref: EC:2.7.4.8
xref: MetaCyc:GUANYL-KIN-RXN
xref: Reactome:R-HSA-110133 "(d)GDP + ADP <=> (d)GMP + ATP (GUK1)"
xref: Reactome:R-HSA-73788 "(d)GMP + ATP <=> (d)GDP + ADP (GUK1)"
+xref: Reactome:R-HSA-9748949 "GUK1 phosphorylates 6TGMP to 6TGDP"
+xref: Reactome:R-HSA-9748963 "GUK1 phosphorylates 6TdGMP to 6TdGDP"
xref: RHEA:20780
is_a: GO:0050145 ! nucleoside monophosphate kinase activity
@@ -38565,7 +38515,6 @@ namespace: molecular_function
alt_id: GO:0008026
def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix." [GOC:jl]
comment: Note that most helicases catalyze processive duplex unwinding.
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_pir
@@ -38582,7 +38531,7 @@ is_a: GO:0140657 ! ATP-dependent activity
id: GO:0004392
name: heme oxygenase (decyclizing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: heme b + 3 O2 + 3 reduced [NADPH-hemoprotein reductase] = biliverdin + CO + Fe2+ + H+ + 3 H2O + 3 oxidized [NADPH-hemoprotein reductase]." [RHEA:21764]
+def: "Catalysis of the reaction: heme b + 3 O2 + 3 reduced [NADPH-hemoprotein reductase] = biliverdin + CO + Fe2+ + H+ + 3 H2O + 3 oxidized [NADPH-hemoprotein reductase]." [RHEA:21764]
synonym: "haem oxidase activity" RELATED [EC:1.14.14.18]
synonym: "haem oxygenase (decyclizing) activity" EXACT []
synonym: "haem oxygenase activity" RELATED [EC:1.14.14.18]
@@ -38604,7 +38553,6 @@ def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + heparan
synonym: "heparan-sulfate 2-O-sulphotransferase activity" EXACT []
synonym: "heparin 2-sulfotransferase activity" RELATED []
synonym: "heparin-sulphate 2-sulphotransferase activity" RELATED []
-xref: EC:2.8.2.-
xref: Reactome:R-HSA-2076508 "HS2ST1 sulfates IdoA at C2 in heparan sulfate"
is_a: GO:0034483 ! heparan sulfate sulfotransferase activity
@@ -38711,7 +38659,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0004401
name: histidinol-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-histidinol phosphate + H(2)O = L-histidinol + phosphate." [EC:3.1.3.15, RHEA:14465]
+def: "Catalysis of the reaction: L-histidinol phosphate + H2O = L-histidinol + phosphate." [EC:3.1.3.15, RHEA:14465]
synonym: "histidinol phosphate phosphatase activity" RELATED [EC:3.1.3.15]
synonym: "histidinolphosphatase activity" RELATED [EC:3.1.3.15]
synonym: "histidinolphosphate phosphatase activity" RELATED [EC:3.1.3.15]
@@ -38735,7 +38683,6 @@ alt_id: GO:0004406
alt_id: GO:0043166
alt_id: GO:0046971
def: "Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone." [EC:2.3.1.48]
-comment: Note that the term 'histone lysine acetyltransferase activity ; GO:0046971' was merged into this term because only lysine residues are ever acetylated in histones, and so the term was redundant.
synonym: "acetyl-CoA:histone acetyltransferase activity" RELATED [EC:2.3.1.48]
synonym: "H2A/H2B histone acetyltransferase activity" NARROW []
synonym: "H3/H4 histone acetyltransferase activity" NARROW []
@@ -38765,6 +38712,7 @@ xref: Reactome:R-HSA-5144542 "CLOCK acetylates lysine-15 of histone H3, H4"
xref: Reactome:R-HSA-5250938 "B-WICH:histone acetyltransferase acetylates histone H3 at lysine-9"
xref: RHEA:21992
is_a: GO:0061733 ! peptide-lysine-N-acetyltransferase activity
+is_a: GO:0140993 ! histone modifying activity
[Term]
id: GO:0004407
@@ -38784,7 +38732,8 @@ xref: Reactome:R-HSA-433672 "NoRC:HDAC:DNMT deacetylates histone H4 and methylat
xref: Reactome:R-HSA-6805650 "MTA2-NuRD complex deacetylates TP53"
xref: RHEA:58196
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
-is_a: GO:0033558 ! protein deacetylase activity
+is_a: GO:0033558 ! protein lysine deacetylase activity
+is_a: GO:0140993 ! histone modifying activity
[Term]
id: GO:0004408
@@ -38806,7 +38755,7 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
id: GO:0004409
name: homoaconitate hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (-)-homoisocitrate = cis-homoaconitate + H(2)O." [EC:4.2.1.36, RHEA:15485]
+def: "Catalysis of the reaction: (-)-homoisocitrate = cis-homoaconitate + H2O." [EC:4.2.1.36, RHEA:15485]
synonym: "(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate hydro-lyase [(Z)-but-1-ene-1,2,4-tricarboxylate-forming]" RELATED [EC:4.2.1.36]
synonym: "2-hydroxybutane-1,2,4-tricarboxylate hydro-lyase activity" RELATED [EC:4.2.1.36]
synonym: "cis-homoaconitase activity" RELATED [EC:4.2.1.36]
@@ -38824,7 +38773,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0004410
name: homocitrate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + acetyl-CoA + H(2)O = CoA + H(+) + homocitrate." [EC:2.3.3.14, RHEA:12929]
+def: "Catalysis of the reaction: 2-oxoglutarate + acetyl-CoA + H2O = CoA + H+ + homocitrate." [RHEA:12929]
comment: Note that this function was formerly EC:4.1.3.21.
synonym: "2-hydroxybutane-1,2,4-tricarboxylate 2-oxoglutarate-lyase (CoA- acetylating) activity" RELATED [EC:2.3.3.14]
synonym: "2-hydroxybutane-1,2,4-tricarboxylate 2-oxoglutarate-lyase (CoA-acetylating)" RELATED [EC:2.3.3.14]
@@ -38835,13 +38784,13 @@ xref: EC:2.3.3.14
xref: KEGG_REACTION:R00271
xref: MetaCyc:HOMOCITRATE-SYNTHASE-RXN
xref: RHEA:12929
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0004411
name: homogentisate 1,2-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: homogentisate + O(2) = 4-maleylacetoacetate + H(+)." [EC:1.13.11.5, RHEA:15449]
+def: "Catalysis of the reaction: homogentisate + O2 = 4-maleylacetoacetate + H+." [EC:1.13.11.5, RHEA:15449]
synonym: "homogentisate dioxygenase activity" RELATED [EC:1.13.11.5]
synonym: "homogentisate oxidase activity" RELATED [EC:1.13.11.5]
synonym: "homogentisate oxygenase activity" RELATED [EC:1.13.11.5]
@@ -38872,7 +38821,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0004413
name: homoserine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-homoserine + ATP = O-phospho-L-homoserine + ADP + 2 H(+)." [EC:2.7.1.39, RHEA:13985]
+def: "Catalysis of the reaction: L-homoserine + ATP = O-phospho-L-homoserine + ADP + 2 H+." [EC:2.7.1.39, RHEA:13985]
synonym: "ATP:L-homoserine O-phosphotransferase activity" RELATED [EC:2.7.1.39]
synonym: "homoserine kinase (phosphorylating)" RELATED [EC:2.7.1.39]
synonym: "HSK" RELATED [EC:2.7.1.39]
@@ -38940,7 +38889,7 @@ is_a: GO:0016790 ! thiolester hydrolase activity
id: GO:0004417
name: hydroxyethylthiazole kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-(2-hydroxyethyl)-4-methylthiazole + ATP = 4-methyl-5-(2-phosphoethyl)-thiazole + ADP + 2 H(+)." [EC:2.7.1.50, RHEA:24212]
+def: "Catalysis of the reaction: 5-(2-hydroxyethyl)-4-methylthiazole + ATP = 4-methyl-5-(2-phosphoethyl)-thiazole + ADP + 2 H+." [EC:2.7.1.50, RHEA:24212]
synonym: "4-methyl-5-(beta-hydroxyethyl)thiazole kinase activity" RELATED [EC:2.7.1.50]
synonym: "ATP:4-methyl-5-(2-hydroxyethyl)thiazole 2-phosphotransferase activity" RELATED [EC:2.7.1.50]
synonym: "hydroxyethylthiazole kinase (phosphorylating)" RELATED [EC:2.7.1.50]
@@ -38955,7 +38904,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0004418
name: hydroxymethylbilane synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + 4 porphobilinogen = hydroxymethylbilane + 4 NH(4)(+)." [EC:2.5.1.61, RHEA:13185]
+def: "Catalysis of the reaction: H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4." [EC:2.5.1.61, RHEA:13185]
comment: Note that this function was formerly EC:4.3.1.8.
synonym: "(4-(2-carboxyethyl)-3-(carboxymethyl)pyrrol-2-yl)methyltransferase (hydrolyzing) activity" RELATED [EC:2.5.1.61]
synonym: "(4-[2-carboxyethyl]-3-[carboxymethyl]pyrrol-2-yl)methyltransferase (hydrolysing)" RELATED [EC:2.5.1.61]
@@ -39002,7 +38951,7 @@ id: GO:0004420
name: hydroxymethylglutaryl-CoA reductase (NADPH) activity
namespace: molecular_function
alt_id: GO:0042282
-def: "Catalysis of the reaction: (R)-mevalonate + CoA + 2 NADP(+) = (S)-3-hydroxy-3-methylglutaryl-CoA + 2 H(+) + 2 NADPH." [PMID:29224355, RHEA:15989]
+def: "Catalysis of the reaction: (R)-mevalonate + CoA + 2 NADP+ = (S)-3-hydroxy-3-methylglutaryl-CoA + 2 H+ + 2 NADPH." [PMID:29224355, RHEA:15989]
synonym: "3-hydroxy-3-methylglutaryl-coenzyme A reductase activity" BROAD [EC:1.1.1.34]
synonym: "HMG-CoA reductase activity" BROAD [EC:1.1.1.34]
synonym: "hydroxymethylglutaryl-CoA reductase activity" RELATED []
@@ -39017,7 +38966,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0004421
name: hydroxymethylglutaryl-CoA synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetoacetyl-CoA + acetyl-CoA + H(2)O = (S)-3-hydroxy-3-methylglutaryl-CoA + CoA + H(+)." [EC:2.3.3.10, RHEA:10188]
+def: "Catalysis of the reaction: acetoacetyl-CoA + acetyl-CoA + H2O = (S)-3-hydroxy-3-methylglutaryl-CoA + CoA + H+." [RHEA:10188]
comment: Note that this function was formerly EC:4.1.3.5.
synonym: "(s)-3-hydroxy-3-methylglutaryl-CoA acetoacetyl-CoA-lyase (CoA- acetylating) activity" RELATED [EC:2.3.3.10]
synonym: "(S)-3-hydroxy-3-methylglutaryl-CoA acetoacetyl-CoA-lyase (CoA-acetylating)" RELATED [EC:2.3.3.10]
@@ -39039,7 +38988,7 @@ xref: MetaCyc:HYDROXYMETHYLGLUTARYL-COA-SYNTHASE-RXN
xref: Reactome:R-HSA-191323 "HMGCS1 condenses Ac-CoA and ACA-CoA to form bHMG-CoA"
xref: Reactome:R-HSA-73918 "acetoacetyl-CoA+acetyl-CoA => HMG-CoA + CoASH"
xref: RHEA:10188
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0004422
@@ -39065,7 +39014,6 @@ synonym: "Transphosphoribosidase activity" BROAD [EC:2.4.2.8]
xref: EC:2.4.2.8
xref: KEGG_REACTION:R01132
xref: MetaCyc:HYPOXANPRIBOSYLTRAN-RXN
-xref: Reactome:R-HSA-74215 "guanine or hypoxanthine + PRPP => GMP or IMP + PPi (HPRT1)"
xref: RHEA:17973
is_a: GO:0106130 ! purine phosphoribosyltransferase activity
@@ -39100,7 +39048,7 @@ is_a: GO:0008484 ! sulfuric ester hydrolase activity
id: GO:0004424
name: imidazoleglycerol-phosphate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H(2)O." [EC:4.2.1.19, RHEA:11040]
+def: "Catalysis of the reaction: D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O." [EC:4.2.1.19, RHEA:11040]
synonym: "D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate hydro-lyase [3-(imidazol-4-yl)-2-oxopropyl-phosphate-forming]" RELATED [EC:4.2.1.19]
synonym: "D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate hydro-lyase activity" RELATED [EC:4.2.1.19]
synonym: "IGP dehydratase activity" RELATED [EC:4.2.1.19]
@@ -39128,10 +39076,11 @@ is_a: GO:0016831 ! carboxy-lyase activity
[Term]
id: GO:0004427
-name: inorganic diphosphatase activity
+name: inorganic diphosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: diphosphate + H(2)O = H(+) + 2 phosphate." [EC:3.6.1.1, RHEA:24576]
+def: "Catalysis of the reaction: diphosphate + H2O = H+ + 2 phosphate." [EC:3.6.1.1, RHEA:24576]
synonym: "diphosphate phosphohydrolase activity" RELATED [EC:3.6.1.1]
+synonym: "inorganic diphosphatase activity" EXACT []
synonym: "inorganic pyrophosphatase activity" RELATED [EC:3.6.1.1]
synonym: "pyrophosphate phosphohydrolase activity" RELATED [EC:3.6.1.1]
xref: EC:3.6.1.1
@@ -39139,7 +39088,7 @@ xref: KEGG_REACTION:R00004
xref: MetaCyc:INORGPYROPHOSPHAT-RXN
xref: Reactome:R-HSA-449937 "pyrophosphate + H2O => 2 orthophosphate [mitochondrial]"
xref: Reactome:R-HSA-6788912 "LHPP:Mg2+ dimer hydrolyses PPi"
-xref: Reactome:R-HSA-71732 "pyrophosphate + H2O => 2 orthophosphate [cytosolic]"
+xref: Reactome:R-HSA-71732 "PPA1 hydrolyzes pyrophosphate to orthophosphate"
xref: RHEA:24576
is_a: GO:0016462 ! pyrophosphatase activity
@@ -39161,7 +39110,7 @@ consider: GO:0052813
id: GO:0004430
name: 1-phosphatidylinositol 4-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = 1-phosphatidyl-1D-myo-inositol 4-phosphate + ADP + 2 H(+)." [EC:2.7.1.67, RHEA:19877]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = 1-phosphatidyl-1D-myo-inositol 4-phosphate + ADP + 2 H+." [EC:2.7.1.67, RHEA:19877]
synonym: "ATP:1-phosphatidyl-1D-myo-inositol 4-phosphotransferase activity" RELATED [EC:2.7.1.67]
synonym: "phosphatidylinositol 4-kinase activity" BROAD [EC:2.7.1.67]
synonym: "phosphatidylinositol kinase (phosphorylating) activity" BROAD [EC:2.7.1.67]
@@ -39208,7 +39157,7 @@ consider: GO:0016308
id: GO:0004435
name: phosphatidylinositol phospholipase C activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1,2-diacylglycerol + 1D-myo-inositol 1,4,5-trisphosphate + H(+)." [EC:3.1.4.11, RHEA:33179]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O = 1,2-diacylglycerol + 1D-myo-inositol 1,4,5-trisphosphate + H+." [EC:3.1.4.11, RHEA:33179]
synonym: "1-phosphatidyl-1D-myo-inositol-4,5-bisphosphate inositoltrisphosphohydrolase activity" RELATED [EC:3.1.4.11]
synonym: "1-phosphatidyl-D-myo-inositol-4,5-bisphosphate inositoltrisphosphohydrolase activity" RELATED [EC:3.1.4.11]
synonym: "1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase activity" EXACT []
@@ -39231,6 +39180,7 @@ xref: Reactome:R-HSA-2730847 "Hydrolysis of PIP2 by PLCG"
xref: Reactome:R-HSA-5607735 "p-Y753,Y759-PLCG2 hydrolyses PIP2"
xref: Reactome:R-HSA-622382 "PIP2 hydrolysis"
xref: Reactome:R-HSA-9032478 "EPOR-associated PLCG hydrolyzes 1-Phosphatidyl-1D-myo-inositol 4,5-bisphosphate"
+xref: Reactome:R-HSA-9717205 "GNB1,3:GNG13:PLCB2:Ca2+ hydrolyzes PI(4,5)P2 to I(1,4,5)P3 and DAG"
xref: RHEA:33179
is_a: GO:0004629 ! phospholipase C activity
@@ -39266,7 +39216,7 @@ consider: GO:0052745
[Term]
id: GO:0004438
-name: phosphatidylinositol-3-phosphatase activity
+name: phosphatidylinositol-3-phosphate phosphatase activity
namespace: molecular_function
alt_id: GO:0016315
def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3-phosphate + H2O = 1-phosphatidyl-1D-myo-inositol + phosphate." [EC:3.1.3.64]
@@ -39275,9 +39225,9 @@ synonym: "1-phosphatidyl-1D-myo-inositol-3-phosphate 3-phosphohydrolase activity
synonym: "D-myo-inositol-1,3-bisphosphate 3-phosphohydrolase activity" RELATED [EC:3.1.3.64]
synonym: "inositol 1,3-bisphosphate phosphatase activity" RELATED [EC:3.1.3.64]
synonym: "inositol-1,3-bisphosphate 3-phosphatase activity" RELATED [EC:3.1.3.64]
-synonym: "inositol-1,4,-bisphosphate 3-phosphatase activity" EXACT []
synonym: "inositol-polyphosphate 3-phosphatase activity" RELATED [EC:3.1.3.64]
synonym: "phosphatidyl-3-phosphate 3-phosphohydrolase activity" RELATED [EC:3.1.3.64]
+synonym: "phosphatidylinositol-3-phosphatase activity" EXACT []
xref: EC:3.1.3.64
xref: MetaCyc:PHOSPHATIDYLINOSITOL-3-PHOSPHATASE-RXN
xref: Reactome:R-HSA-1675795 "PI3P is dephosphorylated to PI by MTM proteins at the late endosome membrane"
@@ -39296,7 +39246,7 @@ id: GO:0004439
name: phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity
namespace: molecular_function
alt_id: GO:0001668
-def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate." [EC:3.1.3.36, RHEA:22764]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate." [RHEA:22764]
synonym: "phosphatidyl-myo-inositol-4,5-bisphosphate phosphatase activity" RELATED [EC:3.1.3.36]
synonym: "phosphatidylinositol 4,5-bisphosphate phosphatase activity" BROAD [EC:3.1.3.36]
synonym: "phosphatidylinositol-bisphosphatase activity" BROAD [EC:3.1.3.36]
@@ -39406,80 +39356,77 @@ is_a: GO:0052745 ! inositol phosphate phosphatase activity
id: GO:0004447
name: iodide peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: iodide + hydrogen peroxide = iodine + 2 H2O." [RHEA:23336]
+def: "Catalysis of the reaction: iodide + H2O2 = iodine + 2 H2O." [RHEA:23336]
synonym: "iodinase activity" RELATED [EC:1.11.1.8]
synonym: "thyroid peroxidase activity" RELATED [EC:1.11.1.8]
synonym: "thyroperoxidase activity" RELATED [EC:1.11.1.8]
synonym: "TPO activity" RELATED [EC:1.11.1.8]
xref: EC:1.11.1.8
xref: MetaCyc:IODIDE-PEROXIDASE-RXN
-is_a: GO:0004601 ! peroxidase activity
+is_a: GO:0140905 ! haloperoxidase activity
[Term]
id: GO:0004448
-name: isocitrate dehydrogenase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: isocitrate + acceptor = 2-oxoglutarate + CO2 + reduced acceptor." [EC:1.1.1.41, EC:1.1.1.42]
-synonym: "beta-ketoglutaric-isocitric carboxylase activity" RELATED [EC:1.1.1.-]
-synonym: "IDH activity" RELATED [EC:1.1.1.-]
-synonym: "IDP activity" RELATED [EC:1.1.1.-]
-synonym: "IDP1" RELATED [EC:1.1.1.-]
-synonym: "IDP2" RELATED [EC:1.1.1.-]
-synonym: "IDP3" RELATED [EC:1.1.1.-]
-synonym: "isocitric acid dehydrogenase activity" RELATED [EC:1.1.1.-]
-synonym: "isocitric dehydrogenase activity" RELATED [EC:1.1.1.-]
-synonym: "oxalosuccinate carboxylase activity" RELATED [EC:1.1.1.-]
-synonym: "oxalosuccinate decarboxylase activity" RELATED [EC:1.1.1.-]
-synonym: "oxalsuccinic decarboxylase activity" RELATED [EC:1.1.1.-]
-xref: MetaCyc:ISOCITDEH-RXN
+name: isocitrate dehydrogenase [NAD(P)+] activity
+namespace: molecular_function
+def: "Catalysis of the reaction: isocitrate + NAD(P)+ = 2-oxoglutarate + CO2 + NAD(P)H." [GOC:curators]
+subset: gocheck_do_not_annotate
+synonym: "IDH activity" RELATED []
+synonym: "IDP activity" RELATED []
+synonym: "isocitrate dehydrogenase activity" EXACT []
+synonym: "isocitric acid dehydrogenase activity" EXACT []
+synonym: "isocitric dehydrogenase activity" EXACT []
+synonym: "oxalosuccinate carboxylase activity" EXACT []
+synonym: "oxalosuccinate decarboxylase activity" EXACT []
+synonym: "oxalosuccinic decarboxylase activity" EXACT []
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0004449
name: isocitrate dehydrogenase (NAD+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH + H+." [EC:1.1.1.41]
-synonym: "isocitrate dehydrogenase (NAD) activity" RELATED [EC:1.1.1.41]
-synonym: "isocitrate:NAD+ oxidoreductase (decarboxylating)" RELATED [EC:1.1.1.41]
-synonym: "NAD dependent isocitrate dehydrogenase activity" RELATED [EC:1.1.1.41]
-synonym: "NAD isocitrate dehydrogenase activity" RELATED [EC:1.1.1.41]
-synonym: "NAD isocitric dehydrogenase activity" RELATED [EC:1.1.1.41]
-synonym: "NAD-linked isocitrate dehydrogenase activity" RELATED [EC:1.1.1.41]
-synonym: "NAD-specific isocitrate dehydrogenase activity" RELATED [EC:1.1.1.41]
-synonym: "nicotinamide adenine dinucleotide isocitrate dehydrogenase activity" RELATED [EC:1.1.1.41]
+def: "Catalysis of the reaction: isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH." [RHEA:23632]
+synonym: "isocitrate dehydrogenase (NAD) activity" EXACT [EC:1.1.1.41]
+synonym: "isocitrate:NAD+ oxidoreductase (decarboxylating)" EXACT [EC:1.1.1.41]
+synonym: "NAD dependent isocitrate dehydrogenase activity" EXACT [EC:1.1.1.41]
+synonym: "NAD isocitrate dehydrogenase activity" EXACT [EC:1.1.1.41]
+synonym: "NAD isocitric dehydrogenase activity" EXACT [EC:1.1.1.41]
+synonym: "NAD-linked isocitrate dehydrogenase activity" EXACT [EC:1.1.1.41]
+synonym: "NAD-specific isocitrate dehydrogenase activity" EXACT [EC:1.1.1.41]
+synonym: "nicotinamide adenine dinucleotide isocitrate dehydrogenase activity" EXACT [EC:1.1.1.41]
xref: EC:1.1.1.41
xref: MetaCyc:ISOCITRATE-DEHYDROGENASE-NAD+-RXN
xref: Reactome:R-HSA-70967 "isocitrate + NAD+ => alpha-ketoglutarate + CO2 + NADH + H+ [IDH3]"
xref: RHEA:23632
-is_a: GO:0004448 ! isocitrate dehydrogenase activity
+is_a: GO:0004448 ! isocitrate dehydrogenase [NAD(P)+] activity
[Term]
id: GO:0004450
name: isocitrate dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+." [EC:1.1.1.42]
+def: "Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH." [RHEA:19629]
synonym: "dual-cofactor-specific isocitrate dehydrogenase activity" RELATED [EC:1.1.1.42]
-synonym: "isocitrate (NADP) dehydrogenase activity" RELATED [EC:1.1.1.42]
-synonym: "isocitrate (nicotinamide adenine dinucleotide phosphate) dehydrogenase activity" RELATED [EC:1.1.1.42]
-synonym: "isocitrate dehydrogenase (NADP) activity" RELATED [EC:1.1.1.42]
-synonym: "isocitrate dehydrogenase (NADP-dependent) activity" RELATED [EC:1.1.1.42]
-synonym: "isocitrate:NADP+ oxidoreductase (decarboxylating)" RELATED [EC:1.1.1.42]
-synonym: "NADP isocitric dehydrogenase activity" RELATED [EC:1.1.1.42]
+synonym: "isocitrate (NADP) dehydrogenase activity" EXACT [EC:1.1.1.42]
+synonym: "isocitrate (nicotinamide adenine dinucleotide phosphate) dehydrogenase activity" EXACT [EC:1.1.1.42]
+synonym: "isocitrate dehydrogenase (NADP) activity" EXACT [EC:1.1.1.42]
+synonym: "isocitrate dehydrogenase (NADP-dependent) activity" EXACT [EC:1.1.1.42]
+synonym: "isocitrate:NADP+ oxidoreductase (decarboxylating)" EXACT [EC:1.1.1.42]
+synonym: "NADP isocitric dehydrogenase activity" EXACT [EC:1.1.1.42]
synonym: "NADP(+)-ICDH activity" RELATED [EC:1.1.1.42]
synonym: "NADP(+)-IDH activity" RELATED [EC:1.1.1.42]
-synonym: "NADP(+)-linked isocitrate dehydrogenase activity" RELATED [EC:1.1.1.42]
-synonym: "NADP-dependent isocitrate dehydrogenase activity" RELATED [EC:1.1.1.42]
-synonym: "NADP-dependent isocitric dehydrogenase activity" RELATED [EC:1.1.1.42]
-synonym: "NADP-linked isocitrate dehydrogenase activity" RELATED [EC:1.1.1.42]
-synonym: "NADP-specific isocitrate dehydrogenase activity" RELATED [EC:1.1.1.42]
-synonym: "triphosphopyridine nucleotide-linked isocitrate dehydrogenase activity" RELATED [EC:1.1.1.42]
+synonym: "NADP(+)-linked isocitrate dehydrogenase activity" EXACT [EC:1.1.1.42]
+synonym: "NADP-dependent isocitrate dehydrogenase activity" EXACT [EC:1.1.1.42]
+synonym: "NADP-dependent isocitric dehydrogenase activity" EXACT [EC:1.1.1.42]
+synonym: "NADP-linked isocitrate dehydrogenase activity" EXACT [EC:1.1.1.42]
+synonym: "NADP-specific isocitrate dehydrogenase activity" EXACT [EC:1.1.1.42]
+synonym: "triphosphopyridine nucleotide-linked isocitrate dehydrogenase activity" EXACT [EC:1.1.1.42]
xref: EC:1.1.1.42
xref: MetaCyc:ISOCITDEH-RXN
xref: Reactome:R-HSA-389540 "isocitrate + NADP+ => 2-oxoglutarate + CO2 + NADPH + H+"
xref: Reactome:R-HSA-389550 "isocitrate + NADP+ => 2-oxoglutarate + CO2 + NADPH + H+"
xref: Reactome:R-HSA-450984 "isocitrate + NADP+ => alpha-ketoglutarate + CO2 + NADPH + H+ [IDH2]"
xref: RHEA:19629
-is_a: GO:0004448 ! isocitrate dehydrogenase activity
+is_a: GO:0004448 ! isocitrate dehydrogenase [NAD(P)+] activity
[Term]
id: GO:0004451
@@ -39503,7 +39450,7 @@ is_a: GO:0016833 ! oxo-acid-lyase activity
id: GO:0004452
name: isopentenyl-diphosphate delta-isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: isopentenyl diphosphate = dimethylallyl diphosphate." [EC:5.3.3.2, RHEA:23284]
+def: "Catalysis of the reaction: isopentenyl diphosphate = dimethylallyl diphosphate." [RHEA:23284]
synonym: "IPP isomerase activity" RELATED [EC:5.3.3.2]
synonym: "isopentenyl-diphosphate D-isomerase activity" EXACT []
synonym: "isopentenyl-diphosphate delta3-delta2-isomerase activity" RELATED [EC:5.3.3.2]
@@ -39574,7 +39521,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0004456
name: phosphogluconate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-phospho-D-gluconate = 2-dehydro-3-deoxy-6-phospho-D-gluconate + H(2)O." [EC:4.2.1.12, RHEA:17277]
+def: "Catalysis of the reaction: 6-phospho-D-gluconate = 2-dehydro-3-deoxy-6-phospho-D-gluconate + H2O." [EC:4.2.1.12, RHEA:17277]
synonym: "6-phospho-D-gluconate hydro-lyase (2-dehydro-3-deoxy-6-phospho-D-gluconate-forming)" RELATED [EC:4.2.1.12]
synonym: "6-phospho-D-gluconate hydro-lyase activity" RELATED [EC:4.2.1.12]
synonym: "6-phosphogluconate dehydrase activity" RELATED [EC:4.2.1.12]
@@ -39692,7 +39639,7 @@ is_a: GO:0016846 ! carbon-sulfur lyase activity
id: GO:0004463
name: leukotriene-A4 hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + leukotriene A(4) = leukotriene B(4)." [EC:3.3.2.6, RHEA:22324]
+def: "Catalysis of the reaction: H2O + leukotriene A(4) = leukotriene B(4)." [EC:3.3.2.6, RHEA:22324]
synonym: "(7E,9E,11Z,14Z)-(5S,6S)-5,6-epoxyicosa-7,9,11,14-tetraenoate hydrolase activity" RELATED [EC:3.3.2.6]
synonym: "leukotriene A(4) hydrolase activity" RELATED [EC:3.3.2.6]
synonym: "leukotriene A4 hydrolase activity" RELATED [EC:3.3.2.6]
@@ -39757,12 +39704,10 @@ is_a: GO:0004806 ! triglyceride lipase activity
id: GO:0004466
name: long-chain-acyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + ETF = 2,3-dehydroacyl-CoA + reduced ETF." [EC:1.3.8.8]
+def: "Catalysis of the reaction: a long-chain 2,3-saturated fatty acyl-CoA + H+ + oxidized [electron-transfer flavoprotein] = a long-chain (2E)-enoyl-CoA + reduced [electron-transfer flavoprotein]." [RHEA:17721]
synonym: "long-chain acyl-coenzyme A dehydrogenase activity" RELATED [EC:1.3.8.8]
-synonym: "long-chain-acyl-CoA:(acceptor) 2,3-oxidoreductase activity" RELATED [EC:1.3.8.8]
-synonym: "long-chain-acyl-CoA:acceptor 2,3-oxidoreductase activity" RELATED [EC:1.3.8.8]
-synonym: "palmitoyl-CoA dehydrogenase activity" RELATED [EC:1.3.8.8]
-synonym: "palmitoyl-coenzyme A dehydrogenase activity" RELATED [EC:1.3.8.8]
+synonym: "palmitoyl-CoA dehydrogenase activity" NARROW []
+synonym: "palmitoyl-coenzyme A dehydrogenase activity" NARROW []
xref: EC:1.3.8.8
xref: MetaCyc:LONG-CHAIN-ACYL-COA-DEHYDROGENASE-RXN
xref: RHEA:17721
@@ -39773,7 +39718,7 @@ id: GO:0004467
name: long-chain fatty acid-CoA ligase activity
namespace: molecular_function
alt_id: GO:0003996
-def: "Catalysis of the reaction: ATP + a long-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA; a long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [RHEA:15421]
+def: "Catalysis of the reaction: ATP + a long-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA. A long-chain fatty acid is a fatty acid with an aliphatic tail of 13 to 21 carbons." [RHEA:15421]
comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "acyl-activating enzyme activity" BROAD []
synonym: "acyl-CoA ligase activity" RELATED []
@@ -39809,6 +39754,7 @@ xref: Reactome:R-HSA-2046085 "Activation of alpha-linolenic acid to alpha-linole
xref: Reactome:R-HSA-2046098 "Activation of linoleic acid to linoleoyl-CoA"
xref: Reactome:R-HSA-548843 "ACSL3,4 ligate CoA to AA to form AA-CoA"
xref: Reactome:R-HSA-5696004 "ACSF2 ligates CoA-SH to MCFA"
+xref: Reactome:R-HSA-9734535 "SLC27A2 ligates CoA to bempedoic acid to form ETC-1002-CoA"
xref: RHEA:15421
xref: UM-BBD_enzymeID:e0025
is_a: GO:0015645 ! fatty acid ligase activity
@@ -39894,7 +39840,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0004474
name: malate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + glyoxylate + H(2)O = (S)-malate + CoA + H(+)." [EC:2.3.3.9, RHEA:18181]
+def: "Catalysis of the reaction: acetyl-CoA + glyoxylate + H2O = (S)-malate + CoA + H+." [RHEA:18181]
comment: Note that this function was formerly EC:4.1.3.2.
synonym: "acetyl-CoA:glyoxylate C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming)" RELATED [EC:2.3.3.9]
synonym: "glyoxylate transacetase activity" RELATED [EC:2.3.3.9]
@@ -39909,13 +39855,13 @@ xref: EC:2.3.3.9
xref: KEGG_REACTION:R00472
xref: MetaCyc:MALSYN-RXN
xref: RHEA:18181
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0004475
-name: mannose-1-phosphate guanylyltransferase activity
+name: mannose-1-phosphate guanylyltransferase (GTP) activity
namespace: molecular_function
-def: "Catalysis of the reaction: alpha-D-mannose 1-phosphate + GTP = diphosphate + GDP-alpha-D-mannose." [EC:2.7.7.13, RHEA:15229]
+def: "Catalysis of the reaction: alpha-D-mannose 1-phosphate + GTP = diphosphate + GDP-alpha-D-mannose." [RHEA:15229]
synonym: "GDP-mannose pyrophosphorylase activity" RELATED [EC:2.7.7.13]
synonym: "GTP-mannose-1-phosphate guanylyltransferase activity" RELATED [EC:2.7.7.13]
synonym: "GTP:alpha-D-mannose-1-phosphate guanylyltransferase activity" RELATED [EC:2.7.7.13]
@@ -39924,13 +39870,14 @@ synonym: "guanosine 5'-diphospho-D-mannose pyrophosphorylase activity" RELATED [
synonym: "guanosine diphosphomannose pyrophosphorylase activity" RELATED [EC:2.7.7.13]
synonym: "guanosine triphosphate-mannose 1-phosphate guanylyltransferase activity" RELATED [EC:2.7.7.13]
synonym: "mannose 1-phosphate guanylyltransferase (guanosine triphosphate)" RELATED [EC:2.7.7.13]
+synonym: "mannose-1-phosphate guanylyltransferase activity" BROAD []
synonym: "PIM-GMP (phosphomannose isomerase-guanosine 5'-diphospho-D-mannose pyrophosphorylase)" RELATED [EC:2.7.7.13]
xref: EC:2.7.7.13
xref: KEGG_REACTION:R00885
xref: MetaCyc:2.7.7.13-RXN
xref: Reactome:R-HSA-446221 "Mannose-1-phosphate converted to GDP-Mannose"
xref: RHEA:15229
-is_a: GO:0008905 ! mannose-phosphate guanylyltransferase activity
+is_a: GO:0070568 ! guanylyltransferase activity
[Term]
id: GO:0004476
@@ -39962,7 +39909,7 @@ synonym: "citrovorum factor cyclodehydrase activity" RELATED [EC:3.5.4.9]
synonym: "formyl-methenyl-methylenetetrahydrofolate synthetase (combined)" RELATED [EC:3.5.4.9]
xref: EC:3.5.4.9
xref: MetaCyc:METHENYLTHFCYCLOHYDRO-RXN
-xref: Reactome:R-HSA-200661 "10-formylTHF polyglutamate <=> 5,10-methenylTHF polyglutamate + H2O"
+xref: Reactome:R-HSA-200661 "MTHFD1 dimer transforms 10-formyl-THFPG to 5,10-methenyl-THFPG"
xref: Reactome:R-HSA-200740 "5,10-methenylTHF polyglutamate + H2O <=> 10-formylTHF polyglutamate"
xref: Reactome:R-HSA-6801328 "MTHFD2, D2L oxidise 5,10-methylene-THF to 5,10-methenyl-THF"
xref: RHEA:23700
@@ -40087,6 +40034,7 @@ xref: EC:2.7.7.50
xref: MetaCyc:MRNA-GUANYLYLTRANSFERASE-RXN
xref: Reactome:R-HSA-77081 "Formation of the CE:GMP intermediate complex"
xref: Reactome:R-HSA-77083 "Transfer of GMP from the capping enzyme GT site to 5'-end of mRNA"
+xref: Reactome:R-HSA-9815529 "nsp12 transfers guanylyl onto SARS-CoV-2 plus strand subgenomic RNAs"
xref: RHEA:54592
is_a: GO:0008192 ! RNA guanylyltransferase activity
@@ -40094,7 +40042,7 @@ is_a: GO:0008192 ! RNA guanylyltransferase activity
id: GO:0004485
name: methylcrotonoyl-CoA carboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-methylbut-2-enoyl-CoA + ATP + bicarbonate = trans-3-methylglutaconyl-CoA + ADP + 2 H(+) + phosphate." [EC:6.4.1.4, RHEA:13589]
+def: "Catalysis of the reaction: 3-methylbut-2-enoyl-CoA + ATP + bicarbonate = trans-3-methylglutaconyl-CoA + ADP + 2 H+ + phosphate." [EC:6.4.1.4, RHEA:13589]
synonym: "3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)" RELATED [EC:6.4.1.4]
synonym: "beta-methylcrotonyl CoA carboxylase activity" RELATED [EC:6.4.1.4]
synonym: "beta-methylcrotonyl coenzyme A carboxylase activity" RELATED [EC:6.4.1.4]
@@ -40119,14 +40067,14 @@ synonym: "5,10-methylene-THF dehydrogenase activity" EXACT [GOC:vw]
synonym: "N5,N10-methylenetetrahydrofolate dehydrogenase activity" RELATED [EC:1.5.1.5]
xref: EC:1.5.1.5
xref: Reactome:R-HSA-200644 "5,10-methyleneTHF polyglutamate + NADP+ <=> 5,10-methenylTHF polyglutamate + NADPH + H+"
-xref: Reactome:R-HSA-200718 "5,10-methenylTHF polyglutamate + NADPH + H+ <=> 5,10-methyleneTHF polyglutamate + NADP+"
+xref: Reactome:R-HSA-200718 "MTHFD1 dimer dehydrogenates 5,10-methenyl-THFPG to 5,10-methylene-THFPG"
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0004487
name: methylenetetrahydrofolate dehydrogenase (NAD+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5,10-methylenetetrahydrofolate + NAD(+) = 5,10-methenyltetrahydrofolate + NADH." [EC:1.5.1.15, RHEA:22892]
+def: "Catalysis of the reaction: 5,10-methylenetetrahydrofolate + NAD+ = 5,10-methenyltetrahydrofolate + NADH." [EC:1.5.1.15, RHEA:22892]
synonym: "5,10-methylenetetrahydrofolate dehydrogenase activity" RELATED [EC:1.5.1.5]
synonym: "5,10-methylenetetrahydrofolate:NAD+ oxidoreductase" RELATED [EC:1.5.1.15]
xref: EC:1.5.1.15
@@ -40140,7 +40088,7 @@ is_a: GO:0004486 ! methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity
id: GO:0004488
name: methylenetetrahydrofolate dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5,10-methylenetetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH." [EC:1.5.1.5, RHEA:22812]
+def: "Catalysis of the reaction: 5,10-methylenetetrahydrofolate + NADP+ = 5,10-methenyltetrahydrofolate + NADPH." [EC:1.5.1.5, RHEA:22812]
synonym: "5,10-methylenetetrahydrofolate:NADP oxidoreductase activity" RELATED [EC:1.5.1.5]
synonym: "5,10-methylenetetrahydrofolate:NADP+ oxidoreductase activity" RELATED [EC:1.5.1.5]
xref: EC:1.5.1.5
@@ -40188,14 +40136,14 @@ xref: EC:1.5.1.20
xref: KEGG_REACTION:R01224
xref: KEGG_REACTION:R07168
xref: MetaCyc:1.5.1.20-RXN
-xref: Reactome:R-HSA-200676 "5,10-methyleneTHF polyglutamate + NADPH + H+ => 5-methylTHF polyglutamate + NADP+"
+xref: Reactome:R-HSA-200676 "MTHFR dimer reduces 5,10-methylene-THFPG to 5-methyl-THFPG"
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0004490
name: methylglutaconyl-CoA hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-3-hydroxy-3-methylglutaryl-CoA = trans-3-methylglutaconyl-CoA + H(2)O." [EC:4.2.1.18, RHEA:21536]
+def: "Catalysis of the reaction: (S)-3-hydroxy-3-methylglutaryl-CoA = trans-3-methylglutaconyl-CoA + H2O." [EC:4.2.1.18, RHEA:21536]
synonym: "(S)-3-hydroxy-3-methylglutaryl-CoA hydro-lyase (trans-3-methylglutaconyl-CoA-forming)" RELATED [EC:4.2.1.18]
synonym: "(S)-3-hydroxy-3-methylglutaryl-CoA hydro-lyase activity" RELATED [EC:4.2.1.18]
synonym: "3-methylglutaconyl CoA hydratase activity" RELATED [EC:4.2.1.18]
@@ -40224,16 +40172,15 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
[Term]
id: GO:0004492
-name: methylmalonyl-CoA decarboxylase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: (S)-2-methyl-3-oxopropanoyl-CoA = propanoyl-CoA + CO2." [EC:7.2.4.3]
-synonym: "(S)-2-methyl-3-oxopropanoyl-CoA carboxy-lyase activity" RELATED [EC:7.2.4.3]
-synonym: "(S)-methylmalonyl-CoA carboxy-lyase (propanoyl-CoA-forming)" RELATED [EC:7.2.4.3]
-synonym: "(S)-methylmalonyl-CoA carboxy-lyase activity" RELATED [EC:7.2.4.3]
-synonym: "methylmalonyl-coenzyme A decarboxylase activity" RELATED [EC:7.2.4.3]
-xref: EC:7.2.4.3
+name: methyl/ethyl malonyl-CoA decarboxylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: (S)-methylmalonyl-CoA + H+ = CO2 + propanoyl-CoA or (2S)-ethylmalonyl-CoA + H+ = butanoyl-CoA + CO2." [PMID:22016388]
+synonym: "(S)-2-methyl-3-oxopropanoyl-CoA carboxy-lyase activity" NARROW []
+synonym: "(S)-methylmalonyl-CoA carboxy-lyase (propanoyl-CoA-forming)" NARROW []
+synonym: "(S)-methylmalonyl-CoA carboxy-lyase activity" NARROW []
+synonym: "ethylmalonyl-CoA decarboxylase activity" NARROW []
+synonym: "methylmalonyl-coenzyme A decarboxylase activity" NARROW []
xref: MetaCyc:METHYLMALONYL-COA-DECARBOXYLASE-RXN
-xref: RHEA:21396
is_a: GO:0016831 ! carboxy-lyase activity
[Term]
@@ -40284,7 +40231,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0004496
name: mevalonate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-mevalonate + ATP = (R)-5-phosphomevalonate + ADP + 2 H(+)." [EC:2.7.1.36, RHEA:17065]
+def: "Catalysis of the reaction: (R)-mevalonate + ATP = (R)-5-phosphomevalonate + ADP + 2 H+." [EC:2.7.1.36, RHEA:17065]
synonym: "ATP:(R)-mevalonate 5-phosphotransferase activity" RELATED [EC:2.7.1.36]
synonym: "ATP:mevalonate 5-phosphotransferase activity" RELATED [EC:2.7.1.36]
synonym: "mevalonate 5-phosphotransferase activity" RELATED [EC:2.7.1.36]
@@ -40366,13 +40313,20 @@ xref: Reactome:R-HSA-9027044 "CYP4 -oxidises 14(R)-HDHA to MaR-L2"
xref: Reactome:R-HSA-9027302 "CYP2E1 oxidises 14(S)-HDHA to 14(S),21(R)-diHDHA and 14(S),21(S)-diHDHA"
xref: Reactome:R-HSA-9027321 "CYP2E1 oxidises 14(R)-HDHA to 14(R),21(R)-diHDHA and 14(R),21(S)-diHDHA"
xref: Reactome:R-HSA-9037761 "CYP1, CYP2 hydroxylate (N)PD1 to 22-OH-(N)PD1"
+xref: Reactome:R-HSA-9749986 "CYP2,3 cytochromes hydroxylate ST to 2,3-DHBA"
+xref: Reactome:R-HSA-9750016 "CYP2,3 cytochromes hydroxylate ST to 2,5-DHBA"
+xref: Reactome:R-HSA-9753285 "CYP2E1 monooxygenates APAP to NAPQI"
+xref: Reactome:R-HSA-9756138 "CYP3A4 monooxygenates ATVL to 2-OH-ATVL"
+xref: Reactome:R-HSA-9756162 "CYP3A4 monooxygenates ATV to 4-OH-ATV"
+xref: Reactome:R-HSA-9756169 "CYP3A4 monooxygenates ATV to 2-OH-ATV"
+xref: Reactome:R-HSA-9756180 "CYP3A4 monooxygenates ATVL to 4-OH-ATVL"
is_a: GO:0016491 ! oxidoreductase activity
[Term]
id: GO:0004498
name: calcidiol 1-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: calcidiol + H(+) + NADPH + O(2) = calcitriol + H(2)O + NADP(+)." [EC:1.14.15.18, RHEA:20573]
+def: "Catalysis of the reaction: calcidiol + H+ + NADPH + O2 = calcitriol + H2O + NADP+." [EC:1.14.15.18, RHEA:20573]
synonym: "1-hydroxylase-25-hydroxyvitamin D3 activity" RELATED [EC:1.14.15.18]
synonym: "25-hydroxy D3-1alpha-hydroxylase activity" RELATED [EC:1.14.15.18]
synonym: "25-hydroxy vitamin D3 1-alpha-hydroxylase activity" EXACT []
@@ -40432,7 +40386,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0004500
name: dopamine beta-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-ascorbate + dopamine + O(2) = (R)-noradrenaline + dehydroascorbate + H(2)O." [EC:1.14.17.1, RHEA:19117]
+def: "Catalysis of the reaction: L-ascorbate + dopamine + O2 = (R)-noradrenaline + dehydroascorbate + H2O." [EC:1.14.17.1, RHEA:19117]
synonym: "(3,4-dihydroxyphenethylamine)beta-mono-oxygenase activity" RELATED [EC:1.14.17.1]
synonym: "3,4-dihydroxyphenethylamine beta-oxidase activity" RELATED [EC:1.14.17.1]
synonym: "3,4-dihydroxyphenethylamine,ascorbate:oxygen oxidoreductase (beta-hydroxylating)" RELATED [EC:1.14.17.1]
@@ -40458,7 +40412,7 @@ is_a: GO:0016715 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0004501
name: ecdysone 20-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + Ecdysone + O(2) = 20-hydroxyecdysone + A + H(2)O." [EC:1.14.99.22, RHEA:14021]
+def: "Catalysis of the reaction: AH(2) + Ecdysone + O2 = 20-hydroxyecdysone + A + H2O." [EC:1.14.99.22, RHEA:14021]
synonym: "alpha-ecdysone C-20 hydroxylase activity" RELATED [EC:1.14.99.22]
synonym: "ecdysone 20-hydroxylase activity" EXACT []
synonym: "ecdysone modification" BROAD []
@@ -40474,7 +40428,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0004502
name: kynurenine 3-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-kynurenine + H(+) + NADPH + O(2) = 3-hydroxy-L-kynurenine + H(2)O + NADP(+)." [EC:1.14.13.9, RHEA:20545]
+def: "Catalysis of the reaction: L-kynurenine + H+ + NADPH + O2 = 3-hydroxy-L-kynurenine + H2O + NADP+." [EC:1.14.13.9, RHEA:20545]
synonym: "kynurenine 3-hydroxylase activity" EXACT []
synonym: "kynurenine hydroxylase activity" RELATED [EC:1.14.13.9]
synonym: "L-kynurenine,NADPH:oxygen oxidoreductase (3-hydroxylating)" RELATED [EC:1.14.13.9]
@@ -40560,7 +40514,7 @@ is_a: GO:0016714 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0004506
name: squalene monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADPH + O(2) + squalene = (S)-2,3-epoxysqualene + H(2)O + NADP(+)." [RHEA:25282]
+def: "Catalysis of the reaction: H+ + NADPH + O2 + squalene = (S)-2,3-epoxysqualene + H2O + NADP+." [RHEA:25282]
synonym: "squalene 2,3-oxidocyclase activity" RELATED [EC:1.14.14.17]
synonym: "squalene epoxidase activity" RELATED [EC:1.14.14.17]
synonym: "squalene hydroxylase activity" RELATED [EC:1.14.14.17]
@@ -40633,7 +40587,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0004509
name: steroid 21-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: A C(21) steroid + [reduced NADPH--hemoprotein reductase] + O(2) = a 21-hydroxy-C(21)-steroid + [oxidized NADPH--hemoprotein reductase] + H(2)O." [RHEA:65612]
+def: "Catalysis of the reaction: A C(21) steroid + [reduced NADPH--hemoprotein reductase] + O2 = a 21-hydroxy-C(21)-steroid + [oxidized NADPH--hemoprotein reductase] + H2O." [RHEA:65612]
synonym: "21-hydroxylase activity" RELATED [EC:1.14.14.16]
synonym: "cytochrome P450 CYP21A1" NARROW []
synonym: "cytochrome p450 XXIA1 activity" NARROW [EC:1.14.14.16]
@@ -40716,7 +40670,7 @@ is_a: GO:0008373 ! sialyltransferase activity
id: GO:0004514
name: nicotinate-nucleotide diphosphorylase (carboxylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: CO(2) + diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+) + quinolinate." [EC:2.4.2.19, RHEA:12733]
+def: "Catalysis of the reaction: CO2 + diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H+ + quinolinate." [EC:2.4.2.19, RHEA:12733]
synonym: "NAD pyrophosphorylase activity" RELATED [EC:2.4.2.19]
synonym: "nicotinate mononucleotide pyrophosphorylase (carboxylating)" RELATED [EC:2.4.2.19]
synonym: "nicotinate-nucleotide pyrophosphorylase (carboxylating) activity" EXACT []
@@ -40758,7 +40712,7 @@ is_a: GO:0070566 ! adenylyltransferase activity
id: GO:0004516
name: nicotinate phosphoribosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + H(+) + nicotinate." [PMID:7503993]
+def: "Catalysis of the reaction: diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + H+ + nicotinate." [PMID:7503993]
synonym: "niacin ribonucleotidase activity" RELATED [EC:6.3.4.21]
synonym: "nicotinate-nucleotide:diphosphate phospho-alpha-D-ribosyltransferase activity" RELATED [EC:6.3.4.21]
synonym: "nicotinic acid mononucleotide glycohydrolase activity" RELATED [EC:6.3.4.21]
@@ -40817,10 +40771,11 @@ is_a: GO:0004518 ! nuclease activity
[Term]
id: GO:0004520
-name: endodeoxyribonuclease activity
+name: DNA endonuclease activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC:mah, ISBN:0198547684]
synonym: "DNA nicking activity" RELATED [GOC:mah]
+synonym: "endodeoxyribonuclease activity" EXACT []
synonym: "endonuclease G activity" RELATED []
xref: Reactome:R-HSA-110359 "APEX1 mediates endonucleolytic cleavage at the 5' side of the AP site"
xref: Reactome:R-HSA-5686440 "MUS81:EME1,EME2 cleaves D-loop"
@@ -40833,14 +40788,15 @@ xref: Reactome:R-HSA-6782204 "5' incision of damaged DNA strand by ERCC1:ERCC4 i
xref: Reactome:R-HSA-6782224 "3' incision by ERCC5 (XPG) in TC-NER"
xref: Reactome:R-HSA-9023941 "MRN:CtIP endonucleolytically cleaves single-strand DNA 3' to SPO11"
is_a: GO:0004519 ! endonuclease activity
-is_a: GO:0004536 ! deoxyribonuclease activity
+is_a: GO:0004536 ! DNA nuclease activity
[Term]
id: GO:0004521
-name: endoribonuclease activity
+name: RNA endonuclease activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks." [GOC:mah, ISBN:0198547684]
synonym: "endonuclease G activity" RELATED []
+synonym: "endoribonuclease activity" EXACT []
xref: Reactome:R-HSA-425923 "IRE1alpha hydrolyzes Xbp1 mRNA and Xbp1 mRNA is spliced"
xref: Reactome:R-HSA-426520 "Endonucleolytic RISC hydrolyzes target RNAs"
xref: Reactome:R-HSA-5601887 "PLD6 dimer cleaves primary piRNA transcript to pre-piRNA"
@@ -40852,8 +40808,10 @@ xref: Reactome:R-HSA-9009941 "RNASEL cleaves viral ssRNA"
xref: Reactome:R-HSA-9023909 "C3PO hydrolyzes cleaved passenger strand"
xref: Reactome:R-HSA-9023912 "AGO2 cleaves passenger strand of duplex siRNA"
xref: Reactome:R-HSA-927836 "SMG6 hydrolyzes mRNA with premature termination codon"
+xref: Reactome:R-HSA-9708327 "ANG cleaves tRNA to yield tRNA halves"
+xref: Reactome:R-HSA-9708812 "ELAC2 cleaves pre-tRNA to yield 3' trailer (type II tRF or tRF-1)"
is_a: GO:0004519 ! endonuclease activity
-is_a: GO:0004540 ! ribonuclease activity
+is_a: GO:0004540 ! RNA nuclease activity
[Term]
id: GO:0004522
@@ -40878,7 +40836,7 @@ synonym: "SLSG glycoproteins" RELATED []
xref: EC:4.6.1.18
xref: MetaCyc:3.1.27.5-RXN
xref: Wikipedia:Ribonuclease_A
-is_a: GO:0016892 ! endoribonuclease activity, producing 3'-phosphomonoesters
+is_a: GO:0016892 ! RNA endonuclease activity, producing 3'-phosphomonoesters
[Term]
id: GO:0004523
@@ -40911,7 +40869,7 @@ xref: Reactome:R-HSA-164528 "RNase H-mediated cleavage of the template strand"
xref: Reactome:R-HSA-173769 "RNase H-mediated digestion of tRNA, 3'PPT and cPPT RNA primers"
xref: Reactome:R-HSA-182795 "RNase H-mediated degradation of the template strand"
xref: Reactome:R-HSA-182859 "RNase H-mediated degradation of the RNA strand of the -sssDNA:RNA duplex"
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0004525
@@ -40926,7 +40884,9 @@ xref: MetaCyc:3.1.26.3-RXN
xref: Reactome:R-HSA-203862 "Dicer cleaves pre-miRNA to yield duplex miRNA"
xref: Reactome:R-HSA-203893 "Microprocessor complex cleaves pri-miRNA to pre-miRNA"
xref: Reactome:R-HSA-426464 "Dicer cleaves double-stranded RNA to yield double-stranded siRNA"
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+xref: Reactome:R-HSA-9708292 "DICER1 cleaves tRNA"
+xref: Reactome:R-HSA-9708408 "DICER1 cleaves tRNA Lys TTT 3 in tRNA:HIV RNA hybrid"
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
is_a: GO:0032296 ! double-stranded RNA-specific ribonuclease activity
[Term]
@@ -40941,7 +40901,7 @@ xref: MetaCyc:3.1.26.5-RXN
xref: Reactome:R-HSA-5696810 "RNase P cleaves the 5' end of pre-tRNA"
xref: Wikipedia:RNase_P
is_a: GO:0004549 ! tRNA-specific ribonuclease activity
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0004527
@@ -40979,11 +40939,11 @@ is_a: GO:0008081 ! phosphoric diester hydrolase activity
[Term]
id: GO:0004529
-name: exodeoxyribonuclease activity
+name: DNA exonuclease activity
namespace: molecular_function
def: "Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of a DNA molecule." [GOC:mah, ISBN:0198547684]
is_a: GO:0004527 ! exonuclease activity
-is_a: GO:0004536 ! deoxyribonuclease activity
+is_a: GO:0004536 ! DNA nuclease activity
[Term]
id: GO:0004530
@@ -41027,16 +40987,17 @@ synonym: "lysosomal DNase II activity" NARROW [EC:3.1.22.1]
synonym: "pancreatic DNase II" RELATED [EC:3.1.22.1]
xref: EC:3.1.22.1
xref: MetaCyc:3.1.22.1-RXN
-is_a: GO:0016889 ! endodeoxyribonuclease activity, producing 3'-phosphomonoesters
+is_a: GO:0016889 ! DNA endonuclease activity, producing 3'-phosphomonoesters
[Term]
id: GO:0004532
-name: exoribonuclease activity
+name: RNA exonuclease activity
namespace: molecular_function
def: "Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of an RNA molecule." [GOC:mah, ISBN:0198547684]
+synonym: "exoribonuclease activity" EXACT []
xref: Reactome:R-HSA-429961 "DCPS scavenges the 7-methylguanosine cap of mRNA"
is_a: GO:0004527 ! exonuclease activity
-is_a: GO:0004540 ! ribonuclease activity
+is_a: GO:0004540 ! RNA nuclease activity
[Term]
id: GO:0004533
@@ -41046,17 +41007,18 @@ def: "Catalysis of the exonucleolytic cleavage of RNA to 5'-phosphomonoester oli
synonym: "retroviral reverse transcriptase RNaseH" RELATED [EC:3.1.13.2]
xref: EC:3.1.13.2
xref: MetaCyc:3.1.13.2-RXN
-is_a: GO:0016896 ! exoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016896 ! RNA exonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0004534
-name: 5'-3' exoribonuclease activity
+name: 5'-3' RNA exonuclease activity
namespace: molecular_function
def: "Catalysis of the sequential cleavage of mononucleotides from a free 5' terminus of an RNA molecule." [GOC:mah, ISBN:0198547684]
+synonym: "5'-3' exoribonuclease activity" EXACT []
xref: EC:3.1.13.-
xref: Reactome:R-HSA-429845 "5' to 3' exoribonuclease hydrolyzes decapped mRNA"
is_a: GO:0008409 ! 5'-3' exonuclease activity
-is_a: GO:0016896 ! exoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016896 ! RNA exonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0004535
@@ -41071,15 +41033,16 @@ xref: MetaCyc:3.1.13.4-RXN
xref: Reactome:R-HSA-429955 "CCR4-NOT complex deadenylates mRNA"
xref: Reactome:R-HSA-429992 "PARN deadenylates mRNA"
xref: Reactome:R-HSA-430021 "PAN2-PAN3 complex partially deadenylates mRNA"
-is_a: GO:0000175 ! 3'-5'-exoribonuclease activity
+is_a: GO:0000175 ! 3'-5'-RNA exonuclease activity
[Term]
id: GO:0004536
-name: deoxyribonuclease activity
+name: DNA nuclease activity
namespace: molecular_function
alt_id: GO:0004537
def: "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid." [GOC:mah, ISBN:0198547684]
synonym: "caspase-activated deoxyribonuclease activity" NARROW []
+synonym: "deoxyribonuclease activity" EXACT []
xref: Reactome:R-HSA-211247 "Cleavage of DNA by DFF40"
xref: Reactome:R-HSA-5685994 "Long-range resection of DNA DSBs by EXO1 or DNA2"
xref: Reactome:R-HSA-6785986 "DNA nucleases unhook the interstrand crosslink (ICL)"
@@ -41088,9 +41051,11 @@ is_a: GO:0140097 ! catalytic activity, acting on DNA
[Term]
id: GO:0004540
-name: ribonuclease activity
+name: RNA nuclease activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA." [GOC:mah, ISBN:0198547684]
+synonym: "https://github.com/geneontology/go-ontology/issues/24408" EXACT []
+synonym: "ribonuclease activity" EXACT []
is_a: GO:0004518 ! nuclease activity
is_a: GO:0140098 ! catalytic activity, acting on RNA
@@ -41104,7 +41069,7 @@ xref: Reactome:R-HSA-5696813 "TSEN complex cleaves the intron from pre-tRNA"
xref: Reactome:R-HSA-5696815 "ELAC2 cleaves the 3' end of pre-tRNA"
xref: Reactome:R-HSA-6785722 "Mitochondrial RNase P (mtRNase P) cleaves the 5' ends of pre-tRNAs and ELAC2 (RNase Z) cleaves the 3' ends of pre-tRNAs in the H strand transcript"
xref: Reactome:R-HSA-6786854 "Mitochondrial RNase P (mtRNase P) cleaves the 5' ends of pre-tRNAs and ELAC2 (RNase Z) cleaves the 3' ends of pre-tRNAs in the L strand transcript"
-is_a: GO:0004540 ! ribonuclease activity
+is_a: GO:0004540 ! RNA nuclease activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
[Term]
@@ -41130,18 +41095,20 @@ xref: Reactome:R-HSA-482621 "(d)NTP + ADP <=> (d)NDP + ATP (NME1,2,3)"
xref: Reactome:R-HSA-482804 "(d)NDP + ATP <=> (d)NTP + ADP (NME4)"
xref: Reactome:R-HSA-482812 "(d)NTP + ADP <=> (d)NDP + ATP (NME4)"
xref: Reactome:R-HSA-6806877 "NME1:NME3 heterohexamer, NME2P1 phosphorylate NDPs to NTPs"
+xref: Reactome:R-HSA-9748969 "NME1:2 hexamer phosphorylates 6TdGDP to 6TdGTP"
+xref: Reactome:R-HSA-9748999 "NME1:2 hexamer phosphorylates 6TGDP to 6TGTP"
+xref: Reactome:R-HSA-9755013 "NME1,2 hexamers phosphorylate RBV-DP"
is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
is_a: GO:0019205 ! nucleobase-containing compound kinase activity
[Term]
id: GO:0004551
-name: nucleotide diphosphatase activity
+name: dinucleotide phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a dinucleotide + H2O = 2 mononucleotides." [EC:3.6.1.9]
-synonym: "dinucleotide nucleotidohydrolase activity" RELATED [EC:3.6.1.9]
+def: "Catalysis of the reaction: a dinucleotide + H2O = 2 mononucleotides." [PMID:2848456, PMID:4405504]
+synonym: "dinucleotide nucleotidohydrolase activity" RELATED []
+synonym: "nucleotide diphosphatase activity" BROAD []
synonym: "nucleotide pyrophosphatase activity" EXACT []
-synonym: "nucleotide-sugar pyrophosphatase activity" RELATED [EC:3.6.1.9]
-xref: EC:3.6.1.9
xref: MetaCyc:NUCLEOTIDE-PYROPHOSPHATASE-RXN
xref: Reactome:R-HSA-196955 "2xENPP1 hydrolyzes FAD to FMN"
is_a: GO:0016462 ! pyrophosphatase activity
@@ -41150,7 +41117,7 @@ is_a: GO:0016462 ! pyrophosphatase activity
id: GO:0004552
name: octanol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-octanol + NAD(+) = 1-octanal + H(+) + NADH." [EC:1.1.1.73, RHEA:24620]
+def: "Catalysis of the reaction: 1-octanol + NAD+ = 1-octanal + H+ + NADH." [EC:1.1.1.73, RHEA:24620]
synonym: "1-octanol dehydrogenase activity" RELATED [EC:1.1.1.73]
synonym: "octanol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.73]
xref: EC:1.1.1.73
@@ -41188,12 +41155,14 @@ is_a: GO:0015927 ! trehalase activity
id: GO:0004556
name: alpha-amylase activity
namespace: molecular_function
-def: "Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units." [EC:3.2.1.1]
-synonym: "1,4-alpha-D-glucan glucanohydrolase activity" RELATED [EC:3.2.1.1]
-synonym: "alpha amylase activity" RELATED [EC:3.2.1.1]
-synonym: "endoamylase activity" RELATED [EC:3.2.1.1]
+alt_id: GO:0103025
+def: "Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units." [PMID:12527308]
+synonym: "1,4-alpha-D-glucan glucanohydrolase activity" RELATED []
+synonym: "alpha amylase activity" RELATED []
+synonym: "alpha-amylase activity (releasing maltohexaose)" NARROW []
+synonym: "endoamylase activity" RELATED []
synonym: "glycogenase activity" BROAD [EC:3.2.1.1]
-synonym: "taka-amylase A" RELATED [EC:3.2.1.1]
+synonym: "taka-amylase A" RELATED []
xref: EC:3.2.1.1
xref: MetaCyc:ALPHA-AMYL-RXN
xref: MetaCyc:RXN-1823
@@ -41206,7 +41175,7 @@ is_a: GO:0016160 ! amylase activity
id: GO:0004557
name: alpha-galactosidase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactohydrolase." [EC:3.2.1.22]
+def: "Catalysis of the hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids." [EC:3.2.1.22, ISBN:0198529171]
synonym: "alpha-D-galactosidase activity" RELATED [EC:3.2.1.22]
synonym: "alpha-D-galactoside galactohydrolase activity" RELATED [EC:3.2.1.22]
synonym: "alpha-galactosidase A" RELATED [EC:3.2.1.22]
@@ -41731,7 +41700,7 @@ is_a: GO:0016743 ! carboxyl- or carbamoyltransferase activity
id: GO:0004586
name: ornithine decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-ornithine + H(+) = CO(2) + putrescine." [EC:4.1.1.17, RHEA:22964]
+def: "Catalysis of the reaction: L-ornithine + H+ = CO2 + putrescine." [EC:4.1.1.17, RHEA:22964]
synonym: "L-ornithine carboxy-lyase (putrescine-forming)" RELATED [EC:4.1.1.17]
synonym: "L-ornithine carboxy-lyase activity" NARROW [EC:4.1.1.17]
synonym: "SpeC" RELATED [EC:4.1.1.17]
@@ -41797,27 +41766,29 @@ synonym: "orotidylic phosphorylase activity" RELATED [EC:2.4.2.10]
synonym: "orotidylic pyrophosphorylase activity" RELATED [EC:2.4.2.10]
xref: EC:2.4.2.10
xref: MetaCyc:OROPRIBTRANS-RXN
-xref: Reactome:R-HSA-73567 "orotate + 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) <=> orotidine 5'-monophosphate (OMP) + pyrophosphate"
+xref: Reactome:R-HSA-73567 "UMPS dimer transfers phosphoribosyl group to ORO to form OMP"
xref: RHEA:10380
is_a: GO:0016763 ! pentosyltransferase activity
[Term]
id: GO:0004589
-name: orotate reductase (NADH) activity
+name: dihydroorotate dehydrogenase (NADH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-dihydroorotate + NAD(+) = H(+) + NADH + orotate." [EC:1.3.1.14, RHEA:13513]
+def: "Catalysis of the reaction: (S)-dihydroorotate + NAD+ = H+ + NADH + orotate." [RHEA:13513]
synonym: "(S)-dihydroorotate:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.14]
+synonym: "orotate reductase (NADH) activity" EXACT []
xref: EC:1.3.1.14
xref: KEGG_REACTION:R01869
xref: MetaCyc:OROTATE-REDUCTASE-NADH-RXN
xref: RHEA:13513
+is_a: GO:0004152 ! dihydroorotate dehydrogenase activity
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0004590
name: orotidine-5'-phosphate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP." [EC:4.1.1.23, RHEA:11596]
+def: "Catalysis of the reaction: H+ + orotidine 5'-phosphate = CO2 + UMP." [EC:4.1.1.23, RHEA:11596]
synonym: "ODCase activity" RELATED [EC:4.1.1.23]
synonym: "OMP decarboxylase activity" RELATED [EC:4.1.1.23]
synonym: "OMP-DC" RELATED [EC:4.1.1.23]
@@ -41839,7 +41810,7 @@ synonym: "uridine 5'-monophosphate synthase activity" RELATED [EC:4.1.1.23]
xref: EC:4.1.1.23
xref: KEGG_REACTION:R00965
xref: MetaCyc:OROTPDECARB-RXN
-xref: Reactome:R-HSA-73564 "orotidine 5'-monophosphate => uridine 5'-monophosphate + CO2"
+xref: Reactome:R-HSA-73564 "UMPS dimer decarboxylates OMP to UMP"
xref: RHEA:11596
is_a: GO:0016831 ! carboxy-lyase activity
@@ -41887,7 +41858,7 @@ is_a: GO:0016881 ! acid-amino acid ligase activity
id: GO:0004593
name: pantothenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-pantothenate + H(2)O = (R)-pantoate + beta-alanine." [EC:3.5.1.22, RHEA:12448]
+def: "Catalysis of the reaction: (R)-pantothenate + H2O = (R)-pantoate + beta-alanine." [EC:3.5.1.22, RHEA:12448]
synonym: "(R)-pantothenate amidohydrolase activity" RELATED [EC:3.5.1.22]
synonym: "pantothenate amidohydrolase activity" RELATED [EC:3.5.1.22]
synonym: "pantothenate hydrolase activity" RELATED [EC:3.5.1.22]
@@ -41950,6 +41921,7 @@ synonym: "nalpha-acetyltransferase activity" EXACT []
synonym: "NAT activity" RELATED []
synonym: "peptide acetyltransferase activity" RELATED []
synonym: "protein N-terminal acetyltransferase activity" EXACT []
+xref: EC:2.3.1.255
xref: MetaCyc:PEPTIDE-ALPHA-N-ACETYLTRANSFERASE-RXN
xref: Reactome:R-HSA-6814090 "NatC acetylates ARFFRP1"
is_a: GO:0034212 ! peptide N-acetyltransferase activity
@@ -41991,7 +41963,7 @@ alt_id: GO:0016685
alt_id: GO:0016686
alt_id: GO:0016687
alt_id: GO:0016693
-def: "Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O." [GOC:curators]
+def: "Catalysis of the reaction: a donor + a peroxide = an oxidized donor + 2 H2O." [GOC:curators]
subset: goslim_metagenomics
synonym: "bacterial catalase-peroxidase activity" NARROW []
synonym: "donor:hydrogen-peroxide oxidoreductase activity" RELATED []
@@ -42004,7 +41976,7 @@ synonym: "japanese radish peroxidase" NARROW []
synonym: "lactoperoxidase activity" NARROW []
synonym: "MPO" RELATED []
synonym: "myeloperoxidase activity" NARROW []
-synonym: "oxyperoxidase activity" RELATED [EC:1.11.1.-]
+synonym: "oxyperoxidase activity" RELATED []
synonym: "peroxidase reaction" EXACT []
synonym: "protoheme peroxidase" NARROW []
synonym: "pyrocatechol peroxidase" NARROW []
@@ -42030,6 +42002,7 @@ xref: Reactome:R-HSA-6789031 "Membrane-bound myeloperoxidase (MPO) produces hypo
xref: Reactome:R-HSA-6789126 "Myeloperoxidase (MPO) produces hypochlorous acid (HOCl)"
xref: Reactome:R-HSA-8855490 "Lactoperoxidase (LPO) produces OSCN-"
xref: Reactome:R-HSA-8933635 "Myeloperoxidase (MPO) catalyzes oxidation of nitrite to nitrogen dioxide"
+xref: Wikipedia:Peroxidase
is_a: GO:0016209 ! antioxidant activity
is_a: GO:0016684 ! oxidoreductase activity, acting on peroxide as acceptor
@@ -42055,7 +42028,7 @@ xref: Reactome:R-HSA-3341277 "GPX2 catalyzes 2 glutathione, reduced + H2O2 => gl
xref: Reactome:R-HSA-3341397 "GPX3 catalyzes 2 glutathione, reduced + H2O2 => glutathione, oxidized + 2 H2O"
xref: Reactome:R-HSA-3343700 "PRDX6:GSTP1 catalyzes 2 glutathione, reduced + H2O2 => glutathione, oxidized + 2 H2O"
xref: Reactome:R-HSA-6799695 "GPX5,6 reduce H2O2 to H2O"
-xref: Reactome:R-HSA-71676 "2 glutathione, reduced + H2O2 => glutathione, oxidized + 2 H2O"
+xref: Reactome:R-HSA-71676 "GPX1 catalyzes reaction of reduced glutathione and H2O2 to form oxidized glutathione and H2O"
xref: RHEA:16833
is_a: GO:0004601 ! peroxidase activity
@@ -42082,7 +42055,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0004604
name: phosphoadenylyl-sulfate reductase (thioredoxin) activity
namespace: molecular_function
-def: "Catalysis of the reaction: adenosine 3',5'-diphosphate + H(+) + sulfite + thioredoxin disulfide = 3'-phospho-5'-adenylyl sulfate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin; 3'-phosphoadenosine 5'-phosphosulfate is also known as PAPS." [EC:1.8.4.8, RHEA:11724]
+def: "Catalysis of the reaction: adenosine 3',5'-diphosphate + H+ + sulfite + thioredoxin disulfide = 3'-phospho-5'-adenylyl sulfate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin; 3'-phosphoadenosine 5'-phosphosulfate is also known as PAPS." [EC:1.8.4.8, RHEA:11724]
synonym: "3'-phosphoadenylylsulfate reductase activity" RELATED [EC:1.8.4.8]
synonym: "adenosine 3',5'-bisphosphate,sulfite:oxidized-thioredoxin oxidoreductase (3'-phosphoadenosine-5'-phosphosulfate-forming)" RELATED [EC:1.8.4.8]
synonym: "adenosine 3',5'-bisphosphate,sulfite:thioredoxin-disulfide oxidoreductase (3'-phosphoadenosine-5'-phosphosulfate-forming)" RELATED [EC:1.8.4.8]
@@ -42148,7 +42121,7 @@ is_a: GO:0008374 ! O-acyltransferase activity
id: GO:0004608
name: phosphatidylethanolamine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + phosphatidylethanolamine = S-adenosyl-L-homocysteine + H(+) + phosphatidyl-N-methylethanolamine." [EC:2.1.1.17, RHEA:11164]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + phosphatidylethanolamine = S-adenosyl-L-homocysteine + H+ + phosphatidyl-N-methylethanolamine." [EC:2.1.1.17, RHEA:11164]
synonym: "lipid methyl transferase activity" RELATED [EC:2.1.1.17]
synonym: "LMTase activity" RELATED [EC:2.1.1.17]
synonym: "PEMT" RELATED [EC:2.1.1.17]
@@ -42168,7 +42141,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0004609
name: phosphatidylserine decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + phosphatidyl-L-serine = CO(2) + phosphatidylethanolamine." [EC:4.1.1.65, RHEA:20828]
+def: "Catalysis of the reaction: H+ + phosphatidyl-L-serine = CO2 + phosphatidylethanolamine." [EC:4.1.1.65, RHEA:20828]
synonym: "phosphatidyl-L-serine carboxy-lyase (phosphatidylethanolamine-forming)" RELATED [EC:4.1.1.65]
synonym: "phosphatidyl-L-serine carboxy-lyase activity" RELATED [EC:4.1.1.65]
synonym: "PS decarboxylase activity" RELATED [EC:4.1.1.65]
@@ -42212,7 +42185,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0004612
name: phosphoenolpyruvate carboxykinase (ATP) activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + oxaloacetate = ADP + CO(2) + H(+) + phosphoenolpyruvate." [EC:4.1.1.49, RHEA:18617]
+def: "Catalysis of the reaction: ATP + oxaloacetate = ADP + CO2 + H+ + phosphoenolpyruvate." [EC:4.1.1.49, RHEA:18617]
synonym: "ATP:oxaloacetate carboxy-lyase (transphosphorylating)" RELATED [EC:4.1.1.49]
synonym: "ATP:oxaloacetate carboxy-lyase (transphosphorylating; phosphoenolpyruvate-forming)" RELATED [EC:4.1.1.49]
synonym: "PEPCK (ATP)" RELATED [EC:4.1.1.49]
@@ -42243,8 +42216,8 @@ synonym: "phosphopyruvate (guanosine triphosphate) carboxykinase activity" RELAT
synonym: "phosphopyruvate carboxylase (GTP)" RELATED [EC:4.1.1.32]
xref: EC:4.1.1.32
xref: MetaCyc:4.1.1.32-RXN
-xref: Reactome:R-HSA-372819 "oxaloacetate + GTP => phosphoenolpyruvate + GDP + CO2 [mitochondrial matrix]"
-xref: Reactome:R-HSA-70241 "oxaloacetate + GTP => phosphoenolpyruvate + GDP + CO2 [cytosol]"
+xref: Reactome:R-HSA-372819 "PCK2 phosphorylates OA to yield PEP"
+xref: Reactome:R-HSA-70241 "PCK1 phosphorylates OA to yield PEP"
xref: RHEA:10388
is_a: GO:0004611 ! phosphoenolpyruvate carboxykinase activity
@@ -42259,8 +42232,6 @@ synonym: "phosphoglucose mutase activity" RELATED [EC:5.4.2.2]
xref: EC:5.4.2.2
xref: MetaCyc:PHOSPHOGLUCMUT-RXN
xref: Reactome:R-HSA-5609939 "Defective PGM1 does not isomerise G6P to G1P"
-xref: Reactome:R-HSA-70272 "PGM:Mg2+ isomerise G6P to G1P"
-xref: Reactome:R-HSA-70427 "PGM:Mg2+ isomerise G1P to G6P"
xref: Reactome:R-HSA-9638125 "PGM1:Mg2+ isomerises G1P to G6P"
xref: Reactome:R-HSA-9638127 "PGM1:Mg2+ isomerises G6P to G1P"
xref: RHEA:23536
@@ -42327,7 +42298,7 @@ synonym: "SerA" RELATED [EC:1.1.1.95]
synonym: "SerA 3PG dehydrogenase activity" RELATED [EC:1.1.1.95]
xref: EC:1.1.1.95
xref: MetaCyc:PGLYCDEHYDROG-RXN
-xref: Reactome:R-HSA-977348 "PHGHD tetramer dehydrogenates 3PG"
+xref: Reactome:R-HSA-977348 "PHGDH tetramer dehydrogenates 3PG"
xref: RHEA:12641
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -42335,7 +42306,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0004618
name: phosphoglycerate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H(+)." [EC:2.7.2.3, RHEA:14801]
+def: "Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H+." [EC:2.7.2.3, RHEA:14801]
synonym: "3-PGK" RELATED [EC:2.7.2.3]
synonym: "3-phosphoglycerate kinase activity" RELATED [EC:2.7.2.3]
synonym: "3-phosphoglycerate phosphokinase activity" RELATED [EC:2.7.2.3]
@@ -42354,7 +42325,7 @@ synonym: "phosphoglycerokinase activity" RELATED [EC:2.7.2.3]
xref: EC:2.7.2.3
xref: KEGG_REACTION:R01512
xref: MetaCyc:PHOSGLYPHOS-RXN
-xref: Reactome:R-HSA-70486 "ATP + 3-Phospho-D-glycerate <=> ADP + 1,3-bisphospho-D-glycerate"
+xref: Reactome:R-HSA-70486 "PGK complexes (PGK1,2) phosphorylate 3PG to form 1,3BPG"
xref: Reactome:R-HSA-71850 "1,3-bisphospho-D-glycerate + ADP <=> 3-phospho-D-glycerate + ATP"
xref: RHEA:14801
is_a: GO:0016301 ! kinase activity
@@ -42364,22 +42335,15 @@ is_a: GO:0016774 ! phosphotransferase activity, carboxyl group as acceptor
id: GO:0004619
name: phosphoglycerate mutase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate." [EC:5.4.2.1]
-synonym: "bisphosphoglyceromutase" RELATED [EC:5.4.2.1]
-synonym: "D-phosphoglycerate 2,3-phosphomutase activity" RELATED [EC:5.4.2.1]
-synonym: "diphosphoglycomutase" RELATED [EC:5.4.2.1]
-synonym: "GriP mutase" NARROW [EC:5.4.2.1]
-synonym: "monophosphoglycerate mutase activity" RELATED [EC:5.4.2.1]
-synonym: "monophosphoglyceromutase activity" RELATED [EC:5.4.2.1]
-synonym: "MPGM" RELATED [EC:5.4.2.1]
-synonym: "PGA mutase activity" RELATED [EC:5.4.2.1]
-synonym: "PGAM activity" RELATED [EC:5.4.2.1]
+def: "Catalysis of the reaction: 2-phosphoglycerate = 3-phosphoglycerate." [RHEA:15901]
+synonym: "D-phosphoglycerate 2,3-phosphomutase activity" RELATED []
+synonym: "PGA mutase activity" RELATED []
+synonym: "PGAM activity" RELATED []
synonym: "PGM" EXACT []
-synonym: "phosphoglycerate phosphomutase activity" RELATED [EC:5.4.2.1]
-synonym: "phosphoglyceromutase activity" RELATED [EC:5.4.2.1]
-xref: EC:5.4.2.1
+synonym: "phosphoglycerate phosphomutase activity" RELATED []
+synonym: "phosphoglyceromutase activity" RELATED []
xref: MetaCyc:3PGAREARR-RXN
-xref: Reactome:R-HSA-71445 "2-Phospho-D-glycerate <=> 3-Phospho-D-glycerate"
+xref: Reactome:R-HSA-71445 "PGAM dimers (PGAM1,2) isomerise 2PG to 3PG"
xref: Reactome:R-HSA-71654 "3-Phospho-D-glycerate <=> 2-Phospho-D-glycerate"
xref: RHEA:15901
is_a: GO:0016868 ! intramolecular transferase activity, phosphotransferases
@@ -42390,7 +42354,6 @@ name: phospholipase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of a glycerophospholipid." [ISBN:0198506732]
subset: goslim_chembl
-xref: EC:3.1.1.-
xref: Reactome:R-HSA-6786650 "DDHD1,2 hydrolyse PA"
xref: Reactome:R-HSA-6792445 "LIPH, I hydrolyse PA to 2-acyl LPA"
is_a: GO:0016298 ! lipase activity
@@ -42553,12 +42516,8 @@ id: GO:0004629
name: phospholipase C activity
namespace: molecular_function
alt_id: GO:0042298
-def: "Catalysis of the reaction: a phospholipid + H2O = 1,2-diacylglycerol + a phosphatidate." [EC:3.1.4.3, GOC:mah]
-synonym: "lecithinase C activity" RELATED [EC:3.1.4.3]
-synonym: "lipophosphodiesterase C" RELATED [EC:3.1.4.3]
-synonym: "phosphatidase C" RELATED [EC:3.1.4.3]
-xref: EC:3.1.4.3
-xref: MetaCyc:PHOSPHOLIPASE-C-RXN
+def: "Catalysis of the reaction: a phospholipid + H2O = 1,2-diacylglycerol + a phosphatidate." [GOC:mah]
+synonym: "phosphatidase C" RELATED []
xref: Reactome:R-HSA-1112666 "BLNK (SLP-65) Signalosome hydrolyzes phosphatidyinositol bisphosphate forming diacylglycerol and inositol-1,4,5-trisphosphate"
xref: Reactome:R-HSA-114688 "PLC-beta hydrolyses PIP2 to DAG and IP3"
xref: Reactome:R-HSA-114689 "PLC gamma 2-mediated PIP2 hydrolysis"
@@ -42591,7 +42550,7 @@ is_a: GO:0008081 ! phosphoric diester hydrolase activity
id: GO:0004631
name: phosphomevalonate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-5-phosphomevalonate + ATP = (R)-5-diphosphomevalonate + ADP + H(+)." [EC:2.7.4.2, RHEA:16341]
+def: "Catalysis of the reaction: (R)-5-phosphomevalonate + ATP = (R)-5-diphosphomevalonate + ADP + H+." [EC:2.7.4.2, RHEA:16341]
synonym: "5-phosphomevalonate kinase activity" RELATED [EC:2.7.4.2]
synonym: "ATP:(R)-5-phosphomevalonate phosphotransferase activity" RELATED [EC:2.7.4.2]
synonym: "ATP:5-phosphomevalonate phosphotransferase activity" RELATED [EC:2.7.4.2]
@@ -42624,7 +42583,7 @@ is_a: GO:0016881 ! acid-amino acid ligase activity
id: GO:0004633
name: phosphopantothenoylcysteine decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-[(R)-4-phosphonatopantothenoyl]-L-cysteinate + H(+) = CO(2) + pantetheine 4'-phosphate." [EC:4.1.1.36, RHEA:16793]
+def: "Catalysis of the reaction: N-[(R)-4-phosphonatopantothenoyl]-L-cysteinate + H+ = CO2 + pantetheine 4'-phosphate." [EC:4.1.1.36, RHEA:16793]
synonym: "4-phosphopantothenoyl-L-cysteine decarboxylase activity" RELATED [EC:4.1.1.36]
synonym: "4-phosphopantotheoylcysteine decarboxylase activity" RELATED [EC:4.1.1.36]
synonym: "N-((R)-4'-phosphopantothenoyl)-L-cysteine carboxy-lyase activity" RELATED [EC:4.1.1.36]
@@ -42656,7 +42615,7 @@ synonym: "nervous-system specific enolase" NARROW [EC:4.2.1.11]
synonym: "phosphoenolpyruvate hydratase activity" RELATED [EC:4.2.1.11]
xref: EC:4.2.1.11
xref: MetaCyc:2PGADEHYDRAT-RXN
-xref: Reactome:R-HSA-70494 "Phosphoenolpyruvate + H2O <=> 2-Phospho-D-glycerate"
+xref: Reactome:R-HSA-70494 "Enolase dimers (ENO1,2,3) convert PEP to 2PG"
xref: Reactome:R-HSA-71660 "2-Phospho-D-glycerate <=> Phosphoenolpyruvate + H2O"
xref: RHEA:10164
is_a: GO:0016836 ! hydro-lyase activity
@@ -42665,7 +42624,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0004635
name: phosphoribosyl-AMP cyclohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-(5-phosphonatoribosyl)-5'-AMP + H(2)O = 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide." [EC:3.5.4.19, RHEA:20049]
+def: "Catalysis of the reaction: 1-(5-phosphonatoribosyl)-5'-AMP + H2O = 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide." [EC:3.5.4.19, RHEA:20049]
synonym: "1-(5-phospho-D-ribosyl)-AMP 1,6-hydrolase activity" RELATED [EC:3.5.4.19]
synonym: "phosphoribosyladenosine monophosphate cyclohydrolase activity" RELATED [EC:3.5.4.19]
synonym: "PRAMP-cyclohydrolase activity" RELATED [EC:3.5.4.19]
@@ -42679,7 +42638,7 @@ is_a: GO:0019238 ! cyclohydrolase activity
id: GO:0004636
name: phosphoribosyl-ATP diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-(5-phospho-D-ribosyl)-ATP + H(2)O = 1-(5-phosphonatoribosyl)-5'-AMP + diphosphate + H(+)." [EC:3.6.1.31, RHEA:22828]
+def: "Catalysis of the reaction: 1-(5-phospho-D-ribosyl)-ATP + H2O = 1-(5-phosphonatoribosyl)-5'-AMP + diphosphate + H+." [EC:3.6.1.31, RHEA:22828]
synonym: "1-(5-phosphoribosyl)-ATP diphosphohydrolase activity" RELATED [EC:3.6.1.31]
synonym: "phosphoribosyl-ATP pyrophosphatase activity" EXACT []
synonym: "phosphoribosyladenosine triphosphate pyrophosphatase activity" RELATED [EC:3.6.1.31]
@@ -42693,7 +42652,7 @@ is_a: GO:0016462 ! pyrophosphatase activity
id: GO:0004637
name: phosphoribosylamine-glycine ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-phospho-D-ribosylamine + ATP + glycine = N(1)-(5-phospho-D-ribosyl)glycinamide + ADP + 2 H(+) + phosphate." [EC:6.3.4.13, RHEA:17453]
+def: "Catalysis of the reaction: 5-phospho-D-ribosylamine + ATP + glycine = N(1)-(5-phospho-D-ribosyl)glycinamide + ADP + 2 H+ + phosphate." [EC:6.3.4.13, RHEA:17453]
synonym: "2-amino-N-ribosylacetamide 5'-phosphate kinosynthase activity" RELATED [EC:6.3.4.13]
synonym: "5'-phosphoribosylglycinamide synthetase activity" RELATED [EC:6.3.4.13]
synonym: "5-phospho-D-ribosylamine:glycine ligase (ADP-forming)" RELATED [EC:6.3.4.13]
@@ -42715,7 +42674,7 @@ is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
id: GO:0004638
name: phosphoribosylaminoimidazole carboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 2 H(+) = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2)." [EC:4.1.1.21, RHEA:10792]
+def: "Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 2 H+ = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO2." [EC:4.1.1.21, RHEA:10792]
synonym: "1-(5-phosphoribosyl)-5-amino-4-imidazolecarboxylate carboxy-lyase activity" RELATED [EC:4.1.1.21]
synonym: "5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate carboxy-lyase [5-amino-1-(5-phospho-D-ribosyl)imidazole-forming]" RELATED [EC:4.1.1.21]
synonym: "5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate carboxy-lyase activity" RELATED [EC:4.1.1.21]
@@ -42735,7 +42694,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0004639
name: phosphoribosylaminoimidazolesuccinocarboxamide synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate + ATP = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H(+) + phosphate." [EC:6.3.2.6, RHEA:22628]
+def: "Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate + ATP = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + 2 H+ + phosphate." [EC:6.3.2.6, RHEA:22628]
synonym: "4-((N-succinylamino)carbonyl)-5-aminoimidazole ribonucleotide synthetase activity" RELATED [EC:6.3.2.6]
synonym: "4-(N-succinocarboxamide)-5-aminoimidazole synthetase activity" RELATED [EC:6.3.2.6]
synonym: "4-[(N-succinylamino)carbonyl]-5-aminoimidazole ribonucleotide synthetase activity" RELATED [EC:6.3.2.6]
@@ -42776,7 +42735,7 @@ is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldos
id: GO:0004641
name: phosphoribosylformylglycinamidine cyclo-ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-D-ribosyl)imidazole + ADP + 2 H(+) + phosphate." [EC:6.3.3.1, RHEA:23032]
+def: "Catalysis of the reaction: 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-D-ribosyl)imidazole + ADP + 2 H+ + phosphate." [EC:6.3.3.1, RHEA:23032]
synonym: "2-(formamido)-1-N-(5-phosphoribosyl)acetamidine cyclo-ligase (ADP-forming)" RELATED [EC:6.3.3.1]
synonym: "2-(formamido)-N1-(5-phosphoribosyl)acetamidine cyclo-ligase (ADP-forming)" RELATED [EC:6.3.3.1]
synonym: "5'-aminoimidazole ribonucleotide synthetase activity" RELATED [EC:6.3.3.1]
@@ -42796,7 +42755,7 @@ is_a: GO:0016882 ! cyclo-ligase activity
id: GO:0004642
name: phosphoribosylformylglycinamidine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide + L-glutamine + ATP + H(2)O = 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + L-glutamate + ADP + 2 H(+) + phosphate." [EC:6.3.5.3, RHEA:17129]
+def: "Catalysis of the reaction: N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide + L-glutamine + ATP + H2O = 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + L-glutamate + ADP + 2 H+ + phosphate." [EC:6.3.5.3, RHEA:17129]
synonym: "2-N-formyl-1-N-(5-phospho-D-ribosyl)glycinamide:L-glutamine amido-ligase (ADP-forming)" RELATED [EC:6.3.5.3]
synonym: "5'-phosphoribosylformylglycinamide:L-glutamine amido-ligase (ADP-forming)" RELATED [EC:6.3.5.3]
synonym: "FGAM synthase activity" RELATED [EC:6.3.5.3]
@@ -42946,13 +42905,14 @@ xref: EC:3.1.3.33
xref: MetaCyc:POLYNUCLEOTIDE-5-PHOSPHATASE-RXN
xref: Reactome:R-HSA-77078 "Hydrolysis of the 5'-end of the nascent transcript by the capping enzyme"
xref: RHEA:11008
-is_a: GO:0098518 ! polynucleotide phosphatase activity
+is_a: GO:0016791 ! phosphatase activity
[Term]
id: GO:0004652
-name: polynucleotide adenylyltransferase activity
+name: obsolete polynucleotide adenylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the template-independent extension of the 3'- end of an RNA or DNA strand by addition of one adenosine molecule at a time. Cannot initiate a chain 'de novo'. The primer, depending on the source of the enzyme, may be an RNA or DNA fragment, or oligo(A) bearing a 3'-OH terminal group." [EC:2.7.7.19]
+def: "OBSOLETE. Catalysis of the template-independent extension of the 3'- end of an RNA or DNA strand by addition of one adenosine molecule at a time. Cannot initiate a chain 'de novo'. The primer, depending on the source of the enzyme, may be an RNA or DNA fragment, or oligo(A) bearing a 3'-OH terminal group." [EC:2.7.7.19]
+comment: This term was obsoleted because it represents the same activity as RNA adenylyltransferase activity ; GO:1990817.
synonym: "adenosine triphosphate:ribonucleic acid adenylyltransferase activity" RELATED [EC:2.7.7.19]
synonym: "AMP polynucleotidylexotransferase activity" RELATED [EC:2.7.7.19]
synonym: "ATP-polynucleotide adenylyltransferase activity" RELATED [EC:2.7.7.19]
@@ -42971,11 +42931,8 @@ synonym: "polyadenylic polymerase activity" RELATED [EC:2.7.7.19]
synonym: "RNA adenylating enzyme activity" RELATED [EC:2.7.7.19]
synonym: "RNA formation factors, PF1" RELATED [EC:2.7.7.19]
synonym: "terminal riboadenylate transferase activity" RELATED [EC:2.7.7.19]
-xref: EC:2.7.7.19
-xref: MetaCyc:POLYNUCLEOTIDE-ADENYLYLTRANSFERASE-RXN
-xref: Reactome:R-HSA-72185 "mRNA polyadenylation"
-xref: RHEA:11332
-is_a: GO:0070566 ! adenylyltransferase activity
+is_obsolete: true
+replaced_by: GO:1990817
[Term]
id: GO:0004653
@@ -43002,7 +42959,7 @@ xref: MetaCyc:2.4.1.41-RXN
xref: Reactome:R-HSA-5096532 "Defective GALNT12 does not transfer GalNAc to mucins"
xref: Reactome:R-HSA-5096537 "Defective GALNT3 does not transfer GalNAc to mucins"
xref: Reactome:R-HSA-8851619 "GALNT3 transfers GalNAc to FGF23"
-xref: Reactome:R-HSA-913675 "GALNTs transfer GalNAc from UDP-GalNAc to mucins to form Tn antigens"
+xref: Reactome:R-HSA-913675 "GALNTs transfer GalNAc to Mucins to form Tn antigens"
xref: Reactome:R-HSA-9683760 "GalNAc is transferred onto 3a"
xref: Reactome:R-HSA-9694438 "GalNAc is transferred onto 3a"
is_a: GO:0008376 ! acetylgalactosaminyltransferase activity
@@ -43026,7 +42983,7 @@ is_a: GO:0016779 ! nucleotidyltransferase activity
id: GO:0004655
name: porphobilinogen synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 5-aminolevulinate = 2 H(2)O + H(+) + porphobilinogen." [EC:4.2.1.24, RHEA:24064]
+def: "Catalysis of the reaction: 2 5-aminolevulinate = 2 H2O + H+ + porphobilinogen." [EC:4.2.1.24, RHEA:24064]
synonym: "5-aminolevulinate hydro-lyase (adding 5-aminolevulinate and cyclizing)" RELATED [EC:4.2.1.24]
synonym: "5-aminolevulinate hydro-lyase (adding 5-aminolevulinate and cyclizing; porphobilinogen-forming)" RELATED [EC:4.2.1.24]
synonym: "5-levulinic acid dehydratase activity" RELATED [EC:4.2.1.24]
@@ -43079,17 +43036,15 @@ is_a: GO:0031545 ! peptidyl-proline 4-dioxygenase activity
id: GO:0004657
name: proline dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor." [EC:1.5.99.8]
-synonym: "L-proline dehydrogenase activity" RELATED [EC:1.5.99.8]
-synonym: "L-proline:(acceptor) oxidoreductase activity" RELATED [EC:1.5.99.8]
-synonym: "L-proline:acceptor oxidoreductase activity" RELATED [EC:1.5.99.8]
-xref: EC:1.5.99.8
+def: "Catalysis of the reaction: L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor." [RHEA:23784]
+synonym: "L-proline dehydrogenase activity" RELATED []
+xref: EC:1.5.5.2
xref: MetaCyc:RXN-7181
xref: Reactome:R-HSA-6784224 "PRODH2:FAD dimer dehydrogenates HPRO to 1-pyrroline-3-hydroxy-5-carboxylate"
xref: Reactome:R-HSA-70670 "PRODH oxidises L-Pro to 1PYR-5COOH"
xref: Reactome:R-HSA-8955817 "PRODH2 oxidises HPRO to 1PYR-5COOH"
xref: RHEA:23784
-is_a: GO:0016645 ! oxidoreductase activity, acting on the CH-NH group of donors
+is_a: GO:0016649 ! oxidoreductase activity, acting on the CH-NH group of donors, quinone or similar compound as acceptor
[Term]
id: GO:0004658
@@ -43120,7 +43075,7 @@ name: protein farnesyltransferase activity
namespace: molecular_function
alt_id: GO:0018223
def: "Catalysis of the reaction: farnesyl diphosphate + protein-cysteine = S-farnesyl protein + diphosphate." [EC:2.5.1.58, PMID:8621375]
-comment: The catalyzed reaction transfers a farnesyl group from farnesyl diphosphate to a target protein. There is no relationship between this activity and farnesyltransferase activity, GO:0004311, where the catalyzed reaction forms (free) geranylgeranyl diphosphate.
+comment: The catalyzed reaction transfers a farnesyl group from farnesyl diphosphate to a target protein. There is no relationship between this activity and farnesyltransferase activity, GO:0004311, where the catalyzed reaction forms (free) geranylgeranyl diphosphate.
synonym: "CAAX farnesyltransferase activity" NARROW [EC:2.5.1.58]
synonym: "farnesyl-diphosphate:protein-cysteine farnesyltransferase activity" RELATED [EC:2.5.1.58]
synonym: "FTase activity" RELATED [EC:2.5.1.58]
@@ -43190,7 +43145,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0004665
name: prephenate dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + prephenate = (4-hydroxyphenyl)pyruvate + CO(2) + NADPH." [EC:1.3.1.13, RHEA:21640]
+def: "Catalysis of the reaction: NADP+ + prephenate = (4-hydroxyphenyl)pyruvate + CO2 + NADPH." [EC:1.3.1.13, RHEA:21640]
synonym: "prephenate (nicotinamide adenine dinucleotide phosphate) dehydrogenase activity" RELATED [EC:1.3.1.13]
synonym: "prephenate:NADP+ oxidoreductase (decarboxylating)" RELATED [EC:1.3.1.13]
xref: EC:1.3.1.13
@@ -43242,7 +43197,7 @@ is_a: GO:0016860 ! intramolecular oxidoreductase activity
id: GO:0004668
name: protein-arginine deiminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: protein L-arginine + H2O = protein L-citrulline + NH3. This reaction is calcium-dependent." [PMID:27393304]
+def: "Catalysis of the reaction: H2O + L-arginyl-[protein] = L-citrullyl-[protein] + NH4+, resulting in citrullination of the target protein. This reaction is calcium-dependent." [PMID:27393304]
synonym: "peptidylarginine deiminase activity" RELATED [EC:3.5.3.15]
synonym: "protein-L-arginine iminohydrolase activity" RELATED [EC:3.5.3.15]
xref: EC:3.5.3.15
@@ -43290,7 +43245,6 @@ namespace: molecular_function
alt_id: GO:0050222
def: "Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP." [MetaCyc:PROTEIN-KINASE-RXN]
comment: Note that triphosphate is used as a phosphate donor by at least one kinase.
-subset: goslim_aspergillus
subset: goslim_candida
synonym: "protamine kinase activity" NARROW []
xref: MetaCyc:PROTEIN-KINASE-RXN
@@ -43310,18 +43264,10 @@ namespace: molecular_function
alt_id: GO:0008896
def: "Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine." [EC:2.7.13.3, GOC:mah]
synonym: "ATP:protein-L-histidine N-phosphotransferase activity" RELATED [EC:2.7.13.3]
-synonym: "EnvZ" NARROW [EC:2.7.13.3]
-synonym: "histidine kinase (ambiguous)" RELATED [EC:2.7.13.3]
synonym: "histidine kinase activity" EXACT []
-synonym: "histidine protein kinase (ambiguous)" RELATED [EC:2.7.13.3]
synonym: "histidine protein kinase activity" RELATED [EC:2.7.13.3]
-synonym: "HK1" RELATED [EC:2.7.13.3]
-synonym: "HP165" RELATED [EC:2.7.13.3]
-synonym: "protein histidine kinase (ambiguous)" RELATED [EC:2.7.13.3]
synonym: "protein kinase (histidine)" RELATED [EC:2.7.13.3]
-synonym: "protein kinase (histidine) (ambiguous)" RELATED [EC:2.7.13.3]
synonym: "protein-histidine kinase activity" EXACT []
-synonym: "Sln1p" NARROW [EC:2.7.13.3]
xref: EC:2.7.13.3
xref: MetaCyc:2.7.13.3-RXN
is_a: GO:0004672 ! protein kinase activity
@@ -43360,7 +43306,7 @@ xref: Reactome:R-HSA-112381 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-
xref: Reactome:R-HSA-1168635 "PRKCB (PKC-beta) phosphorylates CARMA1"
xref: Reactome:R-HSA-1168638 "Activated IKK phosphorylates I-kappaB"
xref: Reactome:R-HSA-1168641 "TAK1 associated with the CBM complex phosphorylates IKKbeta"
-xref: Reactome:R-HSA-1181149 "ACVR2A/B (ActRIIA/B) phosphorylates ACVR1B (ActRIB, ALK4) in response to Activin"
+xref: Reactome:R-HSA-1181149 "ACVR2A,B (ActRIIA,B) phosphorylates ACVR1B (ActRIB, ALK4) in response to Activin"
xref: Reactome:R-HSA-1181156 "Type II Activin Receptor (ActRII/ACVR2) phosphorylates Type I Activin Receptor (ActRIB/ACVR1B) in response to NODAL"
xref: Reactome:R-HSA-1181355 "Phosphorylation of R-SMAD2/3 by NODAL receptor"
xref: Reactome:R-HSA-1225894 "Type II Activin Receptor (ActRIIB/ACVR2B) phosphorylates Type I Activin Receptor (ActRIC/ACVR1C) in response to NODAL"
@@ -43372,7 +43318,7 @@ xref: Reactome:R-HSA-1445144 "p-AKT1,p-AKT2 phosphorylates AS160 (TBC1D4)"
xref: Reactome:R-HSA-1449597 "p-AKT2 phosphorylates Myosin 5A"
xref: Reactome:R-HSA-1454699 "AMPK-alpha2 phosphorylates TBC1D1"
xref: Reactome:R-HSA-1458463 "p-AKT2 phosphorylates RGC2"
-xref: Reactome:R-HSA-1549526 "Phosphorylation of SMAD2/3 by Activin:Activin Receptor"
+xref: Reactome:R-HSA-1549526 "Phosphorylation of SMAD2,3 by Activin:Activin Receptor"
xref: Reactome:R-HSA-156673 "Regulation of KIF23 (MKLP1) by phosphorylation"
xref: Reactome:R-HSA-156678 "Activation of Cdc25C"
xref: Reactome:R-HSA-156682 "PLK1 phosphorylates NUDC"
@@ -43402,7 +43348,8 @@ xref: Reactome:R-HSA-166286 "Multiple IRAK1 autophosphorylation steps"
xref: Reactome:R-HSA-167084 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex"
xref: Reactome:R-HSA-167098 "Phosphorylation (Ser5) of RNA pol II CTD"
xref: Reactome:R-HSA-168053 "Phosphorylated MAPKs phosphorylate ATF-2"
-xref: Reactome:R-HSA-168140 "Phospho-IKK Complex phosphorylates NFkB inhibitor within the NFkB inhibitor:NFkB complex"
+xref: Reactome:R-HSA-168140 "Active IKK Complex phosphorylates NF-kappa-B inhibitor"
+xref: Reactome:R-HSA-168184 "Activated TAK1 mediates phosphorylation of the IKK Complex"
xref: Reactome:R-HSA-170055 "Myt-1 mediated phosphorylation of Cyclin B:Cdc2 complexes"
xref: Reactome:R-HSA-170076 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes"
xref: Reactome:R-HSA-170087 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes"
@@ -43499,7 +43446,7 @@ xref: Reactome:R-HSA-2400001 "AKT1 E17K mutant phosphorylates CHUK (IKKalpha)"
xref: Reactome:R-HSA-2422927 "MAPK3-3 or MAPK1 phosphorylate GORASP2"
xref: Reactome:R-HSA-2430535 "MASTL phosphorylates ENSA"
xref: Reactome:R-HSA-2466068 "Phosphorylation of cohesin by PLK1 at chromosomal arms"
-xref: Reactome:R-HSA-2470508 "ACVR2A/B (ActRIIA/B) phosphorylates ACVR1C (ActRIC, ALK7) in response to Activin"
+xref: Reactome:R-HSA-2470508 "ACVR2A,B (ActRIIA,B) phosphorylates ACVR1C (ActRIC, ALK7) in response to Activin"
xref: Reactome:R-HSA-2529020 "CK2 phosphorylates condensin I subunits"
xref: Reactome:R-HSA-2562526 "PLK1 phosphorylates OPTN"
xref: Reactome:R-HSA-2574840 "AJUBA facilitates AURKA autophosphorylation"
@@ -43579,6 +43526,8 @@ xref: Reactome:R-HSA-448948 "Phosphorylation of E proteins by p38 MAPK"
xref: Reactome:R-HSA-448955 "Phosphorylation of MEF2 proteins by p38"
xref: Reactome:R-HSA-450222 "Active p38 MAPK phosphorylates MAPKAPK2 or 3"
xref: Reactome:R-HSA-450325 "c-FOS activation by phospho ERK1/2"
+xref: Reactome:R-HSA-450337 "Activated TAK1 phosphorylates MKK4/MKK7"
+xref: Reactome:R-HSA-450346 "activated human TAK1 phosphorylates MKK3/MKK6"
xref: Reactome:R-HSA-450463 "MK2 phosphorylates ZFP36 (Tristetraproline, TTP)"
xref: Reactome:R-HSA-450474 "MK2 phosphorylates BRF1"
xref: Reactome:R-HSA-450490 "Protein Kinase B/Akt phosphorylates BRF1"
@@ -43604,7 +43553,7 @@ xref: Reactome:R-HSA-5229343 "AXIN is phosphorylated in the destruction complex"
xref: Reactome:R-HSA-5260201 "p-AKT2 phosphorylates C2CD5"
xref: Reactome:R-HSA-5357472 "PAK1-3 autophosphorylates"
xref: Reactome:R-HSA-5357477 "PAK1-3 phosphorylates VE-cadherin"
-xref: Reactome:R-HSA-5357831 "CYLD is phosphorylated by IKK"
+xref: Reactome:R-HSA-5357831 "CHUK, IKBKB phosphorylate CYLD at S418"
xref: Reactome:R-HSA-5578777 "DMPK phosphorylates PLN"
xref: Reactome:R-HSA-5607722 "Active NIK phosphorylates IKKA dimer"
xref: Reactome:R-HSA-5607726 "Active NIK:p-S176,180-IKKA dimer phosphorylates p100:RELB"
@@ -43743,6 +43692,7 @@ xref: Reactome:R-HSA-8876446 "p-ULK1 phosphorylates DENND3"
xref: Reactome:R-HSA-8877691 "MAP2K6 phosphorylates PIP4K2B"
xref: Reactome:R-HSA-8878050 "HIPK2 phosphorylates RUNX1 and EP300"
xref: Reactome:R-HSA-8878054 "HIPK2 phosphorylates RUNX1"
+xref: Reactome:R-HSA-8932322 "CK2 phosphorylates NFE2L2"
xref: Reactome:R-HSA-8933446 "Active AKT phosphorylates DENND1A and DENND1B in response to insulin signaling"
xref: Reactome:R-HSA-8939963 "Activated AKT phosphorylates RUNX2"
xref: Reactome:R-HSA-8940100 "CDK1 phosphorylates VCPIP1"
@@ -43798,21 +43748,34 @@ xref: Reactome:R-HSA-9656214 "MAP2Ks phosphorylate MAPKs downstream of RAF1 muta
xref: Reactome:R-HSA-9656215 "RAF1 mutant complexes phosphorylate MAP2K dimer"
xref: Reactome:R-HSA-9662823 "PLK2, MAPK14 phosphorylate ADAM17"
xref: Reactome:R-HSA-9673346 "Unknown kinase phosphorylates p-DVL"
-xref: Reactome:R-HSA-9681627 "GSK3 phosphorylates N"
-xref: Reactome:R-HSA-9683664 "GSK3B phosphorylates Ncap"
-xref: Reactome:R-HSA-9694293 "GSK3B phosphorylates Ncap"
-xref: Reactome:R-HSA-9694620 "GSK3 phosphorylates N"
+xref: Reactome:R-HSA-9683664 "GSK3 phosphorylates Nucleoprotein"
xref: Reactome:R-HSA-9699579 "AKT phosphorylates FOXO3 downstream of FLT3"
+xref: Reactome:R-HSA-9705320 "TBK1, IKBKE are autophosphorylated at Ser172"
+xref: Reactome:R-HSA-9705323 "Phosphorylation of TBK1/IKBKE"
+xref: Reactome:R-HSA-9725030 "MAPK1 phsophorylates ZC3HCF1 in a NPM-ALK-dependent manner"
+xref: Reactome:R-HSA-9729260 "GSK3 phosphorylates nucleoprotein"
+xref: Reactome:R-HSA-9729300 "Unknown kinase phosphorylates nucleoprotein"
+xref: Reactome:R-HSA-9729318 "CSNK1A1 phosphorylates nucleoprotein"
+xref: Reactome:R-HSA-9731111 "MAPK1 and MAPK3 phosphorylate SMAD2 and SMAD3"
xref: Reactome:R-HSA-975125 "Multiple IRAK1 autophosphorylation steps within the complex pIRAK4:MyD88:activated TLR7/8 or 9"
xref: Reactome:R-HSA-975134 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88: activated TLR 7/8 or 9"
xref: Reactome:R-HSA-975160 "Phosphorylation of IRAK2 bound to the activated IRAK4:MyD88 oligomer:activated TLR 7/8 or 9"
xref: Reactome:R-HSA-975170 "IRAK4 autophosphorylation in the complex with MyD88:activated TLR 7/8 or 9"
xref: Reactome:R-HSA-975180 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR 7/8 or 9"
+xref: Reactome:R-HSA-9758486 "Unknown kinase phosphorylates 9b"
xref: Reactome:R-HSA-975853 "Multiple IRAK1 autophosphorylation within the complex p-IRAK4:oligo MyD88:activated TLR"
xref: Reactome:R-HSA-975861 "Phosphorylation of IRAK2 bound to the activated IRAK4:MyD88 oligomerl:activated TLR5 or 10 complex"
xref: Reactome:R-HSA-975865 "IRAK4 autophosphorylation within the complex activated TLR:MyD88"
xref: Reactome:R-HSA-975874 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR complex"
xref: Reactome:R-HSA-975878 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR"
+xref: Reactome:R-HSA-9762094 "GSK3B phosphorylates p-NFE2L2"
+xref: Reactome:R-HSA-9766532 "SQSTM1 oligomer is phosphorylated"
+xref: Reactome:R-HSA-9769115 "MAPK1,(MAPK3) phosphorylates NPAS4"
+xref: Reactome:R-HSA-9773803 "Active IKBKB phosphorylates NF-kappa-B inhibitor"
+xref: Reactome:R-HSA-9815501 "MAPKAPK2 phosphorylates RIPK1 at S320"
+xref: Reactome:R-HSA-9817397 "TBK1, IKBKE phosphorylate RIPK1 at T189"
+xref: Reactome:R-HSA-9818789 "CHUK, IKBKB phosphorylate RIPK1 at S25"
+xref: Reactome:R-HSA-9819106 "ULK1 phosphorylates RIPK1 at S357"
is_a: GO:0004672 ! protein kinase activity
[Term]
@@ -44170,7 +44133,6 @@ name: eukaryotic translation initiation factor 2alpha kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + [eukaryotic translation initiation factor 2 alpha subunit] = ADP + [eukaryotic translation initiation factor 2 alpha subunit] phosphate." [GOC:mah, InterPro:IPR015516]
is_a: GO:0004674 ! protein serine/threonine kinase activity
-is_a: GO:0045182 ! translation regulator activity
[Term]
id: GO:0004697
@@ -44209,7 +44171,7 @@ xref: Reactome:R-HSA-198314 "DAG stimulates protein kinase C-delta"
xref: Reactome:R-HSA-2179413 "Activated PKC-alpha activate MMP3"
xref: Reactome:R-HSA-2730863 "Phosphorylation of CARMA1 by PKC-theta"
xref: Reactome:R-HSA-374664 "Phosphorylation and activation of Ezrin"
-xref: Reactome:R-HSA-429698 "PRKD1,2,3 phosphorylates COL4A3BP-2"
+xref: Reactome:R-HSA-429698 "PRKD1,2,3 phosphorylates CERT1-2"
xref: Reactome:R-HSA-450533 "PKCdelta phosphorylates HuR"
xref: Reactome:R-HSA-450550 "PKCalpha phosphorylates HuR"
xref: Reactome:R-HSA-5138432 "DVL2 is phosphorylated by PKC"
@@ -44221,6 +44183,7 @@ xref: Reactome:R-HSA-5625784 "PKN1 phosphorylates histone 3 of nucleosomes assoc
xref: Reactome:R-HSA-5671749 "p-T774-PKN1 phosphorylates CDC25C"
xref: Reactome:R-HSA-74615 "PRKCA/Q phosphorylate RGS9-1:GN5B:RGS9BP"
xref: Reactome:R-HSA-751040 "PKC phosphorylates G alpha (z)"
+xref: Reactome:R-HSA-8932284 "PKC phosphorylates NFE2L2"
xref: Reactome:R-HSA-8934446 "Activated PKC phosphorylates SHC1"
xref: Reactome:R-HSA-9010681 "PKC phosphorylates ROBO3.1"
xref: Reactome:R-HSA-9021357 "PRKCI phosphorylates ELF3"
@@ -44424,11 +44387,8 @@ synonym: "REKS" RELATED [EC:2.7.11.25]
synonym: "STK28" RELATED [EC:2.7.11.25]
xref: EC:2.7.11.25
xref: MetaCyc:2.7.11.25-RXN
-xref: Reactome:R-HSA-168184 "Activated TAK1 mediates phosphorylation of the IKK Complex"
xref: Reactome:R-HSA-2730887 "Autophosphorylation and activation of MEKK1"
xref: Reactome:R-HSA-392530 "p-S400-Cot phosphorylates NIK"
-xref: Reactome:R-HSA-450337 "Activated TAK1 phosphorylates MKK4/MKK7"
-xref: Reactome:R-HSA-450346 "activated human TAK1 phosphorylates MKK3/MKK6"
xref: Reactome:R-HSA-451649 "TPL2 phosphorylates MEK1, SEK1"
xref: Reactome:R-HSA-727819 "TAK1 phosphorylates MKK6"
xref: Reactome:R-HSA-933530 "Activation of IKK by MEKK1"
@@ -44528,6 +44488,7 @@ xref: Reactome:R-HSA-1982066 "Ligand-independent phosphorylation of overexpresse
xref: Reactome:R-HSA-2012073 "Autocatalytic phosphorylation of FGFR3c P250R mutant"
xref: Reactome:R-HSA-2012082 "Autocatalytic phosphorylation of FGFR3 cysteine mutants"
xref: Reactome:R-HSA-2012087 "Autocatalytic phosphorylation of FGFR4 Y367C mutant"
+xref: Reactome:R-HSA-201521 "ALK autophosphorylation downstream of PTN and MDK"
xref: Reactome:R-HSA-202165 "Phosphorylation of ITAM motifs in CD3 complexes"
xref: Reactome:R-HSA-202168 "Phosphorylation of ZAP-70 by Lck"
xref: Reactome:R-HSA-202174 "Activation of ZAP-70"
@@ -44598,6 +44559,7 @@ xref: Reactome:R-HSA-388831 "Phosphorylation of CD28"
xref: Reactome:R-HSA-388833 "Phosphorylation of CTLA-4"
xref: Reactome:R-HSA-389083 "Autophosphorylation of PDGF alpha receptors"
xref: Reactome:R-HSA-389086 "Autophosphorylation of PDGF alpha/beta receptors"
+xref: Reactome:R-HSA-389159 "CSF1R trans-autophosphorylates on multiple tyrosine and serine residues"
xref: Reactome:R-HSA-389354 "Activation of Vav1"
xref: Reactome:R-HSA-389762 "Phosphorylation of PD-1"
xref: Reactome:R-HSA-391156 "Phosphorylation of ITIM motif in SIRP alpha"
@@ -44616,7 +44578,7 @@ xref: Reactome:R-HSA-399934 "Phosphorylation of Plexin-A"
xref: Reactome:R-HSA-399946 "Recruitment and activation of Cdk5"
xref: Reactome:R-HSA-399947 "Tyrosine phosphorylation of CRMPs by Fes"
xref: Reactome:R-HSA-4093332 "p-EPHB phosphorylates SDC2"
-xref: Reactome:R-HSA-418163 "Activated Src activates ERK"
+xref: Reactome:R-HSA-418163 "Activated SRC-1 activates MAPKs (in F2R:ARRB1:MAPKs:active SRC-1)"
xref: Reactome:R-HSA-418859 "Phosphorylation of Unc5C"
xref: Reactome:R-HSA-418872 "Phosphorylation of FADK1"
xref: Reactome:R-HSA-419646 "SEMA4D interacts with Plexin-B1:Met"
@@ -44678,9 +44640,9 @@ xref: Reactome:R-HSA-5654631 "Activated FGFR3 phosphorylates PPTN11"
xref: Reactome:R-HSA-5654634 "Activated FGFR3 phosphorylates SHC1"
xref: Reactome:R-HSA-5654653 "Activated FGFR4 phosphorylates FRS3"
xref: Reactome:R-HSA-5654655 "Activated FGFR4 phosphorylates PPTN11"
-xref: Reactome:R-HSA-5655243 "Activated FGFR3 mutants phosphorylate PLCG1"
+xref: Reactome:R-HSA-5655243 "Activated FGFR3 point and translocation mutants phosphorylate PLCG1"
xref: Reactome:R-HSA-5655268 "Activated FGFR2 mutants phosphorylate FRS2"
-xref: Reactome:R-HSA-5655270 "Activated FGFR3 mutants phosphorylate FRS2"
+xref: Reactome:R-HSA-5655270 "Activated FGFR3 point, translocation and fusion mutants phosphorylate FRS2"
xref: Reactome:R-HSA-5655278 "Activated FGFR1 mutants phosphorylate FRS2"
xref: Reactome:R-HSA-5655284 "Activated FGFR4 mutants phosphorylate FRS2"
xref: Reactome:R-HSA-5655301 "Activated FGFR2 mutants phosphorylate PLCG1"
@@ -44722,7 +44684,6 @@ xref: Reactome:R-HSA-8851890 "MET phosphorylates SHC1-2"
xref: Reactome:R-HSA-8851933 "MET phosphorylates GAB1"
xref: Reactome:R-HSA-8853309 "Autocatalytic phosphorylation of FGFR3 fusions"
xref: Reactome:R-HSA-8853313 "FGFR2 fusions autophosphorylate"
-xref: Reactome:R-HSA-8853315 "Activated FGFR3 fusions phosphorylate FRS2"
xref: Reactome:R-HSA-8853325 "Plasma membrane FGFR1 fusions autophosphorylate"
xref: Reactome:R-HSA-8855237 "FYN phosphorylates DAB1 in RELN:VLDLR:DAB1:SH3KBP1"
xref: Reactome:R-HSA-8857555 "EGFR phosphorylates GPNMB"
@@ -44788,6 +44749,7 @@ xref: Reactome:R-HSA-9606163 "p-SYK and LYN phosphorylate BTK"
xref: Reactome:R-HSA-9612085 "SRC phosphorylates GluN2 (GRIN2) subunits of NMDARs"
xref: Reactome:R-HSA-9612996 "NTRK1,2 in ADCYAP1(2-742):ADCYAP1R1:NTRK1,2 autophosphorylates"
xref: Reactome:R-HSA-9613023 "NTRK1,2 in Ade-Rib:ADORA2A:NTRK1,2 autophosphorylates"
+xref: Reactome:R-HSA-9624014 "SHC1 is phosphorylated downstream of estrogen stimulation of GPER1"
xref: Reactome:R-HSA-9625487 "PTK2 autophosphorylates downstream of EGFR"
xref: Reactome:R-HSA-9634390 "ERBB2 homodimer phosphorylates SHC1"
xref: Reactome:R-HSA-9664261 "Src phosphorylate SYK in IgG:Leishmania surface:p-FCGR3A:SYK"
@@ -44810,15 +44772,35 @@ xref: Reactome:R-HSA-9672173 "Autophosphorylation of PDGFRA extracellular domain
xref: Reactome:R-HSA-9672175 "Autophosphorylation of PDGFR mutant dimers"
xref: Reactome:R-HSA-9673756 "Autophosphorylation of cytosolic PDGFRA and PDGFRB fusion proteins"
xref: Reactome:R-HSA-9673761 "Autophosphorylation of membrane-tethered fusions of PDGFRA or PDGFRB"
+xref: Reactome:R-HSA-9674558 "p-Y-JAK1 phosphorylates CSF3R in CSF3 dimer:2xCSF3R:LYN:p-Y-JAK1"
+xref: Reactome:R-HSA-9674567 "p-Y-JAK1,2 phosphorylates STAT1,3,5 in CSF3 dimer:2xp-4Y-CSF3R:LYN:p-Y-JAK1:p-Y-JAK2:p-TYK2"
xref: Reactome:R-HSA-9680248 "Phosphorylation of extracellular domain KIT mutants"
xref: Reactome:R-HSA-9695834 "Constitutive phosphorylation of FLT3 mutants"
xref: Reactome:R-HSA-9698003 "FLT3 mutants phosphorylate GAB2"
xref: Reactome:R-HSA-9698005 "FLT3 ITD mutants phosphorylate STAT5"
xref: Reactome:R-HSA-9699578 "Active FLT3 phosphorylates CDKN1B"
+xref: Reactome:R-HSA-9700164 "Active ALK phosphorylates FRS2"
+xref: Reactome:R-HSA-9700168 "Active ALK phosphorylates IRS1"
+xref: Reactome:R-HSA-9700171 "Active ALK phosphorylates PLCG1"
+xref: Reactome:R-HSA-9700175 "Active ALK phosphorylates SHC1"
+xref: Reactome:R-HSA-9700181 "Autophosphorylation of ALK fusions"
+xref: Reactome:R-HSA-9700186 "Autophosphorylation of point mutants of ALK"
+xref: Reactome:R-HSA-9700193 "ALK mutants phosphorylate SHC1"
+xref: Reactome:R-HSA-9700647 "Active ALK phosphorylates SRC"
+xref: Reactome:R-HSA-9701488 "Active ALK phosphorylates JAK3"
xref: Reactome:R-HSA-9703437 "FLT3 fusion dimers autophosphorylate"
xref: Reactome:R-HSA-9703438 "FLT3 fusions phosphorylate GAB2"
xref: Reactome:R-HSA-9706344 "FLT3 phosphorylates GRB10"
xref: Reactome:R-HSA-9706350 "FLT3 phosphorylates CBL"
+xref: Reactome:R-HSA-9709918 "PTK6 phosphorylates STAT3"
+xref: Reactome:R-HSA-9712082 "ALK fusions phosphorylate IRS1"
+xref: Reactome:R-HSA-9712085 "ALK mutants phosphorylate STAT3"
+xref: Reactome:R-HSA-9712086 "ALK fusions phosphorylate PLCG1"
+xref: Reactome:R-HSA-9712087 "ALK fusions phosphorylate FRS"
+xref: Reactome:R-HSA-9726848 "SRC phosphorylates RHOU"
+xref: Reactome:R-HSA-9733314 "CSF1R trans-autophosphorylates on tyrosine-561"
+xref: Reactome:R-HSA-9733323 "Src family kinases phosphorylate CBL in CSF1 dimer:p-Y561-CSF1R dimer:CBL"
+xref: Reactome:R-HSA-9762209 "BACH1 is phosphorylated at tyrosine 486"
xref: Reactome:R-HSA-982807 "JAK2 phosphorylation of GHR"
xref: Reactome:R-HSA-983703 "p-6Y-SYK phosphorylates BLNK (SLP65)"
xref: Reactome:R-HSA-983707 "SYK autophosphorylates at the activated BCR"
@@ -44843,7 +44825,6 @@ xref: Reactome:R-HSA-177933 "SHC1 phosphorylation by phosphorylated EGFR"
xref: Reactome:R-HSA-198295 "TRKA phosphorylates IRS"
xref: Reactome:R-HSA-6784324 "p-Y-JAK1,p-Y-TYK2 phosphorylate IL10RA"
xref: Reactome:R-HSA-74711 "Phosphorylation of IRS"
-xref: Reactome:R-HSA-74715 "Autophosphorylation of insulin receptor"
xref: Reactome:R-HSA-74742 "Phosphorylation of SHC1"
xref: Reactome:R-HSA-8852552 "MST1R autophosphorylates"
xref: Reactome:R-HSA-8853792 "RET tyrosine phosphorylation"
@@ -44984,7 +44965,7 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
id: GO:0004721
name: phosphoprotein phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity." [ISBN:0198547684]
+def: "Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cellular proteins and thereby provide an important mechanism for regulating cellular activity." [ISBN:0198547684]
synonym: "phosphoprotein phosphohydrolase activity" EXACT []
synonym: "protein phosphatase activity" EXACT []
synonym: "protein phosphatase-1 activity" NARROW []
@@ -45144,7 +45125,10 @@ xref: Reactome:R-HSA-914036 "SHP1 and SHP2 dephosphorylate Y628 of IL3RB"
xref: Reactome:R-HSA-9603719 "Protein tyrosine phosphatases dephosphorylate NTRK3"
xref: Reactome:R-HSA-9635461 "PtpA dephosphorylates GSK3A"
xref: Reactome:R-HSA-9636439 "PtpA:Ub dephosphorylates p-Y133-VPS33B"
+xref: Reactome:R-HSA-9674816 "p-Y546,Y584-PTPN11 (in CSF3 dimer:2xp-4Y-CSF3R:LYN:p-Y-JAK1:p-JAK2:p-SYK:p-HCK:p-TYK2:SHC:GRB2:PTPN11) dephosphorylates KRAS"
xref: Reactome:R-HSA-9698408 "PTPRJ dephosphorylates active FLT3"
+xref: Reactome:R-HSA-9700200 "PTPRZ dephosphorylates ligand-bound ALK dimers"
+xref: Reactome:R-HSA-9701507 "PTPN6 dephosphorylates JAK3"
xref: Reactome:R-HSA-997309 "Dephosphorylation of STAT1 by SHP2"
xref: Reactome:R-HSA-997311 "Dephosphorylation of TYK2 by PTP1B"
xref: Reactome:R-HSA-997314 "Dephosphorylation of JAK1 by SHP1"
@@ -45185,7 +45169,7 @@ is_obsolete: true
id: GO:0004729
name: oxygen-dependent protoporphyrinogen oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3 O(2) + protoporphyrinogen IX = 3 H(2)O(2) + protoporphyrin IX." [EC:1.3.3.4, RHEA:25576]
+def: "Catalysis of the reaction: 3 O2 + protoporphyrinogen IX = 3 H2O2 + protoporphyrin IX." [EC:1.3.3.4, RHEA:25576]
synonym: "protoporphyrinogen-IX:oxygen oxidoreductase activity" RELATED [EC:1.3.3.4]
xref: EC:1.3.3.4
xref: KEGG_REACTION:R03222
@@ -45199,7 +45183,7 @@ is_a: GO:0070818 ! protoporphyrinogen oxidase activity
id: GO:0004730
name: pseudouridylate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-ribose 5-phosphate + uracil = H(2)O + pseudouridine 5'-phosphate." [EC:4.2.1.70, RHEA:18337]
+def: "Catalysis of the reaction: D-ribose 5-phosphate + uracil = H2O + pseudouridine 5'-phosphate." [EC:4.2.1.70, RHEA:18337]
comment: Note that this term should not be confused with 'pseudouridine synthase activity ; GO:0009982', which refers to the intramolecular isomerization of uridine to pseudouridine.
synonym: "5-ribosyluracil 5-phosphate synthetase activity" RELATED [EC:4.2.1.70]
synonym: "pseudouridine monophosphate synthase activity" EXACT []
@@ -45234,10 +45218,13 @@ synonym: "purine ribonucleoside phosphorylase activity" RELATED [EC:2.4.2.1]
synonym: "purine-nucleoside:phosphate ribosyltransferase activity" RELATED [EC:2.4.2.1]
xref: EC:2.4.2.1
xref: MetaCyc:PNP-RXN
-xref: Reactome:R-HSA-112033 "hypoxanthine + (deoxy)ribose 1-phosphate <=> (deoxy)inosine + orthophosphate (NP)"
-xref: Reactome:R-HSA-112034 "guanine + (deoxy)ribose 1-phosphate <=> (deoxy)guanosine + orthophosphate (NP)"
-xref: Reactome:R-HSA-74242 "(deoxy)inosine + orthophosphate <=> hypoxanthine + (deoxy)ribose 1-phosphate (NP)"
-xref: Reactome:R-HSA-74249 "(deoxy)guanosine + orthophosphate <=> guanine + (deoxy)ribose 1-phosphate (NP)"
+xref: Reactome:R-HSA-112033 "PNP catalyzes the conversion of hypoxanthine and (deoxy)ribose to (deoxy)inosine"
+xref: Reactome:R-HSA-112034 "PNP catalyzes the conversion of guanine and (deoxy)ribose to (deoxy)guanosine"
+xref: Reactome:R-HSA-74242 "PNP catalyzes the conversion of (deoxy)inosine to hypoxanthine and (deoxy)ribose"
+xref: Reactome:R-HSA-74249 "PNP catalyzes the conversion of (deoxy)guanosine to guanine and (deoxy)ribose"
+xref: Reactome:R-HSA-9735775 "Defective PNP does not convert (deoxy)inosine to hypoxanthine and (deoxy)ribose"
+xref: Reactome:R-HSA-9735789 "Defective PNP does not convert (deoxy)guanosine to guanine and (deoxy)ribose"
+xref: Reactome:R-HSA-9755044 "PNP trimer transforms RBV to T-CONH2"
xref: RHEA:19805
is_a: GO:0016763 ! pentosyltransferase activity
@@ -45250,13 +45237,13 @@ synonym: "pyridoxal:oxygen 4-oxidoreductase activity" RELATED [EC:1.2.3.8]
xref: EC:1.2.3.8
xref: MetaCyc:PYRIDOXAL-OXIDASE-RXN
xref: RHEA:23724
-is_a: GO:0016623 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, oxygen as acceptor
+is_a: GO:0004031 ! aldehyde oxidase activity
[Term]
id: GO:0004733
name: pyridoxamine-phosphate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + hydrogen peroxide." [EC:1.4.3.5]
+def: "Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + hydrogen peroxide." [PMID:11786019]
synonym: "PdxH" RELATED [EC:1.4.3.5]
synonym: "PMP oxidase activity" RELATED [EC:1.4.3.5]
synonym: "pyridoxal 5'-phosphate synthase activity" RELATED [EC:1.4.3.5]
@@ -45309,13 +45296,13 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0004736
name: pyruvate carboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + bicarbonate + pyruvate = ADP + 2 H(+) + oxaloacetate + phosphate." [EC:6.4.1.1, RHEA:20844]
+def: "Catalysis of the reaction: ATP + bicarbonate + pyruvate = ADP + 2 H+ + oxaloacetate + phosphate." [EC:6.4.1.1, RHEA:20844]
synonym: "pyruvate:carbon-dioxide ligase (ADP-forming)" RELATED [EC:6.4.1.1]
synonym: "pyruvic carboxylase activity" RELATED [EC:6.4.1.1]
xref: EC:6.4.1.1
xref: KEGG_REACTION:R00344
xref: MetaCyc:PYRUVATE-CARBOXYLASE-RXN
-xref: Reactome:R-HSA-70501 "Pyruvate + CO2 + ATP => ADP + Orthophosphate + Oxaloacetate"
+xref: Reactome:R-HSA-70501 "PC catalyzes the carboxylation of PYR to form OA"
xref: RHEA:20844
is_a: GO:0016885 ! ligase activity, forming carbon-carbon bonds
@@ -45400,11 +45387,13 @@ is_a: GO:0004721 ! phosphoprotein phosphatase activity
id: GO:0004742
name: dihydrolipoyllysine-residue acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + dihydrolipoamide = CoA + S-acetyldihydrolipoamide." [EC:2.3.1.12]
+alt_id: GO:0030523
+def: "Catalysis of the reaction: (R)-N6-dihydrolipoyl-L-lysyl-[protein] + acetyl-CoA = (R)-N6-(S8-acetyldihydrolipoyl)-L-lysyl-[protein] + CoA." [RHEA:17017]
synonym: "acetyl-CoA: enzyme-6-N-(dihydrolipoyl)lysine S-acetyltransferase activity" RELATED [EC:2.3.1.12]
synonym: "acetyl-CoA: enzyme-N6-(dihydrolipoyl)lysine S-acetyltransferase activity" RELATED [EC:2.3.1.12]
synonym: "acetyl-CoA:dihydrolipoamide S-acetyltransferase activity" RELATED [EC:2.3.1.12]
synonym: "dihydrolipoamide S-acetyltransferase activity" EXACT []
+synonym: "dihydrolipoamide S-acyltransferase activity" RELATED []
synonym: "dihydrolipoate acetyltransferase activity" RELATED [EC:2.3.1.12]
synonym: "dihydrolipoic transacetylase activity" RELATED [EC:2.3.1.12]
synonym: "dihydrolipoyl acetyltransferase activity" RELATED [EC:2.3.1.12]
@@ -45418,36 +45407,37 @@ synonym: "lipoylacetyltransferase activity" RELATED [EC:2.3.1.12]
synonym: "thioltransacetylase A activity" NARROW [EC:2.3.1.12]
synonym: "transacetylase X activity" NARROW [EC:2.3.1.12]
xref: EC:2.3.1.12
+xref: RHEA:17017
is_a: GO:0016418 ! S-acetyltransferase activity
-is_a: GO:0030523 ! dihydrolipoamide S-acyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
[Term]
id: GO:0004743
name: pyruvate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: = ADP + H(+) + phosphoenolpyruvate => ATP + pyruvate." [EC:2.7.1.40, RHEA:18159]
+def: "Catalysis of the reaction: = ADP + H+ + phosphoenolpyruvate => ATP + pyruvate." [EC:2.7.1.40, RHEA:18159]
synonym: "ATP:pyruvate 2-O-phosphotransferase activity" RELATED [EC:2.7.1.40]
synonym: "phosphoenol transphosphorylase activity" RELATED [EC:2.7.1.40]
synonym: "phosphoenolpyruvate kinase activity" RELATED [EC:2.7.1.40]
xref: EC:2.7.1.40
xref: MetaCyc:PEPDEPHOS-RXN
-xref: Reactome:R-HSA-71670 "phosphoenolpyruvate + ADP => pyruvate + ATP, Homo sapiens"
+xref: Reactome:R-HSA-71670 "phosphoenolpyruvate + ADP => pyruvate + ATP"
xref: RHEA:18159
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
[Term]
id: GO:0004744
-name: retinal isomerase activity
+name: obsolete retinal isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: all-trans-retinal = 11-cis-retinal." [RHEA:24124]
-synonym: "all-trans-retinal 11-cis-trans-isomerase activity" RELATED [EC:5.2.1.3]
-synonym: "retinene isomerase activity" RELATED [EC:5.2.1.3]
-synonym: "retinoid isomerase activity" BROAD [EC:5.2.1.3]
+def: "OBSOLETE. Catalysis of the reaction: all-trans-retinal = 11-cis-retinal." [PMID:21447403]
+comment: The Enzyme Commission has deleted the EC correspondingj to this term because it is now known to be catalysed by a pathway involving multiple enzymes.
+synonym: "all-trans-retinal 11-cis-trans-isomerase activity" RELATED []
+synonym: "retinene isomerase activity" RELATED []
+synonym: "retinoid isomerase activity" BROAD []
xref: KEGG_REACTION:R02126
xref: MetaCyc:RETINAL-ISOMERASE-RXN
-xref: RHEA:24124
-is_a: GO:0016859 ! cis-trans isomerase activity
+is_obsolete: true
+consider: GO:0106434
[Term]
id: GO:0004745
@@ -45473,7 +45463,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0004746
name: riboflavin synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) = 5-amino-6-(D-ribitylamino)uracil + riboflavin." [EC:2.5.1.9, RHEA:20772]
+def: "Catalysis of the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine + H+ = 5-amino-6-(D-ribitylamino)uracil + riboflavin." [EC:2.5.1.9, RHEA:20772]
synonym: "6,7-dimethyl-8-(1-D-ribityl)lumazine:6,7-dimethyl-8-(1-D-ribityl)lumazine 2,3-butanediyltransferase activity" RELATED [EC:2.5.1.9]
synonym: "heavy riboflavin synthase" NARROW [EC:2.5.1.9]
synonym: "light riboflavin synthase" NARROW [EC:2.5.1.9]
@@ -45526,7 +45516,7 @@ is_a: GO:0061731 ! ribonucleoside-diphosphate reductase activity
id: GO:0004749
name: ribose phosphate diphosphokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + 2 H(+)." [EC:2.7.6.1, RHEA:15609]
+def: "Catalysis of the reaction: D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + 2 H+." [EC:2.7.6.1, RHEA:15609]
comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "5-phosphoribose pyrophosphorylase activity" RELATED [EC:2.7.6.1]
synonym: "5-phosphoribosyl-1-pyrophosphate synthetase activity" RELATED [EC:2.7.6.1]
@@ -45621,7 +45611,7 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0004754
name: saccharopine dehydrogenase (NAD+, L-lysine-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-saccharopine + H(2)O + NAD(+) = 2-oxoglutarate + L-lysine + H(+) + NADH." [EC:1.5.1.7, RHEA:12440]
+def: "Catalysis of the reaction: L-saccharopine + H2O + NAD+ = 2-oxoglutarate + L-lysine + H+ + NADH." [EC:1.5.1.7, RHEA:12440]
synonym: "6-N-(L-1,3-dicarboxypropyl)-L-lysine:NAD+ oxidoreductase (L-lysine-forming)" RELATED [EC:1.5.1.7]
synonym: "dehydrogenase, saccharopine (nicotinamide adenine dinucleotide, lysine forming)" RELATED [EC:1.5.1.7]
synonym: "epsilon-N-(L-glutaryl-2)-L-lysine:NAD oxidoreductase (L-lysine forming)" RELATED [EC:1.5.1.7]
@@ -45637,7 +45627,7 @@ is_a: GO:0004753 ! saccharopine dehydrogenase activity
id: GO:0004755
name: saccharopine dehydrogenase (NADP+, L-glutamate-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-saccharopine + H(2)O + NADP(+) = L-allysine + L-glutamate + H(+) + NADPH." [EC:1.5.1.10, RHEA:10020]
+def: "Catalysis of the reaction: L-saccharopine + H2O + NADP+ = L-allysine + L-glutamate + H+ + NADPH." [EC:1.5.1.10, RHEA:10020]
synonym: "6-N-(L-1,3-dicarboxypropyl)-L-lysine:NADP+ oxidoreductase (L-glutamate-forming)" RELATED [EC:1.5.1.10]
synonym: "aminoadipate semialdehyde-glutamate reductase activity" RELATED [EC:1.5.1.10]
synonym: "aminoadipic semialdehyde-glutamate reductase activity" RELATED [EC:1.5.1.10]
@@ -45656,7 +45646,7 @@ is_a: GO:0004753 ! saccharopine dehydrogenase activity
id: GO:0004756
name: selenide, water dikinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H(2)O + hydrogen selenide = AMP + 3 H(+) + phosphate + selenophosphorate." [EC:2.7.9.3, RHEA:18737]
+def: "Catalysis of the reaction: ATP + H2O + hydrogen selenide = AMP + 3 H+ + phosphate + selenophosphorate." [EC:2.7.9.3, RHEA:18737]
synonym: "ATP:selenide, water phosphotransferase activity" RELATED [EC:2.7.9.3]
synonym: "selenide,water dikinase activity" RELATED [EC:2.7.9.3]
synonym: "selenium donor protein activity" RELATED [EC:2.7.9.3]
@@ -45688,7 +45678,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0004758
name: serine C-palmitoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-serine + H(+) + palmitoyl-CoA = 3-dehydrosphinganine + CO(2) + CoA." [EC:2.3.1.50, RHEA:14761]
+def: "Catalysis of the reaction: L-serine + H+ + palmitoyl-CoA = 3-dehydrosphinganine + CO2 + CoA." [EC:2.3.1.50, RHEA:14761]
synonym: "3-oxosphinganine synthetase activity" RELATED [EC:2.3.1.50]
synonym: "acyl-CoA:serine C-2 acyltransferase decarboxylating" RELATED [EC:2.3.1.50]
synonym: "palmitoyl-CoA:L-serine C-palmitoyltransferase (decarboxylating) activity" RELATED [EC:2.3.1.50]
@@ -45746,7 +45736,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0004765
name: shikimate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + shikimate = 3-phosphoshikimate + ADP + 2 H(+)." [EC:2.7.1.71, RHEA:13121]
+def: "Catalysis of the reaction: ATP + shikimate = 3-phosphoshikimate + ADP + 2 H+." [EC:2.7.1.71, RHEA:13121]
synonym: "ATP:shikimate 3-phosphotransferase activity" RELATED [EC:2.7.1.71]
synonym: "shikimate kinase (phosphorylating)" RELATED [EC:2.7.1.71]
synonym: "shikimate kinase II" RELATED [EC:2.7.1.71]
@@ -45779,7 +45769,7 @@ name: sphingomyelin phosphodiesterase activity
namespace: molecular_function
alt_id: GO:0030230
alt_id: GO:0030231
-def: "Catalysis of the reaction: H(2)O + sphingomyelin = ceramide + choline phosphate + H(+)." [EC:3.1.4.12, RHEA:19253]
+def: "Catalysis of the reaction: H2O + sphingomyelin = ceramide + choline phosphate + H+." [EC:3.1.4.12, RHEA:19253]
subset: goslim_chembl
synonym: "sphingomyelin cholinephosphohydrolase activity" RELATED [EC:3.1.4.12]
synonym: "sphingomyelinase activity" EXACT []
@@ -45801,7 +45791,7 @@ name: stearoyl-CoA 9-desaturase activity
namespace: molecular_function
alt_id: GO:0016214
alt_id: GO:0043735
-def: "Catalysis of the reaction: stearoyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ = oleoyl-CoA + 2 ferricytochrome b5 + 2 H2O." [RHEA:19721]
+def: "Catalysis of the reaction: 2 Fe(II)-[cytochrome b5] + 2 H+ + O2 + octadecanoyl-CoA = (9Z)-octadecenoyl-CoA + 2 Fe(III)-[cytochrome b5] + 2 H2O." [RHEA:19721]
comment: Note that this function was formerly EC:1.14.99.5.
synonym: "acyl-CoA desaturase" BROAD [EC:1.14.19.1]
synonym: "delta(9)-desaturase activity" BROAD [EC:1.14.19.1]
@@ -45969,7 +45959,7 @@ is_a: GO:0009013 ! succinate-semialdehyde dehydrogenase [NAD(P)+] activity
id: GO:0004778
name: succinyl-CoA hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + succinyl-CoA = CoA + H(+) + succinate." [EC:3.1.2.3, RHEA:11516]
+def: "Catalysis of the reaction: H2O + succinyl-CoA = CoA + H+ + succinate." [EC:3.1.2.3, RHEA:11516]
synonym: "succinyl coenzyme A deacylase activity" RELATED [EC:3.1.2.3]
synonym: "succinyl coenzyme A hydrolase activity" RELATED [EC:3.1.2.3]
synonym: "succinyl-CoA acylase activity" RELATED [EC:3.1.2.3]
@@ -45991,7 +45981,7 @@ is_a: GO:0070566 ! adenylyltransferase activity
id: GO:0004780
name: sulfate adenylyltransferase (ADP) activity
namespace: molecular_function
-def: "Catalysis of the reaction: ADP + H(+) + sulfate = 5'-adenylyl sulfate + phosphate." [EC:2.7.7.5, RHEA:16529]
+def: "Catalysis of the reaction: ADP + H+ + sulfate = 5'-adenylyl sulfate + phosphate." [EC:2.7.7.5, RHEA:16529]
synonym: "adenosine diphosphate sulfurylase activity" RELATED [EC:2.7.7.5]
synonym: "ADP-sulfurylase activity" RELATED [EC:2.7.7.5]
synonym: "ADP:sulfate adenylyltransferase activity" EXACT []
@@ -46127,12 +46117,14 @@ consider: GO:0004784
[Term]
id: GO:0004787
-name: thiamine-diphosphatase activity
+name: thiamine diphosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: TPP + H2O = TMP + phosphate." [GOC:ai, RHEA:27998]
+def: "Catalysis of the reaction: thiamine diphosphate + H2O = thiamine monophosphate + phosphate." [GOC:ai, RHEA:27998]
synonym: "thiamin pyrophosphatase activity" EXACT []
synonym: "thiamin-pyrophosphatase activity" EXACT []
+synonym: "thiamine diphosphatase activity" BROAD []
synonym: "thiamine pyrophosphatase activity" EXACT []
+synonym: "thiamine-diphosphatase activity" EXACT []
synonym: "thiaminpyrophosphatase activity" RELATED []
synonym: "TPPase activity" EXACT []
xref: RHEA:27998
@@ -46162,7 +46154,7 @@ is_a: GO:0016778 ! diphosphotransferase activity
id: GO:0004789
name: thiamine-phosphate diphosphorylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-amino-2-methyl-5-diphosphomethylpyrimidine + 4-methyl-5-(2-phosphoethyl)-thiazole + H(+) = diphosphate + thiamine phosphate." [EC:2.5.1.3, RHEA:22328]
+def: "Catalysis of the reaction: 4-amino-2-methyl-5-diphosphomethylpyrimidine + 4-methyl-5-(2-phosphoethyl)-thiazole + H+ = diphosphate + thiamine phosphate." [EC:2.5.1.3, RHEA:22328]
synonym: "2-methyl-4-amino-5-hydroxymethylpyrimidine-diphosphate:4-methyl-5-(2-phosphoethyl)thiazole 2-methyl-4-aminopyrimidine-5-methenyltransferase activity" RELATED [EC:2.5.1.3]
synonym: "thiamin-phosphate diphosphorylase activity" EXACT []
synonym: "thiamin-phosphate pyrophosphorylase activity" EXACT []
@@ -46198,7 +46190,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0004791
name: thioredoxin-disulfide reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + thioredoxin = H(+) + NADPH + thioredoxin disulfide." [RHEA:20345]
+def: "Catalysis of the reaction: NADP+ + thioredoxin = H+ + NADPH + thioredoxin disulfide." [RHEA:20345]
synonym: "NADP--thioredoxin reductase activity" RELATED [EC:1.8.1.9]
synonym: "NADPH--thioredoxin reductase activity" RELATED [EC:1.8.1.9]
synonym: "NADPH2:oxidized thioredoxin oxidoreductase activity" RELATED [EC:1.8.1.9]
@@ -46222,7 +46214,7 @@ is_a: GO:0047134 ! protein-disulfide reductase (NAD(P)) activity
id: GO:0004792
name: thiosulfate sulfurtransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: hydrogen cyanide + thiosulfate = H(+) + sulfite + thiocyanate." [EC:2.8.1.1, RHEA:16881]
+def: "Catalysis of the reaction: hydrogen cyanide + thiosulfate = H+ + sulfite + thiocyanate." [EC:2.8.1.1, RHEA:16881]
synonym: "rhodanase activity" RELATED [EC:2.8.1.1]
synonym: "rhodanese activity" RELATED [EC:2.8.1.1]
synonym: "thiosulfate cyanide transsulfurase activity" RELATED [EC:2.8.1.1]
@@ -46510,7 +46502,7 @@ xref: EC:5.3.1.1
xref: KEGG_REACTION:R01015
xref: MetaCyc:TRIOSEPISOMERIZATION-RXN
xref: Reactome:R-HSA-70454 "dihydroxyacetone phosphate <=> D-glyceraldehyde 3-phosphate"
-xref: Reactome:R-HSA-70481 "D-glyceraldehyde 3-phosphate <=> dihydroxyacetone phosphate"
+xref: Reactome:R-HSA-70481 "TPI1 isomerizes GA3P to DHAP"
xref: RHEA:18585
is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldoses and ketoses
@@ -46554,33 +46546,35 @@ is_a: GO:0016423 ! tRNA (guanine) methyltransferase activity
[Term]
id: GO:0004810
-name: tRNA adenylyltransferase activity
+name: CCA tRNA nucleotidyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + tRNA(n) = diphosphate + tRNA(n+1)." [RHEA:14433]
-synonym: "-C-C-A pyrophosphorylase" BROAD [EC:2.7.7.25]
-synonym: "ATP (CTP):tRNA nucleotidyltransferase" BROAD [EC:2.7.7.25]
-synonym: "ATP(CTP)-tRNA nucleotidyltransferase" BROAD [EC:2.7.7.25]
-synonym: "ATP:tRNA adenylyltransferase activity" EXACT []
+alt_id: GO:0016437
+def: "Catalysis of the reaction: a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate." [PMID:2247609, RHEA:14433]
+synonym: "ATP(CTP)-tRNA nucleotidyltransferase" BROAD []
+synonym: "ATP(CTP):tRNA nucleotidyltransferase activity" BROAD []
synonym: "CCA-adding enzyme activity" RELATED [EC:2.7.7.72]
-synonym: "CTP(ATP):tRNA nucleotidyltransferase" BROAD [EC:2.7.7.25]
-synonym: "ribonucleic cytidylic cytidylic adenylic pyrophosphorylase" BROAD [EC:2.7.7.25]
-synonym: "ribonucleic cytidylyltransferase" BROAD [EC:2.7.7.25]
+synonym: "CTP(ATP):tRNA nucleotidyltransferase" BROAD []
+synonym: "CTP:tRNA cytidylyltransferase activity" BROAD []
+synonym: "ribonucleic cytidylic cytidylic adenylic pyrophosphorylase" BROAD [EC:2.7.7.72]
+synonym: "ribonucleic cytidylyltransferase" BROAD []
synonym: "transfer ribonucleate adenyltransferase activity" RELATED [EC:2.7.7.72]
-synonym: "transfer ribonucleate adenylyltransferase" BROAD [EC:2.7.7.25]
-synonym: "transfer ribonucleate cytidylyltransferase" BROAD [EC:2.7.7.25]
-synonym: "transfer ribonucleate nucleotidyltransferase" BROAD [EC:2.7.7.25]
-synonym: "transfer ribonucleic acid nucleotidyl transferase" BROAD [EC:2.7.7.25]
-synonym: "transfer ribonucleic adenylyl (cytidylyl) transferase" BROAD [EC:2.7.7.25]
-synonym: "transfer ribonucleic-terminal trinucleotide nucleotidyltransferase" BROAD [EC:2.7.7.25]
-synonym: "transfer RNA adenylyltransferase" BROAD [EC:2.7.7.25]
-synonym: "transfer-RNA nucleotidyltransferase" BROAD [EC:2.7.7.25]
-synonym: "tRNA adenylyl(cytidylyl)transferase" BROAD [EC:2.7.7.25]
-synonym: "tRNA CCA-diphosphorylase activity" RELATED [EC:2.7.7.25]
-synonym: "tRNA CCA-pyrophosphorylase activity" RELATED [EC:2.7.7.25]
-synonym: "tRNA-nucleotidyltransferase activity" BROAD [EC:2.7.7.25]
+synonym: "transfer ribonucleate adenylyltransferase" BROAD [EC:2.7.7.72]
+synonym: "transfer ribonucleate nucleotidyltransferase" BROAD []
+synonym: "transfer ribonucleic acid nucleotidyl transferase" BROAD []
+synonym: "transfer ribonucleic adenylyl (cytidylyl) transferase" BROAD [EC:2.7.7.72]
+synonym: "transfer ribonucleic-terminal trinucleotide nucleotidyltransferase" BROAD []
+synonym: "transfer RNA adenylyltransferase" BROAD [EC:2.7.7.72]
+synonym: "transfer-RNA nucleotidyltransferase" BROAD [EC:2.7.7.72]
+synonym: "tRNA adenylyl(cytidylyl)transferase" BROAD [EC:2.7.7.72]
+synonym: "tRNA CCA-diphosphorylase activity" RELATED [EC:2.7.7.72]
+synonym: "tRNA cytidylyltransferase activity" RELATED []
+synonym: "tRNA-nucleotidyltransferase activity" BROAD [EC:2.7.7.72]
xref: EC:2.7.7.72
xref: MetaCyc:TRNA-ADENYLYLTRANSFERASE-RXN
-is_a: GO:1990817 ! RNA adenylyltransferase activity
+xref: MetaCyc:TRNA-CYTIDYLYLTRANSFERASE-RXN
+xref: RHEA:14433
+is_a: GO:0070567 ! cytidylyltransferase activity
+is_a: GO:0140101 ! catalytic activity, acting on a tRNA
[Term]
id: GO:0004812
@@ -46663,7 +46657,7 @@ is_a: GO:0004812 ! aminoacyl-tRNA ligase activity
id: GO:0004816
name: asparagine-tRNA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-asparagine + ATP + tRNA(Asn) = AMP + Asn-tRNA(Asn) + diphosphate + 2 H(+)." [EC:6.1.1.22, RHEA:11180]
+def: "Catalysis of the reaction: L-asparagine + ATP + tRNA(Asn) = AMP + Asn-tRNA(Asn) + diphosphate + 2 H+." [EC:6.1.1.22, RHEA:11180]
synonym: "asparagine translase activity" RELATED [EC:6.1.1.22]
synonym: "asparaginyl transfer ribonucleic acid synthetase activity" RELATED [EC:6.1.1.22]
synonym: "asparaginyl transfer RNA synthetase activity" RELATED [EC:6.1.1.22]
@@ -46773,7 +46767,7 @@ is_a: GO:0004812 ! aminoacyl-tRNA ligase activity
id: GO:0004822
name: isoleucine-tRNA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-isoleucine + ATP + tRNA(Ile) = L-isoleucyl-tRNA(Ile) + AMP + diphosphate + 2 H(+)." [EC:6.1.1.5, RHEA:11060]
+def: "Catalysis of the reaction: L-isoleucine + ATP + tRNA(Ile) = L-isoleucyl-tRNA(Ile) + AMP + diphosphate + 2 H+." [EC:6.1.1.5, RHEA:11060]
synonym: "isoleucine translase activity" RELATED [EC:6.1.1.5]
synonym: "isoleucine-transfer RNA ligase activity" RELATED [EC:6.1.1.5]
synonym: "isoleucine-tRNA synthetase activity" RELATED [EC:6.1.1.5]
@@ -46793,7 +46787,7 @@ is_a: GO:0004812 ! aminoacyl-tRNA ligase activity
id: GO:0004823
name: leucine-tRNA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-leucine + ATP + tRNA(Leu) = AMP + diphosphate + 2 H(+) + Leu-tRNA(Leu)." [EC:6.1.1.4, RHEA:11688]
+def: "Catalysis of the reaction: L-leucine + ATP + tRNA(Leu) = AMP + diphosphate + 2 H+ + Leu-tRNA(Leu)." [EC:6.1.1.4, RHEA:11688]
synonym: "L-leucine:tRNALeu ligase (AMP-forming)" RELATED [EC:6.1.1.4]
synonym: "leucine translase activity" RELATED [EC:6.1.1.4]
synonym: "leucine-tRNA synthetase activity" RELATED [EC:6.1.1.4]
@@ -46956,7 +46950,7 @@ is_a: GO:0004812 ! aminoacyl-tRNA ligase activity
id: GO:0004831
name: tyrosine-tRNA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H(+)." [EC:6.1.1.1, RHEA:10220]
+def: "Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H+." [EC:6.1.1.1, RHEA:10220]
synonym: "L-tyrosine-tRNA(Tyr) ligase (AMP-forming) activity" RELATED [EC:6.1.1.1]
synonym: "L-tyrosine-tRNATyr ligase (AMP-forming)" RELATED [EC:6.1.1.1]
synonym: "L-tyrosine:tRNATyr ligase (AMP-forming)" RELATED [EC:6.1.1.1]
@@ -46981,7 +46975,7 @@ is_a: GO:0004812 ! aminoacyl-tRNA ligase activity
id: GO:0004832
name: valine-tRNA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-valine + ATP + tRNA(Val) = L-valyl-tRNA(Val) + AMP + diphosphate + 2 H(+)." [EC:6.1.1.9, RHEA:10704]
+def: "Catalysis of the reaction: L-valine + ATP + tRNA(Val) = L-valyl-tRNA(Val) + AMP + diphosphate + 2 H+." [EC:6.1.1.9, RHEA:10704]
synonym: "L-valine:tRNAVal ligase (AMP-forming)" RELATED [EC:6.1.1.9]
synonym: "valine transfer ribonucleate ligase activity" RELATED [EC:6.1.1.9]
synonym: "valine translase activity" RELATED [EC:6.1.1.9]
@@ -47229,6 +47223,7 @@ xref: Reactome:R-HSA-5675470 "BIRC2/3 (cIAP1/2) is autoubiquitinated"
xref: Reactome:R-HSA-5684250 "SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2"
xref: Reactome:R-HSA-5691108 "SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2"
xref: Reactome:R-HSA-5693108 "TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains"
+xref: Reactome:R-HSA-68712 "The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1"
xref: Reactome:R-HSA-69598 "Ubiquitination of phosphorylated Cdc25A"
xref: Reactome:R-HSA-741386 "RIP2 induces K63-linked ubiquitination of NEMO"
xref: Reactome:R-HSA-75824 "Ubiquitination of Cyclin D1"
@@ -47239,7 +47234,7 @@ xref: Reactome:R-HSA-9013069 "Ubiquitination of DLL/JAG ligands upon binding to
xref: Reactome:R-HSA-9013974 "Auto-ubiquitination of TRAF3 within activated TLR3 complex"
xref: Reactome:R-HSA-9014342 "K63-linked ubiquitination of RIP1 bound to the activated TLR complex"
xref: Reactome:R-HSA-918224 "DDX58 is K63 polyubiquitinated"
-xref: Reactome:R-HSA-936412 "RNF125 mediated ubiquitination of DDX58, IFIH1 and MADS"
+xref: Reactome:R-HSA-936412 "RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS"
xref: Reactome:R-HSA-936942 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2"
xref: Reactome:R-HSA-936986 "Activated TRAF6 synthesizes unanchored polyubiquitin chains"
xref: Reactome:R-HSA-9628444 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation"
@@ -47247,8 +47242,18 @@ xref: Reactome:R-HSA-9645394 "Activated TRAF6 synthesizes unanchored polyubiquit
xref: Reactome:R-HSA-9645414 "Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer"
xref: Reactome:R-HSA-9688831 "STUB1 ubiquitinates RIPK3 at K55, K363"
xref: Reactome:R-HSA-9701000 "BRCA1:BARD1 heterodimer autoubiquitinates"
+xref: Reactome:R-HSA-9750946 "TRAF2,6 ubiquitinates NLRC5"
xref: Reactome:R-HSA-975118 "TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex"
xref: Reactome:R-HSA-975147 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane"
+xref: Reactome:R-HSA-9758604 "Ubiquitination of IKBKG by TRAF6"
+xref: Reactome:R-HSA-9793444 "ITCH polyubiquitinates MLKL at K50"
+xref: Reactome:R-HSA-9793485 "PRKN polyubiquitinates RIPK3"
+xref: Reactome:R-HSA-9793679 "LUBAC ubiquitinates RIPK1 at K627"
+xref: Reactome:R-HSA-9796346 "MIB2 ubiquitinates RIPK1 at K377, K604, K634"
+xref: Reactome:R-HSA-9796387 "STUB1 ubiquitinates RIPK1 at K571, K604, K627"
+xref: Reactome:R-HSA-9796626 "MIB2 ubiquitinates CFLAR"
+xref: Reactome:R-HSA-9815507 "MIB2 ubiquitinates CYLD at K338, K530"
+xref: Reactome:R-HSA-9817362 "SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex"
xref: Reactome:R-HSA-983140 "Transfer of Ub from E2 to substrate and release of E2"
xref: Reactome:R-HSA-983153 "E1 mediated ubiquitin activation"
xref: Reactome:R-HSA-983156 "Polyubiquitination of substrate"
@@ -47256,14 +47261,15 @@ is_a: GO:0019787 ! ubiquitin-like protein transferase activity
[Term]
id: GO:0004843
-name: thiol-dependent deubiquitinase
+name: cysteine-type deubiquitinase activity
namespace: molecular_function
alt_id: GO:0036459
-def: "Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein." [GOC:jh2, ISBN:0120793709]
-synonym: "deubiquitinase" EXACT [GOC:vw, PMID:19261746]
-synonym: "deubiquitinase activity" NARROW [GOC:bf]
-synonym: "deubiquitinating enzyme" NARROW [PMID:19188440]
-synonym: "deubiquitylase" EXACT [GOC:vw, PMID:15657442]
+def: "An thiol-dependent isopeptidase activity that cleaves ubiquitin from a target protein to which it is conjugated." [GOC:jh2, PMID:30783221]
+synonym: "deubiquitinase" BROAD [GOC:vw, PMID:19261746]
+synonym: "deubiquitinase activity" BROAD [GOC:bf]
+synonym: "deubiquitinating enzyme" BROAD [PMID:19188440]
+synonym: "deubiquitylase" BROAD [GOC:vw, PMID:15657442]
+synonym: "thiol-dependent deubiquitinase" EXACT []
synonym: "thiol-dependent ubiquitin-specific protease activity" EXACT []
synonym: "thiol-dependent ubiquitinyl hydrolase activity" EXACT []
synonym: "ubiquitin C-terminal hydrolase" RELATED [EC:3.4.19.12]
@@ -47337,7 +47343,7 @@ xref: Reactome:R-HSA-8986083 "USP33 deubiquitinates ROBO1"
xref: Reactome:R-HSA-9033478 "USP9X hydrolyzes Ub:PEX5S yielding PEX5S and Ubiquitin"
xref: Reactome:R-HSA-9033491 "USP9X hydrolyzes Ub:PEX5L yielding PEX5L and Ubiquitin"
xref: Reactome:R-HSA-9653514 "USP17L2 deubiquitinates RCE1"
-is_a: GO:0008242 ! omega peptidase activity
+is_a: GO:0008234 ! cysteine-type peptidase activity
is_a: GO:0101005 ! deubiquitinase activity
[Term]
@@ -47346,6 +47352,8 @@ name: uracil DNA N-glycosylase activity
namespace: molecular_function
def: "Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine." [GOC:elh, GOC:pr, PMID:9224623]
synonym: "uracil-DNA glycosylase activity" EXACT []
+xref: EC:3.2.2.27
+xref: https://github.com/geneontology/go-ontology/issues/25051
xref: Reactome:R-HSA-110215 "Cleavage of uracil by UNG glycosylase"
xref: Reactome:R-HSA-110217 "Cleavage of 5-hydroxyluracil by UNG glycosylase"
is_a: GO:0097506 ! deaminated base DNA N-glycosylase activity
@@ -47389,7 +47397,7 @@ is_a: GO:0016663 ! oxidoreductase activity, acting on other nitrogenous compound
id: GO:0004847
name: urea carboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + bicarbonate + urea = ADP + 2 H(+) + phosphate + urea-1-carboxylate." [EC:6.3.4.6, RHEA:20896]
+def: "Catalysis of the reaction: ATP + bicarbonate + urea = ADP + 2 H+ + phosphate + urea-1-carboxylate." [EC:6.3.4.6, RHEA:20896]
synonym: "ATP--urea amidolyase activity" RELATED [EC:6.3.4.6]
synonym: "UALase activity" RELATED [EC:6.3.4.6]
synonym: "UCA activity" RELATED [EC:6.3.4.6]
@@ -47409,7 +47417,7 @@ is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
id: GO:0004848
name: ureidoglycolate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-ureidoglycolate + H(2)O + 2 H(+) = CO(2) + glyoxylate + 2 NH(4)(+)." [EC:3.5.1.116, RHEA:19809]
+def: "Catalysis of the reaction: (S)-ureidoglycolate + H2O + 2 H+ = CO2 + glyoxylate + 2 NH4." [EC:3.5.1.116, RHEA:19809]
comment: Take care to annotate to the reaction, not simply the enzyme name. The name "ureidoglycolate hydrolase" has variously been used to refer to two distinctly different enzymes. Both enzymes act on ureidoglycolate and produce glyoxylate, but the mechanism and reaction products are different. The "ureidoglycolate hydrolase" listed in the Enzyme commission (EC) is a ureidoglycolate amidohydrolase, releasing ammonia, (EC:3.5.3.19, GO:0004848). The "ureidoglycolate hydrolase" characterized in PMID:3915539 (published prior to the EC designation of EC:3.5.3.19) is a ureidoglycolate lyase, releasing urea (EC:4.3.2.3, GO:0050385). The inappropriate labelling of ureidoglycolate lyase as EC:3.5.3.19 has caused much confusion in the literature (see PMID:24107613). Take care to correctly annotate based on the reaction products, rather than name.
synonym: "(S)-ureidoglycolate amidohydrolase (decarboxylating)" EXACT []
xref: EC:3.5.3.19
@@ -47422,15 +47430,9 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0004849
name: uridine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + uridine = ADP + UMP." [EC:2.7.1.48]
-synonym: "ATP:uridine 5'-phosphotransferase activity" RELATED [EC:2.7.1.48]
-synonym: "pyrimidine ribonucleoside kinase activity" RELATED [EC:2.7.1.48]
-synonym: "uridine kinase (phosphorylating)" RELATED [EC:2.7.1.48]
-synonym: "uridine kinase reaction" EXACT []
-synonym: "uridine monophosphokinase activity" RELATED [EC:2.7.1.48]
-synonym: "uridine phosphokinase activity" RELATED [EC:2.7.1.48]
-synonym: "uridine-cytidine kinase activity" RELATED [EC:2.7.1.48]
-xref: EC:2.7.1.48
+def: "Catalysis of the reaction: ATP + uridine = ADP + UMP." [RHEA:16825]
+synonym: "uridine phosphokinase activity" EXACT []
+synonym: "uridine-cytidine kinase activity" NARROW [EC:2.7.1.48]
xref: MetaCyc:URIDINEKIN-RXN
xref: Reactome:R-HSA-8954327 "UCKL1 phosphorylates urindine, cytidine"
xref: RHEA:16825
@@ -47482,7 +47484,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0004852
name: uroporphyrinogen-III synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: hydroxymethylbilane = H(2)O + uroporphyrinogen III." [EC:4.2.1.75, RHEA:18965]
+def: "Catalysis of the reaction: hydroxymethylbilane = H2O + uroporphyrinogen III." [EC:4.2.1.75, RHEA:18965]
synonym: "hydroxymethylbilane hydro-lyase (cyclizing) activity" RELATED [EC:4.2.1.75]
synonym: "hydroxymethylbilane hydro-lyase (cyclizing; uroporphyrinogen-III-forming)" RELATED [EC:4.2.1.75]
synonym: "porphobilinogenase activity" RELATED [EC:4.2.1.75]
@@ -47528,6 +47530,7 @@ synonym: "xanthine/NAD+ oxidoreductase activity" RELATED [EC:1.17.1.4]
synonym: "xanthine:NAD+ oxidoreductase activity" RELATED [EC:1.17.1.4]
xref: EC:1.17.1.4
xref: MetaCyc:RXN0-901
+xref: Reactome:R-HSA-9727349 "XDH dehydrogenates xanthine to form urate"
xref: RHEA:16669
is_a: GO:0016726 ! oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
@@ -47540,14 +47543,13 @@ synonym: "hypoxanthine-xanthine oxidase activity" BROAD [EC:1.17.3.2]
synonym: "schardinger enzyme" RELATED [EC:1.17.3.2]
synonym: "Schardinger enzyme activity" RELATED [EC:1.17.3.2]
synonym: "xanthine oxidoreductase activity" BROAD [EC:1.17.3.2]
-synonym: "xanthine:O(2) oxidoreductase activity" RELATED [EC:1.17.3.2]
synonym: "xanthine:O2 oxidoreductase activity" RELATED [EC:1.17.3.2]
synonym: "xanthine:oxygen oxidoreductase activity" RELATED [EC:1.17.3.2]
synonym: "xanthine:xanthine oxidase activity" RELATED [EC:1.17.3.2]
xref: EC:1.17.3.2
xref: MetaCyc:XANTHINE-OXIDASE-RXN
-xref: Reactome:R-HSA-74247 "Hypoxanthine + H2O + O2 => Xanthine + H2O2"
-xref: Reactome:R-HSA-74258 "Xanthine + H2O + O2 => Urate + H2O2"
+xref: Reactome:R-HSA-74258 "XDH oxidizes xanthine to form urate"
+xref: Reactome:R-HSA-9748991 "XDH oxidises 6MP to 6TU"
xref: RHEA:21132
xref: UM-BBD_enzymeID:e0781
is_a: GO:0016727 ! oxidoreductase activity, acting on CH or CH2 groups, oxygen as acceptor
@@ -47556,7 +47558,7 @@ is_a: GO:0016727 ! oxidoreductase activity, acting on CH or CH2 groups, oxygen a
id: GO:0004856
name: xylulokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-xylulose + ATP = D-xylulose 5-phosphate + ADP + 2 H(+)." [EC:2.7.1.17, RHEA:10964]
+def: "Catalysis of the reaction: D-xylulose + ATP = D-xylulose 5-phosphate + ADP + 2 H+." [EC:2.7.1.17, RHEA:10964]
synonym: "ATP:D-xylulose 5-phosphotransferase activity" RELATED [EC:2.7.1.17]
synonym: "D-xylulokinase activity" RELATED [EC:2.7.1.17]
synonym: "xylulokinase (phosphorylating)" RELATED [EC:2.7.1.17]
@@ -47597,7 +47599,7 @@ is_a: GO:0055102 ! lipase inhibitor activity
id: GO:0004860
name: protein kinase inhibitor activity
namespace: molecular_function
-def: "Binds to and stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein." [GOC:ai]
+def: "Binds to and stops, prevents or reduces the activity of a protein kinase." [GOC:ai]
is_a: GO:0019210 ! kinase inhibitor activity
is_a: GO:0019887 ! protein kinase regulator activity
@@ -47630,7 +47632,7 @@ id: GO:0004864
name: protein phosphatase inhibitor activity
namespace: molecular_function
alt_id: GO:1990681
-def: "Binds to and stops, prevents or reduces the activity of a protein phosphatase, an enzyme that hydrolyzes phosphate groups from phosphorylated proteins." [GOC:ai]
+def: "Binds to and stops, prevents or reduces the activity of a protein phosphatase." [GOC:ai]
synonym: "phosphoprotein phosphatase inhibitor activity" EXACT []
synonym: "protein phosphatase 2 inhibitor activity" NARROW [GOC:dph]
synonym: "protein phosphatase type 2A inhibitor activity" NARROW []
@@ -47648,7 +47650,7 @@ is_a: GO:0004864 ! protein phosphatase inhibitor activity
id: GO:0004866
name: endopeptidase inhibitor activity
namespace: molecular_function
-def: "Binds to and stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides." [GOC:jl]
+def: "Binds to and stops, prevents or reduces the activity of an endopeptidase." [GOC:jl]
synonym: "alpha-2 macroglobulin" RELATED []
synonym: "endoproteinase inhibitor" NARROW []
synonym: "proteinase inhibitor" NARROW []
@@ -47659,7 +47661,7 @@ is_a: GO:0061135 ! endopeptidase regulator activity
id: GO:0004867
name: serine-type endopeptidase inhibitor activity
namespace: molecular_function
-def: "Binds to and stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme." [GOC:ai]
+def: "Binds to and stops, prevents or reduces the activity of a serine-type endopeptidase." [GOC:ai]
synonym: "serine protease inhibitor activity" NARROW []
synonym: "serine proteinase inhibitor activity" NARROW []
synonym: "serpin activity" NARROW []
@@ -47685,7 +47687,7 @@ id: GO:0004869
name: cysteine-type endopeptidase inhibitor activity
namespace: molecular_function
alt_id: GO:0004870
-def: "Binds to and stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile." [GOC:dph, GOC:tb]
+def: "Binds to and stops, prevents or reduces the activity of a cysteine-type endopeptidase." [GOC:dph, GOC:tb]
synonym: "cystatin" NARROW [GOC:jl]
synonym: "cysteine protease inhibitor activity" NARROW [GOC:dph, GOC:tb]
synonym: "thiol protease inhibitor" NARROW []
@@ -47803,10 +47805,11 @@ is_a: GO:0098531 ! ligand-activated transcription factor activity
[Term]
id: GO:0004883
-name: glucocorticoid receptor activity
+name: nuclear glucocorticoid receptor activity
namespace: molecular_function
def: "Combining with a glucocorticoid and transmitting the signal within the cell trigger a change in cell activity or function." [GOC:signaling, PMID:17689856, PMID:20920967]
-is_a: GO:0003707 ! steroid hormone receptor activity
+synonym: "glucocorticoid receptor activity" BROAD []
+is_a: GO:0003707 ! nuclear steroid receptor activity
[Term]
id: GO:0004888
@@ -47959,12 +47962,12 @@ is_a: GO:0004904 ! interferon receptor activity
[Term]
id: GO:0004906
-name: interferon-gamma receptor activity
+name: type II interferon receptor activity
namespace: molecular_function
def: "Combining with interferon-gamma (a type II interferon) and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:ai, GOC:signaling, ISBN:0126896631, PMID:15546383]
synonym: "IFN-gamma receptor activity" EXACT [GOC:mah]
synonym: "IFNG receptor activity" EXACT [GOC:mah]
-synonym: "type II interferon receptor activity" BROAD []
+synonym: "interferon-gamma receptor activity" EXACT []
is_a: GO:0004904 ! interferon receptor activity
[Term]
@@ -48182,25 +48185,26 @@ synonym: "RDC1 receptor activity" NARROW []
synonym: "receptor activity, G-protein coupled" EXACT [GOC:bf]
synonym: "SREB receptor" NARROW []
synonym: "super conserved receptor expressed in brain receptor activity" NARROW []
-xref: Reactome:R-HSA-114552 "G12/13 activation by PAR"
-xref: Reactome:R-HSA-114558 "Gq activation by PAR"
+xref: Reactome:R-HSA-114552 "Thrombin-activated PARs activate G12/13"
+xref: Reactome:R-HSA-114558 "Thrombin-activated PARs activate Gq"
xref: Reactome:R-HSA-167408 "The high affinity receptor complex binds to G-protein"
xref: Wikipedia:GPCR
is_a: GO:0004888 ! transmembrane signaling receptor activity
[Term]
id: GO:0004931
-name: extracellularly ATP-gated cation channel activity
+name: extracellularly ATP-gated monoatomic cation channel activity
namespace: molecular_function
-def: "Enables the transmembrane transfer of a cation by a channel that opens when ATP is bound by the channel complex or one of its constituent parts on the extracellular side of the plasma membrane." [GOC:bf, GOC:mah, PMID:9755289]
+def: "Enables the transmembrane transfer of a monoatomic cation by a channel that opens when ATP is bound by the channel complex or one of its constituent parts on the extracellular side of the plasma membrane." [GOC:bf, GOC:mah, PMID:9755289]
comment: Note that this term refers to an activity and not a gene product. Consider also annotating to the molecular function term 'purinergic nucleotide receptor activity ; GO:0001614'.
+synonym: "extracellularly ATP-gated cation channel activity" BROAD []
synonym: "P2X receptor" RELATED [PMID:9755289]
synonym: "purinoceptor" BROAD []
synonym: "purinoreceptor" BROAD []
xref: Reactome:R-HSA-877187 "P2X7 mediates loss of intracellular K+"
-is_a: GO:0005231 ! excitatory extracellular ligand-gated ion channel activity
+is_a: GO:0005231 ! excitatory extracellular ligand-gated monoatomic ion channel activity
is_a: GO:0035381 ! ATP-gated ion channel activity
-is_a: GO:0099094 ! ligand-gated cation channel activity
+is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
[Term]
id: GO:0004932
@@ -48501,7 +48505,7 @@ namespace: molecular_function
def: "Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts." [ISBN:0198506732]
comment: Note that this term represents an activity and not a gene product. Consider also annotating to the molecular function terms 'glutamate-gated ion channel activity ; GO:0005234' and 'cation channel activity ; GO:0005261'.
is_a: GO:0008066 ! glutamate receptor activity
-is_a: GO:0022824 ! transmitter-gated ion channel activity
+is_a: GO:0022824 ! transmitter-gated monoatomic ion channel activity
[Term]
id: GO:0004971
@@ -48512,20 +48516,20 @@ comment: Note that this term represents an activity and not a gene product. Cons
synonym: "alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity" EXACT []
synonym: "AMPA receptor activity" EXACT []
is_a: GO:0004970 ! ionotropic glutamate receptor activity
-is_a: GO:0099094 ! ligand-gated cation channel activity
+is_a: GO:0022890 ! inorganic cation transmembrane transporter activity
[Term]
id: GO:0004972
name: NMDA glutamate receptor activity
namespace: molecular_function
-def: "An cation channel that opens in response to binding by extracellular glutmate, but only if glycine is also bound and the membrane is depolarized. Voltage gating is indirect, due to ejection of bound magnesium from the pore at permissive voltages." [GOC:mah, PMID:10049997]
+def: "An cation channel that opens in response to binding by extracellular glutmate, but only if glycine is also bound and the membrane is depolarized. Voltage gating is indirect, due to ejection of bound magnesium from the pore at permissive voltages." [GOC:mah, PMID:10049997]
comment: The name of this receptor comes from its selective activation by N-methyl-D-aspartate (NMDA). Note that this term represents an activity and not a gene product.
synonym: "N-methyl-D-aspartate selective glutamate receptor activity" EXACT []
synonym: "NMDA receptor" EXACT []
xref: Wikipedia:NMDA_receptor
is_a: GO:0004970 ! ionotropic glutamate receptor activity
-is_a: GO:0022843 ! voltage-gated cation channel activity
-is_a: GO:0099094 ! ligand-gated cation channel activity
+is_a: GO:0005244 ! voltage-gated monoatomic ion channel activity
+is_a: GO:0022890 ! inorganic cation transmembrane transporter activity
[Term]
id: GO:0004973
@@ -48613,7 +48617,7 @@ name: G protein-coupled opioid receptor activity
namespace: molecular_function
def: "Combining with an opioid (any narcotic derived from or resembling opium), and transmitting the signal across the membrane by activating an associated G-protein." [GOC:ai, GOC:bf, PMID:20494127]
synonym: "opioid receptor activity" BROAD []
-is_a: GO:0008528 ! G protein-coupled peptide receptor activity
+is_a: GO:0004930 ! G protein-coupled receptor activity
[Term]
id: GO:0004986
@@ -48767,7 +48771,7 @@ is_a: GO:0019198 ! transmembrane receptor protein phosphatase activity
id: GO:0005003
name: ephrin receptor activity
namespace: molecular_function
-def: "Combining with an ephrin to initiate a change in cell activity." [GOC:mah, PMID:9530499]
+def: "Combining with an ephrin receptor ligand to initiate a change in cell activity." [GOC:mah, PMID:9530499]
synonym: "Eph receptor activity" EXACT []
is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity
@@ -48789,67 +48793,66 @@ is_a: GO:0005003 ! ephrin receptor activity
[Term]
id: GO:0005006
-name: epidermal growth factor-activated receptor activity
+name: epidermal growth factor receptor activity
namespace: molecular_function
alt_id: GO:0005023
-def: "Combining with an epidermal growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:bf]
-comment: Note that this term represents an activity and not a gene product, and should only be used when the receptor binds the ligand EGF. For receptors that bind other growth factors, consider annotating to other terms under 'transmembrane signaling receptor activity ; GO:0004888.
+def: "Combining with an epidermal growth factor receptor ligand and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:bf]
synonym: "EGF receptor activity" EXACT []
synonym: "EGFR" EXACT []
-synonym: "epidermal growth factor receptor activity" EXACT [GOC:bf, GOC:signaling]
+synonym: "epidermal growth factor-activated receptor activity" EXACT []
synonym: "TGF-alpha receptor activity" EXACT []
synonym: "transforming growth factor-alpha receptor activity" EXACT []
is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity
[Term]
id: GO:0005007
-name: fibroblast growth factor-activated receptor activity
+name: fibroblast growth factor receptor activity
namespace: molecular_function
-def: "Combining with a fibroblast growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:mah]
+def: "Combining with a fibroblast growth factor receptor ligand and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:mah]
comment: Note that this term represents an activity and not a gene product, and should only be used when the receptor binds the ligand FGF. For receptors that bind other growth factors, consider annotating to terms under 'transmembrane signaling receptor activity ; GO:0004888.
synonym: "FGF receptor activity" EXACT []
synonym: "FGF-activated receptor activity" EXACT [GOC:bf, GOC:signaling]
synonym: "FGFR" EXACT []
-synonym: "fibroblast growth factor receptor activity" EXACT [GOC:bf, GOC:signaling]
+synonym: "fibroblast growth factor-activated receptor activity" EXACT []
is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity
[Term]
id: GO:0005008
-name: hepatocyte growth factor-activated receptor activity
+name: hepatocyte growth factor receptor activity
namespace: molecular_function
-def: "Combining with hepatocyte growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:mah]
+def: "Combining with hepatocyte growth factor receptor ligand and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:mah]
comment: Note that this term represents an activity and not a gene product, and should only be used when the receptor binds the ligand HGF. For receptors that bind other growth factors, consider annotating to other terms under 'transmembrane signaling receptor activity ; GO:0004888.
-synonym: "hepatocyte growth factor receptor activity" EXACT [GOC:bf, GOC:signaling]
+synonym: "hepatocyte growth factor-activated receptor activity" EXACT []
synonym: "HGF receptor activity" EXACT []
synonym: "HGF-activated receptor activity" EXACT [GOC:bf, GOC:signaling]
is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity
[Term]
id: GO:0005009
-name: insulin-activated receptor activity
+name: insulin receptor activity
namespace: molecular_function
-def: "Combining with insulin and transmitting the signal across the plasma membrane to initiate a change in cell activity." [ISBN:0198506732]
-comment: Note that this term represents an activity and not a gene product, and should only be used when the receptor binds the ligand insulin. For receptors that bind other extracellular ligands, consider annotating to other terms under 'transmembrane signaling receptor activity ; GO:0004888.
-synonym: "insulin receptor activity" EXACT [GOC:bf, GOC:signaling]
+def: "Combining with insulin receptor ligand and transmitting the signal across the plasma membrane to initiate a change in cell activity." [ISBN:0198506732]
+synonym: "insulin-activated receptor activity" EXACT []
+xref: Reactome:R-HSA-74715 "Autophosphorylation of insulin receptor"
is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity
is_a: GO:0016500 ! protein-hormone receptor activity
[Term]
id: GO:0005010
-name: insulin-like growth factor-activated receptor activity
+name: insulin-like growth factor receptor activity
namespace: molecular_function
-def: "Combining with insulin-like growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:mah]
+def: "Combining with insulin-like growth factor receptor ligand and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:mah]
comment: Note that this term represents an activity and not a gene product, and should only be used when the receptor binds the ligand IGF. For receptors that bind other growth factors, consider annotating to other terms under 'transmembrane signaling receptor activity ; GO:0004888.
synonym: "IGF receptor activity" EXACT []
synonym: "IGF-activated receptor activity" EXACT [GOC:bf, GOC:signaling]
-synonym: "insulin-like growth factor receptor activity" EXACT [GOC:bf, GOC:signaling]
+synonym: "insulin-like growth factor-activated receptor activity" EXACT []
is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity
[Term]
id: GO:0005011
name: macrophage colony-stimulating factor receptor activity
namespace: molecular_function
-def: "Combining with macrophage colony-stimulating factor (M-CSF) and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate." [GOC:mah, GOC:signaling]
+def: "Combining with macrophage colony-stimulating factor (M-CSF) receptor ligand and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate." [GOC:mah, GOC:signaling]
synonym: "CSF-1" NARROW []
synonym: "Fms" NARROW []
synonym: "M-CSF receptor activity" EXACT [GOC:bf]
@@ -48919,14 +48922,14 @@ consider: GO:0043121
[Term]
id: GO:0005017
-name: platelet-derived growth factor-activated receptor activity
+name: platelet-derived growth factor receptor activity
namespace: molecular_function
-def: "Combining with platelet-derived growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:mah]
+def: "Combining with platelet-derived growth factor receptor ligand and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:mah]
comment: Note that this term represents an activity and not a gene product, and should only be used when the receptor binds the ligand PDGF. For receptors that bind other growth factors, consider annotating to other terms under 'transmembrane signaling receptor activity ; GO:0004888.
synonym: "PDGF receptor activity" EXACT []
synonym: "PDGF-activated receptor activity" EXACT [GOC:bf, GOC:signaling]
synonym: "PDGFR activity" EXACT []
-synonym: "platelet-derived growth factor receptor activity" EXACT [GOC:bf, GOC:signaling]
+synonym: "platelet-derived growth factor-activated receptor activity" EXACT []
is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity
[Term]
@@ -48936,7 +48939,7 @@ namespace: molecular_function
def: "Combining with platelet-derived growth factor isoform PDGF-AA, PDGF-BB or PDGF-AB to initiate a change in cell activity." [PMID:1657917]
synonym: "alphaPDGF receptor activity" EXACT [PMID:10372961]
synonym: "PDGF alpha-receptor activity" EXACT []
-is_a: GO:0005017 ! platelet-derived growth factor-activated receptor activity
+is_a: GO:0005017 ! platelet-derived growth factor receptor activity
[Term]
id: GO:0005019
@@ -48945,13 +48948,13 @@ namespace: molecular_function
def: "Combining with platelet-derived growth factor isoform PDGF-BB or PDGF-AB to initiate a change in cell activity." [PMID:1657917]
synonym: "betaPDGF receptor activity" RELATED [PMID:10372961]
synonym: "PDGF beta-receptor activity" EXACT []
-is_a: GO:0005017 ! platelet-derived growth factor-activated receptor activity
+is_a: GO:0005017 ! platelet-derived growth factor receptor activity
[Term]
id: GO:0005020
name: stem cell factor receptor activity
namespace: molecular_function
-def: "Combining with stem cell factor (SCF) and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate. Stem cell factor is a cytokine that stimulates mast cell growth and differentiation." [GOC:jl, GOC:signaling, PMID:10698217]
+def: "Combining with stem cell factor (SCF) receptor ligand and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate. Stem cell factor is a cytokine that stimulates mast cell growth and differentiation." [GOC:jl, GOC:signaling, PMID:10698217]
synonym: "KIT" RELATED [PR:000009345]
synonym: "KIT ligand receptor activity" EXACT [PR:000009345]
synonym: "KL receptor activity" EXACT [PR:000009345]
@@ -48960,17 +48963,17 @@ is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity
[Term]
id: GO:0005021
-name: vascular endothelial growth factor-activated receptor activity
+name: vascular endothelial growth factor receptor activity
namespace: molecular_function
alt_id: GO:0036326
alt_id: GO:0036327
alt_id: GO:0036328
alt_id: GO:0036329
alt_id: GO:0036330
-def: "Combining with a vascular endothelial growth factor (VEGF) and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:mah, GOC:signaling, PMID:19909239]
+def: "Combining with a vascular endothelial growth factor (VEGF) receptor ligand and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:mah, GOC:signaling, PMID:19909239]
comment: Note that this term represents an activity and not a gene product, and should only be used when the receptor binds the ligand VEGF. For receptors that bind other growth factors, consider annotating to terms under 'transmembrane signaling receptor activity ; GO:0004888.
synonym: "vascular endothelial growth factor E-activated receptor activity" EXACT [PMID:19909239]
-synonym: "vascular endothelial growth factor receptor activity" EXACT [GOC:bf, GOC:signaling]
+synonym: "vascular endothelial growth factor-activated receptor activity" EXACT []
synonym: "VEGF receptor activity" EXACT []
synonym: "VEGF-A-activated receptor activity" NARROW []
synonym: "VEGF-activated receptor activity" EXACT [GOC:bf, GOC:signaling]
@@ -48983,7 +48986,7 @@ is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity
[Term]
id: GO:0005024
-name: transforming growth factor beta-activated receptor activity
+name: transforming growth factor beta receptor activity
namespace: molecular_function
def: "Combining with a transforming growth factor beta (TGFbeta) and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate." [GOC:mah, GOC:signaling]
comment: Note that this term represents an activity and not a gene product, and should only be used when the receptor binds the ligand TGFbeta. For binding to other growth factors, consider annotating to terms under 'transmembrane signaling receptor activity ; GO:0004888.
@@ -48991,7 +48994,7 @@ synonym: "TGF-beta receptor activity" EXACT []
synonym: "TGFbeta receptor activity" EXACT []
synonym: "TGFbeta-activated receptor activity" EXACT [GOC:bf, GOC:signaling]
synonym: "TGFbetaR" EXACT []
-synonym: "transforming growth factor beta receptor activity" EXACT [GOC:bf, GOC:signaling]
+synonym: "transforming growth factor beta-activated receptor activity" EXACT []
is_a: GO:0004675 ! transmembrane receptor protein serine/threonine kinase activity
[Term]
@@ -49003,7 +49006,7 @@ synonym: "transforming growth factor beta ligand binding to type I receptor" REL
synonym: "type I TGF-beta receptor activity" EXACT []
synonym: "type I TGFbeta receptor activity" EXACT []
synonym: "type I transforming growth factor beta receptor activity" EXACT []
-is_a: GO:0005024 ! transforming growth factor beta-activated receptor activity
+is_a: GO:0005024 ! transforming growth factor beta receptor activity
[Term]
id: GO:0005026
@@ -49015,7 +49018,7 @@ synonym: "type II TGF-beta receptor activity" EXACT []
synonym: "type II TGFbeta receptor activity" EXACT []
synonym: "type II transforming growth factor beta receptor activity" EXACT []
xref: Reactome:R-HSA-170843 "TGFBR2 phosphorylates TGFBR1"
-is_a: GO:0005024 ! transforming growth factor beta-activated receptor activity
+is_a: GO:0005024 ! transforming growth factor beta receptor activity
[Term]
id: GO:0005027
@@ -49056,7 +49059,7 @@ is_a: GO:0038023 ! signaling receptor activity
[Term]
id: GO:0005031
-name: tumor necrosis factor-activated receptor activity
+name: tumor necrosis factor receptor activity
namespace: molecular_function
alt_id: GO:0005032
alt_id: GO:0005033
@@ -49065,9 +49068,9 @@ synonym: "NGF/TNF (6 C-domain) receptor activity" NARROW []
synonym: "TNF receptor activity" EXACT []
synonym: "TNF receptor activity, type I" NARROW []
synonym: "TNF receptor activity, type II" NARROW []
-synonym: "tumor necrosis factor receptor activity" EXACT [GOC:bf, GOC:signaling]
synonym: "tumor necrosis factor receptor activity, type I" NARROW []
synonym: "tumor necrosis factor receptor activity, type II" NARROW []
+synonym: "tumor necrosis factor-activated receptor activity" EXACT []
is_a: GO:0005035 ! death receptor activity
[Term]
@@ -49530,7 +49533,6 @@ xref: Reactome:R-HSA-180687 "Conversion of Ran-GDP to Ran-GTP"
xref: Reactome:R-HSA-186834 "SOS-mediated nucleotide exchange on RAS (PDGF receptor:GRB2:SOS)"
xref: Reactome:R-HSA-187746 "RIT/RIN are activated"
xref: Reactome:R-HSA-194518 "RhoA is activated by nucleotide exchange and inhibits axonal growth"
-xref: Reactome:R-HSA-194913 "GEFs activate Rho GTPase:GDP"
xref: Reactome:R-HSA-2029445 "An unknown GEF exchanges GTP for GDP on CDC42:GDP"
xref: Reactome:R-HSA-2029451 "Activation of RAC1 by VAV"
xref: Reactome:R-HSA-2029467 "Activation of RAC1 by CRKII:DOCK180:ELMO"
@@ -49563,7 +49565,7 @@ xref: Reactome:R-HSA-3965444 "WNT:FZD complex promotes G-protein nucleotide exch
xref: Reactome:R-HSA-399938 "Activation of Rac1 by FARP2"
xref: Reactome:R-HSA-399995 "Muscarinic Acetylcholine Receptor M3 activates Gq"
xref: Reactome:R-HSA-4093336 "p-TIAM1 exchanges GTP for GDP on RAC1, activating it"
-xref: Reactome:R-HSA-416530 "GPR40:fatty acid activates Gq"
+xref: Reactome:R-HSA-416530 "FFAR1:FFAR1 ligands activates Gq"
xref: Reactome:R-HSA-416588 "Activation of Rho by LARG and PDZ-RhoGEF"
xref: Reactome:R-HSA-418579 "Gq activation by P2Y purinoceptor 1"
xref: Reactome:R-HSA-418850 "Activation of Cdc42"
@@ -49595,7 +49597,7 @@ xref: Reactome:R-HSA-5654618 "Activated FGFR2:p-FRS2:GRB2:SOS1 activates RAS nuc
xref: Reactome:R-HSA-5654647 "Activated FGFR3:p-SHC1:GRB2:SOS1 activates RAS nucleotide exchange"
xref: Reactome:R-HSA-5654663 "Activated FGFR4:p-FRS2:GRB2:SOS1 activates RAS nucleotide exchange"
xref: Reactome:R-HSA-5655241 "Activated FGFR2 mutants:p-FRS2:GRB2:SOS1 activates RAS nucleotide exchange"
-xref: Reactome:R-HSA-5655277 "Activated FGFR3 mutants:p-FRS2:GRB2:SOS1 activates RAS nucleotide exchange"
+xref: Reactome:R-HSA-5655277 "Activated FGFR3 point, translocation and fusion mutants:p-FRS2:GRB2:SOS1 activates RAS nucleotide exchange"
xref: Reactome:R-HSA-5655326 "Activated FGFR1 mutants:p-FRS2:GRB2:SOS1 activates RAS nucleotide exchange"
xref: Reactome:R-HSA-5655347 "Activated FGFR4 mutants:p-FRS2:GRB2:SOS1 activates RAS nucleotide exchange"
xref: Reactome:R-HSA-5672965 "RAS GEFs promote RAS nucleotide exchange"
@@ -49614,7 +49616,6 @@ xref: Reactome:R-HSA-8850041 "RAB3GAP1:RAB3GAP2 promotes nucleotide exchange on
xref: Reactome:R-HSA-8851827 "RAS guanyl nucleotide exchange by MET-bound GRB2:SOS1"
xref: Reactome:R-HSA-8851877 "RAS guanyl nucleotide exchange by SOS1 associated with RANBP9 and MET"
xref: Reactome:R-HSA-8851899 "RAS guanyl nucleotide exchange by SOS1 bound to GRB2, SCH1-2 and MET"
-xref: Reactome:R-HSA-8853307 "FGFR3 fusions:p-FRS2:GRB2:SOS1 activates RAS nucleotide exchange"
xref: Reactome:R-HSA-8875318 "RAB3 GEFs exchange GTP for GDP on RAB3A"
xref: Reactome:R-HSA-8875320 "RAB5 GEFs exchange GTP for GDP on RAB5"
xref: Reactome:R-HSA-8875568 "RAPGEF1 activates RAP1"
@@ -49636,13 +49637,28 @@ xref: Reactome:R-HSA-8877760 "HPS1:HPS4 exchange GTP for GDP on RAB32 and RAB38"
xref: Reactome:R-HSA-8877813 "DENND5A,B exchange GTP for GDP on RAB39"
xref: Reactome:R-HSA-8877998 "RAB3GAP1:RAB3GAP2 exchanges GTP for GDP on RAB18"
xref: Reactome:R-HSA-8964604 "CDC42 in GNB/GNG:PAK1:ARHGEF6:CDC42 is activated"
+xref: Reactome:R-HSA-8980691 "RHOA GEFs activate RHOA"
xref: Reactome:R-HSA-8982637 "Opsins binds G alpha-t"
xref: Reactome:R-HSA-8982640 "G-alpha(t):G-beta-gamma:Opsins complex dissociates to active G-alpha(t)"
+xref: Reactome:R-HSA-9013023 "RHOB GEFs activate RHOB"
+xref: Reactome:R-HSA-9013109 "RHOC GEFs activate RHOC"
+xref: Reactome:R-HSA-9013143 "RAC1 GEFs activate RAC1"
+xref: Reactome:R-HSA-9013159 "CDC42 GEFs activate CDC42"
+xref: Reactome:R-HSA-9013435 "RHOD auto-activates"
+xref: Reactome:R-HSA-9014296 "RAC2 GEFs activate RAC2"
+xref: Reactome:R-HSA-9014433 "RHOG GEFs activate RHOG"
+xref: Reactome:R-HSA-9017491 "RHOJ GEFs activate RHOJ"
+xref: Reactome:R-HSA-9018747 "RHOQ GEFs activate RHOQ"
+xref: Reactome:R-HSA-9018768 "RHOU auto-activates"
+xref: Reactome:R-HSA-9018804 "RAC3 GEFs activate RAC3"
+xref: Reactome:R-HSA-9018817 "RHOT1 GEFs activate RHOT1"
+xref: Reactome:R-HSA-9018825 "RHOT2 GEFs activate RHOT2"
xref: Reactome:R-HSA-9026891 "NTRK2 activates RAS signaling through SHC1"
xref: Reactome:R-HSA-9029158 "EPO:phospho-EPOR:phospho-JAK2:LYN:IRS2:phospho-CRKL:RAPGEF1:GRB2-1:SOS1,phospho-VAV1 mediates exchange of GTP for GDP bound to RAS"
xref: Reactome:R-HSA-9032067 "NTRK2 activates RAS signaling through FRS2"
xref: Reactome:R-HSA-9032798 "DOCK3 activates RAC1"
xref: Reactome:R-HSA-9033292 "NTRK2 and CDK5 promote activation of RAC1 by TIAM1"
+xref: Reactome:R-HSA-9036301 "ESTG stimulates GTP exchange on GPER:heterotrimeric G-protein s"
xref: Reactome:R-HSA-939265 "Activation of Rap1 by membrane-associated GEFs"
xref: Reactome:R-HSA-9607304 "SOS1-mediated nucleotide exchange of RAS downstream of FLT3"
xref: Reactome:R-HSA-9619803 "p-S516-ARHGEF7 activates RAC1"
@@ -49662,8 +49678,11 @@ xref: Reactome:R-HSA-9666430 "p-VAV1,2,3 exchanges GTP for GDP on RAC1:GDP"
xref: Reactome:R-HSA-9670436 "p-KIT mutants:GRB2:SOS catalyzes nucleotide exchange on RAS"
xref: Reactome:R-HSA-9672163 "SOS-mediated nucleotide exchange on RAS downstream of PDGFRA extracellular domain dimers"
xref: Reactome:R-HSA-9672170 "SOS-mediated nucleotide exchange of RAS downstream of mutant PDGFR receptors"
+xref: Reactome:R-HSA-9680385 "CSF1R-associated SOS1 mediates exchange of GTP for GDP bound to RAS"
+xref: Reactome:R-HSA-9693111 "RHOF auto-activates"
xref: Reactome:R-HSA-9695853 "FLT3 mutants:GRB2:SOS1-mediated nucleotide exchange on RAS"
xref: Reactome:R-HSA-9703441 "SOS1-mediated nucleotide exchange of RAS downstream of FLT3 fusion mutants"
+xref: Reactome:R-HSA-9751201 "p-VAV1,2,3 exchange 6TGTP for GDP on RAC1"
is_a: GO:0030695 ! GTPase regulator activity
[Term]
@@ -49740,7 +49759,6 @@ synonym: "Rho GAP activity" NARROW [GOC:pg]
synonym: "Rho GTPase activator activity" NARROW []
synonym: "Sar GAP activity" NARROW [GOC:pg]
synonym: "Sar GTPase activator activity" NARROW []
-xref: Reactome:R-HSA-194922 "GAPs inactivate Rho GTPase:GTP by hydrolysis"
xref: Reactome:R-HSA-392513 "Rap1 signal termination by Rap1GAPs"
xref: Reactome:R-HSA-399935 "Inactivation of R-Ras by Sema3A-Plexin-A GAP activity"
xref: Reactome:R-HSA-4093339 "p120-RasGAP activates GTP hydrolysis on RAS, inactivating it"
@@ -49749,8 +49767,20 @@ xref: Reactome:R-HSA-416559 "Inactivation of Rho-GTP by p190RhoGAP"
xref: Reactome:R-HSA-428522 "Inactivation of RAC1"
xref: Reactome:R-HSA-428533 "Inactivation of CDC42"
xref: Reactome:R-HSA-5638007 "RP2 activates the GTPase activity of ARL3"
+xref: Reactome:R-HSA-8981637 "RHOA GAPs stimulate RHOA GTPase activity"
xref: Reactome:R-HSA-8985594 "MYO9B inactivates RHOA"
+xref: Reactome:R-HSA-9013022 "RHOB GAPs stimulate RHOB GTPase activity"
+xref: Reactome:R-HSA-9013111 "RHOC GAPs stimulate RHOC GTPase activity"
+xref: Reactome:R-HSA-9013144 "RAC1 GAPs stimulate RAC1 GTPase activity"
+xref: Reactome:R-HSA-9013161 "CDC42 GAPs stimulate CDC42 GTPase activity"
+xref: Reactome:R-HSA-9013437 "RHOD GAPs stimulate RHOD GTPase activity"
+xref: Reactome:R-HSA-9014295 "RAC2 GAPs stimulate RAC2 GTPase activity"
+xref: Reactome:R-HSA-9014434 "RHOG GAPs stimulate RHOG GTPase activity"
+xref: Reactome:R-HSA-9017488 "RHOJ GAPs stimulate RHOJ GTPase activity"
+xref: Reactome:R-HSA-9018745 "RHOQ GAPs stimulate RHOQ GTPase activity"
+xref: Reactome:R-HSA-9018806 "RAC3 GAPs stimulate RAC3 GTPase activity"
xref: Reactome:R-HSA-9624893 "RAN stimulates fusion of nuclear envelope (NE) membranes"
+xref: Reactome:R-HSA-9693282 "RHOF GAPs stimulate RHOF GTPase activity"
is_a: GO:0008047 ! enzyme activator activity
is_a: GO:0030695 ! GTPase regulator activity
@@ -49817,8 +49847,7 @@ def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:ai]
comment: This term was made obsolete because it refers to a class of gene products.
synonym: "GPI-linked ephrin" EXACT []
is_obsolete: true
-consider: GO:0046658
-consider: GO:0046875
+consider: GO:0005886
[Term]
id: GO:0005108
@@ -49828,7 +49857,6 @@ def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:ai]
comment: This term was made obsolete because it refers to a class of gene products.
synonym: "transmembrane ephrin" EXACT []
is_obsolete: true
-consider: GO:0005887
consider: GO:0046875
[Term]
@@ -50073,10 +50101,11 @@ is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0005133
-name: interferon-gamma receptor binding
+name: type II interferon receptor binding
namespace: molecular_function
-def: "Binding to an interferon-gamma receptor." [GOC:ai]
+def: "Binding to a type II interferon receptor. Type II interferon is also known as interferon-gamma." [GOC:ai]
synonym: "interferon-gamma" NARROW []
+synonym: "interferon-gamma receptor binding" EXACT []
synonym: "interferon-gamma receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50599,6 +50628,7 @@ subset: goslim_chembl
synonym: "neurohormone" EXACT []
xref: Wikipedia:Neurohormone
is_a: GO:0005179 ! hormone activity
+is_a: GO:0160041 ! neuropeptide activity
[Term]
id: GO:0005185
@@ -50614,7 +50644,7 @@ name: pheromone activity
namespace: molecular_function
def: "The activity of binding to and activating specific cell surface receptors, thereby inducing behavioral, developmental, or physiological response(s) from a responding organism or cell. The substance may be released or retained on the cell surface. Pheromones may serve as a specific attractant, social communicator, or sexual stimulant." [GOC:sgd_curators, ISBN:0198506732]
comment: Also consider annotating to 'receptor agonist activity ; GO:0048018'.
-is_a: GO:0005102 ! signaling receptor binding
+is_a: GO:0048018 ! receptor ligand activity
[Term]
id: GO:0005187
@@ -50692,7 +50722,6 @@ is_obsolete: true
consider: GO:0005102
consider: GO:0005515
consider: GO:0007155
-consider: GO:0016021
consider: GO:0030246
consider: GO:0050839
consider: GO:0098631
@@ -50701,9 +50730,8 @@ consider: GO:0098631
id: GO:0005198
name: structural molecule activity
namespace: molecular_function
-def: "The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell." [GOC:mah, GOC:vw]
+def: "The action of a molecule that contributes to the structural integrity of a complex." [GOC:mah, GOC:vw]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
@@ -50711,6 +50739,7 @@ subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
+subset: prokaryote_subset
is_a: GO:0003674 ! molecular_function
[Term]
@@ -50858,7 +50887,6 @@ def: "Enables the directed movement of substances (such as macromolecules, small
comment: Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.
subset: gocheck_do_not_annotate
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
@@ -50867,27 +50895,28 @@ subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
+subset: prokaryote_subset
synonym: "carrier" RELATED []
-xref: EC:7.-.-.-
xref: Reactome:R-HSA-168313 "Virion-associated M2 protein mediated ion infusion"
xref: Reactome:R-HSA-178215 "SMAD7:SMURF1 complex is exported to the cytosol"
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0005216
-name: ion channel activity
+name: monoatomic ion channel activity
namespace: molecular_function
-def: "Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size)." [GOC:cy, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
-is_a: GO:0015075 ! ion transmembrane transporter activity
+def: "Enables the facilitated diffusion of a monoatomic ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size)." [GOC:cy, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
+synonym: "ion channel activity" BROAD []
+is_a: GO:0015075 ! monoatomic ion transmembrane transporter activity
is_a: GO:0015267 ! channel activity
-is_a: GO:0015318 ! inorganic molecular entity transmembrane transporter activity
[Term]
id: GO:0005217
-name: intracellular ligand-gated ion channel activity
+name: intracellular ligand-gated monoatomic ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a channel that opens when a specific intracellular ligand has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729]
-is_a: GO:0015276 ! ligand-gated ion channel activity
+synonym: "intracellular ligand-gated ion channel activity" BROAD []
+is_a: GO:0015276 ! ligand-gated monoatomic ion channel activity
[Term]
id: GO:0005219
@@ -50912,13 +50941,14 @@ is_a: GO:0015278 ! calcium-release channel activity
[Term]
id: GO:0005221
-name: intracellular cyclic nucleotide activated cation channel activity
+name: intracellular cyclic nucleotide activated monoatomic cation channel activity
namespace: molecular_function
-def: "Enables the transmembrane transfer of a cation by a channel that opens when intracellular cyclic nucleotide has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport]
+def: "Enables the transmembrane transfer of a monoatomic cation by a channel that opens when intracellular cyclic nucleotide has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport]
+synonym: "intracellular cyclic nucleotide activated cation channel activity" BROAD []
xref: Reactome:R-HSA-2514867 "cGMP:CNG transports Na+ and Ca2+ into the rod outer segment"
-is_a: GO:0005217 ! intracellular ligand-gated ion channel activity
-is_a: GO:0043855 ! cyclic nucleotide-gated ion channel activity
-is_a: GO:0099094 ! ligand-gated cation channel activity
+is_a: GO:0005217 ! intracellular ligand-gated monoatomic ion channel activity
+is_a: GO:0043855 ! cyclic nucleotide-gated monoatomic ion channel activity
+is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
[Term]
id: GO:0005222
@@ -50932,7 +50962,7 @@ synonym: "intracellular 3',5'-cAMP activated cation channel activity" EXACT []
synonym: "intracellular adenosine 3',5'-cyclophosphate activated cation channel activity" EXACT []
synonym: "intracellular cAMP activated cation channel activity" EXACT []
synonym: "intracellular cyclic AMP activated cation channel activity" EXACT []
-is_a: GO:0005221 ! intracellular cyclic nucleotide activated cation channel activity
+is_a: GO:0005221 ! intracellular cyclic nucleotide activated monoatomic cation channel activity
[Term]
id: GO:0005223
@@ -50940,16 +50970,16 @@ name: intracellular cGMP-activated cation channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of a cation by a channel that opens when intracellular cGMP has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport]
synonym: "intracellular cGMP activated cation channel activity" EXACT []
-is_a: GO:0005221 ! intracellular cyclic nucleotide activated cation channel activity
+is_a: GO:0005221 ! intracellular cyclic nucleotide activated monoatomic cation channel activity
[Term]
id: GO:0005225
name: volume-sensitive anion channel activity
namespace: molecular_function
-def: "Enables the transmembrane transfer of an anion by a volume-sensitive channel. An anion is a negatively charged ion. A volume-sensitive channel is a channel that responds to changes in the volume of a cell." [GOC:dph, GOC:tb]
+def: "Enables the transmembrane transfer of a monoatomic anion by a volume-sensitive channel. A volume-sensitive channel is a channel that responds to changes in the volume of a cell." [GOC:dph, GOC:tb]
synonym: "volume-regulated channel" BROAD []
xref: Reactome:R-HSA-8941543 "VRAC heteromer transports I-, Cl- from cytosol to extracellular region"
-is_a: GO:0005253 ! anion channel activity
+is_a: GO:0005253 ! monoatomic anion channel activity
[Term]
id: GO:0005227
@@ -50958,8 +50988,9 @@ namespace: molecular_function
def: "Enables the calcium concentration-regulatable energy-independent passage of cations across a lipid bilayer down a concentration gradient." [GOC:dph, GOC:mtg_transport]
synonym: "intracellular calcium-activated potassium channel" NARROW []
synonym: "polycystin" NARROW []
-is_a: GO:0005261 ! cation channel activity
-is_a: GO:0022839 ! ion gated channel activity
+xref: Reactome:R-HSA-9717383 "TRPM4 transports Na+ from the extracellular region to the cytosol"
+is_a: GO:0005261 ! monoatomic cation channel activity
+is_a: GO:0022839 ! monoatomic ion gated channel activity
[Term]
id: GO:0005228
@@ -50967,7 +50998,7 @@ name: intracellular sodium activated potassium channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of potassium by a channel that opens in response to stimulus by a sodium ion or ions. Transport by a channel involves facilitated diffusion of a solute (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel, without evidence for a carrier-mediated mechanism. Sodium activated potassium channels have distinctive properties, including a large single channel conductance, subconductance states, and a block of single channel currents at positive potentials, similar to inward rectification." [GOC:mtg_transport, PMID:12628167]
is_a: GO:0005267 ! potassium channel activity
-is_a: GO:0022839 ! ion gated channel activity
+is_a: GO:0022839 ! monoatomic ion gated channel activity
[Term]
id: GO:0005229
@@ -50978,19 +51009,19 @@ xref: Reactome:R-HSA-2684901 "ANOs transport cytosolic Cl- to extracellular regi
xref: Reactome:R-HSA-2744242 "TTYH2/3 transport cytosolic Cl- to extracellular region"
xref: Reactome:R-HSA-2744361 "BESTs transport cytosolic Cl- to extracellular region"
xref: Reactome:R-HSA-9659568 "ANO1 transports cytosolic Cl- to extracellular region"
-is_a: GO:0022839 ! ion gated channel activity
is_a: GO:0061778 ! intracellular chloride channel activity
[Term]
id: GO:0005230
-name: extracellular ligand-gated ion channel activity
+name: extracellular ligand-gated monoatomic ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a channel that opens when a specific extracellular ligand has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729]
-is_a: GO:0015276 ! ligand-gated ion channel activity
+synonym: "extracellular ligand-gated ion channel activity" BROAD []
+is_a: GO:0015276 ! ligand-gated monoatomic ion channel activity
[Term]
id: GO:0005231
-name: excitatory extracellular ligand-gated ion channel activity
+name: excitatory extracellular ligand-gated monoatomic ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a channel that opens when a specific extracellular ligand has been bound by the channel complex or one of its constituent parts, where channel opening contributes to an increase in membrane potential." [GOC:mah, ISBN:0323037070]
xref: Reactome:R-HSA-399711 "Activation of Ca impermeable AMPA receptors"
@@ -50998,23 +51029,24 @@ xref: Reactome:R-HSA-399712 "Activation of Ca permeable AMPA receptors"
xref: Reactome:R-HSA-420980 "Activation of Ca permeable AMPA receptors"
xref: Reactome:R-HSA-432164 "Ca2+ influx into the post-synaptic cell"
xref: Reactome:R-HSA-438037 "Membrane depolarization upon activation of Ca impermeable AMPA receptors"
-is_a: GO:0005230 ! extracellular ligand-gated ion channel activity
+is_a: GO:0005230 ! extracellular ligand-gated monoatomic ion channel activity
[Term]
id: GO:0005234
name: extracellularly glutamate-gated ion channel activity
namespace: molecular_function
-def: "Enables the transmembrane transfer of an ion by a channel that opens when glutamate is bound by the channel complex or one of its constituent parts on the extracellular side of the plasma membrane." [GOC:mtg_transport, ISBN:0815340729]
+def: "Enables the transmembrane transfer of an ion by a channel that opens when glutamate is bound by the channel complex or one of its constituent parts on the extracellular side of the plasma membrane." [GOC:mtg_transport, ISBN:0815340729]
comment: Note that this term represents an activity and not a gene product. Consider also annotating to the molecular function term 'glutamate receptor activity ; GO:0008066'.
synonym: "extracellular-glutamate-gated ion channel activity" EXACT []
-is_a: GO:0005231 ! excitatory extracellular ligand-gated ion channel activity
+is_a: GO:0005231 ! excitatory extracellular ligand-gated monoatomic ion channel activity
[Term]
id: GO:0005237
-name: inhibitory extracellular ligand-gated ion channel activity
+name: inhibitory extracellular ligand-gated monoatomic ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a channel that opens when a specific extracellular inhibitory ligand has been bound by the channel complex or one of its constituent parts. Inhibitory ligands, such as GABA or glycine, open chloride-selective channels." [GOC:mah, ISBN:0323037070]
-is_a: GO:0005230 ! extracellular ligand-gated ion channel activity
+synonym: "inhibitory extracellular ligand-gated ion channel activity" BROAD []
+is_a: GO:0005230 ! extracellular ligand-gated monoatomic ion channel activity
[Term]
id: GO:0005240
@@ -51047,8 +51079,11 @@ xref: Reactome:R-HSA-1296046 "KCNJs transport K+ from the extracellular region t
xref: Reactome:R-HSA-1369017 "Activation of ATP sensitive Potassium channels in muscle cells"
xref: Reactome:R-HSA-5678261 "KCNJ11:ABCC9 transports K+ from extracellular region to cytosol"
xref: Reactome:R-HSA-5678418 "Defective ABCC9 (in KCNJ11:ABCC9) does not transport K+ from extracellular region to cytosol"
+xref: Reactome:R-HSA-9729870 "KCNJ2 (KIR2.1) transports K+ from the extracellular region to the cytosol"
+xref: Reactome:R-HSA-9730521 "SARS-CoV-2 3a induces potassium efflux"
+xref: Reactome:R-HSA-9731072 "SARS-CoV-1 3a tetramer induces potassium efflux"
is_a: GO:0005249 ! voltage-gated potassium channel activity
-is_a: GO:0099094 ! ligand-gated cation channel activity
+is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
[Term]
id: GO:0005243
@@ -51070,13 +51105,14 @@ is_a: GO:0022829 ! wide pore channel activity
[Term]
id: GO:0005244
-name: voltage-gated ion channel activity
+name: voltage-gated monoatomic ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded." [GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
synonym: "voltage gated ion channel activity" EXACT []
synonym: "voltage-dependent ion channel activity" EXACT []
-is_a: GO:0015075 ! ion transmembrane transporter activity
+synonym: "voltage-gated ion channel activity" BROAD []
is_a: GO:0022832 ! voltage-gated channel activity
+is_a: GO:0022839 ! monoatomic ion gated channel activity
[Term]
id: GO:0005245
@@ -51099,7 +51135,7 @@ xref: Reactome:R-HSA-5577213 "LTCC multimer transports Ca2+ from extracellular r
xref: Reactome:R-HSA-9701055 "TRPA1 tetramer transports Ca2+ from extracellular region to cytosol"
xref: Reactome:R-HSA-9701141 "TRPV1 transports Ca2+ from extracellular region to cytosol"
is_a: GO:0005262 ! calcium channel activity
-is_a: GO:0022843 ! voltage-gated cation channel activity
+is_a: GO:0022843 ! voltage-gated monoatomic cation channel activity
[Term]
id: GO:0005246
@@ -51117,7 +51153,7 @@ synonym: "voltage gated chloride channel activity" EXACT []
synonym: "voltage-dependent chloride channel activity" EXACT []
xref: Reactome:R-HSA-2744228 "CLCN1/2/KA/KB transport cytosolic Cl- to extracellular region"
is_a: GO:0005254 ! chloride channel activity
-is_a: GO:0008308 ! voltage-gated anion channel activity
+is_a: GO:0008308 ! voltage-gated monoatomic anion channel activity
[Term]
id: GO:0005248
@@ -51141,8 +51177,10 @@ synonym: "voltage-dependent potassium channel activity" EXACT []
synonym: "voltage-gated potassium ion channel activity" EXACT []
synonym: "voltage-sensitive potassium channel" EXACT []
xref: Reactome:R-HSA-1296127 "Activation of voltage gated Potassium channels"
+xref: Reactome:R-HSA-9659554 "KCNQ4 transports K+ from the cytosol to the extracellular region"
+xref: Reactome:R-HSA-9667761 "KCNMA1:KCNMB1:LRRC52 transports K+ from the cytosol to the extracellular region"
is_a: GO:0005267 ! potassium channel activity
-is_a: GO:0022843 ! voltage-gated cation channel activity
+is_a: GO:0022843 ! voltage-gated monoatomic cation channel activity
[Term]
id: GO:0005250
@@ -51170,14 +51208,15 @@ is_a: GO:0005249 ! voltage-gated potassium channel activity
[Term]
id: GO:0005253
-name: anion channel activity
+name: monoatomic anion channel activity
namespace: molecular_function
-def: "Enables the energy-independent passage of anions across a lipid bilayer down a concentration gradient." [GOC:dph, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
+def: "Enables the energy-independent passage of a monoatomic anion across a lipid bilayer down a concentration gradient." [GOC:dph, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
+synonym: "anion channel activity" BROAD []
synonym: "non-selective anion channel activity" NARROW []
xref: Reactome:R-HSA-432034 "Aquaporin-6 passively transports anions into vesicles"
xref: Reactome:R-HSA-432036 "Aquaporin-6 passively transports anions out of vesicles"
-is_a: GO:0005216 ! ion channel activity
-is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
+is_a: GO:0005216 ! monoatomic ion channel activity
+is_a: GO:0008509 ! monoatomic anion transmembrane transporter activity
[Term]
id: GO:0005254
@@ -51186,9 +51225,11 @@ namespace: molecular_function
def: "Enables the facilitated diffusion of a chloride (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [GOC:mtg_transport, GOC:pr, ISBN:0815340729]
xref: Reactome:R-HSA-2744349 "TTYH1 transports cytosolic Cl- to extracellular region"
xref: Reactome:R-HSA-427570 "Group 3 - Selective Cl- transport"
+xref: Reactome:R-HSA-9712204 "ANO2:Ca2+ translocates Cl- from the cytosol to the extracellular region"
xref: Reactome:R-HSA-975340 "GABR heteropentamers:GABA transport Cl- from extracellular region to cytosol"
xref: Reactome:R-HSA-975449 "GABRR pentamers:GABA transports extracellular Cl- to cytosol"
-is_a: GO:0005253 ! anion channel activity
+is_a: GO:0005253 ! monoatomic anion channel activity
+is_a: GO:0015108 ! chloride transmembrane transporter activity
[Term]
id: GO:0005260
@@ -51196,24 +51237,26 @@ name: intracellularly ATP-gated chloride channel activity
namespace: molecular_function
alt_id: GO:0005224
def: "Enables passage of a chloride ion through a transmembrane channel that opens when ATP is bound by the channel complex or one of its constituent parts on the intracellular side of the plasma membrane." [PMID:24727426, PMID:9922375]
-synonym: "ATP phosphohydrolase (channel-conductance-controlling)" RELATED [EC:5.6.1.6]
-synonym: "ATP-binding and phosphorylation-dependent chloride channel activity" EXACT []
-synonym: "channel-conductance-controlling ATPase activity" EXACT []
+comment: This activity is a phosphorylation and ATP-gated anion channel, increasing the conductance for certain anions (e.g. Cl-) to flow down their electrochemical gradient. ATP-driven conformational changes in CFTR open and close a gate to allow transmembrane flow of anions down their electrochemical gradient.This in contrast to other ABC proteins, in which ATP-driven conformational changes fuel uphill substrate transport across cellular membranes. Essentially, CFTR is an ion channel that evolved as a 'broken' ABC transporter that leaks when in open conformation (from Wikipedia:Cystic_fibrosis_transmembrane_conductance_regulator).
+synonym: "CFTR" EXACT []
+synonym: "channel-conductance-controlling ATPase activity" RELATED [EC:5.6.1.6]
synonym: "cystic fibrosis transmembrane conductance regulator" NARROW []
-synonym: "cystic-fibrosis membrane-conductance-regulating protein activity" NARROW [EC:5.6.1.6]
xref: EC:5.6.1.6
xref: MetaCyc:3.6.3.49-RXN
+xref: TC:3.A.1.202.1
+xref: Wikipedia:Cystic_fibrosis_transmembrane_conductance_regulator
is_a: GO:0005254 ! chloride channel activity
-is_a: GO:0099095 ! ligand-gated anion channel activity
+is_a: GO:0099095 ! ligand-gated monoatomic anion channel activity
is_a: GO:0099142 ! intracellularly ATP-gated ion channel activity
[Term]
id: GO:0005261
-name: cation channel activity
+name: monoatomic cation channel activity
namespace: molecular_function
alt_id: GO:0015281
alt_id: GO:0015338
-def: "Enables the energy-independent passage of cations across a lipid bilayer down a concentration gradient." [GOC:def, GOC:dph, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
+def: "Enables the energy-independent passage of monoatomic cations across a lipid bilayer down a concentration gradient." [GOC:def, GOC:dph, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
+synonym: "cation channel activity" BROAD []
synonym: "cation diffusion facilitator activity" EXACT []
synonym: "non-selective cation channel activity" NARROW []
xref: Reactome:R-HSA-1168376 "STIM1 oligomerizes"
@@ -51222,8 +51265,11 @@ xref: Reactome:R-HSA-169683 "IP3R:I(1,4,5)P3 tetramer transports Ca2+ from ER lu
xref: Reactome:R-HSA-2089943 "TRPC1 translocates calcium from the extracellular region to the cytosol"
xref: Reactome:R-HSA-426223 "Cation influx mediated by TRPC3/6/7"
xref: Reactome:R-HSA-4420052 "Decreasing cGMP concentration promotes intracellular Ca2+ release in response to WNT"
-is_a: GO:0005216 ! ion channel activity
-is_a: GO:0022890 ! inorganic cation transmembrane transporter activity
+xref: Reactome:R-HSA-9706720 "SARS-CoV-1 E transports Ca2+"
+xref: Reactome:R-HSA-9712190 "cAMP:olfactory CNG channel translocates Na+ and Ca2+ from the extracellular region to the cytosol"
+xref: Reactome:R-HSA-9754616 "SARS-CoV-2 E pentamer transports Ca2+"
+is_a: GO:0005216 ! monoatomic ion channel activity
+is_a: GO:0008324 ! monoatomic cation transmembrane transporter activity
[Term]
id: GO:0005262
@@ -51236,7 +51282,8 @@ xref: Reactome:R-HSA-210420 "Ca2+ influx through voltage gated Ca2+ channels"
xref: Reactome:R-HSA-3295579 "TRPs transport extracellular Ca2+ to cytosol"
xref: Reactome:R-HSA-8949145 "VDAC1,2,3 translocate calcium from the cytosol to the mitochondrial intermembrane space"
xref: Reactome:R-HSA-8949178 "MCU translocates calcium from the mitochondrial intermembrane space to the mitochondrial matrix"
-is_a: GO:0005261 ! cation channel activity
+xref: Reactome:R-HSA-9663785 "CHRNA9:CHRNA10:AcCho transports Ca2+ from the extracellular region to the cytosol"
+is_a: GO:0005261 ! monoatomic cation channel activity
is_a: GO:0015085 ! calcium ion transmembrane transporter activity
[Term]
@@ -51256,7 +51303,7 @@ xref: Reactome:R-HSA-1299338 "Activation of TRESK"
xref: Reactome:R-HSA-1299359 "Activation of TALK"
xref: Reactome:R-HSA-2534365 "Slo3 Potassium Transport"
xref: Reactome:R-HSA-5578910 "KCNK dimers transport K+ from cytosol to extracellular region"
-is_a: GO:0005261 ! cation channel activity
+is_a: GO:0005261 ! monoatomic cation channel activity
is_a: GO:0015079 ! potassium ion transmembrane transporter activity
[Term]
@@ -51266,7 +51313,11 @@ namespace: molecular_function
def: "Enables the facilitated diffusion of a sodium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [GOC:BHF, GOC:mtg_transport, GOC:pr, ISBN:0815340729]
xref: Reactome:R-HSA-2730664 "UNC79:UNC80:NALCN transports Na+ extracellular region to cytosol"
xref: Reactome:R-HSA-3295580 "TRPM4,5 transport extracellular Na+ to cytosol"
-is_a: GO:0005261 ! cation channel activity
+xref: Reactome:R-HSA-9717374 "SCN3A:SCN2B,4B transports Na+ from the extracellular region to the cytosol"
+xref: Reactome:R-HSA-9717382 "SCN9A:SCN1B,2B,4B transports Na+ from the extracellular region to the cytosol"
+xref: Reactome:R-HSA-9717395 "TRPM5 transports Na+ from the extracellular region to the cytosol"
+xref: Reactome:R-HSA-9717396 "SCN2A:SCN1B,2B,4B transports Na+ from the extracellular region to the cytosol"
+is_a: GO:0005261 ! monoatomic cation channel activity
is_a: GO:0015081 ! sodium ion transmembrane transporter activity
[Term]
@@ -51309,8 +51360,9 @@ namespace: molecular_function
def: "Enables the transfer of acetylcholine from one side of a membrane to the other. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions." [GOC:ai]
xref: Reactome:R-HSA-264615 "Loading of acetylcholine in synaptic vesicles"
is_a: GO:0005326 ! neurotransmitter transmembrane transporter activity
-is_a: GO:0015101 ! organic cation transmembrane transporter activity
+is_a: GO:0015651 ! quaternary ammonium group transmembrane transporter activity
is_a: GO:1901375 ! acetate ester transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0005278
@@ -51319,8 +51371,9 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + acetylcholine(in) = H+(in) + acetylcholine(out)." [TC:2.A.1.2.13]
synonym: "acetylcholine:hydrogen antiporter activity" EXACT []
is_a: GO:0005277 ! acetylcholine transmembrane transporter activity
-is_a: GO:0015299 ! solute:proton antiporter activity
-is_a: GO:0015491 ! cation:cation antiporter activity
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0005280
@@ -51330,7 +51383,7 @@ def: "Enables the transfer of a solute or solutes from one side of a membrane to
synonym: "cation/amino acid symporter" BROAD []
synonym: "hydrogen:amino acid symporter activity" EXACT []
xref: Reactome:R-HSA-8875623 "SLC25A18,A22 cotransport Glu, H+ from cytosol to mitochondrial matrix"
-is_a: GO:0005416 ! amino acid:cation symporter activity
+is_a: GO:0005416 ! amino acid:monoatomic cation symporter activity
is_a: GO:0015295 ! solute:proton symporter activity
[Term]
@@ -51363,7 +51416,7 @@ synonym: "sodium:amino acid symporter activity" EXACT []
synonym: "sodium:amino acid transporter activity" BROAD []
synonym: "threonine/serine:sodium symporter activity" NARROW []
is_a: GO:0005343 ! organic acid:sodium symporter activity
-is_a: GO:0005416 ! amino acid:cation symporter activity
+is_a: GO:0005416 ! amino acid:monoatomic cation symporter activity
[Term]
id: GO:0005287
@@ -51392,8 +51445,6 @@ namespace: molecular_function
def: "Enables the transfer of L-histidine from one side of a membrane to the other. L-histidine is 2-amino-3-(1H-imidazol-4-yl)propanoic acid." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
synonym: "histidine/arginine/lysine/ornithine porter activity" NARROW []
synonym: "L-histidine transporter activity" BROAD []
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015173 ! aromatic amino acid transmembrane transporter activity
is_a: GO:0015174 ! basic amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
@@ -51425,19 +51476,20 @@ name: neutral L-amino acid secondary active transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of a neutral L-amino acid from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Secondary active transporters include symporters and antiporters." [GOC:mtg_transport]
synonym: "neutral L-amino acid porter activity" RELATED []
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
[Term]
id: GO:0005295
-name: neutral amino acid:sodium symporter activity
+name: neutral L-amino acid:sodium symporter activity
namespace: molecular_function
alt_id: GO:0005282
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: neutral amino acid(out) + Na+(out) = neutral amino acid(in) + Na+(in)." [TC:2.A.23.3.1]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: neutral L-amino acid(out) + Na+(out) = neutral L-amino acid(in) + Na+(in)." [TC:2.A.23.3.1]
synonym: "neutral amino acid-sodium cotransporter" BROAD []
+synonym: "neutral amino acid:sodium symporter activity" EXACT []
synonym: "sodium/neutral amino acid transporter" BROAD []
is_a: GO:0005283 ! amino acid:sodium symporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
[Term]
id: GO:0005297
@@ -51488,10 +51540,9 @@ def: "Enables the transfer of L-tyrosine from one side of a membrane to the othe
synonym: "L-tyrosine permease activity" EXACT []
synonym: "L-tyrosine transporter activity" BROAD []
synonym: "valine/tyrosine/tryptophan permease activity" RELATED []
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015173 ! aromatic amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0005304
@@ -51503,9 +51554,7 @@ synonym: "L-valine transporter activity" BROAD []
synonym: "leucine/isoleucine/valine porter activity" NARROW []
synonym: "leucine/valine/isoleucine permease activity" NARROW []
synonym: "valine/tyrosine/tryptophan permease activity" NARROW []
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
is_a: GO:0015658 ! branched-chain amino acid transmembrane transporter activity
@@ -51523,7 +51572,7 @@ id: GO:0005308
name: creatine transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of creatine from one side of a membrane to the other. Creatine is a compound synthesized from the amino acids arginine, glycine, and methionine that occurs in muscle." [GOC:ai]
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
[Term]
@@ -51534,7 +51583,7 @@ def: "Enables the transfer of a solute or solutes from one side of a membrane to
synonym: "sodium/chloride-dependent creatine transporter" BROAD []
xref: Reactome:R-HSA-200396 "Creatine transport across the plasma membrane"
is_a: GO:0005308 ! creatine transmembrane transporter activity
-is_a: GO:0015370 ! solute:sodium symporter activity
+is_a: GO:0005343 ! organic acid:sodium symporter activity
[Term]
id: GO:0005310
@@ -51548,7 +51597,7 @@ synonym: "dicarboxylate carrier" NARROW []
synonym: "dicarboxylic acid permease activity" RELATED []
synonym: "sodium:dicarboxylate/tricarboxylate symporter activity" NARROW []
xref: Reactome:R-HSA-1614546 "Sulfate is exported to the cytosol in exchange for dicarboxylate"
-xref: Reactome:R-HSA-372843 "malate [mitochondrial matrix] + orthophosphate [cytosol] <=> malate [cytosol] + orthophosphate [mitochondrial matrix]"
+xref: Reactome:R-HSA-372843 "SLC25A10 mediates exchange of malate and phosphate"
is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
[Term]
@@ -51569,26 +51618,31 @@ id: GO:0005313
name: L-glutamate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of L-glutamate from one side of a membrane to the other. L-glutamate is the anion of 2-aminopentanedioic acid." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
+synonym: "glutamate transmembrane transporter activity" BROAD []
synonym: "glutamate/aspartate porter activity" NARROW []
synonym: "glutamate/aspartate:sodium symporter activity" NARROW []
synonym: "L-glutamate transporter activity" BROAD []
xref: Reactome:R-HSA-210444 "L-Glutamate loading of synaptic vesicle"
xref: Reactome:R-HSA-428052 "SLC17A6,7,8 exchange cytosolic L-Glu for synaptic vesicle H+"
xref: Reactome:R-HSA-5624256 "Defective SLC17A8 does not exchange cytosolic L-Glu for synaptic vesicle H+"
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+xref: RHEA:66336
is_a: GO:0015172 ! acidic amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
+is_a: GO:0042887 ! amide transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0005314
-name: high-affinity glutamate transmembrane transporter activity
+name: high-affinity L-glutamate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of glutamate from one side of a membrane to the other. In high-affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations." [TC:2.A.3.10.5]
+synonym: "high-affinity glutamate transmembrane transporter activity" BROAD []
synonym: "high-affinity glutamate transporter activity" BROAD []
xref: Reactome:R-HSA-210404 "SLC1A1-3,6,7 exchange L-Glu, H+ and 3Na+ for K+"
xref: Reactome:R-HSA-428015 "SLC1A1,2,3,6,7 cotransport L-Glu,L-Asp,D-Asp,H+,3Na+ from extracellular region to cytosol"
xref: Reactome:R-HSA-5625015 "Defective SLC1A3 does not cotransport L-Glu,L-Asp,D-Asp,H+,3Na+ from extracellular region to cytosol"
xref: Reactome:R-HSA-5625029 "SLC1A1 does not cotransport L-Glu,L-Asp,D-Asp,H+,3Na+ from extracellular region to cytosol"
+xref: RHEA:66336
is_a: GO:0005313 ! L-glutamate transmembrane transporter activity
is_a: GO:0015501 ! glutamate:sodium symporter activity
@@ -51690,7 +51744,7 @@ name: long-chain fatty acid transporter activity
namespace: molecular_function
alt_id: GO:0005325
alt_id: GO:0008562
-def: "Enables the transfer of long-chain fatty acids from one side of a membrane to the other. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [ISBN:0198506732]
+def: "Enables the transfer of a long-chain fatty acid from one side of a membrane to the other. A long-chain fatty acid is a fatty acid with an aliphatic tail of 13 to 21 carbons." [ISBN:0198506732]
xref: Reactome:R-HSA-2046087 "Translocation of tetracosahexaenoyl-CoA to peroxisomes"
xref: Reactome:R-HSA-2046093 "Translocation of tetracosapentaenoyl-CoA to peroxisomes"
xref: Reactome:R-HSA-382575 "ABCD1-3 dimers transfer LCFAs from cytosol to peroxisomal matrix"
@@ -51733,18 +51787,21 @@ is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
[Term]
id: GO:0005332
-name: gamma-aminobutyric acid:sodium symporter activity
+name: gamma-aminobutyric acid:sodium:chloride symporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: gamma-aminobutyric acid(out) + Na+(out) = gamma-aminobutyric acid(in) + Na+(in)." [TC:2.A.22.3.2]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: gamma-aminobutyric acid(out) + Na+(out) + Cl-(out) = gamma-aminobutyric acid(in) + Na+(in) + Cl(in)." [PMID:7589472, PMID:7861179]
comment: See also the molecular function term 'neurotransmitter:sodium symporter activity ; GO:0005328'.
synonym: "4-aminobutanoate:sodium symporter activity" EXACT []
synonym: "4-aminobutyrate:sodium symporter activity" EXACT []
synonym: "betaine/GABA:sodium symporter activity" EXACT []
synonym: "GABA:sodium symporter activity" EXACT []
+synonym: "gamma-aminobutyric acid:sodium symporter activity" EXACT []
synonym: "sodium/chloride-dependent GABA transporter activity" BROAD []
xref: Reactome:R-HSA-444007 "GAT1-3 mediate Na+/Cl- dependent GABA transport"
+xref: TC:2.A.22.3.2
is_a: GO:0005283 ! amino acid:sodium symporter activity
is_a: GO:0015185 ! gamma-aminobutyric acid transmembrane transporter activity
+is_a: GO:0015378 ! sodium:chloride symporter activity
is_a: GO:0140161 ! monocarboxylate:sodium symporter activity
[Term]
@@ -51762,21 +51819,23 @@ xref: Reactome:R-HSA-443997 "SLC6A2 cotransports NAd, Na+ from extracellular reg
xref: Reactome:R-HSA-5659764 "Defective SLC6A2 does not cotransport NAd, Na+ from extracellular region to cytosol"
xref: Wikipedia:Norepinephrine_transporter
is_a: GO:0008504 ! monoamine transmembrane transporter activity
+is_a: GO:0015101 ! organic cation transmembrane transporter activity
is_a: GO:0015378 ! sodium:chloride symporter activity
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
[Term]
id: GO:0005335
-name: serotonin:sodium symporter activity
+name: serotonin:sodium:chloride symporter activity
namespace: molecular_function
alt_id: GO:0005336
alt_id: GO:0015222
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: serotonin(out) + Na+(out) + Cl-(out) = serotonin(in) + Na+(in)+ Cl-(in)." [PMID:21752877, PMID:22519513, TC:2.A.22.1.1]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: serotonin(out) + Na+(out) + Cl-(out) = serotonin(in) + Na+(in)+ Cl-(in)." [PMID:21752877, PMID:22519513]
synonym: "serotonin transmembrane transporter activity" EXACT []
-synonym: "serotonin:sodium:chloride symporter activity" EXACT []
+synonym: "serotonin:sodium symporter activity" RELATED []
synonym: "sodium/serotonin symporter activity" EXACT []
xref: Reactome:R-HSA-444008 "SLC6A4 co-transports 5HT, Cl-, Na+ from extracellular region to cytosol"
xref: RHEA:51196
+xref: TC:2.A.22.1.1
is_a: GO:0008504 ! monoamine transmembrane transporter activity
is_a: GO:0015378 ! sodium:chloride symporter activity
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
@@ -51796,6 +51855,10 @@ xref: Reactome:R-HSA-727740 "Equilibrative transport (import) of adenosine and b
xref: Reactome:R-HSA-727749 "SLC29A3 transports nucleosides from lysosomal lumen to cytosol"
xref: Reactome:R-HSA-727767 "SLC29A3 transports nucleosides from cytosol to lysosomal lumen"
xref: Reactome:R-HSA-727768 "Equilibrative transport (export) of adenosine and biogenic amines by solute carrier family 29 (nucleoside transporters), member 4"
+xref: Reactome:R-HSA-9751024 "SLC29A1,2 transport 6MP from extracellular region to cytosol"
+xref: Reactome:R-HSA-9754929 "SLC29A3 transports RBV,RBV-TP from cytosol to mitochondrial matrix"
+xref: Reactome:R-HSA-9755015 "SLC29A1 transports RBV from extracellular region to cytosol"
+xref: Reactome:R-HSA-9755035 "SLC29A1 transports RBV from cytosol to extracellular region"
is_a: GO:0015932 ! nucleobase-containing compound transmembrane transporter activity
is_a: GO:1901505 ! carbohydrate derivative transmembrane transporter activity
@@ -51806,7 +51869,8 @@ namespace: molecular_function
alt_id: GO:0005339
def: "Enables the transfer of a nucleotide-sugar from one side of a membrane to the other. A nucleotide-sugar is any nucleotide in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative." [GOC:ai, GOC:mtg_transport, ISBN:0815340729, PMID:15034926]
xref: Reactome:R-HSA-744230 "SLC35D2 mediates the antiport of GDP-mannose in exchange for GMP"
-xref: Reactome:R-HSA-744231 "SLC35D2 exchanges UDP-sugars for UMP"
+xref: Reactome:R-HSA-744231 "SLC35D2 exchanges UDP-GlcNAc for UMP"
+xref: Reactome:R-HSA-9792608 "SLC35D2 exchanges UDP-D-glucose for UMP"
is_a: GO:0015932 ! nucleobase-containing compound transmembrane transporter activity
is_a: GO:1901505 ! carbohydrate derivative transmembrane transporter activity
@@ -51873,9 +51937,11 @@ name: ATP transmembrane transporter activity
namespace: molecular_function
alt_id: GO:0005348
def: "Enables the transfer of ATP, adenosine triphosphate, from one side of a membrane to the other." [GOC:ai]
+xref: Reactome:R-HSA-9717392 "CALHM1:CALHM3 transports ATP from the cytosol to the extracellular region"
is_a: GO:0000295 ! adenine nucleotide transmembrane transporter activity
is_a: GO:0005346 ! purine ribonucleotide transmembrane transporter activity
is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0005350
@@ -51905,7 +51971,7 @@ synonym: "sugar:hydrogen ion symporter activity" NARROW []
synonym: "sugar:hydrogen symporter activity" EXACT []
synonym: "sugar:proton symporter activity" NARROW []
xref: TC:2.A.1.1
-is_a: GO:0005402 ! carbohydrate:cation symporter activity
+is_a: GO:0005402 ! carbohydrate:monoatomic cation symporter activity
is_a: GO:0015295 ! solute:proton symporter activity
[Term]
@@ -51936,8 +52002,9 @@ is_a: GO:0015149 ! hexose transmembrane transporter activity
id: GO:0005354
name: galactose transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of galactose from one side of a membrane to the other. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
+def: "Enables the transfer of galactose from one side of a membrane to the other. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose." [GOC:ai, GOC:mtg_transport, ISBN:0815340729, RHEA:34915]
synonym: "galactose/glucose (methylgalactoside) porter activity" RELATED []
+xref: RHEA:34915
is_a: GO:0015149 ! hexose transmembrane transporter activity
[Term]
@@ -52073,9 +52140,7 @@ id: GO:0005368
name: taurine transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of taurine from one side of a membrane to the other. Taurine (2-aminoethanesulfonic acid) is a sulphur-containing amino acid derivative which is important in the metabolism of fats." [GOC:ai]
-is_a: GO:0005342 ! organic acid transmembrane transporter activity
is_a: GO:0042959 ! alkanesulfonate transmembrane transporter activity
-is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
[Term]
id: GO:0005369
@@ -52093,9 +52158,8 @@ namespace: molecular_function
alt_id: GO:0005370
def: "Enables the transfer of tricarboxylate from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Secondary active transporters include symporters and antiporters." [GOC:mtg_transport, ISBN:0815340729]
synonym: "tricarboxylate carrier activity" EXACT []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
[Term]
id: GO:0005372
@@ -52103,6 +52167,7 @@ name: water transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of water (H2O) from one side of a membrane to the other." [GOC:ai]
is_a: GO:0015318 ! inorganic molecular entity transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0005373
@@ -52200,9 +52265,8 @@ xref: Reactome:R-HSA-435366 "ZnT1 mediates the efflux of zinc from the cell"
xref: Reactome:R-HSA-435375 "ZnT2 facilitates zinc vesicular sequestration"
xref: Reactome:R-HSA-437084 "ZnT3 transports zinc into synaptic vesicles"
xref: Reactome:R-HSA-437085 "ZnT5 transports zinc into secretory granules in pancreatic beta cells"
-xref: Reactome:R-HSA-437129 "ZnT7 transports zinc into the golgi apparatus"
xref: Reactome:R-HSA-437136 "SLC30A8 transports Zn2+ from cytosol to secretory granule"
-xref: Reactome:R-HSA-437139 "ZnT6 transports zinc into the golgi apparatus"
+xref: Reactome:R-HSA-437139 "ZnT8 transports zinc into the Golgi apparatus"
xref: Reactome:R-HSA-442317 "ZIP6 and ZIP14 mediate zinc influx into cells"
xref: Reactome:R-HSA-442345 "hZIP10 mediates zinc influx into cells"
xref: Reactome:R-HSA-442387 "ZIP8 mediates zinc influx into cells"
@@ -52210,8 +52274,10 @@ xref: Reactome:R-HSA-442393 "ZIP7 mediates zinc efflux from the endoplasmic reti
xref: Reactome:R-HSA-442405 "hZIP5 mediates zinc uptake by cells"
xref: Reactome:R-HSA-442422 "SLC39A1-4 transports Zn2+ from extracellular region to cytosol"
xref: Reactome:R-HSA-5654125 "Defective SLC39A4 does not transport Zn2+ from extracellular region to cytosol"
+xref: Reactome:R-HSA-9820566 "ZnT5 transports zinc into the golgi apparatus"
xref: RHEA:29351
is_a: GO:0046915 ! transition metal ion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0005388
@@ -52235,10 +52301,12 @@ xref: Reactome:R-HSA-418309 "ATP2B1-4 transport cytosolic Ca2+ to extracellular
xref: Reactome:R-HSA-418365 "ATP2A1-3 transport cytosolic Ca2+ to dense tubular network lumen"
xref: Reactome:R-HSA-427910 "ATP2A1-3 transport Ca2+ from cytosol to ER lumen"
xref: Reactome:R-HSA-936883 "ATP2C1/2:Mg2+ transport cytosolic Ca2+ to Golgi lumen"
+xref: Reactome:R-HSA-9662114 "ATP2B2-wa (PMCA2-wa) transports Ca2+ from the cytosol to the extracellular region"
+xref: Reactome:R-HSA-9664214 "ATP2B1 (PMCA1) transports Ca2+ from the cytosol to the extracellular region"
xref: RHEA:18105
is_a: GO:0015085 ! calcium ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
[Term]
id: GO:0005391
@@ -52297,14 +52365,15 @@ consider: GO:0005777
[Term]
id: GO:0005402
-name: carbohydrate:cation symporter activity
+name: carbohydrate:monoatomic cation symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: sugar(out) + cation(out) = sugar(in) + cation(in)." [GOC:ai]
+synonym: "carbohydrate:cation symporter activity" BROAD []
synonym: "cation/sugar symporter activity" EXACT []
synonym: "cation:sugar symporter activity" EXACT []
synonym: "sugar:cation symporter activity" NARROW []
is_a: GO:0015144 ! carbohydrate transmembrane transporter activity
-is_a: GO:0015294 ! solute:cation symporter activity
+is_a: GO:0015294 ! solute:monoatomic cation symporter activity
[Term]
id: GO:0005412
@@ -52318,7 +52387,7 @@ xref: Reactome:R-HSA-5656356 "Defective SLC5A1 does not cotransport Glc and Na+"
xref: Reactome:R-HSA-5658163 "Defective SLC5A2 does not cotransport Glc and Na+ from extracellular region to cytosol"
xref: Reactome:R-HSA-8932955 "SLC5A1 cotransports Glc,Gal with Na+ from extracellular region to cytosol"
is_a: GO:0005355 ! glucose transmembrane transporter activity
-is_a: GO:0005402 ! carbohydrate:cation symporter activity
+is_a: GO:0005402 ! carbohydrate:monoatomic cation symporter activity
is_a: GO:0015370 ! solute:sodium symporter activity
[Term]
@@ -52332,18 +52401,21 @@ synonym: "sodium-dependent nucleoside transporter activity" BROAD []
xref: Reactome:R-HSA-109530 "Concentrative transport (import) of a nucleoside and a sodium ions by solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"
xref: Reactome:R-HSA-109538 "Concentrative transport (import) of a nucleoside and two sodium ions by solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"
xref: Reactome:R-HSA-109539 "Concentrative transport (import) of nucleosides plus sodium ions by solute carrier family 28 (sodium-coupled nucleoside transporter), member 2"
+xref: Reactome:R-HSA-9751037 "SLC28A2,3 cotransport 6MP and Na+ from extracellular region to cytosol"
+xref: Reactome:R-HSA-9754934 "SLC28C2,3 cotransports RBV, Na+ from extracellular region to cytosol"
is_a: GO:0005337 ! nucleoside transmembrane transporter activity
is_a: GO:0015370 ! solute:sodium symporter activity
[Term]
id: GO:0005416
-name: amino acid:cation symporter activity
+name: amino acid:monoatomic cation symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: amino acid(out) + cation(out) = amino acid(in) + cation(in)." [GOC:ai]
+synonym: "amino acid:cation symporter activity" BROAD []
synonym: "cation/amino acid symporter activity" EXACT []
synonym: "cation:amino acid symporter activity" EXACT []
is_a: GO:0015171 ! amino acid transmembrane transporter activity
-is_a: GO:0015294 ! solute:cation symporter activity
+is_a: GO:0015294 ! solute:monoatomic cation symporter activity
[Term]
id: GO:0005427
@@ -52384,7 +52456,7 @@ xref: Reactome:R-HSA-8949688 "SLC8B1 (NCLX) exchanges sodium (mitochondrial inte
xref: Reactome:R-HSA-8949703 "SLC8A3 (NCX3) exchanges sodium (cytosol) for calcium (mitochondrial intermembrane space)"
xref: RHEA:29255
is_a: GO:0015081 ! sodium ion transmembrane transporter activity
-is_a: GO:0015368 ! calcium:cation antiporter activity
+is_a: GO:0015368 ! calcium:monoatomic cation antiporter activity
[Term]
id: GO:0005436
@@ -52408,29 +52480,29 @@ is_a: GO:0015370 ! solute:sodium symporter activity
[Term]
id: GO:0005451
-name: monovalent cation:proton antiporter activity
+name: obsolete monoatomic cation:proton antiporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: monovalent cation(out) + H+(in) = monovalent cation(in) + H+(out)." [GOC:ai]
+def: "OBSOLETE. Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: monoatomic cation(out) + H+(in) = monoatomic cation(in) + H+(out)." [GOC:ai]
+comment: This term was obsoleted because it represents an unnecessary grouping term.
synonym: "monovalent cation:hydrogen antiporter activity" EXACT []
-xref: Reactome:R-HSA-2889070 "SLC9B2 exchanges Na+, Li+ for H+"
-is_a: GO:0015299 ! solute:proton antiporter activity
-is_a: GO:0015491 ! cation:cation antiporter activity
+synonym: "monovalent cation:proton antiporter activity" RELATED []
+is_obsolete: true
[Term]
id: GO:0005452
-name: inorganic anion exchanger activity
+name: solute:inorganic anion antiporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: inorganic anion A(out) + inorganic anion B(in) = inorganic anion A(in) + inorganic anion B(out)." [GOC:mah]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: inorganic anion(out) + solute(in) = inorganic anion (in) + solute(out)." [GOC:mah]
+synonym: "inorganic anion exchanger activity" EXACT []
xref: Reactome:R-HSA-1237038 "SLC4A1 exchanges cytosolic HCO3- for extracellular Cl-"
-xref: Reactome:R-HSA-1247665 "Band 3 Anion Exchanger (AE1, SLC4A1) exchanges cytosolic chloride for extracellular bicarbonate"
+xref: Reactome:R-HSA-1247665 "SLC4A1 exchanges cytosolic Cl- for extracellular HCO3-"
xref: Reactome:R-HSA-425482 "SLC4A1,2,3 exchanges HCO3- for Cl-"
xref: Reactome:R-HSA-425577 "Na+-driven Cl-/HCO3- exchanger transport"
xref: Reactome:R-HSA-427666 "SLC26A3,6 exchange Cl- for HCO3-"
xref: Reactome:R-HSA-5627737 "SLC26A3 does not exchange Cl- for HCO3-"
xref: Reactome:R-HSA-5656248 "Defective SLC4A1 does not exchange Cl- for HCO3- (in erythrocytes)"
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
-is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
[Term]
id: GO:0005456
@@ -52531,7 +52603,7 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: succinate(out) + fumarate(in) = succinate(in) + fumarate(out)." [TC:2.A.29.13.1]
is_a: GO:0015138 ! fumarate transmembrane transporter activity
is_a: GO:0015141 ! succinate transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
+is_a: GO:0015297 ! antiporter activity
[Term]
id: GO:0005471
@@ -52546,7 +52618,7 @@ synonym: "ATP/ADP exchange" EXACT []
synonym: "ATP/ADP exchanger" EXACT []
is_a: GO:0005347 ! ATP transmembrane transporter activity
is_a: GO:0015217 ! ADP transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
+is_a: GO:0015297 ! antiporter activity
[Term]
id: GO:0005476
@@ -52558,7 +52630,7 @@ synonym: "carnitine:acyl carnitine carrier activity" EXACT []
synonym: "fatty acyl carnitine carrier" EXACT []
is_a: GO:0015226 ! carnitine transmembrane transporter activity
is_a: GO:0015227 ! acyl carnitine transmembrane transporter activity
-is_a: GO:0015298 ! solute:cation antiporter activity
+is_a: GO:0015297 ! antiporter activity
[Term]
id: GO:0005477
@@ -52567,7 +52639,6 @@ namespace: molecular_function
def: "Enables the transfer of pyruvate from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Secondary active transporters include symporters and antiporters." [GOC:mtg_transport]
synonym: "pyruvate carrier activity" RELATED []
is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0050833 ! pyruvate transmembrane transporter activity
[Term]
@@ -52844,7 +52915,6 @@ namespace: molecular_function
alt_id: GO:0001948
alt_id: GO:0045308
def: "Binding to a protein." [GOC:go_curators]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
@@ -52922,6 +52992,8 @@ id: GO:0005524
name: ATP binding
namespace: molecular_function
def: "Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN:0198506732]
+synonym: "Mg-ATP binding" EXACT []
+synonym: "MgATP binding" EXACT []
xref: Reactome:R-HSA-265682 "KCNJ11 tetramer:ABCC8 tetramer binds 4xATP, closing the channel"
is_a: GO:0032559 ! adenyl ribonucleotide binding
is_a: GO:0035639 ! purine ribonucleoside triphosphate binding
@@ -53060,7 +53132,6 @@ synonym: "vitamin M binding" EXACT []
is_a: GO:0019842 ! vitamin binding
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0033218 ! amide binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0072341 ! modified amino acid binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -53342,7 +53413,6 @@ namespace: cellular_component
alt_id: GO:0008372
def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome)." [GOC:pdt, NIF_Subcellular:sao1337158144]
comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
@@ -53361,7 +53431,6 @@ namespace: cellular_component
def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators]
comment: Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
@@ -53371,6 +53440,7 @@ subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "extracellular" EXACT []
xref: Wikipedia:Extracellular
is_a: GO:0110165 ! cellular anatomical entity
@@ -53400,7 +53470,6 @@ synonym: "terminal complement complex" EXACT []
xref: Wikipedia:Complement_membrane_attack_complex
is_a: GO:0046930 ! pore complex
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0005580
@@ -53572,8 +53641,8 @@ is_a: GO:0030936 ! transmembrane collagen trimer
id: GO:0005601
name: classical-complement-pathway C3/C5 convertase complex
namespace: cellular_component
-def: "A heterodimeric protein complex that catalyzes the cleavage of complement components C3 and C5, and acts in the classical pathway of complement activation; consists of one monomer of C2a and one monomer of C4b; C2a is the catalytic subunit, but cannot catalyze cleavage alone." [BRENDA:3.4.21.43, GOC:mah, http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Complement.html]
-is_a: GO:0032991 ! protein-containing complex
+def: "A heterodimeric protein complex that catalyzes the cleavage of complement components C3 and C5, and acts in the classical pathway of complement activation; consists of one monomer of C2a and one monomer of C4b; C2a is the catalytic subunit, but cannot catalyze cleavage alone." [BRENDA:3.4.21.43, GOC:mah]
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005615 ! extracellular space
[Term]
@@ -53583,7 +53652,7 @@ namespace: cellular_component
def: "A protein complex composed of six subunits of C1q, each formed of the three homologous polypeptide chains C1QA, C1QB, and C1QB, and tetramer of two C1QR and two C1QS polypeptide chains." [GOC:add, ISBN:0781735149]
synonym: "complement component C1q complex" NARROW []
is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+relationship: part_of GO:0005576 ! extracellular region
[Term]
id: GO:0005603
@@ -53694,6 +53763,7 @@ comment: Note that for multicellular organisms, the extracellular space refers t
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
+subset: prokaryote_subset
synonym: "intercellular space" RELATED []
xref: NIF_Subcellular:sao1425028079
is_a: GO:0110165 ! cellular anatomical entity
@@ -53722,9 +53792,8 @@ id: GO:0005618
name: cell wall
namespace: cellular_component
def: "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins." [GOC:giardia, ISBN:0198547684, PMID:15134259, Wikipedia:Microbial_cyst]
-comment: Not to be used for manual annotation. Please choose a more specific term: for bacteria, annotate to GO:0009274; peptidoglycan-based cell wall, for \nplants: annotate to GO:0009505 ; plant-type cell wall, for fungi: GO:0009277 ; fungal-type cell wall, and for archae, use GO:0030115 S-layer (see PMID:31214995).
+comment: Not to be used for manual annotation. Please choose a more specific term: for bacteria, annotate to GO:0009274; peptidoglycan-based cell wall, for plants: annotate to GO:0009505 ; plant-type cell wall, for fungi: GO:0009277 ; fungal-type cell wall, and for archae, use GO:0030115 S-layer (see PMID:31214995).
subset: gocheck_do_not_annotate
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
@@ -53732,6 +53801,7 @@ subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
+subset: prokaryote_subset
xref: Wikipedia:Cell_wall
is_a: GO:0030312 ! external encapsulating structure
@@ -53759,7 +53829,6 @@ namespace: cellular_component
def: "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732]
subset: gocheck_do_not_annotate
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_plant
synonym: "internal to cell" EXACT []
@@ -53870,7 +53939,6 @@ name: nucleus
namespace: cellular_component
def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -53924,12 +53992,13 @@ relationship: part_of GO:0005652 ! nuclear lamina
[Term]
id: GO:0005639
-name: integral component of nuclear inner membrane
+name: obsolete integral component of nuclear inner membrane
namespace: cellular_component
-def: "The component of the nuclear inner membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:go_curators]
+def: "OBSOLETE. The component of the nuclear inner membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:go_curators]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to nuclear inner membrane" NARROW []
-is_a: GO:0031229 ! intrinsic component of nuclear inner membrane
-is_a: GO:0031301 ! integral component of organelle membrane
+is_obsolete: true
+replaced_by: GO:0005637
[Term]
id: GO:0005640
@@ -54284,7 +54353,7 @@ relationship: part_of GO:0016591 ! RNA polymerase II, holoenzyme
id: GO:0005675
name: transcription factor TFIIH holo complex
namespace: cellular_component
-def: "A complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of the core TFIIH complex and the TFIIK complex." [GOC:ew, GOC:krc, PMID:14500720, PMID:22308316, PMID:22572993, PMID:7813015]
+def: "A complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of the core TFIIH complex and the TFIIK complex." [GOC:ew, GOC:krc, PMID:14500720, PMID:22308316, PMID:22572993, PMID:7813015]
synonym: "holo TFIIH complex" EXACT []
is_a: GO:0032806 ! carboxy-terminal domain protein kinase complex
is_a: GO:0090575 ! RNA polymerase II transcription regulator complex
@@ -54306,7 +54375,6 @@ comment: This term was made obsolete because its definition no longer reflects a
synonym: "chromatin assembly complex" EXACT []
synonym: "nucleosome assembly complex" NARROW []
is_obsolete: true
-consider: GO:0031497
[Term]
id: GO:0005680
@@ -54443,9 +54511,8 @@ id: GO:0005694
name: chromosome
namespace: cellular_component
def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684]
-comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
+comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -54454,6 +54521,7 @@ subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "chromatid" RELATED []
synonym: "interphase chromosome" NARROW []
synonym: "prophase chromosome" NARROW []
@@ -54490,6 +54558,7 @@ namespace: cellular_component
def: "Telomerase is a ribonucleoprotein enzyme complex, with a minimal catalytic core composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. In vivo, the holoenzyme complex often contains additional subunits." [PMID:11884619]
subset: goslim_pir
is_a: GO:0140513 ! nuclear protein-containing complex
+is_a: GO:1902494 ! catalytic complex
is_a: GO:1990904 ! ribonucleoprotein complex
[Term]
@@ -54650,9 +54719,14 @@ name: pericentric heterochromatin
namespace: cellular_component
alt_id: GO:0002137
alt_id: GO:0031618
-def: "Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by methylated H3 histone at lysine 9 (H3K9me2/H3K9me3)." [PMID:12019236, PMID:20206496, PMID:22729156, PMID:9413993]
+alt_id: GO:0034507
+alt_id: GO:0062199
+def: "Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by methylated H3 histone at lysine 9 (H3K9me2/H3K9me3)." [PMID:12019236, PMID:20206496, PMID:21437270, PMID:22729156, PMID:9413993]
synonym: "centric heterochromatin" EXACT []
synonym: "centromeric heterochromatin" EXACT [GOC:dph]
+synonym: "chromosome, centric outer repeat region" RELATED []
+synonym: "chromosome, centromeric inner repeat region" RELATED []
+synonym: "chromosome, centromeric outer repeat region" RELATED []
synonym: "nuclear centric heterochromatin" NARROW []
synonym: "nuclear cluster" NARROW []
synonym: "nuclear pericentric heterochromatin" NARROW []
@@ -54728,7 +54802,6 @@ id: GO:0005730
name: nucleolus
namespace: cellular_component
def: "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN:0198506732]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -54812,11 +54885,11 @@ namespace: cellular_component
def: "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684]
subset: goslim_candida
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
+subset: prokaryote_subset
xref: Wikipedia:Cytoplasm
is_a: GO:0110165 ! cellular anatomical entity
relationship: part_of GO:0005622 ! intracellular anatomical structure
@@ -54828,7 +54901,6 @@ namespace: cellular_component
def: "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [GOC:giardia, ISBN:0198506732]
comment: Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.)
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -54893,7 +54965,7 @@ is_a: GO:0031966 ! mitochondrial membrane
id: GO:0005744
name: TIM23 mitochondrial import inner membrane translocase complex
namespace: cellular_component
-def: "The protein transport machinery of the mitochondrial inner membrane that typically transports proteins that possess a matrix-targeting N-terminal presequence. The TIM23 complex contains three essential Tim proteins: Tim17 and Tim23 are thought to build a preprotein translocation channel while Tim44 interacts transiently with the matrix heat-shock protein Hsp70 to form an ATP-driven import motor." [EC:7.4.2.3, PMID:27554484, PMID:8851659]
+def: "The protein transport machinery of the mitochondrial inner membrane that typically transports proteins that possess a matrix-targeting N-terminal presequence. The TIM23 complex contains three essential Tim proteins: Tim17 and Tim23 are thought to build a preprotein translocation channel while Tim44 interacts transiently with the matrix heat-shock protein Hsp70 to form an ATP-driven import motor." [PMID:27554484, PMID:8851659]
comment: See also the cellular component term 'mitochondrial inner membrane ; GO:0005743'.
subset: goslim_pir
synonym: "mitochondrial inner membrane pre-sequence translocase complex" EXACT []
@@ -54909,7 +54981,6 @@ namespace: cellular_component
def: "Protease complex of the mitochondrial inner membrane that is involved in mitochondrial protein turnover and in processing of proteins imported into mitochondria." [GOC:mcc, PMID:12417197, PMID:21147776]
is_a: GO:0098800 ! inner mitochondrial membrane protein complex
is_a: GO:1905368 ! peptidase complex
-relationship: part_of GO:0031305 ! integral component of mitochondrial inner membrane
[Term]
id: GO:0005746
@@ -55181,7 +55252,6 @@ name: vacuole
namespace: cellular_component
def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -55228,7 +55298,6 @@ name: peroxisome
namespace: cellular_component
alt_id: GO:0019818
def: "A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism." [GOC:pm, PMID:9302272, UniProtKB-KW:KW-0576]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -55252,12 +55321,13 @@ relationship: part_of GO:0005777 ! peroxisome
[Term]
id: GO:0005779
-name: integral component of peroxisomal membrane
+name: obsolete integral component of peroxisomal membrane
namespace: cellular_component
-def: "The component of the peroxisomal membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:mah]
+def: "OBSOLETE. The component of the peroxisomal membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to peroxisomal membrane" NARROW []
-is_a: GO:0031231 ! intrinsic component of peroxisomal membrane
-is_a: GO:0031301 ! integral component of organelle membrane
+is_obsolete: true
+replaced_by: GO:0005778
[Term]
id: GO:0005780
@@ -55296,7 +55366,6 @@ name: endoplasmic reticulum
namespace: cellular_component
def: "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN:0198506732]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -55413,7 +55482,7 @@ consider: GO:0043231
id: GO:0005793
name: endoplasmic reticulum-Golgi intermediate compartment
namespace: cellular_component
-def: "A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport." [GOC:pr, PMID:16723730]
+def: "A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport." [GOC:pr, PMID:16723730]
synonym: "EGTC" EXACT []
synonym: "endoplasmic reticulum-Golgi transport container" EXACT []
synonym: "ER-Golgi intermediate compartment" EXACT []
@@ -55433,7 +55502,6 @@ namespace: cellular_component
def: "A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways." [ISBN:0198506732]
comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -55529,7 +55597,7 @@ id: GO:0005802
name: trans-Golgi network
namespace: cellular_component
def: "The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination." [GOC:vw, ISBN:0815316194]
-comment: There are different opinions about whether the TGN should be considered part of the Golgi apparatus or not. We follow Alberts et al, 1994 (ISBN:0815316194), who consider it to be a part.
+comment: There are different opinions about whether the TGN should be considered part of the Golgi apparatus or not. We follow Alberts et al, 1994 (ISBN:0815316194), who consider it to be a part.
synonym: "Golgi trans face" RELATED []
synonym: "Golgi trans-face" RELATED []
synonym: "late Golgi" RELATED [GOC:mah]
@@ -55744,7 +55812,7 @@ id: GO:0005826
name: actomyosin contractile ring
namespace: cellular_component
alt_id: GO:0030480
-def: "A cytoskeletal structure composed of actin filaments and myosin that forms beneath the plasma membrane of many cells, including animal cells and yeast cells, in a plane perpendicular to the axis of the spindle, i.e. the cell division plane. In animal cells, the contractile ring is located at the cleavage furrow. In budding fungal cells, e.g. mitotic S. cerevisiae cells, the contractile ring forms at the mother-bud neck before mitosis." [GOC:expert_jrp, GOC:sgd_curators, GOC:vw, ISBN:0805319409, ISBN:0815316194, PMID:28914606]
+def: "A cytoskeletal structure composed of actin filaments and myosin that forms beneath the plasma membrane of many cells, including animal cells and yeast cells, in a plane perpendicular to the axis of the spindle, i.e. the cell division plane. In animal cells, the contractile ring is located at the cleavage furrow. In budding fungal cells, e.g. mitotic S. cerevisiae cells, the contractile ring forms at the mother-bud neck before mitosis." [GOC:expert_jrp, GOC:sgd_curators, GOC:vw, ISBN:0805319409, ISBN:0815316194, PMID:28914606]
synonym: "actomyosin ring" RELATED []
synonym: "CAR" EXACT []
synonym: "constriction ring" RELATED []
@@ -55777,7 +55845,6 @@ name: cytosol
namespace: cellular_component
def: "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC:hjd, GOC:jl]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_flybase_ribbon
@@ -55804,7 +55871,7 @@ namespace: cellular_component
def: "A multisubunit ring-shaped complex that mediates protein folding in the cytosol without a cofactor." [GOC:sgd_curators, PMID:11580267]
synonym: "CCT particle" EXACT []
synonym: "TriC" EXACT []
-is_a: GO:0101031 ! chaperone complex
+is_a: GO:0101031 ! protein folding chaperone complex
relationship: part_of GO:0005829 ! cytosol
[Term]
@@ -55846,8 +55913,8 @@ synonym: "FAS complex" EXACT []
synonym: "fatty acid synthetase complex" EXACT []
synonym: "holo-[acyl-carrier-protein] synthase complex" RELATED []
xref: Wikipedia:Fatty_acid_synthetase_complex
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005829 ! cytosol
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0005836
@@ -55892,9 +55959,9 @@ synonym: "20S core complex" NARROW []
synonym: "20S proteasome" NARROW [GOC:cjk]
synonym: "macropain" EXACT []
synonym: "PA28gamma-20S proteasome" NARROW [CORUM:194]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0000502 ! proteasome complex
-relationship: part_of GO:0005622 ! intracellular anatomical structure
[Term]
id: GO:0005840
@@ -55902,7 +55969,6 @@ name: ribosome
namespace: cellular_component
alt_id: GO:0033279
def: "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." [ISBN:0198506732]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
@@ -55910,6 +55976,7 @@ subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "free ribosome" NARROW [NIF_Subcellular:sao1139385046]
synonym: "membrane bound ribosome" NARROW [NIF_Subcellular:sao1291545653]
synonym: "ribosomal RNA" RELATED []
@@ -56031,9 +56098,8 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0005856
name: cytoskeleton
namespace: cellular_component
-def: "Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles." [GOC:mah, ISBN:0198547684, PMID:16959967]
+def: "A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles." [GOC:mah, PMID:16959967, PMID:27419875]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -56043,6 +56109,7 @@ subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
+subset: prokaryote_subset
xref: Wikipedia:Cytoskeleton
is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
@@ -56253,10 +56320,10 @@ relationship: part_of GO:0015629 ! actin cytoskeleton
id: GO:0005886
name: plasma membrane
namespace: cellular_component
+alt_id: GO:0005887
alt_id: GO:0005904
def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -56265,11 +56332,14 @@ subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_plant
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "bacterial inner membrane" NARROW []
synonym: "cell membrane" EXACT []
synonym: "cellular membrane" EXACT [NIF_Subcellular:sao6433132645]
synonym: "cytoplasmic membrane" EXACT []
synonym: "inner endospore membrane" NARROW []
+synonym: "integral component of plasma membrane" NARROW []
+synonym: "integral to plasma membrane" NARROW []
synonym: "juxtamembrane" BROAD []
synonym: "plasma membrane lipid bilayer" NARROW [GOC:mah]
synonym: "plasmalemma" EXACT []
@@ -56278,15 +56348,6 @@ xref: Wikipedia:Cell_membrane
is_a: GO:0016020 ! membrane
relationship: part_of GO:0071944 ! cell periphery
-[Term]
-id: GO:0005887
-name: integral component of plasma membrane
-namespace: cellular_component
-def: "The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:go_curators]
-synonym: "integral to plasma membrane" NARROW []
-is_a: GO:0016021 ! integral component of membrane
-is_a: GO:0031226 ! intrinsic component of plasma membrane
-
[Term]
id: GO:0005888
name: obsolete proteoglycan integral to plasma membrane
@@ -56295,7 +56356,7 @@ def: "OBSOLETE. Penetrating at least one phospholipid bilayer of a plasma membra
comment: This term was made obsolete because it describes the composition (i.e. proteoglycan) and not the location of a gene product.
synonym: "proteoglycan integral to plasma membrane" EXACT []
is_obsolete: true
-replaced_by: GO:0005887
+replaced_by: GO:0005886
[Term]
id: GO:0005889
@@ -56307,7 +56368,6 @@ synonym: "hydrogen:potassium-exchanging ATPase complex" EXACT []
synonym: "proton pump" BROAD []
is_a: GO:0090533 ! cation-transporting ATPase complex
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0005890
@@ -56318,7 +56378,6 @@ synonym: "sodium pump" BROAD []
synonym: "sodium/potassium-exchanging ATPase complex" EXACT []
is_a: GO:0090533 ! cation-transporting ATPase complex
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0005891
@@ -56339,9 +56398,8 @@ namespace: cellular_component
def: "A homo- or hetero-pentameric protein complex that forms a transmembrane channel through which ions may pass in response to acetylcholine binding." [GOC:bf, GOC:mah, PMID:12381728, PMID:15579462]
synonym: "nicotinic acetylcholine receptor" BROAD []
synonym: "nicotinic acetylcholine-gated receptor-channel complex" EXACT [GOC:bf]
-is_a: GO:0034702 ! ion channel complex
+is_a: GO:0034702 ! monoatomic ion channel complex
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0005893
@@ -56350,7 +56408,6 @@ namespace: cellular_component
def: "A protein complex that binds interleukin-2; comprises alpha, beta, and gamma subunits." [GOC:mah, PMID:3116143, PMID:8266078]
synonym: "IL-2 receptor complex" EXACT [GOC:add]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0005894
@@ -56359,7 +56416,6 @@ namespace: cellular_component
def: "A protein complex that binds interleukin-3; comprises an alpha and a beta subunit. The alpha chain is specific to the interleukin-3 receptor, whereas the beta chain is shared with the receptors for granulocyte-macrophage colony-stimulating factor and interleukin-5." [PMID:11839579]
synonym: "IL-3 receptor complex" EXACT [GOC:add]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0005895
@@ -56368,7 +56424,6 @@ namespace: cellular_component
def: "A protein complex that binds interleukin-3; comprises an alpha and a beta subunit. The alpha chain is specific to the interleukin-5 receptor, whereas the beta chain is shared with the receptors for granulocyte-macrophage colony-stimulating factor and interleukin-3." [GOC:mah, PMID:11312115, PMID:11839579]
synonym: "IL-5 receptor complex" EXACT [GOC:add]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0005896
@@ -56377,7 +56432,6 @@ namespace: cellular_component
def: "A hexameric protein complex consisting of two molecules each of interleukin-6, interleukin-6 receptor alpha chain, and gp-130." [PMID:8083235]
synonym: "IL-6 receptor complex" EXACT [GOC:add]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0005897
@@ -56386,7 +56440,6 @@ namespace: cellular_component
def: "A protein complex that binds interleukin-9; comprises an alpha and a beta subunit. The alpha chain is specific to the interleukin-9 receptor, whereas the beta chain is shared with the receptors for several other interleukins." [GOC:mah, PMID:10642536]
synonym: "IL-9 receptor complex" EXACT [GOC:add]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0005898
@@ -56395,7 +56448,6 @@ namespace: cellular_component
def: "A protein complex that binds interleukin-13; consists of two chains, interleukin-13 receptor alpha1 chain and interleukin-4 receptor alpha chain." [PMID:8552669, PMID:9013879]
synonym: "IL-13 receptor complex" EXACT [GOC:add]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0005899
@@ -56404,7 +56456,6 @@ namespace: cellular_component
def: "A disulfide-bonded, heterotetrameric receptor complex. The alpha chains are entirely extracellular, while each beta chain has one transmembrane domain. The ligand binds to the alpha subunit extracellular domain and the kinase is associated with the beta subunit intracellular domain." [ISBN:0198506732]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
is_a: GO:1902911 ! protein kinase complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0005900
@@ -56412,14 +56463,13 @@ name: oncostatin-M receptor complex
namespace: cellular_component
def: "A heterodimeric receptor for the cytokine oncostatin-M (OSM). In humans the receptor complex is made up of the gene products gp130 and OSMR-beta." [GOC:jl, PMID:8999038]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0005901
name: caveola
namespace: cellular_component
alt_id: GO:0016599
-def: "A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm." [GOC:mah, ISBN:0721662544, PMID:16645198]
+def: "A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm." [GOC:mah, ISBN:0721662544, PMID:16645198]
synonym: "caveolae" EXACT []
synonym: "caveolar membrane" RELATED []
xref: Wikipedia:Caveolae
@@ -56757,7 +56807,6 @@ id: GO:0005938
name: cell cortex
namespace: cellular_component
def: "The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins." [GOC:mah, ISBN:0815316194]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_yeast
synonym: "cell periphery" RELATED []
@@ -56879,7 +56928,8 @@ is_obsolete: true
id: GO:0005950
name: anthranilate synthase complex
namespace: cellular_component
-def: "A heterotetrameric enzyme complex made up of two components I and two components II. Catalyzes the formation of anthranilate, pyruvate and L-glutamate from chorismate and L-glutamine." [EC:4.1.3.27, MetaCyc:ANTHRANSYN-CPLX, PMID:4886290]
+def: "A heterotetrameric enzyme complex made up of two components I and two components II. Catalyzes the formation of anthranilate, pyruvate and L-glutamate from chorismate and L-glutamine." [PMID:4886290]
+xref: MetaCyc:ANTHRANSYN-CPLX
is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -56899,13 +56949,14 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0005952
name: cAMP-dependent protein kinase complex
namespace: cellular_component
-def: "An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer." [EC:2.7.11.11, ISBN:0198506732]
+def: "An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer." [PMID:18178622]
synonym: "3',5' cAMP-dependent protein kinase complex" EXACT []
synonym: "3',5'-cAMP-dependent protein kinase complex" EXACT []
synonym: "adenosine 3',5'-cyclophosphate-dependent protein kinase complex" EXACT []
synonym: "cyclic AMP-dependent protein kinase complex" EXACT []
synonym: "PKA" RELATED []
is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902554 ! serine/threonine protein kinase complex
[Term]
id: GO:0005953
@@ -56919,11 +56970,12 @@ is_a: GO:1990234 ! transferase complex
id: GO:0005954
name: calcium- and calmodulin-dependent protein kinase complex
namespace: cellular_component
-def: "An enzyme complex which in eukaryotes is composed of four different chains: alpha, beta, gamma, and delta. The different isoforms assemble into homo- or heteromultimeric holoenzymes composed of 8 to 12 subunits. Catalyzes the phosphorylation of proteins to O-phosphoproteins." [EC:2.7.11.17]
+def: "An enzyme complex which in eukaryotes is composed of four different chains: alpha, beta, gamma, and delta. The different isoforms assemble into homo- or heteromultimeric holoenzymes composed of 8 to 12 subunits. Catalyzes the phosphorylation of proteins to O-phosphoproteins." [PMID:20668654]
synonym: "calcium/calmodulin-dependent protein kinase complex" EXACT []
synonym: "CAMK2" EXACT []
synonym: "CaMKII" RELATED []
is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0005955
@@ -56932,7 +56984,8 @@ namespace: cellular_component
def: "A heterodimeric calcium ion and calmodulin dependent protein phosphatase composed of catalytic and regulatory subunits; the regulatory subunit is very similar in sequence to calmodulin." [PMID:26794871]
synonym: "calcium-dependent protein serine/threonine phosphatase complex" NARROW []
synonym: "protein phosphatase type 2B complex" EXACT []
-is_a: GO:0005963 ! magnesium-dependent protein serine/threonine phosphatase complex
+is_a: GO:0008287 ! protein serine/threonine phosphatase complex
+is_a: GO:0140535 ! intracellular protein-containing complex
[Term]
id: GO:0005956
@@ -56942,6 +56995,7 @@ def: "A protein complex that possesses protein serine/threonine kinase activity,
comment: Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex.
synonym: "casein kinase II complex" EXACT []
is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902554 ! serine/threonine protein kinase complex
[Term]
id: GO:0005957
@@ -56992,7 +57046,7 @@ is_a: GO:0045242 ! isocitrate dehydrogenase complex (NAD+)
id: GO:0005963
name: magnesium-dependent protein serine/threonine phosphatase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the removal of serine- or threonine-bound phosphate groups from a wide range of phosphoproteins, including a number of enzymes that have been phosphorylated under the action of a kinase." [PMID:17517611, PMID:22343722]
+def: "An intracellular enzyme complex that catalyzes the removal of serine- or threonine-bound phosphate groups from a wide range of phosphoproteins, including a number of enzymes that have been phosphorylated under the action of a kinase." [PMID:17517611, PMID:22343722]
is_a: GO:0008287 ! protein serine/threonine phosphatase complex
is_a: GO:0140535 ! intracellular protein-containing complex
@@ -57000,7 +57054,7 @@ is_a: GO:0140535 ! intracellular protein-containing complex
id: GO:0005964
name: phosphorylase kinase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the phosphorylation of phosphorylase b to form phosphorylase a." [EC:2.7.11.19]
+def: "An enzyme complex that catalyzes the phosphorylation of phosphorylase b to form phosphorylase a." [PMID:1370475]
is_a: GO:1902554 ! serine/threonine protein kinase complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -57014,11 +57068,12 @@ relationship: part_of GO:0005737 ! cytoplasm
[Term]
id: GO:0005966
-name: cyclic-nucleotide phosphodiesterase complex
+name: obsolete cyclic-nucleotide phosphodiesterase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the hydrolysis of bonds in a cyclic nucleotide." [EC:3.1.4.-]
+def: "OBSOLETE. An enzyme complex that catalyzes the hydrolysis of bonds in a cyclic nucleotide." [EC:3.1.4.-]
+comment: This term was obsoleted because it described a homomer.
synonym: "photoreceptor cyclic-nucleotide phosphodiesterase complex" NARROW []
-is_a: GO:1902494 ! catalytic complex
+is_obsolete: true
[Term]
id: GO:0005967
@@ -57102,9 +57157,8 @@ name: carbohydrate metabolic process
namespace: biological_process
alt_id: GO:0044261
alt_id: GO:0044723
-def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule." [GOC:mah, ISBN:0198506732]
+def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC:mah, ISBN:0198506732]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -57114,9 +57168,8 @@ subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "carbohydrate metabolism" EXACT []
-synonym: "multicellular organismal carbohydrate metabolic process" NARROW []
-synonym: "single-organism carbohydrate metabolic process" RELATED []
xref: Wikipedia:Carbohydrate_metabolism
is_a: GO:0044238 ! primary metabolic process
is_a: GO:0071704 ! organic substance metabolic process
@@ -57141,8 +57194,8 @@ name: glycogen metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages." [ISBN:0198506732]
synonym: "glycogen metabolism" EXACT []
-is_a: GO:0006073 ! cellular glucan metabolic process
is_a: GO:0006112 ! energy reserve metabolic process
+is_a: GO:0044042 ! glucan metabolic process
[Term]
id: GO:0005978
@@ -57182,7 +57235,6 @@ synonym: "glycogenolysis" EXACT [GOC:sl]
xref: MetaCyc:GLYCOCAT-PWY
is_a: GO:0005977 ! glycogen metabolic process
is_a: GO:0009251 ! glucan catabolic process
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
[Term]
id: GO:0005981
@@ -57193,7 +57245,7 @@ synonym: "regulation of glycogen breakdown" EXACT []
synonym: "regulation of glycogen catabolism" EXACT []
synonym: "regulation of glycogen degradation" EXACT []
synonym: "regulation of glycogenolysis" EXACT [GOC:sl]
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
is_a: GO:0070873 ! regulation of glycogen metabolic process
relationship: regulates GO:0005980 ! glycogen catabolic process
@@ -57203,7 +57255,7 @@ name: starch metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving starch, the most important reserve polysaccharide in plants. It is a glucan consisting of two components, amylose and amylopectin, which are both glucose homopolymers. Starch is synthesized as a temporary storage form of carbon and can be catabolized to produce sucrose." [ISBN:0198506732]
synonym: "starch metabolism" EXACT []
-is_a: GO:0006073 ! cellular glucan metabolic process
+is_a: GO:0044042 ! glucan metabolic process
[Term]
id: GO:0005983
@@ -57216,7 +57268,6 @@ synonym: "starch degradation" EXACT []
xref: MetaCyc:PWY-842
is_a: GO:0005982 ! starch metabolic process
is_a: GO:0009251 ! glucan catabolic process
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
[Term]
id: GO:0005984
@@ -57225,7 +57276,6 @@ namespace: biological_process
def: "The chemical reactions and pathways involving any disaccharide, sugars composed of two monosaccharide units." [GOC:jl, ISBN:0192800981]
synonym: "disaccharide metabolism" EXACT []
is_a: GO:0009311 ! oligosaccharide metabolic process
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
[Term]
id: GO:0005985
@@ -57591,7 +57641,6 @@ synonym: "vitamin Bh metabolic process" EXACT []
synonym: "vitamin Bh metabolism" EXACT []
xref: Wikipedia:Inositol
is_a: GO:0019751 ! polyol metabolic process
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
[Term]
id: GO:0006021
@@ -57607,7 +57656,6 @@ synonym: "myo-inositol biosynthetic process" NARROW []
synonym: "vitamin Bh biosynthesis" EXACT []
synonym: "vitamin Bh biosynthetic process" EXACT []
is_a: GO:0006020 ! inositol metabolic process
-is_a: GO:0034637 ! cellular carbohydrate biosynthetic process
is_a: GO:0046173 ! polyol biosynthetic process
[Term]
@@ -57790,7 +57838,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving cell wall chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues, found in the walls of cells." [GOC:ai]
synonym: "cell wall chitin metabolism" EXACT []
is_a: GO:0006030 ! chitin metabolic process
-relationship: part_of GO:0071554 ! cell wall organization or biogenesis
+is_a: GO:0044036 ! cell wall macromolecule metabolic process
[Term]
id: GO:0006038
@@ -57815,6 +57863,7 @@ synonym: "cell wall chitin catabolism" EXACT []
synonym: "cell wall chitin degradation" EXACT []
is_a: GO:0006032 ! chitin catabolic process
is_a: GO:0006037 ! cell wall chitin metabolic process
+is_a: GO:0016998 ! cell wall macromolecule catabolic process
[Term]
id: GO:0006040
@@ -57982,7 +58031,7 @@ synonym: "sialic acid metabolic process" BROAD []
synonym: "sialic acid metabolism" BROAD []
is_a: GO:0006040 ! amino sugar metabolic process
is_a: GO:0019752 ! carboxylic acid metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
@@ -58027,7 +58076,7 @@ synonym: "mannoprotein catabolism" EXACT []
synonym: "mannoprotein degradation" EXACT []
is_a: GO:0006056 ! mannoprotein metabolic process
is_a: GO:0006516 ! glycoprotein catabolic process
-is_a: GO:0051603 ! proteolysis involved in cellular protein catabolic process
+is_a: GO:0051603 ! proteolysis involved in protein catabolic process
[Term]
id: GO:0006059
@@ -58171,12 +58220,13 @@ is_a: GO:0052646 ! alditol phosphate metabolic process
[Term]
id: GO:0006073
-name: cellular glucan metabolic process
+name: obsolete cellular glucan metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues, occurring at the level of an individual cell." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues, occurring at the level of an individual cell." [ISBN:0198547684]
+comment: This term was obsoleted because it is not different from its parent, glucan metabolic process ; GO:0044042.
synonym: "cellular glucan metabolism" EXACT []
-is_a: GO:0044042 ! glucan metabolic process
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
+is_obsolete: true
+replaced_by: GO:0044042
[Term]
id: GO:0006074
@@ -58306,6 +58356,7 @@ name: acetate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving acetate, the anion of acetic acid." [GOC:go_curators]
synonym: "acetate metabolism" EXACT []
+is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
[Term]
@@ -58341,6 +58392,8 @@ synonym: "acetyl-CoA formation from pyruvate" EXACT []
synonym: "acetyl-CoA synthesis from pyruvate" EXACT []
synonym: "pyruvate dehydrogenase pathway" EXACT []
xref: MetaCyc:PYRUVDEHYD-PWY
+xref: Reactome:R-HSA-372342.1
+xref: Reactome:R-HSA-71397.1
is_a: GO:0006085 ! acetyl-CoA biosynthetic process
is_a: GO:0006090 ! pyruvate metabolic process
@@ -58394,6 +58447,7 @@ subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "energy pathways" BROAD []
synonym: "intermediary metabolism" RELATED [GOC:mah]
synonym: "metabolic energy generation" RELATED []
@@ -58425,7 +58479,6 @@ synonym: "glycolysis" RELATED [GOC:dph]
synonym: "modifed Embden-Meyerhof pathway" RELATED []
xref: MetaCyc:GLYCOLYSIS-VARIANTS
is_a: GO:0006090 ! pyruvate metabolic process
-is_a: GO:0006757 ! ATP generation from ADP
is_a: GO:0016052 ! carbohydrate catabolic process
[Term]
@@ -58436,7 +58489,7 @@ def: "A modification of the TCA cycle occurring in some plants and microorganism
synonym: "glyoxylate bypass" EXACT []
xref: MetaCyc:GLYOXYLATE-BYPASS
xref: Wikipedia:Glyoxylate_cycle
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
+is_a: GO:0005975 ! carbohydrate metabolic process
is_a: GO:0046487 ! glyoxylate metabolic process
[Term]
@@ -58448,7 +58501,7 @@ synonym: "hexose monophosphate pathway" EXACT []
synonym: "pentose phosphate pathway" EXACT []
synonym: "pentose phosphate shunt" EXACT []
synonym: "pentose-phosphate pathway" EXACT []
-xref: KEGG_PATHWAY:00030
+xref: KEGG_PATHWAY:map00030
xref: MetaCyc:PENTOSE-P-PWY
xref: Reactome:R-HSA-71336 "Pentose phosphate pathway (hexose monophosphate shunt), Homo sapiens"
xref: Wikipedia:Pentose_phosphate_pathway
@@ -58500,6 +58553,7 @@ name: citrate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboyxlate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate cycle." [ISBN:0198506732]
synonym: "citrate metabolism" EXACT []
+is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0072350 ! tricarboxylic acid metabolic process
[Term]
@@ -58581,11 +58635,9 @@ namespace: biological_process
alt_id: GO:0090525
def: "Any process that modulates the frequency, rate or extent of glycolysis." [GOC:go_curators]
synonym: "regulation of glycolysis involved in cellular glucose homeostasis" EXACT []
-is_a: GO:0042325 ! regulation of phosphorylation
-is_a: GO:0043467 ! regulation of generation of precursor metabolites and energy
+is_a: GO:0031323 ! regulation of cellular metabolic process
is_a: GO:0043470 ! regulation of carbohydrate catabolic process
-is_a: GO:1900542 ! regulation of purine nucleotide metabolic process
-is_a: GO:1903578 ! regulation of ATP metabolic process
+is_a: GO:0062012 ! regulation of small molecule metabolic process
relationship: regulates GO:0006096 ! glycolytic process
[Term]
@@ -58648,7 +58700,7 @@ is_a: GO:0034309 ! primary alcohol biosynthetic process
id: GO:0006116
name: NADH oxidation
namespace: biological_process
-def: "A metabolic process that results in the oxidation of reduced nicotinamide adenine dinucleotide, NADH, to the oxidized form, NAD." [GOC:ai]
+def: "A metabolic process that results in the oxidation of reduced nicotinamide adenine dinucleotide, NADH, to the oxidized form, NAD+." [GOC:ai]
synonym: "NAD (reduced) dehydrogenation" EXACT []
synonym: "NAD (reduced) oxidation" EXACT []
synonym: "NADH dehydrogenation" EXACT []
@@ -58656,8 +58708,7 @@ synonym: "reduced NAD dehydrogenation" EXACT []
synonym: "reduced NAD oxidation" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide dehydrogenation" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide oxidation" EXACT []
-is_a: GO:0006734 ! NADH metabolic process
-is_a: GO:0019674 ! NAD metabolic process
+is_a: GO:0008152 ! metabolic process
[Term]
id: GO:0006117
@@ -58698,7 +58749,6 @@ subset: goslim_pir
synonym: "respiratory-chain phosphorylation" EXACT []
xref: Wikipedia:Oxidative_phosphorylation
is_a: GO:0009060 ! aerobic respiration
-is_a: GO:0046034 ! ATP metabolic process
[Term]
id: GO:0006120
@@ -58745,7 +58795,7 @@ name: ferredoxin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving ferredoxin, any simple, nonenzymatic iron-sulfur protein that is characterized by having equal numbers of atoms of iron and labile sulfur. Iron and sulfur atoms are present in one or two clusters of two or four atoms of each." [ISBN:0198506732]
synonym: "ferredoxin metabolism" EXACT []
-is_a: GO:0044267 ! cellular protein metabolic process
+is_a: GO:0019538 ! protein metabolic process
[Term]
id: GO:0006125
@@ -59127,12 +59177,11 @@ is_a: GO:0072522 ! purine-containing compound biosynthetic process
[Term]
id: GO:0006165
-name: nucleoside diphosphate phosphorylation
+name: obsolete nucleoside diphosphate phosphorylation
namespace: biological_process
-def: "The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate." [GOC:ai]
-is_a: GO:0009117 ! nucleotide metabolic process
-is_a: GO:0009132 ! nucleoside diphosphate metabolic process
-is_a: GO:0046939 ! nucleotide phosphorylation
+def: "OBSOLETE. The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate." [GOC:ai]
+comment: The reason for obsoletion is that this term represents a single step MF.
+is_obsolete: true
[Term]
id: GO:0006166
@@ -59207,8 +59256,8 @@ synonym: "cAMP synthesis" EXACT []
synonym: "cyclic AMP biosynthesis" EXACT []
synonym: "cyclic AMP biosynthetic process" EXACT []
is_a: GO:0009152 ! purine ribonucleotide biosynthetic process
+is_a: GO:0009190 ! cyclic nucleotide biosynthetic process
is_a: GO:0046058 ! cAMP metabolic process
-is_a: GO:0052652 ! cyclic purine nucleotide metabolic process
[Term]
id: GO:0006172
@@ -59238,12 +59287,11 @@ is_a: GO:0046056 ! dADP metabolic process
[Term]
id: GO:0006174
-name: dADP phosphorylation
+name: obsolete dADP phosphorylation
namespace: biological_process
-def: "The process of introducing a phosphate group into dADP, deoxyadenosine diphosphate, to produce dATP." [ISBN:0198506732]
-is_a: GO:0006165 ! nucleoside diphosphate phosphorylation
-is_a: GO:0009216 ! purine deoxyribonucleoside triphosphate biosynthetic process
-is_a: GO:0046056 ! dADP metabolic process
+def: "OBSOLETE. The process of introducing a phosphate group into dADP, deoxyadenosine diphosphate, to produce dATP." [ISBN:0198506732]
+comment: The reason for obsoletion is that this term represents a single step MF.
+is_obsolete: true
[Term]
id: GO:0006175
@@ -59330,8 +59378,8 @@ synonym: "cGMP biosynthesis" EXACT []
synonym: "cGMP formation" EXACT []
synonym: "cGMP synthesis" EXACT []
is_a: GO:0009152 ! purine ribonucleotide biosynthetic process
+is_a: GO:0009190 ! cyclic nucleotide biosynthetic process
is_a: GO:0046068 ! cGMP metabolic process
-is_a: GO:0052652 ! cyclic purine nucleotide metabolic process
[Term]
id: GO:0006183
@@ -59374,12 +59422,11 @@ is_a: GO:0046066 ! dGDP metabolic process
[Term]
id: GO:0006186
-name: dGDP phosphorylation
+name: obsolete dGDP phosphorylation
namespace: biological_process
-def: "The process of introducing a phosphate group into dGDP, deoxyguanosine diphosphate, to produce dGTP." [ISBN:0198506732]
-is_a: GO:0006165 ! nucleoside diphosphate phosphorylation
-is_a: GO:0009216 ! purine deoxyribonucleoside triphosphate biosynthetic process
-is_a: GO:0046066 ! dGDP metabolic process
+def: "OBSOLETE. The process of introducing a phosphate group into dGDP, deoxyguanosine diphosphate, to produce dGTP." [ISBN:0198506732]
+comment: The reason for obsoletion is that this term represents a single step MF.
+is_obsolete: true
[Term]
id: GO:0006187
@@ -59438,12 +59485,11 @@ is_a: GO:0046095 ! deoxyinosine biosynthetic process
[Term]
id: GO:0006192
-name: IDP phosphorylation
+name: obsolete IDP phosphorylation
namespace: biological_process
-def: "The process of introducing a phosphate group into IDP, inosine (5'-)diphosphate, to produce ITP." [GOC:ai]
-is_a: GO:0006165 ! nucleoside diphosphate phosphorylation
-is_a: GO:0009206 ! purine ribonucleoside triphosphate biosynthetic process
-is_a: GO:0046707 ! IDP metabolic process
+def: "OBSOLETE. The process of introducing a phosphate group into IDP, inosine (5'-)diphosphate, to produce ITP." [GOC:ai]
+comment: The reason for obsoletion is that this term represents a single step MF.
+is_obsolete: true
[Term]
id: GO:0006193
@@ -59460,11 +59506,11 @@ is_a: GO:0046041 ! ITP metabolic process
[Term]
id: GO:0006194
-name: dIDP phosphorylation
+name: obsolete dIDP phosphorylation
namespace: biological_process
-def: "The process of introducing a phosphate group into dIDP, deoxyinosine diphosphate, to produce dITP." [ISBN:0198506732]
-is_a: GO:0006165 ! nucleoside diphosphate phosphorylation
-is_a: GO:0009216 ! purine deoxyribonucleoside triphosphate biosynthetic process
+def: "OBSOLETE. The process of introducing a phosphate group into dIDP, deoxyinosine diphosphate, to produce dITP." [ISBN:0198506732]
+comment: The reason for obsoletion is that this term represents a single step MF.
+is_obsolete: true
[Term]
id: GO:0006195
@@ -60204,7 +60250,6 @@ namespace: biological_process
alt_id: GO:0055132
def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
@@ -60213,7 +60258,6 @@ subset: goslim_pir
subset: goslim_plant
synonym: "cellular DNA metabolism" EXACT []
synonym: "DNA metabolism" EXACT []
-is_a: GO:0044260 ! cellular macromolecule metabolic process
is_a: GO:0090304 ! nucleic acid metabolic process
[Term]
@@ -60221,23 +60265,25 @@ id: GO:0006260
name: DNA replication
namespace: biological_process
alt_id: GO:0055133
-def: "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC:mah]
+def: "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC:mah]
comment: DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'.
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
+subset: prokaryote_subset
xref: Wikipedia:DNA_replication
-is_a: GO:0034645 ! cellular macromolecule biosynthetic process
+is_a: GO:0006259 ! DNA metabolic process
[Term]
id: GO:0006261
-name: DNA-dependent DNA replication
+name: DNA-templated DNA replication
namespace: biological_process
alt_id: GO:0006262
alt_id: GO:0006263
def: "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC:mah, ISBN:0198506732]
+synonym: "DNA-dependent DNA replication" EXACT []
is_a: GO:0006260 ! DNA replication
[Term]
@@ -60249,7 +60295,8 @@ synonym: "mitochondrial DNA synthesis" RELATED []
synonym: "mtDNA replication" EXACT []
synonym: "mtDNA synthesis" RELATED []
synonym: "replication of mitochondrial DNA" EXACT []
-is_a: GO:0006261 ! DNA-dependent DNA replication
+is_a: GO:0006261 ! DNA-templated DNA replication
+is_a: GO:0032042 ! mitochondrial DNA metabolic process
[Term]
id: GO:0006265
@@ -60290,7 +60337,7 @@ comment: Note that this term refers to a geometric change in DNA conformation, a
synonym: "DNA unwinding during replication" RELATED [GOC:dph, GOC:tb]
synonym: "DNA unwinding factor" RELATED []
is_a: GO:0032508 ! DNA duplex unwinding
-relationship: part_of GO:0006261 ! DNA-dependent DNA replication
+relationship: part_of GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:0006269
@@ -60299,19 +60346,19 @@ namespace: biological_process
def: "The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis." [PMID:11395402]
synonym: "replication priming" RELATED []
is_a: GO:0032774 ! RNA biosynthetic process
-relationship: part_of GO:0006261 ! DNA-dependent DNA replication
+relationship: part_of GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:0006270
name: DNA replication initiation
namespace: biological_process
alt_id: GO:0042024
-def: "The process in which DNA-dependent DNA replication is started; this begins with the ATP dependent loading of an initiator complex onto the DNA, this is followed by DNA melting and helicase activity. In bacteria, the gene products that enable the helicase activity are loaded after the initial melting and in archaea and eukaryotes, the gene products that enable the helicase activity are inactive when they are loaded and subsequently activate." [ISBN:071673706X, ISBN:0815316194, PMID:28209641]
+def: "The process in which DNA-dependent DNA replication is started; it begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, followed by DNA unwinding." [PMID:28209641]
synonym: "DNA endoreduplication initiation" NARROW []
synonym: "DNA re-replication initiation" NARROW []
synonym: "DNA-dependent DNA replication initiation" EXACT [GOC:vw]
is_a: GO:0006259 ! DNA metabolic process
-relationship: part_of GO:0006261 ! DNA-dependent DNA replication
+relationship: part_of GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:0006271
@@ -60321,7 +60368,7 @@ def: "The process in which an existing DNA strand is extended by activities incl
synonym: "DNA replication elongation" EXACT []
synonym: "DNA strand elongation during DNA replication" RELATED [GOC:dph, GOC:tb]
is_a: GO:0022616 ! DNA strand elongation
-relationship: part_of GO:0006261 ! DNA-dependent DNA replication
+relationship: part_of GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:0006272
@@ -60343,14 +60390,14 @@ name: DNA replication termination
namespace: biological_process
def: "The process in which DNA replication at a replication fork ceases; occurs when the replication fork reaches a specific termination site or when two replication forks meet." [GOC:mah, PMID:10209736, PMID:12009298]
is_a: GO:0006259 ! DNA metabolic process
-relationship: part_of GO:0006261 ! DNA-dependent DNA replication
+relationship: part_of GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:0006275
name: regulation of DNA replication
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA replication." [GOC:go_curators]
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
+is_a: GO:0051052 ! regulation of DNA metabolic process
relationship: regulates GO:0006260 ! DNA replication
[Term]
@@ -60370,9 +60417,10 @@ is_a: GO:0071897 ! DNA biosynthetic process
[Term]
id: GO:0006278
-name: RNA-dependent DNA biosynthetic process
+name: RNA-templated DNA biosynthetic process
namespace: biological_process
def: "A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand." [GOC:mah, ISBN:0198506732]
+synonym: "RNA-dependent DNA biosynthetic process" EXACT []
is_a: GO:0071897 ! DNA biosynthetic process
[Term]
@@ -60414,9 +60462,10 @@ subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
+subset: prokaryote_subset
xref: Wikipedia:DNA_repair
is_a: GO:0006259 ! DNA metabolic process
-is_a: GO:0006974 ! cellular response to DNA damage stimulus
+is_a: GO:0006974 ! DNA damage response
[Term]
id: GO:0006282
@@ -60425,7 +60474,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA repair." [GOC:go_curators]
subset: goslim_metagenomics
is_a: GO:0051052 ! regulation of DNA metabolic process
-is_a: GO:2001020 ! regulation of response to DNA damage stimulus
+is_a: GO:0080135 ! regulation of cellular response to stress
relationship: regulates GO:0006281 ! DNA repair
[Term]
@@ -60458,12 +60507,13 @@ relationship: part_of GO:0006284 ! base-excision repair
[Term]
id: GO:0006286
-name: base-excision repair, base-free sugar-phosphate removal
+name: obsolete base-excision repair, base-free sugar-phosphate removal
namespace: biological_process
-def: "Excision of the sugar phosphate residue at an AP site, i.e. a deoxyribose sugar with a missing base, by a phosphodiesterase enzyme." [ISBN:0815316194]
-is_a: GO:0006259 ! DNA metabolic process
-is_a: GO:0098502 ! DNA dephosphorylation
-relationship: part_of GO:0006284 ! base-excision repair
+def: "OBSOLETE. Excision of the sugar phosphate residue at an AP site, i.e. a deoxyribose sugar with a missing base, by a phosphodiesterase enzyme." [ISBN:0815316194]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0003906
+consider: GO:0017108
[Term]
id: GO:0006287
@@ -60540,19 +60590,23 @@ relationship: part_of GO:0006289 ! nucleotide-excision repair
[Term]
id: GO:0006295
-name: nucleotide-excision repair, DNA incision, 3'-to lesion
+name: obsolete nucleotide-excision repair, DNA incision, 3'-to lesion
namespace: biological_process
-def: "The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage." [GOC:elh, PMID:10197977]
+def: "OBSOLETE. The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage." [GOC:elh, PMID:10197977]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "nucleotide-excision repair, DNA incision, 3' to lesion" EXACT []
-is_a: GO:0033683 ! nucleotide-excision repair, DNA incision
+is_obsolete: true
+replaced_by: GO:0006289
[Term]
id: GO:0006296
-name: nucleotide-excision repair, DNA incision, 5'-to lesion
+name: obsolete nucleotide-excision repair, DNA incision, 5'-to lesion
namespace: biological_process
-def: "The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage." [GOC:elh, PMID:10197977]
+def: "OBSOLETE. The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage." [GOC:elh, PMID:10197977]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "nucleotide-excision repair, DNA incision, 5' to lesion" EXACT []
-is_a: GO:0033683 ! nucleotide-excision repair, DNA incision
+is_obsolete: true
+replaced_by: GO:0006289
[Term]
id: GO:0006297
@@ -60635,7 +60689,6 @@ def: "The covalent transfer of a methyl group to either N-6 of adenine or C-5 or
xref: Wikipedia:DNA_methylation
is_a: GO:0006305 ! DNA alkylation
is_a: GO:0043414 ! macromolecule methylation
-is_a: GO:0044728 ! DNA methylation or demethylation
[Term]
id: GO:0006307
@@ -60654,8 +60707,8 @@ synonym: "DNA breakdown" EXACT []
synonym: "DNA catabolism" EXACT []
synonym: "DNA degradation" EXACT []
is_a: GO:0006259 ! DNA metabolic process
+is_a: GO:0009057 ! macromolecule catabolic process
is_a: GO:0034655 ! nucleobase-containing compound catabolic process
-is_a: GO:0044265 ! cellular macromolecule catabolic process
[Term]
id: GO:0006309
@@ -60670,7 +60723,7 @@ synonym: "DNA catabolism during apoptosis" EXACT []
synonym: "DNA fragmentation" BROAD []
synonym: "DNA fragmentation involved in apoptotic nuclear change" EXACT [GOC:cjm, GOC:dph, GOC:tb]
synonym: "endonucleolytic DNA catabolic process involved in apoptosis" EXACT []
-is_a: GO:0000737 ! DNA catabolic process, endonucleolytic
+is_a: GO:0006308 ! DNA catabolic process
relationship: part_of GO:0030262 ! apoptotic nuclear changes
[Term]
@@ -60682,6 +60735,7 @@ subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
+subset: prokaryote_subset
is_a: GO:0006259 ! DNA metabolic process
[Term]
@@ -60703,17 +60757,15 @@ is_a: GO:0006310 ! DNA recombination
[Term]
id: GO:0006313
-name: transposition, DNA-mediated
+name: DNA transposition
namespace: biological_process
alt_id: GO:0006317
alt_id: GO:0006318
-def: "Any process involved in a type of transpositional recombination which occurs via a DNA intermediate." [GOC:jp, ISBN:0198506732, ISBN:1555812090]
+def: "A type of transposition in which a transposable element (transposon) is moved to another part of a genome, either by a cut-and-paste mechanism or a replicative mechanism." [ISBN:0198506732, ISBN:1555812090, PMID:26846462, PMID:30416149, PMID:32588192]
synonym: "Class II transposition" EXACT []
-synonym: "DNA transposition" EXACT [GOC:dph]
-synonym: "P-element excision" NARROW []
-synonym: "P-element transposition" NARROW []
-synonym: "Tc1/mariner transposition" NARROW []
-synonym: "Tc3 transposition" NARROW []
+synonym: "transposition, DNA-mediated" EXACT []
+xref: Wikipedia:Transposable_element
+xref: Wikipedia:Transposase
is_a: GO:0006310 ! DNA recombination
is_a: GO:0032196 ! transposition
@@ -60738,17 +60790,6 @@ namespace: biological_process
def: "Lateral transfer of a group I intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron; group I introns are self-splicing introns that use guanosine as a cofactor in the splicing reaction." [GOC:mcc, ISBN:0716743663, PMID:10487208]
is_a: GO:0006314 ! intron homing
-[Term]
-id: GO:0006323
-name: DNA packaging
-namespace: biological_process
-def: "Any process in which DNA and associated proteins are formed into a compact, orderly structure." [GOC:mah, ISBN:0815316194]
-subset: goslim_pir
-synonym: "DNA condensation" EXACT []
-synonym: "DNA organisation" EXACT []
-synonym: "DNA organization" EXACT []
-is_a: GO:0071103 ! DNA conformation change
-
[Term]
id: GO:0006324
name: obsolete S phase-specific histone modification
@@ -60764,16 +60805,29 @@ consider: GO:0016570
id: GO:0006325
name: chromatin organization
namespace: biological_process
+alt_id: GO:0006333
+alt_id: GO:0006336
alt_id: GO:0016568
-def: "Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin." [GOC:mah, GOC:vw, PMID:20404130]
+alt_id: GO:0031497
+alt_id: GO:0034724
+def: "The assembly or remodeling of chromatin composed of DNA complexed with histones, other associated proteins, and sometimes RNA." [PMID:20404130]
subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
+synonym: "chromatin assembly" NARROW []
+synonym: "chromatin assembly or disassembly" RELATED []
+synonym: "chromatin assembly/disassembly" RELATED []
+synonym: "chromatin maintenance" BROAD []
synonym: "chromatin modification" RELATED []
synonym: "chromatin organisation" EXACT [GOC:mah]
+synonym: "DNA replication-independent chromatin assembly" NARROW []
+synonym: "DNA replication-independent chromatin organization" NARROW []
+synonym: "DNA replication-independent nucleosome organisation" NARROW []
+synonym: "DNA replication-independent nuclesome assembly" NARROW []
+synonym: "establishment of chromatin architecture" EXACT [GOC:mah]
synonym: "establishment or maintenance of chromatin architecture" EXACT [GOC:mah]
-is_a: GO:0016043 ! cellular component organization
-relationship: part_of GO:0051276 ! chromosome organization
+synonym: "transcription-coupled nucleosome assembly" NARROW []
+is_a: GO:0071824 ! protein-DNA complex organization
[Term]
id: GO:0006326
@@ -60826,14 +60880,6 @@ synonym: "single-stranded DNA binding" EXACT []
is_obsolete: true
replaced_by: GO:0003697
-[Term]
-id: GO:0006333
-name: chromatin assembly or disassembly
-namespace: biological_process
-def: "The formation or destruction of chromatin structures." [GOC:mah]
-synonym: "chromatin assembly/disassembly" EXACT []
-is_a: GO:0006325 ! chromatin organization
-
[Term]
id: GO:0006334
name: nucleosome assembly
@@ -60843,26 +60889,19 @@ synonym: "histone chaperone" RELATED [GOC:vw]
synonym: "nucleosome modeling" EXACT []
is_a: GO:0034728 ! nucleosome organization
is_a: GO:0065004 ! protein-DNA complex assembly
-relationship: part_of GO:0031497 ! chromatin assembly
+relationship: part_of GO:0006325 ! chromatin organization
[Term]
id: GO:0006335
name: DNA replication-dependent chromatin assembly
namespace: biological_process
-def: "The formation of nucleosomes on newly replicated DNA, coupled to strand elongation." [GOC:mah]
-synonym: "DNA replication-dependent nucleosome assembly" EXACT []
-is_a: GO:0031497 ! chromatin assembly
-is_a: GO:0034723 ! DNA replication-dependent chromatin organization
-
-[Term]
-id: GO:0006336
-name: DNA replication-independent chromatin assembly
-namespace: biological_process
-def: "The formation of chromatin outside the context of DNA replication." [GOC:mah]
-synonym: "DNA replication-independent nucleosome assembly" EXACT []
-synonym: "transcription-coupled nucleosome assembly" EXACT []
-is_a: GO:0031497 ! chromatin assembly
-is_a: GO:0034724 ! DNA replication-independent chromatin organization
+alt_id: GO:0034723
+def: "The formation of nucleosomes on newly synthesized DNA, coupled to strand elongation." [GOC:mah, PMID:28053344]
+synonym: "DNA replication-dependent chromatin organization" RELATED []
+synonym: "DNA replication-dependent nucleosome assembly" BROAD []
+synonym: "DNA replication-dependent nucleosome organisation" RELATED []
+synonym: "DNA replication-dependent nucleosome organization" RELATED []
+is_a: GO:0006325 ! chromatin organization
[Term]
id: GO:0006337
@@ -60871,14 +60910,13 @@ namespace: biological_process
def: "The controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA." [GOC:mah]
is_a: GO:0032986 ! protein-DNA complex disassembly
is_a: GO:0034728 ! nucleosome organization
-relationship: part_of GO:0031498 ! chromatin disassembly
[Term]
id: GO:0006338
name: chromatin remodeling
namespace: biological_process
alt_id: GO:0043044
-def: "Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation." [GOC:jid, GOC:vw, PMID:12042764, PMID:12697820]
+def: "A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication." [GOC:jid, GOC:vw, PMID:12042764, PMID:12697820]
synonym: "ATP-dependent chromatin remodeling" NARROW []
synonym: "ATP-dependent chromatin remodelling" NARROW []
synonym: "chromatin modeling" EXACT []
@@ -60922,12 +60960,13 @@ replaced_by: GO:0043035
[Term]
id: GO:0006346
-name: DNA methylation-dependent heterochromatin assembly
+name: DNA methylation-dependent heterochromatin formation
namespace: biological_process
def: "Repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:mah]
+synonym: "DNA methylation-dependent heterochromatin assembly" EXACT []
synonym: "methylation-dependent chromatin silencing" BROAD []
synonym: "methylation-dependent heterochromatic silencing" BROAD []
-is_a: GO:0140718 ! facultative heterochromatin assembly
+is_a: GO:0140718 ! facultative heterochromatin formation
[Term]
id: GO:0006349
@@ -60937,58 +60976,61 @@ def: "An epigenetic mechanism of regulation of gene expression in which epigenet
synonym: "regulation of gene expression by DNA imprinting" EXACT [GOC:mah]
synonym: "regulation of gene expression by genetic imprinting" RELATED []
xref: Wikipedia:Genomic_imprinting
-is_a: GO:0040029 ! regulation of gene expression, epigenetic
+is_a: GO:0040029 ! epigenetic regulation of gene expression
[Term]
id: GO:0006351
-name: transcription, DNA-templated
+name: DNA-templated transcription
namespace: biological_process
alt_id: GO:0001121
alt_id: GO:0006350
alt_id: GO:0061018
alt_id: GO:0061022
-def: "The cellular synthesis of RNA on a template of DNA." [GOC:jl, GOC:txnOH]
-subset: goslim_aspergillus
+def: "The synthesis of an RNA transcript from a DNA template." [GOC:jl, GOC:txnOH]
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
+subset: prokaryote_subset
synonym: "bacterial transcription" NARROW []
synonym: "cellular transcription" BROAD []
synonym: "DNA-dependent transcription" EXACT []
synonym: "transcription" BROAD []
synonym: "transcription from bacterial-type RNA polymerase promoter" NARROW []
synonym: "transcription, DNA-dependent" EXACT [GOC:txnOH]
+synonym: "transcription, DNA-templated" EXACT []
xref: Wikipedia:Transcription_(genetics)
is_a: GO:0097659 ! nucleic acid-templated transcription
[Term]
id: GO:0006352
-name: DNA-templated transcription, initiation
+name: DNA-templated transcription initiation
namespace: biological_process
alt_id: GO:0001123
-def: "Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription." [GOC:jid, GOC:txnOH, PMID:18280161]
+def: "The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place." [GOC:jid, GOC:txnOH, PMID:18280161]
comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation.
subset: goslim_yeast
synonym: "DNA-dependent RNA polymerase complex assembly at promoter" EXACT []
synonym: "DNA-dependent transcription, initiation" EXACT [GOC:txnOH]
+synonym: "DNA-templated transcription, initiation" EXACT []
synonym: "initiation of DNA-dependent transcription" EXACT [GOC:jh2]
synonym: "initiation of transcription, DNA-dependent" EXACT [GOC:mah]
synonym: "transcription initiation factor activity" RELATED []
synonym: "transcription initiation from bacterial-type RNA polymerase promoter" NARROW []
synonym: "transcription initiation, DNA-dependent" RELATED [GOC:jh2]
is_a: GO:0032774 ! RNA biosynthetic process
-relationship: part_of GO:0006351 ! transcription, DNA-templated
+relationship: part_of GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0006353
-name: DNA-templated transcription, termination
+name: DNA-templated transcription termination
namespace: biological_process
alt_id: GO:0001125
-def: "The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA." [GOC:txnOH, ISBN:0716720094, PMID:15020047, PMID:18280161]
+def: "The completion of transcription: the RNA polymerase pauses, the RNA-DNA hybrid dissociates, followed by the release of the RNA polymerase from its DNA template." [GOC:txnOH, PMID:15020047, PMID:18280161, PMID:30978344]
subset: goslim_yeast
synonym: "DNA-dependent transcription, termination" EXACT [GOC:txnOH]
+synonym: "DNA-templated transcription, termination" EXACT []
synonym: "termination of DNA-dependent transcription" EXACT [GOC:jh2]
synonym: "termination of transcription, DNA-dependent" EXACT [GOC:mah]
synonym: "transcription termination factor activity" RELATED []
@@ -60996,28 +61038,29 @@ synonym: "transcription termination from bacterial-type RNA polymerase promoter"
synonym: "transcription termination, DNA-dependent" RELATED [GOC:jh2]
synonym: "transcriptional complex disassembly" BROAD []
is_a: GO:0032774 ! RNA biosynthetic process
-relationship: part_of GO:0006351 ! transcription, DNA-templated
+relationship: part_of GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0006354
-name: DNA-templated transcription, elongation
+name: DNA-templated transcription elongation
namespace: biological_process
alt_id: GO:0001124
def: "The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase." [GOC:mah, GOC:txnOH, PMID:15020047, PMID:18280161]
subset: goslim_pir
subset: goslim_yeast
synonym: "DNA-dependent transcription, elongation" EXACT [GOC:txnOH]
+synonym: "DNA-templated transcription, elongation" EXACT []
synonym: "RNA elongation" BROAD []
synonym: "RNA elongation from bacterial-type RNA polymerase promoter" NARROW []
synonym: "transcription elongation from bacterial-type RNA polymerase promoter" NARROW []
synonym: "transcription elongation, DNA-dependent" EXACT [GOC:jh2]
synonym: "transcriptional elongation, DNA-dependent" EXACT []
is_a: GO:0032774 ! RNA biosynthetic process
-relationship: part_of GO:0006351 ! transcription, DNA-templated
+relationship: part_of GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0006355
-name: regulation of transcription, DNA-templated
+name: regulation of DNA-templated transcription
namespace: biological_process
alt_id: GO:0032583
alt_id: GO:0045449
@@ -61025,13 +61068,15 @@ alt_id: GO:0061019
def: "Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH]
subset: goslim_drosophila
subset: goslim_generic
+subset: prokaryote_subset
synonym: "regulation of cellular transcription, DNA-dependent" EXACT []
synonym: "regulation of gene-specific transcription" RELATED []
synonym: "regulation of transcription, DNA-dependent" EXACT [GOC:txnOH]
+synonym: "regulation of transcription, DNA-templated" EXACT []
synonym: "transcriptional control" BROAD []
is_a: GO:0010468 ! regulation of gene expression
is_a: GO:1903506 ! regulation of nucleic acid-templated transcription
-relationship: regulates GO:0006351 ! transcription, DNA-templated
+relationship: regulates GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0006356
@@ -61040,7 +61085,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase I." [GOC:go_curators]
synonym: "regulation of transcription from Pol I promoter" EXACT []
synonym: "regulation of transcription from RNA polymerase I promoter" EXACT []
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
relationship: regulates GO:0006360 ! transcription by RNA polymerase I
[Term]
@@ -61056,7 +61101,7 @@ synonym: "regulation of global transcription from Pol II promoter" RELATED []
synonym: "regulation of transcription from Pol II promoter" EXACT []
synonym: "regulation of transcription from RNA polymerase II promoter" EXACT []
synonym: "regulation of transcription from RNA polymerase II promoter, global" RELATED []
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
relationship: regulates GO:0006366 ! transcription by RNA polymerase II
[Term]
@@ -61066,7 +61111,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of transcription mediated by RNA ploymerase III." [GOC:go_curators]
synonym: "regulation of transcription from Pol III promoter" EXACT []
synonym: "regulation of transcription from RNA polymerase III promoter" EXACT []
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
relationship: regulates GO:0006383 ! transcription by RNA polymerase III
[Term]
@@ -61078,29 +61123,33 @@ subset: goslim_yeast
synonym: "RNA polymerase I transcription factor activity" RELATED []
synonym: "transcription from Pol I promoter" EXACT []
synonym: "transcription from RNA polymerase I promoter" EXACT []
-is_a: GO:0006351 ! transcription, DNA-templated
+is_a: GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0006361
-name: transcription initiation from RNA polymerase I promoter
+name: transcription initiation at RNA polymerase I promoter
namespace: biological_process
alt_id: GO:0001180
-def: "Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription." [GOC:mah, GOC:txnOH]
+def: "A transcription initiation process that takes place at a RNA polymerase I gene promoter. Ribosomal RNAs (rRNA) genes are transcribed by RNA polymerase I." [GOC:txnOH]
comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation.
synonym: "transcription initiation from Pol I promoter" EXACT []
+synonym: "transcription initiation from RNA polymerase I promoter" EXACT []
synonym: "transcription initiation from RNA polymerase I promoter for nuclear large rRNA transcript" NARROW []
-is_a: GO:0006352 ! DNA-templated transcription, initiation
+is_a: GO:0006352 ! DNA-templated transcription initiation
relationship: part_of GO:0006360 ! transcription by RNA polymerase I
[Term]
id: GO:0006362
-name: transcription elongation from RNA polymerase I promoter
+name: transcription elongation by RNA polymerase I
namespace: biological_process
+alt_id: GO:0001183
def: "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I." [GOC:mah, GOC:txnOH]
synonym: "RNA elongation from Pol I promoter" EXACT []
synonym: "RNA polymerase I transcription elongation factor activity" RELATED []
-is_a: GO:0006354 ! DNA-templated transcription, elongation
-relationship: part_of GO:0006360 ! transcription by RNA polymerase I
+synonym: "transcription elongation from RNA polymerase I promoter" EXACT []
+synonym: "transcription elongation from RNA polymerase I promoter for nuclear large rRNA transcript" RELATED []
+is_a: GO:0006354 ! DNA-templated transcription elongation
+relationship: part_of GO:0042790 ! nucleolar large rRNA transcription by RNA polymerase I
[Term]
id: GO:0006363
@@ -61108,13 +61157,13 @@ name: termination of RNA polymerase I transcription
namespace: biological_process
alt_id: GO:0001185
alt_id: GO:0019223
-def: "The process in which the synthesis of an RNA molecule by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit." [GOC:mah, GOC:txnOH, PMID:10684922]
+def: "A transcription termination process that completes the production of a ribosomal RNA transcript. RNAP I termination requires binding of a terminator protein to specific sequences downstream of the transcription unit." [GOC:mah, GOC:txnOH, PMID:10684922, PMID:27371117]
synonym: "RNA polymerase I transcription termination" EXACT []
synonym: "RNA polymerase I transcription termination factor activity" RELATED []
synonym: "termination of RNA polymerase I transcription from promoter for nuclear large rRNA transcript" NARROW []
synonym: "transcription termination from Pol I promoter" EXACT []
synonym: "transcription termination from RNA polymerase I promoter" EXACT []
-is_a: GO:0006353 ! DNA-templated transcription, termination
+is_a: GO:0006353 ! DNA-templated transcription termination
relationship: part_of GO:0006360 ! transcription by RNA polymerase I
[Term]
@@ -61143,26 +61192,29 @@ synonym: "RNA polymerase II transcription factor activity" RELATED []
synonym: "specific transcription from RNA polymerase II promoter" RELATED [GOC:mah]
synonym: "transcription from Pol II promoter" EXACT []
synonym: "transcription from RNA polymerase II promoter" EXACT []
-is_a: GO:0006351 ! transcription, DNA-templated
+is_a: GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0006367
-name: transcription initiation from RNA polymerase II promoter
+name: transcription initiation at RNA polymerase II promoter
namespace: biological_process
-def: "Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription." [GOC:mah, GOC:txnOH]
+def: "A transcription initiation process that takes place at a RNA polymerase II gene promoter. Messenger RNAs (mRNA) genes, as well as some non-coding RNAs, are transcribed by RNA polymerase II." [GOC:mah, GOC:txnOH]
comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation.
synonym: "transcription initiation from Pol II promoter" EXACT []
-is_a: GO:0006352 ! DNA-templated transcription, initiation
+synonym: "transcription initiation from RNA polymerase II promoter" EXACT []
+is_a: GO:0006352 ! DNA-templated transcription initiation
relationship: part_of GO:0006366 ! transcription by RNA polymerase II
[Term]
id: GO:0006368
-name: transcription elongation from RNA polymerase II promoter
+name: transcription elongation by RNA polymerase II
namespace: biological_process
def: "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II." [GOC:mah, GOC:txnOH]
synonym: "RNA elongation from Pol II promoter" EXACT []
synonym: "RNA polymerase II transcription elongation factor activity" RELATED []
-is_a: GO:0006354 ! DNA-templated transcription, elongation
+synonym: "transcription elongation by RNA polymerase II promoter" EXACT []
+synonym: "transcription elongation from RNA polymerase II promoter" EXACT []
+is_a: GO:0006354 ! DNA-templated transcription elongation
relationship: part_of GO:0006366 ! transcription by RNA polymerase II
[Term]
@@ -61170,13 +61222,13 @@ id: GO:0006369
name: termination of RNA polymerase II transcription
namespace: biological_process
alt_id: GO:0019224
-def: "The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed." [GOC:mah, GOC:txnOH]
+def: "A transcription termination process that completes the production of a primary RNA polymerase II transcript." [GOC:mah, GOC:txnOH, PMID:27371117]
synonym: "RNA 3'-end formation by RNA polymerase II" EXACT []
synonym: "RNA polymerase II transcription termination" EXACT []
synonym: "RNA polymerase II transcription termination factor activity" RELATED []
synonym: "transcription termination from Pol II promoter" EXACT []
synonym: "transcription termination from RNA polymerase II promoter" EXACT []
-is_a: GO:0006353 ! DNA-templated transcription, termination
+is_a: GO:0006353 ! DNA-templated transcription termination
relationship: part_of GO:0006366 ! transcription by RNA polymerase II
[Term]
@@ -61231,14 +61283,14 @@ consider: GO:0000393
[Term]
id: GO:0006376
-name: mRNA splice site selection
+name: mRNA splice site recognition
namespace: biological_process
def: "Selection of a splice site by components of the assembling spliceosome." [GOC:krc, ISBN:0879695897]
synonym: "spliceosomal commitment complex biosynthesis" NARROW []
synonym: "spliceosomal commitment complex formation" NARROW []
synonym: "spliceosomal E complex biosynthesis" NARROW []
synonym: "spliceosomal E complex formation" NARROW []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0000245 ! spliceosomal complex assembly
[Term]
@@ -61304,34 +61356,37 @@ synonym: "transcription from RNA polymerase III type 2 promoter" NARROW []
synonym: "transcription from RNA polymerase III type 3 promoter" NARROW []
synonym: "U2 snRNA transcription (S. cerevisiae)" NARROW []
synonym: "U6 snRNA transcription (mammalian)" NARROW []
-is_a: GO:0006351 ! transcription, DNA-templated
+is_a: GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0006384
-name: transcription initiation from RNA polymerase III promoter
+name: transcription initiation at RNA polymerase III promoter
namespace: biological_process
alt_id: GO:0001022
alt_id: GO:0001023
alt_id: GO:0001024
alt_id: GO:0001036
-def: "Any process involved in the assembly of the RNA polymerase III preinitiation complex (PIC) at an RNA polymerase III promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription." [GOC:mah, GOC:txnOH]
+def: "A transcription initiation process that takes place at a RNA polymerase III gene promoter. Transfer RNAs (tRNA) genes, as well as some other non-coding RNAs, are transcribed by RNA polymerase III." [GOC:mah, GOC:txnOH]
comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation.
synonym: "transcription initiation from Pol III promoter" EXACT []
synonym: "transcription initiation from RNA polymerase III hybrid type promoter" NARROW []
+synonym: "transcription initiation from RNA polymerase III promoter" EXACT []
synonym: "transcription initiation from RNA polymerase III type 1 promoter" NARROW []
synonym: "transcription initiation from RNA polymerase III type 2 promoter" NARROW []
synonym: "transcription initiation from RNA polymerase III type 3 promoter" NARROW []
-is_a: GO:0006352 ! DNA-templated transcription, initiation
+is_a: GO:0006352 ! DNA-templated transcription initiation
relationship: part_of GO:0006383 ! transcription by RNA polymerase III
[Term]
id: GO:0006385
-name: transcription elongation from RNA polymerase III promoter
+name: transcription elongation by RNA polymerase III
namespace: biological_process
def: "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase III promoter by the addition of ribonucleotides catalyzed by RNA polymerase III." [GOC:mah, GOC:txnOH]
synonym: "RNA elongation from Pol III promoter" EXACT []
synonym: "RNA polymerase III transcription elongation factor activity" RELATED []
-is_a: GO:0006354 ! DNA-templated transcription, elongation
+synonym: "transcription elongation by RNA polymerase III promoter" EXACT []
+synonym: "transcription elongation from RNA polymerase III promoter" EXACT []
+is_a: GO:0006354 ! DNA-templated transcription elongation
relationship: part_of GO:0006383 ! transcription by RNA polymerase III
[Term]
@@ -61339,12 +61394,12 @@ id: GO:0006386
name: termination of RNA polymerase III transcription
namespace: biological_process
alt_id: GO:0019225
-def: "The process in which transcription by RNA polymerase III is terminated; Pol III has an intrinsic ability to terminate transcription upon incorporation of 4 to 6 contiguous U residues." [GOC:mah, PMID:12944462]
+def: "A transcription termination process that completes the production of a primary RNA polymerase II transcript. RNA polymerase III has an intrinsic ability to terminate transcription upon incorporation of at least 4 contiguous U residues." [GOC:mah, PMID:12944462, PMID:27371117]
synonym: "RNA polymerase III transcription termination" EXACT []
synonym: "RNA polymerase III transcription termination factor activity" RELATED []
synonym: "transcription termination from Pol III promoter" EXACT []
synonym: "transcription termination from RNA polymerase III promoter" EXACT []
-is_a: GO:0006353 ! DNA-templated transcription, termination
+is_a: GO:0006353 ! DNA-templated transcription termination
relationship: part_of GO:0006383 ! transcription by RNA polymerase III
[Term]
@@ -61381,40 +61436,42 @@ consider: GO:0006388
id: GO:0006390
name: mitochondrial transcription
namespace: biological_process
-def: "The synthesis of RNA from a mitochondrial DNA template, usually by a specific mitochondrial RNA polymerase." [GOC:jl]
+def: "The synthesis of RNA from a mitochondrial DNA template, usually by a specific mitochondrial RNA polymerase." [GOC:jl, PMID:23632312]
synonym: "transcription from mitochondrial promoter" EXACT []
is_a: GO:0000959 ! mitochondrial RNA metabolic process
-is_a: GO:0006351 ! transcription, DNA-templated
+is_a: GO:0006351 ! DNA-templated transcription
relationship: part_of GO:0140053 ! mitochondrial gene expression
[Term]
id: GO:0006391
-name: transcription initiation from mitochondrial promoter
+name: transcription initiation at mitochondrial promoter
namespace: biological_process
-def: "A transcription initiation process that takes place at a promoter on the mitochondrial chromosome, and results in RNA synthesis by a mitochondrial RNA polymerase." [GOC:mah]
+def: "A transcription initiation process that takes place at a promoter on the mitochondrial chromosome." [PMID:33127643]
+synonym: "transcription initiation from mitochondrial promoter" EXACT []
is_a: GO:0000959 ! mitochondrial RNA metabolic process
-is_a: GO:0006352 ! DNA-templated transcription, initiation
+is_a: GO:0006352 ! DNA-templated transcription initiation
relationship: part_of GO:0006390 ! mitochondrial transcription
[Term]
id: GO:0006392
-name: transcription elongation from mitochondrial promoter
+name: transcription elongation by mitochondrial RNA polymerase
namespace: biological_process
def: "The extension of an RNA molecule after transcription initiation and promoter clearance at mitochondrial promoter by the addition of ribonucleotides catalyzed by a mitchondrial RNA polymerase." [GOC:mah, GOC:txnOH]
synonym: "RNA elongation from mitochondrial promoter" EXACT []
+synonym: "transcription elongation from mitochondrial promoter" EXACT []
is_a: GO:0000959 ! mitochondrial RNA metabolic process
-is_a: GO:0006354 ! DNA-templated transcription, elongation
+is_a: GO:0006354 ! DNA-templated transcription elongation
relationship: part_of GO:0006390 ! mitochondrial transcription
[Term]
id: GO:0006393
name: termination of mitochondrial transcription
namespace: biological_process
-def: "The process in which the synthesis of an RNA molecule using a mitochondrial DNA template is completed." [GOC:mah]
+def: "A transcription termination process that completes the production of a primary mitochondrial transcript." [PMID:29945721]
synonym: "mitochondrial transcription termination" EXACT []
synonym: "RNA transcription termination from mitochondrial promoter" EXACT []
is_a: GO:0000959 ! mitochondrial RNA metabolic process
-is_a: GO:0006353 ! DNA-templated transcription, termination
+is_a: GO:0006353 ! DNA-templated transcription termination
relationship: part_of GO:0006390 ! mitochondrial transcription
[Term]
@@ -61481,9 +61538,9 @@ subset: goslim_yeast
synonym: "RNA breakdown" EXACT []
synonym: "RNA catabolism" EXACT []
synonym: "RNA degradation" EXACT []
+is_a: GO:0009057 ! macromolecule catabolic process
is_a: GO:0016070 ! RNA metabolic process
is_a: GO:0034655 ! nucleobase-containing compound catabolic process
-is_a: GO:0044265 ! cellular macromolecule catabolic process
[Term]
id: GO:0006402
@@ -61598,13 +61655,13 @@ alt_id: GO:0006416
alt_id: GO:0006453
alt_id: GO:0043037
def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
+subset: prokaryote_subset
synonym: "protein anabolism" EXACT []
synonym: "protein biosynthesis" EXACT []
synonym: "protein biosynthetic process" EXACT []
@@ -61612,9 +61669,9 @@ synonym: "protein formation" EXACT []
synonym: "protein synthesis" EXACT []
synonym: "protein translation" EXACT []
xref: Wikipedia:Translation_(genetics)
-is_a: GO:0034645 ! cellular macromolecule biosynthetic process
+is_a: GO:0009059 ! macromolecule biosynthetic process
+is_a: GO:0019538 ! protein metabolic process
is_a: GO:0043043 ! peptide biosynthetic process
-is_a: GO:0044267 ! cellular protein metabolic process
relationship: part_of GO:0010467 ! gene expression
[Term]
@@ -61642,7 +61699,7 @@ def: "The successive addition of amino acid residues to a nascent polypeptide ch
subset: goslim_yeast
synonym: "protein synthesis elongation" BROAD []
synonym: "translation elongation" EXACT []
-is_a: GO:0034645 ! cellular macromolecule biosynthetic process
+is_a: GO:0009059 ! macromolecule biosynthetic process
relationship: part_of GO:0006412 ! translation
[Term]
@@ -61669,17 +61726,18 @@ synonym: "regulation of protein anabolism" EXACT []
synonym: "regulation of protein biosynthesis" EXACT []
synonym: "regulation of protein formation" EXACT []
synonym: "regulation of protein synthesis" EXACT []
-is_a: GO:0010608 ! posttranscriptional regulation of gene expression
-is_a: GO:0032268 ! regulation of cellular protein metabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
+is_a: GO:0010556 ! regulation of macromolecule biosynthetic process
+is_a: GO:0010608 ! post-transcriptional regulation of gene expression
+is_a: GO:0031326 ! regulation of cellular biosynthetic process
+is_a: GO:0034248 ! regulation of amide metabolic process
+is_a: GO:0051246 ! regulation of protein metabolic process
relationship: regulates GO:0006412 ! translation
[Term]
id: GO:0006418
name: tRNA aminoacylation for protein translation
namespace: biological_process
-def: "The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, to be used in ribosome-mediated polypeptide synthesis." [GOC:ma]
+def: "The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, to be used in ribosome-mediated polypeptide synthesis." [GOC:ma]
subset: goslim_yeast
synonym: "tRNA charging" NARROW []
xref: MetaCyc:TRNA-CHARGING-PWY
@@ -61690,126 +61748,126 @@ relationship: part_of GO:0006412 ! translation
id: GO:0006419
name: alanyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling alanine to alanyl-tRNA, catalyzed by alanyl-tRNA synthetase. The alanyl-tRNA synthetase is a class-II synthetases. The activated amino acid is transferred to the 3'-OH group of an alanine accetping tRNA." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling alanine to alanyl-tRNA, catalyzed by alanyl-tRNA synthetase. The alanyl-tRNA synthetase is a class-II synthetases. The activated amino acid is transferred to the 3'-OH group of an alanine accetping tRNA." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006420
name: arginyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling arginine to arginyl-tRNA, catalyzed by arginyl-tRNA synthetase. The arginyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of an alanine accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling arginine to arginyl-tRNA, catalyzed by arginyl-tRNA synthetase. The arginyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of an alanine accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006421
name: asparaginyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling asparagine to asparaginyl-tRNA, catalyzed by asparaginyl-tRNA synthetase. The asparaginyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an asparagine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling asparagine to asparaginyl-tRNA, catalyzed by asparaginyl-tRNA synthetase. The asparaginyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an asparagine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006422
name: aspartyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling aspartate to aspartyl-tRNA, catalyzed by aspartyl-tRNA synthetase. The aspartyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an aspartic acid accetping tRNA." [GOC:mah, ISBN:0716730510]
+def: "The process of coupling aspartate to aspartyl-tRNA, catalyzed by aspartyl-tRNA synthetase. The aspartyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an aspartic acid accetping tRNA." [GOC:mah, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006423
name: cysteinyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling cysteine to cysteinyl-tRNA, catalyzed by cysteinyl-tRNA synthetase. A cysteinyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a cysteine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling cysteine to cysteinyl-tRNA, catalyzed by cysteinyl-tRNA synthetase. A cysteinyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a cysteine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006424
name: glutamyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling glutamate to glutamyl-tRNA, catalyzed by glutamyl-tRNA synthetase. The glutamyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a glutamic acid-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling glutamate to glutamyl-tRNA, catalyzed by glutamyl-tRNA synthetase. The glutamyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a glutamic acid-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006425
name: glutaminyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling glutamine to glutaminyl-tRNA, catalyzed by glutaminyl-tRNA synthetase. The glutaminyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a glutamine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling glutamine to glutaminyl-tRNA, catalyzed by glutaminyl-tRNA synthetase. The glutaminyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a glutamine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006426
name: glycyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-tRNA synthetase. The glycyll-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a glycine-accepting tRNA." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-tRNA synthetase. The glycyll-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a glycine-accepting tRNA." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006427
name: histidyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. The histidyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3''-OH group of a histidine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. The histidyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3''-OH group of a histidine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006428
name: isoleucyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling isoleucine to isoleucyl-tRNA, catalyzed by isoleucyl-tRNA synthetase. The isoleucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a isoleucine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling isoleucine to isoleucyl-tRNA, catalyzed by isoleucyl-tRNA synthetase. The isoleucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a isoleucine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006429
name: leucyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling leucine to leucyl-tRNA, catalyzed by leucyl-tRNA synthetase. The leucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a leucine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling leucine to leucyl-tRNA, catalyzed by leucyl-tRNA synthetase. The leucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a leucine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006430
name: lysyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling lysine to lysyl-tRNA, catalyzed by lysyl-tRNA synthetase. The lysyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a lysine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling lysine to lysyl-tRNA, catalyzed by lysyl-tRNA synthetase. The lysyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a lysine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006431
name: methionyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-tRNA synthetase. The methionyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a methionine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-tRNA synthetase. The methionyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a methionine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006432
name: phenylalanyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. The phenylalanyl-tRNA synthetase is a class-II synthetase. However, unlike other class II enzymes, The activated amino acid is transferred to the 2'-OH group of a phenylalanine-accepting tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. The phenylalanyl-tRNA synthetase is a class-II synthetase. However, unlike other class II enzymes, The activated amino acid is transferred to the 2'-OH group of a phenylalanine-accepting tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006433
name: prolyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling proline to prolyl-tRNA, catalyzed by prolyl-tRNA synthetase. The prolyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a methionine-accetping tRNA." [GOC:mah, ISBN:0716730510]
+def: "The process of coupling proline to prolyl-tRNA, catalyzed by prolyl-tRNA synthetase. The prolyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a methionine-accetping tRNA." [GOC:mah, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006434
name: seryl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling serine to seryl-tRNA, catalyzed by seryl-tRNA synthetase. The seryl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a serine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling serine to seryl-tRNA, catalyzed by seryl-tRNA synthetase. The seryl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a serine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006435
name: threonyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling threonine to threonyl-tRNA, catalyzed by threonyl-tRNA synthetase. The threonyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a threonine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling threonine to threonyl-tRNA, catalyzed by threonyl-tRNA synthetase. The threonyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a threonine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
id: GO:0006436
name: tryptophanyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-tRNA synthetase. The tryptophanyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tryptophan-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-tRNA synthetase. The tryptophanyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tryptophan-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
@@ -61823,7 +61881,7 @@ is_a: GO:0006418 ! tRNA aminoacylation for protein translation
id: GO:0006438
name: valyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling valine to valyl-tRNA, catalyzed by valyl-tRNA synthetase. The valyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a valine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling valine to valyl-tRNA, catalyzed by valyl-tRNA synthetase. The valyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a valine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
@@ -61912,7 +61970,6 @@ alt_id: GO:0007022
alt_id: GO:0007024
alt_id: GO:0007025
def: "The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure." [GOC:go_curators, GOC:rb]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -61921,6 +61978,7 @@ subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "alpha-tubulin folding" NARROW [GOC:mah]
synonym: "beta-tubulin folding" NARROW [GOC:mah]
synonym: "chaperone activity" RELATED []
@@ -61981,22 +62039,6 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a steroid hormone receptor complex, an intracellular receptor that binds steroid hormones. The complex is often a dimer, and forms after the steroid has bound the receptor." [GOC:jl, Wikipedia:Steroid_hormone_receptor]
is_a: GO:0065003 ! protein-containing complex assembly
-[Term]
-id: GO:0006464
-name: cellular protein modification process
-namespace: biological_process
-def: "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:go_curators]
-subset: goslim_aspergillus
-subset: goslim_candida
-subset: goslim_chembl
-subset: goslim_pir
-subset: goslim_plant
-synonym: "process resulting in protein modification" RELATED []
-synonym: "protein modification process" BROAD [GOC:bf, GOC:jl]
-synonym: "protein tagging activity" RELATED []
-is_a: GO:0036211 ! protein modification process
-is_a: GO:0044267 ! cellular protein metabolic process
-
[Term]
id: GO:0006465
name: signal peptide processing
@@ -62005,7 +62047,6 @@ def: "The proteolytic removal of a signal peptide from a protein during or after
synonym: "leader peptide processing" EXACT []
is_a: GO:0006518 ! peptide metabolic process
is_a: GO:0016485 ! protein processing
-is_a: GO:0044267 ! cellular protein metabolic process
[Term]
id: GO:0006466
@@ -62025,8 +62066,8 @@ namespace: biological_process
def: "The process of introducing a phosphate group on to a protein." [GOC:hb]
subset: goslim_yeast
synonym: "protein amino acid phosphorylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
is_a: GO:0016310 ! phosphorylation
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0006469
@@ -62048,14 +62089,15 @@ namespace: biological_process
def: "The process of removing one or more phosphoric residues from a protein." [GOC:hb]
subset: goslim_yeast
synonym: "protein amino acid dephosphorylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
is_a: GO:0016311 ! dephosphorylation
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0006471
-name: protein ADP-ribosylation
+name: obsolete protein ADP-ribosylation
namespace: biological_process
-def: "The transfer, from NAD, of ADP-ribose to protein amino acids." [GOC:pr, RESID:AA0040, RESID:AA0168, RESID:AA0169, RESID:AA0231, RESID:AA0237, RESID:AA0295]
+def: "OBSOLETE. The transfer, from NAD, of ADP-ribose to protein amino acids." [GOC:pr, RESID:AA0040, RESID:AA0168, RESID:AA0169, RESID:AA0231, RESID:AA0237, RESID:AA0295]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "protein amino acid ADP-ribosylation" EXACT [GOC:bf]
xref: RESID:AA0040
xref: RESID:AA0168
@@ -62063,7 +62105,8 @@ xref: RESID:AA0169
xref: RESID:AA0231
xref: RESID:AA0237
xref: RESID:AA0295
-is_a: GO:0006464 ! cellular protein modification process
+is_obsolete: true
+consider: GO:1990404
[Term]
id: GO:0006473
@@ -62105,7 +62148,7 @@ namespace: biological_process
def: "The addition of a sulfate group as an ester to a protein amino acid." [GOC:curators]
synonym: "protein amino acid sulfation" EXACT [GOC:bf]
synonym: "protein amino acid sulphation" EXACT []
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
is_a: GO:0051923 ! sulfation
[Term]
@@ -62162,8 +62205,8 @@ comment: This term was made obsolete because it is a redundant grouping term.
synonym: "aspartic acid/asparagine hydroxylation" EXACT []
synonym: "peptidyl-aspartic acid/asparagine hydroxylation" EXACT []
is_obsolete: true
-consider: GO:0042264
-consider: GO:0042265
+consider: GO:0036140
+consider: GO:0062101
[Term]
id: GO:0006484
@@ -62184,9 +62227,10 @@ def: "A protein modification process that results in the addition of a carbohydr
subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "protein amino acid glycosylation" EXACT [GOC:bf]
synonym: "protein-carbohydrate complex assembly" RELATED []
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
is_a: GO:0043413 ! macromolecule glycosylation
relationship: part_of GO:0009101 ! glycoprotein biosynthetic process
@@ -62216,6 +62260,7 @@ synonym: "N-linked glycan precursor biosynthesis" EXACT [PMID:8666161]
synonym: "N-linked glycan precursor biosynthetic process" EXACT [PMID:8666161]
synonym: "oligosaccharide-PP-dolichol assembly" EXACT []
is_a: GO:0006490 ! oligosaccharide-lipid intermediate biosynthetic process
+is_a: GO:0019348 ! dolichol metabolic process
relationship: part_of GO:0006487 ! protein N-linked glycosylation
[Term]
@@ -62328,7 +62373,7 @@ xref: RESID:AA0307
xref: RESID:AA0308
xref: RESID:AA0309
xref: RESID:AA0316
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
relationship: part_of GO:0042158 ! lipoprotein biosynthetic process
[Term]
@@ -62529,7 +62574,7 @@ synonym: "misfolded or incompletely synthesized protein catabolism" EXACT []
synonym: "misfolded or incompletely synthesized protein degradation" EXACT []
synonym: "protein quality control (PQC)" EXACT []
synonym: "protein quality control by the ubiquitin-proteasome system" BROAD []
-is_a: GO:0051603 ! proteolysis involved in cellular protein catabolic process
+is_a: GO:0051603 ! proteolysis involved in protein catabolic process
[Term]
id: GO:0006516
@@ -62541,7 +62586,6 @@ synonym: "glycoprotein catabolism" EXACT []
synonym: "glycoprotein degradation" EXACT []
is_a: GO:0009100 ! glycoprotein metabolic process
is_a: GO:0030163 ! protein catabolic process
-is_a: GO:0044265 ! cellular macromolecule catabolic process
is_a: GO:1901136 ! carbohydrate derivative catabolic process
[Term]
@@ -62550,8 +62594,8 @@ name: protein deglycosylation
namespace: biological_process
def: "The removal of sugar residues from a glycosylated protein." [GOC:mah]
synonym: "glycoprotein deglycosylation" EXACT []
-is_a: GO:0006464 ! cellular protein modification process
is_a: GO:0009100 ! glycoprotein metabolic process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0006518
@@ -62560,25 +62604,25 @@ namespace: biological_process
def: "The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." [GOC:go_curators]
subset: goslim_pir
synonym: "peptide metabolism" EXACT []
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
id: GO:0006520
-name: cellular amino acid metabolic process
+name: amino acid metabolic process
namespace: biological_process
alt_id: GO:0006519
-def: "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells." [ISBN:0198506732]
-subset: goslim_aspergillus
+def: "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups." [ISBN:0198506732]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
-synonym: "amino acid and derivative metabolism" EXACT []
-synonym: "amino acid metabolic process" EXACT []
-synonym: "cellular amino acid and derivative metabolic process" EXACT []
+subset: prokaryote_subset
+synonym: "amino acid and derivative metabolism" RELATED []
+synonym: "cellular amino acid and derivative metabolic process" RELATED []
+synonym: "cellular amino acid metabolic process" EXACT []
synonym: "cellular amino acid metabolism" EXACT []
is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0044238 ! primary metabolic process
@@ -62591,9 +62635,9 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids." [GOC:go_curators]
synonym: "regulation of amino acid metabolism" EXACT []
is_a: GO:0010565 ! regulation of cellular ketone metabolic process
-is_a: GO:0033238 ! regulation of cellular amine metabolic process
+is_a: GO:0033238 ! regulation of amine metabolic process
is_a: GO:0080090 ! regulation of primary metabolic process
-relationship: regulates GO:0006520 ! cellular amino acid metabolic process
+relationship: regulates GO:0006520 ! amino acid metabolic process
[Term]
id: GO:0006522
@@ -62624,7 +62668,6 @@ synonym: "alanine breakdown" EXACT []
synonym: "alanine catabolism" EXACT []
synonym: "alanine degradation" EXACT []
is_a: GO:0006522 ! alanine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009080 ! pyruvate family amino acid catabolic process
[Term]
@@ -62660,7 +62703,6 @@ synonym: "arginine breakdown" EXACT []
synonym: "arginine catabolism" EXACT []
synonym: "arginine degradation" EXACT []
is_a: GO:0006525 ! arginine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009065 ! glutamine family amino acid catabolic process
[Term]
@@ -62693,7 +62735,6 @@ synonym: "asparagine breakdown" EXACT []
synonym: "asparagine catabolism" EXACT []
synonym: "asparagine degradation" EXACT []
is_a: GO:0006528 ! asparagine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009065 ! glutamine family amino acid catabolic process
is_a: GO:0009068 ! aspartate family amino acid catabolic process
@@ -62728,7 +62769,6 @@ synonym: "aspartate breakdown" EXACT []
synonym: "aspartate catabolism" EXACT []
synonym: "aspartate degradation" EXACT []
is_a: GO:0006531 ! aspartate metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009068 ! aspartate family amino acid catabolic process
is_a: GO:0043649 ! dicarboxylic acid catabolic process
@@ -62764,6 +62804,7 @@ synonym: "glutamic acid metabolic process" EXACT []
synonym: "glutamic acid metabolism" EXACT []
xref: Wikipedia:Glutamic_acid
is_a: GO:0009064 ! glutamine family amino acid metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0043648 ! dicarboxylic acid metabolic process
[Term]
@@ -62783,6 +62824,7 @@ synonym: "glutamic acid biosynthesis" EXACT []
synonym: "glutamic acid biosynthetic process" EXACT []
is_a: GO:0006536 ! glutamate metabolic process
is_a: GO:0009084 ! glutamine family amino acid biosynthetic process
+is_a: GO:0043604 ! amide biosynthetic process
is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
[Term]
@@ -62798,7 +62840,6 @@ synonym: "glutamate degradation" EXACT []
synonym: "glutamic acid catabolic process" EXACT []
synonym: "glutamic acid catabolism" EXACT []
is_a: GO:0006536 ! glutamate metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009065 ! glutamine family amino acid catabolic process
is_a: GO:0043649 ! dicarboxylic acid catabolic process
@@ -62866,7 +62907,6 @@ synonym: "glutamine breakdown" EXACT []
synonym: "glutamine catabolism" EXACT []
synonym: "glutamine degradation" EXACT []
is_a: GO:0006541 ! glutamine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009065 ! glutamine family amino acid catabolic process
[Term]
@@ -62899,7 +62939,6 @@ synonym: "glycine breakdown" EXACT []
synonym: "glycine catabolism" EXACT []
synonym: "glycine degradation" EXACT []
is_a: GO:0006544 ! glycine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009071 ! serine family amino acid catabolic process
[Term]
@@ -62909,7 +62948,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid." [GOC:go_curators]
synonym: "histidine metabolism" EXACT []
xref: Wikipedia:Histidine
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
[Term]
id: GO:0006548
@@ -62920,7 +62959,7 @@ synonym: "histidine breakdown" EXACT []
synonym: "histidine catabolism" EXACT []
synonym: "histidine degradation" EXACT []
is_a: GO:0006547 ! histidine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
[Term]
id: GO:0006549
@@ -62984,7 +63023,6 @@ synonym: "lysine breakdown" EXACT []
synonym: "lysine catabolism" EXACT []
synonym: "lysine degradation" EXACT []
is_a: GO:0006553 ! lysine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009068 ! aspartate family amino acid catabolic process
[Term]
@@ -63018,17 +63056,17 @@ is_a: GO:1901576 ! organic substance biosynthetic process
[Term]
id: GO:0006557
-name: S-adenosylmethioninamine biosynthetic process
+name: obsolete S-adenosylmethioninamine biosynthetic process
namespace: biological_process
alt_id: GO:0006745
-def: "The chemical reactions and pathways resulting in the formation of S-adenosylmethioninamine, (5-deoxy-5-adenosyl)(3-aminopropyl) methylsulfonium salt." [GOC:mah, MetaCyc:S-ADENOSYLMETHIONINAMINE]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of S-adenosylmethioninamine, (5-deoxy-5-adenosyl)(3-aminopropyl) methylsulfonium salt." [GOC:mah, MetaCyc:S-ADENOSYLMETHIONINAMINE]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "S-adenosylmethioninamine anabolism" EXACT []
synonym: "S-adenosylmethioninamine biosynthesis" EXACT []
synonym: "S-adenosylmethioninamine formation" EXACT []
synonym: "S-adenosylmethioninamine synthesis" EXACT []
-is_a: GO:0044272 ! sulfur compound biosynthetic process
-is_a: GO:0046129 ! purine ribonucleoside biosynthetic process
-is_a: GO:0046499 ! S-adenosylmethioninamine metabolic process
+is_obsolete: true
+consider: GO:0004014
[Term]
id: GO:0006558
@@ -63038,7 +63076,7 @@ def: "The chemical reactions and pathways involving L-phenylalanine, the L-enant
synonym: "L-phenylalanine metabolism" EXACT []
synonym: "phenylalanine metabolic process" BROAD []
synonym: "phenylalanine metabolism" BROAD []
-is_a: GO:0009072 ! aromatic amino acid family metabolic process
+is_a: GO:0009072 ! aromatic amino acid metabolic process
is_a: GO:1902221 ! erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process
[Term]
@@ -63052,7 +63090,6 @@ synonym: "L-phenylalanine degradation" EXACT []
synonym: "phenylalanine catabolic process" BROAD []
synonym: "phenylalanine catabolism" BROAD []
is_a: GO:0006558 ! L-phenylalanine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009074 ! aromatic amino acid family catabolic process
is_a: GO:1902222 ! erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process
@@ -63087,7 +63124,6 @@ synonym: "proline breakdown" EXACT []
synonym: "proline catabolism" EXACT []
synonym: "proline degradation" EXACT []
is_a: GO:0006560 ! proline metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009065 ! glutamine family amino acid catabolic process
[Term]
@@ -63121,7 +63157,6 @@ synonym: "L-serine catabolism" EXACT []
synonym: "L-serine degradation" EXACT []
xref: MetaCyc:SERDEG-PWY
is_a: GO:0006563 ! L-serine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009071 ! serine family amino acid catabolic process
[Term]
@@ -63146,7 +63181,6 @@ synonym: "threonine degradation" EXACT []
xref: MetaCyc:THREOCAT-PWY
xref: UM-BBD_pathwayID:met
is_a: GO:0006566 ! threonine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009068 ! aspartate family amino acid catabolic process
[Term]
@@ -63157,7 +63191,7 @@ def: "The chemical reactions and pathways involving tryptophan, the chiral amino
synonym: "tryptophan metabolism" EXACT []
xref: Wikipedia:Tryptophan
is_a: GO:0006586 ! indolalkylamine metabolic process
-is_a: GO:0009072 ! aromatic amino acid family metabolic process
+is_a: GO:0009072 ! aromatic amino acid metabolic process
is_a: GO:1901605 ! alpha-amino acid metabolic process
[Term]
@@ -63171,9 +63205,9 @@ synonym: "tryptophan catabolism" EXACT []
synonym: "tryptophan catabolism, using tryptophanase" NARROW []
synonym: "tryptophan degradation" EXACT []
is_a: GO:0006568 ! tryptophan metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0009074 ! aromatic amino acid family catabolic process
-is_a: GO:0046218 ! indolalkylamine catabolic process
+is_a: GO:0042436 ! indole-containing compound catabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
[Term]
@@ -63184,7 +63218,7 @@ def: "The chemical reactions and pathways involving tyrosine, an aromatic amino
synonym: "tyrosine metabolism" EXACT []
xref: UM-BBD_pathwayID:tyr
xref: Wikipedia:Tyrosine
-is_a: GO:0009072 ! aromatic amino acid family metabolic process
+is_a: GO:0009072 ! aromatic amino acid metabolic process
is_a: GO:1901605 ! alpha-amino acid metabolic process
[Term]
@@ -63241,6 +63275,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents." [GOC:ai]
subset: goslim_drosophila
subset: goslim_generic
+subset: prokaryote_subset
synonym: "amino acid derivative metabolic process" EXACT []
synonym: "cellular amino acid derivative metabolic process" EXACT []
synonym: "cellular amino acid derivative metabolism" EXACT []
@@ -63252,11 +63287,12 @@ is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
id: GO:0006576
-name: cellular biogenic amine metabolic process
+name: biogenic amine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways occurring at the level of individual cells involving any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters." [GOC:jl, ISBN:0395825172]
synonym: "biogenic amine metabolism" EXACT []
-is_a: GO:0044106 ! cellular amine metabolic process
+synonym: "cellular biogenic amine metabolic process" EXACT []
+is_a: GO:0009308 ! amine metabolic process
[Term]
id: GO:0006577
@@ -63316,7 +63352,7 @@ synonym: "acetylcholine catabolism" EXACT []
synonym: "acetylcholine degradation" EXACT []
is_a: GO:0008291 ! acetylcholine metabolic process
is_a: GO:0042135 ! neurotransmitter catabolic process
-is_a: GO:1901575 ! organic substance catabolic process
+is_a: GO:1901565 ! organonitrogen compound catabolic process
[Term]
id: GO:0006582
@@ -63345,7 +63381,7 @@ name: catecholamine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." [GOC:jl, ISBN:0198506732]
synonym: "catecholamine metabolism" EXACT []
-is_a: GO:0006576 ! cellular biogenic amine metabolic process
+is_a: GO:0006576 ! biogenic amine metabolic process
is_a: GO:0009712 ! catechol-containing compound metabolic process
[Term]
@@ -63367,7 +63403,7 @@ def: "The chemical reactions and pathways involving indolalkylamines, indole or
synonym: "indolalkylamine metabolism" EXACT []
synonym: "indolamine metabolic process" BROAD []
synonym: "indolamine metabolism" BROAD []
-is_a: GO:0006576 ! cellular biogenic amine metabolic process
+is_a: GO:0006576 ! biogenic amine metabolic process
is_a: GO:0042430 ! indole-containing compound metabolic process
[Term]
@@ -63383,12 +63419,12 @@ is_a: GO:0042427 ! serotonin biosynthetic process
[Term]
id: GO:0006588
-name: activation of tryptophan 5-monooxygenase activity
+name: obsolete activation of tryptophan 5-monooxygenase activity
namespace: biological_process
-def: "The process in which the tryptophan 5-monooxygenase enzyme is changed so that it can carry out its enzymatic activity." [GOC:dph, GOC:tb]
+def: "OBSOLETE. The process in which the tryptophan 5-monooxygenase enzyme is changed so that it can carry out its enzymatic activity." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "tryptophan hydroxylase activation" RELATED [GOC:dph, GOC:tb]
-is_a: GO:0032770 ! positive regulation of monooxygenase activity
-relationship: part_of GO:0006587 ! serotonin biosynthetic process from tryptophan
+is_obsolete: true
[Term]
id: GO:0006589
@@ -63400,7 +63436,7 @@ synonym: "octopamine biosynthesis" EXACT []
synonym: "octopamine formation" EXACT []
synonym: "octopamine synthesis" EXACT []
is_a: GO:0042136 ! neurotransmitter biosynthetic process
-is_a: GO:0042401 ! cellular biogenic amine biosynthetic process
+is_a: GO:0042401 ! biogenic amine biosynthetic process
is_a: GO:0046165 ! alcohol biosynthetic process
is_a: GO:0046189 ! phenol-containing compound biosynthetic process
is_a: GO:0046333 ! octopamine metabolic process
@@ -63442,7 +63478,7 @@ synonym: "ornithine breakdown" EXACT []
synonym: "ornithine catabolism" EXACT []
synonym: "ornithine degradation" EXACT []
is_a: GO:0006591 ! ornithine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
[Term]
@@ -63452,7 +63488,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving polyamines, any organic compound containing two or more amino groups." [ISBN:0198506732]
subset: goslim_drosophila
synonym: "polyamine metabolism" EXACT []
-is_a: GO:0006576 ! cellular biogenic amine metabolic process
+is_a: GO:0006576 ! biogenic amine metabolic process
[Term]
id: GO:0006596
@@ -63465,7 +63501,7 @@ synonym: "polyamine formation" EXACT []
synonym: "polyamine synthesis" EXACT []
xref: MetaCyc:POLYAMSYN-PWY
is_a: GO:0006595 ! polyamine metabolic process
-is_a: GO:0042401 ! cellular biogenic amine biosynthetic process
+is_a: GO:0042401 ! biogenic amine biosynthetic process
[Term]
id: GO:0006597
@@ -63531,7 +63567,7 @@ synonym: "creatinine breakdown" EXACT []
synonym: "creatinine catabolism" EXACT []
synonym: "creatinine degradation" EXACT []
is_a: GO:0046449 ! creatinine metabolic process
-is_a: GO:0072340 ! cellular lactam catabolic process
+is_a: GO:0072340 ! lactam catabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
@@ -63576,7 +63612,6 @@ synonym: "protein import into cell nucleus" EXACT []
synonym: "protein nucleus import" EXACT []
synonym: "protein transport from cytoplasm to nucleus" EXACT []
is_a: GO:0006886 ! intracellular protein transport
-is_a: GO:0017038 ! protein import
is_a: GO:0034504 ! protein localization to nucleus
is_a: GO:0051170 ! import into nucleus
is_a: GO:0072594 ! establishment of protein localization to organelle
@@ -63730,12 +63765,13 @@ is_obsolete: true
[Term]
id: GO:0006620
-name: posttranslational protein targeting to endoplasmic reticulum membrane
+name: post-translational protein targeting to endoplasmic reticulum membrane
namespace: biological_process
def: "The targeting of proteins to a membrane that occurs after their translation. Some secretory proteins exhibit posttranslational transport into the endoplasmic reticulum (ER) lumen: they are synthesized in their entirety on free cytosolic ribosomes and then released into the cytosol, where they are bound by chaperones which keep them in an unfolded state, and subsequently are translocated across the ER membrane." [ISBN:0716731363]
synonym: "posttranslational endoplasmic reticulum membrane targeting" EXACT []
synonym: "posttranslational endoplasmic reticulum protein-membrane targeting" EXACT []
synonym: "posttranslational protein endoplasmic reticulum membrane targeting" EXACT []
+synonym: "posttranslational protein targeting to endoplasmic reticulum membrane" EXACT []
synonym: "posttranslational protein targeting to ER membrane" EXACT []
synonym: "SRP-independent endoplasmic reticulum protein-membrane targeting" EXACT []
is_a: GO:0006612 ! protein targeting to membrane
@@ -63780,7 +63816,6 @@ def: "Protein processing that takes place in the vacuole. Most protein processin
synonym: "vacuolar protein maturation" RELATED []
synonym: "vacuolar proteolysis" RELATED []
is_a: GO:0016485 ! protein processing
-is_a: GO:0044267 ! cellular protein metabolic process
[Term]
id: GO:0006625
@@ -63834,7 +63869,6 @@ name: lipid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids." [GOC:ma]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -63845,6 +63879,7 @@ subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "lipid metabolism" EXACT []
xref: Wikipedia:Lipid_metabolism
is_a: GO:0044238 ! primary metabolic process
@@ -63936,7 +63971,7 @@ is_a: GO:0009150 ! purine ribonucleotide metabolic process
is_a: GO:0033875 ! ribonucleoside bisphosphate metabolic process
is_a: GO:0034032 ! purine nucleoside bisphosphate metabolic process
is_a: GO:0035383 ! thioester metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
[Term]
id: GO:0006638
@@ -64081,8 +64116,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving any 1,2-diacyl-sn-glycero-3-phosphocholine, the compounds most commonly designated lecithin." [ISBN:0198506732]
synonym: "1,2-diacyl-sn-glycero-3-phosphocholine metabolism" EXACT [GOC:mah]
synonym: "lecithin metabolic process" BROAD []
-is_a: GO:0006807 ! nitrogen compound metabolic process
-is_a: GO:0071704 ! organic substance metabolic process
+is_a: GO:0046470 ! phosphatidylcholine metabolic process
[Term]
id: GO:0006654
@@ -64302,7 +64336,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving ceramides, any N-acylated sphingoid." [ISBN:0198547684]
synonym: "ceramide metabolism" EXACT []
is_a: GO:0006665 ! sphingolipid metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
[Term]
id: GO:0006673
@@ -64424,7 +64458,7 @@ def: "The chemical reactions and pathways involving sphingomyelin, N-acyl-4-sphi
synonym: "sphingomyelin metabolism" EXACT []
is_a: GO:0006644 ! phospholipid metabolic process
is_a: GO:0006665 ! sphingolipid metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
[Term]
id: GO:0006685
@@ -64561,7 +64595,6 @@ synonym: "ergosterol synthesis" EXACT []
is_a: GO:0008204 ! ergosterol metabolic process
is_a: GO:0016126 ! sterol biosynthetic process
is_a: GO:0016129 ! phytosteroid biosynthetic process
-is_a: GO:0044108 ! cellular alcohol biosynthetic process
is_a: GO:0097384 ! cellular lipid biosynthetic process
is_a: GO:1902653 ! secondary alcohol biosynthetic process
@@ -64613,6 +64646,7 @@ synonym: "C21-steroid hormone biosynthesis" EXACT []
synonym: "C21-steroid hormone formation" EXACT []
synonym: "C21-steroid hormone synthesis" EXACT []
is_a: GO:0008207 ! C21-steroid hormone metabolic process
+is_a: GO:0042446 ! hormone biosynthetic process
is_a: GO:0044249 ! cellular biosynthetic process
is_a: GO:0120178 ! steroid hormone biosynthetic process
@@ -64640,7 +64674,7 @@ synonym: "androgen biosynthesis" EXACT []
synonym: "androgen formation" EXACT []
synonym: "androgen synthesis" EXACT []
is_a: GO:0008209 ! androgen metabolic process
-is_a: GO:0044249 ! cellular biosynthetic process
+is_a: GO:0042446 ! hormone biosynthetic process
is_a: GO:0120178 ! steroid hormone biosynthetic process
[Term]
@@ -64655,7 +64689,7 @@ synonym: "estrogen synthesis" EXACT []
synonym: "oestrogen biosynthesis" EXACT []
synonym: "oestrogen biosynthetic process" EXACT []
is_a: GO:0008210 ! estrogen metabolic process
-is_a: GO:0044249 ! cellular biosynthetic process
+is_a: GO:0042446 ! hormone biosynthetic process
is_a: GO:0120178 ! steroid hormone biosynthetic process
[Term]
@@ -64667,8 +64701,8 @@ synonym: "glucocorticoid anabolism" EXACT []
synonym: "glucocorticoid biosynthesis" EXACT []
synonym: "glucocorticoid formation" EXACT []
synonym: "glucocorticoid synthesis" EXACT []
-is_a: GO:0006694 ! steroid biosynthetic process
is_a: GO:0008211 ! glucocorticoid metabolic process
+is_a: GO:0120178 ! steroid hormone biosynthetic process
[Term]
id: GO:0006705
@@ -64680,6 +64714,7 @@ synonym: "mineralocorticoid biosynthesis" EXACT []
synonym: "mineralocorticoid formation" EXACT []
synonym: "mineralocorticoid synthesis" EXACT []
is_a: GO:0008212 ! mineralocorticoid metabolic process
+is_a: GO:0042446 ! hormone biosynthetic process
is_a: GO:0120178 ! steroid hormone biosynthetic process
[Term]
@@ -64810,7 +64845,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:go_curators, ISBN:0198547684]
synonym: "juvenile hormone metabolism" EXACT []
is_a: GO:0006714 ! sesquiterpenoid metabolic process
-is_a: GO:0034754 ! cellular hormone metabolic process
+is_a: GO:0042445 ! hormone metabolic process
[Term]
id: GO:0006717
@@ -65020,7 +65055,7 @@ synonym: "reduced NAD metabolic process" EXACT []
synonym: "reduced NAD metabolism" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide metabolic process" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide metabolism" EXACT []
-is_a: GO:0008152 ! metabolic process
+is_a: GO:0019674 ! NAD metabolic process
[Term]
id: GO:0006735
@@ -65030,8 +65065,7 @@ def: "A metabolic process that generates a pool of NADH by the reduction of NAD+
synonym: "NAD (reduced) regeneration" EXACT []
synonym: "reduced NAD regeneration" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide regeneration" EXACT []
-is_a: GO:0006734 ! NADH metabolic process
-is_a: GO:0019674 ! NAD metabolic process
+is_a: GO:0008152 ! metabolic process
[Term]
id: GO:0006738
@@ -65068,7 +65102,8 @@ synonym: "reduced NADP metabolic process" EXACT []
synonym: "reduced NADP metabolism" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide phosphate metabolic process" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide phosphate metabolism" EXACT []
-is_a: GO:0008152 ! metabolic process
+is_a: GO:0006163 ! purine nucleotide metabolic process
+is_a: GO:0046496 ! nicotinamide nucleotide metabolic process
[Term]
id: GO:0006740
@@ -65106,6 +65141,7 @@ synonym: "reduced NADP biosynthesis" EXACT []
synonym: "reduced NADP biosynthetic process" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide phosphate biosynthesis" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide phosphate biosynthetic process" EXACT []
+is_a: GO:0006164 ! purine nucleotide biosynthetic process
is_a: GO:0006739 ! NADP metabolic process
is_a: GO:0019359 ! nicotinamide nucleotide biosynthetic process
@@ -65133,9 +65169,9 @@ synonym: "reduced NADP catabolic process" EXACT []
synonym: "reduced NADP catabolism" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide phosphate catabolic process" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide phosphate catabolism" EXACT []
+is_a: GO:0006195 ! purine nucleotide catabolic process
is_a: GO:0006739 ! NADP metabolic process
is_a: GO:0019364 ! pyridine nucleotide catabolic process
-is_a: GO:0046496 ! nicotinamide nucleotide metabolic process
[Term]
id: GO:0006743
@@ -65204,7 +65240,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving lipoamide, the functional form of lipoic acid in which the carboxyl group is attached to protein by an amide linkage to a lysine amino group." [GOC:go_curators]
synonym: "lipoamide metabolism" EXACT []
is_a: GO:0006790 ! sulfur compound metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
@@ -65216,9 +65252,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle." [ISBN:0198506732]
synonym: "glutathione metabolism" EXACT []
synonym: "oxidized glutathione reduction" NARROW []
-is_a: GO:0006518 ! peptide metabolic process
-is_a: GO:0006575 ! cellular modified amino acid metabolic process
-is_a: GO:0006790 ! sulfur compound metabolic process
+is_a: GO:0071704 ! organic substance metabolic process
[Term]
id: GO:0006750
@@ -65232,8 +65266,6 @@ synonym: "glutathione synthesis" EXACT []
xref: MetaCyc:GLUTATHIONESYN-PWY
is_a: GO:0006749 ! glutathione metabolic process
is_a: GO:0019184 ! nonribosomal peptide biosynthetic process
-is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
-is_a: GO:0044272 ! sulfur compound biosynthetic process
[Term]
id: GO:0006751
@@ -65244,9 +65276,7 @@ synonym: "glutathione breakdown" EXACT []
synonym: "glutathione catabolism" EXACT []
synonym: "glutathione degradation" EXACT []
is_a: GO:0006749 ! glutathione metabolic process
-is_a: GO:0042219 ! cellular modified amino acid catabolic process
-is_a: GO:0043171 ! peptide catabolic process
-is_a: GO:0044273 ! sulfur compound catabolic process
+is_a: GO:1901575 ! organic substance catabolic process
[Term]
id: GO:0006753
@@ -65294,14 +65324,12 @@ is_a: GO:0046940 ! nucleoside monophosphate phosphorylation
[Term]
id: GO:0006757
-name: ATP generation from ADP
+name: obsolete ATP generation from ADP
namespace: biological_process
-def: "The process of introducing a phosphate group into ADP, adenosine diphosphate, to produce ATP." [GOC:ai]
+def: "OBSOLETE. The process of introducing a phosphate group into ADP, adenosine diphosphate, to produce ATP." [GOC:ai]
+comment: The reason for obsoletion is that this term represents a single step MF.
synonym: "ADP phosphorylation" EXACT [GOC:dph]
-is_a: GO:0006091 ! generation of precursor metabolites and energy
-is_a: GO:0006165 ! nucleoside diphosphate phosphorylation
-is_a: GO:0046031 ! ADP metabolic process
-is_a: GO:0046034 ! ATP metabolic process
+is_obsolete: true
[Term]
id: GO:0006760
@@ -65353,7 +65381,6 @@ id: GO:0006766
name: vitamin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems." [GOC:ai]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_drosophila
subset: goslim_generic
@@ -65385,7 +65412,7 @@ xref: Wikipedia:Biotin
is_a: GO:0006767 ! water-soluble vitamin metabolic process
is_a: GO:0006790 ! sulfur compound metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
@@ -65403,7 +65430,7 @@ synonym: "vitamin B3 metabolism" BROAD []
xref: MetaCyc:PWY-5083
is_a: GO:0006767 ! water-soluble vitamin metabolic process
is_a: GO:0009820 ! alkaloid metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0072524 ! pyridine-containing compound metabolic process
[Term]
@@ -65443,7 +65470,6 @@ comment: This term was made obsolete because it represents a molecular function
synonym: "vitamin B12 reduction" EXACT []
is_obsolete: true
consider: GO:0009235
-consider: GO:0050453
[Term]
id: GO:0006775
@@ -65475,11 +65501,8 @@ synonym: "Moco biosynthesis" EXACT []
synonym: "Moco biosynthetic process" EXACT []
synonym: "molybdenum cofactor biosynthetic process" RELATED []
xref: MetaCyc:PWY-6823
-is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0019720 ! Mo-molybdopterin cofactor metabolic process
-is_a: GO:0090407 ! organophosphate biosynthetic process
-is_a: GO:1901362 ! organic cyclic compound biosynthetic process
-is_a: GO:1901566 ! organonitrogen compound biosynthetic process
+is_a: GO:0032324 ! molybdopterin cofactor biosynthetic process
[Term]
id: GO:0006778
@@ -65577,7 +65600,7 @@ is_a: GO:0046160 ! heme a metabolic process
id: GO:0006785
name: heme B biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of heme B, a Fe(II) porphyrin complex readily isolated from the hemoglobin of beef blood, but also found in other proteins including other hemoglobins, myoglobins, cytochromes P-450, catalases, peroxidases as well as b type cytochromes." [GOC:yaf, PMID:29414780, UniPathway:UPA00252]
+def: "The chemical reactions and pathways resulting in the formation of heme B, a Fe(II) porphyrin complex readily isolated from the hemoglobin of beef blood, but also found in other proteins including other hemoglobins, myoglobins, cytochromes P-450, catalases, peroxidases as well as b type cytochromes." [GOC:yaf, PMID:29414780]
synonym: "haem B biosynthesis" EXACT []
synonym: "haem B biosynthetic process" EXACT []
synonym: "heme B anabolism" EXACT []
@@ -65641,6 +65664,7 @@ subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
+subset: prokaryote_subset
synonym: "sulfur metabolism" EXACT []
synonym: "sulphur metabolic process" EXACT []
synonym: "sulphur metabolism" EXACT []
@@ -65653,7 +65677,7 @@ name: sulfur utilization
namespace: biological_process
def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary sulfur sources and then activates genes to scavenge the last traces of the primary sulfur source and to transport and metabolize alternate sulfur sources. The utilization process begins when the cell or organism detects sulfur levels, includes the activation of genes whose products detect, transport or metabolize sulfur-containing compounds, and ends when the sulfur is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg]
synonym: "sulphur utilization" EXACT []
-is_a: GO:0008150 ! biological_process
+is_a: GO:0031667 ! response to nutrient levels
[Term]
id: GO:0006792
@@ -65661,7 +65685,7 @@ name: regulation of sulfur utilization
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of sulfur utilization." [GOC:go_curators]
synonym: "regulation of sulphur utilization" EXACT []
-is_a: GO:0050789 ! regulation of biological process
+is_a: GO:0032107 ! regulation of response to nutrient levels
relationship: regulates GO:0006791 ! sulfur utilization
[Term]
@@ -65678,14 +65702,14 @@ id: GO:0006794
name: phosphorus utilization
namespace: biological_process
def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary phosphorus source and then activates genes to scavenge the last traces of the primary phosphorus source and to transport and metabolize alternative phosphorus sources. The utilization process begins when the cell or organism detects phosphorus levels, includes the phosphorus-containing substances, and ends when phosphorus is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg]
-is_a: GO:0008150 ! biological_process
+is_a: GO:0006793 ! phosphorus metabolic process
[Term]
id: GO:0006795
name: regulation of phosphorus utilization
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of phosphorus utilization." [GOC:go_curators]
-is_a: GO:0050789 ! regulation of biological process
+is_a: GO:0051174 ! regulation of phosphorus metabolic process
relationship: regulates GO:0006794 ! phosphorus utilization
[Term]
@@ -65833,7 +65857,7 @@ name: regulation of nitrogen utilization
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of nitrogen utilization." [GOC:go_curators]
subset: goslim_metagenomics
-is_a: GO:0050789 ! regulation of biological process
+is_a: GO:0032107 ! regulation of response to nutrient levels
relationship: regulates GO:0019740 ! nitrogen utilization
[Term]
@@ -65855,41 +65879,41 @@ namespace: biological_process
alt_id: GO:0015457
alt_id: GO:0015460
alt_id: GO:0044765
-def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
+def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah]
comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
subset: gocheck_do_not_annotate
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
+subset: prokaryote_subset
synonym: "single-organism transport" RELATED []
-synonym: "small molecule transport" NARROW []
-synonym: "solute:solute exchange" NARROW []
is_a: GO:0051234 ! establishment of localization
[Term]
id: GO:0006811
-name: ion transport
+name: monoatomic ion transport
namespace: biological_process
-def: "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
+def: "The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:ai]
subset: goslim_drosophila
subset: goslim_pir
subset: goslim_yeast
+synonym: "ion transport" BROAD []
is_a: GO:0006810 ! transport
[Term]
id: GO:0006812
-name: cation transport
+name: monoatomic cation transport
namespace: biological_process
alt_id: GO:0006819
alt_id: GO:0015674
alt_id: GO:0072512
-def: "The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
+def: "The directed movement of a monoatomic cation, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom." [GOC:ai]
+synonym: "cation transport" BROAD []
synonym: "di-, tri-valent inorganic cation transport" NARROW [GOC:mah]
synonym: "trivalent inorganic cation transport" NARROW []
-is_a: GO:0006811 ! ion transport
+is_a: GO:0006811 ! monoatomic ion transport
[Term]
id: GO:0006813
@@ -65943,6 +65967,7 @@ synonym: "calcium transport" EXACT []
synonym: "mitochondrial sodium/calcium ion exchange" NARROW []
synonym: "sodium:calcium exchange" NARROW []
is_a: GO:0030001 ! metal ion transport
+is_a: GO:0071702 ! organic substance transport
[Term]
id: GO:0006817
@@ -65954,17 +65979,19 @@ is_a: GO:0015698 ! inorganic anion transport
[Term]
id: GO:0006820
-name: anion transport
+name: monoatomic anion transport
namespace: biological_process
alt_id: GO:0006822
-def: "The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
-is_a: GO:0006811 ! ion transport
+def: "The directed movement of a monoatomic anion, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic anions (also called simple anions) are negatively charged ions consisting of exactly one atom." [GOC:ai]
+synonym: "anion transport" BROAD []
+is_a: GO:0006811 ! monoatomic ion transport
[Term]
id: GO:0006821
name: chloride transport
namespace: biological_process
def: "The directed movement of chloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
+is_a: GO:0006820 ! monoatomic anion transport
is_a: GO:0015698 ! inorganic anion transport
[Term]
@@ -65984,6 +66011,7 @@ namespace: biological_process
def: "The directed movement of cobalt (Co) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "cobalt transport" EXACT []
is_a: GO:0000041 ! transition metal ion transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -66046,6 +66074,7 @@ name: water transport
namespace: biological_process
def: "The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
is_a: GO:0042044 ! fluid transport
+is_a: GO:0071702 ! organic substance transport
[Term]
id: GO:0006835
@@ -66070,7 +66099,6 @@ id: GO:0006837
name: serotonin transport
namespace: biological_process
def: "The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems." [GOC:ai]
-is_a: GO:0006812 ! cation transport
is_a: GO:0015844 ! monoamine transport
is_a: GO:0015850 ! organic hydroxy compound transport
@@ -66122,7 +66150,6 @@ alt_id: GO:1990541
def: "The directed movement of citrate, 2-hydroxy-1,2,3-propanetricarboyxlate, into or out of a mitochondrial matrix." [GOC:ai, PMID:20371607]
synonym: "mitochondrial citrate transport" RELATED []
is_a: GO:0015746 ! citrate transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1990546 ! mitochondrial tricarboxylic acid transmembrane transport
[Term]
@@ -66150,7 +66177,7 @@ name: acetate transport
namespace: biological_process
def: "The directed movement of acetate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
+is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0006847
@@ -66165,7 +66192,6 @@ name: pyruvate transport
namespace: biological_process
def: "The directed movement of pyruvate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
[Term]
id: GO:0006849
@@ -66186,7 +66212,6 @@ synonym: "pyruvate membrane transport in mitochondrion" RELATED []
synonym: "pyruvate transmembrane transport in mitochondria" RELATED []
synonym: "pyruvate transmembrane transport in mitochondrion" RELATED []
is_a: GO:1901475 ! pyruvate transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0006851
@@ -66195,7 +66220,6 @@ namespace: biological_process
def: "The process in which a calcium ion (Ca2+) is transported across a mitochondrial membrane, into or out of the mitochondrion." [GOC:ai]
synonym: "mitochondrial calcium transport" EXACT []
is_a: GO:0070588 ! calcium ion transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0006852
@@ -66218,7 +66242,6 @@ namespace: biological_process
def: "The transfer of acyl groups to and from acyl-CoA molecules to form O-acylcarnitine, which can exchange across the mitochondrial inner membrane with unacylated carnitine." [ISBN:0198547684]
comment: See also the cellular component term 'mitochondrial inner membrane ; GO:0005743'.
xref: Wikipedia:Carnitine#Role_in_fatty_acid_metabolism
-is_a: GO:0006839 ! mitochondrial transport
is_a: GO:0015909 ! long-chain fatty acid transport
is_a: GO:0032365 ! intracellular lipid transport
is_a: GO:1902001 ! fatty acid transmembrane transport
@@ -66270,11 +66293,11 @@ is_a: GO:0006810 ! transport
[Term]
id: GO:0006859
-name: extracellular carbohydrate transport
+name: obsolete extracellular carbohydrate transport
namespace: biological_process
-def: "The directed extracellular movement of carbohydrates." [GOC:ai]
-is_a: GO:0006858 ! extracellular transport
-is_a: GO:0008643 ! carbohydrate transport
+def: "OBSOLETE. The directed extracellular movement of carbohydrates." [GOC:ai]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0006860
@@ -66319,7 +66342,7 @@ alt_id: GO:0006866
def: "The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
subset: goslim_yeast
-is_a: GO:0015849 ! organic acid transport
+is_a: GO:0046942 ! carboxylic acid transport
is_a: GO:0071705 ! nitrogen compound transport
[Term]
@@ -66329,7 +66352,6 @@ namespace: biological_process
def: "The directed movement of asparagine, alpha-aminosuccinamic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "L-asparagine transport" NARROW []
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0006868
@@ -66339,7 +66361,6 @@ alt_id: GO:0015815
def: "The directed movement of glutamine, 2-amino-4-carbamoylbutanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "L-glutamine transport" NARROW []
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0006869
@@ -66354,68 +66375,76 @@ relationship: part_of GO:0010876 ! lipid localization
[Term]
id: GO:0006873
-name: cellular ion homeostasis
+name: intracellular monoatomic ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of ions at the level of a cell." [GOC:mah]
+def: "A homeostatic process involved in the maintenance of a steady state level of monoatomic ions within a cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:mah]
subset: goslim_yeast
-is_a: GO:0050801 ! ion homeostasis
-is_a: GO:0055082 ! cellular chemical homeostasis
+synonym: "cellular ion homeostasis" BROAD []
+synonym: "cellular monoatomic ion homeostasis" EXACT []
+is_a: GO:0050801 ! monoatomic ion homeostasis
+is_a: GO:0055082 ! intracellular chemical homeostasis
[Term]
id: GO:0006874
-name: cellular calcium ion homeostasis
+name: intracellular calcium ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell." [GOC:ceb, GOC:mah]
+def: "A homeostatic process involved in the maintenance of a steady state level of calcium ions within a cell." [GOC:ceb, GOC:mah]
+synonym: "cellular calcium ion homeostasis" EXACT []
synonym: "regulation of calcium ion concentration" BROAD []
-is_a: GO:0006875 ! cellular metal ion homeostasis
+is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
is_a: GO:0055074 ! calcium ion homeostasis
-is_a: GO:0072503 ! cellular divalent inorganic cation homeostasis
[Term]
id: GO:0006875
-name: cellular metal ion homeostasis
+name: obsolete intracellular metal ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of metal ions at the level of a cell." [GOC:ai, GOC:mah]
+def: "OBSOLETE. A homeostatic process involved in the maintenance of a steady state level of metal ions within a cell." [GOC:ai, GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "cellular heavy metal ion homeostasis" NARROW []
-is_a: GO:0030003 ! cellular cation homeostasis
-is_a: GO:0055065 ! metal ion homeostasis
+synonym: "cellular metal ion homeostasis" EXACT []
+is_obsolete: true
+replaced_by: GO:0030003
[Term]
id: GO:0006876
-name: cellular cadmium ion homeostasis
+name: obsolete intracellular cadmium ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of cadmium ions at the level of a cell." [GOC:ai, GOC:mah]
+def: "OBSOLETE. A homeostatic process involved in the maintenance of a steady state level of cadmium ions within a cell." [GOC:ai, GOC:mah]
+comment: This term was obsoleted because it is not a normal process.
synonym: "cadmium homeostasis" BROAD []
-is_a: GO:0046916 ! cellular transition metal ion homeostasis
-is_a: GO:0055073 ! cadmium ion homeostasis
-is_a: GO:0072503 ! cellular divalent inorganic cation homeostasis
+synonym: "cellular cadmium ion homeostasis" EXACT []
+is_obsolete: true
+consider: GO:0098849
[Term]
id: GO:0006877
-name: cellular cobalt ion homeostasis
+name: intracellular cobalt ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of cobalt ions at the level of a cell." [GOC:ai, GOC:mah]
+def: "A homeostatic process involved in the maintenance of a steady state level of cobalt ions within a cell." [GOC:ai, GOC:mah]
+synonym: "cellular cobalt ion homeostasis" EXACT []
synonym: "cobalt homeostasis" BROAD []
-is_a: GO:0046916 ! cellular transition metal ion homeostasis
+is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
is_a: GO:0055068 ! cobalt ion homeostasis
[Term]
id: GO:0006878
-name: cellular copper ion homeostasis
+name: intracellular copper ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell." [GOC:ai, GOC:mah]
+def: "A homeostatic process involved in the maintenance of a steady state level of copper ions within a cell." [GOC:ai, GOC:mah]
+synonym: "cellular copper ion homeostasis" EXACT []
synonym: "copper homeostasis" BROAD []
-is_a: GO:0046916 ! cellular transition metal ion homeostasis
+is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
is_a: GO:0055070 ! copper ion homeostasis
[Term]
id: GO:0006879
-name: cellular iron ion homeostasis
+name: intracellular iron ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell." [GOC:ai, GOC:mah]
+def: "A homeostatic process involved in the maintenance of a steady state level of iron ions within a cell." [GOC:ai, GOC:mah]
+synonym: "cellular iron ion homeostasis" EXACT []
synonym: "iron homeostasis" BROAD []
-is_a: GO:0046916 ! cellular transition metal ion homeostasis
-is_a: GO:0055072 ! iron ion homeostasis
+is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0006880
@@ -66447,21 +66476,21 @@ is_a: GO:0097577 ! sequestering of iron ion
[Term]
id: GO:0006882
-name: cellular zinc ion homeostasis
+name: intracellular zinc ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of zinc ions at the level of a cell." [GOC:ai, GOC:mah]
+def: "A homeostatic process involved in the maintenance of a steady state level of zinc ions within a cell." [GOC:ai, GOC:mah]
+synonym: "cellular zinc ion homeostasis" EXACT []
synonym: "zinc homeostasis" BROAD []
-is_a: GO:0046916 ! cellular transition metal ion homeostasis
-is_a: GO:0055069 ! zinc ion homeostasis
-is_a: GO:0072503 ! cellular divalent inorganic cation homeostasis
+is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0006883
-name: cellular sodium ion homeostasis
+name: intracellular sodium ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of sodium ions at the level of a cell." [GOC:ai, GOC:mah]
-is_a: GO:0006875 ! cellular metal ion homeostasis
-is_a: GO:0030004 ! cellular monovalent inorganic cation homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of sodium ions within a cell." [GOC:ai, GOC:mah]
+synonym: "cellular sodium ion homeostasis" EXACT []
+is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
is_a: GO:0055078 ! sodium ion homeostasis
[Term]
@@ -66479,7 +66508,8 @@ name: regulation of pH
namespace: biological_process
def: "Any process involved in the maintenance of an internal equilibrium of hydrogen ions, thereby modulating the internal pH, within an organism or cell." [GOC:dph, GOC:go_curators, GOC:tb]
synonym: "hydrogen ion homeostasis" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0055067 ! monovalent inorganic cation homeostasis
+is_a: GO:0055080 ! monoatomic cation homeostasis
+is_a: GO:0065007 ! biological regulation
[Term]
id: GO:0006886
@@ -66488,10 +66518,11 @@ namespace: biological_process
alt_id: GO:0032779
def: "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell." [GOC:mah]
subset: goslim_generic
+subset: prokaryote_subset
synonym: "copper-induced intracellular protein transport" RELATED [GOC:al]
is_a: GO:0015031 ! protein transport
is_a: GO:0046907 ! intracellular transport
-relationship: part_of GO:0034613 ! cellular protein localization
+relationship: part_of GO:0008104 ! protein localization
[Term]
id: GO:0006887
@@ -66620,7 +66651,7 @@ namespace: biological_process
alt_id: GO:0016193
alt_id: GO:0016196
alt_id: GO:0098701
-def: "A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle." [GOC:mah, ISBN:0198506732, ISBN:0716731363]
+def: "A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle." [GOC:mah, ISBN:0198506732, ISBN:0716731363, Wikipedia:Endocytosis]
subset: goslim_yeast
synonym: "endocytic import into cell" EXACT []
synonym: "nonselective vesicle endocytosis" RELATED []
@@ -66721,7 +66752,7 @@ name: phagocytosis
namespace: biological_process
def: "A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles." [ISBN:0198506732]
xref: Wikipedia:Phagocytosis
-is_a: GO:0016192 ! vesicle-mediated transport
+is_a: GO:0006897 ! endocytosis
[Term]
id: GO:0006910
@@ -66731,7 +66762,6 @@ def: "The initial step in phagocytosis involving adhesion to bacteria, immune co
comment: Note that cell surface molecules involved in the direct binding of bacteria may be also annotated to the molecular function term 'bacterial cell surface binding ; GO:0051635'. Note that cell surface molecules involved in the direct binding to opsonins such as complement components or antibodies may be also annotated to the term 'opsonin binding ; GO:0001846'.
synonym: "recognition of phagocytosed substance by phagocytic cell" EXACT []
is_a: GO:0008037 ! cell recognition
-relationship: part_of GO:0006897 ! endocytosis
relationship: part_of GO:0006909 ! phagocytosis
[Term]
@@ -66742,7 +66772,6 @@ def: "The internalization of bacteria, immune complexes and other particulate ma
synonym: "phagosome biosynthesis" RELATED []
synonym: "phagosome formation" RELATED []
is_a: GO:0099024 ! plasma membrane invagination
-relationship: part_of GO:0006897 ! endocytosis
relationship: part_of GO:0006909 ! phagocytosis
[Term]
@@ -66934,16 +66963,14 @@ is_obsolete: true
[Term]
id: GO:0006928
-name: movement of cell or subcellular component
+name: obsolete movement of cell or subcellular component
namespace: biological_process
-def: "The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore." [GOC:dgh, GOC:dph, GOC:jl, GOC:mlg]
-comment: Note that in GO cellular components include whole cells (cell is_a cellular component).
-subset: gocheck_do_not_annotate
-subset: goslim_pir
+def: "OBSOLETE. The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore." [GOC:dgh, GOC:dph, GOC:jl, GOC:mlg]
+comment: This term was obsoleted because it mixes cellular and subcellular processes.
synonym: "cell movement" RELATED []
synonym: "cellular component motion" EXACT [GOC:dph, GOC:jl]
synonym: "cellular component movement" EXACT []
-is_a: GO:0009987 ! cellular process
+is_obsolete: true
[Term]
id: GO:0006929
@@ -67084,7 +67111,7 @@ id: GO:0006948
name: induction by virus of host cell-cell fusion
namespace: biological_process
def: "The process of syncytia-forming cell-cell fusion, caused by a virus." [ISBN:0781718325]
-comment: Where syncytium formation results in the spread of virus in the host, also consider annotating to the term 'spread of virus in multicellular host ; GO:0046739'.
+comment: Where syncytium formation results in the spread of virus in the host, also consider annotating to the term 'transport of virus in multicellular host ; GO:0046739'.
synonym: "induction by virus of cell-cell fusion in host" EXACT []
synonym: "viral-induced cell-cell fusion" EXACT []
synonym: "viral-induced host cell-cell fusion" EXACT []
@@ -67107,7 +67134,6 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_manually_annotate
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -67330,25 +67356,17 @@ relationship: part_of GO:0071474 ! cellular hyperosmotic response
[Term]
id: GO:0006974
-name: cellular response to DNA damage stimulus
+name: DNA damage response
namespace: biological_process
alt_id: GO:0034984
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC:go_curators]
subset: goslim_yeast
synonym: "cellular DNA damage response" EXACT []
-synonym: "DNA damage response" EXACT []
+synonym: "cellular response to DNA damage stimulus" EXACT []
synonym: "response to DNA damage stimulus" BROAD []
synonym: "response to genotoxic stress" EXACT []
is_a: GO:0033554 ! cellular response to stress
-[Term]
-id: GO:0006975
-name: DNA damage induced protein phosphorylation
-namespace: biological_process
-def: "The widespread phosphorylation of various molecules, triggering many downstream processes, that occurs in response to the detection of DNA damage." [GOC:go_curators]
-is_a: GO:0006468 ! protein phosphorylation
-is_a: GO:0006974 ! cellular response to DNA damage stimulus
-
[Term]
id: GO:0006977
name: DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
@@ -67396,7 +67414,7 @@ id: GO:0006983
name: ER overload response
namespace: biological_process
alt_id: GO:0006985
-def: "The series of molecular signals generated by the accumulation of normal or misfolded proteins in the endoplasmic reticulum and leading to activation of transcription by NF-kappaB." [PMID:10390516]
+def: "The series of molecular signals initiated by the accumulation of normal or misfolded proteins in the endoplasmic reticulum and leading to activation of transcription by NF-kappaB." [PMID:10390516]
synonym: "endoplasmic reticulum overload response" EXACT []
synonym: "EOR" EXACT []
synonym: "EOR-mediated activation of NF-kappaB" NARROW [GOC:dph, GOC:tb]
@@ -67412,7 +67430,7 @@ is_a: GO:0071216 ! cellular response to biotic stimulus
id: GO:0006984
name: ER-nucleus signaling pathway
namespace: biological_process
-def: "Any series of molecular signals that conveys information from the endoplasmic reticulum to the nucleus, usually resulting in a change in transcriptional regulation." [GOC:mah]
+def: "The series of molecular signals that conveys information from the endoplasmic reticulum to the nucleus, usually resulting in a change in transcriptional regulation." [GOC:mah]
synonym: "endoplasmic reticulum to nucleus signaling pathway" EXACT []
synonym: "endoplasmic reticulum-nuclear signaling pathway" EXACT []
synonym: "ER to nucleus signaling pathway" EXACT []
@@ -67500,7 +67518,6 @@ name: organelle organization
namespace: biological_process
alt_id: GO:1902589
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
synonym: "organelle organisation" EXACT []
@@ -67515,7 +67532,6 @@ name: nucleus organization
namespace: biological_process
alt_id: GO:0048287
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus." [GOC:dph, GOC:ems, GOC:jl, GOC:mah]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_drosophila
subset: goslim_pir
@@ -67584,7 +67600,7 @@ name: telomere maintenance via telomerase
namespace: biological_process
def: "The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase." [GOC:elh]
synonym: "telomerase-dependent telomere maintenance" EXACT []
-is_a: GO:0006278 ! RNA-dependent DNA biosynthetic process
+is_a: GO:0006278 ! RNA-templated DNA biosynthetic process
is_a: GO:0010833 ! telomere maintenance via telomere lengthening
[Term]
@@ -67650,12 +67666,12 @@ id: GO:0007010
name: cytoskeleton organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:dph, GOC:jl, GOC:mah]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "cytoskeletal organization and biogenesis" RELATED [GOC:mah]
synonym: "cytoskeletal regulator activity" RELATED []
synonym: "cytoskeleton organisation" EXACT []
@@ -67714,10 +67730,9 @@ is_a: GO:0009987 ! cellular process
id: GO:0007018
name: microtubule-based movement
namespace: biological_process
-def: "A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules." [GOC:cjm, ISBN:0815316194]
+def: "A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules." [GOC:cjm, ISBN:0815316194]
subset: goslim_drosophila
subset: goslim_generic
-is_a: GO:0006928 ! movement of cell or subcellular component
is_a: GO:0007017 ! microtubule-based process
[Term]
@@ -67887,7 +67902,7 @@ id: GO:0007036
name: vacuolar calcium ion homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of calcium ions in the vacuole or between a vacuole and its surroundings." [GOC:ai, GOC:mah]
-is_a: GO:0006874 ! cellular calcium ion homeostasis
+is_a: GO:0006874 ! intracellular calcium ion homeostasis
[Term]
id: GO:0007038
@@ -67908,7 +67923,7 @@ synonym: "vacuolar protein breakdown" RELATED []
synonym: "vacuolar protein catabolic process" RELATED []
synonym: "vacuolar protein catabolism" RELATED []
synonym: "vacuolar protein degradation" RELATED []
-is_a: GO:0044257 ! cellular protein catabolic process
+is_a: GO:0030163 ! protein catabolic process
[Term]
id: GO:0007040
@@ -67972,7 +67987,6 @@ namespace: biological_process
def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:go_curators, GOC:mtg_cell_cycle]
subset: gocheck_do_not_manually_annotate
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
@@ -68080,10 +68094,11 @@ subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "chromosome division" EXACT []
synonym: "chromosome transmission" RELATED []
xref: Wikipedia:Chromosome_segregation
-is_a: GO:0009987 ! cellular process
+is_a: GO:0022402 ! cell cycle process
[Term]
id: GO:0007060
@@ -68099,11 +68114,9 @@ id: GO:0007062
name: sister chromatid cohesion
namespace: biological_process
def: "The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other." [GOC:jh, GOC:mah, ISBN:0815316194]
-synonym: "coheson-mediated DNA tethering" EXACT []
-synonym: "sister chromatid alignment" RELATED []
+synonym: "cohesion-mediated DNA tethering" EXACT []
is_a: GO:0022402 ! cell cycle process
is_a: GO:0051276 ! chromosome organization
-relationship: part_of GO:0000819 ! sister chromatid segregation
[Term]
id: GO:0007063
@@ -68120,26 +68133,20 @@ name: mitotic sister chromatid cohesion
namespace: biological_process
def: "The cell cycle process in which the sister chromatids of a replicated chromosome are joined along the entire length of the chromosome, from their formation in S phase through metaphase during a mitotic cell cycle. This cohesion cycle is critical for high fidelity chromosome transmission." [GOC:ai, GOC:rn, PMID:10827941, PMID:11389843, PMID:14623866]
is_a: GO:0007062 ! sister chromatid cohesion
-is_a: GO:1903047 ! mitotic cell cycle process
-relationship: part_of GO:0000070 ! mitotic sister chromatid segregation
[Term]
id: GO:0007065
name: male meiosis sister chromatid cohesion
namespace: biological_process
def: "The joining of the sister chromatids of a replicated chromosome along the entire length of the chromosome that occurs during meiosis in a male." [GOC:ai]
-is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
is_a: GO:0051177 ! meiotic sister chromatid cohesion
-relationship: part_of GO:0007140 ! male meiotic nuclear division
[Term]
id: GO:0007066
name: female meiosis sister chromatid cohesion
namespace: biological_process
def: "The joining of the sister chromatids of a replicated chromosome along the entire length of the chromosome that occurs during meiosis in a female." [GOC:ai]
-is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
is_a: GO:0051177 ! meiotic sister chromatid cohesion
-relationship: part_of GO:0007143 ! female meiotic nuclear division
[Term]
id: GO:0007068
@@ -68214,7 +68221,7 @@ name: positive regulation of transcription involved in exit from mitosis
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of transcription as the cell leaves M phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place." [GOC:dph, GOC:isa_complete, GOC:tb]
synonym: "activation of transcription on exit from mitosis" NARROW [GOC:dph, GOC:tb]
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
is_a: GO:1903047 ! mitotic cell cycle process
relationship: part_of GO:0010458 ! exit from mitosis
@@ -68316,12 +68323,11 @@ consider: GO:0007064
[Term]
id: GO:0007083
-name: mitotic chromosome decondensation
+name: obsolete mitotic chromosome decondensation
namespace: biological_process
-def: "The cell cycle process in which chromosome structure is altered from the condensed form taken on during mitosis to the relaxed disperse form held in resting cells." [GOC:ai]
-is_a: GO:0051312 ! chromosome decondensation
-is_a: GO:1903047 ! mitotic cell cycle process
-relationship: part_of GO:0000070 ! mitotic sister chromatid segregation
+def: "OBSOLETE. The cell cycle process in which chromosome structure is altered from the condensed form taken on during mitosis to the relaxed disperse form held in resting cells." [GOC:ai]
+comment: This term was obsoleted because it is a spontaneous process.
+is_obsolete: true
[Term]
id: GO:0007084
@@ -68400,7 +68406,6 @@ namespace: biological_process
def: "The cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin." [GOC:mtg_cell_cycle, PMID:10465783]
synonym: "metaphase/anaphase transition by anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process" EXACT [GOC:vw]
synonym: "mitotic metaphase/anaphase transition" EXACT []
-is_a: GO:0010965 ! regulation of mitotic sister chromatid separation
is_a: GO:0044772 ! mitotic cell cycle phase transition
is_a: GO:0044784 ! metaphase/anaphase transition of cell cycle
@@ -68431,7 +68436,7 @@ namespace: biological_process
alt_id: GO:0044810
alt_id: GO:0072480
alt_id: GO:1902420
-def: "A signal transduction process that contributes to a mitotic cell cycle spindle assembly checkpoint, that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle." [GOC:mtg_cell_cycle, PMID:12360190]
+def: "A mitotic cell cycle checkpoint that delays mitotic sister chromatid separation and consequently the mitotic metaphase/anaphase transition until the spindle is correctly assembled and chromosomes are attached to the spindle. Spindle assembly checkpoint signalling begins with the activated Mph family kinase, and results in the inhibition of the Anaphase Promoting Complex and its activator Sleepy/Cdc20 by the mitotic checkpoint complex (MCC)." [GOC:mtg_cell_cycle, PMID:12360190]
synonym: "Dma1-dependent checkpoint" NARROW []
synonym: "Mad2-dependent checkpoint" NARROW []
synonym: "mitotic cell cycle spindle assembly checkpoint" EXACT []
@@ -68502,7 +68507,6 @@ name: nuclear migration
namespace: biological_process
alt_id: GO:0040023
def: "The directed movement of the nucleus to a specific location within a cell." [GOC:ai]
-subset: goslim_aspergillus
synonym: "establishment of cell nucleus localization" RELATED []
synonym: "establishment of localization of nucleus" RELATED []
synonym: "establishment of nucleus localisation" RELATED [GOC:mah]
@@ -68562,13 +68566,15 @@ is_obsolete: true
[Term]
id: GO:0007105
-name: cytokinesis, site selection
+name: cytokinesis, division site positioning
namespace: biological_process
alt_id: GO:0010687
-def: "The process of marking the place where cytokinesis will occur." [GOC:mtg_cell_cycle]
+def: "The process in which a contractile ring is positioned in a specific location. This process is critical for both for both symmetric and asymmetric cell divisions." [PMID:26553932, PMID:28162898]
+synonym: "cytokinesis, site selection" EXACT []
+synonym: "division plane positioning" EXACT []
synonym: "site selection involved in cell cycle cytokinesis" EXACT []
synonym: "site selection involved in cytokinesis" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0032506 ! cytokinetic process
+is_a: GO:0036214 ! contractile ring localization
[Term]
id: GO:0007106
@@ -69005,7 +69011,6 @@ name: cell adhesion
namespace: biological_process
alt_id: GO:0098602
def: "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules." [GOC:hb, GOC:pf]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -69013,11 +69018,11 @@ subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
+subset: prokaryote_subset
synonym: "cell adhesion molecule activity" RELATED []
synonym: "single organism cell adhesion" RELATED []
xref: Wikipedia:Cell_adhesion
is_a: GO:0009987 ! cellular process
-is_a: GO:0022610 ! biological adhesion
[Term]
id: GO:0007156
@@ -69091,6 +69096,7 @@ def: "Any cellular process that results in the specification, formation or maint
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pombe
+subset: prokaryote_subset
synonym: "cell polarity" RELATED [GOC:mah, GOC:vw]
synonym: "establishment and/or maintenance of cell polarity" RELATED []
synonym: "establishment and/or maintenance of cell polarization" RELATED []
@@ -69114,7 +69120,6 @@ alt_id: GO:0023033
alt_id: GO:0023045
def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11]
comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
@@ -69138,7 +69143,7 @@ relationship: part_of GO:0051716 ! cellular response to stimulus
id: GO:0007166
name: cell surface receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
+def: "The series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:mah, GOC:pr, GOC:signaling]
subset: goslim_drosophila
synonym: "cell surface receptor linked signal transduction" EXACT []
synonym: "cell surface receptor linked signaling pathway" EXACT [GOC:bf]
@@ -69147,9 +69152,10 @@ is_a: GO:0007165 ! signal transduction
[Term]
id: GO:0007167
-name: enzyme linked receptor protein signaling pathway
+name: enzyme-linked receptor protein signaling pathway
namespace: biological_process
-def: "Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, ISBN:0815316194]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, ISBN:0815316194]
+synonym: "enzyme linked receptor protein signaling pathway" EXACT []
synonym: "enzyme linked receptor protein signalling pathway" EXACT []
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -69157,17 +69163,17 @@ is_a: GO:0007166 ! cell surface receptor signaling pathway
id: GO:0007168
name: receptor guanylyl cyclase signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses guanylyl cyclase activity, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, PMID:16815030]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of the target cell where the receptor possesses guanylyl cyclase activity, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, PMID:16815030]
synonym: "receptor guanylyl cyclase signalling pathway" EXACT []
-is_a: GO:0007167 ! enzyme linked receptor protein signaling pathway
+is_a: GO:0007167 ! enzyme-linked receptor protein signaling pathway
[Term]
id: GO:0007169
name: transmembrane receptor protein tyrosine kinase signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:ceb, GOC:signaling]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:ceb, GOC:signaling]
synonym: "transmembrane receptor protein tyrosine kinase signalling pathway" EXACT []
-is_a: GO:0007167 ! enzyme linked receptor protein signaling pathway
+is_a: GO:0007167 ! enzyme-linked receptor protein signaling pathway
[Term]
id: GO:0007170
@@ -69203,7 +69209,7 @@ is_a: GO:0065003 ! protein-containing complex assembly
id: GO:0007173
name: epidermal growth factor receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:ceb]
+def: "The series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:ceb]
synonym: "EGF receptor signaling pathway" EXACT []
synonym: "EGF receptor signalling pathway" EXACT []
synonym: "EGFR signaling pathway" EXACT []
@@ -69226,8 +69232,8 @@ synonym: "epidermal growth factor catabolism" EXACT [GOC:bf]
synonym: "epidermal growth factor ligand processing" RELATED [GOC:bf]
synonym: "intracellular EGF processing" RELATED [PMID:2985587]
synonym: "receptor-mediated EGF processing" RELATED [PMID:1683723]
+is_a: GO:0030163 ! protein catabolic process
is_a: GO:0042059 ! negative regulation of epidermal growth factor receptor signaling pathway
-is_a: GO:0044257 ! cellular protein catabolic process
[Term]
id: GO:0007175
@@ -69263,15 +69269,15 @@ is_a: GO:0061097 ! regulation of protein tyrosine kinase activity
id: GO:0007178
name: transmembrane receptor protein serine/threonine kinase signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses serine/threonine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of the target cell where the receptor possesses serine/threonine kinase activity, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling]
synonym: "transmembrane receptor protein serine/threonine kinase signalling pathway" EXACT []
-is_a: GO:0007167 ! enzyme linked receptor protein signaling pathway
+is_a: GO:0007167 ! enzyme-linked receptor protein signaling pathway
[Term]
id: GO:0007179
name: transforming growth factor beta receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:mah, GOC:signaling]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a transforming growth factor beta receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:mah, GOC:signaling]
synonym: "TGF-beta receptor signaling pathway" EXACT []
synonym: "TGF-beta receptor signalling pathway" EXACT []
synonym: "TGFbeta receptor signaling pathway" EXACT []
@@ -69330,16 +69336,16 @@ relationship: part_of GO:0007178 ! transmembrane receptor protein serine/threoni
id: GO:0007185
name: transmembrane receptor protein tyrosine phosphatase signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses protein tyrosine phosphatase activity, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of the target cell where the receptor possesses protein tyrosine phosphatase activity, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling]
synonym: "transmembrane receptor protein tyrosine phosphatase signalling pathway" EXACT []
-is_a: GO:0007167 ! enzyme linked receptor protein signaling pathway
+is_a: GO:0007167 ! enzyme-linked receptor protein signaling pathway
[Term]
id: GO:0007186
name: G protein-coupled receptor signaling pathway
namespace: biological_process
alt_id: GO:0038042
-def: "A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane." [GOC:bf, GOC:mah, PMID:16902576, PMID:24568158, Wikipedia:G_protein-coupled_receptor]
+def: "The series of molecular signals initiated by a ligand binding to its receptor, in which the activated receptor promotes the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, and ends with regulation of a downstream cellular process. The pathway can start from the plasma membrane, Golgi or nuclear membrane." [GOC:bf, GOC:mah, PMID:16902576, PMID:24568158, Wikipedia:G_protein-coupled_receptor]
subset: goslim_drosophila
synonym: "dimeric G-protein coupled receptor signaling pathway" NARROW []
synonym: "dimeric G-protein coupled receptor signalling pathway" NARROW [GOC:mah]
@@ -69358,7 +69364,7 @@ is_a: GO:0007165 ! signal transduction
id: GO:0007187
name: G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a G protein-coupled receptor binding to its physiological ligand, where the pathway proceeds with activation or inhibition of a nucleotide cyclase activity and a subsequent change in the concentration of a cyclic nucleotide." [GOC:mah, GOC:signaling, ISBN:0815316194]
+def: "A G protein-coupled receptor signaling pathway in which the signal is transmitted via the activation or inhibition of a nucleotide cyclase activity and a subsequent change in the concentration of a cyclic nucleotide." [GOC:mah, GOC:signaling, ISBN:0815316194]
synonym: "G protein signaling, coupled to cyclic nucleotide second messenger" EXACT []
synonym: "G protein signalling, coupled to cyclic nucleotide second messenger" EXACT []
synonym: "G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger" EXACT []
@@ -69371,7 +69377,7 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
id: GO:0007188
name: adenylate cyclase-modulating G protein-coupled receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a G protein-coupled receptor binding to its physiological ligand, where the pathway proceeds through activation or inhibition of adenylyl cyclase activity and a subsequent change in the concentration of cyclic AMP (cAMP)." [GOC:mah, GOC:signaling, ISBN:0815316194]
+def: "A G protein-coupled receptor signaling pathway in which the signal is transmitted via the activation or inhibition of adenylyl cyclase activity and a subsequent change in the intracellular concentration of cyclic AMP (cAMP)." [GOC:mah, GOC:signaling, ISBN:0815316194]
comment: This term is intended to cover steps in a GPCR signaling pathway both upstream and downstream of adenylate-cyclase activity. For steps upstream of adenylate cyclase activity, consider instead annotating to 'regulation of adenylate cyclase activity involved in G protein-coupled receptor signaling pathway ; GO:0010578.
synonym: "adenylate cyclase-modulating GPCR signaling pathway" EXACT [GOC:signaling]
synonym: "G protein signaling, coupled to cAMP nucleotide second messenger" EXACT []
@@ -69392,7 +69398,7 @@ name: adenylate cyclase-activating G protein-coupled receptor signaling pathway
namespace: biological_process
alt_id: GO:0010579
alt_id: GO:0010580
-def: "The series of molecular signals generated as a consequence of a G protein-coupled receptor binding to its physiological ligand, where the pathway proceeds through activation of adenylyl cyclase activity and a subsequent increase in the concentration of cyclic AMP (cAMP)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb, ISBN:0815316194]
+def: "A G protein-coupled receptor signaling pathway in which the signal is transmitted via the activation of adenylyl cyclase activity and a subsequent increase in the intracellular concentration of cyclic AMP (cAMP)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb, ISBN:0815316194]
comment: This term can be used to annotate ligands, receptors and G-proteins that lead to activation of adenylate cyclase activity within a signaling pathway.
synonym: "activation of adenylate cyclase activity by G-protein signaling pathway" RELATED [GOC:bf]
synonym: "activation of adenylate cyclase activity involved in G-protein signaling" RELATED [GOC:signaling]
@@ -69420,13 +69426,13 @@ def: "Any process that initiates the activity of the inactive enzyme adenylate c
synonym: "adenylate cyclase activation" EXACT [GOC:dph, GOC:tb]
synonym: "adenylate cyclase activator" RELATED []
synonym: "adenylyl cyclase activation" EXACT []
-is_a: GO:0050790 ! regulation of catalytic activity
+is_a: GO:0045762 ! positive regulation of adenylate cyclase activity
[Term]
id: GO:0007191
name: adenylate cyclase-activating dopamine receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a dopamine receptor binding to its physiological ligand, where the pathway proceeds with activation of adenylyl cyclase and a subsequent increase in the concentration of cyclic AMP (cAMP)." [GOC:mah, GOC:signaling]
+def: "An adenylate cyclase-activating G protein-coupled receptor signaling pathway initiated by dopamine binding to its receptor, and ending with the regulation of a downstream cellular process." [GOC:mah, GOC:signaling]
synonym: "activation of adenylate cyclase activity by dopamine receptor signaling pathway" RELATED [GOC:signaling]
synonym: "activation of adenylate cyclase activity by dopamine receptor signalling pathway" RELATED [GOC:mah]
synonym: "dopamine receptor, adenylate cyclase activating pathway" EXACT [GOC:dph, GOC:tb]
@@ -69438,7 +69444,7 @@ is_a: GO:0007212 ! dopamine receptor signaling pathway
id: GO:0007192
name: adenylate cyclase-activating serotonin receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a serotonin receptor binding to its physiological ligand, where the pathway proceeds with activation of adenylyl cyclase and a subsequent increase in the concentration of cyclic AMP (cAMP)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
+def: "An adenylate cyclase-activating G protein-coupled receptor signaling pathway initiated by serotonin binding to its receptor, and ending with the regulation of a downstream cellular process." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
synonym: "activation of adenylate cyclase activity by serotonin receptor signalling pathway" RELATED [GOC:mah]
synonym: "serotonin receptor, adenylate cyclase activating pathway" RELATED [GOC:dph, GOC:tb]
synonym: "serotonin receptor, adenylyl cyclase activating pathway" EXACT []
@@ -69449,7 +69455,7 @@ is_a: GO:0007210 ! serotonin receptor signaling pathway
id: GO:0007193
name: adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a G protein-coupled receptor binding to its physiological ligand, where the pathway proceeds through inhibition of adenylyl cyclase activity and a subsequent decrease in the concentration of cyclic AMP (cAMP)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb, ISBN:0815316194]
+def: "A G protein-coupled receptor signaling pathway in which the signal is transmitted via the inhibition of adenylyl cyclase activity and a subsequent decrease in the intracellular concentration of cyclic AMP (cAMP)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb, ISBN:0815316194]
comment: This term is intended to cover steps in a GPCR signaling pathway both upstream and downstream of adenylate-cyclase inhibition.
synonym: "adenylate cyclase-inhibiting GPCR signaling pathway" EXACT [GOC:signaling]
synonym: "G protein signaling, adenylate cyclase inhibiting pathway" EXACT []
@@ -69483,7 +69489,7 @@ is_a: GO:0051350 ! negative regulation of lyase activity
id: GO:0007195
name: adenylate cyclase-inhibiting dopamine receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a dopamine receptor binding to its physiological ligand, where the pathway proceeds with inhibition of adenylyl cyclase and a subsequent decrease in the concentration of cyclic AMP (cAMP)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
+def: "An adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway initiated by dopamine binding to its receptor, and ending with the regulation of a downstream cellular process." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
synonym: "dopamine receptor, adenylate cyclase inhibiting pathway" EXACT [GOC:dph, GOC:tb]
synonym: "dopamine receptor, adenylyl cyclase inhibiting pathway" EXACT []
synonym: "inhibition of adenylate cyclase activity by dopamine receptor signaling pathway" RELATED [GOC:signaling]
@@ -69495,7 +69501,7 @@ is_a: GO:0007212 ! dopamine receptor signaling pathway
id: GO:0007196
name: adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a G protein-coupled glutamate receptor binding to its physiological ligand, where the pathway proceeds with inhibition of adenylyl cyclase and a subsequent decrease in the concentration of cyclic AMP (cAMP)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
+def: "An adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway initiated by glutamate binding to its receptor, and ending with the regulation of a downstream cellular process." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
synonym: "adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway" EXACT []
synonym: "inhibition of adenylate cyclase activity by G-protein-coupled glutamate receptor signaling pathway" RELATED [GOC:signaling]
synonym: "inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway" EXACT [GOC:bf]
@@ -69509,7 +69515,7 @@ is_a: GO:0007216 ! G protein-coupled glutamate receptor signaling pathway
id: GO:0007197
name: adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a G protein-coupled acetylcholine receptor binding to its physiological ligand, where the pathway proceeds with inhibition of adenylyl cyclase and a subsequent decrease in the concentration of cyclic AMP (cAMP)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
+def: "An adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway initiated by acetylcholine binding to its receptor, and ending with the regulation of a downstream cellular process." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
synonym: "inhibition of adenylate cyclase activity by G-protein coupled acetylcholine receptor signaling pathway" RELATED [GOC:signaling]
synonym: "inhibition of adenylate cyclase activity by muscarinic acetylcholine receptor signaling pathway" RELATED [GOC:bf]
synonym: "inhibition of adenylate cyclase activity by muscarinic acetylcholine receptor signalling pathway" RELATED [GOC:mah]
@@ -69522,7 +69528,7 @@ is_a: GO:0007213 ! G protein-coupled acetylcholine receptor signaling pathway
id: GO:0007198
name: adenylate cyclase-inhibiting serotonin receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a serotonin receptor binding to its physiological ligand, where the pathway proceeds with inhibition of adenylyl cyclase and a subsequent decrease in the concentration of cyclic AMP (cAMP)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
+def: "An adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway initiated by serotonin binding to its receptor, and ending with the regulation of a downstream cellular process." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
synonym: "inhibition of adenylate cyclase activity by serotonin receptor signaling pathway" RELATED [GOC:signaling]
synonym: "inhibition of adenylate cyclase activity by serotonin receptor signalling pathway" RELATED [GOC:mah]
synonym: "serotonin receptor, adenylate cyclase inhibiting pathway" EXACT [GOC:dph, GOC:tb]
@@ -69549,7 +69555,7 @@ is_a: GO:0007187 ! G protein-coupled receptor signaling pathway, coupled to cycl
id: GO:0007200
name: phospholipase C-activating G protein-coupled receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a G protein-coupled receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent increase in the concentration of inositol trisphosphate (IP3) and diacylglycerol (DAG)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb, ISBN:0815316194]
+def: "A G protein-coupled receptor signaling pathway in which the signal is transmitted via the activation of phospholipase C (PLC) and a subsequent increase in the intracellular concentration of inositol trisphosphate (IP3) and diacylglycerol (DAG)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb, ISBN:0815316194]
comment: This term is intended to cover steps in a GPCR signaling pathway both upstream and downstream of phospholipase C (PLC) activity.
synonym: "activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger" RELATED [GOC:signaling]
synonym: "G protein signaling, coupled to IP3 second messenger (phospholipase C activating)" EXACT []
@@ -69575,7 +69581,7 @@ is_obsolete: true
id: GO:0007202
name: activation of phospholipase C activity
namespace: biological_process
-def: "The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G protein-coupled receptor binding to its physiological ligand." [GOC:dph, GOC:mah, GOC:tb, PMID:8280098]
+def: "The initiation of the activity of the inactive enzyme phospolipase C as the result of The series of molecular signals generated as a consequence of a G protein-coupled receptor binding to its physiological ligand." [GOC:dph, GOC:mah, GOC:tb, PMID:8280098]
comment: Note that this term refers to a signaling pathway, and should not be confused with function terms such as 'phospholipase activator activity ; GO:0016004'.
synonym: "phospholipase C activation" EXACT [GOC:dph, GOC:tb]
is_a: GO:0010863 ! positive regulation of phospholipase C activity
@@ -69601,7 +69607,7 @@ synonym: "elevation of calcium ion concentration in cytoplasm" BROAD []
synonym: "elevation of calcium ion concentration in cytosol" EXACT []
synonym: "elevation of cytoplasmic calcium ion concentration" BROAD []
synonym: "elevation of cytosolic calcium ion concentration" EXACT []
-is_a: GO:0051480 ! regulation of cytosolic calcium ion concentration
+is_a: GO:0065008 ! regulation of biological quality
[Term]
id: GO:0007205
@@ -69617,7 +69623,7 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
id: GO:0007206
name: phospholipase C-activating G protein-coupled glutamate receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a G protein-coupled glutamate receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent release of inositol trisphosphate (IP3) and diacylglycerol (DAG)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
+def: "A phospholipase C-activating G protein-coupled receptor signaling pathway initiated by glutamate binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
synonym: "activation of phospholipase C activity by G-protein coupled glutamate receptor signaling pathway" RELATED [GOC:signaling]
synonym: "activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway" RELATED [GOC:bf]
synonym: "activation of phospholipase C activity by metabotropic glutamate receptor signalling pathway" RELATED [GOC:mah]
@@ -69630,7 +69636,7 @@ is_a: GO:0007216 ! G protein-coupled glutamate receptor signaling pathway
id: GO:0007207
name: phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a G protein-coupled acetylcholine receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent release of inositol trisphosphate (IP3) and diacylglycerol (DAG)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
+def: "A phospholipase C-activating G protein-coupled receptor signaling pathway initiated by acetylcholine binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
synonym: "activation of phospholipase C activity by G-protein coupled acetylcholine receptor signaling pathway" RELATED [GOC:signaling]
synonym: "activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway" RELATED [GOC:bf]
synonym: "activation of phospholipase C activity by muscarinic acetylcholine receptor signalling pathway" EXACT [GOC:mah]
@@ -69644,7 +69650,7 @@ is_a: GO:0007213 ! G protein-coupled acetylcholine receptor signaling pathway
id: GO:0007208
name: phospholipase C-activating serotonin receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a serotonin receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent release of inositol trisphosphate (IP3) and diacylglycerol (DAG)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
+def: "A phospholipase C-activating receptor G protein-coupled receptor signaling pathway initiated by serotonin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
synonym: "activation of phospholipase C activity by serotonin receptor signaling pathway" RELATED [GOC:signaling]
synonym: "activation of phospholipase C activity by serotonin receptor signalling pathway" RELATED [GOC:mah]
synonym: "serotonin receptor, phospholipase C activating pathway" RELATED [GOC:dph, GOC:tb]
@@ -69655,7 +69661,7 @@ is_a: GO:0098664 ! G protein-coupled serotonin receptor signaling pathway
id: GO:0007209
name: phospholipase C-activating tachykinin receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a tachykinin receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent release of inositol trisphosphate (IP3) and diacylglycerol (DAG)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
+def: "A phospholipase C-activating receptor G protein-coupled receptor signaling pathway initiated by tachykinin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
synonym: "activation of phospholipase C activity by tachykinin receptor signaling pathway" RELATED [GOC:signaling]
synonym: "activation of phospholipase C activity by tachykinin receptor signalling pathway" RELATED [GOC:mah]
synonym: "tachykinin receptor, phospholipase C activating pathway" RELATED [GOC:dph, GOC:tb]
@@ -69675,7 +69681,7 @@ relationship: part_of GO:1903351 ! cellular response to dopamine
id: GO:0007211
name: octopamine or tyramine signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of octopamine or tyramine binding to a cell surface receptor. Octopamine and tyramine are decarboxylation products of tyrosine, and are the invertebrate counterparts of the vertebrate adrenergic transmitters." [GOC:mah, PMID:15355245]
+def: "A G protein-coupled receptor signaling pathway initiated by octopamine or tyramine binding to their receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription, and ending with the regulation of a downstream cellular process. Octopamine and tyramine are decarboxylation products of tyrosine, and are the invertebrate counterparts of the vertebrate adrenergic transmitters." [GOC:mah, PMID:15355245]
synonym: "octopamine or tyramine signalling pathway" EXACT [GOC:mah]
synonym: "octopamine/tyramine signaling pathway" EXACT [GOC:mah]
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -69693,7 +69699,7 @@ relationship: part_of GO:1903351 ! cellular response to dopamine
id: GO:0007213
name: G protein-coupled acetylcholine receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals initiated by an acetylcholine receptor on the surface of the target cell binding to one of its physiological ligands, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction and ends with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, ISBN:0815316194]
+def: "A G protein-coupled receptor signaling pathway initiated by a ligand binding to an acetylcholine receptor on the surface of a target cell, and ends with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, ISBN:0815316194]
synonym: "acetylcholine receptor signalling, muscarinic pathway" EXACT []
synonym: "G-protein coupled acetylcholine receptor signaling pathway" EXACT []
synonym: "muscarinic acetylcholine receptor signaling pathway" EXACT [GOC:bf]
@@ -69704,7 +69710,7 @@ is_a: GO:0095500 ! acetylcholine receptor signaling pathway
id: GO:0007214
name: gamma-aminobutyric acid signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated by the binding of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, to a cell surface receptor." [GOC:mah]
+def: "The series of molecular signals generated by the binding of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, to its receptor on the surface of a target cell." [GOC:mah]
synonym: "4-aminobutanoate signaling pathway" EXACT []
synonym: "4-aminobutanoate signalling pathway" EXACT []
synonym: "4-aminobutyrate signaling pathway" EXACT []
@@ -69718,7 +69724,7 @@ is_a: GO:0007267 ! cell-cell signaling
id: GO:0007215
name: glutamate receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of glutamate to a glutamate receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, PMID:9131252]
+def: "The series of molecular signals initiated by the binding of glutamate to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, PMID:9131252]
synonym: "glutamate signaling pathway" EXACT [GOC:bf]
synonym: "glutamate signalling pathway" EXACT []
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -69727,7 +69733,7 @@ is_a: GO:0007166 ! cell surface receptor signaling pathway
id: GO:0007216
name: G protein-coupled glutamate receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, PMID:9131252]
+def: "A G protein-coupled receptor signaling pathway initiated by glutamate binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:mah, GOC:signaling, PMID:9131252]
synonym: "G-protein coupled glutamate receptor signaling pathway" EXACT []
synonym: "metabotropic glutamate receptor signaling pathway" EXACT [GOC:bf]
synonym: "metabotropic glutamate receptor signalling pathway" EXACT []
@@ -69738,7 +69744,7 @@ is_a: GO:0007215 ! glutamate receptor signaling pathway
id: GO:0007217
name: tachykinin receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a tachykinin, i.e. a short peptide with the terminal sequence (Phe-X-Gly-Leu-Met-NH2), binding to a cell surface receptor." [GOC:mah, PMID:14723970]
+def: "A G protein-coupled receptor signaling pathway initiated by tachykinin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process. Tachykinin is a short peptide with the terminal sequence (Phe-X-Gly-Leu-Met-NH2)." [GOC:mah, PMID:14723970]
synonym: "tachykinin signalling pathway" EXACT []
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -69746,7 +69752,7 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
id: GO:0007218
name: neuropeptide signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor." [GOC:mah, ISBN:0815316194]
+def: "A G protein-coupled receptor signaling pathway initiated by a neuropeptide binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:mah, ISBN:0815316194]
synonym: "neuropeptide signalling pathway" EXACT []
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -69755,7 +69761,7 @@ id: GO:0007219
name: Notch signaling pathway
namespace: biological_process
alt_id: GO:0030179
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:go_curators, GOC:signaling]
+def: "The series of molecular signals initiated by an extracellular ligand binding to the receptor Notch on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:go_curators, GOC:signaling]
synonym: "N signaling pathway" EXACT []
synonym: "N signalling pathway" EXACT []
synonym: "Notch receptor signaling pathway" EXACT []
@@ -69772,7 +69778,7 @@ name: Notch receptor processing
namespace: biological_process
def: "The series of successive proteolytic cleavages of the Notch protein, which result in an active form of the receptor." [PMID:12651094, PMID:14986688]
synonym: "N receptor processing" EXACT []
-is_a: GO:0044267 ! cellular protein metabolic process
+is_a: GO:0019538 ! protein metabolic process
[Term]
id: GO:0007221
@@ -69800,7 +69806,7 @@ is_a: GO:0035567 ! non-canonical Wnt signaling pathway
id: GO:0007224
name: smoothened signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened." [GOC:mah, PMID:15205520]
+def: "The series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened." [GOC:mah, PMID:15205520]
synonym: "hedgehog signaling pathway" EXACT []
synonym: "hh signaling pathway" NARROW []
synonym: "hh signalling pathway" NARROW []
@@ -69842,7 +69848,7 @@ relationship: part_of GO:0007227 ! signal transduction downstream of smoothened
id: GO:0007229
name: integrin-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling]
+def: "The series of molecular signals initiated by an extracellular ligand binding to an integrin on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling]
synonym: "integrin-mediated signalling pathway" EXACT []
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -69874,7 +69880,7 @@ is_a: GO:0071470 ! cellular response to osmotic stress
id: GO:0007232
name: osmosensory signaling pathway via Sho1 osmosensor
namespace: biological_process
-def: "A series of molecular signals generated in response to osmotic change, as mediated through a Sho1 osmosensor system." [GOC:jl]
+def: "The series of molecular signals generated in response to osmotic change, as mediated through a Sho1 osmosensor system." [GOC:jl]
synonym: "osmosensory signalling pathway via Sho1 osmosensor" EXACT []
synonym: "signal transduction during osmotic stress via Sho1 osmosensor" EXACT []
is_a: GO:0007231 ! osmosensory signaling pathway
@@ -69883,7 +69889,7 @@ is_a: GO:0007231 ! osmosensory signaling pathway
id: GO:0007234
name: osmosensory signaling via phosphorelay pathway
namespace: biological_process
-def: "A series of molecular signals generated in response to osmotic change, as mediated through a phosphorelay system." [PMID:9843501]
+def: "The series of molecular signals generated in response to osmotic change, as mediated through a phosphorelay system." [PMID:9843501]
synonym: "osmolarity sensing via two-component system" EXACT []
synonym: "osmolarity signaling pathway via two-component system" EXACT []
synonym: "osmolarity signalling pathway via two-component system" EXACT []
@@ -70170,7 +70176,7 @@ is_a: GO:0019932 ! second-messenger-mediated signaling
id: GO:0007264
name: small GTPase mediated signal transduction
namespace: biological_process
-def: "Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals." [GOC:mah]
+def: "The series of molecular signals in which a small monomeric GTPase relays a signal." [GOC:mah]
synonym: "small GTPase-mediated signal transduction" EXACT []
is_a: GO:0035556 ! intracellular signal transduction
@@ -70178,7 +70184,7 @@ is_a: GO:0035556 ! intracellular signal transduction
id: GO:0007265
name: Ras protein signal transduction
namespace: biological_process
-def: "A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state." [GOC:bf]
+def: "The series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state." [GOC:bf]
synonym: "Ras mediated signal transduction" EXACT []
is_a: GO:0007264 ! small GTPase mediated signal transduction
@@ -70186,7 +70192,7 @@ is_a: GO:0007264 ! small GTPase mediated signal transduction
id: GO:0007266
name: Rho protein signal transduction
namespace: biological_process
-def: "A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state." [GOC:bf]
+def: "The series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state." [GOC:bf]
synonym: "Rho mediated signal transduction" EXACT []
is_a: GO:0007265 ! Ras protein signal transduction
@@ -70194,7 +70200,7 @@ is_a: GO:0007265 ! Ras protein signal transduction
id: GO:0007267
name: cell-cell signaling
namespace: biological_process
-def: "Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions." [GOC:dos, GOC:mah]
+def: "Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions." [GOC:dos, GOC:mah]
subset: goslim_chembl
subset: goslim_plant
synonym: "cell-cell signalling" EXACT []
@@ -70500,13 +70506,13 @@ relationship: part_of GO:0007292 ! female gamete generation
[Term]
id: GO:0007297
-name: ovarian follicle cell migration
+name: follicle cell of egg chamber migration
namespace: biological_process
def: "The directed movement of an ovarian follicle cell that takes place during oogenesis. During egg chamber formation, follicle cells migrate to envelop the germ-line cysts and move in between cysts. At stage 10B, follicle cells migrate centripetally between the nurse cells and the oocyte, enclosing the anterior of the egg. An example of this is found in Drosophila melanogaster." [GOC:mtg_sensu, PMID:10822261]
synonym: "follicle cell migration" BROAD []
is_a: GO:0010631 ! epithelial cell migration
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
-relationship: part_of GO:0030707 ! ovarian follicle cell development
+relationship: part_of GO:0030707 ! follicle cell of egg chamber development
[Term]
id: GO:0007298
@@ -70514,18 +70520,18 @@ name: border follicle cell migration
namespace: biological_process
def: "The directed movement of a border cell through the nurse cells to reach the oocyte. An example of this is found in Drosophila melanogaster." [GOC:mtg_sensu, PMID:10822261]
synonym: "border cell migration" BROAD []
-is_a: GO:0007297 ! ovarian follicle cell migration
+is_a: GO:0007297 ! follicle cell of egg chamber migration
[Term]
id: GO:0007299
-name: ovarian follicle cell-cell adhesion
+name: follicle cell of egg chamber-cell adhesion
namespace: biological_process
def: "The attachment of a somatic follicle cell to another somatic follicle cell or to its substratum, the germline cells. An example of this is found in Drosophila melanogaster." [GOC:bf, GOC:mtg_sensu, PMID:12642496]
synonym: "follicle cell adhesion" BROAD []
synonym: "ovarian follicle cell adhesion" EXACT []
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
is_a: GO:0090136 ! epithelial cell-cell adhesion
-relationship: part_of GO:0030707 ! ovarian follicle cell development
+relationship: part_of GO:0030707 ! follicle cell of egg chamber development
[Term]
id: GO:0007300
@@ -70571,7 +70577,7 @@ namespace: biological_process
def: "The construction of a chorion-containing eggshell. An example of this is found in Drosophila melanogaster." [GOC:mah, GOC:mtg_sensu]
synonym: "eggshell formation" BROAD []
is_a: GO:0030703 ! eggshell formation
-relationship: part_of GO:0030707 ! ovarian follicle cell development
+relationship: part_of GO:0030707 ! follicle cell of egg chamber development
[Term]
id: GO:0007305
@@ -70584,16 +70590,15 @@ relationship: part_of GO:0007304 ! chorion-containing eggshell formation
[Term]
id: GO:0007306
-name: eggshell chorion assembly
+name: egg chorion assembly
namespace: biological_process
-def: "Construction of the chorion portion of the eggshell, which comprises the channels for gas exchange in an insect eggshell." [GOC:dph, GOC:mtg_sensu, GOC:tb, ISBN:0879694238]
-synonym: "eggshell chorion formation" EXACT [GOC:dph, GOC:tb]
+def: "Construction of the chorion portion of the egg, which is a protective, noncellular membrane that surrounds the eggs of various animals including insects and fish." [GOC:dph, GOC:mtg_sensu, GOC:tb, ISBN:0879694238, PMID:24804966]
+synonym: "eggshell chorion formation" RELATED [GOC:dph, GOC:tb]
synonym: "insect chorion formation" RELATED []
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0010927 ! cellular component assembly involved in morphogenesis
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
is_a: GO:0045229 ! external encapsulating structure organization
-relationship: part_of GO:0007304 ! chorion-containing eggshell formation
[Term]
id: GO:0007307
@@ -70602,7 +70607,7 @@ namespace: biological_process
def: "Amplification by up to 60-fold of the loci containing the chorion gene clusters. Amplification is necessary for the rapid synthesis of chorion proteins by the follicle cells, and occurs by repeated firing of one or more origins located within each gene cluster." [GOC:mtg_sensu, PMID:11157771]
is_a: GO:0006277 ! DNA amplification
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
-relationship: part_of GO:0007306 ! eggshell chorion assembly
+relationship: part_of GO:0007306 ! egg chorion assembly
[Term]
id: GO:0007308
@@ -70679,6 +70684,7 @@ synonym: "oocyte nucleus migration during oocyte axis determination" EXACT [GOC:
synonym: "oocyte nucleus migration during oocyte axis specification" RELATED [GOC:dph, GOC:tb]
synonym: "oocyte nucleus positioning during oocyte axis determination" BROAD []
is_a: GO:0007097 ! nuclear migration
+is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
is_a: GO:0051663 ! oocyte nucleus localization involved in oocyte dorsal/ventral axis specification
[Term]
@@ -70748,7 +70754,7 @@ synonym: "establishment and maintenance of pole plasm protein localization" EXAC
synonym: "oocyte pole plasm protein localization" EXACT []
synonym: "pole plasm protein localisation" EXACT [GOC:mah]
is_a: GO:0008104 ! protein localization
-is_a: GO:0022414 ! reproductive process
+is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
relationship: part_of GO:0007315 ! pole plasm assembly
[Term]
@@ -70794,18 +70800,17 @@ is_a: GO:0051604 ! protein maturation
[Term]
id: GO:0007329
-name: positive regulation of transcription from RNA polymerase II promoter by pheromones
+name: obsolete positive regulation of transcription from RNA polymerase II promoter by pheromones
namespace: biological_process
-def: "Any process involving pheromones that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:go_curators]
+def: "OBSOLETE. Any process involving pheromones that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:go_curators]
+comment: This term has been obsoleted because it represents a GO-CAM model.
synonym: "activation of transcription from RNA polymerase II promoter by pheromones" NARROW []
synonym: "positive regulation of transcription from Pol II promoter by pheromones" EXACT []
synonym: "stimulation of transcription from RNA polymerase II promoter by pheromones" NARROW []
synonym: "up regulation of transcription from RNA polymerase II promoter by pheromones" EXACT []
synonym: "up-regulation of transcription from RNA polymerase II promoter by pheromones" EXACT []
synonym: "upregulation of transcription from RNA polymerase II promoter by pheromones" EXACT []
-is_a: GO:0009371 ! positive regulation of transcription by pheromones
-is_a: GO:0046019 ! regulation of transcription from RNA polymerase II promoter by pheromones
-is_a: GO:1901522 ! positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus
+is_obsolete: true
[Term]
id: GO:0007336
@@ -71129,6 +71134,7 @@ namespace: biological_process
def: "The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry." [GOC:dph, GOC:jid]
synonym: "determination of left/right asymmetry" EXACT [GOC:dph]
is_a: GO:0009855 ! determination of bilateral symmetry
+relationship: part_of GO:0060972 ! left/right pattern formation
[Term]
id: GO:0007369
@@ -71517,7 +71523,7 @@ is_a: GO:0007414 ! axonal defasciculation
id: GO:0007416
name: synapse assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional)." [GOC:mah]
+def: "The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional)." [GOC:mah]
subset: goslim_synapse
synonym: "synapse biogenesis" EXACT [GOC:mah]
synonym: "synaptogenesis" EXACT [GOC:mah]
@@ -71765,9 +71771,7 @@ id: GO:0007444
name: imaginal disc development
namespace: biological_process
def: "The process whose specific outcome is the progression of the imaginal disc over time, from its formation to the metamorphosis to form adult structures. Imaginal discs are epithelial infoldings in the larvae of holometabolous insects that develop into adult structures (legs, antennae, wings, etc.)." [GOC:bf, ISBN:0879694238]
-is_a: GO:0035295 ! tube development
is_a: GO:0048513 ! animal organ development
-is_a: GO:0060429 ! epithelium development
[Term]
id: GO:0007445
@@ -71782,7 +71786,7 @@ id: GO:0007446
name: imaginal disc growth
namespace: biological_process
def: "The increase in mass of imaginal discs by cell proliferation prior to metamorphosis. Imaginal discs are epithelial infoldings in the larvae of holometabolous insects that develop into adult structures (legs, antennae, wings, etc.) during metamorphosis from larval to adult form." [GOC:bf, GOC:jid, PMID:10679387]
-is_a: GO:0035265 ! organ growth
+is_a: GO:0048589 ! developmental growth
relationship: part_of GO:0007444 ! imaginal disc development
[Term]
@@ -71914,7 +71918,7 @@ id: GO:0007468
name: obsolete regulation of rhodopsin gene expression
namespace: biological_process
def: "OBSOLETE. Any process that modulates the frequency, rate or extent of rhodopsin gene expression. This includes transcriptional, translational, or posttranslational regulation." [GOC:dph, GOC:go_curators, GOC:tb]
-comment: This term was obsoleted because it referes to a specific gene product. The gene product should be captured as an annotation extension using 'has input'.
+comment: This term was obsoleted because it refers to a specific gene product. The gene product should be captured as an annotation extension using 'has input'.
synonym: "regulation of rhodopsin gene activity" EXACT [GOC:dph, GOC:tb]
is_obsolete: true
consider: GO:0006357
@@ -72241,8 +72245,8 @@ id: GO:0007506
name: gonadal mesoderm development
namespace: biological_process
def: "The process whose specific outcome is the progression of the gonadal mesoderm over time, from its formation to the mature structure. The gonadal mesoderm is the middle layer of the three primary germ layers of the embryo which will go on to form the gonads of the organism." [GOC:ai]
+is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0007498 ! mesoderm development
-is_a: GO:0048608 ! reproductive structure development
is_a: GO:0060485 ! mesenchyme development
relationship: part_of GO:0008406 ! gonad development
@@ -72336,7 +72340,7 @@ namespace: biological_process
alt_id: GO:0048637
def: "The developmental sequence of events leading to the formation of adult skeletal muscle tissue. The main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers." [GOC:mtg_muscle]
synonym: "myogenesis" RELATED []
-is_a: GO:0014706 ! striated muscle tissue development
+is_a: GO:0060537 ! muscle tissue development
relationship: part_of GO:0060538 ! skeletal muscle organ development
[Term]
@@ -72433,7 +72437,6 @@ name: mating type determination
namespace: biological_process
def: "Any process that establishes and transmits the specification of mating type upon an individual. Mating types are the equivalent in microorganisms of the sexes in higher organisms." [http://www.biology-text.com/]
is_a: GO:0007530 ! sex determination
-is_a: GO:0045165 ! cell fate commitment
[Term]
id: GO:0007532
@@ -72442,7 +72445,7 @@ namespace: biological_process
def: "Any mating-type specific process that modulates the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH]
synonym: "mating-type specific transcriptional control" EXACT []
synonym: "regulation of mating-type specific transcription, DNA-dependent" EXACT [GOC:txnOH]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
is_a: GO:0007531 ! mating type determination
[Term]
@@ -72587,9 +72590,9 @@ is_a: GO:0003006 ! developmental process involved in reproduction
id: GO:0007549
name: dosage compensation
namespace: biological_process
-def: "Compensating for the variation in the unpaired sex chromosome:autosome chromosome ratios between sexes by activation or inactivation of genes on one or both of the sex chromosomes." [GOC:ems, ISBN:0140512888, PMID:11498577]
+def: "Compensating for the variation in the unpaired sex chromosome:autosome chromosome ratios between sexes by activation or inactivation of genes on one or both of the sex chromosomes." [GOC:ems, PMID:11498577, PMID:35306885]
xref: Wikipedia:Dosage_compensation
-is_a: GO:0040029 ! regulation of gene expression, epigenetic
+is_a: GO:0040029 ! epigenetic regulation of gene expression
[Term]
id: GO:0007550
@@ -72709,7 +72712,6 @@ alt_id: GO:0007452
def: "The process in which the anatomical structures derived from an imaginal disc are generated and organized. The imaginal discs are epithelial infoldings in the larvae of holometabolous insects that develop into adult appendages (legs, antennae, wings, etc.) during metamorphosis from larval to adult form." [GOC:jid]
synonym: "imaginal disc metamorphosis" EXACT []
is_a: GO:0048563 ! post-embryonic animal organ morphogenesis
-is_a: GO:0060562 ! epithelial tube morphogenesis
relationship: part_of GO:0007444 ! imaginal disc development
relationship: part_of GO:0007552 ! metamorphosis
relationship: part_of GO:0048707 ! instar larval or pupal morphogenesis
@@ -72783,25 +72785,26 @@ is_a: GO:0044706 ! multi-multicellular organism process
[Term]
id: GO:0007568
-name: aging
+name: obsolete aging
namespace: biological_process
alt_id: GO:0016280
-def: "A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700)." [GOC:PO_curators]
+def: "OBSOLETE. A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700)." [GOC:PO_curators]
+comment: The reason for obsoletion is that this represents a phenotype.
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
synonym: "ageing" EXACT []
xref: Wikipedia:Aging
-is_a: GO:0032502 ! developmental process
+is_obsolete: true
[Term]
id: GO:0007569
-name: cell aging
+name: obsolete cell aging
namespace: biological_process
-def: "An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469)." [GOC:PO_curators]
+def: "OBSOLETE. An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469)." [GOC:PO_curators]
+comment: This term was obsoleted because it represents a phenotype.
synonym: "cell ageing" EXACT []
-is_a: GO:0007568 ! aging
-is_a: GO:0048869 ! cellular developmental process
+is_obsolete: true
+consider: GO:0090398
[Term]
id: GO:0007570
@@ -72811,19 +72814,18 @@ def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
comment: This term was made obsolete because it does not describe a biological process.
synonym: "age dependent accumulation of genetic damage" EXACT []
is_obsolete: true
-consider: GO:0001301
[Term]
id: GO:0007571
-name: age-dependent general metabolic decline
+name: obsolete age-dependent general metabolic decline
namespace: biological_process
-def: "A developmental process that arises as the cell progresses toward the end of its lifespan and cause changes cellular metabolism, resulting in a decline in cell function; for example, one aspect of general metabolic decline is a decrease in the efficiency of protein synthesis." [GOC:jh, GOC:mah, PMID:9891807]
+def: "OBSOLETE. A developmental process that arises as the cell progresses toward the end of its lifespan and cause changes cellular metabolism, resulting in a decline in cell function; for example, one aspect of general metabolic decline is a decrease in the efficiency of protein synthesis." [GOC:jh, GOC:mah, PMID:9891807]
+comment: This term was obsolete because it represents a phenotype.
synonym: "age-dependent decreased translational activity" NARROW []
synonym: "age-dependent increased protein content" NARROW []
synonym: "age-dependent yeast cell size increase" RELATED []
synonym: "nucleolar size increase" NARROW []
-is_a: GO:0032502 ! developmental process
-relationship: part_of GO:0007568 ! aging
+is_obsolete: true
[Term]
id: GO:0007572
@@ -72833,7 +72835,6 @@ def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
comment: This term was made obsolete because it does not describe a biological process.
synonym: "age dependent decreased translational activity" EXACT []
is_obsolete: true
-consider: GO:0007571
[Term]
id: GO:0007573
@@ -72843,7 +72844,6 @@ def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
comment: This term was made obsolete because it does not describe a biological process.
synonym: "age dependent increased protein content" EXACT []
is_obsolete: true
-consider: GO:0007571
[Term]
id: GO:0007574
@@ -72853,7 +72853,6 @@ def: "OBSOLETE. Process associated with continued cell division (budding) by the
comment: This term was made obsolete because it does not describe a biological process that is distinct from 'cell aging'.
synonym: "cell aging (sensu Saccharomyces)" EXACT []
is_obsolete: true
-replaced_by: GO:0007569
[Term]
id: GO:0007575
@@ -72863,18 +72862,16 @@ def: "OBSOLETE. The process of nucleolar expansion." [GOC:ai]
comment: This term was made obsolete because it does not describe a biological process.
synonym: "nucleolar size increase" EXACT []
is_obsolete: true
-consider: GO:0007571
-consider: GO:0007576
[Term]
id: GO:0007576
-name: nucleolar fragmentation
+name: obsolete nucleolar fragmentation
namespace: biological_process
alt_id: GO:0046616
-def: "The cell aging process that results in the nucleolus breaking down into fragments." [GOC:mah, PMID:9271578]
+def: "OBSOLETE. The cell aging process that results in the nucleolus breaking down into fragments." [GOC:mah, PMID:9271578]
+comment: This term was obsoleted because it represents a readout.
synonym: "nucleolar size increase" RELATED []
-is_a: GO:0007000 ! nucleolus organization
-relationship: part_of GO:0007569 ! cell aging
+is_obsolete: true
[Term]
id: GO:0007577
@@ -72907,13 +72904,14 @@ is_obsolete: true
[Term]
id: GO:0007580
-name: extrachromosomal circular DNA accumulation involved in cell aging
+name: obsolete extrachromosomal circular DNA accumulation involved in cell aging
namespace: biological_process
-def: "Increase in abundance, as cells age, of circular DNA molecules that originate in the chromosome but are excised and circularized, often by intramolecular homologous recombination between direct tandem repeats, and replicated independently of chromosomal replication." [GOC:jh, PMID:9891807]
-comment: Note that the term string was changed to be consistent with placement of this term in cell aging hierarchy.
+def: "OBSOLETE. Increase in abundance, as cells age, of circular DNA molecules that originate in the chromosome but are excised and circularized, often by intramolecular homologous recombination between direct tandem repeats, and replicated independently of chromosomal replication." [GOC:jh, PMID:9891807]
+comment: This term was obsoleted because it represents a phenotype.
synonym: "extrachromosomal circular DNA accumulation during cell ageing" RELATED []
synonym: "extrachromosomal circular DNA accumulation during cell aging" RELATED [GOC:dph, GOC:tb]
-is_a: GO:0001301 ! progressive alteration of chromatin involved in cell aging
+is_obsolete: true
+consider: GO:0043007
[Term]
id: GO:0007581
@@ -72923,7 +72921,6 @@ def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:sgd_curators
comment: This term was made obsolete because it does not describe a biological process.
synonym: "age-dependent yeast cell size increase" EXACT []
is_obsolete: true
-consider: GO:0007571
[Term]
id: GO:0007583
@@ -73197,7 +73194,7 @@ synonym: "behaviour" EXACT []
synonym: "behavioural response to stimulus" EXACT []
synonym: "single-organism behavior" RELATED []
xref: Wikipedia:Behavior
-is_a: GO:0008150 ! biological_process
+is_a: GO:0032501 ! multicellular organismal process
[Term]
id: GO:0007611
@@ -73254,7 +73251,6 @@ def: "The behavioral interactions between organisms for the purpose of mating, o
synonym: "mating behaviour" EXACT []
xref: Wikipedia:Mating_behaviour
is_a: GO:0019098 ! reproductive behavior
-relationship: part_of GO:0007618 ! mating
[Term]
id: GO:0007618
@@ -73277,7 +73273,7 @@ id: GO:0007620
name: copulation
namespace: biological_process
def: "The act of sexual union between male and female, involving the transfer of sperm." [ISBN:0721662544]
-is_a: GO:0007618 ! mating
+is_a: GO:0007617 ! mating behavior
[Term]
id: GO:0007621
@@ -73299,7 +73295,6 @@ synonym: "rhythmic behavioral response to stimulus" EXACT []
synonym: "rhythmic behaviour" EXACT []
synonym: "rhythmic behavioural response to stimulus" EXACT []
is_a: GO:0007610 ! behavior
-is_a: GO:0048511 ! rhythmic process
[Term]
id: GO:0007623
@@ -73418,7 +73413,6 @@ synonym: "behavioural response to visual stimulus" EXACT []
synonym: "visual behaviour" EXACT []
is_a: GO:0007610 ! behavior
is_a: GO:0009416 ! response to light stimulus
-is_a: GO:0032501 ! multicellular organismal process
[Term]
id: GO:0007633
@@ -73577,7 +73571,6 @@ synonym: "cadherin" NARROW []
synonym: "calcium-dependent cell adhesion molecule activity" EXACT []
is_obsolete: true
consider: GO:0005515
-consider: GO:0016021
consider: GO:0016339
[Term]
@@ -73657,10 +73650,10 @@ relationship: part_of GO:0098793 ! presynapse
[Term]
id: GO:0008022
-name: protein C-terminus binding
+name: obsolete protein C-terminus binding
namespace: molecular_function
-def: "Binding to a protein C-terminus, the end of a peptide chain at which the 1-carboxyl function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN:0198506732]
-subset: goslim_chembl
+def: "OBSOLETE. Binding to a protein C-terminus, the end of a peptide chain at which the 1-carboxyl function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN:0198506732]
+comment: It is out of GO scope.
synonym: "C-terminal binding" EXACT []
synonym: "C-terminal end binding" EXACT [GOC:sl]
synonym: "carboxy-terminal binding" RELATED [GOC:jsg]
@@ -73671,7 +73664,8 @@ synonym: "carboxylate-terminal binding" RELATED [GOC:jsg]
synonym: "carboxylate-terminus binding" NARROW [GOC:jsg]
synonym: "COOH-terminal binding" NARROW [GOC:jsg]
synonym: "COOH-terminus binding" NARROW [GOC:jsg, GOC:sl]
-is_a: GO:0005515 ! protein binding
+is_obsolete: true
+replaced_by: GO:0005515
[Term]
id: GO:0008023
@@ -73929,7 +73923,10 @@ relationship: part_of GO:0007423 ! sensory organ development
id: GO:0008053
name: mitochondrial fusion
namespace: biological_process
-def: "Merging of two or more mitochondria within a cell to form a single compartment." [PMID:11038192]
+alt_id: GO:1990613
+def: "Merging of two or more mitochondria within a cell to form a single compartment." [PMID:11038192, PMID:12052774]
+synonym: "mitochondrial membrane fusion" RELATED []
+synonym: "mitochondrion fusion" EXACT []
is_a: GO:0007005 ! mitochondrion organization
is_a: GO:0048284 ! organelle fusion
@@ -73937,7 +73934,7 @@ is_a: GO:0048284 ! organelle fusion
id: GO:0008055
name: ocellus pigment biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of ocellus pigments, general or particular coloring matter in living organisms, found or utilized in the ocellus, a minute simple eye found in many invertebrates." [GOC:ai, PMID:15176085, PMID:18421706]
+def: "The chemical reactions and pathways resulting in the formation of ocellus pigments, general or particular coloring matter in living organisms, found or utilized in the ocellus, a minute simple eye found in many invertebrates." [GOC:ai, PMID:15176085, PMID:18421706]
synonym: "ocellus pigment anabolism" EXACT []
synonym: "ocellus pigment biosynthesis" EXACT []
synonym: "ocellus pigment formation" EXACT []
@@ -73995,7 +73992,7 @@ relationship: part_of GO:0007562 ! eclosion
id: GO:0008063
name: Toll signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Toll on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:go_curators, PMID:11135568, PMID:19126860]
+def: "The series of molecular signals initiated by an extracellular ligand binding to the receptor Toll on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:go_curators, PMID:11135568, PMID:19126860]
synonym: "Tl signaling pathway" EXACT []
synonym: "Tl signalling pathway" EXACT []
synonym: "Toll signalling pathway" EXACT []
@@ -74045,12 +74042,12 @@ is_obsolete: true
id: GO:0008068
name: extracellularly glutamate-gated chloride channel activity
namespace: molecular_function
-def: "Enables the transmembrane transfer of a chloride ion by a channel that opens when glutamate is bound by the channel complex or one of its constituent parts on the extracellular side of the plasma membrane." [GOC:mtg_transport, ISBN:0815340729]
+def: "Enables the transmembrane transfer of a chloride ion by a channel that opens when glutamate is bound by the channel complex or one of its constituent parts on the extracellular side of the plasma membrane." [GOC:mtg_transport, ISBN:0815340729]
comment: Note that this term represents an activity and not a gene product. Consider also annotating to the molecular function term 'glutamate receptor activity ; GO:0008066'.
synonym: "extracellular-glutamate-gated chloride channel activity" EXACT []
is_a: GO:0005234 ! extracellularly glutamate-gated ion channel activity
is_a: GO:0005254 ! chloride channel activity
-is_a: GO:0099095 ! ligand-gated anion channel activity
+is_a: GO:0099095 ! ligand-gated monoatomic anion channel activity
[Term]
id: GO:0008069
@@ -74065,7 +74062,7 @@ is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0009950 ! dorsal/ventral axis specification
is_a: GO:0016334 ! establishment or maintenance of polarity of follicular epithelium
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
-relationship: part_of GO:0030707 ! ovarian follicle cell development
+relationship: part_of GO:0030707 ! follicle cell of egg chamber development
[Term]
id: GO:0008070
@@ -74100,7 +74097,7 @@ name: guanylate cyclase complex, soluble
namespace: cellular_component
def: "Complex that possesses guanylate cyclase activity and is not bound to a membrane." [GOC:mah]
comment: See also the molecular function term 'guanylate cyclase activity ; GO:0004383'.
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005829 ! cytosol
[Term]
@@ -74125,7 +74122,6 @@ synonym: "voltage-sensitive potassium channel complex" EXACT []
xref: NIF_Subcellular:sao371494298
is_a: GO:0034705 ! potassium channel complex
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0008077
@@ -74213,7 +74209,7 @@ def: "Enables the transmembrane transfer of a calcium ion by a voltage-gated cha
synonym: "light-activated voltage gated calcium channel activity" EXACT []
synonym: "light-activated voltage-dependent calcium channel activity" EXACT []
is_a: GO:0005245 ! voltage-gated calcium channel activity
-is_a: GO:0010461 ! light-activated ion channel activity
+is_a: GO:0010461 ! light-activated monoatomic ion channel activity
[Term]
id: GO:0008087
@@ -74277,6 +74273,7 @@ subset: goslim_flybase_ribbon
subset: goslim_generic
subset: goslim_mouse
subset: goslim_yeast
+subset: prokaryote_subset
is_a: GO:0005515 ! protein binding
[Term]
@@ -74350,14 +74347,19 @@ id: GO:0008104
name: protein localization
namespace: biological_process
alt_id: GO:0008105
+alt_id: GO:0016249
+alt_id: GO:0034613
def: "Any process in which a protein is transported to, or maintained in, a specific location." [GOC:ai]
subset: goslim_drosophila
synonym: "asymmetric protein localisation" RELATED [GOC:mah]
synonym: "asymmetric protein localization" RELATED []
+synonym: "cellular protein localisation" EXACT [GOC:mah]
+synonym: "cellular protein localization" EXACT []
+synonym: "channel localizer activity" NARROW [GOC:mah]
synonym: "establishment and maintenance of asymmetric protein localization" RELATED []
synonym: "establishment and maintenance of protein localization" RELATED []
synonym: "protein localisation" EXACT [GOC:mah]
-is_a: GO:0033036 ! macromolecule localization
+is_a: GO:0070727 ! cellular macromolecule localization
[Term]
id: GO:0008106
@@ -74542,7 +74544,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0008115
name: sarcosine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + O(2) + sarcosine = formaldehyde + glycine + H(2)O(2)." [EC:1.5.3.1, RHEA:13313]
+def: "Catalysis of the reaction: H2O + O2 + sarcosine = formaldehyde + glycine + H2O2." [EC:1.5.3.1, RHEA:13313]
synonym: "sarcosine:oxygen oxidoreductase (demethylating)" RELATED [EC:1.5.3.1]
xref: EC:1.5.3.1
xref: KEGG_REACTION:R00610
@@ -74619,6 +74621,8 @@ xref: EC:2.1.1.67
xref: MetaCyc:THIOPURINE-S-METHYLTRANSFERASE-RXN
xref: Reactome:R-HSA-158609 "TPMT transfers CH3 from AdoMet to 6MP"
xref: Reactome:R-HSA-5603379 "TPMT does not transfer CH3 from AdoMet to 6MP"
+xref: Reactome:R-HSA-9748979 "TPMT transfers methyl group to 6TIMP, forming 6MeTIMP"
+xref: Reactome:R-HSA-9748983 "TPMT transfers methyl group to 6MP, forming 6MeMP"
is_a: GO:0008172 ! S-methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
@@ -74675,7 +74679,7 @@ is_a: GO:0009055 ! electron transfer activity
is_a: GO:0015078 ! proton transmembrane transporter activity
is_a: GO:0015453 ! oxidoreduction-driven active transmembrane transporter activity
is_a: GO:0016679 ! oxidoreductase activity, acting on diphenols and related substances as donors
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0008123
@@ -74698,7 +74702,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0008124
name: 4-alpha-hydroxytetrahydrobiopterin dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (6R)-6-(L-erythro-1,2-dihydroxypropyl)-5,6,7,8-tetrahydro-4a-hydroxypterin = (6R)-6-(L-erythro-1,2-dihydroxypropyl)-7,8-dihydro-6H-pterin + H(2)O." [EC:4.2.1.96, RHEA:11920]
+def: "Catalysis of the reaction: (6R)-6-(L-erythro-1,2-dihydroxypropyl)-5,6,7,8-tetrahydro-4a-hydroxypterin = (6R)-6-(L-erythro-1,2-dihydroxypropyl)-7,8-dihydro-6H-pterin + H2O." [EC:4.2.1.96, RHEA:11920]
synonym: "(6R)-6-(L-erythro-1,2-dihydroxypropyl)-5,6,7,8-tetrahydro-4a-hydroxypterin hydro-lyase [(6R)-6-(L-erythro-1,2-dihydroxypropyl)-7,8-dihydro-6H-pterin-forming]" RELATED [EC:4.2.1.96]
synonym: "4-alpha-hydroxy-tetrahydropterin dehydratase activity" RELATED [EC:4.2.1.96]
synonym: "4a-hydroxytetrahydrobiopterin dehydratase activity" EXACT []
@@ -74749,7 +74753,7 @@ is_a: GO:0034338 ! short-chain carboxylesterase activity
id: GO:0008127
name: quercetin 2,3-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + O(2) + quercetin = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO." [EC:1.13.11.24, RHEA:15381]
+def: "Catalysis of the reaction: H+ + O2 + quercetin = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO." [EC:1.13.11.24, RHEA:15381]
synonym: "flavonol 2,4-oxygenase activity" RELATED [EC:1.13.11.24]
synonym: "quercetin:oxygen 2,3-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.24]
synonym: "quercetinase activity" RELATED [EC:1.13.11.24]
@@ -74844,6 +74848,7 @@ subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_yeast
synonym: "TF binding" EXACT []
+synonym: "transcription regulator binding" RELATED []
is_a: GO:0005515 ! protein binding
[Term]
@@ -74855,14 +74860,13 @@ subset: goslim_chembl
subset: goslim_plant
subset: goslim_yeast
synonym: "translation factor activity, nucleic acid binding" BROAD [GOC:mah]
-is_a: GO:0003723 ! RNA binding
is_a: GO:0090079 ! translation regulator activity, nucleic acid binding
[Term]
id: GO:0008137
name: NADH dehydrogenase (ubiquinone) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADH + ubiquinone + 5 H(+)(in) <=> NAD(+) + ubiquinol + 4 H(+)(out)." [RHEA:29091]
+def: "Catalysis of the reaction: NADH + ubiquinone + 5 H+(in) <=> NAD+ + ubiquinol + 4 H+(out)." [RHEA:29091]
synonym: "coenzyme Q reductase activity" RELATED [EC:7.1.1.2]
synonym: "complex 1 dehydrogenase activity" RELATED [EC:7.1.1.2]
synonym: "complex I (electron transport chain) activity" RELATED [EC:7.1.1.2]
@@ -74988,6 +74992,7 @@ xref: Reactome:R-HSA-176588 "lithocholate + PAPS => lithocholate sulfate + PAP"
xref: Reactome:R-HSA-176604 "taurolithocholate + PAPS => taurolithocholate sulfate + PAP"
xref: Reactome:R-HSA-176669 "N-hydroxy-2-acetylaminofluorene + PAPS => 2-acetylaminofluorene-N-sulfate + PAP"
xref: Reactome:R-HSA-2022061 "Dermatan sulfate can be further sulfated on position 2 of iduronate"
+xref: Reactome:R-HSA-9753277 "SULT dimers sulfate APAP to APAP-SO3"
is_a: GO:0016782 ! transferase activity, transferring sulphur-containing groups
[Term]
@@ -75025,9 +75030,8 @@ namespace: biological_process
alt_id: GO:0000004
alt_id: GO:0007582
alt_id: GO:0044699
-def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt]
+def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt]
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
@@ -75079,7 +75083,7 @@ synonym: "para-aminobenzoic acid formation" EXACT []
synonym: "para-aminobenzoic acid synthesis" EXACT []
synonym: "vitamin Bx biosynthesis" EXACT []
synonym: "vitamin Bx biosynthetic process" EXACT []
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
+is_a: GO:0008652 ! amino acid biosynthetic process
is_a: GO:0009073 ! aromatic amino acid family biosynthetic process
is_a: GO:0046482 ! para-aminobenzoic acid metabolic process
is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
@@ -75112,7 +75116,7 @@ synonym: "down-regulation of DNA replication" EXACT []
synonym: "downregulation of DNA replication" EXACT []
synonym: "inhibition of DNA replication" NARROW []
is_a: GO:0006275 ! regulation of DNA replication
-is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process
+is_a: GO:0051053 ! negative regulation of DNA metabolic process
relationship: negatively_regulates GO:0006260 ! DNA replication
[Term]
@@ -75144,7 +75148,7 @@ consider: GO:0032786
id: GO:0008160
name: protein tyrosine phosphatase activator activity
namespace: molecular_function
-def: "Binds to and increases the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a tyrosyl phenolic group of a protein." [GOC:ai, ISBN:0198506732]
+def: "Binds to and increases the activity of a phosphotyrosine phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a tyrosyl phenolic group of a protein." [GOC:ai, ISBN:0198506732]
is_a: GO:0072542 ! protein phosphatase activator activity
[Term]
@@ -75232,6 +75236,7 @@ xref: Reactome:R-HSA-379387 "COMT transfers Met to DA to form 3MT"
xref: Reactome:R-HSA-379464 "COMT transfers Met to DOPAC to form HVA"
xref: Reactome:R-HSA-6800149 "N6AMT1:TRMT112 transfers CH3 group from AdoMet to MMAIII"
xref: Reactome:R-HSA-71286 "guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine"
+xref: Reactome:R-HSA-9710490 "The GSDME gene promoter is hypermethylated"
is_a: GO:0016741 ! transferase activity, transferring one-carbon groups
[Term]
@@ -75394,6 +75399,8 @@ synonym: "ATPase activity, acting on RNA" EXACT []
synonym: "ATPase, acting on RNA" EXACT []
synonym: "RNA-dependent adenosinetriphosphatase activity" EXACT []
synonym: "RNA-dependent ATPase activity" EXACT []
+xref: Reactome:R-HSA-9770847 "Spliceosomal P complex dissociates yielding the intron-containing complex (ILS) and the spliced mRNP (new)"
+xref: Reactome:R-HSA-9772351 "Disassembly of the Intron Lariat Spliceosome (new)"
is_a: GO:0140657 ! ATP-dependent activity
[Term]
@@ -75443,6 +75450,7 @@ name: RNA guanylyltransferase activity
namespace: molecular_function
def: "Catalysis of the posttranscriptional addition of a guanyl residue to the 5' end of an RNA molecule." [GOC:mah]
is_a: GO:0070568 ! guanylyltransferase activity
+is_a: GO:0140098 ! catalytic activity, acting on RNA
[Term]
id: GO:0008193
@@ -75452,6 +75460,7 @@ def: "Catalysis of the posttranscriptional addition of a guanyl residue to the 5
xref: EC:2.7.7.79
xref: RHEA:54564
is_a: GO:0008192 ! RNA guanylyltransferase activity
+is_a: GO:0140101 ! catalytic activity, acting on a tRNA
[Term]
id: GO:0008194
@@ -75466,7 +75475,7 @@ id: GO:0008195
name: phosphatidate phosphatase activity
namespace: molecular_function
alt_id: GO:0004606
-def: "Catalysis of the reaction: a 1,2-diacylglycerol 3-phosphate + H2O = a 1,2-diacyl-sn-glycerol + phosphate." [EC:3.1.3.4, GOC:pr]
+def: "Catalysis of the reaction: a 1,2-diacylglycerol 3-phosphate + H2O = a 1,2-diacyl-sn-glycerol + phosphate." [GOC:pr, RHEA:27429]
synonym: "3-sn-phosphatidate phosphohydrolase activity" RELATED [EC:3.1.3.4]
synonym: "acid phosphatidyl phosphatase activity" RELATED [EC:3.1.3.4]
synonym: "phosphatic acid phosphatase activity" RELATED [EC:3.1.3.4]
@@ -75519,6 +75528,7 @@ name: ferric iron binding
namespace: molecular_function
def: "Binding to a ferric iron ion, Fe(III)." [GOC:ai]
is_a: GO:0005506 ! iron ion binding
+is_a: GO:1901681 ! sulfur compound binding
[Term]
id: GO:0008200
@@ -75564,7 +75574,6 @@ def: "The chemical reactions and pathways involving ergosterol, (22E)-ergosta-5,
synonym: "ergosterol metabolism" EXACT []
is_a: GO:0016125 ! sterol metabolic process
is_a: GO:0016128 ! phytosteroid metabolic process
-is_a: GO:0044107 ! cellular alcohol metabolic process
is_a: GO:0044255 ! cellular lipid metabolic process
is_a: GO:1902652 ! secondary alcohol metabolic process
@@ -75595,7 +75604,8 @@ namespace: biological_process
def: "The chemical reactions and pathways involving C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones." [GOC:ai]
synonym: "C21-steroid hormone metabolism" EXACT []
is_a: GO:0008202 ! steroid metabolic process
-is_a: GO:0034754 ! cellular hormone metabolic process
+is_a: GO:0009987 ! cellular process
+is_a: GO:0042445 ! hormone metabolic process
[Term]
id: GO:0008208
@@ -75616,7 +75626,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics." [ISBN:0198506732]
synonym: "androgen metabolism" EXACT []
is_a: GO:0008202 ! steroid metabolic process
-is_a: GO:0034754 ! cellular hormone metabolic process
+is_a: GO:0042445 ! hormone metabolic process
[Term]
id: GO:0008210
@@ -75627,7 +75637,7 @@ synonym: "estrogen metabolism" EXACT []
synonym: "oestrogen metabolic process" EXACT []
synonym: "oestrogen metabolism" EXACT []
is_a: GO:0008202 ! steroid metabolic process
-is_a: GO:0034754 ! cellular hormone metabolic process
+is_a: GO:0042445 ! hormone metabolic process
[Term]
id: GO:0008211
@@ -75646,7 +75656,8 @@ namespace: biological_process
def: "The chemical reactions and pathways involving mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Mineralocorticoids act primarily on water and electrolyte balance." [ISBN:0198506732]
synonym: "mineralocorticoid metabolism" EXACT []
is_a: GO:0008202 ! steroid metabolic process
-is_a: GO:0034754 ! cellular hormone metabolic process
+is_a: GO:0009987 ! cellular process
+is_a: GO:0042445 ! hormone metabolic process
[Term]
id: GO:0008213
@@ -75655,7 +75666,7 @@ namespace: biological_process
def: "The addition of an alkyl group to a protein amino acid. Alkyl groups are derived from alkanes by removal of one hydrogen atom." [GOC:ma]
subset: goslim_yeast
synonym: "protein amino acid alkylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0008214
@@ -75663,7 +75674,7 @@ name: protein dealkylation
namespace: biological_process
def: "The removal of an alkyl group from a protein amino acid. Alkyl groups are derived from alkanes by removal of one hydrogen atom." [GOC:ai]
synonym: "protein amino acid dealkylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0008215
@@ -75709,11 +75720,6 @@ name: cell death
namespace: biological_process
def: "Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538)." [GOC:mah, GOC:mtg_apoptosis, PMID:25236395]
comment: This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term.
-subset: goslim_agr
-subset: goslim_chembl
-subset: goslim_drosophila
-subset: goslim_mouse
-subset: goslim_plant
synonym: "accidental cell death" RELATED []
synonym: "necrosis" RELATED []
is_a: GO:0009987 ! cellular process
@@ -75827,7 +75833,6 @@ namespace: molecular_function
alt_id: GO:0070010
alt_id: GO:0070011
def: "Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid." [GOC:jl, ISBN:0815332181]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -75842,7 +75847,8 @@ synonym: "protease activity" EXACT []
synonym: "proteinase activity" NARROW []
xref: EC:3.4.-.-
xref: Reactome:R-HSA-205112 "gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6"
-xref: Reactome:R-HSA-3000243 "Unknown protease degrades GIF:Cbl to release Cbl"
+xref: Reactome:R-HSA-3000243 "Unknown lysosomal protease degrades CBLIF:RCbl to release Cbl"
+xref: Reactome:R-HSA-3000263 "TCN2:RCbl is degraded to release RCbl"
xref: Reactome:R-HSA-3065958 "An unknown protease degrades ACACA"
xref: Reactome:R-HSA-3065959 "An unknown protease degrades hCBXs"
xref: Reactome:R-HSA-3139027 "Maturation of HIV Virion"
@@ -75852,7 +75858,6 @@ xref: Reactome:R-HSA-448678 "CTSG cleaves CASP1(1-404)"
xref: Reactome:R-HSA-5655483 "USP1 autocleavage"
xref: Reactome:R-HSA-5684864 "NAPSA, CTSH, PGA3-5 cleave pro-SFTPB"
xref: Reactome:R-HSA-5685902 "NAPSA, CTSH, PGA3-5 cleave pro-SFTPC"
-xref: Reactome:R-HSA-5693319 "CTRC hydrolyses PRSS1"
xref: Reactome:R-HSA-6803060 "DCD(63-110) is processed to DCD(63-109)"
is_a: GO:0016787 ! hydrolase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -75869,6 +75874,7 @@ xref: Reactome:R-HSA-2022381 "Cathepsin Z (Cathepsin X) hydrolyzes Angiotensin-(
xref: Reactome:R-HSA-2467775 "Autocleavage of ESPL1 (Separase)"
xref: Reactome:R-HSA-2467809 "ESPL1 (Separase) cleaves centromeric cohesin"
xref: Reactome:R-HSA-5660752 "USP9X deubiquitinates Ub-SNCA"
+xref: Reactome:R-HSA-9757951 "CASP8 cleaves N4BP1 at D424, D490"
is_a: GO:0008233 ! peptidase activity
[Term]
@@ -75887,7 +75893,7 @@ def: "Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a c
synonym: "serine protease activity" NARROW []
xref: Reactome:R-HSA-1461993 "pro-HD5 is cleaved by trypsin"
xref: Reactome:R-HSA-2022383 "Chymase hydrolyzes Angiotensin-(1-10) to Angiotensin-(1-8)"
-xref: Reactome:R-HSA-3132753 "Pancreatic proteases degrade TCN1:Cbl"
+xref: Reactome:R-HSA-3132753 "Pancreatic proteases degrade TCN1:RCbl"
xref: Reactome:R-HSA-6801766 "Trypsin cleaves REG3A or REG3G to generate REG3A,G(38-175)"
is_a: GO:0008233 ! peptidase activity
is_a: GO:0017171 ! serine hydrolase activity
@@ -75902,9 +75908,9 @@ synonym: "metalloproteinase activity" NARROW [GOC:mah]
xref: Reactome:R-HSA-157629 "NOTCH2-ligand complex is cleaved to produce NEXT2"
xref: Reactome:R-HSA-157632 "Complex of NOTCH1 with its ligand is cleaved to produce NEXT1"
xref: Reactome:R-HSA-193679 "alpha-secretase cleaves the p75NTR extracellular domain"
-xref: Reactome:R-HSA-2022368 "Neprilysin hydrolyzes Angiotensin-(1-9) to Angiotensin-(1-7)"
+xref: Reactome:R-HSA-2022368 "MME:Zn2+ hydrolyses AGT(34-42)"
xref: Reactome:R-HSA-2022393 "ANPEP hydrolyzes Angiotensin-(2-8) to Angiotensin-(3-8)"
-xref: Reactome:R-HSA-2022396 "Neprilysin hydrolyzes Angiotensin-(1-10) to Angiotensin-(1-7)"
+xref: Reactome:R-HSA-2022396 "MME:Zn2+ hydrolyses AGT(34-43)"
xref: Reactome:R-HSA-2022399 "ENPEP hydrolyzes Angiotensin-(1-8) to Angiotensin-(2-8)"
xref: Reactome:R-HSA-2220944 "ADAM10/17 cleaves ligand-bound NOTCH1 PEST domain mutants to produce NEXT1 PEST domain mutants"
xref: Reactome:R-HSA-2220976 "NOTCH1 HD+PEST domain mutants are cleaved by ADAM10/17 irrespective of ligand binding"
@@ -76115,6 +76121,7 @@ xref: Reactome:R-HSA-5694126 "NT5C3B hydrolyses 7MGP to 7MG"
xref: Reactome:R-HSA-74248 "(d)GMP or (d)IMP + H2O => (2'-deoxy)guanosine or (2'-deoxy)inosine + orthophosphate (NT5C2)"
xref: Reactome:R-HSA-8940070 "NT5E:Zn2+ hydrolyses NAD+"
xref: Reactome:R-HSA-8940074 "NT5E:Zn2+ hydrolyses NMN"
+xref: Reactome:R-HSA-9755078 "NT5C2 tetramer dephosphorylates RBV-MP"
xref: RHEA:12484
is_a: GO:0008252 ! nucleotidase activity
@@ -76146,9 +76153,8 @@ name: protein histidine pros-kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + protein L-histidine = ADP + protein N(pi)-phospho-L-histidine." [EC:2.7.13.1]
synonym: "ATP:protein-L-histidine N-pros-phosphotransferase activity" RELATED [EC:2.7.13.1]
-synonym: "ATP:protein-L-histidine Npi-phosphotransferase activity" RELATED [EC:2.7.13.1]
-synonym: "HK2" RELATED [EC:2.7.13.1]
-synonym: "protein-histidine pros-kinase activity" RELATED [EC:2.7.13.1]
+synonym: "ATP:protein-L-histidine Npi-phosphotransferase activity" EXACT [EC:2.7.13.1]
+synonym: "protein-histidine pros-kinase activity" EXACT []
xref: EC:2.7.13.1
xref: MetaCyc:2.7.13.1-RXN
xref: RHEA:22720
@@ -76161,8 +76167,7 @@ namespace: molecular_function
def: "Catalysis of the reaction: ATP + protein L-histidine = ADP + protein N(tau)-phospho-L-histidine." [EC:2.7.13.2]
synonym: "ATP:protein-L-histidine N-tele-phosphotransferase activity" RELATED [EC:2.7.13.2]
synonym: "ATP:protein-L-histidine Ntau-phosphotransferase activity" RELATED [EC:2.7.13.2]
-synonym: "HK3" RELATED [EC:2.7.13.2]
-synonym: "protein-histidine tele-kinase activity" RELATED [EC:2.7.13.2]
+synonym: "protein-histidine tele-kinase activity" EXACT [EC:2.7.13.2]
xref: EC:2.7.13.2
xref: MetaCyc:2.7.13.2-RXN
xref: RHEA:11860
@@ -76192,24 +76197,24 @@ consider: GO:0050431
[Term]
id: GO:0008260
-name: 3-oxoacid CoA-transferase activity
+name: succinyl-CoA:3-oxo-acid CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: succinyl-CoA + a 3-oxo acid = succinate + a 3-oxo-acyl-CoA." [EC:2.8.3.5]
-synonym: "3-ketoacid CoA-transferase activity" RELATED [EC:2.8.3.5]
-synonym: "3-ketoacid coenzyme A transferase activity" RELATED [EC:2.8.3.5]
+alt_id: GO:0106424
+def: "Catalysis of the reaction: succinyl-CoA + a 3-oxo acid = succinate + a 3-oxo-acyl-CoA." [GOC:vw, PMID:10964512, PMID:8844009, RHEA:24564]
synonym: "3-oxo-CoA transferase activity" RELATED [EC:2.8.3.5]
synonym: "3-oxoacid CoA dehydrogenase activity" RELATED [EC:2.8.3.5]
+synonym: "3-oxoacid CoA-transferase activity" EXACT []
synonym: "3-oxoacid coenzyme A-transferase activity" RELATED [EC:2.8.3.5]
synonym: "acetoacetate succinyl-CoA transferase activity" RELATED [EC:2.8.3.5]
synonym: "acetoacetyl coenzyme A-succinic thiophorase activity" RELATED [EC:2.8.3.5]
synonym: "succinyl coenzyme A-acetoacetyl coenzyme A-transferase activity" RELATED [EC:2.8.3.5]
+synonym: "succinyl-CoA 3-ketoacid-CoA transferase activity" RELATED []
synonym: "succinyl-CoA transferase activity" RELATED [EC:2.8.3.5]
-synonym: "succinyl-CoA:3-ketoacid-CoA transferase activity" RELATED [EC:2.8.3.5]
-synonym: "succinyl-CoA:3-oxo-acid CoA-transferase activity" RELATED [EC:2.8.3.5]
+synonym: "Succinyl-CoA:3-ketoacid-CoA transferase" EXACT []
xref: EC:2.8.3.5
xref: MetaCyc:3-OXOACID-COA-TRANSFERASE-RXN
xref: Reactome:R-HSA-74177 "OXCT dimers transfer CoA from SUCC-CoA to ACA, forming ACA-CoA"
-xref: RHEA:25480
+xref: RHEA:24564
is_a: GO:0008410 ! CoA-transferase activity
[Term]
@@ -76291,7 +76296,6 @@ synonym: "sulfate porter activity" RELATED []
synonym: "sulphate porter activity" EXACT []
is_a: GO:0015116 ! sulfate transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0008272
@@ -76301,6 +76305,7 @@ alt_id: GO:0006870
def: "The directed movement of sulfate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
synonym: "sulphate transport" EXACT []
is_a: GO:0015698 ! inorganic anion transport
+is_a: GO:0071705 ! nitrogen compound transport
is_a: GO:0072348 ! sulfur compound transport
[Term]
@@ -76316,7 +76321,7 @@ xref: Reactome:R-HSA-5626270 "Defective SLC24A4 does not exchange extracellular
xref: Reactome:R-HSA-5626316 "SLC24A5 exchanges cytosolic 4Na+ for Golgi luminal Ca2+, K+"
xref: Reactome:R-HSA-5626356 "Defective SLC24A5 does not exchange cytosolic 4Na+ for Golgi luminal Ca2+, K+"
is_a: GO:0005432 ! calcium:sodium antiporter activity
-is_a: GO:0022821 ! potassium ion antiporter activity
+is_a: GO:0022821 ! solute:potassium antiporter activity
[Term]
id: GO:0008275
@@ -76337,7 +76342,8 @@ is_a: GO:0000930 ! gamma-tubulin complex
id: GO:0008276
name: protein methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a methyl group (CH3-) to a protein." [GOC:jl, ISBN:0198506732]
+def: "Catalysis of the transfer of a methyl group (CH3-) to a protein." [GOC:jl]
+synonym: "protein methylase activity" EXACT []
xref: Reactome:R-HSA-9632182 "PRMT1 methylates ESRs"
is_a: GO:0008168 ! methyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -76361,6 +76367,7 @@ relationship: regulates GO:0007186 ! G protein-coupled receptor signaling pathwa
id: GO:0008278
name: cohesin complex
namespace: cellular_component
+alt_id: GO:0000798
alt_id: GO:0008279
alt_id: GO:0008280
alt_id: GO:0043222
@@ -76369,11 +76376,12 @@ subset: goslim_pir
synonym: "14S cohesin" NARROW []
synonym: "9S cohesin" NARROW []
synonym: "cohesin core heterodimer" RELATED []
+synonym: "nuclear cohesin complex" RELATED []
synonym: "SMC complex" RELATED []
synonym: "SMC/kleisin ring complex" EXACT []
synonym: "Smc1-Smc3 complex" NARROW []
is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0000793 ! condensed chromosome
+relationship: part_of GO:0005694 ! chromosome
[Term]
id: GO:0008281
@@ -76404,7 +76412,6 @@ synonym: "Kir6.x complex" RELATED []
synonym: "Kir6.x-SURx complex" RELATED []
is_a: GO:0034705 ! potassium channel complex
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0008283
@@ -76491,6 +76498,7 @@ subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
+subset: prokaryote_subset
is_a: GO:0005488 ! binding
[Term]
@@ -76508,9 +76516,9 @@ name: acetylcholine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues." [GOC:jl, GOC:nln, ISBN:0192800752]
synonym: "acetylcholine metabolism" EXACT []
-is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0042133 ! neurotransmitter metabolic process
is_a: GO:1900619 ! acetate ester metabolic process
+is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
id: GO:0008292
@@ -76524,12 +76532,13 @@ synonym: "acetylcholine synthesis" EXACT []
is_a: GO:0008291 ! acetylcholine metabolic process
is_a: GO:0042136 ! neurotransmitter biosynthetic process
is_a: GO:1900620 ! acetate ester biosynthetic process
+is_a: GO:1901566 ! organonitrogen compound biosynthetic process
[Term]
id: GO:0008293
name: torso signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to torso (a receptor tyrosine kinase) on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:go_curators, PMID:8343949]
+def: "The series of molecular signals initiated by an extracellular ligand binding to torso (a receptor tyrosine kinase) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:go_curators, PMID:8343949]
synonym: "torso signalling pathway" EXACT []
is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway
@@ -76560,13 +76569,14 @@ is_a: GO:0008216 ! spermidine metabolic process
[Term]
id: GO:0008296
-name: 3'-5'-exodeoxyribonuclease activity
+name: 3'-5'-DNA exonuclease activity
namespace: molecular_function
def: "Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a DNA molecule." [GOC:mah]
synonym: "3'-5' exodeoxyribonuclease activity" EXACT []
+synonym: "3'-5'-exodeoxyribonuclease activity" EXACT []
xref: Reactome:R-HSA-9023943 "MRN:CtIP exonucleolytically hydrolyzes DNA 3' to SPO11 and SPO11:double-strand break dissociates to SPO11:oligonucleotide and resected 5' end"
is_a: GO:0008408 ! 3'-5' exonuclease activity
-is_a: GO:0016895 ! exodeoxyribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016895 ! DNA exonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0008297
@@ -76575,7 +76585,7 @@ namespace: molecular_function
def: "Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of a single-stranded DNA molecule." [GOC:mah]
synonym: "single-stranded DNA specific exodeoxyribonuclease activity" RELATED []
synonym: "ssDNA-specific exodeoxyribonuclease activity" RELATED [GOC:mah]
-is_a: GO:0016895 ! exodeoxyribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016895 ! DNA exonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0008298
@@ -76679,7 +76689,6 @@ def: "A protein complex that is composed of one alpha subunit and one beta subun
synonym: "laminin receptor protein" RELATED []
is_a: GO:0098636 ! protein complex involved in cell adhesion
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0008306
@@ -76702,15 +76711,16 @@ is_a: GO:0005198 ! structural molecule activity
[Term]
id: GO:0008308
-name: voltage-gated anion channel activity
+name: voltage-gated monoatomic anion channel activity
namespace: molecular_function
alt_id: GO:0022844
def: "Enables the transmembrane transfer of an anion by a voltage-gated channel. An anion is a negatively charged ion. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded." [GOC:mtg_transport, GOC:vw, ISBN:0815340729]
synonym: "voltage-dependent ion-selective channel activity" RELATED []
+synonym: "voltage-gated anion channel activity" BROAD []
synonym: "voltage-gated ion-selective channel activity" RELATED []
xref: Reactome:R-HSA-9012374 "VDAC1 transports PYR from cytosol to mitochondrial intermembrane space"
-is_a: GO:0005244 ! voltage-gated ion channel activity
-is_a: GO:0005253 ! anion channel activity
+is_a: GO:0005244 ! voltage-gated monoatomic ion channel activity
+is_a: GO:0005253 ! monoatomic anion channel activity
[Term]
id: GO:0008309
@@ -76718,25 +76728,34 @@ name: double-stranded DNA exodeoxyribonuclease activity
namespace: molecular_function
def: "Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of a double-stranded DNA molecule." [GOC:mah]
synonym: "double-stranded DNA specific exodeoxyribonuclease activity" RELATED []
-is_a: GO:0016895 ! exodeoxyribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016895 ! DNA exonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0008310
-name: single-stranded DNA 3'-5' exodeoxyribonuclease activity
+name: single-stranded DNA 3'-5' DNA exonuclease activity
namespace: molecular_function
def: "Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a single-stranded DNA molecule." [GOC:mah, PMID:22562358]
+synonym: "exonuclease I activity" NARROW []
+synonym: "single-stranded DNA 3'-5' exodeoxyribonuclease activity" EXACT []
synonym: "single-stranded DNA specific 3'-5' exodeoxyribonuclease activity" RELATED []
synonym: "ssDNA-specific 3'-5' exodeoxyribonuclease activity" RELATED [GOC:mah]
-is_a: GO:0008296 ! 3'-5'-exodeoxyribonuclease activity
+xref: EC:3.1.11.1
+xref: MetaCyc:3.1.11.1-RXN
+is_a: GO:0008296 ! 3'-5'-DNA exonuclease activity
is_a: GO:0008297 ! single-stranded DNA exodeoxyribonuclease activity
[Term]
id: GO:0008311
-name: double-stranded DNA 3'-5' exodeoxyribonuclease activity
+name: double-stranded DNA 3'-5' DNA exonuclease activity
namespace: molecular_function
def: "Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA molecule." [GOC:mah, PMID:22562358]
+synonym: "double-stranded DNA 3'-5' exodeoxyribonuclease activity" EXACT []
synonym: "double-stranded DNA specific 3'-5' exodeoxyribonuclease activity" RELATED []
-is_a: GO:0008296 ! 3'-5'-exodeoxyribonuclease activity
+synonym: "exonuclease III activity" NARROW []
+synonym: "exoribonuclease III activity" NARROW []
+xref: EC:3.1.11.2
+xref: MetaCyc:3.1.11.2-RXN
+is_a: GO:0008296 ! 3'-5'-DNA exonuclease activity
is_a: GO:0008309 ! double-stranded DNA exodeoxyribonuclease activity
[Term]
@@ -76748,11 +76767,12 @@ is_a: GO:0003723 ! RNA binding
[Term]
id: GO:0008313
-name: gurken-activated receptor activity
+name: obsolete gurken-activated receptor activity
namespace: molecular_function
-def: "Combining with the ligand Gurken to initiate a change in cell activity." [GOC:bf]
+def: "OBSOLETE. Combining with the ligand Gurken to initiate a change in cell activity." [GOC:bf]
+comment: This term was obsoleted because it represents a receptor by its ligand.
synonym: "gurken receptor activity" EXACT [GOC:bf, GOC:signaling]
-is_a: GO:0005006 ! epidermal growth factor-activated receptor activity
+is_obsolete: true
[Term]
id: GO:0008314
@@ -76820,7 +76840,7 @@ alt_id: GO:0015463
def: "Enables the transfer of a protein from one side of a membrane to the other." [GOC:jl]
synonym: "protein channel activity" RELATED []
xref: Reactome:R-HSA-1268022 "TOMM40 complex translocates proteins from the cytosol to the mitochondrial intermembrane space"
-xref: Reactome:R-HSA-1299475 "TIMM23 PAM translocates proteins from the mitochndrial intermebrane space to the mitochondrial matrix"
+xref: Reactome:R-HSA-1299475 "TIMM23 PAM translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix"
xref: Reactome:R-HSA-184269 "Monoubiquitinated N-myristoyl GAG polyprotein is targeted to the late endosomal vesicle membrane by the ESCRT-I complex"
xref: Reactome:R-HSA-3149434 "Transport of GAG to the Plasma Membrane"
xref: Reactome:R-HSA-5205661 "Pink1 is recruited from the cytoplasm to the mitochondria"
@@ -76854,11 +76874,12 @@ replaced_by: GO:0030536
[Term]
id: GO:0008324
-name: cation transmembrane transporter activity
+name: monoatomic cation transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of cation from one side of a membrane to the other." [GOC:dgf, GOC:mtg_transport, ISBN:0815340729]
+synonym: "cation transmembrane transporter activity" BROAD []
synonym: "transmembrane cation transporter activity" EXACT []
-is_a: GO:0015075 ! ion transmembrane transporter activity
+is_a: GO:0015075 ! monoatomic ion transmembrane transporter activity
[Term]
id: GO:0008327
@@ -76873,9 +76894,8 @@ id: GO:0008328
name: ionotropic glutamate receptor complex
namespace: cellular_component
def: "A multimeric assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand-gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex." [http://www.bris.ac.uk/Depts/Synaptic/info/glutamate.html]
-is_a: GO:0034702 ! ion channel complex
+is_a: GO:0034702 ! monoatomic ion channel complex
is_a: GO:0098878 ! neurotransmitter receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0008330
@@ -76940,7 +76960,7 @@ relationship: part_of GO:0007300 ! ovarian nurse cell to oocyte transport
id: GO:0008336
name: gamma-butyrobetaine dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + 4-(trimethylammonio)butanoate + O(2) = carnitine + CO(2) + succinate." [EC:1.14.11.1, RHEA:24028]
+def: "Catalysis of the reaction: 2-oxoglutarate + 4-(trimethylammonio)butanoate + O2 = carnitine + CO2 + succinate." [EC:1.14.11.1, RHEA:24028]
synonym: "4-trimethylammoniobutanoate,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)" RELATED [EC:1.14.11.1]
synonym: "alpha-butyrobetaine hydroxylase activity" RELATED [EC:1.14.11.1]
synonym: "butyrobetaine hydroxylase activity" RELATED [EC:1.14.11.1]
@@ -76965,7 +76985,6 @@ synonym: "selectin" EXACT []
is_obsolete: true
consider: GO:0005102
consider: GO:0007155
-consider: GO:0016021
consider: GO:0030246
consider: GO:0050839
@@ -76973,9 +76992,8 @@ consider: GO:0050839
id: GO:0008340
name: determination of adult lifespan
namespace: biological_process
-def: "The control of viability and duration in the adult phase of the life-cycle." [GOC:ems]
+def: "The pathways that regulate the duration of the adult phase of the life-cycle of an animal." [PMID:25561524, PMID:273723695, PMID:3424805]
is_a: GO:0032501 ! multicellular organismal process
-relationship: part_of GO:0010259 ! multicellular organism aging
[Term]
id: GO:0008341
@@ -77061,6 +77079,7 @@ synonym: "inhibition of antimicrobial humoral response" NARROW []
is_a: GO:0002759 ! regulation of antimicrobial humoral response
is_a: GO:0002832 ! negative regulation of response to biotic stimulus
is_a: GO:0002921 ! negative regulation of humoral immune response
+is_a: GO:0031348 ! negative regulation of defense response
is_a: GO:0032102 ! negative regulation of response to external stimulus
relationship: negatively_regulates GO:0019730 ! antimicrobial humoral response
@@ -77111,14 +77130,12 @@ relationship: part_of GO:0005815 ! microtubule organizing center
id: GO:0008353
name: RNA polymerase II CTD heptapeptide repeat kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + (DNA-directed RNA polymerase II) = ADP + phospho-(DNA-directed RNA polymerase II); phosphorylation occurs on residues in the carboxy-terminal domain (CTD) repeats." [EC:2.7.11.23, GOC:mah]
+def: "Catalysis of the reaction: ATP + RNA polymerase II large subunit CTD heptapeptide repeat (consensus YSPTSPS) = ADP + H+ + phosphorylated RNA polymerase II." [EC:2.7.11.23, GOC:mah, PMID:28248323]
synonym: "[RNA-polymerase]-subunit kinase activity" BROAD []
-synonym: "ATP:DNA-directed RNA polymerase phosphotransferase activity" BROAD [EC:2.7.11.23]
synonym: "CTD kinase activity" RELATED [EC:2.7.11.23]
synonym: "RNA polymerase II carboxy-terminal domain kinase activity" EXACT []
synonym: "RNA polymerase subunit kinase activity" BROAD [EC:2.7.11.23]
synonym: "RNA-polymerase-subunit kinase activity" BROAD [EC:2.7.11.23]
-synonym: "STK9" RELATED [EC:2.7.11.23]
xref: EC:2.7.11.23
xref: MetaCyc:RNA-POLYMERASE-SUBUNIT-KINASE-RXN
xref: Reactome:R-HSA-167191 "Hyperphosphorylation (Ser2) of RNA Pol II CTD by the P-TEFb(Cyclin T1:Cdk9) complex"
@@ -77126,6 +77143,7 @@ xref: Reactome:R-HSA-170704 "Phosphorylation of DSIF by the P-TEFb(Cyclin T1:Cdk
xref: Reactome:R-HSA-170706 "Phosphorylation of NEFL by the P-TEFb(Cyclin T1:Cdk9) complex"
xref: RHEA:10216
is_a: GO:0004674 ! protein serine/threonine kinase activity
+is_a: GO:0140994 ! RNA polymerase II CTD heptapeptide repeat modifying activity
[Term]
id: GO:0008354
@@ -77284,7 +77302,7 @@ def: "Catalysis of the transfer of sialic acid to an acceptor molecule, typicall
xref: Reactome:R-HSA-9683769 "O-glycosylation of 3a is terminated"
xref: Reactome:R-HSA-9694718 "O-glycosylation of 3a is terminated"
xref: Reactome:R-HSA-9697018 "Addition of sialic acids on some Spike glycosyl sidechains"
-xref: Reactome:R-HSA-981814 "GalNAc alpha-2,6-sialyltransferase II can add a sialic acid to the T antigen at the alpha 6 position"
+xref: Reactome:R-HSA-981814 "ST6GALNAC2 transfers sialic acid to Core 1 mucins"
is_a: GO:0016757 ! glycosyltransferase activity
[Term]
@@ -77354,7 +77372,7 @@ id: GO:0008379
name: thioredoxin peroxidase activity
namespace: molecular_function
alt_id: GO:0009031
-def: "Catalysis of the reaction: thioredoxin + hydrogen peroxide = thioredoxin disulfide + H2O." [RHEA:63528]
+def: "Catalysis of the reaction: [thioredoxin]-dithiol + hydrogen peroxide = [thioredoxin]-disulfide + H2O." [RHEA:63528]
synonym: "thiol peroxidase activity" EXACT []
synonym: "TPx activity" EXACT []
synonym: "TrxPx activity" EXACT []
@@ -77365,8 +77383,7 @@ xref: Reactome:R-HSA-3341343 "PRDX1,2,5 catalyze TXN reduced + H2O2 => TXN oxidi
xref: Reactome:R-HSA-3697882 "PRDX5 reduces peroxynitrite to nitrite using TXN"
xref: Reactome:R-HSA-3697894 "PRDX5 reduces peroxynitrite to nitrite using TXN2"
xref: RHEA:63528
-is_a: GO:0004601 ! peroxidase activity
-is_a: GO:0051920 ! peroxiredoxin activity
+is_a: GO:0140824 ! thioredoxin-dependent peroxiredoxin activity
[Term]
id: GO:0008380
@@ -77381,16 +77398,16 @@ is_a: GO:0006396 ! RNA processing
[Term]
id: GO:0008381
-name: mechanosensitive ion channel activity
+name: mechanosensitive monoatomic ion channel activity
namespace: molecular_function
alt_id: GO:0022833
-def: "Enables the transmembrane transfer of an ion by a channel that opens in response to a mechanical stress." [GOC:mtg_transport, ISBN:0815340729]
+def: "Enables the transmembrane transfer of an monoatomic ion by a channel that opens in response to a mechanical stress." [GOC:mtg_transport, ISBN:0815340729]
synonym: "mechanically gated channel activity" EXACT []
synonym: "mechanically-gated channel activity" EXACT []
synonym: "mechanically-gated ion channel activity" EXACT []
+synonym: "mechanosensitive ion channel activity" BROAD []
xref: TC:1.A.23.2.1
-is_a: GO:0005216 ! ion channel activity
-is_a: GO:0022836 ! gated channel activity
+is_a: GO:0022839 ! monoatomic ion gated channel activity
[Term]
id: GO:0008384
@@ -77551,6 +77568,7 @@ xref: Reactome:R-HSA-5602170 "CYP27A1 does not 27-hydroxylate 5bCHOL3a,7a,12a-tr
xref: Reactome:R-HSA-6785244 "Defective CYP11B2 does not oxidise 18HCORST"
xref: Reactome:R-HSA-6785245 "Defective CYP11B2 does not oxidise CORST"
xref: Reactome:R-HSA-9035960 "Defective CYP27A1 does not 27-hydroxylate 5-CHOL3,7,24(s)-triol"
+xref: Reactome:R-HSA-9758674 "CYP3A4 oxidizes PREDN,PREDL"
xref: RHEA:43836
is_a: GO:0004497 ! monooxygenase activity
@@ -77573,8 +77591,9 @@ name: sterol 12-alpha-hydroxylase activity
namespace: molecular_function
def: "Catalysis of the reaction: a steroid + donor-H2 + O2 = 12-alpha-hydroxysteroid + H2O." [GOC:mah]
synonym: "cytochrome P450 CYP8B1" NARROW []
+xref: EC:1.14.14.139
is_a: GO:0008395 ! steroid hydroxylase activity
-is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0008398
@@ -77725,14 +77744,14 @@ is_a: GO:0002094 ! polyprenyltransferase activity
id: GO:0008413
name: 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) + H2O = 8-oxo-7,8-dihydroguanosine diphosphate (8-oxo-GDP) + phosphate. 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for transcription." [PMID:15878881, RHEA:60032]
+def: "Catalysis of the reaction: 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) + H2O = 8-oxo-7,8-dihydroguanosine diphosphate (8-oxo-GDP) + phosphate. 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for transcription." [PMID:15878881, RHEA:60032]
synonym: "7,8-dihydro-8-oxoguanine-triphosphatase activity" EXACT []
synonym: "8-oxo-7,8-dihydroguanine triphosphatase activity" EXACT []
synonym: "8-oxo-7,8-dihydroguanosine triphosphatase activity" EXACT []
synonym: "8-oxo-GTPase activity" EXACT []
xref: EC:3.6.1.69
xref: RHEA:60032
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0008414
@@ -77753,24 +77772,28 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0008418
name: protein-N-terminal asparagine amidohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: protein-L-asparagine + H2O = protein-L-aspartate + NH3. This reaction is the deamidation of an N-terminal asparagine residue in a peptide or protein." [PMID:8910481]
+def: "Catalysis of the reaction: N-terminal L-asparaginyl-[protein] + H+ + H2O = N-terminal L-aspartyl-[protein] + NH4+. This reaction is the deamidation of an N-terminal asparagine residue in a peptide or protein." [PMID:8910481, RHEA:50676]
+xref: EC:3.5.1.121
+xref: RHEA:50676
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
+is_a: GO:0140096 ! catalytic activity, acting on a protein
[Term]
id: GO:0008419
name: RNA lariat debranching enzyme activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of branched RNA structures that contain vicinal 2'-5'- and 3'-5'-phosphodiester bonds at a branch point nucleotide." [PMID:7519612]
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0008420
name: RNA polymerase II CTD heptapeptide repeat phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phospho-(DNA-directed RNA polymerase II) + H2O = (DNA-directed RNA polymerase II) + phosphate." [PMID:22622228]
+def: "Catalysis of the reaction: RNA polymerase II large subunit CTD heptapeptide repeat--phospho-L-serine/threonine (consensus YSPTSPS) + H2O = RNA polymerase II large subunit + phosphate." [PMID:22622228]
synonym: "CTD phosphatase activity" EXACT []
synonym: "RNA polymerase II carboxy-terminal domain phosphatase activity" EXACT []
is_a: GO:0004722 ! protein serine/threonine phosphatase activity
+is_a: GO:0140994 ! RNA polymerase II CTD heptapeptide repeat modifying activity
[Term]
id: GO:0008421
@@ -77792,27 +77815,30 @@ id: GO:0008422
name: beta-glucosidase activity
namespace: molecular_function
alt_id: GO:0016983
-def: "Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose." [EC:3.2.1.21]
+def: "Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose." [EC:3.2.1.21, PMID:12594539]
synonym: "amygdalase activity" NARROW [EC:3.2.1.21]
-synonym: "amygdalinase" BROAD [EC:3.2.1.21]
-synonym: "arbutinase activity" RELATED [EC:3.2.1.21]
+synonym: "amygdalinase" NARROW [EC:3.2.1.21]
+synonym: "arbutinase activity" NARROW []
synonym: "aryl-beta-glucosidase activity" RELATED [EC:3.2.1.21]
synonym: "beta-1,6-glucosidase activity" RELATED [EC:3.2.1.21]
-synonym: "beta-D-glucosidase activity" RELATED [EC:3.2.1.21]
+synonym: "beta-D-glucosidase activity" EXACT [EC:3.2.1.21]
synonym: "beta-D-glucoside glucohydrolase activity" RELATED [EC:3.2.1.21]
-synonym: "beta-glucoside glucohydrolase activity" RELATED [EC:3.2.1.21]
+synonym: "beta-glucoside glucohydrolase activity" EXACT [EC:3.2.1.21]
synonym: "cellobiase activity" NARROW [EC:3.2.1.21]
synonym: "cytokine beta-glucosidase activity" NARROW []
-synonym: "elaterase activity" NARROW [EC:3.2.1.21]
+synonym: "elaterase activity" NARROW []
synonym: "emulsin" RELATED [EC:3.2.1.21]
-synonym: "gentiobiase activity" NARROW [EC:3.2.1.21]
+synonym: "gentiobiase activity" NARROW []
synonym: "gentobiase activity" NARROW [EC:3.2.1.21]
-synonym: "limarase activity" NARROW [EC:3.2.1.21]
-synonym: "p-nitrophenyl beta-glucosidase activity" RELATED [EC:3.2.1.21]
-synonym: "primeverosidase activity" NARROW [EC:3.2.1.21]
-synonym: "salicilinase activity" NARROW [EC:3.2.1.21]
+synonym: "limarase activity" NARROW []
+synonym: "p-nitrophenyl beta-glucosidase activity" NARROW []
+synonym: "primeverosidase activity" NARROW []
+synonym: "quercetin 3'-O-beta-D-glucopyranoside hydrolase activity" NARROW []
+synonym: "quercetin 4'-O-beta-D-glucopyranoside hydrolase activity" NARROW []
+synonym: "salicilinase activity" NARROW []
xref: EC:3.2.1.21
xref: MetaCyc:3.2.1.21-RXN
+xref: MetaCyc:RXN-13785
is_a: GO:0015926 ! glucosidase activity
[Term]
@@ -77830,7 +77856,7 @@ replaced_by: GO:0004197
id: GO:0008424
name: glycoprotein 6-alpha-L-fucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl}-L-asparagine + GDP-L-fucose = N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-[alpha-L-fucosyl-(1->6)]-N-acetyl-beta-D-glucosaminyl}asparagine + GDP + H(+)." [EC:2.4.1.68, RHEA:12985]
+def: "Catalysis of the reaction: N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl}-L-asparagine + GDP-L-fucose = N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-[alpha-L-fucosyl-(1->6)]-N-acetyl-beta-D-glucosaminyl}asparagine + GDP + H+." [EC:2.4.1.68, RHEA:12985]
synonym: "FucT" RELATED [EC:2.4.1.68]
synonym: "GDP-fucose--glycoprotein fucosyltransferase activity" RELATED [EC:2.4.1.68]
synonym: "GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha(1,6)fucosyltransferase activity" RELATED [EC:2.4.1.68]
@@ -77977,7 +78003,7 @@ replaced_by: GO:0004252
id: GO:0008440
name: inositol-1,4,5-trisphosphate 3-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1D-myo-inositol 1,4,5-trisphosphate + ATP = 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ADP + 2 H(+)." [EC:2.7.1.127, RHEA:11020]
+def: "Catalysis of the reaction: 1D-myo-inositol 1,4,5-trisphosphate + ATP = 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ADP + 2 H+." [EC:2.7.1.127, RHEA:11020]
synonym: "1D-myo-inositol-trisphosphate 3-kinase activity" EXACT []
synonym: "ATP:1D-myo-inositol-1,4,5-trisphosphate 3-phosphotransferase activity" RELATED [EC:2.7.1.127]
synonym: "inositol trisphosphate 3-kinase activity" EXACT []
@@ -78036,7 +78062,7 @@ is_a: GO:0019200 ! carbohydrate kinase activity
id: GO:0008444
name: CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: sn-glycerol 3-phosphate + CDP-diacylglycerol = 3-(3-sn-phosphatidyl)-sn-glycerol 1-phosphate + CMP + H(+)." [EC:2.7.8.5, RHEA:12593]
+def: "Catalysis of the reaction: sn-glycerol 3-phosphate + CDP-diacylglycerol = 3-(3-sn-phosphatidyl)-sn-glycerol 1-phosphate + CMP + H+." [EC:2.7.8.5, RHEA:12593]
synonym: "3-phosphatidyl-1'-glycerol-3'-phosphate synthase activity" RELATED [EC:2.7.8.5]
synonym: "CDP-diacylglycerol:sn-glycerol-3-phosphate 3-phosphatidyltransferase activity" RELATED [EC:2.7.8.5]
synonym: "CDPdiacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity" RELATED [EC:2.7.8.5]
@@ -78065,7 +78091,7 @@ is_a: GO:0017169 ! CDP-alcohol phosphatidyltransferase activity
id: GO:0008445
name: D-aspartate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-aspartate + H2O + O2 = oxaloacetate + NH3 + hydrogen peroxide." [EC:1.4.3.1]
+def: "Catalysis of the reaction: D-aspartate + H2O + O2 = oxaloacetate + NH3 + hydrogen peroxide." [RHEA:12512]
synonym: "aspartic oxidase activity" RELATED [EC:1.4.3.1]
synonym: "D-aspartate:oxygen oxidoreductase (deaminating)" RELATED [EC:1.4.3.1]
synonym: "D-aspartic oxidase activity" RELATED [EC:1.4.3.1]
@@ -78074,13 +78100,12 @@ xref: MetaCyc:D-ASPARTATE-OXIDASE-RXN
xref: Reactome:R-HSA-6810076 "DDO oxidizes D-Asp to OA"
xref: RHEA:12512
is_a: GO:0003884 ! D-amino-acid oxidase activity
-is_a: GO:0015922 ! aspartate oxidase activity
[Term]
id: GO:0008446
name: GDP-mannose 4,6-dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GDP-alpha-D-mannose = GDP-4-dehydro-6-deoxy-alpha-D-mannose + H(2)O." [EC:4.2.1.47, RHEA:23820]
+def: "Catalysis of the reaction: GDP-alpha-D-mannose = GDP-4-dehydro-6-deoxy-alpha-D-mannose + H2O." [EC:4.2.1.47, RHEA:23820]
synonym: "GDP-D-mannose 4,6-dehydratase activity" RELATED [EC:4.2.1.47]
synonym: "GDP-D-mannose dehydratase activity" RELATED [EC:4.2.1.47]
synonym: "GDP-mannose 4,6-hydro-lyase (GDP-4-dehydro-6-deoxy-D-mannose-forming)" RELATED [EC:4.2.1.47]
@@ -78101,7 +78126,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0008447
name: L-ascorbate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4 L-ascorbate + O(2) <=> 4 monodehydroascorbate + 2 H(2)O." [RHEA:30243]
+def: "Catalysis of the reaction: 4 L-ascorbate + O2 <=> 4 monodehydroascorbate + 2 H2O." [RHEA:30243]
synonym: "AA oxidase activity" RELATED [EC:1.10.3.3]
synonym: "AAO" RELATED [EC:1.10.3.3]
synonym: "ascorbase activity" RELATED [EC:1.10.3.3]
@@ -78326,7 +78351,7 @@ is_a: GO:0034481 ! chondroitin sulfotransferase activity
id: GO:0008460
name: dTDP-glucose 4,6-dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H(2)O." [EC:4.2.1.46, RHEA:17221]
+def: "Catalysis of the reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O." [EC:4.2.1.46, RHEA:17221]
synonym: "dTDP-glucose 4,6-hydro-lyase (dTDP-4-dehydro-6-deoxy-D-glucose-forming)" RELATED [EC:4.2.1.46]
synonym: "dTDP-glucose 4,6-hydro-lyase activity" RELATED [EC:4.2.1.46]
synonym: "dTDPglucose 4,6-dehydratase activity" RELATED [EC:4.2.1.46]
@@ -78359,7 +78384,7 @@ replaced_by: GO:0004252
id: GO:0008463
name: formylmethionine deformylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-formyl-L-methionine + H(2)O = L-methionine + formate." [EC:3.5.1.31, RHEA:17781]
+def: "Catalysis of the reaction: N-formyl-L-methionine + H2O = L-methionine + formate." [EC:3.5.1.31, RHEA:17781]
synonym: "N-formyl-L-methionine amidohydrolase activity" RELATED [EC:3.5.1.31]
xref: EC:3.5.1.31
xref: KEGG_REACTION:R00653
@@ -78443,16 +78468,12 @@ is_a: GO:0034483 ! heparan sulfate sulfotransferase activity
[Term]
id: GO:0008469
-name: histone-arginine N-methyltransferase activity
+name: histone arginine N-methyltransferase activity
namespace: molecular_function
alt_id: GO:0016276
def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-arginine = S-adenosyl-L-homocysteine + (histone)-N-methyl-arginine." [PMID:8002954]
-synonym: "histone methyltransferase activity" BROAD []
-synonym: "histone protein methylase activity" EXACT []
-synonym: "histone protein methylase I" RELATED []
synonym: "histone-arginine N-methylase activity" EXACT [GOC:mah]
-synonym: "nuclear protein (histone) N-methyltransferase activity" EXACT []
-synonym: "protein methylase I activity" BROAD []
+synonym: "histone-arginine N-methyltransferase activity" EXACT []
synonym: "S-adenosyl-L-methionine:histone-arginine nomega-methyltransferase activity" EXACT []
synonym: "S-adenosyl-L-methionine:histone-arginine omega-N-methyltransferase activity" EXACT []
xref: Reactome:R-HSA-5205799 "CCND1:CDK4:PRMT5:pT5-WDR77 methylates arginine-9 of histone H3 (H3R8)"
@@ -78470,7 +78491,7 @@ is_a: GO:0042054 ! histone methyltransferase activity
id: GO:0008470
name: isovaleryl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-methylbutanoyl-CoA + ETF = 3-methylbut-2-enoyl-CoA + reduced ETF." [EC:1.3.8.4]
+def: "Catalysis of the reaction: 3-methylbutanoyl-CoA + H+ + oxidized [electron-transfer flavoprotein] = 3-methyl-(2E)-butenoyl-CoA + reduced [electron-transfer flavoprotein]." [PMID:25450250, PMID:7640268, RHEA:12276]
synonym: "3-methylbutanoyl-CoA:(acceptor) oxidoreductase activity" RELATED [EC:1.3.8.4]
synonym: "3-methylbutanoyl-CoA:acceptor oxidoreductase activity" RELATED [EC:1.3.8.4]
synonym: "isovaleroyl-coenzyme A dehydrogenase activity" RELATED [EC:1.3.8.4]
@@ -78510,7 +78531,7 @@ replaced_by: GO:0004181
id: GO:0008473
name: ornithine cyclodeaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-ornithine = L-proline + NH(4)(+)." [EC:4.3.1.12, RHEA:24368]
+def: "Catalysis of the reaction: L-ornithine = L-proline + NH4." [EC:4.3.1.12, RHEA:24368]
comment: Note that cyclodeaminases are lyases according to EC, whereas deaminases are hydrolases.
synonym: "L-ornithine ammonia-lyase (cyclizing)" RELATED [EC:4.3.1.12]
synonym: "L-ornithine ammonia-lyase (cyclizing; L-proline-forming)" RELATED [EC:4.3.1.12]
@@ -78636,15 +78657,18 @@ id: GO:0008479
name: queuine tRNA-ribosyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: tRNA guanine + queuine = tRNA queuine + guanine." [EC:2.4.2.29]
-synonym: "[tRNA]-guanine:queuine tRNA-D-ribosyltransferase activity" RELATED [EC:2.4.2.29]
+synonym: "[tRNA]-guanine:queuine tRNA-D-ribosyltransferase activity" EXACT [EC:2.4.2.29]
+synonym: "eTGT" EXACT []
synonym: "guanine insertion enzyme activity" RELATED [EC:2.4.2.29]
-synonym: "guanine, queuine-tRNA transglycosylase activity" RELATED [EC:2.4.2.29]
-synonym: "Q-insertase activity" RELATED [EC:2.4.2.29]
-synonym: "queuine transfer ribonucleate ribosyltransferase activity" RELATED [EC:2.4.2.29]
-synonym: "transfer ribonucleate glycosyltransferase activity" RELATED [EC:2.4.2.29]
-synonym: "tRNA guanine transglycosidase activity" RELATED [EC:2.4.2.29]
-synonym: "tRNA transglycosylase activity" RELATED [EC:2.4.2.29]
-synonym: "tRNA-guanine transglycosylase activity" RELATED [EC:2.4.2.29]
+synonym: "guanine, queuine-tRNA transglycosylase activity" EXACT [EC:2.4.2.29]
+synonym: "Q-insertase activity" EXACT [EC:2.4.2.29]
+synonym: "queuine transfer ribonucleate ribosyltransferase activity" EXACT [EC:2.4.2.29]
+synonym: "transfer ribonucleate glycosyltransferase activity" EXACT [EC:2.4.2.29]
+synonym: "tRNA guanine transglycosidase activity" EXACT [EC:2.4.2.29]
+synonym: "tRNA guanine transglycosylase" EXACT []
+synonym: "tRNA transglycosylase activity" EXACT [EC:2.4.2.29]
+synonym: "tRNA-guanine transglycosylase activity" EXACT [EC:2.4.2.29]
+synonym: "tRNA-guanosine(34) preQ1 transglycosylase." EXACT []
xref: EC:2.4.2.29
xref: MetaCyc:QUEUOSINE-TRNA-RIBOSYLTRANSFERASE-RXN
xref: Reactome:R-HSA-6782443 "QTRT1:QTRTD1 exchange guanine for queuosine at guanosine-34 of tRNA(Tyr)"
@@ -78691,7 +78715,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0008482
name: sulfite oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + O(2) + sulfite = H(2)O(2) + H(+) + sulfate." [EC:1.8.3.1, RHEA:24600]
+def: "Catalysis of the reaction: H2O + O2 + sulfite = H2O2 + H+ + sulfate." [EC:1.8.3.1, RHEA:24600]
comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "sulfite:oxygen oxidoreductase activity" RELATED [EC:1.8.3.1]
synonym: "sulphite oxidase activity" EXACT []
@@ -78728,10 +78752,10 @@ is_a: GO:0016788 ! hydrolase activity, acting on ester bonds
id: GO:0008486
name: diphosphoinositol-polyphosphate diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: diphospho-myo-inositol polyphosphate + H2O = myo-inositol polyphosphate + phosphate." [EC:3.6.1.52]
-synonym: "diphospho-myo-inositol-polyphosphate diphosphohydrolase activity" RELATED [EC:3.6.1.52]
+def: "Catalysis of the reaction: diphospho-1D-myo-inositol polyphosphate + H2O = 1D-myo-inositol polyphosphate + phosphate." [EC:3.6.1.52]
+synonym: "diphospho-myo-inositol-polyphosphate diphosphohydrolase activity" EXACT [EC:3.6.1.52]
synonym: "diphosphoinositol polyphosphate phosphohydrolase activity" EXACT []
-synonym: "diphosphoinositol-polyphosphate phosphohydrolase activity" RELATED [EC:3.6.1.52]
+synonym: "diphosphoinositol-polyphosphate phosphohydrolase activity" EXACT [EC:3.6.1.52]
synonym: "DIPP activity" RELATED [EC:3.6.1.52]
xref: EC:3.6.1.52
xref: KEGG_REACTION:R05777
@@ -78787,7 +78811,6 @@ def: "Enables the transfer of arsenite from one side of a membrane to the other,
synonym: "arsenite porter activity" RELATED []
is_a: GO:0015105 ! arsenite transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0008492
@@ -78924,7 +78947,7 @@ def: "Enables the transfer of a solute or solutes from one side of a membrane to
synonym: "hydrogen/sucrose transporter activity" BROAD []
synonym: "sucrose:hydrogen symporter activity" EXACT []
is_a: GO:0005351 ! carbohydrate:proton symporter activity
-is_a: GO:0009669 ! sucrose:cation symporter activity
+is_a: GO:0009669 ! sucrose:monoatomic cation symporter activity
[Term]
id: GO:0008507
@@ -78935,7 +78958,7 @@ synonym: "sodium/iodide symporter activity" EXACT []
xref: Reactome:R-HSA-429591 "SLC5A5 cotransports Na+ with I- from extracellular region to cytosol"
xref: Reactome:R-HSA-5658195 "Defective SLC5A5 does not cotransport Na+ with I- from extracellular region to cytosol"
is_a: GO:0015111 ! iodide transmembrane transporter activity
-is_a: GO:0015373 ! anion:sodium symporter activity
+is_a: GO:0015373 ! monoatomic anion:sodium symporter activity
[Term]
id: GO:0008508
@@ -78943,7 +78966,7 @@ name: bile acid:sodium symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: bile acid(out) + Na+(out) = bile acid(in) + Na+(in)." [TC:2.A.28.-.-]
synonym: "sodium/bile acid symporter activity" EXACT []
-xref: Reactome:R-HSA-194121 "Co-transport (influx) of bile salts and sodium ions by NTCP"
+xref: Reactome:R-HSA-194121 "SLC10A1 co-transport bile salts and Na+ from extracellular region to cytosol"
xref: Reactome:R-HSA-194187 "SLC10A2 transports bile salts and acids and Na+ from extracellular region to cytosol"
xref: Reactome:R-HSA-433089 "SOAT can transport taurolithocholate-3-sulphate"
is_a: GO:0015125 ! bile acid transmembrane transporter activity
@@ -78951,12 +78974,13 @@ is_a: GO:0140161 ! monocarboxylate:sodium symporter activity
[Term]
id: GO:0008509
-name: anion transmembrane transporter activity
+name: monoatomic anion transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of a negatively charged ion from one side of a membrane to the other." [GOC:dgf, GOC:mtg_transport, ISBN:0815340729]
+synonym: "anion transmembrane transporter activity" BROAD []
synonym: "anion transporter activity" EXACT []
xref: Reactome:R-HSA-166214 "FA anion flip-flops to the opposite surface"
-is_a: GO:0015075 ! ion transmembrane transporter activity
+is_a: GO:0015075 ! monoatomic ion transmembrane transporter activity
[Term]
id: GO:0008510
@@ -78969,7 +78993,7 @@ xref: Reactome:R-HSA-425483 "SLC4A5,7,9 cotransport Na+ with 3HCO3-"
xref: Reactome:R-HSA-5656219 "Defective SLC4A4 does not cotransport Na+ with 3HCO3-"
xref: Reactome:R-HSA-8878664 "SLC4A4 cotransports Na+ with 3HCO3-"
is_a: GO:0015370 ! solute:sodium symporter activity
-is_a: GO:0140410 ! solute:bicarbonate symporter activity
+is_a: GO:0140410 ! monoatomic cation:bicarbonate symporter activity
[Term]
id: GO:0008511
@@ -78993,7 +79017,6 @@ synonym: "sulfate:hydrogen symporter activity" EXACT []
synonym: "sulphate:hydrogen symporter activity" EXACT []
is_a: GO:0008271 ! secondary active sulfate transmembrane transporter activity
is_a: GO:0015295 ! solute:proton symporter activity
-is_a: GO:0015296 ! anion:cation symporter activity
[Term]
id: GO:0008513
@@ -79006,7 +79029,6 @@ synonym: "polyspecific organic cation transmembrane transporter activity" NARROW
xref: Reactome:R-HSA-549241 "SLC22A4 cotransports ERGT, Na+ from extracellular region to cytosol"
is_a: GO:0015101 ! organic cation transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0008514
@@ -79014,7 +79036,9 @@ name: organic anion transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage." [GOC:ai]
xref: Reactome:R-HSA-2142859 "Growing HA is extruded from the cell by ABCC5"
-is_a: GO:0008509 ! anion transmembrane transporter activity
+xref: Reactome:R-HSA-561041 "OAT1-3 transport organic anions with antiport of dicarboxylic acids"
+xref: Reactome:R-HSA-9794830 "SLC22A8 transports Cipro into renal cell"
+is_a: GO:0022857 ! transmembrane transporter activity
[Term]
id: GO:0008515
@@ -79045,11 +79069,10 @@ synonym: "folic acid transporter activity" RELATED []
synonym: "vitamin B9 transporter activity" EXACT []
synonym: "vitamin M transporter activity" EXACT []
xref: Reactome:R-HSA-200646 "Cytosolic folate export across the plasma membrane"
-xref: Reactome:R-HSA-200652 "Extracellular 5-methyltetrahydrofolate import across the plasma membrane"
-xref: Reactome:R-HSA-200680 "Cytosolic tetrahydrofolate import across the inner mitochondrial membrane"
-xref: Reactome:R-HSA-200720 "Mitochondrial tetrahydrofolate export across the inner mitochondrial membrane"
-xref: Reactome:R-HSA-200729 "Extracellular folate import across the plasma membrane"
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+xref: Reactome:R-HSA-200652 "SLC19A1 transports 5-methyl-THF from extracellular region to cytosol"
+xref: Reactome:R-HSA-200680 "SLC25A32 transports THF from cytosol to mitochondrial matrix"
+xref: Reactome:R-HSA-200720 "SLC25A32 transports THF from mitochondrial matrix to cytosol"
+xref: Reactome:R-HSA-200729 "SLC46A1 transports FOLA from extracellular region to cytosol"
is_a: GO:0042887 ! amide transmembrane transporter activity
is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
@@ -79057,23 +79080,28 @@ is_a: GO:0090482 ! vitamin transmembrane transporter activity
[Term]
id: GO:0008518
-name: folate:anion antiporter activity
+name: folate:monoatomic anion antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Folate derivative (out) + anion (in) = folate derivative (in) + anion (out). The Reduced Folate Carrier (RCF(SLC19A1) acts by an antiport mechanism. RCF carries several folate derivatives: MTX, PMX, ratitrexed, pralatrexate, 5-methyl THF, and 5-formyl THF." [GOC:mtg_transport, PMID:21568705, PMID:24745983, TC:2.A.48]
+synonym: "folate:anion antiporter activity" BROAD []
synonym: "reduced folate carrier activity" RELATED []
synonym: "reduced folate transmembrane transporter activity" RELATED []
synonym: "reduced folate transporter" RELATED []
xref: TC:2.A.48
+is_a: GO:0008509 ! monoatomic anion transmembrane transporter activity
is_a: GO:0008517 ! folic acid transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0008519
name: ammonium transmembrane transporter activity
namespace: molecular_function
+alt_id: GO:0015251
alt_id: GO:0051739
def: "Enables the transfer of ammonium from one side of a membrane to the other. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals." [PMID:17710640]
synonym: "ammonia transmembrane transporter activity" RELATED []
+synonym: "ammonium channel activity" RELATED []
xref: Reactome:R-HSA-444393 "RhCG mediates ammonium influx into kidney collecting duct cells"
xref: Reactome:R-HSA-444416 "RHAG transports NH4+ from cytosol to extracellular region (red blood cells)"
xref: Reactome:R-HSA-444419 "RhBG mediates ammonium effflux out of kidney collecting duct cells"
@@ -79081,7 +79109,8 @@ xref: Reactome:R-HSA-446277 "RhCG mediates ammonium efflux out of kidney collect
xref: Reactome:R-HSA-446278 "RhBG mediates ammonium influx into kidney collecting duct cells"
xref: Reactome:R-HSA-5623051 "Defective RHAG does not transport NH4+ from cytosol to extracellular region (rbc)"
xref: RHEA:28747
-xref: TCBD:1.A.11
+xref: TC:1.A.11
+is_a: GO:0015267 ! channel activity
is_a: GO:0022890 ! inorganic cation transmembrane transporter activity
[Term]
@@ -79094,8 +79123,7 @@ synonym: "sodium-dependent L-ascorbate transmembrane transporter activity" RELAT
synonym: "sodium-dependent L-ascorbic acid transporter" RELATED []
xref: TC:2.A.40.6.1
is_a: GO:0005343 ! organic acid:sodium symporter activity
-is_a: GO:0005402 ! carbohydrate:cation symporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0005402 ! carbohydrate:monoatomic cation symporter activity
is_a: GO:0015145 ! monosaccharide transmembrane transporter activity
is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
@@ -79191,7 +79219,7 @@ consider: GO:0005576
id: GO:0008531
name: riboflavin kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + riboflavin = ADP + FMN + 2 H(+)." [EC:2.7.1.26, RHEA:14357]
+def: "Catalysis of the reaction: ATP + riboflavin = ADP + FMN + 2 H+." [EC:2.7.1.26, RHEA:14357]
synonym: "ATP:riboflavin 5'-phosphotransferase activity" RELATED [EC:2.7.1.26]
synonym: "FK" RELATED [EC:2.7.1.26]
synonym: "flavokinase activity" RELATED [EC:2.7.1.26]
@@ -79439,7 +79467,7 @@ xref: MetaCyc:3.6.3.3-RXN
xref: RHEA:12132
is_a: GO:0015086 ! cadmium ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
[Term]
id: GO:0008552
@@ -79462,14 +79490,14 @@ name: P-type proton-exporting transporter activity
namespace: molecular_function
alt_id: GO:0036442
def: "Enables the transfer of protons from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) -> ADP + phosphate + H+(out). These transporters use a phosphorylative mechanism, which have a phosphorylated intermediate state during the ion transport cycle." [RHEA:20852]
-synonym: "H(+)-transporting ATPase activity" BROAD [EC:7.1.2.1]
synonym: "H+-exporting ATPase activity" RELATED [EC:7.1.2.1]
synonym: "H+-transporting ATPase" BROAD [EC:7.1.2.1]
+synonym: "H+-transporting ATPase activity" BROAD [EC:7.1.2.1]
synonym: "hydrogen exporting ATPase activity, phosphorylative mechanism" EXACT []
synonym: "hydrogen-/sodium-translocating ATPase activity" RELATED []
synonym: "hydrogen-exporting ATPase activity" BROAD []
synonym: "hydrogen-exporting ATPase activity, phosphorylative mechanism" RELATED []
-synonym: "P-type H(+)-exporting ATPase activity" BROAD [EC:7.1.2.1]
+synonym: "P-type H+-exporting ATPase activity" BROAD [EC:7.1.2.1]
synonym: "proton transport ATPase activity" RELATED [EC:7.1.2.1]
synonym: "proton-exporting ATPase activity" BROAD []
synonym: "proton-exporting ATPase activity, phosphorylative mechanism" RELATED []
@@ -79480,7 +79508,7 @@ xref: MetaCyc:3.6.3.6-RXN
xref: RHEA:20852
is_a: GO:0009678 ! pyrophosphate hydrolysis-driven proton transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
[Term]
id: GO:0008554
@@ -79503,7 +79531,7 @@ xref: MetaCyc:3.6.3.7-RXN
xref: RHEA:14633
is_a: GO:0015081 ! sodium ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
[Term]
id: GO:0008556
@@ -79528,7 +79556,7 @@ xref: EC:7.2.2.6
xref: RHEA:16777
is_a: GO:0015079 ! potassium ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
[Term]
id: GO:0008558
@@ -79565,6 +79593,7 @@ synonym: "xenobiotic ABC transporter" NARROW []
synonym: "xenobiotic transmembrane transporting ATPase activity" EXACT []
xref: EC:7.6.2.2
xref: MetaCyc:3.6.3.44-RXN
+xref: Reactome:R-HSA-9757139 "ABCB1,ABCC2 transport ATVs from cytosol to extracellular region"
is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
@@ -79625,17 +79654,19 @@ consider: GO:0007018
[Term]
id: GO:0008568
-name: microtubule-severing ATPase activity
+name: microtubule severing ATPase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate. Catalysis of the severing of a microtubule at a specific spot along its length, coupled to the hydrolysis of ATP." [EC:5.6.1.1, PMID:10910766]
+def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate. Catalysis of the severing of a microtubule at a specific spot along its length, coupled to the hydrolysis of ATP." [PMID:10910766]
comment: See also the cellular component term 'katanin complex ; GO:0008352'.
synonym: "ATP phosphohydrolase (tubulin-dimerizing)" EXACT []
synonym: "katanin activity" NARROW [EC:5.6.1.1]
+synonym: "microtubule-severing ATPase activity" EXACT []
xref: EC:5.6.1.1
xref: MetaCyc:3.6.4.3-RXN
xref: Reactome:R-HSA-9668419 "SPAST (spastin) mediates the severing of microtubules at chromosome attachment sites"
is_a: GO:0140096 ! catalytic activity, acting on a protein
is_a: GO:0140657 ! ATP-dependent activity
+is_a: GO:0140776 ! protein-containing complex destabilizing activity
[Term]
id: GO:0008569
@@ -79683,7 +79714,6 @@ comment: This term was made obsolete because it represents a class of gene produ
synonym: "nucleoplasmin ATPase activity" EXACT []
is_obsolete: true
replaced_by: GO:0016887
-consider: GO:0006333
[Term]
id: GO:0008573
@@ -80118,7 +80148,7 @@ is_a: GO:0031010 ! ISWI-type complex
id: GO:0008625
name: extrinsic apoptotic signaling pathway via death domain receptors
namespace: biological_process
-def: "A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with a ligand binding to a death domain receptor on the cell surface, and ends when the execution phase of apoptosis is triggered." [GOC:mah, GOC:mtg_apoptosis]
+def: "The series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with a ligand binding to a death domain receptor on the cell surface, and ends when the execution phase of apoptosis is triggered." [GOC:mah, GOC:mtg_apoptosis]
comment: Gene products that may be annotated to this term include: 1) ligands such as FASL; 2) receptors such as FAS/CD95 (though care should be taken because FAS can also act as a non-apoptotic signal transducer); 3) signaling molecules such as FADD (FAS-associated protein with a death domain), cIAPs (cellular inhibitor of apoptosis proteins), c-FLIPs and caspases 8 and 10. Examples are TWEAK (TNF12) and FN14 (TNFRSF12A) (UniProt symbols O43508 and Q9NP84) in PMID:21525013.
synonym: "death receptor-mediated apoptosis" NARROW []
synonym: "induction of apoptosis via death domain receptors" RELATED []
@@ -80129,7 +80159,7 @@ is_a: GO:0097191 ! extrinsic apoptotic signaling pathway
id: GO:0008626
name: granzyme-mediated apoptotic signaling pathway
namespace: biological_process
-def: "A series of molecular signals induced by granzymes which triggers the apoptotic death of a cell. The pathway starts with reception of a granzyme signal, and ends when the execution phase of apoptosis is triggered. Granzymes are serine proteases that are secreted by cytotoxic T cells and natural killer cells to induce apoptosis in target cells." [GOC:mtg_apoptosis, PMID:17158907]
+def: "The series of molecular signals induced by granzymes which triggers the apoptotic death of a cell. The pathway starts with reception of a granzyme signal, and ends when the execution phase of apoptosis is triggered. Granzymes are serine proteases that are secreted by cytotoxic T cells and natural killer cells to induce apoptosis in target cells." [GOC:mtg_apoptosis, PMID:17158907]
synonym: "apoptotic signaling pathway in response to granzyme" RELATED []
synonym: "induction of apoptosis by granzyme" RELATED []
is_a: GO:0097190 ! apoptotic signaling pathway
@@ -80139,7 +80169,7 @@ is_a: GO:0140507 ! granzyme-mediated programmed cell death signaling pathway
id: GO:0008627
name: intrinsic apoptotic signaling pathway in response to osmotic stress
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to changes in intracellular ion homeostasis, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis, PMID:11454444, PMID:16483738]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to changes in intracellular ion homeostasis, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis, PMID:11454444, PMID:16483738]
synonym: "induction of apoptosis by ionic changes" RELATED []
is_a: GO:0071470 ! cellular response to osmotic stress
is_a: GO:0097193 ! intrinsic apoptotic signaling pathway
@@ -80148,7 +80178,7 @@ is_a: GO:0097193 ! intrinsic apoptotic signaling pathway
id: GO:0008628
name: hormone-mediated apoptotic signaling pathway
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of a hormone, and which triggers the apoptotic signaling pathway in a cell. The pathway starts with reception of a hormone signal, and ends when the execution phase of apoptosis is triggered." [GOC:bf, GOC:mtg_apoptosis]
+def: "The series of molecular signals mediated by the detection of a hormone, and which triggers the apoptotic signaling pathway in a cell. The pathway starts with reception of a hormone signal, and ends when the execution phase of apoptosis is triggered." [GOC:bf, GOC:mtg_apoptosis]
comment: This term is placed under GO:0097190 apoptotic signaling pathway, rather than under one of its more specific children terms, to cover for the variety of apoptosis signaling mechanisms that different hormones may use.
synonym: "apoptotic signaling pathway in response to hormone" RELATED []
synonym: "induction of apoptosis by hormones" RELATED []
@@ -80159,16 +80189,16 @@ is_a: GO:0097190 ! apoptotic signaling pathway
id: GO:0008630
name: intrinsic apoptotic signaling pathway in response to DNA damage
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered." [GOC:go_curators, GOC:mtg_apoptosis]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered." [GOC:go_curators, GOC:mtg_apoptosis]
synonym: "DNA damage response, signal transduction resulting in induction of apoptosis" RELATED []
-is_a: GO:0006974 ! cellular response to DNA damage stimulus
+is_a: GO:0006974 ! DNA damage response
is_a: GO:0097193 ! intrinsic apoptotic signaling pathway
[Term]
id: GO:0008631
name: intrinsic apoptotic signaling pathway in response to oxidative stress
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, and ends when the execution phase of apoptosis is triggered." [GOC:ai, GOC:mtg_apoptosis]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, and ends when the execution phase of apoptosis is triggered." [GOC:ai, GOC:mtg_apoptosis]
synonym: "induction of apoptosis by oxidative stress" RELATED []
synonym: "oxidative stress-induced intrinsic apoptotic signaling pathway" EXACT [GOC:bf]
is_a: GO:0097193 ! intrinsic apoptotic signaling pathway
@@ -80237,8 +80267,8 @@ comment: This term was made obsolete because it represents a biological process
synonym: "protein tagging activity" EXACT []
is_obsolete: true
consider: GO:0005515
-consider: GO:0006464
consider: GO:0031386
+consider: GO:0036211
[Term]
id: GO:0008641
@@ -80250,6 +80280,7 @@ subset: goslim_pir
synonym: "small protein activating enzyme activity" NARROW []
is_a: GO:0016877 ! ligase activity, forming carbon-sulfur bonds
is_a: GO:0140096 ! catalytic activity, acting on a protein
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0008643
@@ -80322,16 +80353,16 @@ consider: GO:0042802
[Term]
id: GO:0008652
-name: cellular amino acid biosynthetic process
+name: amino acid biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents." [ISBN:0198506732]
-synonym: "amino acid biosynthetic process" EXACT []
-synonym: "cellular amino acid anabolism" EXACT []
-synonym: "cellular amino acid biosynthesis" EXACT []
-synonym: "cellular amino acid formation" EXACT []
-synonym: "cellular amino acid synthesis" EXACT []
+synonym: "amino acid anabolism" EXACT []
+synonym: "amino acid biosynthesis" EXACT []
+synonym: "amino acid formation" EXACT []
+synonym: "amino acid synthesis" EXACT []
+synonym: "cellular amino acid biosynthetic process" EXACT []
xref: Wikipedia:Amino_acid_synthesis
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:1901566 ! organonitrogen compound biosynthetic process
@@ -80342,8 +80373,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving lipopolysaccharides, a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide." [ISBN:0198506732]
synonym: "lipopolysaccharide metabolism" EXACT []
synonym: "LPS metabolic process" EXACT []
-is_a: GO:0044255 ! cellular lipid metabolic process
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
+is_a: GO:0043170 ! macromolecule metabolic process
is_a: GO:1903509 ! liposaccharide metabolic process
[Term]
@@ -80355,12 +80385,10 @@ synonym: "phospholipid anabolism" EXACT []
synonym: "phospholipid biosynthesis" EXACT []
synonym: "phospholipid formation" EXACT []
synonym: "phospholipid synthesis" EXACT []
-xref: MetaCyc:LIPASYN-PWY
xref: MetaCyc:PHOSLIPSYN-PWY
xref: MetaCyc:PHOSLIPSYN2-PWY
is_a: GO:0006644 ! phospholipid metabolic process
is_a: GO:0008610 ! lipid biosynthetic process
-is_a: GO:0044249 ! cellular biosynthetic process
is_a: GO:0090407 ! organophosphate biosynthetic process
[Term]
@@ -80403,7 +80431,6 @@ def: "Binding to penicillin, an antibiotic that contains the condensed beta-lact
subset: goslim_metagenomics
is_a: GO:0033218 ! amide binding
is_a: GO:0033293 ! monocarboxylic acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
is_a: GO:1901681 ! sulfur compound binding
@@ -80424,7 +80451,7 @@ id: GO:0008660
name: 1-aminocyclopropane-1-carboxylate deaminase activity
namespace: molecular_function
alt_id: GO:0018806
-def: "Catalysis of the reaction: 1-aminocyclopropane-1-carboxylate + H(2)O = 2-oxobutanate + NH(4)(+)." [EC:3.5.99.7, RHEA:16933]
+def: "Catalysis of the reaction: 1-aminocyclopropane-1-carboxylate + H2O = 2-oxobutanate + NH4." [EC:3.5.99.7, RHEA:16933]
comment: Note that this function was formerly EC:4.1.99.4.
synonym: "1-aminocyclopropane carboxylic acid deaminase activity" RELATED [EC:3.5.99.7]
synonym: "1-aminocyclopropane-1-carboxylate aminohydrolase (isomerizing)" RELATED [EC:3.5.99.7]
@@ -80435,14 +80462,13 @@ xref: KEGG_REACTION:R00997
xref: MetaCyc:4.1.99.4-RXN
xref: RHEA:16933
xref: UM-BBD_reactionID:r0357
-is_a: GO:0016810 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
is_a: GO:0019239 ! deaminase activity
[Term]
id: GO:0008661
name: 1-deoxy-D-xylulose-5-phosphate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO(2)." [EC:2.2.1.7, RHEA:12605]
+def: "Catalysis of the reaction: D-glyceraldehyde 3-phosphate + H+ + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO2." [EC:2.2.1.7, RHEA:12605]
synonym: "1-deoxy-D-xylulose-5-phosphate pyruvate-lyase (carboxylating) activity" EXACT []
synonym: "1-deoxyxylulose-5-phosphate synthase activity" EXACT []
synonym: "DOXP synthase activity" EXACT []
@@ -80504,7 +80530,7 @@ is_a: GO:0008452 ! RNA ligase activity
id: GO:0008666
name: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + H(2)O + succinyl-CoA = L-2-succinylamino-6-oxopimelate + CoA." [EC:2.3.1.117, RHEA:17325]
+def: "Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + H2O + succinyl-CoA = L-2-succinylamino-6-oxopimelate + CoA." [EC:2.3.1.117, RHEA:17325]
synonym: "succinyl-CoA:(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity" RELATED [EC:2.3.1.117]
synonym: "succinyl-CoA:2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity" RELATED [EC:2.3.1.117]
synonym: "succinyl-CoA:tetrahydrodipicolinate N-succinyltransferase activity" RELATED [EC:2.3.1.117]
@@ -80523,7 +80549,7 @@ is_a: GO:0016749 ! N-succinyltransferase activity
id: GO:0008667
name: 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + NAD(+) = 2,3-dihydroxybenzoate + H(+) + NADH." [EC:1.3.1.28, RHEA:23824]
+def: "Catalysis of the reaction: (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + NAD+ = 2,3-dihydroxybenzoate + H+ + NADH." [EC:1.3.1.28, RHEA:23824]
synonym: "2,3-DHB dehydrogenase activity" RELATED [EC:1.3.1.28]
synonym: "2,3-dihydro-2,3-dihydroxybenzoate:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.28]
xref: EC:1.3.1.28
@@ -80564,7 +80590,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0008671
name: 2-dehydro-3-deoxygalactonokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-dehydro-3-deoxy-D-galactonate + ATP = 6-phospho-2-dehydro-3-deoxy-D-galactonate + ADP + 2 H(+)." [EC:2.7.1.58, RHEA:16525]
+def: "Catalysis of the reaction: 2-dehydro-3-deoxy-D-galactonate + ATP = 6-phospho-2-dehydro-3-deoxy-D-galactonate + ADP + 2 H+." [EC:2.7.1.58, RHEA:16525]
synonym: "2-keto-3-deoxy-galactonokinase activity" RELATED [EC:2.7.1.58]
synonym: "2-keto-3-deoxygalactonate kinase (phosphorylating)" RELATED [EC:2.7.1.58]
synonym: "2-keto-3-deoxygalactonokinase activity" RELATED [EC:2.7.1.58]
@@ -80595,7 +80621,7 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0008673
name: 2-dehydro-3-deoxygluconokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D-gluconate + ADP + 2 H(+)." [EC:2.7.1.45, RHEA:14797]
+def: "Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D-gluconate + ADP + 2 H+." [EC:2.7.1.45, RHEA:14797]
synonym: "2-keto-3-deoxy-D-gluconic acid kinase activity" RELATED [EC:2.7.1.45]
synonym: "2-keto-3-deoxygluconate kinase activity" RELATED [EC:2.7.1.45]
synonym: "2-keto-3-deoxygluconokinase (phosphorylating)" RELATED [EC:2.7.1.45]
@@ -80661,7 +80687,7 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0008676
name: 3-deoxy-8-phosphooctulonate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-arabinose 5-phosphate + H(2)O + phosphoenolpyruvate = 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + 2 H(+) + phosphate." [EC:2.5.1.55, RHEA:14053]
+def: "Catalysis of the reaction: D-arabinose 5-phosphate + H2O + phosphoenolpyruvate = 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + 2 H+ + phosphate." [EC:2.5.1.55, RHEA:14053]
comment: Note that this function was formerly EC:4.1.2.16.
synonym: "2-dehydro-3-deoxy-D-octonate-8-phosphate D-arabinose-5-phosphate-lyase (pyruvate-phosphorylating) activity" RELATED [EC:2.5.1.55]
synonym: "2-dehydro-3-deoxy-phosphooctonate aldolase activity" RELATED [EC:2.5.1.55]
@@ -80686,7 +80712,7 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0008677
name: 2-dehydropantoate 2-reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-pantoate + NADP(+) = 2-dehydropantoate + H(+) + NADPH." [EC:1.1.1.169, RHEA:16233]
+def: "Catalysis of the reaction: (R)-pantoate + NADP+ = 2-dehydropantoate + H+ + NADPH." [EC:1.1.1.169, RHEA:16233]
synonym: "(R)-pantoate:NADP+ 2-oxidoreductase activity" RELATED [EC:1.1.1.169]
synonym: "2-ketopantoate reductase activity" RELATED [EC:1.1.1.169]
synonym: "2-ketopantoic acid reductase activity" RELATED [EC:1.1.1.169]
@@ -80736,21 +80762,23 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
[Term]
id: GO:0008682
-name: 2-octoprenyl-3-methyl-6-methoxy-1,4-benzoquinone hydroxylase activity
+name: 3-demethoxyubiquinol 3-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-octoprenyl-3-methyl-6-methoxy-1,4-benzoquinone + O2 = 2-octoprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone." [RHEA:50908]
+def: "Catalysis of the reaction: a 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol + AH2 + O2 = A + a 3-demethylubiquinol + H2O." [RHEA:50908]
+synonym: "2-octoprenyl-3-methyl-6-methoxy-1,4-benzoquinone hydroxylase activity" NARROW []
synonym: "demethoxy-ubiquinone hydroxylase" RELATED [GOC:vw]
synonym: "demethoxyubiquinone monooxygenase" RELATED [GOC:vw]
xref: EC:1.14.99.60
xref: MetaCyc:OCTAPRENYL-METHYL-METHOXY-BENZOQ-OH-RXN
xref: RHEA:50908
is_a: GO:0004497 ! monooxygenase activity
+is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
[Term]
id: GO:0008683
name: 2-oxoglutarate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + H(+) = CO(2) + succinate semialdehyde." [EC:4.1.1.71, RHEA:10524]
+def: "Catalysis of the reaction: 2-oxoglutarate + H+ = CO2 + succinate semialdehyde." [EC:4.1.1.71, RHEA:10524]
synonym: "2-oxoglutarate carboxy-lyase (succinate-semialdehyde-forming)" RELATED [EC:4.1.1.71]
synonym: "2-oxoglutarate carboxy-lyase activity" RELATED [EC:4.1.1.71]
synonym: "alpha-ketoglutarate decarboxylase activity" RELATED [EC:4.1.1.71]
@@ -80798,7 +80826,7 @@ is_a: GO:0016849 ! phosphorus-oxygen lyase activity
id: GO:0008686
name: 3,4-dihydroxy-2-butanone-4-phosphate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H(+)." [EC:4.1.99.12, RHEA:18457]
+def: "Catalysis of the reaction: D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H+." [EC:4.1.99.12, RHEA:18457]
xref: EC:4.1.99.12
xref: KEGG_REACTION:R07281
xref: MetaCyc:DIOHBUTANONEPSYN-RXN
@@ -80809,7 +80837,7 @@ is_a: GO:0016830 ! carbon-carbon lyase activity
id: GO:0008687
name: 3,4-dihydroxyphenylacetate 2,3-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3,4-dihydroxyphenylacetate + O(2) = 5-formyl-2-hydroxyhepta-2,4-dienedioate + H(+)." [EC:1.13.11.15, RHEA:15633]
+def: "Catalysis of the reaction: 3,4-dihydroxyphenylacetate + O2 = 5-formyl-2-hydroxyhepta-2,4-dienedioate + H+." [EC:1.13.11.15, RHEA:15633]
synonym: "3,4-dihydroxyphenylacetate:oxygen 2,3-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.15]
synonym: "3,4-dihydroxyphenylacetic acid 2,3-dioxygenase activity" RELATED [EC:1.13.11.15]
synonym: "homoprotocatechuate 2,3-dioxygenase activity" RELATED [EC:1.13.11.15]
@@ -80900,27 +80928,22 @@ is_a: GO:0016856 ! racemase and epimerase activity, acting on hydroxy acids and
[Term]
id: GO:0008693
-name: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity
+name: (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (3R)-3-hydroxydecanoyl-[acyl-carrier protein] = 2,3-decenoyl-[acyl-carrier protein] or 3,4-decenoyl-[acyl-carrier protein] + H2O." [EC:4.2.1.59, PMID:8910376, RHEA:41860]
-synonym: "(3R)-3-hydroxydecanoyl-acyl-carrier-protein hydro-lyase activity" RELATED [EC:4.2.1.59]
+def: "Catalysis of the reaction: (3R)-3-hydroxydecanoyl-[acyl-carrier protein] = 2,3-decenoyl-[acyl-carrier protein] or 3,4-decenoyl-[acyl-carrier protein] + H2O." [PMID:8910376, RHEA:41860]
+synonym: "(3R)-3-hydroxydecanoyl-acyl-carrier-protein hydro-lyase activity" RELATED []
synonym: "3-hydroxydecanoyl-[acyl-carrier protein] dehydratase activity" EXACT []
+synonym: "3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity" BROAD []
synonym: "3-hydroxydecanoyl-ACP dehydratase activity" EXACT []
-synonym: "3-hydroxydecanoyl-acyl carrier protein dehydrase activity" RELATED [EC:4.2.1.59]
-synonym: "3-hydroxydecanoyl-acyl carrier protein dehydratase activity" RELATED [EC:4.2.1.59]
-synonym: "3-hydroxydecanoyl-acyl-carrier-protein dehydratase activity" RELATED [EC:4.2.1.59]
-synonym: "beta-hydroxyacyl-ACP dehydrase activity" RELATED [EC:4.2.1.59]
-synonym: "beta-hydroxyacyl-acyl carrier protein dehydratase activity" RELATED [EC:4.2.1.59]
-synonym: "beta-hydroxydecanoate dehydrase activity" RELATED [EC:4.2.1.59]
-synonym: "beta-hydroxydecanoyl thioester dehydrase activity" RELATED [EC:4.2.1.59]
-synonym: "beta-hydroxydecanoyl thiol ester dehydrase activity" RELATED [EC:4.2.1.59]
-synonym: "D-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity" RELATED [EC:4.2.1.59]
-synonym: "D-3-hydroxydecanoyl-acyl-carrier-protein dehydratase activity" RELATED [EC:4.2.1.59]
-synonym: "FabA" RELATED []
-synonym: "HDDase activity" RELATED [EC:4.2.1.59]
-xref: EC:4.2.1.59
+synonym: "3-hydroxydecanoyl-acyl carrier protein dehydrase activity" RELATED []
+synonym: "3-hydroxydecanoyl-acyl carrier protein dehydratase activity" RELATED []
+synonym: "3-hydroxydecanoyl-acyl-carrier-protein dehydratase activity" RELATED []
+synonym: "beta-hydroxyacyl-ACP dehydrase activity" RELATED []
+synonym: "beta-hydroxyacyl-acyl carrier protein dehydratase activity" RELATED []
+synonym: "beta-hydroxydecanoate dehydrase activity" RELATED []
+synonym: "beta-hydroxydecanoyl thioester dehydrase activity" RELATED []
xref: RHEA:41860
-is_a: GO:0019171 ! 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity
+is_a: GO:0019171 ! (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity
[Term]
id: GO:0008694
@@ -80959,7 +80982,7 @@ is_a: GO:0016708 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0008696
name: 4-amino-4-deoxychorismate lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-amino-4-deoxychorismate = 4-aminobenzoate + H(+) + pyruvate." [EC:4.1.3.38, RHEA:16201]
+def: "Catalysis of the reaction: 4-amino-4-deoxychorismate = 4-aminobenzoate + H+ + pyruvate." [EC:4.1.3.38, RHEA:16201]
comment: Note that the name 'para-amino benzoic acid synthase' was initially given to the 'aminodeoxychorismate synthase' activity before the additional 4-amino-4-deoxychorismate lyase activity was discovered. It is the lyase activity that actually produces para-aminobenzoic acid from 4-amino-4-deoxychorismate.
synonym: "4-amino-4-deoxychorismate pyruvate-lyase (4-aminobenzoate-forming)" RELATED [EC:4.1.3.38]
synonym: "4-amino-4-deoxychorismate pyruvate-lyase activity" RELATED [EC:4.1.3.38]
@@ -81037,7 +81060,7 @@ is_a: GO:0016833 ! oxo-acid-lyase activity
id: GO:0008703
name: 5-amino-6-(5-phosphoribosylamino)uracil reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-amino-6-(5-phosphoribitylamino)uracil + NADP(+) = 5-amino-6-(5-phosphoribosylamino)uracil + H(+) + NADPH." [EC:1.1.1.193, RHEA:17845]
+def: "Catalysis of the reaction: 5-amino-6-(5-phosphoribitylamino)uracil + NADP+ = 5-amino-6-(5-phosphoribosylamino)uracil + H+ + NADPH." [EC:1.1.1.193, RHEA:17845]
synonym: "5-amino-6-(5'-phosphoribosylamino)uracil reductase activity" EXACT []
synonym: "5-amino-6-(5-phosphoribitylamino)uracil:NADP+ 1'-oxidoreductase activity" RELATED [EC:1.1.1.193]
synonym: "aminodioxyphosphoribosylaminopyrimidine reductase activity" RELATED [EC:1.1.1.193]
@@ -81097,7 +81120,7 @@ xref: EC:2.1.1.13
xref: KEGG_REACTION:R00946
xref: MetaCyc:HOMOCYSMETB12-RXN
xref: Reactome:R-HSA-174374 "MTR transfers CH3 from MeCbl to HCYS"
-xref: Reactome:R-HSA-3149539 "MTR transfers CH3 group from MTHF to cob(I)alamin"
+xref: Reactome:R-HSA-3149539 "MTR transfers CH3 group from 5-methyl-THF to cob(I)alamin"
xref: RHEA:11172
is_a: GO:0008172 ! S-methyltransferase activity
is_a: GO:0042084 ! 5-methyltetrahydrofolate-dependent methyltransferase activity
@@ -81135,7 +81158,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0008709
name: cholate 7-alpha-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cholate + NAD(+) = 3alpha,12alpha-dihydroxy-7-oxo-5beta-cholanate + H(+) + NADH." [EC:1.1.1.159, RHEA:19409]
+def: "Catalysis of the reaction: cholate + NAD+ = 3alpha,12alpha-dihydroxy-7-oxo-5beta-cholanate + H+ + NADH." [EC:1.1.1.159, RHEA:19409]
synonym: "7-alpha-hydroxysteroid dehydrogenase activity" BROAD [EC:1.1.1.159]
synonym: "7alpha-HSDH" RELATED [EC:1.1.1.159]
synonym: "7alpha-hydroxy steroid dehydrogenase activity" BROAD [EC:1.1.1.159]
@@ -81151,7 +81174,7 @@ is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of
id: GO:0008710
name: 8-amino-7-oxononanoate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-alanine + H(+) + pimelyl-CoA = 8-amino-7-oxononanoate + CO(2) + CoA." [EC:2.3.1.47, RHEA:20712]
+def: "Catalysis of the reaction: L-alanine + H+ + pimelyl-CoA = 8-amino-7-oxononanoate + CO2 + CoA." [EC:2.3.1.47, RHEA:20712]
synonym: "6-carboxyhexanoyl-CoA:L-alanine C-carboxyhexanoyltransferase (decarboxylating)" RELATED [EC:2.3.1.47]
synonym: "7-KAP synthetase activity" RELATED [EC:2.3.1.47]
synonym: "7-keto-8-amino-pelargonic acid synthetase activity" RELATED [EC:2.3.1.47]
@@ -81204,7 +81227,7 @@ is_a: GO:0008920 ! lipopolysaccharide heptosyltransferase activity
id: GO:0008714
name: AMP nucleosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AMP + H(2)O = D-ribose 5-phosphate + adenine." [EC:3.2.2.4, RHEA:20129]
+def: "Catalysis of the reaction: AMP + H2O = D-ribose 5-phosphate + adenine." [EC:3.2.2.4, RHEA:20129]
synonym: "adenosine monophosphate nucleosidase activity" RELATED [EC:3.2.2.4]
synonym: "adenylate nucleosidase activity" RELATED [EC:3.2.2.4]
synonym: "AMP phosphoribohydrolase activity" RELATED [EC:3.2.2.4]
@@ -81218,7 +81241,7 @@ is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
id: GO:0008715
name: CDP-diacylglycerol diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: CDP-diacylglycerol + H(2)O = a phosphatidate + CMP + 2 H(+)." [EC:3.6.1.26, RHEA:15221]
+def: "Catalysis of the reaction: CDP-diacylglycerol + H2O = a phosphatidate + CMP + 2 H+." [EC:3.6.1.26, RHEA:15221]
synonym: "CDP diacylglycerol hydrolase activity" RELATED [EC:3.6.1.26]
synonym: "CDP-diacylglycerol phosphatidylhydrolase activity" RELATED [EC:3.6.1.26]
synonym: "CDP-diacylglycerol pyrophosphatase activity" EXACT []
@@ -81233,7 +81256,7 @@ is_a: GO:0016462 ! pyrophosphatase activity
id: GO:0008716
name: D-alanine-D-alanine ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H(+) + phosphate." [EC:6.3.2.4, RHEA:11224]
+def: "Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H+ + phosphate." [EC:6.3.2.4, RHEA:11224]
synonym: "alanine:alanine ligase (ADP-forming) activity" RELATED [EC:6.3.2.4]
synonym: "alanylalanine synthetase activity" RELATED [EC:6.3.2.4]
synonym: "D-Ala-D-Ala synthetase activity" RELATED [EC:6.3.2.4]
@@ -81284,7 +81307,7 @@ is_a: GO:0016853 ! isomerase activity
id: GO:0008720
name: D-lactate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-lactate + NAD(+) = H(+) + NADH + pyruvate." [EC:1.1.1.28, RHEA:16369]
+def: "Catalysis of the reaction: (R)-lactate + NAD+ = H+ + NADH + pyruvate." [EC:1.1.1.28, RHEA:16369]
synonym: "D-lactic acid dehydrogenase activity" RELATED [EC:1.1.1.28]
synonym: "D-lactic dehydrogenase activity" RELATED [EC:1.1.1.28]
xref: EC:1.1.1.28
@@ -81396,7 +81419,7 @@ is_a: GO:0016778 ! diphosphotransferase activity
id: GO:0008730
name: L(+)-tartrate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tartrate = H(2)O + oxaloacetate." [EC:4.2.1.32, RHEA:15413]
+def: "Catalysis of the reaction: L-tartrate = H2O + oxaloacetate." [EC:4.2.1.32, RHEA:15413]
synonym: "(R,R)-tartrate hydro-lyase (oxaloacetate-forming)" RELATED [EC:4.2.1.32]
synonym: "(R,R)-tartrate hydro-lyase activity" RELATED [EC:4.2.1.32]
synonym: "L-(+)-tartaric acid dehydratase activity" RELATED [EC:4.2.1.32]
@@ -81445,21 +81468,16 @@ xref: MetaCyc:L-ASPARTATE-OXID-RXN
xref: MetaCyc:RXN-9772
xref: RHEA:25876
is_a: GO:0001716 ! L-amino-acid oxidase activity
-is_a: GO:0015922 ! aspartate oxidase activity
[Term]
id: GO:0008735
-name: carnitine dehydratase activity
+name: L-carnitine CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-carnitine = crotono-betaine + H(2)O." [EC:4.2.1.89, RHEA:14577]
+def: "Catalysis of the reactions: (E)-4-(trimethylammonio)but-2-enoyl-CoA + L-carnitine = (E)-4-(trimethylammonio)but-2-enoate + L-carnitinyl-CoA and 4-trimethylammoniobutanoyl-CoA + L-carnitine = 4-trimethylammoniobutanoate + L-carnitinyl-CoA." [PMID:7815937, PMID:8188598]
synonym: "L-carnitine dehydratase activity" EXACT []
-synonym: "L-carnitine hydro-lyase [4-(trimethylammonio)but-2-enoate-forming]" RELATED [EC:4.2.1.89]
-synonym: "L-carnitine hydro-lyase activity" RELATED [EC:4.2.1.89]
-xref: EC:4.2.1.89
-xref: KEGG_REACTION:R01925
-xref: MetaCyc:CARNDEHYDRA-RXN
-xref: RHEA:14577
-is_a: GO:0016836 ! hydro-lyase activity
+synonym: "L-carnitine hydro-lyase [4-(trimethylammonio)but-2-enoate-forming]" RELATED []
+synonym: "L-carnitine hydro-lyase activity" RELATED []
+is_a: GO:0008410 ! CoA-transferase activity
[Term]
id: GO:0008736
@@ -81477,7 +81495,7 @@ is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldos
id: GO:0008737
name: L-fuculokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-fuculose + ATP = L-fuculose 1-phosphate + ADP + 2 H(+)." [EC:2.7.1.51, RHEA:12376]
+def: "Catalysis of the reaction: L-fuculose + ATP = L-fuculose 1-phosphate + ADP + 2 H+." [EC:2.7.1.51, RHEA:12376]
synonym: "ATP:L-fuculose 1-phosphotransferase activity" RELATED [EC:2.7.1.51]
synonym: "L-fuculokinase (phosphorylating)" RELATED [EC:2.7.1.51]
synonym: "L-fuculose kinase activity" RELATED [EC:2.7.1.51]
@@ -81553,7 +81571,7 @@ is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and
id: GO:0008743
name: L-threonine 3-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-threonine + NAD(+) = L-2-amino-3-oxobutanoate + CO(2) + NADH." [EC:1.1.1.103, RHEA:13161]
+def: "Catalysis of the reaction: L-threonine + NAD+ = L-2-amino-3-oxobutanoate + CO2 + NADH." [EC:1.1.1.103, RHEA:13161]
synonym: "L-threonine dehydrogenase activity" RELATED [EC:1.1.1.103]
synonym: "L-threonine:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.103]
synonym: "threonine 3-dehydrogenase activity" BROAD []
@@ -81683,26 +81701,16 @@ consider: GO:0016651
[Term]
id: GO:0008752
-name: FMN reductase activity
+name: FMN reductase (NAD(P)H) activity
namespace: molecular_function
-def: "Catalysis of the reaction: FMNH2 + NAD(P)+ = FMN + NAD(P)H + H+." [EC:1.5.1.39]
+def: "Catalysis of the reaction: FMNH2 + NAD(P)+ = FMN + NAD(P)H + H+. This reaction can utilize NADH and NADPH with similar reaction rates." [EC:1.5.1.39]
synonym: "flavin mononucleotide reductase activity" RELATED []
-synonym: "flavine mononucleotide reductase activity" RELATED [EC:1.5.1.29]
-synonym: "FMNH2:NAD(P)+ oxidoreductase activity" RELATED [EC:1.5.1.29]
+synonym: "FMN reductase activity" BROAD []
synonym: "NAD(P)H dehydrogenase (FMN) activity" EXACT []
-synonym: "NAD(P)H(2) dehydrogenase (FMN) activity" RELATED [EC:1.5.1.29]
-synonym: "NAD(P)H(2):FMN oxidoreductase activity" RELATED [EC:1.5.1.29]
-synonym: "NAD(P)H-dependent FMN reductase activity" RELATED [EC:1.5.1.29]
-synonym: "NAD(P)H-FMN reductase activity" RELATED [EC:1.5.1.29]
-synonym: "NAD(P)H2 dehydrogenase (FMN)" RELATED [EC:1.5.1.29]
-synonym: "NAD(P)H2:FMN oxidoreductase activity" RELATED [EC:1.5.1.29]
-synonym: "NAD(P)H:flavin oxidoreductase activity" RELATED [EC:1.5.1.29]
-synonym: "NAD(P)H:FMN oxidoreductase activity" RELATED [EC:1.5.1.29]
-synonym: "riboflavin mononucleotide (reduced nicotinamide adenine dinucleotide (phosphate)) reductase activity" RELATED [EC:1.5.1.29]
-synonym: "riboflavin mononucleotide reductase activity" BROAD [EC:1.5.1.29]
-synonym: "riboflavine mononucleotide reductase activity" BROAD [EC:1.5.1.29]
-synonym: "SsuE" RELATED [EC:1.5.1.29]
+synonym: "NAD(P)H-dependent FMN reductase activity" RELATED []
xref: EC:1.5.1.39
+xref: RHEA:21620
+xref: RHEA:21624
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
[Term]
@@ -81844,7 +81852,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0008763
name: UDP-N-acetylmuramate-L-alanine ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-alanine + ATP + UDP-N-acetylmuramate = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-alanine." [EC:6.3.2.8, RHEA:23372]
+def: "Catalysis of the reaction: L-alanine + ATP + UDP-N-acetylmuramate = ADP + 2 H+ + phosphate + UDP-N-acetylmuramoyl-L-alanine." [EC:6.3.2.8, RHEA:23372]
synonym: "alanine-adding enzyme activity" RELATED [EC:6.3.2.8]
synonym: "L-Ala ligase activity" RELATED [EC:6.3.2.8]
synonym: "L-alanine-adding enzyme activity" RELATED [EC:6.3.2.8]
@@ -81870,7 +81878,7 @@ is_a: GO:0016881 ! acid-amino acid ligase activity
id: GO:0008764
name: UDP-N-acetylmuramoylalanine-D-glutamate ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glutamate + ATP + UDP-N-acetylmuramoyl-L-alanine = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate." [EC:6.3.2.9, RHEA:16429]
+def: "Catalysis of the reaction: D-glutamate + ATP + UDP-N-acetylmuramoyl-L-alanine = ADP + 2 H+ + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate." [EC:6.3.2.9, RHEA:16429]
synonym: "D-glutamate ligase activity" RELATED [EC:6.3.2.9]
synonym: "D-glutamate-adding enzyme activity" RELATED [EC:6.3.2.9]
synonym: "MurD synthetase activity" RELATED [EC:6.3.2.9]
@@ -81888,7 +81896,7 @@ is_a: GO:0016881 ! acid-amino acid ligase activity
id: GO:0008765
name: UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: meso-2,6-diaminopimelate + ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate." [EC:6.3.2.13, RHEA:23676]
+def: "Catalysis of the reaction: meso-2,6-diaminopimelate + ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate = ADP + 2 H+ + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate." [EC:6.3.2.13, RHEA:23676]
synonym: "MurE synthetase activity" RELATED [EC:6.3.2.13]
synonym: "UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:(L)-meso-2,6-diaminoheptanedioate gamma-ligase (ADP-forming)" RELATED [EC:6.3.2.13]
synonym: "UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-2,6-diamino-heptanedioate ligase (ADP-forming) activity" RELATED [EC:6.3.2.13]
@@ -81928,8 +81936,8 @@ id: GO:0008768
name: UDP-sugar diphosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction: UDP-sugar + H2O = UMP + sugar 1-phosphate." [EC:3.6.1.45]
-synonym: "nucleosidediphosphate-sugar diphosphatase activity" RELATED [EC:3.6.1.45]
-synonym: "nucleosidediphosphate-sugar pyrophosphatase activity" RELATED [EC:3.6.1.45]
+synonym: "nucleosidediphosphate-sugar diphosphatase activity" BROAD [EC:3.6.1.45]
+synonym: "nucleosidediphosphate-sugar pyrophosphatase activity" BROAD [EC:3.6.1.45]
synonym: "UDP-sugar hydrolase activity" RELATED [EC:3.6.1.45]
synonym: "UDP-sugar pyrophosphatase activity" RELATED [EC:3.6.1.45]
synonym: "UDP-sugar sugarphosphohydrolase activity" RELATED [EC:3.6.1.45]
@@ -82181,7 +82189,7 @@ is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
id: GO:0008783
name: agmatinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: agmatine + H(2)O = putrescine + urea." [EC:3.5.3.11, RHEA:13929]
+def: "Catalysis of the reaction: agmatine + H2O = putrescine + urea." [EC:3.5.3.11, RHEA:13929]
synonym: "agmatine amidinohydrolase" BROAD [EC:3.5.3.11]
synonym: "agmatine ureohydrolase activity" RELATED [EC:3.5.3.11]
synonym: "SpeB" RELATED [EC:3.5.3.11]
@@ -82255,7 +82263,7 @@ is_a: GO:0015927 ! trehalase activity
id: GO:0008789
name: altronate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-altronate = 2-dehydro-3-deoxy-D-gluconate + H(2)O." [EC:4.2.1.7, RHEA:15957]
+def: "Catalysis of the reaction: D-altronate = 2-dehydro-3-deoxy-D-gluconate + H2O." [EC:4.2.1.7, RHEA:15957]
synonym: "D-altronate hydro-lyase (2-dehydro-3-deoxy-D-galactonate-forming)" RELATED [EC:4.2.1.7]
synonym: "D-altronate hydro-lyase activity" RELATED [EC:4.2.1.7]
xref: EC:4.2.1.7
@@ -82300,7 +82308,7 @@ is_a: GO:0016749 ! N-succinyltransferase activity
id: GO:0008792
name: arginine decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arginine + H(+) = agmatine + CO(2)." [EC:4.1.1.19, RHEA:17641]
+def: "Catalysis of the reaction: L-arginine + H+ = agmatine + CO2." [EC:4.1.1.19, RHEA:17641]
synonym: "L-arginine carboxy-lyase (agmatine-forming)" RELATED [EC:4.1.1.19]
synonym: "L-arginine carboxy-lyase activity" RELATED [EC:4.1.1.19]
synonym: "SpeA" RELATED [EC:4.1.1.19]
@@ -82365,7 +82373,7 @@ id: GO:0008796
name: bis(5'-nucleosyl)-tetraphosphatase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of P(1),P(4)-bis(5'-nucleosyl)tetraphosphate into two nucleotides." [GOC:ai]
-is_a: GO:0004551 ! nucleotide diphosphatase activity
+is_a: GO:0016462 ! pyrophosphatase activity
[Term]
id: GO:0008797
@@ -82449,7 +82457,7 @@ is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
id: GO:0008803
name: bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity
namespace: molecular_function
-def: "Catalysis of the reaction: P(1),P(4)-bis(5'-adenosyl) tetraphosphate + H(2)O = 2 ADP + 2 H(+)." [EC:3.6.1.41, RHEA:24252]
+def: "Catalysis of the reaction: P(1),P(4)-bis(5'-adenosyl) tetraphosphate + H2O = 2 ADP + 2 H+." [EC:3.6.1.41, RHEA:24252]
synonym: "1-P,4-P-bis(5'-nucleosyl)-tetraphosphate nucleosidebisphosphohydrolase activity" RELATED [EC:3.6.1.41]
synonym: "adenosine tetraphosphate phosphodiesterase activity" RELATED [EC:3.6.1.41]
synonym: "Ap(4)A hydrolase activity" BROAD [EC:3.6.1.41]
@@ -82683,23 +82691,26 @@ is_a: GO:0016833 ! oxo-acid-lyase activity
[Term]
id: GO:0008817
-name: cob(I)yrinic acid a,c-diamide adenosyltransferase activity
+name: corrinoid adenosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + cob(I)alamin + H2O = phosphate + diphosphate + adenosylcobalamin." [EC:2.5.1.17]
-synonym: "aquacob(I)alamin adenosyltransferase activity" RELATED [EC:2.5.1.17]
-synonym: "aquocob(I)alamin vitamin B12s adenosyltransferase activity" RELATED [EC:2.5.1.17]
-synonym: "ATP:cob(I)alamin Co-beta-adenosyltransferase activity" RELATED [EC:2.5.1.17]
+alt_id: GO:0043784
+def: "Catalysis of the reaction: 2 ATP + 2 corrinoid + reduced [electron-transfer flavoprotein] = 2 adenosylcorrinoid + 3 H+ + oxidized [electron-transfer flavoprotein] + 2 triphosphate. The corrinoid can be cob(II)yrinate a,c diamide, cob(II)inamide or cob(II)alamin." [PMID:19933577, PMID:5946606]
+synonym: "aquacob(I)alamin adenosyltransferase activity" NARROW [EC:2.5.1.17]
+synonym: "aquocob(I)alamin vitamin B12s adenosyltransferase activity" NARROW [EC:2.5.1.17]
+synonym: "ATP:cob(I)alamin Co-beta-adenosyltransferase activity" NARROW [EC:2.5.1.17]
synonym: "ATP:cob(I)alamin cobeta-adenosyltransferase activity" RELATED [EC:2.5.1.17]
-synonym: "ATP:cob(I)yrinic acid-a,c-diamide cobeta-adenosyltransferase activity" RELATED [EC:2.5.1.17]
+synonym: "ATP:cob(I)yrinic acid-a,c-diamide cobeta-adenosyltransferase activity" NARROW [EC:2.5.1.17]
synonym: "ATP:corrinoid adenosyltransferase activity" RELATED [EC:2.5.1.17]
-synonym: "cob(I)alamin adenosyltransferase activity" EXACT []
-synonym: "CobA" RELATED [EC:2.5.1.17]
-synonym: "vitamin B12s adenosyltransferase activity" RELATED [EC:2.5.1.17]
+synonym: "cob(I)alamin adenosyltransferase activity" NARROW []
+synonym: "cob(I)yrinic acid a,c-diamide adenosyltransferase activity" NARROW []
+synonym: "cob(II)yrinic acid a,c-diamide reductase activity" NARROW []
+synonym: "cob(II)yrinic acid-a,c-diamide:FMN oxidoreductase activity" NARROW []
+synonym: "vitamin B12s adenosyltransferase activity" RELATED []
xref: EC:2.5.1.17
+xref: KEGG_REACTION:R05218
xref: MetaCyc:COBALADENOSYLTRANS-RXN
-xref: Reactome:R-HSA-3159253 "MMAB transfers adenosyl group from ATP to cob(I)alamin"
+xref: MetaCyc:R343-RXN
xref: Reactome:R-HSA-3322125 "Defective MMAB does not transfer adenosyl group from ATP to B12s"
-xref: RHEA:14725
is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups
[Term]
@@ -82724,7 +82735,7 @@ id: GO:0008820
name: cobinamide phosphate guanylyltransferase activity
namespace: molecular_function
alt_id: GO:0043753
-def: "Catalysis of the reaction: adenosylcobinamide phosphate + GTP + 2 H(+) = adenosylcobinamide-GDP + diphosphate." [EC:2.7.7.62, RHEA:22712]
+def: "Catalysis of the reaction: adenosylcobinamide phosphate + GTP + 2 H+ = adenosylcobinamide-GDP + diphosphate." [RHEA:22712]
synonym: "adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase" BROAD []
synonym: "adenosylcobinamide-phosphate guanylyltransferase activity" EXACT []
synonym: "AdoCbi kinase/AdoCbi-phosphate guanylyltransferase" BROAD []
@@ -82739,34 +82750,29 @@ is_a: GO:0070568 ! guanylyltransferase activity
[Term]
id: GO:0008821
-name: crossover junction endodeoxyribonuclease activity
+name: crossover junction DNA endonuclease activity
namespace: molecular_function
alt_id: GO:0008844
-def: "Catalysis of the endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction)." [EC:3.1.22.4]
+def: "Catalysis of the endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction)." [EC:3.1.21.10]
+synonym: "crossover junction endodeoxyribonuclease activity" EXACT []
synonym: "crossover junction endoribonuclease activity" EXACT []
-synonym: "cruciform-cutting endonuclease activity" RELATED [EC:3.1.22.-]
-synonym: "endo X3" RELATED [EC:3.1.22.4]
-synonym: "Endo X3 activity" NARROW [EC:3.1.22.-]
+synonym: "cruciform-cutting endonuclease activity" RELATED [EC:3.1.21.10]
+synonym: "endo X3" RELATED [EC:3.1.21.10]
synonym: "endodeoxyribonuclease RUS activity" EXACT []
-synonym: "endonuclease RuvC activity" NARROW [EC:3.1.22.-]
-synonym: "endonuclease VII activity" NARROW [EC:3.1.22.-]
-synonym: "endonuclease X3 activity" NARROW [EC:3.1.22.-]
-synonym: "Hje endonuclease activity" RELATED [EC:3.1.22.-]
-synonym: "Holliday junction endonuclease CCE1 activity" NARROW [EC:3.1.22.-]
-synonym: "Holliday junction nuclease activity" RELATED [EC:3.1.22.-]
-synonym: "Holliday junction resolvase activity" NARROW [EC:3.1.22.-]
-synonym: "Holliday junction-cleaving endonuclease activity" RELATED [EC:3.1.22.-]
-synonym: "Holliday junction-resolving endoribonuclease activity" NARROW [EC:3.1.22.-]
-synonym: "resolving enzyme CCE1 activity" NARROW [EC:3.1.22.-]
-synonym: "RusA endonuclease activity" NARROW [EC:3.1.22.-]
-synonym: "RusA holliday junction resolvase" NARROW [EC:3.1.22.4]
-synonym: "RusA Holliday junction resolvase activity" NARROW [EC:3.1.22.-]
-synonym: "RuvC endonuclease activity" NARROW [EC:3.1.22.-]
-synonym: "SpCCe1 holliday junction resolvase" NARROW [EC:3.1.22.4]
-synonym: "SpCCe1 Holliday junction resolvase activity" NARROW [EC:3.1.22.-]
-xref: EC:3.1.22.4
+synonym: "endonuclease RuvC activity" NARROW [EC:3.1.21.10]
+synonym: "endonuclease VII activity" NARROW [EC:3.1.21.10]
+synonym: "endonuclease X3 activity" NARROW [EC:3.1.21.10]
+synonym: "Hje endonuclease activity" RELATED [EC:3.1.21.10]
+synonym: "Holliday junction endonuclease CCE1 activity" NARROW [EC:3.1.21.10]
+synonym: "Holliday junction nuclease activity" RELATED [EC:3.1.21.10]
+synonym: "Holliday junction resolvase activity" NARROW [EC:3.1.21.10]
+synonym: "RusA endonuclease activity" NARROW [EC:3.1.21.10]
+synonym: "RuvC endonuclease activity" NARROW [EC:3.1.21.10]
+synonym: "SpCCe1 holliday junction resolvase" NARROW [EC:3.1.21.10]
+synonym: "SpCCe1 Holliday junction resolvase activity" NARROW [EC:3.1.21.10]
+xref: EC:3.1.21.10
xref: MetaCyc:3.1.22.4-RXN
-is_a: GO:0016889 ! endodeoxyribonuclease activity, producing 3'-phosphomonoesters
+is_a: GO:0016889 ! DNA endonuclease activity, producing 3'-phosphomonoesters
[Term]
id: GO:0008822
@@ -82835,20 +82841,20 @@ is_a: GO:0016846 ! carbon-sulfur lyase activity
[Term]
id: GO:0008828
-name: dATP pyrophosphohydrolase activity
+name: dATP diphosphatase activity
namespace: molecular_function
alt_id: GO:0044713
alt_id: GO:0044714
-def: "Catalysis of the reaction: deoxy-ATP + H2O = dAMP + diphosphate." [GOC:pde, PMID:11139615]
+def: "Catalysis of the reaction: dATP + H2O = dAMP + H+ + diphosphate." [GOC:pde, PMID:11139615, RHEA:28334]
synonym: "2-hydroxy-(d)ATP pyrophosphatase activity" EXACT []
synonym: "2-hydroxy-(deoxy)adenosine-triphosphate pyrophosphatase activity" EXACT []
synonym: "2-hydroxy-adenosine triphosphate pyrophosphatase activity" RELATED []
synonym: "2-hydroxy-ATP pyrophosphatase activity" RELATED []
+synonym: "dATP pyrophosphohydrolase activity" EXACT []
xref: EC:3.6.1.56
xref: MetaCyc:RXN0-384
-xref: Reactome:R-HSA-2395818 "NUDT1 hydrolyses 2-OH-dATP to 2-OH-dAMP"
-xref: Reactome:R-HSA-2395872 "NUDT1 hydrolyses 2-OH-ATP to 2-OH-AMP"
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+xref: RHEA:28334
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0008829
@@ -82885,7 +82891,7 @@ is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and
id: GO:0008831
name: dTDP-4-dehydrorhamnose reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dTDP-6-deoxy-L-mannose + NADP(+) = dTDP-4-dehydro-6-deoxy-L-mannose + H(+) + NADPH." [EC:1.1.1.133, RHEA:21796]
+def: "Catalysis of the reaction: dTDP-6-deoxy-L-mannose + NADP+ = dTDP-4-dehydro-6-deoxy-L-mannose + H+ + NADPH." [EC:1.1.1.133, RHEA:21796]
synonym: "dTDP-4-keto-L-rhamnose reductase activity" RELATED [EC:1.1.1.133]
synonym: "dTDP-4-ketorhamnose reductase activity" RELATED [EC:1.1.1.133]
synonym: "dTDP-6-deoxy-L-mannose dehydrogenase activity" RELATED [EC:1.1.1.133]
@@ -82903,7 +82909,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0008832
name: dGTPase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dGTP + H(2)O = 2'-deoxyguanosine + 2 H(+) + triphosphate." [EC:3.1.5.1, RHEA:15193]
+def: "Catalysis of the reaction: dGTP + H2O = 2'-deoxyguanosine + 2 H+ + triphosphate." [EC:3.1.5.1, RHEA:15193]
synonym: "deoxy-GTPase activity" RELATED [EC:3.1.5.1]
synonym: "deoxyguanosine 5-triphosphate triphosphohydrolase activity" RELATED [EC:3.1.5.1]
synonym: "deoxyguanosine triphosphatase activity" RELATED [EC:3.1.5.1]
@@ -82959,7 +82965,7 @@ id: GO:0008835
name: diaminohydroxyphosphoribosylaminopyrimidine deaminase activity
namespace: molecular_function
alt_id: GO:0008485
-def: "Catalysis of the reaction: 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + H(2)O + H(+) = 5-amino-6-(5-phosphoribosylamino)uracil + NH(4)(+)." [EC:3.5.4.26, RHEA:21868]
+def: "Catalysis of the reaction: 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + H2O + H+ = 5-amino-6-(5-phosphoribosylamino)uracil + NH4." [EC:3.5.4.26, RHEA:21868]
synonym: "2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate deaminase activity" EXACT []
synonym: "2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine 2-aminohydrolase activity" RELATED [EC:3.5.4.26]
synonym: "2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 2-aminohydrolase activity" RELATED [EC:3.5.4.26]
@@ -82974,7 +82980,7 @@ is_a: GO:0019239 ! deaminase activity
id: GO:0008836
name: diaminopimelate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: meso-2,6-diaminopimelate + H(+) = L-lysine + CO(2)." [EC:4.1.1.20, RHEA:15101]
+def: "Catalysis of the reaction: meso-2,6-diaminopimelate + H+ = L-lysine + CO2." [EC:4.1.1.20, RHEA:15101]
synonym: "DAP decarboxylase activity" RELATED [EC:4.1.1.20]
synonym: "DAP-decarboxylase activity" RELATED [EC:4.1.1.20]
synonym: "diaminopimelic acid decarboxylase activity" RELATED [EC:4.1.1.20]
@@ -83029,18 +83035,17 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0008840
name: 4-hydroxy-tetrahydrodipicolinate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O." [EC:4.3.3.7, RHEA:14845]
-synonym: "DHDPS activity" RELATED [EC:4.2.1.52]
+def: "Catalysis of the reaction: pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O." [PMID:8993314, RHEA:34171]
+synonym: "DHDPS activity" RELATED [EC:4.3.3.7]
synonym: "dihydrodipicolinate synthase activity" EXACT []
-synonym: "dihydrodipicolinate synthetase activity" RELATED [EC:4.2.1.52]
-synonym: "dihydrodipicolinic acid synthase activity" RELATED [EC:4.2.1.52]
-synonym: "dihydropicolinate synthetase activity" RELATED [EC:4.2.1.52]
-synonym: "L-aspartate-4-semialdehyde hydro-lyase (adding pyruvate and cyclizing)" RELATED [EC:4.2.1.52]
-synonym: "L-aspartate-4-semialdehyde hydro-lyase [adding pyruvate and cyclizing; (S)-2,3-dihydropyridine-2,6-dicarboxylate-forming]" RELATED [EC:4.2.1.52]
+synonym: "dihydrodipicolinate synthetase activity" RELATED [EC:4.3.3.7]
+synonym: "dihydrodipicolinic acid synthase activity" RELATED [EC:4.3.3.7]
+synonym: "L-aspartate-4-semialdehyde hydro-lyase (adding pyruvate and cyclizing)" RELATED []
+synonym: "L-aspartate-4-semialdehyde hydro-lyase [adding pyruvate and cyclizing; (S)-2,3-dihydropyridine-2,6-dicarboxylate-forming]" RELATED []
xref: EC:4.3.3.7
xref: KEGG_REACTION:R02292
xref: MetaCyc:DIHYDRODIPICSYN-RXN
-xref: RHEA:14845
+xref: RHEA:34171
is_a: GO:0016836 ! hydro-lyase activity
[Term]
@@ -83132,7 +83137,7 @@ def: "Catalysis of the endonucleolytic cleavage to 3'-phosphomononucleotides and
synonym: "Enterobacter RNase activity" EXACT []
xref: EC:4.6.1.21
xref: MetaCyc:3.1.27.6-RXN
-is_a: GO:0016892 ! endoribonuclease activity, producing 3'-phosphomonoesters
+is_a: GO:0016892 ! RNA endonuclease activity, producing 3'-phosphomonoesters
[Term]
id: GO:0008848
@@ -83171,30 +83176,30 @@ is_a: GO:0016841 ! ammonia-lyase activity
[Term]
id: GO:0008852
-name: exodeoxyribonuclease I activity
+name: obsolete exodeoxyribonuclease I activity
namespace: molecular_function
-def: "Catalysis of the degradation of single-stranded DNA. It acts progressively in a 3' to 5' direction, releasing 5'-phosphomononucleotides." [EC:3.1.11.1]
+def: "OBSOLETE. Catalysis of the degradation of single-stranded DNA. It acts progressively in a 3' to 5' direction, releasing 5'-phosphomononucleotides." [EC:3.1.11.1]
+comment: This term was obsoleted because it is the same function as single-stranded DNA 3'-5' exodeoxyribonuclease activity ; GO:0008310.
synonym: "E. coli exonuclease I" RELATED [EC:3.1.11.1]
synonym: "E. coli exonuclease I activity" NARROW [EC:3.1.11.1]
synonym: "Escherichia coli exonuclease I" RELATED [EC:3.1.11.1]
synonym: "exonuclease I activity" RELATED [EC:3.1.11.1]
-xref: EC:3.1.11.1
-xref: MetaCyc:3.1.11.1-RXN
-is_a: GO:0016895 ! exodeoxyribonuclease activity, producing 5'-phosphomonoesters
+is_obsolete: true
+replaced_by: GO:0008310
[Term]
id: GO:0008853
-name: exodeoxyribonuclease III activity
+name: obsolete exodeoxyribonuclease III activity
namespace: molecular_function
-def: "Catalysis of the degradation of double-stranded DNA. It acts progressively in a 3' to 5' direction, releasing 5'-phosphomononucleotides." [EC:3.1.11.2]
+def: "OBSOLETE. Catalysis of the degradation of double-stranded DNA. It acts progressively in a 3' to 5' direction, releasing 5'-phosphomononucleotides." [EC:3.1.11.2]
+comment: This term was obsoleted because it is the same function as double-stranded DNA 3'-5' exodeoxy\nribonuclease activity ; GO:0008311.
synonym: "E. coli exonuclease III" RELATED [EC:3.1.11.2]
synonym: "E. coli exonuclease III activity" NARROW [EC:3.1.11.2]
synonym: "endoribonuclease III" RELATED [EC:3.1.11.2]
synonym: "Escherichia coli exonuclease III" RELATED [EC:3.1.11.2]
synonym: "exonuclease III activity" RELATED [EC:3.1.11.2]
-xref: EC:3.1.11.2
-xref: MetaCyc:3.1.11.2-RXN
-is_a: GO:0016895 ! exodeoxyribonuclease activity, producing 5'-phosphomonoesters
+is_obsolete: true
+replaced_by: GO:0008311
[Term]
id: GO:0008854
@@ -83211,7 +83216,7 @@ synonym: "gene recBCD enzymes" RELATED [EC:3.1.11.5]
synonym: "RecBC deoxyribonuclease activity" RELATED [EC:3.1.11.5]
xref: EC:3.1.11.5
xref: MetaCyc:3.1.11.5-RXN
-is_a: GO:0016895 ! exodeoxyribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016895 ! DNA exonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0008855
@@ -83225,19 +83230,20 @@ synonym: "Escherichia coli exonuclease VII" RELATED [EC:3.1.11.6]
synonym: "exonuclease VII activity" RELATED [EC:3.1.11.6]
xref: EC:3.1.11.6
xref: MetaCyc:3.1.11.6-RXN
-is_a: GO:0016895 ! exodeoxyribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016895 ! DNA exonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0008856
-name: exodeoxyribonuclease X activity
+name: obsolete exodeoxyribonuclease X activity
namespace: molecular_function
-def: "Catalysis of the endonucleolytic cleavage of supercoiled plasma DNA to linear DNA duplexes." [EC:3.1.22.5]
+def: "OBSOLETE. Catalysis of the endonucleolytic cleavage of supercoiled plasma DNA to linear DNA duplexes." [EC:3.1.22.5]
+comment: This term was obsoleted because there is no evidence that this function exists.
synonym: "deoxyribonuclease X activity" RELATED [EC:3.1.22.5]
synonym: "Escherichia coli endodeoxyribonuclease activity" RELATED [EC:3.1.22.5]
synonym: "Escherichia coli endodeoxyribonuclease X activity" NARROW [EC:3.1.22.5]
xref: EC:3.1.11.-
xref: MetaCyc:3.1.22.5-RXN
-is_a: GO:0016895 ! exodeoxyribonuclease activity, producing 5'-phosphomonoesters
+is_obsolete: true
[Term]
id: GO:0008859
@@ -83254,7 +83260,7 @@ synonym: "RNase II activity" EXACT []
xref: EC:3.1.13.1
xref: MetaCyc:3.1.13.1-RXN
is_a: GO:0008408 ! 3'-5' exonuclease activity
-is_a: GO:0016896 ! exoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016896 ! RNA exonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0008860
@@ -83282,7 +83288,7 @@ is_a: GO:0008937 ! ferredoxin-NAD(P) reductase activity
id: GO:0008861
name: formate C-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + formate = CoA + pyruvate." [EC:2.3.1.54]
+def: "Catalysis of the reaction: acetyl-CoA + formate = CoA + pyruvate." [RHEA:11844]
synonym: "acetyl-CoA:formate C-acetyltransferase activity" RELATED [EC:2.3.1.54]
synonym: "formate acetyltransferase activity" RELATED [EC:2.3.1.54]
synonym: "PFL" EXACT []
@@ -83299,7 +83305,7 @@ id: GO:0008863
name: formate dehydrogenase (NAD+) activity
namespace: molecular_function
alt_id: GO:0018476
-def: "Catalysis of the reaction: formate + NAD(+) = CO(2) + NADH." [EC:1.17.1.9, RHEA:15985]
+def: "Catalysis of the reaction: formate + NAD+ = CO2 + NADH." [EC:1.17.1.9, RHEA:15985]
synonym: "formate dehydrogenase (NAD)" RELATED [EC:1.17.1.9]
synonym: "formate hydrogenlyase" RELATED [EC:1.17.1.9]
synonym: "formate-NAD oxidoreductase" RELATED []
@@ -83319,7 +83325,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0008864
name: formyltetrahydrofolate deformylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 10-formyltetrahydrofolate + H(2)O = (6S)-5,6,7,8-tetrahydrofolate + formate + H(+)." [EC:3.5.1.10, RHEA:19833]
+def: "Catalysis of the reaction: 10-formyltetrahydrofolate + H2O = (6S)-5,6,7,8-tetrahydrofolate + formate + H+." [EC:3.5.1.10, RHEA:19833]
synonym: "10-formyltetrahydrofolate amidohydrolase activity" RELATED [EC:3.5.1.10]
synonym: "formyl-FH(4) hydrolase activity" RELATED [EC:3.5.1.10]
synonym: "formyltetrahydrofolate hydrolase activity" RELATED [EC:3.5.1.10]
@@ -83347,7 +83353,7 @@ is_a: GO:0004396 ! hexokinase activity
id: GO:0008866
name: fructuronate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-mannonate + NAD(+) = D-fructuronate + H(+) + NADH." [EC:1.1.1.57, RHEA:15729]
+def: "Catalysis of the reaction: D-mannonate + NAD+ = D-fructuronate + H+ + NADH." [EC:1.1.1.57, RHEA:15729]
synonym: "D-mannonate dehydrogenase activity" RELATED [EC:1.1.1.57]
synonym: "D-mannonate oxidoreductase activity" RELATED [EC:1.1.1.57]
synonym: "D-mannonate:NAD oxidoreductase activity" RELATED [EC:1.1.1.57]
@@ -83364,7 +83370,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0008867
name: galactarate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: galactarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O." [EC:4.2.1.42, RHEA:16005]
+def: "Catalysis of the reaction: galactarate = 5-dehydro-4-deoxy-D-glucarate + H2O." [EC:4.2.1.42, RHEA:16005]
synonym: "D-galactarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming)" RELATED [EC:4.2.1.42]
synonym: "D-galactarate hydro-lyase activity" RELATED [EC:4.2.1.42]
xref: EC:4.2.1.42
@@ -83388,7 +83394,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0008869
name: galactonate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H(2)O." [EC:4.2.1.6, RHEA:18649]
+def: "Catalysis of the reaction: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O." [EC:4.2.1.6, RHEA:18649]
synonym: "D-galactonate dehydrase activity" RELATED [EC:4.2.1.6]
synonym: "D-galactonate dehydratase activity" RELATED [EC:4.2.1.6]
synonym: "D-galactonate hydro-lyase (2-dehydro-3-deoxy-D-galactonate-forming)" RELATED [EC:4.2.1.6]
@@ -83486,7 +83492,9 @@ synonym: "glucose dehydrogenase (PQQ-dependent) activity" RELATED [EC:1.1.5.2]
synonym: "glucose dehydrogenase (pyrroloquinoline-quinone) activity" EXACT []
synonym: "quinoprotein D-glucose dehydrogenase activity" RELATED [EC:1.1.5.2]
xref: EC:1.1.5.2
+xref: KEGG_REACTION:R00305
xref: MetaCyc:GLUCDEHYDROG-RXN
+xref: MetaCyc:GLUCOSE-DEHYDROGENASE-ACCEPTOR-RXN
xref: RHEA:22152
is_a: GO:0004344 ! glucose dehydrogenase activity
is_a: GO:0016901 ! oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor
@@ -83594,7 +83602,7 @@ is_a: GO:0070566 ! adenylyltransferase activity
id: GO:0008883
name: glutamyl-tRNA reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-4-amino-5-oxopentanoate + NADP(+) + tRNA(Glu) = L-glutamyl-tRNA(Glu) + H(+) + NADPH." [EC:1.2.1.70, RHEA:12344]
+def: "Catalysis of the reaction: (S)-4-amino-5-oxopentanoate + NADP+ + tRNA(Glu) = L-glutamyl-tRNA(Glu) + H+ + NADPH." [EC:1.2.1.70, RHEA:12344]
synonym: "L-glutamate-semialdehyde: NADP+ oxidoreductase (L-glutamyl-tRNAGlu-forming)" RELATED [EC:1.2.1.70]
xref: EC:1.2.1.70
xref: KEGG_REACTION:R04109
@@ -83635,7 +83643,7 @@ is_a: GO:0016880 ! acid-ammonia (or amide) ligase activity
id: GO:0008886
name: glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glyceraldehyde 3-phosphate + H(2)O + NADP(+) = 3-phospho-D-glycerate + 2 H(+) + NADPH." [EC:1.2.1.9, RHEA:14669]
+def: "Catalysis of the reaction: D-glyceraldehyde 3-phosphate + H2O + NADP+ = 3-phospho-D-glycerate + 2 H+ + NADPH." [EC:1.2.1.9, RHEA:14669]
synonym: "D-glyceraldehyde-3-phosphate:NADP+ oxidoreductase activity" EXACT []
synonym: "dehydrogenase, glyceraldehyde phosphate (nicotinamide adenine dinucleotide phosphate)" BROAD []
synonym: "glyceraldehyde 3-phosphate dehydrogenase (NADP)" EXACT []
@@ -83656,7 +83664,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0008887
name: glycerate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glycerate + ATP = 3-phospho-D-glycerate + ADP + 2 H(+)." [EC:2.7.1.31, RHEA:23516]
+def: "Catalysis of the reaction: D-glycerate + ATP = 3-phospho-D-glycerate + ADP + 2 H+." [EC:2.7.1.31, RHEA:23516]
synonym: "ATP:(R)-glycerate 3-phosphotransferase activity" RELATED [EC:2.7.1.31]
synonym: "ATP:D-glycerate 2-phosphotransferase activity" RELATED [EC:2.7.1.31]
synonym: "D-glycerate 3-kinase activity" RELATED [EC:2.7.1.31]
@@ -83677,7 +83685,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0008888
name: glycerol dehydrogenase [NAD+] activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycerol + NAD(+) = glycerone + H(+) + NADH." [EC:1.1.1.6, RHEA:13769]
+def: "Catalysis of the reaction: glycerol + NAD+ = glycerone + H+ + NADH." [EC:1.1.1.6, RHEA:13769]
synonym: "glycerol dehydrogenase activity" BROAD []
synonym: "NAD-linked glycerol dehydrogenase activity" RELATED [EC:1.1.1.6]
xref: EC:1.1.1.6
@@ -83706,7 +83714,7 @@ is_a: GO:0008081 ! phosphoric diester hydrolase activity
id: GO:0008890
name: glycine C-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + glycine = L-2-amino-3-oxobutanoate + CoA + H(+)." [EC:2.3.1.29, RHEA:20736]
+def: "Catalysis of the reaction: acetyl-CoA + glycine = L-2-amino-3-oxobutanoate + CoA + H+." [EC:2.3.1.29, RHEA:20736]
synonym: "2-amino-3-ketobutyrate CoA ligase activity" RELATED [EC:2.3.1.29]
synonym: "2-amino-3-ketobutyrate coenzyme A ligase activity" RELATED [EC:2.3.1.29]
synonym: "2-amino-3-ketobutyrate-CoA ligase activity" RELATED [EC:2.3.1.29]
@@ -83848,11 +83856,11 @@ alt_id: GO:0005390
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) + K+(out) = ADP + phosphate + H+(out) + K+(in)." [RHEA:22044]
synonym: "(K+ + H+)-ATPase activity" RELATED [EC:7.2.2.19]
synonym: "ATP phosphohydrolase (H+/K+-exchanging)" RELATED [EC:7.2.2.19]
-synonym: "gastric H(+)/K(+) ATPase activity" NARROW [EC:3.6.3.10]
+synonym: "gastric H+/K(+) ATPase activity" NARROW [EC:3.6.3.10]
synonym: "gastric H+/K+ ATPase" NARROW [EC:7.2.2.19]
-synonym: "H(+)/K(+)-ATPase activity" RELATED [EC:7.2.2.19]
-synonym: "H(+)/K(+)-exchanging ATPase activity" RELATED [EC:7.2.2.19]
synonym: "H+-K+-ATPase activity" RELATED [EC:7.2.2.19]
+synonym: "H+/K(+)-ATPase activity" RELATED [EC:7.2.2.19]
+synonym: "H+/K(+)-exchanging ATPase activity" RELATED [EC:7.2.2.19]
synonym: "H+/K+-ATPase activity" RELATED [EC:7.2.2.19]
synonym: "H+/K+-exchanging ATPase activity" RELATED [EC:7.2.2.19]
synonym: "H,K-ATPase activity" RELATED [EC:7.2.2.19]
@@ -83862,7 +83870,8 @@ synonym: "hydrogen:potassium-exchanging ATPase activity" EXACT []
synonym: "potassium:proton exchanging ATPase activity" RELATED []
synonym: "proton pump activity" BROAD [EC:3.6.3.10]
xref: EC:7.2.2.19
-xref: Reactome:R-HSA-937311 "ATP4A/12A:ATP4B exchanges K+ for H+"
+xref: Reactome:R-HSA-937311 "ATP12A:ATP4B exchanges K+ for H+"
+xref: Reactome:R-HSA-9727198 "ATP4A:ATP4B exchanges K+ for H+"
xref: RHEA:22044
is_a: GO:0008553 ! P-type proton-exporting transporter activity
is_a: GO:0008556 ! P-type potassium transmembrane transporter activity
@@ -83909,7 +83918,7 @@ is_a: GO:0016699 ! oxidoreductase activity, acting on hydrogen as donor, iron-su
id: GO:0008902
name: hydroxymethylpyrimidine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-amino-5-hydroxymethyl-2-methylpyrimidine + ATP = 4-amino-2-methyl-5-phosphomethylpyrimidine + ADP + 2 H(+)." [EC:2.7.1.49, RHEA:23096]
+def: "Catalysis of the reaction: 4-amino-5-hydroxymethyl-2-methylpyrimidine + ATP = 4-amino-2-methyl-5-phosphomethylpyrimidine + ADP + 2 H+." [EC:2.7.1.49, RHEA:23096]
synonym: "ATP:4-amino-5-hydroxymethyl-2-methylpyrimidine 5-phosphotransferase activity" RELATED [EC:2.7.1.49]
synonym: "hydroxymethylpyrimidine kinase (phosphorylating)" RELATED [EC:2.7.1.49]
xref: EC:2.7.1.49
@@ -83936,7 +83945,7 @@ is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldos
id: GO:0008904
name: hygromycin-B 7''-O-phosphotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + hygromycin B = 7''-O-phosphohygromycin B + ADP + 2 H(+)." [EC:2.7.1.119, RHEA:23388]
+def: "Catalysis of the reaction: ATP + hygromycin B = 7''-O-phosphohygromycin B + ADP + 2 H+." [EC:2.7.1.119, RHEA:23388]
synonym: "APH(7'') activity" RELATED [EC:2.7.1.119]
synonym: "ATP:hygromycin-B 7''-O-phosphotransferase activity" RELATED [EC:2.7.1.119]
synonym: "destomic acid ring 7''-O-phosphotransferase activity" EXACT []
@@ -83951,10 +83960,14 @@ is_a: GO:0034071 ! aminoglycoside phosphotransferase activity
[Term]
id: GO:0008905
-name: mannose-phosphate guanylyltransferase activity
+name: obsolete mannose-phosphate guanylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group from GTP or GDP to a mannose molecule." [GOC:mah]
-is_a: GO:0070568 ! guanylyltransferase activity
+def: "OBSOLETE. Catalysis of the transfer of a phosphate group from GTP or GDP to a mannose molecule." [GOC:mah]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
+is_obsolete: true
+consider: GO:0004475
+consider: GO:0008928
+consider: GO:0010471
[Term]
id: GO:0008906
@@ -83983,7 +83996,7 @@ is_a: GO:0140097 ! catalytic activity, acting on DNA
id: GO:0008908
name: isochorismatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + isochorismate = 2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate." [EC:3.3.2.1, RHEA:11112]
+def: "Catalysis of the reaction: H2O + isochorismate = 2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate." [EC:3.3.2.1, RHEA:11112]
synonym: "2,3 dihydro-2,3 dihydroxybenzoate synthase activity" RELATED [EC:3.3.2.1]
synonym: "2,3-dihydro-2,3-dihydroxybenzoate synthase activity" RELATED [EC:3.3.2.1]
synonym: "2,3-dihydroxy-2,3-dihydrobenzoate synthase activity" RELATED [EC:3.3.2.1]
@@ -84014,7 +84027,7 @@ is_a: GO:0050486 ! intramolecular transferase activity, transferring hydroxy gro
id: GO:0008910
name: kanamycin kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + kanamycin = ADP + 2 H(+) + kanamycin 3'-phosphate." [EC:2.7.1.95, RHEA:24256]
+def: "Catalysis of the reaction: ATP + kanamycin = ADP + 2 H+ + kanamycin 3'-phosphate." [EC:2.7.1.95, RHEA:24256]
synonym: "aminoglycoside 3'-phosphotransferase activity" BROAD [EC:2.7.1.95]
synonym: "APH(3') activity" BROAD [EC:2.7.1.95]
synonym: "ATP:kanamycin 3'-O-phosphotransferase activity" RELATED [EC:2.7.1.95]
@@ -84081,7 +84094,7 @@ is_a: GO:0016755 ! aminoacyltransferase activity
id: GO:0008915
name: lipid-A-disaccharide synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate + UDP-2,3-bis(3-hydroxytetradecanoyl)-D-glucosamine = 2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-(1->6)-beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate + H(+) + UDP." [EC:2.4.1.182, RHEA:22668]
+def: "Catalysis of the reaction: 2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate + UDP-2,3-bis(3-hydroxytetradecanoyl)-D-glucosamine = 2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-(1->6)-beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate + H+ + UDP." [EC:2.4.1.182, RHEA:22668]
synonym: "UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine:2,3-bis-(3-hydroxytetradecanoyl)-beta-D-glucosaminyl-1-phosphate 2,3-bis(3-hydroxytetradecanoyl)-glucosaminyltransferase activity" RELATED [EC:2.4.1.182]
xref: EC:2.4.1.182
xref: KEGG_REACTION:R04606
@@ -84159,7 +84172,7 @@ id: GO:0008922
name: long-chain fatty acid [acyl-carrier-protein] ligase activity
namespace: molecular_function
alt_id: GO:0010300
-def: "Catalysis of the reaction: ATP + an acid + [acyl-carrier protein] = AMP + diphosphate + acyl-[acyl-carrier protein]. A long-chain fatty acid is fatty acid with a chain length between C13 and C22." [EC:6.2.1.20]
+def: "Catalysis of the reaction: ATP + an acid + [acyl-carrier protein] = AMP + diphosphate + acyl-[acyl-carrier protein]. A long-chain fatty acid is a fatty acid with an aliphatic tail of 13 to 21 carbons." [EC:6.2.1.20]
synonym: "acyl-[acyl-carrier-protein] synthetase activity" RELATED [EC:6.2.1.20]
synonym: "acyl-ACP synthetase activity" EXACT []
synonym: "acyl-acyl carrier protein synthetase" BROAD [EC:6.2.1.20]
@@ -84182,13 +84195,11 @@ is_a: GO:0015645 ! fatty acid ligase activity
id: GO:0008923
name: lysine decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-lysine + H(+) = cadaverine + CO(2)." [EC:4.1.1.18, RHEA:22352]
-synonym: "L-lysine carboxy-lyase (cadaverine-forming)" RELATED [EC:4.1.1.18]
+def: "Catalysis of the reaction: L-lysine + H+ = cadaverine + CO2." [RHEA:22352]
synonym: "L-lysine carboxy-lyase activity" RELATED [EC:4.1.1.18]
xref: EC:4.1.1.18
xref: KEGG_REACTION:R00462
xref: MetaCyc:LYSDECARBOX-RXN
-xref: MetaCyc:PWY0-461
xref: RHEA:22352
is_a: GO:0016831 ! carboxy-lyase activity
@@ -84233,7 +84244,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0008927
name: mannonate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H(2)O." [EC:4.2.1.8, RHEA:20097]
+def: "Catalysis of the reaction: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O." [EC:4.2.1.8, RHEA:20097]
synonym: "altronate hydrolase activity" RELATED [EC:4.2.1.8]
synonym: "altronic hydro-lyase activity" RELATED [EC:4.2.1.8]
synonym: "D-mannonate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)" RELATED [EC:4.2.1.8]
@@ -84251,23 +84262,23 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0008928
name: mannose-1-phosphate guanylyltransferase (GDP) activity
namespace: molecular_function
-def: "Catalysis of the reaction: alpha-D-mannose 1-phosphate + GDP + H(+) = GDP-alpha-D-mannose + phosphate." [EC:2.7.7.22, RHEA:12905]
+def: "Catalysis of the reaction: alpha-D-mannose 1-phosphate + GDP + H+ = GDP-alpha-D-mannose + phosphate." [RHEA:12905]
synonym: "GDP mannose phosphorylase activity" RELATED [EC:2.7.7.22]
-synonym: "GDP-mannose 1-phosphate guanylyltransferase activity" RELATED [EC:2.7.7.22]
+synonym: "GDP-mannose 1-phosphate guanylyltransferase activity" RELATED []
synonym: "GDP-mannose phosphorylase activity" RELATED [EC:2.7.7.22]
synonym: "GDP-mannose pyrophosphorylase activity" RELATED [EC:2.7.7.22]
-synonym: "GDP:alpha-D-mannose-1-phosphate guanylyltransferase activity" RELATED [EC:2.7.7.22]
-synonym: "GDP:D-mannose-1-phosphate guanylyltransferase activity" RELATED [EC:2.7.7.22]
+synonym: "GDP:alpha-D-mannose-1-phosphate guanylyltransferase activity" RELATED []
+synonym: "GDP:D-mannose-1-phosphate guanylyltransferase activity" RELATED []
synonym: "GDP:mannose-1-phosphate guanylyltransferase activity" EXACT []
-synonym: "guanosine diphosphate-mannose 1-phosphate guanylyltransferase activity" RELATED [EC:2.7.7.22]
-synonym: "guanosine diphosphomannose phosphorylase activity" RELATED [EC:2.7.7.22]
-synonym: "mannose 1-phosphate (guanosine diphosphate) guanylyltransferase activity" RELATED [EC:2.7.7.22]
-synonym: "mannose 1-phosphate guanylyltransferase activity" RELATED [EC:2.7.7.22]
+synonym: "guanosine diphosphate-mannose 1-phosphate guanylyltransferase activity" RELATED []
+synonym: "guanosine diphosphomannose phosphorylase activity" RELATED []
+synonym: "mannose 1-phosphate (guanosine diphosphate) guanylyltransferase activity" RELATED []
+synonym: "mannose 1-phosphate guanylyltransferase activity" RELATED []
xref: EC:2.7.7.22
xref: KEGG_REACTION:R00883
xref: MetaCyc:MANNPGUANYLTRANGDP-RXN
xref: RHEA:12905
-is_a: GO:0008905 ! mannose-phosphate guanylyltransferase activity
+is_a: GO:0070568 ! guanylyltransferase activity
[Term]
id: GO:0008929
@@ -84314,7 +84325,7 @@ name: lytic endotransglycosylase activity
namespace: molecular_function
def: "Catalysis of the specific cleavage of the beta-(1->4) glycosidic linkage between N-acetylmuramyl and N-acetylglucosaminyl residues in peptidoglycan, with the concomitant formation of 1,6-anhydro-N-acetylmuramyl residues. Acts on linkages within peptidoglycan chains (i.e. not at the ends) to produce shorter strands with 1,6-anhydromuramic acid ends." [PMID:10964424, PMID:9642199]
synonym: "murein lytic endotransglycosylase E activity" NARROW []
-xref: EC:2.4.99.-
+xref: EC:4.2.2.n2
is_a: GO:0008933 ! lytic transglycosylase activity
[Term]
@@ -84324,8 +84335,7 @@ namespace: molecular_function
def: "Catalysis of the specific cleavage of the beta-(1->4) glycosidic linkage between N-acetylmuramyl and N-acetylglucosaminyl residues in peptidoglycan, with the concomitant formation of 1,6-anhydro-N-acetylmuramyl residues." [PMID:10964424, PMID:22748813]
synonym: "murein transglycosylase B activity" NARROW []
synonym: "peptidoglycan lytic transglycosylase activity" EXACT []
-xref: EC:3.2.1.-
-is_a: GO:0016757 ! glycosyltransferase activity
+is_a: GO:0016837 ! carbon-oxygen lyase activity, acting on polysaccharides
is_a: GO:0061783 ! peptidoglycan muralytic activity
[Term]
@@ -84383,6 +84393,7 @@ id: GO:0008937
name: ferredoxin-NAD(P) reductase activity
namespace: molecular_function
def: "Catalysis of the reaction: reduced ferredoxin + NAD(P)+ = oxidized ferredoxin + NAD(P)H + H+." [GOC:curators]
+subset: gocheck_do_not_annotate
synonym: "ferredoxin reductase activity" BROAD []
is_a: GO:0016731 ! oxidoreductase activity, acting on iron-sulfur proteins as donors, NAD or NADP as acceptor
@@ -84404,7 +84415,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0008939
name: nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5,6-dimethylbenzimidazole + nicotinate D-ribonucleotide = alpha-ribazole 5'-phosphate + H(+) + nicotinate." [EC:2.4.2.21, RHEA:11196]
+def: "Catalysis of the reaction: 5,6-dimethylbenzimidazole + nicotinate D-ribonucleotide = alpha-ribazole 5'-phosphate + H+ + nicotinate." [EC:2.4.2.21, RHEA:11196]
synonym: "CobT" RELATED [EC:2.4.2.21]
synonym: "N(1)-alpha-phosphoribosyltransferase activity" RELATED [EC:2.4.2.21]
synonym: "N1-alpha-phosphoribosyltransferase activity" RELATED [EC:2.4.2.21]
@@ -84546,7 +84557,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0008949
name: oxalyl-CoA decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + oxalyl-CoA = CO(2) + formyl-CoA." [EC:4.1.1.8, RHEA:19333]
+def: "Catalysis of the reaction: H+ + oxalyl-CoA = CO2 + formyl-CoA." [EC:4.1.1.8, RHEA:19333]
synonym: "oxalyl coenzyme A decarboxylase activity" RELATED [EC:4.1.1.8]
synonym: "oxalyl-CoA carboxy-lyase (formyl-CoA-forming)" RELATED [EC:4.1.1.8]
synonym: "oxalyl-CoA carboxy-lyase activity" RELATED [EC:4.1.1.8]
@@ -84778,7 +84789,7 @@ is_a: GO:0016868 ! intramolecular transferase activity, phosphotransferases
id: GO:0008967
name: phosphoglycolate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-phosphoglycolate + H(2)O = glycolate + phosphate." [EC:3.1.3.18, RHEA:14369]
+def: "Catalysis of the reaction: 2-phosphoglycolate + H2O = glycolate + phosphate." [EC:3.1.3.18, RHEA:14369]
synonym: "2-phosphoglycolate phosphatase activity" RELATED [EC:3.1.3.18]
synonym: "2-phosphoglycolate phosphohydrolase activity" RELATED [EC:3.1.3.18]
synonym: "P-glycolate phosphatase activity" RELATED [EC:3.1.3.18]
@@ -84857,7 +84868,7 @@ is_a: GO:0016868 ! intramolecular transferase activity, phosphotransferases
id: GO:0008974
name: phosphoribulokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-ribulose 5-phosphate + ATP = D-ribulose 1,5-bisphosphate + ADP + 2 H(+)." [EC:2.7.1.19, RHEA:19365]
+def: "Catalysis of the reaction: D-ribulose 5-phosphate + ATP = D-ribulose 1,5-bisphosphate + ADP + 2 H+." [EC:2.7.1.19, RHEA:19365]
synonym: "5-phosphoribulose kinase activity" RELATED [EC:2.7.1.19]
synonym: "ATP:D-ribulose-5-phosphate 1-phosphotransferase activity" RELATED [EC:2.7.1.19]
synonym: "phosphopentokinase activity" RELATED [EC:2.7.1.19]
@@ -84909,7 +84920,7 @@ is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
id: GO:0008977
name: prephenate dehydrogenase (NAD+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD(+) + prephenate = (4-hydroxyphenyl)pyruvate + CO(2) + NADH." [EC:1.3.1.12, RHEA:13869]
+def: "Catalysis of the reaction: NAD+ + prephenate = (4-hydroxyphenyl)pyruvate + CO2 + NADH." [EC:1.3.1.12, RHEA:13869]
synonym: "chorismate mutase--prephenate dehydrogenase activity" RELATED [EC:1.3.1.12]
synonym: "hydroxyphenylpyruvate synthase activity" BROAD [EC:1.3.1.12]
synonym: "prephenate:NAD+ oxidoreductase (decarboxylating)" RELATED [EC:1.3.1.12]
@@ -84935,7 +84946,6 @@ name: prophage integrase activity
namespace: molecular_function
def: "Catalysis of the integration of prophage DNA into a target DNA molecule, usually a bacterial chromosome, via a sequence-specific recombination event which involves the formation of an intasome, a DNA-protein-complex designed for site-specific recombination of the phage and host DNA." [GOC:jl]
synonym: "integrase activity involved in establishment of integrated proviral latency" EXACT []
-is_a: GO:0008907 ! integrase activity
is_a: GO:0009009 ! site-specific recombinase activity
[Term]
@@ -84968,32 +84978,18 @@ name: protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
namespace: molecular_function
alt_id: GO:0015455
alt_id: GO:0015456
-def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + sugar(out) = protein histidine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [EC:2.7.1.69, GOC:mtg_transport, http://www.ucs.mun.ca/~n55lrb/general_pts.html, ISBN:0815340729, TC:4.A.-.-.-]
-synonym: "enzyme II of the phosphotransferase system" NARROW [EC:2.7.1.69]
-synonym: "enzyme IIl4ac" RELATED [EC:2.7.1.69]
-synonym: "gene bglC RNA formation factors" RELATED [EC:2.7.1.69]
-synonym: "gene glC proteins" RELATED [EC:2.7.1.69]
-synonym: "group translocator activity" RELATED [EC:2.7.1.69]
-synonym: "PEP--sugar phosphotransferase enzyme II activity" NARROW [EC:2.7.1.69]
-synonym: "PEP-dependent phosphotransferase enzyme II" RELATED [EC:2.7.1.69]
-synonym: "phosphoenolpyruvate-sugar phosphotransferase enzyme II" RELATED [EC:2.7.1.69]
-synonym: "phosphohistidinoprotein-hexose phosphoribosyltransferase activity" RELATED [EC:2.7.1.69]
-synonym: "phosphohistidinoprotein-hexose phosphotransferase activity" RELATED [EC:2.7.1.69]
-synonym: "phosphoprotein factor-hexose phosophotransferase activity" RELATED [EC:2.7.1.69]
-synonym: "phosphotransfer-driven group translocator" EXACT []
-synonym: "phosphotransferase, phosphohistidinoprotein-hexose activity" RELATED [EC:2.7.1.69]
-synonym: "protein, specific or class, gene bglC" RELATED [EC:2.7.1.69]
+def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + sugar(out) = protein histidine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
+synonym: "enzyme II of the phosphotransferase system" RELATED []
+synonym: "PEP--sugar phosphotransferase enzyme II activity" EXACT []
+synonym: "PEP-dependent phosphotransferase enzyme II" RELATED []
+synonym: "phosphoenolpyruvate-sugar phosphotransferase enzyme II" RELATED []
+synonym: "phosphohistidinoprotein-hexose phosphotransferase activity" RELATED []
+synonym: "phosphoprotein factor-hexose phosophotransferase activity" RELATED []
+synonym: "phosphotransfer-driven group translocator" BROAD []
synonym: "protein-Np-phosphohistidine-sugar phosphotransferase activity" EXACT []
-synonym: "protein-Npi-phospho-L-histidine:sugar N-pros-phosphotransferase activity" RELATED [EC:2.7.1.69]
-synonym: "protein-Npi-phospho-L-histidine:sugar Npi-phosphotransferase activity" RELATED [EC:2.7.1.69]
-synonym: "protein-Npi-phosphohistidine-sugar phosphotransferase activity" RELATED [EC:2.7.1.69]
-synonym: "protein-Npi-phosphohistidine:sugar N-pros-phosphotransferase activity" RELATED [EC:2.7.1.69]
-synonym: "PTS permease activity" RELATED [EC:2.7.1.69]
-synonym: "PTS transporter" RELATED [EC:2.7.1.69]
-synonym: "ribonucleic acid formation factor, gene glC" RELATED [EC:2.7.1.69]
-synonym: "sucrose phosphotransferase system II" RELATED [EC:2.7.1.69]
-xref: EC:2.7.1.69
-xref: MetaCyc:2.7.1.69-RXN
+synonym: "PTS permease activity" RELATED []
+synonym: "PTS transporter" RELATED []
+xref: TC:4.A
is_a: GO:0015144 ! carbohydrate transmembrane transporter activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
is_a: GO:0022804 ! active transmembrane transporter activity
@@ -85002,7 +84998,7 @@ is_a: GO:0022804 ! active transmembrane transporter activity
id: GO:0008983
name: protein-glutamate O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + protein L-glutamate = S-adenosyl-L-homocysteine + protein L-glutamate 5-methyl ester; this reaction is the methylation of peptidyl-L-glutamate to form peptidyl-L-glutamate 5-methyl ester." [EC:2.1.1.80, RESID:AA0072]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + protein L-glutamate = S-adenosyl-L-homocysteine + protein L-glutamate 5-methyl ester; this reaction is the methylation of peptidyl-L-glutamate to form peptidyl-L-glutamate 5-methyl ester." [EC:2.1.1.80]
synonym: "MCP methyltransferase I" RELATED [EC:2.1.1.80]
synonym: "MCP methyltransferase II" RELATED [EC:2.1.1.80]
synonym: "methyl-accepting chemotaxis protein methyltransferase II" RELATED [EC:2.1.1.80]
@@ -85012,6 +85008,8 @@ synonym: "protein carboxyl-O-methyltransferase activity" RELATED [EC:2.1.1.80]
synonym: "protein carboxylmethyltransferase II" RELATED [EC:2.1.1.80]
synonym: "protein carboxymethylase activity" RELATED [EC:2.1.1.80]
synonym: "protein carboxymethyltransferase activity" RELATED [EC:2.1.1.80]
+synonym: "protein glutamate O-methylase activity" EXACT []
+synonym: "protein glutamate O-methyltransferase activity" EXACT []
synonym: "protein methylase II" RELATED [EC:2.1.1.80]
synonym: "protein O-methyltransferase activity" RELATED [EC:2.1.1.80]
synonym: "protein(aspartate)methyltransferase activity" RELATED [EC:2.1.1.80]
@@ -85060,7 +85058,7 @@ replaced_by: GO:0052737
id: GO:0008986
name: pyruvate, water dikinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H(2)O + pyruvate = AMP + 3 H(+) + phosphate + phosphoenolpyruvate." [EC:2.7.9.2, RHEA:11364]
+def: "Catalysis of the reaction: ATP + H2O + pyruvate = AMP + 3 H+ + phosphate + phosphoenolpyruvate." [EC:2.7.9.2, RHEA:11364]
synonym: "ATP:pyruvate, water phosphotransferase activity" RELATED [EC:2.7.9.2]
synonym: "PEP synthase activity" EXACT []
synonym: "PEP synthetase activity" RELATED [EC:2.7.9.2]
@@ -85118,11 +85116,10 @@ is_a: GO:0016435 ! rRNA (guanine) methyltransferase activity
id: GO:0008990
name: rRNA (guanine-N2-)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine." [EC:2.1.1.52]
-synonym: "ribosomal ribonucleate guanine-2-methyltransferase activity" RELATED [EC:2.1.1.52]
-synonym: "S-adenosyl-L-methionine:rRNA (guanine-2-N-)-methyltransferase activity" RELATED [EC:2.1.1.52]
-synonym: "S-adenosyl-L-methionine:rRNA (guanine-N2-)-methyltransferase activity" RELATED [EC:2.1.1.52]
-xref: EC:2.1.1.52
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine." [PMID:17389639]
+synonym: "ribosomal ribonucleate guanine-2-methyltransferase activity" RELATED []
+synonym: "S-adenosyl-L-methionine:rRNA (guanine-2-N-)-methyltransferase activity" RELATED []
+synonym: "S-adenosyl-L-methionine:rRNA (guanine-N2-)-methyltransferase activity" RELATED []
xref: MetaCyc:RRNA-GUANINE-N2--METHYLTRANSFERASE-RXN
is_a: GO:0008170 ! N-methyltransferase activity
is_a: GO:0016435 ! rRNA (guanine) methyltransferase activity
@@ -85187,14 +85184,14 @@ name: ribonuclease E activity
namespace: molecular_function
def: "Catalysis of the cleavage of single-stranded RNA that is monophosphorylated at its 5'-end; cleavage occurs predominantly at 5 nucleotides from the 5'-end and in A + U-rich regions, and is blocked by the presence of a 5'-triphosphate group." [PMID:10722715, PMID:16854990]
xref: MetaCyc:3.1.26.12-RXN
-is_a: GO:0004540 ! ribonuclease activity
+is_a: GO:0004540 ! RNA nuclease activity
[Term]
id: GO:0008996
name: ribonuclease G activity
namespace: molecular_function
def: "Catalysis of the cleavage of single-stranded RNA that is monophosphorylated at its 5'-end; cleavage occurs predominantly at positions 5 and 6 nucleotides from the 5'-end and in A + U-rich regions, and is blocked by the presence of a 5'-triphosphate group." [PMID:10722715, PMID:16854990]
-is_a: GO:0004540 ! ribonuclease activity
+is_a: GO:0004540 ! RNA nuclease activity
[Term]
id: GO:0008997
@@ -85202,7 +85199,7 @@ name: ribonuclease R activity
namespace: molecular_function
def: "Catalysis of the reaction: RNA + H2O = 5'-phosphomononucleotides. Cleaves RNA in the 3' to 5' direction, leaving an undigested core of 3-5 nucleotides." [PMID:11948193]
xref: EC:3.1.11.-
-is_a: GO:0004540 ! ribonuclease activity
+is_a: GO:0004540 ! RNA nuclease activity
[Term]
id: GO:0008998
@@ -85219,14 +85216,14 @@ is_a: GO:0016728 ! oxidoreductase activity, acting on CH or CH2 groups, disulfid
[Term]
id: GO:0008999
-name: ribosomal protein S5-alanine N-acetyltransferase activity
+name: peptide-alanine-alpha-N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + N-terminal L-alanyl-[ribosomal protein] = CoA + H+ + N-terminal N-alpha-acetyl-L-alanyl-[ribosomal protein]." [RHEA:43752]
+def: "Catalysis of the reaction: acetyl-CoA + N-terminal L-alanyl-peptide = CoA + H+ + N-terminal N-alpha-acetyl-L-alanyl-peptide." [RHEA:43752]
synonym: "acetyl-CoA:ribosomal-protein-L-alanine N-acetyltransferase activity" RELATED []
synonym: "ribosomal protein S18 acetyltransferase activity" RELATED []
synonym: "ribosomal-protein-alanine N-acetyltransferase activity" BROAD []
xref: MetaCyc:2.3.1.128-RXN
-xref: RHEA:16433
+xref: RHEA:43756
is_a: GO:0004596 ! peptide alpha-N-acetyltransferase activity
[Term]
@@ -85393,7 +85390,7 @@ def: "Catalysis of the formation of new phosphodiester bonds between a pair of s
comment: Note that this term is not a child of 'recombinase activity ; GO:0000150' because the latter represents activities that do not break or form phosphodiester bonds.
subset: goslim_pir
synonym: "RecA-family recombinase activity" EXACT []
-is_a: GO:0140097 ! catalytic activity, acting on DNA
+is_a: GO:0008907 ! integrase activity
[Term]
id: GO:0009010
@@ -85438,7 +85435,7 @@ is_a: GO:0046527 ! glucosyltransferase activity
id: GO:0009012
name: aminoglycoside 3''-adenylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + streptomycin = 3''-adenylylstreptomycin + diphosphate + H(+)." [EC:2.7.7.47, RHEA:20245]
+def: "Catalysis of the reaction: ATP + streptomycin = 3''-adenylylstreptomycin + diphosphate + H+." [EC:2.7.7.47, RHEA:20245]
synonym: "AAD (3'')" RELATED [EC:2.7.7.47]
synonym: "ATP:streptomycin 3''-adenylyltransferase activity" NARROW []
synonym: "streptomycin 3''-adenylyltransferase activity" NARROW []
@@ -85464,7 +85461,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0009014
name: succinyl-diaminopimelate desuccinylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-succinyl-LL-2,6-diaminopimelate + H(2)O = LL-2,6-diaminopimelate + succinate." [EC:3.5.1.18, RHEA:22608]
+def: "Catalysis of the reaction: N-succinyl-LL-2,6-diaminopimelate + H2O = LL-2,6-diaminopimelate + succinate." [EC:3.5.1.18, RHEA:22608]
synonym: "N-succinyl-L-alpha,epsilon-diaminopimelic acid deacylase activity" RELATED [EC:3.5.1.18]
synonym: "N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase activity" RELATED [EC:3.5.1.18]
xref: EC:3.5.1.18
@@ -85477,7 +85474,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0009015
name: N-succinylarginine dihydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(2)-succinyl-L-arginine + 2 H(2)O + 2 H(+) = N(2)-succinyl-L-ornithine + CO(2) + 2 NH(4)(+)." [EC:3.5.3.23, RHEA:19533]
+def: "Catalysis of the reaction: N(2)-succinyl-L-arginine + 2 H2O + 2 H+ = N(2)-succinyl-L-ornithine + CO2 + 2 NH4." [EC:3.5.3.23, RHEA:19533]
synonym: "2-N-succinyl-L-arginine iminohydrolase (decarboxylating)" RELATED [EC:3.5.3.23]
synonym: "arginine succinylhydrolase activity" EXACT []
synonym: "AruB" RELATED []
@@ -85511,7 +85508,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0009017
name: succinylglutamate desuccinylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-succinyl-L-glutamate + H(2)O = L-glutamate + succinate." [EC:3.5.1.96, RHEA:15169]
+def: "Catalysis of the reaction: N-succinyl-L-glutamate + H2O = L-glutamate + succinate." [EC:3.5.1.96, RHEA:15169]
synonym: "AstE" RELATED []
synonym: "N-succinyl-L-glutamate amidohydrolase activity" RELATED [EC:3.5.1.96]
synonym: "N2-succinylglutamate desuccinylase activity" EXACT []
@@ -85539,11 +85536,11 @@ is_a: GO:0004645 ! 1,4-alpha-oligoglucan phosphorylase activity
id: GO:0009019
name: tRNA (guanine-N1-)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine." [EC:2.1.1.31]
-synonym: "S-adenosyl-L-methionine:tRNA (guanine-1-N-)-methyltransferase activity" RELATED [EC:2.1.1.31]
-synonym: "S-adenosyl-L-methionine:tRNA (guanine-N1-)-methyltransferase activity" RELATED [EC:2.1.1.31]
-synonym: "transfer ribonucleate guanine 1-methyltransferase activity" RELATED [EC:2.1.1.31]
-synonym: "tRNA guanine 1-methyltransferase activity" RELATED [EC:2.1.1.31]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine." [GOC:curators, PMID:782564]
+synonym: "S-adenosyl-L-methionine:tRNA (guanine-1-N-)-methyltransferase activity" RELATED []
+synonym: "S-adenosyl-L-methionine:tRNA (guanine-N1-)-methyltransferase activity" RELATED []
+synonym: "transfer ribonucleate guanine 1-methyltransferase activity" RELATED []
+synonym: "tRNA guanine 1-methyltransferase activity" RELATED []
xref: Reactome:R-HSA-6782859 "TRMT5 methylates guanosine yielding 1-methylguanosine at nucleotide 37 of tRNA(Phe)"
xref: Reactome:R-HSA-6786621 "TRMT10A methylates guanosine-9 in tRNA"
xref: Reactome:R-HSA-6787591 "TRMT10C:HSD17B10 (TRMT10C:SDR5C1) of mitochondrial RNase P methylates guanosine-9 in tRNA yielding 1-methylguanosine-9"
@@ -85571,11 +85568,10 @@ is_a: GO:0106050 ! tRNA 2'-O-methyltransferase activity
[Term]
id: GO:0009022
-name: tRNA nucleotidyltransferase activity
+name: phosphate-dependent exonuclease activity
namespace: molecular_function
-def: "Catalysis of the reaction: tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate." [EC:2.7.7.56]
-comment: Note that, although the enzyme to which this term refers is also known as 'ribonuclease PH', and degrades tRNA in the 3'-5' direction in vivo, the term does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis.
-synonym: "phosphate-dependent exonuclease activity" RELATED [EC:2.7.7.56]
+def: "Catalysis of the reaction: tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate." [PMID:2455297, RHEA:10628]
+comment: Note that, although EC names the enzme tRNA nucleotidyltransferase, the enzyme to which this term refers is also known as 'ribonuclease PH', and degrades tRNA in the 3'-5' direction in vivo, the term does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis It should not be confused with CCA tRNA nucleotidyltransferase..
synonym: "ribonuclease PH activity" RELATED [EC:2.7.7.56]
synonym: "RNase PH activity" RELATED [EC:2.7.7.56]
synonym: "tRNA:phosphate nucleotidyltransferase activity" RELATED [EC:2.7.7.56]
@@ -85632,7 +85628,7 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0009026
name: tagaturonate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-altronate + NAD(+) = D-tagaturonate + H(+) + NADH." [EC:1.1.1.58, RHEA:17813]
+def: "Catalysis of the reaction: D-altronate + NAD+ = D-tagaturonate + H+ + NADH." [EC:1.1.1.58, RHEA:17813]
synonym: "altronate dehydrogenase activity" RELATED [EC:1.1.1.58]
synonym: "altronate oxidoreductase activity" RELATED [EC:1.1.1.58]
synonym: "altronic oxidoreductase activity" RELATED [EC:1.1.1.58]
@@ -85662,7 +85658,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0009028
name: tartronate-semialdehyde synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 glyoxylate + H(+) = 2-hydroxy-3-oxopropanoate + CO(2)." [EC:4.1.1.47, RHEA:10136]
+def: "Catalysis of the reaction: 2 glyoxylate + H+ = 2-hydroxy-3-oxopropanoate + CO2." [EC:4.1.1.47, RHEA:10136]
synonym: "glyoxalate carboligase activity" RELATED [EC:4.1.1.47]
synonym: "glyoxylate carbo-ligase activity" RELATED [EC:4.1.1.47]
synonym: "glyoxylate carboligase activity" RELATED [EC:4.1.1.47]
@@ -85682,7 +85678,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0009029
name: tetraacyldisaccharide 4'-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-(1->6)-beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate + ATP = ADP + 2 H(+) + lipid IV(a)." [EC:2.7.1.130, RHEA:20700]
+def: "Catalysis of the reaction: 2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-(1->6)-beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate + ATP = ADP + 2 H+ + lipid IV(a)." [EC:2.7.1.130, RHEA:20700]
synonym: "ATP:2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D-glucosaminyl-beta-D-1,6-glucosaminyl-beta-phosphate 4'-O-phosphotransferase activity" RELATED [EC:2.7.1.130]
synonym: "lipid-A 4'-kinase activity" RELATED [EC:2.7.1.130]
xref: EC:2.7.1.130
@@ -85696,7 +85692,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0009030
name: thiamine-phosphate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + thiamine phosphate = ADP + H(+) + thiamine diphosphate." [EC:2.7.4.16, RHEA:15913]
+def: "Catalysis of the reaction: ATP + thiamine phosphate = ADP + H+ + thiamine diphosphate." [EC:2.7.4.16, RHEA:15913]
synonym: "ATP:thiamine-phosphate phosphotransferase activity" RELATED [EC:2.7.4.16]
synonym: "thiamin monophosphatase activity" RELATED [EC:2.7.4.16]
synonym: "thiamin monophosphokinase activity" RELATED [EC:2.7.4.16]
@@ -85742,7 +85738,7 @@ is_a: GO:0016657 ! oxidoreductase activity, acting on NAD(P)H, nitrogenous group
id: GO:0009034
name: tryptophanase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tryptophan + H(2)O = indole + NH(4)(+) + pyruvate." [RHEA:19553]
+def: "Catalysis of the reaction: L-tryptophan + H2O = indole + NH4 + pyruvate." [RHEA:19553]
comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "L-tryptophan indole-lyase (deaminating) activity" RELATED [EC:4.1.99.1]
synonym: "L-tryptophan indole-lyase (deaminating; pyruvate forming) activity" RELATED [EC:4.1.99.1]
@@ -85756,7 +85752,6 @@ xref: KEGG_REACTION:R00673
xref: MetaCyc:TRYPDEG-PWY
xref: MetaCyc:TRYPTOPHAN-RXN
xref: RHEA:19553
-xref: UniPathway:UPA00332
is_a: GO:0016830 ! carbon-carbon lyase activity
[Term]
@@ -85793,7 +85788,6 @@ namespace: molecular_function
def: "Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a phosphotyrosyl intermediate in which the target sequence is first cleaved by the nucleophilic attack by a tyrosine in the active site." [GOC:elh, PMID:11090626]
synonym: "site-specific tyrosine recombinase activity" EXACT []
synonym: "tyrosine recombinase" BROAD []
-is_a: GO:0008907 ! integrase activity
is_a: GO:0009009 ! site-specific recombinase activity
[Term]
@@ -85838,10 +85832,9 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
[Term]
id: GO:0009041
-name: uridylate kinase activity
+name: UMP/dUMP kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP." [GOC:go_curators]
-xref: EC:2.7.4.22
is_a: GO:0050145 ! nucleoside monophosphate kinase activity
[Term]
@@ -85911,7 +85904,8 @@ is_a: GO:0004181 ! metallocarboxypeptidase activity
id: GO:0009047
name: dosage compensation by hyperactivation of X chromosome
namespace: biological_process
-def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global hyperactivation of all, or most of, the genes on the X-chromosome in the heterogametic sex, leading to a two-fold increase in gene expression from this chromosome. An example of this is found in Drosophila melanogaster." [GOC:jl, GOC:mr, ISBN:0140512888, PMID:11498577, PMID:20622855, Wikipedia:XY_sex-determination_system]
+def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global hyperactivation of all, or most of, the genes on the X-chromosome in the heterogametic sex, leading to a two-fold increase in gene expression from this chromosome. An example of this is found in Drosophila melanogaster." [GOC:jl, GOC:mr, PMID:11498577, PMID:1568251]
+xref: Wikipedia:XY_sex-determination_system
is_a: GO:0007549 ! dosage compensation
[Term]
@@ -85972,7 +85966,6 @@ synonym: "pentose-phosphate pathway, non-oxidative branch" EXACT []
xref: MetaCyc:NONOXIPENT-PWY
xref: MetaCyc:P21-PWY
is_a: GO:0006091 ! generation of precursor metabolites and energy
-is_a: GO:1901135 ! carbohydrate derivative metabolic process
relationship: part_of GO:0006098 ! pentose-phosphate shunt
[Term]
@@ -86020,6 +86013,9 @@ alt_id: GO:0044266
def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah]
subset: goslim_pir
synonym: "biopolymer catabolic process" EXACT [GOC:mtg_chebi_dec09]
+synonym: "cellular macromolecule catabolic process" RELATED []
+synonym: "cellular macromolecule catabolism" RELATED []
+synonym: "cellular macromolecule degradation" RELATED []
synonym: "macromolecule breakdown" EXACT []
synonym: "macromolecule catabolism" EXACT []
synonym: "macromolecule degradation" EXACT []
@@ -86095,14 +86091,14 @@ is_a: GO:0072329 ! monocarboxylic acid catabolic process
[Term]
id: GO:0009063
-name: cellular amino acid catabolic process
+name: amino acid catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents." [GOC:ai]
-synonym: "amino acid catabolic process" EXACT []
-synonym: "cellular amino acid breakdown" EXACT []
-synonym: "cellular amino acid catabolism" EXACT []
-synonym: "cellular amino acid degradation" EXACT []
-is_a: GO:0006520 ! cellular amino acid metabolic process
+synonym: "amino acid breakdown" EXACT []
+synonym: "amino acid catabolism" EXACT []
+synonym: "amino acid degradation" EXACT []
+synonym: "cellular amino acid catabolic process" EXACT []
+is_a: GO:0006520 ! amino acid metabolic process
is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
@@ -86122,6 +86118,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of amino ac
synonym: "glutamine family amino acid breakdown" EXACT []
synonym: "glutamine family amino acid catabolism" EXACT []
synonym: "glutamine family amino acid degradation" EXACT []
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0009064 ! glutamine family amino acid metabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
@@ -86153,6 +86150,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of amino ac
synonym: "aspartate family amino acid breakdown" EXACT []
synonym: "aspartate family amino acid catabolism" EXACT []
synonym: "aspartate family amino acid degradation" EXACT []
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0009066 ! aspartate family amino acid metabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
@@ -86184,16 +86182,18 @@ def: "The chemical reactions and pathways resulting in the breakdown of amino ac
synonym: "serine family amino acid breakdown" EXACT []
synonym: "serine family amino acid catabolism" EXACT []
synonym: "serine family amino acid degradation" EXACT []
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0009069 ! serine family amino acid metabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
[Term]
id: GO:0009072
-name: aromatic amino acid family metabolic process
+name: aromatic amino acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan)." [GOC:go_curators]
+synonym: "aromatic amino acid family metabolic process" EXACT []
synonym: "aromatic amino acid family metabolism" EXACT []
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
is_a: GO:0006725 ! cellular aromatic compound metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
@@ -86209,9 +86209,9 @@ synonym: "aromatic amino acid family biosynthetic process, shikimate pathway" RE
synonym: "aromatic amino acid family formation" EXACT []
synonym: "aromatic amino acid family synthesis" EXACT []
xref: MetaCyc:COMPLETE-ARO-PWY
-is_a: GO:0009072 ! aromatic amino acid family metabolic process
-is_a: GO:0016053 ! organic acid biosynthetic process
+is_a: GO:0009072 ! aromatic amino acid metabolic process
is_a: GO:0019438 ! aromatic compound biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
is_a: GO:1901566 ! organonitrogen compound biosynthetic process
@@ -86223,9 +86223,9 @@ def: "The chemical reactions and pathways resulting in the breakdown of aromatic
synonym: "aromatic amino acid family breakdown" EXACT []
synonym: "aromatic amino acid family catabolism" EXACT []
synonym: "aromatic amino acid family degradation" EXACT []
-is_a: GO:0009072 ! aromatic amino acid family metabolic process
-is_a: GO:0016054 ! organic acid catabolic process
+is_a: GO:0009072 ! aromatic amino acid metabolic process
is_a: GO:0019439 ! aromatic compound catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
@@ -86295,6 +86295,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of any amin
synonym: "pyruvate family amino acid breakdown" EXACT []
synonym: "pyruvate family amino acid catabolism" EXACT []
synonym: "pyruvate family amino acid degradation" EXACT []
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0009078 ! pyruvate family amino acid metabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
@@ -86304,7 +86305,7 @@ name: branched-chain amino acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine." [GOC:ai]
synonym: "branched chain family amino acid metabolism" EXACT [GOC:ai]
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
[Term]
id: GO:0009082
@@ -86317,7 +86318,7 @@ synonym: "branched chain family amino acid biosynthetic process" EXACT [GOC:ai]
synonym: "branched chain family amino acid formation" EXACT []
synonym: "branched chain family amino acid synthesis" EXACT []
is_a: GO:0009081 ! branched-chain amino acid metabolic process
-is_a: GO:0016053 ! organic acid biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:1901566 ! organonitrogen compound biosynthetic process
[Term]
@@ -86329,7 +86330,7 @@ synonym: "branched chain family amino acid breakdown" EXACT []
synonym: "branched chain family amino acid catabolic process" EXACT [GOC:ai]
synonym: "branched chain family amino acid catabolism" EXACT []
synonym: "branched chain family amino acid degradation" EXACT []
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0009081 ! branched-chain amino acid metabolic process
[Term]
@@ -86381,7 +86382,6 @@ synonym: "methionine degradation" EXACT []
xref: UM-BBD_pathwayID:met
is_a: GO:0000098 ! sulfur amino acid catabolic process
is_a: GO:0006555 ! methionine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009068 ! aspartate family amino acid catabolic process
[Term]
@@ -86435,7 +86435,6 @@ synonym: "homoserine breakdown" EXACT []
synonym: "homoserine catabolism" EXACT []
synonym: "homoserine degradation" EXACT []
xref: MetaCyc:HOMOCYSDEGR-PWY
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009071 ! serine family amino acid catabolic process
is_a: GO:0009092 ! homoserine metabolic process
@@ -86458,7 +86457,6 @@ synonym: "cysteine degradation" EXACT []
xref: Wikipedia:Cysteine
is_a: GO:0000098 ! sulfur amino acid catabolic process
is_a: GO:0006534 ! cysteine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009071 ! serine family amino acid catabolic process
[Term]
@@ -86542,7 +86540,6 @@ def: "The chemical reactions and pathways involving glycoproteins, a protein tha
subset: goslim_drosophila
synonym: "glycoprotein metabolism" EXACT []
is_a: GO:0019538 ! protein metabolic process
-is_a: GO:0044260 ! cellular macromolecule metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
[Term]
@@ -86554,8 +86551,8 @@ synonym: "glycoprotein anabolism" EXACT []
synonym: "glycoprotein biosynthesis" EXACT []
synonym: "glycoprotein formation" EXACT []
synonym: "glycoprotein synthesis" EXACT []
+is_a: GO:0009059 ! macromolecule biosynthetic process
is_a: GO:0009100 ! glycoprotein metabolic process
-is_a: GO:0034645 ! cellular macromolecule biosynthetic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
is_a: GO:1901566 ! organonitrogen compound biosynthetic process
@@ -86593,9 +86590,9 @@ synonym: "lipopolysaccharide formation" EXACT []
synonym: "lipopolysaccharide synthesis" EXACT []
synonym: "LPS biosynthetic process" EXACT []
xref: KEGG_PATHWAY:map00540
+is_a: GO:0000271 ! polysaccharide biosynthetic process
is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:0008653 ! lipopolysaccharide metabolic process
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
[Term]
@@ -86608,8 +86605,8 @@ synonym: "lipopolysaccharide catabolism" EXACT []
synonym: "lipopolysaccharide degradation" EXACT []
synonym: "LPS catabolic process" EXACT []
is_a: GO:0008653 ! lipopolysaccharide metabolic process
-is_a: GO:0044242 ! cellular lipid catabolic process
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
+is_a: GO:0009057 ! macromolecule catabolic process
+is_a: GO:0016042 ! lipid catabolic process
is_a: GO:1901136 ! carbohydrate derivative catabolic process
[Term]
@@ -86721,7 +86718,6 @@ synonym: "purine base synthesis" EXACT []
xref: MetaCyc:PWY-841
is_a: GO:0006144 ! purine nucleobase metabolic process
is_a: GO:0046112 ! nucleobase biosynthetic process
-is_a: GO:0046148 ! pigment biosynthetic process
is_a: GO:0072522 ! purine-containing compound biosynthetic process
[Term]
@@ -87747,7 +87743,6 @@ namespace: biological_process
def: "The chemical reactions and pathways involving pyrimidine deoxyribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleoside triphosphate metabolism" EXACT []
is_a: GO:0009147 ! pyrimidine nucleoside triphosphate metabolic process
-is_a: GO:0009200 ! deoxyribonucleoside triphosphate metabolic process
[Term]
id: GO:0009212
@@ -87759,7 +87754,6 @@ synonym: "pyrimidine deoxyribonucleoside triphosphate biosynthesis" EXACT []
synonym: "pyrimidine deoxyribonucleoside triphosphate formation" EXACT []
synonym: "pyrimidine deoxyribonucleoside triphosphate synthesis" EXACT []
is_a: GO:0009148 ! pyrimidine nucleoside triphosphate biosynthetic process
-is_a: GO:0009202 ! deoxyribonucleoside triphosphate biosynthetic process
is_a: GO:0009211 ! pyrimidine deoxyribonucleoside triphosphate metabolic process
[Term]
@@ -87771,7 +87765,6 @@ synonym: "pyrimidine deoxyribonucleoside triphosphate breakdown" EXACT []
synonym: "pyrimidine deoxyribonucleoside triphosphate catabolism" EXACT []
synonym: "pyrimidine deoxyribonucleoside triphosphate degradation" EXACT []
is_a: GO:0009149 ! pyrimidine nucleoside triphosphate catabolic process
-is_a: GO:0009204 ! deoxyribonucleoside triphosphate catabolic process
is_a: GO:0009211 ! pyrimidine deoxyribonucleoside triphosphate metabolic process
[Term]
@@ -88157,7 +88150,7 @@ synonym: "colanic acid synthesis" EXACT []
synonym: "M antigen biosynthesis" EXACT []
synonym: "M antigen biosynthetic process" EXACT []
xref: MetaCyc:COLANSYN-PWY
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
+is_a: GO:0009059 ! macromolecule biosynthetic process
is_a: GO:0046377 ! colanic acid metabolic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
@@ -88170,7 +88163,7 @@ synonym: "O antigen anabolism" EXACT []
synonym: "O antigen biosynthesis" EXACT []
synonym: "O antigen formation" EXACT []
synonym: "O antigen synthesis" EXACT []
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
+is_a: GO:0000271 ! polysaccharide biosynthetic process
is_a: GO:0046402 ! O antigen metabolic process
relationship: part_of GO:0009103 ! lipopolysaccharide biosynthetic process
@@ -88213,7 +88206,7 @@ synonym: "enterobacterial common antigen biosynthesis" EXACT []
synonym: "enterobacterial common antigen formation" EXACT []
synonym: "enterobacterial common antigen synthesis" EXACT []
xref: MetaCyc:ECASYN-PWY
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
+is_a: GO:0000271 ! polysaccharide biosynthetic process
is_a: GO:0046378 ! enterobacterial common antigen metabolic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
@@ -88240,7 +88233,7 @@ synonym: "K antigen anabolism" EXACT []
synonym: "K antigen biosynthesis" EXACT []
synonym: "K antigen formation" EXACT []
synonym: "K antigen synthesis" EXACT []
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
+is_a: GO:0000271 ! polysaccharide biosynthetic process
is_a: GO:0046375 ! K antigen metabolic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
@@ -88264,8 +88257,8 @@ synonym: "glucan anabolism" EXACT []
synonym: "glucan biosynthesis" EXACT []
synonym: "glucan formation" EXACT []
synonym: "glucan synthesis" EXACT []
-is_a: GO:0006073 ! cellular glucan metabolic process
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
+is_a: GO:0000271 ! polysaccharide biosynthetic process
+is_a: GO:0044042 ! glucan metabolic process
[Term]
id: GO:0009251
@@ -88336,7 +88329,6 @@ synonym: "10-formyl-THF metabolic process" EXACT []
synonym: "10-formyl-THF metabolism" EXACT []
synonym: "10-formyltetrahydrofolate metabolism" EXACT []
is_a: GO:0043648 ! dicarboxylic acid metabolic process
-is_a: GO:0046653 ! tetrahydrofolate metabolic process
[Term]
id: GO:0009257
@@ -88353,7 +88345,6 @@ xref: MetaCyc:1CMET2-PWY
xref: MetaCyc:PWY-3841
is_a: GO:0009256 ! 10-formyltetrahydrofolate metabolic process
is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
-is_a: GO:0046654 ! tetrahydrofolate biosynthetic process
[Term]
id: GO:0009258
@@ -88366,7 +88357,6 @@ synonym: "10-formyltetrahydrofolate breakdown" EXACT []
synonym: "10-formyltetrahydrofolate catabolism" EXACT []
synonym: "10-formyltetrahydrofolate degradation" EXACT []
is_a: GO:0009256 ! 10-formyltetrahydrofolate metabolic process
-is_a: GO:0009397 ! folic acid-containing compound catabolic process
is_a: GO:0043649 ! dicarboxylic acid catabolic process
[Term]
@@ -88583,6 +88573,7 @@ name: cell outer membrane
namespace: cellular_component
def: "A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures." [GOC:md, GOC:mtg_sensu, ISBN:0135712254]
comment: To annotate the plasma (cytoplasmic) membrane, see instead GO:0005886.
+subset: prokaryote_subset
synonym: "outer membrane of cell" EXACT []
is_a: GO:0019867 ! outer membrane
relationship: part_of GO:0030312 ! external encapsulating structure
@@ -88634,41 +88625,46 @@ synonym: "DNA import into cell" BROAD []
synonym: "DNA transport into cell during transformation" RELATED []
is_a: GO:0051027 ! DNA transport
is_a: GO:0098657 ! import into cell
-relationship: part_of GO:0009294 ! DNA mediated transformation
+relationship: part_of GO:0009294 ! DNA-mediated transformation
[Term]
id: GO:0009291
name: unidirectional conjugation
namespace: biological_process
-def: "The process of unidirectional (polarized) transfer of genetic information involving direct cellular contact between a donor and recipient cell; the contact is followed by the formation of a cellular bridge that physically connects the cells; some or all of the chromosome(s) of one cell ('male') is then transferred into the other cell ('female'); unidirectional conjugation occurs between cells of different mating types. Examples of this process are found in prokaryotes." [ISBN:0387520546]
-is_a: GO:0000746 ! conjugation
-is_a: GO:0009292 ! genetic transfer
+def: "The process of unidirectional (polarized) transfer of genetic information involving direct cellular contact between a donor and recipient cell; the contact is followed by the formation of a cellular bridge that physically connects the cells. Some or all of the chromosome(s) of the donor cell is transferred into the recipient cell." [Wikipedia:Bacterial_conjugation]
+comment: Unidirectional conjugation is not a type of not sexual reproduction, since no exchange of gamete occurs and no generation of a new organism: instead an existing organism is transformed.
+subset: goslim_pir
+synonym: "bacterial conjugation" RELATED []
+xref: Wikipedia:Bacterial_conjugation
+is_a: GO:0009292 ! horizontal gene transfer
[Term]
id: GO:0009292
-name: genetic transfer
+name: horizontal gene transfer
namespace: biological_process
-def: "In the absence of a sexual life cycle, the process involved in the introduction of genetic information to create a genetically different individual." [GOC:clt]
-comment: GO:0009292 should not be used for annotation of phage lysogeny (integration of the bacteriophage nucleic acid into the host bacterium's genome).
+def: "The introduction of genetic information into a cell to create a genetically different individual, without production of new individuals." [PMID:26184597]
subset: goslim_pir
synonym: "genetic exchange" BROAD []
-is_a: GO:0044764 ! multi-organism cellular process
+synonym: "genetic transfer" EXACT []
+synonym: "lateral gene transfer" EXACT []
+is_a: GO:0009987 ! cellular process
[Term]
id: GO:0009293
name: transduction
namespace: biological_process
-def: "The transfer of genetic information to a bacterium from a bacteriophage or between bacterial or yeast cells mediated by a phage vector." [ISBN:0198506732]
+def: "A type of horizontal gene transfer in which genetic material is introduced into a cell mediated by a virus." [PMID:18265289, PMID:33597173]
+comment: This process occurs both in prokaryotes and in eukaryotes.
xref: Wikipedia:Transduction_(genetics)
-is_a: GO:0009292 ! genetic transfer
+is_a: GO:0009292 ! horizontal gene transfer
[Term]
id: GO:0009294
-name: DNA mediated transformation
+name: DNA-mediated transformation
namespace: biological_process
-def: "The introduction and uptake of foreign genetic material (DNA or RNA) into a cell, and often the expression of that genetic material." [ISBN:0716720094, Wikipedia:Transformation_(genetics)]
-synonym: "DNA-mediated transformation" EXACT []
-is_a: GO:0009292 ! genetic transfer
+def: "The direct uptake and incorporation of exogenous genetic material (DNA or RNA) into a cell from its surroundings through the cell envelope." [PMID:12706993, PMID:24509783, PMID:27826682]
+synonym: "DNA mediated transformation" EXACT []
+is_a: GO:0009292 ! horizontal gene transfer
[Term]
id: GO:0009295
@@ -88730,7 +88726,7 @@ synonym: "cellular mRNA transcription" EXACT []
synonym: "mRNA biosynthesis" BROAD []
synonym: "mRNA biosynthetic process" BROAD []
synonym: "mRNA synthesis" BROAD []
-is_a: GO:0006351 ! transcription, DNA-templated
+is_a: GO:0006351 ! DNA-templated transcription
is_a: GO:0016071 ! mRNA metabolic process
[Term]
@@ -88783,11 +88779,12 @@ is_a: GO:0098781 ! ncRNA transcription
[Term]
id: GO:0009305
-name: protein biotinylation
+name: obsolete protein biotinylation
namespace: biological_process
-def: "The addition of biotin (vitamin B7 / vitamin H) to a protein amino acid." [GOC:ai]
+def: "OBSOLETE. The addition of biotin (vitamin B7 / vitamin H) to a protein amino acid." [GOC:ai]
+comment: This terms was obsoleted because it represents a molecular function as a biological process.
synonym: "protein amino acid biotinylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_obsolete: true
[Term]
id: GO:0009306
@@ -88816,10 +88813,12 @@ is_a: GO:0044355 ! clearance of foreign intracellular DNA
id: GO:0009308
name: amine metabolic process
namespace: biological_process
+alt_id: GO:0044106
def: "The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom." [GOC:jl, ISBN:0198506732]
subset: goslim_chembl
subset: goslim_pir
synonym: "amine metabolism" EXACT []
+synonym: "cellular amine metabolic process" EXACT []
is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
@@ -88928,7 +88927,7 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0009318
name: exodeoxyribonuclease VII complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes exonucleolytic cleavage in either 5' to 3' or 3' to 5' direction to yield nucleoside 5'-phosphates; it prefers single-stranded DNA." [EC:3.1.11.6]
+def: "An enzyme complex that catalyzes exonucleolytic cleavage in either 5' to 3' or 3' to 5' direction to yield nucleoside 5'-phosphates; it prefers single-stranded DNA." [PMID:6284744]
is_a: GO:0140535 ! intracellular protein-containing complex
is_a: GO:1902494 ! catalytic complex
@@ -88972,8 +88971,8 @@ is_a: GO:1990204 ! oxidoreductase complex
id: GO:0009323
name: obsolete ribosomal-protein-alanine N-acetyltransferase complex
namespace: cellular_component
-def: "OBSOLETE. An enzyme complex that catalyzes the transfer of an acetyl group to ribosomal-protein alanine, forming ribosomal-protein acetylalanine." [EC:2.3.1.128]
-comment: This term was obsoleted because there is no evidence that this complex exists. Enzymes with that activity, such as E. coli rimJ (UniProt:P0A948), act as monomoers.
+def: "OBSOLETE. An enzyme complex that catalyzes the transfer of an acetyl group to ribosomal-protein alanine, forming ribosomal-protein acetylalanine." [GOC:curators]
+comment: This term was obsoleted because there is no evidence that this complex exists. Enzymes with that activity, such as E. coli rimJ (UniProt:P0A948), act as monomers.
is_obsolete: true
[Term]
@@ -88989,7 +88988,7 @@ is_a: GO:1990204 ! oxidoreductase complex
id: GO:0009325
name: nitrate reductase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the formation of nitrate from nitrite with the concomitant reduction of an acceptor." [EC:1.7.99.4]
+def: "An enzyme complex that catalyzes the formation of nitrate from nitrite with the concomitant reduction of an acceptor." [PMID:2139607]
is_a: GO:1990204 ! oxidoreductase complex
[Term]
@@ -88997,21 +88996,21 @@ id: GO:0009326
name: formate dehydrogenase complex
namespace: cellular_component
def: "An enzyme complex that catalyzes the dehydrogenation of formate to produce carbon dioxide (CO2)." [PMID:1504073, PMID:8566699]
-xref: EC:1.17.1.9
is_a: GO:1990204 ! oxidoreductase complex
[Term]
id: GO:0009327
-name: NAD(P)+ transhydrogenase complex (AB-specific)
+name: obsolete NAD(P)+ transhydrogenase complex (AB-specific)
namespace: cellular_component
-def: "A protein complex that possesses NAD(P)+ transhydrogenase (AB-specific) activity. Homodimeric, trimeric, and heterotetrameric complexes have been identified." [BRENDA:1.6.1.2, GOC:mah]
-is_a: GO:0140535 ! intracellular protein-containing complex
+def: "OBSOLETE. A protein complex that possesses NAD(P)+ transhydrogenase (AB-specific) activity. Homodimeric, trimeric, and heterotetrameric complexes have been identified." [BRENDA:1.6.1.2, GOC:mah]
+comment: This term was obsoleted because there is no evidence that this activity exists as part of a complex.
+is_obsolete: true
[Term]
id: GO:0009328
name: phenylalanine-tRNA ligase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the ligation of phenylalanine to tRNA(Phe), forming L-phenylalanyl-tRNA(Phe)." [EC:6.1.1.20]
+def: "An enzyme complex that catalyzes the ligation of phenylalanine to tRNA(Phe), forming L-phenylalanyl-tRNA(Phe)." [PMID:20223217]
is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -89028,13 +89027,13 @@ id: GO:0009330
name: DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
namespace: cellular_component
def: "Complex that possesses DNA topoisomerase II (double strand cut, ATP-hydrolyzing) activity." [GOC:bhm, GOC:krc, GOC:mah, WikiPedia:Type_II_topoisomerase]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0009331
name: glycerol-3-phosphate dehydrogenase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the dehydrogenation of sn-glycerol 3-phosphate to form glycerone phosphate." [EC:1.1.5.3]
+def: "An enzyme complex that catalyzes the dehydrogenation of sn-glycerol 3-phosphate to form glycerone phosphate." [PMID:7576488]
is_a: GO:1990204 ! oxidoreductase complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -89042,7 +89041,7 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0009332
name: glutamate-tRNA ligase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the ligation of glutamate and tRNA(Glu) to form glutamyl-tRNA(Glu)." [EC:6.1.1.17]
+def: "An enzyme complex that catalyzes the ligation of glutamate and tRNA(Glu) to form glutamyl-tRNA(Glu)." [PMID:29679766]
is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -89050,7 +89049,8 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0009333
name: cysteine synthase complex
namespace: cellular_component
-def: "Cysteine synthase is a multienzyme complex made up, in E. coli, of the heteromeric hexamer serine acetyltransferase and the homodimer O-acetylserine (thiol)-lyase A." [EC:4.2.99.8, MetaCyc:CYSSYNMULTI-CPLX]
+def: "Cysteine synthase is a multienzyme complex made up, in E. coli, of the heteromeric hexamer serine acetyltransferase and the homodimer O-acetylserine (thiol)-lyase A." [PMID:10993149]
+xref: MetaCyc:CYSSYNMULTI-CPLX
is_a: GO:1990234 ! transferase complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -89078,7 +89078,7 @@ consider: GO:0005835
id: GO:0009336
name: sulfate adenylyltransferase complex (ATP)
namespace: cellular_component
-def: "An enzyme complex that catalyzes the formation adenylylsulfate from sulfate and ATP." [EC:2.7.7.4]
+def: "An enzyme complex that catalyzes the formation adenylylsulfate from sulfate and ATP." [PMID:15184554]
synonym: "sulphate adenylyltransferase complex (ATP)" EXACT []
is_a: GO:1902503 ! adenylyltransferase complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -89091,12 +89091,13 @@ def: "A multisubunit iron flavoprotein, which in yeast is composed of 2 alpha an
comment: See also the molecular function term 'sulfite reductase (NADPH) activity ; GO:0004783'.
synonym: "sulphite reductase complex (NADPH)" EXACT []
is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0009338
name: exodeoxyribonuclease V complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA." [EC:3.1.11.5]
+def: "An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA." [PMID:1618858]
is_a: GO:0140535 ! intracellular protein-containing complex
is_a: GO:1902494 ! catalytic complex
@@ -89104,7 +89105,7 @@ is_a: GO:1902494 ! catalytic complex
id: GO:0009339
name: glycolate oxidase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the oxidation of 2-hydroxy acid to form 2-oxo acid and hydrogen peroxide (H2O2). The enzyme is a flavoprotein (FMN)." [EC:1.1.3.15]
+def: "An enzyme complex that catalyzes the oxidation of 2-hydroxy acid to form 2-oxo acid and hydrogen peroxide (H2O2). The enzyme is a flavoprotein (FMN)." [PMID:4557653, PMID:8606183]
is_a: GO:1990204 ! oxidoreductase complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -89127,16 +89128,16 @@ is_a: GO:1902494 ! catalytic complex
id: GO:0009342
name: glutamate synthase complex (NADPH)
namespace: cellular_component
-def: "A complex that possesses glutamate synthase (NADPH) activity." [EC:1.4.1.13, GOC:mah]
+def: "A complex that possesses glutamate synthase (NADPH) activity." [GOC:mah, PMID:4565085]
is_a: GO:0031026 ! glutamate synthase complex
[Term]
id: GO:0009343
-name: biotin carboxylase complex
+name: obsolete biotin carboxylase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the formation of carboxybiotin-carboxyl-carrier protein from biotin-carboxyl-carrier protein and carbon dioxide (CO2)." [EC:6.3.4.14]
-is_a: GO:1902494 ! catalytic complex
-relationship: part_of GO:0009317 ! acetyl-CoA carboxylase complex
+def: "OBSOLETE. An enzyme complex that catalyzes the formation of carboxybiotin-carboxyl-carrier protein from biotin-carboxyl-carrier protein and carbon dioxide (CO2)." [EC:6.3.4.14]
+comment: This term was obsoleted because it represents a homomer.
+is_obsolete: true
[Term]
id: GO:0009344
@@ -89144,13 +89145,13 @@ name: nitrite reductase complex [NAD(P)H]
namespace: cellular_component
def: "Complex that possesses nitrite reductase [NAD(P)H] activity." [GOC:mah]
comment: See also the molecular function term 'nitrite reductase [NAD(P)H] activity ; GO:0008942'.
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0009345
name: glycine-tRNA ligase complex
namespace: cellular_component
-def: "A multimeric enzyme complex which, in bacteria, is usually a tetramer of two alpha and two beta chains and in eukaryotes, is usually a homodimer. Functions in the ligation of glycine and tRNA(Gly) to form glycyl-tRNA(Gly)." [EC:6.1.1.14, GOC:jl, PMID:15733854]
+def: "A multimeric enzyme complex which, in bacteria, is usually a tetramer of two alpha and two beta chains and in eukaryotes, is usually a homodimer. Functions in the ligation of glycine and tRNA(Gly) to form glycyl-tRNA(Gly)." [PMID:15733854]
synonym: "glycine-tRNA synthetase complex" EXACT []
is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -89165,8 +89166,8 @@ subset: goslim_metagenomics
synonym: "citrate lyase complex" BROAD []
synonym: "citrate synthase complex" BROAD []
xref: MetaCyc:ACECITLY-CPLX
+is_a: GO:0140535 ! intracellular protein-containing complex
is_a: GO:1902494 ! catalytic complex
-relationship: part_of GO:0005737 ! cytoplasm
[Term]
id: GO:0009347
@@ -89178,17 +89179,17 @@ is_a: GO:1990234 ! transferase complex
[Term]
id: GO:0009348
-name: ornithine carbamoyltransferase complex
+name: obsolete ornithine carbamoyltransferase complex
namespace: cellular_component
-def: "A homotrimeric protein complex that catalyzes the transfer of a carbamoyl group to ornithine, forming citrulline." [EC:2.1.3.3, GOC:mah]
-is_a: GO:1990234 ! transferase complex
-relationship: part_of GO:0005737 ! cytoplasm
+def: "OBSOLETE. A homotrimeric protein complex that catalyzes the transfer of a carbamoyl group to ornithine, forming citrulline." [EC:2.1.3.3, GOC:mah]
+comment: This term was obsoleted because it represents a homomer.
+is_obsolete: true
[Term]
id: GO:0009349
name: riboflavin synthase complex
namespace: cellular_component
-def: "An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine." [EC:2.5.1.9]
+def: "An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine." [PMID:18298940]
subset: goslim_metagenomics
is_a: GO:1990234 ! transferase complex
@@ -89196,7 +89197,7 @@ is_a: GO:1990234 ! transferase complex
id: GO:0009350
name: ethanolamine ammonia-lyase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the breakdown of ethanolamine to form acetaldehyde and ammonia." [EC:4.3.1.7]
+def: "An enzyme complex that catalyzes the breakdown of ethanolamine to form acetaldehyde and ammonia." [PMID:1550360]
is_a: GO:0140535 ! intracellular protein-containing complex
is_a: GO:1902494 ! catalytic complex
@@ -89226,7 +89227,7 @@ consider: GO:0045254
id: GO:0009353
name: mitochondrial oxoglutarate dehydrogenase complex
namespace: cellular_component
-def: "A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2) within the mitochondrial matrix. An example of this complex is found in Mus musculus." [GOC:mtg_sensu, MetaCyc:CPLX66-42, PMID:10848975]
+def: "A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2) within the mitochondrial matrix. An example of this complex is found in Mus musculus." [GOC:mtg_sensu, MetaCyc:CPLX66-42, PMID:10848975]
comment: See also the molecular functions term 'oxoglutarate dehydrogenase (succinyl-transferring) activity ; GO:0004591', 'dihydrolipoyllysine-residue succinyltransferase activity ; GO:0004149' and 'dihydrolipoyl dehydrogenase activity ; GO:0004148'.
is_a: GO:0005947 ! mitochondrial alpha-ketoglutarate dehydrogenase complex
is_a: GO:0045252 ! oxoglutarate dehydrogenase complex
@@ -89257,15 +89258,16 @@ synonym: "4-amino-4-deoxychorismate synthase complex" RELATED []
synonym: "ADC synthase complex" EXACT []
synonym: "p-aminobenzoate synthetase complex" RELATED []
is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0009357
name: protein-N(PI)-phosphohistidine-sugar phosphotransferase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the transfer of a phosphate from protein N(PI)-phosphohistidine to a sugar molecule. It is enzyme II of the phosphotransferase system." [EC:2.7.1.69]
+def: "An enzyme complex that catalyzes the transfer of a phosphate from protein N(PI)-phosphohistidine to a sugar molecule. It is enzyme II of the phosphotransferase system." [PMID:2951378]
is_a: GO:0061695 ! transferase complex, transferring phosphorus-containing groups
+is_a: GO:0140535 ! intracellular protein-containing complex
is_a: GO:1902495 ! transmembrane transporter complex
-relationship: part_of GO:0005737 ! cytoplasm
[Term]
id: GO:0009358
@@ -89311,10 +89313,11 @@ is_a: GO:1902911 ! protein kinase complex
id: GO:0009366
name: enterobactin synthetase complex
namespace: cellular_component
-def: "A multienzyme complex usually composed of four proteins, EntB, EntD, EntE and EntF. Plays a role in the enterobactin biosynthesis pathway." [MetaCyc:ENTMULTI-CPLX, PMID:9485415]
+def: "A multienzyme complex usually composed of four proteins, EntB, EntD, EntE and EntF. Plays a role in the enterobactin biosynthesis pathway." [PMID:9485415]
synonym: "enterochelin synthetase complex" EXACT []
xref: MetaCyc:ENTMULTI-CPLX
is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0009367
@@ -89331,20 +89334,20 @@ name: endopeptidase Clp complex
namespace: cellular_component
def: "A protein complex comprised of members of the ClpX, ClpC, ClpD, ClpP or ClpR protein families. ClpPs are the proteolytic subunit of active complexes, and ClpA and ClpX form the regulatory subunits. Enzymatically active and inactive complexes can form." [GOC:mah, PMID:11352464]
subset: goslim_pir
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0009371
-name: positive regulation of transcription by pheromones
+name: obsolete positive regulation of transcription by pheromones
namespace: biological_process
-def: "Any process involving pheromones that activates or increases the rate of transcription." [GOC:go_curators]
+def: "OBSOLETE. Any process involving pheromones that activates or increases the rate of transcription." [GOC:go_curators]
+comment: This term has been obsoleted because it represents a GO-CAM model.
synonym: "activation of transcription by pheromones" NARROW []
synonym: "stimulation of transcription by pheromones" NARROW []
synonym: "up regulation of transcription by pheromones" EXACT []
synonym: "up-regulation of transcription by pheromones" EXACT []
synonym: "upregulation of transcription by pheromones" EXACT []
-is_a: GO:0009373 ! regulation of transcription by pheromones
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_obsolete: true
[Term]
id: GO:0009372
@@ -89360,16 +89363,15 @@ synonym: "detection of cell density by secreted molecule" RELATED []
synonym: "quorum sensing system" EXACT []
xref: Wikipedia:Quorum_sensing
is_a: GO:0007267 ! cell-cell signaling
-is_a: GO:0044764 ! multi-organism cellular process
is_a: GO:0060245 ! detection of cell density
[Term]
id: GO:0009373
-name: regulation of transcription by pheromones
+name: obsolete regulation of transcription by pheromones
namespace: biological_process
-def: "Any process involving pheromones that modulates the frequency, rate or extent of transcription." [GOC:go_curators]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
-relationship: part_of GO:0071444 ! cellular response to pheromone
+def: "OBSOLETE. Any process involving pheromones that modulates the frequency, rate or extent of transcription." [GOC:go_curators]
+comment: This term has been obsoleted because it represents a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0009374
@@ -89381,7 +89383,6 @@ synonym: "vitamin H binding" EXACT []
is_a: GO:0019842 ! vitamin binding
is_a: GO:0033218 ! amide binding
is_a: GO:0033293 ! monocarboxylic acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
is_a: GO:1901681 ! sulfur compound binding
@@ -89390,8 +89391,7 @@ is_a: GO:1901681 ! sulfur compound binding
id: GO:0009375
name: ferredoxin hydrogenase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the oxidation of reduced ferredoxin. Hydrogenase contains iron-sulfur clusters, and some contain nickel; it can use molecular hydrogen for the reduction of a variety of substances." [EC:1.12.7.2]
-synonym: "hydrogenase complex" BROAD []
+def: "An enzyme complex that catalyzes the oxidation of reduced ferredoxin. Hydrogenase contains iron-sulfur clusters, and some contain nickel; it can use molecular hydrogen for the reduction of a variety of substances." [PMID:12792025, PMID:9836629]
is_a: GO:0140535 ! intracellular protein-containing complex
is_a: GO:1990204 ! oxidoreductase complex
@@ -89447,7 +89447,7 @@ id: GO:0009381
name: excinuclease ABC activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid at sites flanking regions of damaged DNA to which the Uvr ABC excinuclease complexes bind." [GOC:mah, PMID:15192705]
-is_a: GO:0004520 ! endodeoxyribonuclease activity
+is_a: GO:0004520 ! DNA endonuclease activity
[Term]
id: GO:0009382
@@ -89649,9 +89649,9 @@ is_obsolete: true
id: GO:0009401
name: phosphoenolpyruvate-dependent sugar phosphotransferase system
namespace: biological_process
-def: "The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC." [http://www.ucs.mun.ca/~n55lrb/general_pts.html]
+def: "The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC." [PMID:31209249, PMID:33820910]
synonym: "PTS system" NARROW []
-is_a: GO:0008643 ! carbohydrate transport
+is_a: GO:0098704 ! carbohydrate import across plasma membrane
[Term]
id: GO:0009402
@@ -89682,7 +89682,6 @@ id: GO:0009404
name: toxin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving a toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism." [GOC:cab2]
-subset: goslim_aspergillus
subset: goslim_pir
synonym: "toxin metabolism" EXACT []
is_a: GO:0019748 ! secondary metabolic process
@@ -89694,10 +89693,6 @@ name: obsolete pathogenesis
namespace: biological_process
def: "OBSOLETE. The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism." [GOC:go_curators]
comment: This term was obsoleted because it does not describe a single, normal biological process; rather it is the effect of an interaction between two organisms, under specific conditions.
-subset: goslim_aspergillus
-subset: goslim_candida
-subset: goslim_chembl
-subset: goslim_metagenomics
synonym: "virulence" RELATED []
is_obsolete: true
consider: GO:0044003
@@ -89811,8 +89806,10 @@ def: "Any process that results in a change in state or activity of a cell or an
synonym: "response to water stimulus" EXACT [GOC:dos]
is_a: GO:0001101 ! response to acid chemical
is_a: GO:0009628 ! response to abiotic stimulus
+is_a: GO:0010033 ! response to organic substance
is_a: GO:0010035 ! response to inorganic substance
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0009416
@@ -89976,7 +89973,7 @@ name: SOS response
namespace: biological_process
def: "An error-prone process for repairing damaged microbial DNA." [GOC:jl, PMID:16000023]
xref: Wikipedia:SOS_response
-is_a: GO:0006974 ! cellular response to DNA damage stimulus
+is_a: GO:0006974 ! DNA damage response
is_a: GO:0031668 ! cellular response to extracellular stimulus
[Term]
@@ -90015,7 +90012,9 @@ synonym: "reduced NAD biosynthesis" EXACT []
synonym: "reduced NAD biosynthetic process" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide biosynthesis" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide biosynthetic process" EXACT []
+is_a: GO:0006164 ! purine nucleotide biosynthetic process
is_a: GO:0019359 ! nicotinamide nucleotide biosynthetic process
+is_a: GO:0019674 ! NAD metabolic process
[Term]
id: GO:0009436
@@ -90159,7 +90158,7 @@ synonym: "4-aminobutyrate metabolism" EXACT []
synonym: "GABA metabolic process" EXACT []
synonym: "GABA metabolism" EXACT []
synonym: "gamma-aminobutyric acid metabolism" EXACT []
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
[Term]
@@ -90178,7 +90177,7 @@ synonym: "gamma-aminobutyric acid anabolism" EXACT []
synonym: "gamma-aminobutyric acid biosynthesis" EXACT []
synonym: "gamma-aminobutyric acid formation" EXACT []
synonym: "gamma-aminobutyric acid synthesis" EXACT []
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
+is_a: GO:0008652 ! amino acid biosynthetic process
is_a: GO:0009448 ! gamma-aminobutyric acid metabolic process
[Term]
@@ -90197,7 +90196,7 @@ synonym: "gamma-aminobutyric acid breakdown" EXACT []
synonym: "gamma-aminobutyric acid catabolism" EXACT []
synonym: "gamma-aminobutyric acid degradation" EXACT []
xref: MetaCyc:4AMINOBUTMETAB-PWY
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0009448 ! gamma-aminobutyric acid metabolic process
[Term]
@@ -90646,7 +90645,7 @@ replaced_by: GO:0009055
id: GO:0009496
name: plastoquinol--plastocyanin reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 H(+)[side 1] + 2 oxidized plastocyanin + plastoquinol-1 = 2 H(+)[side 2] + 2 reduced plastocyanin + plastoquinone. This reaction involves the concomitant transfer of 2 H+ ions across a membrane." [RHEA:22148]
+def: "Catalysis of the reaction: 2 H+[side 1] + 2 oxidized plastocyanin + plastoquinol-1 = 2 H+[side 2] + 2 reduced plastocyanin + plastoquinone. This reaction involves the concomitant transfer of 2 H+ ions across a membrane." [RHEA:22148]
synonym: "cytochrome b6f" NARROW []
synonym: "cytochrome b6f complex activity" RELATED [EC:7.1.1.6]
synonym: "plastoquinol-plastocyanin reductase activity" RELATED []
@@ -90904,7 +90903,7 @@ is_a: GO:0009521 ! photosystem
id: GO:0009524
name: phragmoplast
namespace: cellular_component
-def: "Fibrous structure (light microscope view) that arises between the daughter nuclei at telophase and within which the initial partition (cell plate), dividing the mother cell in two (cytokinesis), is formed. Appears at first as a spindle connected to the two nuclei, but later spreads laterally in the form of a ring. Consists of microtubules." [ISBN:0471245208]
+def: "The phragmoplast is a plant cell specific cytoplasmic structure composed of cytoskeletal polymers, membranes, and associated cytosolic proteins that functions as the focused secretory module for assembling the cell plate." [PMID:28943203]
xref: Wikipedia:Phragmoplast
is_a: GO:0110165 ! cellular anatomical entity
relationship: part_of GO:0005737 ! cytoplasm
@@ -90995,6 +90994,7 @@ id: GO:0009535
name: chloroplast thylakoid membrane
namespace: cellular_component
def: "The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana." [GOC:lr, GOC:mtg_sensu]
+is_a: GO:0031968 ! organelle outer membrane
is_a: GO:0055035 ! plastid thylakoid membrane
relationship: part_of GO:0009534 ! chloroplast thylakoid
@@ -91360,9 +91360,10 @@ subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
+subset: prokaryote_subset
synonym: "photosynthetic membrane" RELATED []
xref: Wikipedia:Thylakoid
-is_a: GO:0005622 ! intracellular anatomical structure
+is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
[Term]
id: GO:0009580
@@ -91672,15 +91673,16 @@ name: RNAi-mediated antiviral immune response
namespace: biological_process
alt_id: GO:0060145
alt_id: GO:0060150
-def: "RNA-mediated post-transcriptional gene silencing mechanism that protects against foreign organism invasion by restricting viral replication and dissemination." [GOC:jl, PMID:17693253, PMID:21724934, PMID:23686236, PMID:24732439, PMID:31100912]
+def: "A post-transcriptional gene silencing pathway mediated by the action of regulatory RNAs that protects against foreign organism invasion by restricting viral replication and dissemination." [GOC:jl, PMID:17693253, PMID:21724934, PMID:23686236, PMID:24732439, PMID:31100912]
comment: Virus induced gene silencing (VIGS) is used as a technique to control plant gene expression; when used in that context, this does not represent a normal biological process and is outside the scope of GO.
synonym: "RNAi-mediated antiviral immunity" EXACT []
synonym: "VIGS" RELATED []
synonym: "viral gene silencing in virus induced gene silencing" RELATED []
synonym: "viral triggering of virus induced gene silencing" RELATED []
-synonym: "virus induced gene silencing" RELATED []
+synonym: "virus induced gene silencing" EXACT []
synonym: "virus-induced gene silencing" EXACT []
-is_a: GO:0016441 ! posttranscriptional gene silencing
+synonym: "virus-induced PTGS" EXACT []
+is_a: GO:0035194 ! ncRNA-mediated post-transcriptional gene silencing
is_a: GO:0045087 ! innate immune response
is_a: GO:0051607 ! defense response to virus
@@ -91855,6 +91857,8 @@ id: GO:0009637
name: response to blue light
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a blue light stimulus. Blue light is electromagnetic radiation with a wavelength of between 440 and 500nm." [GOC:ai, GOC:mtg_far_red]
+synonym: "blue light response" EXACT []
+synonym: "blue-light response" EXACT []
synonym: "response to blue light stimulus" EXACT []
is_a: GO:0009416 ! response to light stimulus
@@ -92148,12 +92152,13 @@ relationship: part_of GO:0009657 ! plastid organization
[Term]
id: GO:0009669
-name: sucrose:cation symporter activity
+name: sucrose:monoatomic cation symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: sucrose(out) + monovalent cation(out) = sucrose(in) + monovalent cation(in)." [GOC:jy, TC:2.A.2.-.-, TC:2.A.2.4.1]
synonym: "sucrose permease activity" RELATED []
+synonym: "sucrose:cation symporter activity" BROAD []
synonym: "sucrose:monovalent cation symporter activity" EXACT []
-is_a: GO:0005402 ! carbohydrate:cation symporter activity
+is_a: GO:0005402 ! carbohydrate:monoatomic cation symporter activity
is_a: GO:0008515 ! sucrose transmembrane transporter activity
[Term]
@@ -92178,7 +92183,6 @@ synonym: "nitrate(chlorate):hydrogen symporter activity" EXACT []
synonym: "nitrate(chlorate):proton symporter activity" EXACT []
synonym: "nitrate:hydrogen symporter activity" EXACT []
is_a: GO:0015295 ! solute:proton symporter activity
-is_a: GO:0015296 ! anion:cation symporter activity
is_a: GO:0015513 ! high-affinity secondary active nitrite transmembrane transporter activity
[Term]
@@ -92240,7 +92244,7 @@ name: pyrophosphate hydrolysis-driven proton transmembrane transporter activity
namespace: molecular_function
def: "Enables the transmembrane transport of one proton (H+), driven by the hydrolysis of pyrophosphate, and generating a proton motive force." [GOC:mtg_transport, ISBN:0815340729, Wikipedia:Proton-pumping_pyrophosphatase]
synonym: "diphosphate hydrolysis-driven proton transmembrane transporter activity" EXACT []
-synonym: "H(+)-exporting diphosphatase" RELATED [EC:7.1.3.1]
+synonym: "H+-exporting diphosphatase" RELATED [EC:7.1.3.1]
synonym: "hydrogen-translocating pyrophosphatase activity" RELATED [EC:7.1.3.1]
synonym: "PP(i) hydrolysis-driven proton transmembrane transporter activity" EXACT []
synonym: "proton-pumping diphosphatase" RELATED [EC:7.1.3.1]
@@ -92252,7 +92256,7 @@ xref: RHEA:13973
xref: TC:3.A.10
is_a: GO:0015078 ! proton transmembrane transporter activity
is_a: GO:0015399 ! primary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0009679
@@ -92282,7 +92286,6 @@ synonym: "indole acetic acid metabolism" EXACT []
synonym: "indoleacetic acid metabolism" EXACT []
is_a: GO:0009850 ! auxin metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
-is_a: GO:0034754 ! cellular hormone metabolic process
is_a: GO:0042430 ! indole-containing compound metabolic process
[Term]
@@ -92314,8 +92317,8 @@ def: "The chemical reactions and pathways involving gibberellin. Gibberellins ar
synonym: "gibberellic acid metabolic process" NARROW []
synonym: "gibberellic acid metabolism" NARROW []
synonym: "gibberellin metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0016101 ! diterpenoid metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
[Term]
id: GO:0009686
@@ -92333,8 +92336,8 @@ xref: MetaCyc:PWY-5036
xref: MetaCyc:PWY-5052
xref: MetaCyc:PWY-5070
is_a: GO:0009685 ! gibberellin metabolic process
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0016102 ! diterpenoid biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
[Term]
id: GO:0009687
@@ -92386,7 +92389,7 @@ subset: goslim_chembl
synonym: "cytokinin metabolism" EXACT []
is_a: GO:0006725 ! cellular aromatic compound metabolic process
is_a: GO:0009308 ! amine metabolic process
-is_a: GO:0034754 ! cellular hormone metabolic process
+is_a: GO:0042445 ! hormone metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
[Term]
@@ -92438,8 +92441,7 @@ name: jasmonic acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving jasmonic acid, a fatty acid derivative with the formula (1R-(1 alpha, 2 beta(Z)))-3-oxo-2-(2-pentenyl)cyclopentaneacetic acid." [ISBN:0387969845]
synonym: "jasmonic acid metabolism" EXACT []
-is_a: GO:0006629 ! lipid metabolic process
-is_a: GO:0032787 ! monocarboxylic acid metabolic process
+is_a: GO:0001676 ! long-chain fatty acid metabolic process
[Term]
id: GO:0009695
@@ -92451,9 +92453,8 @@ synonym: "jasmonic acid biosynthesis" EXACT []
synonym: "jasmonic acid formation" EXACT []
synonym: "jasmonic acid synthesis" EXACT []
xref: MetaCyc:PWY-735
-is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:0009694 ! jasmonic acid metabolic process
-is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
+is_a: GO:0042759 ! long-chain fatty acid biosynthetic process
[Term]
id: GO:0009696
@@ -92535,7 +92536,7 @@ is_a: GO:0052315 ! phytoalexin biosynthetic process
id: GO:0009702
name: L-arabinokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arabinose + ATP = beta-L-arabinose 1-phosphate + ADP + 2 H(+)." [EC:2.7.1.46, RHEA:20153]
+def: "Catalysis of the reaction: L-arabinose + ATP = beta-L-arabinose 1-phosphate + ADP + 2 H+." [EC:2.7.1.46, RHEA:20153]
synonym: "ATP:L-arabinose 1-phosphotransferase activity" EXACT []
synonym: "L-arabinokinase (phosphorylating)" RELATED [EC:2.7.1.46]
xref: EC:2.7.1.46
@@ -92883,7 +92884,7 @@ is_a: GO:0009725 ! response to hormone
id: GO:0009734
name: auxin-activated signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated by the binding of the plant hormone auxin to a receptor, and ending with modulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:sm, PMID:16990790, PMID:18647826]
+def: "The series of molecular signals generated by the binding of the plant hormone auxin to a receptor, and ending with modulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:sm, PMID:16990790, PMID:18647826]
synonym: "auxin mediated signaling pathway" RELATED []
synonym: "auxin mediated signalling" EXACT []
synonym: "auxin signal transduction" EXACT [PMID:16990790]
@@ -92904,7 +92905,7 @@ is_a: GO:0009725 ! response to hormone
id: GO:0009736
name: cytokinin-activated signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated by the binding of a cytokinin to a receptor, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:sm, PMID:24080474]
+def: "The series of molecular signals generated by the binding of a cytokinin to a receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:sm, PMID:24080474]
synonym: "cytokinin mediated signaling pathway" RELATED []
synonym: "cytokinin mediated signalling" EXACT []
synonym: "cytokinin signaling" EXACT [PMID:24080474]
@@ -92925,7 +92926,7 @@ is_a: GO:0097305 ! response to alcohol
id: GO:0009738
name: abscisic acid-activated signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated by the binding of the plant hormone abscisic acid (ABA) to a receptor, and ending with modulation of a cellular process, e.g. transcription." [GOC:signaling, GOC:sm, PMID:24269821]
+def: "The series of molecular signals generated by the binding of the plant hormone abscisic acid (ABA) to a receptor, and ending with modulation of a cellular process, e.g. transcription." [GOC:signaling, GOC:sm, PMID:24269821]
synonym: "ABA signal transduction" EXACT [PMID:20713515]
synonym: "ABA signaling" EXACT [PMID:24269821]
synonym: "abscisic acid mediated signalling" EXACT []
@@ -92949,7 +92950,7 @@ is_a: GO:1901700 ! response to oxygen-containing compound
id: GO:0009740
name: gibberellic acid mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of gibberellic acid." [GOC:sm]
+def: "The series of molecular signals mediated by the detection of gibberellic acid." [GOC:sm]
synonym: "GA-signaling" EXACT []
synonym: "gibberellic acid mediated signalling" EXACT []
synonym: "gibberellic acid signaling" EXACT []
@@ -92970,7 +92971,7 @@ is_a: GO:1901700 ! response to oxygen-containing compound
id: GO:0009742
name: brassinosteroid mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of brassinosteroid." [GOC:sm]
+def: "The series of molecular signals mediated by the detection of brassinosteroid." [GOC:sm]
synonym: "brassinosteroid mediated signalling" EXACT []
is_a: GO:0043401 ! steroid hormone mediated signaling pathway
relationship: part_of GO:0071367 ! cellular response to brassinosteroid stimulus
@@ -92996,7 +92997,7 @@ is_a: GO:0034285 ! response to disaccharide
id: GO:0009745
name: sucrose mediated signaling
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of sucrose." [GOC:sm]
+def: "The series of molecular signals mediated by the detection of sucrose." [GOC:sm]
synonym: "sucrose mediated signalling" EXACT []
is_a: GO:0010182 ! sugar mediated signaling pathway
relationship: part_of GO:0071329 ! cellular response to sucrose stimulus
@@ -93013,7 +93014,7 @@ is_a: GO:0034284 ! response to monosaccharide
id: GO:0009747
name: hexokinase-dependent signaling
namespace: biological_process
-def: "A series of molecular signals mediated by hexose and dependent on the detection of hexokinase." [GOC:mah, GOC:sm]
+def: "The series of molecular signals mediated by hexose and dependent on the detection of hexokinase." [GOC:mah, GOC:sm]
synonym: "hexokinase-dependent signalling" EXACT []
is_a: GO:0009757 ! hexose mediated signaling
@@ -93021,7 +93022,7 @@ is_a: GO:0009757 ! hexose mediated signaling
id: GO:0009748
name: hexokinase-independent signaling
namespace: biological_process
-def: "A series of molecular signals mediated by hexose and independent of hexokinase." [GOC:mah, GOC:sm]
+def: "The series of molecular signals mediated by hexose and independent of hexokinase." [GOC:mah, GOC:sm]
synonym: "hexokinase-independent signalling" EXACT []
is_a: GO:0009757 ! hexose mediated signaling
@@ -93083,7 +93084,7 @@ is_a: GO:0009753 ! response to jasmonic acid
id: GO:0009755
name: hormone-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of a hormone." [GOC:sm]
+def: "The series of molecular signals mediated by the detection of a hormone." [GOC:sm]
synonym: "hormone mediated signalling" EXACT []
is_a: GO:0007165 ! signal transduction
relationship: part_of GO:0032870 ! cellular response to hormone stimulus
@@ -93092,7 +93093,7 @@ relationship: part_of GO:0032870 ! cellular response to hormone stimulus
id: GO:0009756
name: carbohydrate mediated signaling
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of carbohydrate." [GOC:sm]
+def: "The series of molecular signals mediated by the detection of carbohydrate." [GOC:sm]
synonym: "carbohydrate mediated signalling" EXACT []
is_a: GO:0007165 ! signal transduction
relationship: part_of GO:0071322 ! cellular response to carbohydrate stimulus
@@ -93101,7 +93102,7 @@ relationship: part_of GO:0071322 ! cellular response to carbohydrate stimulus
id: GO:0009757
name: hexose mediated signaling
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of hexose." [GOC:sm]
+def: "The series of molecular signals mediated by the detection of hexose." [GOC:sm]
synonym: "hexose mediated signalling" EXACT []
is_a: GO:0010182 ! sugar mediated signaling pathway
relationship: part_of GO:0071331 ! cellular response to hexose stimulus
@@ -93113,7 +93114,7 @@ namespace: biological_process
alt_id: GO:0007587
def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbohydrate sources,usually glucose, and then activates genes to scavenge the last traces of the primary carbohydrate source and to transport and metabolize alternate carbohydrate sources. The utilization process begins when the cell or organism detects carbohydrate levels, includes the activation of genes whose products detect, transport or metabolize carbohydrates, and ends when the carbohydrate is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mcc2, GOC:mlg]
synonym: "sugar utilization" NARROW [GOC:mcc2]
-is_a: GO:0008150 ! biological_process
+is_a: GO:0031667 ! response to nutrient levels
[Term]
id: GO:0009759
@@ -93251,7 +93252,6 @@ namespace: biological_process
def: "Any metabolic process in which photosynthetic organisms use light energy to convert ADP to ATP without the concomitant reduction of dioxygen (O2) to water that occurs in phosphorylation." [ISBN:0198547684]
synonym: "photosynthetic ATP synthesis" NARROW []
is_a: GO:0016310 ! phosphorylation
-is_a: GO:0046034 ! ATP metabolic process
relationship: part_of GO:0019684 ! photosynthesis, light reaction
[Term]
@@ -93620,7 +93620,7 @@ is_a: GO:1901576 ! organic substance biosynthetic process
id: GO:0009815
name: 1-aminocyclopropane-1-carboxylate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-aminocyclopropane-1-carboxylate + L-ascorbate + O(2) = CO(2) + dehydroascorbate + ethylene + 2 H(2)O + hydrogen cyanide. Ethene is also known as ethylene." [EC:1.14.17.4, RHEA:23640]
+def: "Catalysis of the reaction: 1-aminocyclopropane-1-carboxylate + L-ascorbate + O2 = CO2 + dehydroascorbate + ethylene + 2 H2O + hydrogen cyanide. Ethene is also known as ethylene." [RHEA:23640]
synonym: "1-aminocyclopropane-1-carboxylate oxygenase (ethylene-forming)" RELATED [EC:1.14.17.4]
synonym: "ACC oxidase activity" EXACT []
synonym: "aminocyclopropanecarboxylate oxidase activity" RELATED [EC:1.14.17.4]
@@ -93630,7 +93630,7 @@ xref: EC:1.14.17.4
xref: KEGG_REACTION:R07214
xref: MetaCyc:ETHYL-RXN
xref: RHEA:23640
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+is_a: GO:0016715 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0009819
@@ -93653,14 +93653,14 @@ is_a: GO:1901564 ! organonitrogen compound metabolic process
id: GO:0009821
name: alkaloid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of alkaloids, nitrogen-containing natural products which are not otherwise classified as nonprotein amino acids, amines, peptides, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones, or primary metabolite (such as purine or pyrimidine bases)." [EC:1.1.1.51, GOC:lr, ISBN:0122146743]
+def: "The chemical reactions and pathways resulting in the formation of alkaloids, nitrogen-containing natural products which are not otherwise classified as nonprotein amino acids, amines, peptides, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones, or primary metabolite (such as purine or pyrimidine bases)." [GOC:lr, ISBN:0122146743]
synonym: "alkaloid anabolism" EXACT []
synonym: "alkaloid biosynthesis" EXACT []
synonym: "alkaloid formation" EXACT []
synonym: "alkaloid synthesis" EXACT []
xref: UM-BBD_enzymeID:e0711
is_a: GO:0009820 ! alkaloid metabolic process
-is_a: GO:0044271 ! cellular nitrogen compound biosynthetic process
+is_a: GO:0044550 ! secondary metabolite biosynthetic process
is_a: GO:1901566 ! organonitrogen compound biosynthetic process
[Term]
@@ -93822,13 +93822,12 @@ is_a: GO:0009832 ! plant-type cell wall biogenesis
id: GO:0009835
name: fruit ripening
namespace: biological_process
-def: "An aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal." [GOC:lr]
+def: "An developmental maturation process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal." [GOC:lr]
subset: goslim_plant
synonym: "fruit maturation" RELATED [GOC:PO_curators]
synonym: "fruit senescence" RELATED [GOC:PO_curators]
xref: Wikipedia:Ripening
is_a: GO:0003006 ! developmental process involved in reproduction
-is_a: GO:0007568 ! aging
is_a: GO:0071695 ! anatomical structure maturation
relationship: part_of GO:0010154 ! fruit development
@@ -93935,7 +93934,7 @@ namespace: biological_process
alt_id: GO:0075005
def: "The physiological and developmental changes that occur in a spore following release from dormancy up to the earliest signs of growth (e.g. emergence from a spore wall)." [GOC:lr]
synonym: "spore germination on or near host" NARROW []
-is_a: GO:0030154 ! cell differentiation
+is_a: GO:0048869 ! cellular developmental process
[Term]
id: GO:0009848
@@ -94087,7 +94086,7 @@ relationship: part_of GO:0009627 ! systemic acquired resistance
id: GO:0009863
name: salicylic acid mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals mediated by salicylic acid." [GOC:jy]
+def: "The series of molecular signals mediated by salicylic acid." [GOC:jy]
synonym: "salicylic acid mediated signal transduction" EXACT [GOC:signaling]
synonym: "salicylic acid mediated signalling pathway" EXACT []
synonym: "salicylic acid-mediated signaling pathway" EXACT []
@@ -94136,7 +94135,7 @@ relationship: part_of GO:0009682 ! induced systemic resistance
id: GO:0009867
name: jasmonic acid mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals mediated by jasmonic acid." [GOC:jy, PMID:16478936, PMID:19522558, PMID:20159850]
+def: "The series of molecular signals mediated by jasmonic acid." [GOC:jy, PMID:16478936, PMID:19522558, PMID:20159850]
synonym: "JA signaling" EXACT [PMID:20159850]
synonym: "jasmonate signaling" RELATED [PMID:16478936]
synonym: "jasmonic acid mediated signalling pathway" EXACT []
@@ -94195,7 +94194,7 @@ is_obsolete: true
id: GO:0009873
name: ethylene-activated signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated by the reception of ethylene (ethene, C2H4) by a receptor and ending with modulation of a cellular process, e.g. transcription." [GOC:jy, PMID:24012247]
+def: "The series of molecular signals generated by the reception of ethylene (ethene, C2H4) by a receptor and ending with modulation of a cellular process, e.g. transcription." [GOC:jy, PMID:24012247]
synonym: "ethene mediated signaling pathway" RELATED []
synonym: "ethene mediated signalling pathway" EXACT []
synonym: "ethylene mediated signaling pathway" RELATED []
@@ -94736,7 +94735,7 @@ is_a: GO:0004312 ! fatty acid synthase activity
id: GO:0009923
name: fatty acid elongase complex
namespace: cellular_component
-def: "A tetrameric complex of four different subunits which catalyzes the elongation of fatty acids chains 2 carbon units at a time in the synthesis of very long chain fatty acids." [GOC:tb]
+def: "A tetrameric complex of four different subunits which catalyzes the elongation of a fatty acid chain 2 carbon units at a time in the synthesis of very long chain fatty acids." [GOC:tb]
is_a: GO:0098796 ! membrane protein complex
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
is_a: GO:1990234 ! transferase complex
@@ -95250,6 +95249,7 @@ namespace: molecular_function
def: "Catalysis of a ring closure reaction." [ISBN:0198547684]
subset: goslim_generic
subset: goslim_pir
+subset: prokaryote_subset
is_a: GO:0003824 ! catalytic activity
[Term]
@@ -95377,6 +95377,7 @@ alt_id: GO:0008151
alt_id: GO:0044763
alt_id: GO:0050875
def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete]
+comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
subset: gocheck_do_not_annotate
subset: goslim_plant
synonym: "cell growth and/or maintenance" NARROW []
@@ -95415,13 +95416,13 @@ is_a: GO:0009605 ! response to external stimulus
[Term]
id: GO:0009992
-name: cellular water homeostasis
+name: intracellular water homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of water within a cell." [GOC:dph, GOC:tb]
+def: "A homeostatic process involved in the maintenance of a steady state level of water within a cell." [GOC:dph, GOC:tb]
synonym: "cellular osmoregulation" RELATED [GOC:dph, GOC:tb]
+synonym: "cellular water homeostasis" EXACT []
is_a: GO:0006884 ! cell volume homeostasis
-is_a: GO:0030104 ! water homeostasis
-is_a: GO:0055082 ! cellular chemical homeostasis
+is_a: GO:0055082 ! intracellular chemical homeostasis
[Term]
id: GO:0009994
@@ -95601,7 +95602,6 @@ namespace: molecular_function
def: "Binding to N-1-naphthylphthalamic acid, an auxin transport inhibitor." [GOC:sm]
is_a: GO:0033218 ! amide binding
is_a: GO:0033293 ! monocarboxylic acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
[Term]
@@ -95715,6 +95715,7 @@ synonym: "phytochromobilin biosynthesis" EXACT []
synonym: "phytochromobilin formation" EXACT []
synonym: "phytochromobilin synthesis" EXACT []
is_a: GO:0033014 ! tetrapyrrole biosynthetic process
+is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
is_a: GO:0051202 ! phytochromobilin metabolic process
[Term]
@@ -95812,7 +95813,9 @@ name: response to acetate
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetate stimulus." [GOC:sm]
is_a: GO:0010033 ! response to organic substance
+is_a: GO:1901698 ! response to nitrogen compound
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0010035
@@ -95870,6 +95873,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron(III) ion stimulus." [GOC:sm]
synonym: "response to iron(III)" EXACT []
is_a: GO:0010039 ! response to iron ion
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0010042
@@ -96459,17 +96463,19 @@ name: cellular response to iron ion starvation
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of iron ions." [GOC:mg]
is_a: GO:0009267 ! cellular response to starvation
-relationship: part_of GO:0006879 ! cellular iron ion homeostasis
+relationship: part_of GO:0006879 ! intracellular iron ion homeostasis
[Term]
id: GO:0010108
-name: detection of glutamine
+name: obsolete detection of glutamine
namespace: biological_process
-def: "The series of events in which a glutamine stimulus is received by a cell and converted into a molecular signal." [GOC:sm]
+def: "OBSOLETE. The series of events in which a glutamine stimulus is received by a cell and converted into a molecular signal." [GOC:sm]
+comment: This term was made obsolete because it represents a molecular function GO:0140786 glutamine sensor activity.
synonym: "glutamine detection" EXACT []
synonym: "glutamine perception" RELATED []
synonym: "glutamine sensing" RELATED []
-is_a: GO:0009593 ! detection of chemical stimulus
+is_obsolete: true
+consider: GO:0140786
[Term]
id: GO:0010109
@@ -96629,17 +96635,14 @@ is_a: GO:0006527 ! arginine catabolic process
[Term]
id: GO:0010123
-name: acetate catabolic process to butyrate, ethanol, acetone and butanol
+name: obsolete acetate catabolic process to butyrate, ethanol, acetone and butanol
namespace: biological_process
-def: "The anaerobic chemical reactions and pathways resulting in the breakdown of acetate to form butyrate, ethanol, acetone and butanol." [GOC:pz]
+def: "OBSOLETE. The anaerobic chemical reactions and pathways resulting in the breakdown of acetate to form butyrate, ethanol, acetone and butanol." [GOC:pz]
+comment: This term was obsoleted because it is not believed to exist.
synonym: "acetate fermentation to butyrate, ethanol, acetone and butanol" EXACT []
xref: MetaCyc:CENTFERM-PWY
-is_a: GO:0006067 ! ethanol metabolic process
-is_a: GO:0019605 ! butyrate metabolic process
-is_a: GO:0019654 ! acetate fermentation
-is_a: GO:0043443 ! acetone metabolic process
-is_a: GO:0045733 ! acetate catabolic process
-is_a: GO:0071270 ! 1-butanol metabolic process
+is_obsolete: true
+consider: GO:0044813
[Term]
id: GO:0010124
@@ -96768,6 +96771,7 @@ xref: MetaCyc:PROUT-PWY
xref: MetaCyc:PWY-4561
is_a: GO:0006536 ! glutamate metabolic process
is_a: GO:0006562 ! proline catabolic process
+is_a: GO:0043605 ! amide catabolic process
[Term]
id: GO:0010134
@@ -96785,7 +96789,7 @@ name: ureide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving ureide, allantoin and allantoate, which are the organic forms of nitrogen in nitrogen fixing and transporting plants." [GOC:pz]
synonym: "ureide metabolism" EXACT []
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
[Term]
id: GO:0010136
@@ -96883,6 +96887,7 @@ synonym: "cutin formation" EXACT []
synonym: "cutin synthesis" EXACT []
xref: MetaCyc:PWY-321
is_a: GO:0009059 ! macromolecule biosynthetic process
+relationship: part_of GO:0160062 ! cutin-based cuticle development
[Term]
id: GO:0010144
@@ -96905,7 +96910,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving fructan, a polysaccharide consisting of fructose residues." [GOC:sm]
synonym: "fructan metabolism" EXACT []
synonym: "levan metabolic process" EXACT []
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
+is_a: GO:0005976 ! polysaccharide metabolic process
[Term]
id: GO:0010146
@@ -96919,8 +96924,8 @@ synonym: "fructan synthesis" EXACT []
synonym: "levan biosynthesis" EXACT []
synonym: "levan biosynthetic process" EXACT []
xref: MetaCyc:PWY-822
+is_a: GO:0000271 ! polysaccharide biosynthetic process
is_a: GO:0010145 ! fructan metabolic process
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
[Term]
id: GO:0010147
@@ -96933,8 +96938,8 @@ synonym: "fructan degradation" EXACT []
synonym: "levan catabolic process" EXACT []
synonym: "levan catabolism" EXACT []
xref: MetaCyc:PWY-862
+is_a: GO:0000272 ! polysaccharide catabolic process
is_a: GO:0010145 ! fructan metabolic process
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
[Term]
id: GO:0010148
@@ -96949,7 +96954,7 @@ id: GO:0010149
name: obsolete senescence
namespace: biological_process
def: "OBSOLETE. A preprogrammed process associated with the dismantling of an anatomical structure and an overall decline in metabolism. This may include the breakdown of organelles, membranes and other cellular components. An example of this process is found in Arabidopsis thaliana, when older leaves or floral organs are shed." [GOC:mtg_sensu, ISBN:0387987819]
-comment: This term was made obsolete because its name is ambiguous and it is covered by the two more specific terms: 'organ senescence ; GO:0010260' and 'cell aging ; GO:0007569'.
+comment: This term was made obsolete because its name is ambiguous and it is covered by more specific terms: 'plant organ senescence ; GO:0090693' and 'cellular senescence ; GO:0090398'.
synonym: "senescence" EXACT []
xref: Wikipedia:Senescence
is_obsolete: true
@@ -96958,7 +96963,7 @@ is_obsolete: true
id: GO:0010150
name: leaf senescence
namespace: biological_process
-def: "The process that occurs in a leaf near the end of its active life that is associated with the dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism." [ISBN:0387987819]
+def: "The last stage of leaf development during which programmed degradation of macromolecules and nutrient recycling take place." [ISBN:0387987819, PMID:17177638, PMID:34938309]
is_a: GO:0090693 ! plant organ senescence
relationship: part_of GO:0048366 ! leaf development
@@ -97001,7 +97006,7 @@ id: GO:0010155
name: regulation of proton transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of proton transport into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:sm]
-is_a: GO:1904062 ! regulation of cation transmembrane transport
+is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport
relationship: regulates GO:1902600 ! proton transmembrane transport
[Term]
@@ -97021,6 +97026,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chlorate stimulus." [GOC:sm]
is_a: GO:0010035 ! response to inorganic substance
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0010158
@@ -97104,6 +97110,7 @@ def: "Any process that results in a change in state or activity of a cell or an
is_a: GO:0010035 ! response to inorganic substance
is_a: GO:1901698 ! response to nitrogen compound
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0010168
@@ -97119,8 +97126,8 @@ name: thioglucosidase complex
namespace: cellular_component
def: "A large (200-800 kDa) multiprotein complex formed by 70-kDa and 5-kDa myrosinases, myrosinase- binding proteins (MBPs), MBP-related proteins and myrosinase-associated proteins. The complex has been identified in Brassica napus seeds." [PMID:10682349]
synonym: "myrosinase complex" EXACT []
+is_a: GO:0140535 ! intracellular protein-containing complex
is_a: GO:1902494 ! catalytic complex
-relationship: part_of GO:0005737 ! cytoplasm
[Term]
id: GO:0010170
@@ -97172,7 +97179,7 @@ def: "Catalysis of the reaction: 2-oxo-4-methylthiobutanoate + acetyl-CoA + H2O
synonym: "methylthioalkylmalate synthase activity" BROAD [MetaCyc:RXN-2202]
xref: EC:2.3.3.17
xref: MetaCyc:RXN-2202
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0010178
@@ -97518,19 +97525,24 @@ relationship: part_of GO:0071668 ! plant-type cell wall assembly
[Term]
id: GO:0010216
-name: maintenance of DNA methylation
+name: obsolete negative regulation of gene expression via chromosomal DNA cytosine methylation
namespace: biological_process
-def: "Any process involved in maintaining the methylation state of a nucleotide sequence." [PMID:11898023]
-is_a: GO:0006259 ! DNA metabolic process
+def: "OBSOLETE. An epigenetic gene regulation mechanism that negatively regulates gene expression by methylation of cytosine residues in chromosomal DNA." [PMID:11898023]
+comment: This term was obsoleted because it represents the same process as negative regulation of gene expression via CpG island methylation ; GO:0044027.
+synonym: "maintenance of DNA methylation" BROAD []
+is_obsolete: true
+replaced_by: GO:0044027
[Term]
id: GO:0010217
-name: cellular aluminum ion homeostasis
+name: obsolete intracellular aluminum ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of aluminum ions at the level of a cell." [GOC:lr, GOC:mah]
+def: "OBSOLETE. A homeostatic process involved in the maintenance of a steady state level of aluminium ions within a cell." [GOC:lr, GOC:mah]
+comment: This term was obsoleted because this process is not believed to exist.
synonym: "cellular aluminium ion homeostasis" EXACT [GOC:mah]
-is_a: GO:0006875 ! cellular metal ion homeostasis
-is_a: GO:0055079 ! aluminum ion homeostasis
+synonym: "cellular aluminum ion homeostasis" EXACT []
+is_obsolete: true
+replaced_by: GO:0140982
[Term]
id: GO:0010218
@@ -97628,6 +97640,8 @@ name: response to lithium ion
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lithium (Li+) ion stimulus." [GOC:tb]
is_a: GO:0010038 ! response to metal ion
+is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0010227
@@ -97801,8 +97815,8 @@ synonym: "rhamnogalacturonan I anabolism" EXACT []
synonym: "rhamnogalacturonan I biosynthesis" EXACT []
synonym: "rhamnogalacturonan I formation" EXACT []
synonym: "rhamnogalacturonan I synthesis" EXACT []
-is_a: GO:0000271 ! polysaccharide biosynthetic process
is_a: GO:0010395 ! rhamnogalacturonan I metabolic process
+is_a: GO:0070592 ! cell wall polysaccharide biosynthetic process
[Term]
id: GO:0010247
@@ -97819,7 +97833,7 @@ id: GO:0010248
name: establishment or maintenance of transmembrane electrochemical gradient
namespace: biological_process
def: "The directed movement of ions to establish or maintain an electrochemical gradient across a membrane by means of some agent such as a transporter or pore." [GOC:mah, GOC:sm]
-is_a: GO:0034220 ! ion transmembrane transport
+is_a: GO:0034220 ! monoatomic ion transmembrane transport
[Term]
id: GO:0010249
@@ -97844,10 +97858,13 @@ is_a: GO:0044272 ! sulfur compound biosynthetic process
[Term]
id: GO:0010252
-name: auxin homeostasis
+name: obsolete auxin homeostasis
namespace: biological_process
-def: "A homeostatic process that maintains an endogenous steady-state concentration of primary auxin, or constant level of auxin in a biological system, by a number of biochemical processes including transport, biosynthesis, catabolism and conjugation." [PMID:22504182]
-is_a: GO:0048878 ! chemical homeostasis
+def: "OBSOLETE. A homeostatic process that maintains an endogenous steady-state concentration of primary auxin, or constant level of auxin in a biological system, by a number of biochemical processes including transport, biosynthesis, catabolism and conjugation." [PMID:22504182]
+comment: This term was obsoleted in favor of 'intracellular' and 'multicellular organism-level' auxin homeostasis terms.
+is_obsolete: true
+consider: GO:0140963
+consider: GO:0140964
[Term]
id: GO:0010253
@@ -97907,20 +97924,20 @@ is_a: GO:0010275 ! NAD(P)H dehydrogenase complex assembly
[Term]
id: GO:0010259
-name: multicellular organism aging
+name: obsolete multicellular organism aging
namespace: biological_process
-def: "An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700)." [GOC:PO_curators]
-is_a: GO:0007275 ! multicellular organism development
-is_a: GO:0007568 ! aging
+def: "OBSOLETE. An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700)." [GOC:PO_curators]
+comment: The reason for obsoletion is that this represents a phenotype.
+is_obsolete: true
[Term]
id: GO:0010260
-name: animal organ senescence
+name: obsolete animal organ senescence
namespace: biological_process
alt_id: GO:0010261
-def: "The process that occurs in an animal organ near the end of its active life that is associated with the dismantling of cell components and membranes, and an overall decline in metabolism." [GOC:tb]
-is_a: GO:0007568 ! aging
-relationship: part_of GO:0048513 ! animal organ development
+def: "OBSOLETE. The process that occurs in an animal organ near the end of its active life that is associated with the dismantling of cell components and membranes, and an overall decline in metabolism." [GOC:tb]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0010262
@@ -97975,14 +97992,18 @@ is_a: GO:0010243 ! response to organonitrogen compound
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0033273 ! response to vitamin
is_a: GO:0097305 ! response to alcohol
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0010267
-name: production of ta-siRNAs involved in RNA interference
+name: ta-siRNA processing
namespace: biological_process
-def: "Cleavage of double-stranded RNA to form trans-acting small interfering RNA molecules (siRNAs) of 21-23 nucleotides. ta-siRNAs arise from PolII genes and function like miRNAs to guide cleavage of target mRNAs." [GOC:tb, PMID:16129836]
+def: "A process leading to the generation of a functional trans-acting small interfering RNA (ta-siRNA). ta-siRNAs function like miRNAs to guide cleavage of target mRNAs." [GOC:tb, PMID:16129836, PMID:20687832]
+synonym: "primary ta-siRNA processing" EXACT []
+synonym: "production of small RNA involved in gene silencing by RNA" NARROW []
+synonym: "production of ta-siRNAs involved in RNA interference" EXACT []
synonym: "RNA interference, production of ta-siRNAs" EXACT [GOC:mah]
-is_a: GO:0030422 ! production of siRNA involved in RNA interference
+is_a: GO:0030422 ! siRNA processing
[Term]
id: GO:0010268
@@ -98132,7 +98153,7 @@ id: GO:0010285
name: L,L-diaminopimelate aminotransferase activity
namespace: molecular_function
alt_id: GO:0043742
-def: "Catalysis of the reaction: 2-oxoglutarate + LL-2,6-diaminopimelate = (S)-2,3,4,5-tetrahydrodipicolinate + L-glutamate + H(2)O + H(+)." [EC:2.6.1.83, RHEA:23988]
+def: "Catalysis of the reaction: 2-oxoglutarate + LL-2,6-diaminopimelate = (S)-2,3,4,5-tetrahydrodipicolinate + L-glutamate + H2O + H+." [EC:2.6.1.83, RHEA:23988]
synonym: "LL-2,6-diaminoheptanedioate:2-oxoglutarate aminotransferase activity" EXACT []
synonym: "LL-DAP aminotransferase activity" RELATED [EC:2.6.1.83]
synonym: "LL-DAP-AT activity" RELATED [EC:2.6.1.83]
@@ -98203,14 +98224,14 @@ def: "Catalysis of the reaction: GTP(out) + GDP(in) = GTP(in) + GDP(out)." [PMID
is_a: GO:0001409 ! guanine nucleotide transmembrane transporter activity
is_a: GO:0005346 ! purine ribonucleotide transmembrane transporter activity
is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
+is_a: GO:0015297 ! antiporter activity
[Term]
id: GO:0010293
name: abscisic aldehyde oxidase activity
namespace: molecular_function
alt_id: GO:0033725
-def: "Catalysis of the reaction: (+)-abscisic aldehyde + H(2)O + O(2) = abscisate + H(2)O(2) + H(+)." [EC:1.2.3.14, RHEA:20529]
+def: "Catalysis of the reaction: (+)-abscisic aldehyde + H2O + O2 = abscisate + H2O2 + H+." [EC:1.2.3.14, RHEA:20529]
synonym: "AAO3" RELATED [EC:1.2.3.14]
synonym: "abscisic-aldehyde oxidase activity" RELATED [EC:1.2.3.14]
synonym: "abscisic-aldehyde:oxygen oxidoreductase activity" RELATED [EC:1.2.3.14]
@@ -98234,7 +98255,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0010295
name: (+)-abscisic acid 8'-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (+)-abscisate + H(+) + NADPH + O(2) = (+)-8'-hydroxyabscisate + H(2)O + NADP(+)." [EC:1.14.14.137, RHEA:12897]
+def: "Catalysis of the reaction: (+)-abscisate + H+ + NADPH + O2 = (+)-8'-hydroxyabscisate + H2O + NADP+." [EC:1.14.14.137, RHEA:12897]
synonym: "(+)-ABA 8'-hydroxylase activity" RELATED [EC:1.14.14.137]
synonym: "ABA 8'-hydroxylase activity" RELATED [EC:1.14.14.137]
synonym: "ABA 8'-Hydroxylase activity, Abscisate 8'-hydroxylase activity" RELATED []
@@ -98285,7 +98306,7 @@ id: GO:0010301
name: xanthoxin dehydrogenase activity
namespace: molecular_function
alt_id: GO:0033710
-def: "Catalysis of the reaction: NAD(+) + xanthoxin = (+)-abscisic aldehyde + H(+) + NADH." [EC:1.1.1.288, RHEA:12548]
+def: "Catalysis of the reaction: NAD+ + xanthoxin = (+)-abscisic aldehyde + H+ + NADH." [EC:1.1.1.288, RHEA:12548]
synonym: "ABA2" RELATED [EC:1.1.1.288]
synonym: "xanthoxin oxidase activity" RELATED [EC:1.1.1.288]
synonym: "xanthoxin:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.288]
@@ -98315,7 +98336,7 @@ name: PSII associated light-harvesting complex II catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of one or more components of the light-harvesting complex of photosystem II." [GOC:mah, PMID:16157880]
synonym: "LHCII catabolism" RELATED []
-is_a: GO:0044257 ! cellular protein catabolic process
+is_a: GO:0030163 ! protein catabolic process
[Term]
id: GO:0010305
@@ -98336,14 +98357,14 @@ is_a: GO:0052325 ! cell wall pectin biosynthetic process
id: GO:0010307
name: acetylglutamate kinase regulator activity
namespace: molecular_function
-def: "Modulates the enzyme activity of acetylglutamate kinase." [PMID:16377628]
+def: "Binds to and modulates the activity of acetylglutamate kinase." [PMID:16377628]
is_a: GO:0019207 ! kinase regulator activity
[Term]
id: GO:0010308
name: acireductone dioxygenase (Ni2+-requiring) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O(2) = 3-(methylthio)propanoate + CO + formate." [EC:1.13.11.53, RHEA:14161]
+def: "Catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 3-(methylthio)propanoate + CO + formate." [EC:1.13.11.53, RHEA:14161]
synonym: "1,2-dihydroxy-5-(methylthio)pent-1-en-3-one:oxygen oxidoreductase (formate- and CO-forming)" RELATED [EC:1.13.11.53]
synonym: "2-hydroxy-3-keto-5-thiomethylpent-1-ene dioxygenase activity" BROAD [EC:1.13.11.53]
synonym: "acireductone dioxygenase activity" BROAD [EC:1.13.11.53]
@@ -98359,7 +98380,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0010309
name: acireductone dioxygenase [iron(II)-requiring] activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O(2) = 4-methylthio-2-oxobutanoate + formate + H(+)." [EC:1.13.11.54, RHEA:24504]
+def: "Catalysis of the reaction: 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 4-methylthio-2-oxobutanoate + formate + H+." [EC:1.13.11.54, RHEA:24504]
synonym: "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase activity" EXACT []
synonym: "1,2-dihydroxy-5-(methylthio)pent-1-en-3-one:oxygen oxidoreductase (formate-forming)" RELATED [EC:1.13.11.54]
synonym: "2-hydroxy-3-keto-5-thiomethylpent-1-ene dioxygenase" BROAD []
@@ -98420,12 +98441,14 @@ is_a: GO:1901981 ! phosphatidylinositol phosphate binding
[Term]
id: GO:0010315
-name: auxin efflux
+name: auxin export across the plasma membrane
namespace: biological_process
-def: "The process involved in the transport of auxin out of the cell." [GOC:tair_curators, PMID:16990790]
-synonym: "auxin export" EXACT []
+def: "The directed movement of auxins from inside of a cell, across the plasma membrane and into the extracellular region." [GOC:tair_curators, PMID:16990790]
+synonym: "auxin efflux" BROAD []
+synonym: "auxin export" BROAD []
is_a: GO:0010928 ! regulation of auxin mediated signaling pathway
is_a: GO:0060918 ! auxin transport
+is_a: GO:0140115 ! export across plasma membrane
[Term]
id: GO:0010316
@@ -98434,7 +98457,7 @@ namespace: cellular_component
def: "Heterodimeric complex that catalyzes the pyrophosphate-dependent phosphorylation of D-fructose 6-phosphate into D-fructose 1,6-bisphosphate." [PMID:2170409]
subset: goslim_pir
synonym: "PFK complex" RELATED []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0010317
@@ -98442,7 +98465,7 @@ name: pyrophosphate-dependent phosphofructokinase complex, alpha-subunit complex
namespace: cellular_component
def: "Refers to the alpha subunit of the heterodimeric complex that possesses pyrophosphate-dependent phosphofructokinase activity." [PMID:2170409]
synonym: "PFK complex, alpha-subunit" RELATED []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0010316 ! pyrophosphate-dependent phosphofructokinase complex
[Term]
@@ -98451,7 +98474,7 @@ name: pyrophosphate-dependent phosphofructokinase complex, beta-subunit complex
namespace: cellular_component
def: "Refers to the beta subunit of the heterodimeric complex that possesses pyrophosphate-dependent phosphofructokinase activity." [PMID:2170409]
synonym: "PFK complex, beta-subunit" RELATED []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0010316 ! pyrophosphate-dependent phosphofructokinase complex
[Term]
@@ -98489,8 +98512,8 @@ name: regulation of isopentenyl diphosphate biosynthetic process, methylerythrit
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of isopentenyl diphosphate produced via the methylerythritol (MEP) pathway (mevalonate-independent)." [PMID:16531478]
synonym: "regulation of isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" EXACT []
+is_a: GO:0006109 ! regulation of carbohydrate metabolic process
is_a: GO:0010565 ! regulation of cellular ketone metabolic process
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:0019747 ! regulation of isoprenoid metabolic process
is_a: GO:0071071 ! regulation of phospholipid biosynthetic process
relationship: regulates GO:0019288 ! isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
@@ -98506,8 +98529,8 @@ synonym: "downregulation of isopentenyl diphosphate biosynthetic process, mevalo
synonym: "inhibition of isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" NARROW []
synonym: "negative regulation of isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" EXACT []
is_a: GO:0010322 ! regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
is_a: GO:0045827 ! negative regulation of isoprenoid metabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:0071072 ! negative regulation of phospholipid biosynthetic process
relationship: negatively_regulates GO:0019288 ! isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
@@ -98579,8 +98602,8 @@ def: "Binding to a gibberellin, a plant hormone that regulates aspects of plant
synonym: "gibberellic acid receptor" RELATED []
synonym: "gibberellin receptor" RELATED []
is_a: GO:0019840 ! isoprenoid binding
+is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0042562 ! hormone binding
-is_a: GO:0043177 ! organic acid binding
[Term]
id: GO:0010332
@@ -98723,8 +98746,8 @@ name: lithium:proton antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Li+(in) + H+(out) = Li+(out) + H+(in)." [PMID:17270011]
synonym: "lithium:hydrogen antiporter activity" EXACT []
-is_a: GO:0005451 ! monovalent cation:proton antiporter activity
-is_a: GO:0046873 ! metal ion transmembrane transporter activity
+is_a: GO:0051139 ! metal cation:proton antiporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0010349
@@ -98760,9 +98783,7 @@ def: "The directed movement of lithium ion out of a cell or organelle." [PMID:17
synonym: "lithium export" EXACT []
synonym: "lithium ion efflux" RELATED []
synonym: "lithium ion export" RELATED []
-is_a: GO:0010351 ! lithium ion transport
-is_a: GO:0070839 ! metal ion export
-is_a: GO:0098662 ! inorganic cation transmembrane transport
+is_a: GO:0090452 ! lithium ion transmembrane transport
is_a: GO:0140115 ! export across plasma membrane
[Term]
@@ -98815,8 +98836,8 @@ id: GO:0010359
name: regulation of anion channel activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of anion channel activity." [PMID:17319842]
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
-is_a: GO:1903959 ! regulation of anion transmembrane transport
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
+is_a: GO:1903959 ! regulation of monoatomic anion transmembrane transport
[Term]
id: GO:0010360
@@ -99034,8 +99055,8 @@ id: GO:0010383
name: cell wall polysaccharide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving cell wall polysaccharides." [GOC:tair_curators]
+is_a: GO:0005976 ! polysaccharide metabolic process
is_a: GO:0044036 ! cell wall macromolecule metabolic process
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
[Term]
id: GO:0010384
@@ -99247,8 +99268,8 @@ name: xyloglucan metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving xyloglucan, the cross-linking glycan composed of (1->4)-beta-D-glucan backbone substituted at regular intervals with beta-D-xylosyl-(1->6) residues, which is present in the primary cell wall of most higher plants." [GOC:tair_curators]
synonym: "xyloglucan metabolism" EXACT [GOC:obol]
-is_a: GO:0006073 ! cellular glucan metabolic process
is_a: GO:0010410 ! hemicellulose metabolic process
+is_a: GO:0044042 ! glucan metabolic process
[Term]
id: GO:0010412
@@ -99395,7 +99416,6 @@ synonym: "abscisate binding" RELATED []
is_a: GO:0019840 ! isoprenoid binding
is_a: GO:0033293 ! monocarboxylic acid binding
is_a: GO:0042562 ! hormone binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0043178 ! alcohol binding
[Term]
@@ -99492,7 +99512,6 @@ id: GO:0010439
name: regulation of glucosinolate biosynthetic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glucosinolates, substituted thioglucosides found in rapeseed products and related cruciferae." [PMID:17420480]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0042762 ! regulation of sulfur metabolic process
is_a: GO:0043255 ! regulation of carbohydrate biosynthetic process
@@ -99685,10 +99704,10 @@ is_a: GO:0045823 ! positive regulation of heart contraction
[Term]
id: GO:0010461
-name: light-activated ion channel activity
+name: light-activated monoatomic ion channel activity
namespace: molecular_function
-def: "Enables the transmembrane transfer of an ion by a channel that opens in response to a light stimulus." [GOC:dph, GOC:tb]
-is_a: GO:0005216 ! ion channel activity
+def: "Enables the transmembrane transfer of a monoatomic ion by a channel that opens in response to a light stimulus." [GOC:dph, GOC:tb]
+is_a: GO:0005216 ! monoatomic ion channel activity
[Term]
id: GO:0010462
@@ -99745,7 +99764,7 @@ id: GO:0010468
name: regulation of gene expression
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA)." [GOC:txnOH-2018]
-comment: This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation.
+comment: This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation.
synonym: "gene regulation" RELATED [GOC:cjm]
synonym: "regulation of gene product expression" RELATED []
synonym: "regulation of protein expression" NARROW []
@@ -99776,20 +99795,24 @@ relationship: regulates GO:0007369 ! gastrulation
id: GO:0010471
name: GDP-galactose:mannose-1-phosphate guanylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GDP-L-galactose + alpha-D-mannose 1-phosphate = GDP-alpha-D-mannose + alpha-L-galactose-1-phosphate." [MetaCyc:RXN4FS-12, PMID:17485667]
+def: "Catalysis of the reaction: GDP-beta-L-galactose + alpha-D-mannose 1-phosphate = GDP-alpha-D-mannose + beta-L-galactose-1-phosphate." [PMID:17485667, RHEA:65708]
synonym: "GDP-L-galactose phosphorylase activity" BROAD [MetaCyc:AT4G26850-MONOMER]
synonym: "GDP-L-galactose:mannose-1-phosphate guanylyltransferase activity" EXACT [MetaCyc:RXN4FS-12]
+xref: EC:2.7.7.69
xref: MetaCyc:RXN4FS-12
-is_a: GO:0008905 ! mannose-phosphate guanylyltransferase activity
+xref: RHEA:65708
+is_a: GO:0070568 ! guanylyltransferase activity
[Term]
id: GO:0010472
name: GDP-galactose:glucose-1-phosphate guanylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GDP-L-galactose + alpha-D-glucose 1-phosphate = alpha-L-galactose-1-phosphate + GDP-alpha-D-glucose." [MetaCyc:RXN4FS-13, PMID:17485667]
+def: "Catalysis of the reaction: GDP-beta-L-galactose + alpha-D-glucose 1-phosphate = beta-L-galactose-1-phosphate + GDP-alpha-D-glucose." [PMID:17485667, RHEA:65712]
synonym: "GDP-L-galactose phosphorylase activity" BROAD [MetaCyc:AT4G26850-MONOMER]
synonym: "GDP-L-galactose:glucose-1-phosphate guanylyltransferase activity" EXACT [MetaCyc:RXN4FS-13]
+xref: EC:2.7.7.69
xref: MetaCyc:RXN4FS-13
+xref: RHEA:65712
is_a: GO:0070568 ! guanylyltransferase activity
[Term]
@@ -99799,22 +99822,6 @@ namespace: molecular_function
def: "Catalysis of the reaction: GDP-L-galactose + myo-inositol 1-phosphate = alpha-L-galactose-1-phosphate + GDP-myoinositol." [PMID:17485667]
is_a: GO:0070568 ! guanylyltransferase activity
-[Term]
-id: GO:0010474
-name: glucose-1-phosphate guanylyltransferase (GDP) activity
-namespace: molecular_function
-def: "Catalysis of the reaction: GDP + D-glucose 1-phosphate = phosphate + GDP-glucose." [PMID:17462988]
-synonym: "GDP:glucose-1-phosphate guanyltransferase activity" EXACT []
-is_a: GO:0070568 ! guanylyltransferase activity
-
-[Term]
-id: GO:0010475
-name: galactose-1-phosphate guanylyltransferase (GDP) activity
-namespace: molecular_function
-def: "Catalysis of the reaction: GDP + L-galactose 1-phosphate = phosphate + GDP-galactose." [PMID:17462988]
-synonym: "GDP:galactose-1-phosphate guanyltransferase activity" EXACT []
-is_a: GO:0070568 ! guanylyltransferase activity
-
[Term]
id: GO:0010476
name: gibberellin mediated signaling pathway
@@ -99885,16 +99892,20 @@ relationship: part_of GO:0009856 ! pollination
[Term]
id: GO:0010484
-name: H3 histone acetyltransferase activity
+name: histone H3 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H3 = CoA + acetyl-histone H3." [EC:2.3.1.48]
+synonym: "H3 histone acetylase activity" EXACT []
+synonym: "H3 histone acetyltransferase activity" EXACT []
is_a: GO:0004402 ! histone acetyltransferase activity
[Term]
id: GO:0010485
-name: H4 histone acetyltransferase activity
+name: histone H4 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H4 = CoA + acetyl-histone H4." [EC:2.3.1.48]
+synonym: "H4 histone acetylase activity" EXACT []
+synonym: "H4 histone acetyltransferase activity" EXACT []
is_a: GO:0004402 ! histone acetyltransferase activity
[Term]
@@ -99904,8 +99915,7 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Mn2+(in) + H+(out) = Mn2+(out) + H+(in)." [PMID:17559518]
synonym: "manganese:hydrogen antiporter activity" EXACT []
is_a: GO:0005384 ! manganese ion transmembrane transporter activity
-is_a: GO:0015078 ! proton transmembrane transporter activity
-is_a: GO:0015491 ! cation:cation antiporter activity
+is_a: GO:0051139 ! metal cation:proton antiporter activity
[Term]
id: GO:0010487
@@ -99958,7 +99968,7 @@ name: Lewis a epitope biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of a Lewis a epitope, a trisaccharide (Fuc-alpha-(1->4)[Gal-beta-(1->3)]GlcNAc) characteristic of plant protein N-linked oligosaccharides." [PMID:17630273]
synonym: "LE A biosynthetic process" RELATED []
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
+is_a: GO:0000271 ! polysaccharide biosynthetic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
[Term]
@@ -99973,11 +99983,13 @@ is_a: GO:0036464 ! cytoplasmic ribonucleoprotein granule
[Term]
id: GO:0010495
-name: long-distance posttranscriptional gene silencing
+name: siRNA-mediated long-distance post-transcriptional gene silencing
namespace: biological_process
-def: "A posttranscriptional gene silencing process in which the silencing signal originates in a tissue separate from the tissue in which the silencing takes place." [GOC:dph, GOC:tb, PMID:11590235, PMID:17785412]
-synonym: "long-distance propagation of posttranscriptional gene silencing" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0016441 ! posttranscriptional gene silencing
+def: "An siRNA-mediated posttranscriptional gene silencing pathway in which small interfering RNAs (siRNAs) direct the cleavage of target mRNAs, and in which the silencing signal originates in one tissue and occurs in a different tissue." [GOC:dph, GOC:tb, PMID:11590235, PMID:17785412]
+synonym: "long-distance posttranscriptional gene silencing" BROAD []
+synonym: "long-distance propagation of posttranscriptional gene silencing" BROAD [GOC:dph, GOC:tb]
+synonym: "siRNA-mediated long-distance posttranscriptional gene silencing" EXACT []
+is_a: GO:0090625 ! siRNA-mediated gene silencing by mRNA destabilization
[Term]
id: GO:0010496
@@ -100011,7 +100023,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of a protei
synonym: "proteasome-mediated protein catabolic process" EXACT []
synonym: "proteasome-mediated protein catabolism" EXACT []
is_a: GO:0030163 ! protein catabolic process
-is_a: GO:0051603 ! proteolysis involved in cellular protein catabolic process
+is_a: GO:0051603 ! proteolysis involved in protein catabolic process
[Term]
id: GO:0010499
@@ -100087,10 +100099,11 @@ relationship: positively_regulates GO:0006914 ! autophagy
[Term]
id: GO:0010509
-name: polyamine homeostasis
+name: intracellular polyamine homeostasis
namespace: biological_process
-def: "Any biological process involved in the maintenance of an internal steady state of a polyamine." [GOC:dph, GOC:rph, GOC:tb, PMID:11161802, PMID:9761731]
-is_a: GO:0048878 ! chemical homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of polyamine within a cell." [GOC:dph, GOC:rph, GOC:tb, PMID:11161802, PMID:9761731]
+synonym: "polyamine homeostasis" RELATED []
+is_a: GO:0055082 ! intracellular chemical homeostasis
[Term]
id: GO:0010510
@@ -100105,6 +100118,7 @@ id: GO:0010511
name: regulation of phosphatidylinositol biosynthetic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of phosphatidylinositol." [GOC:dph, GOC:tb, GOC:vw]
+is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0071071 ! regulation of phospholipid biosynthetic process
relationship: regulates GO:0006661 ! phosphatidylinositol biosynthetic process
@@ -100114,6 +100128,7 @@ name: negative regulation of phosphatidylinositol biosynthetic process
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of phosphatidylinositol." [GOC:dph, GOC:tb, GOC:vw]
is_a: GO:0010511 ! regulation of phosphatidylinositol biosynthetic process
+is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
is_a: GO:0071072 ! negative regulation of phospholipid biosynthetic process
relationship: negatively_regulates GO:0006661 ! phosphatidylinositol biosynthetic process
@@ -100123,6 +100138,7 @@ name: positive regulation of phosphatidylinositol biosynthetic process
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of phosphatidylinositol." [GOC:dph, GOC:tb, GOC:vw]
is_a: GO:0010511 ! regulation of phosphatidylinositol biosynthetic process
+is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:0071073 ! positive regulation of phospholipid biosynthetic process
relationship: positively_regulates GO:0006661 ! phosphatidylinositol biosynthetic process
@@ -100196,9 +100212,9 @@ id: GO:0010522
name: regulation of calcium ion transport into cytosol
namespace: biological_process
def: "Any process that modulates the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:dph, GOC:tb]
-is_a: GO:0051924 ! regulation of calcium ion transport
is_a: GO:0060341 ! regulation of cellular localization
is_a: GO:0065008 ! regulation of biological quality
+is_a: GO:1903169 ! regulation of calcium ion transmembrane transport
relationship: regulates GO:0060402 ! calcium ion transport into cytosol
[Term]
@@ -100207,8 +100223,8 @@ name: negative regulation of calcium ion transport into cytosol
namespace: biological_process
def: "Any process that decreases the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:dph, GOC:tb]
is_a: GO:0010522 ! regulation of calcium ion transport into cytosol
-is_a: GO:0048523 ! negative regulation of cellular process
-is_a: GO:0051926 ! negative regulation of calcium ion transport
+is_a: GO:0051481 ! negative regulation of cytosolic calcium ion concentration
+is_a: GO:1903170 ! negative regulation of calcium ion transmembrane transport
relationship: negatively_regulates GO:0060402 ! calcium ion transport into cytosol
[Term]
@@ -100218,35 +100234,36 @@ namespace: biological_process
def: "Any process that increases the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:dph, GOC:tb]
is_a: GO:0007204 ! positive regulation of cytosolic calcium ion concentration
is_a: GO:0010522 ! regulation of calcium ion transport into cytosol
-is_a: GO:0048522 ! positive regulation of cellular process
-is_a: GO:0051928 ! positive regulation of calcium ion transport
+is_a: GO:1904427 ! positive regulation of calcium ion transmembrane transport
relationship: positively_regulates GO:0060402 ! calcium ion transport into cytosol
[Term]
id: GO:0010525
-name: regulation of transposition, RNA-mediated
+name: obsolete regulation of transposition, RNA-mediated
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of RNA-mediated transposition. RNA-mediated transposition is a type of transpositional recombination which occurs via an RNA intermediate." [GOC:dph, GOC:tb]
-is_a: GO:0010528 ! regulation of transposition
-relationship: regulates GO:0032197 ! transposition, RNA-mediated
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of RNA-mediated transposition. RNA-mediated transposition is a type of transpositional recombination which occurs via an RNA intermediate." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because only negative regulation is known to exist (retrotransposon silencing).
+is_obsolete: true
+consider: GO:0032197
[Term]
id: GO:0010526
-name: negative regulation of transposition, RNA-mediated
+name: retrotransposon silencing
namespace: biological_process
-def: "Any process that decreases the frequency, rate or extent of RNA-mediated transposition. RNA-mediated transposition is a type of transpositional recombination which occurs via an RNA intermediate." [GOC:dph, GOC:tb]
-is_a: GO:0010525 ! regulation of transposition, RNA-mediated
+def: "Any process that decreases the frequency, rate or extent of retrotransposition. Retrotransposons are a subset of transposable elements that use an RNA intermediate and reverse transcribe themselves into the genome." [GOC:dph, GOC:tb, PMID:32823517]
+synonym: "negative regulation of transposition, RNA-mediated" EXACT []
+xref: Wikipedia:Retrotransposon_silencing
is_a: GO:0010529 ! negative regulation of transposition
-relationship: negatively_regulates GO:0032197 ! transposition, RNA-mediated
+relationship: negatively_regulates GO:0032197 ! retrotransposition
[Term]
id: GO:0010527
-name: positive regulation of transposition, RNA-mediated
+name: obsolete positive regulation of transposition, RNA-mediated
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of RNA-mediated transposition. RNA-mediated transposition is a type of transpositional recombination which occurs via an RNA intermediate." [GOC:dph, GOC:tb]
-is_a: GO:0010525 ! regulation of transposition, RNA-mediated
-is_a: GO:0010530 ! positive regulation of transposition
-relationship: positively_regulates GO:0032197 ! transposition, RNA-mediated
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of RNA-mediated transposition. RNA-mediated transposition is a type of transpositional recombination which occurs via an RNA intermediate." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
+consider: GO:0032197
[Term]
id: GO:0010528
@@ -100438,7 +100455,7 @@ namespace: biological_process
def: "Any process that modulates the chemical reactions and pathways resulting in the breakdown of one or more components of the light-harvesting complex of photosystem II." [GOC:dph, GOC:tb]
synonym: "regulation of LHCII catabolism" EXACT [GOC:dph, GOC:tb, PMID:17416733]
synonym: "regulation of LHCII degradation" EXACT [PMID:17416733]
-is_a: GO:1903362 ! regulation of cellular protein catabolic process
+is_a: GO:0042176 ! regulation of protein catabolic process
relationship: regulates GO:0010304 ! PSII associated light-harvesting complex II catabolic process
[Term]
@@ -100483,8 +100500,8 @@ id: GO:0010559
name: regulation of glycoprotein biosynthetic process
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:dph, GOC:tb]
+is_a: GO:0010556 ! regulation of macromolecule biosynthetic process
is_a: GO:1903018 ! regulation of glycoprotein metabolic process
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
relationship: regulates GO:0009101 ! glycoprotein biosynthetic process
[Term]
@@ -100494,7 +100511,6 @@ namespace: biological_process
def: "Any process that increases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:dph, GOC:tb]
is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process
is_a: GO:0010559 ! regulation of glycoprotein biosynthetic process
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:1903020 ! positive regulation of glycoprotein metabolic process
relationship: positively_regulates GO:0009101 ! glycoprotein biosynthetic process
@@ -100503,9 +100519,9 @@ id: GO:0010561
name: negative regulation of glycoprotein biosynthetic process
namespace: biological_process
def: "Any process that decreases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:dph, GOC:tb]
+is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process
is_a: GO:0010559 ! regulation of glycoprotein biosynthetic process
is_a: GO:1903019 ! negative regulation of glycoprotein metabolic process
-is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process
relationship: negatively_regulates GO:0009101 ! glycoprotein biosynthetic process
[Term]
@@ -100597,7 +100613,7 @@ synonym: "positive regulation of DNA replication involved in S phase" EXACT []
synonym: "positive regulation of DNA replication involved in S-phase" EXACT []
is_a: GO:0033262 ! regulation of nuclear cell cycle DNA replication
is_a: GO:0090068 ! positive regulation of cell cycle process
-is_a: GO:2000105 ! positive regulation of DNA-dependent DNA replication
+is_a: GO:2000105 ! positive regulation of DNA-templated DNA replication
relationship: positively_regulates GO:0033260 ! nuclear DNA replication
[Term]
@@ -100802,16 +100818,18 @@ id: GO:0010598
name: NAD(P)H dehydrogenase complex (plastoquinone)
namespace: cellular_component
def: "Complex that possesses NAD(P)H dehydrogenase (plastoquinone) activity. The complex is one of the components of the electron transport chain. It is involved in electron transport from an unidentified electron donor, possibly NADH, NADPH or ferredoxin(Fd) to the plastoquinone pool." [PMID:15608332]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0010599
-name: production of lsiRNA involved in RNA interference
+name: lsiRNA processing
namespace: biological_process
-def: "Cleavage of double-stranded RNA to form lsiRNA (long small interfering RNA), a class of siRNAs 30 to 40 nt in length. lsiRNAs are induced by pathogen infection or under specific growth conditions." [PMID:18003861]
+def: "A process leading to the generation of a functional long small interfering RNA (lsiRNA). lsiRNAs are class of siRNAs 30 to 40 nt in length. lsiRNAs are induced by pathogen infection or under specific growth conditions." [PMID:18003861, PMID:20687832]
+synonym: "primary lsiRNA processing" EXACT []
+synonym: "production of lsiRNA involved in RNA interference" RELATED []
synonym: "RNA interference, production of lsiRNA" EXACT [GOC:mah]
-is_a: GO:0070918 ! production of small RNA involved in gene silencing by RNA
-relationship: part_of GO:0016246 ! RNA interference
+is_a: GO:0030422 ! siRNA processing
+relationship: part_of GO:0035194 ! ncRNA-mediated post-transcriptional gene silencing
[Term]
id: GO:0010600
@@ -100886,21 +100904,23 @@ relationship: negatively_regulates GO:0033962 ! P-body assembly
[Term]
id: GO:0010608
-name: posttranscriptional regulation of gene expression
+name: post-transcriptional regulation of gene expression
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript." [GOC:dph, GOC:tb]
+synonym: "posttranscriptional regulation of gene expression" EXACT []
is_a: GO:0010468 ! regulation of gene expression
[Term]
id: GO:0010609
-name: mRNA localization resulting in posttranscriptional regulation of gene expression
+name: mRNA localization resulting in post-transcriptional regulation of gene expression
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of gene expression after the production of a mRNA transcript by its transport into, or maintainance in, a specific location within the cell." [GOC:dph, GOC:tb]
synonym: "mRNA localisation resulting in posttranscriptional regulation of gene expression" EXACT []
+synonym: "mRNA localization resulting in posttranscriptional regulation of gene expression" EXACT []
synonym: "posttranscriptional regulation of gene expression by mRNA localisation" EXACT [GOC:mah]
synonym: "posttranscriptional regulation of gene expression by mRNA localization" EXACT []
is_a: GO:0008298 ! intracellular mRNA localization
-is_a: GO:0010608 ! posttranscriptional regulation of gene expression
+is_a: GO:0010608 ! post-transcriptional regulation of gene expression
[Term]
id: GO:0010610
@@ -100986,7 +101006,7 @@ is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
id: GO:0010619
name: adenylate cyclase-activating glucose-activated G protein-coupled receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of glucose binding to a G protein-coupled receptor, where the pathway proceeds with activation of adenylyl cyclase and a subsequent increase in the concentration of cyclic AMP (cAMP)." [GOC:dph, GOC:signaling, GOC:tb]
+def: "An adenylate cyclase-activating G protein-coupled receptor signaling pathway initiated by glucose binding to its receptor on the surface of the target cell, and ending with the regulation of a downstream cellular process." [GOC:dph, GOC:signaling, GOC:tb]
synonym: "activation of adenylate cyclase activity by glucose involved in G-protein signaling" EXACT [GOC:dph, GOC:tb]
synonym: "activation of adenylate cyclase activity by glucose-triggered G-protein signaling pathway" EXACT [GOC:signaling]
synonym: "activation of adenylate cyclase activity by glucose-triggered G-protein signalling pathway" EXACT [GOC:mah]
@@ -101000,7 +101020,7 @@ name: negative regulation of transcription by transcription factor catabolism
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the catabolism of a sequence-specific DNA-binding transcription factor by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome." [GOC:bf, GOC:dph, GOC:tb]
is_a: GO:0036369 ! transcription factor catabolic process
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
[Term]
id: GO:0010621
@@ -101008,8 +101028,8 @@ name: negative regulation of transcription by transcription factor localization
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the localization of a transcription factor." [GOC:dph, GOC:tb]
synonym: "negative regulation of transcription by transcription factor localisation" EXACT [GOC:mah]
-is_a: GO:0034613 ! cellular protein localization
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0008104 ! protein localization
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
[Term]
id: GO:0010622
@@ -101505,43 +101525,41 @@ is_a: GO:0051038 ! negative regulation of transcription involved in meiotic cell
[Term]
id: GO:0010675
-name: regulation of cellular carbohydrate metabolic process
+name: obsolete regulation of cellular carbohydrate metabolic process
namespace: biological_process
-def: "Any process that modulates the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:dph, GOC:tb]
-is_a: GO:0006109 ! regulation of carbohydrate metabolic process
-is_a: GO:0031323 ! regulation of cellular metabolic process
-relationship: regulates GO:0044262 ! cellular carbohydrate metabolic process
+def: "OBSOLETE. Any process that modulates the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it is not different from its parent, regulation of carbohydrate metabolic process ; GO:0006109.
+is_obsolete: true
+replaced_by: GO:0006109
[Term]
id: GO:0010676
-name: positive regulation of cellular carbohydrate metabolic process
+name: obsolete positive regulation of cellular carbohydrate metabolic process
namespace: biological_process
-def: "Any process that increases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:dph, GOC:tb]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
-is_a: GO:0031325 ! positive regulation of cellular metabolic process
-is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
-relationship: positively_regulates GO:0044262 ! cellular carbohydrate metabolic process
+def: "OBSOLETE. Any process that increases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it is not different from its parent, positive regulation of carbohydrate metabolic process ; GO:0045913.
+is_obsolete: true
+replaced_by: GO:0045913
[Term]
id: GO:0010677
-name: negative regulation of cellular carbohydrate metabolic process
+name: obsolete negative regulation of cellular carbohydrate metabolic process
namespace: biological_process
-def: "Any process that decreases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:dph, GOC:tb]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
-is_a: GO:0031324 ! negative regulation of cellular metabolic process
-is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
-relationship: negatively_regulates GO:0044262 ! cellular carbohydrate metabolic process
+def: "OBSOLETE. Any process that decreases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it is not different from its parent, negative regulation of carbohydrate metabolic process ; GO:0045912.
+is_obsolete: true
+replaced_by: GO:0045912
[Term]
id: GO:0010678
-name: negative regulation of cellular carbohydrate metabolic process by negative regulation of transcription, DNA-templated
+name: obsolete negative regulation of cellular carbohydrate metabolic process by negative regulation of transcription, DNA-templated
namespace: biological_process
-def: "Any cellular process that decreases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates carried out by repression of transcription." [GOC:dph, GOC:tb]
+def: "OBSOLETE. Any cellular process that decreases the rate, extent or frequency of the chemical reactions and pathways involving carbohydrates carried out by repression of transcription." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it is represents a GO-CAM model.
synonym: "negative regulation of cellular carbohydrate metabolic process by negative regulation of transcription, DNA-dependent" EXACT [GOC:txnOH]
synonym: "negative regulation of cellular carbohydrate metabolic process by repression of transcription" EXACT [GOC:bf, GOC:vw]
synonym: "negative regulation of cellular carbohydrate metabolic process by transcriptional repression" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_obsolete: true
[Term]
id: GO:0010679
@@ -102020,7 +102038,7 @@ name: protein glutathionylation
namespace: biological_process
def: "The protein modification process in which a glutathione molecule is added to a protein amino acid through a disulfide linkage." [GOC:BHF, GOC:dph, GOC:rl, GOC:tb]
synonym: "protein amino acid glutathionylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0010732
@@ -102053,10 +102071,12 @@ relationship: negatively_regulates GO:0010731 ! protein glutathionylation
[Term]
id: GO:0010735
-name: positive regulation of transcription via serum response element binding
+name: obsolete positive regulation of transcription via serum response element binding
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of the specifically regulated synthesis of RNA from DNA encoding a specific set of genes as a result of a transcription factor interacting with a serum response element (SRE). A serum response element is a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum." [GOC:BHF, GOC:dph, GOC:rl, GOC:tb]
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of the specifically regulated synthesis of RNA from DNA encoding a specific set of genes as a result of a transcription factor interacting with a serum response element (SRE). A serum response element is a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum." [GOC:BHF, GOC:dph, GOC:rl, GOC:tb]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0010736
[Term]
id: GO:0010736
@@ -102168,7 +102188,7 @@ relationship: negatively_regulates GO:0015911 ! long-chain fatty acid import acr
id: GO:0010749
name: regulation of nitric oxide mediated signal transduction
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is a series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
+def: "Any process that modulates the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
synonym: "regulation of nitric oxide-mediated signal transduction" EXACT []
is_a: GO:1902531 ! regulation of intracellular signal transduction
relationship: regulates GO:0007263 ! nitric oxide mediated signal transduction
@@ -102177,7 +102197,7 @@ relationship: regulates GO:0007263 ! nitric oxide mediated signal transduction
id: GO:0010750
name: positive regulation of nitric oxide mediated signal transduction
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is a series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
+def: "Any process that increases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
synonym: "positive regulation of nitric oxide-mediated signal transduction" EXACT []
is_a: GO:0010749 ! regulation of nitric oxide mediated signal transduction
is_a: GO:1902533 ! positive regulation of intracellular signal transduction
@@ -102187,7 +102207,7 @@ relationship: positively_regulates GO:0007263 ! nitric oxide mediated signal tra
id: GO:0010751
name: negative regulation of nitric oxide mediated signal transduction
namespace: biological_process
-def: "Any process that decreases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is a series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
+def: "Any process that decreases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
synonym: "negative regulation of nitric oxide-mediated signal transduction" EXACT []
is_a: GO:0010749 ! regulation of nitric oxide mediated signal transduction
is_a: GO:1902532 ! negative regulation of intracellular signal transduction
@@ -102197,7 +102217,7 @@ relationship: negatively_regulates GO:0007263 ! nitric oxide mediated signal tra
id: GO:0010752
name: regulation of cGMP-mediated signaling
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of cGMP-mediated signaling. cGMP-mediated signaling is a series of molecular signals in which a cell uses cyclic GMP to convert an extracellular signal into a response." [GOC:BHF, GOC:dph, GOC:tb]
+def: "Any process that modulates the rate, frequency or extent of cGMP-mediated signaling." [GOC:BHF, GOC:dph, GOC:tb]
synonym: "regulation of cGMP-mediated signalling" EXACT [GOC:mah]
is_a: GO:1902531 ! regulation of intracellular signal transduction
relationship: regulates GO:0019934 ! cGMP-mediated signaling
@@ -102206,7 +102226,7 @@ relationship: regulates GO:0019934 ! cGMP-mediated signaling
id: GO:0010753
name: positive regulation of cGMP-mediated signaling
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of cGMP-mediated signaling. cGMP-mediated signaling is a series of molecular signals in which a cell uses cyclic GMP to convert an extracellular signal into a response." [GOC:BHF, GOC:dph, GOC:tb]
+def: "Any process that increases the rate, frequency or extent of cGMP-mediated signaling." [GOC:BHF, GOC:dph, GOC:tb]
synonym: "positive regulation of cGMP-mediated signalling" EXACT [GOC:mah]
is_a: GO:0010752 ! regulation of cGMP-mediated signaling
is_a: GO:1902533 ! positive regulation of intracellular signal transduction
@@ -102216,7 +102236,7 @@ relationship: positively_regulates GO:0019934 ! cGMP-mediated signaling
id: GO:0010754
name: negative regulation of cGMP-mediated signaling
namespace: biological_process
-def: "Any process that decreases the rate, frequency or extent of cGMP-mediated signaling. cGMP-mediated signaling is a series of molecular signals in which a cell uses cyclic GMP to convert an extracellular signal into a response." [GOC:BHF, GOC:dph, GOC:tb]
+def: "Any process that decreases the rate, frequency or extent of cGMP-mediated signaling." [GOC:BHF, GOC:dph, GOC:tb]
synonym: "negative regulation of cGMP-mediated signalling" EXACT [GOC:mah]
is_a: GO:0010752 ! regulation of cGMP-mediated signaling
is_a: GO:1902532 ! negative regulation of intracellular signal transduction
@@ -102323,7 +102343,7 @@ name: positive regulation of sodium ion transport
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:tb]
is_a: GO:0002028 ! regulation of sodium ion transport
-is_a: GO:0043270 ! positive regulation of ion transport
+is_a: GO:0043270 ! positive regulation of monoatomic ion transport
relationship: positively_regulates GO:0006814 ! sodium ion transport
[Term]
@@ -102332,25 +102352,28 @@ name: negative regulation of sodium ion transport
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:tb]
is_a: GO:0002028 ! regulation of sodium ion transport
-is_a: GO:0043271 ! negative regulation of ion transport
+is_a: GO:0043271 ! negative regulation of monoatomic ion transport
relationship: negatively_regulates GO:0006814 ! sodium ion transport
[Term]
id: GO:0010767
-name: regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage
+name: obsolete regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a UV damage stimulus." [GOC:dph, GOC:tb]
-is_a: GO:0006974 ! cellular response to DNA damage stimulus
-is_a: GO:0034644 ! cellular response to UV
-is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a UV damage stimulus." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0006357
+consider: GO:0034644
[Term]
id: GO:0010768
-name: negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage
+name: obsolete negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage
namespace: biological_process
-def: "Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a UV damage stimulus." [GOC:dph, GOC:tb]
-is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:0010767 ! regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage
+def: "OBSOLETE. Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a UV damage stimulus." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0000122
+consider: GO:0034644
[Term]
id: GO:0010769
@@ -102523,7 +102546,6 @@ name: meiotic sister chromatid cohesion involved in meiosis I
namespace: biological_process
def: "The cell cycle process in which sister chromatids of a replicated chromosome are joined along the entire length of the chromosome during meiosis I." [GOC:dph, GOC:tb]
is_a: GO:0051177 ! meiotic sister chromatid cohesion
-relationship: part_of GO:0007127 ! meiosis I
[Term]
id: GO:0010790
@@ -102728,7 +102750,6 @@ id: GO:0010816
name: calcitonin catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of the peptide calcitonin." [GOC:BHF, GOC:rl]
-is_a: GO:0034754 ! cellular hormone metabolic process
is_a: GO:0042447 ! hormone catabolic process
is_a: GO:0043171 ! peptide catabolic process
@@ -102900,8 +102921,7 @@ name: regulation of protein ADP-ribosylation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein ADP-ribosylation. Protein ADP-ribosylation is the transfer, from NAD, of ADP-ribose to protein amino acids." [GOC:dph, GOC:tb]
synonym: "regulation of protein amino acid ADP-ribosylation" EXACT [GOC:bf]
-is_a: GO:0031399 ! regulation of protein modification process
-relationship: regulates GO:0006471 ! protein ADP-ribosylation
+is_a: GO:0051338 ! regulation of transferase activity
[Term]
id: GO:0010836
@@ -102910,8 +102930,7 @@ namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of protein ADP-ribosylation. Protein ADP-ribosylation is the transfer, from NAD, of ADP-ribose to protein amino acids." [GOC:BHF, GOC:dph, GOC:tb]
synonym: "negative regulation of protein amino acid ADP-ribosylation" EXACT [GOC:bf]
is_a: GO:0010835 ! regulation of protein ADP-ribosylation
-is_a: GO:0031400 ! negative regulation of protein modification process
-relationship: negatively_regulates GO:0006471 ! protein ADP-ribosylation
+is_a: GO:0051348 ! negative regulation of transferase activity
[Term]
id: GO:0010837
@@ -102955,7 +102974,6 @@ def: "Any process that increases the frequency, or extent of the wakeful phase o
is_a: GO:0010840 ! regulation of circadian sleep/wake cycle, wakefulness
is_a: GO:0042753 ! positive regulation of circadian rhythm
is_a: GO:0048520 ! positive regulation of behavior
-is_a: GO:0051240 ! positive regulation of multicellular organismal process
relationship: positively_regulates GO:0042746 ! circadian sleep/wake cycle, wakefulness
[Term]
@@ -103010,20 +103028,20 @@ is_a: GO:0010845 ! positive regulation of reciprocal meiotic recombination
[Term]
id: GO:0010847
-name: regulation of chromatin assembly
+name: obsolete regulation of chromatin assembly
namespace: biological_process
-def: "Any process the modulates the frequency, rate or extent of chromatin assembly. Chromatin assembly is the assembly of DNA, histone proteins, and other associated proteins into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus." [GOC:dph, GOC:tb]
-is_a: GO:0001672 ! regulation of chromatin assembly or disassembly
-is_a: GO:0044087 ! regulation of cellular component biogenesis
-relationship: regulates GO:0031497 ! chromatin assembly
+def: "OBSOLETE. Any process the modulates the frequency, rate or extent of chromatin assembly. Chromatin assembly is the assembly of DNA, histone proteins, and other associated proteins into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because 'chromatin assembly' was merged into 'chromatin organization'.
+is_obsolete: true
+replaced_by: GO:0006325
[Term]
id: GO:0010848
-name: regulation of chromatin disassembly
+name: obsolete regulation of chromatin disassembly
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of chromatin disassembly. Chromatin disassembly is the controlled breakdown of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, and other proteins." [GOC:dph, GOC:tb]
-is_a: GO:0001672 ! regulation of chromatin assembly or disassembly
-relationship: regulates GO:0031498 ! chromatin disassembly
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of chromatin disassembly. Chromatin disassembly is the controlled breakdown of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, and other proteins." [GOC:dph, GOC:tb]
+comment: This term has been obsoleted because this process doesn't happen independently from assembly and is always tied to chromatin remodeling.
+is_obsolete: true
[Term]
id: GO:0010849
@@ -103033,7 +103051,7 @@ def: "Any process that modulates the rate of ATP hydrolysis by an ATPase. Enable
synonym: "regulation of hydrogen ion transporting ATPase activity, rotational mechanism" EXACT [GOC:dph, GOC:tb]
synonym: "regulation of V-type ATPase activity" BROAD [GOC:dph, GOC:tb]
is_a: GO:0010155 ! regulation of proton transport
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
is_a: GO:0043462 ! regulation of ATP-dependent activity
[Term]
@@ -103056,7 +103074,7 @@ is_a: GO:0030234 ! enzyme regulator activity
id: GO:0010852
name: cyclase inhibitor activity
namespace: molecular_function
-def: "Decreases the activity of an enzyme that catalyzes a ring closure reaction." [GOC:dph, GOC:tb]
+def: "Binds to and decreases the activity of an enzyme that catalyzes a ring closure reaction." [GOC:dph, GOC:tb]
is_a: GO:0004857 ! enzyme inhibitor activity
is_a: GO:0010851 ! cyclase regulator activity
@@ -103064,30 +103082,32 @@ is_a: GO:0010851 ! cyclase regulator activity
id: GO:0010853
name: cyclase activator activity
namespace: molecular_function
-def: "Increases the activity of an enzyme that catalyzes a ring closure reaction." [GOC:dph, GOC:tb]
+def: "Binds to and increases the activity of an enzyme that catalyzes a ring closure reaction." [GOC:dph, GOC:tb]
+is_a: GO:0008047 ! enzyme activator activity
is_a: GO:0010851 ! cyclase regulator activity
[Term]
id: GO:0010854
name: adenylate cyclase regulator activity
namespace: molecular_function
-def: "Binds to and modulates the activity of the enzyme that catalyzes the reaction: ATP = 3',5'-cyclic AMP + diphosphate." [GOC:dph, GOC:tb]
-is_a: GO:0010852 ! cyclase inhibitor activity
+def: "Binds to and modulates the activity of adenylate cyclase." [GOC:dph, GOC:tb]
+is_a: GO:0010851 ! cyclase regulator activity
[Term]
id: GO:0010855
name: adenylate cyclase inhibitor activity
namespace: molecular_function
-def: "Decreases the activity of the enzyme that catalyzes the reaction: ATP = 3',5'-cyclic AMP + diphosphate." [GOC:dph, GOC:tb]
+def: "Binds to and decreases the activity adenylate cyclase." [GOC:dph, GOC:tb]
+is_a: GO:0010852 ! cyclase inhibitor activity
is_a: GO:0010854 ! adenylate cyclase regulator activity
[Term]
id: GO:0010856
name: adenylate cyclase activator activity
namespace: molecular_function
-def: "Increases the activity of the enzyme that catalyzes the reaction: ATP = 3',5'-cyclic AMP + diphosphate." [GOC:dph, GOC:tb]
-is_a: GO:0008047 ! enzyme activator activity
-is_a: GO:0010851 ! cyclase regulator activity
+def: "Binds to and increases the activity of adenylate cyclase." [GOC:dph, GOC:tb]
+is_a: GO:0010853 ! cyclase activator activity
+is_a: GO:0010854 ! adenylate cyclase regulator activity
[Term]
id: GO:0010857
@@ -103219,22 +103239,21 @@ is_obsolete: true
[Term]
id: GO:0010872
-name: regulation of cholesterol esterification
+name: obsolete regulation of cholesterol esterification
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of cholesterol esterification. Cholesterol esterification is the lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and cholesterol. In the blood this process is associated with the conversion of free cholesterol into cholesteryl ester, which is then sequestered into the core of a lipoprotein particle." [GOC:dph, GOC:tb]
-is_a: GO:0019218 ! regulation of steroid metabolic process
-is_a: GO:0031323 ! regulation of cellular metabolic process
-relationship: regulates GO:0034435 ! cholesterol esterification
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of cholesterol esterification. Cholesterol esterification is the lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and cholesterol. In the blood this process is associated with the conversion of free cholesterol into cholesteryl ester, which is then sequestered into the core of a lipoprotein particle." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0008203
[Term]
id: GO:0010873
-name: positive regulation of cholesterol esterification
+name: obsolete positive regulation of cholesterol esterification
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of cholesterol esterification. Cholesterol esterification is the lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and cholesterol. In the blood this process is associated with the conversion of free cholesterol into cholesteryl ester, which is then sequestered into the core of a lipoprotein particle." [GOC:BHF, GOC:dph, GOC:tb]
-is_a: GO:0010872 ! regulation of cholesterol esterification
-is_a: GO:0031325 ! positive regulation of cellular metabolic process
-is_a: GO:0045940 ! positive regulation of steroid metabolic process
-relationship: positively_regulates GO:0034435 ! cholesterol esterification
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of cholesterol esterification. Cholesterol esterification is the lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and cholesterol. In the blood this process is associated with the conversion of free cholesterol into cholesteryl ester, which is then sequestered into the core of a lipoprotein particle." [GOC:BHF, GOC:dph, GOC:tb]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0008203
[Term]
id: GO:0010874
@@ -103433,7 +103452,7 @@ id: GO:0010895
name: negative regulation of ergosterol biosynthetic process
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ergosterol." [GOC:tb]
-is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
+is_a: GO:0031324 ! negative regulation of cellular metabolic process
is_a: GO:0032443 ! regulation of ergosterol biosynthetic process
is_a: GO:0106119 ! negative regulation of sterol biosynthetic process
is_a: GO:1902931 ! negative regulation of alcohol biosynthetic process
@@ -103535,7 +103554,8 @@ synonym: "regulation of UDP-glucose catabolism" EXACT [GOC:tb]
is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
is_a: GO:0010906 ! regulation of glucose metabolic process
is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
+is_a: GO:0031329 ! regulation of cellular catabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
is_a: GO:0051174 ! regulation of phosphorus metabolic process
relationship: regulates GO:0006258 ! UDP-glucose catabolic process
@@ -103546,9 +103566,9 @@ namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of UDP-glucose catabolism. UDP-glucose catabolic processes are the chemical reactions and pathways resulting in the breakdown of UDP-glucose, uridinediphosphoglucose, a substance composed of glucose in glycosidic linkage with uridine diphosphate." [GOC:BHF, GOC:tb]
synonym: "negative regulation of UDP-glucose catabolism" EXACT [GOC:tb]
is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
is_a: GO:0010904 ! regulation of UDP-glucose catabolic process
is_a: GO:0031330 ! negative regulation of cellular catabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
relationship: negatively_regulates GO:0006258 ! UDP-glucose catabolic process
@@ -103559,7 +103579,7 @@ name: regulation of glucose metabolic process
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose." [GOC:BHF, GOC:tb]
synonym: "regulation of glucose metabolism" EXACT [GOC:tb]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
+is_a: GO:0006109 ! regulation of carbohydrate metabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
relationship: regulates GO:0006006 ! glucose metabolic process
@@ -103569,8 +103589,8 @@ name: positive regulation of glucose metabolic process
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose." [GOC:BHF, GOC:tb]
synonym: "positive regulation of glucose metabolism" EXACT [GOC:tb]
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
is_a: GO:0010906 ! regulation of glucose metabolic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
relationship: positively_regulates GO:0006006 ! glucose metabolic process
@@ -103580,6 +103600,8 @@ name: regulation of heparan sulfate proteoglycan biosynthetic process
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of heparan sulfate proteoglycan biosynthesis. Heparan sulfate proteoglycan biosynthetic processes are the chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues." [GOC:dph, GOC:tb]
is_a: GO:0010559 ! regulation of glycoprotein biosynthetic process
+is_a: GO:0031326 ! regulation of cellular biosynthetic process
+is_a: GO:0042762 ! regulation of sulfur metabolic process
relationship: regulates GO:0015012 ! heparan sulfate proteoglycan biosynthetic process
[Term]
@@ -103588,6 +103610,8 @@ name: positive regulation of heparan sulfate proteoglycan biosynthetic process
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of heparan sulfate proteoglycan biosynthesis. Heparan sulfate proteoglycan biosynthetic processes are the chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues." [GOC:dph, GOC:tb]
is_a: GO:0010908 ! regulation of heparan sulfate proteoglycan biosynthetic process
+is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
+is_a: GO:0051176 ! positive regulation of sulfur metabolic process
is_a: GO:1902730 ! positive regulation of proteoglycan biosynthetic process
relationship: positively_regulates GO:0015012 ! heparan sulfate proteoglycan biosynthetic process
@@ -103678,7 +103702,6 @@ name: regulation of inositol phosphate biosynthetic process
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of inositol phosphate biosynthesis. Inositol phosphate biosynthetic processes are the chemical reactions and pathways resulting in the formation of an inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached." [GOC:BHF, GOC:dph, GOC:tb]
synonym: "regulation of inositol phosphate biosynthesis" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:0019220 ! regulation of phosphate metabolic process
is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0043255 ! regulation of carbohydrate biosynthetic process
@@ -103691,9 +103714,9 @@ name: negative regulation of inositol phosphate biosynthetic process
namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of inositol phosphate biosynthesis. Inositol phosphate biosynthetic processes are the chemical reactions and pathways resulting in the formation of an inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached." [GOC:dph, GOC:tb]
synonym: "negative regulation of inositol phosphate biosynthesis" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
is_a: GO:0010919 ! regulation of inositol phosphate biosynthetic process
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:0045936 ! negative regulation of phosphate metabolic process
is_a: GO:1902931 ! negative regulation of alcohol biosynthetic process
relationship: negatively_regulates GO:0032958 ! inositol phosphate biosynthetic process
@@ -103892,15 +103915,15 @@ relationship: positively_regulates GO:0008219 ! cell death
id: GO:0010943
name: NADPH pyrophosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADPH + H2O = NMNH + ADP." [GOC:tb]
-is_a: GO:0004551 ! nucleotide diphosphatase activity
+def: "Catalysis of the reaction: NADPH + H2O = NMNH + ADP." [GOC:tb, PMID:12790796, RHEA:60820]
+is_a: GO:0004551 ! dinucleotide phosphatase activity
[Term]
id: GO:0010944
name: negative regulation of transcription by competitive promoter binding
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves direct competition for interaction with a promoter binding site." [GOC:tb]
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
[Term]
id: GO:0010945
@@ -104032,7 +104055,7 @@ id: GO:0010959
name: regulation of metal ion transport
namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of metal ion transport. Metal ion transport is the directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:tb]
-is_a: GO:0043269 ! regulation of ion transport
+is_a: GO:0043269 ! regulation of monoatomic ion transport
relationship: regulates GO:0030001 ! metal ion transport
[Term]
@@ -104040,37 +104063,37 @@ id: GO:0010960
name: magnesium ion homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of magnesium ions within an organism or cell." [GOC:dph, GOC:tb]
-is_a: GO:0055065 ! metal ion homeostasis
-is_a: GO:0072507 ! divalent inorganic cation homeostasis
+is_a: GO:0055080 ! monoatomic cation homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0010961
-name: cellular magnesium ion homeostasis
+name: intracellular magnesium ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of magnesium ions at the level of a cell." [GOC:dph, GOC:tb]
-is_a: GO:0006875 ! cellular metal ion homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of magnesium ions within a cell." [GOC:dph, GOC:tb]
+synonym: "cellular magnesium ion homeostasis" EXACT []
is_a: GO:0010960 ! magnesium ion homeostasis
-is_a: GO:0072503 ! cellular divalent inorganic cation homeostasis
+is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
[Term]
id: GO:0010962
name: regulation of glucan biosynthetic process
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of glucan biosynthesis. Glucan biosynthetic processes are the chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues." [GOC:dph, GOC:tb]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:0032885 ! regulation of polysaccharide biosynthetic process
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
relationship: regulates GO:0009250 ! glucan biosynthetic process
[Term]
id: GO:0010964
-name: regulation of heterochromatin assembly by small RNA
+name: regulation of small non-coding RNA-mediated heterochromatin formation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of heterochromatin assembly by small RNA." [GOC:dph, GOC:tb]
+def: "Any process that modulates the frequency, rate or extent of small non-coding RNA-mediated heterochromatin formation." [GOC:dph, GOC:tb]
synonym: "regulation of chromatin silencing by small RNA" RELATED []
+synonym: "regulation of heterochromatin assembly by small RNA" EXACT []
synonym: "regulation of RNAi-mediated heterochromatin assembly" EXACT []
-is_a: GO:0031445 ! regulation of heterochromatin assembly
-relationship: regulates GO:0031048 ! heterochromatin assembly by small RNA
+is_a: GO:0031445 ! regulation of heterochromatin formation
+is_a: GO:0060966 ! regulation of gene silencing by RNA
+relationship: regulates GO:0031048 ! small ncRNA-mediated heterochromatin formation
[Term]
id: GO:0010965
@@ -104085,7 +104108,7 @@ id: GO:0010966
name: regulation of phosphate transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of phosphate transport. Phosphate transport is the directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:tb]
-is_a: GO:0044070 ! regulation of anion transport
+is_a: GO:0051049 ! regulation of transport
relationship: regulates GO:0006817 ! phosphate ion transport
[Term]
@@ -104094,7 +104117,7 @@ name: regulation of polyamine biosynthetic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of polyamine biosynthesis. Polyamine biosynthesis is the chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups." [GOC:dph, GOC:tb]
is_a: GO:0031326 ! regulation of cellular biosynthetic process
-is_a: GO:0033238 ! regulation of cellular amine metabolic process
+is_a: GO:0033238 ! regulation of amine metabolic process
is_a: GO:0080090 ! regulation of primary metabolic process
relationship: regulates GO:0006596 ! polyamine biosynthetic process
@@ -104122,6 +104145,7 @@ def: "The movement of organelles or other particles from one location in the cel
synonym: "establishment of localization by movement along microtubule" EXACT [GOC:dph]
synonym: "microtubule-based transport" BROAD []
synonym: "movement along microtubule" EXACT []
+is_a: GO:0007018 ! microtubule-based movement
is_a: GO:0030705 ! cytoskeleton-dependent intracellular transport
is_a: GO:0099111 ! microtubule-based transport
@@ -104245,7 +104269,6 @@ id: GO:0010981
name: regulation of cell wall macromolecule metabolic process
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of cell wall macromolecule metabolism. Cell wall macromolecule metabolic processes are the chemical reactions and pathways involving macromolecules forming, or destined to form, part of the cell wall. A cell wall is a rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis." [GOC:dph, GOC:tb]
-is_a: GO:0031323 ! regulation of cellular metabolic process
is_a: GO:0060255 ! regulation of macromolecule metabolic process
relationship: regulates GO:0044036 ! cell wall macromolecule metabolic process
@@ -104414,7 +104437,13 @@ namespace: biological_process
alt_id: GO:0016244
def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis]
comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children.
+subset: goslim_agr
+subset: goslim_chembl
+subset: goslim_drosophila
subset: goslim_generic
+subset: goslim_mouse
+subset: goslim_plant
+subset: prokaryote_subset
synonym: "caspase-independent apoptosis" RELATED []
synonym: "caspase-independent cell death" NARROW []
synonym: "non-apoptotic programmed cell death" NARROW []
@@ -104440,7 +104469,6 @@ id: GO:0012505
name: endomembrane system
namespace: cellular_component
def: "A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles." [GOC:lh]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_flybase_ribbon
subset: goslim_yeast
@@ -104708,7 +104736,9 @@ relationship: part_of GO:0014016 ! neuroblast differentiation
id: GO:0014020
name: primary neural tube formation
namespace: biological_process
-def: "The formation of the neural tube from an epithelial cell sheet (the neuroepithelium or neural plate). In primary neurulation, the cells surrounding the neural plate direct the neural plate cells to proliferate, invaginate, and pinch off from the surface to form a hollow epithelial tube. Primary neurulation is the typical mechanism of formation of the anterior neural tube." [GOC:ef, ISBN:0878932585]
+alt_id: GO:0014024
+def: "The formation of the neural tube from an epithelial cell sheet (the neuroepithelium or neural plate). In primary neurulation, the cells surrounding the neural plate direct the neural plate cells to proliferate, invaginate, and pinch off from the surface to form a hollow epithelial tube. Primary neurulation is the typical mechanism of formation of the anterior neural tube." [GOC:ef, ISBN:0878932585, PMID:15327780]
+synonym: "neural rod cavitation" RELATED []
synonym: "primary neural tube morphogenesis" EXACT [GOC:dph]
synonym: "primary neurulation" EXACT []
is_a: GO:0001838 ! embryonic epithelial tube formation
@@ -104719,10 +104749,13 @@ id: GO:0014021
name: secondary neural tube formation
namespace: biological_process
alt_id: GO:0014026
-def: "The formation of the neural tube by coalescence of mesenchymal cells followed by their conversion to epithelial cells to form a solid cord that subsequently hollows out (cavitates) to create a hollow tube. Secondary neurulation is the typical mechanism of formation of the neural tube posterior to the posterior neuropore in mammals." [GOC:ef, ISBN:0878932585]
+alt_id: GO:0014027
+def: "The formation of the neural tube by coalescence of mesenchymal cells followed by their conversion to epithelial cells to form a solid cord that subsequently hollows out (cavitates) to create a hollow tube. Secondary neurulation is the typical mechanism of formation of the neural tube posterior to the posterior neuropore in mammals." [GOC:ef, ISBN:0878932585, PMID:15327780]
synonym: "medullary cord biosynthesis" EXACT []
synonym: "medullary cord formation" EXACT []
+synonym: "medullary rod cavitation" RELATED []
synonym: "neural rod formation" RELATED []
+synonym: "secondary neural tube rod cavitation" RELATED []
synonym: "secondary neurulation" EXACT []
is_a: GO:0001838 ! embryonic epithelial tube formation
relationship: part_of GO:0001841 ! neural tube formation
@@ -104744,14 +104777,6 @@ def: "The formation of a solid rod of neurectoderm derived from the neural keel.
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
relationship: part_of GO:0014020 ! primary neural tube formation
-[Term]
-id: GO:0014024
-name: neural rod cavitation
-namespace: biological_process
-def: "The process of rod cavitation, which is the formation of a lumen in the neural rod during primary neurulation, producing the neural tube." [GOC:ef, PMID:15327780]
-is_a: GO:0060605 ! tube lumen cavitation
-relationship: part_of GO:0014020 ! primary neural tube formation
-
[Term]
id: GO:0014025
name: neural keel formation
@@ -104760,15 +104785,6 @@ def: "The formation of a thickened region of the neurectoderm that is roughly tr
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
relationship: part_of GO:0014023 ! neural rod formation
-[Term]
-id: GO:0014027
-name: secondary neural tube rod cavitation
-namespace: biological_process
-def: "The process of medullary cavitation, which is the formation of a lumen in the medullary cord during secondary neurulation, producing the neural tube." [GOC:ef, PMID:15327780]
-synonym: "medullary rod cavitation" EXACT []
-is_a: GO:0060605 ! tube lumen cavitation
-relationship: part_of GO:0014021 ! secondary neural tube formation
-
[Term]
id: GO:0014028
name: notochord formation
@@ -104808,7 +104824,6 @@ id: GO:0014032
name: neural crest cell development
namespace: biological_process
def: "The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." [GOC:dh, GOC:ef]
-is_a: GO:0014031 ! mesenchymal cell development
is_a: GO:0048864 ! stem cell development
relationship: part_of GO:0014033 ! neural crest cell differentiation
@@ -104959,13 +104974,13 @@ def: "The controlled release of glutamate by a cell. The glutamate is the most a
is_a: GO:0006835 ! dicarboxylic acid transport
is_a: GO:0015800 ! acidic amino acid transport
is_a: GO:0032940 ! secretion by cell
+is_a: GO:0042886 ! amide transport
[Term]
id: GO:0014048
name: regulation of glutamate secretion
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the controlled release of glutamate." [GOC:ef]
-is_a: GO:0044070 ! regulation of anion transport
is_a: GO:0051955 ! regulation of amino acid transport
is_a: GO:1903530 ! regulation of secretion by cell
relationship: regulates GO:0014047 ! glutamate secretion
@@ -104983,7 +104998,6 @@ synonym: "upregulation of glutamate secretion" EXACT []
is_a: GO:0014048 ! regulation of glutamate secretion
is_a: GO:0051957 ! positive regulation of amino acid transport
is_a: GO:1903532 ! positive regulation of secretion by cell
-is_a: GO:1903793 ! positive regulation of anion transport
relationship: positively_regulates GO:0014047 ! glutamate secretion
[Term]
@@ -104998,7 +105012,6 @@ synonym: "inhibition of glutamate secretion" NARROW []
is_a: GO:0014048 ! regulation of glutamate secretion
is_a: GO:0051956 ! negative regulation of amino acid transport
is_a: GO:1903531 ! negative regulation of secretion by cell
-is_a: GO:1903792 ! negative regulation of anion transport
relationship: negatively_regulates GO:0014047 ! glutamate secretion
[Term]
@@ -105016,7 +105029,6 @@ name: regulation of gamma-aminobutyric acid secretion
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the regulated release of gamma-aminobutyric acid." [GOC:ef]
synonym: "regulation of GABA secretion" EXACT []
-is_a: GO:0044070 ! regulation of anion transport
is_a: GO:0051046 ! regulation of secretion
is_a: GO:0051955 ! regulation of amino acid transport
relationship: regulates GO:0014051 ! gamma-aminobutyric acid secretion
@@ -105034,7 +105046,6 @@ synonym: "negative regulation of GABA secretion" EXACT []
is_a: GO:0014052 ! regulation of gamma-aminobutyric acid secretion
is_a: GO:0051048 ! negative regulation of secretion
is_a: GO:0051956 ! negative regulation of amino acid transport
-is_a: GO:1903792 ! negative regulation of anion transport
relationship: negatively_regulates GO:0014051 ! gamma-aminobutyric acid secretion
[Term]
@@ -105051,7 +105062,6 @@ synonym: "upregulation of gamma-aminobutyric acid secretion" EXACT []
is_a: GO:0014052 ! regulation of gamma-aminobutyric acid secretion
is_a: GO:0051047 ! positive regulation of secretion
is_a: GO:0051957 ! positive regulation of amino acid transport
-is_a: GO:1903793 ! positive regulation of anion transport
relationship: positively_regulates GO:0014051 ! gamma-aminobutyric acid secretion
[Term]
@@ -105069,7 +105079,6 @@ name: regulation of acetylcholine secretion, neurotransmission
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the regulated release of acetylcholine." [GOC:ef]
is_a: GO:0032222 ! regulation of synaptic transmission, cholinergic
-is_a: GO:0043269 ! regulation of ion transport
is_a: GO:0046928 ! regulation of neurotransmitter secretion
is_a: GO:0051952 ! regulation of amine transport
relationship: regulates GO:0014055 ! acetylcholine secretion, neurotransmission
@@ -105087,7 +105096,6 @@ synonym: "upregulation of acetylcholine secretion" EXACT []
is_a: GO:0001956 ! positive regulation of neurotransmitter secretion
is_a: GO:0014056 ! regulation of acetylcholine secretion, neurotransmission
is_a: GO:0032224 ! positive regulation of synaptic transmission, cholinergic
-is_a: GO:0043270 ! positive regulation of ion transport
is_a: GO:0051954 ! positive regulation of amine transport
relationship: positively_regulates GO:0014055 ! acetylcholine secretion, neurotransmission
@@ -105102,7 +105110,6 @@ synonym: "downregulation of acetylcholine secretion" EXACT []
synonym: "inhibition of acetylcholine secretion" NARROW []
is_a: GO:0014056 ! regulation of acetylcholine secretion, neurotransmission
is_a: GO:0032223 ! negative regulation of synaptic transmission, cholinergic
-is_a: GO:0043271 ! negative regulation of ion transport
is_a: GO:0046929 ! negative regulation of neurotransmitter secretion
is_a: GO:0051953 ! negative regulation of amine transport
relationship: negatively_regulates GO:0014055 ! acetylcholine secretion, neurotransmission
@@ -105112,7 +105119,6 @@ id: GO:0014059
name: regulation of dopamine secretion
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the regulated release of dopamine." [GOC:ef]
-is_a: GO:0043269 ! regulation of ion transport
is_a: GO:0050433 ! regulation of catecholamine secretion
relationship: regulates GO:0014046 ! dopamine secretion
@@ -105140,7 +105146,7 @@ name: regulation of serotonin secretion
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the regulated release of serotonin." [GOC:ef]
synonym: "regulation of serotonin release" RELATED [GOC:tb]
-is_a: GO:0043269 ! regulation of ion transport
+is_a: GO:0043269 ! regulation of monoatomic ion transport
is_a: GO:1903530 ! regulation of secretion by cell
relationship: regulates GO:0001820 ! serotonin secretion
@@ -105155,7 +105161,7 @@ synonym: "downregulation of serotonin secretion" EXACT []
synonym: "inhibition of serotonin secretion" NARROW []
synonym: "positive regulation of serotonin release" RELATED [GOC:tb]
is_a: GO:0014062 ! regulation of serotonin secretion
-is_a: GO:0043271 ! negative regulation of ion transport
+is_a: GO:0043271 ! negative regulation of monoatomic ion transport
is_a: GO:1903531 ! negative regulation of secretion by cell
relationship: negatively_regulates GO:0001820 ! serotonin secretion
@@ -105171,7 +105177,7 @@ synonym: "up regulation of serotonin secretion" EXACT []
synonym: "up-regulation of serotonin secretion" EXACT []
synonym: "upregulation of serotonin secretion" EXACT []
is_a: GO:0014062 ! regulation of serotonin secretion
-is_a: GO:0043270 ! positive regulation of ion transport
+is_a: GO:0043270 ! positive regulation of monoatomic ion transport
is_a: GO:1903532 ! positive regulation of secretion by cell
relationship: positively_regulates GO:0001820 ! serotonin secretion
@@ -105396,6 +105402,7 @@ id: GO:0014711
name: regulation of branchiomeric skeletal muscle development
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of branchiomeric skeletal muscle development. Branchiomeric skeletal muscle development is the process whose specific outcome is the progression of the branchiomeric skeletal muscle over time, from its formation to the mature structure." [GOC:mtg_muscle]
+is_a: GO:0048634 ! regulation of muscle organ development
is_a: GO:0048641 ! regulation of skeletal muscle tissue development
relationship: regulates GO:0014707 ! branchiomeric skeletal muscle development
@@ -105405,6 +105412,7 @@ name: positive regulation of branchiomeric skeletal muscle development
namespace: biological_process
def: "Any process that activates, maintains or increases the frequency, rate or extent of branchiomeric skeletal muscle development. Branchiomeric skeletal muscle development is the process whose specific outcome is the progression of the branchiomeric skeletal muscle over time, from its formation to the mature structure." [GOC:mtg_muscle]
is_a: GO:0014711 ! regulation of branchiomeric skeletal muscle development
+is_a: GO:0048636 ! positive regulation of muscle organ development
is_a: GO:0048643 ! positive regulation of skeletal muscle tissue development
relationship: positively_regulates GO:0014707 ! branchiomeric skeletal muscle development
@@ -105414,6 +105422,7 @@ name: negative regulation of branchiomeric skeletal muscle development
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of branchiomeric skeletal muscle development. Branchiomeric skeletal muscle development is the process whose specific outcome is the progression of the branchiomeric skeletal muscle over time, from its formation to the mature structure." [GOC:mtg_muscle]
is_a: GO:0014711 ! regulation of branchiomeric skeletal muscle development
+is_a: GO:0048635 ! negative regulation of muscle organ development
is_a: GO:0048642 ! negative regulation of skeletal muscle tissue development
relationship: negatively_regulates GO:0014707 ! branchiomeric skeletal muscle development
@@ -105464,7 +105473,7 @@ relationship: positively_regulates GO:0014901 ! satellite cell activation involv
id: GO:0014719
name: skeletal muscle satellite cell activation
namespace: biological_process
-def: "The change of a skeletal muscle satellite cell from a mitotically quiescent to a mitotically active state following exposure to some activating factor such as a cellular or soluble ligand. In adult muscle, satellite cells become activated to divide and differentiate in response to muscle damage." [GOC:mtg_muscle, PMID:23303905]
+def: "The change of a skeletal muscle satellite cell from a mitotically quiescent to a mitotically active state following exposure to some activating factor such as a cellular or soluble ligand. In adult muscle, satellite cells become activated to divide and differentiate in response to muscle damage." [GOC:mtg_muscle, PMID:23303905]
is_a: GO:0001775 ! cell activation
[Term]
@@ -105511,6 +105520,7 @@ id: GO:0014725
name: regulation of extraocular skeletal muscle development
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of extraocular skeletal muscle development. Extraocular skeletal muscle development is the process whose specific outcome is the progression of the extraocular skeletal muscle over time, from its formation to the mature structure. The extraocular muscle is derived from cranial mesoderm and controls eye movements. The muscle begins its development with the differentiation of the muscle cells and ends with the mature muscle." [GOC:mtg_muscle]
+is_a: GO:0048634 ! regulation of muscle organ development
is_a: GO:0048641 ! regulation of skeletal muscle tissue development
relationship: regulates GO:0002074 ! extraocular skeletal muscle development
@@ -105520,6 +105530,7 @@ name: negative regulation of extraocular skeletal muscle development
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of extraocular skeletal muscle development. Extraocular skeletal muscle development is the process whose specific outcome is the progression of the extraocular skeletal muscle over time, from its formation to the mature structure. The extraocular muscle is derived from cranial mesoderm and controls eye movements. The muscle begins its development with the differentiation of the muscle cells and ends with the mature muscle." [GOC:mtg_muscle]
is_a: GO:0014725 ! regulation of extraocular skeletal muscle development
+is_a: GO:0048635 ! negative regulation of muscle organ development
is_a: GO:0048642 ! negative regulation of skeletal muscle tissue development
relationship: negatively_regulates GO:0002074 ! extraocular skeletal muscle development
@@ -105529,6 +105540,7 @@ name: positive regulation of extraocular skeletal muscle development
namespace: biological_process
def: "Any process that activates, maintains or increases the frequency, rate or extent of extraocular skeletal muscle development. Extraocular skeletal muscle development is the process whose specific outcome is the progression of the extraocular skeletal muscle over time, from its formation to the mature structure. The extraocular muscle is derived from cranial mesoderm and controls eye movements. The muscle begins its development with the differentiation of the muscle cells and ends with the mature muscle." [GOC:mtg_muscle]
is_a: GO:0014725 ! regulation of extraocular skeletal muscle development
+is_a: GO:0048636 ! positive regulation of muscle organ development
is_a: GO:0048643 ! positive regulation of skeletal muscle tissue development
relationship: positively_regulates GO:0002074 ! extraocular skeletal muscle development
@@ -105978,7 +105990,7 @@ relationship: part_of GO:0007519 ! skeletal muscle tissue development
id: GO:0014834
name: skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration
namespace: biological_process
-def: "Any process by which the number of skeletal muscle satellite cells in a skeletal muscle is maintained during muscle regeneration. There are at least three mechanisms by which this is achieved. Skeletal muscle satellite stem cell asymmetric division ensures satellite stem cell numbers are kept constant. Symmetric division of these cells amplifies the number of skeletal muscle satellite stem cells. Some adult skeletal muscle myoblasts (descendants of activated satellite cells) can develop back into quiescent satellite cells, replenishing the overall pool of satellite cells." [GOC:dph, GOC:ef, GOC:mtg_muscle, GOC:tb, PMID:23303905]
+def: "Any process by which the number of skeletal muscle satellite cells in a skeletal muscle is maintained during muscle regeneration. There are at least three mechanisms by which this is achieved. Skeletal muscle satellite stem cell asymmetric division ensures satellite stem cell numbers are kept constant. Symmetric division of these cells amplifies the number of skeletal muscle satellite stem cells. Some adult skeletal muscle myoblasts (descendants of activated satellite cells) can develop back into quiescent satellite cells, replenishing the overall pool of satellite cells." [GOC:dph, GOC:ef, GOC:mtg_muscle, GOC:tb, PMID:23303905]
synonym: "satellite cell compartment self-renewal involved in skeletal muscle regeneration" EXACT [GOC:dph, GOC:tb]
synonym: "satellite cell population maintenance" EXACT []
synonym: "satellite cell self-renewal" BROAD []
@@ -106730,7 +106742,7 @@ synonym: "heparan sulphate proteoglycan biosynthetic process" EXACT []
synonym: "heparin proteoglycan biosynthetic process" RELATED []
xref: RESID:AA0210
is_a: GO:0030166 ! proteoglycan biosynthetic process
-is_a: GO:0030201 ! heparan sulfate proteoglycan metabolic process
+is_a: GO:0044272 ! sulfur compound biosynthetic process
[Term]
id: GO:0015013
@@ -106760,7 +106772,7 @@ synonym: "heparan sulfate proteoglycan synthesis, polysaccharide chain synthesis
synonym: "heparan sulphate proteoglycan biosynthesis, polysaccharide chain biosynthesis" EXACT []
synonym: "heparan sulphate proteoglycan biosynthesis, polysaccharide chain biosynthetic process" EXACT []
synonym: "heparin proteoglycan biosynthetic process, polysaccharide chain biosynthetic process" RELATED []
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
+is_a: GO:0000271 ! polysaccharide biosynthetic process
relationship: part_of GO:0015012 ! heparan sulfate proteoglycan biosynthetic process
[Term]
@@ -106921,6 +106933,7 @@ synonym: "uridine diphosphoglucuronosyltransferase activity" RELATED [EC:2.4.1.1
synonym: "uridine diphosphoglucuronyltransferase activity" RELATED [EC:2.4.1.17]
xref: EC:2.4.1.17
xref: MetaCyc:UDP-GLUCURONOSYLTRANSFERASE-RXN
+xref: Reactome:R-HSA-158546 "UGTs glucuronate APAP to APAP-GlcA"
xref: Reactome:R-HSA-159179 "UGT1A4 transfers GlcA from UDP-GlcA to BMG to form BDG"
xref: Reactome:R-HSA-159194 "UGT1A4 transfers GlcA from UDP-GlcA to BIL to form BMG"
xref: Reactome:R-HSA-174916 "Formation of N-glucuronides"
@@ -106935,6 +106948,11 @@ xref: Reactome:R-HSA-9036104 "Defective UGT1A4 does not transfer GlcA from UDP-G
xref: Reactome:R-HSA-9632038 "UGT1A1 tetramer transfers GlcA from UDP-GlcA to BMG to form BDG"
xref: Reactome:R-HSA-9632039 "UGT1A1 transfers GlcA from UDP-GlcA to BIL to form BMG"
xref: Reactome:R-HSA-9638097 "B4GAT1:LARGE transfers GlcA from UDP-GlcA to Xyl-GlcA"
+xref: Reactome:R-HSA-9749977 "UGT1A6 glucuronates ST"
+xref: Reactome:R-HSA-9756134 "UGT1A3 lactonizes 2-OH-ATV to 2-OH-ATVL"
+xref: Reactome:R-HSA-9756156 "UGT1A3 lactonizes ATV to ATVL"
+xref: Reactome:R-HSA-9756183 "UGT1A3 lactonizes 4-OH-ATV to 4-OH-ATVL"
+xref: Reactome:R-HSA-9758661 "UGT2B7,2B17,1A3 glucuronidates PRED metabolites"
xref: RHEA:21032
is_a: GO:0008194 ! UDP-glycosyltransferase activity
is_a: GO:0016758 ! hexosyltransferase activity
@@ -106984,7 +107002,6 @@ def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:ai]
comment: This term was made obsolete because it contains both component and function information.
synonym: "GPI-anchored membrane-bound receptor" EXACT []
is_obsolete: true
-replaced_by: GO:0031225
[Term]
id: GO:0015026
@@ -107074,7 +107091,9 @@ synonym: "protein disulfide-oxidoreductase activity" EXACT []
synonym: "protein disulphide oxidoreductase activity" EXACT []
xref: MetaCyc:DISULFOXRED-RXN
xref: Reactome:R-HSA-1307802 "MIA40:ERV1 (CHCHD4:GFER) oxidizes cysteine residues to cystine disulfide bonds"
+xref: Reactome:R-HSA-264997 "P4HB mediates disulfide bond formation in Proinsulin"
xref: Reactome:R-HSA-3299753 "CCS transfers Cu to SOD1 and oxidizes cysteine residues in SOD1"
+xref: Reactome:R-HSA-9817575 "ERO1B oxidizes P4HB"
is_a: GO:0015036 ! disulfide oxidoreductase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -107088,7 +107107,6 @@ xref: Reactome:R-HSA-1222417 "TrxA reactivates AhpC"
xref: Reactome:R-HSA-1222644 "TrxA/B1 reactivates Tpx"
xref: Reactome:R-HSA-1222655 "AhpD reactivates AhpC"
xref: Reactome:R-HSA-1222690 "DlaT reactivates AhpD"
-xref: Reactome:R-HSA-264997 "Oxidation of cysteine to cystine in Proinsulin"
is_a: GO:0016667 ! oxidoreductase activity, acting on a sulfur group of donors
[Term]
@@ -107278,7 +107296,6 @@ synonym: "opsin" EXACT []
is_obsolete: true
consider: GO:0007602
consider: GO:0009881
-consider: GO:0016021
consider: GO:0016918
consider: GO:0046876
@@ -107312,7 +107329,7 @@ alt_id: GO:0010655
def: "A G protein-coupled receptor activity that is activated by cleavage by thrombin, which exposes a tethered ligand corresponding to the new N-terminus, which binds to the receptor and activates it." [GOC:ai, GOC:pg, PMID:20423334]
synonym: "thrombin receptor activity" EXACT []
synonym: "thrombin receptor activity, G-protein coupled" EXACT []
-is_a: GO:0008528 ! G protein-coupled peptide receptor activity
+is_a: GO:0001648 ! proteinase-activated receptor activity
[Term]
id: GO:0015058
@@ -107337,7 +107354,6 @@ is_obsolete: true
consider: GO:0007603
consider: GO:0009588
consider: GO:0009881
-consider: GO:0016021
consider: GO:0016918
consider: GO:0046876
@@ -107351,7 +107367,6 @@ synonym: "green-sensitive opsin" EXACT []
is_obsolete: true
consider: GO:0007603
consider: GO:0009881
-consider: GO:0016021
consider: GO:0016918
consider: GO:0046876
@@ -107366,7 +107381,6 @@ is_obsolete: true
consider: GO:0007603
consider: GO:0009585
consider: GO:0009881
-consider: GO:0016021
consider: GO:0016918
consider: GO:0046876
@@ -107381,7 +107395,6 @@ is_obsolete: true
consider: GO:0007603
consider: GO:0009588
consider: GO:0009881
-consider: GO:0016021
consider: GO:0016918
consider: GO:0046876
@@ -107395,7 +107408,6 @@ synonym: "long-wave-sensitive opsin" EXACT []
is_obsolete: true
consider: GO:0007603
consider: GO:0009881
-consider: GO:0016021
consider: GO:0016918
consider: GO:0046876
@@ -107409,7 +107421,6 @@ synonym: "UV-sensitive opsin" EXACT []
is_obsolete: true
consider: GO:0007604
consider: GO:0009881
-consider: GO:0016021
consider: GO:0016918
consider: GO:0046876
@@ -107502,9 +107513,10 @@ is_a: GO:0006259 ! DNA metabolic process
[Term]
id: GO:0015075
-name: ion transmembrane transporter activity
+name: monoatomic ion transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of an ion from one side of a membrane to the other." [GOC:dgf, GOC:mtg_transport, ISBN:0815340729]
+synonym: "ion transmembrane transporter activity" BROAD []
synonym: "ion transporter activity" EXACT []
is_a: GO:0022857 ! transmembrane transporter activity
@@ -107530,6 +107542,7 @@ xref: Reactome:R-HSA-164834 "Enzyme-bound ATP is released"
xref: Reactome:R-HSA-170026 "Protons are translocated from the intermembrane space to the matrix"
xref: Reactome:R-HSA-74723 "Endosome acidification"
xref: Reactome:R-HSA-917841 "Acidification of Tf:TfR1 containing endosome"
+is_a: GO:0008324 ! monoatomic cation transmembrane transporter activity
is_a: GO:0022890 ! inorganic cation transmembrane transporter activity
[Term]
@@ -107544,6 +107557,7 @@ synonym: "potassium uptake permease activity" RELATED []
synonym: "potassium uptake transmembrane transporter activity" RELATED []
xref: RHEA:29463
is_a: GO:0046873 ! metal ion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015080
@@ -107558,9 +107572,11 @@ id: GO:0015081
name: sodium ion transmembrane transporter activity
namespace: molecular_function
alt_id: GO:0022816
-def: "Enables the transfer of sodium ions (Na+) from one side of a membrane to the other." [GOC:ai, GOC:BHF]
+def: "Enables the transfer of sodium ions (Na+) from one side of a membrane to the other." [GOC:ai, GOC:BHF, RHEA:34963]
synonym: "sodium transporter activity" EXACT []
+xref: RHEA:34963
is_a: GO:0046873 ! metal ion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015083
@@ -107571,16 +107587,17 @@ def: "Enables the transfer of aluminum (Al) ions from one side of a membrane to
synonym: "aluminium ion transporter activity" EXACT []
synonym: "aluminium resistance permease activity" EXACT []
synonym: "aluminum resistance permease activity" EXACT []
-is_a: GO:0015075 ! ion transmembrane transporter activity
is_a: GO:0015318 ! inorganic molecular entity transmembrane transporter activity
[Term]
id: GO:0015085
name: calcium ion transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of calcium (Ca) ions from one side of a membrane to the other." [GOC:dgf]
+def: "Enables the transfer of calcium (Ca) ions from one side of a membrane to the other." [GOC:dgf, RHEA:29671]
xref: Reactome:R-HSA-2534359 "CatSper Channel Mediated Calcium Transport"
+xref: RHEA:29671
is_a: GO:0046873 ! metal ion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015086
@@ -107626,6 +107643,8 @@ namespace: molecular_function
def: "Enables the transfer of ferric iron (Fe(III) or Fe3+) ions from one side of a membrane to the other." [ISBN:0198506732]
comment: Ferric iron is rarely transported in the free form. Some bacteria have a system in which an outer membrane protein takes iron away from host ferritin or lactoferrin and transport it to a Fe3+ binding protein in the periplasm. The periplasmic protein then delivers the Fe3+ to a transport system located in the cytoplasmic membrane. Consider also GO:0015343 siderophore transmembrane transporter activity.
is_a: GO:0005381 ! iron ion transmembrane transporter activity
+is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015092
@@ -107654,7 +107673,6 @@ name: lead ion transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of lead (Pb) ions from one side of a membrane to the other." [GOC:ai]
synonym: "zinc, cadmium, cobalt, nickel, lead-efflux ATPase activity" RELATED []
-is_a: GO:0015075 ! ion transmembrane transporter activity
is_a: GO:0015318 ! inorganic molecular entity transmembrane transporter activity
[Term]
@@ -107695,6 +107713,7 @@ namespace: molecular_function
def: "Enables the transfer of molybdate (MoO4 2-) ions from one side of a membrane to the other. Molybdate is the bivalent anion derived from molybdic acid." [ISBN:0198506732]
synonym: "molybdate transporter activity" EXACT []
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015099
@@ -107724,14 +107743,16 @@ xref: Reactome:R-HSA-549304 "OCT3 mediates renal clearance of organic cations"
xref: Reactome:R-HSA-549322 "OCT1 transports organic cations out of hepatic cells"
xref: Reactome:R-HSA-561054 "OCT2 mediates tubular secretion of organic cations in the kidney"
xref: Reactome:R-HSA-561072 "OCT3 mediates renal uptake of organic cations"
-is_a: GO:0008324 ! cation transmembrane transporter activity
+xref: Reactome:R-HSA-9794270 "SLCO1A2 transports Cipro(1+) into the cytosol"
+xref: Reactome:R-HSA-9794523 "SLC22A1 transports Cipro into renal cell"
+xref: Reactome:R-HSA-9795207 "SLC22A1 transports Cipro into hepatic cell"
+is_a: GO:0022857 ! transmembrane transporter activity
[Term]
id: GO:0015103
name: inorganic anion transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of inorganic anions from one side of a membrane to the other. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage." [GOC:ai]
-is_a: GO:0008509 ! anion transmembrane transporter activity
is_a: GO:0015318 ! inorganic molecular entity transmembrane transporter activity
[Term]
@@ -107756,6 +107777,8 @@ def: "Enables the transfer of bicarbonate from one side of a membrane to the oth
xref: Reactome:R-HSA-2752067 "BESTs transport cytosolic HCO3- to extracellular region"
xref: RHEA:28695
is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0015318 ! inorganic molecular entity transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015107
@@ -107763,6 +107786,7 @@ name: chlorate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of chlorate, ClO3-, from one side of a membrane to the other." [GOC:curators]
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015108
@@ -107781,7 +107805,9 @@ xref: Reactome:R-HSA-5678822 "Defective CFTR does not transport Cl- from cytosol
xref: Reactome:R-HSA-5678863 "CFTR transports Cl- from cytosol to extracellular region"
xref: Reactome:R-HSA-5678992 "Ivacaftor:CFTR G551D transports Cl- from cytosol to extracellular region"
xref: RHEA:29823
-is_a: GO:0043225 ! ATPase-coupled inorganic anion transmembrane transporter activity
+is_a: GO:0008509 ! monoatomic anion transmembrane transporter activity
+is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015109
@@ -107790,13 +107816,14 @@ namespace: molecular_function
def: "Enables the transfer of chromate from one side of a membrane to the other. Chromate is the anion of chromic acid, H2CrO4 (aq) or CrO3." [GOC:ai]
xref: RHEA:32819
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015110
name: cyanate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of cyanate, NCO-, the anion of cyanic acid, from one side of a membrane to the other." [GOC:ai]
-is_a: GO:0008509 ! anion transmembrane transporter activity
+is_a: GO:0022857 ! transmembrane transporter activity
[Term]
id: GO:0015111
@@ -107806,6 +107833,7 @@ def: "Enables the transfer of iodide ions from one side of a membrane to the oth
xref: Reactome:R-HSA-209910 "Iodide is taken up by thyroid epithelial cells"
xref: Reactome:R-HSA-5627802 "SLC26A4 transports I- from cytosol to extracellular region"
xref: Reactome:R-HSA-5627870 "SLC26A4 does not transport I- from cytosol to extracellular region"
+is_a: GO:0008509 ! monoatomic anion transmembrane transporter activity
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
[Term]
@@ -107816,6 +107844,7 @@ def: "Enables the transfer of nitrate ions (NO3-) from one side of a membrane to
synonym: "nitrite/nitrate porter activity" RELATED []
xref: RHEA:34923
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015113
@@ -107841,6 +107870,7 @@ name: silicate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of silicates from one side of a membrane to the other. Silicates are the salts of silicic acids, and are usually composed of silicon and oxygen (Si[x]O[y]), one or more metals, and possibly hydrogen. Types of silicate include unisilicates, metasilicates and hydrous silicates." [GOC:ai]
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015116
@@ -107855,6 +107885,7 @@ xref: Reactome:R-HSA-8875871 "SLC26A11 transports SO4(2-) from extracellular reg
xref: RHEA:34983
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015117
@@ -107888,7 +107919,6 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: phosphoenolpyruvate(out) + phosphate(in) = phosphoenolpyruvate(in) + phosphate(out)." [GOC:bf, GOC:jl]
synonym: "phosphoenolpyruvate/phosphate translocator" EXACT []
synonym: "PPT" BROAD [PMID:10488230]
-is_a: GO:0015301 ! anion:anion antiporter activity
is_a: GO:0015315 ! organophosphate:inorganic phosphate antiporter activity
is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
is_a: GO:0089721 ! phosphoenolpyruvate transmembrane transporter activity
@@ -107899,15 +107929,15 @@ name: acetate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of acetate from one side of a membrane to the other. Acetate is the 2-carbon carboxylic acid ethanoic acid." [GOC:ai]
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015124
name: allantoate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of allantoate from one side of a membrane to the other. Allantoate is the end product of purine metabolism in mammals and some fish, formed form allantoin. It is widely distributed in plants as an important source of stored nitrogen." [GOC:ai, ISBN:0198547684]
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0042887 ! amide transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
[Term]
id: GO:0015125
@@ -107919,6 +107949,7 @@ xref: Reactome:R-HSA-194083 "SLCO1B1 transports ALB:(GCCA,TCCA) from extracellul
xref: Reactome:R-HSA-194130 "Transport (influx) of bile salts and acids by OATP-A"
xref: Reactome:R-HSA-5661184 "Defective SLCO1B1 does not transport BIL from extracellular region (blood) to cytosol (hepatocyte)"
xref: Reactome:R-HSA-5661198 "Defective SLCO1B3 does not transport BIL from extracellular region (blood) to cytosol (hepatocyte)"
+xref: Reactome:R-HSA-9733964 "SLC51A:SLC51B transports bile salts from cytosol to extracellular region"
is_a: GO:0005319 ! lipid transporter activity
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
@@ -107939,7 +107970,6 @@ xref: Reactome:R-HSA-5679031 "Defective ABCC2 does not transport BMG,BDG from cy
xref: Reactome:R-HSA-5679041 "ABCC2 transports BMG,BDG from cytosol to extracellular region"
xref: Reactome:R-HSA-9661417 "ABCG2 tetramer transports BMG,BDG from cytosol to extracellular region"
is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
[Term]
id: GO:0015128
@@ -107953,13 +107983,14 @@ is_a: GO:0042879 ! aldonate transmembrane transporter activity
id: GO:0015129
name: lactate transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of lactate from one side of a membrane to the other. Lactate is 2-hydroxypropanoate, CH3-CHOH-COOH; L(+)-lactate is formed by anaerobic glycolysis in animal tissues, and DL-lactate is found in sour milk, molasses and certain fruit juices." [GOC:ai, ISBN:0198506732]
+def: "Enables the transfer of lactate from one side of a membrane to the other. Lactate is 2-hydroxypropanoate, CH3-CHOH-COOH; L(+)-lactate is formed by anaerobic glycolysis in animal tissues, and DL-lactate is found in sour milk, molasses and certain fruit juices." [GOC:ai, ISBN:0198506732, RHEA:34987]
synonym: "monocarboxylate (lactate, pyruvate, mevalonate) uptake/efflux porter activity" RELATED []
xref: Reactome:R-HSA-373867 "BSG:MCTs cotransport LACT, H+ from extracellular region to cytosol"
xref: Reactome:R-HSA-373875 "BSG:MCTs cotransport LACT, H+ from cytosol to extracellular region"
+xref: RHEA:34987
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015130
@@ -107968,7 +107999,6 @@ namespace: molecular_function
def: "Enables the transfer of mevalonate from one side of a membrane to the other. Mevalonate is the anion of mevalonic acid; its (R)-enantiomer is a strategic intermediate derived from hydroxymethylglutaryl-CoA in the biosynthesis of polyprenyl compounds." [GOC:ai, ISBN:0198506732]
synonym: "monocarboxylate (lactate, pyruvate, mevalonate) uptake/efflux porter activity" RELATED []
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
[Term]
@@ -108011,7 +108041,7 @@ id: GO:0015135
name: glucuronate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of glucuronate from one side of a membrane to the other. Glucuronate is the uronic acid formally derived from glucose by oxidation of the hydroxymethylene group at C-6 to a carboxyl group." [GOC:ai]
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
[Term]
id: GO:0015136
@@ -108024,12 +108054,13 @@ is_a: GO:1901505 ! carbohydrate derivative transmembrane transporter activity
id: GO:0015137
name: citrate transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of citrate, 2-hydroxy-1,2,3-propanetricarboyxlate, from one side of a membrane to the other." [GOC:ai]
+def: "Enables the transfer of citrate, 2-hydroxy-1,2,3-propanetricarboyxlate, from one side of a membrane to the other." [GOC:ai, RHEA:33183]
synonym: "tricarboxylate transport protein" RELATED [TC:2.A.29.7.2]
xref: Reactome:R-HSA-433104 "NACT co-transports trivalent citrate and a sodium ion"
+xref: RHEA:33183
xref: TC:2.A.29.7.2
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015142 ! tricarboxylic acid transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015138
@@ -108039,6 +108070,7 @@ def: "Enables the transfer of fumarate from one side of a membrane to the other.
synonym: "dicarboxylate (succinate/fumarate/malate) antiporter activity" RELATED []
is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015556 ! C4-dicarboxylate transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015139
@@ -108048,7 +108080,6 @@ def: "Enables the transfer of alpha-ketoglutarate from one side of a membrane to
synonym: "2-oxoglutarate transporter activity" EXACT []
xref: Reactome:R-HSA-372480 "2-oxoglutarate [mitochondrial matrix] + 2-oxoadipate [cytosol] <=> 2-oxoglutarate [cytosol] + 2-oxoadipate [mitochondrial matrix]"
is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
[Term]
id: GO:0015140
@@ -108067,6 +108098,7 @@ def: "Enables the transfer of succinate, the dianion of ethane dicarboxylic acid
synonym: "dicarboxylate (succinate/fumarate/malate) antiporter activity" RELATED []
is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015556 ! C4-dicarboxylate transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015142
@@ -108074,7 +108106,7 @@ name: tricarboxylic acid transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of tricarboxylic acids from one side of a membrane to the other. Tricarboxylic acid are organic acids with three COOH groups." [GOC:ai]
synonym: "sodium:dicarboxylate/tricarboxylate symporter activity" NARROW []
-xref: Reactome:R-HSA-372449 "phosphoenolpyruvate [mitochondrial matrix] + citrate [cytosol] => phosphoenolpyruvate [cytosol] + citrate [mitochondrial matrix]"
+xref: Reactome:R-HSA-372449 "SLC25A1 may exchange mitochondrial PEP for cytosolic anion"
xref: Reactome:R-HSA-75849 "Transport of Citrate from Mitochondrial Matrix to cytosol"
is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
@@ -108156,7 +108188,7 @@ id: GO:0015152
name: glucose-6-phosphate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of glucose-6-phosphate from one side of a membrane to the other. Glucose-6-phosphate is a monophosphorylated derivative of glucose with the phosphate group attached to C-6." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
-is_a: GO:0022857 ! transmembrane transporter activity
+is_a: GO:0015119 ! hexose phosphate transmembrane transporter activity
[Term]
id: GO:0015153
@@ -108388,9 +108420,10 @@ is_a: GO:0015171 ! amino acid transmembrane transporter activity
[Term]
id: GO:0015175
-name: neutral amino acid transmembrane transporter activity
+name: neutral L-amino acid transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of neutral amino acids from one side of a membrane to the other. Neutral amino acids have side chains with no charge at pH 7.3." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
+def: "Enables the transfer of neutral L-amino acids from one side of a membrane to the other. Neutral amino acids have side chains with no charge at pH 7.3." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
+synonym: "neutral amino acid transmembrane transporter activity" EXACT []
synonym: "neutral amino acid transporter activity" BROAD []
is_a: GO:0015171 ! amino acid transmembrane transporter activity
@@ -108429,9 +108462,7 @@ namespace: molecular_function
def: "Enables the transfer of L-asparagine from one side of a membrane to the other. L-asparagine is the L-enantiomer of alpha-aminosuccinamic acid." [GOC:go_curators, GOC:jsg, GOC:mah, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
synonym: "asparagine/glutamine permease activity" NARROW []
synonym: "L-asparagine transporter activity" BROAD []
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
is_a: GO:0042887 ! amide transmembrane transporter activity
@@ -108457,7 +108488,6 @@ synonym: "cystine/diaminopimelate porter activity" NARROW []
synonym: "L-cystine transporter activity" BROAD []
xref: Reactome:R-HSA-5340130 "CTNS cotransports CySS-, H+ from lysosomal lumen to cytosol"
is_a: GO:0000099 ! sulfur amino acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
@@ -108471,7 +108501,6 @@ synonym: "4-aminobutyrate transporter activity" EXACT []
synonym: "betaine/GABA:sodium symporter activity" NARROW []
synonym: "GABA transporter activity" EXACT []
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015171 ! amino acid transmembrane transporter activity
[Term]
@@ -108480,9 +108509,7 @@ name: L-glutamine transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of L-glutamine from one side of a membrane to the other. L-glutamine is 2-amino-4-carbamoylbutanoic acid." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
synonym: "asparagine/glutamine permease activity" NARROW []
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
[Term]
@@ -108493,9 +108520,7 @@ def: "Enables the transfer of glycine from one side of a membrane to the other.
synonym: "glycine betaine/proline porter activity" NARROW []
synonym: "glycine transporter activity" BROAD []
synonym: "proline/glycine/betaine:hydrogen/sodium symporter activity" NARROW []
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
[Term]
@@ -108507,9 +108532,7 @@ synonym: "isoleucine/valine:sodium symporter activity" NARROW []
synonym: "L-isoleucine transporter activity" BROAD []
synonym: "leucine/isoleucine/valine porter activity" NARROW []
synonym: "leucine/valine/isoleucine permease activity" NARROW []
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
is_a: GO:0015658 ! branched-chain amino acid transmembrane transporter activity
@@ -108522,10 +108545,9 @@ def: "Enables the transfer of L-lysine from one side of a membrane to the other.
synonym: "histidine/arginine/lysine/ornithine porter activity" NARROW []
synonym: "L-lysine permease" RELATED []
synonym: "lysine permease activity" RELATED []
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015174 ! basic amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015190
@@ -108535,9 +108557,7 @@ def: "Enables the transfer of L-leucine from one side of a membrane to the other
synonym: "L-leucine transporter activity" BROAD []
synonym: "leucine/isoleucine/valine porter activity" NARROW []
synonym: "leucine/valine/isoleucine permease activity" NARROW []
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
is_a: GO:0015658 ! branched-chain amino acid transmembrane transporter activity
@@ -108557,8 +108577,6 @@ namespace: molecular_function
def: "Enables the transfer of L-phenylalanine from one side of a membrane to the other. L-phenylalanine is 2-amino-3-phenylpropanoic acid." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
synonym: "L-phenylalanine permease activity" EXACT []
synonym: "L-phenylalanine transporter activity" BROAD []
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015173 ! aromatic amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
@@ -108573,9 +108591,7 @@ synonym: "L-proline permease activity" RELATED []
synonym: "L-proline transporter activity" BROAD []
synonym: "proline/glycine/betaine:hydrogen/sodium symporter activity" NARROW []
xref: Reactome:R-HSA-8870354 "SLC36A4 transports extracellular L-Pro to the cytosol"
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
[Term]
@@ -108602,9 +108618,7 @@ def: "Enables the transfer of L-threonine from one side of a membrane to the oth
synonym: "L-threonine permease activity" RELATED []
synonym: "L-threonine transporter activity" BROAD []
synonym: "threonine/serine:sodium symporter activity" RELATED []
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
[Term]
@@ -108617,8 +108631,6 @@ synonym: "L-tryptophan permease activity" EXACT []
synonym: "L-tryptophan transporter activity" BROAD []
synonym: "valine/tyrosine/tryptophan permease activity" NARROW []
xref: Reactome:R-HSA-8870352 "SLC36A4 transports L-Trp from extracellular region to cytosol"
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015173 ! aromatic amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
@@ -108640,7 +108652,8 @@ name: methylammonium transmembrane transporter activity
namespace: molecular_function
def: "Enables directed movement of methylammonium, CH3NH2, from one side of a membrane to the other." [GOC:ai]
is_a: GO:0005275 ! amine transmembrane transporter activity
-is_a: GO:0008324 ! cation transmembrane transporter activity
+is_a: GO:0015101 ! organic cation transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015203
@@ -108753,6 +108766,7 @@ def: "Enables the transfer of ADP, adenosine diphosphate, from one side of a mem
is_a: GO:0000295 ! adenine nucleotide transmembrane transporter activity
is_a: GO:0005346 ! purine ribonucleotide transmembrane transporter activity
is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015218
@@ -108782,7 +108796,8 @@ xref: Reactome:R-HSA-429594 "SLC5A7 cotransports Cho, Cl-, Na+ from extracellula
xref: Reactome:R-HSA-444433 "Cho transports from the extracellular space to the cytosol"
xref: Reactome:R-HSA-5658483 "Defective SLC5A7 does not cotransport Cho, Cl-, Na+ from extracellular region to cytosol"
xref: Reactome:R-HSA-6797956 "SLC44A1 transports Cho from cytosol to mitochondrial matrix"
-is_a: GO:0015101 ! organic cation transmembrane transporter activity
+is_a: GO:0015651 ! quaternary ammonium group transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015221
@@ -108824,7 +108839,6 @@ synonym: "vitamin B7 transporter activity" RELATED []
synonym: "vitamin H transporter activity" RELATED []
xref: RHEA:28458
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0042887 ! amide transmembrane transporter activity
is_a: GO:0090482 ! vitamin transmembrane transporter activity
is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
@@ -108868,10 +108882,10 @@ def: "Enables the transfer of L-ascorbate from one side of a membrane to the oth
synonym: "L-ascorbate transporter activity" EXACT []
synonym: "vitamin C transporter activity" EXACT []
xref: Reactome:R-HSA-198870 "SLC23A1,2 cotransports AscH-, 2Na+ from extracellular region to cytosol"
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015145 ! monosaccharide transmembrane transporter activity
is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
is_a: GO:0090482 ! vitamin transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015230
@@ -108894,7 +108908,7 @@ name: 5-formyltetrahydrofolate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of 5-formyltetrahydrofolate, the formylated derivative of tetrahydrofolate, from one side of a membrane to the other." [GOC:ai]
synonym: "5-formyltetrahydrofolate transporter activity" EXACT []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
[Term]
@@ -108904,7 +108918,7 @@ namespace: molecular_function
def: "Enables the transfer of heme from one side of a membrane to the other." [PMID:29549126]
synonym: "haem transporter activity" EXACT []
synonym: "heme transporter activity" BROAD []
-xref: Reactome:R-HSA-917870 "SLC46A1 transports FeHM, heme from extracellular region to cytosol"
+xref: Reactome:R-HSA-917870 "SLC46A1 transports hemes from extracellular region to cytosol"
xref: Reactome:R-HSA-917892 "FLVCR1-1 transports heme from cytosol to extracellular region"
xref: Reactome:R-HSA-9661408 "FLVCR1-2 transports heme from mitochondrial matrix to cytosol"
is_a: GO:0022857 ! transmembrane transporter activity
@@ -108916,8 +108930,8 @@ namespace: molecular_function
def: "Enables the directed movement of pantothenate across a membrane. Pantothenate is the anion of pantothenic acid, the amide of beta-alanine and pantoic acid; it is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods." [GOC:ai, ISBN:0721662544]
synonym: "pantothenate transporter activity" BROAD [GOC:mah]
synonym: "vitamin B5 transmembrane transporter activity" EXACT []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0042887 ! amide transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
is_a: GO:0090482 ! vitamin transmembrane transporter activity
@@ -108943,17 +108957,18 @@ is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
[Term]
id: GO:0015240
-name: amiloride transmembrane transporter activity
+name: obsolete amiloride transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of amiloride from one side of a membrane to the other. Amiloride is a potent and specific inhibitor of sodium ion entry into cells. It is used as a potassium-sparing diuretic." [ISBN:0198506732]
+def: "OBSOLETE. Enables the transfer of amiloride from one side of a membrane to the other. Amiloride is a potent and specific inhibitor of sodium ion entry into cells. It is used as a potassium-sparing diuretic." [ISBN:0198506732]
+comment: The reason for obsoletion is that these terms are beyond the scope of GO.
synonym: "amiloride transporter activity" RELATED []
-is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
+is_obsolete: true
[Term]
id: GO:0015243
name: cycloheximide transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of cycloheximide from one side of a membrane to the other. Cycloheximide is an antibiotic produced by Streptomyces which interferes with protein synthesis in eukaryotes." [ISBN:0198506732]
+def: "Enables the transfer of cycloheximide from one side of a membrane to the other. Cycloheximide is an antibiotic produced by Streptomyces which interferes with protein synthesis in eukaryotes." [ISBN:0198506732]
synonym: "cycloheximide transporter activity" RELATED []
is_a: GO:0015665 ! alcohol transmembrane transporter activity
is_a: GO:0042887 ! amide transmembrane transporter activity
@@ -109023,21 +109038,14 @@ xref: RHEA:29667
is_a: GO:0005372 ! water transmembrane transporter activity
is_a: GO:0015267 ! channel activity
-[Term]
-id: GO:0015251
-name: ammonium channel activity
-namespace: molecular_function
-def: "Enables the facilitated diffusion of ammonium (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [GOC:mtg_transport, GOC:pr, ISBN:0815340729]
-is_a: GO:0005261 ! cation channel activity
-is_a: GO:0008519 ! ammonium transmembrane transporter activity
-
[Term]
id: GO:0015252
name: proton channel activity
namespace: molecular_function
def: "Enables the facilitated diffusion of a hydrogen ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [GOC:mtg_transport, GOC:pr, ISBN:0815340729]
synonym: "hydrogen ion channel activity" EXACT []
-is_a: GO:0005261 ! cation channel activity
+xref: Reactome:R-HSA-9729542 "OTOP1 transports H+ from the extracellular region to the cytosol"
+is_a: GO:0005261 ! monoatomic cation channel activity
is_a: GO:0015078 ! proton transmembrane transporter activity
[Term]
@@ -109190,6 +109198,8 @@ id: GO:0015269
name: calcium-activated potassium channel activity
namespace: molecular_function
def: "Enables the calcium concentration-regulatable energy-independent passage of potassium ions across a lipid bilayer down a concentration gradient." [GOC:dph, GOC:mtg_transport]
+xref: Reactome:R-HSA-9663752 "KCNN2 transports K+ from the cytosol to the extracellular region"
+xref: Reactome:R-HSA-9667809 "KCNMA1:KCNMB1 transports potassium ions from the cytosol to the extracellular region"
is_a: GO:0005227 ! calcium activated cation channel activity
is_a: GO:0005267 ! potassium channel activity
@@ -109219,25 +109229,27 @@ is_a: GO:0005247 ! voltage-gated chloride channel activity
[Term]
id: GO:0015275
-name: stretch-activated, cation-selective, calcium channel activity
+name: stretch-activated, monoatomic cation-selective, calcium channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of a calcium ion by a channel that opens in response to a mechanical stress in the form of stretching." [GOC:mtg_transport]
+synonym: "stretch-activated, cation-selective, calcium channel activity" BROAD []
is_a: GO:0005262 ! calcium channel activity
-is_a: GO:0140135 ! mechanosensitive cation channel activity
+is_a: GO:0140135 ! mechanosensitive monoatomic cation channel activity
[Term]
id: GO:0015276
-name: ligand-gated ion channel activity
+name: ligand-gated monoatomic ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729]
synonym: "ionotropic receptor activity" NARROW [GOC:bf, GOC:sart]
+synonym: "ligand-gated ion channel activity" BROAD []
xref: Reactome:R-HSA-451310 "Activation of Edited Kainate receptors"
xref: Reactome:R-HSA-451311 "Activation of Ca-permeable Kainate receptors"
xref: Reactome:R-HSA-622325 "Activation of highly sodium permeable postsynaptic nicotinic acetylcholine receptors"
xref: Reactome:R-HSA-622326 "Activation of highly calcium permeable nicotinic acetylcholine receptors"
xref: Reactome:R-HSA-629595 "Activation of highly calcium permeable postsynaptic nicotinic acetylcholine receptors"
-is_a: GO:0005216 ! ion channel activity
is_a: GO:0022834 ! ligand-gated channel activity
+is_a: GO:0022839 ! monoatomic ion gated channel activity
[Term]
id: GO:0015277
@@ -109248,7 +109260,7 @@ comment: Note that this term represents an activity and not a gene product. Cons
is_a: GO:0004970 ! ionotropic glutamate receptor activity
is_a: GO:0005267 ! potassium channel activity
is_a: GO:0005272 ! sodium channel activity
-is_a: GO:0099094 ! ligand-gated cation channel activity
+is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
[Term]
id: GO:0015278
@@ -109257,7 +109269,8 @@ namespace: molecular_function
alt_id: GO:0005218
def: "Enables the transmembrane transfer of a calcium ion from intracellular stores by a channel that opens when a specific intracellular ligand has been bound by the channel complex or one of its constituent parts." [GOC:mah]
synonym: "intracellular ligand-gated calcium channel activity" RELATED [GO:0015278]
-is_a: GO:0005217 ! intracellular ligand-gated ion channel activity
+xref: Reactome:R-HSA-9717215 "ITPR3 transports Ca2+ from the endoplasmic reticulum to the cytosol"
+is_a: GO:0005217 ! intracellular ligand-gated monoatomic ion channel activity
is_a: GO:0099604 ! ligand-gated calcium channel activity
[Term]
@@ -109279,7 +109292,7 @@ synonym: "ASIC activity" NARROW [GOC:fj]
synonym: "epithelial sodium channel" NARROW [GOC:fj]
xref: Reactome:R-HSA-2672334 "SCNN channels transport extracellular Na+ to cytosol"
is_a: GO:0005272 ! sodium channel activity
-is_a: GO:0099094 ! ligand-gated cation channel activity
+is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
[Term]
id: GO:0015282
@@ -109379,12 +109392,13 @@ is_a: GO:0015291 ! secondary active transmembrane transporter activity
[Term]
id: GO:0015294
-name: solute:cation symporter activity
+name: solute:monoatomic cation symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + cation(out) = solute(in) + cation(in)." [GOC:ai]
+synonym: "solute:cation symporter activity" BROAD []
+is_a: GO:0008324 ! monoatomic cation transmembrane transporter activity
is_a: GO:0015293 ! symporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
-is_a: GO:0022890 ! inorganic cation transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0015295
@@ -109398,15 +109412,16 @@ synonym: "low affinity metal ion uptake transporter activity" NARROW []
synonym: "proline/glycine/betaine:hydrogen/sodium symporter activity" NARROW []
synonym: "solute:hydrogen symporter activity" EXACT []
is_a: GO:0015078 ! proton transmembrane transporter activity
-is_a: GO:0015294 ! solute:cation symporter activity
+is_a: GO:0015294 ! solute:monoatomic cation symporter activity
[Term]
id: GO:0015296
-name: anion:cation symporter activity
+name: monoatomic anion:monoatomic cation symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: anion(out) + cation(out) = anion(in) + cation(in)." [TC:2.A.1.14.-]
-is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
-is_a: GO:0015294 ! solute:cation symporter activity
+synonym: "anion:cation symporter activity" BROAD []
+is_a: GO:0008509 ! monoatomic anion transmembrane transporter activity
+is_a: GO:0015294 ! solute:monoatomic cation symporter activity
[Term]
id: GO:0015297
@@ -109430,37 +109445,37 @@ is_a: GO:0015291 ! secondary active transmembrane transporter activity
[Term]
id: GO:0015298
-name: solute:cation antiporter activity
+name: obsolete solute:monoatomic cation antiporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + cation(in) = solute(in) + cation(out)." [GOC:ai]
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0015297 ! antiporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+def: "OBSOLETE. Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + cation(in) = solute(in) + cation(out)." [GOC:ai]
+comment: This term was obsoleted because it is an unnecessary grouping term.
+synonym: "solute:cation antiporter activity" EXACT []
+is_obsolete: true
[Term]
id: GO:0015299
-name: solute:proton antiporter activity
+name: obsolete solute:proton antiporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + H+(in) = solute(in) + H+(out)." [GOC:ai]
+def: "OBSOLETE. Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + H+(in) = solute(in) + H+(out)." [GOC:ai]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "L-arabinose/beta-D-thiogalactopyranoside:hydrogen antiporter activity" NARROW []
synonym: "solute:hydrogen antiporter activity" EXACT []
xref: Reactome:R-HSA-434650 "MATEs mediate extrusion of xenobiotics"
xref: Reactome:R-HSA-5625574 "Defective SLC22A18 does not exchange extracellular organic cations for cytosolic H+"
xref: Reactome:R-HSA-597628 "SLC22A18 exchanges extracellular organic cations for cytosolic H+"
-is_a: GO:0015078 ! proton transmembrane transporter activity
-is_a: GO:0015298 ! solute:cation antiporter activity
+is_obsolete: true
[Term]
id: GO:0015301
-name: anion:anion antiporter activity
+name: obsolete anion:anion antiporter activity
namespace: molecular_function
alt_id: GO:0015380
alt_id: GO:0015384
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: anion A(out) + anion B(in) = anion A(in) + anion B(out)." [GOC:ai, GOC:mtg_transport]
+def: "OBSOLETE. Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: anion A(out) + anion B(in) = anion A(in) + anion B(out)." [GOC:ai, GOC:mtg_transport]
+comment: This term was obsoleted because it was too general for a grouping class.
synonym: "anion exchanger activity" EXACT []
synonym: "bicarbonate:chloride antiporter" NARROW []
-xref: Reactome:R-HSA-561041 "OAT1-3 transport organic anions with antiport of dicarboxylic acids"
-is_a: GO:0140323 ! solute:anion antiporter activity
+is_obsolete: true
[Term]
id: GO:0015303
@@ -109497,17 +109512,18 @@ consider: GO:0015528
[Term]
id: GO:0015306
-name: sialate:cation symporter activity
+name: sialate:monoatomic cation symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: sialate(out) + cation(out) = sialate(in) + cation(in)." [TC:2.A.1.14.10]
synonym: "cation/sialate symporter activity" EXACT []
synonym: "cation:sialate symporter activity" EXACT []
synonym: "sialate transporter activity" BROAD []
synonym: "sialate/cation symporter activity" EXACT []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+synonym: "sialate:cation symporter activity" BROAD []
is_a: GO:0015136 ! sialic acid transmembrane transporter activity
-is_a: GO:0015294 ! solute:cation symporter activity
+is_a: GO:0015294 ! solute:monoatomic cation symporter activity
is_a: GO:0042887 ! amide transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
[Term]
id: GO:0015307
@@ -109521,12 +109537,12 @@ is_obsolete: true
[Term]
id: GO:0015308
-name: amiloride:proton antiporter activity
+name: obsolete amiloride:proton antiporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + amiloride(in) = H+(in) + amiloride(out)." [TC:2.A.1.2.1]
+def: "OBSOLETE. Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + amiloride(in) = H+(in) + amiloride(out)." [TC:2.A.1.2.1]
+comment: The reason for obsoletion is that these terms are beyond the scope of GO.
synonym: "amiloride:hydrogen antiporter activity" EXACT []
-is_a: GO:0015240 ! amiloride transmembrane transporter activity
-is_a: GO:0015299 ! solute:proton antiporter activity
+is_obsolete: true
[Term]
id: GO:0015309
@@ -109534,8 +109550,10 @@ name: cycloheximide:proton antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + cycloheximide(in) = H+(in) + cycloheximide(out)." [TC:2.A.1.2.2]
synonym: "cycloheximide:hydrogen antiporter activity" EXACT []
+is_a: GO:0015078 ! proton transmembrane transporter activity
is_a: GO:0015243 ! cycloheximide transmembrane transporter activity
-is_a: GO:0015299 ! solute:proton antiporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0015310
@@ -109543,8 +109561,10 @@ name: benomyl:proton antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + benomyl(in) = H+(in) + benomyl(out)." [TC:2.A.1.2.6]
synonym: "benomyl:hydrogen antiporter activity" EXACT []
-is_a: GO:0015299 ! solute:proton antiporter activity
-is_a: GO:1901479 ! benomyl transmembrane transporter activity
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
+is_a: GO:0042887 ! amide transmembrane transporter activity
[Term]
id: GO:0015311
@@ -109553,7 +109573,9 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + monoamine(in) = H+(in) + monoamine(out)." [TC:2.A.1.2.11, TC:2.A.1.2.12]
synonym: "monoamine:hydrogen antiporter activity" EXACT []
is_a: GO:0008504 ! monoamine transmembrane transporter activity
-is_a: GO:0015299 ! solute:proton antiporter activity
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0015312
@@ -109561,8 +109583,10 @@ name: polyamine:proton antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + polyamine(in) = H+(in) + polyamine(out)." [TC:2.A.1.2.16]
synonym: "polyamine:hydrogen antiporter activity" EXACT []
+is_a: GO:0015078 ! proton transmembrane transporter activity
is_a: GO:0015203 ! polyamine transmembrane transporter activity
-is_a: GO:0015299 ! solute:proton antiporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0015313
@@ -109579,7 +109603,6 @@ name: aminotriazole:proton antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + aminotriazole(in) = H+(in) + aminotriazole(out)." [TC:2.A.1.3.1]
synonym: "aminotriazole:hydrogen antiporter activity" EXACT []
-is_a: GO:0005451 ! monovalent cation:proton antiporter activity
is_a: GO:0045119 ! azole:proton antiporter activity
is_a: GO:1901478 ! aminotriazole transmembrane transporter activity
@@ -109588,8 +109611,8 @@ id: GO:0015315
name: organophosphate:inorganic phosphate antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: organophosphate(out) + inorganic phosphate(in) = organophosphate(in) + inorganic phosphate(out)." [TC:2.A.1.4.-]
+is_a: GO:0005452 ! solute:inorganic anion antiporter activity
is_a: GO:0015114 ! phosphate ion transmembrane transporter activity
-is_a: GO:0140323 ! solute:anion antiporter activity
[Term]
id: GO:0015316
@@ -109664,7 +109687,7 @@ namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA(out) + CoA(in) = acetyl-CoA(in) + CoA(out)." [TC:2.A.1.25.1]
is_a: GO:0008521 ! acetyl-CoA transmembrane transporter activity
is_a: GO:0015228 ! coenzyme A transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
+is_a: GO:0015297 ! antiporter activity
is_a: GO:0015324 ! peptide-acetyl-CoA secondary active transmembrane transporter activity
[Term]
@@ -109673,8 +109696,8 @@ name: cystine:glutamate antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: cystine(out) + glutamate(in) = cystine(in) + glutamate(out)." [TC:2.A.3.8.5]
is_a: GO:0005313 ! L-glutamate transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
is_a: GO:0015328 ! cystine secondary active transmembrane transporter activity
-is_a: GO:0140323 ! solute:anion antiporter activity
[Term]
id: GO:0015328
@@ -109807,7 +109830,7 @@ namespace: molecular_function
def: "Enables the transfer of a zinc ion or zinc ions from the inside of the cell to the outside of the cell across a membrane: Zn2+(out) = Zn2+(in). The activity is driven by proton motive force." [GOC:mtg_transport, ISBN:0815340729, TC:2.A.4.1.4, TC:2.A.4.2.3]
synonym: "zinc efflux permease activity" BROAD []
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
is_a: GO:0022883 ! zinc efflux transmembrane transporter activity
[Term]
@@ -109823,17 +109846,17 @@ consider: GO:0005385
[Term]
id: GO:0015343
-name: siderophore transmembrane transporter activity
+name: siderophore-iron transmembrane transporter activity
namespace: molecular_function
alt_id: GO:0015236
alt_id: GO:0015237
alt_id: GO:0042927
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(out) + H+(out) = siderophore-iron(in) + H+(in)." [TC:2.A.1.16.-]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(out) + H+(out) = siderophore-iron(in) + H+(in)." [PMID:20376388, PMID:31748738]
synonym: "iron-siderophore transporter activity" EXACT []
synonym: "siderochrome transporter activity" NARROW []
synonym: "siderochrome-iron transporter activity" NARROW []
+synonym: "siderophore transmembrane transporter activity" RELATED []
synonym: "siderophore transporter activity" RELATED []
-synonym: "siderophore-iron transmembrane transporter activity" RELATED []
synonym: "siderophore-iron transporter activity" RELATED []
xref: Reactome:R-HSA-1222597 "Loaded mycobactin gets imported"
is_a: GO:0022857 ! transmembrane transporter activity
@@ -109846,7 +109869,7 @@ def: "Enables the transfer of a solute or solutes from one side of a membrane to
synonym: "ferrioxamine uptake transmembrane transporter activity" RELATED []
synonym: "siderochrome-iron (ferrioxamine) uptake transporter" NARROW []
synonym: "siderophore-iron uptake transmembrane transporter activity" RELATED []
-is_a: GO:0015343 ! siderophore transmembrane transporter activity
+is_a: GO:0015343 ! siderophore-iron transmembrane transporter activity
[Term]
id: GO:0015345
@@ -109857,6 +109880,7 @@ synonym: "ferric enterobactin:hydrogen symporter activity" EXACT []
synonym: "ferric-enterobactin:proton symporter activity" EXACT []
is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015295 ! solute:proton symporter activity
+is_a: GO:0015603 ! iron chelate transmembrane transporter activity
[Term]
id: GO:0015346
@@ -109865,7 +109889,7 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ferric triacetylfusarinine C(out) + H+(out) = ferric triacetylfusarinine C(in) + H+(in)." [TC:2.A.1.16.3]
synonym: "ferric triacetylfusarinine C:hydrogen symporter activity" EXACT []
is_a: GO:0015295 ! solute:proton symporter activity
-is_a: GO:0015343 ! siderophore transmembrane transporter activity
+is_a: GO:0015343 ! siderophore-iron transmembrane transporter activity
is_a: GO:0015621 ! ferric triacetylfusarinine C transmembrane transporter activity
[Term]
@@ -109881,9 +109905,11 @@ xref: Reactome:R-HSA-9661397 "SLCO1B1 transports BIL from extracellular region (
xref: Reactome:R-HSA-9661446 "BMG, BDG translocates from ER lumen to cytosol"
xref: Reactome:R-HSA-9661723 "SLCO2B1-3 transports BIL from extracellular region (blood) to cytosol (hepatocyte)"
xref: Reactome:R-HSA-9661799 "SLCO1B3 transports BIL from extracellular region (blood) to cytosol (hepatocyte)"
+xref: Reactome:R-HSA-9749583 "SLC22A7 transports ASA-,ST from extracellular region to cytosol of hepatocytes"
+xref: Reactome:R-HSA-9749607 "SLCO2B1-1 transports ASA- from extracellular region to cytosol of GI cells"
+xref: Reactome:R-HSA-9757010 "SLCO1B1,1B3,2B1-3 transport ATV from extracelluar region to cytosol"
is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0015348
@@ -109912,9 +109938,10 @@ namespace: molecular_function
def: "Enables the transfer of methotrexate, 4-amino-10-methylformic acid from one side of a membrane to the other. Methotrexate is a folic acid analogue and a potent competitive inhibitor of dihydrofolate reductase." [GOC:ai]
synonym: "methotrexate transporter activity" RELATED []
is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0042887 ! amide transmembrane transporter activity
is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
+is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015351
@@ -109925,7 +109952,6 @@ synonym: "bilirubin porter activity" RELATED []
synonym: "bilitranslocase" NARROW []
is_a: GO:0015127 ! bilirubin transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0015352
@@ -109978,7 +110004,7 @@ def: "Enables the transfer of a solute or solutes from one side of a membrane to
synonym: "acetate:hydrogen symporter activity" EXACT []
synonym: "hydrogen:acetate symporter activity" EXACT []
is_a: GO:0015295 ! solute:proton symporter activity
-is_a: GO:0043893 ! acetate:cation symporter activity
+is_a: GO:0043893 ! acetate:monoatomic cation symporter activity
[Term]
id: GO:0015361
@@ -110020,8 +110046,8 @@ name: dicarboxylate:inorganic phosphate antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: dicarboxylate(out) + inorganic phosphate(in) = dicarboxylate(in) + inorganic phosphate(out)." [TC:2.A.29.2.3]
is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
+is_a: GO:0005452 ! solute:inorganic anion antiporter activity
is_a: GO:0015114 ! phosphate ion transmembrane transporter activity
-is_a: GO:0140323 ! solute:anion antiporter activity
[Term]
id: GO:0015366
@@ -110041,32 +110067,32 @@ name: oxoglutarate:malate antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: oxoglutarate(out) + malate(in) = oxoglutarate(in) + malate(out)." [TC:2.A.29.2.1]
synonym: "2-oxoglutarate/malate carrier protein" EXACT [Wikipedia:Mitochondrial_carrier]
-xref: Reactome:R-HSA-198440 "malate [mitochondrial matrix] + alpha-ketoglutarate [cytosol] <=> malate [cytosol] + alpha-ketoglutarate [mitochondrial matrix]"
-xref: Reactome:R-HSA-376851 "Exchange of alpha-ketoglutarate (2-oxoglutarate) and malate across the inner mitochondrial membrane"
+xref: Reactome:R-HSA-198440 "SLC25A11 exchanges malate and alpha-ketoglutarate (2-oxoglutarate) across the inner mitochondrial membrane"
+xref: Reactome:R-HSA-376851 "SLC25A11 exchanges alpha-ketoglutarate (2-oxoglutarate) and malate across the inner mitochondrial membrane"
is_a: GO:0015139 ! alpha-ketoglutarate transmembrane transporter activity
is_a: GO:0015140 ! malate transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
+is_a: GO:0015297 ! antiporter activity
[Term]
id: GO:0015368
-name: calcium:cation antiporter activity
+name: calcium:monoatomic cation antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Ca2+(in) + cation(out) = Ca2+(out) + cation(in)." [TC:2.A.19.-.-]
+synonym: "calcium:cation antiporter activity" BROAD []
xref: Reactome:R-HSA-425822 "K+-independent Li+/Ca2+ exchanger transport"
is_a: GO:0015085 ! calcium ion transmembrane transporter activity
-is_a: GO:0015491 ! cation:cation antiporter activity
+is_a: GO:0140828 ! metal cation:monoatomic cation antiporter activity
[Term]
id: GO:0015369
name: calcium:proton antiporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Ca2+(in) + H+(out) = Ca2+(out) + H+(in)." [TC:2.A.19.2.-]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Ca2+(in) + H+(out) = Ca2+(out) + H+(in)." [RHEA:71799, TC:2.A.19.2.-]
synonym: "calcium:hydrogen antiporter activity" EXACT []
xref: Reactome:R-HSA-8949687 "LETM1 exchanges protons (mitochondrial intermembrane space) for calcium (mitochondrial matrix)"
-xref: RHEA:29671
-is_a: GO:0005451 ! monovalent cation:proton antiporter activity
-is_a: GO:0015368 ! calcium:cation antiporter activity
-is_a: GO:0051139 ! metal ion:proton antiporter activity
+xref: RHEA:71799
+is_a: GO:0015368 ! calcium:monoatomic cation antiporter activity
+is_a: GO:0051139 ! metal cation:proton antiporter activity
[Term]
id: GO:0015370
@@ -110076,7 +110102,7 @@ def: "Enables the transfer of a solute or solutes from one side of a membrane to
synonym: "proline/glycine/betaine:hydrogen/sodium symporter activity" NARROW []
xref: Reactome:R-HSA-8876283 "SLC5A10 cotransports Na+ with Man, Fru from extracellular region to cytosol"
is_a: GO:0015081 ! sodium ion transmembrane transporter activity
-is_a: GO:0015294 ! solute:cation symporter activity
+is_a: GO:0015294 ! solute:monoatomic cation symporter activity
[Term]
id: GO:0015371
@@ -110084,7 +110110,7 @@ name: galactose:sodium symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: galactose(out) + Na+(out) = glucose(in) + Na+(in)." [TC:2.A.21.3.-]
is_a: GO:0005354 ! galactose transmembrane transporter activity
-is_a: GO:0005402 ! carbohydrate:cation symporter activity
+is_a: GO:0005402 ! carbohydrate:monoatomic cation symporter activity
is_a: GO:0015370 ! solute:sodium symporter activity
[Term]
@@ -110101,11 +110127,12 @@ consider: GO:0015183
[Term]
id: GO:0015373
-name: anion:sodium symporter activity
+name: monoatomic anion:sodium symporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: monovalent anion(out) + Na+(out) = monovalent anion(in) + Na+(in)." [TC:2.A.21.5.-]
-synonym: "monovalent anion:sodium symporter activity" EXACT []
-is_a: GO:0015296 ! anion:cation symporter activity
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: monoatomic anion(out) + Na+(out) = monoatomic anion(in) + Na+(in)." [TC:2.A.21.5.-]
+synonym: "anion:sodium symporter activity" BROAD []
+synonym: "monovalent anion:sodium symporter activity" RELATED []
+is_a: GO:0015296 ! monoatomic anion:monoatomic cation symporter activity
is_a: GO:0015370 ! solute:sodium symporter activity
[Term]
@@ -110124,7 +110151,7 @@ alt_id: GO:0015656
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: glycine(out) + Na+(out) = glycine(in) + Na+(in)." [GOC:ai]
xref: Reactome:R-HSA-444120 "SLC6A5,9 cotransport Gly, Cl-, Na+ from extracellular region to cytosol"
xref: Reactome:R-HSA-5660840 "Defective SLC6A5 does not cotransport Gly, Cl-, Na+ from extracellular region to cytosol"
-is_a: GO:0005295 ! neutral amino acid:sodium symporter activity
+is_a: GO:0005295 ! neutral L-amino acid:sodium symporter activity
is_a: GO:0015187 ! glycine transmembrane transporter activity
[Term]
@@ -110142,11 +110169,14 @@ consider: GO:0015370
[Term]
id: GO:0015377
-name: cation:chloride symporter activity
+name: chloride:monoatomic cation symporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: cation(out) + Cl-(out) = cation(in) + Cl-(in)." [TC:2.A.30.-.-]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: cation(out) + Cl-(out) = cation(in) + Cl-(in)." [PMID:31747317]
synonym: "cation:chloride cotransporter activity" BROAD []
-is_a: GO:0015296 ! anion:cation symporter activity
+synonym: "cation:chloride symporter activity" BROAD []
+xref: TC:2.A.30
+is_a: GO:0015108 ! chloride transmembrane transporter activity
+is_a: GO:0015296 ! monoatomic anion:monoatomic cation symporter activity
[Term]
id: GO:0015378
@@ -110155,20 +110185,21 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Na+(out) + Cl-(out) = Na+(in) + Cl-(in)." [TC:2.A.30.4.-]
xref: Reactome:R-HSA-426130 "SLC12A3 cotransports Cl-, Na+ from extracellular region to cytosol"
xref: Reactome:R-HSA-5623705 "Defective SLC12A3 does not cotransport Cl-, Na+ from extracellular region to cytosol"
-is_a: GO:0015373 ! anion:sodium symporter activity
-is_a: GO:0015377 ! cation:chloride symporter activity
+is_a: GO:0015373 ! monoatomic anion:sodium symporter activity
+is_a: GO:0015377 ! chloride:monoatomic cation symporter activity
[Term]
id: GO:0015379
name: potassium:chloride symporter activity
namespace: molecular_function
alt_id: GO:0022820
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: K+(out) + Cl-(out) = K+(in) + Cl-(in)." [TC:2.A.30.5.-]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: K+(out) + Cl-(out) = K+(in) + Cl-(in)." [TC:2.A.30.1.5]
synonym: "potassium ion symporter activity" BROAD []
xref: Reactome:R-HSA-426155 "SLC12A4,5,6,7 cotransport K+, Cl- from cytosol to extracellular region"
xref: Reactome:R-HSA-5623806 "Defective SLC12A6 does not cotransport K+, Cl- from cytosol to extracellular region"
+xref: TC:2.A.30.1.5
is_a: GO:0015079 ! potassium ion transmembrane transporter activity
-is_a: GO:0015377 ! cation:chloride symporter activity
+is_a: GO:0015377 ! chloride:monoatomic cation symporter activity
[Term]
id: GO:0015381
@@ -110190,7 +110221,7 @@ synonym: "sodium:sulphate symporter activity" EXACT []
xref: Reactome:R-HSA-433099 "NaS2 co-transports sulphate and two sodium ions"
xref: Reactome:R-HSA-433114 "NaS1 co-transports sulphate and a sodium ion"
is_a: GO:0008271 ! secondary active sulfate transmembrane transporter activity
-is_a: GO:0015373 ! anion:sodium symporter activity
+is_a: GO:0015370 ! solute:sodium symporter activity
[Term]
id: GO:0015383
@@ -110198,9 +110229,9 @@ name: sulfate:bicarbonate antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: sulfate(out) + bicarbonate(in) = sulfate(in) + bicarbonate(out)." [TC:2.A.53.2.2]
synonym: "sulphate:bicarbonate antiporter activity" EXACT []
+is_a: GO:0005452 ! solute:inorganic anion antiporter activity
is_a: GO:0008271 ! secondary active sulfate transmembrane transporter activity
is_a: GO:0015106 ! bicarbonate transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
[Term]
id: GO:0015385
@@ -110216,6 +110247,7 @@ synonym: "sodium:hydrogen exchange activity" EXACT []
synonym: "sodium:hydrogen exchanger" EXACT []
xref: Reactome:R-HSA-2872444 "SLC9B1/C2 exchange Na+ for H+"
xref: Reactome:R-HSA-2872463 "SLC9C1 exchanges Na+ for H+"
+xref: Reactome:R-HSA-2889070 "SLC9B2 exchanges Na+ for H+"
xref: Reactome:R-HSA-425965 "SLC9A9 exchanges Na+ for H+ across the late endosome membrane"
xref: Reactome:R-HSA-425983 "SLC9A6,7 exchange Na+ for H+ across the early endosome membrane"
xref: Reactome:R-HSA-425994 "Na+/H+ exchanger transport (at cell membrane)"
@@ -110223,9 +110255,8 @@ xref: Reactome:R-HSA-426015 "Na+/H+ exchanger transport (at trans-golgi membrane
xref: Reactome:R-HSA-5661039 "Defective SLC9A6 does not exchange Na+ for H+ across the early endosome membrane"
xref: Reactome:R-HSA-5661086 "Defective SLC9A9 does not exchange Na+ for H+ across the late endosome membrane"
xref: RHEA:29251
-is_a: GO:0005451 ! monovalent cation:proton antiporter activity
is_a: GO:0015081 ! sodium ion transmembrane transporter activity
-is_a: GO:0051139 ! metal ion:proton antiporter activity
+is_a: GO:0051139 ! metal cation:proton antiporter activity
[Term]
id: GO:0015386
@@ -110234,8 +110265,8 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: K+(in) + H+(out) = K+(out) + H+(in)." [TC:2.A.37.-.-]
synonym: "potassium:hydrogen antiporter activity" EXACT []
xref: RHEA:29467
-is_a: GO:0005451 ! monovalent cation:proton antiporter activity
-is_a: GO:0022821 ! potassium ion antiporter activity
+is_a: GO:0022821 ! solute:potassium antiporter activity
+is_a: GO:0051139 ! metal cation:proton antiporter activity
[Term]
id: GO:0015387
@@ -110249,13 +110280,15 @@ is_a: GO:0015295 ! solute:proton symporter activity
[Term]
id: GO:0015389
-name: pyrimidine- and adenine-specific:sodium symporter activity
+name: pyrimidine- and adenosine-specific:sodium symporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: (pyrimidine nucleoside or adenine)(out) + Na+(out) = (pyrimidine nucleoside or adenine)(in) + Na+(in)." [TC:2.A.41.2.3]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: (pyrimidine nucleoside or adenosine)(out) + Na+(out) = (pyrimidine nucleoside or adenosine)(in) + Na+(in)." [TC:2.A.41.2.3]
+synonym: "pyrimidine- and adenine-specific:sodium symporter activity" RELATED []
+xref: TC:2.A.41.2.3
is_a: GO:0005345 ! purine nucleobase transmembrane transporter activity
is_a: GO:0005350 ! pyrimidine nucleobase transmembrane transporter activity
is_a: GO:0005415 ! nucleoside:sodium symporter activity
-is_a: GO:0015391 ! nucleobase:cation symporter activity
+is_a: GO:0015391 ! nucleobase:monoatomic cation symporter activity
[Term]
id: GO:0015390
@@ -110266,11 +110299,12 @@ is_a: GO:0015370 ! solute:sodium symporter activity
[Term]
id: GO:0015391
-name: nucleobase:cation symporter activity
+name: nucleobase:monoatomic cation symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: nucleobase(out) + cation(out) = nucleobase(in) + cation(in)." [GOC:ai]
+synonym: "nucleobase:cation symporter activity" BROAD []
is_a: GO:0015205 ! nucleobase transmembrane transporter activity
-is_a: GO:0015294 ! solute:cation symporter activity
+is_a: GO:0015294 ! solute:monoatomic cation symporter activity
[Term]
id: GO:0015393
@@ -110314,14 +110348,14 @@ def: "Enables the transfer of ammonium from one side of a membrane to the other,
synonym: "high affinity secondary active ammonium transmembrane transporter activity" EXACT []
is_a: GO:0008519 ! ammonium transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0015399
name: primary active transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute from one side of a membrane to the other, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is powered by a primary energy source, directly using ATP. Primary energy sources known to be coupled to transport are chemical, electrical and solar sources." [GOC:mtg_transport, ISBN:0815340729, TC:3.-.-.-.-]
+def: "Enables the transfer of a solute from one side of a membrane to the other, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is powered by a primary energy source. Primary energy sources known to be coupled to transport are chemical such as ATP hydrolysis, redox energy and photon energy." [GOC:mtg_transport, PMID:31613498]
synonym: "primary active transporter" RELATED []
+xref: EC:7.-.-.-
xref: TC:3
is_a: GO:0022804 ! active transmembrane transporter activity
@@ -110334,7 +110368,6 @@ synonym: "low affinity ammonium transmembrane transporter activity" RELATED []
synonym: "low affinity secondary active ammonium transmembrane transporter activity" EXACT []
is_a: GO:0008519 ! ammonium transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0015401
@@ -110386,7 +110419,7 @@ xref: EC:7.2.2.7
xref: MetaCyc:3.6.3.30-RXN
xref: RHEA:12332
is_a: GO:0015091 ! ferric iron transmembrane transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
[Term]
@@ -110405,7 +110438,7 @@ xref: MetaCyc:3.6.3.35-RXN
xref: Reactome:R-HSA-5692462 "ATP13A1 transports Mn2+ from cytosol to ER lumen"
xref: RHEA:17365
is_a: GO:0005384 ! manganese ion transmembrane transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
[Term]
@@ -110423,7 +110456,6 @@ xref: MetaCyc:ABC-64-RXN
xref: RHEA:14613
is_a: GO:0005368 ! taurine transmembrane transporter activity
is_a: GO:0008559 ! ABC-type xenobiotic transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0033283 ! ATPase-coupled organic acid transmembrane transporter activity
[Term]
@@ -110462,7 +110494,7 @@ xref: MetaCyc:3.6.3.24-RXN
xref: MetaCyc:ABC-20-RXN
xref: RHEA:15557
is_a: GO:0015099 ! nickel cation transmembrane transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
[Term]
@@ -110551,7 +110583,7 @@ id: GO:0015418
name: ABC-type quaternary ammonium compound transporting activity
namespace: molecular_function
alt_id: GO:0102908
-def: "Catalysis of the reaction: ATP + H2O + quaternary ammonium(out) = ADP + H(+) + phosphate + quaternary ammonium(in)." [GOC:pz, RHEA:11036]
+def: "Catalysis of the reaction: ATP + H2O + quaternary ammonium(out) = ADP + H+ + phosphate + quaternary ammonium(in)." [GOC:pz, RHEA:11036]
synonym: "ATP-dependent quaternary-ammonium compound transmembrane transporting activity" RELATED []
synonym: "ATPase-coupled quaternary ammonium compound transmembrane transporting activity" RELATED []
synonym: "glycine betaine/proline porter activity" NARROW []
@@ -110565,7 +110597,6 @@ xref: MetaCyc:3.6.3.32-RXN
xref: MetaCyc:RXN-8638
xref: RHEA:11036
is_a: GO:0015651 ! quaternary ammonium group transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
[Term]
@@ -110608,9 +110639,10 @@ synonym: "vitamin B12-transporting ATPase activity" BROAD []
xref: EC:7.6.2.8
xref: MetaCyc:3.6.3.33-RXN
xref: MetaCyc:ABC-5-RXN
-xref: Reactome:R-HSA-3000238 "LMBRD1 transports lysosomal Cbl to cytosol"
-xref: Reactome:R-HSA-3095901 "ABCC1 transports cytosolic Cbl to extracellular region"
-xref: Reactome:R-HSA-3315437 "Defective LMBRD1 does not transport lysosomal Cbl to cytosol"
+xref: Reactome:R-HSA-3095901 "ABCC1 transports cytosolic RCbl to extracellular region"
+xref: Reactome:R-HSA-5223313 "ABCD4:LMBRD1 transports RCbl from lysosomal lumen to cytosol (gut mucosal cells)"
+xref: Reactome:R-HSA-5683325 "Defective ABCD4:LMBRD1 does not transport Cbl from lysosomal lumen to cytosol"
+xref: Reactome:R-HSA-9759206 "ABCD4:LMBRD1 transports RCbl from lysosomal lumen to cytosol"
xref: RHEA:17873
is_a: GO:0090482 ! vitamin transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
@@ -110769,7 +110801,6 @@ xref: EC:7.6.2.10
xref: MetaCyc:3.6.3.20-RXN
xref: RHEA:21668
is_a: GO:0015169 ! glycerol-3-phosphate transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
[Term]
@@ -110800,7 +110831,7 @@ synonym: "ATPase-coupled bile acid transmembrane transporter activity" RELATED [
synonym: "bile acid porter activity" NARROW []
synonym: "bile acid-exporting ATPase activity" NARROW []
xref: Reactome:R-HSA-193362 "ABCB11 transports bile salts from cytosol to extracellular region"
-xref: Reactome:R-HSA-194153 "Transport (efflux) of bile salts by ABCC3 (MRP3)"
+xref: Reactome:R-HSA-194153 "ABCC3 transports bile salts from cytosol to extracellular region"
xref: Reactome:R-HSA-5678517 "Defective ABCB11 does not transport bile salts from cytosol to extracellular region"
xref: RHEA:50048
xref: TC:3.A.1.207.2
@@ -110837,7 +110868,7 @@ synonym: "cadmium-transporting ATPase activity" RELATED [EC:7.2.2.2]
xref: EC:7.2.2.2
xref: MetaCyc:3.6.3.46-RXN
is_a: GO:0015086 ! cadmium ion transmembrane transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
[Term]
@@ -110863,8 +110894,7 @@ synonym: "capsular-polysaccharide ABC transporter" NARROW []
synonym: "capsular-polysaccharide-transporting ATPase activity" EXACT []
xref: EC:7.6.2.12
xref: MetaCyc:3.6.3.38-RXN
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0033284 ! ATPase-coupled carboxylic acid transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
[Term]
@@ -110991,7 +111021,7 @@ xref: MetaCyc:3.6.3.2-RXN
xref: RHEA:10260
is_a: GO:0015095 ! magnesium ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
[Term]
id: GO:0015445
@@ -111008,7 +111038,7 @@ xref: MetaCyc:3.6.3.53-RXN
xref: RHEA:14733
is_a: GO:0015080 ! silver ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
[Term]
id: GO:0015446
@@ -111028,7 +111058,6 @@ xref: EC:7.3.2.7
xref: MetaCyc:3.6.3.16-RXN
xref: RHEA:11348
xref: TC:3.A.4.1.1
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0042626 ! ATPase-coupled transmembrane transporter activity
is_a: GO:1901683 ! arsenate ion transmembrane transporter activity
@@ -111104,13 +111133,15 @@ is_a: GO:0015399 ! primary active transmembrane transporter activity
[Term]
id: GO:0015454
-name: light-driven active transmembrane transporter activity
+name: light-driven active monoatomic ion transmembrane transporter activity
namespace: molecular_function
-def: "Primary active transport of a solute across a membrane, driven by light. Primary active transport is catalysis of the transport of a solute across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by a primary energy source." [GOC:mtg_transport, ISBN:0815340729, TC:3.E.-.-.-]
-synonym: "Light absorption-driven transporters" EXACT []
+def: "Active transport of an ion across a membrane, driven by light." [GOC:mtg_transport, PMID:23994288, PMID:26442282]
+synonym: "light absorption-driven transporter" EXACT []
+synonym: "light-driven active ion transmembrane transporter activity" BROAD []
+synonym: "light-driven active transmembrane transporter activity" RELATED []
synonym: "light-driven pumps" EXACT []
xref: TC:3.E
-is_a: GO:0015399 ! primary active transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0015459
@@ -111151,7 +111182,7 @@ is_a: GO:0140359 ! ABC-type transporter activity
id: GO:0015464
name: acetylcholine receptor activity
namespace: molecular_function
-def: "Combining with acetylcholine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:jl, GOC:signaling]
+def: "Combining with an acetylcholine receptor ligand and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:jl, GOC:signaling]
comment: For nicotinic acetylcholine receptors that act as ion channels, instead use 'acetylcholine-gated cation channel activity ; GO:0022848'.
is_a: GO:0004888 ! transmembrane signaling receptor activity
is_a: GO:0098960 ! postsynaptic neurotransmitter receptor activity
@@ -111316,7 +111347,6 @@ comment: This term was made obsolete because it represents a class of gene produ
synonym: "secretin (sensu Bacteria)" EXACT []
is_obsolete: true
consider: GO:0008320
-consider: GO:0045203
[Term]
id: GO:0015481
@@ -111342,7 +111372,7 @@ is_obsolete: true
id: GO:0015483
name: long-chain fatty acid transporting porin activity
namespace: molecular_function
-def: "Enables the transfer of long-chain fatty acids from one side of a membrane to the other. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22. This transporter is a porin and so enables the energy independent passage of substances, sized less than 1000 Da, across a membrane. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria." [GOC:mtg_transport, TC:1.B.9.1.1]
+def: "Enables the transfer of a long-chain fatty acid from one side of a membrane to the other. A long-chain fatty acid is a fatty acid with an aliphatic tail of 13 to 21 carbons. This transporter is a porin and so enables the energy independent passage of substances, sized less than 1000 Da, across a membrane. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria." [GOC:mtg_transport, TC:1.B.9.1.1]
xref: TC:1.B.9.1.1
is_a: GO:0005324 ! long-chain fatty acid transporter activity
is_a: GO:0015245 ! fatty acid transmembrane transporter activity
@@ -111371,16 +111401,17 @@ id: GO:0015486
name: glycoside-pentoside-hexuronide:cation symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: (glycoside, pentoside or hexuronide)(out) + monovalent cation(out) = (glycoside, pentoside or hexuronide)(in) + monovalent cation(in). The cation is Na+, Li+ or H+." [TC:2.A.2.-.-]
-is_a: GO:0005402 ! carbohydrate:cation symporter activity
+is_a: GO:0005402 ! carbohydrate:monoatomic cation symporter activity
[Term]
id: GO:0015487
-name: melibiose:cation symporter activity
+name: melibiose:monoatomic cation symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: melibiose(out) + monovalent cation(out) = melibiose(in) + monovalent cation(in)." [TC:2.A.2.1.1]
synonym: "melibiose permease activity" RELATED []
+synonym: "melibiose:cation symporter activity" BROAD []
synonym: "melibiose:monovalent cation symporter activity" EXACT []
-is_a: GO:0005402 ! carbohydrate:cation symporter activity
+is_a: GO:0005402 ! carbohydrate:monoatomic cation symporter activity
is_a: GO:0015156 ! melibiose transmembrane transporter activity
[Term]
@@ -111403,10 +111434,11 @@ is_a: GO:0015203 ! polyamine transmembrane transporter activity
[Term]
id: GO:0015491
-name: cation:cation antiporter activity
+name: obsolete cation:cation antiporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: cation A(out) + cation B(in) = cation A(in) + cation B(out)." [GOC:ai]
-is_a: GO:0015298 ! solute:cation antiporter activity
+def: "OBSOLETE. Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: cation A(out) + cation B(in) = cation A(in) + cation B(out)." [GOC:ai]
+comment: This term was obsoleted because it was too general for a grouping class.
+is_obsolete: true
[Term]
id: GO:0015492
@@ -111423,7 +111455,6 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: lysine(out) + H+(out) = lysine(in) + H+(in)." [TC:2.A.3.1.2]
synonym: "lysine:hydrogen symporter activity" EXACT []
is_a: GO:0005280 ! amino acid:proton symporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
[Term]
id: GO:0015494
@@ -111464,18 +111495,17 @@ synonym: "putrescine-ornithine antiporter activity" EXACT []
synonym: "putrescine/ornithine antiporter activity" EXACT []
synonym: "putrescine:hydrogen symporter activity" EXACT []
is_a: GO:0000064 ! L-ornithine transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
is_a: GO:0015489 ! putrescine transmembrane transporter activity
-is_a: GO:0015491 ! cation:cation antiporter activity
-is_a: GO:0140323 ! solute:anion antiporter activity
[Term]
id: GO:0015498
name: pantothenate:sodium symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: pantothenate(out) + Na+(out) = pantothenate(in) + Na+(in)." [TC:2.A.21.1.1]
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015370 ! solute:sodium symporter activity
+is_a: GO:0005343 ! organic acid:sodium symporter activity
is_a: GO:0042887 ! amide transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
[Term]
@@ -111488,7 +111518,7 @@ synonym: "formate uptake permease activity" EXACT []
synonym: "formate uptake transmembrane transporter activity" RELATED []
xref: RHEA:29679
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015500
@@ -111512,7 +111542,7 @@ synonym: "sodium/excitatory glutamate cotransporter activity" BROAD []
synonym: "sodium/excitatory glutamate symporter activity" EXACT []
xref: RHEA:29031
is_a: GO:0005283 ! amino acid:sodium symporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0042887 ! amide transmembrane transporter activity
[Term]
id: GO:0015503
@@ -111521,7 +111551,7 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: K+(in) + H+(out) = K+(out) + H+(in), where glutathione maintains the closed state." [PMID:11053405, TC:2.A.37.1.1, TC:2.A.37.1.2]
is_a: GO:0015079 ! potassium ion transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0015504
@@ -111532,16 +111562,17 @@ synonym: "cytosine permease activity" RELATED []
synonym: "cytosine:hydrogen ion symporter activity" EXACT []
is_a: GO:0015209 ! cytosine transmembrane transporter activity
is_a: GO:0015295 ! solute:proton symporter activity
-is_a: GO:0015391 ! nucleobase:cation symporter activity
+is_a: GO:0015391 ! nucleobase:monoatomic cation symporter activity
[Term]
id: GO:0015505
-name: uracil:cation symporter activity
+name: uracil:monoatomic cation symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: uracil(out) + cation(out) = uracil(in) + cation(in)." [GOC:mtg_transport]
synonym: "uracil permease activity" RELATED []
+synonym: "uracil:cation symporter activity" BROAD []
is_a: GO:0015210 ! uracil transmembrane transporter activity
-is_a: GO:0015391 ! nucleobase:cation symporter activity
+is_a: GO:0015391 ! nucleobase:monoatomic cation symporter activity
[Term]
id: GO:0015506
@@ -111574,7 +111605,6 @@ def: "Catalysis of the transfer of nitrite from one side of the membrane to the
synonym: "nitrite uptake permease activity" EXACT []
is_a: GO:0015112 ! nitrate transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0015514
@@ -111585,7 +111615,6 @@ synonym: "nitrite extrusion permease activity" EXACT []
is_a: GO:0015113 ! nitrite transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
is_a: GO:0015562 ! efflux transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0015515
@@ -111593,7 +111622,7 @@ name: citrate:succinate antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: citrate(out) + succinate(in) = citrate(in) + succinate(out)." [TC:2.A.47.3.2]
is_a: GO:0015141 ! succinate transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
+is_a: GO:0015297 ! antiporter activity
is_a: GO:0071913 ! citrate secondary active transmembrane transporter activity
[Term]
@@ -111602,7 +111631,7 @@ name: tartrate:succinate antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: tartrate(out) + succinate(in) = tartrate(in) + succinate(out)." [TC:2.A.47.3.3]
is_a: GO:0015141 ! succinate transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
+is_a: GO:0015297 ! antiporter activity
is_a: GO:0015554 ! tartrate transmembrane transporter activity
[Term]
@@ -111645,7 +111674,9 @@ synonym: "tetracyclin:hydrogen antiporter activity" EXACT []
synonym: "tetracyclin:proton antiporter activity" EXACT []
synonym: "tetracycline:hydrogen antiporter activity" EXACT []
is_a: GO:0008493 ! tetracycline transmembrane transporter activity
-is_a: GO:0015299 ! solute:proton antiporter activity
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0015521
@@ -111680,7 +111711,6 @@ synonym: "L-arabinose/beta-D-thiogalactopyranoside:hydrogen antiporter activity"
synonym: "L-arabinose/beta-D-thiogalactopyranoside:proton antiporter activity" EXACT []
is_obsolete: true
consider: GO:0015147
-consider: GO:0015299
consider: GO:0051119
[Term]
@@ -111692,9 +111722,7 @@ comment: This term was made obsolete because it represents a multifunctional gen
synonym: "carbonyl cyanide m-chlorophenylhydrazone/nalidixic acid/organomercurials:hydrogen antiporter activity" EXACT []
synonym: "carbonyl cyanide m-chlorophenylhydrazone/nalidixic acid/organomercurials:proton antiporter activity" EXACT []
is_obsolete: true
-consider: GO:0015547
consider: GO:0015548
-consider: GO:0015549
[Term]
id: GO:0015526
@@ -111738,7 +111766,6 @@ name: shikimate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of shikimate from one side of a membrane to the other. Shikimate is an important intermediate in the biosynthesis of aromatic amino acids." [GOC:ai]
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
[Term]
@@ -111823,13 +111850,14 @@ is_a: GO:0015295 ! solute:proton symporter activity
[Term]
id: GO:0015539
-name: hexuronate:cation symporter activity
+name: hexuronate:monoatomic cation symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: hexuronate(out) + cation(out) = hexuronate(in) + cation(in). The hexuronate may be glucuronate or galacturonate." [TC:2.A.1.14.2]
synonym: "hexuronate (glucuronate/galacturonate) porter activity" NARROW []
synonym: "hexuronate porter activity" RELATED []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015294 ! solute:cation symporter activity
+synonym: "hexuronate:cation symporter activity" BROAD []
+is_a: GO:0015294 ! solute:monoatomic cation symporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
[Term]
id: GO:0015540
@@ -111849,7 +111877,6 @@ def: "Enables the transfer of cyanate from one side of a membrane to the other."
synonym: "cyanate porter activity" RELATED []
is_a: GO:0015110 ! cyanate transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0015543
@@ -111870,7 +111897,6 @@ synonym: "phenyl propionate permease activity" RELATED []
is_a: GO:0015292 ! uniporter activity
is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
is_a: GO:0015552 ! propionate transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0015545
@@ -111894,14 +111920,13 @@ is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
[Term]
id: GO:0015547
-name: nalidixic acid transmembrane transporter activity
+name: obsolete nalidixic acid transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of nalidixic acid from one side of a membrane to the other. Nalidixic acid is a synthetic antibiotic that interferes with DNA gyrase and inhibits prokaryotic replication." [GOC:curators, PMID:12702699, PubChem_Compound:4221]
+def: "OBSOLETE. Enables the transfer of nalidixic acid from one side of a membrane to the other. Nalidixic acid is a synthetic antibiotic that interferes with DNA gyrase and inhibits prokaryotic replication." [GOC:curators, PMID:12702699, PubChem_Compound:4221]
+comment: The reason for obsoletion is that these terms are beyond the scope of GO.
synonym: "carbonyl cyanide m-chlorophenylhydrazone/nalidixic acid/organomercurials:hydrogen antiporter activity" RELATED []
synonym: "nalidixic acid transporter activity" RELATED []
-is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
+is_obsolete: true
[Term]
id: GO:0015548
@@ -111914,20 +111939,21 @@ is_a: GO:0022857 ! transmembrane transporter activity
[Term]
id: GO:0015549
-name: carbonyl cyanide m-chlorophenylhydrazone transmembrane transporter activity
+name: obsolete carbonyl cyanide m-chlorophenylhydrazone transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of carbonyl cyanide m-chlorophenylhydrazone from one side of a membrane to the other. Carbonyl cyanide m-chlorophenylhydrazone is a proton ionophore, commonly used as an uncoupling agent and inhibitor of photosynthesis because of its effects on mitochondrial and chloroplast membranes." [GOC:curators]
+def: "OBSOLETE. Enables the transfer of carbonyl cyanide m-chlorophenylhydrazone from one side of a membrane to the other. Carbonyl cyanide m-chlorophenylhydrazone is a proton ionophore, commonly used as an uncoupling agent and inhibitor of photosynthesis because of its effects on mitochondrial and chloroplast membranes." [GOC:curators]
+comment: The reason for obsoletion is that these terms are beyond the scope of GO.
synonym: "carbonyl cyanide m-chlorophenylhydrazone transporter activity" RELATED []
synonym: "carbonyl cyanide m-chlorophenylhydrazone/nalidixic acid/organomercurials:hydrogen antiporter activity" RELATED []
synonym: "CCCP transporter activity" EXACT []
-is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
+is_obsolete: true
[Term]
id: GO:0015550
name: galacturonate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of galacturonate from one side of a membrane to the other. Galacturonate is the uronic acid formally derived from galactose by oxidation of the hydroxymethylene group at C-6 to a carboxyl group." [GOC:ai]
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
[Term]
id: GO:0015551
@@ -111942,8 +111968,8 @@ id: GO:0015552
name: propionate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of propionate from one side of a membrane to the other. Propionate (or propanoate) is the organic acid CH3-CH2-COOH." [GOC:ai]
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015636 ! short-chain fatty acid transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015553
@@ -111964,22 +111990,21 @@ id: GO:0015556
name: C4-dicarboxylate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of C4-dicarboxylate from one side of a membrane to the other." [GOC:krc]
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
[Term]
id: GO:0015558
name: secondary active p-aminobenzoyl-glutamate transmembrane transporter activity
namespace: molecular_function
alt_id: GO:0015569
-def: "Enables the transfer of p-aminobenzoyl-glutamate from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Secondary active transporters include symporters and antiporters. p-aminobenzoyl-glutamate is the anion of p-aminobenzoyl-glutamic acid." [GOC:ai]
+def: "Enables the transfer of p-aminobenzoyl-glutamate from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Secondary active transporters include symporters and antiporters. p-aminobenzoyl-glutamate is the anion of p-aminobenzoyl-glutamic acid." [GOC:ai, RHEA:35043]
synonym: "p-aminobenzoyl-glutamate transmembrane transporter activity" NARROW []
synonym: "p-aminobenzoyl-glutamate transporter activity" RELATED []
synonym: "p-aminobenzoyl-glutamate uptake permease activity" RELATED []
synonym: "p-aminobenzoyl-glutamate uptake transmembrane transporter activity" RELATED []
+xref: RHEA:35043
is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0071916 ! dipeptide transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
@@ -112020,24 +112045,25 @@ is_a: GO:0022857 ! transmembrane transporter activity
id: GO:0015565
name: threonine efflux transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of threonine from the inside of the cell to the outside of the cell across a membrane." [GOC:mtg_transport, ISBN:0815340729]
+def: "Enables the transfer of threonine from the inside of the cell to the outside of the cell across a membrane." [GOC:mtg_transport, ISBN:0815340729, RHEA:35019]
synonym: "threonine efflux permease activity" EXACT []
synonym: "threonine export protein" RELATED []
synonym: "threonine export transporter activity" EXACT []
+xref: RHEA:35019
is_a: GO:0015195 ! L-threonine transmembrane transporter activity
is_a: GO:0034639 ! L-amino acid efflux transmembrane transporter activity
[Term]
id: GO:0015566
-name: acriflavine transmembrane transporter activity
+name: obsolete acriflavine transmembrane transporter activity
namespace: molecular_function
alt_id: GO:0015555
-def: "Enables the directed movement of acriflavin from one side of a membrane to the other. Acriflavin is a fluorescent dye used as a local antiseptic and also as a biological stain. It intercalates into nucleic acids thereby inhibiting bacterial and viral replication." [PubChem_Compound:6842]
+def: "OBSOLETE. Enables the directed movement of acriflavin from one side of a membrane to the other. Acriflavin is a fluorescent dye used as a local antiseptic and also as a biological stain. It intercalates into nucleic acids thereby inhibiting bacterial and viral replication." [PubChem_Compound:6842]
+comment: The reason for obsoletion is that these terms are beyond the scope of GO.
synonym: "acriflavin resistant pump activity" RELATED [GOC:dph, GOC:tb]
synonym: "acriflavin transporter activity" RELATED [GOC:dph, GOC:tb]
synonym: "acriflavine transporter activity" RELATED []
-is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
-is_a: GO:1901702 ! salt transmembrane transporter activity
+is_obsolete: true
[Term]
id: GO:0015567
@@ -112125,7 +112151,7 @@ id: GO:0015577
name: galactitol transmembrane transporter activity
namespace: molecular_function
alt_id: GO:0015588
-def: "Enables the transfer of a galactitol from one side of a membrane to the other. Galactitol is the hexitol derived by the reduction of the aldehyde group of either D- or L-galactose." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
+def: "Enables the transfer of a galactitol from one side of a membrane to the other. Galactitol is the hexitol derived by the reduction of the aldehyde group of either D- or L-galactose." [GOC:ai, GOC:mtg_transport, ISBN:0815340729, RHEA:33143]
synonym: "galactitol permease activity" EXACT []
xref: RHEA:33143
is_a: GO:0015144 ! carbohydrate transmembrane transporter activity
@@ -112183,7 +112209,6 @@ xref: EC:7.6.2.16
xref: RHEA:29995
is_a: GO:0015417 ! ABC-type polyamine transporter activity
is_a: GO:0015489 ! putrescine transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0015596
@@ -112224,7 +112249,6 @@ xref: EC:7.4.2.1
xref: MetaCyc:ABC-12-RXN
is_a: GO:0015186 ! L-glutamine transmembrane transporter activity
is_a: GO:0015426 ! ATPase-coupled polar amino acid-transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0015600
@@ -112281,7 +112305,8 @@ is_a: GO:0022857 ! transmembrane transporter activity
id: GO:0015606
name: spermidine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of spermidine, N-(3-aminopropyl)-1,4-diaminobutane, from one side of a membrane to the other." [GOC:ai]
+def: "Enables the transfer of spermidine, N-(3-aminopropyl)-1,4-diaminobutane, from one side of a membrane to the other." [GOC:ai, RHEA:35039]
+xref: RHEA:35039
is_a: GO:0015101 ! organic cation transmembrane transporter activity
is_a: GO:0015203 ! polyamine transmembrane transporter activity
@@ -112289,7 +112314,7 @@ is_a: GO:0015203 ! polyamine transmembrane transporter activity
id: GO:0015607
name: ABC-type fatty-acyl-CoA transporter activity
namespace: molecular_function
-def: "Catalysis of the reaction ATP + H(2)O + fatty acyl CoA(Side 1) <=> ADP + phosphate + fatty acyl CoA(Side 2). A fatty acyl CoA group is any acyl group derived from a fatty acid with a coenzyme A group attached to it." [RHEA:15181]
+def: "Catalysis of the reaction ATP + H2O + fatty acyl CoA(Side 1) <=> ADP + phosphate + fatty acyl CoA(Side 2). A fatty acyl CoA group is any acyl group derived from a fatty acid with a coenzyme A group attached to it." [RHEA:15181]
synonym: "ABC-type fatty-acyl-CoA transporter" EXACT []
synonym: "ATPase-coupled fatty-acyl-CoA transmembrane transporter activity" RELATED []
synonym: "fatty acyl CoA transporter activity" RELATED []
@@ -112297,6 +112322,8 @@ synonym: "fatty-acyl-CoA transmembrane transporter activity" BROAD []
synonym: "fatty-acyl-CoA-transporting ATPase" RELATED [EC:7.6.2.4]
xref: EC:7.6.2.4
xref: RHEA:15181
+is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0034040 ! ATPase-coupled lipid transmembrane transporter activity
is_a: GO:0042887 ! amide transmembrane transporter activity
is_a: GO:0071077 ! adenosine 3',5'-bisphosphate transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
@@ -112398,7 +112425,7 @@ id: GO:0015620
name: ferric-enterobactin transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of ferric-enterobactin from one side of a membrane to the other." [GOC:ai]
-is_a: GO:0015343 ! siderophore transmembrane transporter activity
+is_a: GO:0015343 ! siderophore-iron transmembrane transporter activity
[Term]
id: GO:0015621
@@ -112421,7 +112448,7 @@ xref: EC:7.2.2.17
xref: MetaCyc:ABC-10-RXN
xref: RHEA:58492
is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0015603 ! iron chelate transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
[Term]
@@ -112491,7 +112518,6 @@ id: GO:0015629
name: actin cytoskeleton
namespace: cellular_component
def: "The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes." [GOC:jl, ISBN:0395825172, ISBN:0815316194]
-subset: goslim_aspergillus
is_a: GO:0005856 ! cytoskeleton
[Term]
@@ -112499,7 +112525,6 @@ id: GO:0015630
name: microtubule cytoskeleton
namespace: cellular_component
def: "The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins." [GOC:jl, ISBN:0395825172]
-subset: goslim_aspergillus
is_a: GO:0005856 ! cytoskeleton
[Term]
@@ -112521,7 +112546,7 @@ synonym: "zinc transporting ATPase activity" BROAD []
synonym: "zinc-transporting ATPase activity" BROAD []
xref: EC:7.2.2.20
xref: RHEA:29795
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
is_a: GO:0046915 ! transition metal ion transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
@@ -112539,7 +112564,7 @@ id: GO:0015636
name: short-chain fatty acid transmembrane transporter activity
namespace: molecular_function
alt_id: GO:0015635
-def: "Enables the transfer of short-chain fatty acids from one side of a membrane to the other. Short-chain fatty acids are fatty acids with a chain length of less than C6." [GOC:mah]
+def: "Enables the transfer of short-chain fatty acids from one side of a membrane to the other. A short-chain fatty acid is a fatty acid with an aliphatic tail of less than 6 carbons." [GOC:mah]
synonym: "short-chain fatty acid transporter activity" RELATED []
synonym: "short-chain fatty acid uptake transporter activity" RELATED []
is_a: GO:0015245 ! fatty acid transmembrane transporter activity
@@ -112633,10 +112658,10 @@ is_a: GO:0015647 ! peptidoglycan transmembrane transporter activity
id: GO:0015649
name: 2-keto-3-deoxygluconate:proton symporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: 2-keto-3-deoxygluconate(out) + H+(out) = 2-keto-3-deoxygluconate(in) + H+(in)." [TC:2.A.10.1.1]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: 2-keto-3-deoxygluconate(out) + H+(out) = 2-keto-3-deoxygluconate(in) + H+(in)." [RHEA:29943, TC:2.A.10.1.1]
synonym: "2-keto-3-deoxygluconate:hydrogen symporter activity" EXACT []
+xref: RHEA:29943
is_a: GO:0005351 ! carbohydrate:proton symporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015145 ! monosaccharide transmembrane transporter activity
is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
@@ -112691,6 +112716,7 @@ synonym: "tellurite uptake transmembrane transporter activity" RELATED []
synonym: "tellurite-resistance uptake permease activity" RELATED []
synonym: "tellurite-resistance uptake transmembrane transporter activity" RELATED []
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0015655
@@ -112709,7 +112735,6 @@ name: branched-chain amino acid:sodium symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: branched-chain amino acid(out) + cation(out) = branched-chain amino acid(in) + cation(in)." [TC:2.A.26.1.1]
is_a: GO:0005283 ! amino acid:sodium symporter activity
-is_a: GO:0015297 ! antiporter activity
is_a: GO:0015658 ! branched-chain amino acid transmembrane transporter activity
[Term]
@@ -112754,8 +112779,6 @@ synonym: "ATPase activity, coupled to transmembrane movement of ions, phosphoryl
synonym: "ion transmembrane transporter activity, phosphorylative mechanism" RELATED []
synonym: "P-type ATPase activity" EXACT []
synonym: "zinc, cadmium, cobalt, nickel, lead-efflux ATPase activity" NARROW []
-xref: Reactome:R-HSA-429157 "ABCC4 accumulation of dense granule contents"
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0140358 ! P-type transmembrane transporter activity
[Term]
@@ -112783,7 +112806,7 @@ namespace: molecular_function
def: "Catalysis of endonucleolytic cleavage of DNA in a site-specific manner, resulting in double-strand breaks." [GOC:mlg]
synonym: "restriction endonuclease activity" EXACT []
synonym: "restriction enzyme activity" EXACT []
-is_a: GO:0004520 ! endodeoxyribonuclease activity
+is_a: GO:0004520 ! DNA endonuclease activity
[Term]
id: GO:0015667
@@ -112893,8 +112916,7 @@ namespace: biological_process
def: "A process in which ferric-enterobactin, the iron-bound form of the siderophore enterobactin, is transported into the cell by specific cell surface receptors." [GOC:pg, PMID:23192658]
synonym: "ferric-enterobactin transport" BROAD []
is_a: GO:0015711 ! organic anion transport
-is_a: GO:0033212 ! iron import into cell
-is_a: GO:1901678 ! iron coordination entity transport
+is_a: GO:0033214 ! siderophore-dependent iron import into cell
[Term]
id: GO:0015686
@@ -112920,6 +112942,7 @@ name: molybdate ion transport
namespace: biological_process
def: "The directed movement of molybdate (MoO4 2-) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Molybdate is the bivalent anion derived from molybdic acid." [GOC:ai]
is_a: GO:0015698 ! inorganic anion transport
+is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0015690
@@ -112963,6 +112986,7 @@ def: "The directed movement of mercury (Hg) ions into, out of or within a cell,
synonym: "mercuric ion transport" NARROW []
synonym: "mercury transport" EXACT []
is_a: GO:0000041 ! transition metal ion transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
relationship: part_of GO:0050787 ! detoxification of mercury ion
@@ -112971,7 +112995,6 @@ id: GO:0015695
name: organic cation transport
namespace: biological_process
def: "The directed movement of organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage." [GOC:ai]
-is_a: GO:0006812 ! cation transport
is_a: GO:0071702 ! organic substance transport
[Term]
@@ -112990,7 +113013,7 @@ id: GO:0015698
name: inorganic anion transport
namespace: biological_process
def: "The directed movement of inorganic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage." [GOC:krc]
-is_a: GO:0006820 ! anion transport
+is_a: GO:0006810 ! transport
[Term]
id: GO:0015699
@@ -113012,6 +113035,7 @@ name: bicarbonate transport
namespace: biological_process
def: "The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
is_a: GO:0015711 ! organic anion transport
+is_a: GO:0019755 ! one-carbon compound transport
[Term]
id: GO:0015702
@@ -113032,7 +113056,6 @@ id: GO:0015704
name: cyanate transport
namespace: biological_process
def: "The directed movement of cyanate, NCO-, the anion of cyanic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
-is_a: GO:0006820 ! anion transport
is_a: GO:0019755 ! one-carbon compound transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -113041,19 +113064,21 @@ id: GO:0015705
name: iodide transport
namespace: biological_process
def: "The directed movement of iodide into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
+is_a: GO:0006820 ! monoatomic anion transport
is_a: GO:0015698 ! inorganic anion transport
[Term]
id: GO:0015706
-name: nitrate transport
+name: nitrate transmembrane transport
namespace: biological_process
alt_id: GO:0006872
alt_id: GO:0080055
def: "The directed movement of nitrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
synonym: "low affinity nitrate transport" NARROW []
synonym: "low-affinity nitrate transport" NARROW []
-is_a: GO:0015698 ! inorganic anion transport
-is_a: GO:0071705 ! nitrogen compound transport
+synonym: "nitrate transport" BROAD []
+is_a: GO:0098661 ! inorganic anion transmembrane transport
+is_a: GO:1902025 ! nitrate import
[Term]
id: GO:0015707
@@ -113074,9 +113099,7 @@ synonym: "silicate transport" BROAD []
synonym: "silicic acid import" RELATED []
synonym: "silicic acid transport" EXACT []
synonym: "silicon uptake" RELATED []
-is_a: GO:0098657 ! import into cell
-is_a: GO:0098661 ! inorganic anion transmembrane transport
-is_a: GO:0098739 ! import across plasma membrane
+is_a: GO:0098658 ! inorganic anion import across plasma membrane
[Term]
id: GO:0015709
@@ -113085,6 +113108,7 @@ namespace: biological_process
def: "The directed movement of thiosulfate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
synonym: "thiosulphate transport" EXACT []
is_a: GO:0015698 ! inorganic anion transport
+is_a: GO:0071705 ! nitrogen compound transport
is_a: GO:0072348 ! sulfur compound transport
[Term]
@@ -113099,7 +113123,6 @@ id: GO:0015711
name: organic anion transport
namespace: biological_process
def: "The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage." [GOC:ai, GOC:krc]
-is_a: GO:0006820 ! anion transport
is_a: GO:0071702 ! organic substance transport
[Term]
@@ -113125,7 +113148,6 @@ namespace: biological_process
def: "The directed movement of phosphoenolpyruvate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0015748 ! organophosphate ester transport
-is_a: GO:0015849 ! organic acid transport
[Term]
id: GO:0015715
@@ -113189,7 +113211,6 @@ synonym: "bile acid transport" NARROW []
synonym: "bile salt transport" NARROW []
is_a: GO:0006869 ! lipid transport
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
[Term]
@@ -113206,7 +113227,6 @@ name: bilirubin transport
namespace: biological_process
def: "The directed movement of bilirubin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
is_a: GO:0006835 ! dicarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0071705 ! nitrogen compound transport
[Term]
@@ -113215,7 +113235,8 @@ name: formate transport
namespace: biological_process
def: "The directed movement of formate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
+is_a: GO:0019755 ! one-carbon compound transport
+is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0015726
@@ -113225,7 +113246,6 @@ def: "The process in which L-idonate is transported across a lipid bilayer, from
synonym: "L-idonate transport" RELATED []
is_a: GO:0034219 ! carbohydrate transmembrane transport
is_a: GO:0042873 ! aldonate transmembrane transport
-is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:0015727
@@ -113233,7 +113253,6 @@ name: lactate transport
namespace: biological_process
def: "The directed movement of lactate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lactate is 2-hydroxypropanoate, CH3-CHOH-COOH; L(+)-lactate is formed by anaerobic glycolysis in animal tissues, and DL-lactate is found in sour milk, molasses and certain fruit juices." [GOC:ai, ISBN:0198506732]
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
[Term]
@@ -113242,7 +113261,6 @@ name: mevalonate transport
namespace: biological_process
def: "The directed movement of mevalonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
[Term]
@@ -113251,16 +113269,16 @@ name: oxaloacetate transport
namespace: biological_process
def: "The directed movement of oxaloacetate, the anion of oxobutanedioic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
is_a: GO:0015740 ! C4-dicarboxylate transport
-is_a: GO:0015849 ! organic acid transport
[Term]
id: GO:0015730
-name: propanoate transport
+name: propanoate transmembrane transport
namespace: biological_process
def: "The directed movement of propionate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
+synonym: "propanoate transport" BROAD []
synonym: "propionate transport" EXACT []
-is_a: GO:0015908 ! fatty acid transport
-is_a: GO:0015912 ! short-chain fatty acid transport
+is_a: GO:0015913 ! short-chain fatty acid transmembrane transport
+is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0015731
@@ -113275,8 +113293,7 @@ id: GO:0015732
name: prostaglandin transport
namespace: biological_process
def: "The directed movement of prostaglandins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
-is_a: GO:0006869 ! lipid transport
-is_a: GO:0015718 ! monocarboxylic acid transport
+is_a: GO:0015908 ! fatty acid transport
is_a: GO:0071715 ! icosanoid transport
[Term]
@@ -113287,7 +113304,6 @@ def: "The process in which shikimate is transported across a lipid bilayer, from
synonym: "shikimate transport" RELATED []
is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -113295,10 +113311,8 @@ id: GO:0015734
name: taurine transport
namespace: biological_process
def: "The directed movement of taurine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0042918 ! alkanesulfonate transport
is_a: GO:0071705 ! nitrogen compound transport
-is_a: GO:0072348 ! sulfur compound transport
[Term]
id: GO:0015735
@@ -113307,7 +113321,7 @@ namespace: biological_process
def: "The process in which uronic acid is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:krc]
synonym: "uronic acid transport" RELATED []
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:0015736
@@ -113353,7 +113367,6 @@ name: fumarate transport
namespace: biological_process
def: "The directed movement of fumarate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
is_a: GO:0015740 ! C4-dicarboxylate transport
-is_a: GO:0015849 ! organic acid transport
[Term]
id: GO:0015742
@@ -113363,7 +113376,6 @@ def: "The directed movement of alpha-ketoglutarate into, out of or within a cell
synonym: "2-oxoglutarate transport" EXACT []
synonym: "mitochondrial alpha-ketoglutarate/malate transport" RELATED []
is_a: GO:0006835 ! dicarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
[Term]
id: GO:0015743
@@ -113372,7 +113384,6 @@ namespace: biological_process
def: "The directed movement of malate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
synonym: "mitochondrial alpha-ketoglutarate/malate transport" RELATED []
is_a: GO:0015740 ! C4-dicarboxylate transport
-is_a: GO:0015849 ! organic acid transport
[Term]
id: GO:0015744
@@ -113380,7 +113391,6 @@ name: succinate transport
namespace: biological_process
def: "The directed movement of succinate, the dianion of ethane dicarboxylic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
is_a: GO:0015740 ! C4-dicarboxylate transport
-is_a: GO:0015849 ! organic acid transport
[Term]
id: GO:0015745
@@ -113391,7 +113401,7 @@ synonym: "tartrate transport" RELATED []
is_a: GO:0015740 ! C4-dicarboxylate transport
is_a: GO:0034219 ! carbohydrate transmembrane transport
is_a: GO:0042869 ! aldarate transmembrane transport
-is_a: GO:1905039 ! carboxylic acid transmembrane transport
+is_a: GO:0072348 ! sulfur compound transport
[Term]
id: GO:0015746
@@ -113399,7 +113409,7 @@ name: citrate transport
namespace: biological_process
def: "The directed movement of citrate, 2-hydroxy-1,2,3-propanetricarboyxlate, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
is_a: GO:0006842 ! tricarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
+is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0015747
@@ -113409,6 +113419,7 @@ def: "The directed movement of urate into, out of or within a cell, or between c
synonym: "urate transmembrane transport" EXACT [GOC:mah]
synonym: "uric acid transport" EXACT []
is_a: GO:0015711 ! organic anion transport
+is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0015748
@@ -113580,7 +113591,7 @@ is_a: GO:0015766 ! disaccharide transport
id: GO:0015771
name: trehalose transport
namespace: biological_process
-def: "The directed movement of trehalose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Trehalose is a disaccharide isomeric with sucrose and obtained from certain lichens and fungi." [GOC:ai]
+def: "The directed movement of trehalose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Trehalose is a disaccharide isomeric with sucrose and obtained from certain lichens and fungi." [GOC:ai, PMID:17606922, PMID:20035867]
is_a: GO:0015766 ! disaccharide transport
[Term]
@@ -113630,10 +113641,11 @@ is_a: GO:1901264 ! carbohydrate derivative transport
[Term]
id: GO:0015778
-name: hexuronide transport
+name: hexuronide transmembrane transport
namespace: biological_process
-def: "The directed movement of hexuronide into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Hexuronides are any compound formed by combination of glycosidic linkage of a hydroxy compound (e.g. an alcohol or a saccharide) with the anomeric carbon atom of a hexuronate." [GOC:ai]
-is_a: GO:0008643 ! carbohydrate transport
+def: "The directed movement of hexuronide across a membrane. Hexuronides are any compound formed by combination of glycosidic linkage of a hydroxy compound (e.g. an alcohol or a saccharide) with the anomeric carbon atom of a hexuronate." [GOC:ai]
+synonym: "hexuronide transport" BROAD []
+is_a: GO:0034219 ! carbohydrate transmembrane transport
[Term]
id: GO:0015779
@@ -113662,7 +113674,6 @@ synonym: "CMP-N-acetylneuraminate transport" RELATED []
synonym: "CMP-sialic acid transport" BROAD []
is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0015783
@@ -113679,7 +113690,6 @@ namespace: biological_process
def: "The process in which UDP-glucose is transported across a membrane." [GOC:ai]
is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0015787
@@ -113687,9 +113697,8 @@ name: UDP-glucuronic acid transmembrane transport
namespace: biological_process
def: "The directed movement of UDP-glucuronic acid into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. UDP-glucuronic acid is a substance composed of glucuronic acid in glycosidic linkage with uridine diphosphate." [GOC:ai]
synonym: "UDP-glucuronic acid transport" RELATED []
-is_a: GO:0046942 ! carboxylic acid transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:0015789
@@ -113699,7 +113708,6 @@ def: "The directed movement of UDP-N-acetylgalactosamine into, out of or within
synonym: "UDP-N-acetylgalactosamine transport" RELATED []
is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0015790
@@ -113709,15 +113717,15 @@ def: "The directed movement of UDP-xylose into, out of or within a cell, or betw
synonym: "UDP-xylose transport" RELATED []
is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0015791
-name: polyol transport
+name: polyol transmembrane transport
namespace: biological_process
-def: "The directed movement of polyols, any polyhydric alcohol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
+def: "The directed movement of polyols, any polyhydric alcohol, across a membrane." [GOC:ai]
subset: goslim_pir
is_a: GO:0015850 ! organic hydroxy compound transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0015792
@@ -113726,16 +113734,17 @@ namespace: biological_process
def: "The process in which arabitol is transported across a lipid bilayer, from one side of a membrane to the other. Arabitol is the pentitol derived from arabinose or lyxose by reduction of the aldehyde group. The D enantiomer is present in lichens and mushrooms." [ISBN:0198506732]
synonym: "arabinitol transport" RELATED []
synonym: "arabitol transport" RELATED [GOC:dph, GOC:tb]
-is_a: GO:0015791 ! polyol transport
+is_a: GO:0015791 ! polyol transmembrane transport
is_a: GO:0034219 ! carbohydrate transmembrane transport
[Term]
id: GO:0015793
-name: glycerol transport
+name: glycerol transmembrane transport
namespace: biological_process
-def: "The directed movement of glycerol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Glycerol is 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids." [GOC:ai]
-is_a: GO:0008643 ! carbohydrate transport
-is_a: GO:0015791 ! polyol transport
+def: "The directed movement of glycerol across a membrane. Glycerol is 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids." [GOC:ai]
+synonym: "glycerol transport" BROAD []
+is_a: GO:0015791 ! polyol transmembrane transport
+is_a: GO:0034219 ! carbohydrate transmembrane transport
[Term]
id: GO:0015794
@@ -113745,33 +113754,36 @@ def: "The process in which glycerol-3-phosphate is transported across a membrane
synonym: "glycerol-3-phosphate transport" RELATED []
is_a: GO:0015711 ! organic anion transport
is_a: GO:0015748 ! organophosphate ester transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
is_a: GO:1901264 ! carbohydrate derivative transport
[Term]
id: GO:0015795
-name: sorbitol transport
+name: sorbitol transmembrane transport
namespace: biological_process
-def: "The directed movement of sorbitol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Sorbitol, also known as glucitol, is the hexitol derived by the reduction of the aldehyde group of glucose." [GOC:ai, ISBN:0198506732]
+def: "The directed movement of sorbitol across a membrane. Sorbitol, also known as glucitol, is the hexitol derived by the reduction of the aldehyde group of glucose." [GOC:ai, ISBN:0198506732]
synonym: "glucitol transport" EXACT []
-is_a: GO:0008643 ! carbohydrate transport
-is_a: GO:0015791 ! polyol transport
+synonym: "sorbitol transport" BROAD []
+is_a: GO:0015791 ! polyol transmembrane transport
+is_a: GO:0034219 ! carbohydrate transmembrane transport
[Term]
id: GO:0015796
-name: galactitol transport
+name: galactitol transmembrane transport
namespace: biological_process
-def: "The directed movement of galactitol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Galactitol is the hexitol derived by the reduction of the aldehyde group of either D- or L-galactose." [GOC:ai]
-is_a: GO:0008643 ! carbohydrate transport
-is_a: GO:0015791 ! polyol transport
+def: "The directed movement of galactitol across a membrane. Galactitol is the hexitol derived by the reduction of the aldehyde group of either D- or L-galactose." [GOC:ai]
+synonym: "galactitol transport" BROAD []
+is_a: GO:0015791 ! polyol transmembrane transport
+is_a: GO:0034219 ! carbohydrate transmembrane transport
[Term]
id: GO:0015797
-name: mannitol transport
+name: mannitol transmembrane transport
namespace: biological_process
-def: "The directed movement of mannitol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Mannitol is the alditol derived from D-mannose by reduction of the aldehyde group." [GOC:ai]
-is_a: GO:0008643 ! carbohydrate transport
-is_a: GO:0015791 ! polyol transport
+def: "The directed movement of mannitol across a membrane. Mannitol is the alditol derived from D-mannose by reduction of the aldehyde group." [GOC:ai]
+synonym: "mannitol transport" BROAD []
+is_a: GO:0015791 ! polyol transmembrane transport
+is_a: GO:0034219 ! carbohydrate transmembrane transport
[Term]
id: GO:0015798
@@ -113779,14 +113791,14 @@ name: myo-inositol transport
namespace: biological_process
def: "The directed movement of myo-inositol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Myo-inositol is 1,2,3,4,5/4,6-cyclohexanehexol, a growth factor for animals and microorganisms." [GOC:ai]
synonym: "vitamin Bh transport" EXACT []
-is_a: GO:0015791 ! polyol transport
+is_a: GO:0015850 ! organic hydroxy compound transport
[Term]
id: GO:0015799
name: propanediol transport
namespace: biological_process
def: "The directed movement of propanediol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Propanediol is a sweet colorless, viscous, hygroscopic liquid used as an antifreeze and in brake fluid; it is also as a humectant in cosmetics and personal care items, although it can be absorbed through the skin with harmful effects." [http://www.rhymezone.com]
-is_a: GO:0015791 ! polyol transport
+is_a: GO:0015850 ! organic hydroxy compound transport
[Term]
id: GO:0015800
@@ -113851,8 +113863,7 @@ id: GO:0015807
name: L-amino acid transport
namespace: biological_process
def: "The directed movement of L-enantiomer amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai, GOC:jsg, GOC:mah]
-is_a: GO:0046942 ! carboxylic acid transport
-is_a: GO:0071705 ! nitrogen compound transport
+is_a: GO:0006865 ! amino acid transport
[Term]
id: GO:0015808
@@ -113871,8 +113882,6 @@ synonym: "aspartate transport" BROAD []
synonym: "mitochondrial aspartate/glutamate transport" RELATED []
is_a: GO:0003333 ! amino acid transmembrane transport
is_a: GO:0015740 ! C4-dicarboxylate transport
-is_a: GO:0015800 ! acidic amino acid transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0015811
@@ -113894,7 +113903,6 @@ synonym: "4-aminobutanoate transport" EXACT []
synonym: "4-aminobutyrate transport" EXACT []
synonym: "GABA transport" EXACT []
is_a: GO:0006865 ! amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0015813
@@ -113904,10 +113912,7 @@ alt_id: GO:0089711
def: "The directed movement of L-glutamate across a membrane." [PMID:21307582]
synonym: "L-glutamate transport" BROAD []
synonym: "mitochondrial aspartate/glutamate transport" RELATED []
-is_a: GO:0006835 ! dicarboxylic acid transport
-is_a: GO:0015800 ! acidic amino acid transport
-is_a: GO:0015807 ! L-amino acid transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0051938 ! L-glutamate import
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -113916,7 +113921,6 @@ name: p-aminobenzoyl-glutamate transport
namespace: biological_process
def: "The directed movement of p-aminobenzoyl-glutamate, the anion of p-aminobenzoyl-glutamic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
is_a: GO:0006835 ! dicarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0042938 ! dipeptide transport
is_a: GO:0072337 ! modified amino acid transport
@@ -113925,9 +113929,8 @@ id: GO:0015816
name: glycine transport
namespace: biological_process
def: "The directed movement of glycine, aminoethanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
-is_a: GO:0006812 ! cation transport
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
+is_a: GO:0015807 ! L-amino acid transport
[Term]
id: GO:0015817
@@ -113936,7 +113939,6 @@ namespace: biological_process
def: "The directed movement of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "L-histidine transport" NARROW []
is_a: GO:0015802 ! basic amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0015818
@@ -113955,12 +113957,11 @@ alt_id: GO:0034226
alt_id: GO:0061461
def: "The directed movement of lysine, 2,6-diaminohexanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "L-lysine import" NARROW []
-synonym: "L-lysine transport" NARROW []
+synonym: "L-lysine transport" RELATED []
synonym: "lysine import" NARROW []
synonym: "lysine uptake" NARROW []
-is_a: GO:0006812 ! cation transport
is_a: GO:0015802 ! basic amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
+is_a: GO:1902022 ! L-lysine transport
[Term]
id: GO:0015820
@@ -113978,8 +113979,6 @@ namespace: biological_process
def: "The directed movement of methionine, 2-amino-4-(methylthio)butanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "L-methionine transport" NARROW []
is_a: GO:0000101 ! sulfur amino acid transport
-is_a: GO:0006812 ! cation transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0015822
@@ -113987,9 +113986,7 @@ name: ornithine transport
namespace: biological_process
def: "The directed movement of ornithine, 2,5-diaminopentanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "L-ornithine transport" NARROW []
-is_a: GO:0006812 ! cation transport
is_a: GO:0006865 ! amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0015823
@@ -114007,7 +114004,6 @@ namespace: biological_process
def: "The directed movement of proline, pyrrolidine-2-carboxylic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "L-proline transport" NARROW []
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0015825
@@ -114026,7 +114022,6 @@ namespace: biological_process
def: "The directed movement of threonine, (2R*,3S*)-2-amino-3-hydroxybutanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "L-threonine transport" NARROW []
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0015827
@@ -114034,9 +114029,7 @@ name: tryptophan transport
namespace: biological_process
def: "The directed movement of tryptophan, 2-amino-3-(1H-indol-3-yl)propanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "L-tryptophan transport" NARROW []
-is_a: GO:0006812 ! cation transport
is_a: GO:0015801 ! aromatic amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0015828
@@ -114061,6 +114054,7 @@ name: diaminopimelate transport
namespace: biological_process
def: "The directed movement of diaminopimelate, the anion of 2,6-diaminoheptanedioic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators, ISBN:0198506732]
is_a: GO:0006865 ! amino acid transport
+is_a: GO:1901571 ! fatty acid derivative transport
[Term]
id: GO:0015832
@@ -114155,7 +114149,7 @@ is_a: GO:0015837 ! amine transport
id: GO:0015842
name: aminergic neurotransmitter loading into synaptic vesicle
namespace: biological_process
-def: "The active transport of aminergic neurotransmitters into a synaptic vesicle. This import is fuelled by an electrochemical gradient across the vesicle membrane, established by the action proton pumps." [GOC:ai]
+def: "The active transport of aminergic neurotransmitters into a synaptic vesicle. This import is fuelled by an electrochemical gradient across the vesicle membrane, established by the action proton pumps." [GOC:ai]
is_a: GO:0015837 ! amine transport
is_a: GO:0098700 ! neurotransmitter loading into synaptic vesicle
@@ -114164,7 +114158,7 @@ id: GO:0015843
name: methylammonium transport
namespace: biological_process
def: "The directed movement of methylammonium into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
-is_a: GO:0006812 ! cation transport
+is_a: GO:0015695 ! organic cation transport
is_a: GO:0015837 ! amine transport
is_a: GO:0019755 ! one-carbon compound transport
@@ -114372,7 +114366,7 @@ name: acetylcholine transport
namespace: biological_process
def: "The directed movement of acetylcholine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions." [GOC:ai]
is_a: GO:0015695 ! organic cation transport
-is_a: GO:0071705 ! nitrogen compound transport
+is_a: GO:0015697 ! quaternary ammonium group transport
is_a: GO:1901374 ! acetate ester transport
[Term]
@@ -114381,14 +114375,13 @@ name: choline transport
namespace: biological_process
def: "The directed movement of choline into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Choline (2-hydroxyethyltrimethylammonium) is an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine." [GOC:ai]
is_a: GO:0015695 ! organic cation transport
-is_a: GO:0071705 ! nitrogen compound transport
+is_a: GO:0015697 ! quaternary ammonium group transport
[Term]
id: GO:0015872
name: dopamine transport
namespace: biological_process
def: "The directed movement of dopamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Dopamine is a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline." [GOC:ai]
-is_a: GO:0006812 ! cation transport
is_a: GO:0051937 ! catecholamine transport
[Term]
@@ -114398,6 +114391,7 @@ namespace: biological_process
def: "The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine." [GOC:ai, ISBN:0198506732]
synonym: "levarterenol transport" EXACT []
synonym: "noradrenaline transport" EXACT []
+is_a: GO:0015695 ! organic cation transport
is_a: GO:0051937 ! catecholamine transport
[Term]
@@ -114415,7 +114409,6 @@ id: GO:0015876
name: acetyl-CoA transport
namespace: biological_process
def: "The directed movement of acetyl-CoA into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetyl-CoA is a derivative of coenzyme A in which the sulfhydryl group is acetylated; it is a metabolite derived from several pathways (e.g. glycolysis, fatty acid oxidation, amino-acid catabolism) and is further metabolized by the tricarboxylic acid cycle. It is a key intermediate in lipid and terpenoid biosynthesis." [GOC:ai]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015916 ! fatty-acyl-CoA transport
[Term]
@@ -114434,7 +114427,6 @@ def: "The directed movement of biotin into, out of or within a cell, or between
synonym: "vitamin B7 transport" EXACT []
synonym: "vitamin H transport" EXACT []
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0042886 ! amide transport
is_a: GO:0051180 ! vitamin transport
is_a: GO:0072348 ! sulfur compound transport
@@ -114466,7 +114458,7 @@ def: "The directed movement of creatine across a membrane." [GO_REF:0000069, GOC
synonym: "creatine transport" BROAD []
is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0072337 ! modified amino acid transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:0015882
@@ -114478,8 +114470,6 @@ synonym: "L-ascorbic acid transport" RELATED []
synonym: "vitamin C transport" EXACT []
is_a: GO:0015749 ! monosaccharide transmembrane transport
is_a: GO:0035461 ! vitamin transmembrane transport
-is_a: GO:0046942 ! carboxylic acid transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -114501,7 +114491,6 @@ synonym: "folate transport" EXACT []
synonym: "vitamin B9 transport" EXACT []
synonym: "vitamin M transport" EXACT []
is_a: GO:0006835 ! dicarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0042886 ! amide transport
is_a: GO:0051180 ! vitamin transport
is_a: GO:0072337 ! modified amino acid transport
@@ -114537,7 +114526,7 @@ is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0035461 ! vitamin transmembrane transport
is_a: GO:0042886 ! amide transport
is_a: GO:0072337 ! modified amino acid transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:0015888
@@ -114585,11 +114574,12 @@ is_a: GO:1901678 ! iron coordination entity transport
[Term]
id: GO:0015894
-name: acriflavine transport
+name: obsolete acriflavine transport
namespace: biological_process
-def: "The directed movement of acriflavine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acriflavine is a fluorescent dye used as a local antiseptic and also as a biological stain. It intercalates into nucleic acids thereby inhibiting bacterial and viral replication." [GOC:curators, PubChem_Compound:6842]
+def: "OBSOLETE. The directed movement of acriflavine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acriflavine is a fluorescent dye used as a local antiseptic and also as a biological stain. It intercalates into nucleic acids thereby inhibiting bacterial and viral replication." [GOC:curators, PubChem_Compound:6842]
+comment: This term is out of scope for GO.
synonym: "acriflavin transport" RELATED [GOC:dph, GOC:tb]
-is_a: GO:0042908 ! xenobiotic transport
+is_obsolete: true
[Term]
id: GO:0015895
@@ -114600,12 +114590,11 @@ is_a: GO:0071702 ! organic substance transport
[Term]
id: GO:0015896
-name: nalidixic acid transport
+name: obsolete nalidixic acid transport
namespace: biological_process
-def: "The directed movement of nalidixic acid into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Nalidixic acid is a synthetic antibiotic that interferes with DNA gyrase and inhibits prokaryotic replication." [GOC:curators, PMID:12702699, PubChem_Compound:4221]
-is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
-is_a: GO:0071705 ! nitrogen compound transport
+def: "OBSOLETE. The directed movement of nalidixic acid into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Nalidixic acid is a synthetic antibiotic that interferes with DNA gyrase and inhibits prokaryotic replication." [GOC:curators, PMID:12702699, PubChem_Compound:4221]
+comment: This term is out of scope for GO.
+is_obsolete: true
[Term]
id: GO:0015897
@@ -114617,11 +114606,11 @@ is_a: GO:0071702 ! organic substance transport
[Term]
id: GO:0015898
-name: amiloride transport
+name: obsolete amiloride transport
namespace: biological_process
-def: "The directed movement amiloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Amiloride is a potent and specific inhibitor of sodium ion entry into cells. It is used as a potassium-sparing diuretic." [GOC:ai]
-is_a: GO:0071702 ! organic substance transport
-is_a: GO:0071705 ! nitrogen compound transport
+def: "OBSOLETE. The directed movement amiloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Amiloride is a potent and specific inhibitor of sodium ion entry into cells. It is used as a potassium-sparing diuretic." [GOC:ai]
+comment: This term is out of scope for GO.
+is_obsolete: true
[Term]
id: GO:0015899
@@ -114633,11 +114622,11 @@ is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0015900
-name: benomyl transport
+name: obsolete benomyl transport
namespace: biological_process
-def: "The directed movement of benomyl into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Benomyl, methyl 1-(butylcarbamoyl)-2-benzimidazolecarbamate, is a systemic agricultural fungicide used for control of certain fungal diseases of stone fruit." [GOC:curators]
-is_a: GO:0042886 ! amide transport
-is_a: GO:0071702 ! organic substance transport
+def: "OBSOLETE. The directed movement of benomyl into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Benomyl, methyl 1-(butylcarbamoyl)-2-benzimidazolecarbamate, is a systemic agricultural fungicide used for control of certain fungal diseases of stone fruit." [GOC:curators]
+comment: This term is out of scope for GO.
+is_obsolete: true
[Term]
id: GO:0015901
@@ -114649,12 +114638,12 @@ is_a: GO:0042886 ! amide transport
[Term]
id: GO:0015902
-name: carbonyl cyanide m-chlorophenylhydrazone transport
+name: obsolete carbonyl cyanide m-chlorophenylhydrazone transport
namespace: biological_process
-def: "The directed movement of carbonyl cyanide m-chlorophenylhydrazone into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbonyl cyanide m-chlorophenylhydrazone is a proton ionophore, commonly used as an uncoupling agent and inhibitor of photosynthesis because of its effects on mitochondrial and chloroplast membranes." [GOC:curators]
+def: "OBSOLETE. The directed movement of carbonyl cyanide m-chlorophenylhydrazone into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbonyl cyanide m-chlorophenylhydrazone is a proton ionophore, commonly used as an uncoupling agent and inhibitor of photosynthesis because of its effects on mitochondrial and chloroplast membranes." [GOC:curators]
+comment: This term is out of scope for GO.
synonym: "CCCP transport" EXACT []
-is_a: GO:0071702 ! organic substance transport
-is_a: GO:0071705 ! nitrogen compound transport
+is_obsolete: true
[Term]
id: GO:0015903
@@ -114673,7 +114662,7 @@ synonym: "tetracyclin transport" BROAD []
synonym: "tetracycline transport" BROAD []
is_a: GO:0015711 ! organic anion transport
is_a: GO:0015850 ! organic hydroxy compound transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0015905
@@ -114691,20 +114680,20 @@ name: fatty acid transport
namespace: biological_process
def: "The directed movement of fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Fatty acids are aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [GOC:ai]
is_a: GO:0006869 ! lipid transport
-is_a: GO:0015849 ! organic acid transport
+is_a: GO:0015718 ! monocarboxylic acid transport
[Term]
id: GO:0015909
name: long-chain fatty acid transport
namespace: biological_process
-def: "The directed movement of long-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [GOC:ai]
+def: "The directed movement of a long-chain fatty acid into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid is a fatty acid with an aliphatic tail of 13 to 21 carbons." [GOC:ai]
is_a: GO:0015908 ! fatty acid transport
[Term]
id: GO:0015910
name: long-chain fatty acid import into peroxisome
namespace: biological_process
-def: "The directed movement of long-chain fatty acids into a peroxisome. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [GOC:ai]
+def: "The directed movement of a long-chain fatty acid into a peroxisome. A long-chain fatty acid is a fatty acid with an aliphatic tail of 13 to 21 carbons." [GOC:ai]
synonym: "peroxisomal long-chain fatty acid import" EXACT []
synonym: "peroxisomal long-chain fatty acid uptake" EXACT [GOC:dph, GOC:tb]
is_a: GO:0015909 ! long-chain fatty acid transport
@@ -114716,7 +114705,7 @@ is_a: GO:1902001 ! fatty acid transmembrane transport
id: GO:0015911
name: long-chain fatty acid import across plasma membrane
namespace: biological_process
-def: "The directed movement of long-chain fatty acids from outside of a cell, across the plasma membrane and into the cytosol. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [GOC:ai]
+def: "The directed movement of a long-chain fatty acid from outside of a cell, across the plasma membrane and into the cytosol. A long-chain fatty acid is a fatty acid with an aliphatic tail of 13 to 21 carbons." [GOC:ai]
synonym: "plasma membrane long-chain fatty acid transport" EXACT []
is_a: GO:0044539 ! long-chain fatty acid import into cell
is_a: GO:0098739 ! import across plasma membrane
@@ -114726,17 +114715,18 @@ is_a: GO:1902001 ! fatty acid transmembrane transport
id: GO:0015912
name: short-chain fatty acid transport
namespace: biological_process
-def: "The directed movement of short-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Short-chain fatty acids are fatty acids with a chain length of less than C6." [GOC:ai]
-is_a: GO:0006869 ! lipid transport
-is_a: GO:0015718 ! monocarboxylic acid transport
+def: "The directed movement of short-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A short-chain fatty acid is a fatty acid with an aliphatic tail of less than 6 carbons." [GOC:ai]
+is_a: GO:0015908 ! fatty acid transport
[Term]
id: GO:0015913
-name: short-chain fatty acid import
+name: short-chain fatty acid transmembrane transport
namespace: biological_process
-def: "The directed movement of short-chain fatty acids into a cell or organelle. Short-chain fatty acids are fatty acids with a chain length of less than C6." [GOC:ai]
+def: "The directed movement of short-chain fatty acids into a cell or organelle. A short-chain fatty acid is a fatty acid with an aliphatic tail of less than 6 carbons." [GOC:ai]
+synonym: "short-chain fatty acid import" RELATED []
synonym: "short-chain fatty acid uptake" EXACT []
-is_a: GO:0015908 ! fatty acid transport
+is_a: GO:0015912 ! short-chain fatty acid transport
+is_a: GO:1902001 ! fatty acid transmembrane transport
[Term]
id: GO:0015914
@@ -114748,11 +114738,12 @@ is_a: GO:0015748 ! organophosphate ester transport
[Term]
id: GO:0015915
-name: fatty-acyl group transport
+name: obsolete fatty-acyl group transport
namespace: biological_process
-def: "The directed movement of fatty acyl groups into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A fatty acyl group is any acyl group derived from a fatty acid." [GOC:ai]
+def: "OBSOLETE. The directed movement of fatty acyl groups into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A fatty acyl group is any acyl group derived from a fatty acid." [GOC:ai]
+comment: This term was obsoleted because it was created by error; individual groups in molecules are not transported.
synonym: "fatty acyl transport" EXACT []
-is_a: GO:0006810 ! transport
+is_obsolete: true
[Term]
id: GO:0015916
@@ -114762,6 +114753,7 @@ def: "The directed movement of fatty acyl coenzyme A into, out of or within a ce
synonym: "fatty acyl CoA transport" EXACT []
synonym: "fatty acyl coenzyme A transport" EXACT []
synonym: "fatty acyl-CoA transport" EXACT []
+is_a: GO:0015711 ! organic anion transport
is_a: GO:0015868 ! purine ribonucleotide transport
is_a: GO:0042886 ! amide transport
is_a: GO:0051503 ! adenine nucleotide transport
@@ -114794,26 +114786,24 @@ is_a: GO:0043574 ! peroxisomal transport
id: GO:0015920
name: lipopolysaccharide transport
namespace: biological_process
+alt_id: GO:0015921
def: "The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide." [GOC:ai]
subset: goslim_pir
+synonym: "lipopolysaccharide export" NARROW []
+synonym: "LPS export" NARROW []
synonym: "LPS transport" EXACT []
is_a: GO:0006869 ! lipid transport
is_a: GO:1901264 ! carbohydrate derivative transport
-[Term]
-id: GO:0015921
-name: lipopolysaccharide export
-namespace: biological_process
-def: "The directed movement of lipopolysaccharides out of a cell or organelle." [GOC:ai]
-synonym: "LPS export" EXACT []
-is_a: GO:0015920 ! lipopolysaccharide transport
-
[Term]
id: GO:0015922
-name: aspartate oxidase activity
+name: obsolete aspartate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: aspartate + O2 = iminosuccinate + hydrogen peroxide." [EC:1.4.3.1, EC:1.4.3.16]
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+def: "OBSOLETE. Catalysis of the reaction: aspartate + O2 = iminosuccinate + hydrogen peroxide." [EC:1.4.3.1, EC:1.4.3.16]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+consider: GO:0008445
+consider: GO:0008734
[Term]
id: GO:0015923
@@ -114826,8 +114816,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0015924
name: mannosyl-oligosaccharide mannosidase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of the terminal alpha-D-mannose residues in oligo-mannose oligosaccharides." [EC:3.2.1.-, GOC:ai]
-xref: EC:3.2.1.-
+def: "Catalysis of the hydrolysis of the terminal alpha-D-mannose residues in oligo-mannose oligosaccharides." [GOC:ai]
is_a: GO:0004559 ! alpha-mannosidase activity
[Term]
@@ -114978,7 +114967,7 @@ synonym: "vitamin B5 metabolism" EXACT []
is_a: GO:0006575 ! cellular modified amino acid metabolic process
is_a: GO:0006767 ! water-soluble vitamin metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
[Term]
id: GO:0015940
@@ -115035,6 +115024,7 @@ name: formate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving formate, also known as methanoate, the anion HCOO- derived from methanoic (formic) acid." [ISBN:0198506732]
synonym: "formate metabolism" EXACT []
+is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
[Term]
@@ -115392,7 +115382,7 @@ subset: goslim_pir
synonym: "carbon utilization by utilization of organic compounds" EXACT [GOC:mah]
synonym: "heterotrophy" EXACT []
xref: Wikipedia:Heterotroph
-is_a: GO:0008150 ! biological_process
+is_a: GO:0031667 ! response to nutrient levels
[Term]
id: GO:0015977
@@ -115416,6 +115406,7 @@ subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
+subset: prokaryote_subset
xref: Wikipedia:Photosynthesis
is_a: GO:0044237 ! cellular metabolic process
@@ -115476,12 +115467,12 @@ is_a: GO:1902600 ! proton transmembrane transport
[Term]
id: GO:0015986
-name: ATP synthesis coupled proton transport
+name: proton motive force-driven ATP synthesis
namespace: biological_process
def: "The transport of protons across a membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis." [ISBN:0716731363]
+synonym: "ATP synthesis coupled proton transport" EXACT []
synonym: "chemiosmosis" BROAD [GOC:rs]
is_a: GO:0006754 ! ATP biosynthetic process
-is_a: GO:0015985 ! energy coupled proton transport, down electrochemical gradient
[Term]
id: GO:0015987
@@ -115499,10 +115490,12 @@ is_a: GO:1902600 ! proton transmembrane transport
[Term]
id: GO:0015989
-name: light-driven proton transport
+name: obsolete light-driven proton transport
namespace: biological_process
-def: "The transport of protons against an electrochemical gradient, using energy from light." [GOC:mah]
-is_a: GO:0015988 ! energy coupled proton transmembrane transport, against electrochemical gradient
+def: "OBSOLETE. The transport of protons against an electrochemical gradient, using energy from light." [GOC:mah]
+comment: This term has been obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0015454
[Term]
id: GO:0015990
@@ -115585,14 +115578,14 @@ is_a: GO:0016667 ! oxidoreductase activity, acting on a sulfur group of donors
id: GO:0016004
name: phospholipase activator activity
namespace: molecular_function
-def: "Increases the activity of a phospholipase, an enzyme that catalyzes of the hydrolysis of a glycerophospholipid." [GOC:ai]
+def: "Binds to and increases the activity of a phospholipase, an enzyme that catalyzes of the hydrolysis of a glycerophospholipid." [GOC:ai]
is_a: GO:0060229 ! lipase activator activity
[Term]
id: GO:0016005
name: phospholipase A2 activator activity
namespace: molecular_function
-def: "Increases the activity of the enzyme phospholipase A2." [GOC:ai]
+def: "Binds to and increases the activity of the enzyme phospholipase A2." [GOC:ai]
is_a: GO:0016004 ! phospholipase activator activity
[Term]
@@ -115686,7 +115679,6 @@ is_obsolete: true
consider: GO:0007603
consider: GO:0009588
consider: GO:0009881
-consider: GO:0016021
consider: GO:0016918
consider: GO:0046876
@@ -115712,10 +115704,10 @@ is_a: GO:0038187 ! pattern recognition receptor activity
id: GO:0016020
name: membrane
namespace: cellular_component
+alt_id: GO:0016021
alt_id: GO:0098589
alt_id: GO:0098805
-def: "A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it." [GOC:dos, GOC:mah, ISBN:0815316194]
-subset: goslim_aspergillus
+def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
@@ -115723,22 +115715,15 @@ subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
+synonym: "integral component of membrane" NARROW []
+synonym: "integral to membrane" NARROW []
synonym: "membrane region" NARROW []
synonym: "region of membrane" NARROW []
+synonym: "transmembrane" RELATED [GOC:mah]
synonym: "whole membrane" NARROW []
xref: Wikipedia:Biological_membrane
-is_a: GO:0110165 ! cellular anatomical entity
-
-[Term]
-id: GO:0016021
-name: integral component of membrane
-namespace: cellular_component
-def: "The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:go_curators]
-subset: goslim_chembl
-synonym: "integral to membrane" NARROW []
-synonym: "transmembrane" RELATED [GOC:mah]
xref: Wikipedia:Transmembrane_protein
-is_a: GO:0031224 ! intrinsic component of membrane
+is_a: GO:0110165 ! cellular anatomical entity
[Term]
id: GO:0016024
@@ -115888,7 +115873,7 @@ is_a: GO:0016037 ! light absorption
id: GO:0016040
name: glutamate synthase (NADH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 L-glutamate + NAD(+) = 2-oxoglutarate + L-glutamine + H(+) + NADH." [EC:1.4.1.14, RHEA:13753]
+def: "Catalysis of the reaction: 2 L-glutamate + NAD+ = 2-oxoglutarate + L-glutamine + H+ + NADH." [EC:1.4.1.14, RHEA:13753]
synonym: "glutamate (reduced nicotinamide adenine dinucleotide) synthase" RELATED [EC:1.4.1.14]
synonym: "GOGAT activity" BROAD []
synonym: "L-glutamate synthase (NADH)" RELATED [EC:1.4.1.14]
@@ -116113,7 +116098,7 @@ id: GO:0016056
name: rhodopsin mediated signaling pathway
namespace: biological_process
alt_id: GO:0009586
-def: "The series of molecular signals generated as a consequence of excitation of rhodopsin by a photon and the events that convert the absorbed photons into a cellular response." [GOC:bf, GOC:dph, GOC:hb, GOC:signaling, GOC:tb]
+def: "A G protein-coupled receptor signaling pathway initiated by the excitation of rhodopsin by a photon, and ending with the regulation of a downstream cellular process." [GOC:bf, GOC:dph, GOC:hb, GOC:signaling, GOC:tb]
synonym: "rhodopsin mediated phototransduction" EXACT [GOC:bf]
synonym: "rhodopsin mediated signalling pathway" EXACT [GOC:dph, GOC:tb]
synonym: "rhodopsin signaling" EXACT [GOC:bf]
@@ -116161,7 +116146,7 @@ id: GO:0016061
name: regulation of light-activated channel activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of light-activated channel activity." [GOC:go_curators]
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
[Term]
id: GO:0016062
@@ -116223,10 +116208,10 @@ name: RNA metabolic process
namespace: biological_process
def: "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_metagenomics
subset: goslim_pir
+subset: prokaryote_subset
synonym: "RNA metabolism" EXACT []
is_a: GO:0090304 ! nucleic acid metabolic process
@@ -116238,6 +116223,7 @@ def: "The chemical reactions and pathways involving mRNA, messenger RNA, which i
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pombe
+subset: prokaryote_subset
synonym: "mRNA metabolism" EXACT []
is_a: GO:0016070 ! RNA metabolic process
@@ -116344,7 +116330,7 @@ relationship: part_of GO:0016079 ! synaptic vesicle exocytosis
id: GO:0016081
name: synaptic vesicle docking
namespace: biological_process
-def: "The initial (indirect) attachment of a synaptic vesicle membrane to the presynaptic active zone membrane, mediated by proteins protruding from the membrane and proteins of the presynaptic active zone cytoplasmic component. Synaptic vesicle tethering is the first step in this process." [PMID:15217342]
+def: "The initial (indirect) attachment of a synaptic vesicle membrane to the presynaptic active zone membrane, mediated by proteins protruding from the membrane and proteins of the presynaptic active zone cytoplasmic component. Synaptic vesicle tethering is the first step in this process." [PMID:15217342]
comment: Although this process can occur outside of synaptic transmission, by convention we treat it as a part of synaptic transmission (dos, pvn, fk synapse project 2015).
subset: goslim_synapse
synonym: "synaptic vesicle docking during exocytosis" RELATED [GOC:dph, GOC:tb]
@@ -116357,7 +116343,7 @@ id: GO:0016082
name: synaptic vesicle priming
namespace: biological_process
def: "A process that converts synaptic vesicles to a state of competence for calcium triggered fusion with the active zone membrane by bringing the two membranes into very close proximity. Priming typically (but not always) occurs after docking (Jahn and Fasshauer, 2012). Primed vesicles are also capable of spontaneously fusing with the active zone membrane." [GOC:mah, PMID:15217342, PMID:23060190]
-comment: Although this process can occur outside of synaptic transmission, by convention we treat it as a part of synaptic transmission. (dos, pvn, fk synapse project 2015)
+comment: Although this process can occur outside of synaptic transmission, by convention we treat it as a part of synaptic transmission. (dos, pvn, fk synapse project 2015)
subset: goslim_synapse
is_a: GO:0065003 ! protein-containing complex assembly
is_a: GO:0140029 ! exocytic process
@@ -116894,7 +116880,6 @@ xref: MetaCyc:PWY-2582
xref: MetaCyc:PWY-699
is_a: GO:0016129 ! phytosteroid biosynthetic process
is_a: GO:0016131 ! brassinosteroid metabolic process
-is_a: GO:0120178 ! steroid hormone biosynthetic process
[Term]
id: GO:0016133
@@ -117091,7 +117076,7 @@ id: GO:0016152
name: mercury (II) reductase activity
namespace: molecular_function
alt_id: GO:0018692
-def: "Catalysis of the reaction: H(+) + Hg + NADP(+) = Hg(2+) + NADPH." [RHEA:23856]
+def: "Catalysis of the reaction: H+ + Hg + NADP+ = Hg2+ + NADPH." [RHEA:23856]
synonym: "Hg:NADP+ oxidoreductase activity" RELATED [EC:1.16.1.1]
synonym: "mer A" RELATED [EC:1.16.1.1]
synonym: "mercurate(II) reductase activity" RELATED [EC:1.16.1.1]
@@ -117111,7 +117096,7 @@ is_a: GO:0016723 ! oxidoreductase activity, acting on metal ions, NAD or NADP as
id: GO:0016153
name: urocanate hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-imidazolone-5-propanoate + H(+) = trans-urocanate + H(2)O." [EC:4.2.1.49, RHEA:13101]
+def: "Catalysis of the reaction: 4-imidazolone-5-propanoate + H+ = trans-urocanate + H2O." [EC:4.2.1.49, RHEA:13101]
synonym: "3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate hydro-lyase (urocanate-forming)" RELATED [EC:4.2.1.49]
synonym: "3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate hydro-lyase activity" RELATED [EC:4.2.1.49]
synonym: "imidazolonepropionate hydrolase activity" RELATED [EC:4.2.1.49]
@@ -117138,7 +117123,7 @@ is_a: GO:0016763 ! pentosyltransferase activity
id: GO:0016155
name: formyltetrahydrofolate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 10-formyltetrahydrofolate + H(2)O + NADP(+) = (6S)-5,6,7,8-tetrahydrofolate + CO(2) + H(+) + NADPH." [EC:1.5.1.6, RHEA:10180]
+def: "Catalysis of the reaction: 10-formyltetrahydrofolate + H2O + NADP+ = (6S)-5,6,7,8-tetrahydrofolate + CO2 + H+ + NADPH." [EC:1.5.1.6, RHEA:10180]
synonym: "10-formyl tetrahydrofolate:NADP oxidoreductase activity" RELATED [EC:1.5.1.6]
synonym: "10-formyl-H2PtGlu:NADP oxidoreductase activity" RELATED [EC:1.5.1.6]
synonym: "10-formyl-H4folate dehydrogenase activity" RELATED [EC:1.5.1.6]
@@ -117155,7 +117140,7 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0016156
name: fumarate reductase (NADH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD(+) + succinate = fumarate + H(+) + NADH." [EC:1.3.1.6, RHEA:18281]
+def: "Catalysis of the reaction: NAD+ + succinate = fumarate + H+ + NADH." [EC:1.3.1.6, RHEA:18281]
synonym: "NADH-dependent fumarate reductase activity" RELATED [EC:1.3.1.6]
synonym: "NADH-fumarate reductase activity" RELATED [EC:1.3.1.6]
synonym: "succinate:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.6]
@@ -117201,7 +117186,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0016159
name: muconolactone delta-isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,5-dihydro-5-oxofuran-2-acetate = 3,4-dihydro-5-oxofuran-2-acetate." [EC:5.3.3.4]
+def: "Catalysis of the reaction: (S)-muconolactone = (4,5-dihydro-5-oxofuran-2-yl)-acetate." [RHEA:12348]
synonym: "5-oxo-4,5-dihydrofuran-2-acetate delta3-delta2-isomerase activity" RELATED [EC:5.3.3.4]
synonym: "muconolactone D-isomerase activity" EXACT []
synonym: "muconolactone isomerase activity" RELATED [EC:5.3.3.4]
@@ -117221,9 +117206,9 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0016161
name: beta-amylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (1,4-alpha-D-glucosyl)(n+1) + H2O = (1,4-alpha-D-glucosyl)(n-1) + alpha-maltose. This reaction is the hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains." [EC:3.2.1.2]
-synonym: "1,4-alpha-D-glucan maltohydrolase activity" RELATED [EC:3.2.1.2]
-synonym: "beta amylase activity" RELATED [EC:3.2.1.2]
+def: "Catalysis of the reaction: (1,4-alpha-D-glucosyl)(n+1) + H2O = (1,4-alpha-D-glucosyl)(n-1) + alpha-maltose. This reaction is the hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains." [PMID:18390594]
+synonym: "4-alpha-D-glucan maltohydrolase activity" RELATED [EC:3.2.1.2]
+synonym: "beta amylase activity" RELATED []
synonym: "glycogenase activity" BROAD [EC:3.2.1.2]
synonym: "saccharogen amylase activity" RELATED [EC:3.2.1.2]
xref: EC:3.2.1.2
@@ -117398,7 +117383,6 @@ name: superoxide-generating NAD(P)H oxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: NAD(P)H + O2 = NAD(P)H + O2-." [GOC:ai, PMID:10806195]
synonym: "cytochrome B-245" RELATED []
-xref: EC:1.6.3.-
xref: Reactome:R-HSA-1222376 "NOX2 generates superoxide from oxygen"
xref: Reactome:R-HSA-1236967 "Alkalization of the phagosomal lumen by NOX2"
xref: Reactome:R-HSA-1497810 "Uncoupled eNOS favours the formation of superoxide"
@@ -117415,7 +117399,7 @@ is_a: GO:0050664 ! oxidoreductase activity, acting on NAD(P)H, oxygen as accepto
id: GO:0016176
name: superoxide-generating NADPH oxidase activator activity
namespace: molecular_function
-def: "Increases the activity of the enzyme superoxide-generating NADPH oxidase." [GOC:ai]
+def: "Binds to and increases the activity of the enzyme superoxide-generating NADPH oxidase." [GOC:ai]
synonym: "neutrophil cytosol factor 2" NARROW []
is_a: GO:0008047 ! enzyme activator activity
@@ -117423,7 +117407,9 @@ is_a: GO:0008047 ! enzyme activator activity
id: GO:0016180
name: snRNA processing
namespace: biological_process
-def: "Any process involved in the conversion of a primary small nuclear RNA (snRNA) transcript into a mature snRNA molecule." [GOC:jl]
+def: "Any process involved in the conversion of a primary small nuclear RNA (snRNA) transcript into a mature snRNA molecule. The primary function of snRNAs is processing pre-messenger RNA in the nucleus. They have also been shown to aid in the regulation of transcription factors (7SK RNA) or RNA polymerase II (B2 RNA), and maintaining the telomeres." [PMID:15196465, PMID:31815536]
+synonym: "snRNA maturation" EXACT []
+synonym: "snRNA production" EXACT []
is_a: GO:0016073 ! snRNA metabolic process
is_a: GO:0034470 ! ncRNA processing
@@ -117503,7 +117489,7 @@ id: GO:0016189
name: synaptic vesicle to endosome fusion
namespace: biological_process
def: "Fusion of a synaptic vesicle with an endosome." [GOC:curators, PMID:10099709]
-comment: This covers fusion of synaptic vesicles trafficked to the synapse as well as fusion of endocytosed vesicles as part of recycling. It is there for not part of the synaptic vesicle cycle.
+comment: This covers fusion of synaptic vesicles trafficked to the synapse as well as fusion of endocytosed vesicles as part of recycling. It is there for not part of the synaptic vesicle cycle.
subset: goslim_synapse
is_a: GO:0007032 ! endosome organization
is_a: GO:0048284 ! organelle fusion
@@ -117526,7 +117512,6 @@ name: vesicle-mediated transport
namespace: biological_process
alt_id: GO:0006899
def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -117687,6 +117672,7 @@ def: "Inhibition of the reactions brought about by dioxygen (O2) or peroxides. U
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
+subset: prokaryote_subset
is_a: GO:0003674 ! molecular_function
[Term]
@@ -117733,7 +117719,7 @@ is_a: GO:0036137 ! kynurenine aminotransferase activity
id: GO:0016213
name: linoleoyl-CoA desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: linoleoyl-CoA + reduced acceptor + O2 = gamma-linolenoyl-CoA + acceptor + 2 H2O." [PMID:12713571, PMID:7212717, RHEA:47140]
+def: "Catalysis of the reaction: (9Z,12Z)-octadecadienoyl-CoA + 2 Fe(II)-[cytochrome b5] + 2 H+ + O2 = (6Z,9Z,12Z)-octadecatrienoyl-CoA + 2 Fe(III)-[cytochrome b5] + 2 H2O. Can also use a substrate with 3 double bonds (a (9Z,12Z,15Z)-octadecatrienoyl-CoA and add a fourth double bond (a (6Z,9Z,12Z,15Z)-octadecatetraenoyl-CoA)." [PMID:12713571, PMID:7212717, RHEA:47140, RHEA:47144]
comment: Note that this function was formerly EC:1.14.99.25.
synonym: "delta(6)-acyl CoA desaturase activity" BROAD []
synonym: "delta(6)-desaturase activity" BROAD []
@@ -117757,22 +117743,22 @@ xref: Reactome:R-HSA-2046084 "Desaturation of alpha-linoleoyl-CoA to Stearidonoy
xref: Reactome:R-HSA-2046096 "Desaturation of Linoleoyl-CoA to gamma-linolenoyl-CoA"
xref: Reactome:R-HSA-2046097 "Desaturation of tetracosatetraenoyl-CoA to tetracosapentaenoyl-CoA"
xref: Reactome:R-HSA-2046099 "Desaturation of tetracosapentaenoyl-CoA to tetracosahexaenoyl-CoA"
-xref: RHEA:47140
is_a: GO:0016215 ! acyl-CoA desaturase activity
[Term]
id: GO:0016215
name: acyl-CoA desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + reduced acceptor + O2 = desaturated-acyl-CoA + acceptor + 2 H2O." [GOC:mah]
+def: "Catalysis of the reaction: AH2 + O2 + octadecanoyl-CoA = (9Z)-octadecenoyl-CoA + A + 2 H2O." [RHEA:25416]
synonym: "CoA desaturase activity" BROAD []
+xref: RHEA:25416
is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
[Term]
id: GO:0016216
name: isopenicillin-N synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine + O(2) = 2 H(2)O + isopenicillin N." [EC:1.21.3.1, RHEA:22428]
+def: "Catalysis of the reaction: N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine + O2 = 2 H2O + isopenicillin N." [EC:1.21.3.1, RHEA:22428]
synonym: "isopenicillin N synthase activity" RELATED [EC:1.21.3.1]
synonym: "isopenicillin-N synthetase activity" EXACT []
synonym: "N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine:oxygen oxidoreductase (cyclizing)" RELATED [EC:1.21.3.1]
@@ -117792,14 +117778,11 @@ is_a: GO:0019120 ! hydrolase activity, acting on acid halide bonds, in C-halide
[Term]
id: GO:0016218
-name: obsolete polyketide synthase activity
+name: polyketide synthase activity
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
-comment: This term was made obsolete because the activity it describes does not exist, and the gene product with the name 'polyketide synthase' has multiple functional domains, so using the name to describe a single function would be misleading.
-synonym: "polyketide synthase activity" EXACT []
-is_obsolete: true
-replaced_by: GO:0030639
-consider: GO:0034081
+def: "Catalysis of a multistep reaction that produce polyketides through decarboxylative condensation of carboxylic acids. The key chain-building reaction, a C-N bond-forming reaction, involves the generation of the characteristic peptide bond by nucleophilic attack of the amino group of an amino-acyl donor unit covalently bound to a downstream peptidyl carrier protein module (amino acyl-S-PCP) on the acyl group of an upstream electrophilic acyl- or peptidyl acyl-S-PCP chain, catalyzed by a condensation (C) domain. Supplementing these core chain-elongation domains are variable numbers of auxiliary domains that are responsible for modification of the growing polypeptide chain by a small set of iterated reactions including epimerization, N-methylation, and heterocyclization." [PMID:10631508]
+synonym: "PKS activity" RELATED []
+is_a: GO:0003824 ! catalytic activity
[Term]
id: GO:0016222
@@ -117868,7 +117851,7 @@ is_a: GO:0016491 ! oxidoreductase activity
id: GO:0016230
name: sphingomyelin phosphodiesterase activator activity
namespace: molecular_function
-def: "Increases the activity of the enzyme sphingomyelin phosphodiesterase." [GOC:ai]
+def: "Binds to and increases the activity of the enzyme sphingomyelin phosphodiesterase." [GOC:ai]
synonym: "neutral sphingomyelinase activator" EXACT []
is_a: GO:0016004 ! phospholipase activator activity
@@ -117920,8 +117903,8 @@ id: GO:0016236
name: macroautophagy
namespace: biological_process
alt_id: GO:0034262
-def: "The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Some types of macroautophagy, e.g. pexophagy, mitophagy, involve selective targeting of the targets to be degraded." [PMID:11099404, PMID:12914914, PMID:15798367, PMID:16973210, PMID:20159618, PMID:9412464]
-comment: Targeted macroautophagy sometimes targets regions of cytoplasm containing non-self, such as virus particles or components (e.g. see PMID:20159618). As this is essentially the same process as macroautophagy that encloses and digests only self, the term autophagy is still used despite the enclosure of some non-self (non-auto) entities.
+def: "The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Some types of macroautophagy, e.g. pexophagy, mitophagy, involve selective targeting of the targets to be degraded." [PMID:11099404, PMID:12914914, PMID:15798367, PMID:16973210, PMID:20159618, PMID:9412464]
+comment: Targeted macroautophagy sometimes targets regions of cytoplasm containing non-self, such as virus particles or components (e.g. see PMID:20159618). As this is essentially the same process as macroautophagy that encloses and digests only self, the term autophagy is still used despite the enclosure of some non-self (non-auto) entities.
synonym: "autophagy" BROAD []
is_a: GO:0006914 ! autophagy
@@ -117988,23 +117971,12 @@ synonym: "regulation of autophagic vacuole size" EXACT [GOC:autophagy]
is_a: GO:0032535 ! regulation of cellular component size
is_a: GO:1905037 ! autophagosome organization
-[Term]
-id: GO:0016246
-name: RNA interference
-namespace: biological_process
-def: "The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes." [GOC:ems, PMID:11201747, PMID:11713190, PMID:18771919]
-comment: Note that this term refers specifically to posttranscriptional mechanisms by which small interfering RNAs down-regulate gene expression. Also consider annotating to other descendants of 'gene silencing by RNA ; GO:0031047'.
-synonym: "posttranscriptional gene silencing by siRNA" EXACT [GOC:mah]
-synonym: "RNAi" EXACT []
-xref: Wikipedia:RNA_interference
-is_a: GO:0035194 ! post-transcriptional gene silencing by RNA
-
[Term]
id: GO:0016247
name: channel regulator activity
namespace: molecular_function
-def: "Bonds to and modulates the activity of a channel. A channel catalyzes energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel." [GOC:mah]
-is_a: GO:0098772 ! molecular function regulator
+def: "Binds to and modulates the activity of a channel. A channel catalyzes energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel." [GOC:mah]
+is_a: GO:0098772 ! molecular function regulator activity
[Term]
id: GO:0016248
@@ -118012,7 +117984,6 @@ name: channel inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents, or reduces the activity of a channel." [GOC:mah]
is_a: GO:0016247 ! channel regulator activity
-is_a: GO:0140678 ! molecular function inhibitor activity
[Term]
id: GO:0016250
@@ -118078,7 +118049,7 @@ id: GO:0016255
name: attachment of GPI anchor to protein
namespace: biological_process
def: "A transamidation reaction that results in the cleavage of the polypeptide chain and the concomitant transfer of the GPI anchor to the newly formed carboxy-terminal amino acid of the anchored protein. The cleaved C-terminal contains the C-terminal GPI signal sequence of the newly synthesized polypeptide chain." [ISBN:0879695595]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
relationship: part_of GO:0006506 ! GPI anchor biosynthetic process
[Term]
@@ -118141,6 +118112,7 @@ namespace: molecular_function
alt_id: GO:0016253
def: "Catalysis of the reaction: UDP-N-acetyl-D-glucosamine + protein = UDP + 4-N-(N-acetyl-D-glucosaminyl)-protein." [EC:2.4.1.94]
synonym: "N-GlcNAc transferase activity" RELATED [EC:2.4.1.94]
+synonym: "protein N-GlcNAc transferase activity" EXACT []
synonym: "UDP-N-acetyl-D-glucosamine:protein beta-N-acetyl-D-glucosaminyl-transferase activity" EXACT []
synonym: "UDP-N-acetylglucosamine-peptide N-acetylglucosaminyltransferase activity" EXACT []
synonym: "uridine diphospho-N-acetylglucosamine:polypeptide beta-N-acetylglucosaminyltransferase activity" EXACT []
@@ -118271,29 +118243,23 @@ is_a: GO:0016273 ! arginine N-methyltransferase activity
[Term]
id: GO:0016275
-name: [cytochrome c]-arginine N-methyltransferase activity
+name: obsolete [cytochrome c]-arginine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + (cytochrome c)-arginine = S-adenosyl-L-homocysteine + (cytochrome c)-N(omega)-methyl-arginine." [EC:2.1.1.124, GOC:ma]
-synonym: "cytochrome c-arginine N-methyltransferase activity" RELATED [EC:2.1.1.124]
-synonym: "S-adenosyl-L-methionine:cytochrome c-arginine nomega-methyltransferasea" RELATED [EC:2.1.1.124]
-synonym: "S-adenosyl-L-methionine:cytochrome c-arginine omega-N-methyltransferasea" RELATED [EC:2.1.1.124]
-xref: EC:2.1.1.124
-xref: MetaCyc:2.1.1.124-RXN
-xref: RHEA:21872
-is_a: GO:0016274 ! protein-arginine N-methyltransferase activity
+def: "OBSOLETE. Catalysis of the reaction: S-adenosyl-L-methionine + (cytochrome c)-arginine = S-adenosyl-L-homocysteine + (cytochrome c)-N(omega)-methyl-arginine." [GOC:ma]
+comment: Specific substrate mentioned
+synonym: "cytochrome c-arginine N-methyltransferase activity" RELATED []
+synonym: "S-adenosyl-L-methionine:cytochrome c-arginine nomega-methyltransferasea" RELATED []
+synonym: "S-adenosyl-L-methionine:cytochrome c-arginine omega-N-methyltransferasea" RELATED []
+is_obsolete: true
+replaced_by: GO:0035241
[Term]
id: GO:0016277
-name: [myelin basic protein]-arginine N-methyltransferase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + (myelin basic protein)-arginine = S-adenosyl-L-homocysteine + (myelin basic protein)-N(omega)-methyl-arginine." [PMID:6177833]
-synonym: "myelin basic protein methylase activity" RELATED [EC:2.1.1.126]
-synonym: "myelin basic protein methylase I" RELATED [EC:2.1.1.126]
-synonym: "myelin basic protein-arginine N-methyltransferase activity" RELATED [EC:2.1.1.126]
-synonym: "protein methylase I activity" BROAD [EC:2.1.1.126]
-synonym: "S-adenosyl-L-methionine:myelin-basic-protein-arginine nomega-methyltransferase activity" RELATED [EC:2.1.1.126]
-synonym: "S-adenosyl-L-methionine:myelin-basic-protein-arginine omega-N-methyltransferase activity" RELATED [EC:2.1.1.126]
-is_a: GO:0016274 ! protein-arginine N-methyltransferase activity
+name: obsolete [myelin basic protein]-arginine N-methyltransferase activity
+namespace: molecular_function
+def: "OBSOLETE. Catalysis of the reaction: S-adenosyl-L-methionine + (myelin basic protein)-arginine = S-adenosyl-L-homocysteine + (myelin basic protein)-N(omega)-methyl-arginine." [PMID:6177833]
+comment: This term represents an activity acting on a specfic gene product (not a class). the myelin bsic protein is often used as a substrate for assaying for enzyme activity. The orginal EC for this entry has been depreciated and transferred to 4 other ECs.
+is_obsolete: true
[Term]
id: GO:0016278
@@ -118312,6 +118278,8 @@ id: GO:0016279
name: protein-lysine N-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate." [PMID:12054878]
+synonym: "protein (lysine) methyltransferase activity" EXACT []
+synonym: "protein lysine methylase activity" EXACT []
xref: Reactome:R-HSA-212263 "PRC2 trimethylates histone H3 at lysine-27"
xref: Reactome:R-HSA-8865237 "SETD6 methylates RELA in the NFkB complex"
xref: Reactome:R-HSA-8931858 "ETFBKMT transfers 3xCH3 from 3xAdoMet to ETFB"
@@ -118321,6 +118289,7 @@ xref: Reactome:R-HSA-8932243 "EEF2KMT transfers 3xCH3 from 3xAdoMet to EEF2"
xref: Reactome:R-HSA-8932275 "METTL22 transfers 3xCH3 from 3xAdoMet to KIN"
xref: Reactome:R-HSA-8932276 "VCPKMT (METTL21D) transfers 3xCH3 from 3xAdoMet to VCP"
xref: Reactome:R-HSA-8932413 "METTL10 transfers 3xCH3 from 3xAdoMet to EEF1A1"
+xref: RHEA:51736
is_a: GO:0008276 ! protein methyltransferase activity
is_a: GO:0016278 ! lysine N-methyltransferase activity
@@ -118338,7 +118307,7 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0016282
name: eukaryotic 43S preinitiation complex
namespace: cellular_component
-def: "A protein complex composed of the 40S ribosomal subunit plus eIF1A, eIF3, and eIF2-GTP-bound methionyl-initiator methionine tRNA." [GOC:hjd, PMID:15145049]
+def: "A protein complex composed of the 40S ribosomal subunit plus eIF1, eIF1A, eIF3, eIF5, and eIF2-GTP-bound methionyl-initiator methionine tRNA." [GOC:hjd, PMID:15145049, PMID:16510876, PMID:25742741, PMID:29735639]
synonym: "eukaryotic 43S pre-initiation complex" EXACT []
is_a: GO:0070993 ! translation preinitiation complex
@@ -118482,11 +118451,9 @@ is_a: GO:0016790 ! thiolester hydrolase activity
id: GO:0016298
name: lipase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of a lipid or phospholipid." [GOC:mah]
-subset: goslim_aspergillus
+def: "Catalysis of the hydrolysis of a lipid or phospholipid." [GOC:mah, ISBN:0198506732]
subset: goslim_chembl
subset: goslim_drosophila
-xref: EC:3.1.1.-
xref: Reactome:R-HSA-163402 "diacylglycerol + H2O -> 2-acylglycerol + fatty acid"
xref: Reactome:R-HSA-163432 "cholesterol ester + H2O -> cholesterol + fatty acid"
is_a: GO:0016788 ! hydrolase activity, acting on ester bonds
@@ -118538,7 +118505,7 @@ id: GO:0016303
name: 1-phosphatidylinositol-3-kinase activity
namespace: molecular_function
alt_id: GO:0004429
-def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ADP + 2 H(+)." [EC:2.7.1.137, RHEA:12709]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ADP + 2 H+." [EC:2.7.1.137, RHEA:12709]
synonym: "1-phosphatidylinositol 3-kinase activity" EXACT []
synonym: "ATP:1-phosphatidyl-1D-myo-inositol 3-phosphotransferase activity" RELATED [EC:2.7.1.137]
synonym: "phosphatidylinositol 3-kinase activity, class I" NARROW []
@@ -118605,7 +118572,7 @@ name: phosphatidylinositol phosphate kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + a phosphatidylinositol phosphate = ADP + a phosphatidylinositol bisphosphate." [EC:2.7.1.-, PMID:9759495]
synonym: "phosphatidylinositol monophosphate kinase activity" EXACT [GOC:bf]
-is_a: GO:0016301 ! kinase activity
+is_a: GO:0001727 ! lipid kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
[Term]
@@ -118614,7 +118581,7 @@ name: 1-phosphatidylinositol-4-phosphate 5-kinase activity
namespace: molecular_function
alt_id: GO:0004431
alt_id: GO:0045215
-def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4-phosphate + ATP = 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ADP + 2 H(+)." [EC:2.7.1.68, RHEA:14425]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4-phosphate + ATP = 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ADP + 2 H+." [EC:2.7.1.68, RHEA:14425]
synonym: "1-phosphatidylinositol-4-phosphate kinase activity" BROAD []
synonym: "1-phosphatidylinositol-4-phosphate kinase, class IA" NARROW []
synonym: "1-phosphatidylinositol-4-phosphate kinase, class IB" NARROW []
@@ -118622,6 +118589,7 @@ synonym: "ATP:1-phosphatidyl-1D-myo-inositol-4-phosphate 5-phosphotransferase ac
synonym: "diphosphoinositide kinase activity" BROAD [EC:2.7.1.68]
synonym: "phosphatidylinositol 4-phosphate kinase activity" BROAD [EC:2.7.1.68]
synonym: "phosphatidylinositol-4-phosphate 5-kinase activity" RELATED [EC:2.7.1.68]
+synonym: "PI(4)5K" RELATED []
synonym: "PIP kinase activity" BROAD [EC:2.7.1.68]
synonym: "PIP5K" EXACT []
synonym: "PtdIns(4)P-5-kinase activity" RELATED [EC:2.7.1.68]
@@ -118713,13 +118681,14 @@ id: GO:0016316
name: phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity
namespace: molecular_function
alt_id: GO:0004440
-def: "Catalysis of the reaction: 1-phosphatidyl-myo-inositol 3,4-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 3-phosphate + phosphate." [EC:3.1.3.66, GOC:hb]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 3-phosphate + phosphate." [GOC:hb, RHEA:17193]
synonym: "1-phosphatidyl-1D-myo-inositol-3,4-bisphosphate 4-phosphohydrolase activity" RELATED [EC:3.1.3.66]
synonym: "inositol polyphosphate 4-phosphatase type II activity" RELATED [EC:3.1.3.66]
xref: EC:3.1.3.66
xref: MetaCyc:3.1.3.66-RXN
xref: Reactome:R-HSA-1676162 "PI(3,4)P2 is dephosphorylated to PI3P by INPP4A/B at the early endosome membrane"
xref: Reactome:R-HSA-1676164 "PI(3,4)P2 is dephosphorylated to PI3P by INPP4A/B at the plasma membrane"
+xref: RHEA:17193
is_a: GO:0034596 ! phosphatidylinositol phosphate 4-phosphatase activity
is_a: GO:0106017 ! phosphatidylinositol-3,4-bisphosphate phosphatase activity
@@ -118985,7 +118954,6 @@ synonym: "calcium-independent cell adhesion molecule activity" EXACT []
is_obsolete: true
consider: GO:0005515
consider: GO:0007161
-consider: GO:0016021
consider: GO:0016338
[Term]
@@ -119089,7 +119057,7 @@ name: activin receptor activity, type I
namespace: molecular_function
def: "Combining with activin-bound type II activin receptor to initiate a change in cell activity; upon binding, acts as a downstream transducer of activin signals." [GOC:mah, PMID:8622651]
synonym: "type I activin receptor activity" EXACT []
-is_a: GO:0017002 ! activin-activated receptor activity
+is_a: GO:0017002 ! activin receptor activity
[Term]
id: GO:0016362
@@ -119098,7 +119066,7 @@ namespace: molecular_function
def: "Combining with activin to initiate a change in cell activity; upon ligand binding, binds to and catalyses the phosphorylation of a type I activin receptor." [GOC:mah, PMID:8622651]
synonym: "type II activin receptor activity" EXACT []
xref: Reactome:R-HSA-201443 "Type II receptor phosphorylates type I receptor"
-is_a: GO:0017002 ! activin-activated receptor activity
+is_a: GO:0017002 ! activin receptor activity
[Term]
id: GO:0016363
@@ -119115,7 +119083,6 @@ id: GO:0016401
name: palmitoyl-CoA oxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: palmitoyl-CoA + O2 = trans-2,3-dehydropalmitoyl-CoA + hydrogen peroxide." [GOC:jsg]
-xref: EC:1.3.3.-
is_a: GO:0003997 ! acyl-CoA oxidase activity
[Term]
@@ -119171,9 +119138,10 @@ name: CoA-ligase activity
namespace: molecular_function
def: "Catalysis of the reaction: substrate + ATP + CoASH = AMP + diphosphate + substrate-CoA." [GOC:ai]
xref: Reactome:R-HSA-159443 "benzoate + Coenzyme A + ATP => benzoyl-CoA + AMP + pyrophosphate"
-xref: Reactome:R-HSA-159567 "salicylic acid + Coenzyme A + ATP => salicylate-CoA + AMP + pyrophosphate"
+xref: Reactome:R-HSA-159567 "ACSM2B-like proteins transform ST to ST-CoA"
xref: Reactome:R-HSA-177157 "phenylacetate + Coenzyme A + ATP => phenylacetyl-CoA + AMP + pyrophosphate"
xref: Reactome:R-HSA-6798345 "PXLP-GCAT dimer ligates CoASH to 2A-3OB to form Gly and Ac-CoA"
+xref: Reactome:R-HSA-9749971 "ACSM2B-like proteins transform 2,5-DHBA to 2,5-DHB-CoA"
is_a: GO:0016877 ! ligase activity, forming carbon-sulfur bonds
[Term]
@@ -119285,7 +119253,6 @@ id: GO:0016418
name: S-acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of an acetyl group to a sulfur atom on the acceptor molecule." [GOC:ai]
-xref: EC:2.3.1.38
is_a: GO:0016407 ! acetyltransferase activity
is_a: GO:0016417 ! S-acyltransferase activity
@@ -119355,10 +119322,11 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0016428
name: tRNA (cytosine-5-)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 5-methylcytosine." [EC:2.1.1.29]
-synonym: "S-adenosyl-L-methionine:tRNA (cytosine-5-)-methyltransferase activity" RELATED [EC:2.1.1.29]
-synonym: "transfer ribonucleate cytosine 5-methyltransferase activity" RELATED [EC:2.1.1.29]
-synonym: "transfer RNA cytosine 5-methyltransferase activity" RELATED [EC:2.1.1.29]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 5-methylcytosine." [GOC:curators]
+synonym: "S-adenosyl-L-methionine:tRNA (cytosine-5-)-methyltransferase activity" RELATED []
+synonym: "transfer ribonucleate cytosine 5-methyltransferase activity" RELATED []
+synonym: "transfer RNA cytosine 5-methyltransferase activity" RELATED []
+xref: EC:2.1.1.202
xref: Reactome:R-HSA-6782388 "NSUN2 methylates cytidine-34, cytidine-48 of unspliced tRNA(Leu)(CAA)"
xref: Reactome:R-HSA-6782419 "TRDMT1 (DNMT2) methylates cytidine-38 of tRNA(Asp)"
xref: Reactome:R-HSA-6785409 "NSUN2 methylates cytidine-48 and cytidine-49 of tRNA(Asp)(GUC)"
@@ -119435,35 +119403,6 @@ namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methyluridine." [GOC:go-curators]
is_a: GO:0008649 ! rRNA methyltransferase activity
-[Term]
-id: GO:0016437
-name: tRNA cytidylyltransferase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: CTP + tRNA(n) = diphosphate + tRNA(n+1)." [EC:2.7.7.21]
-synonym: "-C-C-A pyrophosphorylase" BROAD [EC:2.7.7.21]
-synonym: "ATP (CTP):tRNA nucleotidyltransferase" BROAD []
-synonym: "ATP(CTP)-tRNA nucleotidyltransferase" BROAD []
-synonym: "ATP(CTP):tRNA nucleotidyltransferase activity" BROAD []
-synonym: "CTP(ATP):tRNA nucleotidyltransferase" BROAD []
-synonym: "CTP:tRNA cytidylyltransferase activity" BROAD []
-synonym: "ribonucleic cytidylic cytidylic adenylic pyrophosphorylase" BROAD []
-synonym: "ribonucleic cytidylyltransferase" BROAD []
-synonym: "transfer ribonucleate adenylyltransferase" BROAD []
-synonym: "transfer ribonucleate cytidylyltransferase" BROAD [EC:2.7.7.21]
-synonym: "transfer ribonucleate nucleotidyltransferase" BROAD []
-synonym: "transfer ribonucleic acid nucleotidyl transferase" BROAD []
-synonym: "transfer ribonucleic adenylyl (cytidylyl) transferase" BROAD []
-synonym: "transfer ribonucleic-terminal trinucleotide nucleotidyltransferase" BROAD []
-synonym: "transfer RNA adenylyltransferase" BROAD []
-synonym: "transfer-RNA nucleotidyltransferase" BROAD []
-synonym: "tRNA adenylyl(cytidylyl)transferase" BROAD []
-synonym: "tRNA CCA-diphosphorylase activity" RELATED [EC:2.7.7.21]
-synonym: "tRNA CCA-pyrophosphorylase activity" RELATED [EC:2.7.7.21]
-xref: EC:2.7.7.72
-xref: MetaCyc:TRNA-CYTIDYLYLTRANSFERASE-RXN
-is_a: GO:0070567 ! cytidylyltransferase activity
-is_a: GO:0140101 ! catalytic activity, acting on a tRNA
-
[Term]
id: GO:0016438
name: tRNA-queuosine beta-mannosyltransferase activity
@@ -119478,15 +119417,13 @@ is_a: GO:0140101 ! catalytic activity, acting on a tRNA
[Term]
id: GO:0016441
-name: posttranscriptional gene silencing
+name: post-transcriptional gene silencing
namespace: biological_process
-def: "The inactivation of gene expression by a posttranscriptional mechanism." [GOC:mah, PMID:15020054]
-synonym: "cosuppression" RELATED []
-synonym: "post-transcriptional gene silencing" EXACT [GOC:vw]
+def: "The inactivation of gene expression that occurs after transcription." [GOC:mah, PMID:15020054]
+synonym: "posttranscriptional gene silencing" EXACT [GOC:vw]
synonym: "PTGS" EXACT []
-synonym: "quelling" EXACT []
xref: Wikipedia:Post_transcriptional_gene_silencing
-is_a: GO:0010608 ! posttranscriptional regulation of gene expression
+is_a: GO:0010608 ! post-transcriptional regulation of gene expression
is_a: GO:0010629 ! negative regulation of gene expression
[Term]
@@ -119621,7 +119558,7 @@ is_a: GO:0016459 ! myosin complex
id: GO:0016462
name: pyrophosphatase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments." [GOC:curators, https://en.wikipedia.org/wiki/Pyrophosphatase]
+def: "Catalysis of the hydrolysis of a pyrophosphate bond (diphosphate bond) between two phosphate groups." [GOC:curators, https://en.wikipedia.org/wiki/Pyrophosphatase]
xref: Reactome:R-HSA-6810472 "NUDT13 hydrolyses AP6A to AP4 and ADP"
is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
@@ -119643,7 +119580,7 @@ xref: EC:7.2.2.12
xref: MetaCyc:3.6.3.5-RXN
xref: RHEA:20621
is_a: GO:0015662 ! P-type ion transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
is_a: GO:0046915 ! transition metal ion transmembrane transporter activity
[Term]
@@ -119661,8 +119598,8 @@ is_a: GO:0015450 ! protein-transporting ATPase activity
id: GO:0016465
name: chaperonin ATPase complex
namespace: cellular_component
-def: "Multisubunit protein complex with 2x7 (Type I, in most cells) or 2x8 (Type II, in Archaea) ATP-binding sites involved in maintaining an unfolded polypeptide structure before folding or to entry into mitochondria and chloroplasts." [EC:3.6.4.9]
-is_a: GO:0101031 ! chaperone complex
+def: "Multisubunit protein complex with 2x7 (Type I, in most cells) or 2x8 (Type II, in Archaea) ATP-binding sites involved in maintaining an unfolded polypeptide structure before folding or to entry into mitochondria and chloroplasts." [PMID:24816391]
+is_a: GO:0101031 ! protein folding chaperone complex
relationship: part_of GO:0005829 ! cytosol
[Term]
@@ -119712,6 +119649,7 @@ subset: goslim_pir
synonym: "hydrogen-transporting two-sector ATPase complex" EXACT []
synonym: "vacuolar hydrogen-transporting ATPase" RELATED []
is_a: GO:0098796 ! membrane protein complex
+is_a: GO:1904949 ! ATPase complex
[Term]
id: GO:0016471
@@ -119731,7 +119669,6 @@ def: "A large protein complex that catalyzes the synthesis or hydrolysis of ATP
subset: goslim_pir
synonym: "sodium-transporting two-sector ATPase complex" EXACT []
is_a: GO:0098796 ! membrane protein complex
-relationship: part_of GO:0016021 ! integral component of membrane
[Term]
id: GO:0016473
@@ -119772,7 +119709,7 @@ is_a: GO:0045995 ! regulation of embryonic development
id: GO:0016477
name: cell migration
namespace: biological_process
-def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, Wikipedia:Cell_migration]
+def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, Wikipedia:Cell_migration]
xref: Wikipedia:Cell_migration
is_a: GO:0048870 ! cell motility
@@ -119788,7 +119725,7 @@ synonym: "inhibition of transcription from RNA polymerase I promoter" NARROW []
synonym: "negative regulation of transcription from Pol I promoter" EXACT []
synonym: "negative regulation of transcription from RNA polymerase I promoter" EXACT []
is_a: GO:0006356 ! regulation of transcription by RNA polymerase I
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
relationship: negatively_regulates GO:0006360 ! transcription by RNA polymerase I
[Term]
@@ -119803,7 +119740,7 @@ synonym: "inhibition of transcription from RNA polymerase III promoter" NARROW [
synonym: "negative regulation of transcription from Pol III promoter" EXACT []
synonym: "negative regulation of transcription from RNA polymerase III promoter" EXACT []
is_a: GO:0006359 ! regulation of transcription by RNA polymerase III
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
relationship: negatively_regulates GO:0006383 ! transcription by RNA polymerase III
[Term]
@@ -119889,7 +119826,6 @@ id: GO:0016491
name: oxidoreductase activity
namespace: molecular_function
def: "Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC:go_curators]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -119898,13 +119834,14 @@ subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "oxidoreductase activity, acting on other substrates" NARROW []
synonym: "redox activity" EXACT []
xref: EC:1.-.-.-
xref: Reactome:R-HSA-1614362 "SUMF1 mediates the oxidation of cysteine to formylglycine, producing active arylsulfatases"
xref: Reactome:R-HSA-209921 "Monoiodinated tyrosine can be deiodinated"
xref: Reactome:R-HSA-209960 "Diiodinated tyrosine can be deiodinated"
-xref: Reactome:R-HSA-3095889 "MMACHC reduces Cbl"
+xref: Reactome:R-HSA-3095889 "MMACHC dealkylates RCbl"
xref: Reactome:R-HSA-390425 "FAR1 reduces PalmCoA to HXOL"
xref: Reactome:R-HSA-390438 "FAR2 reduces PalmCoA to HXOL"
xref: Reactome:R-HSA-5662660 "Dopachrome is transformed to DHICA by DCT"
@@ -120020,7 +119957,7 @@ is_a: GO:0004930 ! G protein-coupled receptor activity
id: GO:0016504
name: peptidase activator activity
namespace: molecular_function
-def: "Binds to and increases the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds." [GOC:ai]
+def: "Binds to and increases the activity of a peptidase." [GOC:ai]
synonym: "protease activator activity" NARROW [GOC:mah]
xref: Reactome:R-HSA-168865 "NA activation of TGF-beta"
is_a: GO:0008047 ! enzyme activator activity
@@ -120057,25 +119994,20 @@ relationship: part_of GO:0005759 ! mitochondrial matrix
[Term]
id: GO:0016508
-name: long-chain-enoyl-CoA hydratase activity
+name: obsolete long-chain-enoyl-CoA hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a long-chain (3S)-3-hydroxyacyl-CoA = a long-chain trans-2-enoyl-CoA + H2O. A long-chain acyl-CoA is an acyl-CoA thioester where the acyl chain contains 13 to 22 carbon atoms." [EC:4.2.1.74]
+def: "OBSOLETE. Catalysis of the reaction: a medium-chain (3S)-3-hydroxyacyl-CoA = a medium-chain (2E)-enoyl-CoA + H2O. A long-chain acyl-CoA is an acyl-CoA thioester where the acyl chain contains 13 to 22 carbon atoms." [RHEA:71647]
+comment: This term was obsoleted because it represents a specific substrate of 3-hydroxyacyl-CoA dehydratase activity ; GO:0018812.
synonym: "long-chain enoyl coenzyme A hydratase activity" RELATED [EC:4.2.1.74]
synonym: "long-chain-(3S)-3-hydroxyacyl-CoA hydro-lyase activity" RELATED [EC:4.2.1.74]
-xref: EC:4.2.1.74
-xref: MetaCyc:LONG-CHAIN-ENOYL-COA-HYDRATASE-RXN
-xref: Reactome:R-HSA-2066778 "Hydration of delta2-tetracosaheptaenoyl-CoA to 3-hydroxy tetracosahexaenoyl-CoA"
-xref: Reactome:R-HSA-2066780 "Dehydrogenation of 3-hydroxy tetracosahexaenoyl-CoA"
-xref: Reactome:R-HSA-389986 "trans-2,3-dehydropristanoyl-CoA + H2O => 3-hydroxypristanoyl-CoA"
-xref: Reactome:R-HSA-390252 "HSD17B4 hydrates trans-2,3-dehydrohexacosanoyl-CoA"
-xref: Reactome:R-HSA-6809263 "EHHADH hydrates trans-2,3-dehydrohexacosanoyl-CoA"
-is_a: GO:0016836 ! hydro-lyase activity
+is_obsolete: true
+replaced_by: GO:0018812
[Term]
id: GO:0016509
name: long-chain-3-hydroxyacyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD(P)+ = 3-oxoacyl-CoA + NAD(P)H + H+, where the acyl group is a long-chain fatty acid residue. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [EC:1.1.1.211, GOC:pde]
+def: "Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD(P)+ = 3-oxoacyl-CoA + NAD(P)H + H+, where the acyl group is a long-chain fatty acid residue. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [EC:1.1.1.211, GOC:pde, RHEA:52656]
comment: Also see '3-hydroxyacyl-CoA dehydrogenase activity ; GO:0003857'.
synonym: "beta-hydroxyacyl-CoA dehydrogenase activity" RELATED [EC:1.1.1.211]
synonym: "LCHAD" RELATED [EC:1.1.1.211]
@@ -120084,6 +120016,7 @@ synonym: "long-chain-(S)-3-hydroxyacyl-CoA:NAD+ oxidoreductase activity" RELATED
xref: EC:1.1.1.211
xref: MetaCyc:1.1.1.211-RXN
xref: Reactome:R-HSA-548818 "HSD17B3,12 hydrogenates 3OOD-CoA to 3HODC-CoA"
+xref: RHEA:52656
is_a: GO:0003857 ! 3-hydroxyacyl-CoA dehydrogenase activity
[Term]
@@ -120141,7 +120074,6 @@ namespace: cellular_component
def: "A protein complex that binds interleukin-4 (IL-4) and consists of an alpha chain that binds IL-4 with high affinity and a gamma common chain that also forms part of the interleukin-2 receptor." [PMID:10358772]
synonym: "IL-4 receptor complex" EXACT [GOC:add]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0016517
@@ -120576,7 +120508,7 @@ namespace: biological_process
def: "The covalent alteration of one or more amino acid residues within a histone protein." [GOC:krc]
subset: goslim_yeast
xref: Wikipedia:Histone#Histone_modifications_in_chromatin_regulation
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0016571
@@ -120589,11 +120521,11 @@ is_a: GO:0016570 ! histone modification
[Term]
id: GO:0016572
-name: histone phosphorylation
+name: obsolete histone phosphorylation
namespace: biological_process
-def: "The modification of histones by addition of phosphate groups." [GOC:ai]
-is_a: GO:0006468 ! protein phosphorylation
-is_a: GO:0016570 ! histone modification
+def: "OBSOLETE. The modification of histones by addition of phosphate groups." [GOC:ai]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0016573
@@ -120623,11 +120555,12 @@ is_a: GO:0016570 ! histone modification
[Term]
id: GO:0016576
-name: histone dephosphorylation
+name: obsolete histone dephosphorylation
namespace: biological_process
-def: "The modification of histones by removal of phosphate groups." [GOC:ai]
-is_a: GO:0006470 ! protein dephosphorylation
-is_a: GO:0016570 ! histone modification
+def: "OBSOLETE. The modification of histones by removal of phosphate groups." [GOC:ai]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0140789
[Term]
id: GO:0016577
@@ -120670,7 +120603,7 @@ id: GO:0016581
name: NuRD complex
namespace: cellular_component
def: "An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins." [PMID:10589671, PMID:11743021, PMID:17289569]
-synonym: "Mi-2 complex" EXACT []
+synonym: "Mi-2 complex" NARROW []
synonym: "NRD complex" EXACT []
synonym: "nucleosome remodeling and histone deacetylation complex" EXACT []
is_a: GO:0000118 ! histone deacetylase complex
@@ -120697,12 +120630,15 @@ consider: GO:0006334
[Term]
id: GO:0016584
-name: nucleosome positioning
+name: obsolete nucleosome positioning
namespace: biological_process
-def: "Ordering of successions of nucleosomes into regular arrays so that nucleosomes are positioned at defined distances from one another." [GOC:bf, PMID:11447119, PMID:8676389]
+def: "OBSOLETE. Ordering of successions of nucleosomes into regular arrays so that nucleosomes are positioned at defined distances from one another." [GOC:bf, PMID:11447119, PMID:8676389]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "nucleosome spacing" EXACT []
-is_a: GO:0031497 ! chromatin assembly
-is_a: GO:0034728 ! nucleosome organization
+is_obsolete: true
+consider: GO:0140658
+consider: GO:0140750
+consider: GO:0140751
[Term]
id: GO:0016585
@@ -120793,7 +120729,6 @@ synonym: "aminoacetic acid binding" EXACT []
synonym: "aminoethanoic acid binding" EXACT []
synonym: "Gly binding" EXACT []
is_a: GO:0016597 ! amino acid binding
-is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0043169 ! cation binding
[Term]
@@ -120803,7 +120738,7 @@ namespace: molecular_function
def: "Binding to glutamate, the anion of 2-aminopentanedioic acid." [GOC:ai]
synonym: "glutamic acid binding" EXACT []
is_a: GO:0016597 ! amino acid binding
-is_a: GO:0031406 ! carboxylic acid binding
+is_a: GO:0033218 ! amide binding
[Term]
id: GO:0016596
@@ -120822,7 +120757,7 @@ namespace: molecular_function
def: "Binding to an amino acid, organic acids containing one or more amino substituents." [GOC:ai]
subset: goslim_metagenomics
subset: goslim_pir
-is_a: GO:0043177 ! organic acid binding
+is_a: GO:0031406 ! carboxylic acid binding
[Term]
id: GO:0016598
@@ -120831,7 +120766,7 @@ namespace: biological_process
alt_id: GO:0019130
def: "The conjugation of arginine to the N-terminal aspartate or glutamate of a protein; required for the degradation of the protein via the ubiquitin pathway." [PMID:17896865]
synonym: "protein amino acid arginylation" EXACT []
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
relationship: part_of GO:0006511 ! ubiquitin-dependent protein catabolic process
[Term]
@@ -120847,7 +120782,7 @@ relationship: part_of GO:0005901 ! caveola
id: GO:0016601
name: Rac protein signal transduction
namespace: biological_process
-def: "A series of molecular signals within the cell that are mediated by a member of the Rac family of proteins switching to a GTP-bound active state." [GOC:bf]
+def: "The series of molecular signals within the cell that are mediated by a member of the Rac family of proteins switching to a GTP-bound active state." [GOC:bf]
synonym: "Rac mediated signal transduction" EXACT []
is_a: GO:0007265 ! Ras protein signal transduction
@@ -120928,7 +120863,7 @@ is_a: GO:0005179 ! hormone activity
id: GO:0016610
name: nitrogenase complex
namespace: cellular_component
-def: "An enzyme complex composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase is tetrameric with an alpha2-beta2 structure and nitrogenase reductase is a homodimer, and both are associated with metal ions, which differ between species. Both proteins are required for the enzyme activity of the complex, the formation of oxidized ferredoxin and ammonia from reduced ferredoxin and nitrogen." [EC:1.18.6.1, MetaCyc:CPLX-186, MetaCyc:CPLX-525]
+def: "An enzyme complex composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase is tetrameric with an alpha2-beta2 structure and nitrogenase reductase is a homodimer, and both are associated with metal ions, which differ between species. Both proteins are required for the enzyme activity of the complex, the formation of oxidized ferredoxin and ammonia from reduced ferredoxin and nitrogen." [PMID:10852721]
subset: goslim_pir
is_a: GO:0140535 ! intracellular protein-containing complex
is_a: GO:1990204 ! oxidoreductase complex
@@ -120937,7 +120872,7 @@ is_a: GO:1990204 ! oxidoreductase complex
id: GO:0016611
name: iron-iron nitrogenase complex
namespace: cellular_component
-def: "An enzyme complex containing an iron-iron cluster found in species such as the photosynthetic bacterium Rhodobacter capsulatus. It is composed of two main subunits, dinitrogenase and nitrogenase reductase. Dinitrogenase, the iron-iron containing subunit, has an alpha1-beta2 or alpha2-beta2 structure, and the nitrogenase reductase subunit is a homodimer. Functions in the catalysis of the formation of oxidized ferredoxin and ammonia from reduced ferredoxin and nitrogen." [EC:1.18.6.1, GOC:jl, PMID:11848850]
+def: "An enzyme complex containing an iron-iron cluster found in species such as the photosynthetic bacterium Rhodobacter capsulatus. It is composed of two main subunits, dinitrogenase and nitrogenase reductase. Dinitrogenase, the iron-iron containing subunit, has an alpha1-beta2 or alpha2-beta2 structure, and the nitrogenase reductase subunit is a homodimer. Functions in the catalysis of the formation of oxidized ferredoxin and ammonia from reduced ferredoxin and nitrogen." [GOC:jl, PMID:11848850]
comment: Note that it is not established whether the nitrogenase exists in vivo in a specific particle or whether the nitrogenase proteins are bound nonspecifically to the membranes of some cells.
is_a: GO:0016610 ! nitrogenase complex
@@ -120945,15 +120880,17 @@ is_a: GO:0016610 ! nitrogenase complex
id: GO:0016612
name: molybdenum-iron nitrogenase complex
namespace: cellular_component
-def: "An enzyme complex containing a molybdenum-iron cluster found in many species. It is composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase, the molybdenum-iron protein, is tetrameric with an alpha2-beta2 structure, and nitrogenase reductase is a homodimer." [EC:1.18.6.1]
+def: "An enzyme complex containing a molybdenum-iron cluster found in many species. It is composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase, the molybdenum-iron protein, is tetrameric with an alpha2-beta2 structure, and nitrogenase reductase is a homodimer." [PMID:11566366]
synonym: "molybdenum-iron nitrogenase activity" RELATED []
+xref: MetaCyc:CPLX-186
+xref: MetaCyc:CPLX-525
is_a: GO:0016610 ! nitrogenase complex
[Term]
id: GO:0016613
name: vanadium-iron nitrogenase complex
namespace: cellular_component
-def: "An enzyme complex containing a vanadium-iron cluster found in some species, such as Azotobacter vinelandii. It is composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase, the vanadium-iron protein, is tetrameric with an alpha2-beta2 structure, and nitrogenase reductase is a homodimer." [EC:1.18.6.1, PMID:3474027]
+def: "An enzyme complex containing a vanadium-iron cluster found in some species, such as Azotobacter vinelandii. It is composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase, the vanadium-iron protein, is tetrameric with an alpha2-beta2 structure, and nitrogenase reductase is a homodimer." [PMID:3474027]
synonym: "vanadium-iron nitrogenase activity" RELATED []
is_a: GO:0016610 ! nitrogenase complex
@@ -121112,7 +121049,7 @@ is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
id: GO:0016629
name: 12-oxophytodienoate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 8-[(1R,2R)-3-oxo-2-{(Z)-pent-2-en-1-yl}cyclopentyl]octanoate + NADP(+) = (15Z)-12-oxophyto-10,15-dienoate + H(+) + NADPH." [EC:1.3.1.42, RHEA:21888]
+def: "Catalysis of the reaction: 8-[(1R,2R)-3-oxo-2-{(Z)-pent-2-en-1-yl}cyclopentyl]octanoate + NADP+ = (15Z)-12-oxophyto-10,15-dienoate + H+ + NADPH." [EC:1.3.1.42, RHEA:21888]
synonym: "12-oxo-phytodienoate reductase activity" EXACT []
synonym: "12-oxo-phytodienoic acid reductase activity" RELATED [EC:1.3.1.42]
synonym: "8-[(1R,2R)-3-oxo-2-{(Z)-pent-2-enyl}cyclopentyl]octanoate:NADP+ 4-oxidoreductase activity" RELATED [EC:1.3.1.42]
@@ -121571,7 +121508,7 @@ id: GO:0016676
name: obsolete oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor
namespace: molecular_function
def: "OBSOLETE. Catalysis of an oxidation-reduction (redox) reaction in which a heme group acts as a hydrogen or electron donor and reduces oxygen." [GOC:jl]
-comment: This term was obsoleted because Enzyme Commission (EC) has rehoused all its descendant classes, and this is now a grouping term with not children.
+comment: This term was obsoleted because Enzyme Commission (EC) has rehoused all its descendant classes, and this is now a grouping term with not children.
synonym: "oxidoreductase activity, acting on haem group of donors, oxygen as acceptor" EXACT []
xref: EC:1.9.3.-
is_obsolete: true
@@ -121703,7 +121640,7 @@ alt_id: GO:0016955
alt_id: GO:0016956
alt_id: GO:0016957
alt_id: GO:0016958
-def: "Catalysis of the reaction: 2 R-H + 2 chloride + hydrogen peroxide = 2 R-Cl + 2 H2O." [EC:1.11.1.10]
+def: "Catalysis of the reaction: 2 R-H + 2 chloride + H2O2 = 2 R-Cl + 2 H2O." [EC:1.11.1.10]
synonym: "chloride:hydrogen-peroxide oxidoreductase" RELATED [EC:1.11.1.10]
synonym: "chloroperoxidase activity" RELATED [EC:1.11.1.10]
synonym: "cofactor-free chloroperoxidase activity" NARROW []
@@ -121714,13 +121651,13 @@ synonym: "heme chloroperoxidase activity" NARROW []
synonym: "vanadium chloroperoxidase activity" NARROW []
xref: EC:1.11.1.10
xref: MetaCyc:CHLORIDE-PEROXIDASE-RXN
-is_a: GO:0004601 ! peroxidase activity
+is_a: GO:0140905 ! haloperoxidase activity
[Term]
id: GO:0016692
name: NADH peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O(2) + H(+) + NADH = 2 H(2)O + NAD(+)." [EC:1.11.1.1, RHEA:18509]
+def: "Catalysis of the reaction: H2O2 + NADH + H+ = 2 H2O + NAD+." [EC:1.11.1.1, RHEA:18509]
synonym: "diphosphopyridine nucleotide peroxidase activity" RELATED [EC:1.11.1.1]
synonym: "DPNH peroxidase activity" RELATED [EC:1.11.1.1]
synonym: "NAD peroxidase activity" RELATED [EC:1.11.1.1]
@@ -122021,19 +121958,19 @@ consider: GO:0016705
id: GO:0016719
name: carotene 7,8-desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: neurosporene + donor-H2 + O2 = lycopene + acceptor + 2 H2O." [RHEA:15701]
+def: "Catalysis of the reaction: neurosporene + donor-H2 + O2 = lycopene + acceptor + 2 H2O." [RHEA:30955]
synonym: "carotene,hydrogen-donor:oxygen oxidoreductase activity" RELATED []
synonym: "zeta-carotene desaturase activity" RELATED [EC:1.3.5.6]
xref: EC:1.3.5.6
xref: MetaCyc:1.14.99.30-RXN
-xref: RHEA:15701
+xref: RHEA:30955
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
[Term]
id: GO:0016720
name: delta12-fatty acid dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + linoleate + O(2) = A + crepenynate + 2 H(2)O." [EC:1.14.99.33, RHEA:23456]
+def: "Catalysis of the reaction: AH(2) + linoleate + O2 = A + crepenynate + 2 H2O." [EC:1.14.99.33, RHEA:23456]
synonym: "crepenynate synthase activity" NARROW [EC:1.14.99.33]
synonym: "D12-fatty acid dehydrogenase activity" EXACT []
synonym: "delta-12 fatty acid acetylenase activity" RELATED [EC:1.14.99.33]
@@ -122219,7 +122156,6 @@ id: GO:0016740
name: transferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -122229,6 +122165,7 @@ subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
+subset: prokaryote_subset
xref: EC:2.-.-.-
xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2"
xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1"
@@ -122508,6 +122445,7 @@ subset: goslim_chembl
subset: goslim_drosophila
synonym: "transferase activity, transferring alkyl or aryl groups, other than methyl groups" EXACT []
xref: EC:2.5.1.-
+xref: Reactome:R-HSA-3159253 "MMAB adenosylates cob(I)alamin"
xref: Reactome:R-HSA-4419978 "DHDDS:NUS1 elongates E,E-FPP with (n)IPPP to form pPPP"
xref: Reactome:R-HSA-4755545 "Defective DHDDS does not elongate E,E-FPP"
xref: Reactome:R-HSA-6782893 "TRMT12 transforms yW-187 yielding yW-86 at nucleotide 37 of tRNA(Phe)"
@@ -122617,7 +122555,6 @@ id: GO:0016779
name: nucleotidyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a nucleotidyl group to a reactant." [ISBN:0198506732]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -122659,7 +122596,6 @@ name: sulfurtransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor)." [GOC:ai, ISBN:0721662544]
synonym: "sulphurtransferase activity" EXACT []
-synonym: "tRNA sulfurtransferase activity" NARROW [GOC:mah]
xref: EC:2.8.1.-
xref: Reactome:R-HSA-1614618 "Persulfide sulfur is transferred onto sulfite"
xref: Reactome:R-HSA-6782264 "CTU1:CTU2:URM1 thiolates uridine-34 in tRNAs"
@@ -122698,8 +122634,7 @@ is_a: GO:0016740 ! transferase activity
id: GO:0016787
name: hydrolase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN:0198506732]
-subset: goslim_aspergillus
+def: "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc." [ISBN:0198506732]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -122709,6 +122644,7 @@ subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
+subset: prokaryote_subset
xref: EC:3.-.-.-
xref: Reactome:R-HSA-1236938 "Partial proteolysis of antigen in phagolysosomes"
xref: Reactome:R-HSA-2029475 "Production of AA by iPLA2 upon FCGR activation"
@@ -122731,6 +122667,7 @@ xref: EC:3.1.-.-
xref: Reactome:R-HSA-162729 "uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid"
xref: Reactome:R-HSA-9023617 "Butyrylcholinesterase hydrolyzes acyl Ghrelin"
xref: Reactome:R-HSA-9023619 "Platelet-activating factor acetylhydrolase (PLA2G7) hydrolyzes acyl Ghrelin"
+xref: Reactome:R-HSA-9749609 "BCHE hydrolyzes ASA-"
is_a: GO:0016787 ! hydrolase activity
[Term]
@@ -122749,7 +122686,6 @@ namespace: molecular_function
alt_id: GO:0003869
alt_id: GO:0016302
def: "Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate." [GOC:curators, GOC:pg]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -123006,6 +122942,9 @@ name: hydrolase activity, acting on acid anhydrides, in phosphorus-containing an
namespace: molecular_function
def: "Catalysis of the hydrolysis of any acid anhydride which contains phosphorus." [GOC:jl]
xref: EC:3.6.1.-
+xref: Reactome:R-HSA-9731590 "NUDT1 hydrolyzes O6-methyl-dGTP to O6-methyl-dGMP"
+xref: Reactome:R-HSA-9731613 "NUDT1 hydrolyzes N6-methyl-dATP to N6-methyl-dAMP"
+xref: Reactome:R-HSA-9731632 "NUDT1 hydrolyzes N6-methyl-ATP to N6-methyl-AMP"
is_a: GO:0016817 ! hydrolase activity, acting on acid anhydrides
[Term]
@@ -123090,7 +123029,6 @@ id: GO:0016829
name: lyase activity
namespace: molecular_function
def: "Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [ISBN:0198547684]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -123098,6 +123036,7 @@ subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "other lyase activity" NARROW []
xref: EC:4.-.-.-
xref: Reactome:R-HSA-5696408 "PXLP-K278-PHYKPL tetramer hydrolyses 5PHL"
@@ -123134,6 +123073,9 @@ alt_id: GO:0016228
def: "Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone." [GOC:curators]
synonym: "aldolase activity" BROAD []
xref: EC:4.1.2.-
+xref: Reactome:R-HSA-200651 "5,10-methyleneTHF polyglutamate + glycine <=> tetrahydrofolate polyglutamate (THF polyglutamate) + serine"
+xref: Reactome:R-HSA-200735 "SHMT1 tetramer transfers hydroxymethyl group to THFPG to form 5,10-methylene-THFPG"
+xref: Reactome:R-HSA-71249 "SHMT1 tetramer cleaves HTMLYS to yield TEABL and Gly"
is_a: GO:0016830 ! carbon-carbon lyase activity
[Term]
@@ -123178,7 +123120,7 @@ is_a: GO:0016835 ! carbon-oxygen lyase activity
id: GO:0016837
name: carbon-oxygen lyase activity, acting on polysaccharides
namespace: molecular_function
-def: "Catalysis of the cleavage of a carbon-oxygen bond by the elimination of an alcohol from a polysaccharide." [EC:4.2.-.-]
+def: "Catalysis of the cleavage of a carbon-oxygen bond by the elimination of an alcohol from a polysaccharide." [GOC:curators]
xref: EC:4.2.2.-
is_a: GO:0016835 ! carbon-oxygen lyase activity
@@ -123186,7 +123128,7 @@ is_a: GO:0016835 ! carbon-oxygen lyase activity
id: GO:0016838
name: carbon-oxygen lyase activity, acting on phosphates
namespace: molecular_function
-def: "Catalysis of the cleavage of a carbon-oxygen bond by elimination of a phosphate." [EC:4.2.-.-]
+def: "Catalysis of the cleavage of a carbon-oxygen bond by elimination of a phosphate." [EC:4.2.3.-]
xref: EC:4.2.3.-
is_a: GO:0016835 ! carbon-oxygen lyase activity
@@ -123237,7 +123179,7 @@ is_a: GO:0016840 ! carbon-nitrogen lyase activity
id: GO:0016844
name: strictosidine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3alpha(S)-strictosidine + H(2)O = secologanin + tryptamine." [EC:4.3.3.2, RHEA:15013]
+def: "Catalysis of the reaction: 3alpha(S)-strictosidine + H2O = secologanin + tryptamine." [EC:4.3.3.2, RHEA:15013]
synonym: "3-alpha(S)-strictosidine tryptamine-lyase (secologanin-forming)" RELATED [EC:4.3.3.2]
synonym: "3-alpha(S)-strictosidine tryptamine-lyase activity" RELATED [EC:4.3.3.2]
synonym: "STR activity" RELATED [EC:4.3.3.2]
@@ -123273,7 +123215,7 @@ id: GO:0016847
name: 1-aminocyclopropane-1-carboxylate synthase activity
namespace: molecular_function
alt_id: GO:0034100
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) = 1-aminocyclopropane-1-carboxylate + S-methyl-5'-thioadenosine + H(+)." [EC:4.4.1.14, RHEA:21744]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) = 1-aminocyclopropane-1-carboxylate + S-methyl-5'-thioadenosine + H+." [EC:4.4.1.14, RHEA:21744]
comment: Note that this function was formerly EC:4.1.99.4.
synonym: "1-aminocyclopropane-1-carboxylate synthetase activity" RELATED [EC:4.4.1.14]
synonym: "1-aminocyclopropane-1-carboxylic acid synthase activity" RELATED [EC:4.4.1.14]
@@ -123321,8 +123263,7 @@ consider: GO:0016829
id: GO:0016851
name: magnesium chelatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H(2)O + Mg(2+) + protoporphyrin IX = ADP + 2 H(+) + magnesium protoporphyrin IX + phosphate." [EC:6.6.1.1, RHEA:13961]
-comment: Note that this was EC:4.99.1.1.
+def: "Catalysis of the reaction: ATP + H2O + Mg2+ + protoporphyrin IX = ADP + 3 H+ + Mg-protoporphyrin IX + phosphate." [RHEA:13961]
synonym: "magnesium-chelatase activity" RELATED [EC:6.6.1.1]
synonym: "magnesium-protoporphyrin chelatase activity" RELATED [EC:6.6.1.1]
synonym: "magnesium-protoporphyrin IX chelatase activity" RELATED [EC:6.6.1.1]
@@ -123342,13 +123283,11 @@ is_a: GO:0051003 ! ligase activity, forming nitrogen-metal bonds, forming coordi
id: GO:0016852
name: sirohydrochlorin cobaltochelatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: sirohydrochlorin + Co2+ = cobalt-sirohydrochlorin + 2 H+." [EC:4.99.1.3]
-synonym: "anaerobic cobalt chelatase activity" EXACT []
-synonym: "CbiK" NARROW []
-synonym: "CbiX" RELATED [EC:4.99.1.3]
-synonym: "CbiXS" RELATED [EC:4.99.1.3]
-synonym: "cobalt-sirohydrochlorin cobalt-lyase (sirohydrochlorin-forming)" RELATED [EC:4.99.1.3]
-synonym: "sirohydrochlorin cobalt-lyase activity" RELATED [EC:4.99.1.3]
+def: "Catalysis of the reaction: sirohydrochlorin + Co2+ = cobalt-sirohydrochlorin + 2 H+." [RHEA:15893]
+synonym: "anaerobic cobalt chelatase activity" EXACT [EC:4.99.1.3]
+synonym: "cobalt-sirohydrochlorin cobalt-lyase (sirohydrochlorin-forming)" RELATED []
+synonym: "cobaltochelatase" EXACT [EC:4.99.1.3]
+synonym: "sirohydrochlorin cobalt-lyase activity" RELATED []
xref: EC:4.99.1.3
xref: MetaCyc:4.99.1.3-RXN
xref: RHEA:15893
@@ -123359,7 +123298,6 @@ id: GO:0016853
name: isomerase activity
namespace: molecular_function
def: "Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5." [ISBN:0198506732]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -123367,6 +123305,7 @@ subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "other isomerase activity" NARROW []
xref: EC:5.-.-.-
xref: Reactome:R-HSA-6787623 "TSTA3 dimer epimerises GDP-DHDMan to GDP-KDGal"
@@ -123569,8 +123508,7 @@ consider: GO:0016853
id: GO:0016874
name: ligase activity
namespace: molecular_function
-def: "Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient." [EC:6.-.-.-, GOC:mah]
-subset: goslim_aspergillus
+def: "Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient." [GOC:mah]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -123579,6 +123517,7 @@ subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "synthetase activity" EXACT [GOC:jh2]
xref: EC:6.-.-.-
is_a: GO:0003824 ! catalytic activity
@@ -123639,7 +123578,7 @@ is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
id: GO:0016882
name: cyclo-ligase activity
namespace: molecular_function
-def: "Catalysis of the joining of two groups within a single molecule via a carbon-nitrogen bond, forming heterocyclic ring, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [EC:6.3.3.1, EC:6.3.3.2, EC:6.3.3.4, GOC:jl, GOC:mah]
+def: "Catalysis of the joining of two groups within a single molecule via a carbon-nitrogen bond, forming heterocyclic ring, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [GOC:jl, GOC:mah]
xref: EC:6.3.3.-
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
@@ -123684,8 +123623,8 @@ name: ATP hydrolysis activity
namespace: molecular_function
alt_id: GO:0004002
alt_id: GO:0042623
-def: "Catalysis of the reaction: ATP + H2O = ADP + H+ Pi. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient." [RHEA:13065]
-comment: Note that this term is meant to specifically represent the ATPase activity of proteins using ATPase as a source of energy to drive a reaction. If possible, gene products should also be annotated to a child of 'ATP-dependent activity ; GO:0140657', to capture their overall function.
+def: "Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient." [RHEA:13065]
+comment: Note that this term is meant to specifically represent the ATPase activity of proteins using ATP as a source of energy to drive a reaction. If possible, gene products should also be annotated to a child of 'ATP-dependent activity ; GO:0140657', to capture their overall function.
synonym: "adenosine 5'-triphosphatase activity" EXACT []
synonym: "adenosine triphosphatase activity" EXACT []
synonym: "adenosinetriphosphatase activity" EXACT []
@@ -123703,7 +123642,6 @@ xref: Reactome:R-HSA-6811422 "NSF ATPase activity dissociates cis-SNARE at the E
xref: Reactome:R-HSA-6814670 "ATP hydrolysis by RHOBTB3 promotes PLIN3 dissociation"
xref: Reactome:R-HSA-6814678 "ATP hydrolysis by NSF disassembles the cis-SNARE at the TGN"
xref: Reactome:R-HSA-6814683 "NSF-dependent ATP hydrolysis disassembles the cis-SNARE at the TGN"
-xref: Reactome:R-HSA-72139 "Formation of the active Spliceosomal C (B*) complex"
xref: Reactome:R-HSA-8847638 "ATP hydrolysis by NSF disassembles the cis-SNARE at the Golgi membrane"
xref: Reactome:R-HSA-8868658 "HSPA8-mediated ATP hydrolysis promotes vesicle uncoating"
xref: Reactome:R-HSA-8939203 "HSP90-dependent ATP hydrolysis promotes release of ESR:ESTG from chaperone complex"
@@ -123712,8 +123650,9 @@ xref: Reactome:R-HSA-917693 "ESCRT Disassembly"
xref: Reactome:R-HSA-9609860 "Tail-anchored protein:SGTA:BAG6:GET4:UBL4A:ASNA1:ATP dissociates and ASNA1 hydrolyzes ATP yielding Tail-anchored protein:ASNA1:ADP"
xref: Reactome:R-HSA-9668415 "VPS4 mediates disassembly of ESCRTIII subunits to promote sealing of holes in the nuclear envelope"
xref: Reactome:R-HSA-9706399 "RHOBTB3 hydrolyzes ATP"
+xref: Reactome:R-HSA-9749350 "ATP-dependent release of CDT1 from the OCCM complex"
xref: RHEA:13065
-is_a: GO:0017111 ! nucleoside-triphosphatase activity
+is_a: GO:0017111 ! ribonucleoside triphosphate phosphatase activity
relationship: part_of GO:0140657 ! ATP-dependent activity
[Term]
@@ -123724,17 +123663,18 @@ def: "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid
synonym: "endodeoxyribonuclease activity, producing 5' phosphomonoesters" EXACT []
xref: EC:3.1.21.-
xref: Reactome:R-HSA-912368 "SPO11 hydrolyzes DNA forming double-strand breaks"
-is_a: GO:0004520 ! endodeoxyribonuclease activity
+is_a: GO:0004520 ! DNA endonuclease activity
is_a: GO:0016893 ! endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters
[Term]
id: GO:0016889
-name: endodeoxyribonuclease activity, producing 3'-phosphomonoesters
+name: DNA endonuclease activity, producing 3'-phosphomonoesters
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acids by creating internal breaks to yield 3'-phosphomonoesters." [GOC:ai]
+synonym: "endodeoxyribonuclease activity, producing 3'-phosphomonoesters" EXACT []
synonym: "endodeoxyribonuclease activity, producing other than 5'-phosphomonoesters" EXACT []
xref: EC:3.1.22.-
-is_a: GO:0004520 ! endodeoxyribonuclease activity
+is_a: GO:0004520 ! DNA endonuclease activity
is_a: GO:0016894 ! endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters
[Term]
@@ -123743,25 +123683,29 @@ name: site-specific endodeoxyribonuclease activity, specific for altered base
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages at specific sites within a deoxyribonucleic acid molecule by creating internal breaks." [GOC:jl]
xref: EC:3.1.25.-
-is_a: GO:0004520 ! endodeoxyribonuclease activity
+is_a: GO:0004520 ! DNA endonuclease activity
[Term]
id: GO:0016891
-name: endoribonuclease activity, producing 5'-phosphomonoesters
+name: RNA endonuclease activity, producing 5'-phosphomonoesters
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters." [GOC:ai]
+synonym: "endoribonuclease activity, producing 5'-phosphomonoesters" EXACT []
xref: EC:3.1.26.-
-is_a: GO:0004521 ! endoribonuclease activity
+is_a: GO:0004521 ! RNA endonuclease activity
is_a: GO:0016893 ! endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters
[Term]
id: GO:0016892
-name: endoribonuclease activity, producing 3'-phosphomonoesters
+name: RNA endonuclease activity, producing 3'-phosphomonoesters
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 3'-phosphomonoesters." [GOC:ai]
+synonym: "endoribonuclease activity, producing 3'-phosphomonoesters" EXACT []
synonym: "endoribonuclease activity, producing other than 5'-phosphomonoesters" EXACT []
xref: EC:3.1.27.-
-is_a: GO:0004521 ! endoribonuclease activity
+xref: Reactome:R-HSA-9705961 "nsp15 cleaves viral poly(U)-RNA"
+xref: Reactome:R-HSA-9755252 "nsp15 cleaves viral poly(U)-RNA"
+is_a: GO:0004521 ! RNA endonuclease activity
is_a: GO:0016894 ! endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters
[Term]
@@ -123783,39 +123727,41 @@ def: "Catalysis of the hydrolysis of ester linkages within nucleic acids by crea
comment: Note that this activity can catalyze cleavage of DNA or RNA.
synonym: "3'-endonuclease activity" EXACT []
synonym: "endoribonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters" RELATED []
-xref: EC:3.1.31.-
+xref: EC:3.1.31.1
is_a: GO:0004519 ! endonuclease activity
[Term]
id: GO:0016895
-name: exodeoxyribonuclease activity, producing 5'-phosphomonoesters
+name: DNA exonuclease activity, producing 5'-phosphomonoesters
namespace: molecular_function
alt_id: GO:0008858
def: "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acids by removing nucleotide residues from the 3' or 5' end to yield 5' phosphomonoesters." [GOC:ai]
synonym: "exodeoxyribonuclease activity, producing 5' phosphomonoesters" EXACT []
synonym: "exonuclease VIII activity" NARROW []
xref: EC:3.1.11.-
-is_a: GO:0004529 ! exodeoxyribonuclease activity
+is_a: GO:0004529 ! DNA exonuclease activity
is_a: GO:0016796 ! exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters
[Term]
id: GO:0016896
-name: exoribonuclease activity, producing 5'-phosphomonoesters
+name: RNA exonuclease activity, producing 5'-phosphomonoesters
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within ribonucleic acids by removing nucleotide residues from the 3' or 5' end to yield 5' phosphomonoesters." [GOC:ai]
synonym: "exoribonuclease activity, producing 5' phosphomonoesters" EXACT []
+synonym: "exoribonuclease activity, producing 5'-phosphomonoesters" EXACT []
xref: EC:3.1.13.-
xref: Reactome:R-HSA-429860 "DCP1-DCP2 complex decaps mRNA"
-is_a: GO:0004532 ! exoribonuclease activity
+is_a: GO:0004532 ! RNA exonuclease activity
is_a: GO:0016796 ! exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters
[Term]
id: GO:0016897
-name: exoribonuclease activity, producing 3'-phosphomonoesters
+name: RNA exonuclease activity, producing 3'-phosphomonoesters
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within ribonucleic acids by removing nucleotide residues from the 3' or 5' end to yield 3' phosphomonoesters." [GOC:ai]
+synonym: "exoribonuclease activity, producing 3'-phosphomonoesters" EXACT []
xref: EC:3.1.14.-
-is_a: GO:0004532 ! exoribonuclease activity
+is_a: GO:0004532 ! RNA exonuclease activity
is_a: GO:0016797 ! exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters
[Term]
@@ -124056,8 +124002,7 @@ replaced_by: GO:0004222
id: GO:0016920
name: pyroglutamyl-peptidase activity
namespace: molecular_function
-def: "Catalysis of the release of the N-terminal pyroglutamyl group from a peptide or protein." [EC:3.4.19.3, EC:3.4.19.6, GOC:mah]
-xref: EC:3.4.19.-
+def: "Catalysis of the release of the N-terminal pyroglutamyl group from a peptide or protein." [GOC:mah, PMID:9920379]
is_a: GO:0008234 ! cysteine-type peptidase activity
is_a: GO:0008242 ! omega peptidase activity
@@ -124143,14 +124088,16 @@ is_a: GO:0070646 ! protein modification by small protein removal
[Term]
id: GO:0016929
-name: SUMO-specific protease activity
+name: deSUMOylase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of peptide or isopeptide bonds within SUMO, or between the SUMO and a larger protein to which it has been conjugated." [GOC:rn, PMID:10094048, PMID:11031248, PMID:11265250]
-comment: This term should not be used for direct manual annotation because the supporting experiments should always distinguish whether the activity is part of maturation or SUMO removal.
-subset: gocheck_do_not_manually_annotate
+alt_id: GO:0070140
+def: "An thiol-dependent isopeptidase activity that cleaves SUMO from a target protein to which it is conjugated." [GOC:rn, PMID:10094048, PMID:11031248, PMID:11265250, PMID:23746258]
+synonym: "SUMO-specific isopeptidase activity" EXACT []
+synonym: "SUMO-specific protease activity" EXACT []
synonym: "SUSP" NARROW []
synonym: "ULP" NARROW []
-is_a: GO:0019783 ! ubiquitin-like protein-specific protease activity
+is_a: GO:0008234 ! cysteine-type peptidase activity
+is_a: GO:0019783 ! ubiquitin-like protein peptidase activity
[Term]
id: GO:0016933
@@ -124159,7 +124106,7 @@ namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a channel that opens when glycine is bound by the channel complex or one of its constituent parts on the extracellular side of the plasma membrane." [GOC:mtg_transport, ISBN:0815340729]
synonym: "extracellular-glycine-gated ion channel activity" EXACT []
synonym: "glycine receptor" BROAD []
-is_a: GO:0005231 ! excitatory extracellular ligand-gated ion channel activity
+is_a: GO:0005231 ! excitatory extracellular ligand-gated monoatomic ion channel activity
[Term]
id: GO:0016934
@@ -124171,10 +124118,10 @@ synonym: "extracellular-glycine-gated chloride channel activity" EXACT []
synonym: "glycine receptor" BROAD []
synonym: "glycine-inhibited chloride channel activity" RELATED []
xref: Reactome:R-HSA-975389 "GLRA:GLRB:Gly transports extracellular Cl- to cytosol"
-is_a: GO:0005237 ! inhibitory extracellular ligand-gated ion channel activity
+is_a: GO:0005237 ! inhibitory extracellular ligand-gated monoatomic ion channel activity
is_a: GO:0005254 ! chloride channel activity
is_a: GO:0016933 ! extracellularly glycine-gated ion channel activity
-is_a: GO:0099095 ! ligand-gated anion channel activity
+is_a: GO:0099095 ! ligand-gated monoatomic anion channel activity
[Term]
id: GO:0016935
@@ -124183,7 +124130,6 @@ namespace: cellular_component
def: "A protein complex that forms a transmembrane channel through which chloride ions may pass in response to glycine binding to the channel complex or one of its constituent parts." [GOC:mah]
is_a: GO:0034707 ! chloride channel complex
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0016936
@@ -124195,10 +124141,11 @@ is_a: GO:0097367 ! carbohydrate derivative binding
[Term]
id: GO:0016937
-name: short-branched-chain-acyl-CoA dehydrogenase activity
+name: short-chain-acyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor, where the acyl group is a short branched chain fatty acid residue." [GOC:mah]
-xref: EC:1.3.99.-
+def: "Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor, where the acyl group is a short chain fatty acid residue." [GOC:mah]
+xref: EC:1.3.8.1
+xref: RHEA:47196
is_a: GO:0003995 ! acyl-CoA dehydrogenase activity
[Term]
@@ -124310,7 +124257,7 @@ name: nitric oxide reductase activity
namespace: molecular_function
alt_id: GO:0016967
alt_id: GO:0016968
-def: "Catalysis of the reaction: H(2)O + 2 ferricytochrome c + nitrous oxide = 2 H(+) + 2 ferrocytochrome c + 2 nitric oxide." [EC:1.7.2.5]
+def: "Catalysis of the reaction: H2O + 2 ferricytochrome c + nitrous oxide = 2 H+ + 2 ferrocytochrome c + 2 nitric oxide." [EC:1.7.2.5]
synonym: "CYP55" NARROW []
synonym: "cytochrome bc nitric oxide reductase activity" NARROW []
synonym: "nitric-oxide reductase activity" RELATED [EC:1.7.2.5]
@@ -124406,7 +124353,7 @@ namespace: molecular_function
alt_id: GO:0008916
alt_id: GO:0016978
alt_id: GO:0102315
-def: "Catalysis of the lipoylation of a protein in two steps: ATP + (R)-lipoate + a [lipoyl-carrier protein]-L-lysine = a [lipoyl-carrier protein]-N6-(lipoyl)lysine + AMP + diphosphate (overall reaction): (1) ATP + (R)-lipoate = lipoyl-AMP + diphosphate; (2) lipoyl-AMP + a [lipoyl-carrier protein]-L-lysine = a [lipoyl-carrier protein]-N6-(lipoyl)lysine + AMP." [RHEA:49288]
+def: "Catalysis of the lipoylation of a protein in two steps: ATP + (R)-lipoate + a [lipoyl-carrier protein]-L-lysine = a [lipoyl-carrier protein]-N6-(lipoyl)lysine + AMP + diphosphate (overall reaction): (1) ATP + (R)-lipoate = lipoyl-AMP + diphosphate; (2) lipoyl-AMP + a [lipoyl-carrier protein]-L-lysine = a [lipoyl-carrier protein]-N6-(lipoyl)lysine + AMP." [PMID:16141198, PMID:17570395, RHEA:49288]
synonym: "lipoate-protein ligase A activity" NARROW []
synonym: "lipoate-protein ligase activity (lipoylation of glycine cleavage complex)" NARROW []
synonym: "lipoate-protein ligase B activity" NARROW []
@@ -124424,7 +124371,7 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
id: GO:0016980
name: creatinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: creatine + H(2)O = sarcosine + urea." [EC:3.5.3.3, RHEA:22456]
+def: "Catalysis of the reaction: creatine + H2O = sarcosine + urea." [EC:3.5.3.3, RHEA:22456]
synonym: "creatine amidinohydrolase activity" RELATED [EC:3.5.3.3]
xref: EC:3.5.3.3
xref: KEGG_REACTION:R01566
@@ -124544,6 +124491,9 @@ synonym: "LS" RELATED [EC:2.8.1.8]
synonym: "protein 6-N-(octanoyl)lysine:sulfur sulfurtransferase activity" RELATED [EC:2.8.1.8]
synonym: "protein N6-(octanoyl)lysine:sulfur sulfurtransferase activity" RELATED [EC:2.8.1.8]
xref: EC:2.8.1.8
+xref: MetaCyc:RXN-14950
+xref: MetaCyc:RXN-14957
+xref: MetaCyc:RXN-14959
xref: MetaCyc:RXN0-949
xref: Reactome:R-HSA-6793591 "LIAS:2(4Fe-4S) transforms octanoyl-K107-GCSH to lipoyl-K107-GCSH"
xref: RHEA:16585
@@ -124585,7 +124535,6 @@ def: "Catalysis of the reaction: cholesterol + O2 = cholest-5-en-3-one + H2O2."
synonym: "3beta-hydroxy steroid oxidoreductase activity" RELATED [EC:1.1.3.6]
synonym: "3beta-hydroxysteroid:oxygen oxidoreductase activity" RELATED [EC:1.1.3.6]
synonym: "cholesterol- O2 oxidoreductase activity" RELATED [EC:1.1.3.6]
-synonym: "cholesterol-O(2) oxidoreductase activity" RELATED [EC:1.1.3.6]
synonym: "cholesterol-O2 oxidoreductase activity" RELATED [EC:1.1.3.6]
synonym: "cholesterol:oxygen oxidoreductase activity" RELATED [EC:1.1.3.6]
xref: EC:1.1.3.6
@@ -124631,8 +124580,8 @@ synonym: "cellular cell wall macromolecule breakdown" EXACT [GOC:mah]
synonym: "cellular cell wall macromolecule catabolic process" EXACT []
synonym: "cellular cell wall macromolecule catabolism" EXACT [GOC:mah]
synonym: "cellular cell wall macromolecule degradation" EXACT [GOC:mah]
+is_a: GO:0009057 ! macromolecule catabolic process
is_a: GO:0044036 ! cell wall macromolecule metabolic process
-is_a: GO:0044265 ! cellular macromolecule catabolic process
[Term]
id: GO:0016999
@@ -124652,8 +124601,8 @@ synonym: "antibiotic anabolism" EXACT []
synonym: "antibiotic biosynthesis" EXACT []
synonym: "antibiotic formation" EXACT []
synonym: "antibiotic synthesis" EXACT []
+is_a: GO:0009058 ! biosynthetic process
is_a: GO:0016999 ! antibiotic metabolic process
-is_a: GO:0044249 ! cellular biosynthetic process
[Term]
id: GO:0017001
@@ -124663,16 +124612,16 @@ def: "The chemical reactions and pathways resulting in the breakdown of antibiot
synonym: "antibiotic breakdown" EXACT []
synonym: "antibiotic catabolism" EXACT []
synonym: "antibiotic degradation" EXACT []
+is_a: GO:0009056 ! catabolic process
is_a: GO:0016999 ! antibiotic metabolic process
-is_a: GO:0044248 ! cellular catabolic process
[Term]
id: GO:0017002
-name: activin-activated receptor activity
+name: activin receptor activity
namespace: molecular_function
def: "Combining with activin and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Activin is one of two gonadal glycoproteins related to transforming growth factor beta." [GOC:mah, GOC:signaling, ISBN:0198506732]
comment: Note that this term represents an activity and not a gene product, and should only be used when the receptor binds the ligand activin. For binding to other extracellular ligands, consider annotating to terms under 'transmembrane signaling receptor activity ; GO:0004888.
-synonym: "activin receptor activity" EXACT [GOC:bf, GOC:signaling]
+synonym: "activin-activated receptor activity" EXACT []
is_a: GO:0004675 ! transmembrane receptor protein serine/threonine kinase activity
[Term]
@@ -124705,7 +124654,7 @@ id: GO:0017006
name: protein-tetrapyrrole linkage
namespace: biological_process
def: "The covalent linking of a tetrapyrrole to a protein." [GOC:ai]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0017007
@@ -124760,7 +124709,7 @@ name: protein flavinylation
namespace: biological_process
def: "The addition of a flavin group to a protein amino acid." [GOC:ai]
synonym: "protein amino acid flavinylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0017014
@@ -124768,7 +124717,7 @@ name: protein nitrosylation
namespace: biological_process
def: "The covalent addition of a nitric oxide group to an amino acid within a protein." [GOC:ai, PMID:20972426]
synonym: "protein amino acid nitrosylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0017015
@@ -124920,14 +124869,14 @@ name: amino acid:potassium symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: amino acid(out) + K+(out) = amino acid(in) + K+(in)." [GOC:ai]
synonym: "potassium:amino acid symporter activity" EXACT []
-is_a: GO:0005416 ! amino acid:cation symporter activity
+is_a: GO:0005416 ! amino acid:monoatomic cation symporter activity
is_a: GO:0015079 ! potassium ion transmembrane transporter activity
[Term]
id: GO:0017038
name: protein import
namespace: biological_process
-def: "The targeting and directed movement of proteins into a cell or organelle. Not all import involves an initial targeting event." [GOC:ai]
+def: "The targeting and directed movement of proteins into a cell or organelle. Not all import involves an initial targeting event." [GOC:ai]
synonym: "protein uptake" EXACT []
is_a: GO:0015031 ! protein transport
@@ -124982,15 +124931,10 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0017042
name: glycosylceramidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycosyl-N-acylsphingosine + H2O = a sugar + N-acylsphingosine." [EC:3.2.1.62]
+def: "Catalysis of the reaction: glycosyl-N-acylsphingosine + H2O = a sugar + N-acylsphingosine." [PMID:10692580, PMID:9762914]
synonym: "cerebrosidase activity" RELATED [EC:3.2.1.62]
synonym: "glycosyl ceramide glycosylhydrolase activity" RELATED [EC:3.2.1.62]
synonym: "glycosyl-N-acylsphingosine glycohydrolase activity" RELATED [EC:3.2.1.62]
-synonym: "lactase-phlorizin hydrolase" BROAD [EC:3.2.1.62]
-synonym: "phloretin-glucosidase activity" RELATED [EC:3.2.1.62]
-synonym: "phloridzin beta-glucosidase activity" RELATED [EC:3.2.1.62]
-synonym: "phloridzin glucosidase activity" RELATED [EC:3.2.1.62]
-synonym: "phlorizin hydrolase activity" RELATED [EC:3.2.1.62]
xref: EC:3.2.1.62
xref: MetaCyc:GLYCOSYLCERAMIDASE-RXN
is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
@@ -125042,13 +124986,15 @@ name: D-erythro-sphingosine kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: sphingosine + ATP = sphingosine 1-phosphate + ADP." [MetaCyc:RXN3DJ-11417]
synonym: "sphingosine kinase activity" EXACT []
+xref: EC:2.7.1.91
xref: MetaCyc:RXN3DJ-11417
xref: Reactome:R-HSA-428273 "SPHK1 phosphorylates SPG to S1P"
xref: Reactome:R-HSA-5218845 "p-SPHK1 phosphorylates sphingosine to sphingosine 1-phosphate"
xref: Reactome:R-HSA-9625814 "SPHK1 phosphorylates sphingosine in response to E2 stimulation"
xref: Reactome:R-HSA-9695949 "SPHK2 phosphorylates SPG to S1P"
xref: RHEA:35847
-is_a: GO:0016301 ! kinase activity
+is_a: GO:0001727 ! lipid kinase activity
+is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
[Term]
id: GO:0017051
@@ -125103,7 +125049,7 @@ synonym: "negative regulation of RNA polymerase II transcriptional preinitiation
synonym: "negative regulation of RNA polymerase II transcriptional preinitiation complex formation" EXACT []
is_a: GO:0031333 ! negative regulation of protein-containing complex assembly
is_a: GO:0045898 ! regulation of RNA polymerase II transcription preinitiation complex assembly
-is_a: GO:0060633 ! negative regulation of transcription initiation from RNA polymerase II promoter
+is_a: GO:0060633 ! negative regulation of transcription initiation by RNA polymerase II
relationship: negatively_regulates GO:0051123 ! RNA polymerase II preinitiation complex assembly
[Term]
@@ -125129,7 +125075,7 @@ is_a: GO:0005198 ! structural molecule activity
id: GO:0017057
name: 6-phosphogluconolactonase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-O-phosphono-D-glucono-1,5-lactone + H(2)O = 6-phospho-D-gluconate + H(+)." [EC:3.1.1.31, RHEA:12556]
+def: "Catalysis of the reaction: 6-O-phosphono-D-glucono-1,5-lactone + H2O = 6-phospho-D-gluconate + H+." [EC:3.1.1.31, RHEA:12556]
synonym: "6-PGL" RELATED [EC:3.1.1.31]
synonym: "6-phospho-D-glucono-1,5-lactone lactonohydrolase activity" RELATED [EC:3.1.1.31]
synonym: "phosphogluconolactonase activity" RELATED [EC:3.1.1.31]
@@ -125151,7 +125097,7 @@ is_a: GO:0019904 ! protein domain specific binding
id: GO:0017059
name: serine C-palmitoyltransferase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the transfer of a palmitoyl on to serine, forming 3-dehydro-D-sphinganine." [EC:2.3.1.50]
+def: "An enzyme complex that catalyzes the transfer of a palmitoyl on to serine, forming 3-dehydro-D-sphinganine." [PMID:19416851]
is_a: GO:0031211 ! endoplasmic reticulum palmitoyltransferase complex
[Term]
@@ -125243,7 +125189,14 @@ id: GO:0017064
name: fatty acid amide hydrolase activity
namespace: molecular_function
alt_id: GO:0017073
+alt_id: GO:0102077
+alt_id: GO:0103073
def: "Catalysis of the hydrolysis of a fatty acid amide to yield a fatty acid." [PMID:15952893]
+synonym: "anandamide amidohydrolase activity" NARROW []
+synonym: "oleamide hydrolase activity" NARROW []
+xref: EC:3.5.1.99
+xref: MetaCyc:RXN-10756
+xref: MetaCyc:RXN6666-2
xref: Reactome:R-HSA-5693742 "FAAH hydrolyses AEA to AA and ETA"
xref: Reactome:R-HSA-5693751 "FAAH2 hydrolyses AEA to AA and ETA"
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
@@ -125262,7 +125215,7 @@ id: GO:0017067
name: tyrosine-ester sulfotransferase activity
namespace: molecular_function
alt_id: GO:0008128
-def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + L-tyrosine methyl ester = L-tyrosine methyl ester 4-sulfate + adenosine 3',5'-diphosphate + H(+)." [EC:2.8.2.9, RHEA:19977]
+def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + L-tyrosine methyl ester = L-tyrosine methyl ester 4-sulfate + adenosine 3',5'-diphosphate + H+." [EC:2.8.2.9, RHEA:19977]
synonym: "3'-phosphoadenylyl-sulfate:L-tyrosine-methyl-ester sulfotransferase activity" RELATED [EC:2.8.2.9]
synonym: "aryl sulfotransferase IV" RELATED [EC:2.8.2.9]
synonym: "L-tyrosine methyl ester sulfotransferase activity" RELATED [EC:2.8.2.9]
@@ -125430,10 +125383,10 @@ id: GO:0017086
name: 3-methyl-2-oxobutanoate dehydrogenase (lipoamide) complex
namespace: cellular_component
alt_id: GO:0031212
-def: "A protein complex that catalyzes the reaction 3-methyl-2-oxobutanoate + lipoamide = S-(2-methylpropanoyl)-dihydrolipoamide + carbon dioxide (CO2). This requires thiamine diphosphate; the enzyme also acts on (S)-3-methyl-2-oxopentanoate and 4-methyl-2-oxo-pentanoate." [EC:1.2.4.4]
+def: "A protein complex that catalyzes the reaction 3-methyl-2-oxobutanoate + lipoamide = S-(2-methylpropanoyl)-dihydrolipoamide + carbon dioxide (CO2). This requires thiamine diphosphate; the enzyme also acts on (S)-3-methyl-2-oxopentanoate and 4-methyl-2-oxo-pentanoate." [PMID:15612914]
synonym: "BCADH" EXACT []
synonym: "branched-chain alpha-ketoacid dehydrogenase complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0017087
@@ -125442,6 +125395,7 @@ namespace: cellular_component
def: "A protein complex consisting of a regulatory subunit (alpha-MPP) and a catalytic subunit (beta-MPP) that catalyzes the release of N-terminal targeting peptides from precursor proteins imported into the mitochondrion." [GOC:mah]
comment: Note that monomeric mitochondrial processing peptidases have been observed.
is_a: GO:0098798 ! mitochondrial protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005759 ! mitochondrial matrix
[Term]
@@ -125478,7 +125432,6 @@ namespace: cellular_component
def: "A protein complex that is located in the cell membrane, and is involved in the metabolism of peptides, including neuropeptides. The complex has metalloendopeptidase activity that catalyzes the hydrolysis of protein and peptide substrates, preferentially on carboxyl side of hydrophobic residues." [GOC:mah, MEROPS_fam:M12]
synonym: "PABA peptide hydrolase complex" EXACT []
is_a: GO:0098796 ! membrane protein complex
-relationship: part_of GO:0016021 ! integral component of membrane
[Term]
id: GO:0017092
@@ -125520,7 +125473,6 @@ namespace: molecular_function
def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + heparan sulfate = adenosine 3',5'-bisphosphate + heparan sulfate 6-O-sulfate; results in 6-O-sulfation of glucosamine residues in heparan sulfate." [PMID:8631808]
synonym: "heparan sulphate 6-O-sulphotransferase activity" EXACT []
synonym: "heparin 6-O-sulfotransferase activity" RELATED []
-xref: EC:2.8.2.-
xref: Reactome:R-HSA-2076419 "HS6STs sulfate GlcN at C6 in heparan sulfate/heparin"
is_a: GO:0034483 ! heparan sulfate sulfotransferase activity
@@ -125554,10 +125506,12 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0017099
name: very-long-chain-acyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor, where the acyl group is a very long chain fatty acid residue. A very long-chain fatty acid is a fatty acid which has a chain length greater than C22." [GOC:mah]
+def: "Catalysis of the reaction: a very-long-chain 2,3-saturated fatty acyl-CoA + H+ + oxidized [electron-transfer flavoprotein] = a very-long-chain (2E)-enoyl-CoA + reduced [electron-transfer flavoprotein]. A very long-chain fatty acid is a fatty acid which has a chain length greater than C22." [RHEA:19181]
synonym: "very long-chain-acyl-CoA dehydrogenase activity" EXACT []
+xref: EC:1.3.8.9
xref: Reactome:R-HSA-548831 "TECR,TECRL dehydrogenate TOD-CoA to ST-CoA"
-is_a: GO:0004466 ! long-chain-acyl-CoA dehydrogenase activity
+xref: RHEA:19181
+is_a: GO:0003995 ! acyl-CoA dehydrogenase activity
[Term]
id: GO:0017101
@@ -125566,8 +125520,8 @@ namespace: cellular_component
def: "A multienzyme complex found in all multicellular eukaryotes composed of eight proteins with aminoacyl-tRNA synthetase activities (abbreviated as: ArgRS, AspRS, GluProRS, GlnRS, IleRS, LeuRS, LysRS, MetRS where RS is the enzyme, preceded by the amino acid it uses as a substrate) as well as three non-synthetase proteins (p43, p38, and p18) with diverse functions. Several of these subunits are known dimers, so the total polypeptide count in the multisynthetase complex is at least fifteen. All of the enzymes in this assembly catalyze the same reaction, the covalent attachment of an amino acid to either the 2'- or 3'-hydroxyl of the 3'-terminal adenosine of tRNA, but using different substrates." [GOC:jl, PMID:16169847]
synonym: "aminoacyl-tRNA synthetase complex" EXACT []
synonym: "multisynthetase complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005622 ! intracellular anatomical structure
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0017102
@@ -125602,12 +125556,22 @@ is_a: GO:0051748 ! UTP-monosaccharide-1-phosphate uridylyltransferase activity
[Term]
id: GO:0017105
-name: acyl-CoA delta11-desaturase activity
+name: acyl-CoA delta11-(Z)-desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + reduced acceptor + O2 = delta11-acyl-CoA + acceptor + 2 H2O. The enzyme introduces a cis double bond at position C-11 of saturated fatty acyl-CoAs." [EC:1.14.19.5]
+alt_id: GO:0050601
+def: "Catalysis of the reaction: an 11,12-saturated fatty acyl-CoA + 2 Fe(II)-[cytochrome b5] + 2 H+ + O2 = an (11Z)-delta-11-fatty acyl-CoA + 2 Fe(III)-[cytochrome b5] + 2 H2O." [PMID:15063718, PMID:15544945, RHEA:25852]
synonym: "acyl-CoA D11-desaturase activity" EXACT []
synonym: "acyl-CoA delta(11)-desaturase activity" EXACT []
+synonym: "acyl-CoA delta11-desaturase activity" BROAD []
+synonym: "delta(11) desaturase" BROAD [EC:1.14.19.5]
+synonym: "delta(11)-fatty-acid desaturase" BROAD [EC:1.14.19.5]
+synonym: "delta(11)-palmitoyl-CoA desaturase" NARROW [EC:1.14.19.5]
+synonym: "fatty acid delta(11)-desaturase" BROAD [EC:1.14.19.5]
+synonym: "myristoyl-CoA 11-(Z) desaturase activity" NARROW []
+synonym: "Z/E11-desaturase" BROAD [EC:1.14.19.5]
xref: EC:1.14.19.5
+xref: MetaCyc:1.14.99.32-RXN
+xref: RHEA:25852
is_a: GO:0016215 ! acyl-CoA desaturase activity
[Term]
@@ -125647,30 +125611,29 @@ is_a: GO:0048256 ! flap endonuclease activity
id: GO:0017109
name: glutamate-cysteine ligase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the ligation of glutamate to cysteine, forming glutamylcysteine." [EC:6.3.2.2]
+def: "An enzyme complex that catalyzes the ligation of glutamate to cysteine, forming glutamylcysteine." [PMID:9675072]
synonym: "gamma-glutamylcysteine synthetase complex" EXACT []
is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005737 ! cytoplasm
[Term]
id: GO:0017110
-name: nucleoside-diphosphatase activity
+name: nucleoside diphosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a nucleoside diphosphate + H2O = a nucleoside monophosphate + phosphate." [EC:3.6.1.6]
+def: "Catalysis of the reaction: a nucleoside diphosphate + H2O = a nucleoside monophosphate + phosphate." [EC:3.6.1.6]
synonym: "apyrase activity" BROAD []
synonym: "inosine 5'-diphosphatase" NARROW [EC:3.6.1.6]
synonym: "inosine diphosphatase" NARROW [EC:3.6.1.6]
synonym: "NDPase activity" RELATED [EC:3.6.1.6]
synonym: "nucleoside 5'-diphosphatase activity" RELATED [EC:3.6.1.6]
synonym: "nucleoside diphosphatase activity" EXACT []
-synonym: "nucleoside diphosphate phosphatase activity" RELATED [EC:3.6.1.6]
synonym: "nucleoside diphosphate phosphohydrolase activity" RELATED [EC:3.6.1.6]
+synonym: "nucleoside-diphosphatase activity" EXACT []
synonym: "nucleoside-diphosphate phosphohydrolase activity" RELATED [EC:3.6.1.6]
synonym: "type B nucleoside diphosphatase" NARROW [EC:3.6.1.6]
synonym: "type L nucleoside diphosphatase" NARROW [EC:3.6.1.6]
xref: EC:3.6.1.6
xref: MetaCyc:NUCLEOSIDE-DIPHOSPHATASE-RXN
-xref: Reactome:R-HSA-2395876 "NUDT15 hydrolyses 8-oxo-dGDP to 8-oxo-dGMP"
xref: Reactome:R-HSA-8850854 "NTPDase1 hydrolyzes nucleoside diphosphates"
xref: Reactome:R-HSA-8851129 "NTPDase3 hydrolyzes nucleoside diphosphates"
xref: Reactome:R-HSA-8851225 "NTPDase4 hydrolyzes nucleoside diphosphates"
@@ -125682,19 +125645,21 @@ is_a: GO:0016462 ! pyrophosphatase activity
[Term]
id: GO:0017111
-name: nucleoside-triphosphatase activity
+name: ribonucleoside triphosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate." [RHEA:23680]
+def: "Catalysis of the reaction: a ribonucleoside triphosphate + H2O = a ribonucleoside diphosphate + H+ + phosphate." [RHEA:23680]
subset: goslim_chembl
subset: goslim_metagenomics
synonym: "apyrase activity" BROAD []
-synonym: "NTPase activity" RELATED []
-synonym: "nucleoside 5-triphosphatase activity" RELATED []
-synonym: "nucleoside triphosphatase activity" EXACT []
-synonym: "nucleoside triphosphate hydrolase activity" RELATED []
+synonym: "NTPase activity" EXACT []
+synonym: "nucleoside 5-triphosphatase activity" BROAD [EC:3.6.1.15]
+synonym: "nucleoside triphosphatase activity" BROAD []
+synonym: "nucleoside triphosphate hydrolase activity" BROAD []
+synonym: "nucleoside triphosphate phosphatase activity" BROAD []
synonym: "nucleoside triphosphate phosphohydrolase activity" RELATED []
synonym: "nucleoside-5-triphosphate phosphohydrolase activity" RELATED []
-synonym: "unspecific diphosphate phosphohydrolase activity" RELATED []
+synonym: "nucleoside-triphosphatase activity" BROAD []
+xref: EC:3.6.1.15
xref: MetaCyc:NUCLEOSIDE-TRIPHOSPHATASE-RXN
xref: Reactome:R-HSA-8850846 "NTPDase1 hydrolyzes nucleoside triphosphates"
xref: Reactome:R-HSA-8851089 "NTPDase2 hydrolyzes nucleoside triphosphates"
@@ -125763,7 +125728,7 @@ is_a: GO:0033202 ! DNA helicase complex
id: GO:0017118
name: lipoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of the lipoyl group from lipoyl-AMP to the lysine residue of lipoate-dependent enzyme." [PMID:10103005, RHEA:20473]
+def: "Catalysis of the reaction: (R)-lipoyl-5'-AMP + L-lysyl-[lipoyl-carrier protein] = (R)-N6-lipoyl-L-lysyl-[lipoyl-carrier protein] + AMP + 2 H+." [PMID:10103005, RHEA:20473]
xref: RHEA:20473
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
@@ -125771,7 +125736,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0017119
name: Golgi transport complex
namespace: cellular_component
-def: "A multisubunit tethering complex of the CATCHR family (complexes associated with tethering containing helical rods) that has a role in tethering vesicles to the Golgi prior to fusion. Composed of 8 subunits COG1-8." [GOC:krc, PMID:11980916, PMID:20972446, PMID:9792665]
+def: "A multisubunit tethering complex of the CATCHR family (complexes associated with tethering containing helical rods) that has a role in tethering vesicles to the Golgi prior to fusion. Composed of 8 subunits COG1-8." [GOC:krc, PMID:11980916, PMID:20972446, PMID:9792665]
synonym: "COG complex" EXACT []
synonym: "conserved oligomeric Golgi complex" EXACT []
synonym: "Sec34/35 complex" NARROW []
@@ -125985,7 +125950,6 @@ def: "An assembly of four or five subunits which form a structure with an extrac
synonym: "N-methyl-D-aspartate selective glutamate receptor complex" EXACT []
synonym: "NMDA-selective glutamate receptor" EXACT []
is_a: GO:0008328 ! ionotropic glutamate receptor complex
-is_a: GO:0034703 ! cation channel complex
[Term]
id: GO:0017147
@@ -126013,10 +125977,11 @@ synonym: "negative regulation of protein synthesis" EXACT []
synonym: "protein biosynthesis inhibitor activity" RELATED []
synonym: "protein biosynthetic process inhibitor activity" RELATED []
is_a: GO:0006417 ! regulation of translation
+is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process
is_a: GO:0010629 ! negative regulation of gene expression
-is_a: GO:0032269 ! negative regulation of cellular protein metabolic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
-is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process
+is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
+is_a: GO:0051248 ! negative regulation of protein metabolic process
relationship: negatively_regulates GO:0006412 ! translation
[Term]
@@ -126082,7 +126047,7 @@ id: GO:0017156
name: calcium-ion regulated exocytosis
namespace: biological_process
def: "The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell, induced by a rise in cytosolic calcium-ion levels." [GOC:go_curators]
-comment: Note that the calcium regulated exocytosis pathway can be leaky: some level of exocytosis via this pathway occurs spontaneously. This phenomenon underlies spontaneous neurotransmitter release from presynapses. This phenomenon is distinct from the unregulated, calcium independent exocytosis pathway.
+comment: Note that the calcium regulated exocytosis pathway can be leaky: some level of exocytosis via this pathway occurs spontaneously. This phenomenon underlies spontaneous neurotransmitter release from presynapses. This phenomenon is distinct from the unregulated, calcium independent exocytosis pathway.
synonym: "calcium ion-dependent exocytosis" EXACT []
is_a: GO:0045055 ! regulated exocytosis
@@ -126107,7 +126072,7 @@ relationship: regulates GO:0017156 ! calcium-ion regulated exocytosis
id: GO:0017159
name: pantetheine hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-pantetheine + H(2)O = (R)-pantothenate + cysteamine." [EC:3.5.1.92, RHEA:13445]
+def: "Catalysis of the reaction: (R)-pantetheine + H2O = (R)-pantothenate + cysteamine." [EC:3.5.1.92, RHEA:13445]
synonym: "(R)-pantetheine amidohydrolase activity" RELATED [EC:3.5.1.92]
synonym: "pantetheinase activity" RELATED [EC:3.5.1.92]
synonym: "vanin" RELATED [EC:3.5.1.92]
@@ -126184,7 +126149,7 @@ is_a: GO:0008092 ! cytoskeletal protein binding
id: GO:0017168
name: 5-oxoprolinase (ATP-hydrolyzing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-oxo-L-proline + ATP + 2 H(2)O = L-glutamate + ADP + 2 H(+) + phosphate." [EC:3.5.2.9, RHEA:10348]
+def: "Catalysis of the reaction: 5-oxo-L-proline + ATP + 2 H2O = L-glutamate + ADP + 2 H+ + phosphate." [EC:3.5.2.9, RHEA:10348]
synonym: "5-OPase activity" RELATED [EC:3.5.2.9]
synonym: "5-oxo-L-prolinase activity" RELATED [EC:3.5.2.9]
synonym: "5-oxo-L-proline amidohydrolase (ATP-hydrolysing)" RELATED [EC:3.5.2.9]
@@ -126233,7 +126198,7 @@ is_a: GO:0016787 ! hydrolase activity
id: GO:0017172
name: cysteine dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-cysteine + O(2) = 3-sulfino-L-alanine + H(+)." [EC:1.13.11.20, RHEA:20441]
+def: "Catalysis of the reaction: L-cysteine + O2 = 3-sulfino-L-alanine + H+." [EC:1.13.11.20, RHEA:20441]
xref: EC:1.13.11.20
xref: KEGG_REACTION:R00893
xref: MetaCyc:CYSTEINE-DIOXYGENASE-RXN
@@ -126293,12 +126258,13 @@ def: "A heterodimeric complex that catalyzes the trimming of glucose residues fr
comment: Note that alpha-glucosidase I functions as a monomer, and therefore does not have a corresponding cellular component term.
synonym: "alpha-glucosidase II complex" RELATED [GOC:19605557, GOC:vw]
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0017178
name: diphthine-ammonia ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + diphthine + NH(4)(+) = ADP + diphthamide + H(+) + phosphate." [EC:6.3.1.14, RHEA:19753]
+def: "Catalysis of the reaction: ATP + diphthine + NH4 = ADP + diphthamide + H+ + phosphate." [EC:6.3.1.14, RHEA:19753]
synonym: "diphthamide synthase activity" RELATED [EC:6.3.1.14]
synonym: "diphthamide synthetase activity" RELATED [EC:6.3.1.14]
synonym: "diphthine:ammonia ligase (ADP-forming)" RELATED [EC:6.3.1.14]
@@ -126407,7 +126373,7 @@ is_a: GO:0018214 ! protein carboxylation
id: GO:0017188
name: aspartate N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-aspartate + acetyl-CoA = N-acetyl-L-aspartate + CoA + H(+)." [EC:2.3.1.17, RHEA:14165]
+def: "Catalysis of the reaction: L-aspartate + acetyl-CoA = N-acetyl-L-aspartate + CoA + H+." [EC:2.3.1.17, RHEA:14165]
synonym: "acetyl-CoA:L-aspartate N-acetyltransferase activity" RELATED [EC:2.3.1.17]
synonym: "aspartate acetyltransferase activity" RELATED [EC:2.3.1.17]
synonym: "L-aspartate N-acetyltransferase activity" RELATED [EC:2.3.1.17]
@@ -126604,14 +126570,14 @@ is_a: GO:0018198 ! peptidyl-cysteine modification
[Term]
id: GO:0018010
-name: glycoprotein N-palmitoyltransferase activity
+name: obsolete glycoprotein N-palmitoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: palmitoyl-CoA + glycoprotein = CoA + N-palmitoylglycoprotein." [EC:2.3.1.96]
+def: "OBSOLETE. Catalysis of the reaction: palmitoyl-CoA + glycoprotein = CoA + N-palmitoylglycoprotein." [EC:2.3.1.96]
+comment: This term was obsoleted because it has been deleted from EC. The glycoprotein is the product of the reaction.
synonym: "mucus glycoprotein fatty acyltransferase" NARROW [EC:2.3.1.96]
synonym: "palmitoyl-CoA:glycoprotein N-palmitoyltransferase activity" RELATED [EC:2.3.1.96]
xref: MetaCyc:GLYCOPROTEIN-N-PALMITOYLTRANSFERASE-RXN
-is_a: GO:0019105 ! N-palmitoyltransferase activity
-is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
+is_obsolete: true
[Term]
id: GO:0018011
@@ -126710,19 +126676,15 @@ is_a: GO:0018022 ! peptidyl-lysine methylation
[Term]
id: GO:0018024
-name: histone-lysine N-methyltransferase activity
+name: obsolete histone lysine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives." [RESID:AA0074, RESID:AA0075, RESID:AA0076]
-synonym: "histone H1-specific S-adenosylmethionine:protein-lysine N-methyltransferase activity" RELATED []
+def: "OBSOLETE. Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives." [RHEA:10024]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+synonym: "histone H1-specific S-adenosylmethionine:protein-lysine N-methyltransferase activity" NARROW []
synonym: "histone-lysine N-methylase activity" EXACT [GOC:mah]
-synonym: "protein (lysine) methyltransferase activity" RELATED []
-synonym: "protein methylase 3 activity" NARROW []
-synonym: "protein methylase III activity" NARROW []
-synonym: "protein methyltransferase II activity" NARROW []
+synonym: "histone-lysine N-methyltransferase activity" EXACT []
synonym: "S-adenosyl-L-methionine:histone-L-lysine 6-N-methyltransferase activity" RELATED []
synonym: "S-adenosyl-L-methionine:histone-L-lysine N6-methyltransferase activity" RELATED []
-xref: EC:2.1.1.354
-xref: MetaCyc:HISTONE-LYSINE-N-METHYLTRANSFERASE-RXN
xref: Reactome:R-HSA-3788745 "EHMT1:EHMT2 methylates IL8 promoter"
xref: Reactome:R-HSA-3788748 "EHMT1:EHMT2 methylates IL6 promoter"
xref: Reactome:R-HSA-4827382 "SUV39H1 (KMT1A), SUV39H2 (KTM1B), SETDB1 (KMT1E), SETDB2 (KMT1F) methylate dimethyl-lysine-10 of histone H3 (H3K9)"
@@ -126745,12 +126707,10 @@ xref: Reactome:R-HSA-5649801 "DOT1L (KMT4) methylates lysine-80 of histone H3 (H
xref: Reactome:R-HSA-5649802 "WHSC1L1 (KMT3F) methylates dimethyl-lysine-28 of histone H3 (H3K27)"
xref: Reactome:R-HSA-5651654 "SUV420H1 (KMT5B), SUV420H2 (KMT5C), (possibly SMYD3 (KMT3E)) methylate methyl-lysine-21 of histone H4 (H4K20)"
xref: Reactome:R-HSA-5651657 "SUV420H1, SUV420H2, (possibly SMYD3 (KMT3E)) methylate dimethyl-lysine-21 of histone H4 (H4K20)"
-xref: RESID:AA0074
-xref: RESID:AA0075
-xref: RESID:AA0076
-xref: RHEA:10024
-is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
-is_a: GO:0042054 ! histone methyltransferase activity
+is_obsolete: true
+consider: GO:0140938
+consider: GO:0140939
+consider: GO:0140940
[Term]
id: GO:0018025
@@ -126804,16 +126764,16 @@ is_a: GO:0018205 ! peptidyl-lysine modification
id: GO:0018030
name: peptidyl-lysine N6-myristoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a myristoyl group to the N6 nitrogen atom on a lysine residue of a peptide or protein molecule." [GOC:mah]
+def: "Catalysis of the transfer of a myristoyl group to the N6 nitrogen atom on a lysine residue of a peptide or protein molecule." [GOC:mah, PMID:1402651]
is_a: GO:0019107 ! myristoyltransferase activity
+is_a: GO:0140096 ! catalytic activity, acting on a protein
[Term]
id: GO:0018031
name: peptidyl-lysine N6-palmitoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a palmitoyl group to the N6 nitrogen atom on a lysine residue of a peptide or protein molecule." [GOC:mah]
-xref: EC:2.3.1.-
-is_a: GO:0019105 ! N-palmitoyltransferase activity
+def: "Catalysis of the transfer of a palmitoyl group to the N6 nitrogen atom on a lysine residue of a peptide or protein molecule." [GOC:mah, PMID:29074776]
+is_a: GO:0016410 ! N-acyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
[Term]
@@ -126822,203 +126782,206 @@ name: protein amidation
namespace: biological_process
def: "Addition of an amide group from a glycine to a protein amino acid." [UniProtKB-KW:KW-0027]
synonym: "protein amino acid amidation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018033
-name: protein C-terminal amidation
+name: obsolete protein C-terminal amidation
namespace: biological_process
-def: "The formation of a C-terminal amide by hydrolysis and oxidation of an interior peptide in a secreted protein." [GOC:ai]
-is_a: GO:0018032 ! protein amidation
-is_a: GO:0018410 ! C-terminal protein amino acid modification
+def: "OBSOLETE. The formation of a C-terminal amide by hydrolysis and oxidation of an interior peptide in a secreted protein." [GOC:ai]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0018034
-name: C-terminal peptidyl-alanine amidation
+name: obsolete C-terminal peptidyl-alanine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-alanine amide by hydrolysis and oxidation of an interior Ala-Gly peptide in a secreted protein." [RESID:AA0081]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-alanine amide by hydrolysis and oxidation of an interior Ala-Gly peptide in a secreted protein." [RESID:AA0081]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0081
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018194 ! peptidyl-alanine modification
+is_obsolete: true
[Term]
id: GO:0018035
-name: C-terminal peptidyl-arginine amidation
+name: obsolete C-terminal peptidyl-arginine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-arginine amide by hydrolysis and oxidation of an interior Arg-Gly peptide in a secreted protein." [RESID:AA0082]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-arginine amide by hydrolysis and oxidation of an interior Arg-Gly peptide in a secreted protein." [RESID:AA0082]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0082
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018195 ! peptidyl-arginine modification
+is_obsolete: true
[Term]
id: GO:0018036
-name: C-terminal peptidyl-asparagine amidation
+name: obsolete C-terminal peptidyl-asparagine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-asparagine amide by hydrolysis and oxidation of an interior Asn-Gly peptide in a secreted protein." [RESID:AA0083]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-asparagine amide by hydrolysis and oxidation of an interior Asn-Gly peptide in a secreted protein." [RESID:AA0083]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0083
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018196 ! peptidyl-asparagine modification
+is_obsolete: true
[Term]
id: GO:0018037
-name: C-terminal peptidyl-aspartic acid amidation
+name: obsolete C-terminal peptidyl-aspartic acid amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-aspartic acid 1-amide by hydrolysis and oxidation of an interior Asp-Gly peptide in a secreted protein." [RESID:AA0084]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-aspartic acid 1-amide by hydrolysis and oxidation of an interior Asp-Gly peptide in a secreted protein." [RESID:AA0084]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0084
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018197 ! peptidyl-aspartic acid modification
+is_obsolete: true
[Term]
id: GO:0018038
-name: C-terminal peptidyl-cysteine amidation
+name: obsolete C-terminal peptidyl-cysteine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-cysteine amide by hydrolysis and oxidation of an interior Cys-Gly peptide in a secreted protein." [RESID:AA0085]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-cysteine amide by hydrolysis and oxidation of an interior Cys-Gly peptide in a secreted protein." [RESID:AA0085]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0085
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018198 ! peptidyl-cysteine modification
+is_obsolete: true
[Term]
id: GO:0018039
-name: C-terminal peptidyl-glutamine amidation
+name: obsolete C-terminal peptidyl-glutamine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-glutamine amide by hydrolysis and oxidation of an interior Gln-Gly peptide in a secreted protein." [RESID:AA0086]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-glutamine amide by hydrolysis and oxidation of an interior Gln-Gly peptide in a secreted protein." [RESID:AA0086]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0086
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018199 ! peptidyl-glutamine modification
+is_obsolete: true
[Term]
id: GO:0018040
-name: C-terminal peptidyl-glutamic acid amidation
+name: obsolete C-terminal peptidyl-glutamic acid amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-glutamic acid amide by hydrolysis and oxidation of an interior Glu-Gly peptide in a secreted protein." [RESID:AA0087]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-glutamic acid amide by hydrolysis and oxidation of an interior Glu-Gly peptide in a secreted protein." [RESID:AA0087]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0087
-is_a: GO:0018033 ! protein C-terminal amidation
+is_obsolete: true
[Term]
id: GO:0018041
-name: C-terminal peptidyl-glycine amidation
+name: obsolete C-terminal peptidyl-glycine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-glycine acid amide by hydrolysis and oxidation of an interior Gly-Gly peptide in a secreted protein." [RESID:AA0088]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-glycine acid amide by hydrolysis and oxidation of an interior Gly-Gly peptide in a secreted protein." [RESID:AA0088]
+comment: This term was obsoleted because it represents a molecular function.
xref: RESID:AA0088
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018201 ! peptidyl-glycine modification
+is_obsolete: true
+consider: GO:0004504
+consider: GO:0004598
[Term]
id: GO:0018042
-name: C-terminal peptidyl-histidine amidation
+name: obsolete C-terminal peptidyl-histidine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-histidine amide by hydrolysis and oxidation of an interior His-Gly peptide in a secreted protein." [RESID:AA0089]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-histidine amide by hydrolysis and oxidation of an interior His-Gly peptide in a secreted protein." [RESID:AA0089]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0089
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018202 ! peptidyl-histidine modification
+is_obsolete: true
[Term]
id: GO:0018043
-name: C-terminal peptidyl-isoleucine amidation
+name: obsolete C-terminal peptidyl-isoleucine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-isoleucine amide by hydrolysis and oxidation of an interior Ile-Gly peptide in a secreted protein." [RESID:AA0090]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-isoleucine amide by hydrolysis and oxidation of an interior Ile-Gly peptide in a secreted protein." [RESID:AA0090]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0090
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018203 ! peptidyl-isoleucine modification
+is_obsolete: true
[Term]
id: GO:0018044
-name: C-terminal peptidyl-leucine amidation
+name: obsolete C-terminal peptidyl-leucine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-leucine amide by hydrolysis and oxidation of an interior Leu-Gly peptide in a secreted protein." [RESID:AA0091]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-leucine amide by hydrolysis and oxidation of an interior Leu-Gly peptide in a secreted protein." [RESID:AA0091]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0091
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018204 ! peptidyl-leucine modification
+is_obsolete: true
[Term]
id: GO:0018045
-name: C-terminal peptidyl-lysine amidation
+name: obsolete C-terminal peptidyl-lysine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-lysine amide by hydrolysis and oxidation of an interior Lys-Gly peptide in a secreted protein." [RESID:AA0092]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-lysine amide by hydrolysis and oxidation of an interior Lys-Gly peptide in a secreted protein." [RESID:AA0092]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0092
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018205 ! peptidyl-lysine modification
+is_obsolete: true
[Term]
id: GO:0018046
-name: C-terminal peptidyl-methionine amidation
+name: obsolete C-terminal peptidyl-methionine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-methionine amide by hydrolysis and oxidation of an interior Met-Gly peptide in a secreted protein." [RESID:AA0093]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-methionine amide by hydrolysis and oxidation of an interior Met-Gly peptide in a secreted protein." [RESID:AA0093]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0093
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018206 ! peptidyl-methionine modification
+is_obsolete: true
[Term]
id: GO:0018047
-name: C-terminal peptidyl-phenylalanine amidation
+name: obsolete C-terminal peptidyl-phenylalanine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-phenylalanine amide by hydrolysis and oxidation of an interior Phe-Gly peptide in a secreted protein." [RESID:AA0094]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-phenylalanine amide by hydrolysis and oxidation of an interior Phe-Gly peptide in a secreted protein." [RESID:AA0094]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0094
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018207 ! peptidyl-phenylalanine modification
+is_obsolete: true
[Term]
id: GO:0018048
-name: C-terminal peptidyl-proline amidation
+name: obsolete C-terminal peptidyl-proline amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-proline amide by hydrolysis and oxidation of an interior Pro-Gly peptide in a secreted protein." [RESID:AA0095]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-proline amide by hydrolysis and oxidation of an interior Pro-Gly peptide in a secreted protein." [RESID:AA0095]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0095
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018208 ! peptidyl-proline modification
+is_obsolete: true
[Term]
id: GO:0018049
-name: C-terminal peptidyl-serine amidation
+name: obsolete C-terminal peptidyl-serine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-serine amide by hydrolysis and oxidation of an interior Ser-Gly peptide in a secreted protein." [RESID:AA0096]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-serine amide by hydrolysis and oxidation of an interior Ser-Gly peptide in a secreted protein." [RESID:AA0096]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0096
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018209 ! peptidyl-serine modification
+is_obsolete: true
[Term]
id: GO:0018050
-name: C-terminal peptidyl-threonine amidation
+name: obsolete C-terminal peptidyl-threonine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-threonine amide by hydrolysis and oxidation of an interior Thr-Gly peptide in a secreted protein." [RESID:AA0097]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-threonine amide by hydrolysis and oxidation of an interior Thr-Gly peptide in a secreted protein." [RESID:AA0097]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0097
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018210 ! peptidyl-threonine modification
+is_obsolete: true
[Term]
id: GO:0018051
-name: C-terminal peptidyl-tryptophan amidation
+name: obsolete C-terminal peptidyl-tryptophan amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-tryptophan amide by hydrolysis and oxidation of an interior Trp-Gly peptide in a secreted protein." [RESID:AA0098]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-tryptophan amide by hydrolysis and oxidation of an interior Trp-Gly peptide in a secreted protein." [RESID:AA0098]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0098
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018211 ! peptidyl-tryptophan modification
+is_obsolete: true
[Term]
id: GO:0018052
-name: C-terminal peptidyl-tyrosine amidation
+name: obsolete C-terminal peptidyl-tyrosine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-tyrosine amide by hydrolysis and oxidation of an interior Tyr-Gly peptide in a secreted protein." [RESID:AA0099]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-tyrosine amide by hydrolysis and oxidation of an interior Tyr-Gly peptide in a secreted protein." [RESID:AA0099]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0099
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018212 ! peptidyl-tyrosine modification
+is_obsolete: true
[Term]
id: GO:0018053
-name: C-terminal peptidyl-valine amidation
+name: obsolete C-terminal peptidyl-valine amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-valine amide by hydrolysis and oxidation of an interior Val-Gly peptide in a secreted protein." [RESID:AA0100]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-valine amide by hydrolysis and oxidation of an interior Val-Gly peptide in a secreted protein." [RESID:AA0100]
+comment: This term was obsoleted because it represents a molecular function, and this modification is not known to exist; only c-terminal peptidylglycine has been identified, see PMID:35124797.
xref: RESID:AA0100
-is_a: GO:0018033 ! protein C-terminal amidation
-is_a: GO:0018213 ! peptidyl-valine modification
+is_obsolete: true
[Term]
id: GO:0018054
-name: peptidyl-lysine biotinylation
+name: obsolete peptidyl-lysine biotinylation
namespace: biological_process
-def: "The covalent modification of peptidyl-lysine by biotin to form peptidyl-N6-biotinyl-L-lysine." [RESID:AA0117]
+def: "OBSOLETE. The covalent modification of peptidyl-lysine by biotin to form peptidyl-N6-biotinyl-L-lysine." [RESID:AA0117]
+comment: This terms was obsoleted because it represents a molecular function as a biological process.
xref: RESID:AA0117
-is_a: GO:0009305 ! protein biotinylation
-is_a: GO:0018205 ! peptidyl-lysine modification
+is_obsolete: true
[Term]
id: GO:0018057
@@ -127174,31 +127137,29 @@ is_a: GO:0018200 ! peptidyl-glutamic acid modification
[Term]
id: GO:0018073
-name: protein bromination
+name: obsolete protein bromination
namespace: biological_process
-def: "The addition of one or more bromine atoms to an amino acid residue in a protein." [GOC:mah]
+def: "OBSOLETE. The addition of one or more bromine atoms to an amino acid residue in a protein." [GOC:mah]
synonym: "protein amino acid bromination" EXACT [GOC:bf]
-is_a: GO:0018079 ! protein halogenation
+is_obsolete: true
[Term]
id: GO:0018074
-name: peptidyl-histidine bromination
+name: obsolete peptidyl-histidine bromination
namespace: biological_process
-def: "The bromination of peptidyl-histidine to form peptidyl-L-bromohistidine; the position of the bromine substitution is unknown." [RESID:AA0173]
+def: "OBSOLETE. The bromination of peptidyl-histidine to form peptidyl-L-bromohistidine; the position of the bromine substitution is unknown." [RESID:AA0173]
xref: RESID:AA0173
-is_a: GO:0018073 ! protein bromination
-is_a: GO:0018202 ! peptidyl-histidine modification
+is_obsolete: true
[Term]
id: GO:0018075
-name: peptidyl-phenylalanine bromination
+name: obsolete peptidyl-phenylalanine bromination
namespace: biological_process
-def: "The bromination of phenylalanine." [RESID:AA0174, RESID:AA0175, RESID:AA0176]
+def: "OBSOLETE. The bromination of phenylalanine." [RESID:AA0174, RESID:AA0175, RESID:AA0176]
xref: RESID:AA0174
xref: RESID:AA0175
xref: RESID:AA0176
-is_a: GO:0018073 ! protein bromination
-is_a: GO:0018207 ! peptidyl-phenylalanine modification
+is_obsolete: true
[Term]
id: GO:0018076
@@ -127210,39 +127171,36 @@ is_a: GO:0018394 ! peptidyl-lysine acetylation
[Term]
id: GO:0018077
-name: protein iodination
+name: obsolete protein iodination
namespace: biological_process
-def: "The addition of one or more iodine atoms to an amino acid residue in a protein." [GOC:mah]
+def: "OBSOLETE. The addition of one or more iodine atoms to an amino acid residue in a protein." [GOC:mah]
synonym: "protein amino acid iodination" EXACT [GOC:bf]
-is_a: GO:0018079 ! protein halogenation
+is_obsolete: true
[Term]
id: GO:0018078
-name: peptidyl-thyronine iodination
+name: obsolete peptidyl-thyronine iodination
namespace: biological_process
-def: "The iodination of peptidyl-thyronine, formed from tyrosine." [RESID:AA0177, RESID:AA0178]
+def: "OBSOLETE. The iodination of peptidyl-thyronine, formed from tyrosine." [RESID:AA0177, RESID:AA0178]
xref: RESID:AA0177
xref: RESID:AA0178
-is_a: GO:0018077 ! protein iodination
-is_a: GO:0018212 ! peptidyl-tyrosine modification
+is_obsolete: true
[Term]
id: GO:0018079
-name: protein halogenation
+name: obsolete protein halogenation
namespace: biological_process
-def: "The addition of a halogen to a protein amino acid." [GOC:ai]
+def: "OBSOLETE. The addition of a halogen to a protein amino acid." [GOC:ai]
synonym: "protein amino acid halogenation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
-is_a: GO:0070276 ! halogen metabolic process
+is_obsolete: true
[Term]
id: GO:0018080
-name: peptidyl-tryptophan bromination
+name: obsolete peptidyl-tryptophan bromination
namespace: biological_process
-def: "The bromination of peptidyl-tryptophan, to form peptidyl-L-6'-bromotryptophan." [RESID:AA0179]
+def: "OBSOLETE. The bromination of peptidyl-tryptophan, to form peptidyl-L-6'-bromotryptophan." [RESID:AA0179]
xref: RESID:AA0179
-is_a: GO:0018073 ! protein bromination
-is_a: GO:0018211 ! peptidyl-tryptophan modification
+is_obsolete: true
[Term]
id: GO:0018081
@@ -127311,14 +127269,13 @@ consider: GO:0019122
[Term]
id: GO:0018091
-name: peptidyl-asparagine racemization
+name: obsolete peptidyl-asparagine racemization
namespace: biological_process
alt_id: GO:0018373
alt_id: GO:0019127
-def: "The racemization of peptidyl-asparagine." [RESID:AA0196]
-xref: RESID:AA0196
-is_a: GO:0018085 ! peptidyl-L-amino acid racemization
-is_a: GO:0018196 ! peptidyl-asparagine modification
+def: "OBSOLETE. The racemization of peptidyl-asparagine." [RESID:AA0196]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0018094
@@ -127348,27 +127305,28 @@ is_a: GO:0018209 ! peptidyl-serine modification
[Term]
id: GO:0018097
-name: protein-chromophore linkage via peptidyl-S-4-hydroxycinnamyl-L-cysteine
+name: obsolete protein-chromophore linkage via peptidyl-S-4-hydroxycinnamyl-L-cysteine
namespace: biological_process
-def: "The synthesis of the chromophore S-4-hydroxycinnamyl-L-cysteine." [RESID:AA0207]
+def: "OBSOLETE. The synthesis of the chromophore S-4-hydroxycinnamyl-L-cysteine." [RESID:AA0207]
+comment: Term describes modified products or self-catalyzed processes.
synonym: "protein amino acid cinnamylation" BROAD []
xref: RESID:AA0207
-is_a: GO:0018198 ! peptidyl-cysteine modification
-is_a: GO:0018298 ! protein-chromophore linkage
+is_obsolete: true
[Term]
id: GO:0018101
-name: protein citrullination
+name: obsolete protein citrullination
namespace: biological_process
-def: "The hydrolysis of peptidyl-arginine to form peptidyl-citrulline." [PMID:23175390, RESID:AA0214]
-comment: Citrullination is distinct from the formation of the free amino acid citrulline (e.g. as part of the urea cycle).
+def: "OBSOLETE. The hydrolysis of peptidyl-arginine to form peptidyl-citrulline." [PMID:23175390, RESID:AA0214]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "deimination" EXACT [Wikipedia:Citrullination]
synonym: "peptidyl-citrulline anabolism from peptidyl-arginine" EXACT []
synonym: "peptidyl-citrulline biosynthetic process from peptidyl-arginine" EXACT [RESID:AA0214]
synonym: "peptidyl-citrulline formation from peptidyl-arginine" EXACT []
synonym: "peptidyl-citrulline synthesis from peptidyl-arginine" EXACT []
xref: RESID:AA0214
-is_a: GO:0018195 ! peptidyl-arginine modification
+is_obsolete: true
+consider: GO:0004668
[Term]
id: GO:0018102
@@ -127443,13 +127401,12 @@ is_a: GO:0018195 ! peptidyl-arginine modification
[Term]
id: GO:0018110
-name: histone arginine kinase activity
+name: obsolete histone arginine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: histone L-arginine + ATP = histone N(omega)-phospho-L-arginine + ADP + 2 H(+)." [GOC:mah]
+def: "OBSOLETE. Catalysis of the reaction: histone L-arginine + ATP = histone N(omega)-phospho-L-arginine + ADP + 2 H+." [GOC:mah]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "histone-arginine kinase activity" EXACT []
-xref: EC:2.7.3.-
-is_a: GO:0004054 ! arginine kinase activity
-is_a: GO:0035173 ! histone kinase activity
+is_obsolete: true
[Term]
id: GO:0018111
@@ -127528,16 +127485,16 @@ is_a: GO:0018175 ! protein nucleotidylation
[Term]
id: GO:0018118
-name: peptidyl-L-cysteine glutathione disulfide biosynthetic process from peptidyl-cysteine
+name: obsolete peptidyl-L-cysteine glutathione disulfide biosynthetic process from peptidyl-cysteine
namespace: biological_process
-def: "The modification of peptidyl-cysteine by covalent addition of glutathione to form peptidyl-L-cysteine glutathione disulfide." [RESID:AA0229]
+def: "OBSOLETE. The modification of peptidyl-cysteine by covalent addition of glutathione to form peptidyl-L-cysteine glutathione disulfide." [RESID:AA0229]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-L-cysteine glutathione disulfide anabolism from peptidyl-cysteine" EXACT []
synonym: "peptidyl-L-cysteine glutathione disulfide formation from peptidyl-cysteine" EXACT []
synonym: "peptidyl-L-cysteine glutathione disulfide synthesis from peptidyl-cysteine" EXACT []
synonym: "peptidyl-L-cysteine glutathione disulphide biosynthesis from peptidyl-cysteine" EXACT []
synonym: "peptidyl-L-cysteine glutathione disulphide biosynthetic process from peptidyl-cysteine" EXACT []
-xref: RESID:AA0229
-is_a: GO:0018198 ! peptidyl-cysteine modification
+is_obsolete: true
[Term]
id: GO:0018119
@@ -127552,12 +127509,13 @@ is_a: GO:0018198 ! peptidyl-cysteine modification
[Term]
id: GO:0018120
-name: peptidyl-arginine ADP-ribosylation
+name: obsolete peptidyl-arginine ADP-ribosylation
namespace: biological_process
-def: "The transfer, from NAD, of ADP-ribose to peptidyl-arginine to form omega-N-(ADP-ribosyl)-L-arginine." [RESID:AA0168]
+def: "OBSOLETE. The transfer, from NAD, of ADP-ribose to peptidyl-arginine to form omega-N-(ADP-ribosyl)-L-arginine." [RESID:AA0168]
+comment: This term was obsoleted because it represents a molecular function.
xref: RESID:AA0168
-is_a: GO:0006471 ! protein ADP-ribosylation
-is_a: GO:0018195 ! peptidyl-arginine modification
+is_obsolete: true
+consider: GO:0106274
[Term]
id: GO:0018121
@@ -127568,21 +127526,23 @@ is_a: GO:0016763 ! pentosyltransferase activity
[Term]
id: GO:0018122
-name: peptidyl-asparagine ADP-ribosylation
+name: obsolete peptidyl-asparagine ADP-ribosylation
namespace: biological_process
-def: "The transfer, from NAD, of ADP-ribose to peptidyl-asparagine to form peptidyl-N4-(ADP-ribosyl)-L-asparagine." [RESID:AA0231]
+def: "OBSOLETE. The transfer, from NAD, of ADP-ribose to peptidyl-asparagine to form peptidyl-N4-(ADP-ribosyl)-L-asparagine." [RESID:AA0231]
+comment: This term was obsoleted because it represents a molecular function.
xref: RESID:AA0231
-is_a: GO:0006471 ! protein ADP-ribosylation
-is_a: GO:0018196 ! peptidyl-asparagine modification
+is_obsolete: true
+consider: GO:0018121
[Term]
id: GO:0018123
-name: peptidyl-cysteine ADP-ribosylation
+name: obsolete peptidyl-cysteine ADP-ribosylation
namespace: biological_process
-def: "The transfer, from NAD, of ADP-ribose to peptidyl-cysteine to form peptidyl-S-(ADP-ribosyl)-L-cysteine." [RESID:AA0169]
+def: "OBSOLETE. The transfer, from NAD, of ADP-ribose to peptidyl-cysteine to form peptidyl-S-(ADP-ribosyl)-L-cysteine." [RESID:AA0169]
+comment: This term was obsoleted because it represents a molecular function.
xref: RESID:AA0169
-is_a: GO:0006471 ! protein ADP-ribosylation
-is_a: GO:0018198 ! peptidyl-cysteine modification
+is_obsolete: true
+consider: GO:0018071
[Term]
id: GO:0018124
@@ -127609,7 +127569,7 @@ name: protein hydroxylation
namespace: biological_process
def: "The addition of a hydroxy group to a protein amino acid." [GOC:ai]
synonym: "protein amino acid hydroxylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018127
@@ -127768,7 +127728,7 @@ id: GO:0018143
name: nucleic acid-protein covalent cross-linking
namespace: biological_process
def: "The formation of a covalent cross-link between a nucleic acid and a protein." [GOC:ma]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018144
@@ -127826,7 +127786,7 @@ id: GO:0018149
name: peptide cross-linking
namespace: biological_process
def: "The formation of a covalent cross-link between or within protein chains." [GOC:jsg]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018150
@@ -127911,7 +127871,7 @@ name: protein oxidation
namespace: biological_process
def: "The modification of a protein amino acid by oxidation." [GOC:ai]
synonym: "protein amino acid oxidation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018159
@@ -127991,14 +127951,12 @@ is_a: GO:0018212 ! peptidyl-tyrosine modification
[Term]
id: GO:0018166
-name: C-terminal protein-tyrosinylation
+name: obsolete C-terminal protein-tyrosinylation
namespace: biological_process
-def: "The ATP-dependent addition of a tyrosine residue to the C-terminus of a protein; typically the addition of tyrosine to the C-terminus of detyrosinated alpha-tubulin by the enzyme tubulin-tyrosine ligase." [RESID:AA0257]
-comment: See also the molecular function term 'tubulin-tyrosine ligase activity ; GO:0004835'.
+def: "OBSOLETE. The ATP-dependent addition of a tyrosine residue to the C-terminus of a protein; typically the addition of tyrosine to the C-terminus of detyrosinated alpha-tubulin by the enzyme tubulin-tyrosine ligase." [RESID:AA0257]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
xref: RESID:AA0257
-is_a: GO:0018212 ! peptidyl-tyrosine modification
-is_a: GO:0018322 ! protein tyrosinylation
-is_a: GO:0018410 ! C-terminal protein amino acid modification
+is_obsolete: true
[Term]
id: GO:0018167
@@ -128027,12 +127985,12 @@ is_a: GO:0070739 ! protein-glutamic acid ligase activity
[Term]
id: GO:0018170
-name: C-terminal peptidyl-polyglutamic acid amidation
+name: obsolete C-terminal peptidyl-polyglutamic acid amidation
namespace: biological_process
-def: "The formation of a C-terminal peptidyl-polyglutamic acid to form a peptidyl-N-L-glutamyl-poly-L-glutamic acid C-terminus." [RESID:AA0261]
+def: "OBSOLETE. The formation of a C-terminal peptidyl-polyglutamic acid to form a peptidyl-N-L-glutamyl-poly-L-glutamic acid C-terminus." [RESID:AA0261]
+comment: This term was obsoleted because it represents a molecular function.
xref: RESID:AA0261
-is_a: GO:0018040 ! C-terminal peptidyl-glutamic acid amidation
-is_a: GO:0018200 ! peptidyl-glutamic acid modification
+is_obsolete: true
[Term]
id: GO:0018171
@@ -128087,7 +128045,7 @@ name: protein nucleotidylation
namespace: biological_process
def: "The addition of a nucleotide to a protein amino acid." [GOC:ai]
synonym: "protein amino acid nucleotidylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018177
@@ -128127,16 +128085,17 @@ synonym: "protein amino acid desulfurisation" EXACT []
synonym: "protein amino acid desulfurization" EXACT [GOC:bf]
synonym: "protein amino acid desulphurisation" EXACT []
synonym: "protein amino acid desulphurization" EXACT []
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018181
-name: peptidyl-arginine C5-methylation
+name: obsolete peptidyl-arginine C5-methylation
namespace: biological_process
-def: "The methylation of peptidyl-arginine on the carbon 5 (C5) residue to form peptidyl-5-methyl-L-arginine." [GOC:bf, http://www.uni-marburg.de/mpi/thauer/thauer_res.html, RESID:AA0272]
+def: "OBSOLETE. The methylation of peptidyl-arginine on the carbon 5 (C5) residue to form peptidyl-5-methyl-L-arginine." [GOC:bf, http://www.uni-marburg.de/mpi/thauer/thauer_res.html, RESID:AA0272]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-arginine 5-methylation" EXACT []
-xref: RESID:AA0272
-is_a: GO:0035245 ! peptidyl-arginine C-methylation
+is_obsolete: true
+replaced_by: GO:0035244
[Term]
id: GO:0018182
@@ -128163,7 +128122,7 @@ name: protein polyamination
namespace: biological_process
def: "The modification of a protein amino acid by polyamination." [GOC:ai]
synonym: "protein amino acid polyamination" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018185
@@ -128259,7 +128218,7 @@ name: peptidyl-amino acid modification
namespace: biological_process
def: "The alteration of an amino acid residue in a peptide." [GOC:mah]
subset: goslim_yeast
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018194
@@ -128277,10 +128236,11 @@ is_a: GO:0018193 ! peptidyl-amino acid modification
[Term]
id: GO:0018196
-name: peptidyl-asparagine modification
+name: obsolete peptidyl-asparagine modification
namespace: biological_process
-def: "The modification of peptidyl-asparagine." [GOC:go_curators]
-is_a: GO:0018193 ! peptidyl-amino acid modification
+def: "OBSOLETE. The modification of peptidyl-asparagine." [GOC:go_curators]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0018197
@@ -128407,7 +128367,7 @@ name: protein carboxylation
namespace: biological_process
def: "The addition of a carboxy group to a protein amino acid." [GOC:ai]
synonym: "protein amino acid carboxylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018215
@@ -128415,7 +128375,7 @@ name: protein phosphopantetheinylation
namespace: biological_process
def: "The modification of a protein amino acid by phosphopantetheinylation." [GOC:ai]
synonym: "protein amino acid phosphopantetheinylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018216
@@ -128475,16 +128435,16 @@ is_a: GO:0018345 ! protein palmitoylation
[Term]
id: GO:0018222
-name: peptidyl-L-cysteine methyl disulfide biosynthetic process from peptidyl-cysteine
+name: obsolete peptidyl-L-cysteine methyl disulfide biosynthetic process from peptidyl-cysteine
namespace: biological_process
-def: "The modification of peptidyl-cysteine to form peptidyl-L-cysteine methyl disulfide." [RESID:AA0101]
+def: "OBSOLETE. The modification of peptidyl-cysteine to form peptidyl-L-cysteine methyl disulfide." [RESID:AA0101]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-L-cysteine methyl disulfide anabolism from peptidyl-cysteine" EXACT []
synonym: "peptidyl-L-cysteine methyl disulfide formation from peptidyl-cysteine" EXACT []
synonym: "peptidyl-L-cysteine methyl disulfide synthesis from peptidyl-cysteine" EXACT []
synonym: "peptidyl-L-cysteine methyl disulphide biosynthesis from peptidyl-cysteine" EXACT []
synonym: "peptidyl-L-cysteine methyl disulphide biosynthetic process from peptidyl-cysteine" EXACT []
-xref: RESID:AA0101
-is_a: GO:0018198 ! peptidyl-cysteine modification
+is_obsolete: true
[Term]
id: GO:0018226
@@ -128524,15 +128484,14 @@ is_a: GO:0018344 ! protein geranylgeranylation
[Term]
id: GO:0018229
-name: peptidyl-L-cysteine methyl ester biosynthetic process from peptidyl-cysteine
+name: obsolete peptidyl-L-cysteine methyl ester biosynthetic process from peptidyl-cysteine
namespace: biological_process
-def: "The modification of a C-terminal peptidyl-cysteine to form peptidyl-L-cysteine methyl ester." [RESID:AA0105]
+def: "OBSOLETE. The modification of a C-terminal peptidyl-cysteine to form peptidyl-L-cysteine methyl ester." [RESID:AA0105]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-L-cysteine methyl ester anabolism from peptidyl-cysteine" EXACT []
synonym: "peptidyl-L-cysteine methyl ester formation from peptidyl-cysteine" EXACT []
synonym: "peptidyl-L-cysteine methyl ester synthesis from peptidyl-cysteine" EXACT []
-xref: RESID:AA0105
-is_a: GO:0006481 ! C-terminal protein methylation
-is_a: GO:0018351 ! peptidyl-cysteine esterification
+is_obsolete: true
[Term]
id: GO:0018230
@@ -128682,7 +128641,7 @@ id: GO:0018246
name: protein-coenzyme A linkage
namespace: biological_process
def: "The formation of a linkage between a protein amino acid and coenzyme A." [GOC:mah]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018247
@@ -128708,7 +128667,7 @@ name: protein dehydration
namespace: biological_process
def: "The removal of a water group from a protein amino acid." [GOC:ai]
synonym: "protein amino acid dehydration" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018250
@@ -128737,16 +128696,14 @@ is_a: GO:0018249 ! protein dehydration
[Term]
id: GO:0018252
-name: peptide cross-linking via L-seryl-5-imidazolinone glycine
+name: obsolete peptide cross-linking via L-seryl-5-imidazolinone glycine
namespace: biological_process
-def: "The formation of the green fluorescent protein chromophore cross-link from the alpha-carboxyl carbon of residue n, a serine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons." [RESID:AA0184]
-comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'.
+def: "OBSOLETE. The formation of the green fluorescent protein chromophore cross-link from the alpha-carboxyl carbon of residue n, a serine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons." [RESID:AA0184]
+comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'. Term describes modified products or self-catalyzed processes.
synonym: "biosynthesis of protein-protein cross-link via L-seryl-5-imidazolinone glycine" EXACT []
synonym: "biosynthetic process of protein-protein cross-link via L-seryl-5-imidazolinone glycine" EXACT []
xref: RESID:AA0184
-is_a: GO:0018209 ! peptidyl-serine modification
-is_a: GO:0018253 ! peptide cross-linking via 5-imidazolinone glycine
-is_a: GO:0018298 ! protein-chromophore linkage
+is_obsolete: true
[Term]
id: GO:0018253
@@ -128843,23 +128800,19 @@ is_a: GO:0018149 ! peptide cross-linking
[Term]
id: GO:0018263
-name: isopeptide cross-linking via N-(L-isoaspartyl)-L-cysteine
+name: obsolete isopeptide cross-linking via N-(L-isoaspartyl)-L-cysteine
namespace: biological_process
-def: "The formation of an isopeptide cross-link between peptidyl-asparagine and peptidyl-cysteine to produce N-(L-isoaspartyl)-L-cysteine." [RESID:AA0216]
-xref: RESID:AA0216
-is_a: GO:0018196 ! peptidyl-asparagine modification
-is_a: GO:0018198 ! peptidyl-cysteine modification
-is_a: GO:0018262 ! isopeptide cross-linking
+def: "OBSOLETE. The formation of an isopeptide cross-link between peptidyl-asparagine and peptidyl-cysteine to produce N-(L-isoaspartyl)-L-cysteine." [RESID:AA0216]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0018264
-name: isopeptide cross-linking via N-(L-isoaspartyl)-glycine
+name: obsolete isopeptide cross-linking via N-(L-isoaspartyl)-glycine
namespace: biological_process
-def: "The formation of an isopeptide cross-link between peptidyl-asparagine and peptidyl-glycine to produce N-(L-isoaspartyl)-glycine." [RESID:AA0126]
-xref: RESID:AA0126
-is_a: GO:0018196 ! peptidyl-asparagine modification
-is_a: GO:0018201 ! peptidyl-glycine modification
-is_a: GO:0018262 ! isopeptide cross-linking
+def: "OBSOLETE. The formation of an isopeptide cross-link between peptidyl-asparagine and peptidyl-glycine to produce N-(L-isoaspartyl)-glycine." [RESID:AA0126]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0018265
@@ -128871,7 +128824,6 @@ synonym: "GPI anchor formation via N-asparaginyl-glycosylphosphatidylinositoleth
synonym: "GPI anchor synthesis via N-asparaginyl-glycosylphosphatidylinositolethanolamine" EXACT []
xref: RESID:AA0158
is_a: GO:0006506 ! GPI anchor biosynthetic process
-is_a: GO:0018196 ! peptidyl-asparagine modification
[Term]
id: GO:0018266
@@ -128965,12 +128917,12 @@ is_a: GO:0018352 ! protein-pyridoxal-5-phosphate linkage
[Term]
id: GO:0018273
-name: protein-chromophore linkage via peptidyl-N6-retinal-L-lysine
+name: obsolete protein-chromophore linkage via peptidyl-N6-retinal-L-lysine
namespace: biological_process
-def: "The modification of peptidyl-lysine to form N6-retinal-L-lysine." [RESID:AA0120]
+def: "OBSOLETE. The modification of peptidyl-lysine to form N6-retinal-L-lysine." [RESID:AA0120]
+comment: Term describes modified products or self-catalyzed processes.
xref: RESID:AA0120
-is_a: GO:0018205 ! peptidyl-lysine modification
-is_a: GO:0018298 ! protein-chromophore linkage
+is_obsolete: true
[Term]
id: GO:0018274
@@ -129011,7 +128963,7 @@ name: protein deamination
namespace: biological_process
def: "The removal of an amino group from a protein amino acid." [GOC:ai]
synonym: "protein amino acid deamination" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018278
@@ -129029,7 +128981,6 @@ namespace: biological_process
def: "The glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine and N4 glucosyl asparagine also occur. This modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification." [GOC:jsg, RESID:AA0151, RESID:AA0420, RESID:AA0421]
synonym: "protein amino acid N-linked glycosylation via asparagine" EXACT [GOC:bf]
is_a: GO:0006487 ! protein N-linked glycosylation
-is_a: GO:0018196 ! peptidyl-asparagine modification
[Term]
id: GO:0018280
@@ -129057,7 +129008,7 @@ name: metal incorporation into metallo-sulfur cluster
namespace: biological_process
def: "The formation of a cluster of several metal atoms, including iron, nickel, molybdenum, vanadium, or copper, with one or more bridging (mu-bond) sulfur atoms; amino acids residues in proteins that may ligate the metal sulfur cluster are cysteine, histidine, aspartate, glutamate, serine and cysteine persulfide." [GOC:jsg]
synonym: "metal incorporation into metallo-sulphur cluster" EXACT []
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
relationship: part_of GO:0031163 ! metallo-sulfur cluster assembly
[Term]
@@ -129162,7 +129113,7 @@ id: GO:0018293
name: protein-FAD linkage
namespace: biological_process
def: "The formation of a linkage between a protein amino acid and flavin-adenine dinucleotide (FAD)." [GOC:ai]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018294
@@ -129202,10 +129153,11 @@ is_a: GO:0018293 ! protein-FAD linkage
[Term]
id: GO:0018298
-name: protein-chromophore linkage
+name: obsolete protein-chromophore linkage
namespace: biological_process
-def: "The covalent or noncovalent attachment of a chromophore to a protein." [GOC:ma]
-is_a: GO:0006464 ! cellular protein modification process
+def: "OBSOLETE. The covalent or noncovalent attachment of a chromophore to a protein." [GOC:ma]
+comment: Term describes modified products or self-catalyzed processes.
+is_obsolete: true
[Term]
id: GO:0018299
@@ -129317,39 +129269,41 @@ is_obsolete: true
[Term]
id: GO:0018309
-name: protein-FMN linkage
+name: obsolete protein-FMN linkage
namespace: biological_process
-def: "The formation of a linkage between a protein amino acid and flavin mononucleotide (FMN)." [GOC:mah]
-is_a: GO:0006464 ! cellular protein modification process
+def: "OBSOLETE. The formation of a linkage between a protein amino acid and flavin mononucleotide (FMN)." [GOC:mah]
+comment: This is a molecular function.
+is_obsolete: true
[Term]
id: GO:0018310
-name: protein-FMN linkage via S-(6-FMN)-L-cysteine
+name: obsolete protein-FMN linkage via S-(6-FMN)-L-cysteine
namespace: biological_process
-def: "The formation of a protein-FMN linkage via S-(6-FMN)-L-cysteine." [RESID:AA0220]
+def: "OBSOLETE. The formation of a protein-FMN linkage via S-(6-FMN)-L-cysteine." [RESID:AA0220]
+comment: This is a molecular function.
xref: RESID:AA0220
-is_a: GO:0018198 ! peptidyl-cysteine modification
-is_a: GO:0018309 ! protein-FMN linkage
+is_obsolete: true
[Term]
id: GO:0018311
-name: peptidyl-N4-hydroxymethyl-L-asparagine biosynthetic process from peptidyl-asparagine
+name: obsolete peptidyl-N4-hydroxymethyl-L-asparagine biosynthetic process from peptidyl-asparagine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of N4-hydroxymethyl-L-asparagine from other compounds, including peptidyl-asparagine." [RESID:AA0236]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of N4-hydroxymethyl-L-asparagine from other compounds, including peptidyl-asparagine." [RESID:AA0236]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-N4-hydroxymethyl-L-asparagine anabolism from peptidyl-asparagine" EXACT []
synonym: "peptidyl-N4-hydroxymethyl-L-asparagine formation from peptidyl-asparagine" EXACT []
synonym: "peptidyl-N4-hydroxymethyl-L-asparagine synthesis from peptidyl-asparagine" EXACT []
-xref: RESID:AA0236
-is_a: GO:0018196 ! peptidyl-asparagine modification
+is_obsolete: true
[Term]
id: GO:0018312
-name: peptidyl-serine ADP-ribosylation
+name: obsolete peptidyl-serine ADP-ribosylation
namespace: biological_process
-def: "The transfer, from NAD, of ADP-ribose to peptidyl-serine to form peptidyl-O-(ADP-ribosyl)-L-serine." [RESID:AA0237]
+def: "OBSOLETE. The transfer, from NAD, of ADP-ribose to peptidyl-serine to form peptidyl-O-(ADP-ribosyl)-L-serine." [RESID:AA0237]
+comment: This term was obsoleted because it represents a molecular function.
xref: RESID:AA0237
-is_a: GO:0006471 ! protein ADP-ribosylation
-is_a: GO:0018209 ! peptidyl-serine modification
+is_obsolete: true
+consider: GO:0018127
[Term]
id: GO:0018313
@@ -129367,7 +129321,6 @@ namespace: biological_process
def: "OBSOLETE. The covalent cross-linking of pyrroloquinoline-quinone to peptidyl-glutamic acid and peptidyl-tyrosine." [PMID:7665488, RESID:AA0283]
synonym: "protein-pyrroloquinoline-quinone linkage" EXACT []
is_obsolete: true
-replaced_by: GO:0006464
[Term]
id: GO:0018315
@@ -129413,15 +129366,15 @@ namespace: biological_process
def: "The modification of a protein by amino acid glucuronylation, the addition of a glucuronate group, the uronic acid derived from glucose." [GOC:ai, GOC:pr]
synonym: "protein amino acid glucuronylation" EXACT [GOC:bf]
is_a: GO:0006486 ! protein glycosylation
-is_a: GO:1901135 ! carbohydrate derivative metabolic process
[Term]
id: GO:0018322
-name: protein tyrosinylation
+name: obsolete protein tyrosinylation
namespace: biological_process
-def: "The addition of a tyrosine molecule to a protein amino acid." [GOC:ai]
+def: "OBSOLETE. The addition of a tyrosine molecule to a protein amino acid." [GOC:ai]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
synonym: "protein amino acid tyrosinylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_obsolete: true
[Term]
id: GO:0018323
@@ -129567,10 +129520,9 @@ id: GO:0018338
name: obsolete protein amino acid cinnamylation
namespace: biological_process
def: "OBSOLETE. The modification of a protein amino acid by cinnamylation." [GOC:ai]
-comment: This term was made obsolete because it was an unnecessary grouping term.
+comment: This term was made obsolete because it was an unnecessary grouping term. Consider GO:0018097 has been obsoleted.
synonym: "protein amino acid cinnamylation" EXACT []
is_obsolete: true
-consider: GO:0018097
[Term]
id: GO:0018339
@@ -129616,7 +129568,7 @@ alt_id: GO:0018346
def: "The covalent attachment of a prenyl group to a protein; geranyl, farnesyl, or geranylgeranyl groups may be added." [GOC:di, ISBN:0198506732]
synonym: "C-terminal protein prenylation" NARROW []
synonym: "protein amino acid prenylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
is_a: GO:0097354 ! prenylation
[Term]
@@ -129652,26 +129604,27 @@ is_a: GO:0043543 ! protein acylation
[Term]
id: GO:0018350
-name: protein esterification
+name: obsolete protein esterification
namespace: biological_process
-def: "The addition of an ester group to a protein amino acid." [GOC:ai]
+def: "OBSOLETE. The addition of an ester group to a protein amino acid." [GOC:ai]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "protein amino acid esterification" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_obsolete: true
[Term]
id: GO:0018351
-name: peptidyl-cysteine esterification
+name: obsolete peptidyl-cysteine esterification
namespace: biological_process
-def: "The addition of an ester group to a cysteine residue in a protein." [GOC:mah]
-is_a: GO:0018198 ! peptidyl-cysteine modification
-is_a: GO:0018350 ! protein esterification
+def: "OBSOLETE. The addition of an ester group to a cysteine residue in a protein." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0018352
name: protein-pyridoxal-5-phosphate linkage
namespace: biological_process
def: "The formation of a linkage between a protein amino acid and pyridoxal-5-phosphate." [GOC:mah]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018353
@@ -129687,7 +129640,7 @@ is_a: GO:0018198 ! peptidyl-cysteine modification
id: GO:0018355
name: protein-phosphoribosyl dephospho-coenzyme A linkage via O-(phosphoribosyl dephospho-coenzyme A)-L-serine
namespace: biological_process
-def: "The formation of a protein-phosphoribosyl dephospho-coenzyme A linkage via O-(phosphoribosyl dephospho-coenzyme A)-L-serine." [RESID:AA00167]
+def: "The formation of a protein-phosphoribosyl dephospho-coenzyme A linkage via O-(phosphoribosyl dephospho-coenzyme A)-L-serine." [RESID:AA0167]
is_a: GO:0018247 ! protein-phosphoribosyl dephospho-coenzyme A linkage
[Term]
@@ -129798,7 +129751,7 @@ id: GO:0018366
name: chiral amino acid racemization
namespace: biological_process
def: "The formation of a mixture of the two possible enantiomers from the D- or L-enantiomer of a chiral amino acid." [GOC:jsg, ISBN:0198506732]
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
[Term]
id: GO:0018367
@@ -129812,12 +129765,12 @@ consider: GO:0006520
[Term]
id: GO:0018376
-name: peptidyl-asparagine hydroxylation to form L-erythro-beta-hydroxyasparagine
+name: obsolete peptidyl-asparagine hydroxylation to form L-erythro-beta-hydroxyasparagine
namespace: biological_process
-def: "The hydroxylation of peptidyl-asparagine to form peptidyl-L-erythro-beta-hydroxyasparagine; catalyzed by peptide-aspartate beta-dioxygenase (EC:1.14.11.16)." [RESID:AA0026]
-comment: See also the molecular function term 'peptide-aspartate beta-dioxygenase activity ; GO:0004597'.
-xref: RESID:AA0026
-is_a: GO:0042265 ! peptidyl-asparagine hydroxylation
+def: "OBSOLETE. The hydroxylation of peptidyl-asparagine to form peptidyl-L-erythro-beta-hydroxyasparagine; catalyzed by peptide-aspartate beta-dioxygenase (EC:1.14.11.16)." [RESID:AA0026]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+replaced_by: GO:0062101
[Term]
id: GO:0018377
@@ -129883,29 +129836,28 @@ is_a: GO:0018058 ! N-terminal protein amino acid deamination, from amino carbon
[Term]
id: GO:0018390
-name: peptidyl-L-glutamic acid 5-methyl ester biosynthetic process from peptidyl-glutamic acid or peptidyl-glutamine
+name: obsolete peptidyl-L-glutamic acid 5-methyl ester biosynthetic process from peptidyl-glutamic acid or peptidyl-glutamine
namespace: biological_process
-def: "The methyl esterification of peptidyl-glutamic acid or peptidyl-glutamine to form the derivative glutamic acid 5-methyl ester." [RESID:AA0072]
+def: "OBSOLETE. The methyl esterification of peptidyl-glutamic acid or peptidyl-glutamine to form the derivative glutamic acid 5-methyl ester." [RESID:AA0072]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-L-glutamic acid 5-methyl ester anabolism from peptidyl-glutamic acid or peptidyl-glutamine" EXACT []
synonym: "peptidyl-L-glutamic acid 5-methyl ester formation from peptidyl-glutamic acid or peptidyl-glutamine" EXACT []
synonym: "peptidyl-L-glutamic acid 5-methyl ester synthesis from peptidyl-glutamic acid or peptidyl-glutamine" EXACT []
-xref: RESID:AA0072
-is_a: GO:0018199 ! peptidyl-glutamine modification
-is_a: GO:0018442 ! peptidyl-glutamic acid esterification
+is_obsolete: true
[Term]
id: GO:0018391
-name: C-terminal peptidyl-glutamic acid tyrosinylation
+name: obsolete C-terminal peptidyl-glutamic acid tyrosinylation
namespace: biological_process
-def: "The ATP-dependent addition of a tyrosine residue to a glutamic acid residue at the C-terminus of a protein." [GOC:mah]
-is_a: GO:0018166 ! C-terminal protein-tyrosinylation
-is_a: GO:0018200 ! peptidyl-glutamic acid modification
+def: "OBSOLETE. The ATP-dependent addition of a tyrosine residue to a glutamic acid residue at the C-terminus of a protein." [GOC:mah]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
+is_obsolete: true
[Term]
id: GO:0018392
name: glycoprotein 3-alpha-L-fucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl}-L-asparagine + GDP-L-fucose = N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosaminyl}-L-asparagine + GDP + H(+)." [EC:2.4.1.214, RHEA:24444]
+def: "Catalysis of the reaction: N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl}-L-asparagine + GDP-L-fucose = N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosaminyl}-L-asparagine + GDP + H+." [EC:2.4.1.214, RHEA:24444]
synonym: "GDP-fucose:beta-N-acetylglucosamine (Fuc to (Fuc-alpha-1->6-GlcNAc)-Asn-peptide) alpha-1->3-fucosyltransferase activity" RELATED [EC:2.4.1.214]
synonym: "GDP-fucose:beta-N-acetylglucosamine (Fuc to (Fucalpha1->6-GlcNAc)-Asn-peptide) alpha1->3-fucosyltransferase activity" RELATED [EC:2.4.1.214]
synonym: "GDP-fucose:beta-N-acetylglucosamine (Fuc to (Fucalpha1->6GlcNAc)-Asn-peptide) alpha1->3-fucosyltransferase activity" RELATED [EC:2.4.1.214]
@@ -129957,27 +129909,27 @@ is_a: GO:0017185 ! peptidyl-lysine hydroxylation
[Term]
id: GO:0018397
-name: peptidyl-phenylalanine bromination to L-2'-bromophenylalanine
+name: obsolete peptidyl-phenylalanine bromination to L-2'-bromophenylalanine
namespace: biological_process
-def: "The bromination of peptidyl-phenylalanine to form L-2'-bromophenylalanine." [RESID:AA0174]
+def: "OBSOLETE. The bromination of peptidyl-phenylalanine to form L-2'-bromophenylalanine." [RESID:AA0174]
xref: RESID:AA0174
-is_a: GO:0018075 ! peptidyl-phenylalanine bromination
+is_obsolete: true
[Term]
id: GO:0018398
-name: peptidyl-phenylalanine bromination to L-3'-bromophenylalanine
+name: obsolete peptidyl-phenylalanine bromination to L-3'-bromophenylalanine
namespace: biological_process
-def: "The bromination of peptidyl-phenylalanine to form L-3'-bromophenylalanine." [RESID:AA0175]
+def: "OBSOLETE. The bromination of peptidyl-phenylalanine to form L-3'-bromophenylalanine." [RESID:AA0175]
xref: RESID:AA0175
-is_a: GO:0018075 ! peptidyl-phenylalanine bromination
+is_obsolete: true
[Term]
id: GO:0018399
-name: peptidyl-phenylalanine bromination to L-4'-bromophenylalanine
+name: obsolete peptidyl-phenylalanine bromination to L-4'-bromophenylalanine
namespace: biological_process
-def: "The bromination of peptidyl-phenylalanine to form L-4'-bromophenylalanine." [RESID:AA0176]
+def: "OBSOLETE. The bromination of peptidyl-phenylalanine to form L-4'-bromophenylalanine." [RESID:AA0176]
xref: RESID:AA0176
-is_a: GO:0018075 ! peptidyl-phenylalanine bromination
+is_obsolete: true
[Term]
id: GO:0018400
@@ -130048,20 +130000,20 @@ is_a: GO:0035268 ! protein mannosylation
[Term]
id: GO:0018407
-name: peptidyl-thyronine iodination to form 3',3'',5'-triiodo-L-thyronine
+name: obsolete peptidyl-thyronine iodination to form 3',3'',5'-triiodo-L-thyronine
namespace: biological_process
-def: "The iodination of peptidyl-thyronine to form peptidyl-3',3'',5'-triiodo-L-thyronine (triiodothyronine)." [RESID:AA0177]
+def: "OBSOLETE. The iodination of peptidyl-thyronine to form peptidyl-3',3'',5'-triiodo-L-thyronine (triiodothyronine)." [RESID:AA0177]
synonym: "peptidyl-thyronine iodination to form triiodothyronine" BROAD []
xref: RESID:AA0177
-is_a: GO:0018078 ! peptidyl-thyronine iodination
+is_obsolete: true
[Term]
id: GO:0018408
-name: peptidyl-thyronine iodination to form 3',3'',5',5''-tetraiodo-L-thyronine
+name: obsolete peptidyl-thyronine iodination to form 3',3'',5',5''-tetraiodo-L-thyronine
namespace: biological_process
-def: "The iodination of peptidyl-thyronine to form peptidyl-3',3'',5',5''-tetraiodo-L-thyronine (L-thyroxine)." [RESID:AA0178]
+def: "OBSOLETE. The iodination of peptidyl-thyronine to form peptidyl-3',3'',5',5''-tetraiodo-L-thyronine (L-thyroxine)." [RESID:AA0178]
xref: RESID:AA0178
-is_a: GO:0018078 ! peptidyl-thyronine iodination
+is_obsolete: true
[Term]
id: GO:0018410
@@ -130078,7 +130030,7 @@ name: protein glucuronidation
namespace: biological_process
def: "The modification of a protein by amino acid glucuronidation." [GOC:ai]
synonym: "protein amino acid glucuronidation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018412
@@ -130149,7 +130101,7 @@ name: nickel incorporation into iron-sulfur cluster via tris-L-cysteinyl L-cyste
namespace: biological_process
def: "The incorporation of nickel into a 3Fe-2S complex by tris-L-cysteinyl L-cysteine persulfido L-glutamato L-histidino L-serinyl nickel triiron disulfide trioxide." [RESID:AA0293]
synonym: "nickel incorporation into iron-sulphur cluster via tris-L-cysteinyl L-cysteine persulphido L-glutamato L-histidino L-serinyl nickel triiron disulphide trioxide" EXACT []
-xref: RESID:AA0
+xref: RESID:AA0293
is_a: GO:0016226 ! iron-sulfur cluster assembly
is_a: GO:0018198 ! peptidyl-cysteine modification
is_a: GO:0018200 ! peptidyl-glutamic acid modification
@@ -130165,13 +130117,11 @@ is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0018420
-name: peptide cross-linking via N6-(L-isoaspartyl)-L-lysine
+name: obsolete peptide cross-linking via N6-(L-isoaspartyl)-L-lysine
namespace: biological_process
-def: "The formation of isopeptide bonds by ligation of peptidyl-lysine and peptidyl-asparagine residues." [RESID:AA0294]
-xref: RESID:AA0294
-is_a: GO:0018149 ! peptide cross-linking
-is_a: GO:0018196 ! peptidyl-asparagine modification
-is_a: GO:0018205 ! peptidyl-lysine modification
+def: "OBSOLETE. The formation of isopeptide bonds by ligation of peptidyl-lysine and peptidyl-asparagine residues." [RESID:AA0294]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0018421
@@ -130200,12 +130150,13 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
[Term]
id: GO:0018424
-name: peptidyl-glutamic acid poly-ADP-ribosylation
+name: obsolete peptidyl-glutamic acid poly-ADP-ribosylation
namespace: biological_process
-def: "This modification produces peptidyl-glutamic acid poly-ADP-ribose found in a number of nuclear proteins under certain conditions including the repair of single strand DNA breaks. The activated form of the generating enzyme poly(ADP-ribose) polymerase is itself modified in this way." [RESID:AA0295]
+def: "OBSOLETE. This modification produces peptidyl-glutamic acid poly-ADP-ribose found in a number of nuclear proteins under certain conditions including the repair of single strand DNA breaks. The activated form of the generating enzyme poly(ADP-ribose) polymerase is itself modified in this way." [RESID:AA0295]
+comment: This term was obsoleted because it represents a molecular function.
xref: RESID:AA0295
-is_a: GO:0006471 ! protein ADP-ribosylation
-is_a: GO:0018200 ! peptidyl-glutamic acid modification
+is_obsolete: true
+consider: GO:0140807
[Term]
id: GO:0018425
@@ -130263,15 +130214,13 @@ is_a: GO:0018428 ! copper incorporation into copper-sulfur cluster
[Term]
id: GO:0018439
-name: peptidyl-L-leucine methyl ester biosynthetic process from peptidyl-leucine
+name: obsolete peptidyl-L-leucine methyl ester biosynthetic process from peptidyl-leucine
namespace: biological_process
alt_id: GO:0018440
-def: "The modification of a C-terminal peptidyl-leucine to form peptidyl-L-leucine methyl ester." [RESID:AA0299]
+def: "OBSOLETE. The modification of a C-terminal peptidyl-leucine to form peptidyl-L-leucine methyl ester." [RESID:AA0299]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-leucine esterification" EXACT []
-xref: RESID:AA0299
-is_a: GO:0006481 ! C-terminal protein methylation
-is_a: GO:0018203 ! peptidyl-isoleucine modification
-is_a: GO:0018350 ! protein esterification
+is_obsolete: true
[Term]
id: GO:0018441
@@ -130286,11 +130235,11 @@ is_a: GO:0018418 ! nickel incorporation into iron-sulfur cluster via tris-L-cyst
[Term]
id: GO:0018442
-name: peptidyl-glutamic acid esterification
+name: obsolete peptidyl-glutamic acid esterification
namespace: biological_process
-def: "The addition of an ester group to a glutamic acid residue in a protein." [GOC:mah]
-is_a: GO:0018200 ! peptidyl-glutamic acid modification
-is_a: GO:0018350 ! protein esterification
+def: "OBSOLETE. The addition of an ester group to a glutamic acid residue in a protein." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0018443
@@ -130437,7 +130386,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0018457
name: perillyl-alcohol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD(+) + perillyl alcohol = H(+) + NADH + perillyl aldehyde." [EC:1.1.1.144, RHEA:10664]
+def: "Catalysis of the reaction: NAD+ + perillyl alcohol = H+ + NADH + perillyl aldehyde." [EC:1.1.1.144, RHEA:10664]
synonym: "perillyl alcohol dehydrogenase activity" RELATED [EC:1.1.1.144]
synonym: "perillyl-alcohol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.144]
xref: EC:1.1.1.144
@@ -130451,7 +130400,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0018458
name: isopiperitenol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (1S,6R)-isopiperitenol + NAD(+) = (6R)-isoperitenone + H(+) + NADH." [EC:1.1.1.223, RHEA:20860]
+def: "Catalysis of the reaction: (1S,6R)-isopiperitenol + NAD+ = (6R)-isoperitenone + H+ + NADH." [EC:1.1.1.223, RHEA:20860]
synonym: "(-)-trans-isopiperitenol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.223]
xref: EC:1.1.1.223
xref: KEGG_REACTION:R03261
@@ -130464,7 +130413,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0018459
name: carveol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (1S,5R)-carveol + NADP(+) = (R)-carvone + H(+) + NADPH." [EC:1.1.1.243, RHEA:13629]
+def: "Catalysis of the reaction: (1S,5R)-carveol + NADP+ = (R)-carvone + H+ + NADPH." [EC:1.1.1.243, RHEA:13629]
synonym: "(-)-trans-carveol dehydrogenase activity" RELATED [EC:1.1.1.243]
synonym: "(-)-trans-carveol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.243]
xref: EC:1.1.1.243
@@ -130502,7 +130451,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0018462
name: 4-(hydroxymethyl)benzenesulfonate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-(hydroxymethyl)benzenesulfonate + NAD(+) = 4-formylbenzenesulfonate + H(+) + NADH." [EC:1.1.1.257, RHEA:24412]
+def: "Catalysis of the reaction: 4-(hydroxymethyl)benzenesulfonate + NAD+ = 4-formylbenzenesulfonate + H+ + NADH." [EC:1.1.1.257, RHEA:24412]
synonym: "4-(hydroxymethyl)benzenesulfonate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.257]
synonym: "4-(hydroxymethyl)benzenesulphonate dehydrogenase activity" EXACT []
synonym: "4-sulfobenzyl alcohol dehydrogenase activity" EXACT []
@@ -130517,7 +130466,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0018463
name: 6-hydroxyhexanoate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-hydroxyhexanoate + NAD(+) = 6-oxohexanoate + H(+) + NADH." [EC:1.1.1.258, RHEA:14225]
+def: "Catalysis of the reaction: 6-hydroxyhexanoate + NAD+ = 6-oxohexanoate + H+ + NADH." [EC:1.1.1.258, RHEA:14225]
synonym: "6-hydroxyhexanoate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.258]
xref: EC:1.1.1.258
xref: KEGG_REACTION:R05283
@@ -130530,7 +130479,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0018464
name: 3-hydroxypimeloyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxypimelyl-CoA + NAD(+) = 3-oxopimelyl-CoA + H(+) + NADH." [EC:1.1.1.259, RHEA:11168]
+def: "Catalysis of the reaction: 3-hydroxypimelyl-CoA + NAD+ = 3-oxopimelyl-CoA + H+ + NADH." [EC:1.1.1.259, RHEA:11168]
synonym: "3-hydroxypimeloyl-CoA:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.259]
xref: EC:1.1.1.259
xref: KEGG_REACTION:R05305
@@ -130543,7 +130492,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0018465
name: vanillyl-alcohol oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O(2) + vanillyl alcohol = H(2)O(2) + vanillin." [EC:1.1.3.38, RHEA:10036]
+def: "Catalysis of the reaction: O2 + vanillyl alcohol = H2O2 + vanillin." [EC:1.1.3.38, RHEA:10036]
synonym: "4-hydroxy-2-methoxybenzyl alcohol oxidase activity" RELATED [EC:1.1.3.38]
synonym: "vanillyl alcohol:oxygen oxidoreductase activity" RELATED [EC:1.1.3.38]
xref: EC:1.1.3.38
@@ -130566,7 +130515,7 @@ is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
id: GO:0018467
name: formaldehyde dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: formaldehyde + H(2)O + NAD(+) = formate + 2 H(+) + NADH." [EC:1.2.1.46, RHEA:16425]
+def: "Catalysis of the reaction: formaldehyde + H2O + NAD+ = formate + 2 H+ + NADH." [EC:1.2.1.46, RHEA:16425]
synonym: "formaldehyde:NAD+ oxidoreductase activity" RELATED [EC:1.2.1.46]
synonym: "glutathione-independent formaldehyde dehydrogenase activity" EXACT []
xref: EC:1.2.1.46
@@ -130691,7 +130640,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0018481
name: 4-hydroxymuconic-semialdehyde dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cis,trans-4-hydroxymuconate semialdehyde + H(2)O + NAD(+) = 2 H(+) + maleylacetate + NADH." [EC:1.2.1.61, RHEA:22420]
+def: "Catalysis of the reaction: cis,trans-4-hydroxymuconate semialdehyde + H2O + NAD+ = 2 H+ + maleylacetate + NADH." [EC:1.2.1.61, RHEA:22420]
synonym: "4-hydroxymuconic-semialdehyde:NAD+ oxidoreductase activity" RELATED [EC:1.2.1.61]
xref: EC:1.2.1.61
xref: KEGG_REACTION:R05236
@@ -130704,7 +130653,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0018482
name: 4-formylbenzenesulfonate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-formylbenzenesulfonate + H(2)O + NAD(+) = 4-sulfobenzoate + 2 H(+) + NADH." [EC:1.2.1.62, RHEA:18833]
+def: "Catalysis of the reaction: 4-formylbenzenesulfonate + H2O + NAD+ = 4-sulfobenzoate + 2 H+ + NADH." [EC:1.2.1.62, RHEA:18833]
synonym: "4-formylbenzenesulfonate:NAD+ oxidoreductase activity" RELATED [EC:1.2.1.62]
synonym: "4-formylbenzenesulphonate dehydrogenase activity" EXACT []
synonym: "toluene-sulfonate aldehyde dehydrogenase activity" EXACT []
@@ -130784,7 +130733,7 @@ is_a: GO:0004031 ! aldehyde oxidase activity
id: GO:0018489
name: vanillate monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADH + O(2) + vanillate = 3,4-dihydroxybenzoate + formaldehyde + H(2)O + NAD(+)." [EC:1.14.13.82, RHEA:13021]
+def: "Catalysis of the reaction: H+ + NADH + O2 + vanillate = 3,4-dihydroxybenzoate + formaldehyde + H2O + NAD+." [EC:1.14.13.82, RHEA:13021]
comment: Note that this was EC:1.2.3.12.
synonym: "4-hydroxy-3-methoxybenzoate demethylase activity" RELATED [EC:1.14.13.82]
synonym: "vanillate demethylase (aerobic) activity" EXACT []
@@ -130803,7 +130752,7 @@ is_a: GO:0032451 ! demethylase activity
id: GO:0018490
name: 4-hydroxyphenylpyruvate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 (4-hydroxyphenyl)pyruvate + O(2) = 2 (4-hydroxyphenyl)acetate + 2 CO(2)." [EC:1.2.3.13, RHEA:17197]
+def: "Catalysis of the reaction: 2 (4-hydroxyphenyl)pyruvate + O2 = 2 (4-hydroxyphenyl)acetate + 2 CO2." [EC:1.2.3.13, RHEA:17197]
synonym: "4-hydroxyphenylpyruvate:oxygen oxidoreductase (decarboxylating)" BROAD [EC:1.2.3.13]
xref: EC:1.2.3.13
xref: KEGG_REACTION:R00042
@@ -130845,7 +130794,7 @@ is_a: GO:0016903 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0018493
name: formylmethanofuran dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-formylmethanofuran + A + H(2)O + H(+) = AH(2) + CO(2) + methanofuran." [EC:1.2.7.12, RHEA:19841]
+def: "Catalysis of the reaction: N-formylmethanofuran + A + H2O + H+ = AH(2) + CO2 + methanofuran." [EC:1.2.7.12, RHEA:19841]
synonym: "formylmethanofuran:(acceptor) oxidoreductase activity" RELATED [EC:1.2.7.12]
synonym: "formylmethanofuran:acceptor oxidoreductase activity" RELATED [EC:1.2.7.12]
xref: EC:1.2.7.12
@@ -130990,7 +130939,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0018507
name: cis-3,4-dihydrophenanthrene-3,4-diol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (3S,4R)-3,4-dihydrophenanthrene-3,4-diol + NAD(+) = H(+) + NADH + phenanthrene-3,4-diol." [EC:1.3.1.49, RHEA:16253]
+def: "Catalysis of the reaction: (3S,4R)-3,4-dihydrophenanthrene-3,4-diol + NAD+ = H+ + NADH + phenanthrene-3,4-diol." [EC:1.3.1.49, RHEA:16253]
synonym: "(+)-cis-3,4-dihydrophenanthrene-3,4-diol:NAD+ 3,4-oxidoreductase activity" RELATED [EC:1.3.1.49]
synonym: "cis-3,4-dihydroxy-3,4-dihydrophenanthrene dehydrogenase activity" EXACT []
xref: EC:1.3.1.49
@@ -131027,7 +130976,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0018510
name: phloroglucinol reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dihydrophloroglucinol + NADP(+) = H(+) + NADPH + phloroglucinol." [EC:1.3.1.57, RHEA:10080]
+def: "Catalysis of the reaction: dihydrophloroglucinol + NADP+ = H+ + NADPH + phloroglucinol." [EC:1.3.1.57, RHEA:10080]
synonym: "dihydrophloroglucinol:NADP+ oxidoreductase activity" RELATED [EC:1.3.1.57]
xref: EC:1.3.1.57
xref: KEGG_REACTION:R05308
@@ -131040,7 +130989,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0018511
name: 2,3-dihydroxy-2,3-dihydro-p-cumate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cis-2,3-dihydroxy-2,3-dihydro-p-cumate + NAD(+) = 2,3-dihydroxy-p-cumate + H(+) + NADH." [EC:1.3.1.58, RHEA:23772]
+def: "Catalysis of the reaction: cis-2,3-dihydroxy-2,3-dihydro-p-cumate + NAD+ = 2,3-dihydroxy-p-cumate + H+ + NADH." [EC:1.3.1.58, RHEA:23772]
synonym: "cis-2,3-dihydroxy-2,3-dihydro-p-cumate:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.58]
xref: EC:1.3.1.58
xref: KEGG_REACTION:R05240
@@ -131064,7 +131013,7 @@ is_obsolete: true
id: GO:0018513
name: dibenzothiophene dihydrodiol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene + NAD(+) = 1,2-dihydroxydibenzothiophene + H(+) + NADH." [EC:1.3.1.60, RHEA:24188]
+def: "Catalysis of the reaction: cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene + NAD+ = 1,2-dihydroxydibenzothiophene + H+ + NADH." [EC:1.3.1.60, RHEA:24188]
synonym: "cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.60]
xref: EC:1.3.1.60
xref: KEGG_REACTION:R05310
@@ -131077,7 +131026,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0018515
name: pimeloyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD(+) + pimelyl-CoA = 2,3-didehydropimeloyl-CoA + H(+) + NADH." [EC:1.3.1.62, RHEA:19665]
+def: "Catalysis of the reaction: NAD+ + pimelyl-CoA = 2,3-didehydropimeloyl-CoA + H+ + NADH." [EC:1.3.1.62, RHEA:19665]
synonym: "pimeloyl-CoA:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.62]
xref: EC:1.3.1.62
xref: KEGG_REACTION:R05311
@@ -131090,7 +131039,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0018516
name: 2,4-dichlorobenzoyl-CoA reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-chlorobenzoyl-CoA + chloride + NADP(+) = 2,4-dichlorobenzoyl-CoA + NADPH." [EC:1.3.1.63, RHEA:23076]
+def: "Catalysis of the reaction: 4-chlorobenzoyl-CoA + chloride + NADP+ = 2,4-dichlorobenzoyl-CoA + NADPH." [EC:1.3.1.63, RHEA:23076]
synonym: "4-chlorobenzoyl-CoA:NADP+ oxidoreductase (halogenating)" RELATED [EC:1.21.1.2]
xref: EC:1.21.1.2
xref: KEGG_REACTION:R05276
@@ -131103,7 +131052,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0018517
name: phthalate 4,5-cis-dihydrodiol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cis-4,5-dihydroxycyclohexa-2,6-diene-1,2-dicarboxylate + NAD(+) = 4,5-dihydroxyphthalate + H(+) + NADH." [EC:1.3.1.64, RHEA:13837]
+def: "Catalysis of the reaction: cis-4,5-dihydroxycyclohexa-2,6-diene-1,2-dicarboxylate + NAD+ = 4,5-dihydroxyphthalate + H+ + NADH." [EC:1.3.1.64, RHEA:13837]
synonym: "cis-4,5-dihydroxycyclohexa-1(6),2-diene-1,2-dicarboxylate:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.64]
xref: EC:1.3.1.64
xref: KEGG_REACTION:R05275
@@ -131116,7 +131065,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0018518
name: 5,6-dihydroxy-3-methyl-2-oxo-1,2,5,6-tetrahydroquinoline dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5,6-dihydroxy-3-methyl-5,6-dihydroquinolin-2(1H)-one + NAD(+) = 5,6-dihydroxy-3-methyl-2-oxo-1,2-dihydroquinoline + H(+) + NADH." [EC:1.3.1.65, RHEA:24556]
+def: "Catalysis of the reaction: 5,6-dihydroxy-3-methyl-5,6-dihydroquinolin-2(1H)-one + NAD+ = 5,6-dihydroxy-3-methyl-2-oxo-1,2-dihydroquinoline + H+ + NADH." [EC:1.3.1.65, RHEA:24556]
synonym: "5,6-dihydrodiol-3-methyl-2-oxo-1,2-dihydroquinoline dehydrogenase" RELATED []
synonym: "5,6-dihydroxy-3-methyl-2-oxo-1,2,5,6-tetrahydroquinoline:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.65]
xref: EC:1.3.1.65
@@ -131130,7 +131079,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0018519
name: cis-dihydroethylcatechol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cis-1,2-dihydro-3-ethylcatechol + NAD(+) = 3-ethylcatechol + H(+) + NADH." [EC:1.3.1.66, RHEA:18101]
+def: "Catalysis of the reaction: cis-1,2-dihydro-3-ethylcatechol + NAD+ = 3-ethylcatechol + H+ + NADH." [EC:1.3.1.66, RHEA:18101]
synonym: "cis-1,2-dihydro-3-ethylcatechol:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.66]
synonym: "cis-ethylbenzene glycol dehydrogenase activity" EXACT []
xref: EC:1.3.1.66
@@ -131156,7 +131105,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0018521
name: 1,2-dihydroxy-6-methylcyclohexa-3,5-dienecarboxylate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,6-dihydroxy-2-methylcyclohexa-2,4-dienecarboxylate + NAD(+) = 3-methylcatechol + CO(2) + NADH." [EC:1.3.1.68, RHEA:15657]
+def: "Catalysis of the reaction: 1,6-dihydroxy-2-methylcyclohexa-2,4-dienecarboxylate + NAD+ = 3-methylcatechol + CO2 + NADH." [EC:1.3.1.68, RHEA:15657]
synonym: "1,2-dihydroxy-6-methylcyclohexa-3,5-dienecarboxylate:NAD+ oxidoreductase (decarboxylating)" RELATED [EC:1.3.1.68]
xref: EC:1.3.1.68
xref: KEGG_REACTION:R05314
@@ -131169,7 +131118,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0018522
name: benzoyl-CoA reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 ADP + cyclohexa-1,5-diene-1-carbonyl-CoA + oxidized ferredoxin + 2 phosphate = 2 ATP + 2 H(2)O + benzoyl-CoA + reduced ferredoxin." [EC:1.3.7.8]
+def: "Catalysis of the reaction: 2 ADP + cyclohexa-1,5-diene-1-carbonyl-CoA + oxidized ferredoxin + 2 phosphate = 2 ATP + 2 H2O + benzoyl-CoA + reduced ferredoxin." [EC:1.3.7.8]
synonym: "benzoyl-CoA reductase (dearomatizing) activity" RELATED [EC:1.3.7.8]
synonym: "cyclohexa-1,5-diene-1-carbonyl-CoA:ferredoxin oxidoreductase (aromatizing, ATP-forming) activity" EXACT [KEGG_REACTION:R02451]
xref: EC:1.3.7.8
@@ -131227,13 +131176,13 @@ is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0018527
name: cyclohexylamine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cyclohexylamine + O2 + H2O = cyclohexanone + NH3 + hydrogen peroxide." [EC:1.4.3.12]
+def: "Catalysis of the reaction: cyclohexylamine + O2 + H2O = cyclohexanone + NH3 + hydrogen peroxide." [PMID:18451, RHEA:18433]
synonym: "cyclohexylamine:oxygen oxidoreductase (deaminating)" RELATED [EC:1.4.3.12]
xref: EC:1.4.3.12
xref: MetaCyc:CYCLOHEXYLAMINE-OXIDASE-RXN
xref: RHEA:18433
xref: UM-BBD_reactionID:r0754
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+is_a: GO:0008131 ! primary amine oxidase activity
[Term]
id: GO:0018528
@@ -131257,7 +131206,7 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0018530
name: (R)-6-hydroxynicotine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-6-hydroxynicotine + H(2)O + O(2) = 6-hydroxypseudooxynicotine + H(2)O(2)." [EC:1.5.3.6, RHEA:10012]
+def: "Catalysis of the reaction: (R)-6-hydroxynicotine + H2O + O2 = 6-hydroxypseudooxynicotine + H2O2." [EC:1.5.3.6, RHEA:10012]
synonym: "(R)-6-hydroxynicotine:oxygen oxidoreductase activity" RELATED [EC:1.5.3.6]
synonym: "6-hydroxy-D-nicotine oxidase activity" EXACT []
synonym: "D-6-hydroxynicotine oxidase activity" RELATED [EC:1.5.3.6]
@@ -131272,7 +131221,7 @@ is_a: GO:0019116 ! hydroxy-nicotine oxidase activity
id: GO:0018531
name: (S)-6-hydroxynicotine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-6-hydroxynicotine + H(2)O + O(2) = 6-hydroxypseudooxynicotine + H(2)O(2)." [EC:1.5.3.5, RHEA:11880]
+def: "Catalysis of the reaction: (S)-6-hydroxynicotine + H2O + O2 = 6-hydroxypseudooxynicotine + H2O2." [EC:1.5.3.5, RHEA:11880]
synonym: "(S)-6-hydroxynicotine:oxygen oxidoreductase activity" RELATED [EC:1.5.3.5]
synonym: "6-hydroxy-L-nicotine oxidase activity" EXACT []
synonym: "6-hydroxy-L-nicotine:oxygen oxidoreductase activity" RELATED [EC:1.5.3.5]
@@ -131333,7 +131282,7 @@ is_a: GO:0016645 ! oxidoreductase activity, acting on the CH-NH group of donors
id: GO:0018537
name: coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-methyltetrahydromethanopterin + coenzyme F420 + H(+) = 5,10-methylenetetrahydromethanopterin + reduced coenzyme F420." [EC:1.5.98.2, RHEA:21144]
+def: "Catalysis of the reaction: 5-methyltetrahydromethanopterin + coenzyme F420 + H+ = 5,10-methylenetetrahydromethanopterin + reduced coenzyme F420." [EC:1.5.98.2, RHEA:21144]
synonym: "5,10-methylenetetrahydromethanopterin cyclohydrolase activity" RELATED [EC:1.5.98.2]
synonym: "5,10-methylenetetrahydromethanopterin reductase activity" RELATED [EC:1.5.98.2]
synonym: "5-methyltetrahydromethanopterin:coenzyme-F420 oxidoreductase activity" RELATED [EC:1.5.98.2]
@@ -131363,7 +131312,7 @@ is_a: GO:0016651 ! oxidoreductase activity, acting on NAD(P)H
id: GO:0018541
name: p-benzoquinone reductase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,4-benzoquinone + H(+) + NADPH = hydroquinone + NADP(+)." [EC:1.6.5.6, RHEA:23488]
+def: "Catalysis of the reaction: 1,4-benzoquinone + H+ + NADPH = hydroquinone + NADP+." [EC:1.6.5.6, RHEA:23488]
synonym: "NADPH:p-benzoquinone oxidoreductase activity" RELATED [EC:1.6.5.6]
xref: EC:1.6.5.6
xref: KEGG_REACTION:R05244
@@ -131411,10 +131360,11 @@ id: GO:0018546
name: nitrobenzene nitroreductase activity
namespace: molecular_function
def: "Catalysis of the reaction: nitrobenzene + 2 NADPH + 2 H+ = hydroxyaminobenzene + 2 NADP+ + H2O." [MetaCyc:RXN-8815]
+xref: EC:1.7.1.16
xref: MetaCyc:RXN-8815
xref: RHEA:52884
xref: UM-BBD_enzymeID:e0245
-is_a: GO:0016657 ! oxidoreductase activity, acting on NAD(P)H, nitrogenous group as acceptor
+is_a: GO:0046857 ! oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor
[Term]
id: GO:0018547
@@ -131422,6 +131372,7 @@ name: nitroglycerin reductase activity
namespace: molecular_function
def: "Catalysis of the removal of one or more nitrite (NO2-) groups from nitroglycerin or a derivative." [UM-BBD_enzymeID:e0038]
synonym: "NG reductase activity" EXACT []
+xref: Reactome:R-HSA-9620103 "ALDH2 transforms GTN to NO"
xref: UM-BBD_enzymeID:e0038
is_a: GO:0016663 ! oxidoreductase activity, acting on other nitrogenous compounds as donors, oxygen as acceptor
@@ -131771,7 +131722,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0018580
name: nitronate monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ethylnitronate + O(2) = acetaldehyde + nitrite." [EC:1.13.12.16, RHEA:28767]
+def: "Catalysis of the reaction: ethylnitronate + O2 = acetaldehyde + nitrite." [EC:1.13.12.16, RHEA:28767]
comment: Where non-covalently bound FMN is used as the cofactor, see instead 'nitronate monooxygenase (FMN-linked) activity ; GO:0036434'.
synonym: "2-nitropropane dioxygenase activity" RELATED [EC:1.13.11.32]
synonym: "nitronate:oxygen 2-oxidoreductase (nitrite-forming) activity" EXACT systematic_synonym [EC:1.13.12.16]
@@ -131983,7 +131934,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018601
name: 4-nitrophenol 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-nitrophenol + H(+) + NADH + O(2) = 4-nitrocatechol + H(2)O + NAD(+)." [EC:1.14.13.29, RHEA:12568]
+def: "Catalysis of the reaction: 4-nitrophenol + H+ + NADH + O2 = 4-nitrocatechol + H2O + NAD+." [EC:1.14.13.29, RHEA:12568]
synonym: "4-nitrophenol hydroxylase activity" RELATED [EC:1.14.13.29]
synonym: "4-nitrophenol,NADH:oxygen oxidoreductase (2-hydroxylating)" RELATED [EC:1.14.13.29]
synonym: "4-nitrophenol-2-hydroxylase activity" RELATED [EC:1.14.13.29]
@@ -132157,7 +132108,7 @@ is_a: GO:0016708 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018619
name: benzene 1,2-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: benzene + H(+) + NADH + O(2) = cis-cyclohexa-3,5-diene-1,2-diol + NAD(+)." [EC:1.14.12.3, RHEA:13813]
+def: "Catalysis of the reaction: benzene + H+ + NADH + O2 = cis-cyclohexa-3,5-diene-1,2-diol + NAD+." [EC:1.14.12.3, RHEA:13813]
synonym: "benzene dioxygenase activity" RELATED [EC:1.14.12.3]
synonym: "benzene hydroxylase activity" RELATED [EC:1.14.12.3]
synonym: "benzene,NADH:oxygen oxidoreductase (1,2-hydroxylating)" RELATED [EC:1.14.12.3]
@@ -132172,7 +132123,7 @@ is_a: GO:0016708 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018620
name: phthalate 4,5-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADH + O(2) + phthalate = cis-4,5-dihydroxycyclohexa-2,6-diene-1,2-dicarboxylate + NAD(+)." [EC:1.14.12.7, RHEA:17489]
+def: "Catalysis of the reaction: H+ + NADH + O2 + phthalate = cis-4,5-dihydroxycyclohexa-2,6-diene-1,2-dicarboxylate + NAD+." [EC:1.14.12.7, RHEA:17489]
synonym: "PDO activity" RELATED [EC:1.14.12.7]
synonym: "phthalate dioxygenase activity" BROAD [EC:1.14.12.7]
synonym: "phthalate,NADH:oxygen oxidoreductase (4,5-hydroxylating)" RELATED [EC:1.14.12.7]
@@ -132187,7 +132138,7 @@ is_a: GO:0016708 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018621
name: 4-sulfobenzoate 3,4-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-sulfobenzoate + H(+) + NADH + O(2) = 3,4-dihydroxybenzoate + NAD(+) + sulfite." [EC:1.14.12.8, RHEA:13937]
+def: "Catalysis of the reaction: 4-sulfobenzoate + H+ + NADH + O2 = 3,4-dihydroxybenzoate + NAD+ + sulfite." [EC:1.14.12.8, RHEA:13937]
synonym: "4-sulfobenzoate 3,4-dioxygenase system" RELATED [EC:1.14.12.8]
synonym: "4-sulfobenzoate dioxygenase activity" RELATED [EC:1.14.12.8]
synonym: "4-sulfobenzoate,NADH:oxygen oxidoreductase (3,4-hydroxylating, sulfite-forming)" RELATED [EC:1.14.12.8]
@@ -132203,7 +132154,7 @@ is_a: GO:0016708 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018622
name: 4-chlorophenylacetate 3,4-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-chlorophenylacetate + NADH + O(2) = 3,4-dihydroxyphenylacetate + chloride + NAD(+)." [EC:1.14.12.9, RHEA:14689]
+def: "Catalysis of the reaction: 4-chlorophenylacetate + NADH + O2 = 3,4-dihydroxyphenylacetate + chloride + NAD+." [EC:1.14.12.9, RHEA:14689]
synonym: "4-chlorophenylacetate,NADH:oxygen oxidoreductase (3,4-hydroxylating, dechlorinating)" RELATED [EC:1.14.12.9]
xref: EC:1.14.12.9
xref: KEGG_REACTION:R03306
@@ -132232,7 +132183,7 @@ is_a: GO:0016708 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018624
name: toluene dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADH + O(2) + toluene = (1S,2R)-3-methylcyclohexa-3,5-diene-1,2-diol + NAD(+)." [EC:1.14.12.11, RHEA:16737]
+def: "Catalysis of the reaction: H+ + NADH + O2 + toluene = (1S,2R)-3-methylcyclohexa-3,5-diene-1,2-diol + NAD+." [EC:1.14.12.11, RHEA:16737]
synonym: "toluene 1,2-dioxygenase activity" RELATED [EC:1.14.12.11]
synonym: "toluene 2,3-dioxygenase activity" RELATED [EC:1.14.12.11]
synonym: "toluene,NADH:oxygen oxidoreductase (1,2-hydroxylating)" RELATED [EC:1.14.12.11]
@@ -132275,7 +132226,7 @@ id: GO:0018627
name: 2-aminobenzenesulfonate 2,3-dioxygenase activity
namespace: molecular_function
alt_id: GO:0018605
-def: "Catalysis of the reaction: 2-aminobenzenesulfonate + 2 H(+) + NADH + O(2) = 2,3-dihydroxybenzenesulfonate + NAD(+) + NH(4)(+). 2,3-dihydroxybenzenesulfonate is also known as 3-sulfocatechol." [EC:1.14.12.14, RHEA:23468]
+def: "Catalysis of the reaction: 2-aminobenzenesulfonate + 2 H+ + NADH + O2 = 2,3-dihydroxybenzenesulfonate + NAD+ + NH4. 2,3-dihydroxybenzenesulfonate is also known as 3-sulfocatechol." [EC:1.14.12.14, RHEA:23468]
synonym: "2-aminobenzenesulfonate dioxygenase activity" EXACT []
synonym: "2-aminobenzenesulfonate,NADH:oxygen oxidoreductase (2,3-hydroxylating, ammonia-forming)" RELATED [EC:1.14.12.14]
synonym: "2-aminobenzenesulphonate 2,3-dioxygenase activity" EXACT []
@@ -132292,7 +132243,7 @@ is_a: GO:0016708 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018628
name: terephthalate 1,2-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADH + O(2) + terephthalate = (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate + NAD(+)." [EC:1.14.12.15, RHEA:10312]
+def: "Catalysis of the reaction: H+ + NADH + O2 + terephthalate = (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate + NAD+." [EC:1.14.12.15, RHEA:10312]
synonym: "1,4-dicarboxybenzoate 1,2-dioxygenase activity" RELATED [EC:1.14.12.15]
synonym: "benzene-1,4-dicarboxylate 1,2-dioxygenase activity" RELATED [EC:1.14.12.15]
synonym: "benzene-1,4-dicarboxylate,NADH:oxygen oxidoreductase (1,2-hydroxylating)" RELATED [EC:1.14.12.15]
@@ -132639,24 +132590,23 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
[Term]
id: GO:0018660
-name: 4-hydroxyphenylacetate,NADH:oxygen oxidoreductase (3-hydroxylating) activity
+name: obsolete 4-hydroxyphenylacetate,NADH:oxygen oxidoreductase (3-hydroxylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-hydroxyphenylacetate + NADH + H+ + O2 = 3,4-dihydroxyphenylacetate + NAD+ + H2O." [RHEA:16681]
-synonym: "4 HPA 3-hydroxylase activity" BROAD [EC:1.14.14.9]
+def: "OBSOLETE. Catalysis of the reaction: 4-hydroxyphenylacetate + NADH + H+ + O2 = 3,4-dihydroxyphenylacetate + NAD+ + H2O." [GOC:curators]
+comment: RHEA:16681 (RHEA:16681 has been replaced by RHEA:30595); The EC assigned this term does not use NAD but FAD\nGO:0052881 already assigned RHEA:30595 using FADH; \nSince GO:0018660 was assigned to RHEA 16681 with NAD vs FAD; 3 IEA; suggest obsoletion of GO:0018660
+synonym: "4 HPA 3-hydroxylase activity" BROAD []
synonym: "4-hydroxyphenylacetate 3-hydroxylase activity" BROAD []
synonym: "4-hydroxyphenylacetate 3-monooxygenase activity" BROAD []
-synonym: "p-hydroxyphenylacetate 3-hydroxylase activity" BROAD [EC:1.14.14.9]
-synonym: "p-hydroxyphenylacetate hydroxylase activity" BROAD [EC:1.14.14.9]
-xref: EC:1.14.14.9
+synonym: "p-hydroxyphenylacetate 3-hydroxylase activity" BROAD []
+synonym: "p-hydroxyphenylacetate hydroxylase activity" BROAD []
xref: KEGG_REACTION:R02698
-xref: RHEA:16681
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+is_obsolete: true
[Term]
id: GO:0018661
name: orcinol 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADH + O(2) + orcinol = 2,3,5-trihydroxytoluene + H(2)O + NAD(+)." [EC:1.14.13.6, RHEA:19601]
+def: "Catalysis of the reaction: H+ + NADH + O2 + orcinol = 2,3,5-trihydroxytoluene + H2O + NAD+." [EC:1.14.13.6, RHEA:19601]
synonym: "orcinol hydroxylase activity" EXACT []
synonym: "orcinol,NADH:oxygen oxidoreductase (2-hydroxylating)" RELATED [EC:1.14.13.6]
xref: EC:1.14.13.6
@@ -132684,7 +132634,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018663
name: 2,6-dihydroxypyridine 3-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,6-dihydroxypyridine + H(+) + NADH + O(2) = 2,3,6-trihydroxypyridine + H(2)O + NAD(+)." [EC:1.14.13.10, RHEA:16917]
+def: "Catalysis of the reaction: 2,6-dihydroxypyridine + H+ + NADH + O2 = 2,3,6-trihydroxypyridine + H2O + NAD+." [EC:1.14.13.10, RHEA:16917]
synonym: "2,6-dihydroxypyridine oxidase activity" EXACT []
synonym: "2,6-dihydroxypyridine,NADH:oxygen oxidoreductase (3-hydroxylating)" RELATED [EC:1.14.13.10]
xref: EC:1.14.13.10
@@ -132698,7 +132648,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018664
name: benzoate 4-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: benzoate + H(+) + NADPH + O(2) = 4-hydroxybenzoate + H(2)O + NADP(+)." [EC:1.14.14.92, RHEA:18033]
+def: "Catalysis of the reaction: benzoate + H+ + NADPH + O2 = 4-hydroxybenzoate + H2O + NADP+." [EC:1.14.14.92, RHEA:18033]
synonym: "4-hydroxybenzoic hydroxylase activity" EXACT []
synonym: "benzoate 4-hydroxylase activity" RELATED [EC:1.14.14.92]
synonym: "benzoate,NADPH:oxygen oxidoreductase (4-hydroxylating)" RELATED [EC:1.14.14.92]
@@ -132762,7 +132712,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018668
name: 3-hydroxybenzoate 4-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxybenzoate + H(+) + NADPH + O(2) = 3,4-dihydroxybenzoate + H(2)O + NADP(+)." [EC:1.14.13.23, RHEA:11480]
+def: "Catalysis of the reaction: 3-hydroxybenzoate + H+ + NADPH + O2 = 3,4-dihydroxybenzoate + H2O + NADP+." [EC:1.14.13.23, RHEA:11480]
synonym: "3-hydroxybenzoate 4-hydroxylase activity" EXACT []
synonym: "3-hydroxybenzoate,NADPH:oxygen oxidoreductase (4-hydroxylating)" RELATED [EC:1.14.13.23]
xref: EC:1.14.13.23
@@ -132776,7 +132726,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018669
name: 3-hydroxybenzoate 6-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxybenzoate + H(+) + NADH + O(2) = 2,5-dihydroxybenzoate + H(2)O + NAD(+)." [EC:1.14.13.24, RHEA:22692]
+def: "Catalysis of the reaction: 3-hydroxybenzoate + H+ + NADH + O2 = 2,5-dihydroxybenzoate + H2O + NAD+." [EC:1.14.13.24, RHEA:22692]
synonym: "3-hydroxybenzoate 6-hydroxylase activity" EXACT []
synonym: "3-hydroxybenzoate,NADH:oxygen oxidoreductase (6-hydroxylating)" RELATED [EC:1.14.13.24]
synonym: "3-hydroxybenzoic acid-6-hydroxylase activity" RELATED [EC:1.14.13.24]
@@ -132819,7 +132769,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018672
name: anthranilate 3-monooxygenase (deaminating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: anthranilate + 2 H(+) + NADPH + O(2) = 2,3-dihydroxybenzoate + NADP(+) + NH(4)(+)." [EC:1.14.13.35, RHEA:21236]
+def: "Catalysis of the reaction: anthranilate + 2 H+ + NADPH + O2 = 2,3-dihydroxybenzoate + NADP+ + NH4." [EC:1.14.13.35, RHEA:21236]
synonym: "anthranilate 2,3-dioxygenase (deaminating)" RELATED [EC:1.14.13.35]
synonym: "anthranilate 2,3-hydroxylase (deaminating) activity" RELATED [EC:1.14.13.35]
synonym: "anthranilate hydroxylase (deaminating) activity" EXACT []
@@ -132849,7 +132799,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018674
name: (S)-limonene 3-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (4S)-limonene + H(+) + NADPH + O(2) = (1S,6R)-isopiperitenol + H(2)O + NADP(+)." [EC:1.14.14.99, RHEA:15129]
+def: "Catalysis of the reaction: (4S)-limonene + H+ + NADPH + O2 = (1S,6R)-isopiperitenol + H2O + NADP+." [EC:1.14.14.99, RHEA:15129]
synonym: "(-)-limonene 3-hydroxylase activity" RELATED [EC:1.14.14.99]
synonym: "(-)-limonene 3-monooxygenase activity" EXACT []
synonym: "(-)-limonene,NADPH:oxygen oxidoreductase (3-hydroxylating) activity" RELATED [EC:1.14.14.99]
@@ -132882,7 +132832,7 @@ is_a: GO:0019113 ! limonene monooxygenase activity
id: GO:0018676
name: (S)-limonene 7-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (4S)-limonene + H(+) + NADPH + O(2) = (4S)-perillyl alcohol + H(2)O + NADP(+)." [EC:1.14.14.52, RHEA:23432]
+def: "Catalysis of the reaction: (4S)-limonene + H+ + NADPH + O2 = (4S)-perillyl alcohol + H2O + NADP+." [EC:1.14.14.52, RHEA:23432]
synonym: "(-)-limonene 7-monooxygenase activity" EXACT []
xref: EC:1.14.14.52
xref: KEGG_REACTION:R02470
@@ -133068,7 +133018,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018690
name: 4-methoxybenzoate monooxygenase (O-demethylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-methoxybenzoate + AH(2) + O(2) = 4-hydroxybenzoate + A + formaldehyde + H(2)O." [EC:1.14.99.15, RHEA:18613]
+def: "Catalysis of the reaction: 4-methoxybenzoate + AH(2) + O2 = 4-hydroxybenzoate + A + formaldehyde + H2O." [EC:1.14.99.15, RHEA:18613]
synonym: "4-methoxybenzoate 4-monooxygenase (O-demethylating)" RELATED [EC:1.14.99.15]
synonym: "4-methoxybenzoate monooxygenase activity" EXACT []
synonym: "4-methoxybenzoate O-demethylase activity" RELATED [EC:1.14.99.15]
@@ -133087,7 +133037,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018693
name: ethylbenzene hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: A + ethylbenzene + H(2)O = (S)-1-phenylethanol + AH(2)." [EC:1.17.99.2, RHEA:17897]
+def: "Catalysis of the reaction: A + ethylbenzene + H2O = (S)-1-phenylethanol + AH(2)." [EC:1.17.99.2, RHEA:17897]
synonym: "ethylbenzene dehydrogenase activity" RELATED [EC:1.17.99.2]
synonym: "ethylbenzene:(acceptor) oxidoreductase activity" RELATED [EC:1.17.99.2]
xref: EC:1.17.99.2
@@ -133253,7 +133203,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0018710
name: acetone carboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetone + ATP + CO(2) + 2 H(2)O = acetoacetate + AMP + 4 H(+) + 2 phosphate." [EC:6.4.1.6, RHEA:18385]
+def: "Catalysis of the reaction: acetone + ATP + CO2 + 2 H2O = acetoacetate + AMP + 4 H+ + 2 phosphate." [EC:6.4.1.6, RHEA:18385]
synonym: "acetone:carbon-dioxide ligase (AMP-forming)" RELATED [EC:6.4.1.6]
xref: EC:6.4.1.6
xref: KEGG_REACTION:R05735
@@ -133485,7 +133435,7 @@ is_a: GO:0016823 ! hydrolase activity, acting on acid carbon-carbon bonds, in ke
id: GO:0018738
name: S-formylglutathione hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-formylglutathione + H(2)O = formate + glutathione + H(+)." [EC:3.1.2.12, RHEA:14961]
+def: "Catalysis of the reaction: S-formylglutathione + H2O = formate + glutathione + H+." [EC:3.1.2.12, RHEA:14961]
subset: goslim_chembl
xref: EC:3.1.2.12
xref: KEGG_REACTION:R00527
@@ -133499,7 +133449,7 @@ is_a: GO:0016790 ! thiolester hydrolase activity
id: GO:0018739
name: 4-hydroxybenzoyl-CoA thioesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-hydroxybenzoyl-CoA + H(2)O = 4-hydroxybenzoate + CoA + H(+)." [EC:3.1.2.23, RHEA:11948]
+def: "Catalysis of the reaction: 4-hydroxybenzoyl-CoA + H2O = 4-hydroxybenzoate + CoA + H+." [EC:3.1.2.23, RHEA:11948]
synonym: "4-hydroxybenzoyl-CoA hydrolase activity" RELATED [EC:3.1.2.23]
synonym: "4-hydroxybenzoyl-CoA thiolesterase activity" EXACT []
xref: EC:3.1.2.23
@@ -133513,7 +133463,7 @@ is_a: GO:0016289 ! CoA hydrolase activity
id: GO:0018740
name: 2'-hydroxybiphenyl-2-sulfinate desulfinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2'-hydroxybiphenyl-2-sulfinate + H(2)O = biphenyl-2-ol + sulfite." [EC:3.13.1.3, RHEA:12945]
+def: "Catalysis of the reaction: 2'-hydroxybiphenyl-2-sulfinate + H2O = biphenyl-2-ol + sulfite." [EC:3.13.1.3, RHEA:12945]
synonym: "2'-hydroxybiphenyl-2-sulfinate sulfinolyase activity" EXACT []
synonym: "2'-hydroxybiphenyl-2-sulfinate sulfohydrolase activity" RELATED [EC:3.13.1.3]
synonym: "2-(2'-hydroxyphenyl)benzenesulfinate desulfinase activity" RELATED [EC:3.13.1.3]
@@ -133536,11 +133486,12 @@ is_a: GO:0046508 ! hydrolase activity, acting on carbon-sulfur bonds
[Term]
id: GO:0018741
-name: alkyl sulfatase activity
+name: linear primary-alkylsulfatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dodecyl sulfate + H2O = sulfate + H+ + 1-dodecanol." [UM-BBD_reactionID:r0602]
-synonym: "alkyl sulphatase activity" EXACT []
-xref: EC:3.1.6.-
+def: "Catalysis of the reaction: a primary linear alkyl sulfate ester + H2O =>a primary alcohol + H(+) + sulfate." [RHEA:67908, UM-BBD_reactionID:r0602]
+synonym: "alkyl sulfatase activity" BROAD []
+xref: EC:3.1.6.21
+xref: RHEA:67908
xref: UM-BBD_reactionID:r0602
is_a: GO:0008484 ! sulfuric ester hydrolase activity
@@ -133698,7 +133649,7 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0018759
name: methenyltetrahydromethanopterin cyclohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H(2)O = N(5)-formyl-5,6,7,8-tetrahydromethanopterin + H(+)." [EC:3.5.4.27, RHEA:19053]
+def: "Catalysis of the reaction: 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H2O = N(5)-formyl-5,6,7,8-tetrahydromethanopterin + H+." [EC:3.5.4.27, RHEA:19053]
synonym: "5,10-methenyltetrahydromethanopterin 10-hydrolase (decyclizing)" RELATED [EC:3.5.4.27]
synonym: "5,10-methenyltetrahydromethanopterin cyclohydrolase activity" RELATED [EC:3.5.4.27]
synonym: "methenyl-H(4)MPT cyclohydrolase activity" RELATED [EC:3.5.4.27]
@@ -133715,7 +133666,7 @@ is_a: GO:0019238 ! cyclohydrolase activity
id: GO:0018760
name: thiocyanate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + 2 H(+) + thiocyanate = carbonyl sulfide + NH(4)(+)." [EC:3.5.5.8, RHEA:21464]
+def: "Catalysis of the reaction: H2O + 2 H+ + thiocyanate = carbonyl sulfide + NH4." [EC:3.5.5.8, RHEA:21464]
synonym: "thiocyanate aminohydrolase activity" RELATED [EC:3.5.5.8]
xref: EC:3.5.5.8
xref: KEGG_REACTION:R05780
@@ -133728,7 +133679,7 @@ is_a: GO:0016815 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0018761
name: bromoxynil nitrilase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3,5-dibromo-4-hydroxybenzonitrile + 2 H(2)O = 3,5-dibromo-4-hydroxybenzoate + NH(4)(+). Involved in the bacterial degradation of the herbicide bromoxynil." [EC:3.5.5.6, RHEA:22100]
+def: "Catalysis of the reaction: 3,5-dibromo-4-hydroxybenzonitrile + 2 H2O = 3,5-dibromo-4-hydroxybenzoate + NH4. Involved in the bacterial degradation of the herbicide bromoxynil." [EC:3.5.5.6, RHEA:22100]
synonym: "3,5-dibromo-4-hydroxybenzonitrile aminohydrolase activity" EXACT []
synonym: "bromoxynil-specific nitrilase activity" EXACT []
xref: EC:3.5.5.6
@@ -133857,7 +133808,7 @@ is_a: GO:0016823 ! hydrolase activity, acting on acid carbon-carbon bonds, in ke
id: GO:0018773
name: acetylpyruvate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetylpyruvate + H(2)O = acetate + H(+) + pyruvate." [EC:3.7.1.6, RHEA:16097]
+def: "Catalysis of the reaction: acetylpyruvate + H2O = acetate + H+ + pyruvate." [EC:3.7.1.6, RHEA:16097]
synonym: "2,4-dioxopentanoate acetylhydrolase activity" RELATED [EC:3.7.1.6]
xref: EC:3.7.1.6
xref: KEGG_REACTION:R00324
@@ -133998,7 +133949,7 @@ is_a: GO:0019120 ! hydrolase activity, acting on acid halide bonds, in C-halide
id: GO:0018786
name: haloalkane dehalogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-haloalkane + H2O = a primary alcohol + halide." [RHEA:19081]
+def: "Catalysis of the reaction: 1-haloalkane + H2O = a primary alcohol + halide." [PMID:3624201, RHEA:19081]
synonym: "1-chlorohexane halidohydrolase activity" RELATED [EC:3.8.1.5]
synonym: "1-haloalkane dehalogenase activity" RELATED [EC:3.8.1.5]
synonym: "1-haloalkane halidohydrolase activity" RELATED [EC:3.8.1.5]
@@ -134024,7 +133975,7 @@ is_a: GO:0019120 ! hydrolase activity, acting on acid halide bonds, in C-halide
id: GO:0018788
name: atrazine chlorohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: atrazine + H(2)O = 4-(ethylamino)-2-hydroxy-6-(isopropylamino)-1,3,5-triazine + chloride + H(+)." [EC:3.8.1.8, RHEA:11312]
+def: "Catalysis of the reaction: atrazine + H2O = 4-(ethylamino)-2-hydroxy-6-(isopropylamino)-1,3,5-triazine + chloride + H+." [EC:3.8.1.8, RHEA:11312]
synonym: "AtzA" RELATED [EC:3.8.1.8]
xref: EC:3.8.1.8
xref: KEGG_REACTION:R05558
@@ -134037,7 +133988,7 @@ is_a: GO:0019120 ! hydrolase activity, acting on acid halide bonds, in C-halide
id: GO:0018789
name: cyclamate sulfohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cyclohexylsulfamate + H(2)O = cyclohexylamine + sulfate." [EC:3.10.1.2, RHEA:18481]
+def: "Catalysis of the reaction: cyclohexylsulfamate + H2O = cyclohexylamine + sulfate." [EC:3.10.1.2, RHEA:18481]
synonym: "cyclamate sulfamatase activity" EXACT []
synonym: "cyclamate sulfamidase activity" RELATED [EC:3.10.1.2]
synonym: "cyclamate sulphohydrolase activity" EXACT []
@@ -134108,7 +134059,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0018798
name: gallate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: gallate + H(+) = CO(2) + pyrogallol." [EC:4.1.1.59, RHEA:12749]
+def: "Catalysis of the reaction: gallate + H+ = CO2 + pyrogallol." [EC:4.1.1.59, RHEA:12749]
synonym: "gallate carboxy-lyase (pyrogallol-forming)" RELATED [EC:4.1.1.59]
synonym: "gallate carboxy-lyase activity" RELATED [EC:4.1.1.59]
synonym: "gallic acid decarboxylase activity" EXACT []
@@ -134123,7 +134074,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0018799
name: 4-hydroxybenzoate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-hydroxybenzoate + H(+) = CO(2) + phenol." [EC:4.1.1.61, RHEA:10876]
+def: "Catalysis of the reaction: 4-hydroxybenzoate + H+ = CO2 + phenol." [EC:4.1.1.61, RHEA:10876]
synonym: "4-hydroxybenzoate carboxy-lyase (phenol-forming)" RELATED [EC:4.1.1.61]
synonym: "4-hydroxybenzoate carboxy-lyase activity" RELATED [EC:4.1.1.61]
synonym: "p-hydroxybenzoate decarboxylase activity" RELATED [EC:4.1.1.61]
@@ -134156,7 +134107,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0018801
name: glutaconyl-CoA decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: trans-glutaconyl-CoA + H(+) = but-2-enoyl-CoA + CO(2)." [PMID:11248185, RHEA:23972]
+def: "Catalysis of the reaction: trans-glutaconyl-CoA + H+ = but-2-enoyl-CoA + CO2." [PMID:11248185, RHEA:23972]
synonym: "4-carboxybut-2-enoyl-CoA carboxy-lyase (but-2-enoyl-CoA-forming)" EXACT []
synonym: "4-carboxybut-2-enoyl-CoA carboxy-lyase activity" RELATED [EC:7.2.4.5]
synonym: "glutaconyl coenzyme A decarboxylase activity" RELATED [EC:7.2.4.5]
@@ -134254,9 +134205,18 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0018812
name: 3-hydroxyacyl-CoA dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: alkene-CoA + H2O = alcohol-CoA. Substrates are crotonoyl-CoA (producing 3-hydroxyacyl-CoA) and 2,3-didehydro-pimeloyl-CoA (producing 3-hydroxypimeloyl-CoA)." [UM-BBD_ruleID:bt0291]
+def: "Catalysis of the reaction: a 3-hydroxy-fatty acyl-CoA = a (2E)-enoyl-CoA + H2O. The stereospecifity of the hydroxyacyl in this reaction is not specified." [RHEA:33767]
+xref: EC:4.2.1.74
+xref: MetaCyc:LONG-CHAIN-ENOYL-COA-HYDRATASE-RXN
+xref: Reactome:R-HSA-2066778 "Hydration of delta2-tetracosaheptaenoyl-CoA to 3-hydroxy tetracosahexaenoyl-CoA"
+xref: Reactome:R-HSA-2066780 "Dehydrogenation of 3-hydroxy tetracosahexaenoyl-CoA"
+xref: Reactome:R-HSA-389986 "trans-2,3-dehydropristanoyl-CoA + H2O => 3-hydroxypristanoyl-CoA"
+xref: Reactome:R-HSA-390252 "HSD17B4 hydrates trans-2,3-dehydrohexacosanoyl-CoA"
+xref: Reactome:R-HSA-5676637 "PTPLs dehydrate VLC3HA-CoA to VLCTDA-CoA"
+xref: Reactome:R-HSA-6809263 "EHHADH hydrates trans-2,3-dehydrohexacosanoyl-CoA"
xref: Reactome:R-HSA-8957389 "RPP14 (HTD2) dehydrates 3HA-CoA to t2E-CoA"
-is_a: GO:0016836 ! hydro-lyase activity
+xref: RHEA:33767
+is_a: GO:0004300 ! enoyl-CoA hydratase activity
[Term]
id: GO:0018813
@@ -134272,7 +134232,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0018814
name: phenylacetaldoxime dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (trans)-phenylacetaldoxime = H(2)O + phenylacetonitrile." [EC:4.99.1.7, RHEA:20069]
+def: "Catalysis of the reaction: (trans)-phenylacetaldoxime = H2O + phenylacetonitrile." [EC:4.99.1.7, RHEA:20069]
synonym: "(Z)-phenylacetaldehyde-oxime hydro-lyase (phenylacetonitrile-forming) activity" RELATED [EC:4.99.1.7]
synonym: "(Z)-phenylacetaldehyde-oxime hydro-lyase activity" RELATED [EC:4.99.1.7]
synonym: "arylacetaldoxime dehydratase activity" RELATED [EC:4.99.1.7]
@@ -134319,7 +134279,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0018818
name: acetylene hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetaldehyde = acetylene + H(2)O." [EC:4.2.1.112, RHEA:17885]
+def: "Catalysis of the reaction: acetaldehyde = acetylene + H2O." [EC:4.2.1.112, RHEA:17885]
synonym: "acetaldehyde hydro-lyase activity" RELATED [EC:4.2.1.112]
synonym: "AH" RELATED [EC:4.2.1.112]
synonym: "AHy" RELATED [EC:4.2.1.112]
@@ -134334,7 +134294,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0018819
name: lactoyl-CoA dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: lactoyl-CoA = acryloyl-CoA + H2O." [EC:4.2.1.54]
+def: "Catalysis of the reaction: lactoyl-CoA = acryloyl-CoA + H2O." [EC:4.2.1.54, RHEA:34691]
synonym: "acrylyl coenzyme A hydratase activity" RELATED [EC:4.2.1.54]
synonym: "lactoyl coenzyme A dehydratase activity" RELATED [EC:4.2.1.54]
synonym: "lactoyl-CoA hydro-lyase (acryloyl-CoA-forming)" RELATED [EC:4.2.1.54]
@@ -134344,7 +134304,7 @@ synonym: "lactyl-coenzyme A dehydrase activity" RELATED [EC:4.2.1.54]
xref: EC:4.2.1.54
xref: MetaCyc:LACTOYL-COA-DEHYDRATASE-RXN
xref: MetaCyc:RXN-781
-xref: RHEA:21056
+xref: RHEA:34691
xref: UM-BBD_reactionID:r0086
is_a: GO:0016836 ! hydro-lyase activity
@@ -134352,7 +134312,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0018820
name: cyanamide hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: urea = cyanamide + H(2)O." [EC:4.2.1.69, RHEA:23056]
+def: "Catalysis of the reaction: urea = cyanamide + H2O." [EC:4.2.1.69, RHEA:23056]
synonym: "urea hydro-lyase (cyanamide-forming)" RELATED [EC:4.2.1.69]
synonym: "urea hydro-lyase activity" RELATED [EC:4.2.1.69]
xref: EC:4.2.1.69
@@ -134385,7 +134345,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0018823
name: cyclohexa-1,5-dienecarbonyl-CoA hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cyclohexa-1,5-diene-1-carbonyl-CoA + H(2)O = 6-hydroxycyclohex-1-enecarbonyl-CoA." [EC:4.2.1.100, RHEA:21856]
+def: "Catalysis of the reaction: cyclohexa-1,5-diene-1-carbonyl-CoA + H2O = 6-hydroxycyclohex-1-enecarbonyl-CoA." [EC:4.2.1.100, RHEA:21856]
synonym: "6-hydroxycyclohex-1-enecarbonyl-CoA (cyclohexa-1,5-dienecarbonyl-CoA-forming)" RELATED [EC:4.2.1.100]
synonym: "cyclohex-1,5-diene-1-carbonyl-CoA hydratase activity" EXACT []
synonym: "cyclohexa-1,5-diene-1-carbonyl-CoA hydratase activity" RELATED [EC:4.2.1.100]
@@ -134497,7 +134457,7 @@ is_a: GO:0019181 ! halohydrin hydrogen-halide-lyase activity
id: GO:0018833
name: DDT-dehydrochlorinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane = 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene + chloride + H(+)." [EC:4.5.1.1, RHEA:19217]
+def: "Catalysis of the reaction: 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane = 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene + chloride + H+." [EC:4.5.1.1, RHEA:19217]
synonym: "1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane chloride-lyase [1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene-forming]" RELATED [EC:4.5.1.1]
synonym: "1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane chloride-lyase activity" RELATED [EC:4.5.1.1]
synonym: "DDT dehydrochlorinase activity" EXACT []
@@ -134515,7 +134475,7 @@ is_a: GO:0016848 ! carbon-halide lyase activity
id: GO:0018834
name: dichloromethane dehalogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dichloromethane + H(2)O = 2 chloride + formaldehyde + 2 H(+)." [EC:4.5.1.3, RHEA:15397]
+def: "Catalysis of the reaction: dichloromethane + H2O = 2 chloride + formaldehyde + 2 H+." [EC:4.5.1.3, RHEA:15397]
synonym: "dichloromethane chloride-lyase (adding H2O; chloride-hydrolysing; formaldehyde-forming)" RELATED [EC:4.5.1.3]
synonym: "dichloromethane chloride-lyase (chloride-hydrolysing)" RELATED [EC:4.5.1.3]
xref: EC:4.5.1.3
@@ -134538,7 +134498,7 @@ is_a: GO:0016829 ! lyase activity
id: GO:0018836
name: alkylmercury lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: R-Hg+ + H+ = R-H + Hg2+." [EC:4.99.1.2]
+def: "Catalysis of the reaction: an alkylmercury + H+ = an alkane + Hg2+." [RHEA:18777]
synonym: "alkylmercury mercuric-lyase (alkane-forming)" RELATED [EC:4.99.1.2]
synonym: "alkylmercury mercuric-lyase activity" RELATED [EC:4.99.1.2]
synonym: "organomercurial lyase activity" RELATED [EC:4.99.1.2]
@@ -134835,6 +134795,7 @@ synonym: "ethyne metabolic process" EXACT []
synonym: "ethyne metabolism" EXACT []
xref: UM-BBD_pathwayID:atl
is_a: GO:0006805 ! xenobiotic metabolic process
+is_a: GO:0018942 ! organometal metabolic process
is_a: GO:0043452 ! cellular alkyne metabolic process
is_a: GO:0120244 ! terminal acetylenic compound metabolic process
@@ -134911,8 +134872,8 @@ namespace: biological_process
def: "The chemical reactions and pathways involving arsonoacetate, a synthetic, organic compound containing a single arsenic atom. Arsonoacetate and other arsenic containing compounds are used in agricultural applications as animal feed additives, cotton defoliants and post-emergence grass herbicides." [UM-BBD_pathwayID:ara]
synonym: "arsonoacetate metabolism" EXACT []
xref: UM-BBD_pathwayID:ara
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0006805 ! xenobiotic metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
[Term]
id: GO:0018873
@@ -135025,9 +134986,7 @@ def: "The chemical reactions and pathways involving caprolactam, hexahydro-2h-az
synonym: "caprolactam metabolism" EXACT []
xref: UM-BBD_pathwayID:cap
is_a: GO:0006805 ! xenobiotic metabolic process
-is_a: GO:0072338 ! cellular lactam metabolic process
-is_a: GO:1901360 ! organic cyclic compound metabolic process
-is_a: GO:1901564 ! organonitrogen compound metabolic process
+is_a: GO:0072338 ! lactam metabolic process
[Term]
id: GO:0018884
@@ -135094,7 +135053,7 @@ synonym: "propachlor metabolic process" EXACT []
synonym: "propachlor metabolism" EXACT []
xref: UM-BBD_pathwayID:ppc
is_a: GO:0042537 ! benzene-containing compound metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
@@ -135235,19 +135194,20 @@ xref: UM-BBD_pathwayID:2\,4-d
is_a: GO:0018904 ! ether metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:0042537 ! benzene-containing compound metabolic process
+is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
id: GO:0018902
-name: 1,3-dichloro-2-propanol metabolic process
+name: obsolete 1,3-dichloro-2-propanol metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving 1,3-dichloro-2-propanol (DCP), a halohydrin suspected of being carcinogenic, mutagenic and genotoxic. DCP is used as a general solvent, as an intermediate in organic synthesis and in paints, varnishes, lacquers, water colors, binders and photographic lacquers." [GOC:jl, UM-BBD_pathwayID:dcp]
+def: "OBSOLETE. The chemical reactions and pathways involving 1,3-dichloro-2-propanol (DCP), a halohydrin suspected of being carcinogenic, mutagenic and genotoxic. DCP is used as a general solvent, as an intermediate in organic synthesis and in paints, varnishes, lacquers, water colors, binders and photographic lacquers." [GOC:jl, UM-BBD_pathwayID:dcp]
+comment: 1,3-dichloro-2-propanol is not a natural compound.
synonym: "1,3-dichloro-2-propanol metabolism" EXACT []
synonym: "DCP metabolic process" EXACT []
synonym: "DCP metabolism" EXACT []
xref: UM-BBD_pathwayID:dcp
-is_a: GO:0006805 ! xenobiotic metabolic process
-is_a: GO:0044107 ! cellular alcohol metabolic process
-is_a: GO:1902652 ! secondary alcohol metabolic process
+is_obsolete: true
+consider: GO:0006805
[Term]
id: GO:0018903
@@ -135438,7 +135398,7 @@ def: "The chemical reactions and pathways involving prodione, a colorless, odorl
synonym: "iprodione metabolism" EXACT []
xref: UM-BBD_pathwayID:ipd
is_a: GO:0042537 ! benzene-containing compound metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0052803 ! imidazole-containing compound metabolic process
[Term]
@@ -135488,8 +135448,6 @@ synonym: "methanesulfonic acid metabolism" EXACT []
synonym: "methanesulphonic acid metabolic process" EXACT []
synonym: "methanesulphonic acid metabolism" EXACT []
xref: UM-BBD_pathwayID:msa
-is_a: GO:0006082 ! organic acid metabolic process
-is_a: GO:0006790 ! sulfur compound metabolic process
is_a: GO:0006805 ! xenobiotic metabolic process
is_a: GO:0019694 ! alkanesulfonate metabolic process
@@ -136074,15 +136032,14 @@ is_a: GO:0042537 ! benzene-containing compound metabolic process
[Term]
id: GO:0018981
-name: triethanolamine metabolic process
+name: obsolete triethanolamine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving triethanolamine, a combustible, hygroscopic, colorless liquid commonly used in dry-cleaning solutions, cosmetics, detergents, textile processing, wool scouring, and as a corrosion inhibitor and pharmaceutical alkalizing agent." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways involving triethanolamine, a combustible, hygroscopic, colorless liquid commonly used in dry-cleaning solutions, cosmetics, detergents, textile processing, wool scouring, and as a corrosion inhibitor and pharmaceutical alkalizing agent." [GOC:jl]
+comment: Triethanolamine is not a natural compound.
synonym: "triethanolamine metabolism" EXACT []
xref: UM-BBD_pathwayID:tea
-is_a: GO:0006805 ! xenobiotic metabolic process
-is_a: GO:0019751 ! polyol metabolic process
-is_a: GO:0044106 ! cellular amine metabolic process
-is_a: GO:0044107 ! cellular alcohol metabolic process
+is_obsolete: true
+consider: GO:0006805
[Term]
id: GO:0018982
@@ -136117,7 +136074,8 @@ synonym: "naphthalenesulfonate metabolism" EXACT []
synonym: "naphthalenesulphonate metabolic process" EXACT []
synonym: "naphthalenesulphonate metabolism" EXACT []
xref: UM-BBD_pathwayID:nphs
-is_a: GO:0071704 ! organic substance metabolic process
+is_a: GO:0006082 ! organic acid metabolic process
+is_a: GO:0006790 ! sulfur compound metabolic process
[Term]
id: GO:0018985
@@ -136158,12 +136116,13 @@ relationship: part_of GO:0007591 ! molting cycle, chitin-based cuticle
[Term]
id: GO:0018991
-name: oviposition
+name: egg-laying behavior
namespace: biological_process
alt_id: GO:0060403
-def: "The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water." [GOC:ems]
+def: "A reproductive behavior that results in the deposition of eggs (either fertilized or not) upon a surface or into a medium such as water." [GOC:ems, PMID:18050396, PMID:31164023]
synonym: "egg laying" BROAD []
synonym: "egg-laying" BROAD []
+synonym: "oviposition" EXACT []
synonym: "post-mating oviposition" NARROW []
xref: Wikipedia:Oviposition
is_a: GO:0019098 ! reproductive behavior
@@ -136279,7 +136238,8 @@ alt_id: GO:0019009
def: "A protein complex that possesses molybdopterin synthase activity. In E. coli, the complex is a heterotetramer consisting of two MoaD and two MoaE subunits." [GOC:mah, PMID:12571227, PMID:15709772]
subset: goslim_metagenomics
synonym: "molybdopterin converting factor complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0019010
@@ -136497,11 +136457,11 @@ is_a: GO:0032991 ! protein-containing complex
[Term]
id: GO:0019037
-name: viral assembly intermediate
+name: obsolete viral assembly intermediate
namespace: cellular_component
-def: "Specific locations and structures in the virus infected cell involved in assembling new virions." [ISBN:0781718325]
-is_a: GO:0110165 ! cellular anatomical entity
-relationship: part_of GO:0005737 ! cytoplasm
+def: "OBSOLETE. Specific locations and structures in the virus infected cell involved in assembling new virions." [ISBN:0781718325]
+comment: This term was obsoleted because the concept it represented was too vague.
+is_obsolete: true
[Term]
id: GO:0019038
@@ -136609,40 +136569,58 @@ is_a: GO:0044003 ! modulation by symbiont of host process
[Term]
id: GO:0019049
-name: mitigation of host defenses by virus
+name: mitigation of host antiviral defense response
namespace: biological_process
+alt_id: GO:0019052
+alt_id: GO:0019053
+alt_id: GO:0030683
+alt_id: GO:0050690
def: "A process by which a virus avoids or tolerates the effects of its host organism's defenses. Host defenses may be induced by the presence of the virus or may be preformed (e.g. physical barriers). The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:1555811272]
synonym: "evasion of host defenses by virus" NARROW [GOC:bf, GOC:bm, GOC:jl]
-synonym: "evasion or tolerance of host defenses by virus" RELATED []
+synonym: "mitigation of host defenses by virus" EXACT []
+synonym: "regulation by virus of antiviral response" EXACT []
+synonym: "regulation of defense response to virus by virus" EXACT []
synonym: "viral host defence evasion" NARROW []
synonym: "viral host defense evasion" NARROW []
-is_a: GO:0019048 ! modulation by virus of host process
-is_a: GO:0030682 ! mitigation of host defenses by symbiont
+synonym: "viral regulation of antiviral response" EXACT []
+is_a: GO:0019054 ! modulation by virus of host cellular process
+is_a: GO:0052031 ! modulation by symbiont of host defense response
[Term]
id: GO:0019050
name: suppression by virus of host apoptotic process
namespace: biological_process
+alt_id: GO:0039650
def: "Any viral process that inhibits apoptosis of infected host cells, facilitating prolonged cell survival during viral replication." [GOC:mtg_apoptosis, ISBN:0781718325]
+synonym: "inhibition of host caspases by virus" NARROW []
synonym: "negative regulation by virus of host apoptosis" EXACT []
synonym: "negative regulation of apoptosis by virus" EXACT []
synonym: "suppression by virus of host apoptosis" EXACT []
+synonym: "suppression by virus of host cysteine-type endopeptidase activity involved in apoptotic process" NARROW []
synonym: "suppression of apoptosis in host by virus" EXACT []
-is_a: GO:0033668 ! negative regulation by symbiont of host apoptotic process
+is_a: GO:0033668 ! suppression by symbiont of host apoptotic process
is_a: GO:0039526 ! modulation by virus of host apoptotic process
[Term]
id: GO:0019051
name: induction by virus of host apoptotic process
namespace: biological_process
-def: "The set of viral processes that induce an apoptotic process in infected host cells, facilitating release and spread of progeny virions." [GOC:mtg_apoptosis, ISBN:0781718325]
+alt_id: GO:0039651
+alt_id: GO:0060139
+def: "Any viral process that activates or increases the frequency, rate or extent of cell death by apoptotic process." [GOC:dph, GOC:mtg_apoptosis]
synonym: "activation by virus of host apoptosis" EXACT []
synonym: "activation by virus of host apoptotic programmed cell death" EXACT []
synonym: "activation of apoptosis in host by virus" EXACT []
+synonym: "activation of host caspases by virus" NARROW []
synonym: "induction by virus of host apoptosis" NARROW []
synonym: "induction by virus of host apoptotic programmed cell death" EXACT []
+synonym: "induction by virus of host caspase activity" NARROW []
+synonym: "induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process" NARROW []
synonym: "induction of apoptosis in host by virus" EXACT []
-is_a: GO:0060139 ! positive regulation of apoptotic process by virus
+synonym: "positive regulation of apoptosis by virus" NARROW []
+synonym: "positive regulation of apoptotic process by virus" EXACT []
+is_a: GO:0039526 ! modulation by virus of host apoptotic process
+is_a: GO:0052151 ! positive regulation by symbiont of host apoptotic process
[Term]
id: GO:0019054
@@ -136675,7 +136653,6 @@ namespace: biological_process
def: "Any process in which a virus modulates the frequency, rate or extent of its host's transcription." [ISBN:0781718325]
synonym: "modification by virus of host transcription" EXACT []
synonym: "viral perturbation of host cell transcription" EXACT []
-is_a: GO:0019054 ! modulation by virus of host cellular process
is_a: GO:0039656 ! modulation by virus of host gene expression
is_a: GO:0052026 ! modulation by symbiont of host transcription
@@ -136693,7 +136670,6 @@ synonym: "regulation of host translation by virus" EXACT []
synonym: "regulation of translation in host by virus" EXACT []
synonym: "viral host shutoff protein" RELATED []
synonym: "viral perturbation of host cell mRNA translation" EXACT []
-is_a: GO:0019054 ! modulation by virus of host cellular process
is_a: GO:0039656 ! modulation by virus of host gene expression
is_a: GO:0044073 ! modulation by symbiont of host translation
@@ -136880,7 +136856,7 @@ relationship: part_of GO:0019058 ! viral life cycle
id: GO:0019076
name: viral release from host cell
namespace: biological_process
-def: "The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane." [GOC:jl]
+def: "The dissemination of mature viral particles from a host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane." [GOC:jl]
synonym: "release of virus from host" EXACT []
synonym: "viral exit" EXACT []
synonym: "viral release" EXACT []
@@ -136987,7 +136963,7 @@ synonym: "viral immortalization" EXACT []
synonym: "viral transformation" EXACT []
synonym: "viral transformation of host cell" EXACT []
xref: Wikipedia:Viral_transformation
-is_a: GO:0019048 ! modulation by virus of host process
+is_a: GO:0019054 ! modulation by virus of host cellular process
[Term]
id: GO:0019089
@@ -137010,7 +136986,7 @@ synonym: "mitochondrial rRNA export out of mitochondrion" EXACT []
synonym: "mitochondrial rRNA transport from mitochondrion" EXACT []
synonym: "mitochondrial rRNA, mitochondrial export" EXACT []
is_a: GO:0051029 ! rRNA transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0019091
@@ -137111,7 +137087,8 @@ synonym: "reproductive behavior in a multicellular organism" EXACT []
synonym: "reproductive behaviour" EXACT []
synonym: "single-organism reproductive behavior" RELATED []
is_a: GO:0007610 ! behavior
-is_a: GO:0048609 ! multicellular organismal reproductive process
+is_a: GO:0022414 ! reproductive process
+relationship: part_of GO:0032504 ! multicellular organism reproduction
[Term]
id: GO:0019099
@@ -137193,11 +137170,12 @@ is_a: GO:0140097 ! catalytic activity, acting on DNA
[Term]
id: GO:0019105
-name: N-palmitoyltransferase activity
+name: obsolete N-palmitoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a palmitoyl group to a nitrogen atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0016409 ! palmitoyltransferase activity
-is_a: GO:0016410 ! N-acyltransferase activity
+def: "OBSOLETE. Catalysis of the transfer of a palmitoyl group to a nitrogen atom on the acceptor molecule." [GOC:ai]
+comment: This term has been obsoleted because it represents an unnecessary grouping class and is not consistent with the ontology structure.
+is_obsolete: true
+consider: GO:0016410
[Term]
id: GO:0019107
@@ -137421,7 +137399,7 @@ is_a: GO:0016713 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0019134
name: glucosamine-1-phosphate N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: alpha-D-glucosamine 1-phosphate + acetyl-CoA = N-acetyl-alpha-D-glucosamine 1-phosphate + CoA + H(+)." [EC:2.3.1.157, RHEA:13725]
+def: "Catalysis of the reaction: alpha-D-glucosamine 1-phosphate + acetyl-CoA = N-acetyl-alpha-D-glucosamine 1-phosphate + CoA + H+." [EC:2.3.1.157, RHEA:13725]
synonym: "acetyl-CoA:alpha-D-glucosamine-1-phosphate N-acetyltransferase activity" RELATED [EC:2.3.1.157]
synonym: "acetyl-CoA:D-glucosamine-1-phosphate N-acetyltransferase activity" RELATED [EC:2.3.1.157]
xref: EC:2.3.1.157
@@ -137462,6 +137440,7 @@ synonym: "multispecific deoxynucleoside kinase activity" RELATED [EC:2.7.1.145]
synonym: "multisubstrate deoxyribonucleoside kinase activity" RELATED [EC:2.7.1.145]
xref: EC:2.7.1.145
xref: MetaCyc:2.7.1.145-RXN
+xref: Reactome:R-HSA-74207 "dA, dG, or dI + ATP => dAMP, dGMP, or dIMP + ADP (DGUOK)"
xref: RHEA:12140
is_a: GO:0019206 ! nucleoside kinase activity
@@ -137530,7 +137509,7 @@ is_a: GO:0036441 ! 2-dehydropantolactone reductase activity
id: GO:0019142
name: 2-hydroxyglutarate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glyoxylate + H(2)O + propanoyl-CoA = 2-hydroxyglutarate + CoA + H(+)." [EC:2.3.3.11, RHEA:19185]
+def: "Catalysis of the reaction: glyoxylate + H2O + propanoyl-CoA = 2-hydroxyglutarate + CoA + H+." [RHEA:19185]
comment: Note that this function was formerly EC:4.1.3.9.
synonym: "2-hydroxyglutarate glyoxylate-lyase (CoA-propanoylating) activity" RELATED [EC:2.3.3.11]
synonym: "2-hydroxyglutaratic synthetase activity" RELATED [EC:2.3.3.11]
@@ -137542,13 +137521,13 @@ xref: EC:2.3.3.11
xref: KEGG_REACTION:R00932
xref: MetaCyc:HYDGLUTSYN-RXN
xref: RHEA:19185
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0019143
name: 3-deoxy-manno-octulosonate-8-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate." [EC:3.1.3.45, RHEA:11500]
+def: "Catalysis of the reaction: 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + H2O = 3-deoxy-D-manno-octulosonate + phosphate." [EC:3.1.3.45, RHEA:11500]
synonym: "3-deoxy-D-manno-octulosonate-8-phosphate 8-phosphohydrolase activity" RELATED [EC:3.1.3.45]
xref: EC:3.1.3.45
xref: KEGG_REACTION:R03350
@@ -137589,7 +137568,7 @@ is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
id: GO:0019146
name: arabinose-5-phosphate isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-arabinose 5-phosphate = D-ribulose 5-phosphate + 2 H(+)." [EC:5.3.1.13, RHEA:23104]
+def: "Catalysis of the reaction: D-arabinose 5-phosphate = D-ribulose 5-phosphate + 2 H+." [EC:5.3.1.13, RHEA:23104]
synonym: "arabinose phosphate isomerase activity" RELATED [EC:5.3.1.13]
synonym: "D-arabinose-5-phosphate aldose-ketose-isomerase activity" RELATED [EC:5.3.1.13]
synonym: "D-arabinose-5-phosphate ketol-isomerase activity" RELATED [EC:5.3.1.13]
@@ -137604,7 +137583,7 @@ is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldos
id: GO:0019147
name: (R)-aminopropanol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-1-aminopropan-2-ol + NAD(+) = aminoacetone + H(+) + NADH." [EC:1.1.1.75, RHEA:16517]
+def: "Catalysis of the reaction: (R)-1-aminopropan-2-ol + NAD+ = aminoacetone + H+ + NADH." [EC:1.1.1.75, RHEA:16517]
synonym: "(R)-1-aminopropan-2-ol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.75]
synonym: "1-aminopropan-2-ol-dehydrogenase activity" RELATED [EC:1.1.1.75]
synonym: "1-aminopropan-2-ol-NAD+ dehydrogenase activity" RELATED [EC:1.1.1.75]
@@ -137747,14 +137726,13 @@ xref: EC:3.2.1.68
xref: MetaCyc:3.2.1.68-RXN
xref: MetaCyc:RXN-12280
xref: MetaCyc:RXN-14380
-is_a: GO:0004133 ! glycogen debranching enzyme activity
is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
[Term]
id: GO:0019157
name: obsolete malate oxidase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: (S)-malate + O(2) = H(2)O(2) + oxaloacetate." [GOC:curators]
+def: "OBSOLETE. Catalysis of the reaction: (S)-malate + O2 = H2O2 + oxaloacetate." [GOC:curators]
comment: This term is slated for obsoletion because RHEA indicates there is not enough experimental evidence.
synonym: "(S)-malate:oxygen oxidoreductase activity" EXACT []
synonym: "FAD-dependent malate oxidase activity" EXACT []
@@ -137794,7 +137772,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0019160
name: NMN nucleosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + nicotinamide mononucleotide = D-ribose 5-phosphate + H(+) + nicotinamide." [EC:3.2.2.14, RHEA:23140]
+def: "Catalysis of the reaction: H2O + nicotinamide mononucleotide = D-ribose 5-phosphate + H+ + nicotinamide." [EC:3.2.2.14, RHEA:23140]
synonym: "nicotinamide mononucleotidase activity" RELATED [EC:3.2.2.14]
synonym: "nicotinamide mononucleotide nucleosidase activity" RELATED [EC:3.2.2.14]
synonym: "nicotinamide-nucleotide phosphoribohydrolase activity" RELATED [EC:3.2.2.14]
@@ -137874,7 +137852,7 @@ is_a: GO:0016625 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0019165
name: thiamine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + thiamine = ADP + 2 H(+) + thiamine phosphate." [EC:2.7.1.89, RHEA:12012]
+def: "Catalysis of the reaction: ATP + thiamine = ADP + 2 H+ + thiamine phosphate." [EC:2.7.1.89, RHEA:12012]
synonym: "ATP:thiamin phosphotransferase activity" RELATED [EC:2.7.1.89]
synonym: "ATP:thiamine phosphotransferase activity" RELATED [EC:2.7.1.89]
synonym: "thiamin kinase (phosphorylating)" RELATED [EC:2.7.1.89]
@@ -137927,10 +137905,12 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
[Term]
id: GO:0019171
-name: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity
+name: (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a (3R)-3-hydroxyacyl-[acyl-carrier protein] = H2O + a trans-delta2-enoyl-acyl-[acyl-carrier protein]." [MetaCyc:3-HYDROXYDECANOYL-ACP-DEHYDR-RXN]
+def: "Catalysis of the reaction: a (3R)-hydroxyacyl-[acyl-carrier-protein] = a (2E)-enoyl-[acyl-carrier-protein] + H2O." [RHEA:13097]
+synonym: "(3R)-3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity" RELATED []
synonym: "3-hydroxyacyl-[acyl-carrier protein] dehydratase activity" EXACT []
+synonym: "3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity" BROAD []
synonym: "3-hydroxyacyl-ACP dehydratase activity" EXACT []
xref: EC:4.2.1.59
xref: MetaCyc:3-HYDROXYDECANOYL-ACP-DEHYDR-RXN
@@ -137973,7 +137953,8 @@ is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-
id: GO:0019177
name: dihydroneopterin triphosphate pyrophosphohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dihydroneopterin triphosphate = dihydroneopterin phosphate + diphosphate." [MetaCyc:H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN]
+def: "Catalysis of the reaction: dihydroneopterin triphosphate = dihydroneopterin phosphate + diphosphate." [RHEA:25302]
+xref: EC:3.6.1.67
xref: MetaCyc:H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN
xref: RHEA:25302
is_a: GO:0016462 ! pyrophosphatase activity
@@ -138041,7 +138022,6 @@ namespace: cellular_component
def: "A protein complex that forms a transmembrane channel through which chloride ions may pass in response to histamine binding to the channel complex or one of its constituent parts." [GOC:mah]
is_a: GO:0034707 ! chloride channel complex
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0019184
@@ -138113,7 +138093,7 @@ id: GO:0019197
name: phosphoenolpyruvate-dependent sugar phosphotransferase complex
namespace: cellular_component
def: "Includes phosphoenolpyruvate-protein phosphatase (enzyme I of the phosphotransferase system) and protein-N(PI)-phosphohistidine-sugar phosphotransferase (enzyme II of the phosphotransferase system)." [GOC:ma]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005737 ! cytoplasm
[Term]
@@ -138164,11 +138144,9 @@ id: GO:0019204
name: obsolete nucleotide phosphatase activity
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: phosphopolynucleotide + H2O = polynucleotide + phosphate." [GOC:mah]
-comment: This term was defined to cover phosphatase activity against polynucleotides, but had subclasses and annotations for phosphatase activity against free nucleotides. It has therefore been split. Use GO:0098519 (nucleotide phosphatase activity, acting against free nucleotides) or GO:0098518 (polynucleotide phosphatase activity).
+comment: This term was defined to cover phosphatase activity against polynucleotides, but had subclasses and annotations for phosphatase activity against free nucleotides.
synonym: "nucleotide phosphatase activity" EXACT []
is_obsolete: true
-consider: GO:0098518
-consider: GO:0098519
[Term]
id: GO:0019205
@@ -138191,7 +138169,6 @@ xref: Reactome:R-HSA-110138 "AK5,7,8,9 phosphorylates (d)NMPs to (d)NDPs"
xref: Reactome:R-HSA-73598 "(2'-deoxy)cytidine + ATP => (d)CMP + ADP (DCK)"
xref: Reactome:R-HSA-73599 "cytidine or uridine + ATP => CMP or UMP + ADP [UCK1]"
xref: Reactome:R-HSA-73632 "thymidine + ATP => TMP (deoxythymidine 5'-monophosphate) + ADP [TK1]"
-xref: Reactome:R-HSA-74207 "dA, dG, or dI + ATP => dAMP, dGMP, or dIMP + ADP (DGUOK)"
is_a: GO:0019205 ! nucleobase-containing compound kinase activity
[Term]
@@ -138228,7 +138205,7 @@ is_a: GO:0019207 ! kinase regulator activity
id: GO:0019211
name: phosphatase activator activity
namespace: molecular_function
-def: "Binds to and increases the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule." [GOC:ai]
+def: "Binds to and increases the activity of a phosphatase." [GOC:ai]
is_a: GO:0008047 ! enzyme activator activity
is_a: GO:0019208 ! phosphatase regulator activity
@@ -138236,7 +138213,7 @@ is_a: GO:0019208 ! phosphatase regulator activity
id: GO:0019212
name: phosphatase inhibitor activity
namespace: molecular_function
-def: "Binds to and stops, prevents or reduces the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule." [GOC:ai]
+def: "Binds to and stops, prevents or reduces the activity of a phosphatase." [GOC:ai]
is_a: GO:0004857 ! enzyme inhibitor activity
is_a: GO:0019208 ! phosphatase regulator activity
@@ -138257,7 +138234,7 @@ def: "OBSOLETE. The action of reducing the surface tension of a liquid." [GOC:jl
comment: This term was made obsolete because it represents involvement in a process.
synonym: "surfactant activity" EXACT []
is_obsolete: true
-consider: GO:0050828
+consider: GO:0043129
[Term]
id: GO:0019215
@@ -138320,7 +138297,7 @@ relationship: regulates GO:0006796 ! phosphate-containing compound metabolic pro
id: GO:0019221
name: cytokine-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, PMID:19295629]
+def: "The series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, PMID:19295629]
synonym: "cytokine and chemokine mediated signaling pathway" EXACT []
synonym: "cytokine mediated signalling pathway" EXACT []
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -138346,7 +138323,6 @@ namespace: biological_process
def: "The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission." [GOC:curators, ISBN:0815316194]
synonym: "conduction of nerve impulse" EXACT [GOC:dph]
synonym: "signal transmission along a neuron" EXACT []
-is_a: GO:0035637 ! multicellular organismal signaling
is_a: GO:0050877 ! nervous system process
relationship: part_of GO:0007154 ! cell communication
@@ -138406,7 +138382,7 @@ id: GO:0019233
name: sensory perception of pain
namespace: biological_process
def: "The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process." [GOC:curators]
-synonym: "nociception" EXACT []
+synonym: "nociception" RELATED []
synonym: "perception of physiological pain" NARROW []
xref: Wikipedia:Nociception
is_a: GO:0007600 ! sensory perception
@@ -138454,8 +138430,11 @@ name: deaminase activity
namespace: molecular_function
def: "Catalysis of the removal of an amino group from a substrate, producing a substituted or nonsubstituted ammonia (NH3/NH2R)." [GOC:jl]
subset: goslim_pir
+xref: Reactome:R-HSA-74241 "ADA catalyzes the deamination of (deoxy)adenosine"
xref: Reactome:R-HSA-9014641 "HRSP12 deaminates 2AA to 2OBUTA"
-is_a: GO:0016787 ! hydrolase activity
+xref: Reactome:R-HSA-9734745 "Defective ADA does not deaminate (deoxy)adenosine"
+xref: Reactome:R-HSA-9754964 "ADA deamidates RBV"
+is_a: GO:0016810 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
[Term]
id: GO:0019240
@@ -139043,7 +139022,7 @@ name: rhizobactin 1021 biosynthetic process
namespace: biological_process
alt_id: GO:0031193
alt_id: GO:0031194
-def: "The chemical reactions and pathways resulting in the formation of rhizobactin 1021, (E)-4-((3-(acetylhydroxyamino)propyl)-amino)-2-hydroxy-(2-(2-(3-(hydroxy(1-oxo-2-decenyl)amino)propyl)amino)-2-oxoethyl)-4-oxobutanoic acid, a siderophore produced by Sinorhizobium meliloti." [MetaCyc:PWY-761, PMID:11274118]
+def: "The chemical reactions and pathways resulting in the formation of rhizobactin 1021, (E)-4-((3-(acetylhydroxyamino)propyl)-amino)-2-hydroxy-(2-(2-(3-(hydroxy(1-oxo-2-decenyl)amino)propyl)amino)-2-oxoethyl)-4-oxobutanoic acid, a siderophore produced by Sinorhizobium meliloti." [PMID:11274118]
synonym: "rhizobactin 1021 anabolism" EXACT []
synonym: "rhizobactin 1021 biosynthesis" EXACT []
synonym: "rhizobactin 1021 biosynthetic process, peptide formation" NARROW []
@@ -139051,9 +139030,10 @@ synonym: "rhizobactin 1021 biosynthetic process, peptide modification" NARROW []
synonym: "rhizobactin 1021 formation" EXACT []
synonym: "rhizobactin 1021 synthesis" EXACT []
xref: MetaCyc:PWY-761
-is_a: GO:0016053 ! organic acid biosynthetic process
-is_a: GO:0019540 ! catechol-containing siderophore biosynthetic process
+is_a: GO:0043604 ! amide biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:0046494 ! rhizobactin 1021 metabolic process
+is_a: GO:1901566 ! organonitrogen compound biosynthetic process
is_a: GO:1902645 ! tertiary alcohol biosynthetic process
[Term]
@@ -139309,7 +139289,6 @@ synonym: "vitamin Bh catabolic process" EXACT []
synonym: "vitamin Bh catabolism" EXACT []
xref: MetaCyc:P562-PWY
is_a: GO:0006020 ! inositol metabolic process
-is_a: GO:0044275 ! cellular carbohydrate catabolic process
is_a: GO:0046174 ! polyol catabolic process
[Term]
@@ -139827,17 +139806,6 @@ xref: MetaCyc:PWY-5194
is_a: GO:0006783 ! heme biosynthetic process
is_a: GO:0046156 ! siroheme metabolic process
-[Term]
-id: GO:0019355
-name: nicotinamide nucleotide biosynthetic process from aspartate
-namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of nicotinamide nucleotide from other compounds, including aspartate." [GOC:go_curators]
-synonym: "nicotinamide nucleotide anabolism from aspartate" EXACT []
-synonym: "nicotinamide nucleotide formation from aspartate" EXACT []
-synonym: "nicotinamide nucleotide synthesis from aspartate" EXACT []
-is_a: GO:0006531 ! aspartate metabolic process
-is_a: GO:0019359 ! nicotinamide nucleotide biosynthetic process
-
[Term]
id: GO:0019356
name: nicotinate nucleotide biosynthetic process from tryptophan
@@ -140134,7 +140102,7 @@ synonym: "caprolactam degradation" EXACT []
xref: MetaCyc:P621-PWY
is_a: GO:0018883 ! caprolactam metabolic process
is_a: GO:0042178 ! xenobiotic catabolic process
-is_a: GO:0072340 ! cellular lactam catabolic process
+is_a: GO:0072340 ! lactam catabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
@@ -140189,7 +140157,6 @@ synonym: "glucuronide metabolic process" EXACT []
synonym: "glucuronide metabolism" EXACT []
synonym: "glucuronoside metabolism" EXACT []
is_a: GO:0016137 ! glycoside metabolic process
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
[Term]
id: GO:0019390
@@ -140204,7 +140171,6 @@ synonym: "glucuronoside formation" EXACT []
synonym: "glucuronoside synthesis" EXACT []
is_a: GO:0016138 ! glycoside biosynthetic process
is_a: GO:0019389 ! glucuronoside metabolic process
-is_a: GO:0034637 ! cellular carbohydrate biosynthetic process
[Term]
id: GO:0019391
@@ -140219,7 +140185,6 @@ synonym: "glucuronoside degradation" EXACT []
xref: MetaCyc:GLUCUROCAT-PWY
is_a: GO:0016139 ! glycoside catabolic process
is_a: GO:0019389 ! glucuronoside metabolic process
-is_a: GO:0044275 ! cellular carbohydrate catabolic process
[Term]
id: GO:0019392
@@ -140322,8 +140287,8 @@ name: alditol metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving alditols, any polyhydric alcohol derived from the acyclic form of a monosaccharide by reduction of its aldehyde or keto group to an alcoholic group." [ISBN:0198506732]
synonym: "alditol metabolism" EXACT []
+is_a: GO:0005975 ! carbohydrate metabolic process
is_a: GO:0019751 ! polyol metabolic process
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
[Term]
id: GO:0019401
@@ -140334,8 +140299,8 @@ synonym: "alditol anabolism" EXACT []
synonym: "alditol biosynthesis" EXACT []
synonym: "alditol formation" EXACT []
synonym: "alditol synthesis" EXACT []
+is_a: GO:0016051 ! carbohydrate biosynthetic process
is_a: GO:0019400 ! alditol metabolic process
-is_a: GO:0034637 ! cellular carbohydrate biosynthetic process
is_a: GO:0046173 ! polyol biosynthetic process
[Term]
@@ -140378,8 +140343,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of alditols
synonym: "alditol breakdown" EXACT []
synonym: "alditol catabolism" EXACT []
synonym: "alditol degradation" EXACT []
+is_a: GO:0016052 ! carbohydrate catabolic process
is_a: GO:0019400 ! alditol metabolic process
-is_a: GO:0044275 ! cellular carbohydrate catabolic process
is_a: GO:0046174 ! polyol catabolic process
[Term]
@@ -140771,6 +140736,7 @@ synonym: "tryptophan degradation to acetyl-CoA" EXACT []
xref: MetaCyc:TRYPTOPHAN-DEGRADATION-1
is_a: GO:0006084 ! acetyl-CoA metabolic process
is_a: GO:0006569 ! tryptophan catabolic process
+is_a: GO:0043605 ! amide catabolic process
[Term]
id: GO:0019443
@@ -140839,6 +140805,7 @@ synonym: "L-cysteine breakdown" EXACT []
synonym: "L-cysteine catabolism" EXACT []
synonym: "L-cysteine degradation" EXACT []
is_a: GO:0009093 ! cysteine catabolic process
+is_a: GO:0042219 ! cellular modified amino acid catabolic process
is_a: GO:0046439 ! L-cysteine metabolic process
[Term]
@@ -140927,6 +140894,7 @@ synonym: "methionine degradation to succinyl-CoA" EXACT []
xref: MetaCyc:METHIONINE-DEG1-PWY
is_a: GO:0006104 ! succinyl-CoA metabolic process
is_a: GO:0009087 ! methionine catabolic process
+is_a: GO:0043605 ! amide catabolic process
[Term]
id: GO:0019458
@@ -141031,7 +140999,7 @@ synonym: "nopaline breakdown" EXACT []
synonym: "nopaline catabolism" EXACT []
synonym: "nopaline degradation" EXACT []
xref: MetaCyc:NOPALINEDEG-PWY
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0042219 ! cellular modified amino acid catabolic process
is_a: GO:0046418 ! nopaline metabolic process
@@ -141057,9 +141025,11 @@ synonym: "4-hydroxyproline breakdown" EXACT []
synonym: "4-hydroxyproline catabolism" EXACT []
synonym: "4-hydroxyproline degradation" EXACT []
xref: MetaCyc:HYDROXYPRODEG-PWY
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0019471 ! 4-hydroxyproline metabolic process
is_a: GO:0042219 ! cellular modified amino acid catabolic process
+is_a: GO:0046700 ! heterocycle catabolic process
+is_a: GO:1901361 ! organic cyclic compound catabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
[Term]
@@ -141069,6 +141039,8 @@ namespace: biological_process
def: "The chemical reactions and pathways involving 4-hydroxyproline, C5H9NO3, a derivative of the amino acid proline. The presence of hydroxyproline is essential to produce stable triple helical tropocollagen, hence the problems caused by ascorbate deficiency in scurvy. This unusual amino acid is also present in considerable amounts in the major glycoprotein of primary plant cell walls." [GOC:ai]
synonym: "4-hydroxyproline metabolism" EXACT []
is_a: GO:0006575 ! cellular modified amino acid metabolic process
+is_a: GO:0046483 ! heterocycle metabolic process
+is_a: GO:1901360 ! organic cyclic compound metabolic process
is_a: GO:1901605 ! alpha-amino acid metabolic process
[Term]
@@ -141080,8 +141052,10 @@ synonym: "4-hydroxyproline anabolism" EXACT []
synonym: "4-hydroxyproline biosynthesis" EXACT []
synonym: "4-hydroxyproline formation" EXACT []
synonym: "4-hydroxyproline synthesis" EXACT []
+is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0019471 ! 4-hydroxyproline metabolic process
is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
[Term]
@@ -141103,6 +141077,7 @@ synonym: "L-lysine breakdown to acetyl-CoA" EXACT []
synonym: "L-lysine degradation to acetyl-CoA" EXACT []
is_a: GO:0006084 ! acetyl-CoA metabolic process
is_a: GO:0019477 ! L-lysine catabolic process
+is_a: GO:0043605 ! amide catabolic process
[Term]
id: GO:0019475
@@ -141148,7 +141123,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of D-amino
synonym: "D-amino acid breakdown" EXACT []
synonym: "D-amino acid catabolism" EXACT []
synonym: "D-amino acid degradation" EXACT []
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0046416 ! D-amino acid metabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
@@ -141185,7 +141160,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving beta-alanine (3-aminopropanoic acid), an achiral amino acid and an isomer of alanine. It occurs free (e.g. in brain) and in combination (e.g. in pantothenate) but it is not a constituent of proteins." [GOC:jl, ISBN:0198506732]
synonym: "beta-alanine metabolism" EXACT []
xref: Wikipedia:Beta-alanine
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
[Term]
id: GO:0019483
@@ -141196,7 +141171,7 @@ synonym: "beta-alanine anabolism" EXACT []
synonym: "beta-alanine biosynthesis" EXACT []
synonym: "beta-alanine formation" EXACT []
synonym: "beta-alanine synthesis" EXACT []
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
+is_a: GO:0008652 ! amino acid biosynthetic process
is_a: GO:0019482 ! beta-alanine metabolic process
[Term]
@@ -141207,7 +141182,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of beta-ala
synonym: "beta-alanine breakdown" EXACT []
synonym: "beta-alanine catabolism" EXACT []
synonym: "beta-alanine degradation" EXACT []
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0019482 ! beta-alanine metabolic process
[Term]
@@ -141244,7 +141219,6 @@ xref: MetaCyc:P161-PWY
is_a: GO:0018864 ! acetylene metabolic process
is_a: GO:0042178 ! xenobiotic catabolic process
is_a: GO:0043454 ! alkyne catabolic process
-is_a: GO:0120245 ! terminal acetylenic compound catabolic process
[Term]
id: GO:0019488
@@ -141359,7 +141333,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving cyanide, NC-, the anion of hydrocyanic acid. Cyanide is a potent inhibitor of respiration, reacting with the ferric form of cytochrome aa3 and thus blocking the electron transport chain." [ISBN:0198506732]
synonym: "cyanide metabolism" EXACT []
is_a: GO:0034641 ! cellular nitrogen compound metabolic process
-is_a: GO:0071704 ! organic substance metabolic process
+is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
id: GO:0019500
@@ -141372,7 +141346,7 @@ synonym: "cyanide degradation" EXACT []
xref: MetaCyc:P401-PWY
is_a: GO:0019499 ! cyanide metabolic process
is_a: GO:0044270 ! cellular nitrogen compound catabolic process
-is_a: GO:1901575 ! organic substance catabolic process
+is_a: GO:1901565 ! organonitrogen compound catabolic process
[Term]
id: GO:0019501
@@ -141383,15 +141357,16 @@ synonym: "arsonoacetate breakdown" EXACT []
synonym: "arsonoacetate catabolism" EXACT []
synonym: "arsonoacetate degradation" EXACT []
xref: MetaCyc:P482-PWY
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0018872 ! arsonoacetate metabolic process
is_a: GO:0042178 ! xenobiotic catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
[Term]
id: GO:0019502
-name: stachydrine metabolic process
+name: L-proline betaine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving stachydrine, N-methylproline methylbetaine, the betaine derivative of L-proline found in alfalfa, chrysanthemum, and citrus plants." [GOC:curators, MetaCyc:CPD-821]
+def: "The chemical reactions and pathways involving stachydrine, N-methylproline methylbetaine, the betaine derivative of L-proline found in alfalfa, chrysanthemum, and citrus plants." [GOC:curators]
+synonym: "stachydrine metabolic process" EXACT []
synonym: "stachydrine metabolism" EXACT []
is_a: GO:0006577 ! amino-acid betaine metabolic process
is_a: GO:0009820 ! alkaloid metabolic process
@@ -141399,30 +141374,33 @@ is_a: GO:1901605 ! alpha-amino acid metabolic process
[Term]
id: GO:0019503
-name: stachydrine biosynthetic process
+name: L-proline betaine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of stachydrine, N-methylproline methylbetaine, the betaine derivative of L-proline." [GOC:ai]
+def: "The chemical reactions and pathways resulting in the formation of stachydrine, N-methylproline methylbetaine, the betaine derivative of L-proline." [GOC:ai, PMID:14367364]
synonym: "stachydrine anabolism" EXACT []
synonym: "stachydrine biosynthesis" EXACT []
+synonym: "stachydrine biosynthetic process" EXACT []
synonym: "stachydrine formation" EXACT []
synonym: "stachydrine synthesis" EXACT []
is_a: GO:0006578 ! amino-acid betaine biosynthetic process
is_a: GO:0009821 ! alkaloid biosynthetic process
-is_a: GO:0019502 ! stachydrine metabolic process
+is_a: GO:0019502 ! L-proline betaine metabolic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
[Term]
id: GO:0019504
-name: stachydrine catabolic process
+name: L-proline betaine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of stachydrine, N-methylproline methylbetaine, the betaine derivative of L-proline." [GOC:ai]
+def: "The chemical reactions and pathways resulting in the breakdown of stachydrine, N-methylproline methylbetaine, the betaine derivative of L-proline." [PMID:10689197, PMID:1804402, PMID:24520058]
synonym: "stachydrine breakdown" EXACT []
+synonym: "stachydrine catabolic process" EXACT []
synonym: "stachydrine catabolism" EXACT []
synonym: "stachydrine degradation" EXACT []
xref: MetaCyc:P561-PWY
is_a: GO:0006579 ! amino-acid betaine catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:0019502 ! stachydrine metabolic process
+is_a: GO:0019502 ! L-proline betaine metabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
[Term]
@@ -141497,7 +141475,7 @@ synonym: "S-adenosylhomocysteine breakdown" EXACT []
synonym: "S-adenosylhomocysteine catabolism" EXACT []
synonym: "S-adenosylhomocysteine degradation" EXACT []
xref: MetaCyc:ADENOSYLHOMOCYSCAT-PWY
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0042219 ! cellular modified amino acid catabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
is_a: GO:0046130 ! purine ribonucleoside catabolic process
@@ -141603,8 +141581,8 @@ name: aldonic acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving aldonic acid, a monocarboxylic acid with a chain of three or more carbon atoms, derived from an aldose by oxidation of the aldehydic group." [ISBN:0198506732]
synonym: "aldonic acid metabolism" EXACT []
+is_a: GO:0005975 ! carbohydrate metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
[Term]
id: GO:0019521
@@ -141612,6 +141590,7 @@ name: D-gluconate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving D-gluconate, the anion of D-gluconic acid, the aldonic acid derived from glucose." [ISBN:0198506732]
synonym: "D-gluconate metabolism" EXACT []
+is_a: GO:0009311 ! oligosaccharide metabolic process
is_a: GO:0019520 ! aldonic acid metabolic process
[Term]
@@ -141697,9 +141676,7 @@ synonym: "taurine breakdown" EXACT []
synonym: "taurine catabolism" EXACT []
synonym: "taurine degradation" EXACT []
xref: MetaCyc:TAURINEDEG-PWY
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0019530 ! taurine metabolic process
-is_a: GO:0044273 ! sulfur compound catabolic process
is_a: GO:0046306 ! alkanesulfonate catabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
@@ -141709,8 +141686,6 @@ name: taurine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving taurine (2-aminoethanesulfonic acid), a sulphur-containing amino acid derivative important in the metabolism of fats." [GOC:jl, ISBN:0198600461]
synonym: "taurine metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
-is_a: GO:0006790 ! sulfur compound metabolic process
is_a: GO:0019694 ! alkanesulfonate metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
@@ -141721,7 +141696,7 @@ namespace: molecular_function
def: "Enables the transfer of oxalate from one side of a membrane to the other. Oxalate, or ethanedioic acid, occurs in many plants and is highly toxic to animals." [ISBN:0198506732]
synonym: "oxalic acid transporter activity" EXACT []
is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0019532
@@ -141732,7 +141707,7 @@ synonym: "ethanedioate transport" EXACT []
synonym: "ethanedioic acid transport" EXACT []
synonym: "oxalic acid transport" EXACT []
is_a: GO:0006835 ! dicarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
+is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0019533
@@ -141763,7 +141738,7 @@ def: "The chemical reactions and pathways involving vibriobactin, the major side
synonym: "vibriobactin metabolism" EXACT []
is_a: GO:0006725 ! cellular aromatic compound metabolic process
is_a: GO:0009237 ! siderophore metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
@@ -141793,6 +141768,7 @@ id: GO:0019538
name: protein metabolic process
namespace: biological_process
alt_id: GO:0006411
+alt_id: GO:0044267
alt_id: GO:0044268
def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma]
subset: goslim_agr
@@ -141800,6 +141776,8 @@ subset: goslim_flybase_ribbon
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
+synonym: "cellular protein metabolic process" EXACT []
+synonym: "cellular protein metabolism" EXACT []
synonym: "multicellular organismal protein metabolic process" NARROW []
synonym: "protein metabolic process and modification" EXACT []
synonym: "protein metabolism" EXACT []
@@ -141836,6 +141814,7 @@ def: "The chemical reactions and pathways involving propionate, the anion derive
synonym: "propanoate metabolic process" EXACT []
synonym: "propanoate metabolism" EXACT []
synonym: "propionate metabolism" EXACT []
+is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0046459 ! short-chain fatty acid metabolic process
[Term]
@@ -141872,6 +141851,7 @@ xref: MetaCyc:ARG-GLU-PWY
xref: MetaCyc:ARGASEDEG-PWY
is_a: GO:0006527 ! arginine catabolic process
is_a: GO:0006536 ! glutamate metabolic process
+is_a: GO:0043605 ! amide catabolic process
[Term]
id: GO:0019545
@@ -142010,6 +141990,7 @@ synonym: "histidine degradation to glutamate and formamide" EXACT []
xref: MetaCyc:HISDEG-PWY
is_a: GO:0006536 ! glutamate metabolic process
is_a: GO:0006548 ! histidine catabolic process
+is_a: GO:0043605 ! amide catabolic process
is_a: GO:0043606 ! formamide metabolic process
[Term]
@@ -142022,6 +142003,7 @@ synonym: "histidine degradation to glutamate and formate" EXACT []
is_a: GO:0006536 ! glutamate metabolic process
is_a: GO:0006548 ! histidine catabolic process
is_a: GO:0015942 ! formate metabolic process
+is_a: GO:0043605 ! amide catabolic process
[Term]
id: GO:0019558
@@ -142246,7 +142228,6 @@ name: aldaric acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving aldaric acid, any dicarboxylic acid formed by oxidation of by the terminal groups of an aldose to carboxyl group." [ISBN:0198506732]
synonym: "aldaric acid metabolism" EXACT []
-is_a: GO:0005975 ! carbohydrate metabolic process
is_a: GO:0043648 ! dicarboxylic acid metabolic process
[Term]
@@ -142269,7 +142250,6 @@ def: "The chemical reactions and pathways resulting in the breakdown of aldaric
synonym: "aldaric acid breakdown" EXACT []
synonym: "aldaric acid catabolism" EXACT []
synonym: "aldaric acid degradation" EXACT []
-is_a: GO:0016052 ! carbohydrate catabolic process
is_a: GO:0019577 ! aldaric acid metabolic process
is_a: GO:0043649 ! dicarboxylic acid catabolic process
@@ -142658,12 +142638,13 @@ synonym: "protocatechuate degradation, ortho-cleavage" EXACT []
xref: MetaCyc:PROTOCATECHUATE-ORTHO-CLEAVAGE-PWY
is_a: GO:0019619 ! 3,4-dihydroxybenzoate catabolic process
is_a: GO:0043648 ! dicarboxylic acid metabolic process
+is_a: GO:1901568 ! fatty acid derivative metabolic process
[Term]
id: GO:0019619
name: 3,4-dihydroxybenzoate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 3,4-dihydroxybenzoate." [GOC:ai]
+def: "The chemical reactions and pathways resulting in the breakdown of 3,4-dihydroxybenzoate." [GOC:ai]
synonym: "protocatechuate breakdown" EXACT []
synonym: "protocatechuate catabolic process" EXACT []
synonym: "protocatechuate catabolism" EXACT []
@@ -142715,6 +142696,7 @@ synonym: "atrazine breakdown to urea" EXACT []
synonym: "atrazine degradation to urea" EXACT []
is_a: GO:0019381 ! atrazine catabolic process
is_a: GO:0019627 ! urea metabolic process
+is_a: GO:0043605 ! amide catabolic process
[Term]
id: GO:0019624
@@ -142741,7 +142723,7 @@ is_a: GO:0042199 ! cyanuric acid metabolic process
id: GO:0019626
name: short-chain fatty acid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of fatty acids with a chain length of less than C6." [ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a fatty acid with an aliphatic tail of less than 6 carbons." [ISBN:0198506732]
synonym: "short-chain fatty acid breakdown" EXACT []
synonym: "short-chain fatty acid catabolism" EXACT []
synonym: "short-chain fatty acid degradation" EXACT []
@@ -142755,7 +142737,7 @@ name: urea metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving urea, the water soluble compound O=C-(NH2)2." [ISBN:0198506732]
synonym: "urea metabolism" EXACT []
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0044281 ! small molecule metabolic process
is_a: GO:0071941 ! nitrogen cycle metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
@@ -142772,7 +142754,7 @@ synonym: "uric acid catabolic process" EXACT []
xref: MetaCyc:P165-PWY
is_a: GO:0044282 ! small molecule catabolic process
is_a: GO:0046415 ! urate metabolic process
-is_a: GO:1901575 ! organic substance catabolic process
+is_a: GO:0072523 ! purine-containing compound catabolic process
[Term]
id: GO:0019629
@@ -143005,6 +142987,7 @@ synonym: "citrate fermentation to diacetyl" EXACT []
synonym: "diacetyl fermentation" EXACT []
is_a: GO:0006101 ! citrate metabolic process
is_a: GO:0019662 ! non-glycolytic fermentation
+is_a: GO:0019666 ! nitrogenous compound fermentation
is_a: GO:0042180 ! cellular ketone metabolic process
is_a: GO:0072352 ! tricarboxylic acid catabolic process
@@ -143043,15 +143026,20 @@ namespace: biological_process
def: "The anaerobic chemical reactions and pathways resulting in the breakdown of acetate, yielding energy in the form of ATP." [GOC:jl, MetaCyc:P142-PWY]
xref: MetaCyc:P142-PWY
is_a: GO:0006083 ! acetate metabolic process
-is_a: GO:0006113 ! fermentation
+is_a: GO:0019666 ! nitrogenous compound fermentation
[Term]
id: GO:0019655
name: glycolytic fermentation to ethanol
namespace: biological_process
+alt_id: GO:0043458
def: "The anaerobic chemical reactions and pathways resulting in the breakdown of glucose; it is converted into ethanol and carbon dioxide (CO2), producing two molecules of ATP for each molecule of glucose." [GOC:dph, GOC:nr, ISBN:0716720094]
synonym: "alcoholic fermentation" RELATED [ISBN:0716720094]
+synonym: "ethanol anabolism during fermentation" RELATED []
+synonym: "ethanol biosynthetic process involved in glucose fermentation to ethanol" RELATED []
synonym: "ethanol fermentation" EXACT []
+synonym: "ethanol formation during fermentation" RELATED []
+synonym: "ethanol synthesis during fermentation" RELATED []
synonym: "glucose catabolic process to ethanol" EXACT [GOC:dph]
synonym: "glucose fermentation to ethanol" EXACT []
xref: Wikipedia:Ethanol_fermentation
@@ -143069,9 +143057,9 @@ synonym: "heterofermentative pathway" EXACT []
synonym: "heterolactate fermentation" EXACT []
synonym: "heterolactic fermentation" EXACT []
xref: MetaCyc:P122-PWY
+is_a: GO:0006067 ! ethanol metabolic process
is_a: GO:0019659 ! glucose catabolic process to lactate
is_a: GO:0019662 ! non-glycolytic fermentation
-is_a: GO:1902707 ! hexose catabolic process to ethanol
[Term]
id: GO:0019657
@@ -143115,7 +143103,6 @@ namespace: biological_process
def: "Fermentation that includes the anaerobic conversion of glucose to pyruvate via the glycolytic pathway." [GOC:curators]
xref: MetaCyc:Pyruvate-Degredation
is_a: GO:0006113 ! fermentation
-is_a: GO:0046034 ! ATP metabolic process
[Term]
id: GO:0019661
@@ -143129,10 +143116,8 @@ synonym: "homofermentative pathway" EXACT []
synonym: "homolactate fermentation" EXACT []
synonym: "homolactic fermentation" EXACT [ISBN:0716720094]
xref: MetaCyc:ANAEROFRUCAT-PWY
-is_a: GO:0006734 ! NADH metabolic process
is_a: GO:0019659 ! glucose catabolic process to lactate
is_a: GO:0019660 ! glycolytic fermentation
-is_a: GO:0019674 ! NAD metabolic process
[Term]
id: GO:0019662
@@ -143157,7 +143142,7 @@ name: anaerobic amino acid catabolic process
namespace: biological_process
def: "The anaerobic chemical reactions and pathways resulting in the breakdown of amino acids, yielding energy in the form of ATP." [GOC:curators, GOC:jl, MetaCyc:Fermentation]
synonym: "amino acid fermentation" EXACT []
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0019666 ! nitrogenous compound fermentation
[Term]
@@ -143243,7 +143228,8 @@ synonym: "oxidized NAD metabolic process" EXACT []
synonym: "oxidized NAD metabolism" EXACT []
synonym: "oxidized nicotinamide adenine dinucleotide metabolic process" EXACT []
synonym: "oxidized nicotinamide adenine dinucleotide metabolism" EXACT []
-is_a: GO:0008152 ! metabolic process
+is_a: GO:0006163 ! purine nucleotide metabolic process
+is_a: GO:0046496 ! nicotinamide nucleotide metabolic process
[Term]
id: GO:0019675
@@ -143295,8 +143281,9 @@ synonym: "reduced NAD catabolic process" EXACT []
synonym: "reduced NAD catabolism" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide catabolic process" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide catabolism" EXACT []
+is_a: GO:0006195 ! purine nucleotide catabolic process
is_a: GO:0019364 ! pyridine nucleotide catabolic process
-is_a: GO:0046496 ! nicotinamide nucleotide metabolic process
+is_a: GO:0019674 ! NAD metabolic process
[Term]
id: GO:0019678
@@ -143464,7 +143451,8 @@ synonym: "alkanesulfonate metabolism" EXACT []
synonym: "alkanesulphonate metabolic process" EXACT []
synonym: "alkanesulphonate metabolism" EXACT []
xref: MetaCyc:ALKANEMONOX-PWY
-is_a: GO:0071704 ! organic substance metabolic process
+is_a: GO:0006082 ! organic acid metabolic process
+is_a: GO:0006790 ! sulfur compound metabolic process
[Term]
id: GO:0019695
@@ -143472,8 +143460,8 @@ name: choline metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine." [GOC:jl, ISBN:0192801023]
synonym: "choline metabolism" EXACT []
-is_a: GO:0071704 ! organic substance metabolic process
is_a: GO:0097164 ! ammonium ion metabolic process
+is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
id: GO:0019696
@@ -143532,11 +143520,13 @@ is_a: GO:0035246 ! peptidyl-arginine N-methylation
[Term]
id: GO:0019702
-name: protein-arginine N5-methyltransferase activity
+name: protein arginine N5-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the delta-nitrogen atom of peptidyl-arginine residues. The reaction is S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N5-methyl-L-arginine." [EC:2.1.1.322, PMID:9873020]
-comment: This enzyme, characterized from the yeast Saccharomyces cerevisiae, methylates the delta-nitrogen atom of arginine residues within proteins. Among its substrates are Arg67 of the ribosomal protein L12.
+def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the delta-nitrogen atom of peptidyl-arginine residues. The reaction is S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N5-methyl-L-arginine." [EC:2.1.1.322, PMID:11856739, PMID:9873020]
+comment: This enzyme, characterized from the yeast Saccharomyces cerevisiae, methylates the delta-nitrogen atom of arginine residues within proteins. Among its substrates are R67 of the ribosomal protein L12.
+synonym: "protein arginine N5-methylase activity" EXACT []
synonym: "protein-arginine delta-N-methyltransferase activity" EXACT []
+synonym: "protein-arginine N5-methyltransferase activity" EXACT []
synonym: "S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-N5-methyl-L-arginine-forming)" RELATED [EC:2.1.1.322]
synonym: "type IV PRMT activity" EXACT []
synonym: "type IV protein arginine methyltransferase activity" EXACT []
@@ -143584,6 +143574,7 @@ xref: EC:2.3.1.225
xref: Reactome:R-HSA-5682084 "ZDHCC8 transfers PALM from PALM-CoA to ABCA1 tetramer"
xref: Reactome:R-HSA-9021072 "ZDHHC7, ZDHHC21 palmitoylate ESR1"
xref: Reactome:R-HSA-9647982 "S-farn Me-HRAS, -NRAS and -KRAS4A are palmitoylated"
+xref: Reactome:R-HSA-9694341 "Spike protein gets palmitoylated"
xref: RHEA:36683
is_a: GO:0016409 ! palmitoyltransferase activity
is_a: GO:0019707 ! protein-cysteine S-acyltransferase activity
@@ -143624,13 +143615,12 @@ is_a: GO:0018283 ! iron incorporation into metallo-sulfur cluster
[Term]
id: GO:0019710
-name: peptidyl-asparagine methylation
+name: obsolete peptidyl-asparagine methylation
namespace: biological_process
alt_id: GO:0018018
-def: "The methylation of peptidyl-asparagine to form peptidyl-N4-methyl-L-asparagine or peptidyl-N4,N4-dimethyl-L-asparagine." [RESID:AA0070, RESID:AA0311]
-xref: RESID:AA0070
-xref: RESID:AA0311
-is_a: GO:0018196 ! peptidyl-asparagine modification
+def: "OBSOLETE. The methylation of peptidyl-asparagine to form peptidyl-N4-methyl-L-asparagine or peptidyl-N4,N4-dimethyl-L-asparagine." [RESID:AA0070, RESID:AA0311]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0019711
@@ -143644,35 +143634,33 @@ is_a: GO:0018197 ! peptidyl-aspartic acid modification
[Term]
id: GO:0019712
-name: peptidyl-L-glutamic acid 5-methyl ester biosynthetic process from glutamic acid
+name: obsolete peptidyl-L-glutamic acid 5-methyl ester biosynthetic process from glutamic acid
namespace: biological_process
-def: "The methyl esterification of peptidyl-glutamic acid." [RESID:AA0072]
+def: "OBSOLETE. The methyl esterification of peptidyl-glutamic acid." [RESID:AA0072]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-L-glutamic acid 5-methyl ester anabolism from glutamic acid" EXACT []
synonym: "peptidyl-L-glutamic acid 5-methyl ester formation from glutamic acid" EXACT []
synonym: "peptidyl-L-glutamic acid 5-methyl ester synthesis from glutamic acid" EXACT []
-xref: RESID:AA0072
-is_a: GO:0018390 ! peptidyl-L-glutamic acid 5-methyl ester biosynthetic process from peptidyl-glutamic acid or peptidyl-glutamine
+is_obsolete: true
[Term]
id: GO:0019713
-name: peptidyl-L-glutamic acid 5-methyl ester biosynthetic process from glutamine
+name: obsolete peptidyl-L-glutamic acid 5-methyl ester biosynthetic process from glutamine
namespace: biological_process
-def: "The coupled methyl esterification and deamidation of peptidyl-glutamine." [RESID:AA0072]
+def: "OBSOLETE. The coupled methyl esterification and deamidation of peptidyl-glutamine." [RESID:AA0072]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-L-glutamic acid 5-methyl ester anabolism from glutamine" EXACT []
synonym: "peptidyl-L-glutamic acid 5-methyl ester formation from glutamine" EXACT []
synonym: "peptidyl-L-glutamic acid 5-methyl ester synthesis from glutamine" EXACT []
-xref: RESID:AA0072
-is_a: GO:0006541 ! glutamine metabolic process
-is_a: GO:0018390 ! peptidyl-L-glutamic acid 5-methyl ester biosynthetic process from peptidyl-glutamic acid or peptidyl-glutamine
-is_a: GO:0019714 ! peptidyl-glutamine esterification
+is_obsolete: true
[Term]
id: GO:0019714
-name: peptidyl-glutamine esterification
+name: obsolete peptidyl-glutamine esterification
namespace: biological_process
-def: "The addition of an ester group to a glutamine residue in a protein." [GOC:mah]
-is_a: GO:0018199 ! peptidyl-glutamine modification
-is_a: GO:0018350 ! protein esterification
+def: "OBSOLETE. The addition of an ester group to a glutamine residue in a protein." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0019715
@@ -143763,17 +143751,15 @@ id: GO:0019725
name: cellular homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state at the level of the cell." [GOC:isa_complete, GOC:jl, ISBN:0395825172]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_plant
-is_a: GO:0009987 ! cellular process
is_a: GO:0042592 ! homeostatic process
[Term]
id: GO:0019726
name: mevaldate reductase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-mevalonate + NADP(+) = H(+) + mevaldate + NADPH." [EC:1.1.1.33, RHEA:20193]
+def: "Catalysis of the reaction: (R)-mevalonate + NADP+ = H+ + mevaldate + NADPH." [EC:1.1.1.33, RHEA:20193]
synonym: "(R)-mevalonate:NADP+ oxidoreductase" RELATED [EC:1.1.1.33]
synonym: "mevaldate (reduced nicotinamide adenine dinucleotide phosphate) reductase" RELATED [EC:1.1.1.33]
xref: EC:1.1.1.33
@@ -143786,7 +143772,7 @@ is_a: GO:0004495 ! mevaldate reductase activity
id: GO:0019727
name: mevaldate reductase (NAD+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-mevalonate + NAD(+) = H(+) + mevaldate + NADH." [EC:1.1.1.32, RHEA:13221]
+def: "Catalysis of the reaction: (R)-mevalonate + NAD+ = H+ + mevaldate + NADH." [EC:1.1.1.32, RHEA:13221]
xref: EC:1.1.1.32
xref: KEGG_REACTION:R02246
xref: MetaCyc:MEVALDATE-REDUCTASE-RXN
@@ -143804,17 +143790,14 @@ is_a: GO:0018205 ! peptidyl-lysine modification
[Term]
id: GO:0019729
-name: peptide cross-linking via 2-imino-glutaminyl-5-imidazolinone glycine
+name: obsolete peptide cross-linking via 2-imino-glutaminyl-5-imidazolinone glycine
namespace: biological_process
-def: "The formation of the fluorescent protein FP583 chromophore cross-link from the alpha-carboxyl carbon of residue n, a glutamine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons." [RESID:AA0189]
-comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'.
+def: "OBSOLETE. The formation of the fluorescent protein FP583 chromophore cross-link from the alpha-carboxyl carbon of residue n, a glutamine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons." [RESID:AA0189]
+comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'. Term describes modified products or self-catalyzed processes.
synonym: "biosynthesis of protein-protein cross-link via 2-imino-glutaminyl-5-imidazolinone glycine" EXACT []
synonym: "biosynthetic process of protein-protein cross-link via 2-imino-glutaminyl-5-imidazolinone glycine" EXACT []
xref: RESID:AA0189
-is_a: GO:0018149 ! peptide cross-linking
-is_a: GO:0018199 ! peptidyl-glutamine modification
-is_a: GO:0018201 ! peptidyl-glycine modification
-is_a: GO:0018298 ! protein-chromophore linkage
+is_obsolete: true
[Term]
id: GO:0019730
@@ -143824,7 +143807,7 @@ alt_id: GO:0006960
alt_id: GO:0019735
def: "An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus." [GOC:go_curators, GOC:mtg_sensu]
is_a: GO:0006959 ! humoral immune response
-is_a: GO:0051707 ! response to other organism
+is_a: GO:0098542 ! defense response to other organism
[Term]
id: GO:0019731
@@ -143859,7 +143842,7 @@ id: GO:0019740
name: nitrogen utilization
namespace: biological_process
def: "A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary nitrogen source, usually ammonia, and then activates genes to scavenge the last traces of the primary nitrogen source and to transport and metabolize alternative nitrogen sources. The utilization process begins when the cell or organism detects nitrogen levels, includes the activation of genes whose products detect, transport or metabolize nitrogen-containing substances, and ends when nitrogen is incorporated into the cell or organism's metabolism." [GOC:mah, GOC:mlg]
-is_a: GO:0008150 ! biological_process
+is_a: GO:0031667 ! response to nutrient levels
[Term]
id: GO:0019741
@@ -143941,7 +143924,6 @@ id: GO:0019748
name: secondary metabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients." [GOC:go_curators]
-subset: goslim_aspergillus
subset: goslim_chembl
subset: goslim_pir
subset: goslim_plant
@@ -144174,6 +144156,7 @@ name: proteasome core complex, alpha-subunit complex
namespace: cellular_component
def: "The proteasome core subcomplex that constitutes the two outer rings of the proteasome core complex. An example of this component is found in Mus musculus." [GOC:jl, GOC:mtg_sensu, GOC:rb, PMID:10854779]
is_a: GO:0032991 ! protein-containing complex
+relationship: part_of GO:0005622 ! intracellular anatomical structure
relationship: part_of GO:0005839 ! proteasome core complex
[Term]
@@ -144182,6 +144165,7 @@ name: proteasome core complex, beta-subunit complex
namespace: cellular_component
def: "The proteasome core subcomplex that constitutes the two inner rings of the proteasome core complex. An example of this component is found in Mus musculus." [GOC:jl, GOC:mtg_sensu, GOC:rb, PMID:10854779]
is_a: GO:0032991 ! protein-containing complex
+relationship: part_of GO:0005622 ! intracellular anatomical structure
relationship: part_of GO:0005839 ! proteasome core complex
[Term]
@@ -144259,47 +144243,61 @@ is_a: GO:0008641 ! ubiquitin-like modifier activating enzyme activity
[Term]
id: GO:0019783
-name: ubiquitin-like protein-specific protease activity
+name: ubiquitin-like protein peptidase activity
namespace: molecular_function
+alt_id: GO:0070138
+alt_id: GO:0140491
alt_id: GO:1904454
alt_id: GO:1904455
-def: "Catalysis of the hydrolysis of peptide or isopeptide bonds within small proteins such as ubiquitin or ubiquitin-like proteins (e.g. APG8, ISG15, NEDD8, SUMO), or between the small protein and a larger protein to which it has been conjugated." [GOC:ma, GOC:mah]
+def: "An isopeptidase activity that cleaves ubiquitin or ubiquitin-like proteins (ULP; e.g. ATG8, ISG15, NEDD8, SUMO) from target proteins." [PMID:19489724]
+comment: While ubiquitin-like proteins can be rarely linked to substrates via bonds other than isopeptide bonds, all known ubiquitin-like peptidases cleave the isopeptide bond.
+synonym: "small conjugating protein-specific isopeptidase activity" EXACT [GOC:dph]
synonym: "small conjugating protein-specific protease activity" EXACT [GOC:dph]
+synonym: "ubiquitin-like hydrolase activity" EXACT []
+synonym: "ubiquitin-like protein-specific isopeptidase activity" EXACT []
+synonym: "ubiquitin-like protein-specific protease activity" EXACT []
synonym: "ubiquitin-like specific protease activity" NARROW []
synonym: "ubiquitin-like-protein-specific protease activity" NARROW []
synonym: "ubiquitin-specific protease activity involved in negative regulation of ERAD pathway" NARROW []
synonym: "ubiquitin-specific protease activity involved in positive regulation of ERAD pathway" NARROW []
-is_a: GO:0008234 ! cysteine-type peptidase activity
+synonym: "ubiquitinyl-like hydrolase activity" EXACT []
+is_a: GO:0008233 ! peptidase activity
[Term]
id: GO:0019784
-name: NEDD8-specific protease activity
+name: deNEDDylase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of NEDD8, a small ubiquitin-related modifier, from previously neddylated substrates." [GOC:mah]
-synonym: "deneddylase activity" EXACT [GOC:dph]
+def: "An isopeptidase activity that cleaves NEDD8 from a target protein to which it is conjugated." [GOC:mah, PMID:25628956]
+synonym: "NEDD8-specific protease activity" EXACT []
xref: Reactome:R-HSA-5690808 "UCHL3, SENP8 cleave NEDD8"
xref: Reactome:R-HSA-8863723 "COP9 and TOR1 deneddylate STON2"
xref: Reactome:R-HSA-8956040 "COP9 signalosome deneddylates cytosolic CRL E3 ubiquitin ligase complexes"
xref: Reactome:R-HSA-8956045 "COP9 signalosome deneddylates nuclear CRL4 E3 ubiquitin ligase complex"
-is_a: GO:0019783 ! ubiquitin-like protein-specific protease activity
+is_a: GO:0019783 ! ubiquitin-like protein peptidase activity
[Term]
id: GO:0019785
-name: ISG15-specific protease activity
+name: ISG15-specific peptidase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of ISG15, a small ubiquitin-related modifier, from previously modified substrates." [GOC:mah]
+def: "A thiol-dependent isopeptidase activity that cleaves ISG15 from a target protein to which it is conjugated." [GOC:mah, PMID:30213559]
+synonym: "ISG15-specific protease activity" EXACT []
xref: Reactome:R-HSA-1678841 "Regulation of protein ISGylation by ISG15 deconjugating enzyme USP18"
xref: Reactome:R-HSA-5653786 "USP43 deISGylates ISG:K164,ISG:K168-PCNA"
-is_a: GO:0019783 ! ubiquitin-like protein-specific protease activity
+xref: Reactome:R-HSA-9729725 "SARS-CoV-2 nsp3 deISGylates ISGylated IRF3"
+xref: Reactome:R-HSA-9755244 "SARS-CoV-2 nsp3 deISGylates ISGylated IFIH1"
+is_a: GO:0008234 ! cysteine-type peptidase activity
+is_a: GO:0019783 ! ubiquitin-like protein peptidase activity
[Term]
id: GO:0019786
-name: Atg8-specific protease activity
+name: Atg8-specific peptidase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of APG8, a small ubiquitin-related modifier." [GOC:mah]
+def: "A thiol-dependent isopeptidase activity that cleaves APG8 from a target protein to which it is conjugated." [GOC:mah, PMID:28901328]
synonym: "APG8-PE hydrolase" RELATED []
synonym: "APG8-specific protease activity" RELATED [GOC:vw]
-is_a: GO:0019783 ! ubiquitin-like protein-specific protease activity
+synonym: "Atg8-specific protease activity" EXACT []
+is_a: GO:0008234 ! cysteine-type peptidase activity
+is_a: GO:0019783 ! ubiquitin-like protein peptidase activity
[Term]
id: GO:0019787
@@ -144319,8 +144317,7 @@ synonym: "ubiquitin-like conjugating enzyme activity" NARROW []
synonym: "ubiquitin-like-protein ligase activity" NARROW []
xref: Reactome:R-HSA-5678490 "ATG16L1 complex transfers LC3 from ATG3 to PE"
xref: Reactome:R-HSA-688137 "RIP2 is K63 polyubiquitinated"
-is_a: GO:0016740 ! transferase activity
-is_a: GO:0140096 ! catalytic activity, acting on a protein
+is_a: GO:0016755 ! aminoacyltransferase activity
[Term]
id: GO:0019788
@@ -144338,6 +144335,8 @@ xref: Reactome:R-HSA-8951661 "Transfer of NEDD8 to AcM-UBE2M"
xref: Reactome:R-HSA-8951764 "Transfer of NEDD8 to AcM-UBE2F"
xref: Reactome:R-HSA-8952044 "AcM-UBE2F transfers NEDD8 to CRL5 E3 ubiquitin ligase complex"
xref: Reactome:R-HSA-8952618 "AcM-UBE2M transfers NEDD8 to CRL1 E3 ubiquitin ligase complex"
+xref: Reactome:R-HSA-8952626 "AcM-UBE2M transfers NEDD8 to CRL2 E3 ubiquitin ligase complex"
+xref: Reactome:R-HSA-8952631 "AcM-UBE2M transfers NEDD8 to CRL3 E3 ubiquitin ligase complex"
xref: Reactome:R-HSA-8952638 "AcM-UBE2M transfers NEDD8 to CRL4 E3 ubiquitin ligase complex"
xref: Reactome:R-HSA-8956025 "AcM-UBE2M transfers NEDD8 to CUL9:RBX1"
is_a: GO:0019787 ! ubiquitin-like protein transferase activity
@@ -144679,10 +144678,10 @@ is_a: GO:0072525 ! pyridine-containing compound biosynthetic process
id: GO:0019806
name: bromide peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 R-H + 2 bromide + hydrogen peroxide = 2 R-Br + 2 H2O. Enzymes with this activity often accept other halide ions as substrates, including chloride and iodide." [EC:1.11.1.18]
+def: "Catalysis of the reaction: 2 R-H + 2 bromide + H2O2 = 2 R-Br + 2 H2O. Enzymes with this activity often accept other halide ions as substrates, including chloride and iodide." [EC:1.11.1.18]
synonym: "bromoperoxidase activity" EXACT []
xref: EC:1.11.1.18
-is_a: GO:0004601 ! peroxidase activity
+is_a: GO:0140905 ! haloperoxidase activity
[Term]
id: GO:0019807
@@ -144872,7 +144871,7 @@ is_a: GO:0140299 ! small molecule sensor activity
id: GO:0019827
name: stem cell population maintenance
namespace: biological_process
-def: "The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types." [GOC:mah, ISBN:0878932437]
+def: "The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types." [GOC:mah, ISBN:0878932437]
synonym: "maintenance of pluripotency" RELATED [GOC:vk]
is_a: GO:0032501 ! multicellular organismal process
is_a: GO:0098727 ! maintenance of cell number
@@ -144881,23 +144880,24 @@ is_a: GO:0098727 ! maintenance of cell number
id: GO:0019828
name: aspartic-type endopeptidase inhibitor activity
namespace: molecular_function
-def: "Binds to and stops, prevents or reduces the activity of aspartic-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; the optimum reaction pH is below 5 due to an aspartic residue involved in the catalytic process." [GOC:ai]
+def: "Binds to and stops, prevents or reduces the activity of aspartic-type endopeptidases." [GOC:ai]
synonym: "aspartic protease inhibitor activity" NARROW []
is_a: GO:0004866 ! endopeptidase inhibitor activity
[Term]
id: GO:0019829
-name: ATPase-coupled cation transmembrane transporter activity
+name: ATPase-coupled monoatomic cation transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + cation(out) = ADP + phosphate + cation(in)." [GOC:ai]
synonym: "ATP-dependent cation transmembrane transporter activity" EXACT []
+synonym: "ATPase-coupled cation transmembrane transporter activity" BROAD []
synonym: "cation ABC transporter" NARROW []
synonym: "cation-transporting ATPase activity" EXACT []
synonym: "plasma membrane cation-transporting ATPase" NARROW []
xref: Reactome:R-HSA-5251989 "ATP13A4,5 transport divalent ions from extracellular region to cytosol"
xref: Reactome:R-HSA-5692480 "ATP13A2 transports cations from cytosol to lysosomal lumen"
-is_a: GO:0022853 ! active ion transmembrane transporter activity
-is_a: GO:0022890 ! inorganic cation transmembrane transporter activity
+is_a: GO:0008324 ! monoatomic cation transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
is_a: GO:0042626 ! ATPase-coupled transmembrane transporter activity
[Term]
@@ -145271,6 +145271,7 @@ id: GO:0019869
name: chloride channel inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents, or reduces the activity of a chloride channel." [GOC:mah]
+is_a: GO:0008200 ! ion channel inhibitor activity
is_a: GO:0017081 ! chloride channel regulator activity
[Term]
@@ -145300,6 +145301,7 @@ synonym: "streptomycin biosynthesis" EXACT []
synonym: "streptomycin formation" EXACT []
synonym: "streptomycin synthesis" EXACT []
is_a: GO:0030648 ! aminoglycoside antibiotic biosynthetic process
+is_a: GO:0044272 ! sulfur compound biosynthetic process
is_a: GO:0046173 ! polyol biosynthetic process
is_a: GO:0046343 ! streptomycin metabolic process
@@ -145317,7 +145319,7 @@ replaced_by: GO:0046690
id: GO:0019874
name: 6-aminohexanoate-cyclic-dimer hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,8-diazacyclotetradecane-2,9-dione + H(2)O = N-(6-aminohexanoyl)-6-aminohexanoate." [EC:3.5.2.12, RHEA:16225]
+def: "Catalysis of the reaction: 1,8-diazacyclotetradecane-2,9-dione + H2O = N-(6-aminohexanoyl)-6-aminohexanoate." [EC:3.5.2.12, RHEA:16225]
synonym: "1,8-diazacyclotetradecane-2,9-dione lactamhydrolase activity" RELATED [EC:3.5.2.12]
xref: EC:3.5.2.12
xref: KEGG_REACTION:R03448
@@ -145477,7 +145479,7 @@ alt_id: GO:0008599
alt_id: GO:0008601
alt_id: GO:0030359
alt_id: GO:0030362
-def: "Binds to and modulates the activity of a protein phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a protein substrate molecule." [GOC:ai]
+def: "Binds to and modulates the activity of a protein phosphatase." [GOC:ai]
synonym: "calcineurin regulator activity" NARROW [GOC:dph, GOC:rl]
synonym: "calcineurin, intrinsic regulator activity" NARROW [GOC:dph, GOC:rl]
synonym: "protein phosphatase 2 regulator activity" NARROW [GOC:dph, GOC:rl]
@@ -145651,6 +145653,7 @@ name: [pyruvate dehydrogenase (lipoamide)] phosphatase regulator activity
namespace: molecular_function
def: "Binds to and modulates of the activity of [pyruvate dehydrogenase (lipoamide)] phosphatase." [EC:3.1.3.43, GOC:ai]
synonym: "[pyruvate dehydrogenase (lipoamide)] phosphatase, intrinsic regulator activity" NARROW []
+xref: EC:3.1.3.43
is_a: GO:0019888 ! protein phosphatase regulator activity
[Term]
@@ -145765,19 +145768,20 @@ is_a: GO:0018173 ! peptidyl-1-thioglycine biosynthetic process from peptidyl-gly
[Term]
id: GO:0019922
-name: protein-chromophore linkage via peptidyl-cysteine
+name: obsolete protein-chromophore linkage via peptidyl-cysteine
namespace: biological_process
-def: "The covalent linking of a chromophore to a protein via peptidyl-cysteines." [GOC:ma]
-is_a: GO:0018198 ! peptidyl-cysteine modification
-is_a: GO:0018298 ! protein-chromophore linkage
+def: "OBSOLETE. The covalent linking of a chromophore to a protein via peptidyl-cysteines." [GOC:ma]
+comment: Term describes modified products or self-catalyzed processes.
+is_obsolete: true
[Term]
id: GO:0019923
-name: alpha-1-microglobulin-chromophore linkage
+name: obsolete alpha-1-microglobulin-chromophore linkage
namespace: biological_process
-def: "The covalent linking of the alpha-1-microglobulin chromophore to the protein; the structure of the chromophore is not known. It is probably heterogeneous and involving two cysteines in thioether bonds." [RESID:AA0224]
+def: "OBSOLETE. The covalent linking of the alpha-1-microglobulin chromophore to the protein; the structure of the chromophore is not known. It is probably heterogeneous and involving two cysteines in thioether bonds." [RESID:AA0224]
+comment: Term describes modified products or self-catalyzed processes.
xref: RESID:AA0224
-is_a: GO:0019922 ! protein-chromophore linkage via peptidyl-cysteine
+is_obsolete: true
[Term]
id: GO:0019926
@@ -145831,12 +145835,12 @@ is_a: GO:0018197 ! peptidyl-aspartic acid modification
[Term]
id: GO:0019931
-name: protein-chromophore linkage via peptidyl-N6-3-dehydroretinal-L-lysine
+name: obsolete protein-chromophore linkage via peptidyl-N6-3-dehydroretinal-L-lysine
namespace: biological_process
-def: "The modification of peptidyl-lysine to form N6-3,4-didehydroretinylidene-L-lysine." [RESID:AA0312]
+def: "OBSOLETE. The modification of peptidyl-lysine to form N6-3,4-didehydroretinylidene-L-lysine." [RESID:AA0312]
+comment: Term describes modified products or self-catalyzed processes.
xref: RESID:AA0312
-is_a: GO:0018205 ! peptidyl-lysine modification
-is_a: GO:0018298 ! protein-chromophore linkage
+is_obsolete: true
[Term]
id: GO:0019932
@@ -145900,21 +145904,20 @@ consider: GO:0048017
[Term]
id: GO:0019937
-name: protein catenane formation via N6-(L-isoaspartyl)-L-lysine, autocatalytic
+name: obsolete protein catenane formation via N6-(L-isoaspartyl)-L-lysine, autocatalytic
namespace: biological_process
-def: "The autocatalytic formation of isopeptide bonds by ligation of peptidyl-lysine and peptidyl-asparagine residues; known to occur in the capsid of some bacteriophage, such as HK97, where it is thought to provide a mechanism for stabilizing the capsid." [RESID:AA0294]
-xref: RESID:AA0294
-is_a: GO:0018419 ! protein catenane formation
-is_a: GO:0018420 ! peptide cross-linking via N6-(L-isoaspartyl)-L-lysine
+def: "OBSOLETE. The autocatalytic formation of isopeptide bonds by ligation of peptidyl-lysine and peptidyl-asparagine residues; known to occur in the capsid of some bacteriophage, such as HK97, where it is thought to provide a mechanism for stabilizing the capsid." [RESID:AA0294]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0019938
-name: peptide cross-linking via N6-(L-isoaspartyl)-L-lysine, presumed catalytic
+name: obsolete peptide cross-linking via N6-(L-isoaspartyl)-L-lysine, presumed catalytic
namespace: biological_process
alt_id: GO:0042266
-def: "The formation of isopeptide bonds by ligation of peptidyl-lysine and peptidyl-asparagine residues; occurs in mammals in proteins as yet unidentified by a mechanism probably analogous to that of transglutaminase reactions." [RESID:AA0294]
-xref: RESID:AA0294
-is_a: GO:0018420 ! peptide cross-linking via N6-(L-isoaspartyl)-L-lysine
+def: "OBSOLETE. The formation of isopeptide bonds by ligation of peptidyl-lysine and peptidyl-asparagine residues; occurs in mammals in proteins as yet unidentified by a mechanism probably analogous to that of transglutaminase reactions." [RESID:AA0294]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0019939
@@ -145958,7 +145961,7 @@ synonym: "protein degradation tagging activity" RELATED []
synonym: "protein-ligand-dependent protein catabolic process" NARROW []
synonym: "protein-ligand-dependent protein catabolism" NARROW []
is_a: GO:0043632 ! modification-dependent macromolecule catabolic process
-is_a: GO:0051603 ! proteolysis involved in cellular protein catabolic process
+is_a: GO:0051603 ! proteolysis involved in protein catabolic process
[Term]
id: GO:0019942
@@ -146005,17 +146008,16 @@ is_obsolete: true
id: GO:0019953
name: sexual reproduction
namespace: biological_process
-def: "A reproduction process that creates a new organism by combining the genetic material of two gametes, which may come from two organisms or from a single organism, in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two gametes join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny." [GOC:jl, GOC:kmv, GOC:krc, GOC:tb, ISBN:0387520546, Wikipedia:Sexual_reproduction]
-comment: Sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.
+def: "A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid)." [Wikipedia:Sexual_reproduction]
+comment: Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.
xref: Wikipedia:Sexual_reproduction
is_a: GO:0000003 ! reproduction
-is_a: GO:0044703 ! multi-organism reproductive process
[Term]
id: GO:0019954
name: asexual reproduction
namespace: biological_process
-def: "The biological process in which new individuals are produced by either a single cell or a group of cells, in the absence of any sexual process." [ISBN:0387520546]
+def: "A type of reproduction in which new individuals are produced from a single organism, either from an unfertilized egg or from a single cell or group of cells." [ISBN:0387520546, PMID:22977071, PMID:28779329, PMID:29559496]
synonym: "parthenogenesis" RELATED [Wikipedia:Parthenogenesis]
xref: Wikipedia:Asexual_reproduction
is_a: GO:0000003 ! reproduction
@@ -146093,12 +146095,12 @@ is_a: GO:0019961 ! interferon binding
[Term]
id: GO:0019964
-name: interferon-gamma binding
+name: type II interferon binding
namespace: molecular_function
-def: "Binding to interferon-gamma. Interferon gamma is the only member of the type II interferon found so far." [GOC:add, GOC:ai, ISBN:0126896631, PMID:15546383]
+def: "Binding to type II interferon, also known as interferon-gamma." [GOC:add, GOC:ai, ISBN:0126896631, PMID:15546383]
synonym: "IFN-gamma binding" EXACT [GOC:mah]
synonym: "IFNG binding" EXACT [GOC:mah]
-synonym: "type II interferon binding" BROAD [PMID:15546383, PR:000024990]
+synonym: "interferon-gamma binding" BROAD [PMID:15546383, PR:000024990]
is_a: GO:0019961 ! interferon binding
[Term]
@@ -146268,7 +146270,6 @@ synonym: "pre-translational protein modification" EXACT []
synonym: "pretranslation protein modification" EXACT []
synonym: "pretranslational amino acid modification" EXACT []
is_a: GO:0006400 ! tRNA modification
-is_a: GO:0006464 ! cellular protein modification process
[Term]
id: GO:0019990
@@ -146500,7 +146501,6 @@ synonym: "haemoglobin metabolic process" EXACT []
synonym: "haemoglobin metabolism" EXACT []
synonym: "hemoglobin metabolism" EXACT []
is_a: GO:0019538 ! protein metabolic process
-is_a: GO:0044260 ! cellular macromolecule metabolic process
[Term]
id: GO:0020028
@@ -146511,7 +146511,7 @@ synonym: "endocytic hemoglobin import" RELATED []
synonym: "haemoglobin uptake" EXACT []
synonym: "hemoglobin uptake" EXACT []
is_a: GO:0006898 ! receptor-mediated endocytosis
-is_a: GO:0017038 ! protein import
+is_a: GO:0015031 ! protein transport
is_a: GO:0072594 ! establishment of protein localization to organelle
is_a: GO:0098657 ! import into cell
@@ -146555,15 +146555,16 @@ is_a: GO:0042783 ! evasion of host immune response
[Term]
id: GO:0020035
-name: cytoadherence to microvasculature, mediated by symbiont protein
+name: adhesion of symbiont to microvasculature
namespace: biological_process
alt_id: GO:0043706
def: "The adherence of symbiont-infected erythrocytes to microvascular endothelium via symbiont proteins embedded in the membrane of the erythrocyte." [GOC:mb, PMID:10362584]
synonym: "cytoadherence to microvasculature, mediated by parasite protein" NARROW []
+synonym: "cytoadherence to microvasculature, mediated by symbiont protein" EXACT []
synonym: "heterophilic cell adhesion involved in cytoadherence to microvasculature, mediated by parasite protein" NARROW []
synonym: "parasite-protein-mediated cytoadherence to microvasculature" NARROW []
synonym: "symbiont-protein-mediated cytoadherence to microvasculature" BROAD []
-is_a: GO:0044406 ! adhesion of symbiont to host
+is_a: GO:0044650 ! adhesion of symbiont to host cell
[Term]
id: GO:0020036
@@ -146994,7 +146995,7 @@ synonym: "MHB formation" EXACT [GOC:cls]
synonym: "midbrain-hindbrain boundary biosynthesis" EXACT [GOC:cls]
synonym: "midbrain-hindbrain boundary formation" EXACT [GOC:cls]
is_a: GO:0003002 ! regionalization
-is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
+is_a: GO:0048859 ! formation of anatomical boundary
relationship: part_of GO:0021999 ! neural plate anterior/posterior regionalization
relationship: part_of GO:0030917 ! midbrain-hindbrain boundary development
@@ -149024,7 +149025,7 @@ relationship: part_of GO:0021520 ! spinal cord motor neuron cell fate specificat
id: GO:0021777
name: obsolete BMP signaling pathway involved in spinal cord association neuron specification
namespace: biological_process
-def: "OBSOLETE. A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to its commitment to an association neuron fate." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12593981]
+def: "OBSOLETE. The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to its commitment to an association neuron fate." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12593981]
comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "BMP signalling pathway involved in spinal cord association neuron specification" EXACT []
synonym: "bone morphogenetic protein signaling pathway involved in spinal cord association neuron specification" EXACT []
@@ -150127,8 +150128,8 @@ id: GO:0021905
name: forebrain-midbrain boundary formation
namespace: biological_process
def: "The process whose specific outcome is the creation of the forebrain-midbrain boundary." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:11262869]
-is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
is_a: GO:0048856 ! anatomical structure development
+is_a: GO:0048859 ! formation of anatomical boundary
relationship: part_of GO:0021903 ! rostrocaudal neural tube patterning
[Term]
@@ -150264,7 +150265,7 @@ consider: GO:0021917
id: GO:0021919
name: BMP signaling pathway involved in spinal cord dorsal/ventral patterning
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the spatial identity of regions along the dorsal-ventral axis of the spinal cord." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12593981]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the spatial identity of regions along the dorsal-ventral axis of the spinal cord." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12593981]
synonym: "BMP signaling pathway in spinal cord dorsoventral patterning" EXACT [GOC:mah]
synonym: "BMP signaling pathway involved in spinal cord dorsal-ventral patterning" EXACT [GOC:mah]
synonym: "BMP signalling pathway involved in spinal cord dorsal-ventral patterning" EXACT []
@@ -151178,7 +151179,7 @@ relationship: part_of GO:0021861 ! forebrain radial glial cell differentiation
id: GO:0022024
name: BMP signaling pathway involved in forebrain neuron fate commitment
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the commitment of a neuroblast to a neuronal fate. The neuron will reside in the forebrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the commitment of a neuroblast to a neuronal fate. The neuron will reside in the forebrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid]
synonym: "BMP signalling pathway involved in forebrain neuron fate commitment" EXACT []
synonym: "bone morphogenetic protein signaling pathway involved in forebrain neuron fate commitment" EXACT []
synonym: "bone morphogenetic protein signalling pathway involved in forebrain neuron fate commitment" EXACT []
@@ -151189,7 +151190,7 @@ relationship: part_of GO:0021898 ! commitment of multipotent stem cells to neuro
id: GO:0022025
name: leukemia inhibitory factor signaling pathway involved in forebrain neuron fate commitment
namespace: biological_process
-def: "Any series of molecular signals initiated by the binding of leukemia inhibitory factor to a receptor on the surface of the target cell, that contributes to the commitment of a neuroblast to a neuronal fate. The neuron will reside in the forebrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:signaling]
+def: "The series of molecular signals initiated by the binding of leukemia inhibitory factor to its receptor on the surface of the target cell, that contributes to the commitment of a neuroblast to a neuronal fate. The neuron will reside in the forebrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, GOC:signaling]
synonym: "leukemia inhibitory factor signalling pathway involved in forebrain neuron fate commitment" EXACT []
is_a: GO:0048861 ! leukemia inhibitory factor signaling pathway
relationship: part_of GO:0021898 ! commitment of multipotent stem cells to neuronal lineage in forebrain
@@ -151542,7 +151543,6 @@ id: GO:0022608
name: multicellular organism adhesion
namespace: biological_process
def: "The attachment of a multicellular organism to a substrate or other organism." [GOC:isa_complete]
-is_a: GO:0022610 ! biological adhesion
is_a: GO:0032501 ! multicellular organismal process
[Term]
@@ -151554,11 +151554,11 @@ is_a: GO:0022608 ! multicellular organism adhesion
[Term]
id: GO:0022610
-name: biological adhesion
+name: obsolete biological adhesion
namespace: biological_process
-def: "The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions." [GOC:isa_complete]
-subset: goslim_pir
-is_a: GO:0008150 ! biological_process
+def: "OBSOLETE. The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions." [GOC:isa_complete]
+comment: This term was obsoleted because it represents an unnecessary grouping class by mixing cellular and multi-cellular organism level processes.
+is_obsolete: true
[Term]
id: GO:0022611
@@ -151620,15 +151620,15 @@ is_a: GO:0030198 ! extracellular matrix organization
[Term]
id: GO:0022618
-name: ribonucleoprotein complex assembly
+name: protein-RNA complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex." [GOC:jl]
subset: goslim_chembl
-synonym: "protein-RNA complex assembly" EXACT []
+synonym: "ribonucleoprotein complex assembly" EXACT []
synonym: "RNA-protein complex assembly" EXACT []
synonym: "RNP complex assembly" EXACT []
is_a: GO:0065003 ! protein-containing complex assembly
-is_a: GO:0071826 ! ribonucleoprotein complex subunit organization
+is_a: GO:0071826 ! protein-RNA complex organization
relationship: part_of GO:0022613 ! ribonucleoprotein complex biogenesis
[Term]
@@ -151641,10 +151641,11 @@ relationship: part_of GO:0055046 ! microgametogenesis
[Term]
id: GO:0022620
-name: vegetative cell differentiation
+name: microgametophyte vegetative cell differentiation
namespace: biological_process
-def: "The process in which a relatively unspecialized cell acquires specialized features of a vegetative cell. The vegetative cell is gives rise to the pollen tube." [GOC:isa_complete]
-synonym: "tube cell differentiation" EXACT []
+def: "The process in which a relatively unspecialized cell acquires specialized features of a microgametophyte. The microgametophyte vegetative cell gives rise to the pollen tube." [GOC:isa_complete]
+synonym: "tube cell differentiation" RELATED []
+synonym: "vegetative cell differentiation" RELATED []
is_a: GO:0030154 ! cell differentiation
relationship: part_of GO:0055046 ! microgametogenesis
@@ -151795,7 +151796,7 @@ namespace: molecular_function
def: "Catalysis of the active transport of a sodium ion across a membrane by a mechanism involving conformational change, where energy for active transport is derived from membrane potential if the solute is charged." [GOC:mtg_transport, ISBN:0815340729]
is_a: GO:0015081 ! sodium ion transmembrane transporter activity
is_a: GO:0022810 ! membrane potential driven uniporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0022819
@@ -151804,24 +151805,25 @@ namespace: molecular_function
def: "Catalysis of the active transport of a potassium ion across a membrane by a mechanism involving conformational change, where energy for active transport is derived from membrane potential if the solute is charged." [GOC:mtg_transport, ISBN:0815340729]
is_a: GO:0015079 ! potassium ion transmembrane transporter activity
is_a: GO:0022810 ! membrane potential driven uniporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0022821
-name: potassium ion antiporter activity
+name: solute:potassium antiporter activity
namespace: molecular_function
def: "Catalysis of the active transport of a potassium ion across a membrane by a mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy." [GOC:mtg_transport, ISBN:0815340729]
-is_a: GO:0008509 ! anion transmembrane transporter activity
+synonym: "potassium ion antiporter activity" EXACT []
is_a: GO:0015079 ! potassium ion transmembrane transporter activity
-is_a: GO:0015298 ! solute:cation antiporter activity
+is_a: GO:0140828 ! metal cation:monoatomic cation antiporter activity
[Term]
id: GO:0022824
-name: transmitter-gated ion channel activity
+name: transmitter-gated monoatomic ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a channel that opens when a specific neurotransmitter has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729]
synonym: "ionotropic neurotransmitter receptor activity" NARROW [GOC:bf, GOC:sart]
-is_a: GO:0005230 ! extracellular ligand-gated ion channel activity
+synonym: "transmitter-gated ion channel activity" BROAD []
+is_a: GO:0005230 ! extracellular ligand-gated monoatomic ion channel activity
is_a: GO:0022835 ! transmitter-gated channel activity
[Term]
@@ -151892,9 +151894,11 @@ is_a: GO:0015267 ! channel activity
[Term]
id: GO:0022839
-name: ion gated channel activity
+name: monoatomic ion gated channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of a solute by a channel that opens in response to a specific ion stimulus." [GOC:mtg_transport]
+synonym: "ion gated channel activity" BROAD []
+is_a: GO:0005216 ! monoatomic ion channel activity
is_a: GO:0022836 ! gated channel activity
[Term]
@@ -151921,30 +151925,32 @@ is_a: GO:0015267 ! channel activity
[Term]
id: GO:0022843
-name: voltage-gated cation channel activity
+name: voltage-gated monoatomic cation channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of a cation by a voltage-gated channel. A cation is a positively charged ion. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded." [GOC:mtg_transport, ISBN:0815340729]
+synonym: "voltage-gated cation channel activity" BROAD []
xref: Reactome:R-HSA-2534378 "Hv1 Mediated H+ Permeability"
xref: Reactome:R-HSA-6788999 "HV1-mediated H+ transfer"
-is_a: GO:0005244 ! voltage-gated ion channel activity
-is_a: GO:0005261 ! cation channel activity
+is_a: GO:0005244 ! voltage-gated monoatomic ion channel activity
+is_a: GO:0005261 ! monoatomic cation channel activity
[Term]
id: GO:0022848
-name: acetylcholine-gated cation-selective channel activity
+name: acetylcholine-gated monoatomic cation-selective channel activity
namespace: molecular_function
alt_id: GO:0004889
alt_id: GO:0016904
def: "Selectively enables the transmembrane transfer of a cation by a channel that opens upon binding acetylcholine." [GOC:mah, PMID:2466967]
synonym: "acetylcholine-activated cation-selective channel activity" EXACT []
synonym: "acetylcholine-gated cation channel activity" EXACT []
+synonym: "acetylcholine-gated cation-selective channel activity" BROAD []
synonym: "ionotropic acetylcholine receptor activity" EXACT []
synonym: "nAChR" EXACT []
synonym: "nicotinergic acetylcholine receptor activity" EXACT []
synonym: "nicotinic acetylcholine-activated cation-selective channel activity" EXACT [GOC:bf]
-is_a: GO:0005231 ! excitatory extracellular ligand-gated ion channel activity
-is_a: GO:0099094 ! ligand-gated cation channel activity
-is_a: GO:1904315 ! transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential
+is_a: GO:0005231 ! excitatory extracellular ligand-gated monoatomic ion channel activity
+is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
+is_a: GO:1904315 ! transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential
[Term]
id: GO:0022849
@@ -151956,7 +151962,7 @@ is_a: GO:0099604 ! ligand-gated calcium channel activity
[Term]
id: GO:0022850
-name: serotonin-gated cation-selective channel activity
+name: serotonin-gated monoatomic cation-selective channel activity
namespace: molecular_function
alt_id: GO:0005232
def: "Enables the transmembrane transfer of a cation by a channel that opens when serotonin has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729]
@@ -151964,10 +151970,12 @@ comment: Note that this term represents an activity and not a gene product. Cons
synonym: "5-hydroxytryptamine-gated receptor-channel" NARROW []
synonym: "serotonin-activated cation-selective channel activity" EXACT []
synonym: "serotonin-gated cation channel activity" NARROW []
+synonym: "serotonin-gated cation-selective channel activity" BROAD []
xref: Reactome:R-HSA-9648983 "HTR3A pentamer:5HT transports Na+,K+,Ca2+"
xref: Reactome:R-HSA-975311 "HTR3 pentamers:5HT transport Na+,K+,Ca2+"
-is_a: GO:0022824 ! transmitter-gated ion channel activity
-is_a: GO:0099094 ! ligand-gated cation channel activity
+is_a: GO:0022824 ! transmitter-gated monoatomic ion channel activity
+is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
+is_a: GO:0099589 ! serotonin receptor activity
[Term]
id: GO:0022851
@@ -151976,8 +151984,8 @@ namespace: molecular_function
def: "Enables the transmembrane transfer of a chloride ion by a channel that opens when GABA has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729]
is_a: GO:0005254 ! chloride channel activity
is_a: GO:0016917 ! GABA receptor activity
-is_a: GO:0022824 ! transmitter-gated ion channel activity
-is_a: GO:0099095 ! ligand-gated anion channel activity
+is_a: GO:0022824 ! transmitter-gated monoatomic ion channel activity
+is_a: GO:0099095 ! ligand-gated monoatomic anion channel activity
[Term]
id: GO:0022852
@@ -151985,15 +151993,16 @@ name: glycine-gated chloride ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of a chloride ion by a channel that opens when glycine has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729]
is_a: GO:0005254 ! chloride channel activity
-is_a: GO:0022824 ! transmitter-gated ion channel activity
-is_a: GO:0099095 ! ligand-gated anion channel activity
+is_a: GO:0022824 ! transmitter-gated monoatomic ion channel activity
+is_a: GO:0099095 ! ligand-gated monoatomic anion channel activity
[Term]
id: GO:0022853
-name: active ion transmembrane transporter activity
+name: active monoatomic ion transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of an ion from one side of a membrane to the other up the solute's concentration gradient. This is carried out by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction." [GOC:mtg_transport, ISBN:0815340729]
-is_a: GO:0015075 ! ion transmembrane transporter activity
+synonym: "active ion transmembrane transporter activity" BROAD []
+is_a: GO:0015075 ! monoatomic ion transmembrane transporter activity
is_a: GO:0022804 ! active transmembrane transporter activity
[Term]
@@ -152054,9 +152063,7 @@ id: GO:0022858
name: alanine transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of alanine from one side of a membrane to the other. Alanine is 2-aminopropanoic acid." [GOC:mtg_transport, ISBN:0815340729]
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
[Term]
id: GO:0022859
@@ -152232,7 +152239,7 @@ namespace: molecular_function
def: "Enables the transfer of a zinc ion or zinc ions from the inside of the cell to the outside of the cell across a membrane." [GOC:mtg_transport, ISBN:0815340729]
synonym: "zinc efflux permease activity" EXACT []
is_a: GO:0005385 ! zinc ion transmembrane transporter activity
-is_a: GO:0046583 ! cation efflux transmembrane transporter activity
+is_a: GO:0046583 ! monoatomic cation efflux transmembrane transporter activity
[Term]
id: GO:0022884
@@ -152261,10 +152268,9 @@ is_a: GO:0015267 ! channel activity
id: GO:0022889
name: serine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of serine from one side of a membrane to the other. Serine is 2-amino-3-hydroxypropanoic acid." [GOC:mtg_transport, ISBN:0815340729]
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+def: "Enables the transfer of serine from one side of a membrane to the other. Serine is 2-amino-3-hydroxypropanoic acid." [GOC:mtg_transport, ISBN:0815340729, RHEA:35031]
+xref: RHEA:35031
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
[Term]
id: GO:0022890
@@ -152279,7 +152285,6 @@ synonym: "di-, tri-valent inorganic cation transmembrane transporter activity" N
synonym: "divalent inorganic cation transmembrane transporter activity" NARROW []
synonym: "monovalent inorganic cation transmembrane transporter activity" NARROW []
synonym: "trivalent inorganic cation transmembrane transporter activity" NARROW []
-is_a: GO:0008324 ! cation transmembrane transporter activity
is_a: GO:0015318 ! inorganic molecular entity transmembrane transporter activity
[Term]
@@ -152591,7 +152596,7 @@ is_a: GO:0023029 ! MHC class Ib protein binding
id: GO:0023035
name: CD40 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the cell surface receptor CD40 to one of its physiological ligands, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mtg_signal, GOC:signaling, PMID:11348017]
+def: "The series of molecular signals initiated by the binding of the cell surface receptor CD40 to one of its physiological ligands, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mtg_signal, GOC:signaling, PMID:11348017]
synonym: "CD40 signalling pathway" EXACT [GOC:mah]
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -152767,12 +152772,13 @@ subset: goslim_generic
subset: goslim_mouse
subset: goslim_pombe
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "biological signaling" EXACT []
synonym: "signaling process" EXACT []
synonym: "signalling" EXACT []
synonym: "signalling process" RELATED [GOC:mah]
synonym: "single organism signaling" RELATED []
-is_a: GO:0008150 ! biological_process
+is_a: GO:0050789 ! regulation of biological process
[Term]
id: GO:0023053
@@ -152946,34 +152952,42 @@ id: GO:0030001
name: metal ion transport
namespace: biological_process
alt_id: GO:0070838
+alt_id: GO:0070839
def: "The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
+synonym: "divalent metal ion export" NARROW []
synonym: "divalent metal ion transport" NARROW []
synonym: "heavy metal ion transport" NARROW []
-is_a: GO:0006812 ! cation transport
+synonym: "metal ion export" NARROW []
+is_a: GO:0006812 ! monoatomic cation transport
[Term]
id: GO:0030002
-name: cellular anion homeostasis
+name: intracellular monoatomic anion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of anions at the level of a cell." [GOC:ceb, GOC:mah]
-is_a: GO:0006873 ! cellular ion homeostasis
-is_a: GO:0055081 ! anion homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of monoatomic anions within a cell. Monatomic anions (also called simple anions) are anions consisting of exactly one atom." [GOC:ceb, GOC:mah]
+synonym: "cellular anion homeostasis" BROAD []
+synonym: "cellular monoatomic anion homeostasis" EXACT []
+is_a: GO:0006873 ! intracellular monoatomic ion homeostasis
+is_a: GO:0055081 ! monoatomic anion homeostasis
[Term]
id: GO:0030003
-name: cellular cation homeostasis
+name: intracellular monoatomic cation homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of cations at the level of a cell." [GOC:ceb, GOC:mah]
-is_a: GO:0006873 ! cellular ion homeostasis
-is_a: GO:0055080 ! cation homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of monoatomic cations within a cell. Monatomic cations (also called simple cations) are cations consisting of exactly one atom." [GOC:ceb, GOC:mah]
+synonym: "cellular cation homeostasis" BROAD []
+synonym: "cellular monoatomic cation homeostasis" EXACT []
+is_a: GO:0006873 ! intracellular monoatomic ion homeostasis
+is_a: GO:0055080 ! monoatomic cation homeostasis
[Term]
id: GO:0030004
-name: cellular monovalent inorganic cation homeostasis
+name: obsolete cellular monovalent inorganic cation homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of monovalent inorganic cations at the level of a cell." [GOC:ai, GOC:mah]
-is_a: GO:0030003 ! cellular cation homeostasis
-is_a: GO:0055067 ! monovalent inorganic cation homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of monovalent inorganic cations at the level of a cell." [GOC:ai, GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0030003
[Term]
id: GO:0030005
@@ -152982,8 +152996,7 @@ namespace: biological_process
def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of divalent or trivalent cations at the level of a cell." [GOC:ceb, GOC:mah]
synonym: "cellular di-, tri-valent inorganic cation homeostasis" EXACT []
is_obsolete: true
-consider: GO:0072503
-consider: GO:0072504
+consider: GO:0030003
[Term]
id: GO:0030006
@@ -152993,16 +153006,16 @@ def: "OBSOLETE. Regulation of the levels, transport, and metabolism of ions of a
comment: This term was made obsolete because 'heavy metal' is an ambiguous grouping term which has no set meaning (see Pure Appl. Chem. Vol. 74, No. 5, pp. 793-807, 2002, for more information).
synonym: "heavy cellular metal ion homeostasis" EXACT []
is_obsolete: true
-consider: GO:0006875
+consider: GO:0030003
[Term]
id: GO:0030007
-name: cellular potassium ion homeostasis
+name: intracellular potassium ion homeostasis
namespace: biological_process
alt_id: GO:0017079
-def: "Any process involved in the maintenance of an internal steady state of potassium ions at the level of a cell." [GOC:mah]
-is_a: GO:0006875 ! cellular metal ion homeostasis
-is_a: GO:0030004 ! cellular monovalent inorganic cation homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of potassium ions within a cell." [GOC:mah]
+synonym: "cellular potassium ion homeostasis" EXACT []
+is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
is_a: GO:0055075 ! potassium ion homeostasis
[Term]
@@ -153060,7 +153073,7 @@ id: GO:0030015
name: CCR4-NOT core complex
namespace: cellular_component
def: "The core of the CCR4-NOT complex. In Saccharomyces the CCR4-NOT core complex comprises Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p." [GOC:sart, PMID:11113136]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140535 ! intracellular protein-containing complex
relationship: part_of GO:0030014 ! CCR4-NOT complex
[Term]
@@ -153159,11 +153172,12 @@ is_a: GO:0097493 ! structural molecule activity conferring elasticity
[Term]
id: GO:0030026
-name: cellular manganese ion homeostasis
+name: intracellular manganese ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of manganese ions at the level of a cell." [GOC:mah]
+def: "A homeostatic process involved in the maintenance of a steady state level of manganese ions within a cell." [GOC:mah]
+synonym: "cellular manganese ion homeostasis" EXACT []
synonym: "manganese homeostasis" BROAD []
-is_a: GO:0046916 ! cellular transition metal ion homeostasis
+is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
is_a: GO:0055071 ! manganese ion homeostasis
[Term]
@@ -153188,6 +153202,7 @@ id: GO:0030030
name: cell projection organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/]
+subset: prokaryote_subset
synonym: "cell projection organisation" EXACT []
synonym: "cell projection organization and biogenesis" RELATED [GOC:mah]
synonym: "cell surface structure organization and biogenesis" RELATED [GOC:mah]
@@ -153322,15 +153337,14 @@ name: actin modification
namespace: biological_process
alt_id: GO:0007013
def: "Covalent modification of an actin molecule." [GOC:mah]
-is_a: GO:0006464 ! cellular protein modification process
is_a: GO:0030036 ! actin cytoskeleton organization
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0030048
name: actin filament-based movement
namespace: biological_process
def: "Movement of organelles or other particles along actin filaments, or sliding of actin filaments past each other, mediated by motor proteins." [GOC:BHF, GOC:mah]
-is_a: GO:0006928 ! movement of cell or subcellular component
is_a: GO:0030029 ! actin filament-based process
[Term]
@@ -153470,9 +153484,9 @@ synonym: "NAD-malic dehydrogenase activity" RELATED [EC:1.1.1.37]
synonym: "NAD-specific malate dehydrogenase activity" RELATED [EC:1.1.1.37]
xref: EC:1.1.1.37
xref: MetaCyc:MALATE-DEH-RXN
-xref: Reactome:R-HSA-198508 "malate + NAD+ <=> oxaloacetate + NADH + H+"
+xref: Reactome:R-HSA-198508 "MDH1 oxidizes MAL to OA"
xref: Reactome:R-HSA-70979 "(S)-Malate + NAD+ <=> Oxaloacetate + NADH + H+"
-xref: Reactome:R-HSA-71783 "Oxaloacetate + NADH + H+ <=> (S)-Malate + NAD+"
+xref: Reactome:R-HSA-71783 "MDH2 reduces OA to MAL"
xref: RHEA:21432
is_a: GO:0016615 ! malate dehydrogenase activity
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -153565,7 +153579,6 @@ id: GO:0030071
name: regulation of mitotic metaphase/anaphase transition
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin." [GOC:mah]
-is_a: GO:0010965 ! regulation of mitotic sister chromatid separation
is_a: GO:1901990 ! regulation of mitotic cell cycle phase transition
is_a: GO:1902099 ! regulation of metaphase/anaphase transition of cell cycle
relationship: regulates GO:0007091 ! metaphase/anaphase transition of mitotic cell cycle
@@ -153603,7 +153616,6 @@ namespace: cellular_component
def: "A thylakoid that is derived from and attached to, but not necessarily continuous with, the plasma membrane, and is not enclosed in a plastid. It bears the photosynthetic pigments in photosynthetic cyanobacteria." [GOC:mah, GOC:mtg_sensu]
synonym: "plasma membrane-derived thylakoid" EXACT []
is_a: GO:0009579 ! thylakoid
-is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
[Term]
id: GO:0030076
@@ -153736,7 +153748,7 @@ id: GO:0030091
name: protein repair
namespace: biological_process
def: "The process of restoring a protein to its original state after damage by such things as oxidation or spontaneous decomposition of residues." [GOC:mlg]
-is_a: GO:0044267 ! cellular protein metabolic process
+is_a: GO:0019538 ! protein metabolic process
[Term]
id: GO:0030092
@@ -153800,7 +153812,7 @@ synonym: "blood cell formation" EXACT []
synonym: "haemopoiesis" EXACT []
synonym: "hematopoiesis" EXACT []
xref: Wikipedia:Haematopoiesis
-is_a: GO:0048534 ! hematopoietic or lymphoid organ development
+is_a: GO:0048468 ! cell development
[Term]
id: GO:0030098
@@ -153849,14 +153861,18 @@ is_a: GO:0030072 ! peptide hormone secretion
[Term]
id: GO:0030104
-name: water homeostasis
+name: obsolete water homeostasis
namespace: biological_process
alt_id: GO:0018987
-def: "Any process involved in the maintenance of an internal steady state of water within an organism or cell." [GOC:dph, GOC:mah, GOC:tb]
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of water within an organism or cell." [GOC:dph, GOC:mah, GOC:tb]
+comment: The reason for obsoletion is that this term does not specify whether the process is intracellular or organism-level.
synonym: "osmoregulation" RELATED []
synonym: "regulation of osmotic pressure" EXACT []
xref: Wikipedia:Osmoregulation
-is_a: GO:0048878 ! chemical homeostasis
+is_obsolete: true
+consider: GO:0003091
+consider: GO:0009992
+consider: GO:0050891
[Term]
id: GO:0030105
@@ -154311,7 +154327,6 @@ def: "The import of proteins across the outer and inner mitochondrial membranes
synonym: "mitochondrial matrix protein import" EXACT []
synonym: "mitochondrial translocation" BROAD []
synonym: "protein transport into mitochondrial matrix" EXACT []
-is_a: GO:0006839 ! mitochondrial transport
is_a: GO:0044743 ! protein transmembrane import into intracellular organelle
is_a: GO:0065002 ! intracellular protein transmembrane transport
is_a: GO:0072655 ! establishment of protein localization to mitochondrion
@@ -154351,7 +154366,7 @@ is_a: GO:0009404 ! toxin metabolic process
id: GO:0030154
name: cell differentiation
namespace: biological_process
-def: "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN:0198506732]
+def: "The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." [ISBN:0198506732]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
@@ -154454,13 +154469,18 @@ id: GO:0030163
name: protein catabolic process
namespace: biological_process
alt_id: GO:0044254
+alt_id: GO:0044257
def: "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:mah]
comment: This term refers to the breakdown of mature proteins. For cleavage events involved in generating a mature protein from a precursor, consider instead the term 'protein maturation ; GO:0051604' and its children.
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pombe
+subset: prokaryote_subset
+synonym: "cellular protein breakdown" EXACT []
+synonym: "cellular protein catabolic process" EXACT []
+synonym: "cellular protein catabolism" EXACT []
+synonym: "cellular protein degradation" EXACT []
synonym: "multicellular organismal protein catabolic process" NARROW []
synonym: "pheromone catabolic process" RELATED []
synonym: "pheromone catabolism" RELATED []
@@ -154478,7 +154498,7 @@ name: protein denaturation
namespace: biological_process
def: "Structural change in proteins which destroys the native, active configuration without rupture of peptide bonds." [GOC:kd, ISBN:3110145359]
xref: Wikipedia:Denaturation#Protein_denaturation
-is_a: GO:0044257 ! cellular protein catabolic process
+is_a: GO:0030163 ! protein catabolic process
[Term]
id: GO:0030165
@@ -154547,7 +154567,7 @@ def: "Enables the transmembrane transfer of a proton by a voltage-gated channel.
synonym: "voltage gated proton channel activity" EXACT []
synonym: "voltage-dependent proton channel activity" EXACT []
is_a: GO:0015252 ! proton channel activity
-is_a: GO:0022843 ! voltage-gated cation channel activity
+is_a: GO:0022843 ! voltage-gated monoatomic cation channel activity
[Term]
id: GO:0030172
@@ -154558,24 +154578,25 @@ is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
id: GO:0030173
-name: integral component of Golgi membrane
+name: obsolete integral component of Golgi membrane
namespace: cellular_component
-def: "The component of the Golgi membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:go_curators]
+def: "OBSOLETE. The component of the Golgi membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:go_curators]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "Golgi integral membrane protein" RELATED []
synonym: "integral to Golgi membrane" NARROW []
-is_a: GO:0031228 ! intrinsic component of Golgi membrane
-is_a: GO:0031301 ! integral component of organelle membrane
+is_obsolete: true
+replaced_by: GO:0000139
[Term]
id: GO:0030174
-name: regulation of DNA-dependent DNA replication initiation
+name: regulation of DNA-templated DNA replication initiation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of initiation of DNA-dependent DNA replication; the process in which DNA becomes competent to replicate. In eukaryotes, replication competence is established in early G1 and lost during the ensuing S phase." [GOC:mah]
synonym: "DNA replication licencing" EXACT []
synonym: "DNA replication licensing" EXACT []
synonym: "regulation of DNA replication initiation" BROAD [GOC:vw]
-is_a: GO:0051052 ! regulation of DNA metabolic process
-is_a: GO:0090329 ! regulation of DNA-dependent DNA replication
+synonym: "regulation of DNA-dependent DNA replication initiation" EXACT []
+is_a: GO:0090329 ! regulation of DNA-templated DNA replication
relationship: regulates GO:0006270 ! DNA replication initiation
[Term]
@@ -154592,14 +154613,15 @@ is_a: GO:0098858 ! actin-based cell projection
[Term]
id: GO:0030176
-name: integral component of endoplasmic reticulum membrane
+name: obsolete integral component of endoplasmic reticulum membrane
namespace: cellular_component
-def: "The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "ER integral membrane protein" EXACT []
synonym: "integral to endoplasmic reticulum membrane" NARROW []
synonym: "integral to ER membrane" EXACT []
-is_a: GO:0031227 ! intrinsic component of endoplasmic reticulum membrane
-is_a: GO:0031301 ! integral component of organelle membrane
+is_obsolete: true
+replaced_by: GO:0005789
[Term]
id: GO:0030177
@@ -154714,9 +154736,9 @@ name: melatonin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving melatonin (N-acetyl-5-methoxytryptamine)." [GOC:mah, ISBN:0198506732]
synonym: "melatonin metabolism" EXACT []
-is_a: GO:0034754 ! cellular hormone metabolic process
is_a: GO:0042430 ! indole-containing compound metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0042445 ! hormone metabolic process
+is_a: GO:0043603 ! amide metabolic process
[Term]
id: GO:0030187
@@ -154838,7 +154860,7 @@ relationship: negatively_regulates GO:0007596 ! blood coagulation
id: GO:0030196
name: cyanide hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: formamide = H(2)O + hydrogen cyanide." [EC:4.2.1.66, RHEA:21720]
+def: "Catalysis of the reaction: formamide = H2O + hydrogen cyanide." [EC:4.2.1.66, RHEA:21720]
synonym: "formamide dehydratase activity" RELATED [EC:4.2.1.66]
synonym: "formamide hydro-lyase (cyanide-forming)" RELATED [EC:4.2.1.66]
synonym: "formamide hydro-lyase activity" RELATED [EC:4.2.1.66]
@@ -154893,7 +154915,7 @@ synonym: "heparan sulphate proteoglycan catabolic process" EXACT []
synonym: "heparan sulphate proteoglycan catabolism" EXACT []
synonym: "heparin proteoglycan catabolic process" RELATED []
is_a: GO:0030167 ! proteoglycan catabolic process
-is_a: GO:0030201 ! heparan sulfate proteoglycan metabolic process
+is_a: GO:0044273 ! sulfur compound catabolic process
[Term]
id: GO:0030201
@@ -154946,7 +154968,10 @@ synonym: "chondroitin sulfate B metabolism" EXACT []
synonym: "dermatan sulfate metabolism" EXACT []
synonym: "dermatan sulphate metabolic process" EXACT []
synonym: "dermatan sulphate metabolism" EXACT []
+is_a: GO:0005996 ! monosaccharide metabolic process
is_a: GO:0006790 ! sulfur compound metabolic process
+is_a: GO:0032787 ! monocarboxylic acid metabolic process
+is_a: GO:0052779 ! amino disaccharide metabolic process
is_a: GO:1903510 ! mucopolysaccharide metabolic process
relationship: part_of GO:0050655 ! dermatan sulfate proteoglycan metabolic process
@@ -154996,6 +155021,8 @@ synonym: "dermatan sulphate biosynthetic process" EXACT []
is_a: GO:0006024 ! glycosaminoglycan biosynthetic process
is_a: GO:0030205 ! dermatan sulfate metabolic process
is_a: GO:0044272 ! sulfur compound biosynthetic process
+is_a: GO:0046364 ! monosaccharide biosynthetic process
+is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
relationship: part_of GO:0050651 ! dermatan sulfate proteoglycan biosynthetic process
[Term]
@@ -155013,6 +155040,9 @@ synonym: "dermatan sulphate catabolism" EXACT []
is_a: GO:0006027 ! glycosaminoglycan catabolic process
is_a: GO:0030205 ! dermatan sulfate metabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
+is_a: GO:0046365 ! monosaccharide catabolic process
+is_a: GO:0052782 ! amino disaccharide catabolic process
+is_a: GO:0072329 ! monocarboxylic acid catabolic process
[Term]
id: GO:0030210
@@ -155246,7 +155276,6 @@ alt_id: GO:0010576
def: "Binds to and modulates the activity of an enzyme." [GOC:dph, GOC:mah, GOC:tb]
comment: This term should only be used in cases when the regulator directly interacts with the enzyme.
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -155257,7 +155286,7 @@ subset: goslim_yeast
synonym: "catalytic regulator activity" EXACT [GOC:dph]
synonym: "enzyme modulator" EXACT []
synonym: "metalloenzyme regulator activity" NARROW []
-is_a: GO:0098772 ! molecular function regulator
+is_a: GO:0098772 ! molecular function regulator activity
[Term]
id: GO:0030235
@@ -155401,7 +155430,6 @@ name: guanylate cyclase activator activity
namespace: molecular_function
def: "Binds to and increases the activity of guanylate cyclase." [GOC:mah]
synonym: "guanylin" NARROW []
-is_a: GO:0008047 ! enzyme activator activity
is_a: GO:0010853 ! cyclase activator activity
is_a: GO:0030249 ! guanylate cyclase regulator activity
@@ -155409,7 +155437,7 @@ is_a: GO:0030249 ! guanylate cyclase regulator activity
id: GO:0030251
name: guanylate cyclase inhibitor activity
namespace: molecular_function
-def: "Stops, prevents or reduces the activity of guanylate cyclase." [GOC:mah]
+def: "Binds to and stops, prevents or reduces the activity of guanylate cyclase." [GOC:mah]
is_a: GO:0010852 ! cyclase inhibitor activity
is_a: GO:0030249 ! guanylate cyclase regulator activity
@@ -155501,7 +155529,7 @@ def: "The progressive compaction of dispersed interphase chromatin into threadli
synonym: "DNA condensation" BROAD [Wikipedia:DNA_condensation]
synonym: "eukaryotic chromosome condensation" EXACT [GOC:bf]
synonym: "nuclear chromosome condensation" EXACT [GOC:bf]
-is_a: GO:0006323 ! DNA packaging
+is_a: GO:0051276 ! chromosome organization
[Term]
id: GO:0030262
@@ -155536,7 +155564,7 @@ relationship: part_of GO:0030262 ! apoptotic nuclear changes
id: GO:0030265
name: phospholipase C-activating rhodopsin mediated signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a rhodopsin molecule being activated by a photon, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent release of inositol trisphosphate (IP3) and diacylglycerol (DAG)." [GOC:mah, GOC:signaling, PMID:22498302, PMID:8823931]
+def: "A phospholipase C-activating receptor G protein-coupled receptor signaling pathway initiated by a rhodopsin molecule being activated by a photon, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, PMID:22498302, PMID:8823931]
synonym: "phospholipase C-activating rhodopsin mediated G-protein coupled receptor signaling pathway" EXACT [GOC:bf]
synonym: "PLC-activating rhodopsin mediated signaling pathway" EXACT [GOC:bf]
synonym: "rhodopsin mediated G protein signaling, coupled to IP3 second messenger" EXACT []
@@ -155583,7 +155611,7 @@ id: GO:0030268
name: methylenetetrahydromethanopterin dehydrogenase activity
namespace: molecular_function
alt_id: GO:0018536
-def: "Catalysis of the reaction: 5,10-methylenetetrahydromethanopterin + coenzyme F420 + 2 H(+) = 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + reduced coenzyme F420." [EC:1.5.98.1, RHEA:16721]
+def: "Catalysis of the reaction: 5,10-methylenetetrahydromethanopterin + coenzyme F420 + 2 H+ = 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + reduced coenzyme F420." [EC:1.5.98.1, RHEA:16721]
synonym: "5,10-methylenetetrahydromethanopterin dehydrogenase activity" RELATED [EC:1.5.98.1]
synonym: "5,10-methylenetetrahydromethanopterin:coenzyme-F420 oxidoreductase activity" RELATED [EC:1.5.98.1]
synonym: "N(5),N(10)-methylenetetrahydromethanopterin dehydrogenase activity" RELATED [EC:1.5.98.1]
@@ -155617,7 +155645,7 @@ id: GO:0030270
name: formylmethanofuran-tetrahydromethanopterin N-formyltransferase activity
namespace: molecular_function
alt_id: GO:0018714
-def: "Catalysis of the reaction: 5,6,7,8-tetrahydromethanopterin + N-formylmethanofuran + H(+) = N(5)-formyl-5,6,7,8-tetrahydromethanopterin + methanofuran." [EC:2.3.1.101, RHEA:18061]
+def: "Catalysis of the reaction: 5,6,7,8-tetrahydromethanopterin + N-formylmethanofuran + H+ = N(5)-formyl-5,6,7,8-tetrahydromethanopterin + methanofuran." [EC:2.3.1.101, RHEA:18061]
synonym: "formylmethanofuran-tetrahydromethanopterin formyltransferase activity" RELATED [EC:2.3.1.101]
synonym: "formylmethanofuran:5,6,7,8-tetrahydromethanopterin 5-formyltransferase activity" RELATED [EC:2.3.1.101]
synonym: "formylmethanofuran:5,6,7,8-tetrahydromethanopterin N5-formyltransferase activity" RELATED [EC:2.3.1.101]
@@ -155652,7 +155680,7 @@ id: GO:0030272
name: 5-formyltetrahydrofolate cyclo-ligase activity
namespace: molecular_function
alt_id: GO:0019006
-def: "Catalysis of the reaction: 5-formyltetrahydrofolate + ATP = 5,10-methenyltetrahydrofolate + ADP + H(+) + phosphate." [EC:6.3.3.2, RHEA:10488]
+def: "Catalysis of the reaction: 5-formyltetrahydrofolate + ATP = 5,10-methenyltetrahydrofolate + ADP + H+ + phosphate." [EC:6.3.3.2, RHEA:10488]
synonym: "5,10-methenyltetrahydrofolate synthetase activity" RELATED [EC:6.3.3.2]
synonym: "5-formyltetrahydrofolate cyclo-ligase (ADP-forming)" RELATED [EC:6.3.3.2]
synonym: "5-formyltetrahydrofolate cyclodehydrase" BROAD [EC:6.3.3.2]
@@ -155771,21 +155799,21 @@ is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of
[Term]
id: GO:0030284
-name: estrogen receptor activity
+name: nuclear estrogen receptor activity
namespace: molecular_function
def: "Combining with estrogen and transmitting the signal within the cell to trigger a change in cell activity or function." [GOC:signaling, PMID:17615392]
-comment: For estrogen receptors that function within the nucleus to modulate transcription, consider instead annotating to the child terms 'estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity ; GO:0038052' or 'estrogen-activated RNA polymerase II transcription factor binding transcription factor activity ; GO:0038053'.
-is_a: GO:0003707 ! steroid hormone receptor activity
+synonym: "estrogen receptor activity" BROAD []
+is_a: GO:0003707 ! nuclear steroid receptor activity
[Term]
id: GO:0030285
-name: integral component of synaptic vesicle membrane
+name: obsolete integral component of synaptic vesicle membrane
namespace: cellular_component
-def: "The component of the synaptic vesicle membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:go_curators]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the synaptic vesicle membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:go_curators]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to synaptic vesicle membrane" NARROW []
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:0098563 ! intrinsic component of synaptic vesicle membrane
+is_obsolete: true
+replaced_by: GO:0030672
[Term]
id: GO:0030286
@@ -155822,7 +155850,7 @@ id: GO:0030289
name: protein phosphatase 4 complex
namespace: cellular_component
def: "A protein serine/threonine phosphatase complex formed by the catalytic subunit of protein phosphatase 4 plus one or more regulatory subunits." [GOC:bhm, PMID:10026142]
-is_a: GO:0005963 ! magnesium-dependent protein serine/threonine phosphatase complex
+is_a: GO:0008287 ! protein serine/threonine phosphatase complex
[Term]
id: GO:0030290
@@ -155958,7 +155986,6 @@ namespace: molecular_function
def: "Catalysis of the cleavage of heparan sulfate; can degrade both heparan sulfate and heparin glycosaminoglycan chains." [PMID:10916150]
synonym: "heparinase activity" RELATED []
xref: Reactome:R-HSA-1667005 "Heparanase (HPSE) cleaves heparan sulfate from its proteoglycan (lysosome)"
-xref: Reactome:R-HSA-1678694 "Heparanase 2 (HPSE2) cleaves heparan sulfate from its proteoglycan (plasma membrane)"
is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
[Term]
@@ -155997,7 +156024,6 @@ namespace: biological_process
def: "The chemical reactions and pathways involving poly-N-acetyllactosamine, a carbohydrate composed of N-acetyllactosamine repeats (Gal-beta-1,4-GlcNAc-beta-1,3)n." [GOC:mah, PMID:9405606]
synonym: "poly-N-acetyllactosamine metabolism" EXACT []
is_a: GO:0006022 ! aminoglycan metabolic process
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
[Term]
id: GO:0030310
@@ -156009,7 +156035,6 @@ synonym: "poly-N-acetyllactosamine catabolism" EXACT []
synonym: "poly-N-acetyllactosamine degradation" EXACT []
is_a: GO:0006026 ! aminoglycan catabolic process
is_a: GO:0030309 ! poly-N-acetyllactosamine metabolic process
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
[Term]
id: GO:0030311
@@ -156022,7 +156047,6 @@ synonym: "poly-N-acetyllactosamine formation" EXACT []
synonym: "poly-N-acetyllactosamine synthesis" EXACT []
is_a: GO:0006023 ! aminoglycan biosynthetic process
is_a: GO:0030309 ! poly-N-acetyllactosamine metabolic process
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
[Term]
id: GO:0030312
@@ -156110,16 +156134,16 @@ def: "OBSOLETE. Any process involved in the maintenance of an internal steady st
comment: This term was made obsolete because it has been split.
synonym: "cellular di-, tri-valent inorganic anion homeostasis" EXACT []
is_obsolete: true
-consider: GO:0072501
-consider: GO:0072502
+consider: GO:0030002
[Term]
id: GO:0030320
-name: cellular monovalent inorganic anion homeostasis
+name: obsolete cellular monovalent inorganic anion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of monovalent inorganic anions at the level of a cell." [GOC:ai, GOC:mah]
-is_a: GO:0030002 ! cellular anion homeostasis
-is_a: GO:0055083 ! monovalent inorganic anion homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of monovalent inorganic anions at the level of a cell." [GOC:ai, GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0030002
[Term]
id: GO:0030321
@@ -156214,9 +156238,10 @@ is_a: GO:0072331 ! signal transduction by p53 class mediator
[Term]
id: GO:0030331
-name: estrogen receptor binding
+name: nuclear estrogen receptor binding
namespace: molecular_function
-def: "Binding to an estrogen receptor." [GOC:ai]
+def: "Binding to a nuclear estrogen receptor." [GOC:ai]
+synonym: "estrogen receptor binding" BROAD []
is_a: GO:0016922 ! nuclear receptor binding
[Term]
@@ -156708,7 +156733,7 @@ name: fructoselysine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving fructoselysine, a fructose molecule containing a lysine group in place of a hydroxyl group." [GOC:ai]
synonym: "fructoselysine metabolism" EXACT []
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
is_a: GO:0030389 ! fructosamine metabolic process
[Term]
@@ -156717,8 +156742,8 @@ name: fructoseglycine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving fructoseglycine, a fructose molecule containing a glycine group in place of a hydroxyl group." [GOC:ai]
synonym: "fructoseglycine metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0006575 ! cellular modified amino acid metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0030389 ! fructosamine metabolic process
[Term]
@@ -156884,7 +156909,7 @@ is_a: GO:0016742 ! hydroxymethyl-, formyl- and related transferase activity
id: GO:0030410
name: nicotianamine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3 S-adenosyl-L-methionine(1+) = 3 S-methyl-5'-thioadenosine + 3 H(+) + nicotianamine." [EC:2.5.1.43, RHEA:16481]
+def: "Catalysis of the reaction: 3 S-adenosyl-L-methionine(1+) = 3 S-methyl-5'-thioadenosine + 3 H+ + nicotianamine." [EC:2.5.1.43, RHEA:16481]
synonym: "S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-adenosyl-L-methionine 3-amino-3-carboxypropyltransferase activity" RELATED [EC:2.5.1.43]
xref: EC:2.5.1.43
xref: KEGG_REACTION:R00075
@@ -156896,7 +156921,7 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0030411
name: scytalone dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: scytalone = 1,3,8-trihydroxynaphthalene + H(2)O." [EC:4.2.1.94, RHEA:24396]
+def: "Catalysis of the reaction: scytalone = 1,3,8-trihydroxynaphthalene + H2O." [EC:4.2.1.94, RHEA:24396]
synonym: "scytalone 7,8-hydro-lyase (1,3,8-trihydroxynaphthalene-forming)" RELATED [EC:4.2.1.94]
synonym: "scytalone 7,8-hydro-lyase activity" RELATED [EC:4.2.1.94]
xref: EC:4.2.1.94
@@ -156909,7 +156934,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0030412
name: formimidoyltetrahydrofolate cyclodeaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-formimidoyltetrahydrofolate + 2 H(+) = 5,10-methenyltetrahydrofolate + NH(4)(+)." [EC:4.3.1.4, RHEA:22736]
+def: "Catalysis of the reaction: 5-formimidoyltetrahydrofolate + 2 H+ = 5,10-methenyltetrahydrofolate + NH4." [EC:4.3.1.4, RHEA:22736]
comment: Note that cyclodeaminases are lyases according to EC, whereas deaminases are hydrolases.
synonym: "5-formimidoyltetrahydrofolate ammonia-lyase (cyclizing)" RELATED [EC:4.3.1.4]
synonym: "5-formimidoyltetrahydrofolate ammonia-lyase (cyclizing; 5,10-methenyltetrahydrofolate-forming)" RELATED [EC:4.3.1.4]
@@ -156964,7 +156989,7 @@ name: nicotianamine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving nicotianamine, 2(S),3'2(S),3''(S)-N-(N-(3-amino-3-carboxypropyl)-3-amino-3-carboxypropyl)-azetidine-2-carboxylic acid." [GOC:mah, PMID:10069850]
synonym: "nicotianamine metabolism" EXACT []
-is_a: GO:0006576 ! cellular biogenic amine metabolic process
+is_a: GO:0006576 ! biogenic amine metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:0072350 ! tricarboxylic acid metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
@@ -156980,7 +157005,7 @@ synonym: "nicotianamine formation" EXACT []
synonym: "nicotianamine synthesis" EXACT []
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0030417 ! nicotianamine metabolic process
-is_a: GO:0042401 ! cellular biogenic amine biosynthetic process
+is_a: GO:0042401 ! biogenic amine biosynthetic process
is_a: GO:0072351 ! tricarboxylic acid biosynthetic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
@@ -157004,7 +157029,7 @@ name: establishment of competence for transformation
namespace: biological_process
def: "The process in which a naturally transformable bacterium acquires the ability to take up exogenous DNA. This term should be applied only to naturally transformable bacteria, and should not be used in the context of artificially induced bacterial transformation." [GOC:mah, ISBN:1555811027]
is_a: GO:0031668 ! cellular response to extracellular stimulus
-relationship: part_of GO:0009294 ! DNA mediated transformation
+relationship: part_of GO:0009294 ! DNA-mediated transformation
[Term]
id: GO:0030421
@@ -157017,23 +157042,23 @@ is_a: GO:0022600 ! digestive system process
[Term]
id: GO:0030422
-name: production of siRNA involved in RNA interference
+name: siRNA processing
namespace: biological_process
-def: "Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference." [GOC:mah, PMID:11524674]
+alt_id: GO:0070919
+def: "A process leading to the generation of a functional small interfering RNA (siRNA). Includes the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides. May also include amplification of the siRNA by RNA-directed RNA polymerase." [GOC:mah, PMID:11524674, PMID:19239886, PMID:20687832]
+synonym: "chromatin silencing by small RNA, production of guide RNAs" EXACT []
+synonym: "chromatin silencing by small RNA, production of siRNA" EXACT [GOC:mah]
+synonym: "production of guide RNAs involved in chromatin silencing by small RNA" EXACT [GOC:mah]
synonym: "production of guide RNAs involved in RNA interference" EXACT [GOC:mah]
+synonym: "production of siRNA" RELATED []
+synonym: "production of siRNA involved in chromatin silencing by small RNA" EXACT []
+synonym: "production of siRNA involved in gene silencing by small RNA" NARROW []
+synonym: "production of siRNA involved in post-transcriptional gene silencing by RNA" EXACT []
+synonym: "production of siRNA involved in PTGS" RELATED []
+synonym: "production of siRNA involved in RNA interference" EXACT []
synonym: "RNA interference, production of guide RNAs" EXACT []
synonym: "RNA interference, production of siRNA" EXACT [GOC:mah]
-is_a: GO:0070918 ! production of small RNA involved in gene silencing by RNA
-relationship: part_of GO:0016246 ! RNA interference
-
-[Term]
-id: GO:0030423
-name: targeting of mRNA for destruction involved in RNA interference
-namespace: biological_process
-def: "The process in which small interfering RNAs target cognate mRNA molecules for degradation." [PMID:11524674]
-synonym: "RNA interference, targeting of mRNA for destruction" EXACT [GOC:mah]
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
-relationship: part_of GO:0016246 ! RNA interference
+is_a: GO:0070918 ! regulatory ncRNA processing
[Term]
id: GO:0030424
@@ -157070,7 +157095,6 @@ namespace: cellular_component
alt_id: GO:0000134
alt_id: GO:0030483
def: "Any part of a cell where non-isotropic growth takes place." [GOC:mah]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
subset: goslim_yeast
@@ -157156,7 +157180,6 @@ synonym: "spore biosynthesis" EXACT []
synonym: "spore differentiation" EXACT []
synonym: "spore formation" EXACT []
xref: Wikipedia:Sporogenesis
-is_a: GO:0030154 ! cell differentiation
is_a: GO:0043934 ! sporulation
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
@@ -157165,7 +157188,6 @@ id: GO:0030436
name: asexual sporulation
namespace: biological_process
def: "The formation of spores derived from the products of an asexual cell division. Examples of this process are found in bacteria and fungi." [GOC:mah, PMID:9529886]
-subset: goslim_aspergillus
synonym: "asexual reproductive sporulation" EXACT []
synonym: "asexual spore formation" EXACT []
synonym: "mitotic spore formation" EXACT []
@@ -157187,6 +157209,7 @@ synonym: "sporulation" BROAD []
is_a: GO:0022413 ! reproductive process in single-celled organism
is_a: GO:0043935 ! sexual sporulation resulting in formation of a cellular spore
is_a: GO:0048468 ! cell development
+is_a: GO:1903046 ! meiotic cell cycle process
[Term]
id: GO:0030438
@@ -157273,7 +157296,6 @@ id: GO:0030447
name: filamentous growth
namespace: biological_process
def: "The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape." [GOC:mcc, PMID:11729141]
-subset: goslim_aspergillus
subset: goslim_candida
is_a: GO:0040007 ! growth
@@ -157389,7 +157411,6 @@ def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
comment: This term was made obsolete because it does not describe a biological process that is distinct from 'cell aging'.
synonym: "cell aging (sensu Fungi)" EXACT []
is_obsolete: true
-replaced_by: GO:0007569
[Term]
id: GO:0030464
@@ -157413,7 +157434,7 @@ consider: GO:0048102
[Term]
id: GO:0030466
-name: silent mating-type cassette heterochromatin assembly
+name: silent mating-type cassette heterochromatin formation
namespace: biological_process
alt_id: GO:0006347
alt_id: GO:0035389
@@ -157424,7 +157445,8 @@ synonym: "chromatin silencing at silent mating-type cassette" EXACT []
synonym: "establishment of chromatin silencing at silent mating-type cassette" RELATED []
synonym: "heterochromatic silencing at silent mating-type cassette" EXACT []
synonym: "silent mating-type cassette chromatin silencing" EXACT [GOC:mah]
-is_a: GO:0140719 ! constitutive heterochromatin assembly
+synonym: "silent mating-type cassette heterochromatin assembly" EXACT []
+is_a: GO:0140719 ! constitutive heterochromatin formation
[Term]
id: GO:0030470
@@ -157514,7 +157536,7 @@ id: GO:0030479
name: actin cortical patch
namespace: cellular_component
alt_id: GO:0005857
-def: "An endocytic patch that consists of an actin-containing structure found at the plasma membrane in cells; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. An example of this is the actin cortical patch found in Saccharomyces cerevisiae." [GOC:mah, GOC:vw, ISBN:0879693568, ISBN:0879693649, PMID:16959963]
+def: "An endocytic patch that consists of an actin-containing structure found at the plasma membrane in cells; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. An example of this is the actin cortical patch found in Saccharomyces cerevisiae." [GOC:mah, GOC:vw, ISBN:0879693568, ISBN:0879693649, PMID:16959963]
synonym: "actin patch" EXACT []
is_a: GO:0061645 ! endocytic patch
relationship: part_of GO:0030864 ! cortical actin cytoskeleton
@@ -157731,7 +157753,7 @@ id: GO:0030509
name: BMP signaling pathway
namespace: biological_process
alt_id: GO:0008101
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, ISBN:0878932437, PMID:17428827]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, ISBN:0878932437, PMID:17428827]
synonym: "BMP receptor signaling pathway" RELATED []
synonym: "BMP signalling pathway" EXACT []
synonym: "bone morphogenetic protein signaling pathway" EXACT []
@@ -157875,7 +157897,7 @@ relationship: negatively_regulates GO:0048675 ! axon extension
id: GO:0030518
name: intracellular steroid hormone receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of a intracellular steroid hormone receptor binding to one of its physiological ligands." [GOC:mah, GOC:signaling]
+def: "The series of molecular signals initiated by a steroid binding to an intracellular steroid hormone receptor." [GOC:mah, GOC:signaling]
synonym: "steroid hormone receptor signaling pathway" BROAD [GOC:bf]
synonym: "steroid hormone receptor signalling pathway" BROAD [GOC:bf]
is_a: GO:0030522 ! intracellular receptor signaling pathway
@@ -157892,7 +157914,7 @@ is_a: GO:0043021 ! ribonucleoprotein complex binding
id: GO:0030520
name: intracellular estrogen receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of an intracellular estrogen receptor binding to one of its physiological ligands. The pathway begins with receptor-ligand binding, and ends with regulation of a downstream cellular process (e.g. transcription)." [GOC:mah, GOC:signaling]
+def: "The series of molecular signals initiated by estrogen binding to an intracellular receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling]
synonym: "estrogen receptor signaling pathway" BROAD [GOC:bf]
synonym: "estrogen receptor signalling pathway" BROAD [GOC:bf]
is_a: GO:0030518 ! intracellular steroid hormone receptor signaling pathway
@@ -157901,7 +157923,7 @@ is_a: GO:0030518 ! intracellular steroid hormone receptor signaling pathway
id: GO:0030521
name: androgen receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of an androgen binding to its receptor." [GOC:mah]
+def: "The series of molecular signals initiated by androgen binding to its receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah]
synonym: "androgen receptor signalling pathway" EXACT []
is_a: GO:0030518 ! intracellular steroid hormone receptor signaling pathway
@@ -157909,20 +157931,12 @@ is_a: GO:0030518 ! intracellular steroid hormone receptor signaling pathway
id: GO:0030522
name: intracellular receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals initiated by a ligand binding to an receptor located within a cell." [GOC:bf, GOC:mah]
+def: "The series of molecular signals initiated by a ligand binding to a receptor located within a cell." [GOC:bf, GOC:mah]
synonym: "intracellular receptor mediated signaling pathway" EXACT []
synonym: "intracellular receptor-mediated signaling pathway" EXACT []
synonym: "intracellular receptor-mediated signalling pathway" EXACT []
is_a: GO:0007165 ! signal transduction
-[Term]
-id: GO:0030523
-name: dihydrolipoamide S-acyltransferase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + dihydrolipoamide = CoA + S-acyldihydrolipoamide." [EC:2.3.1.12, GOC:mah]
-xref: EC:2.3.1.12
-is_a: GO:0016417 ! S-acyltransferase activity
-
[Term]
id: GO:0030526
name: granulocyte macrophage colony-stimulating factor receptor complex
@@ -157931,7 +157945,6 @@ def: "The heterodimeric receptor for granulocyte macrophage colony-stimulating f
synonym: "GM-CSF receptor complex" EXACT [GOC:vk]
synonym: "granulocyte macrophage colony stimulating factor receptor complex" EXACT []
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0030527
@@ -157996,7 +158009,6 @@ name: triplet codon-amino acid adaptor activity
namespace: molecular_function
def: "The codon binding activity of a tRNA that positions an activated amino acid, mediating its insertion at the correct point in the sequence of a nascent polypeptide chain during protein synthesis." [GOC:hjd, GOC:mtg_MIT_16mar07, ISBN:0198506732]
comment: Note that this term can be used in place of the obsolete term 'transfer RNA ; GO:0005563'.
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_yeast
@@ -158015,7 +158027,6 @@ synonym: "adult behavioral response to stimulus" EXACT []
synonym: "adult behaviour" EXACT []
synonym: "adult behavioural response to stimulus" EXACT []
is_a: GO:0007610 ! behavior
-is_a: GO:0032501 ! multicellular organismal process
[Term]
id: GO:0030535
@@ -158046,7 +158057,6 @@ def: "Behavior in a larval form of an organism, an immature organism that must u
comment: See also the biological process term 'behavior ; GO:0007610'.
synonym: "larval behaviour" EXACT []
is_a: GO:0007610 ! behavior
-is_a: GO:0032501 ! multicellular organismal process
[Term]
id: GO:0030538
@@ -158097,6 +158107,7 @@ name: Hsp70 protein binding
namespace: molecular_function
def: "Binding to a Hsp70 protein, heat shock proteins around 70kDa in size." [ISBN:0198506732]
is_a: GO:0031072 ! heat shock protein binding
+is_a: GO:0051087 ! protein-folding chaperone binding
[Term]
id: GO:0030545
@@ -158104,7 +158115,7 @@ name: signaling receptor regulator activity
namespace: molecular_function
def: "Binds to and modulates the activity of a receptor." [GOC:ceb]
synonym: "receptor regulator activity" BROAD []
-is_a: GO:0098772 ! molecular function regulator
+is_a: GO:0098772 ! molecular function regulator activity
[Term]
id: GO:0030546
@@ -158458,7 +158469,7 @@ id: GO:0030582
name: reproductive fruiting body development
namespace: biological_process
def: "The process whose specific outcome is the progression of a reproductive fruiting body over time, from its formation to the mature structure. A reproductive fruiting body is a multicellular reproductive structure that contains spores." [GOC:mah, GOC:mtg_sensu]
-comment: This term describes the development of a fruiting body that is a spore-bearing organ. It is not intended to describe the development of myxococcal fruiting bodies.
+comment: This term describes the development of a fruiting body that is a spore-bearing organ. It is not intended to describe the development of myxococcal fruiting bodies.
synonym: "fruiting body formation" EXACT []
is_a: GO:0075259 ! spore-bearing structure development
@@ -158468,11 +158479,11 @@ name: myxococcal fruiting body development
namespace: biological_process
alt_id: GO:0055084
def: "The process whose specific outcome is the progression of the myxococcal fruiting body over time, from its formation to the mature structure. The process begins when myxococci respond to a lack of nutrients in the environment and ends when the myxococcal fruiting body is a mature structure." [GOC:mtg_sensu, ISBN:0815316194, PMID:11121786]
-comment: For example, as seen in myxobacterium. It is not intended to describe fruiting body development as is Dictyostelium.
+comment: For example, as seen in myxobacterium. It is not intended to describe fruiting body development as is Dictyostelium.
synonym: "fruiting body development in cellular response to starvation" BROAD []
synonym: "fruiting body development in response to starvation" BROAD []
+is_a: GO:0032502 ! developmental process
is_a: GO:0042594 ! response to starvation
-is_a: GO:0044764 ! multi-organism cellular process
[Term]
id: GO:0030584
@@ -158486,7 +158497,7 @@ is_a: GO:0030582 ! reproductive fruiting body development
id: GO:0030585
name: phosphoenolpyruvate carboxykinase (diphosphate) activity
namespace: molecular_function
-def: "Catalysis of the reaction: diphosphate + oxaloacetate = CO(2) + phosphate + phosphoenolpyruvate." [EC:4.1.1.38, RHEA:22356]
+def: "Catalysis of the reaction: diphosphate + oxaloacetate = CO2 + phosphate + phosphoenolpyruvate." [EC:4.1.1.38, RHEA:22356]
synonym: "diphosphate:oxaloacetate carboxy-lyase (transphosphorylating)" RELATED [EC:4.1.1.38]
synonym: "diphosphate:oxaloacetate carboxy-lyase (transphosphorylating; phosphoenolpyruvate-forming)" RELATED [EC:4.1.1.38]
synonym: "PEP carboxyphosphotransferase activity" RELATED [EC:4.1.1.38]
@@ -158709,7 +158720,7 @@ replaced_by: GO:0004190
id: GO:0030603
name: oxaloacetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + oxaloacetate = acetate + H(+) + oxalate." [EC:3.7.1.1, RHEA:24432]
+def: "Catalysis of the reaction: H2O + oxaloacetate = acetate + H+ + oxalate." [EC:3.7.1.1, RHEA:24432]
synonym: "oxalacetic hydrolase activity" RELATED [EC:3.7.1.1]
synonym: "oxaloacetate acetylhydrolase activity" RELATED [EC:3.7.1.1]
xref: EC:3.7.1.1
@@ -158722,7 +158733,7 @@ is_a: GO:0016823 ! hydrolase activity, acting on acid carbon-carbon bonds, in ke
id: GO:0030604
name: 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH." [EC:1.1.1.267, RHEA:13717]
+def: "Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + NADP+ = 1-deoxy-D-xylulose 5-phosphate + H+ + NADPH." [EC:1.1.1.267, RHEA:13717]
synonym: "1-deoxy-D-xylulose-5-phosphate isomeroreductase activity" RELATED [EC:1.1.1.267]
synonym: "1-deoxyxylulose-5-phosphate reductoisomerase activity" RELATED [EC:1.1.1.267]
synonym: "2-C-methyl-D-erythritol-4-phosphate:NADP+ oxidoreductase (isomerizing)" RELATED [EC:1.1.1.267]
@@ -158790,7 +158801,7 @@ id: GO:0030617
name: obsolete transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity
namespace: molecular_function
def: "OBSOLETE. A TGF-beta cytoplasmic mediator that inhibits the signaling function of common-partner and pathway-specific mediators." [PMID:9759503]
-comment: This term was obsoleted because it represents the same activity as GO:0140416 ; DNA-binding transcription factor inhibitor activity', occurs_in cytosol.
+comment: This term was obsoleted because it represents the same activity as GO:0140416 ; DNA-binding transcription factor inhibitor activity', occurs in cytosol.
synonym: "inhibitory SMAD protein" RELATED []
synonym: "TGF-beta receptor, inhibitory cytoplasmic mediator activity" EXACT []
synonym: "TGFbeta receptor, inhibitory cytoplasmic mediator activity" EXACT []
@@ -158915,20 +158926,20 @@ synonym: "D-alanine anabolism" EXACT []
synonym: "D-alanine biosynthesis" EXACT []
synonym: "D-alanine formation" EXACT []
synonym: "D-alanine synthesis" EXACT []
-is_a: GO:0046145 ! D-alanine family amino acid biosynthetic process
+is_a: GO:0006523 ! alanine biosynthetic process
is_a: GO:0046436 ! D-alanine metabolic process
is_a: GO:0046437 ! D-amino acid biosynthetic process
[Term]
id: GO:0030633
-name: D-alanine family amino acid catabolic process
+name: obsolete D-alanine family amino acid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of D-alanine and related amino acids." [GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of D-alanine and related amino acids." [GOC:mah]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "D-alanine family amino acid breakdown" EXACT []
synonym: "D-alanine family amino acid catabolism" EXACT []
synonym: "D-alanine family amino acid degradation" EXACT []
-is_a: GO:0006524 ! alanine catabolic process
-is_a: GO:0046144 ! D-alanine family amino acid metabolic process
+is_obsolete: true
[Term]
id: GO:0030634
@@ -159022,31 +159033,35 @@ def: "Any process involved in the maintenance of an internal equilibrium of hydr
synonym: "cellular hydrogen ion homeostasis" EXACT [GOC:dph, GOC:tb]
synonym: "proton homeostasis" EXACT []
is_a: GO:0006885 ! regulation of pH
-is_a: GO:0030004 ! cellular monovalent inorganic cation homeostasis
+is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
[Term]
id: GO:0030642
-name: cellular sulfate ion homeostasis
+name: intracellular sulfate ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of sulfate ions at the level of a cell." [GOC:mah]
+def: "A homeostatic process involved in the maintenance of a steady state level of sulfate ions within a cell." [GOC:mah, PMID:24193406]
+synonym: "cellular sulfate ion homeostasis" EXACT []
synonym: "sulphate ion homeostasis" BROAD []
is_a: GO:0055063 ! sulfate ion homeostasis
-is_a: GO:0072501 ! cellular divalent inorganic anion homeostasis
+is_a: GO:0055082 ! intracellular chemical homeostasis
[Term]
id: GO:0030643
-name: cellular phosphate ion homeostasis
+name: intracellular phosphate ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of phosphate ions at the level of a cell." [GOC:mah]
+def: "A homeostatic process involved in the maintenance of a steady state level of phosphate ions within a cell." [GOC:mah]
+subset: goslim_pombe
+synonym: "cellular phosphate ion homeostasis" EXACT []
is_a: GO:0055062 ! phosphate ion homeostasis
-is_a: GO:0072502 ! cellular trivalent inorganic anion homeostasis
+is_a: GO:0055082 ! intracellular chemical homeostasis
[Term]
id: GO:0030644
-name: cellular chloride ion homeostasis
+name: intracellular chloride ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of chloride ions at the level of a cell." [GOC:mah]
-is_a: GO:0030320 ! cellular monovalent inorganic anion homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of chloride ions within a cell." [GOC:mah]
+synonym: "cellular chloride ion homeostasis" EXACT []
+is_a: GO:0030002 ! intracellular monoatomic anion homeostasis
is_a: GO:0055064 ! chloride ion homeostasis
[Term]
@@ -159058,7 +159073,7 @@ synonym: "butyrate fermentation" EXACT []
synonym: "glucose fermentation to butyrate" EXACT []
is_a: GO:0006007 ! glucose catabolic process
is_a: GO:0006113 ! fermentation
-is_a: GO:1902705 ! hexose catabolic process to butyrate
+is_a: GO:0019605 ! butyrate metabolic process
[Term]
id: GO:0030647
@@ -159133,10 +159148,9 @@ name: beta-lactam antibiotic metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins." [GOC:mah, ISBN:0198506732]
synonym: "beta-lactam antibiotic metabolism" EXACT []
+is_a: GO:0009308 ! amine metabolic process
is_a: GO:0016999 ! antibiotic metabolic process
-is_a: GO:0044106 ! cellular amine metabolic process
-is_a: GO:0072338 ! cellular lactam metabolic process
-is_a: GO:1901360 ! organic cyclic compound metabolic process
+is_a: GO:0072338 ! lactam metabolic process
[Term]
id: GO:0030654
@@ -159149,9 +159163,7 @@ synonym: "beta-lactam antibiotic formation" EXACT []
synonym: "beta-lactam antibiotic synthesis" EXACT []
is_a: GO:0017000 ! antibiotic biosynthetic process
is_a: GO:0030653 ! beta-lactam antibiotic metabolic process
-is_a: GO:0072339 ! cellular lactam biosynthetic process
-is_a: GO:1901362 ! organic cyclic compound biosynthetic process
-is_a: GO:1901566 ! organonitrogen compound biosynthetic process
+is_a: GO:0072339 ! lactam biosynthetic process
[Term]
id: GO:0030655
@@ -159163,7 +159175,7 @@ synonym: "beta-lactam antibiotic catabolism" EXACT []
synonym: "beta-lactam antibiotic degradation" EXACT []
is_a: GO:0017001 ! antibiotic catabolic process
is_a: GO:0030653 ! beta-lactam antibiotic metabolic process
-is_a: GO:0072340 ! cellular lactam catabolic process
+is_a: GO:0072340 ! lactam catabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
@@ -159184,7 +159196,6 @@ def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the
comment: This term was made obsolete because it was replaced by more specific terms.
synonym: "regulation of coenzyme and prosthetic group metabolic process" EXACT []
is_obsolete: true
-consider: GO:0051199
[Term]
id: GO:0030658
@@ -159335,6 +159346,7 @@ def: "The binding activity of a protein that brings together two or more macromo
subset: goslim_chembl
subset: goslim_yeast
synonym: "protein binding, bridging" EXACT []
+synonym: "protein recruiting activity" RELATED []
synonym: "protein-protein adaptor" NARROW []
is_a: GO:0060090 ! molecular adaptor activity
@@ -159408,30 +159420,6 @@ synonym: "evasion or tolerance of host defense response" NARROW []
synonym: "evasion or tolerance of host defenses" RELATED []
is_a: GO:0052200 ! response to host defenses
-[Term]
-id: GO:0030683
-name: mitigation of host immune response by virus
-namespace: biological_process
-alt_id: GO:0019052
-alt_id: GO:0019053
-def: "A process by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mah, GOC:pk]
-synonym: "evasion by virus of host immune response" NARROW [GOC:bf, GOC:bm, GOC:jl]
-synonym: "evasion or tolerance by virus of host immune response" RELATED []
-synonym: "inhibition of extracellular antiviral response" EXACT []
-synonym: "mitigation by virus of host immune response" EXACT []
-synonym: "negative regulation by virus of extracellular antiviral response" EXACT []
-synonym: "negative regulation by virus of intracellular antiviral response" EXACT []
-synonym: "negative regulation of host extracellular antiviral response by virus" EXACT []
-synonym: "negative regulation of host intracellular antiviral response by virus" EXACT []
-synonym: "suppression by virus of host extracellular antiviral response" EXACT []
-synonym: "suppression by virus of host immune response" NARROW [GOC:bf]
-synonym: "suppression by virus of host intracellular antiviral response" EXACT []
-synonym: "suppression of host extracellular antiviral response by virus" EXACT []
-synonym: "suppression of host intracellular antiviral response by virus" EXACT []
-synonym: "viral inhibition of intracellular antiviral response" EXACT []
-is_a: GO:0019049 ! mitigation of host defenses by virus
-is_a: GO:0050690 ! regulation of defense response to virus by virus
-
[Term]
id: GO:0030684
name: preribosome
@@ -159603,7 +159591,7 @@ is_a: GO:0042083 ! 5,10-methylenetetrahydrofolate-dependent methyltransferase ac
id: GO:0030699
name: glycine reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl phosphate + H(2)O + NH(4)(+) + thioredoxin disulfide = glycine + H(+) + phosphate + thioredoxin." [EC:1.21.4.2, RHEA:12232]
+def: "Catalysis of the reaction: acetyl phosphate + H2O + NH4 + thioredoxin disulfide = glycine + H+ + phosphate + thioredoxin." [EC:1.21.4.2, RHEA:12232]
synonym: "acetyl-phosphate ammonia:thioredoxin disulfide oxidoreductase (glycine-forming)" RELATED [EC:1.21.4.2]
xref: EC:1.21.4.2
xref: KEGG_REACTION:R07226
@@ -159674,7 +159662,7 @@ relationship: part_of GO:0007293 ! germarium-derived egg chamber formation
[Term]
id: GO:0030707
-name: ovarian follicle cell development
+name: follicle cell of egg chamber development
namespace: biological_process
def: "The process that occurs during oogenesis involving the ovarian follicle cells, somatic cells which surround the germ cells of an ovary. An example of this is found in Drosophila melanogaster." [GOC:mtg_sensu, PMID:10822261]
is_a: GO:0002064 ! epithelial cell development
@@ -159689,7 +159677,7 @@ namespace: biological_process
def: "Formation of a single follicular epithelium around the germ-line derived cells of a cyst formed in the germarium. An example of this process is found in Drosophila melanogaster." [GOC:mtg_sensu, PMID:11591336]
is_a: GO:0048139 ! female germ-line cyst encapsulation
relationship: part_of GO:0007293 ! germarium-derived egg chamber formation
-relationship: part_of GO:0030707 ! ovarian follicle cell development
+relationship: part_of GO:0030707 ! follicle cell of egg chamber development
[Term]
id: GO:0030709
@@ -159699,7 +159687,7 @@ def: "The delamination process that results in the splitting off of border cells
synonym: "border cell delamination" BROAD []
is_a: GO:0022414 ! reproductive process
is_a: GO:0060232 ! delamination
-relationship: part_of GO:0030707 ! ovarian follicle cell development
+relationship: part_of GO:0030707 ! follicle cell of egg chamber development
[Term]
id: GO:0030710
@@ -159743,12 +159731,12 @@ relationship: negatively_regulates GO:0030709 ! border follicle cell delaminatio
[Term]
id: GO:0030713
-name: ovarian follicle cell stalk formation
+name: follicle cell of egg chamber stalk formation
namespace: biological_process
def: "Development of ovarian follicle cells to create the interfollicular stalks that connect the egg chambers of progressive developmental stages. An example of this process is found in Drosophila melanogaster." [GOC:mtg_sensu, PMID:10822261]
is_a: GO:0000904 ! cell morphogenesis involved in differentiation
is_a: GO:0003006 ! developmental process involved in reproduction
-relationship: part_of GO:0030707 ! ovarian follicle cell development
+relationship: part_of GO:0030707 ! follicle cell of egg chamber development
[Term]
id: GO:0030714
@@ -159760,7 +159748,7 @@ is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0009798 ! axis specification
is_a: GO:0016334 ! establishment or maintenance of polarity of follicular epithelium
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
-relationship: part_of GO:0030707 ! ovarian follicle cell development
+relationship: part_of GO:0030707 ! follicle cell of egg chamber development
[Term]
id: GO:0030715
@@ -159893,7 +159881,7 @@ relationship: part_of GO:0007292 ! female gamete generation
id: GO:0030729
name: acetoacetate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetoacetate + ATP + CoA = acetoacetyl-CoA + AMP + diphosphate + H(+)." [EC:6.2.1.16, RHEA:16117]
+def: "Catalysis of the reaction: acetoacetate + ATP + CoA = acetoacetyl-CoA + AMP + diphosphate + H+." [EC:6.2.1.16, RHEA:16117]
synonym: "acetoacetate:CoA ligase (AMP-forming)" RELATED [EC:6.2.1.16]
synonym: "acetoacetyl-CoA synthetase activity" EXACT []
xref: EC:6.2.1.16
@@ -159930,7 +159918,7 @@ is_a: GO:0019915 ! lipid storage
id: GO:0030731
name: guanidinoacetate N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanidinoacetate = S-adenosyl-L-homocysteine + creatine + H(+)." [EC:2.1.1.2, RHEA:10656]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanidinoacetate = S-adenosyl-L-homocysteine + creatine + H+." [EC:2.1.1.2, RHEA:10656]
synonym: "GA methylpherase activity" RELATED [EC:2.1.1.2]
synonym: "guanidinoacetate methyltransferase activity" RELATED [EC:2.1.1.2]
synonym: "guanidinoacetate transmethylase activity" RELATED [EC:2.1.1.2]
@@ -159987,7 +159975,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030735
name: carnosine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + carnosine = S-adenosyl-L-homocysteine + anserine + H(+)." [EC:2.1.1.22, RHEA:14205]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + carnosine = S-adenosyl-L-homocysteine + anserine + H+." [EC:2.1.1.22, RHEA:14205]
synonym: "S-adenosyl-L-methionine:carnosine N-methyltransferase activity" RELATED [EC:2.1.1.22]
xref: EC:2.1.1.22
xref: KEGG_REACTION:R02144
@@ -160000,7 +159988,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030736
name: phenol O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + phenol = S-adenosyl-L-homocysteine + anisole + H(+)." [EC:2.1.1.25, RHEA:14809]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + phenol = S-adenosyl-L-homocysteine + anisole + H+." [EC:2.1.1.25, RHEA:14809]
synonym: "PMT" RELATED [EC:2.1.1.25]
synonym: "S-adenosyl-L-methionine:phenol O-methyltransferase activity" RELATED [EC:2.1.1.25]
xref: EC:2.1.1.25
@@ -160013,7 +160001,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030737
name: iodophenol O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-iodophenol + S-adenosyl-L-methionine = 1-iodo-2-methoxybenzene + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.26, RHEA:14313]
+def: "Catalysis of the reaction: 2-iodophenol + S-adenosyl-L-methionine = 1-iodo-2-methoxybenzene + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.26, RHEA:14313]
synonym: "S-adenosyl-L-methionine:2-iodophenol O-methyltransferase activity" RELATED [EC:2.1.1.26]
xref: EC:2.1.1.26
xref: KEGG_REACTION:R03746
@@ -160025,7 +160013,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030738
name: tyramine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + tyramine = N-methyltyramine + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.27, RHEA:14865]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + tyramine = N-methyltyramine + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.27, RHEA:14865]
synonym: "DIB O-methyltransferase (3,5-diiodo-4-hydroxy-benzoic acid)" RELATED [EC:2.1.1.27]
synonym: "S-adenosyl-L-methionine:tyramine N-methyltransferase activity" RELATED [EC:2.1.1.27]
synonym: "S-adenosyl-methionine:tyramine N-methyltransferase activity" RELATED [EC:2.1.1.27]
@@ -160052,7 +160040,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030740
name: inositol 3-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + myo-inositol = 1D-3-O-methyl-myo-inositol + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.39, RHEA:18877]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + myo-inositol = 1D-3-O-methyl-myo-inositol + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.39, RHEA:18877]
synonym: "inositol L-1-methyltransferase activity" RELATED [EC:2.1.1.39]
synonym: "myo-inositol 1-methyltransferase activity" RELATED [EC:2.1.1.39]
synonym: "myo-inositol 1-O-methyltransferase (name based on 1L-numbering system and not 1D-numbering)" RELATED [EC:2.1.1.39]
@@ -160070,7 +160058,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030741
name: inositol 1-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + myo-inositol = 1D-1-O-methyl-myo-inositol + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.40, RHEA:17565]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + myo-inositol = 1D-1-O-methyl-myo-inositol + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.40, RHEA:17565]
synonym: "inositol 3-O-methyltransferase (name based on 1L-numbering system and not 1D-numbering)" RELATED [EC:2.1.1.40]
synonym: "inositol 3-O-methyltransferase activity" RELATED [EC:2.1.1.40]
synonym: "inositol D-1-methyltransferase activity" RELATED [EC:2.1.1.40]
@@ -160112,7 +160100,7 @@ is_a: GO:0062105 ! RNA 2'-O-methyltransferase activity
id: GO:0030744
name: luteolin O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + luteolin = 4',5,7-trihydroxy-3'-methoxyflavone + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.42, RHEA:14589]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + luteolin = 4',5,7-trihydroxy-3'-methoxyflavone + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.42, RHEA:14589]
synonym: "luteolin 3'-O-methyltransferase activity" RELATED [EC:2.1.1.42]
synonym: "luteolin methyltransferase activity" RELATED [EC:2.1.1.42]
synonym: "o-dihydric phenol meta-O-methyltransferase activity" RELATED [EC:2.1.1.42]
@@ -160201,7 +160189,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030750
name: putrescine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + putrescine = N-methylputrescine + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.53, RHEA:15037]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + putrescine = N-methylputrescine + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.53, RHEA:15037]
synonym: "putrescine methyltransferase activity" RELATED [EC:2.1.1.53]
synonym: "S-adenosyl-L-methionine:putrescine N-methyltransferase activity" RELATED [EC:2.1.1.53]
xref: EC:2.1.1.53
@@ -160214,7 +160202,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030751
name: licodione 2'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + licodione = 2'-O-methyllicodione + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.65, RHEA:18521]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + licodione = 2'-O-methyllicodione + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.65, RHEA:18521]
synonym: "S-adenosyl-L-methionine:licodione 2'-O-methyltransferase activity" RELATED [EC:2.1.1.65]
xref: EC:2.1.1.65
xref: KEGG_REACTION:R03623
@@ -160292,7 +160280,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030756
name: isoorientin 3'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + isoorientin = S-adenosyl-L-homocysteine + H(+) + isoscoparin." [EC:2.1.1.78, RHEA:24096]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + isoorientin = S-adenosyl-L-homocysteine + H+ + isoscoparin." [EC:2.1.1.78, RHEA:24096]
synonym: "isoorientin 3'-methyltransferase activity" RELATED [EC:2.1.1.78]
synonym: "S-adenosyl-L-methionine:isoorientin 3'-O-methyltransferase activity" RELATED [EC:2.1.1.78]
xref: EC:2.1.1.78
@@ -160322,7 +160310,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030758
name: 3,7-dimethylquercitin 4'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3',4',5-trihydroxy-3,7-dimethoxyflavone + S-adenosyl-L-methionine(1+) = 3',5-dihydroxy-3,4',7-trimethoxyflavone + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.83, RHEA:21832]
+def: "Catalysis of the reaction: 3',4',5-trihydroxy-3,7-dimethoxyflavone + S-adenosyl-L-methionine(1+) = 3',5-dihydroxy-3,4',7-trimethoxyflavone + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.83, RHEA:21832]
synonym: "3,7-dimethylquercetin 4'-O-methyltransferase activity" RELATED [EC:2.1.1.83]
synonym: "4'-OMT activity" RELATED [EC:2.1.1.83]
synonym: "flavonol 4'-methyltransferase activity" RELATED [EC:2.1.1.83]
@@ -160339,7 +160327,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030759
name: methylquercetagetin 6-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3',4',5,6-tetrahydroxy-3,7-dimethoxyflavone + S-adenosyl-L-methionine(1+) = 3',4',5-trihydroxy-3,6,7-trimethoxyflavone + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.84, RHEA:18717]
+def: "Catalysis of the reaction: 3',4',5,6-tetrahydroxy-3,7-dimethoxyflavone + S-adenosyl-L-methionine(1+) = 3',4',5-trihydroxy-3,6,7-trimethoxyflavone + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.84, RHEA:18717]
synonym: "6-OMT" RELATED [EC:2.1.1.84]
synonym: "flavonol 6-methyltransferase activity" RELATED [EC:2.1.1.84]
synonym: "flavonol 6-O-methyltransferase activity" RELATED [EC:2.1.1.84]
@@ -160368,7 +160356,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030761
name: 8-hydroxyquercitin 8-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3,3',4',5,7,8-hexahydroxyflavone + S-adenosyl-L-methionine(1+) = 3,3',4',5,7-pentahydroxy-8-methoxyflavone + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.88, RHEA:16593]
+def: "Catalysis of the reaction: 3,3',4',5,7,8-hexahydroxyflavone + S-adenosyl-L-methionine(1+) = 3,3',4',5,7-pentahydroxy-8-methoxyflavone + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.88, RHEA:16593]
synonym: "8-hydroxyquercetin 8-O-methyltransferase activity" RELATED [EC:2.1.1.88]
synonym: "flavonol 8-methyltransferase activity" RELATED [EC:2.1.1.88]
synonym: "flavonol 8-O-methyltransferase activity" RELATED [EC:2.1.1.88]
@@ -160383,7 +160371,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030762
name: tetrahydrocolumbamine 2-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-tetrahydrocolumbamine + S-adenosyl-L-methionine(1+) = S-adenosyl-L-homocysteine + H(+) + tetrahydropalmatine." [EC:2.1.1.89, RHEA:22536]
+def: "Catalysis of the reaction: (S)-tetrahydrocolumbamine + S-adenosyl-L-methionine(1+) = S-adenosyl-L-homocysteine + H+ + tetrahydropalmatine." [EC:2.1.1.89, RHEA:22536]
synonym: "S-adenosyl-L-methionine:5,8,13,13a-tetrahydrocolumbamine 2-O-methyltransferase activity" RELATED [EC:2.1.1.89]
synonym: "tetrahydrocolumbamine methyltransferase activity" RELATED [EC:2.1.1.89]
xref: EC:2.1.1.89
@@ -160396,7 +160384,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030763
name: isobutyraldoxime O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-methylpropanal oxime + S-adenosyl-L-methionine = 2-methylpropanal O-methyloxime + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.91, RHEA:10996]
+def: "Catalysis of the reaction: 2-methylpropanal oxime + S-adenosyl-L-methionine = 2-methylpropanal O-methyloxime + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.91, RHEA:10996]
synonym: "aldoxime methyltransferase activity" RELATED [EC:2.1.1.91]
synonym: "aldoxime O-methyltransferase activity" RELATED [EC:2.1.1.91]
synonym: "S-adenosyl-L-methionine:2-methylpropanal-oxime O-methyltransferase activity" RELATED [EC:2.1.1.91]
@@ -160425,7 +160413,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030767
name: 3-hydroxyanthranilate 4-C-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxyanthranilate + S-adenosyl-L-methionine = 3-hydroxy-4-methylanthranilate + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.97, RHEA:17833]
+def: "Catalysis of the reaction: 3-hydroxyanthranilate + S-adenosyl-L-methionine = 3-hydroxy-4-methylanthranilate + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.97, RHEA:17833]
synonym: "3-hydroxyanthranilate 4-methyltransferase activity" RELATED [EC:2.1.1.97]
synonym: "S-adenosyl-L-methionine:3-hydroxyanthranilate 4-C-methyltransferase activity" RELATED [EC:2.1.1.97]
xref: EC:2.1.1.97
@@ -160438,7 +160426,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030768
name: 16-methoxy-2,3-dihydro-3-hydroxytabersonine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (3R)-3-hydroxy-16-methoxy-2,3-dihydrotabersonine + S-adenosyl-L-methionine = S-adenosyl-L-homocysteine + deacetoxyvindoline + H(+)." [EC:2.1.1.99, RHEA:11336]
+def: "Catalysis of the reaction: (3R)-3-hydroxy-16-methoxy-2,3-dihydrotabersonine + S-adenosyl-L-methionine = S-adenosyl-L-homocysteine + deacetoxyvindoline + H+." [EC:2.1.1.99, RHEA:11336]
synonym: "16-methoxy-2,3-dihydro-3-hydroxytabersonine methyltransferase activity" RELATED [EC:2.1.1.99]
synonym: "3-hydroxy-16-methoxy-2,3-dihydrotabersonine N-methyltransferase activity" RELATED [EC:2.1.1.99]
synonym: "NMT activity" RELATED [EC:2.1.1.99]
@@ -160454,7 +160442,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030769
name: macrocin O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + macrocin = S-adenosyl-L-homocysteine + H(+) + tylosin." [EC:2.1.1.101, RHEA:17269]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + macrocin = S-adenosyl-L-homocysteine + H+ + tylosin." [EC:2.1.1.101, RHEA:17269]
synonym: "macrocin methyltransferase activity" RELATED [EC:2.1.1.101]
synonym: "S-adenosyl-L-methionine-macrocin O-methyltransferase activity" RELATED [EC:2.1.1.101]
synonym: "S-adenosyl-L-methionine:macrocin 3'''-O-methyltransferase activity" RELATED [EC:2.1.1.101]
@@ -160468,7 +160456,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030770
name: demethylmacrocin O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + demethylmacrocin = S-adenosyl-L-homocysteine + H(+) + macrocin." [EC:2.1.1.102, RHEA:17573]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + demethylmacrocin = S-adenosyl-L-homocysteine + H+ + macrocin." [EC:2.1.1.102, RHEA:17573]
synonym: "demethylmacrocin methyltransferase activity" RELATED [EC:2.1.1.102]
synonym: "S-adenosyl-L-methionine:demethylmacrocin 2'''-O-methyltransferase activity" RELATED [EC:2.1.1.102]
xref: EC:2.1.1.102
@@ -160481,7 +160469,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030771
name: N-benzoyl-4-hydroxyanthranilate 4-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-benzoyl-4-hydroxyanthranilate + S-adenosyl-L-methionine(1+) = N-benzoyl-4-methoxyanthranilate + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.105, RHEA:17405]
+def: "Catalysis of the reaction: N-benzoyl-4-hydroxyanthranilate + S-adenosyl-L-methionine(1+) = N-benzoyl-4-methoxyanthranilate + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.105, RHEA:17405]
synonym: "benzoyl-CoA:anthranilate N-benzoyltransferase" BROAD [EC:2.1.1.105]
synonym: "N-benzoyl-4-hydroxyanthranilate 4-methyltransferase activity" RELATED [EC:2.1.1.105]
synonym: "S-adenosyl-L-methionine:N-benzoyl-4-O-hydroxyanthranilate 4-O-methyltransferase activity" RELATED [EC:2.1.1.105]
@@ -160495,7 +160483,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030772
name: tryptophan 2-C-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + L-tryptophan = S-adenosyl-L-homocysteine + L-2-methyltryptophan + H(+)." [EC:2.1.1.106, RHEA:17321]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + L-tryptophan = S-adenosyl-L-homocysteine + L-2-methyltryptophan + H+." [EC:2.1.1.106, RHEA:17321]
synonym: "S-adenosyl-L-methionine:L-tryptophan 2-C-methyltransferase activity" RELATED [EC:2.1.1.106]
synonym: "S-adenosylmethionine:tryptophan 2-methyltransferase activity" RELATED [EC:2.1.1.106]
synonym: "tryptophan 2-methyltransferase activity" RELATED [EC:2.1.1.106]
@@ -160509,7 +160497,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030773
name: 6-hydroxymellein O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-hydroxymellein + S-adenosyl-L-methionine = 6-methoxymellein + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.108, RHEA:15201]
+def: "Catalysis of the reaction: 6-hydroxymellein + S-adenosyl-L-methionine = 6-methoxymellein + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.108, RHEA:15201]
synonym: "6-hydroxymellein methyltransferase activity" RELATED [EC:2.1.1.108]
synonym: "S-adenosyl-L-methionine:6-hydroxymellein 6-O-methyltransferase activity" RELATED [EC:2.1.1.108]
xref: EC:2.1.1.108
@@ -160522,7 +160510,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030774
name: anthranilate N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + anthranilate = N-methylanthranilate + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.111, RHEA:12180]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + anthranilate = N-methylanthranilate + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.111, RHEA:12180]
synonym: "anthranilic acid N-methyltransferase activity" RELATED [EC:2.1.1.111]
synonym: "S-adenosyl-L-methionine:anthranilate N-methyltransferase activity" RELATED [EC:2.1.1.111]
xref: EC:2.1.1.111
@@ -160559,7 +160547,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030777
name: (S)-scoulerine 9-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-scoulerine + S-adenosyl-L-methionine(1+) = (S)-tetrahydrocolumbamine + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.117, RHEA:23808]
+def: "Catalysis of the reaction: (S)-scoulerine + S-adenosyl-L-methionine(1+) = (S)-tetrahydrocolumbamine + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.117, RHEA:23808]
synonym: "S-adenosyl-L-methionine:(S)-scoclaurine 9-O-methyltransferase activity" RELATED [EC:2.1.1.117]
synonym: "S-adenosyl-L-methionine:(S)-scoulerine 9-O-methyltransferase activity" RELATED [EC:2.1.1.117]
xref: EC:2.1.1.117
@@ -160572,7 +160560,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030778
name: columbamine O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + columbamine = S-adenosyl-L-homocysteine + H(+) + palmatine." [EC:2.1.1.118, RHEA:15373]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + columbamine = S-adenosyl-L-homocysteine + H+ + palmatine." [EC:2.1.1.118, RHEA:15373]
synonym: "S-adenosyl-L-methionine:columbamine O-methyltransferase activity" RELATED [EC:2.1.1.118]
xref: EC:2.1.1.118
xref: KEGG_REACTION:R03721
@@ -160584,7 +160572,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030779
name: 10-hydroxydihydrosanguinarine 10-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 10-hydroxydihydrosanguinarine + S-adenosyl-L-methionine(1+) = S-adenosyl-L-homocysteine + dihydrochelirubine + H(+)." [EC:2.1.1.119, RHEA:18541]
+def: "Catalysis of the reaction: 10-hydroxydihydrosanguinarine + S-adenosyl-L-methionine(1+) = S-adenosyl-L-homocysteine + dihydrochelirubine + H+." [EC:2.1.1.119, RHEA:18541]
synonym: "S-adenosyl-L-methionine:10-hydroxydihydrosanguinarine 10-O-methyltransferase activity" RELATED [EC:2.1.1.119]
xref: EC:2.1.1.119
xref: KEGG_REACTION:R04707
@@ -160596,7 +160584,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030780
name: 12-hydroxydihydrochelirubine 12-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 12-hydroxydihydrochelirubine + S-adenosyl-L-methionine(1+) = S-adenosyl-L-homocysteine + dihydromacarpine + H(+)." [EC:2.1.1.120, RHEA:21092]
+def: "Catalysis of the reaction: 12-hydroxydihydrochelirubine + S-adenosyl-L-methionine(1+) = S-adenosyl-L-homocysteine + dihydromacarpine + H+." [EC:2.1.1.120, RHEA:21092]
synonym: "S-adenosyl-L-methionine:12-hydroxydihydrochelirubine 12-O-methyltransferase activity" RELATED [EC:2.1.1.120]
xref: EC:2.1.1.120
xref: KEGG_REACTION:R04705
@@ -160681,7 +160669,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030787
name: inositol 4-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + myo-inositol = 1D-4-O-methyl-myo-inositol + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.129, RHEA:23248]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + myo-inositol = 1D-4-O-methyl-myo-inositol + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.129, RHEA:23248]
synonym: "myo-inositol 4-O-methyltransferase activity" RELATED [EC:2.1.1.129]
synonym: "myo-inositol 6-O-methyltransferase activity" RELATED [EC:2.1.1.129]
synonym: "S-adenosyl-L-methionine:1D-myo-inositol 4-methyltransferase activity" RELATED [EC:2.1.1.129]
@@ -160696,7 +160684,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030788
name: precorrin-2 C20-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + precorrin-2 = S-adenosyl-L-homocysteine + H(+) + precorrin-3A." [EC:2.1.1.130, RHEA:16841]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + precorrin-2 = S-adenosyl-L-homocysteine + H+ + precorrin-3A." [EC:2.1.1.130, RHEA:16841]
synonym: "S-adenosyl-L-methionine--precorrin-2 methyltransferase activity" RELATED [EC:2.1.1.130]
synonym: "S-adenosyl-L-methionine:precorrin-4 C20-methyltransferase activity" RELATED [EC:2.1.1.130]
xref: EC:2.1.1.130
@@ -160745,7 +160733,6 @@ xref: EC:2.1.1.137
xref: MetaCyc:2.1.1.137-RXN
xref: Reactome:R-HSA-5696213 "AS3MT transfers CH3 from AdoMet to methylarsonite"
xref: Reactome:R-HSA-5696220 "AS3MT transfers CH3 from AdoMet to arsenite(3-)"
-xref: RHEA:15293
xref: UM-BBD_reactionID:r0805
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
@@ -160763,7 +160750,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030793
name: 3'-demethylstaurosporine O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-demethylstaurosporine + S-adenosyl-L-methionine = S-adenosyl-L-homocysteine + H(+) + staurosporine." [EC:2.1.1.139, RHEA:11696]
+def: "Catalysis of the reaction: 3'-demethylstaurosporine + S-adenosyl-L-methionine = S-adenosyl-L-homocysteine + H+ + staurosporine." [EC:2.1.1.139, RHEA:11696]
synonym: "3'-demethoxy-3'-hydroxystaurosporine O-methyltransferase activity" RELATED [EC:2.1.1.139]
synonym: "S-adenosyl-L-methionine:3'-demethylstaurosporine O-methyltransferase activity" RELATED [EC:2.1.1.139]
synonym: "staurosporine synthase activity" RELATED [EC:2.1.1.139]
@@ -160803,7 +160790,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030796
name: cycloartenol 24-C-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + cycloartenol = (24R)-24-methylcycloart-25-en-3beta-ol + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.142, RHEA:13137]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + cycloartenol = (24R)-24-methylcycloart-25-en-3beta-ol + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.142, RHEA:13137]
synonym: "S-adenosyl-L-methionine:cycloartenol 24-C-methyltransferase activity" RELATED [EC:2.1.1.142]
synonym: "sterol C-methyltransferase activity" BROAD [EC:2.1.1.142]
xref: EC:2.1.1.142
@@ -160816,7 +160803,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030797
name: 24-methylenesterol C-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 24-methylidenelophenol + S-adenosyl-L-methionine(1+) = (Z)-24-ethylidenelophenol + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.143, RHEA:21044]
+def: "Catalysis of the reaction: 24-methylidenelophenol + S-adenosyl-L-methionine(1+) = (Z)-24-ethylidenelophenol + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.143, RHEA:21044]
synonym: "24-methylenelophenol C-24(1)-methyltransferase activity" RELATED [EC:2.1.1.143]
synonym: "24-methylenelophenol C-241-methyltransferase activity" RELATED [EC:2.1.1.143]
synonym: "S-adenosyl-L-methionine:24-methylenelophenol C-methyltransferase activity" RELATED [EC:2.1.1.143]
@@ -161325,7 +161312,7 @@ id: GO:0030828
name: obsolete positive regulation of cGMP biosynthetic process
namespace: biological_process
def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cGMP." [GOC:mah]
-comment: The reason for obsoletion is that this term represent the regulation of a signaling pathway, not regulation of metabolism.
+comment: The reason for obsoletion is that this term represent the regulation of a signaling pathway, not regulation of metabolism.
synonym: "activation of cGMP biosynthetic process" NARROW []
synonym: "positive regulation of cGMP anabolism" EXACT []
synonym: "positive regulation of cGMP biosynthesis" EXACT []
@@ -161343,7 +161330,7 @@ id: GO:0030829
name: obsolete regulation of cGMP catabolic process
namespace: biological_process
def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of cGMP." [GOC:mah]
-comment: The reason for obsoletion is that this term represent the regulation of a signaling pathway, not regulation of metabolism.
+comment: The reason for obsoletion is that this term represent the regulation of a signaling pathway, not regulation of metabolism.
synonym: "regulation of cGMP breakdown" EXACT []
synonym: "regulation of cGMP catabolism" EXACT []
synonym: "regulation of cGMP degradation" EXACT []
@@ -161590,7 +161577,7 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
id: GO:0030846
name: termination of RNA polymerase II transcription, poly(A)-coupled
namespace: biological_process
-def: "The process in which transcription of polyadenylated RNA polymerase II transcripts is terminated; cleavage and polyadenylylation of the mRNA 3' end is coupled to transcription termination." [GOC:txnOH, PMID:12944462, PMID:18679429]
+def: "An RNA polymerase II transcription termination process in which cleavage and polyadenylylation of the mRNA 3' end are coupled to transcription termination." [GOC:txnOH, PMID:12944462, PMID:18679429, PMID:27371117]
synonym: "termination of RNA polymerase II transcription, polyadenylation-coupled" RELATED []
synonym: "transcription termination from Pol II promoter, poly(A) coupled" RELATED []
synonym: "transcription termination from Pol II promoter, RNA polymerase(A) coupled" RELATED []
@@ -161600,7 +161587,7 @@ is_a: GO:0006369 ! termination of RNA polymerase II transcription
id: GO:0030847
name: termination of RNA polymerase II transcription, exosome-dependent
namespace: biological_process
-def: "The process in which transcription of nonpolyadenylated RNA polymerase II transcripts is terminated; coupled to the maturation of the RNA 3'-end." [GOC:txnOH, PMID:12944462, PMID:18679429]
+def: "The process in which transcription of nonpolyadenylated RNA polymerase II transcripts is terminated; coupled to the maturation of the RNA 3'-end." [GOC:txnOH, PMID:12944462, PMID:18679429, PMID:27371117]
synonym: "termination of RNA polymerase II transcription, poly(A)-independent" EXACT []
synonym: "transcription termination from Pol II promoter, poly(A)-independent" EXACT []
synonym: "transcription termination from Pol II promoter, RNA polymerase(A)-independent" EXACT []
@@ -161610,7 +161597,7 @@ is_a: GO:0006369 ! termination of RNA polymerase II transcription
id: GO:0030848
name: threo-3-hydroxyaspartate ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (3S)-3-hydroxy-L-aspartate = NH(4)(+) + oxaloacetate." [EC:4.3.1.16, RHEA:12424]
+def: "Catalysis of the reaction: (3S)-3-hydroxy-L-aspartate = NH4 + oxaloacetate." [EC:4.3.1.16, RHEA:12424]
synonym: "3-hydroxyaspartate dehydratase activity" BROAD [GOC:mcc, PMID:10481099]
synonym: "L-threo-3-hydroxyaspartate dehydratase activity" RELATED [EC:4.3.1.16]
synonym: "threo-3-hydroxy-L-aspartate ammonia-lyase (oxaloacetate-forming)" RELATED [EC:4.3.1.16]
@@ -161883,7 +161870,6 @@ namespace: cellular_component
def: "A protein complex composed of an alpha and a beta receptor subunit and an interleukin ligand. In human, Interleukin-19, -20 and -24 bind IL20RA/IL20RB receptor subunits and Interleukin-20 and -24 bind IL22RA1/IL20RB receptor subunits." [PMID:12351624]
synonym: "IL-20 receptor complex" EXACT [GOC:add]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0030877
@@ -161898,8 +161884,8 @@ synonym: "APC-Axin-1-beta-catenin complex" EXACT []
synonym: "Axin-APC-beta-catenin-GSK3B complex" EXACT []
synonym: "BDC" EXACT [GOC:bf, GOC:PARL, PMID:22899650]
synonym: "beta-catenin degradation complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005737 ! cytoplasm
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0030878
@@ -162053,14 +162039,18 @@ is_a: GO:0000153 ! cytoplasmic ubiquitin ligase complex
id: GO:0030892
name: mitotic cohesin complex
namespace: cellular_component
+alt_id: GO:0034990
def: "A cohesin complex that mediates sister chromatid cohesion during mitosis; has a subunit composition distinct from that of the meiotic cohesin complex." [GOC:mah, PMID:12750522]
+synonym: "nuclear mitotic cohesin complex" RELATED []
is_a: GO:0008278 ! cohesin complex
[Term]
id: GO:0030893
name: meiotic cohesin complex
namespace: cellular_component
+alt_id: GO:0034991
def: "A cohesin complex that mediates sister chromatid cohesion during meiosis; has a subunit composition distinct from that of the mitotic cohesin complex." [GOC:mah, PMID:12750522]
+synonym: "nuclear meiotic cohesin complex" RELATED []
is_a: GO:0008278 ! cohesin complex
[Term]
@@ -162080,9 +162070,11 @@ relationship: part_of GO:0005657 ! replication fork
id: GO:0030895
name: apolipoprotein B mRNA editing enzyme complex
namespace: cellular_component
-def: "Protein complex that mediates editing of the mRNA encoding apolipoprotein B; catalyzes the deamination of C to U (residue 6666 in the human mRNA). Contains a catalytic subunit, APOBEC-1, and other proteins (e.g. human ASP; rat ASP and KSRP)." [PMID:10781591]
+def: "Protein complex that mediates editing of the mRNA encoding apolipoprotein B; catalyzes the deamination of C to U (residue 6666 in the human mRNA). Contains a catalytic subunit, APOBEC-1, and other proteins (e.g. human ASP; rat ASP and KSRP)." [PMID:10781591, PMID:12683974]
+comment: ASP = APOBEC1 complementation factor 1, a1cf, acf; KSRP = Khsrp (KH-type splicing regulatory protein)
synonym: "apoB mRNA editing enzyme complex" EXACT []
synonym: "APOBEC" EXACT []
+is_a: GO:0045293 ! mRNA editing complex
is_a: GO:0140513 ! nuclear protein-containing complex
[Term]
@@ -162306,40 +162298,45 @@ is_a: GO:0018251 ! peptidyl-tyrosine dehydrogenation
[Term]
id: GO:0030923
-name: metal incorporation into metallo-oxygen cluster
+name: obsolete metal incorporation into metallo-oxygen cluster
namespace: biological_process
-def: "The formation of a cluster of several metal atoms, including manganese or calcium, with one or more bridging (mu-bond) oxygen atoms; amino acids residues in proteins that may ligate the metal oxygen cluster are histidine, aspartate, and glutamate." [GOC:jsg]
-is_a: GO:0006464 ! cellular protein modification process
+def: "OBSOLETE. The formation of a cluster of several metal atoms, including manganese or calcium, with one or more bridging (mu-bond) oxygen atoms; amino acids residues in proteins that may ligate the metal oxygen cluster are histidine, aspartate, and glutamate." [GOC:jsg]
+comment: This term represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0030924
-name: manganese incorporation into metallo-oxygen cluster
+name: obsolete manganese incorporation into metallo-oxygen cluster
namespace: biological_process
-def: "The incorporation of manganese into a metallo-oxygen cluster." [GOC:jsg]
-is_a: GO:0030923 ! metal incorporation into metallo-oxygen cluster
+def: "OBSOLETE. The incorporation of manganese into a metallo-oxygen cluster." [GOC:jsg]
+comment: This term represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0030925
-name: calcium incorporation into metallo-oxygen cluster
+name: obsolete calcium incorporation into metallo-oxygen cluster
namespace: biological_process
-def: "The incorporation of calcium into a metallo-oxygen cluster." [GOC:jsg]
-is_a: GO:0030923 ! metal incorporation into metallo-oxygen cluster
+def: "OBSOLETE. The incorporation of calcium into a metallo-oxygen cluster." [GOC:jsg]
+comment: This term represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0030926
-name: calcium incorporation into metallo-oxygen cluster via bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide
+name: obsolete calcium incorporation into metallo-oxygen cluster via bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide
namespace: biological_process
-def: "The incorporation of calcium into a 4Mn-Ca-4O complex by bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide as in the photosystem II catalytic site." [PMID:14764885, RESID:AA0366]
+def: "OBSOLETE. The incorporation of calcium into a 4Mn-Ca-4O complex by bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide as in the photosystem II catalytic site." [PMID:14764885, RESID:AA0366]
+comment: This term represents a molecular function.
xref: RESID:AA0366
-is_a: GO:0030925 ! calcium incorporation into metallo-oxygen cluster
+is_obsolete: true
[Term]
id: GO:0030927
-name: manganese incorporation into metallo-oxygen cluster via bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide
+name: obsolete manganese incorporation into metallo-oxygen cluster via bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide
namespace: biological_process
-def: "The incorporation of manganese into a 4Mn-Ca-4O complex by bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide as in the photosystem II catalytic site." [PMID:14764885, RESID:AA0366]
+def: "OBSOLETE. The incorporation of manganese into a 4Mn-Ca-4O complex by bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide as in the photosystem II catalytic site." [PMID:14764885, RESID:AA0366]
+comment: This term represents a molecular function.
xref: RESID:AA0366
-is_a: GO:0030924 ! manganese incorporation into metallo-oxygen cluster
+is_obsolete: true
[Term]
id: GO:0030929
@@ -162347,8 +162344,8 @@ name: ADPG pyrophosphorylase complex
namespace: cellular_component
def: "Complex that possesses ADPG pyrophosphorylase activity. In all organisms where it has been found, the complex is a tetramer. In bacteria, it is a homotetramer. In plants, the complex is a heterotetramer composed small and large subunits." [GOC:tb, PMID:9680965]
subset: goslim_pir
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005737 ! cytoplasm
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0030930
@@ -162407,7 +162404,6 @@ def: "Any collagen trimer that passes through a lipid bilayer membrane." [ISBN:0
synonym: "MACIT" EXACT [ISBN:0198599587]
is_a: GO:0005581 ! collagen trimer
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0030937
@@ -162596,6 +162592,7 @@ synonym: "AdT" RELATED [GOC:rb]
synonym: "GatCAB" NARROW [GOC:rb]
synonym: "GatFAB" NARROW [GOC:rb]
is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0030957
@@ -162780,7 +162777,6 @@ is_a: GO:0015697 ! quaternary ammonium group transport
is_a: GO:0015711 ! organic anion transport
is_a: GO:0015748 ! organophosphate ester transport
is_a: GO:0071934 ! thiamine transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0030975
@@ -162819,9 +162815,7 @@ id: GO:0030977
name: taurine binding
namespace: molecular_function
def: "Binding to taurine." [GOC:mlg]
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0043210 ! alkanesulfonate binding
-is_a: GO:1901681 ! sulfur compound binding
[Term]
id: GO:0030978
@@ -162829,7 +162823,7 @@ name: alpha-glucan metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving alpha-glucans, compounds composed of glucose residues linked by alpha-D-glucosidic bonds." [GOC:mah]
synonym: "alpha-glucan metabolism" EXACT []
-is_a: GO:0006073 ! cellular glucan metabolic process
+is_a: GO:0044042 ! glucan metabolic process
[Term]
id: GO:0030979
@@ -162853,7 +162847,6 @@ synonym: "alpha-glucan catabolism" EXACT []
synonym: "alpha-glucan degradation" EXACT []
is_a: GO:0009251 ! glucan catabolic process
is_a: GO:0030978 ! alpha-glucan metabolic process
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
[Term]
id: GO:0030981
@@ -162919,7 +162912,6 @@ name: high molecular weight kininogen receptor complex
namespace: cellular_component
def: "A protein complex that acts as a receptor for high molecular weight kininogens. In humans, this receptor includes the CK1 and uPAR proteins." [GOC:mah, PMID:11290596]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0030989
@@ -163000,6 +162992,7 @@ synonym: "cell septum edging hydrolysis" EXACT []
synonym: "hydrolysis of cell septum edging" EXACT []
synonym: "hydrolysis of edging of cell septum" EXACT []
synonym: "septum edging hydrolysis" BROAD []
+is_a: GO:0044248 ! cellular catabolic process
is_a: GO:0071999 ! extracellular polysaccharide catabolic process
relationship: part_of GO:0000920 ! septum digestion after cytokinesis
@@ -163137,6 +163130,7 @@ subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
+subset: prokaryote_subset
synonym: "matrisome" NARROW []
synonym: "proteinaceous extracellular matrix" EXACT []
xref: NIF_Subcellular:nlx_subcell_20090513
@@ -163173,7 +163167,7 @@ consider: GO:0044613
id: GO:0031016
name: pancreas development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes." [GOC:cvs]
+def: "The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones." [GOC:cvs]
xref: Wikipedia:Pancreas
is_a: GO:0048513 ! animal organ development
@@ -163465,87 +163459,79 @@ is_a: GO:0030141 ! secretory granule
[Term]
id: GO:0031047
-name: gene silencing by RNA
+name: RNA-mediated gene silencing
namespace: biological_process
-def: "Any process in which RNA molecules inactivate expression of target genes." [GOC:dph, GOC:mah, GOC:tb, PMID:15020054]
+def: "A process in which an RNA molecule reduces expression of target genes. This can occur pre-transcriptionally by assembly of heterochromatin and prevention of transcription or co- or post-transcriptionally by targeting RNAs for degradation or by interfering with splicing or translation. This process starts once the inhibitory RNA molecule has been transcribed, and includes processing of the RNA such as cleavage, modifications, transport from the nucleus to the cytoplasm, loading onto the RISC complex, and the effect on transcription or translation." [PMID:15020054]
subset: goslim_drosophila
subset: goslim_generic
-synonym: "RNA-mediated gene silencing" EXACT [GOC:dph, GOC:tb]
+synonym: "gene silencing by RNA" RELATED []
+synonym: "RNA-dependent gene silencing" EXACT []
is_a: GO:0010629 ! negative regulation of gene expression
[Term]
id: GO:0031048
-name: heterochromatin assembly by small RNA
+name: small ncRNA-mediated heterochromatin formation
namespace: biological_process
alt_id: GO:0070924
-def: "Assembly of heterochromatin, directed by small RNAs sharing sequence identity to the repressed region." [GOC:dph, GOC:mtg_lung, GOC:ns, PMID:19239886]
+alt_id: GO:0140458
+def: "A heterochromatin formation-based gene silencing process mediated by a small non-coding RNA molecule that occur before the beginnning of trancription." [PMID:19239886, PMID:21420348]
synonym: "chromatin silencing by small RNA" RELATED []
+synonym: "heterochromatin assembly by small RNA" EXACT []
synonym: "heterochromatin assembly involved in chromatin silencing by small RNA" RELATED []
synonym: "heterochromatin formation involved in chromatin silencing by small RNA" RELATED []
+synonym: "pre-transcriptional gene silencing by RNA" BROAD []
+synonym: "pre-transcriptional gene silencing by small non-coding RNA" EXACT []
synonym: "RNA interference-like chromatin silencing" EXACT []
+synonym: "RNA-dependent heterochromatin formation" EXACT []
synonym: "RNA-mediated chromatin silencing" EXACT [GOC:dph, GOC:tb]
+synonym: "RNA-mediated heterochromatin formation" RELATED []
synonym: "RNA-mediated TGS" BROAD []
synonym: "RNA-mediated transcriptional silencing" EXACT []
synonym: "RNAi-directed chromatin silencing" EXACT [GOC:vw]
synonym: "RNAi-like chromatin silencing" EXACT []
+synonym: "small non-coding RNA-dependent heterochromatin formation" NARROW []
synonym: "small RNA-mediated heterochromatic silencing" EXACT []
synonym: "small RNA-mediated heterochromatin formation" RELATED [GOC:mah]
-is_a: GO:0031507 ! heterochromatin assembly
+is_a: GO:0031047 ! RNA-mediated gene silencing
+is_a: GO:0031507 ! heterochromatin formation
[Term]
id: GO:0031049
name: programmed DNA elimination
namespace: biological_process
-def: "The DNA metabolic process in which micronuclear-limited sequences, internal eliminated sequences (IES) and breakage eliminated sequences (BES) are removed from the developing macronucleus (anlage) of a ciliate." [GOC:mah, GOC:ns]
+def: "A process in which genomic fragments or entire chromosomes are eliminated from somatic cells or from micronuclei of ciliates. This process occurs in the developing macronucleus (anlage) of a ciliate, as well as in other species, including vertebrates and is an irreversible mechanism of gene silencing." [GOC:mah, GOC:ns, PMID:18708581, PMID:24886889, PMID:32986476]
subset: goslim_pir
-is_a: GO:0006259 ! DNA metabolic process
-
-[Term]
-id: GO:0031050
-name: dsRNA processing
-namespace: biological_process
-def: "Cleavage of double-stranded RNA molecules by an RNaseIII-family enzyme to produce small RNAs (generally 20-30 nucleotides, depending on species) with biological function." [GOC:ns]
-synonym: "double-stranded RNA fragmentation" RELATED []
-synonym: "dsRNA fragmentation" RELATED []
-is_a: GO:0006396 ! RNA processing
-
-[Term]
-id: GO:0031051
-name: scnRNA processing
-namespace: biological_process
-def: "Cleavage of noncoding, double-stranded RNAs transcribed from the micronuclear genome to produce scnRNAs, small RNAs (~28 nucleotides) that direct the deletion of micronuclear-limited sequences from the developing macronuclear genome." [PMID:15196465]
-synonym: "scnRNA production" BROAD []
-is_a: GO:0031050 ! dsRNA processing
-relationship: part_of GO:0031049 ! programmed DNA elimination
+is_a: GO:0040029 ! epigenetic regulation of gene expression
[Term]
id: GO:0031052
-name: chromosome breakage
+name: programmed DNA elimination by chromosome breakage
namespace: biological_process
-def: "Regulated cleavage of the developing macronuclear genome at a limited number of chromosome breakage sites (CBS). The macronuclear destined segment (MDS) sequence adjacent to the CBS (or separated from it by a BES) receives a macronuclear telomere following chromosome breakage." [GOC:ns]
-comment: Note that this term refers to breakage of chromosomes during normal DNA rearrangements characteristic of ciliates; it is not to be used for DNA damage or other abnormal occurrences.
-synonym: "establishment or maintenance of heterochromatin architecture" EXACT [GOC:mah]
-is_a: GO:0051276 ! chromosome organization
-relationship: part_of GO:0031049 ! programmed DNA elimination
+def: "Regulated cleavage of the developing macronuclear genome at a limited number of chromosome breakage sites (CBS). The macronuclear destined segment (MDS) sequence adjacent to the CBS (or separated from it by a BES) receives a macronuclear telomere following chromosome breakage." [GOC:ns, PMID:15956677, PMID:25303953, PMID:32165395]
+comment: Note that this term refers to breakage of chromosomes during normal DNA well characterized in ciliates but also present in many vertebrates; it is not to be used for DNA damage or other abnormal occurrences.
+synonym: "chromosome breakage" RELATED []
+is_a: GO:0031049 ! programmed DNA elimination
[Term]
id: GO:0031053
name: primary miRNA processing
namespace: biological_process
-def: "Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule." [GOC:sl, PMID:15211354]
+alt_id: GO:1990729
+alt_id: GO:1990744
+def: "A process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule." [GOC:sl, PMID:15211354, PMID:25799998]
synonym: "pri-miRNA processing" EXACT []
synonym: "primary microRNA processing" EXACT []
-is_a: GO:0034470 ! ncRNA processing
-relationship: part_of GO:0035196 ! production of miRNAs involved in gene silencing by miRNA
+synonym: "primary miRNA methylation" NARROW []
+synonym: "primary miRNA modification" EXACT []
+is_a: GO:0035196 ! miRNA processing
[Term]
id: GO:0031054
name: pre-miRNA processing
namespace: biological_process
-def: "Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule." [GOC:sl, PMID:15211354]
+def: "A process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule." [GOC:sl, PMID:15211354]
synonym: "pre-microRNA processing" EXACT []
-is_a: GO:0034470 ! ncRNA processing
-relationship: part_of GO:0035196 ! production of miRNAs involved in gene silencing by miRNA
+is_a: GO:0035196 ! miRNA processing
[Term]
id: GO:0031055
@@ -163564,37 +163550,40 @@ relationship: regulates GO:0016570 ! histone modification
[Term]
id: GO:0031057
-name: negative regulation of histone modification
+name: obsolete negative regulation of histone modification
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent alteration of a histone." [GOC:mah]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent alteration of a histone." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of histone modification" EXACT []
synonym: "down-regulation of histone modification" EXACT []
synonym: "downregulation of histone modification" EXACT []
synonym: "inhibition of histone modification" NARROW []
-is_a: GO:0031056 ! regulation of histone modification
-is_a: GO:0031400 ! negative regulation of protein modification process
-relationship: negatively_regulates GO:0016570 ! histone modification
+is_obsolete: true
+consider: GO:0006338
+consider: GO:0040029
[Term]
id: GO:0031058
-name: positive regulation of histone modification
+name: obsolete positive regulation of histone modification
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the covalent alteration of a histone." [GOC:mah]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the covalent alteration of a histone." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of histone modification" NARROW []
synonym: "stimulation of histone modification" NARROW []
synonym: "up regulation of histone modification" EXACT []
synonym: "up-regulation of histone modification" EXACT []
synonym: "upregulation of histone modification" EXACT []
-is_a: GO:0031056 ! regulation of histone modification
-is_a: GO:0031401 ! positive regulation of protein modification process
-relationship: positively_regulates GO:0016570 ! histone modification
+is_obsolete: true
+consider: GO:0006338
+consider: GO:0040029
[Term]
id: GO:0031059
-name: histone deacetylation at centromere
+name: obsolete histone deacetylation at centromere
namespace: biological_process
-def: "The removal of acetyl groups from histones in centromeric DNA." [GOC:mah]
-is_a: GO:0016575 ! histone deacetylation
+def: "OBSOLETE. The removal of acetyl groups from histones in centromeric DNA." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function as a biological process, and contains cellular component information.
+is_obsolete: true
[Term]
id: GO:0031060
@@ -163613,8 +163602,8 @@ synonym: "down regulation of histone methylation" EXACT []
synonym: "down-regulation of histone methylation" EXACT []
synonym: "downregulation of histone methylation" EXACT []
synonym: "inhibition of histone methylation" NARROW []
-is_a: GO:0031057 ! negative regulation of histone modification
is_a: GO:0031060 ! regulation of histone methylation
+is_a: GO:0031400 ! negative regulation of protein modification process
relationship: negatively_regulates GO:0016571 ! histone methylation
[Term]
@@ -163627,8 +163616,8 @@ synonym: "stimulation of histone methylation" NARROW []
synonym: "up regulation of histone methylation" EXACT []
synonym: "up-regulation of histone methylation" EXACT []
synonym: "upregulation of histone methylation" EXACT []
-is_a: GO:0031058 ! positive regulation of histone modification
is_a: GO:0031060 ! regulation of histone methylation
+is_a: GO:0031401 ! positive regulation of protein modification process
relationship: positively_regulates GO:0016571 ! histone methylation
[Term]
@@ -163649,8 +163638,8 @@ synonym: "down regulation of histone deacetylation" EXACT []
synonym: "down-regulation of histone deacetylation" EXACT []
synonym: "downregulation of histone deacetylation" EXACT []
synonym: "inhibition of histone deacetylation" NARROW []
-is_a: GO:0031057 ! negative regulation of histone modification
is_a: GO:0031063 ! regulation of histone deacetylation
+is_a: GO:0031400 ! negative regulation of protein modification process
relationship: negatively_regulates GO:0016575 ! histone deacetylation
[Term]
@@ -163663,45 +163652,42 @@ synonym: "stimulation of histone deacetylation" NARROW []
synonym: "up regulation of histone deacetylation" EXACT []
synonym: "up-regulation of histone deacetylation" EXACT []
synonym: "upregulation of histone deacetylation" EXACT []
-is_a: GO:0031058 ! positive regulation of histone modification
is_a: GO:0031063 ! regulation of histone deacetylation
is_a: GO:0090312 ! positive regulation of protein deacetylation
relationship: positively_regulates GO:0016575 ! histone deacetylation
[Term]
id: GO:0031066
-name: regulation of histone deacetylation at centromere
+name: obsolete regulation of histone deacetylation at centromere
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the removal of acetyl groups from histones in centromeric DNA." [GOC:mah]
-is_a: GO:0031063 ! regulation of histone deacetylation
-relationship: regulates GO:0031059 ! histone deacetylation at centromere
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the removal of acetyl groups from histones in centromeric DNA." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function as a biological process, and contains cellular component information.
+is_obsolete: true
[Term]
id: GO:0031067
-name: negative regulation of histone deacetylation at centromere
+name: obsolete negative regulation of histone deacetylation at centromere
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the removal of acetyl groups to histones in centromeric DNA." [GOC:mah]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the removal of acetyl groups to histones in centromeric DNA." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function as a biological process, and contains cellular component information.
synonym: "down regulation of histone deacetylation at centromere" EXACT []
synonym: "down-regulation of histone deacetylation at centromere" EXACT []
synonym: "downregulation of histone deacetylation at centromere" EXACT []
synonym: "inhibition of histone deacetylation at centromere" NARROW []
-is_a: GO:0031064 ! negative regulation of histone deacetylation
-is_a: GO:0031066 ! regulation of histone deacetylation at centromere
-relationship: negatively_regulates GO:0031059 ! histone deacetylation at centromere
+is_obsolete: true
[Term]
id: GO:0031068
-name: positive regulation of histone deacetylation at centromere
+name: obsolete positive regulation of histone deacetylation at centromere
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the removal of acetyl groups from histones in centromeric DNA." [GOC:mah]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the removal of acetyl groups from histones in centromeric DNA." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function as a biological process, and contains cellular component information.
synonym: "activation of histone deacetylation at centromere" NARROW []
synonym: "stimulation of histone deacetylation at centromere" NARROW []
synonym: "up regulation of histone deacetylation at centromere" EXACT []
synonym: "up-regulation of histone deacetylation at centromere" EXACT []
synonym: "upregulation of histone deacetylation at centromere" EXACT []
-is_a: GO:0031065 ! positive regulation of histone deacetylation
-is_a: GO:0031066 ! regulation of histone deacetylation at centromere
-relationship: positively_regulates GO:0031059 ! histone deacetylation at centromere
+is_obsolete: true
[Term]
id: GO:0031069
@@ -163781,9 +163767,11 @@ relationship: part_of GO:0009791 ! post-embryonic development
[Term]
id: GO:0031078
-name: histone deacetylase activity (H3-K14 specific)
+name: histone H3K14 deacetylase activity
namespace: molecular_function
def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein." [PMID:28450737]
+synonym: "histone deacetylase activity (H3-K14 specific)" EXACT []
+synonym: "histone H3-K14 deacetylase activity" EXACT []
is_a: GO:0004407 ! histone deacetylase activity
[Term]
@@ -163828,8 +163816,7 @@ namespace: cellular_component
def: "Any of several protein complexes required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes, platelet dense granules, and other related organelles; acronym for biogenesis of lysosomal-related organelles complex." [PMID:15102850, PMID:15261680]
subset: goslim_pir
synonym: "BLOC-1 related complex" EXACT [PMID:25898167]
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005829 ! cytosol
+is_a: GO:0140535 ! intracellular protein-containing complex
[Term]
id: GO:0031083
@@ -163970,7 +163957,7 @@ relationship: part_of GO:0032153 ! cell division site
id: GO:0031098
name: stress-activated protein kinase signaling cascade
namespace: biological_process
-def: "A series of molecular signals in which a stress-activated protein kinase (SAPK) cascade relays one or more of the signals." [GOC:mah]
+def: "The series of molecular signals in which a stress-activated protein kinase (SAPK) cascade relays a signal." [GOC:mah]
synonym: "JNK signaling pathway" NARROW []
synonym: "JNK signalling pathway" NARROW []
synonym: "SAPK signaling pathway" EXACT []
@@ -164034,7 +164021,7 @@ is_a: GO:0031102 ! neuron projection regeneration
id: GO:0031105
name: septin complex
namespace: cellular_component
-def: "A protein complex containing septins. Typically, these complexes contain multiple septins and are oligomeric." [GOC:mah, PMID:15385632]
+def: "A protein complex containing septins. Typically, these complexes contain multiple septins and are oligomeric." [GOC:mah, PMID:15385632]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0005938 ! cell cortex
@@ -164075,6 +164062,7 @@ id: GO:0031109
name: microtubule polymerization or depolymerization
namespace: biological_process
def: "Assembly or disassembly of microtubules by the addition or removal of tubulin heterodimers from a microtubule." [GOC:mah]
+synonym: "microtubule dynamics" EXACT []
is_a: GO:0000226 ! microtubule cytoskeleton organization
[Term]
@@ -164250,7 +164238,7 @@ namespace: biological_process
def: "Any process involved in forming the mature 3' end of an rRNA molecule." [GOC:mah]
synonym: "rRNA 3' end processing" EXACT []
is_a: GO:0006364 ! rRNA processing
-is_a: GO:0043628 ! ncRNA 3'-end processing
+is_a: GO:0043628 ! regulatory ncRNA 3'-end processing
[Term]
id: GO:0031126
@@ -164261,7 +164249,7 @@ synonym: "sno(s)RNA 3' end processing" EXACT []
synonym: "snoRNA 3'-end processing" NARROW []
synonym: "sRNA 3'-end processing" NARROW []
is_a: GO:0043144 ! sno(s)RNA processing
-is_a: GO:0043628 ! ncRNA 3'-end processing
+is_a: GO:0043628 ! regulatory ncRNA 3'-end processing
[Term]
id: GO:0031127
@@ -164289,11 +164277,11 @@ is_a: GO:0031128 ! developmental induction
[Term]
id: GO:0031130
-name: creation of an inductive signal
+name: obsolete creation of an inductive signal
namespace: biological_process
-def: "The process in which one cell or group of cells sends a signal over a short range to another cell or group of cells of different ancestry and developmental potential, thereby effecting a developmental change in the latter." [GOC:mah]
-is_a: GO:0048869 ! cellular developmental process
-relationship: part_of GO:0031129 ! inductive cell-cell signaling
+def: "OBSOLETE. The process in which one cell or group of cells sends a signal over a short range to another cell or group of cells of different ancestry and developmental potential, thereby effecting a developmental change in the latter." [GOC:mah]
+comment: The reason for obsoletion is that the term is not clearly defined and there is no annotations.
+is_obsolete: true
[Term]
id: GO:0031131
@@ -164307,7 +164295,7 @@ relationship: part_of GO:0031129 ! inductive cell-cell signaling
id: GO:0031132
name: serine 3-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-serine + NADP(+) = L-alpha-formylglycine + 2 H(+) + NADPH." [EC:1.1.1.276, RHEA:21596]
+def: "Catalysis of the reaction: L-serine + NADP+ = L-alpha-formylglycine + 2 H+ + NADPH." [EC:1.1.1.276, RHEA:21596]
synonym: "L-serine:NADP+ 3-oxidoreductase activity" RELATED [EC:1.1.1.276]
xref: EC:1.1.1.276
xref: KEGG_REACTION:R06126
@@ -164336,38 +164324,35 @@ relationship: part_of GO:0000819 ! sister chromatid segregation
[Term]
id: GO:0031135
-name: negative regulation of conjugation
+name: obsolete negative regulation of conjugation
namespace: biological_process
-def: "Any process that decreases the rate of conjugation." [GOC:mah]
+def: "OBSOLETE. Any process that decreases the rate of conjugation." [GOC:mah]
+comment: This term was obsoleted because its target (conjugation) was not clearly defined.
synonym: "down regulation of conjugation" EXACT []
synonym: "down-regulation of conjugation" EXACT []
synonym: "downregulation of conjugation" EXACT []
synonym: "inhibition of conjugation" NARROW []
-is_a: GO:0046999 ! regulation of conjugation
-is_a: GO:0048523 ! negative regulation of cellular process
-relationship: negatively_regulates GO:0000746 ! conjugation
+is_obsolete: true
[Term]
id: GO:0031136
-name: positive regulation of conjugation
+name: obsolete positive regulation of conjugation
namespace: biological_process
-def: "Any process that increases the rate or frequency of conjugation." [GOC:mah]
+def: "OBSOLETE. Any process that increases the rate or frequency of conjugation." [GOC:mah]
+comment: This term was obsoleted because its target (conjugation) was not clearly defined.
synonym: "activation of conjugation" NARROW []
synonym: "stimulation of conjugation" NARROW []
synonym: "up regulation of conjugation" EXACT []
synonym: "up-regulation of conjugation" EXACT []
synonym: "upregulation of conjugation" EXACT []
-is_a: GO:0046999 ! regulation of conjugation
-is_a: GO:0048522 ! positive regulation of cellular process
-relationship: positively_regulates GO:0000746 ! conjugation
+is_obsolete: true
[Term]
id: GO:0031137
name: regulation of conjugation with cellular fusion
namespace: biological_process
def: "Any process that modulates the rate or frequency of conjugation with cellular fusion." [GOC:mah]
-is_a: GO:0046999 ! regulation of conjugation
-is_a: GO:2000241 ! regulation of reproductive process
+is_a: GO:0050789 ! regulation of biological process
relationship: regulates GO:0000747 ! conjugation with cellular fusion
[Term]
@@ -164379,9 +164364,8 @@ synonym: "down regulation of conjugation with cellular fusion" EXACT []
synonym: "down-regulation of conjugation with cellular fusion" EXACT []
synonym: "downregulation of conjugation with cellular fusion" EXACT []
synonym: "inhibition of conjugation with cellular fusion" NARROW []
-is_a: GO:0031135 ! negative regulation of conjugation
is_a: GO:0031137 ! regulation of conjugation with cellular fusion
-is_a: GO:2000242 ! negative regulation of reproductive process
+is_a: GO:0048519 ! negative regulation of biological process
relationship: negatively_regulates GO:0000747 ! conjugation with cellular fusion
[Term]
@@ -164394,9 +164378,8 @@ synonym: "stimulation of conjugation with cellular fusion" NARROW []
synonym: "up regulation of conjugation with cellular fusion" EXACT []
synonym: "up-regulation of conjugation with cellular fusion" EXACT []
synonym: "upregulation of conjugation with cellular fusion" EXACT []
-is_a: GO:0031136 ! positive regulation of conjugation
is_a: GO:0031137 ! regulation of conjugation with cellular fusion
-is_a: GO:2000243 ! positive regulation of reproductive process
+is_a: GO:0048518 ! positive regulation of biological process
relationship: positively_regulates GO:0000747 ! conjugation with cellular fusion
[Term]
@@ -164525,12 +164508,16 @@ relationship: part_of GO:0031154 ! culmination involved in sorocarp development
[Term]
id: GO:0031151
-name: histone methyltransferase activity (H3-K79 specific)
+name: histone H3K79 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 79) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 79). This reaction is the addition of a methyl group onto lysine at position 79 of the histone H3 protein." [GOC:mah, PMID:15371351]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 79) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 79). This reaction is the addition of a methyl group to the lysine residue at position 79 of the histone H3 protein." [GOC:mah, PMID:15371351]
+synonym: "histone H3K79 methylase activity" EXACT []
synonym: "histone lysine N-methyltransferase activity (H3-K79 specific)" EXACT []
synonym: "histone methylase activity (H3-K79 specific)" EXACT [GOC:mah]
-is_a: GO:0018024 ! histone-lysine N-methyltransferase activity
+synonym: "histone methyltransferase activity (H3-K79 specific)" EXACT []
+synonym: "histone-H3K79 methyltransferase activity" EXACT []
+is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
+is_a: GO:0140938 ! histone H3 methyltransferase activity
[Term]
id: GO:0031152
@@ -164647,8 +164634,8 @@ name: sulfur incorporation into metallo-sulfur cluster
namespace: biological_process
def: "The incorporation of exogenous sulfur into a metallo-sulfur cluster." [GOC:mah]
synonym: "sulphur incorporation into metallo-sulphur cluster" EXACT []
-is_a: GO:0006464 ! cellular protein modification process
is_a: GO:0006790 ! sulfur compound metabolic process
+is_a: GO:0036211 ! protein modification process
relationship: part_of GO:0031163 ! metallo-sulfur cluster assembly
[Term]
@@ -164673,21 +164660,23 @@ relationship: part_of GO:0000331 ! contractile vacuole
[Term]
id: GO:0031165
-name: integral component of contractile vacuolar membrane
+name: obsolete integral component of contractile vacuolar membrane
namespace: cellular_component
-def: "The component of the contractile vacuolar membrane consisting of gene products that have some part that penetrates at least one leaflet of the membrane bilayer. This component includes gene products that are buried in the bilayer with no exposure outside the bilayer." [GOC:dos, GOC:pg]
+def: "OBSOLETE. The component of the contractile vacuolar membrane consisting of gene products that have some part that penetrates at least one leaflet of the membrane bilayer. This component includes gene products that are buried in the bilayer with no exposure outside the bilayer." [GOC:dos, GOC:pg]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to contractile vacuolar membrane" EXACT []
-is_a: GO:0031166 ! integral component of vacuolar membrane
-is_a: GO:0031311 ! intrinsic component of contractile vacuolar membrane
+is_obsolete: true
+replaced_by: GO:0031164
[Term]
id: GO:0031166
-name: integral component of vacuolar membrane
+name: obsolete integral component of vacuolar membrane
namespace: cellular_component
-def: "The component of the vacuolar membrane consisting of gene products and protein complexes that have some part that penetrates at least one leaflet of the membrane bilayer. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the vacuolar membrane consisting of gene products and protein complexes that have some part that penetrates at least one leaflet of the membrane bilayer. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to vacuolar membrane" NARROW []
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:0031310 ! intrinsic component of vacuolar membrane
+is_obsolete: true
+replaced_by: GO:0005774
[Term]
id: GO:0031167
@@ -164832,24 +164821,26 @@ relationship: part_of GO:0005737 ! cytoplasm
[Term]
id: GO:0031203
-name: posttranslational protein targeting to membrane, docking
+name: post-translational protein targeting to membrane, docking
namespace: biological_process
def: "The process in which the signal sequence of a translated protein binds to and forms a complex with the Sec complex." [PMID:12518217, PMID:8707814]
synonym: "posttranslational protein membrane targeting, docking" EXACT []
+synonym: "posttranslational protein targeting to membrane, docking" EXACT []
synonym: "protein docking during posttranslational protein targeting to membrane" EXACT []
synonym: "Sec-translated protein complex assembly" EXACT []
is_a: GO:0065003 ! protein-containing complex assembly
-relationship: part_of GO:0006620 ! posttranslational protein targeting to endoplasmic reticulum membrane
+relationship: part_of GO:0006620 ! post-translational protein targeting to endoplasmic reticulum membrane
[Term]
id: GO:0031204
-name: posttranslational protein targeting to membrane, translocation
+name: post-translational protein targeting to membrane, translocation
namespace: biological_process
def: "The process in which a protein translocates through the ER membrane posttranslationally." [PMID:12518317, PMID:8707814]
synonym: "posttranslational protein membrane targeting, translocation" EXACT []
+synonym: "posttranslational protein targeting to membrane, translocation" EXACT []
synonym: "protein translocation during posttranslational protein targeting to membrane" EXACT []
is_a: GO:0065002 ! intracellular protein transmembrane transport
-relationship: part_of GO:0006620 ! posttranslational protein targeting to endoplasmic reticulum membrane
+relationship: part_of GO:0006620 ! post-translational protein targeting to endoplasmic reticulum membrane
[Term]
id: GO:0031205
@@ -164906,10 +164897,8 @@ id: GO:0031211
name: endoplasmic reticulum palmitoyltransferase complex
namespace: cellular_component
def: "A complex of the endoplasmic reticulum that catalyzes S-palmitoylation, the addition of palmitate (C16:0) or other long-chain fatty acids to proteins at a cysteine residue." [GOC:jh]
-is_a: GO:0098796 ! membrane protein complex
+is_a: GO:0002178 ! palmitoyltransferase complex
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
-is_a: GO:1905961 ! protein-cysteine S-palmitoyltransferase complex
-relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
[Term]
id: GO:0031213
@@ -164926,7 +164915,6 @@ namespace: biological_process
def: "Formation of hard tissues that consist mainly of inorganic compounds, and also contain a small amounts of organic matrices that are believed to play important roles in their formation." [PMID:15132736]
xref: Wikipedia:Biomineralization
is_a: GO:0009888 ! tissue development
-is_a: GO:0110148 ! biomineralization
relationship: part_of GO:0048513 ! animal organ development
[Term]
@@ -165031,76 +165019,83 @@ relationship: part_of GO:0010996 ! response to auditory stimulus
[Term]
id: GO:0031224
-name: intrinsic component of membrane
+name: obsolete intrinsic component of membrane
namespace: cellular_component
-def: "The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane." [GOC:mah]
-comment: Note that proteins intrinsic to membranes cannot be removed without disrupting the membrane, e.g. by detergent.
-subset: goslim_metagenomics
+def: "OBSOLETE. The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane." [GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to membrane" NARROW []
-is_a: GO:0110165 ! cellular anatomical entity
-relationship: part_of GO:0016020 ! membrane
+is_obsolete: true
+replaced_by: GO:0016020
[Term]
id: GO:0031225
-name: anchored component of membrane
+name: obsolete anchored component of membrane
namespace: cellular_component
-def: "The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "anchored to membrane" EXACT []
-is_a: GO:0031224 ! intrinsic component of membrane
+is_obsolete: true
+replaced_by: GO:0016020
[Term]
id: GO:0031226
-name: intrinsic component of plasma membrane
+name: obsolete intrinsic component of plasma membrane
namespace: cellular_component
-def: "The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to plasma membrane" NARROW []
-is_a: GO:0031224 ! intrinsic component of membrane
-relationship: part_of GO:0005886 ! plasma membrane
+is_obsolete: true
+replaced_by: GO:0005886
[Term]
id: GO:0031227
-name: intrinsic component of endoplasmic reticulum membrane
+name: obsolete intrinsic component of endoplasmic reticulum membrane
namespace: cellular_component
-def: "The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to endoplasmic reticulum membrane" NARROW []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
+is_obsolete: true
+replaced_by: GO:0005789
[Term]
id: GO:0031228
-name: intrinsic component of Golgi membrane
+name: obsolete intrinsic component of Golgi membrane
namespace: cellular_component
-def: "The component of the Golgi membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the Golgi membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to Golgi membrane" NARROW []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0000139 ! Golgi membrane
+is_obsolete: true
+replaced_by: GO:0000139
[Term]
id: GO:0031229
-name: intrinsic component of nuclear inner membrane
+name: obsolete intrinsic component of nuclear inner membrane
namespace: cellular_component
-def: "The component of the nuclear inner membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the nuclear inner membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to nuclear inner membrane" NARROW []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0005637 ! nuclear inner membrane
+is_obsolete: true
+replaced_by: GO:0005637
[Term]
id: GO:0031230
-name: intrinsic component of cell outer membrane
+name: obsolete intrinsic component of cell outer membrane
namespace: cellular_component
-def: "The component of the cell outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah, GOC:mtg_sensu]
+def: "OBSOLETE. The component of the cell outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah, GOC:mtg_sensu]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to cell outer membrane" NARROW []
-is_a: GO:0031224 ! intrinsic component of membrane
-relationship: part_of GO:0009279 ! cell outer membrane
+is_obsolete: true
+replaced_by: GO:0009279
[Term]
id: GO:0031231
-name: intrinsic component of peroxisomal membrane
+name: obsolete intrinsic component of peroxisomal membrane
namespace: cellular_component
-def: "The component of the peroxisomal membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the peroxisomal membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to peroxisomal membrane" NARROW []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0005778 ! peroxisomal membrane
+is_obsolete: true
+replaced_by: GO:0005778
[Term]
id: GO:0031232
@@ -165114,13 +165109,14 @@ relationship: part_of GO:0009897 ! external side of plasma membrane
[Term]
id: GO:0031233
-name: intrinsic component of external side of plasma membrane
+name: obsolete intrinsic component of external side of plasma membrane
namespace: cellular_component
-def: "The component of a plasma membrane consisting of gene products and protein complexes that penetrate the external side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of a plasma membrane consisting of gene products and protein complexes that penetrate the external side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to external leaflet of plasma membrane" EXACT [GOC:ab]
synonym: "intrinsic to external side of plasma membrane" NARROW []
-is_a: GO:0031226 ! intrinsic component of plasma membrane
-relationship: part_of GO:0009897 ! external side of plasma membrane
+is_obsolete: true
+replaced_by: GO:0009897
[Term]
id: GO:0031234
@@ -165136,14 +165132,15 @@ relationship: part_of GO:0009898 ! cytoplasmic side of plasma membrane
[Term]
id: GO:0031235
-name: intrinsic component of the cytoplasmic side of the plasma membrane
+name: obsolete intrinsic component of the cytoplasmic side of the plasma membrane
namespace: cellular_component
-def: "The component of a plasma membrane consisting of gene products and protein complexes that have some covalently attached part (e.g. peptide sequence or GPI anchor) which is embedded in the cytoplasmic side of the plasma membrane only." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of a plasma membrane consisting of gene products and protein complexes that have some covalently attached part (e.g. peptide sequence or GPI anchor) which is embedded in the cytoplasmic side of the plasma membrane only." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to cytoplasmic side of plasma membrane" NARROW []
synonym: "intrinsic to internal leaflet of plasma membrane" EXACT [GOC:ab]
synonym: "intrinsic to internal side of plasma membrane" EXACT []
-is_a: GO:0031226 ! intrinsic component of plasma membrane
-relationship: part_of GO:0009898 ! cytoplasmic side of plasma membrane
+is_obsolete: true
+replaced_by: GO:0009898
[Term]
id: GO:0031236
@@ -165158,14 +165155,15 @@ relationship: part_of GO:0098567 ! periplasmic side of plasma membrane
[Term]
id: GO:0031237
-name: intrinsic component of periplasmic side of plasma membrane
+name: obsolete intrinsic component of periplasmic side of plasma membrane
namespace: cellular_component
alt_id: GO:0031239
-def: "The component of a plasma membrane consisting of gene products and protein complexes that penetrate the periplasmic side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor." [GOC:mah, GOC:mtg_sensu]
+def: "OBSOLETE. The component of a plasma membrane consisting of gene products and protein complexes that penetrate the periplasmic side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor." [GOC:mah, GOC:mtg_sensu]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to external leaflet of plasma membrane, in periplasmic space" EXACT [GOC:ab]
synonym: "intrinsic to periplasmic side of plasma membrane" EXACT []
-is_a: GO:0031233 ! intrinsic component of external side of plasma membrane
-relationship: part_of GO:0098567 ! periplasmic side of plasma membrane
+is_obsolete: true
+replaced_by: GO:0098567
[Term]
id: GO:0031240
@@ -165203,14 +165201,15 @@ relationship: part_of GO:0031240 ! external side of cell outer membrane
[Term]
id: GO:0031243
-name: intrinsic component of external side of cell outer membrane
+name: obsolete intrinsic component of external side of cell outer membrane
namespace: cellular_component
-def: "The component of the cell outer membrane consisting of the gene products and protein complexes that penetrate the external side of the cell outer membrane only, either directly or via some covalently attached hydrophobic anchor." [GOC:dos, GOC:mah, GOC:mtg_sensu]
+def: "OBSOLETE. The component of the cell outer membrane consisting of the gene products and protein complexes that penetrate the external side of the cell outer membrane only, either directly or via some covalently attached hydrophobic anchor." [GOC:dos, GOC:mah, GOC:mtg_sensu]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to external leaflet of cell outer membrane" EXACT [GOC:ab]
synonym: "intrinsic to external side of cell outer membrane" NARROW []
synonym: "intrinsic to external side of outer membrane" EXACT []
-is_a: GO:0031230 ! intrinsic component of cell outer membrane
-relationship: part_of GO:0031240 ! external side of cell outer membrane
+is_obsolete: true
+replaced_by: GO:0031240
[Term]
id: GO:0031244
@@ -165235,15 +165234,16 @@ relationship: part_of GO:0031241 ! periplasmic side of cell outer membrane
[Term]
id: GO:0031246
-name: intrinsic component of periplasmic side of cell outer membrane
+name: obsolete intrinsic component of periplasmic side of cell outer membrane
namespace: cellular_component
-def: "The component of the cell outer membrane consisting of the gene products that that penetrate the periplasmic side of the cell outer membrane only, either directly or via some covalently attached hydrophobic anchor." [GOC:dos, GOC:mah, GOC:mtg_sensu]
+def: "OBSOLETE. The component of the cell outer membrane consisting of the gene products that that penetrate the periplasmic side of the cell outer membrane only, either directly or via some covalently attached hydrophobic anchor." [GOC:dos, GOC:mah, GOC:mtg_sensu]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to external side of cell outer membrane" NARROW []
synonym: "intrinsic to internal leaflet of cell outer membrane" EXACT [GOC:ab]
synonym: "intrinsic to internal side of cell outer membrane" EXACT []
synonym: "intrinsic to internal side of outer membrane" EXACT []
-is_a: GO:0031230 ! intrinsic component of cell outer membrane
-relationship: part_of GO:0031241 ! periplasmic side of cell outer membrane
+is_obsolete: true
+replaced_by: GO:0031241
[Term]
id: GO:0031247
@@ -165275,7 +165275,7 @@ id: GO:0031250
name: anaerobic ribonucleoside-triphosphate reductase complex
namespace: cellular_component
def: "An enzyme complex composed of 4 subunits, 2 copies of the large protein (nrdD in E. coli) and 2 copies of the small protein (nrdG in E. coli). It catalyzes the generation of 2'deoxyribonucleotides under anaerobic growth conditions. The larger subunit is the catalytic unit that is activated by the smaller iron-binding subunit." [GOC:mlg]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005737 ! cytoplasm
[Term]
@@ -165384,10 +165384,10 @@ relationship: part_of GO:0005654 ! nucleoplasm
id: GO:0031262
name: Ndc80 complex
namespace: cellular_component
-def: "An outer kinetochore protein complex that is part of the KMN kinetochore network (also known as the NMS complex) providing the platform with which the plus ends of spindle microtubules directly interact to form stable kinetochore-microtubule attachments. A common subunit nomenclature is used from yeast to human: Ndc80, Nuf2, Spc24, and Spc25." [GOC:krc, GOC:vw, PMID:15509863, PMID:15661517, PMID:28502666]
+def: "An essential outer kinetochore complex involved in the attachment of microtubule ends to the chromosomes during mitosis." [GOC:vw, PMID:28502666, PMID:34810257]
synonym: "Nuf2-Ndc80 complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0031617 ! NMS complex
+relationship: part_of GO:0000940 ! outer kinetochore
[Term]
id: GO:0031263
@@ -165726,7 +165726,7 @@ is_a: GO:0007411 ! axon guidance
id: GO:0031291
name: Ran protein signal transduction
namespace: biological_process
-def: "A series of molecular signals within the cell that are mediated by a member of the Ran family of proteins switching to a GTP-bound active state." [GOC:mah]
+def: "The series of molecular signals within the cell that are mediated by a member of the Ran family of proteins switching to a GTP-bound active state." [GOC:mah]
is_a: GO:0007265 ! Ras protein signal transduction
[Term]
@@ -165789,7 +165789,7 @@ synonym: "replication fork processing at rDNA locus" NARROW []
synonym: "replication fork processing at ribosomal DNA locus" NARROW []
synonym: "replication fork restart" RELATED [PMID:20842177]
synonym: "replication restart" RELATED [GOC:bhm, PMID:15780929]
-is_a: GO:0045005 ! DNA-dependent DNA replication maintenance of fidelity
+is_a: GO:0045005 ! DNA-templated DNA replication maintenance of fidelity
[Term]
id: GO:0031298
@@ -165817,111 +165817,123 @@ is_a: GO:0008483 ! transaminase activity
[Term]
id: GO:0031300
-name: intrinsic component of organelle membrane
+name: obsolete intrinsic component of organelle membrane
namespace: cellular_component
-def: "The component of the organelle membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the organelle membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to organelle membrane" NARROW []
-is_a: GO:0031224 ! intrinsic component of membrane
-relationship: part_of GO:0031090 ! organelle membrane
+is_obsolete: true
+replaced_by: GO:0031090
[Term]
id: GO:0031301
-name: integral component of organelle membrane
+name: obsolete integral component of organelle membrane
namespace: cellular_component
-def: "The component of the organelle membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the organelle membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to organelle membrane" EXACT []
-is_a: GO:0016021 ! integral component of membrane
-is_a: GO:0031300 ! intrinsic component of organelle membrane
+is_obsolete: true
+replaced_by: GO:0031090
[Term]
id: GO:0031302
-name: intrinsic component of endosome membrane
+name: obsolete intrinsic component of endosome membrane
namespace: cellular_component
-def: "The component of the endosome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the endosome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to endosome membrane" NARROW []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0010008 ! endosome membrane
+is_obsolete: true
+replaced_by: GO:0010008
[Term]
id: GO:0031303
-name: integral component of endosome membrane
+name: obsolete integral component of endosome membrane
namespace: cellular_component
-def: "The component of the endosome membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the endosome membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to endosome membrane" NARROW []
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:0031302 ! intrinsic component of endosome membrane
+is_obsolete: true
+replaced_by: GO:0010008
[Term]
id: GO:0031304
-name: intrinsic component of mitochondrial inner membrane
+name: obsolete intrinsic component of mitochondrial inner membrane
namespace: cellular_component
-def: "The component of the mitochondrial inner membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the mitochondrial inner membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to mitochondrial inner membrane" NARROW []
-is_a: GO:0098573 ! intrinsic component of mitochondrial membrane
-relationship: part_of GO:0005743 ! mitochondrial inner membrane
+is_obsolete: true
+replaced_by: GO:0005743
[Term]
id: GO:0031305
-name: integral component of mitochondrial inner membrane
+name: obsolete integral component of mitochondrial inner membrane
namespace: cellular_component
-def: "The component of the mitochondrial inner membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
-synonym: "integral to mitochondrial inner membrane" EXACT []
-is_a: GO:0031304 ! intrinsic component of mitochondrial inner membrane
-is_a: GO:0032592 ! integral component of mitochondrial membrane
+def: "OBSOLETE. The component of the mitochondrial inner membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+synonym: "integral to mitochondrial inner membrane" NARROW []
+is_obsolete: true
+replaced_by: GO:0005743
[Term]
id: GO:0031306
-name: intrinsic component of mitochondrial outer membrane
+name: obsolete intrinsic component of mitochondrial outer membrane
namespace: cellular_component
-def: "The component of the mitochondrial outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the mitochondrial outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to mitochondrial outer membrane" NARROW []
-is_a: GO:0098573 ! intrinsic component of mitochondrial membrane
-relationship: part_of GO:0005741 ! mitochondrial outer membrane
+is_obsolete: true
+replaced_by: GO:0005741
[Term]
id: GO:0031307
-name: integral component of mitochondrial outer membrane
+name: obsolete integral component of mitochondrial outer membrane
namespace: cellular_component
-def: "The component of the mitochondrial outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the mitochondrial outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to mitochondrial outer membrane" NARROW []
-is_a: GO:0031306 ! intrinsic component of mitochondrial outer membrane
-is_a: GO:0032592 ! integral component of mitochondrial membrane
+is_obsolete: true
+replaced_by: GO:0005741
[Term]
id: GO:0031308
-name: intrinsic component of nuclear outer membrane
+name: obsolete intrinsic component of nuclear outer membrane
namespace: cellular_component
-def: "The component of the nuclear outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the nuclear outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to nuclear outer membrane" NARROW []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0005640 ! nuclear outer membrane
+is_obsolete: true
+replaced_by: GO:0005640
[Term]
id: GO:0031309
-name: integral component of nuclear outer membrane
+name: obsolete integral component of nuclear outer membrane
namespace: cellular_component
-def: "The component of the nuclear outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the nuclear outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to nuclear outer membrane" NARROW []
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:0031308 ! intrinsic component of nuclear outer membrane
+is_obsolete: true
+replaced_by: GO:0005640
[Term]
id: GO:0031310
-name: intrinsic component of vacuolar membrane
+name: obsolete intrinsic component of vacuolar membrane
namespace: cellular_component
-def: "The component of the vacuolar membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the vacuolar membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to vacuolar membrane" NARROW []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0005774 ! vacuolar membrane
+is_obsolete: true
+replaced_by: GO:0005774
[Term]
id: GO:0031311
-name: intrinsic component of contractile vacuolar membrane
+name: obsolete intrinsic component of contractile vacuolar membrane
namespace: cellular_component
-def: "The component of the contractile vacuolar membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the contractile vacuolar membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to contractile vacuolar membrane" NARROW []
-is_a: GO:0031310 ! intrinsic component of vacuolar membrane
-relationship: part_of GO:0031164 ! contractile vacuolar membrane
+is_obsolete: true
+replaced_by: GO:0031164
[Term]
id: GO:0031312
@@ -166416,121 +166428,134 @@ relationship: positively_regulates GO:0006952 ! defense response
[Term]
id: GO:0031350
-name: intrinsic component of plastid membrane
+name: obsolete intrinsic component of plastid membrane
namespace: cellular_component
-def: "The component of the plastid membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the plastid membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to plastid membrane" NARROW []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0042170 ! plastid membrane
+is_obsolete: true
+replaced_by: GO:0042170
[Term]
id: GO:0031351
-name: integral component of plastid membrane
+name: obsolete integral component of plastid membrane
namespace: cellular_component
-def: "The component of the plastid membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the plastid membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to plastid membrane" NARROW []
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:0031350 ! intrinsic component of plastid membrane
+is_obsolete: true
+replaced_by: GO:0042170
[Term]
id: GO:0031352
-name: intrinsic component of plastid inner membrane
+name: obsolete intrinsic component of plastid inner membrane
namespace: cellular_component
-def: "The component of the plastid inner membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the plastid inner membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to plastid inner membrane" NARROW []
-is_a: GO:0031350 ! intrinsic component of plastid membrane
-relationship: part_of GO:0009528 ! plastid inner membrane
+is_obsolete: true
+replaced_by: GO:0009528
[Term]
id: GO:0031353
-name: integral component of plastid inner membrane
+name: obsolete integral component of plastid inner membrane
namespace: cellular_component
-def: "The component of the plastid inner membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the plastid inner membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to plastid inner membrane" NARROW []
-is_a: GO:0031351 ! integral component of plastid membrane
-is_a: GO:0031352 ! intrinsic component of plastid inner membrane
+is_obsolete: true
+replaced_by: GO:0009528
[Term]
id: GO:0031354
-name: intrinsic component of plastid outer membrane
+name: obsolete intrinsic component of plastid outer membrane
namespace: cellular_component
-def: "The component of the plastid outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the plastid outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to plastid outer membrane" NARROW []
-is_a: GO:0031350 ! intrinsic component of plastid membrane
-relationship: part_of GO:0009527 ! plastid outer membrane
+is_obsolete: true
+replaced_by: GO:0009527
[Term]
id: GO:0031355
-name: integral component of plastid outer membrane
+name: obsolete integral component of plastid outer membrane
namespace: cellular_component
-def: "The component of the plastid outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the plastid outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to plastid outer membrane" NARROW []
-is_a: GO:0031351 ! integral component of plastid membrane
-is_a: GO:0031354 ! intrinsic component of plastid outer membrane
+is_obsolete: true
+replaced_by: GO:0009527
[Term]
id: GO:0031356
-name: intrinsic component of chloroplast inner membrane
+name: obsolete intrinsic component of chloroplast inner membrane
namespace: cellular_component
-def: "The component of the chloroplast inner membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the chloroplast inner membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to chloroplast inner membrane" NARROW []
-is_a: GO:0031352 ! intrinsic component of plastid inner membrane
-relationship: part_of GO:0009706 ! chloroplast inner membrane
+is_obsolete: true
+replaced_by: GO:0009706
[Term]
id: GO:0031357
-name: integral component of chloroplast inner membrane
+name: obsolete integral component of chloroplast inner membrane
namespace: cellular_component
-def: "The component of the chloroplast inner membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the chloroplast inner membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to chloroplast inner membrane" NARROW []
-is_a: GO:0031353 ! integral component of plastid inner membrane
-is_a: GO:0031356 ! intrinsic component of chloroplast inner membrane
+is_obsolete: true
+replaced_by: GO:0009706
[Term]
id: GO:0031358
-name: intrinsic component of chloroplast outer membrane
+name: obsolete intrinsic component of chloroplast outer membrane
namespace: cellular_component
-def: "The component of the chloroplast outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the chloroplast outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to chloroplast outer membrane" NARROW []
-is_a: GO:0031354 ! intrinsic component of plastid outer membrane
-relationship: part_of GO:0009707 ! chloroplast outer membrane
+is_obsolete: true
+replaced_by: GO:0009707
[Term]
id: GO:0031359
-name: integral component of chloroplast outer membrane
+name: obsolete integral component of chloroplast outer membrane
namespace: cellular_component
-def: "The component of the chloroplast outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the chloroplast outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to chloroplast outer membrane" NARROW []
-is_a: GO:0031355 ! integral component of plastid outer membrane
-is_a: GO:0031358 ! intrinsic component of chloroplast outer membrane
+is_obsolete: true
+replaced_by: GO:0009707
[Term]
id: GO:0031360
-name: intrinsic component of thylakoid membrane
+name: obsolete intrinsic component of thylakoid membrane
namespace: cellular_component
-def: "The component of the thylakoid membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the thylakoid membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to thylakoid membrane" NARROW []
-is_a: GO:0031224 ! intrinsic component of membrane
-relationship: part_of GO:0042651 ! thylakoid membrane
+is_obsolete: true
+replaced_by: GO:0042651
[Term]
id: GO:0031361
-name: integral component of thylakoid membrane
+name: obsolete integral component of thylakoid membrane
namespace: cellular_component
-def: "The component of the thylakoid membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the thylakoid membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to thylakoid membrane" NARROW []
-is_a: GO:0016021 ! integral component of membrane
-is_a: GO:0031360 ! intrinsic component of thylakoid membrane
+is_obsolete: true
+replaced_by: GO:0042651
[Term]
id: GO:0031362
-name: anchored component of external side of plasma membrane
+name: obsolete anchored component of external side of plasma membrane
namespace: cellular_component
-def: "The component of the plasma membrane consisting of the gene products that are tethered to the external side of the membrane only by a covalently attached anchor, such as a lipid group embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the plasma membrane consisting of the gene products that are tethered to the external side of the membrane only by a covalently attached anchor, such as a lipid group embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "anchored to external leaflet of plasma membrane" EXACT [GOC:ab]
synonym: "anchored to external side of plasma membrane" EXACT []
-is_a: GO:0031233 ! intrinsic component of external side of plasma membrane
-is_a: GO:0046658 ! anchored component of plasma membrane
+is_obsolete: true
+replaced_by: GO:0009897
[Term]
id: GO:0031363
@@ -166554,7 +166579,7 @@ alt_id: GO:0018409
def: "The alteration of the N-terminal amino acid residue in a protein." [GOC:mah]
synonym: "peptide or protein amino-terminal blocking" RELATED []
synonym: "peptide/protein amino-terminal blocking" RELATED []
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0031366
@@ -166730,6 +166755,7 @@ comment: Use this term to annotate conjugated tags, not for conjugating enzymes.
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
+subset: prokaryote_subset
synonym: "covalent modifier" RELATED [GOC:vw]
synonym: "protein tagging activity" RELATED []
synonym: "ubiquitin" RELATED []
@@ -166771,7 +166797,7 @@ def: "A heptameric complex related to replication factor C, which loads the DNA
synonym: "Ctf18-RFC" EXACT []
synonym: "Ctf18-RLC" EXACT []
synonym: "RFC (Ctf18)" EXACT []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140513 ! nuclear protein-containing complex
relationship: part_of GO:0005694 ! chromosome
[Term]
@@ -166838,7 +166864,7 @@ name: bursicon neuropeptide hormone complex
namespace: cellular_component
def: "A neuropeptide hormone secreted by the central nervous system of insects that stimulates the tanning and sclerotization of the adult cuticle following eclosion. The active hormone consists of an obligate heterodimer of the alpha and beta subunits." [GOC:rc]
is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+relationship: part_of GO:0005576 ! extracellular region
[Term]
id: GO:0031396
@@ -166881,8 +166907,8 @@ name: regulation of protein modification process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein." [GOC:mah, GOC:tb]
subset: goslim_yeast
-is_a: GO:0032268 ! regulation of cellular protein metabolic process
-relationship: regulates GO:0006464 ! cellular protein modification process
+is_a: GO:0051246 ! regulation of protein metabolic process
+relationship: regulates GO:0036211 ! protein modification process
[Term]
id: GO:0031400
@@ -166894,8 +166920,8 @@ synonym: "down-regulation of protein modification" EXACT []
synonym: "downregulation of protein modification" EXACT []
synonym: "inhibition of protein modification" NARROW []
is_a: GO:0031399 ! regulation of protein modification process
-is_a: GO:0032269 ! negative regulation of cellular protein metabolic process
-relationship: negatively_regulates GO:0006464 ! cellular protein modification process
+is_a: GO:0051248 ! negative regulation of protein metabolic process
+relationship: negatively_regulates GO:0036211 ! protein modification process
[Term]
id: GO:0031401
@@ -166908,8 +166934,8 @@ synonym: "up regulation of protein modification" EXACT []
synonym: "up-regulation of protein modification" EXACT []
synonym: "upregulation of protein modification" EXACT []
is_a: GO:0031399 ! regulation of protein modification process
-is_a: GO:0032270 ! positive regulation of cellular protein metabolic process
-relationship: positively_regulates GO:0006464 ! cellular protein modification process
+is_a: GO:0051247 ! positive regulation of protein metabolic process
+relationship: positively_regulates GO:0036211 ! protein modification process
[Term]
id: GO:0031402
@@ -166942,7 +166968,6 @@ name: lipoic acid binding
namespace: molecular_function
def: "Binding to lipoic acid, 1,2-dithiolane-3-pentanoic acid." [GOC:mah, ISBN:0198506732]
is_a: GO:0005504 ! fatty acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
is_a: GO:1901681 ! sulfur compound binding
@@ -166954,6 +166979,7 @@ namespace: molecular_function
def: "Binding to a carboxylic acid, an organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC:mah, ISBN:0198506732]
subset: goslim_pir
is_a: GO:0043168 ! anion binding
+is_a: GO:0043177 ! organic acid binding
[Term]
id: GO:0031407
@@ -166990,7 +167016,6 @@ namespace: cellular_component
alt_id: GO:0016023
def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
@@ -167030,7 +167055,7 @@ name: regulation of buoyancy
namespace: biological_process
def: "Any process that modulates an organism's tendency or ability to rise or float in a fluid medium such as water or air, often through the use of stored gases." [GOC:mah, PATO:0001420]
synonym: "buoyancy regulation" EXACT []
-is_a: GO:0065008 ! regulation of biological quality
+is_a: GO:0065007 ! biological regulation
[Term]
id: GO:0031414
@@ -167074,7 +167099,6 @@ synonym: "L-ascorbate binding" EXACT []
synonym: "vitamin C binding" EXACT []
is_a: GO:0019842 ! vitamin binding
is_a: GO:0031406 ! carboxylic acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0048029 ! monosaccharide binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -167100,8 +167124,8 @@ id: GO:0031421
name: invertasome
namespace: cellular_component
def: "A complex formed by a recombinase, a regulatory protein, and the DNA sequences bound by each protein; catalyzes a reversible site-specific recombination reaction that results in the alternate expression of one or more genes in various contexts." [PMID:11114897, PMID:9732277]
-is_a: GO:0032993 ! protein-DNA complex
is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0031422
@@ -167110,7 +167134,7 @@ namespace: cellular_component
def: "A complex containing a RecQ family helicase and a topoisomerase III homologue (a member of the topoisomerase type IA subfamily); may also include one or more additional proteins; conserved from E. coli to human." [GOC:bhm, GOC:krc, PMID:15889139]
synonym: "RecQ helicase-Topo III complex" EXACT [PMID:15889139]
synonym: "Sgs1-Top3 complex" NARROW [PMID:15889139]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005694 ! chromosome
[Term]
@@ -167150,6 +167174,7 @@ def: "Any process that results in a change in state or activity of a cell or an
is_a: GO:0010243 ! response to organonitrogen compound
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0031428
@@ -167196,7 +167221,8 @@ def: "A heterodimeric protein complex required for the activation of DNA replica
synonym: "Cdc7-Dbf4 complex" NARROW []
synonym: "DDK" EXACT []
synonym: "Hsk1-Dfp1 kinase complex" NARROW []
-is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:0140513 ! nuclear protein-containing complex
+is_a: GO:1902554 ! serine/threonine protein kinase complex
[Term]
id: GO:0031432
@@ -167327,14 +167353,13 @@ is_a: GO:0014721 ! twitch skeletal muscle contraction
[Term]
id: GO:0031445
-name: regulation of heterochromatin assembly
+name: regulation of heterochromatin formation
namespace: biological_process
def: "Any process that modulates the frequency, rate, extent or location of heterochromatin formation." [GOC:mah]
-synonym: "regulation of heterochromatin formation" EXACT []
+synonym: "regulation of heterochromatin assembly" EXACT []
is_a: GO:0010468 ! regulation of gene expression
-is_a: GO:0010847 ! regulation of chromatin assembly
is_a: GO:0120261 ! regulation of heterochromatin organization
-relationship: regulates GO:0031507 ! heterochromatin assembly
+relationship: regulates GO:0031507 ! heterochromatin formation
[Term]
id: GO:0031446
@@ -167414,36 +167439,36 @@ relationship: positively_regulates GO:0031444 ! slow-twitch skeletal muscle fibe
[Term]
id: GO:0031452
-name: negative regulation of heterochromatin assembly
+name: negative regulation of heterochromatin formation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of heterochromatin formation." [GOC:mah]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of heterochromatin formation." [PMID:16855380]
+synonym: "chromatin decompaction" EXACT []
+synonym: "chromatin decondensation" EXACT [PMID:16855380]
synonym: "down regulation of heterochromatin formation" EXACT []
synonym: "down-regulation of heterochromatin formation" EXACT []
synonym: "downregulation of heterochromatin formation" EXACT []
synonym: "inhibition of heterochromatin formation" NARROW []
-synonym: "negative regulation of heterochromatin formation" EXACT []
+synonym: "negative regulation of heterochromatin assembly" EXACT []
is_a: GO:0010628 ! positive regulation of gene expression
-is_a: GO:0031445 ! regulation of heterochromatin assembly
-is_a: GO:0045798 ! negative regulation of chromatin assembly or disassembly
+is_a: GO:0031445 ! regulation of heterochromatin formation
is_a: GO:0120262 ! negative regulation of heterochromatin organization
-relationship: negatively_regulates GO:0031507 ! heterochromatin assembly
+relationship: negatively_regulates GO:0031507 ! heterochromatin formation
[Term]
id: GO:0031453
-name: positive regulation of heterochromatin assembly
+name: positive regulation of heterochromatin formation
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of heterochromatin formation." [GOC:mah]
synonym: "activation of heterochromatin formation" NARROW []
-synonym: "positive regulation of heterochromatin formation" EXACT []
+synonym: "positive regulation of heterochromatin assembly" EXACT []
synonym: "stimulation of heterochromatin formation" NARROW []
synonym: "up regulation of heterochromatin formation" EXACT []
synonym: "up-regulation of heterochromatin formation" EXACT []
synonym: "upregulation of heterochromatin formation" EXACT []
-is_a: GO:0031445 ! regulation of heterochromatin assembly
+is_a: GO:0031445 ! regulation of heterochromatin formation
is_a: GO:0044089 ! positive regulation of cellular component biogenesis
-is_a: GO:0045799 ! positive regulation of chromatin assembly or disassembly
is_a: GO:0120263 ! positive regulation of heterochromatin organization
-relationship: positively_regulates GO:0031507 ! heterochromatin assembly
+relationship: positively_regulates GO:0031507 ! heterochromatin formation
[Term]
id: GO:0031455
@@ -167492,9 +167517,7 @@ synonym: "ATP-dependent betaine transporter activity" EXACT []
synonym: "ATPase-coupled betaine transporter activity" RELATED []
synonym: "betaine ABC transporter" NARROW []
synonym: "betaine-transporting ATPase activity" EXACT []
-is_a: GO:0015101 ! organic cation transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
-is_a: GO:0140359 ! ABC-type transporter activity
+is_a: GO:0015418 ! ABC-type quaternary ammonium compound transporting activity
[Term]
id: GO:0031459
@@ -167626,7 +167649,7 @@ is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
id: GO:0031470
name: carboxysome
namespace: cellular_component
-def: "An organelle consisting of a proteinaceous coat and enzymes for the fixation of CO(2). It augments the concentration of CO(2) in the vicinity of RuBisCO to increase the efficiency of CO(2) fixation under atmospheric conditions." [GOC:js, PMID:28934381, PMID:8157606, PMID:8491708]
+def: "An organelle consisting of a proteinaceous coat and enzymes for the fixation of CO2. It augments the concentration of CO2 in the vicinity of RuBisCO to increase the efficiency of CO2 fixation under atmospheric conditions." [GOC:js, PMID:28934381, PMID:8157606, PMID:8491708]
xref: Wikipedia:Carboxysome
is_a: GO:0031469 ! bacterial microcompartment
@@ -167778,7 +167801,6 @@ name: nucleosome binding
namespace: molecular_function
def: "Binding to a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures." [GOC:mah]
is_a: GO:0003682 ! chromatin binding
-is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0031492
@@ -167803,7 +167825,7 @@ id: GO:0031494
name: regulation of mating type switching
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of mating type switching, the conversion of a single-cell organism from one mating type to another by the precise replacement of a DNA sequence at the expressed mating type locus with a copy of a sequence from a donor locus." [GOC:mah]
-is_a: GO:0010453 ! regulation of cell fate commitment
+is_a: GO:0050793 ! regulation of developmental process
is_a: GO:2000241 ! regulation of reproductive process
relationship: regulates GO:0007533 ! mating type switching
@@ -167816,8 +167838,8 @@ synonym: "down regulation of mating type switching" EXACT []
synonym: "down-regulation of mating type switching" EXACT []
synonym: "downregulation of mating type switching" EXACT []
synonym: "inhibition of mating type switching" NARROW []
-is_a: GO:0010454 ! negative regulation of cell fate commitment
is_a: GO:0031494 ! regulation of mating type switching
+is_a: GO:0051093 ! negative regulation of developmental process
is_a: GO:2000242 ! negative regulation of reproductive process
relationship: negatively_regulates GO:0007533 ! mating type switching
@@ -167831,30 +167853,19 @@ synonym: "stimulation of mating type switching" NARROW []
synonym: "up regulation of mating type switching" EXACT []
synonym: "up-regulation of mating type switching" EXACT []
synonym: "upregulation of mating type switching" EXACT []
-is_a: GO:0010455 ! positive regulation of cell fate commitment
is_a: GO:0031494 ! regulation of mating type switching
+is_a: GO:0051094 ! positive regulation of developmental process
is_a: GO:2000243 ! positive regulation of reproductive process
relationship: positively_regulates GO:0007533 ! mating type switching
-[Term]
-id: GO:0031497
-name: chromatin assembly
-namespace: biological_process
-def: "The assembly of DNA, histone proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus." [http://www.infobiogen.fr/services/chromcancer/IntroItems/ChromatinEducEng.html, PMID:20404130]
-synonym: "chromatin maintenance" BROAD []
-synonym: "establishment of chromatin architecture" EXACT [GOC:mah]
-is_a: GO:0006333 ! chromatin assembly or disassembly
-is_a: GO:0022607 ! cellular component assembly
-relationship: part_of GO:0006323 ! DNA packaging
-
[Term]
id: GO:0031498
-name: chromatin disassembly
+name: obsolete chromatin disassembly
namespace: biological_process
-def: "The controlled breakdown of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, other proteins, and sometimes RNA." [http://www.infobiogen.fr/services/chromcancer/IntroItems/ChromatinEducEng.html, PMID:20404130]
+def: "OBSOLETE. The controlled breakdown of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, other proteins, and sometimes RNA." [http://www.infobiogen.fr/services/chromcancer/IntroItems/ChromatinEducEng.html, PMID:20404130]
+comment: This term has been obsoleted because this process doesn't happen independently from assembly and is always tied to chromatin remodeling.
synonym: "chromatin maintenance" BROAD []
-is_a: GO:0006333 ! chromatin assembly or disassembly
-is_a: GO:0022411 ! cellular component disassembly
+is_obsolete: true
[Term]
id: GO:0031499
@@ -167946,18 +167957,18 @@ synonym: "cell wall glycoprotein biosynthesis" EXACT []
synonym: "cell wall glycoprotein formation" EXACT []
synonym: "cell wall glycoprotein synthesis" EXACT []
is_a: GO:0009101 ! glycoprotein biosynthetic process
-is_a: GO:0044038 ! cell wall macromolecule biosynthetic process
+is_a: GO:0044036 ! cell wall macromolecule metabolic process
[Term]
id: GO:0031507
-name: heterochromatin assembly
+name: heterochromatin formation
namespace: biological_process
alt_id: GO:0006342
alt_id: GO:0006343
alt_id: GO:0016440
alt_id: GO:0070869
alt_id: GO:1904497
-def: "An epigenetic gene silencing mechanism that involves the assembly of chromatin into heterochromatin, resulting in a chromatin conformation refractory to transcription. This process starts with heterochromatin nucleation, its spreading, and ends with heterochromatin boundary formation." [GOC:mah, PMID:25192661, PMID:33827924]
+def: "An epigenetic gene silencing mechanism in which chromatin is compacted into heterochromatin, resulting in a chromatin conformation refractory to transcription. This process starts with heterochromatin nucleation, its spreading, and ends with heterochromatin boundary formation." [PMID:25192661, PMID:33827924]
synonym: "chromatin silencing" EXACT []
synonym: "chromatin-mediated silencing" EXACT []
synonym: "establishment of chromatin silencing" RELATED []
@@ -167966,27 +167977,26 @@ synonym: "establishment of heterochromatin architecture" EXACT [GOC:mah]
synonym: "establishment of heterochromatin architecture involved in chromatin silencing at centromere outer repeat region" NARROW [GOC:TermGenie]
synonym: "establishment of heterochromatin architecture involved in chromatin silencing at pericentric region" NARROW [GOC:TermGenie]
synonym: "heterochromatic silencing" RELATED []
+synonym: "heterochromatin assembly" EXACT []
synonym: "heterochromatin assembly involved in chromatin silencing" RELATED []
synonym: "heterochromatin assembly involved in chromatin silencing at centromere outer repeat region" NARROW []
synonym: "heterochromatin assembly involved in chromatin silencing at pericentric region" NARROW [GOC:TermGenie]
-synonym: "heterochromatin formation" EXACT []
synonym: "heterochromatin formation involved in chromatin silencing" RELATED []
synonym: "heterochromatin formation involved in chromatin silencing at centromere outer repeat region" NARROW [GOC:TermGenie]
synonym: "heterochromatin formation involved in chromatin silencing at pericentric region" NARROW [GOC:TermGenie]
synonym: "heterochromatin maintenance" BROAD []
synonym: "TGS" BROAD []
-synonym: "transcriptional gene silencing" EXACT []
-is_a: GO:0031497 ! chromatin assembly
+synonym: "transcriptional gene silencing" RELATED []
is_a: GO:0045814 ! negative regulation of gene expression, epigenetic
is_a: GO:0070828 ! heterochromatin organization
[Term]
id: GO:0031508
-name: pericentric heterochromatin assembly
+name: pericentric heterochromatin formation
namespace: biological_process
alt_id: GO:0030702
alt_id: GO:1990141
-def: "The assembly of chromatin located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3, into heterochromatin, resulting in the repression of transcription of centromeric DNA." [GOC:mah, PMID:20206496, PMID:22729156]
+def: "The compaction of chromatin located adjacent to the CENP-A rich centromere 'central core' and characterized by methylation of histone H3K9, into heterochromatin, resulting in the repression of transcription at pericentric DNA." [GOC:mah, PMID:14612388, PMID:20206496, PMID:22729156]
synonym: "centric heterochromatin formation" RELATED []
synonym: "centromere chromatin silencing" EXACT [GOC:mah]
synonym: "centromeric heterochromatin biosynthesis" EXACT []
@@ -167996,19 +168006,17 @@ synonym: "chromatin silencing at centromere" EXACT []
synonym: "chromatin silencing at centromere outer repeat region" NARROW []
synonym: "chromatin silencing at pericentric region" RELATED [GOC:mah]
synonym: "heterochromatic silencing at centromere" EXACT []
-is_a: GO:0031055 ! chromatin remodeling at centromere
-is_a: GO:0140462 ! pericentric heterochromatin organization
-is_a: GO:0140719 ! constitutive heterochromatin assembly
-relationship: part_of GO:0034508 ! centromere complex assembly
+synonym: "pericentric heterochromatin assembly" EXACT []
+is_a: GO:0140719 ! constitutive heterochromatin formation
[Term]
id: GO:0031509
-name: subtelomeric heterochromatin assembly
+name: subtelomeric heterochromatin formation
namespace: biological_process
alt_id: GO:0006348
alt_id: GO:0035390
alt_id: GO:0099114
-def: "The assembly of chromatin into heterochromatin at the subtelomeric region, resulting in a chromatin conformation refractory to transcription." [GOC:mah, PMID:10219245, PMID:26205977]
+def: "The compaction of chromatin into heterochromatin at the subtelomeric region." [GOC:mah, PMID:10219245, PMID:26205977]
synonym: "chromatin silencing at subtelomere" RELATED []
synonym: "chromatin silencing at telomere" EXACT []
synonym: "establishment of chromatin silencing at telomere" RELATED []
@@ -168017,13 +168025,14 @@ synonym: "heterochromatic silencing at telomere" EXACT []
synonym: "regulation of chromatin silencing at telomere" RELATED []
synonym: "regulation of subtelomeric heterochromatin assembly" RELATED []
synonym: "subtelomere chromatin silencing" RELATED [GOC:mah]
+synonym: "subtelomeric heterochromatin assembly" EXACT []
synonym: "subtelomeric silencing" EXACT [GOC:mah]
synonym: "telomere chromatin silencing" EXACT [GOC:mah]
synonym: "Telomere Position Effect" EXACT [GOC:BHF, GOC:BHF_telomere, GOC:nc, PMID:21847107]
synonym: "telomeric heterochromatin assembly" RELATED []
synonym: "telomeric heterochromatin formation" RELATED []
synonym: "telomeric silencing" EXACT [GOC:bf]
-is_a: GO:0140719 ! constitutive heterochromatin assembly
+is_a: GO:0140719 ! constitutive heterochromatin formation
relationship: part_of GO:0032200 ! telomere organization
[Term]
@@ -168041,6 +168050,7 @@ id: GO:0031511
name: Mis6-Sim4 complex
namespace: cellular_component
def: "A protein complex that forms part of the inner kinetochore, which is involved in the loading of the centromeric histone h3 variant CENP-A onto centromeres and in centromere specific heterochromatin formation. The complex contains about 12 proteins, of which two are known as Mis6 and Sim4 in S. pombe and CENP-I and CENP-H in human." [GOC:vw, PMID:12719471, PMID:15897182]
+synonym: "Mcm21" RELATED []
synonym: "Mis6 centromere subcomplex" NARROW []
synonym: "Mis6-Mal2-Sim4 centromere complex" EXACT [GOC:vw, PMID:21445296]
synonym: "Sim4 complex" EXACT []
@@ -168088,7 +168098,7 @@ id: GO:0031518
name: CBF3 complex
namespace: cellular_component
def: "A multisubunit protein complex that binds to centromeric DNA and initiates kinetochore assembly. In yeast, this complex consists of four subunits, namely Ctf13p, Skp1p, Cep3p and Cbf2p." [PMID:13679521, PMID:9407032]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140513 ! nuclear protein-containing complex
relationship: part_of GO:0000775 ! chromosome, centromeric region
[Term]
@@ -168128,7 +168138,7 @@ synonym: "plasma membrane Sec complex" RELATED []
synonym: "Sec complex" BROAD []
synonym: "Sec secretion complex" NARROW []
synonym: "Sec translocation complex" NARROW []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140535 ! intracellular protein-containing complex
[Term]
id: GO:0031523
@@ -168491,24 +168501,25 @@ is_a: GO:2000273 ! positive regulation of signaling receptor activity
[Term]
id: GO:0031554
-name: regulation of DNA-templated transcription, termination
+name: regulation of termination of DNA-templated transcription
namespace: biological_process
def: "Any process that modulates the frequency, rate, extent, or location of DNA-templated transcription termination, the process in which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA." [GOC:mlg, GOC:txnOH]
synonym: "regulation of DNA-dependent transcription, termination" EXACT [GOC:txnOH]
-synonym: "regulation of termination of DNA-dependent transcription" EXACT [GOC:jh2]
+synonym: "regulation of DNA-templated transcription, termination" EXACT []
synonym: "regulation of transcription termination, DNA-dependent" EXACT [GOC:jh2]
synonym: "transcription antiterminator activity" RELATED []
is_a: GO:0043244 ! regulation of protein-containing complex disassembly
is_a: GO:2001141 ! regulation of RNA biosynthetic process
-relationship: regulates GO:0006353 ! DNA-templated transcription, termination
+relationship: regulates GO:0006353 ! DNA-templated transcription termination
[Term]
id: GO:0031555
name: transcriptional attenuation
namespace: biological_process
-def: "Regulation of transcription through variation in where transcription termination occurs." [GOC:dh, GOC:mlg, ISBN:0198542682]
+def: "A negative regulation of gene expression mechanism by which bacteria and archae can direct RNA polymerase to prematurely terminate transcription in response to a specific metabolic signal." [PMID:12210530, PMID:15851059, PMID:7007895]
xref: Wikipedia:Attenuator_(genetics)
-is_a: GO:0031554 ! regulation of DNA-templated transcription, termination
+is_a: GO:0010629 ! negative regulation of gene expression
+is_a: GO:0060566 ! positive regulation of termination of DNA-templated transcription
[Term]
id: GO:0031556
@@ -168583,9 +168594,10 @@ relationship: part_of GO:0043332 ! mating projection tip
id: GO:0031564
name: transcription antitermination
namespace: biological_process
-def: "Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s)." [ISBN:0198577788, PMID:12456320]
+def: "A positive regulation of gene expression mechanism that allows RNA polymerase to continue transcription beyond a termination site, thus allowing expression of downstream genes under specific conditions." [ISBN:0198577788, PMID:12456320, PMID:21478900, PMID:30191803]
synonym: "transcriptional readthrough" EXACT []
-is_a: GO:0031554 ! regulation of DNA-templated transcription, termination
+is_a: GO:0010628 ! positive regulation of gene expression
+is_a: GO:0060567 ! negative regulation of termination of DNA-templated transcription
[Term]
id: GO:0031565
@@ -168773,7 +168785,7 @@ is_a: GO:0043111 ! replication fork arrest
id: GO:0031583
name: phospholipase D-activating G protein-coupled receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a G protein-coupled receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase D (PLD) and a subsequent increase in cellular levels of phosphatidic acid (PA)." [GOC:mah, GOC:signaling, PMID:11812783, PMID:15924269]
+def: "A G protein-coupled receptor signaling pathway in which the signal is transmitted via the activation of phospholipase D (PLD) and a subsequent increase in the intracellular concentration of phosphatidic acid (PA)." [GOC:mah, GOC:signaling, PMID:11812783, PMID:15924269]
comment: This term is intended to cover steps in a GPCR signaling pathway both upstream and downstream of phospholipase D (PLD) activation.
synonym: "activation of phospholipase D activity by G-protein coupled receptor protein signaling pathway" RELATED [GOC:signaling]
synonym: "G-protein signalling, phospholipase D activating pathway" EXACT []
@@ -168900,7 +168912,7 @@ id: GO:0031594
name: neuromuscular junction
namespace: cellular_component
def: "The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential." [GOC:nln]
-comment: In vertebrates, the term 'neuromuscular junction' is limited to synapses targeting skeletal muscle fibers - all of which are cholinergic and excitatory. Both inhibitory and excitatory neuromuscular junctions exist in invertebrates, utilizing a range of neurotransmitters including glutamate, GABA and 5-HT.
+comment: In vertebrates, the term 'neuromuscular junction' is limited to synapses targeting skeletal muscle fibers - all of which are cholinergic and excitatory. Both inhibitory and excitatory neuromuscular junctions exist in invertebrates, utilizing a range of neurotransmitters including glutamate, GABA and 5-HT.
synonym: "motor endplate" RELATED [NIF_Subcellular:nlx_subcell_20090512]
synonym: "NMJ" RELATED [GOC:ha]
xref: NIF_Subcellular:sao1124888485
@@ -169090,17 +169102,6 @@ def: "A centrosome from which one pole of a mitotic or meiotic spindle is organi
is_a: GO:0005813 ! centrosome
relationship: part_of GO:0000922 ! spindle pole
-[Term]
-id: GO:0031617
-name: NMS complex
-namespace: cellular_component
-def: "A supercomplex formed by the association of two subcomplexes (known as MIND and Ndc80 in Schizosaccharomyces) with additional proteins at the kinetochores of condensed nuclear chromosomes." [PMID:16079914]
-synonym: "KMN kinetochore network" EXACT []
-synonym: "KNL-1-Mis12-Ndc80" EXACT []
-synonym: "Ndc80-MIND-Spc7 complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0000776 ! kinetochore
-
[Term]
id: GO:0031619
name: homologous chromosome orientation involved in meiotic metaphase I plate congression
@@ -169158,7 +169159,6 @@ name: receptor internalization
namespace: biological_process
def: "A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane." [GOC:bf, GOC:mah, GOC:signaling, PMID:15006537, PMID:19643732]
is_a: GO:0006898 ! receptor-mediated endocytosis
-is_a: GO:0043112 ! receptor metabolic process
[Term]
id: GO:0031624
@@ -169285,7 +169285,7 @@ is_a: GO:1990837 ! sequence-specific double-stranded DNA binding
id: GO:0031635
name: adenylate cyclase-inhibiting opioid receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of an opioid receptor binding to its physiological ligand, where the pathway proceeds with inhibition of adenylyl cyclase and a subsequent decrease in the concentration of cyclic AMP (cAMP)." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
+def: "An adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway initiated by an opioid binding to its receptor, and ending with the regulation of a downstream cellular process." [GOC:dph, GOC:mah, GOC:signaling, GOC:tb]
synonym: "inhibition of adenylate cyclase activity by opioid receptor signaling pathway" RELATED [GOC:signaling]
synonym: "inhibition of adenylate cyclase activity by opioid receptor signalling pathway" RELATED [GOC:mah]
synonym: "opioid receptor, adenylate cyclase inhibiting pathway" EXACT [GOC:dph, GOC:tb]
@@ -169441,7 +169441,6 @@ name: regulation of heat generation
namespace: biological_process
def: "Any process that modulates the rate or extent of heat generation." [GOC:dph, GOC:mah, GOC:tb]
is_a: GO:0051239 ! regulation of multicellular organismal process
-is_a: GO:0065008 ! regulation of biological quality
relationship: regulates GO:0031649 ! heat generation
[Term]
@@ -169484,7 +169483,6 @@ name: regulation of heat dissipation
namespace: biological_process
def: "Any process that modulates the rate or extent of heat dissipation." [GOC:dph, GOC:mah, GOC:tb]
is_a: GO:0051239 ! regulation of multicellular organismal process
-is_a: GO:0065008 ! regulation of biological quality
relationship: regulates GO:0031653 ! heat dissipation
[Term]
@@ -169588,7 +169586,7 @@ consider: GO:0010389
id: GO:0031663
name: lipopolysaccharide-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system." [GOC:mah, GOC:signaling, PMID:15379975]
+def: "The series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system." [GOC:mah, GOC:signaling, PMID:15379975]
synonym: "lipopolysaccharide-mediated signalling pathway" EXACT []
synonym: "LPS-mediated signaling pathway" EXACT []
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -170473,21 +170471,23 @@ is_a: GO:0071855 ! neuropeptide receptor binding
[Term]
id: GO:0031771
-name: type 1 hypocretin receptor binding
+name: type 1 orexin receptor binding
namespace: molecular_function
-def: "Binding to a type 1 hypocretin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 orexin receptor." [GOC:mah, GOC:nln]
+synonym: "OX1 orexin receptor binding" EXACT []
+synonym: "type 1 hypocretin receptor binding" EXACT []
synonym: "type 1 hypocretin receptor ligand" NARROW []
-synonym: "type 1 orexin receptor binding" EXACT []
-is_a: GO:0042324 ! hypocretin receptor binding
+is_a: GO:0042324 ! orexin receptor binding
[Term]
id: GO:0031772
-name: type 2 hypocretin receptor binding
+name: type 2 orexin receptor binding
namespace: molecular_function
-def: "Binding to a type 2 hypocretin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 orexin receptor." [GOC:mah, GOC:nln]
+synonym: "OX2 orexin receptor binding" EXACT []
+synonym: "type 2 hypocretin receptor binding" EXACT []
synonym: "type 2 hypocretin receptor ligand" NARROW []
-synonym: "type 2 orexin receptor binding" EXACT []
-is_a: GO:0042324 ! hypocretin receptor binding
+is_a: GO:0042324 ! orexin receptor binding
[Term]
id: GO:0031773
@@ -171758,6 +171758,7 @@ def: "Enables the transfer of pyridoxal from one side of a membrane to the other
synonym: "pyridoxal transporter activity" BROAD []
is_a: GO:0015101 ! organic cation transmembrane transporter activity
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0031926
@@ -171775,6 +171776,7 @@ namespace: molecular_function
def: "Enables the transfer of pyridoxamine from one side of a membrane to the other. Pyridoxamine, 4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol, is one of the vitamin B6 compounds. Pyridoxal, pyridoxamine and pyridoxine are collectively known as vitamin B6, and are efficiently converted to the biologically active form of vitamin B6, pyridoxal phosphate." [GOC:mah]
is_a: GO:0015101 ! organic cation transmembrane transporter activity
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0031928
@@ -171783,12 +171785,13 @@ namespace: molecular_function
def: "Enables the transfer of pyridoxine from one side of a membrane to the other. Pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, is one of the vitamin B6 compounds. Pyridoxal, pyridoxamine and pyridoxine are collectively known as vitamin B6, and are efficiently converted to the biologically active form of vitamin B6, pyridoxal phosphate." [GOC:mah]
synonym: "pyridoxine transporter activity" BROAD []
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0031929
name: TOR signaling
namespace: biological_process
-def: "A series of molecular signals mediated by TOR (Target of rapamycin) proteins, members of the phosphoinositide (PI) 3-kinase related kinase (PIKK) family that act as serine/threonine kinases in response to nutrient availability or growth factors." [PMID:12372295]
+def: "The series of molecular signals mediated by TOR (Target of rapamycin) proteins, members of the phosphoinositide (PI) 3-kinase related kinase (PIKK) family that act as serine/threonine kinases in response to nutrient availability or growth factors." [PMID:12372295]
comment: Note that this term should not be confused with 'torso signaling pathway ; GO:0008293', although torso is abbreviated 'tor'.
synonym: "target of rapamycin signaling pathway" EXACT []
synonym: "target of rapamycin signalling pathway" EXACT []
@@ -171802,7 +171805,7 @@ is_a: GO:0035556 ! intracellular signal transduction
id: GO:0031930
name: mitochondria-nucleus signaling pathway
namespace: biological_process
-def: "A series of molecular signals that forms a pathway of communication from the mitochondria to the nucleus and initiates cellular changes in response to changes in mitochondrial function." [GOC:jh, PMID:15068799]
+def: "The series of molecular signals that forms a pathway of communication from the mitochondria to the nucleus and initiates cellular changes in response to changes in mitochondrial function." [GOC:jh, PMID:15068799]
synonym: "mitochondria-nucleus signal transduction" EXACT [GOC:signaling]
synonym: "mitochondrial signaling pathway" EXACT []
synonym: "mitochondrial signalling pathway" EXACT []
@@ -172112,7 +172115,7 @@ relationship: positively_regulates GO:0046777 ! protein autophosphorylation
id: GO:0031955
name: short-chain fatty acid-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + a short-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA; short-chain fatty acids are fatty acids with a chain length of less than C6." [EC:6.2.1.3, GOC:mah]
+def: "Catalysis of the reaction: ATP + a short-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA. A short-chain fatty acid is a fatty acid with an aliphatic tail of less than 6 carbons." [GOC:mah, PMID:34904027]
synonym: "short-chain fatty acid activation" RELATED []
synonym: "short-chain fatty-acid-CoA ligase activity" EXACT [GOC:bf]
synonym: "short-chain-fatty-acid-CoA ligase activity" EXACT []
@@ -172123,7 +172126,7 @@ is_a: GO:0016405 ! CoA-ligase activity
id: GO:0031956
name: medium-chain fatty acid-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + a medium-chain carboxylic acid + CoA = AMP + diphosphate + an acyl-CoA; a medium-chain fatty acid is any fatty acid with a chain length of between C6 and C12." [GOC:mah, RHEA:48340]
+def: "Catalysis of the reaction: ATP + a medium-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA. A medium-chain fatty acid is a fatty acid with an aliphatic tail of 6 to 12 carbons." [GOC:mah, RHEA:48340]
synonym: "medium-chain fatty acid activation" RELATED []
synonym: "medium-chain fatty-acid-CoA ligase activity" EXACT [GOC:bf]
synonym: "medium-chain-fatty-acid-CoA ligase activity" EXACT []
@@ -172136,7 +172139,7 @@ is_a: GO:0016405 ! CoA-ligase activity
id: GO:0031957
name: very long-chain fatty acid-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + a very-long-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA; a very long-chain fatty acid is a fatty acid which has a chain length greater than C22." [EC:6.2.1.3, GOC:mah]
+def: "Catalysis of the reaction: ATP + a very-long-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA; a very long-chain fatty acid is a fatty acid which has a chain length greater than C22." [GOC:mah, PMID:18024425]
synonym: "very-long-chain fatty acid activation" RELATED []
synonym: "very-long-chain fatty acid-CoA ligase activity" EXACT []
synonym: "very-long-chain-fatty-acid-CoA ligase activity" EXACT []
@@ -172150,7 +172153,7 @@ is_a: GO:0016405 ! CoA-ligase activity
id: GO:0031958
name: corticosteroid receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of a corticosteroid binding to its receptor." [GOC:mah, PMID:11027914, PMID:12606724]
+def: "The series of molecular signals initiated by corticosteroid binding to its receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, PMID:11027914, PMID:12606724]
synonym: "corticosteroid receptor signalling pathway" EXACT []
is_a: GO:0030518 ! intracellular steroid hormone receptor signaling pathway
@@ -172158,7 +172161,7 @@ is_a: GO:0030518 ! intracellular steroid hormone receptor signaling pathway
id: GO:0031959
name: mineralocorticoid receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of a mineralocorticoid binding to its receptor." [GOC:mah, PMID:11027914, PMID:12606724]
+def: "The series of molecular signals initiated by mineralocorticoid binding to its receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, PMID:11027914, PMID:12606724]
synonym: "mineralocorticoid receptor signalling pathway" EXACT []
is_a: GO:0031958 ! corticosteroid receptor signaling pathway
@@ -172172,25 +172175,27 @@ is_a: GO:0048545 ! response to steroid hormone
[Term]
id: GO:0031961
-name: cortisol receptor binding
+name: nuclear cortisol receptor binding
namespace: molecular_function
-def: "Binding to a cortisol receptor." [GOC:mah, PMID:12511169]
-is_a: GO:0035259 ! glucocorticoid receptor binding
+def: "Binding to a nuclear cortisol receptor." [GOC:mah, PMID:12511169]
+synonym: "cortisol receptor binding" BROAD []
+is_a: GO:0035259 ! nuclear glucocorticoid receptor binding
[Term]
id: GO:0031962
-name: mineralocorticoid receptor binding
+name: nuclear mineralocorticoid receptor binding
namespace: molecular_function
-def: "Binding to a mineralocorticoid receptor." [GOC:mah, PMID:12511169]
+def: "Binding to a nuclear mineralocorticoid receptor." [GOC:mah, PMID:12511169]
+synonym: "mineralocorticoid receptor binding" BROAD []
is_a: GO:0016922 ! nuclear receptor binding
[Term]
id: GO:0031963
-name: cortisol receptor activity
+name: nuclear cortisol receptor activity
namespace: molecular_function
def: "Combining with cortisol and transmitting the signal within the cell to trigger a change in cell activity or function." [GOC:mah, PMID:12511169]
-comment: For cortisol receptors that act in the nucleus to regulate transcription, consider also annotating to the terms: ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity ; GO:0038049' or ligand-activated RNA polymerase II transcription factor binding transcription factor activity ; GO:0038049'.
-is_a: GO:0004883 ! glucocorticoid receptor activity
+synonym: "cortisol receptor activity" BROAD []
+is_a: GO:0004883 ! nuclear glucocorticoid receptor activity
[Term]
id: GO:0031964
@@ -172293,7 +172298,6 @@ name: plastid thylakoid
namespace: cellular_component
def: "Any thylakoid within a plastid." [GOC:pz]
is_a: GO:0009579 ! thylakoid
-is_a: GO:0031984 ! organelle subcompartment
relationship: part_of GO:0009536 ! plastid
[Term]
@@ -172395,7 +172399,7 @@ relationship: part_of GO:0007626 ! locomotory behavior
id: GO:0031989
name: bombesin receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a bombesin receptor binding to one of its physiological ligands." [GOC:mah]
+def: "A G protein-coupled receptor signaling pathway initiated by a bombesin binding to its receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah]
synonym: "bombesin receptor signalling pathway" EXACT []
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -172407,7 +172411,9 @@ def: "The directed movement of mRNA from the nucleus to the cytoplasm during a h
synonym: "mRNA export from cell nucleus during heat stress" EXACT []
synonym: "mRNA export from nucleus during heat stress" RELATED [GOC:dph, GOC:tb]
is_a: GO:0006406 ! mRNA export from nucleus
+is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0034605 ! cellular response to heat
+is_a: GO:1901698 ! response to nitrogen compound
[Term]
id: GO:0031991
@@ -172466,10 +172472,12 @@ is_a: GO:0019899 ! enzyme binding
[Term]
id: GO:0031997
-name: N-terminal myristoylation domain binding
+name: obsolete N-terminal myristoylation domain binding
namespace: molecular_function
-def: "Binding to the N-terminus of a protein that has the potential to be, or has been, modified by N-terminal myristoylation. Binding affinity is typically altered by myristoylation; for example, N-terminal myristoylation of HIV Nef increases its affinity for calmodulin." [GOC:dl, GOC:jsg, PMID:15632291]
-is_a: GO:0047485 ! protein N-terminus binding
+def: "OBSOLETE. Binding to the N-terminus of a protein that has the potential to be, or has been, modified by N-terminal myristoylation. Binding affinity is typically altered by myristoylation; for example, N-terminal myristoylation of HIV Nef increases its affinity for calmodulin." [GOC:dl, GOC:jsg, PMID:15632291]
+comment: It is beyond GO scope.
+is_obsolete: true
+replaced_by: GO:0005515
[Term]
id: GO:0031998
@@ -172533,7 +172541,6 @@ namespace: cellular_component
def: "A protein complex that binds interleukin-28 and interleukin-29. It is composed of an alpha and a beta receptor subunit (in human IFNLR1/IL28Ralpha & IL10RB) and either Interleukin-28 (IFNL2 or IFNL3) or Interleukin-29 (IFNL1)." [GOC:rph]
synonym: "IL-28 receptor complex" EXACT [GOC:add]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0032003
@@ -172625,7 +172632,7 @@ is_a: GO:0045335 ! phagocytic vesicle
id: GO:0032011
name: ARF protein signal transduction
namespace: biological_process
-def: "A series of molecular signals within the cell that are mediated by a member of the ARF family of proteins switching to a GTP-bound active state." [GOC:mah]
+def: "The series of molecular signals within the cell that are mediated by a member of the ARF family of proteins switching to a GTP-bound active state." [GOC:mah]
is_a: GO:0007265 ! Ras protein signal transduction
[Term]
@@ -172879,11 +172886,13 @@ is_a: GO:0030684 ! preribosome
[Term]
id: GO:0032041
-name: NAD-dependent histone deacetylase activity (H3-K14 specific)
+name: NAD-dependent histone H3K14 deacetylase activity
namespace: molecular_function
def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein." [PMID:28450737]
+synonym: "NAD-dependent histone deacetylase activity (H3-K14 specific)" EXACT []
+synonym: "NAD-dependent histone H3-K14 deacetylase activity" EXACT []
is_a: GO:0017136 ! NAD-dependent histone deacetylase activity
-is_a: GO:0031078 ! histone deacetylase activity (H3-K14 specific)
+is_a: GO:0031078 ! histone H3K14 deacetylase activity
[Term]
id: GO:0032042
@@ -173403,7 +173412,7 @@ is_a: GO:0043433 ! negative regulation of DNA-binding transcription factor activ
id: GO:0032089
name: NACHT domain binding
namespace: molecular_function
-def: "Binding to a NACHT (NAIP, CIITA, HET-E and TP1) domain. The NACHT domain consists of seven distinct conserved motifs, including an ATP/GTPase specific P-loop, a Mg(2+)-binding site and five more specific motifs." [GOC:rl]
+def: "Binding to a NACHT (NAIP, CIITA, HET-E and TP1) domain. The NACHT domain consists of seven distinct conserved motifs, including an ATP/GTPase specific P-loop, a Mg2+-binding site and five more specific motifs." [GOC:rl]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -173649,12 +173658,13 @@ is_a: GO:0045859 ! regulation of protein kinase activity
[Term]
id: GO:0032111
-name: activation of protein histidine kinase activity
+name: obsolete activation of protein histidine kinase activity
namespace: biological_process
-def: "Any process that initiates the activity of an inactive protein histidine kinase." [GOC:mah]
+def: "OBSOLETE. Any process that initiates the activity of an inactive protein histidine kinase." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "protein histidine kinase activator" RELATED []
-is_a: GO:0010864 ! positive regulation of protein histidine kinase activity
-is_a: GO:0032147 ! activation of protein kinase activity
+is_obsolete: true
+consider: GO:0030295
[Term]
id: GO:0032112
@@ -173687,7 +173697,7 @@ is_a: GO:0032113 ! regulation of carbohydrate phosphatase activity
id: GO:0032115
name: sorbose reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glucitol + NADP(+) = L-sorbose + H(+) + NADPH. The reaction may occur, to a minor extent, in the reverse direction." [EC:1.1.1.289, RHEA:14609]
+def: "Catalysis of the reaction: D-glucitol + NADP+ = L-sorbose + H+ + NADPH. The reaction may occur, to a minor extent, in the reverse direction." [EC:1.1.1.289, RHEA:14609]
synonym: "D-glucitol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.289]
synonym: "Sou1p" RELATED [EC:1.1.1.289]
xref: EC:1.1.1.289
@@ -173734,7 +173744,7 @@ namespace: biological_process
def: "The process of binding or confining zinc ions such that they are separated from other components of a biological system." [GOC:mah]
is_a: GO:0051238 ! sequestering of metal ion
is_a: GO:0051651 ! maintenance of location in cell
-relationship: part_of GO:0006882 ! cellular zinc ion homeostasis
+relationship: part_of GO:0006882 ! intracellular zinc ion homeostasis
[Term]
id: GO:0032120
@@ -173826,9 +173836,11 @@ relationship: part_of GO:0031045 ! dense core granule
[Term]
id: GO:0032129
-name: histone deacetylase activity (H3-K9 specific)
+name: histone H3K9 deacetylase activity
namespace: molecular_function
def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 9) + H2O = histone H3 L-lysine (position 9) + acetate. This reaction represents the removal of an acetyl group from lysine at position 9 of the histone H3 protein." [PMID:28450737]
+synonym: "histone deacetylase activity (H3-K9 specific)" EXACT []
+synonym: "histone H3-K9 deacetylase activity" EXACT []
is_a: GO:0004407 ! histone deacetylase activity
[Term]
@@ -174293,13 +174305,13 @@ synonym: "cellular bud neck septin ring organisation" EXACT [GOC:mah]
is_a: GO:0031106 ! septin ring organization
is_a: GO:1903047 ! mitotic cell cycle process
relationship: part_of GO:0000281 ! mitotic cytokinesis
-relationship: part_of GO:0007105 ! cytokinesis, site selection
+relationship: part_of GO:0007105 ! cytokinesis, division site positioning
[Term]
id: GO:0032187
name: actomyosin contractile ring localization
namespace: biological_process
-def: "The process in which a contractile ring is assembled and/or maintained in a specific location, in the context of cytokinesis that takes place as part of a cell cycle." [GOC:mah]
+def: "The process in which a contractile ring is positioned or maintained in a specific location, in the context of cytokinesis that takes place as part of a cell cycle." [GOC:mah]
synonym: "contractile ring localisation involved in cell cycle cytokinesis" EXACT [GOC:mah]
synonym: "contractile ring localization involved in cell cycle cytokinesis" EXACT [GOC:mah, GOC:vw]
is_a: GO:0036214 ! contractile ring localization
@@ -174316,7 +174328,7 @@ synonym: "establishment of contractile ring localisation involved in cell cycle
synonym: "establishment of contractile ring localization involved in cell cycle cytokinesis" EXACT [GOC:mah, GOC:vw]
synonym: "establishment of contractile ring localization involved in cytokinesis during cell cycle" RELATED [GOC:dph, GOC:tb]
is_a: GO:0032187 ! actomyosin contractile ring localization
-relationship: part_of GO:0007105 ! cytokinesis, site selection
+relationship: part_of GO:0007105 ! cytokinesis, division site positioning
[Term]
id: GO:0032189
@@ -174369,8 +174381,7 @@ is_a: GO:0030139 ! endocytic vesicle
id: GO:0032196
name: transposition
namespace: biological_process
-def: "Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites." [GOC:jp, ISBN:1555812090]
-subset: goslim_aspergillus
+def: "Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites. For elements that are transcribed as the first step of transposition, the process starts with the transcription of the transposable element, its translation and maturation, and ending with integration into DNA. For elements that are cut out, the process starts with the excision of the donor DNA and integrated into another site." [ISBN:1555812090, PMID:14682279, PMID:25893143]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_pir
@@ -174380,18 +174391,19 @@ is_a: GO:0009987 ! cellular process
[Term]
id: GO:0032197
-name: transposition, RNA-mediated
+name: retrotransposition
namespace: biological_process
alt_id: GO:0006319
alt_id: GO:0006320
alt_id: GO:0006321
alt_id: GO:0006322
-def: "Any process involved in a type of transpositional recombination which occurs via an RNA intermediate." [GOC:jp, ISBN:1555812090]
+def: "A type of transposition in which a transposable element (transposon) copies and pastes itself into a different genomic location by transcription and convertsion of the transcribed RNA back into DNA through reverse transcription." [ISBN:1555812090, PMID:26912865, PMID:30416149, PMID:30958115, PMID:32588192]
synonym: "Class I transposition" EXACT []
-synonym: "retrotransposition" EXACT []
synonym: "retrotransposon transposition" EXACT []
synonym: "RNA-mediated transposition" EXACT [GOC:dph, GOC:tb]
synonym: "Tf transposition" NARROW []
+synonym: "transposition via RNA intermediate" EXACT []
+synonym: "transposition, RNA-mediated" EXACT []
synonym: "Ty element transposition" NARROW []
synonym: "Ty1 element transposition" NARROW []
synonym: "Ty2 element transposition" NARROW []
@@ -174401,20 +174413,22 @@ is_a: GO:0032196 ! transposition
[Term]
id: GO:0032198
-name: MITE transposition
+name: obsolete MITE transposition
namespace: biological_process
-def: "Any process involved in the transposition of miniature inverted-repeat transposable elements (MITEs)." [GOC:jp, ISBN:1555812090]
-synonym: "Class III transposition" EXACT []
-is_a: GO:0032196 ! transposition
+def: "OBSOLETE. Any process involved in the transposition of miniature inverted-repeat transposable elements (MITEs)." [GOC:jp, ISBN:1555812090]
+comment: This term was obsoleted because it represents a specific substrate.
+is_obsolete: true
+replaced_by: GO:0006313
[Term]
id: GO:0032199
-name: reverse transcription involved in RNA-mediated transposition
+name: obsolete reverse transcription involved in RNA-mediated transposition
namespace: biological_process
-def: "The synthesis of DNA from an RNA transposon intermediate." [GOC:jp, GOC:txnOH, ISBN:1555812090]
+def: "OBSOLETE. The synthesis of DNA from an RNA transposon intermediate." [GOC:jp, GOC:txnOH, ISBN:1555812090]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "reverse transcription during retrotransposition" EXACT []
-is_a: GO:0001171 ! reverse transcription
-relationship: part_of GO:0032197 ! transposition, RNA-mediated
+is_obsolete: true
+replaced_by: GO:0032197
[Term]
id: GO:0032200
@@ -174632,6 +174646,7 @@ xref: Reactome:R-HSA-3165230 "SLC52A1,2,3 transport RIB from extracellular regio
xref: RHEA:35015
is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0090482 ! vitamin transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0032218
@@ -175179,47 +175194,6 @@ xref: EC:6.3.4.-
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
-[Term]
-id: GO:0032268
-name: regulation of cellular protein metabolic process
-namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell." [GOC:mah]
-synonym: "regulation of cellular protein metabolism" EXACT []
-is_a: GO:0031323 ! regulation of cellular metabolic process
-is_a: GO:0051246 ! regulation of protein metabolic process
-relationship: regulates GO:0044267 ! cellular protein metabolic process
-
-[Term]
-id: GO:0032269
-name: negative regulation of cellular protein metabolic process
-namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell." [GOC:mah]
-synonym: "down regulation of cellular protein metabolic process" EXACT []
-synonym: "down-regulation of cellular protein metabolic process" EXACT []
-synonym: "downregulation of cellular protein metabolic process" EXACT []
-synonym: "inhibition of cellular protein metabolic process" NARROW []
-synonym: "negative regulation of cellular protein metabolism" EXACT []
-is_a: GO:0031324 ! negative regulation of cellular metabolic process
-is_a: GO:0032268 ! regulation of cellular protein metabolic process
-is_a: GO:0051248 ! negative regulation of protein metabolic process
-relationship: negatively_regulates GO:0044267 ! cellular protein metabolic process
-
-[Term]
-id: GO:0032270
-name: positive regulation of cellular protein metabolic process
-namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell." [GOC:mah]
-synonym: "activation of cellular protein metabolic process" NARROW []
-synonym: "positive regulation of cellular protein metabolism" EXACT []
-synonym: "stimulation of cellular protein metabolic process" NARROW []
-synonym: "up regulation of cellular protein metabolic process" EXACT []
-synonym: "up-regulation of cellular protein metabolic process" EXACT []
-synonym: "upregulation of cellular protein metabolic process" EXACT []
-is_a: GO:0031325 ! positive regulation of cellular metabolic process
-is_a: GO:0032268 ! regulation of cellular protein metabolic process
-is_a: GO:0051247 ! positive regulation of protein metabolic process
-relationship: positively_regulates GO:0044267 ! cellular protein metabolic process
-
[Term]
id: GO:0032271
name: regulation of protein polymerization
@@ -175316,7 +175290,7 @@ relationship: positively_regulates GO:0032274 ! gonadotropin secretion
id: GO:0032279
name: asymmetric synapse
namespace: cellular_component
-def: "A type of synapse occurring between an axon and a dendritic spine or dendritic shaft. Asymmetric synapses, the most abundant synapse type in the central nervous system, involve axons that contain predominantly spherical vesicles and contain a thickened postsynaptic density. Most or all synapses of this type are excitatory." [GOC:dgh, GOC:ef]
+def: "A type of synapse occurring between an axon and a dendritic spine or dendritic shaft. Asymmetric synapses, the most abundant synapse type in the central nervous system, involve axons that contain predominantly spherical vesicles and contain a thickened postsynaptic density. Most or all synapses of this type are excitatory." [GOC:dgh, GOC:ef]
synonym: "Gray's type I synapse" EXACT []
is_a: GO:0098984 ! neuron to neuron synapse
@@ -175325,7 +175299,7 @@ id: GO:0032280
name: symmetric synapse
namespace: cellular_component
def: "A synapse that lacks an electron dense postsynaptic specialization. In vertebtrates, these occur primarily on dendrite shafts and neuronal cell bodies and involve persynapses containing clusters of predominantly flattened or elongated vesicles and are typcially inhibitory." [GOC:dgh, GOC:ef]
-comment: The term 'symmetric' in this name refers only to gross morphology. There is no implication of functional symmetry.
+comment: The term 'symmetric' in this name refers only to gross morphology. There is no implication of functional symmetry.
synonym: "Gray's type II synapse" EXACT []
is_a: GO:0098984 ! neuron to neuron synapse
@@ -175338,7 +175312,6 @@ synonym: "alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glu
synonym: "AMPA receptor" RELATED []
synonym: "AMPA-selective glutamate receptor complex" EXACT []
is_a: GO:0008328 ! ionotropic glutamate receptor complex
-is_a: GO:0034703 ! cation channel complex
[Term]
id: GO:0032282
@@ -175359,11 +175332,11 @@ relationship: part_of GO:0032282 ! plastid acetyl-CoA carboxylase complex
[Term]
id: GO:0032284
-name: plastid biotin carboxylase complex
+name: obsolete plastid biotin carboxylase complex
namespace: cellular_component
-def: "A biotin carboxylase complex located in the stroma of a plastid." [GOC:mah]
-is_a: GO:0009343 ! biotin carboxylase complex
-relationship: part_of GO:0032282 ! plastid acetyl-CoA carboxylase complex
+def: "OBSOLETE. A biotin carboxylase complex located in the stroma of a plastid." [GOC:mah]
+comment: This term was obsoleted because it represents a homomer.
+is_obsolete: true
[Term]
id: GO:0032285
@@ -175467,11 +175440,11 @@ def: "Catalysis of the hydrolysis of phosphodiester bonds in double-stranded RNA
synonym: "double-stranded RNA-specific RNase activity" EXACT []
synonym: "dsRNA-specific ribonuclease activity" EXACT []
synonym: "dsRNA-specific RNase activity" EXACT []
-is_a: GO:0004540 ! ribonuclease activity
+is_a: GO:0004540 ! RNA nuclease activity
[Term]
id: GO:0032297
-name: negative regulation of DNA-dependent DNA replication initiation
+name: negative regulation of DNA-templated DNA replication initiation
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of initiation of DNA-dependent DNA replication." [GOC:mah]
synonym: "down regulation of DNA replication initiation" EXACT []
@@ -175479,25 +175452,25 @@ synonym: "down-regulation of DNA replication initiation" EXACT []
synonym: "downregulation of DNA replication initiation" EXACT []
synonym: "inhibition of DNA replication initiation" NARROW []
synonym: "negative regulation of DNA replication initiation" BROAD [GOC:vw]
-is_a: GO:0030174 ! regulation of DNA-dependent DNA replication initiation
-is_a: GO:0051053 ! negative regulation of DNA metabolic process
-is_a: GO:2000104 ! negative regulation of DNA-dependent DNA replication
+synonym: "negative regulation of DNA-dependent DNA replication initiation" EXACT []
+is_a: GO:0030174 ! regulation of DNA-templated DNA replication initiation
+is_a: GO:2000104 ! negative regulation of DNA-templated DNA replication
relationship: negatively_regulates GO:0006270 ! DNA replication initiation
[Term]
id: GO:0032298
-name: positive regulation of DNA-dependent DNA replication initiation
+name: positive regulation of DNA-templated DNA replication initiation
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of initiation of DNA-dependent DNA replication." [GOC:mah]
synonym: "activation of DNA replication initiation" NARROW []
synonym: "negative regulation of DNA replication initiation" BROAD [GOC:vw]
+synonym: "positive regulation of DNA-dependent DNA replication initiation" EXACT []
synonym: "stimulation of DNA replication initiation" NARROW []
synonym: "up regulation of DNA replication initiation" EXACT []
synonym: "up-regulation of DNA replication initiation" EXACT []
synonym: "upregulation of DNA replication initiation" EXACT []
-is_a: GO:0030174 ! regulation of DNA-dependent DNA replication initiation
-is_a: GO:0051054 ! positive regulation of DNA metabolic process
-is_a: GO:2000105 ! positive regulation of DNA-dependent DNA replication
+is_a: GO:0030174 ! regulation of DNA-templated DNA replication initiation
+is_a: GO:2000105 ! positive regulation of DNA-templated DNA replication
relationship: positively_regulates GO:0006270 ! DNA replication initiation
[Term]
@@ -175507,6 +175480,7 @@ namespace: cellular_component
def: "A protein complex that possesses ribonuclease H activity, in which the catalytic subunit is a member of the RNase H2 (or HII) class. For example, in Saccharomyces the complex contains Rnh201p, Rnh202p and Rnh203p." [GOC:mah, PMID:14734815]
synonym: "RNase H2 complex" EXACT []
is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0032300
@@ -175514,7 +175488,7 @@ name: mismatch repair complex
namespace: cellular_component
def: "Any complex formed of proteins that act in mismatch repair." [GOC:mah]
subset: goslim_pir
-is_a: GO:1990391 ! DNA repair complex
+is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0005622 ! intracellular anatomical structure
[Term]
@@ -175543,7 +175517,6 @@ name: regulation of icosanoid secretion
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the controlled release of an icosanoid from a cell." [GOC:mah]
synonym: "regulation of eicosanoid secretion" EXACT []
-is_a: GO:0044070 ! regulation of anion transport
is_a: GO:0051046 ! regulation of secretion
is_a: GO:2000191 ! regulation of fatty acid transport
relationship: regulates GO:0032309 ! icosanoid secretion
@@ -175560,7 +175533,6 @@ synonym: "inhibition of icosanoid secretion" NARROW []
synonym: "negative regulation of eicosanoid secretion" EXACT []
is_a: GO:0032303 ! regulation of icosanoid secretion
is_a: GO:0051048 ! negative regulation of secretion
-is_a: GO:1903792 ! negative regulation of anion transport
is_a: GO:2000192 ! negative regulation of fatty acid transport
relationship: negatively_regulates GO:0032309 ! icosanoid secretion
@@ -175577,7 +175549,6 @@ synonym: "up-regulation of icosanoid secretion" EXACT []
synonym: "upregulation of icosanoid secretion" EXACT []
is_a: GO:0032303 ! regulation of icosanoid secretion
is_a: GO:0051047 ! positive regulation of secretion
-is_a: GO:1903793 ! positive regulation of anion transport
is_a: GO:2000193 ! positive regulation of fatty acid transport
relationship: positively_regulates GO:0032309 ! icosanoid secretion
@@ -175734,9 +175705,7 @@ id: GO:0032328
name: alanine transport
namespace: biological_process
def: "The directed movement of alanine, 2-aminopropanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
-is_a: GO:0006812 ! cation transport
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0032329
@@ -175745,9 +175714,7 @@ namespace: biological_process
alt_id: GO:0090478
def: "The directed movement of L-serine, 2-amino-3-hydroxypropanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
synonym: "serine import" NARROW []
-is_a: GO:0006812 ! cation transport
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0032330
@@ -176146,10 +176113,12 @@ is_a: GO:0046444 ! FMN metabolic process
[Term]
id: GO:0032364
-name: oxygen homeostasis
+name: intracellular oxygen homeostasis
namespace: biological_process
-def: "A homeostatic process involved in the maintenance of an internal steady state of oxygen within an organism or cell." [GOC:rph]
-is_a: GO:0033483 ! gas homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of oxygen within a cell." [GOC:rph]
+synonym: "cellular oxygen homeostasis" EXACT []
+synonym: "oxygen homeostasis" BROAD []
+is_a: GO:0055082 ! intracellular chemical homeostasis
[Term]
id: GO:0032365
@@ -176635,12 +176604,12 @@ is_a: GO:0051050 ! positive regulation of transport
[Term]
id: GO:0032412
-name: regulation of ion transmembrane transporter activity
+name: regulation of monoatomic ion transmembrane transporter activity
namespace: biological_process
def: "Any process that modulates the activity of an ion transporter." [GOC:mah, GOC:tb]
+synonym: "regulation of ion transmembrane transporter activity" BROAD []
synonym: "regulation of ion transporter activity" EXACT [GOC:tb]
is_a: GO:0022898 ! regulation of transmembrane transporter activity
-is_a: GO:0034765 ! regulation of ion transmembrane transport
[Term]
id: GO:0032413
@@ -176653,8 +176622,8 @@ synonym: "downregulation of ion transporter activity" EXACT []
synonym: "inhibition of ion transporter activity" NARROW []
synonym: "negative regulation of ion transporter activity" EXACT [GOC:tb]
is_a: GO:0032410 ! negative regulation of transporter activity
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
-is_a: GO:0034766 ! negative regulation of ion transmembrane transport
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
+is_a: GO:0034766 ! negative regulation of monoatomic ion transmembrane transport
[Term]
id: GO:0032414
@@ -176668,8 +176637,8 @@ synonym: "up regulation of ion transporter activity" EXACT []
synonym: "up-regulation of ion transporter activity" EXACT []
synonym: "upregulation of ion transporter activity" EXACT []
is_a: GO:0032411 ! positive regulation of transporter activity
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
-is_a: GO:0034767 ! positive regulation of ion transmembrane transport
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
+is_a: GO:0034767 ! positive regulation of monoatomic ion transmembrane transport
[Term]
id: GO:0032415
@@ -176717,13 +176686,14 @@ is_a: GO:1990849 ! vacuolar localization
[Term]
id: GO:0032419
-name: extrinsic component of lysosome membrane
+name: obsolete extrinsic component of lysosome membrane
namespace: cellular_component
-def: "The component of an lysosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of an lysosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "extrinsic to lysosomal membrane" EXACT []
synonym: "extrinsic to lysosome membrane" EXACT []
-is_a: GO:0000306 ! extrinsic component of vacuolar membrane
-relationship: part_of GO:0005765 ! lysosomal membrane
+is_obsolete: true
+consider: GO:0005765
[Term]
id: GO:0032420
@@ -176950,7 +176920,7 @@ id: GO:0032443
name: regulation of ergosterol biosynthetic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ergosterol." [GOC:mah]
-is_a: GO:0031326 ! regulation of cellular biosynthetic process
+is_a: GO:0031323 ! regulation of cellular metabolic process
is_a: GO:0106118 ! regulation of sterol biosynthetic process
is_a: GO:1902930 ! regulation of alcohol biosynthetic process
relationship: regulates GO:0006696 ! ergosterol biosynthetic process
@@ -176964,14 +176934,6 @@ comment: Note that this term should not be confused with any of the molecular fu
synonym: "ARF complex" EXACT []
is_a: GO:0090575 ! RNA polymerase II transcription regulator complex
-[Term]
-id: GO:0032445
-name: fructose import
-namespace: biological_process
-def: "The directed movement of the hexose monosaccharide fructose into a cell or organelle." [GOC:mah]
-synonym: "fructose uptake" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0015755 ! fructose transmembrane transport
-
[Term]
id: GO:0032446
name: protein modification by small protein conjugation
@@ -176999,8 +176961,7 @@ name: CBM complex
namespace: cellular_component
def: "A protein complex comprising Bcl10, MALT1 and a CARD domain-containing protein (CARD9, CARD10 or CARD11); plays a role in signal transduction during NF-kappaB activation." [PMID:12909454, PMID:30467369]
synonym: "CARMA1-BCL10-Malt1 complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005737 ! cytoplasm
+is_a: GO:0140535 ! intracellular protein-containing complex
[Term]
id: GO:0032450
@@ -177046,23 +177007,27 @@ xref: Reactome:R-HSA-5661123 "KDM1A, KDM1B demethylate Me2K5-histone H3"
xref: Reactome:R-HSA-5661124 "JMJD6 demethylates MeR4-HIST1H4"
xref: Reactome:R-HSA-5661125 "JMJD6 demethylates Me2sR4-HIST1H4"
is_a: GO:0140457 ! protein demethylase activity
+is_a: GO:0140993 ! histone modifying activity
[Term]
id: GO:0032453
-name: histone H3-methyl-lysine-4 demethylase activity
+name: histone H3K4 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a modified lysine residue at position 4 of the histone H3 protein." [GOC:mah]
synonym: "histone demethylase activity (H3-K4 specific)" EXACT []
-synonym: "histone H3K4 demethylase activity" EXACT []
+synonym: "histone demethylase activity (H3K4-specific)" EXACT []
+synonym: "histone H3-K4 demethylase activity" EXACT []
+synonym: "histone H3-methyl-lysine-4 demethylase activity" EXACT []
is_a: GO:0032452 ! histone demethylase activity
[Term]
id: GO:0032454
-name: histone H3-methyl-lysine-9 demethylase activity
+name: histone H3K9 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a modified lysine residue at position 9 of the histone H3 protein." [PMID:16362057]
-synonym: "H3K49 demethylase activity" EXACT []
synonym: "histone demethylase activity (H3-K9 specific)" EXACT []
+synonym: "histone H3-K49 demethylase activity" EXACT []
+synonym: "histone H3-methyl-lysine-9 demethylase activity" EXACT []
xref: Reactome:R-HSA-9011949 "KDM4B demethylates H3K9me3 on estrogen-responsive target enhancers"
xref: Reactome:R-HSA-9011985 "KDM1A demethylates H3 on MYC and BCL genes in response to estrogen"
xref: Reactome:R-HSA-997263 "JMJD1C demethylates H3K9 mono- and di-methylation"
@@ -177228,7 +177193,7 @@ synonym: "calcium ion homeostasis in Golgi" EXACT []
synonym: "Golgi calcium ion concentration regulation" EXACT []
synonym: "regulation of calcium ion concentration in Golgi" EXACT []
synonym: "regulation of Golgi calcium ion concentration" EXACT []
-is_a: GO:0006874 ! cellular calcium ion homeostasis
+is_a: GO:0006874 ! intracellular calcium ion homeostasis
[Term]
id: GO:0032469
@@ -177244,7 +177209,7 @@ synonym: "regulation of calcium ion concentration in endoplasmic reticulum" EXAC
synonym: "regulation of calcium ion concentration in ER" EXACT []
synonym: "regulation of endoplasmic reticulum calcium ion concentration" EXACT []
synonym: "regulation of ER calcium ion concentration" EXACT []
-is_a: GO:0006874 ! cellular calcium ion homeostasis
+is_a: GO:0006874 ! intracellular calcium ion homeostasis
[Term]
id: GO:0032470
@@ -177374,7 +177339,7 @@ relationship: positively_regulates GO:0032606 ! type I interferon production
id: GO:0032482
name: Rab protein signal transduction
namespace: biological_process
-def: "A series of molecular signals within the cell that are mediated by a member of the Rab family of proteins switching to a GTP-bound active state." [GOC:mah]
+def: "The series of molecular signals within the cell that are mediated by a member of the Rab family of proteins switching to a GTP-bound active state." [GOC:mah]
is_a: GO:0007265 ! Ras protein signal transduction
[Term]
@@ -177389,7 +177354,7 @@ relationship: regulates GO:0032482 ! Rab protein signal transduction
id: GO:0032484
name: Ral protein signal transduction
namespace: biological_process
-def: "A series of molecular signals within the cell that are mediated by a member of the Ral family of proteins switching to a GTP-bound active state." [GOC:mah]
+def: "The series of molecular signals within the cell that are mediated by a member of the Ral family of proteins switching to a GTP-bound active state." [GOC:mah]
is_a: GO:0007265 ! Ras protein signal transduction
[Term]
@@ -177404,7 +177369,7 @@ relationship: regulates GO:0032484 ! Ral protein signal transduction
id: GO:0032486
name: Rap protein signal transduction
namespace: biological_process
-def: "A series of molecular signals within the cell that are mediated by a member of the Rap family of proteins switching to a GTP-bound active state." [GOC:mah]
+def: "The series of molecular signals within the cell that are mediated by a member of the Rap family of proteins switching to a GTP-bound active state." [GOC:mah]
is_a: GO:0007265 ! Ras protein signal transduction
[Term]
@@ -177419,7 +177384,7 @@ relationship: regulates GO:0032486 ! Rap protein signal transduction
id: GO:0032488
name: Cdc42 protein signal transduction
namespace: biological_process
-def: "A series of molecular signals within the cell that are mediated by the Cdc42 protein switching to a GTP-bound active state." [GOC:mah, PMID:18558478]
+def: "The series of molecular signals within the cell that are mediated by the Cdc42 protein switching to a GTP-bound active state." [GOC:mah, PMID:18558478]
synonym: "Cdc42 signaling" RELATED [GOC:vw]
synonym: "Cdc42 signaling pathway" RELATED [GOC:vw]
synonym: "cdc42 signalling pathway" RELATED [GOC:vw]
@@ -177553,7 +177518,6 @@ namespace: biological_process
alt_id: GO:0044767
def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete]
subset: goslim_agr
-subset: goslim_aspergillus
subset: goslim_flybase_ribbon
subset: goslim_pir
synonym: "development" NARROW []
@@ -177592,7 +177556,6 @@ def: "Any process in which a protein is maintained in a specific location within
synonym: "maintenance of protein localization in cell" RELATED [GOC:dph, GOC:tb]
is_a: GO:0045185 ! maintenance of protein location
is_a: GO:0051651 ! maintenance of location in cell
-relationship: part_of GO:0034613 ! cellular protein localization
[Term]
id: GO:0032508
@@ -177721,7 +177684,7 @@ name: silicon efflux transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of silicon from the inside of the cell to the outside of the cell across a membrane." [GOC:mah, PMID:17625566]
synonym: "silicon efflux transporter activity" EXACT []
-is_a: GO:0008324 ! cation transmembrane transporter activity
+is_a: GO:0008324 ! monoatomic cation transmembrane transporter activity
is_a: GO:0015562 ! efflux transmembrane transporter activity
[Term]
@@ -177914,6 +177877,7 @@ synonym: "Srx1" RELATED [EC:1.8.98.2]
synonym: "sulphiredoxin activity" EXACT []
xref: EC:1.8.98.2
xref: MetaCyc:1.8.98.2-RXN
+xref: Reactome:R-HSA-9760094 "SRXN1 reduces hyperoxidized PRDX1 dimer"
xref: RHEA:17545
is_a: GO:0016209 ! antioxidant activity
is_a: GO:0016667 ! oxidoreductase activity, acting on a sulfur group of donors
@@ -178301,12 +178265,13 @@ relationship: part_of GO:0043197 ! dendritic spine
[Term]
id: GO:0032592
-name: integral component of mitochondrial membrane
+name: obsolete integral component of mitochondrial membrane
namespace: cellular_component
-def: "The component of the mitochondrial membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the mitochondrial membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to mitochondrial membrane" NARROW []
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:0098573 ! intrinsic component of mitochondrial membrane
+is_obsolete: true
+replaced_by: GO:0031966
[Term]
id: GO:0032593
@@ -178516,7 +178481,7 @@ is_a: GO:0032606 ! type I interferon production
[Term]
id: GO:0032609
-name: interferon-gamma production
+name: type II interferon production
namespace: biological_process
alt_id: GO:0042095
alt_id: GO:0072643
@@ -178524,9 +178489,9 @@ def: "The appearance of interferon-gamma due to biosynthesis or secretion follow
subset: gocheck_do_not_annotate
synonym: "IFNG production" EXACT [GOC:mah]
synonym: "interferon-gamma biosynthetic process" NARROW []
+synonym: "interferon-gamma production" EXACT []
synonym: "interferon-gamma secretion" NARROW []
-synonym: "type II IFN production" BROAD [GOC:mah]
-synonym: "type II interferon production" BROAD []
+synonym: "type II IFN production" EXACT [GOC:mah]
is_a: GO:0001816 ! cytokine production
[Term]
@@ -179087,16 +179052,16 @@ relationship: regulates GO:0032608 ! interferon-beta production
[Term]
id: GO:0032649
-name: regulation of interferon-gamma production
+name: regulation of type II interferon production
namespace: biological_process
alt_id: GO:0045072
alt_id: GO:1902713
def: "Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah, PMID:15546383]
synonym: "regulation of interferon-gamma biosynthetic process" NARROW []
+synonym: "regulation of interferon-gamma production" EXACT []
synonym: "regulation of interferon-gamma secretion" NARROW []
-synonym: "regulation of type II interferon production" BROAD []
is_a: GO:0001817 ! regulation of cytokine production
-relationship: regulates GO:0032609 ! interferon-gamma production
+relationship: regulates GO:0032609 ! type II interferon production
[Term]
id: GO:0032650
@@ -179628,7 +179593,7 @@ relationship: negatively_regulates GO:0032608 ! interferon-beta production
[Term]
id: GO:0032689
-name: negative regulation of interferon-gamma production
+name: negative regulation of type II interferon production
namespace: biological_process
alt_id: GO:0045077
alt_id: GO:1902714
@@ -179638,11 +179603,11 @@ synonym: "down-regulation of interferon-gamma production" EXACT []
synonym: "downregulation of interferon-gamma production" EXACT []
synonym: "inhibition of interferon-gamma production" NARROW []
synonym: "negative regulation of interferon-gamma biosynthetic process" NARROW []
+synonym: "negative regulation of interferon-gamma production" EXACT []
synonym: "negative regulation of interferon-gamma secretion" NARROW []
-synonym: "negative regulation of type II interferon production" BROAD []
is_a: GO:0001818 ! negative regulation of cytokine production
-is_a: GO:0032649 ! regulation of interferon-gamma production
-relationship: negatively_regulates GO:0032609 ! interferon-gamma production
+is_a: GO:0032649 ! regulation of type II interferon production
+relationship: negatively_regulates GO:0032609 ! type II interferon production
[Term]
id: GO:0032690
@@ -180328,22 +180293,22 @@ relationship: positively_regulates GO:0032608 ! interferon-beta production
[Term]
id: GO:0032729
-name: positive regulation of interferon-gamma production
+name: positive regulation of type II interferon production
namespace: biological_process
alt_id: GO:0045078
alt_id: GO:1902715
def: "Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon." [GOC:add, GOC:mah, PMID:15546383]
synonym: "activation of interferon-gamma production" NARROW []
synonym: "positive regulation of interferon-gamma biosynthetic process" NARROW []
+synonym: "positive regulation of interferon-gamma production" EXACT []
synonym: "positive regulation of interferon-gamma secretion" NARROW []
-synonym: "positive regulation of type II interferon production" BROAD []
synonym: "stimulation of interferon-gamma production" NARROW []
synonym: "up regulation of interferon-gamma production" EXACT []
synonym: "up-regulation of interferon-gamma production" EXACT []
synonym: "upregulation of interferon-gamma production" EXACT []
is_a: GO:0001819 ! positive regulation of cytokine production
-is_a: GO:0032649 ! regulation of interferon-gamma production
-relationship: positively_regulates GO:0032609 ! interferon-gamma production
+is_a: GO:0032649 ! regulation of type II interferon production
+relationship: positively_regulates GO:0032609 ! type II interferon production
[Term]
id: GO:0032730
@@ -181070,8 +181035,14 @@ is_a: GO:0032771 ! regulation of tyrosinase activity
id: GO:0032774
name: RNA biosynthetic process
namespace: biological_process
+alt_id: GO:0062103
def: "The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication." [GOC:mah, GOC:txnOH]
comment: Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study.
+subset: gocheck_do_not_annotate
+synonym: "double-stranded RNA biosynthesis" NARROW []
+synonym: "double-stranded RNA biosynthetic process" NARROW []
+synonym: "dsRNA biosynthesis" NARROW []
+synonym: "dsRNA biosynthetic process" NARROW [GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:rl]
synonym: "RNA anabolism" EXACT []
synonym: "RNA biosynthesis" EXACT []
synonym: "RNA formation" EXACT []
@@ -181117,7 +181088,7 @@ synonym: "cobalt-transporting ATPase activity" RELATED []
xref: RHEA:32779
is_a: GO:0015087 ! cobalt ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
[Term]
id: GO:0032780
@@ -181167,16 +181138,17 @@ is_a: GO:0008023 ! transcription elongation factor complex
[Term]
id: GO:0032784
-name: regulation of DNA-templated transcription, elongation
+name: regulation of DNA-templated transcription elongation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase." [GOC:mah, GOC:txnOH]
synonym: "regulation of DNA-dependent transcription, elongation" EXACT [GOC:txnOH]
+synonym: "regulation of DNA-templated transcription, elongation" EXACT []
synonym: "regulation of RNA elongation" BROAD []
synonym: "regulation of transcription elongation, DNA-dependent" EXACT [GOC:jh2]
synonym: "regulation of transcriptional elongation" BROAD []
synonym: "transcription elongation regulator activity" RELATED []
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
-relationship: regulates GO:0006354 ! DNA-templated transcription, elongation
+is_a: GO:0006355 ! regulation of DNA-templated transcription
+relationship: regulates GO:0006354 ! DNA-templated transcription elongation
[Term]
id: GO:0032785
@@ -181192,9 +181164,9 @@ synonym: "negative regulation of transcription elongation" BROAD []
synonym: "negative regulation of transcription elongation, DNA-dependent" EXACT [GOC:jh2]
synonym: "negative regulation of transcriptional elongation" BROAD []
synonym: "negative transcription elongation regulator activity" RELATED []
-is_a: GO:0032784 ! regulation of DNA-templated transcription, elongation
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
-relationship: negatively_regulates GO:0006354 ! DNA-templated transcription, elongation
+is_a: GO:0032784 ! regulation of DNA-templated transcription elongation
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
+relationship: negatively_regulates GO:0006354 ! DNA-templated transcription elongation
[Term]
id: GO:0032786
@@ -181211,9 +181183,9 @@ synonym: "stimulation of RNA elongation" BROAD []
synonym: "up regulation of RNA elongation" BROAD []
synonym: "up-regulation of RNA elongation" BROAD []
synonym: "upregulation of RNA elongation" BROAD []
-is_a: GO:0032784 ! regulation of DNA-templated transcription, elongation
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
-relationship: positively_regulates GO:0006354 ! DNA-templated transcription, elongation
+is_a: GO:0032784 ! regulation of DNA-templated transcription elongation
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
+relationship: positively_regulates GO:0006354 ! DNA-templated transcription elongation
[Term]
id: GO:0032787
@@ -181232,7 +181204,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving saturated monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-) and fully saturated C-C bonds." [GOC:mah, GOC:vk]
synonym: "saturated monocarboxylate metabolic process" EXACT []
synonym: "saturated monocarboxylic acid metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
[Term]
id: GO:0032789
@@ -181373,9 +181345,9 @@ synonym: "low-density lipoprotein receptor breakdown" EXACT []
synonym: "low-density lipoprotein receptor catabolic process" EXACT [GOC:dph]
synonym: "low-density lipoprotein receptor catabolism" EXACT []
synonym: "low-density lipoprotein receptor degradation" EXACT []
+is_a: GO:0030163 ! protein catabolic process
is_a: GO:0032799 ! low-density lipoprotein receptor particle metabolic process
is_a: GO:0032801 ! receptor catabolic process
-is_a: GO:0044257 ! cellular protein catabolic process
[Term]
id: GO:0032803
@@ -181388,7 +181360,7 @@ synonym: "regulation of low-density lipoprotein receptor breakdown" EXACT []
synonym: "regulation of low-density lipoprotein receptor catabolic process" EXACT [GOC:bf, GOC:dph]
synonym: "regulation of low-density lipoprotein receptor catabolism" EXACT []
synonym: "regulation of low-density lipoprotein receptor degradation" EXACT []
-is_a: GO:1903362 ! regulation of cellular protein catabolic process
+is_a: GO:0042176 ! regulation of protein catabolic process
is_a: GO:2000644 ! regulation of receptor catabolic process
relationship: regulates GO:0032802 ! low-density lipoprotein particle receptor catabolic process
@@ -181406,7 +181378,7 @@ synonym: "negative regulation of low-density lipoprotein receptor catabolic proc
synonym: "negative regulation of low-density lipoprotein receptor catabolism" EXACT []
synonym: "negative regulation of low-density lipoprotein receptor degradation" EXACT []
is_a: GO:0032803 ! regulation of low-density lipoprotein particle receptor catabolic process
-is_a: GO:1903363 ! negative regulation of cellular protein catabolic process
+is_a: GO:0042177 ! negative regulation of protein catabolic process
is_a: GO:2000645 ! negative regulation of receptor catabolic process
relationship: negatively_regulates GO:0032802 ! low-density lipoprotein particle receptor catabolic process
@@ -181425,7 +181397,7 @@ synonym: "up regulation of low-density lipoprotein receptor catabolic process" E
synonym: "up-regulation of low-density lipoprotein receptor catabolic process" EXACT []
synonym: "upregulation of low-density lipoprotein receptor catabolic process" EXACT []
is_a: GO:0032803 ! regulation of low-density lipoprotein particle receptor catabolic process
-is_a: GO:1903364 ! positive regulation of cellular protein catabolic process
+is_a: GO:0045732 ! positive regulation of protein catabolic process
is_a: GO:2000646 ! positive regulation of receptor catabolic process
relationship: positively_regulates GO:0032802 ! low-density lipoprotein particle receptor catabolic process
@@ -181444,6 +181416,7 @@ name: DNA ligase IV complex
namespace: cellular_component
def: "A eukaryotically conserved protein complex that contains DNA ligase IV and is involved in DNA repair by non-homologous end joining; in addition to the ligase, the complex also contains XRCC4 or a homolog, e.g. Saccharomyces Lif1p." [PMID:16314503]
synonym: "DNA ligase IV-XRCC4 complex" EXACT [GOC:mah]
+is_a: GO:0070419 ! nonhomologous end joining complex
is_a: GO:0140513 ! nuclear protein-containing complex
[Term]
@@ -181921,7 +181894,7 @@ synonym: "regulation of intracellular acidification" RELATED []
synonym: "regulation of intracellular pH reduction" EXACT []
synonym: "regulation of reduction of cellular pH" EXACT []
synonym: "regulation of reduction of pH in cell" EXACT []
-is_a: GO:0050794 ! regulation of cellular process
+is_a: GO:0050789 ! regulation of biological process
is_a: GO:0051453 ! regulation of intracellular pH
relationship: regulates GO:0051452 ! intracellular pH reduction
@@ -181941,8 +181914,7 @@ synonym: "negative regulation of intracellular pH reduction" EXACT []
synonym: "negative regulation of reduction of cellular pH" EXACT []
synonym: "negative regulation of reduction of pH in cell" EXACT []
is_a: GO:0032847 ! regulation of cellular pH reduction
-is_a: GO:0048523 ! negative regulation of cellular process
-is_a: GO:0051454 ! intracellular pH elevation
+is_a: GO:0048519 ! negative regulation of biological process
relationship: negatively_regulates GO:0051452 ! intracellular pH reduction
[Term]
@@ -181962,8 +181934,8 @@ synonym: "up regulation of cellular pH reduction" EXACT []
synonym: "up-regulation of cellular pH reduction" EXACT []
synonym: "upregulation of cellular pH reduction" EXACT []
is_a: GO:0032847 ! regulation of cellular pH reduction
-is_a: GO:0048522 ! positive regulation of cellular process
-relationship: positively_regulates GO:0051452 ! intracellular pH reduction
+is_a: GO:0048518 ! positive regulation of biological process
+is_a: GO:0051452 ! intracellular pH reduction
[Term]
id: GO:0032865
@@ -182102,7 +182074,7 @@ def: "Any process that modulates the frequency, rate or extent of DNA endoredupl
synonym: "regulation of DNA endoreplication" EXACT []
synonym: "regulation of DNA re-duplication" EXACT []
is_a: GO:0010564 ! regulation of cell cycle process
-is_a: GO:0090329 ! regulation of DNA-dependent DNA replication
+is_a: GO:0090329 ! regulation of DNA-templated DNA replication
relationship: regulates GO:0042023 ! DNA endoreduplication
[Term]
@@ -182118,7 +182090,7 @@ synonym: "negative regulation of DNA endoreplication" EXACT []
synonym: "negative regulation of DNA re-duplication" EXACT []
is_a: GO:0010948 ! negative regulation of cell cycle process
is_a: GO:0032875 ! regulation of DNA endoreduplication
-is_a: GO:2000104 ! negative regulation of DNA-dependent DNA replication
+is_a: GO:2000104 ! negative regulation of DNA-templated DNA replication
relationship: negatively_regulates GO:0042023 ! DNA endoreduplication
[Term]
@@ -182135,7 +182107,7 @@ synonym: "up-regulation of DNA endoreduplication" EXACT []
synonym: "upregulation of DNA endoreduplication" EXACT []
is_a: GO:0032875 ! regulation of DNA endoreduplication
is_a: GO:0090068 ! positive regulation of cell cycle process
-is_a: GO:2000105 ! positive regulation of DNA-dependent DNA replication
+is_a: GO:2000105 ! positive regulation of DNA-templated DNA replication
relationship: positively_regulates GO:0042023 ! DNA endoreduplication
[Term]
@@ -182165,7 +182137,7 @@ subset: goslim_chembl
synonym: "regulation of cellular protein localisation" EXACT [GOC:TermGenie]
synonym: "regulation of cellular protein localization" EXACT []
synonym: "regulation of protein localisation" EXACT [GOC:mah]
-is_a: GO:0032879 ! regulation of localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0008104 ! protein localization
[Term]
@@ -182598,7 +182570,6 @@ synonym: "diurnal variation of gene expression" RELATED []
synonym: "diurnal variation of protein expression" RELATED []
is_a: GO:0007623 ! circadian rhythm
is_a: GO:0010468 ! regulation of gene expression
-is_a: GO:0032501 ! multicellular organismal process
[Term]
id: GO:0032923
@@ -182614,7 +182585,7 @@ is_a: GO:0090407 ! organophosphate biosynthetic process
id: GO:0032924
name: activin receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to an activin receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:rl, GOC:signaling]
+def: "The series of molecular signals initiated by an extracellular ligand binding to an activin receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:rl, GOC:signaling]
synonym: "activin receptor signalling pathway" EXACT []
is_a: GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway
@@ -182702,11 +182673,14 @@ relationship: positively_regulates GO:0042554 ! superoxide anion generation
[Term]
id: GO:0032931
-name: histone acetyltransferase activity (H3-K56 specific)
+name: histone H3K56 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 56) = CoA + histone H3 N6-acetyl-L-lysine (position 56)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H3-K56 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H3-K56 specific)" EXACT []
+synonym: "histone H3-K56 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H3-K56 specific)" EXACT []
-is_a: GO:0010484 ! H3 histone acetyltransferase activity
+is_a: GO:0010484 ! histone H3 acetyltransferase activity
[Term]
id: GO:0032932
@@ -182726,7 +182700,7 @@ namespace: biological_process
alt_id: GO:0006994
alt_id: GO:0030967
alt_id: GO:0035104
-def: "A series of molecular signals from the endoplasmic reticulum to the nucleus generated as a consequence of decreased levels of one or more sterols (and in some yeast, changes in oxygen levels) and which proceeds through activation of a sterol response element binding transcription factor (SREBP) to result in up-regulation of target gene transcription." [GOC:bf, GOC:mah, GOC:signaling, GOC:vw, PMID:12923525, PMID:22017871]
+def: "The series of molecular signals from the endoplasmic reticulum to the nucleus generated as a consequence of decreased levels of one or more sterols (and in some yeast, changes in oxygen levels) and which proceeds through activation of a sterol response element binding transcription factor (SREBP) to result in up-regulation of target gene transcription." [GOC:bf, GOC:mah, GOC:signaling, GOC:vw, PMID:12923525, PMID:22017871]
synonym: "activation of sterol regulatory element binding protein target gene transcription" NARROW []
synonym: "endoplasmic reticulum to nucleus sterol response pathway" EXACT []
synonym: "endoplasmic reticulum-nuclear sterol response pathway" EXACT []
@@ -182764,6 +182738,7 @@ id: GO:0032935
name: sterol sensor activity
namespace: molecular_function
def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of a sterol." [GOC:mah]
+synonym: "sterol sensing activity" EXACT []
synonym: "sterol-sensing domain" NARROW []
is_a: GO:0032934 ! sterol binding
is_a: GO:0106254 ! lipid sensor activity
@@ -182783,7 +182758,7 @@ namespace: cellular_component
def: "A protein complex formed by the association of sterol regulatory element binding protein (SREBP), SREBP-cleavage-activating protein (SCAP), and an Insig protein (Insig-1 or Insig-2) in the ER membrane." [PMID:12923525]
is_a: GO:0098796 ! membrane protein complex
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
-relationship: part_of GO:0030176 ! integral component of endoplasmic reticulum membrane
+relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
[Term]
id: GO:0032938
@@ -182889,7 +182864,6 @@ name: regulation of alpha-glucan metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving alpha-glucans." [GOC:mah]
synonym: "regulation of alpha-glucan metabolism" EXACT []
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:0032881 ! regulation of polysaccharide metabolic process
relationship: regulates GO:0030978 ! alpha-glucan metabolic process
@@ -182912,7 +182886,6 @@ name: regulation of beta-glucan metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving beta-glucans." [GOC:mah]
synonym: "regulation of beta-glucan metabolism" EXACT []
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:0032881 ! regulation of polysaccharide metabolic process
relationship: regulates GO:0051273 ! beta-glucan metabolic process
@@ -183138,16 +183111,17 @@ relationship: positively_regulates GO:0032964 ! collagen biosynthetic process
[Term]
id: GO:0032968
-name: positive regulation of transcription elongation from RNA polymerase II promoter
+name: positive regulation of transcription elongation by RNA polymerase II
namespace: biological_process
alt_id: GO:0090040
def: "Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II." [GOC:mah, GOC:txnOH]
synonym: "positive regulation of gene-specific transcription elongation from RNA polymerase II promoter" RELATED []
synonym: "positive regulation of RNA elongation from RNA polymerase II promoter" EXACT []
+synonym: "positive regulation of transcription elongation from RNA polymerase II promoter" EXACT []
is_a: GO:0032786 ! positive regulation of DNA-templated transcription, elongation
-is_a: GO:0034243 ! regulation of transcription elongation from RNA polymerase II promoter
+is_a: GO:0034243 ! regulation of transcription elongation by RNA polymerase II
is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
-relationship: positively_regulates GO:0006368 ! transcription elongation from RNA polymerase II promoter
+relationship: positively_regulates GO:0006368 ! transcription elongation by RNA polymerase II
[Term]
id: GO:0032969
@@ -183215,7 +183189,6 @@ def: "The directed movement of amino acids into the vacuole across the vacuolar
synonym: "vacuolar amino acid import" EXACT []
is_a: GO:0003333 ! amino acid transmembrane transport
is_a: GO:0034486 ! vacuolar transmembrane transport
-is_a: GO:0043090 ! amino acid import
[Term]
id: GO:0032976
@@ -183323,7 +183296,7 @@ namespace: biological_process
def: "The disaggregation of a protein-DNA complex into its constituent components." [GOC:mah]
synonym: "DNA-protein complex disassembly" EXACT [GOC:mah]
is_a: GO:0032984 ! protein-containing complex disassembly
-is_a: GO:0071824 ! protein-DNA complex subunit organization
+is_a: GO:0071824 ! protein-DNA complex organization
[Term]
id: GO:0032987
@@ -183331,18 +183304,18 @@ name: protein-lipid complex disassembly
namespace: biological_process
def: "The disaggregation of a protein-lipid complex into its constituent components." [GOC:mah]
is_a: GO:0032984 ! protein-containing complex disassembly
-is_a: GO:0071825 ! protein-lipid complex subunit organization
+is_a: GO:0071825 ! protein-lipid complex organization
[Term]
id: GO:0032988
-name: ribonucleoprotein complex disassembly
+name: protein-RNA complex disassembly
namespace: biological_process
def: "The disaggregation of a protein-RNA complex into its constituent components." [GOC:mah]
-synonym: "protein-RNA complex disassembly" EXACT []
+synonym: "ribonucleoprotein complex disassembly" EXACT []
synonym: "RNA-protein complex disassembly" EXACT []
synonym: "RNP complex disassembly" EXACT []
is_a: GO:0032984 ! protein-containing complex disassembly
-is_a: GO:0071826 ! ribonucleoprotein complex subunit organization
+is_a: GO:0071826 ! protein-RNA complex organization
[Term]
id: GO:0032989
@@ -183372,7 +183345,7 @@ comment: A protein complex in this context is meant as a stable set of interacti
subset: goslim_agr
subset: goslim_chembl
subset: goslim_flybase_ribbon
-subset: goslim_generic
+subset: goslim_mouse
subset: goslim_pir
synonym: "macromolecular complex" EXACT []
synonym: "macromolecule complex" EXACT []
@@ -183385,7 +183358,7 @@ is_a: GO:0005575 ! cellular_component
id: GO:0032992
name: protein-carbohydrate complex
namespace: cellular_component
-def: "A macromolecular complex containing separate protein and carbohydrate molecules. Separate in this context means not covalently bound to each other." [GOC:mah]
+def: "A macromolecular complex containing separate protein and carbohydrate molecules. Separate in this context means not covalently bound to each other." [GOC:mah]
comment: Macromolecular complexes in which the carbohydrate component is all covalently bound to protein are not considered protein carbohydrate complexes.
is_a: GO:0032991 ! protein-containing complex
@@ -183403,7 +183376,7 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:0032994
name: protein-lipid complex
namespace: cellular_component
-def: "A macromolecular complex containing separate protein and lipid molecules. Separate in this context means not covalently bound to each other." [GOC:mah]
+def: "A macromolecular complex containing separate protein and lipid molecules. Separate in this context means not covalently bound to each other." [GOC:mah]
comment: Macromolecular complexes in which the lipid component is all covalently bound to protein are not considered protein-lipid complexes.
is_a: GO:0032991 ! protein-containing complex
@@ -183585,6 +183558,7 @@ name: tetrapyrrole metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next." [GOC:mah]
subset: goslim_pombe
+subset: prokaryote_subset
synonym: "tetrapyrrole metabolism" EXACT []
is_a: GO:0006725 ! cellular aromatic compound metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
@@ -183920,7 +183894,6 @@ id: GO:0033045
name: regulation of sister chromatid segregation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of sister chromatid segregation." [GOC:mah]
-is_a: GO:0010564 ! regulation of cell cycle process
is_a: GO:0033044 ! regulation of chromosome organization
is_a: GO:0051983 ! regulation of chromosome segregation
relationship: regulates GO:0000819 ! sister chromatid segregation
@@ -183930,7 +183903,6 @@ id: GO:0033046
name: negative regulation of sister chromatid segregation
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation." [GOC:mah]
-is_a: GO:0010948 ! negative regulation of cell cycle process
is_a: GO:0033045 ! regulation of sister chromatid segregation
is_a: GO:0051985 ! negative regulation of chromosome segregation
is_a: GO:2001251 ! negative regulation of chromosome organization
@@ -183960,10 +183932,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving clavulanic acid, (2R,3Z,5R)-3-(2-hydroxyethylidene)-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid." [GOC:mah]
synonym: "clavulanic acid metabolism" EXACT []
is_a: GO:0032787 ! monocarboxylic acid metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
-is_a: GO:0046483 ! heterocycle metabolic process
-is_a: GO:1901360 ! organic cyclic compound metabolic process
-is_a: GO:1901564 ! organonitrogen compound metabolic process
+is_a: GO:0072338 ! lactam metabolic process
[Term]
id: GO:0033050
@@ -183975,12 +183944,9 @@ synonym: "clavulanic acid biosynthesis" EXACT []
synonym: "clavulanic acid formation" EXACT []
synonym: "clavulanic acid synthesis" EXACT []
xref: Wikipedia:Clavulanic_acid
-is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0033049 ! clavulanic acid metabolic process
-is_a: GO:0043604 ! amide biosynthetic process
is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
-is_a: GO:1901362 ! organic cyclic compound biosynthetic process
-is_a: GO:1901566 ! organonitrogen compound biosynthetic process
+is_a: GO:0072339 ! lactam biosynthetic process
[Term]
id: GO:0033051
@@ -183998,7 +183964,7 @@ name: cyanoamino acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving cyanoamino acids, amino acid derivatives that contain a cyanide group." [GOC:mah, PMID:11575729]
synonym: "cyanoamino acid metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0050898 ! nitrile metabolic process
[Term]
@@ -184008,7 +183974,6 @@ namespace: biological_process
def: "The chemical reactions and pathways involving D-glutamine, the D-enantiomer of the amino acid glutamine, i.e. (2R)-2,5-diamino-5-oxopentanoic acid." [GOC:jsg, GOC:mah]
synonym: "D-glutamine metabolism" EXACT []
is_a: GO:0006541 ! glutamine metabolic process
-is_a: GO:0046144 ! D-alanine family amino acid metabolic process
is_a: GO:0046416 ! D-amino acid metabolic process
[Term]
@@ -184018,7 +183983,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving D-glutamate, the D-enantiomer of the amino acid glutamate, i.e. (2R)-2-aminopentanedioic acid." [GOC:jsg, GOC:mah]
synonym: "D-glutamate metabolism" EXACT []
is_a: GO:0006536 ! glutamate metabolic process
-is_a: GO:0046144 ! D-alanine family amino acid metabolic process
+is_a: GO:0043170 ! macromolecule metabolic process
is_a: GO:0046416 ! D-amino acid metabolic process
[Term]
@@ -184028,7 +183993,6 @@ namespace: biological_process
def: "The chemical reactions and pathways involving D-arginine, the D-enantiomer of the amino acid arginine, i.e. (2R)-2-amino-5-(carbamimidamido)pentanoic acid." [GOC:jsg, GOC:mah]
synonym: "D-arginine metabolism" EXACT []
is_a: GO:0006525 ! arginine metabolic process
-is_a: GO:0046144 ! D-alanine family amino acid metabolic process
is_a: GO:0046416 ! D-amino acid metabolic process
[Term]
@@ -184038,7 +184002,6 @@ namespace: biological_process
def: "The chemical reactions and pathways involving D-ornithine, the D-enantiomer of the amino acid ornithine, i.e. (2R)-2,5-diaminopentanoic acid." [GOC:jsg, GOC:mah]
synonym: "D-ornithine metabolism" EXACT []
is_a: GO:0006591 ! ornithine metabolic process
-is_a: GO:0046144 ! D-alanine family amino acid metabolic process
is_a: GO:0046416 ! D-amino acid metabolic process
[Term]
@@ -184072,15 +184035,6 @@ comment: Many paralogs of Rad51 act as recombinase mediators. These paralogs dim
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
-[Term]
-id: GO:0033062
-name: Rhp55-Rhp57 complex
-namespace: cellular_component
-def: "A conserved heterodimeric DNA recombinase mediator complex that contains the RecA family proteins Rhp55p and Rph57 in Schizosaccharomyces, or orthologs thereof (e.g. Rad55p and Rad57p in Saccharomyces)." [GOC:mah, GOC:vw]
-synonym: "Rad55-Rad57 complex" EXACT []
-is_a: GO:0033061 ! DNA recombinase mediator complex
-is_a: GO:0140513 ! nuclear protein-containing complex
-
[Term]
id: GO:0033063
name: Rad51B-Rad51C-Rad51D-XRCC2 complex
@@ -184103,8 +184057,11 @@ is_a: GO:0140513 ! nuclear protein-containing complex
id: GO:0033065
name: Rad51C-XRCC3 complex
namespace: cellular_component
-def: "A DNA recombinase mediator complex that contains the Rad51 paralogs RAD51C and XRCC3, or orthologs thereof." [GOC:mah, PMID:16093548, PMID:17114795]
+alt_id: GO:0033062
+def: "A DNA recombinase mediator complex that contains the Rad51 paralogs RAD51C and XRCC3, or orthologs thereof." [GOC:mah, GOC:vw, PMID:12427746, PMID:16093548, PMID:17114795]
synonym: "CX3 complex" EXACT []
+synonym: "Rad55-Rad57 complex" EXACT []
+synonym: "Rhp55-Rhp57 complex" RELATED []
is_a: GO:0033061 ! DNA recombinase mediator complex
is_a: GO:0140513 ! nuclear protein-containing complex
@@ -184149,10 +184106,7 @@ def: "The chemical reactions and pathways involving ansamycins, any of a group o
synonym: "ansamycin metabolism" EXACT []
is_a: GO:0016999 ! antibiotic metabolic process
is_a: GO:0030638 ! polyketide metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
-is_a: GO:0046483 ! heterocycle metabolic process
-is_a: GO:1901360 ! organic cyclic compound metabolic process
-is_a: GO:1901564 ! organonitrogen compound metabolic process
+is_a: GO:0072338 ! lactam metabolic process
[Term]
id: GO:0033070
@@ -184163,12 +184117,9 @@ synonym: "ansamycin anabolism" EXACT []
synonym: "ansamycin biosynthesis" EXACT []
synonym: "ansamycin formation" EXACT []
synonym: "ansamycin synthesis" EXACT []
-is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0030639 ! polyketide biosynthetic process
is_a: GO:0033069 ! ansamycin metabolic process
-is_a: GO:0043604 ! amide biosynthetic process
-is_a: GO:1901362 ! organic cyclic compound biosynthetic process
-is_a: GO:1901566 ! organonitrogen compound biosynthetic process
+is_a: GO:0072339 ! lactam biosynthetic process
[Term]
id: GO:0033071
@@ -184223,10 +184174,7 @@ synonym: "isoquinoline alkaloid biosynthesis" EXACT []
synonym: "isoquinoline alkaloid formation" EXACT []
synonym: "isoquinoline alkaloid synthesis" EXACT []
is_a: GO:0009821 ! alkaloid biosynthetic process
-is_a: GO:0018130 ! heterocycle biosynthetic process
-is_a: GO:0019438 ! aromatic compound biosynthetic process
is_a: GO:0033076 ! isoquinoline alkaloid metabolic process
-is_a: GO:1901362 ! organic cyclic compound biosynthetic process
[Term]
id: GO:0033076
@@ -184235,11 +184183,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving isoquinoline alkaloids, alkaloid compounds that contain bicyclic N-containing aromatic rings and are derived from a 3,4-dihydroxytyramine (dopamine) precursor that undergoes a Schiff base addition with aldehydes of different origin." [GOC:mah, http://www.life.uiuc.edu/ib/425/lecture32.html]
synonym: "ipecac alkaloid metabolism" RELATED []
synonym: "isoquinoline alkaloid metabolism" EXACT []
-is_a: GO:0006725 ! cellular aromatic compound metabolic process
is_a: GO:0009820 ! alkaloid metabolic process
-is_a: GO:0034641 ! cellular nitrogen compound metabolic process
-is_a: GO:0046483 ! heterocycle metabolic process
-is_a: GO:1901360 ! organic cyclic compound metabolic process
[Term]
id: GO:0033077
@@ -184578,7 +184522,7 @@ relationship: part_of GO:0033107 ! Cvt vesicle
id: GO:0033111
name: attachment organelle membrane
namespace: cellular_component
-def: "The lipid bilayer surrounding an attachment organelle. This is a region of the cell membrane facing the environment - in mycoplasma, part of the mycolate outer membrane." [GOC:ecd]
+def: "The lipid bilayer surrounding an attachment organelle. This is a region of the cell membrane facing the environment - in mycoplasma, part of the mycolate outer membrane." [GOC:ecd]
is_a: GO:0098588 ! bounding membrane of organelle
relationship: part_of GO:0033099 ! attachment organelle
@@ -184735,32 +184679,30 @@ consider: GO:0043547
[Term]
id: GO:0033127
-name: regulation of histone phosphorylation
+name: obsolete regulation of histone phosphorylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein." [GOC:mah]
-is_a: GO:0001932 ! regulation of protein phosphorylation
-is_a: GO:0031056 ! regulation of histone modification
-relationship: regulates GO:0016572 ! histone phosphorylation
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0019887
[Term]
id: GO:0033128
-name: negative regulation of histone phosphorylation
+name: obsolete negative regulation of histone phosphorylation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein." [GOC:mah]
-is_a: GO:0001933 ! negative regulation of protein phosphorylation
-is_a: GO:0031057 ! negative regulation of histone modification
-is_a: GO:0033127 ! regulation of histone phosphorylation
-relationship: negatively_regulates GO:0016572 ! histone phosphorylation
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0004860
[Term]
id: GO:0033129
-name: positive regulation of histone phosphorylation
+name: obsolete positive regulation of histone phosphorylation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein." [GOC:mah]
-is_a: GO:0001934 ! positive regulation of protein phosphorylation
-is_a: GO:0031058 ! positive regulation of histone modification
-is_a: GO:0033127 ! regulation of histone phosphorylation
-relationship: positively_regulates GO:0016572 ! histone phosphorylation
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0030295
[Term]
id: GO:0033130
@@ -184879,9 +184821,10 @@ relationship: positively_regulates GO:0042501 ! serine phosphorylation of STAT p
[Term]
id: GO:0033142
-name: progesterone receptor binding
+name: nuclear progesterone receptor binding
namespace: molecular_function
-def: "Binding to a progesterone receptor." [GOC:mah]
+def: "Binding to a nuclear progesterone receptor." [GOC:mah]
+synonym: "progesterone receptor binding" BROAD []
is_a: GO:0016922 ! nuclear receptor binding
[Term]
@@ -185033,7 +184976,6 @@ def: "Any process that modulates the frequency, rate or extent of the directed m
is_a: GO:0032386 ! regulation of intracellular transport
is_a: GO:0051223 ! regulation of protein transport
relationship: regulates GO:0006886 ! intracellular protein transport
-relationship: regulates GO:0034613 ! cellular protein localization
[Term]
id: GO:0033158
@@ -185091,7 +185033,7 @@ relationship: part_of GO:0020009 ! microneme
id: GO:0033164
name: glycolipid 1,6-alpha-mannosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of an alpha-D-mannosyl residue from GDP-mannose into lipid-linked oligosaccharide, forming an alpha-(1->6)-D-mannosyl-D-mannose linkage." [GOC:mcc, PMID:16878994]
+def: "Catalysis of the transfer of an alpha-D-mannosyl residue from GDP-mannose into lipid-linked oligosaccharide, forming an alpha-(1->6)-D-mannosyl-D-mannose linkage." [GOC:mcc, PMID:16878994, PMID:2644248]
synonym: "GDP-mannose:glycolipid 1,6-alpha-D-mannosyltransferase activity" RELATED [EC:2.4.1.232]
synonym: "GDP-mannose:oligosaccharide 1,6-alpha-D-mannosyltransferase activity" RELATED [EC:2.4.1.232]
synonym: "GDP-mannose:oligosaccharide 6-alpha-D-mannosyltransferase activity" RELATED [EC:2.4.1.232]
@@ -185134,7 +185076,6 @@ comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "RNA interference, conversion of ds siRNA to ss siRNA" EXACT [GOC:mah]
is_obsolete: true
consider: GO:0004521
-consider: GO:0016246
[Term]
id: GO:0033169
@@ -185256,7 +185197,6 @@ id: GO:0033183
name: negative regulation of histone ubiquitination
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of a ubiquitin group to a histone protein." [GOC:mah]
-is_a: GO:0031057 ! negative regulation of histone modification
is_a: GO:0031397 ! negative regulation of protein ubiquitination
is_a: GO:0033182 ! regulation of histone ubiquitination
relationship: negatively_regulates GO:0016574 ! histone ubiquitination
@@ -185266,7 +185206,6 @@ id: GO:0033184
name: positive regulation of histone ubiquitination
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the addition of a ubiquitin group to a histone protein." [GOC:mah]
-is_a: GO:0031058 ! positive regulation of histone modification
is_a: GO:0031398 ! positive regulation of protein ubiquitination
is_a: GO:0033182 ! regulation of histone ubiquitination
relationship: positively_regulates GO:0016574 ! histone ubiquitination
@@ -185385,11 +185324,10 @@ is_a: GO:0033194 ! response to hydroperoxide
id: GO:0033196
name: tryparedoxin peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: tryparedoxin + hydrogen peroxide = tryparedoxin disulfide + H2O." [GOC:mah]
+def: "Catalysis of the reaction: tryparedoxin + hydrogen peroxide = tryparedoxin disulfide + H2O." [GOC:mah, PMID:32388269]
synonym: "TXNPx activity" EXACT []
xref: MetaCyc:1.11.1.15-RXN
is_a: GO:0004601 ! peroxidase activity
-is_a: GO:0051920 ! peroxiredoxin activity
[Term]
id: GO:0033197
@@ -185413,6 +185351,7 @@ synonym: "response to adenosine triphosphate" EXACT []
is_a: GO:0014074 ! response to purine-containing compound
is_a: GO:0046683 ! response to organophosphorus
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0033199
@@ -185452,7 +185391,6 @@ def: "A protein complex that possesses DNA helicase activity." [GOC:mah]
subset: goslim_metagenomics
subset: goslim_pir
is_a: GO:1902494 ! catalytic complex
-relationship: part_of GO:0005622 ! intracellular anatomical structure
[Term]
id: GO:0033203
@@ -185500,7 +185438,7 @@ is_a: GO:0033207 ! beta-1,4-N-acetylgalactosaminyltransferase activity
id: GO:0033209
name: tumor necrosis factor-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling]
+def: "The series of molecular signals initiated by tumor necrosis factor binding to its receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling]
synonym: "adipocytokine signaling pathway" RELATED []
synonym: "TNF-alpha-mediated signaling pathway" NARROW []
synonym: "tumor necrosis factor alpha-mediated signaling pathway" NARROW []
@@ -185512,7 +185450,7 @@ relationship: part_of GO:0071356 ! cellular response to tumor necrosis factor
id: GO:0033210
name: leptin-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of leptin to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Leptin is a hormone manufactured primarily in the adipocytes of white adipose tissue, and the level of circulating leptin is directly proportional to the total amount of fat in the body." [GOC:mah, GOC:signaling, GOC:yaf]
+def: "The series of molecular signals initiated by leptin binding to its receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription. Leptin is a hormone manufactured primarily in the adipocytes of white adipose tissue, and the level of circulating leptin is directly proportional to the total amount of fat in the body." [GOC:mah, GOC:signaling, GOC:yaf]
synonym: "adipocytokine signaling pathway" RELATED []
synonym: "leptin-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -185522,7 +185460,7 @@ relationship: part_of GO:0044320 ! cellular response to leptin stimulus
id: GO:0033211
name: adiponectin-activated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of adiponectin to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, PMID:20536390]
+def: "The series of molecular signals initiated by adiponectin binding to its receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling, PMID:20536390]
synonym: "adipocytokine signaling pathway" RELATED []
synonym: "adiponectin-mediated signaling pathway" RELATED []
synonym: "adiponectin-mediated signalling pathway" EXACT []
@@ -185540,7 +185478,7 @@ synonym: "ferrous iron import" NARROW []
synonym: "ferrous iron uptake" NARROW []
synonym: "iron assimilation" RELATED []
is_a: GO:0006826 ! iron ion transport
-is_a: GO:0006879 ! cellular iron ion homeostasis
+is_a: GO:0006879 ! intracellular iron ion homeostasis
is_a: GO:0051649 ! establishment of localization in cell
is_a: GO:0098657 ! import into cell
@@ -185676,27 +185614,24 @@ is_a: GO:1903712 ! cysteine transmembrane transport
id: GO:0033229
name: cysteine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of cysteine from one side of a membrane to the other." [GOC:mah, RHEA:32795]
-xref: RHEA:32795
+def: "Enables the transfer of cysteine from one side of a membrane to the other." [GOC:mah]
is_a: GO:0000099 ! sulfur amino acid transmembrane transporter activity
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
[Term]
id: GO:0033230
name: ABC-type cysteine transporter activity
namespace: molecular_function
alt_id: GO:0032519
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + cysteine(out/in) = ADP + phosphate + cysteine(in/out)." [GOC:mlg, PMID:25837721, PMID:32144203]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + cysteine(out/in) = ADP + phosphate + cysteine(in/out)." [GOC:mlg, PMID:25837721, PMID:32144203, RHEA:32795]
synonym: "ATP-dependent cysteine transporter activity" EXACT []
synonym: "ATPase-coupled cysteine transmembrane transporter activity" RELATED []
synonym: "ATPase-coupled cysteine transporter activity" RELATED []
synonym: "cysteine exporter" RELATED []
synonym: "cysteine-exporting ATPase activity" RELATED []
synonym: "cysteine-transporting ATPase activity" EXACT []
+xref: RHEA:32795
is_a: GO:0015424 ! ABC-type amino acid transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0033229 ! cysteine transmembrane transporter activity
[Term]
@@ -185730,7 +185665,6 @@ synonym: "methionine transmembrane-transporting ATPase activity" RELATED []
xref: EC:7.4.2.11
xref: RHEA:29779
is_a: GO:0015424 ! ABC-type amino acid transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0042943 ! D-amino acid transmembrane transporter activity
is_a: GO:0043865 ! methionine transmembrane transporter activity
@@ -185786,72 +185720,74 @@ replaced_by: GO:0070524
[Term]
id: GO:0033238
-name: regulation of cellular amine metabolic process
+name: regulation of amine metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines." [GOC:mah]
synonym: "regulation of amine metabolism" EXACT []
-is_a: GO:0031323 ! regulation of cellular metabolic process
+synonym: "regulation of cellular amine metabolic process" EXACT []
is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
-relationship: regulates GO:0044106 ! cellular amine metabolic process
+relationship: regulates GO:0009308 ! amine metabolic process
[Term]
id: GO:0033239
-name: negative regulation of cellular amine metabolic process
+name: negative regulation of amine metabolic process
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines." [GOC:mah]
synonym: "negative regulation of amine metabolism" EXACT []
-is_a: GO:0031324 ! negative regulation of cellular metabolic process
-is_a: GO:0033238 ! regulation of cellular amine metabolic process
+synonym: "negative regulation of cellular amine metabolic process" EXACT []
+is_a: GO:0033238 ! regulation of amine metabolic process
is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
-relationship: negatively_regulates GO:0044106 ! cellular amine metabolic process
+relationship: negatively_regulates GO:0009308 ! amine metabolic process
[Term]
id: GO:0033240
-name: positive regulation of cellular amine metabolic process
+name: positive regulation of amine metabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines." [GOC:mah]
synonym: "positive regulation of amine metabolism" EXACT []
-is_a: GO:0031325 ! positive regulation of cellular metabolic process
-is_a: GO:0033238 ! regulation of cellular amine metabolic process
+synonym: "positive regulation of cellular amine metabolic process" EXACT []
+is_a: GO:0033238 ! regulation of amine metabolic process
is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
-relationship: positively_regulates GO:0044106 ! cellular amine metabolic process
+relationship: positively_regulates GO:0009308 ! amine metabolic process
[Term]
id: GO:0033241
-name: regulation of cellular amine catabolic process
+name: regulation of amine catabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines." [GOC:mah]
synonym: "regulation of amine breakdown" EXACT []
synonym: "regulation of amine catabolism" EXACT []
synonym: "regulation of amine degradation" EXACT []
-is_a: GO:0031329 ! regulation of cellular catabolic process
-is_a: GO:0033238 ! regulation of cellular amine metabolic process
+synonym: "regulation of cellular amine catabolic process" EXACT []
+is_a: GO:0009894 ! regulation of catabolic process
+is_a: GO:0033238 ! regulation of amine metabolic process
relationship: regulates GO:0009310 ! amine catabolic process
[Term]
id: GO:0033242
-name: negative regulation of cellular amine catabolic process
+name: negative regulation of amine catabolic process
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines." [GOC:mah]
synonym: "negative regulation of amine breakdown" EXACT []
synonym: "negative regulation of amine catabolism" EXACT []
synonym: "negative regulation of amine degradation" EXACT []
-is_a: GO:0031330 ! negative regulation of cellular catabolic process
-is_a: GO:0033239 ! negative regulation of cellular amine metabolic process
-is_a: GO:0033241 ! regulation of cellular amine catabolic process
+synonym: "negative regulation of cellular amine catabolic process" EXACT []
+is_a: GO:0009895 ! negative regulation of catabolic process
+is_a: GO:0033239 ! negative regulation of amine metabolic process
+is_a: GO:0033241 ! regulation of amine catabolic process
relationship: negatively_regulates GO:0009310 ! amine catabolic process
[Term]
id: GO:0033243
-name: positive regulation of cellular amine catabolic process
+name: positive regulation of amine catabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines." [GOC:mah]
synonym: "positive regulation of amine breakdown" EXACT []
synonym: "positive regulation of amine catabolism" EXACT []
synonym: "positive regulation of amine degradation" EXACT []
-is_a: GO:0031331 ! positive regulation of cellular catabolic process
-is_a: GO:0033240 ! positive regulation of cellular amine metabolic process
-is_a: GO:0033241 ! regulation of cellular amine catabolic process
+is_a: GO:0009896 ! positive regulation of catabolic process
+is_a: GO:0033240 ! positive regulation of amine metabolic process
+is_a: GO:0033241 ! regulation of amine catabolic process
relationship: positively_regulates GO:0009310 ! amine catabolic process
[Term]
@@ -185861,8 +185797,8 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving any antibiotic that contains the condensed beta-lactamthiazolidine ring system." [GOC:mah]
synonym: "regulation of penicillin metabolism" EXACT []
is_a: GO:0010565 ! regulation of cellular ketone metabolic process
-is_a: GO:0033238 ! regulation of cellular amine metabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0033238 ! regulation of amine metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0042762 ! regulation of sulfur metabolic process
is_a: GO:0043455 ! regulation of secondary metabolic process
relationship: regulates GO:0042316 ! penicillin metabolic process
@@ -185873,9 +185809,9 @@ name: negative regulation of penicillin metabolic process
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving any antibiotic that contains the condensed beta-lactamthiazolidine ring system." [GOC:mah]
synonym: "negative regulation of penicillin metabolism" EXACT []
-is_a: GO:0033239 ! negative regulation of cellular amine metabolic process
+is_a: GO:0033239 ! negative regulation of amine metabolic process
is_a: GO:0033244 ! regulation of penicillin metabolic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0051175 ! negative regulation of sulfur metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
relationship: negatively_regulates GO:0042316 ! penicillin metabolic process
@@ -185886,9 +185822,9 @@ name: positive regulation of penicillin metabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving any antibiotic that contains the condensed beta-lactamthiazolidine ring system." [GOC:mah]
synonym: "positive regulation of penicillin metabolism" EXACT []
-is_a: GO:0033240 ! positive regulation of cellular amine metabolic process
+is_a: GO:0033240 ! positive regulation of amine metabolic process
is_a: GO:0033244 ! regulation of penicillin metabolic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0051176 ! positive regulation of sulfur metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
relationship: positively_regulates GO:0042316 ! penicillin metabolic process
@@ -185901,8 +185837,8 @@ def: "Any process that modulates the frequency, rate or extent of the chemical r
synonym: "regulation of penicillin breakdown" EXACT []
synonym: "regulation of penicillin catabolism" EXACT []
synonym: "regulation of penicillin degradation" EXACT []
+is_a: GO:0031329 ! regulation of cellular catabolic process
is_a: GO:0033244 ! regulation of penicillin metabolic process
-is_a: GO:0034251 ! regulation of cellular amide catabolic process
relationship: regulates GO:0042317 ! penicillin catabolic process
[Term]
@@ -185913,9 +185849,9 @@ def: "Any process that stops, prevents, or reduces the frequency, rate or extent
synonym: "negative regulation of penicillin breakdown" EXACT []
synonym: "negative regulation of penicillin catabolism" EXACT []
synonym: "negative regulation of penicillin degradation" EXACT []
+is_a: GO:0031330 ! negative regulation of cellular catabolic process
is_a: GO:0033245 ! negative regulation of penicillin metabolic process
is_a: GO:0033247 ! regulation of penicillin catabolic process
-is_a: GO:0034252 ! negative regulation of cellular amide catabolic process
relationship: negatively_regulates GO:0042317 ! penicillin catabolic process
[Term]
@@ -185926,9 +185862,9 @@ def: "Any process that activates or increases the frequency, rate or extent of t
synonym: "positive regulation of penicillin breakdown" EXACT []
synonym: "positive regulation of penicillin catabolism" EXACT []
synonym: "positive regulation of penicillin degradation" EXACT []
+is_a: GO:0031331 ! positive regulation of cellular catabolic process
is_a: GO:0033246 ! positive regulation of penicillin metabolic process
is_a: GO:0033247 ! regulation of penicillin catabolic process
-is_a: GO:0034253 ! positive regulation of cellular amide catabolic process
relationship: positively_regulates GO:0042317 ! penicillin catabolic process
[Term]
@@ -185965,10 +185901,10 @@ is_a: GO:0033252 ! regulation of beta-lactamase activity
id: GO:0033254
name: vacuolar transporter chaperone complex
namespace: cellular_component
-def: "A protein complex that contains four related proteins that have been implicated in several membrane-related processes, such as sorting of H+-translocating ATPases, endocytosis, ER-Golgi trafficking, vacuole fusion, vacuolar polyphosphate homeostasis and the microautophagic scission of vesicles into the vacuolar lumen. The complex is enriched at the vacuolar membrane, but also found in other cellular compartments, including the ER and the cell periphery. In Saccharomyces, the subunits are Vtc1p, Vtc2p, Vtc3p and Vtc4p." [PMID:11823419, PMID:17079729]
+def: "A protein complex that contains four related proteins that have been implicated in several membrane-related processes, such as sorting of H+-translocating ATPases, endocytosis, ER-Golgi trafficking, vacuole fusion, vacuolar polyphosphate homeostasis and the microautophagic scission of vesicles into the vacuolar lumen. The complex is enriched at the vacuolar membrane, but also found in other cellular compartments, including the ER and the cell periphery. In Saccharomyces, the subunits are Vtc1p, Vtc2p, Vtc3p and Vtc4p." [PMID:11823419, PMID:17079729, PMID:34544285]
synonym: "VTC complex" EXACT []
-is_a: GO:0101031 ! chaperone complex
-relationship: part_of GO:0005737 ! cytoplasm
+is_a: GO:0098796 ! membrane protein complex
+is_a: GO:0140535 ! intracellular protein-containing complex
[Term]
id: GO:0033255
@@ -186011,7 +185947,7 @@ namespace: biological_process
def: "The process in which new strands of DNA are synthesized in a plastid." [GOC:mah]
synonym: "plastid DNA synthesis" RELATED []
synonym: "replication of plastid DNA" EXACT []
-is_a: GO:0006261 ! DNA-dependent DNA replication
+is_a: GO:0006261 ! DNA-templated DNA replication
is_a: GO:0033258 ! plastid DNA metabolic process
[Term]
@@ -186049,7 +185985,7 @@ synonym: "regulation of DNA replication during S phase" RELATED [GOC:dph, GOC:tb
synonym: "regulation of DNA replication involved in S phase" EXACT []
synonym: "regulation of DNA replication involved in S-phase" EXACT []
is_a: GO:0010564 ! regulation of cell cycle process
-is_a: GO:0090329 ! regulation of DNA-dependent DNA replication
+is_a: GO:0090329 ! regulation of DNA-templated DNA replication
relationship: regulates GO:0033260 ! nuclear DNA replication
[Term]
@@ -186078,6 +186014,7 @@ name: choline binding
namespace: molecular_function
def: "Binding to choline, the amine 2-hydroxy-N,N,N-trimethylethanaminium." [GOC:mlg]
is_a: GO:0043169 ! cation binding
+is_a: GO:0050997 ! quaternary ammonium group binding
[Term]
id: GO:0033266
@@ -186089,8 +186026,7 @@ synonym: "ATP-dependent choline transmembrane transporter activity" RELATED []
synonym: "ATPase-coupled choline transmembrane transporter activity" RELATED []
synonym: "choline-transporting ATPase activity" RELATED []
is_a: GO:0015220 ! choline transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
-is_a: GO:0140359 ! ABC-type transporter activity
+is_a: GO:0015418 ! ABC-type quaternary ammonium compound transporting activity
[Term]
id: GO:0033267
@@ -186141,7 +186077,7 @@ name: myo-inositol phosphate transport
namespace: biological_process
def: "The directed movement of any phosphorylated myo-inositol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
is_a: GO:0015748 ! organophosphate ester transport
-is_a: GO:0015791 ! polyol transport
+is_a: GO:0015850 ! organic hydroxy compound transport
[Term]
id: GO:0033272
@@ -186169,6 +186105,7 @@ is_a: GO:0010243 ! response to organonitrogen compound
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0033273 ! response to vitamin
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0033275
@@ -186189,12 +186126,12 @@ relationship: part_of GO:0016591 ! RNA polymerase II, holoenzyme
[Term]
id: GO:0033277
-name: abortive mitotic cell cycle
+name: obsolete abortive mitotic cell cycle
namespace: biological_process
-def: "A cell cycle in which mitosis is begun and progresses normally through the end of anaphase, but not completed, resulting in a cell with increased ploidy." [GOC:mah, PMID:9573008]
-comment: Note that this term should be used only for abortive mitotic events that occur normally, e.g. during megakaryocyte differentiation; it should not be used for incomplete mitosis resulting from mutation or other abnormal occurrences. Note that this term should not be confused with 'endomitotic cell cycle ; GO:0007113', which describes a process in which no mitotic spindle forms.
+def: "OBSOLETE. A cell cycle in which mitosis is begun and progresses normally through the end of anaphase, but not completed, resulting in a cell with increased ploidy." [GOC:mah, PMID:9573008]
+comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
synonym: "abortive mitosis" RELATED []
-is_a: GO:0000278 ! mitotic cell cycle
+is_obsolete: true
[Term]
id: GO:0033278
@@ -186283,8 +186220,6 @@ synonym: "ATP-dependent ectoine transmembrane transporter activity" EXACT []
synonym: "ectoine transmembrane transporter activity" BROAD []
synonym: "ectoine-transporting ATPase activity" EXACT []
xref: RHEA:32787
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0033285 ! ATPase-coupled monocarboxylic acid transmembrane transporter activity
[Term]
@@ -186296,10 +186231,8 @@ def: "Enables the transfer of a solute or solutes from one side of a membrane to
synonym: "ATP-dependent hydroxyectoine transmembrane transporter activity" EXACT []
synonym: "hydroxyectoine transmembrane transporter activity" BROAD []
synonym: "hydroxyectoine-transporting ATPase activity" EXACT []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015651 ! quaternary ammonium group transmembrane transporter activity
is_a: GO:0015665 ! alcohol transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0033285 ! ATPase-coupled monocarboxylic acid transmembrane transporter activity
[Term]
@@ -186315,7 +186248,7 @@ id: GO:0033290
name: eukaryotic 48S preinitiation complex
namespace: cellular_component
alt_id: GO:0016283
-def: "A protein complex composed of the small ribosomal subunit, eIF3, eIF1A, methionyl-initiatior methionine and a capped mRNA. The complex is initially positioned at the 5'-end of the capped mRNA." [GOC:hjd, PMID:15145049]
+def: "The protein-ribosome-tRNA complex that has just recognized the start codon of a capped mRNA. It is composed of the small ribosomal subunit, eukaryote initiation factors (eIF) eIF3 complex, eIF1, eIF1A, eIF2-GDP, eIF4 complex and initiatior-methionine-tRNA. Recognition of the start codon triggers downstream steps in the pathway, including eIF1 dissociation; Pi release from eIF2; and conversion to the closed, scanning-arrested conformation of the PIC." [GOC:hjd, PMID:16510876, PMID:24319994, PMID:24499181, PMID:29735639]
synonym: "eukaryotic 48S initiation complex" RELATED []
synonym: "eukaryotic 48S pre-initiation complex" EXACT []
is_a: GO:0070993 ! translation preinitiation complex
@@ -186352,7 +186285,6 @@ name: ectoine binding
namespace: molecular_function
def: "Binding to ectoine, 1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid." [GOC:mah]
is_a: GO:0033293 ! monocarboxylic acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -186362,7 +186294,6 @@ name: hydroxyectoine binding
namespace: molecular_function
def: "Binding to hydroxyectoine." [GOC:mlg]
is_a: GO:0033293 ! monocarboxylic acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0043178 ! alcohol binding
is_a: GO:0050997 ! quaternary ammonium group binding
is_a: GO:0097159 ! organic cyclic compound binding
@@ -186482,7 +186413,6 @@ namespace: biological_process
def: "The directed movement of hydroxyectoine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mlg]
is_a: GO:0015697 ! quaternary ammonium group transport
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
[Term]
@@ -186615,7 +186545,7 @@ name: homomethionine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving homomethionine, a non-protein amino acid synthesized from methionine via chain elongation." [GOC:mah, MetaCyc:PWY-1186]
synonym: "homomethionine metabolism" EXACT []
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
[Term]
id: GO:0033322
@@ -186627,7 +186557,7 @@ synonym: "homomethionine biosynthesis" EXACT []
synonym: "homomethionine formation" EXACT []
synonym: "homomethionine synthesis" EXACT []
xref: MetaCyc:PWY-1186
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
+is_a: GO:0008652 ! amino acid biosynthetic process
is_a: GO:0033321 ! homomethionine metabolic process
[Term]
@@ -187065,7 +186995,7 @@ namespace: biological_process
def: "A process in which a protein is transported to, or maintained in, a location within an organelle." [GOC:mah]
synonym: "protein localisation to organelle" EXACT [GOC:mah]
synonym: "protein localization in organelle" EXACT [GOC:mah]
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
[Term]
id: GO:0033366
@@ -188301,18 +188231,21 @@ is_a: GO:0046396 ! D-galacturonate metabolic process
[Term]
id: GO:0033483
-name: gas homeostasis
+name: obsolete gas homeostasis
namespace: biological_process
-def: "A homeostatic process involved in the maintenance of an internal steady state of a gas within an organism or cell." [GOC:mah]
-is_a: GO:0048878 ! chemical homeostasis
+def: "OBSOLETE. A homeostatic process involved in the maintenance of an internal steady state of a gas within an organism or cell." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
[Term]
id: GO:0033484
-name: nitric oxide homeostasis
+name: intracellular nitric oxide homeostasis
namespace: biological_process
-def: "A homeostatic process involved in the maintenance of an internal steady state of nitric oxide within an organism or cell." [GOC:mah]
-synonym: "NO homeostasis" EXACT []
-is_a: GO:0033483 ! gas homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of nitric oxide within a cell." [GOC:mah]
+synonym: "cellular nitric oxide homeostasis" EXACT []
+synonym: "nitric oxide homeostasis" BROAD []
+synonym: "NO homeostasis" BROAD []
+is_a: GO:0055082 ! intracellular chemical homeostasis
[Term]
id: GO:0033485
@@ -188351,7 +188284,7 @@ synonym: "pelargonidin 3-O-glucoside biosynthesis" EXACT []
synonym: "pelargonidin 3-O-glucoside formation" EXACT []
synonym: "pelargonidin 3-O-glucoside synthesis" EXACT []
xref: MetaCyc:PWY-5125
-is_a: GO:0009813 ! flavonoid biosynthetic process
+is_a: GO:0009718 ! anthocyanin-containing compound biosynthetic process
is_a: GO:1901806 ! beta-glucoside biosynthetic process
[Term]
@@ -188512,19 +188445,22 @@ is_a: GO:0048878 ! chemical homeostasis
[Term]
id: GO:0033501
-name: galactose homeostasis
+name: obsolete galactose homeostasis
namespace: biological_process
-def: "A homeostatic process involved in the maintenance of an internal steady state of galactose within an organism or cell." [GOC:mah]
-is_a: GO:0033500 ! carbohydrate homeostasis
+def: "OBSOLETE. A homeostatic process involved in the maintenance of an internal steady state of galactose within an organism or cell." [GOC:mah]
+comment: This term was obsoleted because it does not specify whether it represent an intracellular or an organism-level process.
+is_obsolete: true
+consider: GO:0033502
[Term]
id: GO:0033502
-name: cellular galactose homeostasis
+name: intracellular galactose homeostasis
namespace: biological_process
-def: "A cellular homeostatic process involved in the maintenance of an internal steady state of galactose within a cell or between a cell and its external environment." [GOC:dph, GOC:mah, GOC:tb]
+def: "A homeostatic process involved in the maintenance of a steady state level of galactose within a cell." [GOC:dph, GOC:mah, GOC:tb, PMID:21621292]
synonym: "cell galactose homeostasis" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0033501 ! galactose homeostasis
-is_a: GO:0055082 ! cellular chemical homeostasis
+synonym: "cellular galactose homeostasis" EXACT []
+is_a: GO:0033500 ! carbohydrate homeostasis
+is_a: GO:0055082 ! intracellular chemical homeostasis
[Term]
id: GO:0033503
@@ -188575,7 +188511,7 @@ synonym: "glucosinolate biosynthesis from phenylalanine" EXACT []
synonym: "glucosinolate formation from phenylalanine" EXACT []
synonym: "glucosinolate synthesis from phenylalanine" EXACT []
xref: MetaCyc:PWY-2821
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
is_a: GO:0019761 ! glucosinolate biosynthetic process
[Term]
@@ -188687,14 +188623,12 @@ is_a: GO:0043647 ! inositol phosphate metabolic process
[Term]
id: GO:0033518
-name: myo-inositol hexakisphosphate dephosphorylation
+name: obsolete myo-inositol hexakisphosphate dephosphorylation
namespace: biological_process
-def: "The process of removing one or more phosphate group from myo-inositol hexakisphosphate." [GOC:mah]
+def: "OBSOLETE. The process of removing one or more phosphate group from myo-inositol hexakisphosphate." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "phytate dephosphorylation" EXACT []
-xref: MetaCyc:PWY-4702
-xref: MetaCyc:PWY-4781
-is_a: GO:0033517 ! myo-inositol hexakisphosphate metabolic process
-is_a: GO:0046855 ! inositol phosphate dephosphorylation
+is_obsolete: true
[Term]
id: GO:0033519
@@ -189098,12 +189032,15 @@ relationship: part_of GO:0000228 ! nuclear chromosome
[Term]
id: GO:0033558
-name: protein deacetylase activity
+name: protein lysine deacetylase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of an acetyl group or groups from a protein substrate." [GOC:mah]
+def: "Catalysis of the reaction: H2O + N6-acetyl-L-lysyl-[protein] = acetate + L-lysyl-[protein]." [PMID:27296530, RHEA:58108]
+synonym: "protein deacetylase activity" EXACT []
xref: Reactome:R-HSA-5693092 "Unknown deacetylase deacetylates 7K-BACE1(46-501)"
xref: Reactome:R-HSA-8952069 "HDAC4 deacetylates RUNX3"
xref: Reactome:R-HSA-9626962 "SIRT1 deacetylates FOXO1"
+xref: Reactome:R-HSA-9701565 "HDACs deacetylate p-STAT3 dimers"
+xref: RHEA:58108
is_a: GO:0019213 ! deacetylase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -189122,18 +189059,22 @@ id: GO:0033560
name: folate reductase activity
namespace: molecular_function
def: "Catalysis of the reaction: 7,8-dihydrofolate + NADP+ = folate + NADPH + H+." [GOC:pde]
-xref: Reactome:R-HSA-197963 "Folate is reduced to dihydrofolate (DHF)"
+xref: Reactome:R-HSA-197963 "DHFR2 reduces FOLA to DHF"
xref: Reactome:R-HSA-197972 "DHF is reduced to tetrahydrofolate (THF)"
+xref: Reactome:R-HSA-9709098 "DHFR dimer reduces FOLA to DHF"
xref: RHEA:31103
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0033561
-name: regulation of water loss via skin
+name: obsolete regulation of water loss via skin
namespace: biological_process
-def: "A process that modulates the rate or extent of water loss from an organism via the skin." [GOC:mah]
+def: "OBSOLETE. A process that modulates the rate or extent of water loss from an organism via the skin." [GOC:mah]
+comment: This term was obsoleted because it represents a readout.
synonym: "skin barrier function" RELATED []
-is_a: GO:0050891 ! multicellular organismal water homeostasis
+is_obsolete: true
+consider: GO:0043589
+consider: GO:0098773
[Term]
id: GO:0033562
@@ -189145,7 +189086,7 @@ synonym: "cotranscriptional gene silencing by RNA interference machinery" RELATE
synonym: "cotranscriptional gene silencing by small RNA" RELATED []
synonym: "RNAi-mediated CTGS" EXACT [GOC:vw]
synonym: "small RNA-mediated cotranscriptional gene silencing" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0031047 ! gene silencing by RNA
+is_a: GO:0031047 ! RNA-mediated gene silencing
[Term]
id: GO:0033563
@@ -189253,75 +189194,83 @@ is_a: GO:1901654 ! response to ketone
[Term]
id: GO:0033575
-name: protein glycosylation at cell surface
+name: obsolete protein glycosylation at cell surface
namespace: biological_process
-def: "The addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid at the surface of a cell." [GOC:mah, GOC:pr, PMID:12042244]
+def: "OBSOLETE. The addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid at the surface of a cell." [GOC:mah, GOC:pr, PMID:12042244]
+comment: This term was obsoleted because it represented both a process and a cellular component.
synonym: "protein amino acid glycosylation at cell surface" EXACT [GOC:bf]
-is_a: GO:0006486 ! protein glycosylation
+is_obsolete: true
+replaced_by: GO:0006486
[Term]
id: GO:0033576
-name: protein glycosylation in cytosol
+name: obsolete protein glycosylation in cytosol
namespace: biological_process
-def: "The addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in the cytosol." [GOC:mah, GOC:pr, PMID:12042244]
+def: "OBSOLETE. The addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in the cytosol." [GOC:mah, GOC:pr, PMID:12042244]
+comment: This term was obsoleted because it represented both a process and a cellular component.
synonym: "protein amino acid glycosylation in cytosol" EXACT [GOC:bf]
-is_a: GO:0006486 ! protein glycosylation
+is_obsolete: true
+replaced_by: GO:0006486
[Term]
id: GO:0033577
-name: protein glycosylation in endoplasmic reticulum
+name: obsolete protein glycosylation in endoplasmic reticulum
namespace: biological_process
-def: "The addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in the endoplasmic reticulum." [GOC:mah, GOC:pr, PMID:12042244]
+def: "OBSOLETE. The addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in the endoplasmic reticulum." [GOC:mah, GOC:pr, PMID:12042244]
synonym: "core glycosylation" RELATED [PMID:6345657]
synonym: "protein amino acid glycosylation in endoplasmic reticulum" EXACT [GOC:bf]
synonym: "protein amino acid glycosylation in ER" EXACT []
-is_a: GO:0006486 ! protein glycosylation
+is_obsolete: true
+replaced_by: GO:0006486
[Term]
id: GO:0033578
-name: protein glycosylation in Golgi
+name: obsolete protein glycosylation in Golgi
namespace: biological_process
-def: "The addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in any compartment of the Golgi apparatus." [GOC:mah, GOC:pr, PMID:12042244]
+def: "OBSOLETE. The addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in any compartment of the Golgi apparatus." [GOC:mah, GOC:pr, PMID:12042244]
synonym: "protein amino acid glycosylation in Golgi" EXACT [GOC:bf]
synonym: "terminal glycosylation" NARROW [PMID:6345657]
-is_a: GO:0006486 ! protein glycosylation
+is_obsolete: true
+replaced_by: GO:0006486
[Term]
id: GO:0033579
-name: protein galactosylation in endoplasmic reticulum
+name: obsolete protein galactosylation in endoplasmic reticulum
namespace: biological_process
-def: "The addition of a galactose unit to a protein amino acid in the endoplasmic reticulum." [GOC:mah]
+def: "OBSOLETE. The addition of a galactose unit to a protein amino acid in the endoplasmic reticulum." [GOC:mah]
synonym: "protein amino acid galactosylation in endoplasmic reticulum" EXACT [GOC:bf]
synonym: "protein amino acid galactosylation in ER" EXACT []
-is_a: GO:0033577 ! protein glycosylation in endoplasmic reticulum
-is_a: GO:0042125 ! protein galactosylation
+is_obsolete: true
+replaced_by: GO:0042125
[Term]
id: GO:0033580
-name: protein galactosylation at cell surface
+name: obsolete protein galactosylation at cell surface
namespace: biological_process
-def: "The addition of a galactose unit to a protein amino acid at the surface of a cell." [GOC:mah]
+def: "OBSOLETE. The addition of a galactose unit to a protein amino acid at the surface of a cell." [GOC:mah]
+comment: This term was obsoleted because it represented both a process and a cellular component.
synonym: "protein amino acid galactosylation at cell surface" EXACT [GOC:bf]
-is_a: GO:0033575 ! protein glycosylation at cell surface
-is_a: GO:0042125 ! protein galactosylation
+is_obsolete: true
+replaced_by: GO:0042125
[Term]
id: GO:0033581
-name: protein galactosylation in Golgi
+name: obsolete protein galactosylation in Golgi
namespace: biological_process
-def: "The addition of a galactose unit to a protein amino acid in any compartment of the Golgi apparatus." [GOC:mah]
+def: "OBSOLETE. The addition of a galactose unit to a protein amino acid in any compartment of the Golgi apparatus." [GOC:mah]
synonym: "protein amino acid galactosylation in Golgi" EXACT [GOC:bf]
-is_a: GO:0033578 ! protein glycosylation in Golgi
-is_a: GO:0042125 ! protein galactosylation
+is_obsolete: true
+replaced_by: GO:0042125
[Term]
id: GO:0033582
-name: protein galactosylation in cytosol
+name: obsolete protein galactosylation in cytosol
namespace: biological_process
-def: "The addition of a galactose unit to a protein amino acid in the cytosol." [GOC:mah]
+def: "OBSOLETE. The addition of a galactose unit to a protein amino acid in the cytosol." [GOC:mah]
+comment: This term was obsoleted because it represented both a process and a cellular component.
synonym: "protein amino acid galactosylation in cytosol" EXACT [GOC:bf]
-is_a: GO:0033576 ! protein glycosylation in cytosol
-is_a: GO:0042125 ! protein galactosylation
+is_obsolete: true
+replaced_by: GO:0042125
[Term]
id: GO:0033583
@@ -189378,6 +189327,7 @@ def: "A heterohexameric protein complex composed two discrete heterotrimeric sub
comment: Despite its name, this complex is not directly involved in transcriptional elongation (PMID:23165209).
synonym: "Elongator core complex" RELATED []
is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0033590
@@ -189401,6 +189351,7 @@ synonym: "response to vitamin C" EXACT []
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0033273 ! response to vitamin
is_a: GO:0034284 ! response to monosaccharide
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0033592
@@ -189507,7 +189458,6 @@ synonym: "downregulation of dopamine secretion" EXACT []
synonym: "inhibition of dopamine secretion" NARROW []
is_a: GO:0014059 ! regulation of dopamine secretion
is_a: GO:0033604 ! negative regulation of catecholamine secretion
-is_a: GO:0043271 ! negative regulation of ion transport
relationship: negatively_regulates GO:0014046 ! dopamine secretion
[Term]
@@ -189522,7 +189472,6 @@ synonym: "up-regulation of dopamine secretion" EXACT []
synonym: "upregulation of dopamine secretion" EXACT []
is_a: GO:0014059 ! regulation of dopamine secretion
is_a: GO:0033605 ! positive regulation of catecholamine secretion
-is_a: GO:0043270 ! positive regulation of ion transport
relationship: positively_regulates GO:0014046 ! dopamine secretion
[Term]
@@ -189592,6 +189541,7 @@ synonym: "ethanedioate metabolic process" EXACT []
synonym: "ethanedioic acid metabolic process" EXACT []
synonym: "oxalate metabolism" EXACT []
synonym: "oxalic acid metabolic process" EXACT []
+is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0043648 ! dicarboxylic acid metabolic process
[Term]
@@ -189749,7 +189699,7 @@ relationship: positively_regulates GO:0033622 ! integrin activation
id: GO:0033626
name: positive regulation of integrin activation by cell surface receptor linked signal transduction
namespace: biological_process
-def: "Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell that lead to the increased affinity of an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits, for its extracellular ligands." [GOC:add, PMID:12213832, PMID:14754902]
+def: "Any process that activates or increases the frequency, rate, or extent of integrin activation by cell surface receptor linked signal transduction. This can occur by increased affinity of an integrin for its extracellular ligands." [GOC:add, PMID:12213832, PMID:14754902]
synonym: "cell surface receptor linked signal transduction leading to integrin activation" EXACT [GOC:bf, GOC:signaling]
synonym: "cell surface receptor linked signal transduction leading to integrin complex activation" EXACT []
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -189839,64 +189789,66 @@ name: modulation by symbiont of host response to abiotic stimulus
namespace: biological_process
def: "Any process in which an organism modulates a change in the state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
is_a: GO:0044003 ! modulation by symbiont of host process
-relationship: regulates GO:0009628 ! response to abiotic stimulus
[Term]
id: GO:0033636
-name: modulation by symbiont of host response to temperature stimulus
+name: obsolete modulation by symbiont of host response to temperature stimulus
namespace: biological_process
-def: "Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+def: "OBSOLETE. Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "modulation by symbiont of host response to thermal stimulus" EXACT []
-is_a: GO:0033635 ! modulation by symbiont of host response to abiotic stimulus
-relationship: regulates GO:0009266 ! response to temperature stimulus
+is_obsolete: true
[Term]
id: GO:0033637
-name: modulation by symbiont of host response to cold
+name: obsolete modulation by symbiont of host response to cold
namespace: biological_process
-def: "Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+def: "OBSOLETE. Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "freezing tolerance" RELATED []
-is_a: GO:0033636 ! modulation by symbiont of host response to temperature stimulus
+is_obsolete: true
[Term]
id: GO:0033638
-name: modulation by symbiont of host response to heat
+name: modulation by symbiont of host heat acclimation
namespace: biological_process
-def: "Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+def: "Any process in which an organism modulates the host's tolerance to high temperatures, above the optimal temperature for that organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators, PMID:17425405, PMID:35350854]
+synonym: "modulation by symbiont of host response to heat" RELATED []
synonym: "response to heat shock" RELATED []
-is_a: GO:0033636 ! modulation by symbiont of host response to temperature stimulus
+is_a: GO:0033635 ! modulation by symbiont of host response to abiotic stimulus
[Term]
id: GO:0033639
-name: modulation by symbiont of host response to water
+name: obsolete modulation by symbiont of host response to water
namespace: biological_process
-def: "Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-is_a: GO:0033635 ! modulation by symbiont of host response to abiotic stimulus
+def: "OBSOLETE. Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0033640
-name: modulation by symbiont of host response to osmotic stress
+name: obsolete modulation by symbiont of host response to osmotic stress
namespace: biological_process
-def: "Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-is_a: GO:0033635 ! modulation by symbiont of host response to abiotic stimulus
-relationship: regulates GO:0006970 ! response to osmotic stress
+def: "OBSOLETE. Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0033641
-name: modulation by symbiont of host response to pH
+name: obsolete modulation by symbiont of host response to pH
namespace: biological_process
-def: "Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-is_a: GO:0033635 ! modulation by symbiont of host response to abiotic stimulus
-relationship: regulates GO:0009268 ! response to pH
+def: "OBSOLETE. Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0033642
-name: modulation by symbiont of host response to gravitational stimulus
+name: obsolete modulation by symbiont of host response to gravitational stimulus
namespace: biological_process
-def: "Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gravitational stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+def: "OBSOLETE. Any process in which an organism modulates a change in state or activity of a host cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gravitational stimulus. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "response to gravitational stimulus" BROAD []
-is_a: GO:0033635 ! modulation by symbiont of host response to abiotic stimulus
-relationship: regulates GO:0009629 ! response to gravity
+is_obsolete: true
[Term]
id: GO:0033643
@@ -189963,7 +189915,6 @@ name: host cell plastid
namespace: cellular_component
def: "Any member of a family of organelles as found in the cytoplasm of host cells, which are membrane-bounded and contain DNA. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
is_a: GO:0033648 ! host intracellular membrane-bounded organelle
-is_a: GO:0033655 ! host cell cytoplasm part
[Term]
id: GO:0033652
@@ -190131,7 +190082,7 @@ consider: GO:0044131
[Term]
id: GO:0033668
-name: negative regulation by symbiont of host apoptotic process
+name: suppression by symbiont of host apoptotic process
namespace: biological_process
def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of programmed cell death in the host, where programmed cell death proceeds by apoptosis. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
comment: Note that term is to be used to annotate gene products in the symbiont. To annotate host gene products, consider the biological process term 'negative regulation of apoptosis ; GO:0043066'.
@@ -190140,8 +190091,9 @@ synonym: "down-regulation by organism of host apoptotic programmed cell death" E
synonym: "downregulation by organism of host apoptotic programmed cell death" EXACT []
synonym: "inhibition by organism of host apoptotic programmed cell death" NARROW []
synonym: "negative regulation by symbiont of host apoptosis" NARROW []
+synonym: "negative regulation by symbiont of host apoptotic process" EXACT []
is_a: GO:0043066 ! negative regulation of apoptotic process
-is_a: GO:0052041 ! negative regulation by symbiont of host programmed cell death
+is_a: GO:0052041 ! suppression by symbiont of host programmed cell death
is_a: GO:0052150 ! modulation by symbiont of host apoptotic process
[Term]
@@ -190251,13 +190203,14 @@ is_a: GO:0033677 ! DNA/RNA helicase activity
[Term]
id: GO:0033683
-name: nucleotide-excision repair, DNA incision
+name: obsolete nucleotide-excision repair, DNA incision
namespace: biological_process
-def: "A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound." [GOC:elh, PMID:8631896]
+def: "OBSOLETE. A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound." [GOC:elh, PMID:8631896]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "DNA incision involved in nucleotide-excision repair" EXACT [GOC:dph, GOC:tb]
synonym: "nucleic acid cleavage involved in nucleotide-excision repair" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0090305 ! nucleic acid phosphodiester bond hydrolysis
-relationship: part_of GO:0006289 ! nucleotide-excision repair
+is_obsolete: true
+replaced_by: GO:0006289
[Term]
id: GO:0033684
@@ -190347,19 +190300,18 @@ is_a: GO:0097367 ! carbohydrate derivative binding
[Term]
id: GO:0033692
-name: cellular polysaccharide biosynthetic process
+name: obsolete cellular polysaccharide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, occurring at the level of an individual cell." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, occurring at the level of an individual cell." [GOC:go_curators]
+comment: This term was obsoleted because it is not different from its parent, polysaccharide biosynthetic process ; GO:0000271.
synonym: "cellular glycan biosynthesis" EXACT []
synonym: "cellular glycan biosynthetic process" EXACT []
synonym: "cellular polysaccharide anabolism" EXACT []
synonym: "cellular polysaccharide biosynthesis" EXACT []
synonym: "cellular polysaccharide formation" EXACT []
synonym: "cellular polysaccharide synthesis" EXACT []
-is_a: GO:0000271 ! polysaccharide biosynthetic process
-is_a: GO:0034637 ! cellular carbohydrate biosynthetic process
-is_a: GO:0034645 ! cellular macromolecule biosynthetic process
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
+is_obsolete: true
+replaced_by: GO:0000271
[Term]
id: GO:0033693
@@ -190399,7 +190351,7 @@ synonym: "regulation of extent of heterochromatin assembly" RELATED []
synonym: "regulation of extent of heterochromatin formation" EXACT []
synonym: "regulation of heterochromatin spreading" RELATED []
is_a: GO:0070828 ! heterochromatin organization
-relationship: part_of GO:0031507 ! heterochromatin assembly
+relationship: part_of GO:0031507 ! heterochromatin formation
[Term]
id: GO:0033697
@@ -190433,7 +190385,8 @@ synonym: "DNA 5'-adenylate hydrolase activity" EXACT []
synonym: "DNA adenylate hydrolysis activity" BROAD []
synonym: "DNA de-adenylation" RELATED []
synonym: "DNA deadenylation" RELATED []
-is_a: GO:0035312 ! 5'-3' exodeoxyribonuclease activity
+xref: EC:3.6.1.71
+is_a: GO:0035312 ! 5'-3' DNA exonuclease activity
[Term]
id: GO:0033700
@@ -190460,7 +190413,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0033702
name: (+)-trans-carveol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (1R,5S)-carveol + NAD(+) = (S)-carvone + H(+) + NADH." [EC:1.1.1.275, RHEA:14825]
+def: "Catalysis of the reaction: (1R,5S)-carveol + NAD+ = (S)-carvone + H+ + NADH." [EC:1.1.1.275, RHEA:14825]
synonym: "(+)-trans-carveol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.275]
xref: EC:1.1.1.275
xref: KEGG_REACTION:R06117
@@ -190472,7 +190425,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0033703
name: 3beta-hydroxy-5beta-steroid dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3beta-hydroxy-5beta-pregnane-20-one + NADP(+) = 5beta-pregnan-3,20-dione + H(+) + NADPH." [EC:1.1.1.277, RHEA:22944]
+def: "Catalysis of the reaction: 3beta-hydroxy-5beta-pregnane-20-one + NADP+ = 5beta-pregnan-3,20-dione + H+ + NADPH." [EC:1.1.1.277, RHEA:22944]
synonym: "3beta-hydroxy-5beta-steroid:NADP+ 3-oxidoreductase activity" RELATED [EC:1.1.1.277]
synonym: "3beta-hydroxysteroid 5beta-oxidoreductase activity" RELATED [EC:1.1.1.277]
synonym: "3beta-hydroxysteroid 5beta-progesterone oxidoreductase activity" RELATED [EC:1.1.1.277]
@@ -190486,7 +190439,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0033704
name: 3beta-hydroxy-5alpha-steroid dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3beta-hydroxy-5alpha-pregnane-20-one + NADP(+) = 5alpha-pregnane-3,20-dione + H(+) + NADPH." [EC:1.1.1.278, RHEA:18137]
+def: "Catalysis of the reaction: 3beta-hydroxy-5alpha-pregnane-20-one + NADP+ = 5alpha-pregnane-3,20-dione + H+ + NADPH." [EC:1.1.1.278, RHEA:18137]
synonym: "3beta-hydroxy-5alpha-steroid:NADP+ 3-oxidoreductase activity" RELATED [EC:1.1.1.278]
xref: EC:1.1.1.278
xref: KEGG_REACTION:R07138
@@ -190563,7 +190516,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0033711
name: 4-phosphoerythronate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-phospho-D-erythronate + NAD(+) = (R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + H(+) + NADH." [EC:1.1.1.290, RHEA:18829]
+def: "Catalysis of the reaction: 4-phospho-D-erythronate + NAD+ = (R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + H+ + NADH." [EC:1.1.1.290, RHEA:18829]
synonym: "4-O-phosphoerythronate dehydrogenase activity" RELATED [EC:1.1.1.290]
synonym: "4-phospho-D-erythronate:NAD+ 2-oxidoreductase activity" RELATED [EC:1.1.1.290]
synonym: "4PE dehydrogenase activity" RELATED [EC:1.1.1.290]
@@ -190580,7 +190533,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0033712
name: 1,5-anhydro-D-fructose reductase (1,5-anhydro-D-mannitol-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,5-anhydro-D-mannitol + NADP(+) = 1,5-anhydro-D-fructose + H(+) + NADPH." [EC:1.1.1.292, RHEA:24208]
+def: "Catalysis of the reaction: 1,5-anhydro-D-mannitol + NADP+ = 1,5-anhydro-D-fructose + H+ + NADPH." [EC:1.1.1.292, RHEA:24208]
synonym: "1,5-anhydro-D-mannitol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.292]
synonym: "AFR" RELATED [EC:1.1.1.292]
xref: EC:1.1.1.292
@@ -190604,7 +190557,7 @@ is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0033714
name: secondary-alcohol oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O(2) + secondary alcohol = H(2)O(2) + ketone." [EC:1.1.3.18, RHEA:23180]
+def: "Catalysis of the reaction: secondary alcohol + O2 = H2O2 + ketone." [EC:1.1.3.18, RHEA:23180]
synonym: "polyvinyl alcohol oxidase activity" RELATED [EC:1.1.3.18]
synonym: "secondary alcohol oxidase activity" RELATED [EC:1.1.3.18]
synonym: "secondary-alcohol:oxygen oxidoreductase activity" RELATED [EC:1.1.3.18]
@@ -190822,7 +190775,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0033732
name: pyrroloquinoline-quinone synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-(2-amino-2-carboxyethyl)-7,8-dioxo-1,2,3,4,7,8-hexahydroquinoline-2,4-dicarboxylate + 3 O(2) = 2 H(2)O + 2 H(2)O(2) + H(+) + pyrroloquinoline quinone." [EC:1.3.3.11, RHEA:10692]
+def: "Catalysis of the reaction: 6-(2-amino-2-carboxyethyl)-7,8-dioxo-1,2,3,4,7,8-hexahydroquinoline-2,4-dicarboxylate + 3 O2 = 2 H2O + 2 H2O2 + H+ + pyrroloquinoline quinone." [EC:1.3.3.11, RHEA:10692]
synonym: "6-(2-amino-2-carboxyethyl)-7,8-dioxo-1,2,3,4,5,6,7,8-octahydroquinoline-2,4-dicarboxylate:oxygen oxidoreductase (cyclizing) activity" RELATED [EC:1.3.3.11]
synonym: "PqqC" RELATED [EC:1.3.3.11]
xref: EC:1.3.3.11
@@ -190848,8 +190801,12 @@ is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
id: GO:0033735
name: aspartate dehydrogenase activity
namespace: molecular_function
+alt_id: GO:0106351
+alt_id: GO:0106352
def: "Catalysis of the reaction: L-aspartate + H2O + NAD(P)+ = oxaloacetate + NH3 + NAD(P)H + H+." [EC:1.4.1.21]
-synonym: "L-aspartate:NAD(P)+ oxidoreductase (deaminating) activity" RELATED [EC:1.4.1.21]
+synonym: "aspartate dehydrogenase NAD activity" NARROW []
+synonym: "aspartate dehydrogenase NADP activity" NARROW []
+synonym: "L-aspartate:NAD(P)+ oxidoreductase (deaminating) activity" RELATED []
synonym: "NAD-dependent aspartate dehydrogenase activity" RELATED [EC:1.4.1.21]
synonym: "NADH2-dependent aspartate dehydrogenase activity" RELATED [EC:1.4.1.21]
synonym: "NADP+-dependent aspartate dehydrogenase activity" RELATED [EC:1.4.1.21]
@@ -190863,7 +190820,7 @@ is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0033736
name: L-lysine 6-oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-lysine + H(2)O + O(2) = allysine + H(2)O(2) + NH(4)(+)." [EC:1.4.3.20, RHEA:22548]
+def: "Catalysis of the reaction: L-lysine + H2O + O2 = allysine + H2O2 + NH4." [RHEA:22548]
synonym: "L-lysine-epsilon-oxidase activity" RELATED [EC:1.4.3.20]
synonym: "L-lysine:oxygen 6-oxidoreductase (deaminating) activity" RELATED [EC:1.4.3.20]
synonym: "Lod" RELATED [EC:1.4.3.20]
@@ -190904,7 +190861,7 @@ is_a: GO:0033694 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0033739
name: preQ1 synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7-aminomethyl-7-deazaguanine + 2 NADP(+) = 7-cyano-7-deazaguanine + 3 H(+) + 2 NADPH." [EC:1.7.1.13, RHEA:13409]
+def: "Catalysis of the reaction: 7-aminomethyl-7-deazaguanine + 2 NADP+ = 7-cyano-7-deazaguanine + 3 H+ + 2 NADPH." [EC:1.7.1.13, RHEA:13409]
synonym: "7-aminomethyl-7-carbaguanine:NADP+ oxidoreductase activity" EXACT systematic_synonym [EC:1.7.1.13]
synonym: "7-cyano-7-deazaguanine reductase activity" RELATED [EC:1.7.1.13]
synonym: "preQ0 oxidoreductase activity" RELATED [EC:1.7.1.13]
@@ -190918,7 +190875,7 @@ xref: KEGG_REACTION:R07605
xref: MetaCyc:RXN0-4022
xref: RHEA:13409
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
-is_a: GO:0016657 ! oxidoreductase activity, acting on NAD(P)H, nitrogenous group as acceptor
+is_a: GO:0046857 ! oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor
[Term]
id: GO:0033740
@@ -190935,7 +190892,7 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0033741
name: adenylyl-sulfate reductase (glutathione) activity
namespace: molecular_function
-def: "Catalysis of the reaction: AMP + glutathione disulfide + H(+) + sulfite = 5'-adenylyl sulfate + 2 glutathione." [EC:1.8.4.9, RHEA:14141]
+def: "Catalysis of the reaction: AMP + glutathione disulfide + H+ + sulfite = 5'-adenylyl sulfate + 2 glutathione." [EC:1.8.4.9, RHEA:14141]
synonym: "5'-adenylylsulfate reductase activity" RELATED [EC:1.8.4.9]
synonym: "AMP,sulfite:glutathione-disulfide oxidoreductase (adenosine-5'-phosphosulfate-forming) activity" RELATED [EC:1.8.4.9]
synonym: "AMP,sulfite:oxidized-glutathione oxidoreductase (adenosine-5'-phosphosulfate-forming) activity" RELATED [EC:1.8.4.9]
@@ -190951,7 +190908,7 @@ id: GO:0033743
name: peptide-methionine (R)-S-oxide reductase activity
namespace: molecular_function
alt_id: GO:0000318
-def: "Catalysis of the reaction: peptide-L-methionine + H(2)O + thioredoxin disulfide = peptide-L-methionine (R)-S-oxide + thioredoxin. Can act on oxidized methionine in peptide linkage with specificity for the R enantiomer. Thioredoxin disulfide is the oxidized form of thioredoxin." [EC:1.8.4.12, GOC:mah, GOC:vw, RHEA:24164]
+def: "Catalysis of the reaction: peptide-L-methionine + H2O + thioredoxin disulfide = peptide-L-methionine (R)-S-oxide + thioredoxin. Can act on oxidized methionine in peptide linkage with specificity for the R enantiomer. Thioredoxin disulfide is the oxidized form of thioredoxin." [EC:1.8.4.12, GOC:mah, GOC:vw, RHEA:24164]
synonym: "methionine S-oxide reductase (R-form oxidizing) activity" RELATED [EC:1.8.4.12]
synonym: "methionine S-oxide reductase activity" BROAD [EC:1.8.4.12]
synonym: "methionine sulfoxide reductase activity" BROAD [EC:1.8.4.12]
@@ -191008,10 +190965,12 @@ is_a: GO:0016671 ! oxidoreductase activity, acting on a sulfur group of donors,
[Term]
id: GO:0033746
-name: histone H3-methyl-arginine-2 demethylase activity
+name: histone H3R2 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of the methyl group from a modified arginine residue at position 2 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:17947579, PMID:22483719, PMID:29233856]
synonym: "histone demethylase activity (H3-R2 specific)" EXACT []
+synonym: "histone H3-methyl-arginine-2 demethylase activity" EXACT []
+synonym: "histone H3-R2 demethylase activity" EXACT []
synonym: "histone H3R2me demethylase activity" EXACT []
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0032452 ! histone demethylase activity
@@ -191049,11 +191008,14 @@ is_a: GO:0016695 ! oxidoreductase activity, acting on hydrogen as donor
[Term]
id: GO:0033749
-name: histone H3-methyl-arginine-3 demethylase activity
+name: histone H3R3 demethylase activity
namespace: molecular_function
-def: "Catalysis of the removal of the methyl group from a modified arginine residue at position 3 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:17947579]
+def: "Catalysis of the removal of the methyl group from a modified arginine residue at position 3 of the histone H4 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:17947579]
synonym: "histone demethylase activity (H4-R3 specific)" EXACT []
-synonym: "histone H3R3me demethylase activity" EXACT []
+synonym: "histone H4-methyl-arginine-3 demethylase activity" EXACT []
+synonym: "histone H4-R3 demethylase activity" EXACT []
+synonym: "histone H4R3 demethylase activity" RELATED []
+synonym: "histone H4R3me demethylase activity" EXACT []
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0032452 ! histone demethylase activity
@@ -191073,7 +191035,7 @@ id: GO:0033751
name: obsolete linoleate 8R-lipoxygenase
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: linoleate + O2 = (9Z,12Z)-(7S,8S)-dihydroxyoctadeca-9,12-dienoate." [GOC:curators]
-comment: The reason for obsoletion is because there is no support for the reaction. EC and RHEA mappings have been obsoleted at their source.
+comment: The reason for obsoletion is because there is no support for the reaction. EC and RHEA mappings have been obsoleted at their source.
synonym: "5,8-linoleate diol synthase (bifunctional enzyme)" RELATED []
synonym: "7,8-linoleate diol synthase (bifunctional enzyme)" RELATED []
synonym: "linoleate diol synthase activity" RELATED []
@@ -191181,7 +191143,7 @@ is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
id: GO:0033760
name: 2'-deoxymugineic-acid 2'-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2'-deoxymugineate + 2-oxoglutarate + O(2) = CO(2) + H(+) + mugineate + succinate." [EC:1.14.11.24, RHEA:12200]
+def: "Catalysis of the reaction: 2'-deoxymugineate + 2-oxoglutarate + O2 = CO2 + H+ + mugineate + succinate." [EC:1.14.11.24, RHEA:12200]
synonym: "2'-deoxymugineic acid,2-oxoglutarate:oxygen oxidoreductase (2-hydroxylating) activity" RELATED [EC:1.14.11.24]
synonym: "IDS3" RELATED [EC:1.14.11.24]
xref: EC:1.14.11.24
@@ -191228,6 +191190,7 @@ id: GO:0033764
name: steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
namespace: molecular_function
def: "Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP, and in which one substrate is a sterol derivative." [GOC:mah]
+xref: Reactome:R-HSA-9758682 "AKR1C1 hydrogenates PREDN,PREDL"
is_a: GO:0016229 ! steroid dehydrogenase activity
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -191243,7 +191206,7 @@ is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
id: GO:0033766
name: 2-hydroxyquinoline 8-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADH + O(2) + quinolin-2-ol = H(2)O + NAD(+) + quinoline-2,8-diol." [EC:1.14.13.61, RHEA:22080]
+def: "Catalysis of the reaction: H+ + NADH + O2 + quinolin-2-ol = H2O + NAD+ + quinoline-2,8-diol." [EC:1.14.13.61, RHEA:22080]
synonym: "2-oxo-1,2-dihydroquinoline 8-monooxygenase activity" RELATED [EC:1.14.13.61]
synonym: "quinolin-2(1H)-one,NADH:oxygen oxidoreductase (8-oxygenating) activity" RELATED [EC:1.14.13.61]
xref: EC:1.14.13.61
@@ -191256,7 +191219,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0033767
name: 4-hydroxyacetophenone monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4'-hydroxyacetophenone + H(+) + NADPH + O(2) = 4-hydroxyphenyl acetate + H(2)O + NADP(+)." [EC:1.14.13.84, RHEA:22916]
+def: "Catalysis of the reaction: 4'-hydroxyacetophenone + H+ + NADPH + O2 = 4-hydroxyphenyl acetate + H2O + NADP+." [EC:1.14.13.84, RHEA:22916]
synonym: "(4-hydroxyphenyl)ethan-1-one,NADPH:oxygen oxidoreductase (ester-forming) activity" EXACT systematic_synonym [EC:1.14.13.84]
synonym: "HAPMO" RELATED [EC:1.14.13.84]
xref: EC:1.14.13.84
@@ -191277,30 +191240,31 @@ is_a: GO:0000152 ! nuclear ubiquitin ligase complex
id: GO:0033769
name: glyceollin synthase activity
namespace: molecular_function
-def: "Catalysis of the reactions: 2-dimethylallyl-(6aS,11aS)-3,6a,9-trihydroxypterocarpan + NADPH + H+ + O2 = glyceollin + NADP+ + 2 H2O, and 4-dimethylallyl-(6aS,11aS)-3,6a,9-trihydroxypterocarpan + NADPH + H+ + O2 = glyceollin + NADP+ + 2 H2O." [EC:1.14.13.85]
-synonym: "2-(or 4-)dimethylallyl-(6aS,11aS)-3,6a,9-trihydroxypterocarpan,NADPH:oxygen oxidoreductase (cyclizing) activity" RELATED [EC:1.14.13.85]
-synonym: "dimethylallyl-3,6a,9-trihydroxypterocarpan cyclase activity" RELATED [EC:1.14.13.85]
-xref: EC:1.14.13.85
+def: "Catalysis of the reactions: 2-dimethylallyl-(6aS,11aS)-3,6a,9-trihydroxypterocarpan + NADPH + H+ + O2 = glyceollin II or glyceollin III + NADP+ + 2 H2O, and 4-dimethylallyl-(6aS,11aS)-3,6a,9-trihydroxypterocarpan + NADPH + H+ + O2 = glyceollin I + NADP+ + 2 H2O." [EC:1.14.14.135]
+synonym: "dimethylallyl-3,6a,9-trihydroxypterocarpan cyclase activity" EXACT [EC:1.14.14.135]
+xref: EC:1.14.14.135
xref: MetaCyc:2.5.1.36-RXN
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0033770
name: 2-hydroxyisoflavanone synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: apigenin + 2 NADPH + 2 H+ + O2 = 2-hydroxy-2,3-dihydrogenistein + 2 NADP+ + H2O." [EC:1.14.13.86]
-synonym: "2-HIS" RELATED [EC:1.14.13.86]
-synonym: "apigenin,NADPH:oxygen oxidoreductase (isoflavanone-forming) activity" RELATED [EC:1.14.13.86]
-xref: EC:1.14.13.86
+alt_id: GO:0102604
+alt_id: GO:0102668
+def: "Catalysis of the reactions: liquiritigenin + O2 + [reduced NADPH--hemoprotein reductase] = 2,4',7-trihydroxyisoflavanone + H2O + [oxidized NADPH--hemoprotein reductase] and (2S)-naringenin + O2 + [reduced NADPH--hemoprotein reductase] = 2,4',5,7-tetrahydroxyisoflavanone + H2O + [oxidized NADPH--hemoprotein reductase]." [EC:1.14.14.87]
+synonym: "isoflavonoid synthase" BROAD [EC:1.14.14.87]
+xref: EC:1.14.14.87
+xref: MetaCyc:RXN-1541
+xref: MetaCyc:RXN-3283
xref: MetaCyc:RXN-7750
-xref: RHEA:14897
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0033771
name: licodione synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + liquiritigenin + NADPH + O(2) = H(2)O + licodione + NADP(+)." [EC:1.14.14.140, RHEA:15697]
+def: "Catalysis of the reaction: H+ + liquiritigenin + NADPH + O2 = H2O + licodione + NADP+." [EC:1.14.14.140, RHEA:15697]
synonym: "(2S)-flavanone 2-hydroxylase activity" RELATED [EC:1.14.14.140]
synonym: "liquiritigenin,NADPH:oxygen oxidoreductase (licodione-forming) activity" RELATED [EC:1.14.14.140]
xref: EC:1.14.14.140
@@ -191349,7 +191313,7 @@ relationship: part_of GO:0045178 ! basal part of cell
id: GO:0033775
name: deoxysarpagine hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 10-deoxysarpagine + H(+) + NADPH + O(2) = H(2)O + NADP(+) + sarpagine." [EC:1.14.14.136, RHEA:14237]
+def: "Catalysis of the reaction: 10-deoxysarpagine + H+ + NADPH + O2 = H2O + NADP+ + sarpagine." [EC:1.14.14.136, RHEA:14237]
synonym: "10-deoxysarpagine,NADPH:oxygen oxidoreductase (10-hydroxylating) activity" RELATED [EC:1.14.14.136]
synonym: "DOSH" RELATED [EC:1.14.14.136]
xref: EC:1.14.14.136
@@ -191362,7 +191326,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0033776
name: phenylacetone monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADPH + O(2) + phenylacetone = benzyl acetate + H(2)O + NADP(+)." [EC:1.14.13.92, RHEA:10124]
+def: "Catalysis of the reaction: H+ + NADPH + O2 + phenylacetone = benzyl acetate + H2O + NADP+." [EC:1.14.13.92, RHEA:10124]
synonym: "PAMO" RELATED [EC:1.14.13.92]
synonym: "phenylacetone,NADPH:oxygen oxidoreductase activity" RELATED [EC:1.14.13.92]
xref: EC:1.14.13.92
@@ -191375,7 +191339,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0033777
name: lithocholate 6beta-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + lithocholate + NADPH + O(2) = 6-beta-hydroxylithocholate + H(2)O + NADP(+)." [EC:1.14.14.138, RHEA:18857]
+def: "Catalysis of the reaction: H+ + lithocholate + NADPH + O2 = 6-beta-hydroxylithocholate + H2O + NADP+." [EC:1.14.14.138, RHEA:18857]
synonym: "6beta-hydroxylase activity" BROAD [EC:1.14.14.138]
synonym: "CYP3A10" RELATED [EC:1.14.14.138]
synonym: "cytochrome P450 3A10/lithocholic acid 6beta-hydroxylase activity" RELATED [EC:1.14.14.138]
@@ -191391,47 +191355,38 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0033778
name: 7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7alpha-hydroxycholest-4-en-3-one + H(+) + NADPH + O(2) = 7alpha,12alpha-dihydroxycholest-4-en-3-one + H(2)O + NADP(+)." [PMID:10051404, PMID:1400444, RHEA:46752]
-synonym: "7alpha-hydroxy-4-cholesten-3-one 12alpha-monooxygenase activity" RELATED [EC:1.14.13.95]
-synonym: "7alpha-hydroxycholest-4-en-3-one,NADPH:oxygen oxidoreductase (12alpha-hydroxylating) activity" RELATED [EC:1.14.13.95]
-synonym: "CYP12" RELATED [EC:1.14.13.95]
-synonym: "HCO 12alpha-hydroxylase activity" RELATED [EC:1.14.13.95]
-synonym: "sterol 12alpha-hydroxylase activity" BROAD [EC:1.14.13.95]
-xref: EC:1.14.14.139
+def: "Catalysis of the reaction: 7alpha-hydroxycholest-4-en-3-one + H+ + NADPH + O2 = 7alpha,12alpha-dihydroxycholest-4-en-3-one + H2O + NADP+." [PMID:10051404, PMID:1400444, RHEA:46752]
+synonym: "7alpha-hydroxy-4-cholesten-3-one 12alpha-monooxygenase activity" RELATED [EC:1.14.14.139]
xref: KEGG_REACTION:R04826
xref: MetaCyc:1.14.13.95-RXN
xref: Reactome:R-HSA-192157 "CYP8B1 12-hydroxylates 4CHOL7aOLONE"
xref: Reactome:R-HSA-193709 "CYP8B1 12-hydroxylates 4CHOL7a,24(S)DIOL"
xref: Reactome:R-HSA-193845 "CYP8B1 12-hydroxylates 4CHOL7a,27DONE"
-xref: RHEA:10504
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+xref: RHEA:46752
+is_a: GO:0008397 ! sterol 12-alpha-hydroxylase activity
[Term]
id: GO:0033779
name: 5beta-cholestane-3alpha,7alpha-diol 12alpha-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5beta-cholestane-3alpha,7alpha-diol + H(+) + NADPH + O(2) = 5beta-cholestane-3alpha,7alpha,12alpha-triol + H(2)O + NADP(+)." [EC:1.14.14.139, RHEA:15261]
+def: "Catalysis of the reaction: 5beta-cholestane-3alpha,7alpha-diol + H+ + NADPH + O2 = 5beta-cholestane-3alpha,7alpha,12alpha-triol + H2O + NADP+." [RHEA:15261]
synonym: "5beta-cholestane-3alpha,7alpha-diol 12alpha-monooxygenase activity" RELATED [EC:1.14.14.139]
synonym: "5beta-cholestane-3alpha,7alpha-diol,NADPH:oxygen oxidoreductase (12alpha-hydroxylating) activity" RELATED [EC:1.14.14.139]
-synonym: "CYP8B1" RELATED [EC:1.14.14.139]
-synonym: "cytochrome P450 8B1" RELATED [EC:1.14.14.139]
-synonym: "sterol 12alpha-hydroxylase activity" BROAD [EC:1.14.14.139]
-xref: EC:1.14.14.139
xref: KEGG_REACTION:R07204
xref: MetaCyc:1.14.13.96-RXN
xref: RHEA:15261
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+is_a: GO:0008397 ! sterol 12-alpha-hydroxylase activity
[Term]
id: GO:0033780
name: taurochenodeoxycholate 6alpha-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reactions: taurochenodeoxycholate + NADPH + H+ + O2 = taurohyocholate + NADP+ + H2O, and lithocholate + NADPH + H+ + O2 = hyodeoxycholate + NADP+ + H2O." [EC:1.14.13.97]
-synonym: "CYP3A4" RELATED [EC:1.14.13.97]
+def: "Catalysis of the reactions: taurochenodeoxycholate + NADPH + H+ + O2 = taurohyocholate + NADP+ + H2O, and lithocholate + NADPH + H+ + O2 = hyodeoxycholate + NADP+ + H2O." [RHEA:23644]
+synonym: "CYP3A4" RELATED [EC:1.14.14.57]
synonym: "CYP4A21" RELATED [EC:1.14.13.97]
-synonym: "taurochenodeoxycholate 6alpha-monooxygenase activity" RELATED [EC:1.14.13.97]
-synonym: "taurochenodeoxycholate,NADPH:oxygen oxidoreductase (6alpha-hydroxylating) activity" RELATED [EC:1.14.13.97]
-xref: EC:1.14.13.97
+synonym: "taurochenodeoxycholate 6alpha-monooxygenase activity" RELATED [EC:1.14.14.57]
+synonym: "taurochenodeoxycholate,NADPH:oxygen oxidoreductase (6alpha-hydroxylating) activity" RELATED []
+xref: EC:1.14.14.57
xref: MetaCyc:RXN-7977
xref: RHEA:23644
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
@@ -191440,7 +191395,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0033781
name: cholesterol 24-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cholesterol + H(+) + NADPH + O(2) = (24S)-24-hydroxycholesterol + H(2)O + NADP(+)." [EC:1.14.14.25, RHEA:22716]
+def: "Catalysis of the reaction: cholesterol + H+ + NADPH + O2 = (24S)-24-hydroxycholesterol + H2O + NADP+." [EC:1.14.14.25, RHEA:22716]
synonym: "cholesterol 24-monooxygenase activity" RELATED [EC:1.14.14.25]
synonym: "cholesterol 24S-hydroxylase activity" RELATED [EC:1.14.14.25]
synonym: "cholesterol,NADPH:oxygen oxidoreductase (24-hydroxylating) activity" RELATED [EC:1.14.14.25]
@@ -191487,7 +191442,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0033784
name: senecionine N-oxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADPH + O(2) + senecionine = H(2)O + NADP(+) + senecionine N-oxide." [EC:1.14.13.101, RHEA:11420]
+def: "Catalysis of the reaction: H+ + NADPH + O2 + senecionine = H2O + NADP+ + senecionine N-oxide." [EC:1.14.13.101, RHEA:11420]
synonym: "senecionine monooxygenase (N-oxide-forming) activity" RELATED [EC:1.14.13.101]
synonym: "senecionine,NADPH:oxygen oxidoreductase (N-oxide-forming) activity" RELATED [EC:1.14.13.101]
synonym: "SNO" RELATED [EC:1.14.13.101]
@@ -191523,7 +191478,7 @@ is_a: GO:0070566 ! adenylyltransferase activity
id: GO:0033787
name: cyanocobalamin reductase (cyanide-eliminating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: cob(I)alamin + hydrogen cyanide + NADP(+) = cyanocob(III)alamin + H(+) + NADPH." [RHEA:16113]
+def: "Catalysis of the reaction: cob(I)alamin + hydrogen cyanide + NADP+ = cyanocob(III)alamin + H+ + NADPH." [RHEA:16113]
comment: Formerly EC:1.6.99.12.
synonym: "cob(I)alamin, cyanide:NADP+ oxidoreductase activity" RELATED [EC:1.16.1.6]
synonym: "cyanocobalamin reductase (NADPH, cyanide-eliminating) activity" RELATED [EC:1.16.1.6]
@@ -191554,7 +191509,7 @@ is_a: GO:0016726 ! oxidoreductase activity, acting on CH or CH2 groups, NAD or N
id: GO:0033789
name: phenylacetyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 1,4-benzoquinone + H(2)O + phenylacetyl-CoA = 2 hydroquinone + phenylglyoxylyl-CoA." [RHEA:15705]
+def: "Catalysis of the reaction: 2 1,4-benzoquinone + H2O + phenylacetyl-CoA = 2 hydroquinone + phenylglyoxylyl-CoA." [RHEA:15705]
synonym: "phenylacetyl-CoA:acceptor oxidoreductase activity" RELATED [EC:1.17.5.1]
synonym: "phenylacetyl-CoA:quinone oxidoreductase activity" RELATED [EC:1.17.5.1]
xref: EC:1.17.5.1
@@ -191588,18 +191543,17 @@ is_a: GO:0016725 ! oxidoreductase activity, acting on CH or CH2 groups
[Term]
id: GO:0033792
-name: bile-acid 7alpha-dehydroxylase activity
-namespace: molecular_function
-def: "Catalysis of the reactions: deoxycholate + FAD + H2O = cholate + FADH2, and lithocholate + FAD + H2O = chenodeoxycholate + FADH2." [EC:1.17.99.5]
-synonym: "7alpha-dehydroxylase activity" RELATED [EC:1.17.99.5]
-synonym: "bile acid 7-dehydroxylase activity" RELATED [EC:1.17.99.5]
-synonym: "cholate 7alpha-dehydroxylase activity" RELATED [EC:1.17.99.5]
-synonym: "deoxycholate:FAD oxidoreductase (7alpha-dehydroxylating) activity" RELATED [EC:1.17.99.5]
-synonym: "deoxycholate:NAD+ oxidoreductase activity" RELATED [EC:1.17.99.5]
-xref: EC:1.17.99.5
-xref: MetaCyc:RXN-8658
-xref: MetaCyc:RXN-8659
-is_a: GO:0016725 ! oxidoreductase activity, acting on CH or CH2 groups
+name: 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase activity
+namespace: molecular_function
+def: "Catalysis of the reactions: a 3alpha-hydroxy bile acid CoA + NAD+ = a 3-oxo bile acid CoA + H+ + NADH." [PMID:23836456, RHEA:55380]
+comment: Formerly EC:1.17.99.5. Was originally descibed as bile acid 7-dehydroxylase (PubMed:3549693). In fact, the 7-dehydroxylation process is catalyzed by multiple enzymes.
+synonym: "7alpha-dehydroxylase activity" RELATED []
+synonym: "bile acid 7-dehydroxylase activity" RELATED []
+synonym: "bile-acid 7alpha-dehydroxylase activity" RELATED []
+synonym: "cholate 7alpha-dehydroxylase activity" RELATED []
+xref: EC:1.1.1.395
+xref: RHEA:55380
+is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0033793
@@ -191646,7 +191600,7 @@ is_a: GO:0016491 ! oxidoreductase activity
id: GO:0033797
name: selenate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 e(-) + 2 H(+) + selenate = H(2)O + selenite." [EC:1.97.1.9, RHEA:14029]
+def: "Catalysis of the reaction: 2 e(-) + 2 H+ + selenate = H2O + selenite." [EC:1.97.1.9, RHEA:14029]
synonym: "selenite:reduced acceptor oxidoreductase activity" RELATED [EC:1.97.1.9]
xref: EC:1.97.1.9
xref: KEGG_REACTION:R07229
@@ -191682,7 +191636,7 @@ synonym: "CrCOMT2" RELATED []
synonym: "flavonoid 3',5'-O-dimethyltransferase activity" RELATED []
synonym: "myricetin 3-O-methyltransferase activity" RELATED []
synonym: "S-adenosyl-L-methionine:myricetin O-methyltransferase activity" RELATED []
-xref: EC:2.1.1.267;
+xref: EC:2.1.1.267
xref: KEGG_REACTION:R06815
xref: MetaCyc:RXN-13912
xref: MetaCyc:RXN-8451
@@ -191718,7 +191672,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0033802
name: isoliquiritigenin 2'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + isoliquiritigenin = 2'-O-methylisoliquiritigenin + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.154, RHEA:21608]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + isoliquiritigenin = 2'-O-methylisoliquiritigenin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.154, RHEA:21608]
synonym: "chalcone OMT" RELATED [EC:2.1.1.154]
synonym: "CHMT" RELATED [EC:2.1.1.154]
synonym: "S-adenosyl-L-methionine:isoliquiritigenin 2'-O-methyltransferase activity" RELATED [EC:2.1.1.154]
@@ -191733,7 +191687,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0033803
name: kaempferol 4'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + kaempferol = S-adenosyl-L-homocysteine + H(+) + kaempferide." [EC:2.1.1.155, RHEA:15105]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + kaempferol = S-adenosyl-L-homocysteine + H+ + kaempferide." [EC:2.1.1.155, RHEA:15105]
synonym: "F 4'-OMT" RELATED [EC:2.1.1.155]
synonym: "S-adenosyl-L-methionine:flavonoid 4'-O-methyltransferase activity" RELATED [EC:2.1.1.155]
synonym: "S-adenosyl-L-methionine:kaempferol 4'-O-methyltransferase activity" RELATED [EC:2.1.1.155]
@@ -191913,7 +191867,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0033816
name: diaminobutyrate acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-2,4-diaminobutyrate + acetyl-CoA = N(4)-acetyl-L-2,4-diaminobutyrate + CoA + H(+)." [EC:2.3.1.178, RHEA:16901]
+def: "Catalysis of the reaction: L-2,4-diaminobutyrate + acetyl-CoA = N(4)-acetyl-L-2,4-diaminobutyrate + CoA + H+." [EC:2.3.1.178, RHEA:16901]
synonym: "2,4-diaminobutanoate acetyltransferase activity" RELATED [EC:2.3.1.178]
synonym: "acetyl-CoA:L-2,4-diaminobutanoate 4-N-acetyltransferase activity" RELATED [EC:2.3.1.178]
synonym: "acetyl-CoA:L-2,4-diaminobutanoate N4-acetyltransferase activity" RELATED [EC:2.3.1.178]
@@ -191953,18 +191907,21 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0033819
name: lipoyl(octanoyl) transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: octanoyl-[acyl-carrier protein] + protein = protein N6-(octanoyl)lysine + acyl-carrier protein." [EC:2.3.1.181]
-synonym: "LipB" RELATED [EC:2.3.1.181]
-synonym: "lipoate/octanoate transferase activity" RELATED [EC:2.3.1.181]
-synonym: "lipoyl (octanoyl)-acyl carrier protein:protein transferase activity" RELATED [EC:2.3.1.181]
-synonym: "lipoyl (octanoyl)-acyl-carrier-protein-protein N-lipoyltransferase activity" RELATED [EC:2.3.1.181]
-synonym: "octanoyl-acyl carrier protein-protein N-octanoyltransferase activity" RELATED [EC:2.3.1.181]
-synonym: "octanoyl-acyl-carrier-protein-protein N-octanoyltransferase activity" RELATED [EC:2.3.1.181]
-synonym: "octanoyl-acyl-carrier-protein:protein N-octanoyltransferase activity" RELATED [EC:2.3.1.181]
+alt_id: GO:0102555
+def: "Catalysis of the reaction: L-lysyl-[protein] + octanoyl-[ACP] = H+ + holo-[ACP] + N6-octanoyl-L-lysyl-[protein]." [RHEA:17665]
+synonym: "lipoate/octanoate transferase activity" EXACT [EC:2.3.1.181]
+synonym: "lipoyl (octanoyl)-acyl carrier protein:protein transferase activity" EXACT [EC:2.3.1.181]
+synonym: "lipoyl (octanoyl)-acyl-carrier-protein-protein N-lipoyltransferase activity" EXACT [EC:2.3.1.181]
+synonym: "octanoyl transferase activity (acting on glycine-cleavage complex H protein)" NARROW []
+synonym: "octanoyl-acyl carrier protein-protein N-octanoyltransferase activity" EXACT [EC:2.3.1.181]
+synonym: "octanoyl-acyl-carrier-protein-protein N-octanoyltransferase activity" EXACT [EC:2.3.1.181]
+synonym: "octanoyl-acyl-carrier-protein:protein N-octanoyltransferase activity" EXACT [EC:2.3.1.181]
xref: EC:2.3.1.181
+xref: MetaCyc:RXN-14966
xref: MetaCyc:RXN0-947
xref: Reactome:R-HSA-6793590 "LIPT2 transfers octanoyl group to GCSH"
-is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+xref: RHEA:17665
+is_a: GO:0016415 ! octanoyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
[Term]
@@ -192090,7 +192047,7 @@ is_a: GO:0008375 ! acetylglucosaminyltransferase activity
id: GO:0033828
name: glucosylglycerol-phosphate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: sn-glycerol 3-phosphate + ADP-glucose = 2-O-(beta-D-glucosyl)-sn-glycerol 3-phosphate + ADP + H(+)." [EC:2.4.1.213, RHEA:12881]
+def: "Catalysis of the reaction: sn-glycerol 3-phosphate + ADP-glucose = 2-O-(beta-D-glucosyl)-sn-glycerol 3-phosphate + ADP + H+." [EC:2.4.1.213, RHEA:12881]
synonym: "ADP-glucose:sn-glycerol-3-phosphate 2-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.213]
synonym: "ADPglucose:sn-glycerol-3-phosphate 2-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.213]
synonym: "GG-phosphate synthase activity" RELATED [EC:2.4.1.213]
@@ -192349,7 +192306,7 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0033848
name: N2-(2-carboxyethyl)arginine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glyceraldehyde 3-phosphate + L-arginine = N(2)-(2-carboxyethyl)-L-arginine + H(+) + phosphate." [EC:2.5.1.66, RHEA:10556]
+def: "Catalysis of the reaction: D-glyceraldehyde 3-phosphate + L-arginine = N(2)-(2-carboxyethyl)-L-arginine + H+ + phosphate." [EC:2.5.1.66, RHEA:10556]
synonym: "CEA synthetase activity" RELATED [EC:2.5.1.66]
synonym: "CEAS" RELATED [EC:2.5.1.66]
synonym: "glyceraldehyde-3-phosphate:L-arginine 2-N-(2-hydroxy-3-oxopropyl) transferase (2-carboxyethyl-forming) activity" RELATED [EC:2.5.1.66]
@@ -192467,7 +192424,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0033856
name: pyridoxine 5'-phosphate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = 2 H(2)O + H(+) + phosphate + pyridoxine 5'-phosphate." [RHEA:15265]
+def: "Catalysis of the reaction: 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = 2 H2O + H+ + phosphate + pyridoxine 5'-phosphate." [RHEA:15265]
synonym: "1-deoxy-D-xylulose-5-phosphate:3-amino-2-oxopropyl phosphate 3-amino-2-oxopropyltransferase (phosphate-hydrolysing; cyclizing) activity" RELATED [EC:2.6.99.2]
synonym: "PNP synthase activity" RELATED [EC:2.6.99.2]
synonym: "pyridoxine 5-phosphate phospho lyase activity" RELATED [EC:2.6.99.2]
@@ -192481,18 +192438,15 @@ is_a: GO:0016769 ! transferase activity, transferring nitrogenous groups
id: GO:0033857
name: diphosphoinositol-pentakisphosphate kinase activity
namespace: molecular_function
+alt_id: GO:0102092
def: "Catalysis of the reaction: ATP + 1D-myo-inositol 5-diphosphate pentakisphosphate = ADP + 1D-myo-inositol bisdiphosphate tetrakisphosphate." [EC:2.7.4.24]
-synonym: "ATP:5-diphospho-1D-myo-inositol-pentakisphosphate phosphotransferase activity" RELATED [EC:2.7.4.24]
+synonym: "5-diphosphoinositol pentakisphosphate 3-kinase activity" EXACT []
synonym: "PP-InsP5 kinase activity" RELATED [EC:2.7.4.24]
synonym: "PP-IP5 kinase activity" RELATED [EC:2.7.4.24]
-synonym: "PPIP5K" RELATED [EC:2.7.4.24]
-synonym: "PPIP5K1" RELATED [EC:2.7.4.24]
-synonym: "PPIP5K2" RELATED [EC:2.7.4.24]
-synonym: "VIP1" NARROW [EC:2.7.4.24]
-synonym: "VIP2" NARROW [EC:2.7.4.24]
+synonym: "PPIP5K" RELATED []
xref: EC:2.7.4.24
+xref: MetaCyc:RXN-10979
is_a: GO:0016301 ! kinase activity
-is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
[Term]
id: GO:0033858
@@ -192552,13 +192506,13 @@ synonym: "uridine monophosphate kinase activity" RELATED [EC:2.7.4.22]
xref: EC:2.7.4.22
xref: MetaCyc:2.7.4.22-RXN
xref: RHEA:24400
-is_a: GO:0009041 ! uridylate kinase activity
+is_a: GO:0009041 ! UMP/dUMP kinase activity
[Term]
id: GO:0033863
name: ribose 1,5-bisphosphate phosphokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-ribose 1,5-diphosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + ADP + H(+)." [EC:2.7.4.23, RHEA:20109]
+def: "Catalysis of the reaction: D-ribose 1,5-diphosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + ADP + H+." [EC:2.7.4.23, RHEA:20109]
synonym: "ATP:ribose-1,5-bisphosphate phosphotransferase activity" RELATED [EC:2.7.4.23]
synonym: "PhnN" RELATED [EC:2.7.4.23]
synonym: "ribose 1,5-bisphosphokinase activity" RELATED [EC:2.7.4.23]
@@ -192692,7 +192646,7 @@ is_a: GO:0034483 ! heparan sulfate sulfotransferase activity
id: GO:0033873
name: petromyzonol sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + 5alpha-cholane-3alpha,7alpha,12alpha,24-tetrol = 3alpha,7alpha,12alpha-trihydroxy-5alpha-cholan-24-yl sulfate + adenosine 3',5'-diphosphate + H(+)." [EC:2.8.2.31, RHEA:16997]
+def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + 5alpha-cholane-3alpha,7alpha,12alpha,24-tetrol = 3alpha,7alpha,12alpha-trihydroxy-5alpha-cholan-24-yl sulfate + adenosine 3',5'-diphosphate + H+." [EC:2.8.2.31, RHEA:16997]
synonym: "3'-phosphoadenylyl-sulfate:5alpha-cholan-3alpha,7alpha,12alpha,24-tetrol sulfotransferase activity" RELATED [EC:2.8.2.31]
synonym: "PZ-SULT" RELATED [EC:2.8.2.31]
xref: EC:2.8.2.31
@@ -192705,7 +192659,7 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0033874
name: scymnol sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + 5beta-scymnol = 5beta-scymnol sulfate + adenosine 3',5'-diphosphate + H(+)." [EC:2.8.2.32, RHEA:15477]
+def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + 5beta-scymnol = 5beta-scymnol sulfate + adenosine 3',5'-diphosphate + H+." [EC:2.8.2.32, RHEA:15477]
xref: EC:2.8.2.32
xref: KEGG_REACTION:R07798
xref: MetaCyc:2.8.2.32-RXN
@@ -192724,7 +192678,7 @@ is_a: GO:0033865 ! nucleoside bisphosphate metabolic process
id: GO:0033876
name: glycochenodeoxycholate sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + glycochenodeoxycholate = adenosine 3',5'-diphosphate + glycochenodeoxycholate 7-sulfate + H(+)." [EC:2.8.2.34, RHEA:17689]
+def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + glycochenodeoxycholate = adenosine 3',5'-diphosphate + glycochenodeoxycholate 7-sulfate + H+." [EC:2.8.2.34, RHEA:17689]
synonym: "3'-phosphoadenylyl-sulfate:glycochenodeoxycholate 7-sulfotransferase activity" RELATED [EC:2.8.2.34]
synonym: "BAST" RELATED [EC:2.8.2.34]
synonym: "bile acid:3'-phosphoadenosine-5'-phosphosulfate sulfotransferase activity" BROAD [EC:2.8.2.34]
@@ -192781,7 +192735,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0033880
name: phenylacetyl-CoA hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + phenylglyoxylyl-CoA = CoA + H(+) + phenylglyoxylate." [EC:3.1.2.25, RHEA:15337]
+def: "Catalysis of the reaction: H2O + phenylglyoxylyl-CoA = CoA + H+ + phenylglyoxylate." [EC:3.1.2.25, RHEA:15337]
synonym: "phenylglyoxylyl-CoA hydrolase activity" RELATED [EC:3.1.2.25]
xref: EC:3.1.2.25
xref: KEGG_REACTION:R07294
@@ -192791,16 +192745,16 @@ is_a: GO:0016289 ! CoA hydrolase activity
[Term]
id: GO:0033881
-name: bile-acid-CoA hydrolase activity
+name: bile-acid-CoA transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: deoxycholoyl-CoA + H(2)O = CoA + deoxycholate + H(+)." [EC:3.1.2.26, RHEA:17693]
-synonym: "bile acid-coenzyme A hydrolase activity" RELATED [EC:3.1.2.26]
-synonym: "deoxycholoyl-CoA hydrolase activity" RELATED [EC:3.1.2.26]
-xref: EC:3.1.2.26
+def: "Catalysis of the reaction: deoxycholoyl-CoA + cholate = deoxycholate + choloyl-CoA." [PMID:22021638, RHEA:49436]
+comment: Formerly EC:3.1.2.26 and RHEA:17693.
+synonym: "bile-acid-CoA hydrolase activity" RELATED []
+synonym: "deoxycholoyl-CoA transferase activity" RELATED []
+xref: EC:2.8.3.25
xref: KEGG_REACTION:R07295
-xref: MetaCyc:BACOAHYDRO-RXN
-xref: RHEA:17693
-is_a: GO:0016289 ! CoA hydrolase activity
+xref: RHEA:49436
+is_a: GO:0008410 ! CoA-transferase activity
[Term]
id: GO:0033882
@@ -192849,7 +192803,7 @@ consider: GO:0052732
id: GO:0033885
name: 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoate + H(2)O = (9S,10S)-9,10-dihydroxyoctadecanoate + phosphate." [EC:3.1.3.76, RHEA:16537]
+def: "Catalysis of the reaction: (9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoate + H2O = (9S,10S)-9,10-dihydroxyoctadecanoate + phosphate." [EC:3.1.3.76, RHEA:16537]
synonym: "(9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity" RELATED [EC:3.1.3.76]
synonym: "(9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoate phosphohydrolase activity" EXACT systematic_synonym [EC:3.1.3.76]
synonym: "dihydroxy fatty acid phosphatase activity" BROAD [EC:3.1.3.76]
@@ -192878,7 +192832,7 @@ is_a: GO:0008484 ! sulfuric ester hydrolase activity
id: GO:0033887
name: chondro-4-sulfatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-deoxy-beta-D-gluc-4-enuronosyl-(1->3)-N-acetyl-D-galactosamine 4-sulfate + H(2)O = 4-deoxy-beta-D-gluc-4-enuronosyl-(1->3)-N-acetyl-D-galactosamine + H(+) + sulfate." [EC:3.1.6.9, RHEA:11444]
+def: "Catalysis of the reaction: 4-deoxy-beta-D-gluc-4-enuronosyl-(1->3)-N-acetyl-D-galactosamine 4-sulfate + H2O = 4-deoxy-beta-D-gluc-4-enuronosyl-(1->3)-N-acetyl-D-galactosamine + H+ + sulfate." [EC:3.1.6.9, RHEA:11444]
synonym: "4-deoxy-beta-D-gluc-4-enuronosyl-(1,3)-N-acetyl-D-galactosamine-4-sulfate 4-sulfohydrolase activity" RELATED [EC:3.1.6.9]
xref: EC:3.1.6.9
xref: KEGG_REACTION:R03517
@@ -192890,7 +192844,7 @@ is_a: GO:0008484 ! sulfuric ester hydrolase activity
id: GO:0033888
name: chondro-6-sulfatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-deoxy-beta-D-gluc-4-enuronosyl-(1->3)-N-acetyl-D-galactosamine 6-sulfate + H(2)O = 4-deoxy-beta-D-gluc-4-enuronosyl-(1->3)-N-acetyl-D-galactosamine + H(+) + sulfate." [EC:3.1.6.10, RHEA:10536]
+def: "Catalysis of the reaction: 4-deoxy-beta-D-gluc-4-enuronosyl-(1->3)-N-acetyl-D-galactosamine 6-sulfate + H2O = 4-deoxy-beta-D-gluc-4-enuronosyl-(1->3)-N-acetyl-D-galactosamine + H+ + sulfate." [EC:3.1.6.10, RHEA:10536]
synonym: "4-deoxy-beta-D-gluc-4-enuronosyl-(1,3)-N-acetyl-D-galactosamine-6-sulfate 6-sulfohydrolase activity" RELATED [EC:3.1.6.10]
xref: EC:3.1.6.10
xref: KEGG_REACTION:R03518
@@ -192917,7 +192871,7 @@ def: "Catalysis of the exonucleolytic cleavage that removes extra residues from
synonym: "RNase D activity" RELATED [EC:3.1.13.5]
xref: EC:3.1.13.5
xref: MetaCyc:3.1.13.5-RXN
-is_a: GO:0016896 ! exoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016896 ! RNA exonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0033891
@@ -192952,7 +192906,7 @@ def: "Catalysis of the endonucleolytic cleavage of poly(A) to fragments terminat
synonym: "endoribonuclease IV activity" RELATED [EC:3.1.26.6]
xref: EC:3.1.26.6
xref: MetaCyc:3.1.26.6-RXN
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0033894
@@ -192961,7 +192915,7 @@ namespace: molecular_function
def: "Catalysis of the endonucleolytic cleavage of RNA, removing 3'-extranucleotides from tRNA precursor." [EC:3.1.26.7]
xref: EC:3.1.26.7
xref: MetaCyc:3.1.26.7-RXN
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0033895
@@ -192972,7 +192926,7 @@ synonym: "ribonuclease (uracil-specific) activity" RELATED [EC:3.1.26.9]
synonym: "uracil-specific endoribonuclease activity" RELATED [EC:3.1.26.9]
synonym: "uracil-specific RNase activity" RELATED [EC:3.1.26.9]
xref: EC:3.1.26.9
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0033896
@@ -192982,7 +192936,7 @@ def: "Catalysis of the endonucleolytic cleavage of poly(U) or poly(C) to fragmen
synonym: "poly(U)- and poly(C)-specific endoribonuclease activity" RELATED [EC:3.1.26.10]
xref: EC:3.1.26.10
xref: MetaCyc:3.1.26.10-RXN
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0033897
@@ -193014,7 +192968,7 @@ synonym: "RNase Ms activity" EXACT []
synonym: "RNase T2 activity" RELATED [EC:4.6.1.19]
xref: EC:4.6.1.19
xref: MetaCyc:3.1.27.1-RXN
-is_a: GO:0004521 ! endoribonuclease activity
+is_a: GO:0004521 ! RNA endonuclease activity
is_a: GO:0016849 ! phosphorus-oxygen lyase activity
[Term]
@@ -193026,7 +192980,7 @@ synonym: "proteus mirabilis RNase activity" EXACT []
synonym: "ribonucleate nucleotido-2'-transferase (cyclizing) activity" BROAD []
xref: EC:4.6.1.22
xref: MetaCyc:3.1.27.2-RXN
-is_a: GO:0016892 ! endoribonuclease activity, producing 3'-phosphomonoesters
+is_a: GO:0016892 ! RNA endonuclease activity, producing 3'-phosphomonoesters
[Term]
id: GO:0033899
@@ -193042,7 +192996,7 @@ synonym: "RNase U2 activity" RELATED [EC:4.6.1.20]
synonym: "trichoderma koningi RNase III activity" EXACT []
xref: EC:4.6.1.20
xref: MetaCyc:3.1.27.4-RXN
-is_a: GO:0016892 ! endoribonuclease activity, producing 3'-phosphomonoesters
+is_a: GO:0016892 ! RNA endonuclease activity, producing 3'-phosphomonoesters
[Term]
id: GO:0033900
@@ -193053,7 +193007,7 @@ synonym: "ribonuclease F (E. coli) activity" RELATED [EC:3.1.27.7]
synonym: "RNase F activity" RELATED [EC:3.1.27.7]
xref: EC:3.1.27.7
xref: MetaCyc:3.1.27.7-RXN
-is_a: GO:0016892 ! endoribonuclease activity, producing 3'-phosphomonoesters
+is_a: GO:0016892 ! RNA endonuclease activity, producing 3'-phosphomonoesters
[Term]
id: GO:0033901
@@ -193063,7 +193017,7 @@ def: "Catalysis of the hydrolysis of poly(A), forming oligoribonucleotides and u
synonym: "endoribonuclease V activity" RELATED [EC:3.1.27.8]
xref: EC:3.1.27.8
xref: MetaCyc:3.1.27.8-RXN
-is_a: GO:0016892 ! endoribonuclease activity, producing 3'-phosphomonoesters
+is_a: GO:0016892 ! RNA endonuclease activity, producing 3'-phosphomonoesters
[Term]
id: GO:0033902
@@ -193073,7 +193027,7 @@ def: "Catalysis of the hydrolysis of the phosphodiester linkage between guanosin
synonym: "alpha-sarcin" RELATED []
xref: EC:4.6.1.23
xref: MetaCyc:3.1.27.10-RXN
-is_a: GO:0004540 ! ribonuclease activity
+is_a: GO:0004540 ! RNA nuclease activity
[Term]
id: GO:0033903
@@ -193311,7 +193265,7 @@ is_a: GO:0090600 ! alpha-1,3-glucosidase activity
id: GO:0033920
name: 6-phospho-beta-galactosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 6-phospho-beta-D-galactoside + H2O = 6-phospho-D-galactose + an alcohol." [EC:3.2.1.85]
+def: "Catalysis of the reaction: a 6-phospho-beta-D-galactoside + H2O = 6-phospho-D-galactose + an alcohol." [RHEA:24568]
synonym: "6-phospho-beta-D-galactosidase activity" RELATED [EC:3.2.1.85]
synonym: "6-phospho-beta-D-galactoside 6-phosphogalactohydrolase activity" RELATED [EC:3.2.1.85]
synonym: "beta-D-phosphogalactoside galactohydrolase activity" RELATED [EC:3.2.1.85]
@@ -193615,7 +193569,7 @@ synonym: "galactan (1,3)-beta-D-galactosidase activity" RELATED [EC:3.2.1.145]
synonym: "galactan (1->3)-beta-D-galactosidase activity" RELATED [EC:3.2.1.145]
xref: EC:3.2.1.145
xref: MetaCyc:3.2.1.145-RXN
-is_a: GO:0015925 ! galactosidase activity
+is_a: GO:0004565 ! beta-galactosidase activity
[Term]
id: GO:0033944
@@ -193826,7 +193780,7 @@ is_a: GO:0140097 ! catalytic activity, acting on DNA
id: GO:0033960
name: N-methyl nucleosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7-methylxanthosine + H(2)O = 7-methylxanthine + H(+) + ribofuranose." [EC:3.2.2.25, RHEA:10880]
+def: "Catalysis of the reaction: 7-methylxanthosine + H2O = 7-methylxanthine + H+ + ribofuranose." [EC:3.2.2.25, RHEA:10880]
synonym: "7-methylxanthosine nucleosidase activity" RELATED [EC:3.2.2.25]
synonym: "7-methylxanthosine ribohydrolase activity" RELATED [EC:3.2.2.25]
synonym: "methylpurine nucleosidase activity" RELATED [EC:3.2.2.25]
@@ -193950,7 +193904,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0033969
name: gamma-glutamyl-gamma-aminobutyrate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-(L-gamma-glutamylamino)butanoate + H(2)O = 4-aminobutanoate + L-glutamate." [EC:3.5.1.94, RHEA:19737]
+def: "Catalysis of the reaction: 4-(L-gamma-glutamylamino)butanoate + H2O = 4-aminobutanoate + L-glutamate." [EC:3.5.1.94, RHEA:19737]
synonym: "4-(glutamylamino)butanoate amidohydrolase activity" RELATED [EC:3.5.1.94]
synonym: "gamma-glutamyl-GABA hydrolase activity" RELATED [EC:3.5.1.94]
synonym: "PuuD" RELATED [EC:3.5.1.94]
@@ -193965,7 +193919,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0033970
name: N-malonylurea hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-oxo-3-ureidopropanoate + H(2)O = H(+) + malonate + urea." [EC:3.5.1.95, RHEA:17361]
+def: "Catalysis of the reaction: 3-oxo-3-ureidopropanoate + H2O = H+ + malonate + urea." [EC:3.5.1.95, RHEA:17361]
synonym: "3-oxo-3-ureidopropanoate amidohydrolase (urea- and malonate-forming) activity" RELATED [EC:3.5.1.95]
synonym: "ureidomalonase activity" RELATED [EC:3.5.1.95]
xref: EC:3.5.1.95
@@ -193978,7 +193932,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0033971
name: hydroxyisourate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate + H(+)." [EC:3.5.2.17, RHEA:23736]
+def: "Catalysis of the reaction: 5-hydroxyisourate + H2O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate + H+." [EC:3.5.2.17, RHEA:23736]
synonym: "5-hydroxyisourate amidohydrolase activity" RELATED [EC:3.5.2.17]
synonym: "5-hydroxyisourate hydrolase activity" RELATED [EC:3.5.2.17]
synonym: "HIUHase activity" RELATED [EC:3.5.2.17]
@@ -193992,7 +193946,7 @@ is_a: GO:0016812 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0033972
name: proclavaminate amidinohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: amidinoproclavaminate + H(2)O = proclavaminate + urea." [EC:3.5.3.22, RHEA:17001]
+def: "Catalysis of the reaction: amidinoproclavaminate + H2O = proclavaminate + urea." [EC:3.5.3.22, RHEA:17001]
synonym: "PAH" RELATED [EC:3.5.3.22]
synonym: "proclavaminate amidino hydrolase activity" RELATED [EC:3.5.3.22]
synonym: "proclavaminic acid amidino hydrolase activity" RELATED [EC:3.5.3.22]
@@ -194006,7 +193960,7 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0033973
name: dCTP deaminase (dUMP-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: dCTP + 2 H(2)O = diphosphate + dUMP + H(+) + NH(4)(+)." [EC:3.5.4.30, RHEA:19205]
+def: "Catalysis of the reaction: dCTP + 2 H2O = diphosphate + dUMP + H+ + NH4." [EC:3.5.4.30, RHEA:19205]
synonym: "dCTP aminohydrolase (dUMP-forming) activity" RELATED [EC:3.5.4.30]
xref: EC:3.5.4.30
xref: KEGG_REACTION:R07307
@@ -194071,7 +194025,7 @@ is_a: GO:0019120 ! hydrolase activity, acting on acid halide bonds, in C-halide
id: GO:0033978
name: phosphonopyruvate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-phosphonopyruvate + H(2)O = phosphate + pyruvate." [EC:3.11.1.3, RHEA:16673]
+def: "Catalysis of the reaction: 3-phosphonopyruvate + H2O = phosphate + pyruvate." [EC:3.11.1.3, RHEA:16673]
synonym: "PPH" RELATED [EC:3.11.1.3]
xref: EC:3.11.1.3
xref: KEGG_REACTION:R08200
@@ -194092,7 +194046,7 @@ is_a: GO:0016074 ! sno(s)RNA metabolic process
id: GO:0033980
name: phosphonopyruvate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-phosphonopyruvate + 2 H(+) = CO(2) + phosphonoacetaldehyde." [EC:4.1.1.82, RHEA:20768]
+def: "Catalysis of the reaction: 3-phosphonopyruvate + 2 H+ = CO2 + phosphonoacetaldehyde." [EC:4.1.1.82, RHEA:20768]
synonym: "3-phosphonopyruvate carboxy-lyase (2-phosphonoacetaldehyde-forming) activity" RELATED [EC:4.1.1.82]
synonym: "3-phosphonopyruvate carboxy-lyase activity" RELATED [EC:4.1.1.82]
xref: EC:4.1.1.82
@@ -194106,7 +194060,7 @@ id: GO:0033981
name: D-dopachrome decarboxylase activity
namespace: molecular_function
alt_id: GO:0030928
-def: "Catalysis of the reaction: D-dopachrome + H(+) = 5,6-dihydroxyindole + CO(2)." [EC:4.1.1.84, RHEA:18441]
+def: "Catalysis of the reaction: D-dopachrome + H+ = 5,6-dihydroxyindole + CO2." [EC:4.1.1.84, RHEA:18441]
synonym: "D-dopachrome carboxy-lyase (5,6-dihydroxyindole-forming) activity" RELATED [EC:4.1.1.84]
synonym: "D-dopachrome carboxy-lyase activity" RELATED [EC:4.1.1.84]
synonym: "D-dopachrome tautomerase activity" RELATED [EC:4.1.1.84]
@@ -194124,7 +194078,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0033982
name: 3-dehydro-L-gulonate-6-phosphate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-dehydro-L-gulonate 6-phosphate + H(+) = L-xylulose 5-phosphate + CO(2)." [EC:4.1.1.85, RHEA:14353]
+def: "Catalysis of the reaction: 3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2." [EC:4.1.1.85, RHEA:14353]
synonym: "3-dehydro-L-gulonate-6-phosphate carboxy-lyase (L-xylulose-5-phosphate-forming) activity" RELATED [EC:4.1.1.85]
synonym: "3-dehydro-L-gulonate-6-phosphate carboxy-lyase activity" RELATED [EC:4.1.1.85]
synonym: "3-keto-L-gulonate 6-phosphate decarboxylase activity" RELATED [EC:4.1.1.85]
@@ -194142,7 +194096,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0033983
name: diaminobutyrate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-2,4-diaminobutyrate + H(+) = 1,3-diaminopropane + CO(2)." [EC:4.1.1.86, RHEA:15689]
+def: "Catalysis of the reaction: L-2,4-diaminobutyrate + H+ = 1,3-diaminopropane + CO2." [EC:4.1.1.86, RHEA:15689]
synonym: "DABA DC" RELATED [EC:4.1.1.86]
synonym: "L-2,4-diaminobutanoate carboxy-lyase (propane-1,3-diamine-forming) activity" RELATED [EC:4.1.1.86]
synonym: "L-2,4-diaminobutanoate carboxy-lyase activity" RELATED [EC:4.1.1.86]
@@ -194208,7 +194162,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0033988
name: bile-acid 7alpha-dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7alpha,12alpha-dihydroxy-3-oxochol-4-en-24-oate = 12alpha-hydroxy-3-oxochola-4,6-dien-24-oate + H(2)O." [EC:4.2.1.106, RHEA:10436]
+def: "Catalysis of the reaction: 7alpha,12alpha-dihydroxy-3-oxochol-4-en-24-oate = 12alpha-hydroxy-3-oxochola-4,6-dien-24-oate + H2O." [PMID:26650892, RHEA:10436]
synonym: "7alpha,12alpha-dihydroxy-3-oxochol-4-enoate hydro-lyase (12alpha-hydroxy-3-oxochola-4,6-dienoate-forming) activity" RELATED [EC:4.2.1.106]
synonym: "7alpha,12alpha-dihydroxy-3-oxochol-4-enoate hydro-lyase activity" RELATED [EC:4.2.1.106]
synonym: "BA7 alpha dehydratase activity" RELATED [EC:4.2.1.106]
@@ -194238,7 +194192,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0033990
name: ectoine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(4)-acetyl-L-2,4-diaminobutyrate = ectoine + H(2)O." [EC:4.2.1.108, RHEA:17281]
+def: "Catalysis of the reaction: N(4)-acetyl-L-2,4-diaminobutyrate = ectoine + H2O." [EC:4.2.1.108, RHEA:17281]
synonym: "4-N-acetyl-L-2,4-diaminobutanoate hydro-lyase (L-ectoine-forming) activity" RELATED [EC:4.2.1.108]
synonym: "EctC" RELATED [EC:4.2.1.108]
synonym: "L-ectoine synthase activity" RELATED [EC:4.2.1.108]
@@ -194383,7 +194337,7 @@ synonym: "ChS ABC lyase activity" BROAD [EC:4.2.2.20]
synonym: "ChS ABC lyase I activity" RELATED [EC:4.2.2.20]
xref: EC:4.2.2.20
xref: MetaCyc:4.2.2.20-RXN
-is_a: GO:0047486 ! chondroitin ABC lyase activity
+is_a: GO:0016837 ! carbon-oxygen lyase activity, acting on polysaccharides
[Term]
id: GO:0034001
@@ -194400,7 +194354,7 @@ synonym: "ChS ABC lyase activity" BROAD [EC:4.2.2.21]
synonym: "ChS ABC lyase II activity" RELATED [EC:4.2.2.21]
xref: EC:4.2.2.21
xref: MetaCyc:4.2.2.21-RXN
-is_a: GO:0047486 ! chondroitin ABC lyase activity
+is_a: GO:0016837 ! carbon-oxygen lyase activity, acting on polysaccharides
[Term]
id: GO:0034002
@@ -194479,7 +194433,7 @@ is_a: GO:0010334 ! sesquiterpene synthase activity
id: GO:0034007
name: S-linalool synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: geranyl diphosphate + H(2)O = (S)-linalool + diphosphate." [EC:4.2.3.25, RHEA:24116]
+def: "Catalysis of the reaction: geranyl diphosphate + H2O = (S)-linalool + diphosphate." [EC:4.2.3.25, RHEA:24116]
synonym: "3S-linalool synthase activity" RELATED [EC:4.2.3.25]
synonym: "geranyl-diphosphate diphosphate-lyase [(3S)-linalool-forming] activity" RELATED [EC:4.2.3.25]
synonym: "LIS" RELATED [EC:4.2.3.25]
@@ -194493,7 +194447,7 @@ is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
id: GO:0034008
name: R-linalool synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: geranyl diphosphate + H(2)O = (R)-linalool + diphosphate." [EC:4.2.3.26, RHEA:15809]
+def: "Catalysis of the reaction: geranyl diphosphate + H2O = (R)-linalool + diphosphate." [EC:4.2.3.26, RHEA:15809]
synonym: "(-)-3R-linalool synthase activity" RELATED [EC:4.2.3.26]
synonym: "(3R)-linalool synthase activity" RELATED [EC:4.2.3.26]
synonym: "geranyl-diphosphate diphosphate-lyase [(3R)-linalool-forming] activity" RELATED [EC:4.2.3.26]
@@ -194536,7 +194490,7 @@ is_a: GO:0016846 ! carbon-sulfur lyase activity
id: GO:0034011
name: L-cysteate sulfo-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-cysteate + H(2)O = NH(4)(+) + pyruvate + sulfite." [EC:4.4.1.25, RHEA:13441]
+def: "Catalysis of the reaction: L-cysteate + H2O = NH4 + pyruvate + sulfite." [EC:4.4.1.25, RHEA:13441]
synonym: "CuyA" RELATED [EC:4.4.1.25]
synonym: "L-cysteate bisulfite-lyase (deaminating; pyruvate-forming) activity" RELATED [EC:4.4.1.25]
synonym: "L-cysteate sulfo-lyase (deaminating) activity" RELATED [EC:4.4.1.25]
@@ -194599,7 +194553,7 @@ is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and
id: GO:0034016
name: polyenoic fatty acid isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: all-cis-icosa-5,8,11,14,17-pentaenoate = (5Z,7E,9E,14Z,17Z)-icosapentaenoate." [EC:5.3.3.13, RHEA:14889]
+def: "Catalysis of the reaction: all-cis-icosa-5,8,11,14,17-pentaenoate = (5Z,7E,9E,14Z,17Z)-icosapentaenoate." [RHEA:14889]
synonym: "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate delta8,11-delta7,8-isomerase activity" RELATED [EC:5.3.3.13]
synonym: "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate delta8,11-delta7,9-isomerase (trans-double-bond-forming) activity" RELATED [EC:5.3.3.13]
synonym: "(5Z,8Z,11Z,14Z,17Z)-icosapentaenoate delta8,11-delta7,9-isomerase (trans-double-bond-forming) activity" RELATED [EC:5.3.3.13]
@@ -194616,10 +194570,9 @@ id: GO:0034017
name: trans-2-decenoyl-acyl-carrier-protein isomerase activity
namespace: molecular_function
alt_id: GO:0043832
-def: "Catalysis of the reaction: trans-dec-2-enoyl-[acyl-carrier protein] = cis-dec-3-enoyl-[acyl-carrier protein]." [EC:5.3.3.14]
+def: "Catalysis of the reaction: trans-dec-2-enoyl-[acyl-carrier protein] = cis-dec-3-enoyl-[acyl-carrier protein]." [RHEA:23568]
synonym: "beta-hydroxydecanoyl thioester dehydrase activity" BROAD [EC:5.3.3.14]
synonym: "decenoyl-acyl-carrier-protein delta2-trans-delta3-cis-isomerase activity" RELATED [EC:5.3.3.14]
-synonym: "FabM" RELATED [EC:5.3.3.14]
synonym: "trans-2, cis-3 decenoyl-[acyl-carrier-protein] isomerase activity" EXACT []
synonym: "trans-2, cis-3 decenoyl-ACP isomerase activity" EXACT []
synonym: "trans-2,cis-3-decenoyl-ACP isomerase activity" RELATED [EC:5.3.3.14]
@@ -194645,7 +194598,7 @@ synonym: "ascopyrone P tautomerase activity" RELATED [EC:5.3.2.7]
xref: EC:5.3.2.7
xref: MetaCyc:5.3.3.15-RXN
xref: RHEA:22568
-is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds
+is_a: GO:0016862 ! intramolecular oxidoreductase activity, interconverting keto- and enol-groups
[Term]
id: GO:0034019
@@ -194719,7 +194672,7 @@ is_a: GO:0016866 ! intramolecular transferase activity
id: GO:0034024
name: glutamate-putrescine ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-glutamate + ATP + putrescine = gamma-L-glutamylputrescine + ADP + 2 H(+) + phosphate." [EC:6.3.1.11, RHEA:13633]
+def: "Catalysis of the reaction: L-glutamate + ATP + putrescine = gamma-L-glutamylputrescine + ADP + 2 H+ + phosphate." [EC:6.3.1.11, RHEA:13633]
synonym: "gamma-glutamylputrescine synthetase activity" RELATED [EC:6.3.1.11]
synonym: "L-glutamate:putrescine ligase (ADP-forming) activity" RELATED [EC:6.3.1.11]
synonym: "YcjK" RELATED [EC:6.3.1.11]
@@ -194761,7 +194714,7 @@ is_a: GO:0016881 ! acid-amino acid ligase activity
id: GO:0034027
name: (carboxyethyl)arginine beta-lactam-synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(2)-(2-carboxyethyl)-L-arginine + ATP = AMP + deoxyamidinoproclavaminate + diphosphate + 2 H(+)." [EC:6.3.3.4, RHEA:23620]
+def: "Catalysis of the reaction: N(2)-(2-carboxyethyl)-L-arginine + ATP = AMP + deoxyamidinoproclavaminate + diphosphate + 2 H+." [EC:6.3.3.4, RHEA:23620]
synonym: "beta-lactam synthetase activity" RELATED [EC:6.3.3.4]
synonym: "L-2-N-(2-carboxyethyl)arginine cyclo-ligase (AMP-forming) activity" RELATED [EC:6.3.3.4]
synonym: "L-N2-(2-carboxyethyl)arginine cyclo-ligase (AMP-forming) activity" RELATED [EC:6.3.3.4]
@@ -194775,7 +194728,7 @@ is_a: GO:0016882 ! cyclo-ligase activity
id: GO:0034028
name: 5-(carboxyamino)imidazole ribonucleotide synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole + ATP + bicarbonate = 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + ADP + 3 H(+) + phosphate." [EC:6.3.4.18, RHEA:19317]
+def: "Catalysis of the reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole + ATP + bicarbonate = 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + ADP + 3 H+ + phosphate." [EC:6.3.4.18, RHEA:19317]
synonym: "5-amino-1-(5-phospho-D-ribosyl)imidazole:carbon-dioxide ligase (ADP-forming) activity" RELATED [EC:6.3.4.18]
synonym: "N5-CAIR synthetase activity" RELATED [EC:6.3.4.18]
synonym: "N5-carboxyaminoimidazole ribonucleotide synthetase activity" RELATED [EC:6.3.4.18]
@@ -194790,7 +194743,7 @@ is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
id: GO:0034029
name: 2-oxoglutarate carboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + ATP + bicarbonate = ADP + 2 H(+) + oxalosuccinate + phosphate." [EC:6.4.1.7, RHEA:20425]
+def: "Catalysis of the reaction: 2-oxoglutarate + ATP + bicarbonate = ADP + 2 H+ + oxalosuccinate + phosphate." [EC:6.4.1.7, RHEA:20425]
synonym: "carboxylating factor for ICDH" RELATED [EC:6.4.1.7]
synonym: "CFI" RELATED [EC:6.4.1.7]
synonym: "OGC" RELATED [EC:6.4.1.7]
@@ -195068,7 +195021,7 @@ synonym: "suppression of HR" NARROW [GOC:pamgo_curators]
is_a: GO:0034053 ! modulation by symbiont of host defense-related programmed cell death
is_a: GO:0043069 ! negative regulation of programmed cell death
is_a: GO:0044414 ! suppression of host defenses by symbiont
-is_a: GO:0052041 ! negative regulation by symbiont of host programmed cell death
+is_a: GO:0052041 ! suppression by symbiont of host programmed cell death
[Term]
id: GO:0034055
@@ -195085,7 +195038,7 @@ synonym: "up regulation by symbiont of host defense-related programmed cell deat
synonym: "up-regulation by symbiont of host defense-related programmed cell death" EXACT [GOC:pamgo_curators]
synonym: "upregulation by symbiont of host defense-related programmed cell death" EXACT [GOC:pamgo_curators]
is_a: GO:0034053 ! modulation by symbiont of host defense-related programmed cell death
-is_a: GO:0052042 ! positive regulation by symbiont of host programmed cell death
+is_a: GO:0052042 ! induction by symbiont of host programmed cell death
is_a: GO:0052170 ! suppression by symbiont of host innate immune response
is_a: GO:0140418 ! effector-mediated modulation of host process by symbiont
@@ -195164,6 +195117,7 @@ synonym: "RNA transcriptase activity" RELATED [EC:2.7.7.6]
synonym: "transcriptase" BROAD [EC:2.7.7.6]
xref: Reactome:R-HSA-5696807 "TRNT1 polymerizes CCA at the 3' end of pre-tRNA"
xref: Reactome:R-HSA-6786881 "TRNT1 polymerizes CCA at the 3' end of pre-tRNA"
+xref: RHEA:21248
is_a: GO:0097747 ! RNA polymerase activity
[Term]
@@ -195241,7 +195195,7 @@ name: aminoglycoside phosphotransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + aminoglycoside = ADP + phosphoaminoglycoside." [GOC:cb, GOC:mah]
synonym: "aminoglycoside kinase activity" EXACT []
-xref: EC 2.7.1.190
+xref: EC:2.7.1.190
is_a: GO:0016301 ! kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
@@ -195331,22 +195285,21 @@ id: GO:0034080
name: CENP-A containing chromatin assembly
namespace: biological_process
alt_id: GO:0034509
-def: "The formation of chromatin containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres." [GOC:mah, GOC:vw, PMID:18158900, PMID:19217403]
+alt_id: GO:0061641
+def: "The formation of chromatin containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres." [GOC:mah, GOC:vw, PMID:18158900, PMID:19217403]
synonym: "CenH3-containing nucleosome assembly at centromere" RELATED []
+synonym: "CENP-A containing chromatin organization" RELATED []
synonym: "CENP-A containing nucleosome assembly" RELATED []
synonym: "CENP-A containing nucleosome assembly at centromere" EXACT [GOC:vw]
synonym: "CENP-A deposition" RELATED [GOC:vw]
synonym: "CENP-A loading" RELATED [GOC:vw]
synonym: "centromere specific nucleosome exchange" RELATED [GOC:mah]
synonym: "centromere-specific histone exchange" EXACT [GOC:mah, GOC:vw]
+synonym: "centromeric chromatin organization" RELATED [GOC:dph]
synonym: "centromeric DNA replication-independent nucleosome assembly" EXACT [GOC:mah]
synonym: "DNA replication-independent nucleosome assembly at centromere" EXACT [GOC:mah]
-is_a: GO:0006334 ! nucleosome assembly
-is_a: GO:0006336 ! DNA replication-independent chromatin assembly
is_a: GO:0031055 ! chromatin remodeling at centromere
-is_a: GO:0043486 ! histone exchange
relationship: part_of GO:0034508 ! centromere complex assembly
-relationship: part_of GO:0061641 ! CENP-A containing chromatin organization
[Term]
id: GO:0034081
@@ -195355,7 +195308,7 @@ namespace: cellular_component
def: "A protein complex that carries out enzymatic reactions involved in the biosynthesis of polyketides, any of a diverse group of natural products synthesized via linear poly-beta-ketones." [GOC:mah, PMID:12636085]
synonym: "PKS" RELATED []
synonym: "PKS complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005737 ! cytoplasm
[Term]
@@ -195418,7 +195371,6 @@ namespace: biological_process
def: "The process in which the association between sister chromatids of a replicated chromosome is maintained as chromosomes condense, attach to the spindle in a bipolar orientation, and congress to the metaphase plate during a mitotic cell cycle." [GOC:mah]
synonym: "mitotic cohesion stability" RELATED []
is_a: GO:0034086 ! maintenance of sister chromatid cohesion
-is_a: GO:1903047 ! mitotic cell cycle process
relationship: part_of GO:0007064 ! mitotic sister chromatid cohesion
[Term]
@@ -195427,7 +195379,6 @@ name: establishment of meiotic sister chromatid cohesion
namespace: biological_process
def: "The process in which the sister chromatids of a replicated chromosome become joined along the entire length of the chromosome during S phase during a meiotic cell cycle." [GOC:mah]
is_a: GO:0034085 ! establishment of sister chromatid cohesion
-is_a: GO:1903046 ! meiotic cell cycle process
relationship: part_of GO:0051177 ! meiotic sister chromatid cohesion
[Term]
@@ -195436,7 +195387,6 @@ name: maintenance of meiotic sister chromatid cohesion
namespace: biological_process
def: "The process in which the association between sister chromatids of a replicated chromosome is maintained as chromosomes condense, attach to the spindle in a bipolar orientation, and congress to the metaphase plate during a meiotic cell cycle." [GOC:mah]
is_a: GO:0034086 ! maintenance of sister chromatid cohesion
-is_a: GO:1903046 ! meiotic cell cycle process
relationship: part_of GO:0051177 ! meiotic sister chromatid cohesion
[Term]
@@ -195471,7 +195421,6 @@ name: regulation of maintenance of meiotic sister chromatid cohesion
namespace: biological_process
def: "Any process that modulates the extent to which the association between sister chromatids of a replicated chromosome is maintained during a meiotic cell cycle." [GOC:mah, GOC:vw]
is_a: GO:0034091 ! regulation of maintenance of sister chromatid cohesion
-is_a: GO:2000241 ! regulation of reproductive process
relationship: regulates GO:0034090 ! maintenance of meiotic sister chromatid cohesion
[Term]
@@ -195481,7 +195430,6 @@ namespace: biological_process
def: "Any process that decreases the extent to which the association between sister chromatids of a replicated chromosome is maintained during a meiotic cell cycle." [GOC:mah, GOC:vw]
is_a: GO:0034092 ! negative regulation of maintenance of sister chromatid cohesion
is_a: GO:0034094 ! regulation of maintenance of meiotic sister chromatid cohesion
-is_a: GO:2000242 ! negative regulation of reproductive process
relationship: negatively_regulates GO:0034090 ! maintenance of meiotic sister chromatid cohesion
[Term]
@@ -195491,7 +195439,6 @@ namespace: biological_process
def: "Any process that increases the extent to which the association between sister chromatids of a replicated chromosome is maintained during a meiotic cell cycle." [GOC:mah, GOC:vw]
is_a: GO:0034093 ! positive regulation of maintenance of sister chromatid cohesion
is_a: GO:0034094 ! regulation of maintenance of meiotic sister chromatid cohesion
-is_a: GO:2000243 ! positive regulation of reproductive process
relationship: positively_regulates GO:0034090 ! maintenance of meiotic sister chromatid cohesion
[Term]
@@ -195732,6 +195679,7 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor signalling pathway" EXACT []
+is_a: GO:0002683 ! negative regulation of immune system process
is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
relationship: negatively_regulates GO:0002224 ! toll-like receptor signaling pathway
@@ -195816,10 +195764,10 @@ relationship: positively_regulates GO:0002756 ! MyD88-independent toll-like rece
id: GO:0034130
name: toll-like receptor 1 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 1." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to toll-like receptor 1." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR1 signaling pathway" EXACT []
synonym: "toll-like receptor 1 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0002752 ! cell surface pattern recognition receptor signaling pathway
[Term]
id: GO:0034131
@@ -195828,7 +195776,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 1 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR1 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 1 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0062207 ! regulation of pattern recognition receptor signaling pathway
relationship: regulates GO:0034130 ! toll-like receptor 1 signaling pathway
[Term]
@@ -195838,7 +195786,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 1 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR1 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 1 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
+is_a: GO:0002683 ! negative regulation of immune system process
+is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:0034131 ! regulation of toll-like receptor 1 signaling pathway
relationship: negatively_regulates GO:0034130 ! toll-like receptor 1 signaling pathway
@@ -195849,18 +195798,18 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 1 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR1 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 1 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034131 ! regulation of toll-like receptor 1 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034130 ! toll-like receptor 1 signaling pathway
[Term]
id: GO:0034134
name: toll-like receptor 2 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 2." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to toll-like receptor 2." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR2 signaling pathway" EXACT []
synonym: "toll-like receptor 2 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140895 ! cell surface toll-like receptor signaling pathway
[Term]
id: GO:0034135
@@ -195869,7 +195818,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 2 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR2 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 2 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0062207 ! regulation of pattern recognition receptor signaling pathway
relationship: regulates GO:0034134 ! toll-like receptor 2 signaling pathway
[Term]
@@ -195879,7 +195828,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 2 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR2 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 2 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
+is_a: GO:0002683 ! negative regulation of immune system process
+is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:0034135 ! regulation of toll-like receptor 2 signaling pathway
relationship: negatively_regulates GO:0034134 ! toll-like receptor 2 signaling pathway
@@ -195890,18 +195840,18 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 2 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR2 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 2 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034135 ! regulation of toll-like receptor 2 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034134 ! toll-like receptor 2 signaling pathway
[Term]
id: GO:0034138
name: toll-like receptor 3 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 3." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to the endolysosomal toll-like receptor 3." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR3 signaling pathway" EXACT []
synonym: "toll-like receptor 3 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140894 ! endolysosomal toll-like receptor signaling pathway
[Term]
id: GO:0034139
@@ -195910,7 +195860,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 3 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR3 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 3 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0039531 ! regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: regulates GO:0034138 ! toll-like receptor 3 signaling pathway
[Term]
@@ -195920,8 +195870,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 3 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR3 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 3 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
is_a: GO:0034139 ! regulation of toll-like receptor 3 signaling pathway
+is_a: GO:0039532 ! negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: negatively_regulates GO:0034138 ! toll-like receptor 3 signaling pathway
[Term]
@@ -195931,18 +195881,18 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 3 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR3 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 3 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034139 ! regulation of toll-like receptor 3 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034138 ! toll-like receptor 3 signaling pathway
[Term]
id: GO:0034142
name: toll-like receptor 4 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 4." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to toll-like receptor 4." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR4 signaling pathway" EXACT []
synonym: "toll-like receptor 4 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140895 ! cell surface toll-like receptor signaling pathway
[Term]
id: GO:0034143
@@ -195951,7 +195901,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 4 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR4 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 4 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0062207 ! regulation of pattern recognition receptor signaling pathway
relationship: regulates GO:0034142 ! toll-like receptor 4 signaling pathway
[Term]
@@ -195961,7 +195911,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 4 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR4 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 4 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
+is_a: GO:0002683 ! negative regulation of immune system process
+is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:0034143 ! regulation of toll-like receptor 4 signaling pathway
relationship: negatively_regulates GO:0034142 ! toll-like receptor 4 signaling pathway
@@ -195972,18 +195923,18 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 4 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR4 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 4 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034143 ! regulation of toll-like receptor 4 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034142 ! toll-like receptor 4 signaling pathway
[Term]
id: GO:0034146
name: toll-like receptor 5 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 5." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to toll-like receptor 5." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR5 signaling pathway" EXACT []
synonym: "toll-like receptor 5 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140895 ! cell surface toll-like receptor signaling pathway
[Term]
id: GO:0034147
@@ -195992,7 +195943,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 5 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR5 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 5 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0062207 ! regulation of pattern recognition receptor signaling pathway
relationship: regulates GO:0034146 ! toll-like receptor 5 signaling pathway
[Term]
@@ -196002,7 +195953,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 5 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR5 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 5 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
+is_a: GO:0002683 ! negative regulation of immune system process
+is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:0034147 ! regulation of toll-like receptor 5 signaling pathway
relationship: negatively_regulates GO:0034146 ! toll-like receptor 5 signaling pathway
@@ -196013,18 +195965,18 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 5 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR5 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 5 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034147 ! regulation of toll-like receptor 5 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034146 ! toll-like receptor 5 signaling pathway
[Term]
id: GO:0034150
name: toll-like receptor 6 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 6." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to toll-like receptor 6." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR6 signaling pathway" EXACT []
synonym: "toll-like receptor 6 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140895 ! cell surface toll-like receptor signaling pathway
[Term]
id: GO:0034151
@@ -196033,7 +195985,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 6 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR6 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 6 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0062207 ! regulation of pattern recognition receptor signaling pathway
relationship: regulates GO:0034150 ! toll-like receptor 6 signaling pathway
[Term]
@@ -196043,7 +195995,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 6 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR6 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 6 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
+is_a: GO:0002683 ! negative regulation of immune system process
+is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:0034151 ! regulation of toll-like receptor 6 signaling pathway
relationship: negatively_regulates GO:0034150 ! toll-like receptor 6 signaling pathway
@@ -196054,18 +196007,18 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 6 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR6 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 6 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034151 ! regulation of toll-like receptor 6 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034150 ! toll-like receptor 6 signaling pathway
[Term]
id: GO:0034154
name: toll-like receptor 7 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 7." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to the endolysosomal toll-like receptor 7." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR7 signaling pathway" EXACT []
synonym: "toll-like receptor 7 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140894 ! endolysosomal toll-like receptor signaling pathway
[Term]
id: GO:0034155
@@ -196074,7 +196027,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 7 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR7 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 7 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0039531 ! regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: regulates GO:0034154 ! toll-like receptor 7 signaling pathway
[Term]
@@ -196084,8 +196037,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 7 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR7 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 7 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
is_a: GO:0034155 ! regulation of toll-like receptor 7 signaling pathway
+is_a: GO:0039532 ! negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: negatively_regulates GO:0034154 ! toll-like receptor 7 signaling pathway
[Term]
@@ -196095,18 +196048,18 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 7 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR7 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 7 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034155 ! regulation of toll-like receptor 7 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034154 ! toll-like receptor 7 signaling pathway
[Term]
id: GO:0034158
name: toll-like receptor 8 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 8." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to the endolysosomal toll-like receptor 8." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR8 signaling pathway" EXACT []
synonym: "toll-like receptor 8 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140894 ! endolysosomal toll-like receptor signaling pathway
[Term]
id: GO:0034159
@@ -196115,7 +196068,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 8 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR8 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 8 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0039531 ! regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: regulates GO:0034158 ! toll-like receptor 8 signaling pathway
[Term]
@@ -196125,8 +196078,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 8 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR8 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 8 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
is_a: GO:0034159 ! regulation of toll-like receptor 8 signaling pathway
+is_a: GO:0039532 ! negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: negatively_regulates GO:0034158 ! toll-like receptor 8 signaling pathway
[Term]
@@ -196136,18 +196089,18 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 8 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR8 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 8 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034159 ! regulation of toll-like receptor 8 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034158 ! toll-like receptor 8 signaling pathway
[Term]
id: GO:0034162
name: toll-like receptor 9 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 9." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to the endolysosomal toll-like receptor 9." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR9 signaling pathway" EXACT []
synonym: "toll-like receptor 9 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140894 ! endolysosomal toll-like receptor signaling pathway
[Term]
id: GO:0034163
@@ -196156,7 +196109,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 9 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR9 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 9 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0039531 ! regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: regulates GO:0034162 ! toll-like receptor 9 signaling pathway
[Term]
@@ -196166,8 +196119,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 9 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR9 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 9 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
is_a: GO:0034163 ! regulation of toll-like receptor 9 signaling pathway
+is_a: GO:0039532 ! negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: negatively_regulates GO:0034162 ! toll-like receptor 9 signaling pathway
[Term]
@@ -196177,18 +196130,18 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 9 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR9 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 9 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034163 ! regulation of toll-like receptor 9 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034162 ! toll-like receptor 9 signaling pathway
[Term]
id: GO:0034166
name: toll-like receptor 10 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 10." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to toll-like receptor 10." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR10 signaling pathway" EXACT []
synonym: "toll-like receptor 10 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140895 ! cell surface toll-like receptor signaling pathway
[Term]
id: GO:0034167
@@ -196197,7 +196150,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 10 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR10 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 10 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0062207 ! regulation of pattern recognition receptor signaling pathway
relationship: regulates GO:0034166 ! toll-like receptor 10 signaling pathway
[Term]
@@ -196207,7 +196160,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 10 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR10 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 10 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
+is_a: GO:0002683 ! negative regulation of immune system process
+is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:0034167 ! regulation of toll-like receptor 10 signaling pathway
relationship: negatively_regulates GO:0034166 ! toll-like receptor 10 signaling pathway
@@ -196218,18 +196172,18 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 10 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR10 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 10 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034167 ! regulation of toll-like receptor 10 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034166 ! toll-like receptor 10 signaling pathway
[Term]
id: GO:0034170
name: toll-like receptor 11 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 11." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to the endolysosomal toll-like receptor 11." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR11 signaling pathway" EXACT []
synonym: "toll-like receptor 11 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140894 ! endolysosomal toll-like receptor signaling pathway
[Term]
id: GO:0034171
@@ -196238,7 +196192,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 11 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR11 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 11 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0039531 ! regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: regulates GO:0034170 ! toll-like receptor 11 signaling pathway
[Term]
@@ -196248,8 +196202,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 11 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR11 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 11 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
is_a: GO:0034171 ! regulation of toll-like receptor 11 signaling pathway
+is_a: GO:0039532 ! negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: negatively_regulates GO:0034170 ! toll-like receptor 11 signaling pathway
[Term]
@@ -196259,18 +196213,18 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 11 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR11 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 11 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034171 ! regulation of toll-like receptor 11 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034170 ! toll-like receptor 11 signaling pathway
[Term]
id: GO:0034174
name: toll-like receptor 12 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 12." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to the endolysosomal toll-like receptor 12." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR12 signaling pathway" EXACT []
synonym: "toll-like receptor 12 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140894 ! endolysosomal toll-like receptor signaling pathway
[Term]
id: GO:0034175
@@ -196279,7 +196233,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 12 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR12 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 12 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0039531 ! regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: regulates GO:0034174 ! toll-like receptor 12 signaling pathway
[Term]
@@ -196289,8 +196243,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 12 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR12 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 12 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
is_a: GO:0034175 ! regulation of toll-like receptor 12 signaling pathway
+is_a: GO:0039532 ! negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: negatively_regulates GO:0034174 ! toll-like receptor 12 signaling pathway
[Term]
@@ -196300,18 +196254,18 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 12 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR12 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 12 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034175 ! regulation of toll-like receptor 12 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034174 ! toll-like receptor 12 signaling pathway
[Term]
id: GO:0034178
name: toll-like receptor 13 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 13." [GOC:add, PMID:16551253, PMID:17328678]
+def: "The series of molecular signals initiated by a ligand binding to the endolysosomal toll-like receptor 13." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "TLR13 signaling pathway" EXACT []
synonym: "toll-like receptor 13 signalling pathway" EXACT []
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140894 ! endolysosomal toll-like receptor signaling pathway
[Term]
id: GO:0034179
@@ -196320,7 +196274,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of toll-like receptor 13 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "regulation of TLR13 signaling pathway" EXACT []
synonym: "regulation of toll-like receptor 13 signalling pathway" EXACT []
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0039531 ! regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: regulates GO:0034178 ! toll-like receptor 13 signaling pathway
[Term]
@@ -196330,8 +196284,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 13 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "negative regulation of TLR13 signaling pathway" EXACT []
synonym: "negative regulation of toll-like receptor 13 signalling pathway" EXACT []
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
is_a: GO:0034179 ! regulation of toll-like receptor 13 signaling pathway
+is_a: GO:0039532 ! negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: negatively_regulates GO:0034178 ! toll-like receptor 13 signaling pathway
[Term]
@@ -196341,8 +196295,8 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate, or extent of toll-like receptor 13 signaling pathway." [GOC:add, PMID:16551253, PMID:17328678]
synonym: "positive regulation of TLR13 signaling pathway" EXACT []
synonym: "positive regulation of toll-like receptor 13 signalling pathway" EXACT []
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
is_a: GO:0034179 ! regulation of toll-like receptor 13 signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0034178 ! toll-like receptor 13 signaling pathway
[Term]
@@ -196399,7 +196353,7 @@ replaced_by: GO:0034185
id: GO:0034188
name: apolipoprotein A-I receptor activity
namespace: molecular_function
-def: "Combining with apolipoprotein A-I and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:bf, GOC:BHF, GOC:rl, GOC:signaling, PMID:16443932]
+def: "Combining with an apolipoprotein A-I receptor ligand and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:bf, GOC:BHF, GOC:rl, GOC:signaling, PMID:16443932]
is_a: GO:0004888 ! transmembrane signaling receptor activity
is_a: GO:0030226 ! apolipoprotein receptor activity
@@ -196453,6 +196407,7 @@ synonym: "D-galactonate breakdown" EXACT []
synonym: "D-galactonate catabolism" EXACT []
synonym: "D-galactonate degradation" EXACT []
xref: MetaCyc:GALACTCAT-PWY
+is_a: GO:0016052 ! carbohydrate catabolic process
is_a: GO:0019584 ! galactonate catabolic process
is_a: GO:0034192 ! D-galactonate metabolic process
@@ -196465,6 +196420,7 @@ synonym: "L-galactonate breakdown" EXACT []
synonym: "L-galactonate catabolism" EXACT []
synonym: "L-galactonate degradation" EXACT []
xref: MetaCyc:GALACTCAT-PWY
+is_a: GO:0016052 ! carbohydrate catabolic process
is_a: GO:0019584 ! galactonate catabolic process
is_a: GO:0034193 ! L-galactonate metabolic process
@@ -196571,35 +196527,39 @@ is_a: GO:0032993 ! protein-DNA complex
[Term]
id: GO:0034207
-name: steroid acetylation
+name: obsolete steroid acetylation
namespace: biological_process
-def: "The addition of an acetyl group to a steroid molecule. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." [GOC:mah]
-is_a: GO:0008202 ! steroid metabolic process
-is_a: GO:0030258 ! lipid modification
+def: "OBSOLETE. The addition of an acetyl group to a steroid molecule. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0008202
[Term]
id: GO:0034208
-name: steroid deacetylation
+name: obsolete steroid deacetylation
namespace: biological_process
-def: "The removal of an acetyl group from a steroid molecule. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." [GOC:mah]
-is_a: GO:0008202 ! steroid metabolic process
-is_a: GO:0030258 ! lipid modification
+def: "OBSOLETE. The removal of an acetyl group from a steroid molecule. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0008202
[Term]
id: GO:0034209
-name: sterol acetylation
+name: obsolete sterol acetylation
namespace: biological_process
-def: "The addition of an acetyl group to a sterol molecule. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." [GOC:rb, PMID:18034159]
-is_a: GO:0016125 ! sterol metabolic process
-is_a: GO:0034207 ! steroid acetylation
+def: "OBSOLETE. The addition of an acetyl group to a sterol molecule. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." [GOC:rb, PMID:18034159]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0016125
[Term]
id: GO:0034210
-name: sterol deacetylation
+name: obsolete sterol deacetylation
namespace: biological_process
-def: "The removal of an acetyl group from a sterol molecule. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." [GOC:rb, PMID:18034159]
-is_a: GO:0016125 ! sterol metabolic process
-is_a: GO:0034208 ! steroid deacetylation
+def: "OBSOLETE. The removal of an acetyl group from a sterol molecule. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid." [GOC:rb, PMID:18034159]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0016125
[Term]
id: GO:0034211
@@ -196615,6 +196575,7 @@ name: peptide N-acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the acetylation of an amino acid residue of a peptide or protein, according to the reaction: acetyl-CoA + peptide = CoA + N-acetylpeptide." [GOC:mah]
xref: Reactome:R-HSA-3371554 "HSF1 acetylation at Lys80"
+xref: Reactome:R-HSA-9760081 "CREBBP, EP300 acetylates NFE2L2"
is_a: GO:0008080 ! N-acetyltransferase activity
[Term]
@@ -196671,10 +196632,10 @@ synonym: "ascospore wall chitin anabolism" EXACT []
synonym: "ascospore wall chitin biosynthesis" EXACT []
synonym: "ascospore wall chitin formation" EXACT []
synonym: "ascospore wall chitin synthesis" EXACT []
+is_a: GO:0009308 ! amine metabolic process
+is_a: GO:0022414 ! reproductive process
is_a: GO:0034218 ! ascospore wall chitin metabolic process
is_a: GO:0034221 ! fungal-type cell wall chitin biosynthetic process
-is_a: GO:0044106 ! cellular amine metabolic process
-is_a: GO:1903046 ! meiotic cell cycle process
relationship: part_of GO:0070591 ! ascospore wall biogenesis
[Term]
@@ -196699,15 +196660,16 @@ is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0034220
-name: ion transmembrane transport
+name: monoatomic ion transmembrane transport
namespace: biological_process
alt_id: GO:0099131
-def: "A process in which an ion is transported across a membrane." [GOC:mah]
+def: "A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:mah]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "ATP hydrolysis coupled ion transmembrane transport" NARROW []
synonym: "ion membrane transport" EXACT []
+synonym: "ion transmembrane transport" BROAD []
synonym: "transmembrane ion transport" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0006811 ! ion transport
+is_a: GO:0006811 ! monoatomic ion transport
is_a: GO:0055085 ! transmembrane transport
[Term]
@@ -196728,6 +196690,7 @@ name: regulation of cell wall chitin metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving chitin in a cell wall." [GOC:mah]
synonym: "regulation of cell wall chitin metabolism" EXACT []
+is_a: GO:0010981 ! regulation of cell wall macromolecule metabolic process
is_a: GO:0032882 ! regulation of chitin metabolic process
is_a: GO:0051128 ! regulation of cellular component organization
relationship: regulates GO:0006037 ! cell wall chitin metabolic process
@@ -196741,12 +196704,9 @@ synonym: "regulation of ascospore wall chitin anabolism" EXACT []
synonym: "regulation of ascospore wall chitin biosynthesis" EXACT []
synonym: "regulation of ascospore wall chitin formation" EXACT []
synonym: "regulation of ascospore wall chitin synthesis" EXACT []
-is_a: GO:0010564 ! regulation of cell cycle process
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
-is_a: GO:0010981 ! regulation of cell wall macromolecule metabolic process
is_a: GO:0032884 ! regulation of cell wall chitin biosynthetic process
is_a: GO:0032995 ! regulation of fungal-type cell wall biogenesis
-is_a: GO:0033238 ! regulation of cellular amine metabolic process
+is_a: GO:0033238 ! regulation of amine metabolic process
is_a: GO:2000241 ! regulation of reproductive process
relationship: regulates GO:0034217 ! ascospore wall chitin biosynthetic process
@@ -196836,7 +196796,6 @@ synonym: "ascospore wall chitin catabolism" EXACT []
synonym: "ascospore wall chitin degradation" EXACT []
is_a: GO:0006039 ! cell wall chitin catabolic process
is_a: GO:0034218 ! ascospore wall chitin metabolic process
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
is_a: GO:0044347 ! cell wall polysaccharide catabolic process
is_a: GO:0071854 ! cell wall macromolecule catabolic process involved in fungal-type cell wall disassembly
@@ -196861,7 +196820,6 @@ synonym: "regulation of ascospore wall chitin breakdown" EXACT []
synonym: "regulation of ascospore wall chitin catabolism" EXACT []
synonym: "regulation of ascospore wall chitin degradation" EXACT []
is_a: GO:0034233 ! regulation of cell wall chitin catabolic process
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
is_a: GO:2000966 ! regulation of cell wall polysaccharide catabolic process
relationship: regulates GO:0034232 ! ascospore wall chitin catabolic process
@@ -196938,26 +196896,28 @@ relationship: negatively_regulates GO:0000768 ! syncytium formation by plasma me
[Term]
id: GO:0034243
-name: regulation of transcription elongation from RNA polymerase II promoter
+name: regulation of transcription elongation by RNA polymerase II
namespace: biological_process
alt_id: GO:0090039
def: "Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II." [GOC:mah, GOC:txnOH]
synonym: "regulation of gene-specific transcription elongation from RNA polymerase II promoter" RELATED []
synonym: "regulation of RNA elongation from RNA polymerase II promoter" EXACT []
-is_a: GO:0032784 ! regulation of DNA-templated transcription, elongation
-relationship: regulates GO:0006368 ! transcription elongation from RNA polymerase II promoter
+synonym: "regulation of transcription elongation from RNA polymerase II promoter" EXACT []
+is_a: GO:0032784 ! regulation of DNA-templated transcription elongation
+relationship: regulates GO:0006368 ! transcription elongation by RNA polymerase II
[Term]
id: GO:0034244
-name: negative regulation of transcription elongation from RNA polymerase II promoter
+name: negative regulation of transcription elongation by RNA polymerase II
namespace: biological_process
alt_id: GO:0090041
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II." [GOC:mah, GOC:txnOH]
synonym: "negative regulation of gene-specific transcription elongation from RNA polymerase II promoter" RELATED []
synonym: "negative regulation of RNA elongation from RNA polymerase II promoter" EXACT []
+synonym: "negative regulation of transcription elongation from RNA polymerase II promoter" EXACT []
is_a: GO:0032785 ! negative regulation of DNA-templated transcription, elongation
-is_a: GO:0034243 ! regulation of transcription elongation from RNA polymerase II promoter
-relationship: negatively_regulates GO:0006368 ! transcription elongation from RNA polymerase II promoter
+is_a: GO:0034243 ! regulation of transcription elongation by RNA polymerase II
+relationship: negatively_regulates GO:0006368 ! transcription elongation by RNA polymerase II
[Term]
id: GO:0034245
@@ -196992,7 +196952,7 @@ synonym: "sequence-specific DNA binding mitochondrial RNA polymerase transcripti
synonym: "transcription factor activity, mitochondrial proximal promoter sequence-specific binding" EXACT []
synonym: "transcription factor activity, mitochondrial RNA polymerase core promoter proximal region sequence-specific binding" EXACT []
synonym: "transcription factor activity, mitochondrial RNA polymerase core promoter sequence-specific DNA binding" EXACT []
-is_a: GO:0003700 ! DNA-binding transcription factor activity
+is_a: GO:0140110 ! transcription regulator activity
[Term]
id: GO:0034247
@@ -197004,73 +196964,76 @@ is_a: GO:0043144 ! sno(s)RNA processing
[Term]
id: GO:0034248
-name: regulation of cellular amide metabolic process
+name: regulation of amide metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides." [GOC:mah]
synonym: "regulation of amide metabolism" EXACT []
-is_a: GO:0031323 ! regulation of cellular metabolic process
+synonym: "regulation of cellular amide metabolic process" EXACT []
is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
-relationship: regulates GO:0043603 ! cellular amide metabolic process
+relationship: regulates GO:0043603 ! amide metabolic process
[Term]
id: GO:0034249
-name: negative regulation of cellular amide metabolic process
+name: negative regulation of amide metabolic process
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides." [GOC:mah]
synonym: "negative regulation of amide metabolism" EXACT []
-is_a: GO:0031324 ! negative regulation of cellular metabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+synonym: "negative regulation of cellular amide metabolic process" EXACT []
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
-relationship: negatively_regulates GO:0043603 ! cellular amide metabolic process
+relationship: negatively_regulates GO:0043603 ! amide metabolic process
[Term]
id: GO:0034250
-name: positive regulation of cellular amide metabolic process
+name: positive regulation of amide metabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides." [GOC:mah]
synonym: "positive regulation of amide metabolism" EXACT []
-is_a: GO:0031325 ! positive regulation of cellular metabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+synonym: "positive regulation of cellular amide metabolic process" EXACT []
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
-relationship: positively_regulates GO:0043603 ! cellular amide metabolic process
+relationship: positively_regulates GO:0043603 ! amide metabolic process
[Term]
id: GO:0034251
-name: regulation of cellular amide catabolic process
+name: regulation of amide catabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides." [GOC:mah]
synonym: "regulation of amide breakdown" EXACT []
synonym: "regulation of amide catabolism" EXACT []
synonym: "regulation of amide degradation" EXACT []
-is_a: GO:0031329 ! regulation of cellular catabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
-relationship: regulates GO:0043605 ! cellular amide catabolic process
+synonym: "regulation of cellular amide catabolic process" EXACT []
+is_a: GO:0009894 ! regulation of catabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
+relationship: regulates GO:0043605 ! amide catabolic process
[Term]
id: GO:0034252
-name: negative regulation of cellular amide catabolic process
+name: negative regulation of amide catabolic process
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides." [GOC:mah]
synonym: "negative regulation of amide breakdown" EXACT []
synonym: "negative regulation of amide catabolism" EXACT []
synonym: "negative regulation of amide degradation" RELATED []
-is_a: GO:0031330 ! negative regulation of cellular catabolic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
-is_a: GO:0034251 ! regulation of cellular amide catabolic process
-relationship: negatively_regulates GO:0043605 ! cellular amide catabolic process
+synonym: "negative regulation of cellular amide catabolic process" EXACT []
+is_a: GO:0009895 ! negative regulation of catabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
+is_a: GO:0034251 ! regulation of amide catabolic process
+relationship: negatively_regulates GO:0043605 ! amide catabolic process
[Term]
id: GO:0034253
-name: positive regulation of cellular amide catabolic process
+name: positive regulation of amide catabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides." [GOC:mah]
synonym: "positive regulation of amide breakdown" EXACT []
synonym: "positive regulation of amide catabolism" EXACT []
synonym: "positive regulation of amide degradation" RELATED []
-is_a: GO:0031331 ! positive regulation of cellular catabolic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
-is_a: GO:0034251 ! regulation of cellular amide catabolic process
-relationship: positively_regulates GO:0043605 ! cellular amide catabolic process
+synonym: "positive regulation of cellular amide catabolic process" EXACT []
+is_a: GO:0009896 ! positive regulation of catabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
+is_a: GO:0034251 ! regulation of amide catabolic process
+relationship: positively_regulates GO:0043605 ! amide catabolic process
[Term]
id: GO:0034254
@@ -197080,7 +197043,7 @@ def: "Any process that modulates the frequency, rate or extent of the chemical r
synonym: "regulation of urea breakdown" EXACT []
synonym: "regulation of urea catabolism" EXACT []
synonym: "regulation of urea degradation" EXACT []
-is_a: GO:0034251 ! regulation of cellular amide catabolic process
+is_a: GO:0034251 ! regulation of amide catabolic process
is_a: GO:0034255 ! regulation of urea metabolic process
relationship: regulates GO:0043419 ! urea catabolic process
@@ -197090,7 +197053,7 @@ name: regulation of urea metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving urea." [GOC:mah]
synonym: "regulation of urea metabolism" EXACT []
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
is_a: GO:1903314 ! regulation of nitrogen cycle metabolic process
relationship: regulates GO:0019627 ! urea metabolic process
@@ -197240,7 +197203,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of discaden
synonym: "discadenine breakdown" EXACT []
synonym: "discadenine catabolism" EXACT []
synonym: "discadenine degradation" EXACT []
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0009823 ! cytokinin catabolic process
is_a: GO:0034267 ! discadenine metabolic process
is_a: GO:0072523 ! purine-containing compound catabolic process
@@ -197451,40 +197414,16 @@ synonym: "perception of maltose stimulus" RELATED []
is_a: GO:0034286 ! response to maltose
is_a: GO:0034288 ! detection of disaccharide stimulus
-[Term]
-id: GO:0034290
-name: holin activity
-namespace: molecular_function
-def: "A compound function consisting of the regulated formation of a pore via oligomerisation of an existing pool of subunits in the plasma membrane. The resulting channel activity directly or indirectly allows murein hydrolyases to access their cell wall substrate." [GOC:jh2, PMID:1406491, PMID:25157079]
-is_a: GO:0015267 ! channel activity
-
-[Term]
-id: GO:0034291
-name: canonical holin activity
-namespace: molecular_function
-def: "A compound function consisting of the regulated formation of a pore via oligomerisation of an existing pool of subunits in the plasma membrane. The resulting channel activity directly allows release of a fully-folded phage-encoded endolysin (murein-degradase) from the cell." [GOC:jh2, GOC:mah, PMID:1406491, PMID:25157079]
-is_a: GO:0034290 ! holin activity
-
-[Term]
-id: GO:0034292
-name: pinholin activity
-namespace: molecular_function
-def: "A compound function consisting of the regulated formation of a pore via oligomerisation of an existing pool of subunits in the plasma membrane. The resulting ion channel activity indirectly allows endolysin (murein hydrolyases) to access their cell wall substrate by collapsing the proton motive force (PMF) across the membrane, allowing the endolysin to fold to an active form and hydrolyze bonds in the peptidoglycan cell wall." [GOC:jh2, GOC:mah, PMID:1406491, PMID:25157079]
-is_a: GO:0005216 ! ion channel activity
-is_a: GO:0034290 ! holin activity
-
[Term]
id: GO:0034293
name: sexual sporulation
namespace: biological_process
def: "The formation of spores derived from the products of meiosis." [GOC:mah]
-subset: goslim_aspergillus
synonym: "meiotic spore formation" EXACT []
synonym: "meiotic sporulation" EXACT []
synonym: "sexual spore formation" EXACT []
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0043934 ! sporulation
-relationship: part_of GO:0019953 ! sexual reproduction
relationship: part_of GO:0051321 ! meiotic cell cycle
[Term]
@@ -197607,6 +197546,7 @@ name: regulation of ascospore formation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of ascospore formation. An example of this process is found in Saccharomyces cerevisiae." [GOC:mah]
synonym: "MAPKKK cascade during sporulation" RELATED []
+is_a: GO:0010564 ! regulation of cell cycle process
is_a: GO:0043940 ! regulation of sexual sporulation resulting in formation of a cellular spore
is_a: GO:0060284 ! regulation of cell development
relationship: regulates GO:0030437 ! ascospore formation
@@ -197924,13 +197864,13 @@ relationship: part_of GO:0045087 ! innate immune response
[Term]
id: GO:0034341
-name: response to interferon-gamma
+name: response to type II interferon
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon-gamma is also known as type II interferon." [GOC:add, ISBN:0126896631, PMID:15546383]
synonym: "response to gamma-interferon" RELATED []
synonym: "response to immune interferon" EXACT []
+synonym: "response to interferon-gamma" BROAD []
synonym: "response to type II IFN" BROAD []
-synonym: "response to type II interferon" BROAD []
is_a: GO:0034097 ! response to cytokine
relationship: part_of GO:0045087 ! innate immune response
@@ -198071,9 +198011,10 @@ relationship: positively_regulates GO:0034349 ! glial cell apoptotic process
[Term]
id: GO:0034353
-name: RNA pyrophosphohydrolase activity
+name: mRNA 5'-diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the removal of a 5' terminal pyrophosphate from the 5'-triphosphate end of an RNA, leaving a 5'-monophosphate end." [GOC:jh2, PMID:17612492, PMID:18202662]
+def: "Catalysis of the removal of a 5' terminal diphosphate from the 5'-triphosphate end of an mRNA, leaving a 5'-monophosphate end." [GOC:jh2, PMID:17612492, PMID:18202662]
+synonym: "RNA pyrophosphohydrolase activity" BROAD []
is_a: GO:0016462 ! pyrophosphatase activity
is_a: GO:0140098 ! catalytic activity, acting on RNA
@@ -198090,10 +198031,11 @@ is_a: GO:0034627 ! 'de novo' NAD biosynthetic process
id: GO:0034355
name: NAD salvage
namespace: biological_process
-def: "Any process that generates nicotinamide adenine dinucleotide (NAD) from derivatives of it, without de novo synthesis; salvage is usually from the degradation products nicotinic acid (Na) and nicotinamide (Nam)." [GOC:mah, PMID:12648681]
+def: "Any process that generates nicotinamide adenine dinucleotide (NAD) from derivatives of it, without de novo synthesis; salvage is usually from the degradation products nicotinic acid (Na) and nicotinamide (Nam)." [GOC:mah, PMID:12648681, PMID:27374990]
synonym: "NAD salvage pathway" EXACT []
is_a: GO:0009435 ! NAD biosynthetic process
is_a: GO:0019365 ! pyridine nucleotide salvage
+is_a: GO:0032261 ! purine nucleotide salvage
[Term]
id: GO:0034356
@@ -198210,7 +198152,7 @@ name: protein-lipid complex remodeling
namespace: biological_process
def: "The acquisition, loss or modification of a protein or lipid within a protein-lipid complex." [GOC:BHF, GOC:mah, GOC:rl]
is_a: GO:0034367 ! protein-containing complex remodeling
-is_a: GO:0071825 ! protein-lipid complex subunit organization
+is_a: GO:0071825 ! protein-lipid complex organization
[Term]
id: GO:0034369
@@ -198482,7 +198424,7 @@ namespace: biological_process
def: "A process in which a protein is transported to, or maintained in, a location within the external part of the cell wall and/or plasma membrane." [GOC:mah]
synonym: "protein localisation at cell surface" EXACT [GOC:mah]
synonym: "protein localization at cell surface" EXACT []
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
[Term]
id: GO:0034395
@@ -198574,8 +198516,8 @@ id: GO:0034402
name: recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex
namespace: biological_process
def: "The process in which proteins required for 3'-end transcript processing become associated with the RNA polymerase II holoenzyme complex and the 3' end of a transcript." [PMID:18195044]
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
-relationship: part_of GO:0031124 ! mRNA 3'-end processing
+is_a: GO:0022618 ! protein-RNA complex assembly
+relationship: part_of GO:0180010 ! co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway
[Term]
id: GO:0034403
@@ -198635,8 +198577,8 @@ name: ascospore wall beta-glucan metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving beta-glucans, compounds composed of glucose residues linked by beta-D-glucosidic bonds, found in the walls of ascospores." [GOC:mah]
synonym: "ascospore wall beta-glucan metabolism" EXACT []
+is_a: GO:0022414 ! reproductive process
is_a: GO:0070879 ! fungal-type cell wall beta-glucan metabolic process
-is_a: GO:1903046 ! meiotic cell cycle process
relationship: part_of GO:0070591 ! ascospore wall biogenesis
[Term]
@@ -198741,27 +198683,29 @@ is_a: GO:0090503 ! RNA phosphodiester bond hydrolysis, exonucleolytic
[Term]
id: GO:0034416
-name: bisphosphoglycerate phosphatase activity
+name: obsolete bisphosphoglycerate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,3-diphosphoglycerate + H2O = phosphoglycerate + phosphate." [EC:3.1.3.80, GOC:mah, PMID:18413611]
+def: "OBSOLETE. Catalysis of the reaction: 2,3-diphosphoglycerate + H2O = phosphoglycerate + phosphate." [GOC:mah, PMID:18413611]
+comment: This term was obsoleted because it is not different from its child bisphosphoglycerate 3-phosphatase activity ; GO:0034417.
synonym: "2,3-bisphosphoglycerate phosphatase activity" EXACT []
synonym: "2,3-diphosphoglycerate phosphatase activity" EXACT []
synonym: "2,3-diphosphoglyceric acid phosphatase activity" EXACT []
synonym: "diphosphoglycerate phosphatase activity" EXACT []
synonym: "glycerate-2,3-diphosphate phosphatase activity" EXACT []
-is_a: GO:0016791 ! phosphatase activity
+is_obsolete: true
+replaced_by: GO:0034417
[Term]
id: GO:0034417
name: bisphosphoglycerate 3-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,3-diphosphoglycerate + H2O = 2-phospho-D-glycerate + phosphate." [EC:3.1.3.80, GOC:mah, PMID:18413611]
+def: "Catalysis of the reaction: (2R)-2,3-bisphosphoglycerate + H2O = (2R)-2-phosphoglycerate + phosphate." [GOC:mah, PMID:18413611, RHEA:27381]
synonym: "2,3-bisphospho-D-glycerate 3-phosphohydrolase activity" RELATED [EC:3.1.3.80]
xref: EC:3.1.3.80
xref: KEGG_REACTION:R09532
xref: MetaCyc:RXN-11102
xref: RHEA:27381
-is_a: GO:0034416 ! bisphosphoglycerate phosphatase activity
+is_a: GO:0016791 ! phosphatase activity
[Term]
id: GO:0034418
@@ -198775,7 +198719,7 @@ synonym: "urate synthesis" EXACT []
synonym: "uric acid biosynthetic process" EXACT []
is_a: GO:0044283 ! small molecule biosynthetic process
is_a: GO:0046415 ! urate metabolic process
-is_a: GO:1901576 ! organic substance biosynthetic process
+is_a: GO:0072522 ! purine-containing compound biosynthetic process
[Term]
id: GO:0034419
@@ -198895,7 +198839,7 @@ synonym: "AP-6-A hydrolase activity" EXACT []
synonym: "AP6A hydrolase activity" EXACT []
synonym: "diadenosine 5',5'''-P1,P6-hexaphosphate hydrolase activity" EXACT []
xref: RHEA:32047
-is_a: GO:0004551 ! nucleotide diphosphatase activity
+is_a: GO:0016462 ! pyrophosphatase activity
[Term]
id: GO:0034432
@@ -198907,29 +198851,33 @@ synonym: "AP-5-A hydrolase activity" EXACT []
synonym: "AP5A hydrolase activity" EXACT []
synonym: "Ap5a pyrophosphohydrolase activity" EXACT [GOC:tb]
synonym: "diadenosine 5',5'''-P1,P6-pentaphosphate hydrolase activity" EXACT []
-is_a: GO:0004551 ! nucleotide diphosphatase activity
+is_a: GO:0016462 ! pyrophosphatase activity
[Term]
id: GO:0034433
-name: steroid esterification
+name: obsolete steroid esterification
namespace: biological_process
-def: "A lipid modification process in which a steroid ester is formed by the combination of a carboxylic acid (often a fatty acid) and a steroid molecule (e.g. cholesterol)." [GOC:BHF, GOC:mah, GOC:pde, GOC:rl]
-is_a: GO:0008202 ! steroid metabolic process
-is_a: GO:0030258 ! lipid modification
+def: "OBSOLETE. A lipid modification process in which a steroid ester is formed by the combination of a carboxylic acid (often a fatty acid) and a steroid molecule (e.g. cholesterol)." [GOC:BHF, GOC:mah, GOC:pde, GOC:rl]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0034434
-name: sterol esterification
+name: obsolete sterol esterification
namespace: biological_process
-def: "A lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and a sterol molecule (e.g. cholesterol)." [GOC:BHF, GOC:mah, GOC:pde, GOC:rl]
-is_a: GO:0034433 ! steroid esterification
+def: "OBSOLETE. A lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and a sterol molecule (e.g. cholesterol)." [GOC:BHF, GOC:mah, GOC:pde, GOC:rl]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0008203
[Term]
id: GO:0034435
-name: cholesterol esterification
+name: obsolete cholesterol esterification
namespace: biological_process
-def: "A lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and cholesterol. In the blood this process is associated with the conversion of free cholesterol into cholesteryl ester, which is then sequestered into the core of a lipoprotein particle." [GOC:BHF, GOC:mah, GOC:pde, GOC:rl]
-is_a: GO:0034434 ! sterol esterification
+def: "OBSOLETE. A lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and cholesterol. In the blood this process is associated with the conversion of free cholesterol into cholesteryl ester, which is then sequestered into the core of a lipoprotein particle." [GOC:BHF, GOC:mah, GOC:pde, GOC:rl]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0008203
[Term]
id: GO:0034436
@@ -199026,7 +198974,6 @@ namespace: biological_process
def: "The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate." [GOC:mah, GOC:pf, PMID:17050732]
synonym: "cell spreading during cell substrate adhesion" EXACT []
synonym: "substrate adhesion dependent cell spreading" EXACT []
-is_a: GO:0000904 ! cell morphogenesis involved in differentiation
is_a: GO:0031589 ! cell-substrate adhesion
[Term]
@@ -199141,7 +199088,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a small-subunit processome." [GOC:mah]
synonym: "small subunit processome assembly" EXACT []
synonym: "SSU processome assembly" EXACT []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0000028 ! ribosomal small subunit assembly
[Term]
@@ -199149,7 +199096,7 @@ id: GO:0034463
name: 90S preribosome assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a 90S preribosome. The 90S preribosome represents the complex that forms on the primary rRNA transcript before it splits into the small subunit and large subunit portions." [GOC:krc, GOC:mah, GOC:tb]
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0000027 ! ribosomal large subunit assembly
relationship: part_of GO:0000028 ! ribosomal small subunit assembly
@@ -199206,7 +199153,11 @@ relationship: part_of GO:0005795 ! Golgi stack
id: GO:0034470
name: ncRNA processing
namespace: biological_process
-def: "Any process that results in the conversion of one or more primary non-coding RNA (ncRNA) transcripts into one or more mature ncRNA molecules." [GOC:mah]
+alt_id: GO:0031050
+def: "Any process that results in the conversion of one or more primary non-coding RNA (ncRNA) transcripts into one or more mature ncRNA molecules." [GOC:mah, PMID:27573892]
+synonym: "double-stranded RNA fragmentation" RELATED []
+synonym: "dsRNA fragmentation" RELATED []
+synonym: "dsRNA processing" RELATED []
is_a: GO:0006396 ! RNA processing
is_a: GO:0034660 ! ncRNA metabolic process
@@ -199218,6 +199169,7 @@ def: "Any process involved in forming the mature 5' end of a non-coding RNA mole
synonym: "ncRNA 5' end processing" EXACT []
is_a: GO:0000966 ! RNA 5'-end processing
is_a: GO:0034470 ! ncRNA processing
+is_a: GO:0036260 ! RNA capping
[Term]
id: GO:0034472
@@ -199226,7 +199178,7 @@ namespace: biological_process
def: "Any process involved in forming the mature 3' end of an snRNA molecule." [GOC:mah]
synonym: "snRNA 3' end processing" EXACT []
is_a: GO:0016180 ! snRNA processing
-is_a: GO:0043628 ! ncRNA 3'-end processing
+is_a: GO:0031123 ! RNA 3'-end processing
[Term]
id: GO:0034473
@@ -199290,16 +199242,16 @@ is_a: GO:0004629 ! phospholipase C activity
id: GO:0034480
name: phosphatidylcholine phospholipase C activity
namespace: molecular_function
-def: "Catalysis of the reaction: phosphatidylcholine + H2O = 1,2-diacylglycerol + a choline phosphate." [EC:3.1.4.3, GOC:mah]
-synonym: "alpha-toxin" NARROW [EC:3.1.4.3]
+def: "Catalysis of the reaction: a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1,2-diacyl-sn-glycerol + H+ + phosphocholine." [GOC:mah, RHEA:10604]
synonym: "Clostridium oedematiens beta- and gamma-toxins activity" NARROW [EC:3.1.4.3]
synonym: "Clostridium welchii alpha-toxin activity" NARROW [EC:3.1.4.3]
synonym: "heat-labile hemolysin" NARROW [EC:3.1.4.3]
synonym: "lipophosphodiesterase I activity" RELATED [EC:3.1.4.3]
-synonym: "phosphatidylcholine cholinephosphohydrolase activity" RELATED [EC:3.1.4.3]
+synonym: "phosphatidylcholine cholinephosphohydrolase activity" RELATED []
synonym: "phospholipase C, acting on phosphatidylcholine" EXACT []
xref: EC:3.1.4.3
xref: MetaCyc:PHOSPHOLIPASE-C-RXN
+xref: Reactome:R-HSA-9680388 "CSF1R-associated PLCG2 hydrolyzes phosphatidylcholine"
xref: RHEA:10604
is_a: GO:0004629 ! phospholipase C activity
@@ -199371,7 +199323,7 @@ id: GO:0034488
name: basic amino acid transmembrane export from vacuole
namespace: biological_process
def: "The directed movement of basic amino acids out of the vacuole, across the vacuolar membrane." [GOC:mah]
-is_a: GO:0034486 ! vacuolar transmembrane transport
+is_a: GO:0032974 ! amino acid transmembrane export from vacuole
is_a: GO:0034487 ! vacuolar amino acid transmembrane transport
is_a: GO:1990822 ! basic amino acid transmembrane transport
@@ -199448,7 +199400,7 @@ def: "Any process in which a protein is transported to, or maintained at, the ph
synonym: "protein localisation to phagophore assembly site" EXACT [GOC:mah]
synonym: "protein localization to PAS" EXACT []
synonym: "protein localization to pre-autophagosomal structure" NARROW []
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
relationship: part_of GO:0000045 ! autophagosome assembly
[Term]
@@ -199531,15 +199483,6 @@ synonym: "chromosome, centromeric core region" EXACT [GOC:vw]
is_a: GO:0098687 ! chromosomal region
relationship: part_of GO:0000775 ! chromosome, centromeric region
-[Term]
-id: GO:0034507
-name: chromosome, centromeric outer repeat region
-namespace: cellular_component
-def: "The portion of the centromeric region of a chromosome that flanks the core region, encompassing repeated regions of a chromosome centromere and the proteins that bind to it." [GOC:mah, GOC:vw]
-synonym: "chromosome, centric outer repeat region" RELATED []
-is_a: GO:0098687 ! chromosomal region
-relationship: part_of GO:0000775 ! chromosome, centromeric region
-
[Term]
id: GO:0034508
name: centromere complex assembly
@@ -199948,9 +199891,8 @@ id: GO:0034556
name: nitrobenzoate nitroreductase activity
namespace: molecular_function
def: "Catalysis of the reaction: o-nitrobenzoate + NADPH + H+ = o-hydroxylaminobenzoate + NADP+." [UM-BBD_reactionID:r0849]
-xref: EC:1.7.1.-
xref: UM-BBD_reactionID:r0849
-is_a: GO:0016657 ! oxidoreductase activity, acting on NAD(P)H, nitrogenous group as acceptor
+is_a: GO:0046857 ! oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor
[Term]
id: GO:0034557
@@ -200201,25 +200143,32 @@ is_a: GO:0034661 ! ncRNA catabolic process
[Term]
id: GO:0034587
-name: piRNA metabolic process
+name: piRNA processing
namespace: biological_process
-def: "The chemical reactions and pathways involving piRNAs, Piwi-associated RNAs, a class of 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism." [GOC:kmv]
+alt_id: GO:1990511
+def: "A process leading to the generation of a functional piRNA. piRNAs (Piwi-associated RNAs) are a class of 24- to 30-nucleotide RNAs derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism." [GOC:kmv, PMID:23329111, PMID:24696457, PMID:34724117]
subset: goslim_drosophila
-synonym: "piRNA metabolism" EXACT []
-synonym: "Piwi-associated RNA metabolic process" EXACT []
-is_a: GO:0034660 ! ncRNA metabolic process
+synonym: "piRNA biogenesis" EXACT []
+synonym: "piRNA biosynthetic process" RELATED []
+synonym: "piRNA metabolic process" RELATED []
+synonym: "piRNA metabolism" RELATED []
+synonym: "PIWI-associated RNA biogenesis" EXACT []
+synonym: "Piwi-associated RNA biosynthetic process" RELATED []
+synonym: "Piwi-associated RNA metabolic process" RELATED []
+synonym: "PIWI-associated RNA processing" EXACT []
+is_a: GO:0070918 ! regulatory ncRNA processing
[Term]
id: GO:0034588
-name: piRNA catabolic process
+name: obsolete piRNA catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of piRNAs, Piwi-associated RNAs, a class of 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism." [GOC:kmv]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of piRNAs, Piwi-associated RNAs, a class of 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism." [GOC:kmv]
+comment: This term has been obsoleted because there is no evidence for a specific pathway for piRNA degradation.
synonym: "piRNA breakdown" EXACT []
synonym: "piRNA catabolism" EXACT []
synonym: "piRNA degradation" EXACT []
synonym: "Piwi-associated RNA catabolic process" EXACT []
-is_a: GO:0034587 ! piRNA metabolic process
-is_a: GO:0034661 ! ncRNA catabolic process
+is_obsolete: true
[Term]
id: GO:0034589
@@ -200229,7 +200178,6 @@ def: "The directed movement of hydroxyproline into, out of or within a cell, or
synonym: "4-hydroxyproline transport" EXACT []
synonym: "L-hydroxyproline transport" NARROW []
is_a: GO:0006865 ! amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
is_a: GO:0072337 ! modified amino acid transport
[Term]
@@ -200239,7 +200187,7 @@ namespace: molecular_function
def: "Enables the transfer of L-hydroxyproline from one side of a membrane to the other." [GOC:mah, PMID:14502423]
synonym: "4-hydroxyproline transmembrane transporter activity" BROAD []
xref: Reactome:R-HSA-6784213 "Unknown hydroxyproline carrier transports cytosolic HPRO into the mitochondrial matrix"
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
@@ -200264,7 +200212,7 @@ relationship: part_of GO:0008021 ! synaptic vesicle
id: GO:0034593
name: phosphatidylinositol bisphosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phosphatidylinositol bisphosphate + H2O = phosphatidylinositol phosphate + phosphate." [GOC:mah]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol bisphosphate + H2O = phosphatidylinositol phosphate + phosphate." [GOC:mah]
synonym: "diphosphoinositide phosphatase activity" RELATED []
synonym: "phosphatidyl-inositol-bisphosphate phosphatase activity" EXACT []
synonym: "phosphatidylinositol-bisphosphatase activity" RELATED []
@@ -200308,13 +200256,12 @@ is_a: GO:0052866 ! phosphatidylinositol phosphate phosphatase activity
id: GO:0034597
name: phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 3-phosphate + phosphate." [GOC:mah]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 3-phosphate + phosphate." [GOC:mah, RHEA:25674]
synonym: "1-phosphatidyl-1D-myo-inositol-4,5-bisphosphate 4-phosphohydrolase activity" EXACT []
-synonym: "inositol polyphosphate 4-phosphatase type II activity" RELATED [EC:3.1.3.66]
synonym: "phosphatidyl-myo-inositol-4,5-bisphosphate 4-phosphohydrolase activity" EXACT []
-xref: EC:3.1.3.66
-xref: MetaCyc:3.1.3.66-RXN
+xref: EC:3.1.3.78
xref: Reactome:R-HSA-6810410 "PI(4,5)P2 is dephosphorylated to PI5P by TMEM55B in the nucleus"
+xref: RHEA:25674
is_a: GO:0034596 ! phosphatidylinositol phosphate 4-phosphatase activity
is_a: GO:0106019 ! phosphatidylinositol-4,5-bisphosphate phosphatase activity
@@ -200395,7 +200342,6 @@ name: turning behavior involved in mating
namespace: biological_process
def: "The sharp ventral turn performed by the male as he approaches either the hermaphrodite head or tail, whilst trying to locate his partner's vulva. Turning occurs via a sharp ventral coil of the male's tail." [PMID:18050467, WB_REF:WBPaper00002109]
synonym: "turning behavior during mating" EXACT []
-is_a: GO:0035178 ! turning behavior
is_a: GO:0060179 ! male mating behavior
[Term]
@@ -200418,7 +200364,7 @@ name: oligodeoxyribonucleotidase activity
namespace: molecular_function
def: "Catalysis of the exonucleolytic cleavage of oligodeoxyribonucleotides to yield deoxyribonucleoside 5'-phosphates." [GOC:mah]
synonym: "DNA oligonucleotidase activity" EXACT []
-is_a: GO:0004536 ! deoxyribonuclease activity
+is_a: GO:0004536 ! DNA nuclease activity
is_a: GO:0008946 ! oligonucleotidase activity
[Term]
@@ -200429,7 +200375,7 @@ def: "Catalysis of the exonucleolytic cleavage of oligoribonucleotides to yield
synonym: "RNA oligonucleotidase activity" EXACT []
xref: Reactome:R-HSA-9009950 "PDE12 cleaves 2'-5' oligoadenylates"
xref: Reactome:R-HSA-9615042 "Viral 2',5'-PDE cleaves 2'-5' oligoadenylates"
-is_a: GO:0004540 ! ribonuclease activity
+is_a: GO:0004540 ! RNA nuclease activity
is_a: GO:0008946 ! oligonucleotidase activity
[Term]
@@ -200440,17 +200386,6 @@ def: "Any process that results in a change in state or activity of a cell or an
synonym: "response to TNF" EXACT []
is_a: GO:0034097 ! response to cytokine
-[Term]
-id: GO:0034613
-name: cellular protein localization
-namespace: biological_process
-alt_id: GO:0016249
-def: "Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GOC:mah]
-synonym: "cellular protein localisation" EXACT [GOC:mah]
-synonym: "channel localizer activity" NARROW [GOC:mah]
-is_a: GO:0008104 ! protein localization
-is_a: GO:0070727 ! cellular macromolecule localization
-
[Term]
id: GO:0034614
name: cellular response to reactive oxygen species
@@ -200501,7 +200436,6 @@ def: "Binding to 2-amino-5-(carbamimidamido)pentanoic acid." [GOC:BHF, GOC:rl]
synonym: "aminopentanoic acid binding" RELATED []
synonym: "Arg binding" EXACT []
is_a: GO:0016597 ! amino acid binding
-is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0043169 ! cation binding
[Term]
@@ -200548,9 +200482,14 @@ is_a: GO:0009435 ! NAD biosynthetic process
id: GO:0034628
name: 'de novo' NAD biosynthetic process from aspartate
namespace: biological_process
+alt_id: GO:0019355
def: "The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of aspartate from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH." [GOC:imk]
synonym: "de novo NAD biosynthetic process from aspartate" RELATED []
-is_a: GO:0019355 ! nicotinamide nucleotide biosynthetic process from aspartate
+synonym: "nicotinamide nucleotide anabolism from aspartate" EXACT []
+synonym: "nicotinamide nucleotide biosynthetic process from aspartate" EXACT []
+synonym: "nicotinamide nucleotide formation from aspartate" EXACT []
+synonym: "nicotinamide nucleotide synthesis from aspartate" EXACT []
+is_a: GO:0006531 ! aspartate metabolic process
is_a: GO:0034627 ! 'de novo' NAD biosynthetic process
[Term]
@@ -200603,9 +200542,6 @@ name: glutathione transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of glutathione, the tripeptide glutamylcysteinylglycine, from one side of a membrane to the other." [GOC:mah]
is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0042937 ! tripeptide transmembrane transporter activity
-is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
-is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
[Term]
id: GO:0034635
@@ -200613,18 +200549,15 @@ name: glutathione transport
namespace: biological_process
def: "The directed movement of glutathione, the tripeptide glutamylcysteinylglycine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
is_a: GO:0015711 ! organic anion transport
-is_a: GO:0042939 ! tripeptide transport
-is_a: GO:0072337 ! modified amino acid transport
-is_a: GO:0072348 ! sulfur compound transport
[Term]
id: GO:0034637
-name: cellular carbohydrate biosynthetic process
+name: obsolete cellular carbohydrate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, carried out by individual cells." [GOC:mah]
-is_a: GO:0016051 ! carbohydrate biosynthetic process
-is_a: GO:0044249 ! cellular biosynthetic process
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, carried out by individual cells." [GOC:mah]
+comment: This term was obsoleted because it is not different from its parent, carbohydrate biosynthetic process ; GO:0016051.
+is_obsolete: true
+replaced_by: GO:0016051
[Term]
id: GO:0034638
@@ -200709,18 +200642,18 @@ is_a: GO:0071482 ! cellular response to light stimulus
[Term]
id: GO:0034645
-name: cellular macromolecule biosynthetic process
+name: obsolete cellular macromolecule biosynthetic process
namespace: biological_process
alt_id: GO:0034961
-def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells." [GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells." [GOC:mah]
+comment: This term was obsoleted because it is not different from its parent, macromolecule biosynthetic process ; GO:0009059.
synonym: "cellular biopolymer biosynthetic process" EXACT [GOC:mtg_chebi_dec09]
synonym: "cellular macromolecule anabolism" EXACT [GOC:mah]
synonym: "cellular macromolecule biosynthesis" EXACT [GOC:mah]
synonym: "cellular macromolecule formation" EXACT [GOC:mah]
synonym: "cellular macromolecule synthesis" EXACT [GOC:mah]
-is_a: GO:0009059 ! macromolecule biosynthetic process
-is_a: GO:0044249 ! cellular biosynthetic process
-is_a: GO:0044260 ! cellular macromolecule metabolic process
+is_obsolete: true
+replaced_by: GO:0009059
[Term]
id: GO:0034646
@@ -200732,7 +200665,7 @@ relationship: part_of GO:0043229 ! intracellular organelle
[Term]
id: GO:0034647
-name: histone H3-tri/di/monomethyl-lysine-4 demethylase activity
+name: histone H3K4me/H3K4me2/H3K4me3 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a tri, a di or a monomethyl-lysine residue at position 4 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:17550896, PMID:22473470]
synonym: "H3K4me3 demethylase activity" RELATED []
@@ -200740,11 +200673,12 @@ synonym: "histone demethylase activity (H3-K4-me3 specific)" EXACT []
synonym: "histone demethylase activity (H3-trimethyl-K4 specific)" EXACT []
synonym: "histone H3-K4me2 demethylase activity" BROAD []
synonym: "histone H3-K4me3 demethylase activity" RELATED []
+synonym: "histone H3-tri/di/monomethyl-lysine-4 demethylase activity" EXACT []
synonym: "histone H3K4me2 demethylase activity" BROAD []
xref: EC:1.14.11.67
xref: RHEA:60208
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
-is_a: GO:0032453 ! histone H3-methyl-lysine-4 demethylase activity
+is_a: GO:0032453 ! histone H3K4 demethylase activity
[Term]
id: GO:0034648
@@ -200798,14 +200732,14 @@ is_a: GO:1902645 ! tertiary alcohol biosynthetic process
[Term]
id: GO:0034652
-name: extrachromosomal circular DNA localization involved in cell aging
+name: obsolete extrachromosomal circular DNA localization involved in cell aging
namespace: biological_process
-def: "A process in which extrachromosomal circular DNA molecules are transported to, or maintained in, a specific location in cells contributing to their aging." [GOC:dph, GOC:jp, GOC:tb, PMID:18660802]
-comment: Note that the term string was changed to be consistent with placement of this term in cell aging hierarchy.
+def: "OBSOLETE. A process in which extrachromosomal circular DNA molecules are transported to, or maintained in, a specific location in cells contributing to their aging." [GOC:dph, GOC:jp, GOC:tb, PMID:18660802]
+comment: This term was obsoleted because it represents a phenotype.
synonym: "extrachromosomal circular DNA localisation involved in cell aging" EXACT [GOC:mah]
synonym: "extrachromosomal circular DNA localization during cell ageing" EXACT []
synonym: "extrachromosomal circular DNA localization during cell aging" RELATED [GOC:dph, GOC:tb]
-is_a: GO:0001301 ! progressive alteration of chromatin involved in cell aging
+is_obsolete: true
[Term]
id: GO:0034653
@@ -200869,7 +200803,9 @@ id: GO:0034657
name: GID complex
namespace: cellular_component
def: "A protein complex with ubiquitin ligase activity that is involved in proteasomal degradation of fructose-1,6-bisphosphatase (FBPase) and phosphoenolpyruvate carboxykinase during the transition from gluconeogenic to glycolytic growth conditions. In S. cerevisiae, the GID (Glucose Induced degradation Deficient) complex consists of Vid30p, Rmd5p, Vid24p, Vid28p, Gid7p, Gid8p, and Fyv10p." [PMID:12686616, PMID:18508925]
-is_a: GO:0140535 ! intracellular protein-containing complex
+synonym: "C-terminal to LisH complex" EXACT [PMID:29911972]
+synonym: "CTLH complex" EXACT [PMID:29911972]
+is_a: GO:0000151 ! ubiquitin ligase complex
[Term]
id: GO:0034658
@@ -200884,7 +200820,7 @@ name: isopropylmalate transport
namespace: biological_process
def: "The directed movement of isopropylmalate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
is_a: GO:0006835 ! dicarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
+is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
[Term]
@@ -200930,7 +200866,7 @@ namespace: cellular_component
def: "A protein complex that is located in the endoplasmic reticulum (ER) and is formed by the association of an immunoglobulin heavy chain with the proteins of the ER chaperone complex; the latter include BiP, GRP94; CaBP1, protein disulfide isomerase (PDI), ERdj3, cyclophilin B, ERp72, GRP170, UDP-glucosyltransferase, and SDF2-L1." [PMID:12475965]
synonym: "Ig heavy chain-bound ER chaperone complex" EXACT []
synonym: "immunoglobulin heavy chain-bound endoplasmic reticulum chaperone complex" EXACT []
-is_a: GO:0101031 ! chaperone complex
+is_a: GO:0101031 ! protein folding chaperone complex
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
[Term]
@@ -201200,6 +201136,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a prostagladin stimulus." [GOC:BHF, GOC:vk]
synonym: "response to prostaglandin stimulus" EXACT [GOC:dos]
is_a: GO:0009725 ! response to hormone
+is_a: GO:0033993 ! response to lipid
[Term]
id: GO:0034695
@@ -201260,15 +201197,14 @@ id: GO:0034701
name: tripeptidase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of a tripeptide." [GOC:mah]
-xref: EC:3.4.13.-
xref: MetaCyc:3.4.11.4-RXN
is_a: GO:0008238 ! exopeptidase activity
[Term]
id: GO:0034702
-name: ion channel complex
+name: monoatomic ion channel complex
namespace: cellular_component
-def: "A protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient." [GOC:mah, ISBN:071673706X]
+def: "A protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective monoatomic ion transport down its electrochemical gradient." [GOC:mah, ISBN:071673706X]
is_a: GO:1902495 ! transmembrane transporter complex
[Term]
@@ -201276,7 +201212,7 @@ id: GO:0034703
name: cation channel complex
namespace: cellular_component
def: "An ion channel complex through which cations pass." [GOC:mah]
-is_a: GO:0034702 ! ion channel complex
+is_a: GO:0034702 ! monoatomic ion channel complex
[Term]
id: GO:0034704
@@ -201304,7 +201240,7 @@ id: GO:0034707
name: chloride channel complex
namespace: cellular_component
def: "An ion channel complex through which chloride ions pass." [GOC:mah]
-is_a: GO:0034702 ! ion channel complex
+is_a: GO:0034702 ! monoatomic ion channel complex
[Term]
id: GO:0034708
@@ -201454,23 +201390,6 @@ xref: RHEA:56784
is_a: GO:0008234 ! cysteine-type peptidase activity
is_a: GO:0008242 ! omega peptidase activity
-[Term]
-id: GO:0034723
-name: DNA replication-dependent chromatin organization
-namespace: biological_process
-def: "The formation or destruction of chromatin structures on newly replicated DNA, coupled to strand elongation." [GOC:mah, PMID:17510629]
-synonym: "DNA replication-dependent nucleosome organisation" EXACT []
-synonym: "DNA replication-dependent nucleosome organization" EXACT []
-is_a: GO:0006325 ! chromatin organization
-
-[Term]
-id: GO:0034724
-name: DNA replication-independent chromatin organization
-namespace: biological_process
-def: "The formation or destruction of chromatin structures, occurring outside the context of DNA replication." [GOC:mah, PMID:17510629]
-synonym: "DNA replication-independent nucleosome organisation" EXACT []
-is_a: GO:0006325 ! chromatin organization
-
[Term]
id: GO:0034725
name: obsolete DNA replication-dependent nucleosome disassembly
@@ -201506,7 +201425,6 @@ namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of one or more nucleosomes." [GOC:mah]
synonym: "nucleosome organisation" EXACT []
is_a: GO:0006338 ! chromatin remodeling
-is_a: GO:0071824 ! protein-DNA complex subunit organization
[Term]
id: GO:0034729
@@ -201601,9 +201519,11 @@ is_a: GO:0004772 ! sterol O-acyltransferase activity
[Term]
id: GO:0034739
-name: histone deacetylase activity (H4-K16 specific)
+name: histone H4K16 deacetylase activity
namespace: molecular_function
def: "Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein." [GOC:vw, PMID:28450737]
+synonym: "histone deacetylase activity (H4-K16 specific)" EXACT []
+synonym: "histone H4-K16 deacetylase activity" EXACT []
is_a: GO:0004407 ! histone deacetylase activity
[Term]
@@ -201621,8 +201541,8 @@ namespace: cellular_component
def: "A protein complex that contains the tumor suppressor protein adenomatous polyposis coli (APC), alpha-tubulin, gamma-tubulin, and the Rac1 and Cdc42 effector IQGAP1; may play a role in cytoskeleton organization." [PMID:17126424]
comment: Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'.
synonym: "60S APC complex" NARROW []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005737 ! cytoplasm
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1905360 ! GTPase complex
[Term]
id: GO:0034743
@@ -201630,8 +201550,8 @@ name: APC-IQGAP complex
namespace: cellular_component
def: "A protein complex that contains the tumor suppressor protein adenomatous polyposis coli (APC) and the Rac1 and Cdc42 effector IQGAP1; may play a role in cytoskeleton organization and cell migration." [PMID:15572129]
comment: Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'.
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005737 ! cytoplasm
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1905360 ! GTPase complex
relationship: part_of GO:0031252 ! cell leading edge
[Term]
@@ -201640,8 +201560,8 @@ name: APC-IQGAP1-Cdc42 complex
namespace: cellular_component
def: "A protein complex that contains the tumor suppressor protein adenomatous polyposis coli (APC), the small GTPase Cdc42, and the Rac1 and Cdc42 effector IQGAP1; may play a role in cytoskeleton organization and cell migration." [PMID:15572129]
comment: Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'.
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005737 ! cytoplasm
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1905360 ! GTPase complex
relationship: part_of GO:0031252 ! cell leading edge
[Term]
@@ -201650,8 +201570,8 @@ name: APC-IQGAP1-Rac1 complex
namespace: cellular_component
def: "A protein complex that contains the tumor suppressor protein adenomatous polyposis coli (APC), the small GTPase Rac1, and the Rac1 and Cdc42 effector IQGAP1; may play a role in cytoskeleton organization and cell migration." [PMID:15572129]
comment: Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'.
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005737 ! cytoplasm
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1905360 ! GTPase complex
relationship: part_of GO:0031252 ! cell leading edge
[Term]
@@ -201660,8 +201580,8 @@ name: APC-IQGAP1-CLIP-170 complex
namespace: cellular_component
def: "A protein complex that contains the tumor suppressor protein adenomatous polyposis coli (APC), the small GTPase Cdc42, and CLIP-170; may play a role in cytoskeleton organization and cell migration." [PMID:15572129]
comment: Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'.
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005737 ! cytoplasm
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1905360 ! GTPase complex
relationship: part_of GO:0031252 ! cell leading edge
[Term]
@@ -201725,14 +201645,6 @@ synonym: "nuclear AHRC" EXACT []
is_a: GO:0034751 ! aryl hydrocarbon receptor complex
is_a: GO:0140513 ! nuclear protein-containing complex
-[Term]
-id: GO:0034754
-name: cellular hormone metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone, as carried out by individual cells." [GOC:mah]
-is_a: GO:0042445 ! hormone metabolic process
-is_a: GO:0044237 ! cellular metabolic process
-
[Term]
id: GO:0034755
name: iron ion transmembrane transport
@@ -201757,6 +201669,7 @@ synonym: "low-affinity iron ion transmembrane transport" NARROW []
synonym: "low-affinity iron ion transport" NARROW []
synonym: "transmembrane iron transport" EXACT []
is_a: GO:0006826 ! iron ion transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -201783,7 +201696,7 @@ synonym: "downregulation of iron ion transport" EXACT []
synonym: "inhibition of iron ion transport" NARROW []
synonym: "negative regulation of iron transport" EXACT []
is_a: GO:0034756 ! regulation of iron ion transport
-is_a: GO:0043271 ! negative regulation of ion transport
+is_a: GO:0043271 ! negative regulation of monoatomic ion transport
relationship: negatively_regulates GO:0006826 ! iron ion transport
[Term]
@@ -201798,7 +201711,7 @@ synonym: "up regulation of iron ion transport" EXACT []
synonym: "up-regulation of iron ion transport" EXACT []
synonym: "upregulation of iron ion transport" EXACT []
is_a: GO:0034756 ! regulation of iron ion transport
-is_a: GO:0043270 ! positive regulation of ion transport
+is_a: GO:0043270 ! positive regulation of monoatomic ion transport
relationship: positively_regulates GO:0006826 ! iron ion transport
[Term]
@@ -201811,7 +201724,7 @@ synonym: "regulation of transmembrane Fe transport" EXACT []
synonym: "regulation of transmembrane iron ion transport" EXACT [GOC:dph, GOC:tb]
synonym: "regulation of transmembrane iron transport" EXACT []
is_a: GO:0034756 ! regulation of iron ion transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
+is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport
relationship: regulates GO:0034755 ! iron ion transmembrane transport
[Term]
@@ -201892,18 +201805,19 @@ relationship: positively_regulates GO:0055085 ! transmembrane transport
[Term]
id: GO:0034765
-name: regulation of ion transmembrane transport
+name: regulation of monoatomic ion transmembrane transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other." [GOC:mah]
synonym: "regulation of ion membrane transport" EXACT []
+synonym: "regulation of ion transmembrane transport" BROAD []
synonym: "regulation of transmembrane ion transport" EXACT [GOC:dph, GOC:tb]
is_a: GO:0034762 ! regulation of transmembrane transport
-is_a: GO:0043269 ! regulation of ion transport
-relationship: regulates GO:0034220 ! ion transmembrane transport
+is_a: GO:0043269 ! regulation of monoatomic ion transport
+relationship: regulates GO:0034220 ! monoatomic ion transmembrane transport
[Term]
id: GO:0034766
-name: negative regulation of ion transmembrane transport
+name: negative regulation of monoatomic ion transmembrane transport
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other." [GOC:mah]
synonym: "down regulation of transmembrane ion transport" EXACT []
@@ -201911,28 +201825,30 @@ synonym: "down-regulation of transmembrane ion transport" EXACT []
synonym: "downregulation of transmembrane ion transport" EXACT []
synonym: "inhibition of transmembrane ion transport" NARROW []
synonym: "negative regulation of ion membrane transport" EXACT []
+synonym: "negative regulation of ion transmembrane transport" BROAD []
synonym: "negative regulation of transmembrane ion transport" EXACT [GOC:dph, GOC:tb]
is_a: GO:0034763 ! negative regulation of transmembrane transport
-is_a: GO:0034765 ! regulation of ion transmembrane transport
-is_a: GO:0043271 ! negative regulation of ion transport
-relationship: negatively_regulates GO:0034220 ! ion transmembrane transport
+is_a: GO:0034765 ! regulation of monoatomic ion transmembrane transport
+is_a: GO:0043271 ! negative regulation of monoatomic ion transport
+relationship: negatively_regulates GO:0034220 ! monoatomic ion transmembrane transport
[Term]
id: GO:0034767
-name: positive regulation of ion transmembrane transport
+name: positive regulation of monoatomic ion transmembrane transport
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other." [GOC:mah]
synonym: "activation of transmembrane ion transport" NARROW []
synonym: "positive regulation of ion membrane transport" EXACT []
+synonym: "positive regulation of ion transmembrane transport" BROAD []
synonym: "positive regulation of transmembrane ion transport" EXACT []
synonym: "stimulation of transmembrane ion transport" NARROW []
synonym: "up regulation of transmembrane ion transport" EXACT []
synonym: "up-regulation of transmembrane ion transport" EXACT []
synonym: "upregulation of transmembrane ion transport" EXACT []
is_a: GO:0034764 ! positive regulation of transmembrane transport
-is_a: GO:0034765 ! regulation of ion transmembrane transport
-is_a: GO:0043270 ! positive regulation of ion transport
-relationship: positively_regulates GO:0034220 ! ion transmembrane transport
+is_a: GO:0034765 ! regulation of monoatomic ion transmembrane transport
+is_a: GO:0043270 ! positive regulation of monoatomic ion transport
+relationship: positively_regulates GO:0034220 ! monoatomic ion transmembrane transport
[Term]
id: GO:0034768
@@ -201967,13 +201883,14 @@ is_a: GO:0034968 ! histone lysine methylation
[Term]
id: GO:0034771
-name: histone H4-K20 monomethylation
+name: obsolete histone H4-K20 monomethylation
namespace: biological_process
-def: "The modification of histone H4 by addition of one methyl group to lysine at position 20 of the histone." [GOC:mah]
+def: "OBSOLETE. The modification of histone H4 by addition of one methyl group to lysine at position 20 of the histone." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H4 K20 monomethylation" EXACT []
synonym: "histone lysine H4 K20 monomethylation" EXACT []
-is_a: GO:0018026 ! peptidyl-lysine monomethylation
-is_a: GO:0034770 ! histone H4-K20 methylation
+is_obsolete: true
+consider: GO:0042799
[Term]
id: GO:0034772
@@ -202012,8 +201929,7 @@ comment: Note that this term is not intended for use in annotating lateral movem
synonym: "glutathione membrane transport" EXACT []
synonym: "transmembrane glutathione transport" EXACT [GOC:dph, GOC:tb]
is_a: GO:0034635 ! glutathione transport
-is_a: GO:0035443 ! tripeptide transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0034776
@@ -203581,7 +203497,7 @@ relationship: part_of GO:0003100 ! regulation of systemic arterial blood pressur
id: GO:0034963
name: box C/D RNA processing
namespace: biological_process
-def: "Any process involved in the conversion of a primary box C/D type small RNA transcript into a mature box C/D RNA." [GOC:krc, GOC:mah]
+def: "Any process involved in the conversion of a primary box C/D type small RNA transcript into a mature box C/D RNA." [GOC:krc, GOC:mah]
synonym: "box C/D snoRNA processing" NARROW []
synonym: "box C/D sRNA processing" NARROW []
is_a: GO:0033967 ! box C/D RNA metabolic process
@@ -203591,7 +203507,7 @@ is_a: GO:0043144 ! sno(s)RNA processing
id: GO:0034964
name: box H/ACA RNA processing
namespace: biological_process
-def: "Any process involved in the conversion of a primary box H/ACA type small RNA transcript into a mature box H/ACA RNA." [GOC:krc, GOC:mah]
+def: "Any process involved in the conversion of a primary box H/ACA type small RNA transcript into a mature box H/ACA RNA." [GOC:krc, GOC:mah]
synonym: "box H/ACA snoRNA processing" NARROW []
synonym: "box H/ACA sRNA processing" NARROW []
is_a: GO:0033979 ! box H/ACA RNA metabolic process
@@ -203720,6 +203636,7 @@ namespace: cellular_component
def: "A protein complex that contains the precursor form of NF-kappaB (p105), the NF-kappaB inhibitor ABIN-2, and the kinase TPL-2 (MAP3K8); the complex stabilizes TPL-2 and is involved in signaling in lipopolysaccharide (LPS)-stimulated macrophages." [PMID:15169888]
synonym: "ABIN2-NFKB1-TPL-1 complex" EXACT []
is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902554 ! serine/threonine protein kinase complex
[Term]
id: GO:0034978
@@ -203741,7 +203658,7 @@ xref: Reactome:R-HSA-5688289 "SIRT3 deacetylates ACCS2, GLUD, IDH2, SOD2"
xref: Reactome:R-HSA-5688294 "SIRT5 deacetylates Cytochrome C"
xref: Reactome:R-HSA-9620532 "SIRT1,SIRT3 deacetylate FOXO3"
xref: Reactome:R-HSA-9667952 "ANKLE2 is deacetylated by SIRT2"
-is_a: GO:0033558 ! protein deacetylase activity
+is_a: GO:0033558 ! protein lysine deacetylase activity
[Term]
id: GO:0034980
@@ -203766,7 +203683,6 @@ namespace: biological_process
def: "The peptide cleavage of mitochondrial proteins, including cleavage contributing to their import." [GOC:curators]
synonym: "mitochondrial protein modification" RELATED []
is_a: GO:0016485 ! protein processing
-is_a: GO:0044267 ! cellular protein metabolic process
[Term]
id: GO:0034983
@@ -203808,23 +203724,6 @@ def: "Binding to one or more specific sites on the Fc-gamma receptor I complex.
is_a: GO:0034987 ! immunoglobulin receptor binding
is_a: GO:0044877 ! protein-containing complex binding
-[Term]
-id: GO:0034990
-name: nuclear mitotic cohesin complex
-namespace: cellular_component
-def: "A cohesin complex that mediates sister chromatid cohesion in the nucleus during mitosis; has a subunit composition distinct from that of the meiotic cohesin complex." [GOC:mah]
-comment: Note that this term should be used to annotate gene products found in cohesin complexes in organisms that undergo closed mitosis (i. e. where the nuclear envelope does not break down, as in fungi). For organisms in which the nuclear envelope breaks down during mitosis, the parent should be used.
-is_a: GO:0000798 ! nuclear cohesin complex
-is_a: GO:0030892 ! mitotic cohesin complex
-
-[Term]
-id: GO:0034991
-name: nuclear meiotic cohesin complex
-namespace: cellular_component
-def: "A cohesin complex that mediates sister chromatid cohesion in the nucleus during meiosis; has a subunit composition distinct from that of the mitotic cohesin complex." [GOC:mah]
-is_a: GO:0000798 ! nuclear cohesin complex
-is_a: GO:0030893 ! meiotic cohesin complex
-
[Term]
id: GO:0034992
name: microtubule organizing center attachment site
@@ -203841,7 +203740,7 @@ relationship: part_of GO:0005635 ! nuclear envelope
id: GO:0034993
name: meiotic nuclear membrane microtubule tethering complex
namespace: cellular_component
-def: "A nuclear membrane protein complex which connects the nuclear outer and inner membranes together, and links links the nuclear lumen to cytoplasmic microtubules during meiosis." [GOC:mah, PMID:18692466]
+def: "A nuclear membrane protein complex which connects the nuclear outer and inner membranes together, and links links the nuclear lumen to cytoplasmic microtubules during meiosis." [GOC:mah, PMID:18692466]
synonym: "LINC complex" EXACT []
synonym: "LInker of Nucleoskeleton and Cytoskeleton complex" EXACT []
synonym: "SUN-KASH complex" EXACT []
@@ -203865,7 +203764,6 @@ name: SC5b-7 complex
namespace: cellular_component
def: "A protein complex that consist of complement components C5b6 and C7 stably inserted in a cell membrane. Formation of the SC5b-7 complex is the first phase of membrane attack complex assembly." [PMID:10090939]
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0034996
@@ -203884,7 +203782,6 @@ namespace: cellular_component
def: "A protein complex that comprises one integrin alphav subunit, one integrin beta5 subunit, and vitronectin." [PMID:1694173]
synonym: "ITGAV-ITGB5-VTN complex" NARROW [CORUM:3117]
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0034998
@@ -203947,14 +203844,15 @@ xref: Reactome:R-HSA-1433514 "Synthesis of PIP3 from PIP2 by PI3K"
xref: Reactome:R-HSA-2045911 "BCAP Signalosome phosphorylates PI(4,5)P2 forming PI(3,4,5)P3"
xref: Reactome:R-HSA-9028519 "NTRK2-activated PI3K generates PIP3"
xref: Reactome:R-HSA-9670433 "KIT mutants:PI3K catalyze synthesis of PIP3"
+xref: Reactome:R-HSA-9680389 "CSF1R-associated phosphatidylinositol 3-kinase (PI3K) phosphorylates PI(4,5)P2"
xref: Wikipedia:Phosphoinositide_3-kinase
-is_a: GO:0016301 ! kinase activity
+is_a: GO:0001727 ! lipid kinase activity
[Term]
id: GO:0035005
name: 1-phosphatidylinositol-4-phosphate 3-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4-phosphate + ATP = 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + ADP + 2 H(+)." [EC:2.7.1.154, RHEA:18373]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4-phosphate + ATP = 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + ADP + 2 H+." [EC:2.7.1.154, RHEA:18373]
synonym: "ATP:1-phosphatidyl-1D-myo-inositol-4-phosphate 3-phosphotransferase activity" RELATED [EC:2.7.1.154]
synonym: "C2-domain-containing phosphoinositide 3-kinase activity" NARROW [EC:2.7.1.154]
synonym: "phosphatidylinositol 3-kinase activity, class I" NARROW []
@@ -204291,7 +204189,7 @@ relationship: part_of GO:0035039 ! male pronucleus assembly
id: GO:0035041
name: sperm DNA decondensation
namespace: biological_process
-def: "Unwinding of the condensed nuclear chromatin of an inactive sperm nucleus." [GOC:bf, PMID:11735001]
+def: "Unwinding of the condensed nuclear chromatin of an inactive male pronucleus after fertilization." [GOC:bf, PMID:11735001, PMID:23352575]
synonym: "sperm chromatin decondensation" EXACT []
is_a: GO:0006325 ! chromatin organization
is_a: GO:0022414 ! reproductive process
@@ -204299,14 +204197,15 @@ relationship: part_of GO:0035039 ! male pronucleus assembly
[Term]
id: GO:0035042
-name: fertilization, exchange of chromosomal proteins
+name: obsolete fertilization, exchange of chromosomal proteins
namespace: biological_process
-def: "Replacement of sperm-specific chromosomal proteins with somatic histones, to allow the paternal genome to acquire a nucleosomal chromatin organization compatible with nuclear activity." [GOC:bf, PMID:11735001]
+def: "OBSOLETE. Replacement of sperm-specific chromosomal proteins with somatic histones, to allow the paternal genome to acquire a nucleosomal chromatin organization compatible with nuclear activity." [GOC:bf, PMID:11735001]
+comment: This term has been obsoleted because it represents a molecular function (histone chaperone activity) and a process (sperm DNA decondensation).
synonym: "sperm-specific histone exchange" EXACT []
synonym: "sperm-specific histone replacement" EXACT []
-is_a: GO:0022414 ! reproductive process
-is_a: GO:0043486 ! histone exchange
-relationship: part_of GO:0035041 ! sperm DNA decondensation
+is_obsolete: true
+consider: GO:0035041
+consider: GO:0140713
[Term]
id: GO:0035043
@@ -204468,7 +204367,7 @@ is_a: GO:0030575 ! nuclear body organization
id: GO:0035064
name: methylated histone binding
namespace: molecular_function
-def: "Binding to a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:bf, PMID:14585615]
+def: "Binding to a histone in which a residue has been modified by methylation." [GOC:bf, PMID:14585615]
is_a: GO:0042393 ! histone binding
is_a: GO:0140034 ! methylation-dependent protein binding
@@ -204491,7 +204390,6 @@ synonym: "stimulation of histone acetylation" NARROW []
synonym: "up regulation of histone acetylation" EXACT []
synonym: "up-regulation of histone acetylation" EXACT []
synonym: "upregulation of histone acetylation" EXACT []
-is_a: GO:0031058 ! positive regulation of histone modification
is_a: GO:0035065 ! regulation of histone acetylation
is_a: GO:2000758 ! positive regulation of peptidyl-lysine acetylation
relationship: positively_regulates GO:0016573 ! histone acetylation
@@ -204505,7 +204403,6 @@ synonym: "down regulation of histone acetylation" EXACT []
synonym: "down-regulation of histone acetylation" EXACT []
synonym: "downregulation of histone acetylation" EXACT []
synonym: "inhibition of histone acetylation" NARROW []
-is_a: GO:0031057 ! negative regulation of histone modification
is_a: GO:0035065 ! regulation of histone acetylation
is_a: GO:2000757 ! negative regulation of peptidyl-lysine acetylation
relationship: negatively_regulates GO:0016573 ! histone acetylation
@@ -204651,15 +204548,6 @@ is_a: GO:0001578 ! microtubule bundle formation
is_a: GO:0022607 ! cellular component assembly
relationship: part_of GO:0060271 ! cilium assembly
-[Term]
-id: GO:0035087
-name: siRNA loading onto RISC involved in RNA interference
-namespace: biological_process
-def: "The transfer of small interfering RNA molecules (siRNAs) from the Dicer family of enzymes that cleave the double-stranded RNA, onto the nuclease-containing RNA-initiated silencing complex (RISC), in the context of RNA interference." [GOC:bf, GOC:mah, PMID:14512631]
-synonym: "RNA interference, siRNA loading onto RISC" EXACT [GOC:mah]
-is_a: GO:0070922 ! small RNA loading onto RISC
-relationship: part_of GO:0016246 ! RNA interference
-
[Term]
id: GO:0035088
name: establishment or maintenance of apical/basal cell polarity
@@ -204695,22 +204583,14 @@ is_a: GO:0005543 ! phospholipid binding
id: GO:0035092
name: sperm DNA condensation
namespace: biological_process
+alt_id: GO:0035093
def: "The progressive compaction of the spermatid chromatin so that it reaches a level of condensation that is not compatible with nuclear activities such as transcription or DNA replication." [GOC:bf, PMID:11735001]
synonym: "sperm chromatin condensation" EXACT []
-is_a: GO:0006323 ! DNA packaging
+synonym: "spermatogenesis, exchange of chromosomal proteins" RELATED []
is_a: GO:0006325 ! chromatin organization
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
relationship: part_of GO:0007289 ! spermatid nucleus differentiation
-[Term]
-id: GO:0035093
-name: spermatogenesis, exchange of chromosomal proteins
-namespace: biological_process
-def: "The replacement of somatic histones within sperm chromatin with sperm-specific histones or protamines with unique DNA-binding properties, resulting in condensation of the sperm chromatin." [GOC:bf, PMID:11735001]
-is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
-is_a: GO:0043486 ! histone exchange
-relationship: part_of GO:0035092 ! sperm DNA condensation
-
[Term]
id: GO:0035094
name: response to nicotine
@@ -204797,16 +204677,15 @@ is_a: GO:0031519 ! PcG protein complex
[Term]
id: GO:0035103
-name: sterol regulatory element binding protein cleavage
+name: obsolete sterol regulatory element binding protein cleavage
namespace: biological_process
alt_id: GO:0006992
-def: "The proteolytic release of a transcriptionally active sterol regulatory element binding protein (SREBP) from intracellular membranes, freeing it to move to the nucleus to upregulate transcription of target genes, in response to altered levels of one or more lipids." [GOC:bf, GOC:vw, PMID:12923525]
+def: "OBSOLETE. The proteolytic release of a transcriptionally active sterol regulatory element binding protein (SREBP) from intracellular membranes, freeing it to move to the nucleus to upregulate transcription of target genes, in response to altered levels of one or more lipids." [GOC:bf, GOC:vw, PMID:12923525]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "SREBP cleavage" EXACT []
synonym: "sterol depletion response, SREBP cleavage" EXACT []
synonym: "sterol regulatory element binding protein cleavage involved in ER-nuclear sterol response pathway" NARROW [GOC:vw]
-is_a: GO:0016485 ! protein processing
-is_a: GO:0044267 ! cellular protein metabolic process
-relationship: part_of GO:0032933 ! SREBP signaling pathway
+is_obsolete: true
[Term]
id: GO:0035105
@@ -205279,7 +205158,7 @@ def: "Ensuring that a tube in an open tracheal system is of the correct diameter
synonym: "regulation of tracheal tube diameter" EXACT []
synonym: "tracheal tube dilation" NARROW []
synonym: "tracheal tube expansion" NARROW []
-is_a: GO:0035159 ! regulation of tube length, open tracheal system
+is_a: GO:0035151 ! regulation of tube size, open tracheal system
is_a: GO:0035296 ! regulation of tube diameter
[Term]
@@ -205416,28 +205295,33 @@ is_a: GO:0008283 ! cell population proliferation
id: GO:0035173
name: histone kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to a histone. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:bf]
+def: "Catalysis of the transfer of a phosphate group to a histone." [GOC:bf]
is_a: GO:0004672 ! protein kinase activity
+is_a: GO:0140993 ! histone modifying activity
[Term]
id: GO:0035174
-name: histone serine kinase activity
+name: obsolete histone serine kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to a serine residue of a histone. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:bf]
+def: "OBSOLETE. Catalysis of the transfer of a phosphate group to a serine residue of a histone." [GOC:bf]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "histone-serine kinase activity" EXACT []
-is_a: GO:0004674 ! protein serine/threonine kinase activity
-is_a: GO:0035173 ! histone kinase activity
+is_obsolete: true
+consider: GO:0140995
+consider: GO:0140996
+consider: GO:0140997
+consider: GO:0140998
[Term]
id: GO:0035175
-name: histone kinase activity (H3-S10 specific)
+name: histone H3S10 kinase activity
namespace: molecular_function
alt_id: GO:0044021
-def: "Catalysis of the transfer of a phosphate group to the serine-10 residue of the N-terminal tail of histone H3." [GOC:bf, PMID:15041176]
-synonym: "histone kinase activity (H3-S3 specific)" EXACT []
+def: "Catalysis of the reaction: histone H3-serine (position 10) + ATP = histone H3-phosphoserine (position 10) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 10 of histone H3." [GOC:bf, PMID:15041176]
+synonym: "histone kinase activity (H3-S10 specific)" EXACT []
synonym: "histone serine kinase activity (H3-S10 specific)" EXACT []
synonym: "histone-serine kinase activity (H3-S10 specific)" EXACT []
-is_a: GO:0035174 ! histone serine kinase activity
+is_a: GO:0140996 ! histone H3 kinase activity
[Term]
id: GO:0035176
@@ -205503,6 +205387,7 @@ synonym: "germline ring canal outer rim" BROAD []
synonym: "nurse cell ring canal outer rim" NARROW []
synonym: "ovarian ring canal outer rim" NARROW []
is_a: GO:0110165 ! cellular anatomical entity
+relationship: part_of GO:0005576 ! extracellular region
relationship: part_of GO:0035324 ! female germline ring canal
[Term]
@@ -205515,16 +205400,21 @@ synonym: "germline ring canal inner rim" BROAD []
synonym: "nurse cell ring canal inner rim" NARROW []
synonym: "ovarian ring canal inner rim" NARROW []
is_a: GO:0110165 ! cellular anatomical entity
+relationship: part_of GO:0005576 ! extracellular region
relationship: part_of GO:0035324 ! female germline ring canal
[Term]
id: GO:0035184
-name: histone threonine kinase activity
+name: obsolete histone threonine kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to a threonine residue of a histone. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:bf]
+def: "OBSOLETE. Catalysis of the transfer of a phosphate group to a threonine residue of a histone." [GOC:bf]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "histone-threonine kinase activity" EXACT []
-is_a: GO:0004674 ! protein serine/threonine kinase activity
-is_a: GO:0035173 ! histone kinase activity
+is_obsolete: true
+consider: GO:0140995
+consider: GO:0140996
+consider: GO:0140997
+consider: GO:0140998
[Term]
id: GO:0035185
@@ -205549,7 +205439,6 @@ namespace: biological_process
def: "The specific behavior of an organism during the emergence from an egg shell. In Drosophila for example, the larva swings its head reiteratively through a semicircular arc, using its mouth hooks to tear apart the chorion in front of it and thus free itself from within the egg shell." [GOC:pr, PMID:10436051]
synonym: "hatching behaviour" EXACT []
is_a: GO:0007610 ! behavior
-is_a: GO:0032501 ! multicellular organismal process
relationship: part_of GO:0035188 ! hatching
[Term]
@@ -205605,46 +205494,55 @@ relationship: part_of GO:0007417 ! central nervous system development
[Term]
id: GO:0035194
-name: post-transcriptional gene silencing by RNA
+name: ncRNA-mediated post-transcriptional gene silencing
namespace: biological_process
-def: "Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger RNA (often mRNA) degradation or negatively regulate mRNA translation." [GOC:aruk, GOC:bc, GOC:mah, GOC:rl, PMID:15020054, PMID:15066275, PMID:15066283, PMID:23985560, PMID:28379604]
+alt_id: GO:0016246
+def: "A posttranscriptional gene silencing pathway in which regulatory RNAs elicit silencing of specific target genes, either by mRNA destabilization or inhibition of translation." [GOC:ems, PMID:11201747, PMID:11713190, PMID:15020054, PMID:15066275, PMID:18771919, PMID:32885814, PMID:33184244]
+synonym: "cosuppression" RELATED []
+synonym: "post-transcriptional gene silencing by RNA" RELATED []
synonym: "posttranscriptional gene silencing by RNA" EXACT []
+synonym: "PTGS" BROAD []
+synonym: "quelling" RELATED []
+synonym: "RNA interference" BROAD []
+synonym: "RNA-dependent post-transcriptional gene silencing" EXACT []
+synonym: "RNA-mediated post-transcriptional gene silencing" EXACT []
synonym: "RNA-mediated posttranscriptional gene silencing" EXACT [GOC:dph, GOC:tb]
-synonym: "sense-PTGS" RELATED []
-is_a: GO:0016441 ! posttranscriptional gene silencing
-is_a: GO:0031047 ! gene silencing by RNA
+synonym: "RNAi" BROAD []
+xref: Wikipedia:RNA_interference
+is_a: GO:0016441 ! post-transcriptional gene silencing
+is_a: GO:0031047 ! RNA-mediated gene silencing
[Term]
id: GO:0035195
-name: gene silencing by miRNA
+name: miRNA-mediated gene silencing
namespace: biological_process
-def: "Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: endolytic cleavage of the RNA (often mRNA) or mRNA translational repression, usually accompanied by poly-A tail shortening and subsequent degradation of the mRNA." [GOC:aruk, GOC:bc, GOC:rl, PMID:14744438, PMID:15066275, PMID:15066283, PMID:23209154, PMID:23985560, PMID:28379604]
+def: "A post-transcriptional gene silencing pathway in which regulatory microRNAs (miRNAs) elicit silencing of specific target genes. miRNAs are endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate protein production by either of two posttranscriptional mechanisms: endonucleolytic cleavage of the RNA (often mRNA) or mRNA translational repression, usually accompanied by poly-A tail shortening and subsequent degradation of the mRNA. miRNAs are present in all the animals and in plants, whereas siRNAs are present in lower animals and in plants." [GOC:aruk, GOC:bc, GOC:rl, PMID:14744438, PMID:15066275, PMID:15066283, PMID:23209154, PMID:23985560, PMID:28379604]
synonym: "gene silencing by microRNA" EXACT [GOC:pr]
+synonym: "gene silencing by miRNA" EXACT [GOC:dph, GOC:tb]
synonym: "microRNA-mediated gene silencing" EXACT []
-synonym: "miRNA-mediated gene silencing" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0035194 ! post-transcriptional gene silencing by RNA
+is_a: GO:0035194 ! ncRNA-mediated post-transcriptional gene silencing
[Term]
id: GO:0035196
-name: production of miRNAs involved in gene silencing by miRNA
+name: miRNA processing
namespace: biological_process
alt_id: GO:0030918
-def: "Cleavage of stem-loop RNA precursors into microRNAs (miRNAs), a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein, or by increasing the degradation of non-protein-coding RNA transcripts." [GOC:aruk, GOC:bc, GOC:dph, GOC:rl, GOC:tb, PMID:15066275, PMID:15066283, PMID:23985560, PMID:28379604]
+def: "A process leading to the generation of a functional miRNA. Includes the cleavage of stem-loop RNA precursors into microRNAs (miRNAs). miRNAs are a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein, or by increasing the degradation of non-protein-coding RNA transcripts." [GOC:aruk, GOC:bc, GOC:dph, GOC:rl, GOC:tb, PMID:15066275, PMID:15066283, PMID:23985560, PMID:28379604]
synonym: "gene silencing by miRNA, production of miRNAs" EXACT [GOC:mah]
-synonym: "microRNA biogenesis" RELATED [GOC:tb]
-synonym: "microRNA biosynthesis" RELATED []
-synonym: "microRNA biosynthetic process" RELATED []
-synonym: "microRNA metabolic process" RELATED []
-synonym: "microRNA metabolism" RELATED []
-synonym: "microRNA processing" BROAD []
+synonym: "microRNA biogenesis" EXACT [GOC:tb]
+synonym: "microRNA biosynthesis" BROAD []
+synonym: "microRNA biosynthetic process" BROAD []
+synonym: "microRNA metabolic process" BROAD []
+synonym: "microRNA metabolism" BROAD []
+synonym: "microRNA processing" EXACT []
synonym: "microRNA-mediated gene silencing, production of microRNAs" EXACT []
-synonym: "miRNA biogenesis" RELATED [GOC:tb]
-synonym: "miRNA biosynthetic process" EXACT []
-synonym: "miRNA processing" EXACT []
+synonym: "miRNA biogenesis" RELATED []
+synonym: "miRNA biosynthetic process" BROAD []
+synonym: "miRNA maturation" EXACT []
synonym: "miRNA-mediated gene silencing, production of miRNAs" EXACT [GOC:dph, GOC:tb]
synonym: "production of microRNAs involved in gene silencing by microRNA" EXACT [GOC:pr]
-is_a: GO:0070918 ! production of small RNA involved in gene silencing by RNA
-relationship: part_of GO:0035195 ! gene silencing by miRNA
+synonym: "production of miRNAs involved in gene silencing by miRNA" EXACT []
+is_a: GO:0070918 ! regulatory ncRNA processing
[Term]
id: GO:0035197
@@ -205998,7 +205896,7 @@ is_a: GO:0010623 ! programmed cell death involved in cell development
id: GO:0035235
name: ionotropic glutamate receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, ISBN:0198506732]
+def: "The series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, ISBN:0198506732]
synonym: "ionotropic glutamate receptor signalling pathway" EXACT []
is_a: GO:0007215 ! glutamate receptor signaling pathway
is_a: GO:1990806 ! ligand-gated ion channel signaling pathway
@@ -206050,12 +205948,13 @@ is_a: GO:1901338 ! catecholamine binding
id: GO:0035241
name: protein-arginine omega-N monomethyltransferase activity
namespace: molecular_function
-def: "Catalysis of the addition of a methyl group to either of the unmethylated terminal nitrogen atoms (also called omega nitrogen) in peptidyl-arginine to form an omega-N-G-monomethylated arginine residue. The reaction is S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-Nomega-methyl-L-arginine." [EC:2.1.1.321, PMID:14705965, RESID:AA0069]
+def: "Catalysis of the addition of a methyl group to either of the unmethylated terminal nitrogen atoms (also called omega nitrogen) in peptidyl-arginine to form an omega-N-G-monomethylated arginine residue. The reaction is S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-Nomega-methyl-L-arginine." [EC:2.1.1.321, PMID:14705965, RESID:AA0069]
comment: Type III protein arginine methyltransferases catalyze the single methylation of one of the terminal nitrogen atoms of the guanidino group in an L-arginine residue within a protein. Unlike type I and type II protein arginine methyltransferases, which also catalyze this reaction, type III enzymes do not methylate the substrate any further.
+synonym: "protein arginine omega-N monomethylase activity" EXACT []
synonym: "S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-Nomega-methyl-L-arginine-forming)" RELATED [EC:2.1.1.321]
synonym: "type III protein arginine methyltransferase activity" RELATED [EC:2.1.1.321]
xref: EC:2.1.1.321
-xref: RESID:AA0069
+xref: MetaCyc:2.1.1.124-RXN
xref: RHEA:48100
is_a: GO:0016274 ! protein-arginine N-methyltransferase activity
@@ -206063,14 +205962,15 @@ is_a: GO:0016274 ! protein-arginine N-methyltransferase activity
id: GO:0035242
name: protein-arginine omega-N asymmetric methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the addition of a second methyl group to methylated peptidyl-arginine. Methylation is on the same terminal nitrogen (omega nitrogen) residue that was previously methylated, resulting in asymmetrical peptidyl-N(omega),N(omega)-dimethylated arginine residues." [PMID:14705965, RESID:AA0068, RESID:AA0069, RHEA:48096]
+def: "Catalysis of the addition of a second methyl group to methylated peptidyl-arginine. Methylation is on the same terminal nitrogen (omega nitrogen) residue that was previously methylated, resulting in asymmetrical peptidyl-N(omega),N(omega)-dimethylated arginine residues." [PMID:14705965]
comment: Note that type I protein arginine N-methyltransferase enzymes possess 'protein-arginine omega-N monomethyltransferase activity ; GO:0035241' and 'protein-arginine omega-N asymmetric methyltransferase activity ; GO:0035242'.
+synonym: "protein arginine omega-N asymmetric methylase activity" EXACT []
+synonym: "protein arginine omega-N asymmetric methyltransferase activity" EXACT []
synonym: "S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-Nomega,Nomega-dimethyl-L-arginine-forming)" RELATED [EC:2.1.1.319]
synonym: "type I PRMT activity" RELATED []
synonym: "type I protein arginine methyltransferase activity" RELATED [EC:2.1.1.319]
xref: EC:2.1.1.319
-xref: RESID:AA0068
-xref: RESID:AA0069
+xref: Reactome:R-HSA-9729283 "Nucleoprotein is methylated by PRMT1"
xref: RHEA:48096
is_a: GO:0016274 ! protein-arginine N-methyltransferase activity
@@ -206080,6 +205980,8 @@ name: protein-arginine omega-N symmetric methyltransferase activity
namespace: molecular_function
def: "Catalysis of the addition of a second methyl group to methylated peptidyl-arginine. Methylation is on the terminal nitrogen (omega nitrogen) residue that is not already methylated, resulting in symmetrical peptidyl-N(omega),N'(omega)-dimethyled arginine residues." [EC:2.1.1.320, PMID:14705965, RESID:AA0067, RESID:AA0069]
comment: Note that type II protein arginine N-methyltransferase enzymes possess 'protein-arginine omega-N monomethyltransferase activity ; GO:0035241' and 'protein-arginine omega-N symmetric methyltransferase activity ; GO:0035243'.
+synonym: "protein arginine omega-N symmetric methylase activity" EXACT []
+synonym: "protein arginine omega-N symmetric methyltransferase activity" EXACT []
synonym: "S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-Nomega,Nomega'-dimethyl-L-arginine-forming)" RELATED [EC:2.1.1.320]
synonym: "type II PRMT activity" RELATED []
synonym: "type II protein arginine methyltransferase activity" RELATED []
@@ -206092,19 +205994,28 @@ is_a: GO:0016274 ! protein-arginine N-methyltransferase activity
[Term]
id: GO:0035244
-name: peptidyl-arginine C-methyltransferase activity
-namespace: molecular_function
-def: "Catalysis of the transfer of a methyl group to the carbon atom of an arginine residue in a protein." [GOC:bf]
+name: protein-arginine C-methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a methyl group to the carbon atom of an arginine residue in a protein. This modification has been detected in anaerobic bacteria." [GOC:bf, PMID:29743535, PMID:33162960, RHEA:66028]
+synonym: "peptidyl arginine C-methyltransferase activity" EXACT []
+synonym: "peptidyl-arginine C-methylase activity" EXACT []
+synonym: "peptidyl-arginine C-methyltransferase activity" EXACT []
+synonym: "protein-arginine C-methylase activity" EXACT []
+xref: EC:2.1.1.379
+xref: RESID:AA0272
+xref: RHEA:66028
is_a: GO:0008169 ! C-methyltransferase activity
is_a: GO:0008276 ! protein methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
[Term]
id: GO:0035245
-name: peptidyl-arginine C-methylation
+name: obsolete peptidyl-arginine C-methylation
namespace: biological_process
-def: "The addition of a methyl group onto a carbon atom of an arginine residue in a protein." [GOC:bf]
-is_a: GO:0018216 ! peptidyl-arginine methylation
+def: "OBSOLETE. The addition of a methyl group onto a carbon atom of an arginine residue in a protein." [GOC:bf]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+replaced_by: GO:0035244
[Term]
id: GO:0035246
@@ -206206,9 +206117,10 @@ is_a: GO:0035254 ! glutamate receptor binding
[Term]
id: GO:0035259
-name: glucocorticoid receptor binding
+name: nuclear glucocorticoid receptor binding
namespace: molecular_function
-def: "Binding to a glucocorticoid receptor." [GOC:bf]
+def: "Binding to a nuclear glucocorticoid receptor." [GOC:bf]
+synonym: "glucocorticoid receptor binding" BROAD []
is_a: GO:0016922 ! nuclear receptor binding
[Term]
@@ -206350,7 +206262,6 @@ id: GO:0035276
name: ethanol binding
namespace: molecular_function
def: "Binding to ethanol, CH(3)-CH(2)-OH." [ISBN:0198506732]
-is_a: GO:0043168 ! anion binding
is_a: GO:0043178 ! alcohol binding
[Term]
@@ -206366,7 +206277,7 @@ relationship: part_of GO:0007424 ! open tracheal system development
id: GO:0035278
name: miRNA-mediated gene silencing by inhibition of translation
namespace: biological_process
-def: "The process in which microRNAs (miRNAs) block the translation of target mRNAs into proteins. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA will typically mediate repression of translation if the miRNA imperfectly base-pairs with the 3' untranslated regions of target mRNAs." [PMID:14744438, PMID:15196554]
+def: "An RNA interference pathway in which microRNAs (miRNAs) block the translation of target mRNAs into proteins. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA will typically mediate repression of translation if the miRNA imperfectly base-pairs with the 3' untranslated regions of target mRNAs." [PMID:14744438, PMID:15196554]
synonym: "down regulation of translation involved in gene silencing by miRNA" EXACT [GOC:mah]
synonym: "down-regulation of translation involved in gene silencing by miRNA" EXACT [GOC:mah]
synonym: "downregulation of translation involved in gene silencing by miRNA" EXACT [GOC:mah]
@@ -206375,33 +206286,25 @@ synonym: "inhibition of translation involved in gene silencing by miRNA" NARROW
synonym: "miRNA mediated inhibition of translation" EXACT []
synonym: "miRNA-mediated gene silencing, negative regulation of translation" RELATED [GOC:dph, GOC:tb]
synonym: "negative regulation of translation involved in gene silencing by microRNA" EXACT [GOC:pr]
-is_a: GO:0035195 ! gene silencing by miRNA
-is_a: GO:0040033 ! RNA-mediated gene silencing by inhibition of translation
+is_a: GO:0017148 ! negative regulation of translation
+is_a: GO:0035195 ! miRNA-mediated gene silencing
[Term]
id: GO:0035279
name: miRNA-mediated gene silencing by mRNA destabilization
namespace: biological_process
-def: "The process in which microRNAs (miRNAs) direct the cleavage of target mRNAs. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA base pairing with near-perfect complementarity to the target mRNA will typically direct targeted endonucleolytic cleavage of the mRNA. Many plant miRNAs downregulate gene expression through this mechanism." [GOC:dph, GOC:mtg_lung, PMID:14744438, PMID:15196554]
+def: "An RNA interference pathway in which microRNAs (miRNAs) direct the cleavage of target mRNAs. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA base pairing with near-perfect complementarity to the target mRNA will typically direct targeted endonucleolytic cleavage of the mRNA. Many plant miRNAs downregulate gene expression through this mechanism." [GOC:dph, GOC:mtg_lung, PMID:14744438, PMID:15196554, PMID:21118121, PMID:23209154]
+synonym: "deadenylation involved in gene silencing by miRNA" RELATED []
synonym: "gene silencing by miRNA, mRNA cleavage" EXACT [GOC:mah]
+synonym: "gene silencing by mRNA cleavage" BROAD []
+synonym: "miRNA-mediated gene silencing by mRNA deadenylation" RELATED []
synonym: "miRNA-mediated gene silencing, mRNA cleavage" EXACT [GOC:dph, GOC:tb]
synonym: "mRNA cleavage involved in gene silencing by microRNA" EXACT [GOC:pr]
synonym: "mRNA cleavage involved in gene silencing by miRNA" EXACT []
+synonym: "mRNA deadenylation-mediated gene silencing by miRNA" RELATED []
synonym: "mRNA destabilization-mediated gene silencing by miRNA" EXACT []
-is_a: GO:0035195 ! gene silencing by miRNA
-is_a: GO:0098795 ! mRNA destabilization-mediated gene silencing
-
-[Term]
-id: GO:0035280
-name: miRNA loading onto RISC involved in gene silencing by miRNA
-namespace: biological_process
-def: "The transfer of a microRNA (miRNA) strand from a miRNA:miRNA duplex onto the RNA-initiated silencing complex (RISC)." [PMID:14744438]
-synonym: "gene silencing by miRNA, miRNA loading onto RISC" EXACT [GOC:mah]
-synonym: "microRNA loading onto RISC involved in gene silencing by microRNA" EXACT [GOC:pr]
-synonym: "miRISC assembly" BROAD []
-synonym: "miRNA-mediated gene silencing, miRNA loading onto RISC" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0070922 ! small RNA loading onto RISC
-relationship: part_of GO:0035195 ! gene silencing by miRNA
+is_a: GO:0035195 ! miRNA-mediated gene silencing
+is_a: GO:0061157 ! mRNA destabilization
[Term]
id: GO:0035281
@@ -206414,7 +206317,7 @@ synonym: "pre-microRNA export out of nucleus" EXACT []
synonym: "pre-microRNA transport from nucleus to cytoplasm" EXACT []
synonym: "pre-microRNA-nucleus export" EXACT []
is_a: GO:0006405 ! RNA export from nucleus
-relationship: part_of GO:0035195 ! gene silencing by miRNA
+relationship: part_of GO:0035195 ! miRNA-mediated gene silencing
[Term]
id: GO:0035282
@@ -206565,7 +206468,7 @@ relationship: part_of GO:0007443 ! Malpighian tubule morphogenesis
id: GO:0035299
name: inositol pentakisphosphate 2-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ATP = 1D-myo-inositol hexakisphosphate + ADP + 2 H(+)." [RHEA:20313]
+def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ATP = 1D-myo-inositol hexakisphosphate + ADP + 2 H+." [RHEA:20313]
synonym: "ATP:1D-myo-inositol 1,3,4,5,6-pentakisphosphate 2-phosphotransferase activity" RELATED [EC:2.7.1.158]
synonym: "Gsl1p" RELATED [EC:2.7.1.158]
synonym: "inositol 1,3,4,5,6-pentakisphosphate 2-kinase activity" RELATED [EC:2.7.1.158]
@@ -206720,11 +206623,12 @@ relationship: part_of GO:0035309 ! wing and notum subfield formation
[Term]
id: GO:0035312
-name: 5'-3' exodeoxyribonuclease activity
+name: 5'-3' DNA exonuclease activity
namespace: molecular_function
def: "Catalysis of the sequential cleavage of mononucleotides from a free 5' terminus of a DNA molecule." [ISBN:0198547684]
+synonym: "5'-3' exodeoxyribonuclease activity" EXACT []
is_a: GO:0008409 ! 5'-3' exonuclease activity
-is_a: GO:0016895 ! exodeoxyribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016895 ! DNA exonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0035313
@@ -207048,7 +206952,6 @@ comment: Note that this term is not intended for use in annotating lateral movem
synonym: "acetyl-CoA membrane transport" EXACT []
is_a: GO:0015876 ! acetyl-CoA transport
is_a: GO:0071106 ! adenosine 3',5'-bisphosphate transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0035349
@@ -207059,7 +206962,6 @@ comment: Note that this term is not intended for use in annotating lateral movem
synonym: "coenzyme A membrane transport" EXACT []
is_a: GO:0015880 ! coenzyme A transport
is_a: GO:0071106 ! adenosine 3',5'-bisphosphate transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0035350
@@ -207069,7 +206971,6 @@ def: "The process in which flavin-adenine dinucleotide (FAD) is transported acro
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "FAD membrane transport" EXACT []
is_a: GO:0015883 ! FAD transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1901679 ! nucleotide transmembrane transport
[Term]
@@ -207090,6 +206991,7 @@ def: "The process in which a nicotinamide adenine dinucleotide is transported ac
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "NAD membrane transport" EXACT []
is_a: GO:0043132 ! NAD transport
+is_a: GO:0072530 ! purine-containing compound transmembrane transport
is_a: GO:1901679 ! nucleotide transmembrane transport
[Term]
@@ -207128,10 +207030,11 @@ is_a: GO:0098802 ! plasma membrane signaling receptor complex
[Term]
id: GO:0035356
-name: cellular triglyceride homeostasis
+name: intracellular triglyceride homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of triglyceride within a cell or between a cell and its external environment." [GOC:BHF]
-is_a: GO:0055082 ! cellular chemical homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of triglyceride within a cell." [GOC:BHF]
+synonym: "cellular triglyceride homeostasis" EXACT []
+is_a: GO:0055082 ! intracellular chemical homeostasis
is_a: GO:0070328 ! triglyceride homeostasis
[Term]
@@ -207338,10 +207241,10 @@ id: GO:0035379
name: carbon dioxide transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of carbon dioxide (CO2) from one side of a membrane to the other." [GOC:yaf]
-xref: Reactome:R-HSA-1237042 "AQP1 passively tranlocates carbon dioxide from the extracellular region to the cytosol"
-xref: Reactome:R-HSA-1237069 "RhAG passively translocates carbon dioxide from the extracellular region to the cytosol"
-xref: Reactome:R-HSA-1247645 "RhAG passively translocates carbon dioxide from the cytosol to the extracellular region"
-xref: Reactome:R-HSA-1247649 "AQP1 passively translocates carbon dioxide from the cytosol to the extracellular region"
+xref: Reactome:R-HSA-1237042 "AQP1 tetramer transports CO2 from extracellular region to cytosol"
+xref: Reactome:R-HSA-1237069 "RHAG transports CO2 from extracellular region to cytosol"
+xref: Reactome:R-HSA-1247645 "RHAG transports CO2 from cytosol to extracellular region"
+xref: Reactome:R-HSA-1247649 "AQP1 tetramer transports CO2 from cytosol to extracellular region"
is_a: GO:0022857 ! transmembrane transporter activity
[Term]
@@ -207357,7 +207260,6 @@ id: GO:0035381
name: ATP-gated ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a channel that opens when ATP has been bound by the channel complex or one of its constituent parts." [GOC:bf]
-is_a: GO:0015075 ! ion transmembrane transporter activity
is_a: GO:0022834 ! ligand-gated channel activity
[Term]
@@ -207396,7 +207298,7 @@ is_a: GO:1901576 ! organic substance biosynthetic process
id: GO:0035385
name: Roundabout signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a SLIT protein to a Roundabout (ROBO) family receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling]
+def: "The series of molecular signals initiated by a SLIT protein binding to a Roundabout (ROBO) family receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling]
synonym: "ROBO signaling pathway" EXACT []
synonym: "ROBO/SLIT signaling pathway" EXACT []
synonym: "Roundabout signalling pathway" EXACT [GOC:mah]
@@ -207520,87 +207422,105 @@ is_a: GO:0035397 ! helper T cell enhancement of adaptive immune response
[Term]
id: GO:0035400
-name: histone tyrosine kinase activity
+name: obsolete histone tyrosine kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to a tyrosine residue of a histone. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:bf]
+def: "OBSOLETE. Catalysis of the transfer of a phosphate group to a tyrosine residue of a histone." [GOC:bf]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "histone-tyrosine kinase activity" EXACT []
-is_a: GO:0004715 ! non-membrane spanning protein tyrosine kinase activity
-is_a: GO:0035173 ! histone kinase activity
+is_obsolete: true
+consider: GO:0140995
+consider: GO:0140996
+consider: GO:0140997
+consider: GO:0140998
[Term]
id: GO:0035401
-name: histone kinase activity (H3-Y41 specific)
+name: histone H3Y41 kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to the tyrosine-41 residue of histone H3." [GOC:bf]
+def: "Catalysis of the reaction: histone H3-tyrosine (position 41) + ATP = histone H3-phosphotyrosine (position 41) + ADP. This reaction is the addition of a phosphate group to the tyrosine residue at position 41 of histone H3." [GOC:bf]
+synonym: "histone H3-Y41 kinase activity" EXACT []
+synonym: "histone kinase activity (H3-Y41 specific)" EXACT []
synonym: "histone tyrosine kinase activity (H3-Y41 specific)" EXACT []
synonym: "histone-tyrosine kinase activity (H3-Y41 specific)" EXACT []
-is_a: GO:0035400 ! histone tyrosine kinase activity
+is_a: GO:0140996 ! histone H3 kinase activity
[Term]
id: GO:0035402
-name: histone kinase activity (H3-T11 specific)
+name: histone H3T11 kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to the threonine-11 residue of the N-terminal tail of histone H3." [GOC:bf]
+def: "Catalysis of the reaction: histone H3-threonine (position 11) + ATP = histone H3-phosphothreonine (position 11) + ADP. This reaction is the addition of a phosphate group to the threonine residue at position 11 of histone H3." [GOC:bf]
+synonym: "histone H3-T11 kinase activity" EXACT []
+synonym: "histone kinase activity (H3-T11 specific)" EXACT []
synonym: "histone threonine kinase activity (H3-T11 specific)" EXACT []
synonym: "histone-threonine kinase activity (H3-T11 specific)" EXACT []
-is_a: GO:0035184 ! histone threonine kinase activity
+is_a: GO:0140996 ! histone H3 kinase activity
[Term]
id: GO:0035403
-name: histone kinase activity (H3-T6 specific)
+name: histone H3T6 kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to the threonine-6 residue of the N-terminal tail of histone H3." [GOC:bf]
+def: "Catalysis of the reaction: histone H3-threonine (position 6) + ATP = histone H3-phosphothreonine (position 6) + ADP. This reaction is the addition of a phosphate group to the threonine residue at position 6 of histone H3." [GOC:bf]
+synonym: "histone H3-T6 kinase activity" EXACT []
+synonym: "histone kinase activity (H3-T6 specific)" EXACT []
synonym: "histone threonine kinase activity (H3-T6 specific)" EXACT []
synonym: "histone-threonine kinase activity (H3-T6 specific)" EXACT []
-is_a: GO:0035184 ! histone threonine kinase activity
+is_a: GO:0140996 ! histone H3 kinase activity
[Term]
id: GO:0035404
-name: histone-serine phosphorylation
+name: obsolete histone-serine phosphorylation
namespace: biological_process
-def: "The modification of histones by addition of a phosphate group to a serine residue." [GOC:bf]
+def: "OBSOLETE. The modification of histones by addition of a phosphate group to a serine residue." [GOC:bf]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone serine phosphorylation" EXACT []
-is_a: GO:0016572 ! histone phosphorylation
-is_a: GO:0018105 ! peptidyl-serine phosphorylation
+is_obsolete: true
+consider: GO:0035173
[Term]
id: GO:0035405
-name: histone-threonine phosphorylation
+name: obsolete histone-threonine phosphorylation
namespace: biological_process
-def: "The modification of histones by addition of a phosphate group to a threonine residue." [GOC:bf]
+def: "OBSOLETE. The modification of histones by addition of a phosphate group to a threonine residue." [GOC:bf]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone threonine phosphorylation" EXACT []
-is_a: GO:0016572 ! histone phosphorylation
-is_a: GO:0018107 ! peptidyl-threonine phosphorylation
+is_obsolete: true
[Term]
id: GO:0035406
-name: histone-tyrosine phosphorylation
+name: obsolete histone-tyrosine phosphorylation
namespace: biological_process
-def: "The modification of histones by addition of a phosphate group to a tyrosine residue." [GOC:bf]
+def: "OBSOLETE. The modification of histones by addition of a phosphate group to a tyrosine residue." [GOC:bf]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone tyrosine phosphorylation" EXACT []
-is_a: GO:0016572 ! histone phosphorylation
-is_a: GO:0018108 ! peptidyl-tyrosine phosphorylation
+is_obsolete: true
+consider: GO:0035173
[Term]
id: GO:0035407
-name: histone H3-T11 phosphorylation
+name: obsolete histone H3-T11 phosphorylation
namespace: biological_process
-def: "The modification of histone H3 by the addition of an phosphate group to a threonine residue at position 11 of the histone." [GOC:bf]
-is_a: GO:0035405 ! histone-threonine phosphorylation
+def: "OBSOLETE. The modification of histone H3 by the addition of an phosphate group to a threonine residue at position 11 of the histone." [GOC:bf]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0035402
[Term]
id: GO:0035408
-name: histone H3-T6 phosphorylation
+name: obsolete histone H3-T6 phosphorylation
namespace: biological_process
-def: "The modification of histone H3 by the addition of an phosphate group to a threonine residue at position 6 of the histone." [GOC:bf]
-is_a: GO:0035405 ! histone-threonine phosphorylation
+def: "OBSOLETE. The modification of histone H3 by the addition of an phosphate group to a threonine residue at position 6 of the histone." [GOC:bf]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0035403
[Term]
id: GO:0035409
-name: histone H3-Y41 phosphorylation
+name: obsolete histone H3-Y41 phosphorylation
namespace: biological_process
-def: "The modification of histone H3 by the addition of a phosphate group to a tyrosine residue at position 41 of the histone." [GOC:bf]
-is_a: GO:0035406 ! histone-tyrosine phosphorylation
+def: "OBSOLETE. The modification of histone H3 by the addition of a phosphate group to a tyrosine residue at position 41 of the histone." [GOC:bf]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0035401
[Term]
id: GO:0035410
@@ -207732,7 +207652,8 @@ alt_id: GO:0032893
def: "Any process that modulates the frequency, rate or extent of the directed movement of a gluconate across a membrane by means of some agent such as a transporter or pore." [GOC:vw]
synonym: "regulation of gluconate membrane transport" EXACT []
synonym: "regulation of gluconate transport" RELATED []
-is_a: GO:1903959 ! regulation of anion transmembrane transport
+is_a: GO:0032890 ! regulation of organic acid transport
+is_a: GO:0034762 ! regulation of transmembrane transport
relationship: regulates GO:0035429 ! gluconate transmembrane transport
[Term]
@@ -207747,8 +207668,9 @@ synonym: "downregulation of gluconate transport" EXACT []
synonym: "inhibition of gluconate transport" NARROW []
synonym: "negative regulation of gluconate membrane transport" EXACT []
synonym: "negative regulation of gluconate transport" RELATED []
+is_a: GO:0032891 ! negative regulation of organic acid transport
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:0035430 ! regulation of gluconate transmembrane transport
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
relationship: negatively_regulates GO:0035429 ! gluconate transmembrane transport
[Term]
@@ -207765,8 +207687,9 @@ synonym: "stimulation of gluconate transport" NARROW []
synonym: "up regulation of gluconate transport" EXACT []
synonym: "up-regulation of gluconate transport" EXACT []
synonym: "upregulation of gluconate transport" EXACT []
+is_a: GO:0032892 ! positive regulation of organic acid transport
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:0035430 ! regulation of gluconate transmembrane transport
-is_a: GO:1903961 ! positive regulation of anion transmembrane transport
relationship: positively_regulates GO:0035429 ! gluconate transmembrane transport
[Term]
@@ -207777,7 +207700,6 @@ def: "The process in which acetate is transported across a membrane. Acetate is
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "acetate membrane transport" EXACT []
is_a: GO:0006846 ! acetate transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -207790,6 +207712,7 @@ comment: Note that this term is not intended for use in annotating lateral movem
synonym: "copper cation transmembrane transport" EXACT []
synonym: "copper ion membrane transport" EXACT []
is_a: GO:0006825 ! copper ion transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -207811,7 +207734,7 @@ comment: Note that this term is not intended for use in annotating lateral movem
synonym: "triose phosphate membrane transport" EXACT []
is_a: GO:0015711 ! organic anion transport
is_a: GO:0015717 ! triose phosphate transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0035437
@@ -207900,6 +207823,7 @@ def: "The directed movement of nickel (Ni) cations across a membrane by means of
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "nickel cation membrane transport" EXACT []
is_a: GO:0015675 ! nickel cation transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -208096,7 +208020,7 @@ relationship: part_of GO:0021536 ! diencephalon development
id: GO:0035463
name: transforming growth factor beta receptor signaling pathway involved in determination of left/right asymmetry
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, which contributes to determination of organismal asymmetry with respect to the left and right halves." [GOC:dgh, GOC:signaling]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a transforming growth factor beta receptor on the surface of a target cell, which contributes to determination of organismal asymmetry with respect to the left and right halves." [GOC:dgh, GOC:signaling]
synonym: "TGF-beta receptor signaling pathway involved in determination of left/right asymmetry" EXACT []
synonym: "TGF-beta receptor signalling pathway involved in determination of left/right asymmetry" EXACT []
synonym: "TGFbeta receptor signaling pathway involved in determination of left/right asymmetry" EXACT []
@@ -208496,18 +208420,21 @@ is_a: GO:0006304 ! DNA modification
[Term]
id: GO:0035511
-name: oxidative DNA demethylation
+name: obsolete oxidative DNA demethylation
namespace: biological_process
-def: "Removal of the methyl group from one or more nucleotides within a DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms." [PMID:12594517, PMID:16482161, PMID:18775698]
-is_a: GO:0070989 ! oxidative demethylation
-is_a: GO:0080111 ! DNA demethylation
+def: "OBSOLETE. Removal of the methyl group from one or more nucleotides within a DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms." [PMID:12594517, PMID:16482161, PMID:18775698]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0035516
[Term]
id: GO:0035512
-name: hydrolytic DNA demethylation
+name: obsolete hydrolytic DNA demethylation
namespace: biological_process
-def: "The hydrolytic removal of the methyl group from one or more nucleotides within a DNA molecule." [GOC:bf]
-is_a: GO:0080111 ! DNA demethylation
+def: "OBSOLETE. The hydrolytic removal of the methyl group from one or more nucleotides within a DNA molecule." [GOC:bf]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0051747
[Term]
id: GO:0035513
@@ -208543,7 +208470,7 @@ namespace: molecular_function
alt_id: GO:0103051
alt_id: GO:0103052
alt_id: GO:0103053
-def: "Catalysis of the reaction: a methylated nucleobase within DNA + 2-oxoglutarate + O(2) = a nucleobase within DNA + formaldehyde + succinate + CO(2)." [PMID:12594517, PMID:16482161, PMID:18775698, RHEA:30299]
+def: "Catalysis of the reaction: a methylated nucleobase within DNA + 2-oxoglutarate + O2 = a nucleobase within DNA + formaldehyde + succinate + CO2." [PMID:12594517, PMID:16482161, PMID:18775698, RHEA:30299]
synonym: "1-ethyladenine demethylase activity" NARROW []
synonym: "2-oxoglutarate-dependent DNA demethylase" EXACT [PMID:17991826]
synonym: "N1-methyladenine demethylase activity" NARROW []
@@ -208679,14 +208606,15 @@ is_obsolete: true
id: GO:0035529
name: NADH pyrophosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADH + H2O = AMP + NMNH + 2 H+." [MetaCyc:RXN0-4401, PMID:12399474, PMID:20181750]
+def: "Catalysis of the reaction: NADH + H2O = AMP + NMNH + 2 H+." [PMID:12399474, PMID:20181750, RHEA:48868]
synonym: "NADH diphosphatase activity" EXACT []
synonym: "NADH pyrophosphohydrolase activity" EXACT []
-xref: EC:3.6.1.9
+xref: EC:3.6.1.22
xref: KEGG_REACTION:R00103
xref: MetaCyc:RXN0-4401
xref: Reactome:R-HSA-6809287 "NUDT12 hydrolyses NADH to NMNH"
-is_a: GO:0004551 ! nucleotide diphosphatase activity
+xref: RHEA:48868
+is_a: GO:0004551 ! dinucleotide phosphatase activity
[Term]
id: GO:0035530
@@ -208755,8 +208683,9 @@ synonym: "8-oxo-dGTPase activity" EXACT [PMID:7782328]
xref: EC:3.6.1.55
xref: Reactome:R-HSA-2395849 "NUDT1 hydrolyses 8-oxo-dGTP to 8-oxo-dGMP"
xref: Reactome:R-HSA-2395869 "NUDT15 hydrolyses 8-oxo-dGTP to 8-oxo-dGMP"
+xref: Reactome:R-HSA-9750555 "NUDT15 dimer dephosphorylates 6TdGTP to 6TdGMP"
xref: RHEA:31575
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0035540
@@ -208838,7 +208767,7 @@ name: oxidative single-stranded DNA demethylation
namespace: biological_process
def: "Removal of the methyl group from one or more nucleotides within a single-stranded DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms." [GOC:BHF, GOC:rl, PMID:18775698]
synonym: "oxidative ssDNA demethylation" EXACT []
-is_a: GO:0035511 ! oxidative DNA demethylation
+is_a: GO:0080111 ! DNA demethylation
[Term]
id: GO:0035553
@@ -209049,17 +208978,22 @@ is_a: GO:0035570 ! N-terminal peptidyl-serine methylation
[Term]
id: GO:0035574
-name: histone H4-K20 demethylation
+name: obsolete histone H4-K20 demethylation
namespace: biological_process
-def: "The modification of histone H4 by the removal of a methyl group from lysine at position 20 of the histone." [GOC:sp, PMID:20622853]
-is_a: GO:0070076 ! histone lysine demethylation
+def: "OBSOLETE. The modification of histone H4 by the removal of a methyl group from lysine at position 20 of the histone." [GOC:sp, PMID:20622853]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0035575
[Term]
id: GO:0035575
-name: histone H4-methyl-lysine-20 demethylase activity
+name: histone H4K20 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of the methyl group from a modified lysine residue at position 20 of the histone H4 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:20622853, PMID:26214369, PMID:32209475]
synonym: "histone demethylase activity (H4-K20 specific)" EXACT []
+synonym: "histone demethylase activity (H4K20-specific)" EXACT []
+synonym: "histone H4-K20 demethylase activity" EXACT []
+synonym: "histone H4-methyl-lysine-20 demethylase activity" EXACT []
synonym: "histone H4K20me demethylase activity" EXACT []
xref: Reactome:R-HSA-2172678 "PHF8 demethylates histone H4K20me1"
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
@@ -209153,7 +209087,7 @@ is_a: GO:0071694 ! maintenance of protein location in extracellular region
id: GO:0035584
name: calcium-mediated signaling using intracellular calcium source
namespace: biological_process
-def: "A series of molecular signals in which a cell uses calcium ions released from an intracellular store to convert a signal into a response." [GOC:bf, GOC:BHF, PMID:20192754]
+def: "The series of molecular signals in which a cell uses calcium ions released from an intracellular store to convert a signal into a response." [GOC:bf, GOC:BHF, PMID:20192754]
synonym: "calcium signaling using intracellular calcium source" EXACT []
synonym: "calcium signalling using intracellular calcium source" EXACT []
synonym: "calcium-mediated signalling using intracellular calcium source" EXACT []
@@ -209163,7 +209097,7 @@ is_a: GO:0019722 ! calcium-mediated signaling
id: GO:0035585
name: calcium-mediated signaling using extracellular calcium source
namespace: biological_process
-def: "A series of molecular signals in which a cell uses calcium ions imported from an extracellular source to convert a signal into a response." [GOC:bf, GOC:BHF, PMID:20192754]
+def: "The series of molecular signals in which a cell uses calcium ions imported from an extracellular source to convert a signal into a response." [GOC:bf, GOC:BHF, PMID:20192754]
synonym: "calcium signaling using extracellular calcium source" EXACT []
synonym: "calcium signalling using extracellular calcium source" EXACT []
synonym: "calcium-mediated signalling using extracellular calcium source" EXACT []
@@ -209174,7 +209108,7 @@ is_a: GO:0019722 ! calcium-mediated signaling
id: GO:0035588
name: G protein-coupled purinergic receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a receptor binding to an extracellular purine or purine derivative and transmitting the signal to a heterotrimeric G-protein complex to initiate a change in cell activity." [GOC:BHF, PMID:9755289]
+def: "A G protein-coupled receptor signaling pathway initiated by an extracellular purine or purine derivative binding to its receptor, and ending with the regulation of a downstream cellular process." [GOC:BHF, PMID:9755289]
synonym: "G-protein coupled purinergic receptor signaling pathway" EXACT []
synonym: "G-protein coupled purinergic receptor signalling pathway" EXACT [GOC:mah]
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -209184,7 +209118,7 @@ is_a: GO:0035590 ! purinergic nucleotide receptor signaling pathway
id: GO:0035589
name: G protein-coupled purinergic nucleotide receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a receptor binding to an extracellular purine nucleotide and transmitting the signal to a heterotrimeric G-protein complex to initiate a change in cell activity." [GOC:BHF, PMID:9755289]
+def: "A G protein-coupled receptor signaling pathway initiated by an extracellular purine nucleotide binding to its receptor, and ending with the regulation of a downstream cellular process." [GOC:BHF, PMID:9755289]
synonym: "G-protein coupled purinergic nucleotide receptor signaling pathway" EXACT []
synonym: "G-protein coupled purinergic nucleotide receptor signalling pathway" EXACT [GOC:mah]
synonym: "P2Y receptor signaling pathway" EXACT [PMID:9755289]
@@ -209195,7 +209129,7 @@ id: GO:0035590
name: purinergic nucleotide receptor signaling pathway
namespace: biological_process
alt_id: GO:0035587
-def: "The series of molecular signals generated as a consequence of a receptor binding to an extracellular purine nucleotide to initiate a change in cell activity." [GOC:BHF, PMID:9755289]
+def: "The series of molecular signals initiated by an extracellular purine nucleotide binding to its receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, PMID:9755289]
synonym: "P2 receptor signaling pathway" RELATED [PMID:9755289]
synonym: "purinergic nucleotide receptor signalling pathway" EXACT [GOC:mah]
synonym: "purinergic receptor signaling pathway" RELATED []
@@ -209209,6 +209143,7 @@ name: signaling adaptor activity
namespace: molecular_function
def: "The binding activity of a molecule that brings together two or more molecules in a signaling pathway, permitting those molecules to function in a coordinated way. Adaptor molecules themselves do not have catalytic activity." [GOC:bf, PMID:19104498]
comment: A signaling adaptor can bring together both protein and non-protein molecules within a signaling pathway. Scaffold proteins act in at least four ways: tethering signaling components, localizing these components to specific areas of the cell, regulating signal transduction by coordinating positive and negative feedback signals, and insulating correct signaling proteins from competing proteins (PMID:19104498).
+synonym: "signaling protein recruiting activity" EXACT []
synonym: "signaling scaffold activity" RELATED []
synonym: "signalling adaptor activity" EXACT [GOC:mah]
is_a: GO:0030674 ! protein-macromolecule adaptor activity
@@ -209309,7 +209244,7 @@ name: protein deacylation
namespace: biological_process
def: "The removal of an acyl group, any group or radical of the form RCO- where R is an organic group, from a protein amino acid." [GOC:se, PMID:12080046]
synonym: "protein amino acid deacylation" EXACT [GOC:se]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
is_a: GO:0098732 ! macromolecule deacylation
[Term]
@@ -209352,7 +209287,7 @@ relationship: part_of GO:0071864 ! positive regulation of cell proliferation in
id: GO:0035605
name: peptidyl-cysteine S-nitrosylase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a nitric oxide (NO) group to a sulphur atom within a cysteine residue of a protein." [EC:2.6.99.-, GOC:sp, PMID:20972425, PMID:20972426]
+def: "Catalysis of the transfer of a nitric oxide (NO) group to a sulphur atom within a cysteine residue of a protein." [GOC:sp, PMID:20972425, PMID:20972426]
comment: This term should not be used to annotate the nitrosylating action of nitric oxide synthase (NOS) if the nitroso group is synthesized directly on the substrate.
synonym: "protein nitrosylase activity" RELATED [GOC:sp]
synonym: "S-nitrosylase activity" EXACT [PMID:20972426]
@@ -209467,7 +209402,7 @@ name: stress granule disassembly
namespace: biological_process
def: "The disaggregation of a stress granule into its constituent protein and RNA parts." [GOC:BHF, PMID:19825938]
synonym: "SG disassembly" EXACT [PMID:19825938]
-is_a: GO:0032988 ! ribonucleoprotein complex disassembly
+is_a: GO:0032988 ! protein-RNA complex disassembly
is_a: GO:1903008 ! organelle disassembly
[Term]
@@ -209541,7 +209476,7 @@ is_obsolete: true
id: GO:0035626
name: juvenile hormone mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of juvenile hormone to a receptor, and ending with regulation of cell state or activity." [GOC:bf, GOC:sart]
+def: "The series of molecular signals initiated by a juvenile hormone binding to its receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:sart]
synonym: "juvenile hormone mediated signalling pathway" EXACT [GOC:bf]
synonym: "juvenile hormone-mediated signaling pathway" EXACT [GOC:bf]
is_a: GO:0009755 ! hormone-mediated signaling pathway
@@ -209559,7 +209494,7 @@ is_a: GO:0042886 ! amide transport
id: GO:0035628
name: cystic duct development
namespace: biological_process
-def: "The progression of the cystic duct over time, from its formation to the mature structure. The cystic duct runs from the gall bladder to the common bile duct." [PMID:20614624]
+def: "The progression of the cystic duct over time, from its formation to the mature structure. The cystic duct runs from the gallbladder to the common bile duct." [PMID:20614624]
is_a: GO:0061009 ! common bile duct development
[Term]
@@ -209586,7 +209521,6 @@ name: CD40 receptor complex
namespace: cellular_component
def: "A protein complex that contains at least CD40 (a cell surface receptor of the tumour necrosis factor receptor (TNFR) superfamily), and other signaling molecules." [GOC:BHF, PMID:20614026, PMID:9221764]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0035632
@@ -209637,12 +209571,12 @@ is_obsolete: true
[Term]
id: GO:0035637
-name: multicellular organismal signaling
+name: obsolete multicellular organismal signaling
namespace: biological_process
-def: "The transfer of information occurring at the level of a multicellular organism." [GOC:go_curators]
+def: "OBSOLETE. The transfer of information occurring at the level of a multicellular organism." [GOC:go_curators]
+comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "multicellular organismal signalling" EXACT [GOC:bf]
-is_a: GO:0023052 ! signaling
-is_a: GO:0032501 ! multicellular organismal process
+is_obsolete: true
[Term]
id: GO:0035639
@@ -209675,12 +209609,15 @@ is_a: GO:0035640 ! exploration behavior
[Term]
id: GO:0035642
-name: histone methyltransferase activity (H3-R17 specific)
+name: histone H3R17 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 17) = S-adenosyl-L-homocysteine + (histone H3)-N-methyl-arginine (position 17). This reaction is the addition of a methyl group to arginine at position 17 of histone H3." [GOC:sp, PMID:11341840]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 17) = S-adenosyl-L-homocysteine + (histone H3)-N-methyl-arginine (position 17). This reaction is the addition of a methyl group to the arginine residue at position 17 of histone H3." [GOC:sp, PMID:11341840]
synonym: "histone methylase activity (H3-R17 specific)" EXACT [GOC:bf]
+synonym: "histone methyltransferase activity (H3-R17 specific)" EXACT []
synonym: "histone-arginine N-methyltransferase activity (H3-R17 specific)" EXACT [GOC:bf]
-is_a: GO:0008469 ! histone-arginine N-methyltransferase activity
+synonym: "histone-H3R17 methyltransferase activity" EXACT []
+is_a: GO:0016274 ! protein-arginine N-methyltransferase activity
+is_a: GO:0140938 ! histone H3 methyltransferase activity
[Term]
id: GO:0035643
@@ -209717,7 +209654,7 @@ is_a: GO:0043485 ! endosome to pigment granule transport
id: GO:0035647
name: 3-oxo-delta(4,5)-steroid 5-beta-reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 3-oxo-delta-4,5-steroid + NADPH + H(+) = a 5-beta-3-oxo-steroid + NADP(+)." [GOC:kad, MetaCyc:RXN-9726, PMID:19166903]
+def: "Catalysis of the reaction: a 3-oxo-delta-4,5-steroid + NADPH + H+ = a 5-beta-3-oxo-steroid + NADP+." [GOC:kad, MetaCyc:RXN-9726, PMID:19166903]
synonym: "3-oxo-delta4,5-steroid 5beta-reductase" EXACT [GOC:kad]
is_a: GO:0035671 ! enone reductase activity
@@ -209780,7 +209717,7 @@ is_a: GO:0035652 ! clathrin-coated vesicle cargo loading
id: GO:0035655
name: interleukin-18-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-18 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:BHF, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-18 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:BHF, GOC:signaling]
synonym: "interleukin-18-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
relationship: part_of GO:0071351 ! cellular response to interleukin-18
@@ -209816,7 +209753,7 @@ relationship: part_of GO:0005770 ! late endosome
id: GO:0035659
name: Wnt signaling pathway involved in wound healing, spreading of epidermal cells
namespace: biological_process
-def: "The series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of a cell in the epidermis that contributes to the migration of an epidermal cell along or through a wound gap to reestablish a continuous epidermis." [GOC:BHF]
+def: "The series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of a target cell in the epidermis that contributes to the migration of an epidermal cell along or through a wound gap to reestablish a continuous epidermis." [GOC:BHF]
synonym: "Wnt receptor signaling pathway involved in wound healing, spreading of epidermal cells" EXACT []
synonym: "Wnt receptor signalling pathway involved in wound healing, spreading of epidermal cells" EXACT [GOC:mah]
synonym: "Wnt-activated signaling pathway involved in wound healing, spreading of epidermal cells" EXACT [GOC:signaling]
@@ -209827,7 +209764,7 @@ relationship: part_of GO:0035313 ! wound healing, spreading of epidermal cells
id: GO:0035660
name: MyD88-dependent toll-like receptor 4 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a toll-like 4 receptor, where the MyD88 adaptor molecule mediates transduction of the signal. Toll-like 4 receptors bind bacterial lipopolysaccharide (LPS) to initiate an innate immune response." [GOC:BHF, PMID:18304834, PMID:20385024]
+def: "The series of molecular signals initiated by a ligand binding to a toll-like 4 receptor, where the MyD88 adaptor molecule mediates transduction of the signal. Toll-like 4 receptors bind bacterial lipopolysaccharide (LPS) to initiate an innate immune response." [GOC:BHF, PMID:18304834, PMID:20385024]
synonym: "MyD88-dependent TLR4 signaling pathway" EXACT [GOC:bf]
synonym: "MyD88-dependent toll-like receptor 4 signalling pathway" EXACT [GOC:bf]
is_a: GO:0002755 ! MyD88-dependent toll-like receptor signaling pathway
@@ -209837,7 +209774,7 @@ is_a: GO:0034142 ! toll-like receptor 4 signaling pathway
id: GO:0035661
name: MyD88-dependent toll-like receptor 2 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a toll-like 2 receptor where the MyD88 adaptor molecule mediates transduction of the signal. Toll-like 2 receptors are pattern recognition receptors that bind microbial pattern motifs to initiate an innate immune response." [GOC:BHF, PMID:20385024]
+def: "The series of molecular signals initiated by a ligand binding to a toll-like 2 receptor where the MyD88 adaptor molecule mediates transduction of the signal. Toll-like 2 receptors are pattern recognition receptors that bind microbial pattern motifs to initiate an innate immune response." [GOC:BHF, PMID:20385024]
synonym: "MyD88-dependent TLR2 signaling pathway" EXACT [GOC:bf]
synonym: "MyD88-dependent toll-like receptor 2 signalling pathway" EXACT [GOC:bf]
is_a: GO:0002755 ! MyD88-dependent toll-like receptor signaling pathway
@@ -209863,7 +209800,7 @@ is_a: GO:0035325 ! Toll-like receptor binding
id: GO:0035664
name: TIRAP-dependent toll-like receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TIRAP/MAL adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response." [GOC:BHF, PMID:11526399, PMID:11544529, PMID:12447442]
+def: "The series of molecular signals initiated by a ligand binding to a toll-like receptor where the TIRAP/MAL adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate an innate immune response." [GOC:BHF, PMID:11526399, PMID:11544529, PMID:12447442]
synonym: "MAL-dependent toll-like receptor signaling pathway" EXACT [PMID:11544529]
synonym: "MyD88 adapter-like dependent toll-like receptor signaling pathway" EXACT [PMID:11544529]
synonym: "TIRAP-dependent TLR signaling pathway" EXACT [GOC:bf]
@@ -209874,7 +209811,7 @@ is_a: GO:0002224 ! toll-like receptor signaling pathway
id: GO:0035665
name: TIRAP-dependent toll-like receptor 4 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a toll-like receptor 4 where the TIRAP/MAL adaptor mediates transduction of the signal. Toll-like 4 receptors are pattern recognition receptors that bind bacterial lipopolysaccharide (LPS) to initiate an innate immune response." [GOC:BHF, PMID:12447441]
+def: "The series of molecular signals initiated by a ligand binding to a toll-like receptor 4 where the TIRAP/MAL adaptor mediates transduction of the signal. Toll-like 4 receptors are pattern recognition receptors that bind bacterial lipopolysaccharide (LPS) to initiate an innate immune response." [GOC:BHF, PMID:12447441]
synonym: "MAL-dependent toll-like receptor 4 signaling pathway" EXACT [PMID:11544529]
synonym: "MyD88 adapter-like dependent toll-like receptor 4 signaling pathway" EXACT [GOC:11544529]
synonym: "TIRAP-dependent TLR4 signaling pathway" EXACT [GOC:bf]
@@ -209886,7 +209823,7 @@ is_a: GO:0035664 ! TIRAP-dependent toll-like receptor signaling pathway
id: GO:0035666
name: TRIF-dependent toll-like receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response." [GOC:BHF, PMID:12855817]
+def: "The series of molecular signals initiated by a ligand binding to a toll-like receptor where the TRIF adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate an innate immune response." [GOC:BHF, PMID:12855817]
synonym: "Toll/IL-1 receptor (TIR) domain-containing adaptor-dependent TLR signaling pathway" EXACT [PMID:12855817]
synonym: "TRIF-dependent TLR signaling pathway" EXACT [GOC:bf]
synonym: "TRIF-dependent toll-like receptor signalling pathway" EXACT [GOC:bf]
@@ -209896,7 +209833,7 @@ is_a: GO:0002756 ! MyD88-independent toll-like receptor signaling pathway
id: GO:0035667
name: TRIF-dependent toll-like receptor 4 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a toll-like 4 receptor where the TRIF adaptor mediates transduction of the signal. Toll-like 4 receptors are pattern recognition receptors that bind bacterial lipopolysaccharide (LPS) to initiate an innate immune response." [GOC:BHF, PMID:18641322, PMID:20511708]
+def: "The series of molecular signals initiated by a ligand binding to a toll-like 4 receptor where the TRIF adaptor mediates transduction of the signal. Toll-like 4 receptors are pattern recognition receptors that bind bacterial lipopolysaccharide (LPS) to initiate an innate immune response." [GOC:BHF, PMID:18641322, PMID:20511708]
synonym: "Toll/IL-1 receptor (TIR) domain-containing adaptor-dependent TLR4 signaling pathway" EXACT [PMID:12855817]
synonym: "TRIF-dependent TLR4 signaling pathway" EXACT [GOC:bf]
synonym: "TRIF-dependent toll-like receptor 4 signalling pathway" EXACT [GOC:bf]
@@ -209907,7 +209844,7 @@ is_a: GO:0035666 ! TRIF-dependent toll-like receptor signaling pathway
id: GO:0035668
name: TRAM-dependent toll-like receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the TRAM adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response." [GOC:BHF, PMID:14556004]
+def: "The series of molecular signals initiated by a ligand binding to a toll-like receptor where the TRAM adaptor mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate an innate immune response." [GOC:BHF, PMID:14556004]
synonym: "TRAM-dependent TLR signaling pathway" EXACT [GOC:bf]
synonym: "TRAM-dependent toll-like receptor signalling pathway" EXACT [GOC:bf]
is_a: GO:0002756 ! MyD88-independent toll-like receptor signaling pathway
@@ -209916,7 +209853,7 @@ is_a: GO:0002756 ! MyD88-independent toll-like receptor signaling pathway
id: GO:0035669
name: TRAM-dependent toll-like receptor 4 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a toll-like receptor 4 where the TRAM adaptor mediates transduction of the signal. Toll-like 4 receptors are pattern recognition receptors that bind bacterial lipopolysaccharide (LPS) to initiate an innate immune response." [GOC:BHF, PMID:14556004, PMID:18297073]
+def: "The series of molecular signals initiated by a ligand binding to a toll-like receptor 4 where the TRAM adaptor mediates transduction of the signal. Toll-like 4 receptors are pattern recognition receptors that bind bacterial lipopolysaccharide (LPS) to initiate an innate immune response." [GOC:BHF, PMID:14556004, PMID:18297073]
synonym: "TRAM-dependent TLR4 signaling pathway" EXACT [GOC:bf]
synonym: "TRAM-dependent toll-like receptor 4 signalling pathway" EXACT [GOC:bf]
is_a: GO:0034142 ! toll-like receptor 4 signaling pathway
@@ -210018,16 +209955,16 @@ relationship: part_of GO:0035677 ! posterior lateral line neuromast hair cell de
id: GO:0035681
name: toll-like receptor 15 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 15." [GOC:pde]
+def: "The series of molecular signals initiated by a ligand binding to toll-like receptor 15." [GOC:pde]
synonym: "TLR15 signaling pathway" EXACT [GOC:bf]
synonym: "toll-like receptor 15 signalling pathway" EXACT [GOC:mah]
-is_a: GO:0002224 ! toll-like receptor signaling pathway
+is_a: GO:0140895 ! cell surface toll-like receptor signaling pathway
[Term]
id: GO:0035682
name: toll-like receptor 21 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to toll-like receptor 21." [GOC:pde]
+def: "The series of molecular signals initiated by a ligand binding to toll-like receptor 21." [GOC:pde]
synonym: "TLR21 signaling pathway" EXACT [GOC:bf]
synonym: "toll-like receptor 21 signalling pathway" EXACT [GOC:mah]
is_a: GO:0002224 ! toll-like receptor signaling pathway
@@ -210092,7 +210029,7 @@ relationship: part_of GO:0035687 ! T-helper 1 cell extravasation
id: GO:0035689
name: chemokine (C-C motif) ligand 5 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the chemokine CCL5 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, PMID:18337562]
+def: "The series of molecular signals initiated by chemokine CCL5 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, PMID:18337562]
synonym: "CCL5-mediated signaling pathway" EXACT [PMID:18337562]
synonym: "chemokine (C-C motif) ligand 5 signalling pathway" EXACT [GOC:mah]
synonym: "RANTES-mediated signaling pathway" EXACT [PMID:19122644]
@@ -210102,7 +210039,7 @@ is_a: GO:0070098 ! chemokine-mediated signaling pathway
id: GO:0035691
name: macrophage migration inhibitory factor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of macrophage migration inhibitory factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling, PMID:12782713, PMID:19413900]
+def: "The series of molecular signals initiated by macrophage migration inhibitory factor binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling, PMID:12782713, PMID:19413900]
synonym: "macrophage migration inhibitory factor signalling pathway" EXACT [GOC:mah]
synonym: "MIF signaling pathway" EXACT [GOC:ebc]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -210128,7 +210065,7 @@ namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of a mitochondrial protein. This process is necessary to maintain the healthy state of mitochondria and is thought to occur via the induction of an intramitochondrial lysosome-like organelle that acts to eliminate the damaged oxidised mitochondrial proteins without destroying the mitochondrial structure." [GOC:sp, PMID:21264221, PMID:21264228]
synonym: "catabolism of mitochondrial protein" EXACT [GOC:bf]
synonym: "degradation of damaged mitochondrial protein" EXACT [GOC:bf]
-is_a: GO:0044257 ! cellular protein catabolic process
+is_a: GO:0030163 ! protein catabolic process
relationship: part_of GO:0007005 ! mitochondrion organization
[Term]
@@ -210360,7 +210297,7 @@ is_a: GO:0042073 ! intraciliary transport
id: GO:0035722
name: interleukin-12-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-12 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-12 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling]
synonym: "IL-12-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-12-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -210370,7 +210307,7 @@ relationship: part_of GO:0071349 ! cellular response to interleukin-12
id: GO:0035723
name: interleukin-15-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-15 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-15 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling]
synonym: "IL-15-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-15-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -210395,6 +210332,7 @@ def: "A process in which a sodium ion is transported from one side of a membrane
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "sodium ion membrane transport" EXACT []
is_a: GO:0006814 ! sodium ion transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -210438,6 +210376,7 @@ name: S-nitrosoglutathione binding
namespace: molecular_function
def: "Binding to S-nitrosoglutathione, a nitrosothiol considered to be a natural nitric oxide (NO) donor involved in S-nitrosylation, and in the storage and transport of nitric oxide in biological systems." [GOC:BHF]
synonym: "GSNO binding" EXACT []
+is_a: GO:0043168 ! anion binding
is_a: GO:1901681 ! sulfur compound binding
[Term]
@@ -210457,7 +210396,7 @@ namespace: biological_process
def: "The accumulation and maintenance in cells or tissues of nitric oxide (NO). Nitric oxide is stored in the form of dinitrosyl-iron complexes, which are stabilized, and possibly sequestered, by binding to glutathione S-transferase proteins." [GOC:BHF, PMID:12871945]
synonym: "NO storage" EXACT [GOC:bf]
is_a: GO:0051179 ! localization
-relationship: part_of GO:0033484 ! nitric oxide homeostasis
+relationship: part_of GO:0033484 ! intracellular nitric oxide homeostasis
[Term]
id: GO:0035733
@@ -210488,10 +210427,11 @@ relationship: part_of GO:0001745 ! compound eye morphogenesis
[Term]
id: GO:0035737
-name: injection of substance in to other organism
+name: obsolete injection of substance in to other organism
namespace: biological_process
-def: "The process of forcing a substance into another organism, either by penetrating the skin of the other organism or by applying the substance externally to a sensitive tissue such as those that surround the eyes." [GOC:pamgo_curators]
-is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms
+def: "OBSOLETE. The process of forcing a substance into another organism, either by penetrating the skin of the other organism or by applying the substance externally to a sensitive tissue such as those that surround the eyes." [GOC:pamgo_curators]
+comment: This term was obsoleted because it is specific to species that delivers venoms by biting; other organisms deliver venoms by other mechanisms, such as direct skin contact. Hence this terms describes a species rather than a specific process.
+is_obsolete: true
[Term]
id: GO:0035738
@@ -210500,7 +210440,7 @@ namespace: biological_process
def: "The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the manifestation of some change or damage to the bitten organism." [GOC:pamgo_curators]
synonym: "envenomation resulting in modification of morphology or physiology of other organism" EXACT []
synonym: "envenomation resulting in modulation of process in other organism" EXACT []
-is_a: GO:0035737 ! injection of substance in to other organism
+is_a: GO:0035821 ! modulation of process of another organism
[Term]
id: GO:0035739
@@ -210601,7 +210541,7 @@ name: protein localization to myelin sheath abaxonal region
namespace: biological_process
def: "Any process in which a protein is transported to, and/or maintained in, the abaxonal region of the myelin sheath. The abaxonal region is the region of the myelin sheath furthest from the axon." [GOC:BHF, PMID:20237282]
synonym: "protein localisation to myelin sheath abaxonal region" EXACT [GOC:mah]
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
[Term]
id: GO:0035751
@@ -210774,7 +210714,7 @@ is_a: GO:0099080 ! supramolecular complex
id: GO:0035771
name: interleukin-4-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-4 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-4 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling]
synonym: "IL-4-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-4-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -210784,7 +210724,7 @@ relationship: part_of GO:0071353 ! cellular response to interleukin-4
id: GO:0035772
name: interleukin-13-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-13 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-13 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling]
synonym: "IL-13-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-13-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -210894,22 +210834,23 @@ is_a: GO:2000516 ! positive regulation of CD4-positive, alpha-beta T cell activa
[Term]
id: GO:0035784
-name: nickel cation homeostasis
+name: obsolete obsolete nickel cation homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of nickel cations within an organism or cell." [GOC:kmv]
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of nickel cations within an organism or cell." [GOC:kmv]
+comment: The term is not clearly defined and usage has been inconsistent. For homeostasis terms, we would like to specify whether the homeostasis takes place intracellularly or at the level of the organism.
synonym: "nickel homeostasis" EXACT [GOC:bf]
-is_a: GO:0055076 ! transition metal ion homeostasis
-is_a: GO:0072507 ! divalent inorganic cation homeostasis
+is_obsolete: true
+consider: GO:0035785
[Term]
id: GO:0035785
-name: cellular nickel ion homeostasis
+name: intracellular nickel ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of nickel ions at the level of a cell." [GOC:kmv]
+def: "A homeostatic process involved in the maintenance of a steady state level of nickel ions within a cell." [GOC:kmv]
synonym: "cellular nickel homeostasis" EXACT [GOC:bf]
-is_a: GO:0035784 ! nickel cation homeostasis
-is_a: GO:0046916 ! cellular transition metal ion homeostasis
-is_a: GO:0072503 ! cellular divalent inorganic cation homeostasis
+synonym: "cellular nickel ion homeostasis" EXACT []
+is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0035787
@@ -210940,7 +210881,7 @@ is_a: GO:0035788 ! cell migration involved in metanephros development
id: GO:0035790
name: platelet-derived growth factor receptor-alpha signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a ligand to an alpha-type platelet-derived growth factor receptor (PDGFalpha) on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:yaf, PMID:10372961]
+def: "The series of molecular signals initiated a ligand binding to an alpha-type platelet-derived growth factor receptor (PDGFalpha) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:yaf, PMID:10372961]
synonym: "alphaPDGF receptor signaling pathway" EXACT [PMID:10372961]
synonym: "PDGF receptor-alpha signaling pathway" EXACT [GOC:bf]
synonym: "PDGFR-alpha signaling pathway" RELATED [GOC:bf]
@@ -210951,7 +210892,7 @@ is_a: GO:0048008 ! platelet-derived growth factor receptor signaling pathway
id: GO:0035791
name: platelet-derived growth factor receptor-beta signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a ligand to a beta-type platelet-derived growth factor receptor (PDGFbeta) on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:signaling, GOC:yaf, PMID:10372961]
+def: "The series of molecular signals initiated by the binding of a ligand to a beta-type platelet-derived growth factor receptor (PDGFbeta) on the surface of a signal-receiving cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:signaling, GOC:yaf, PMID:10372961]
synonym: "betaPDGF receptor signaling pathway" EXACT [PMID:10372961]
synonym: "PDGF receptor-beta signaling pathway" EXACT [GOC:bf]
synonym: "PDGFR-beta signaling pathway" EXACT [GOC:bf]
@@ -210972,7 +210913,7 @@ relationship: part_of GO:0033644 ! host cell membrane
id: GO:0035793
name: positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of metanephric mesenchymal cell migration as a result of the series of molecular signals generated as a consequence of a platelet-derived growth factor receptor-beta binding to one of its physiological ligands." [GOC:bf, GOC:mtg_kidney_jan10, GOC:yaf, PMID:10734101]
+def: "Any process that increases the frequency, rate or extent of metanephric mesenchymal cell migration resulting from the platelet-derived growth factor receptor-beta signaling pathway." [GOC:bf, GOC:mtg_kidney_jan10, GOC:yaf, PMID:10734101]
synonym: "positive regulation of metanephric mesenchymal cell migration by betaPDGF receptor signaling pathway" EXACT [PMID:10734101]
synonym: "positive regulation of metanephric mesenchymal cell migration by PDGF receptor-beta signaling pathway" EXACT [GOC:bf]
synonym: "positive regulation of metanephric mesenchymal cell migration by PDGFR-beta signaling pathway" EXACT [GOC:bf]
@@ -211045,7 +210986,7 @@ relationship: part_of GO:0072189 ! ureter development
id: GO:0035800
name: deubiquitinase activator activity
namespace: molecular_function
-def: "Binds to and increases the activity of deubiquitinase, an enzyme that catalyzes the hydrolysis of various forms of polymeric ubiquitin sequences." [GOC:sart, ISBN:0120793709]
+def: "Binds to and increases the activity of a deubiquitinase." [GOC:sart, ISBN:0120793709]
is_a: GO:0016504 ! peptidase activator activity
[Term]
@@ -211174,7 +211115,6 @@ name: regulation of renal sodium excretion
namespace: biological_process
def: "Any process that modulates the amount of sodium excreted in urine over a unit of time." [GOC:mtg_25march11, GOC:yaf]
is_a: GO:0044062 ! regulation of excretion
-is_a: GO:0065008 ! regulation of biological quality
is_a: GO:0098801 ! regulation of renal system process
relationship: regulates GO:0035812 ! renal sodium excretion
@@ -211203,11 +211143,11 @@ relationship: positively_regulates GO:0035812 ! renal sodium excretion
[Term]
id: GO:0035816
-name: renal water absorption involved in negative regulation of urine volume
+name: obsolete renal water absorption involved in negative regulation of urine volume
namespace: biological_process
-def: "Any process where water is taken up from the collecting ducts and proximal and distal loops of the nephron, which acts to decrease the amount of urine that is excreted from the body per unit time." [GOC:mtg_25march11, GOC:yaf]
-is_a: GO:0070295 ! renal water absorption
-relationship: part_of GO:0035811 ! negative regulation of urine volume
+def: "OBSOLETE. Any process where water is taken up from the collecting ducts and proximal and distal loops of the nephron, which acts to decrease the amount of urine that is excreted from the body per unit time." [GOC:mtg_25march11, GOC:yaf]
+comment: The reason for obsoletion is that there are no annotations and should be captured in GO-CAM and annotation extensions.
+is_obsolete: true
[Term]
id: GO:0035817
@@ -211334,21 +211274,25 @@ is_obsolete: true
id: GO:0035830
name: palmatine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving palmatine, a berberine alkaloid found in many plants." [GOC:yaf]
+def: "The chemical reactions and pathways involving palmatine, a berberine alkaloid found in many plants." [GOC:yaf, PMID:25285405]
synonym: "palmatine metabolism" EXACT [GOC:bf]
is_a: GO:0033076 ! isoquinoline alkaloid metabolic process
+is_a: GO:0046483 ! heterocycle metabolic process
+is_a: GO:1901360 ! organic cyclic compound metabolic process
[Term]
id: GO:0035831
name: palmatine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of palmatine, a berberine alkaloid found in many plants." [GOC:yaf]
+def: "The chemical reactions and pathways resulting in the formation of palmatine, a berberine alkaloid found in many plants." [GOC:yaf, PMID:21327819]
synonym: "palmatine anabolism" EXACT [GOC:bf]
synonym: "palmatine biosynthesis" EXACT [GOC:bf]
synonym: "palmatine formation" EXACT [GOC:bf]
synonym: "palmatine synthesis" EXACT [GOC:bf]
+is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0033075 ! isoquinoline alkaloid biosynthetic process
is_a: GO:0035830 ! palmatine metabolic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
[Term]
id: GO:0035832
@@ -211357,6 +211301,9 @@ namespace: biological_process
def: "The chemical reactions and pathways involving berbamunine, an isoquinoline alkaloid." [GOC:yaf]
synonym: "berbamunine metabolism" EXACT [GOC:bf]
is_a: GO:0046445 ! benzyl isoquinoline alkaloid metabolic process
+is_a: GO:0046483 ! heterocycle metabolic process
+is_a: GO:1901360 ! organic cyclic compound metabolic process
+is_a: GO:1901615 ! organic hydroxy compound metabolic process
[Term]
id: GO:0035833
@@ -211368,7 +211315,10 @@ synonym: "berbamunine biosynthesis" EXACT [GOC:bf]
synonym: "berbamunine formation" EXACT [GOC:bf]
synonym: "berbamunine synthesis" EXACT [GOC:bf]
is_a: GO:0009708 ! benzyl isoquinoline alkaloid biosynthetic process
+is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0035832 ! berbamunine metabolic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+is_a: GO:1901617 ! organic hydroxy compound biosynthetic process
[Term]
id: GO:0035834
@@ -211410,7 +211360,6 @@ synonym: "ergot alkaloid formation" EXACT [GOC:bf]
synonym: "ergot alkaloid synthesis" EXACT [GOC:bf]
is_a: GO:0009709 ! terpenoid indole alkaloid biosynthetic process
is_a: GO:0035836 ! ergot alkaloid metabolic process
-is_a: GO:0044550 ! secondary metabolite biosynthetic process
[Term]
id: GO:0035838
@@ -211493,7 +211442,7 @@ name: oviduct epithelium development
namespace: biological_process
def: "The progression of the oviduct epithelium over time from its initial formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism. The oviduct epithelium is the specialized epithelium that lines the oviduct." [GOC:yaf, http://www.thefreedictionary.com/oviduct]
synonym: "fallopian tube epithelium development" NARROW [GOC:yaf]
-is_a: GO:0048608 ! reproductive structure development
+is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0060429 ! epithelium development
relationship: part_of GO:0060066 ! oviduct development
@@ -211584,7 +211533,6 @@ namespace: biological_process
def: "The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow." [CL:0000556, GOC:BHF, GOC:vk]
synonym: "megakaryocyte cell development" EXACT [GOC:bf]
is_a: GO:0061515 ! myeloid cell development
-is_a: GO:0098751 ! bone cell development
relationship: part_of GO:0030219 ! megakaryocyte differentiation
[Term]
@@ -211610,7 +211558,7 @@ id: GO:0035859
name: Seh1-associated complex
namespace: cellular_component
def: "A GTPase-activating protein (GAP) complex that regulates TORC1 signaling by interacting with the Rag GTPase. In S. cerevisiae the complex contains Seh1p, Sec13p, Npr2p, Npr3p, Iml1p, Mtc5p, Rtc1p, and Sea4p." [GOC:jh, PMID:21454883, PMID:23974112]
-comment: The Rag GTPase complex corresponds to Gtr1-Gtr2 GTPase complex ; GO:1990131.
+comment: The Rag GTPase complex corresponds to Gtr1-Gtr2 GTPase complex ; GO:1990131.
synonym: "GATOR complex" EXACT [GOC:rb, PMID:23723238]
synonym: "SEA complex" EXACT [GOC:jh, PMID:21454883]
is_a: GO:0032991 ! protein-containing complex
@@ -211619,7 +211567,7 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:0035860
name: glial cell-derived neurotrophic factor receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a glial cell-derived neurotrophic factor receptor binding to one of its physiological ligands." [GOC:yaf, PMID:12953054]
+def: "The series of molecular signals initiated by a ligand binding to a glial cell-derived neurotrophic factor receptor." [GOC:yaf, PMID:12953054]
synonym: "GDNF receptor signaling pathway" EXACT [GOC:yaf]
synonym: "glial cell derived neurotrophic factor receptor signaling pathway" EXACT [GOC:bf]
synonym: "glial cell line-derived neurotrophic factor receptor signalling pathway" EXACT [GOC:yaf]
@@ -211675,6 +211623,8 @@ def: "Any process that results in a change in state or activity of a cell or an
synonym: "response to K+ ion" EXACT [GOC:bf]
synonym: "response to potassium" EXACT [GOC:bf]
is_a: GO:0010038 ! response to metal ion
+is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0035865
@@ -211685,6 +211635,8 @@ synonym: "cellular response to K+ ion" EXACT [GOC:bf]
synonym: "cellular response to potassium" EXACT [GOC:bf]
is_a: GO:0035864 ! response to potassium ion
is_a: GO:0071248 ! cellular response to metal ion
+is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0035866
@@ -211726,8 +211678,8 @@ relationship: part_of GO:0005929 ! cilium
id: GO:0035870
name: dITP diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dITP + H2O = dIMP + diphosphate." [GOC:dgf, PMID:21548881, RHEA:28342]
-synonym: "2'-Deoxyinosine-5'-triphosphate pyrophosphohydrolase activity" EXACT [KEGG_REACTION:R03531]
+def: "Catalysis of the reaction: dITP + H2O = dIMP + H+ + diphosphate." [GOC:dgf, PMID:21548881, RHEA:28342]
+synonym: "2'-deoxyinosine-5'-triphosphate pyrophosphohydrolase activity" EXACT [KEGG_REACTION:R03531]
synonym: "deoxyinosine triphosphate pyrophosphatase activity" EXACT [GOC:bf]
synonym: "dITP pyrophosphatase activity" EXACT [GOC:bf]
xref: EC:3.6.1.66
@@ -211735,7 +211687,7 @@ xref: KEGG_REACTION:R03531
xref: MetaCyc:RXN0-1602
xref: Reactome:R-HSA-2509838 "ITPA hydrolyses dITP to dIMP"
xref: RHEA:28342
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0035871
@@ -211750,7 +211702,7 @@ is_a: GO:0016579 ! protein deubiquitination
id: GO:0035872
name: nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of a nucleotide-binding domain, leucine rich repeat containing receptor (NLR) binding to one of its physiological ligands. NLRs are cytoplasmic receptors defined by their tripartite domain architecture that contains: a variable C-terminus, a middle nucleotide-binding domain, and a LRR domain that is variable in the repeats composition and number. The NLR signaling pathway begins with binding of a ligand to a NLR receptor and ends with regulation of a downstream cellular process." [GOC:sj, PMID:18280719, Reactome:168643]
+def: "The series of molecular signals initiated by a ligand binding to a nucleotide-binding domain, leucine rich repeat containing receptor (NLR), and ending with the regulation of a downstream cellular process. NLRs are cytoplasmic receptors defined by their tripartite domain architecture that contains: a variable C-terminus, a middle nucleotide-binding domain, and a LRR domain that is variable in the repeats composition and number." [GOC:sj, PMID:18280719]
synonym: "NLR signaling pathway" EXACT [PMID:18280719]
synonym: "NOD-like receptor signaling pathway" RELATED [Wikipedia:NOD-like_receptor]
synonym: "nucleotide-binding domain leucine-rich repeat containing receptor signaling pathway" EXACT [PMID:18280719]
@@ -211767,7 +211719,6 @@ def: "The process in which lactate is transported across a membrane. Lactate is
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "lactate membrane transport" EXACT []
is_a: GO:0015727 ! lactate transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -211914,22 +211865,17 @@ def: "The attachment of a developing otolith to the kinocilia of tether cells in
is_a: GO:0032501 ! multicellular organismal process
relationship: part_of GO:0048840 ! otolith development
-[Term]
-id: GO:0035890
-name: exit from host
-namespace: biological_process
-def: "The directed movement of an organism out of the body, tissues or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:bf]
-synonym: "ejection from host" RELATED [GOC:bf]
-is_a: GO:0052126 ! movement in host environment
-
[Term]
id: GO:0035891
name: exit from host cell
namespace: biological_process
-def: "The directed movement of an organism out of a cell of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:bf, GOC:rs, PMID:19325115]
+alt_id: GO:0035890
+def: "The movement of an organism out of a cell of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:bf, GOC:rs, PMID:19325115]
+synonym: "ejection from host" RELATED [GOC:bf]
synonym: "ejection from host cell" RELATED [PMID:19325115]
+synonym: "exit from host" RELATED []
synonym: "host cell exit" EXACT [PMID:19325115]
-is_a: GO:0035890 ! exit from host
+is_a: GO:0044000 ! movement in host
[Term]
id: GO:0035892
@@ -211940,7 +211886,6 @@ synonym: "modulation by organism of platelet aggregation in other organism" EXAC
synonym: "modulation of platelet aggregation in other organism" EXACT []
synonym: "regulation of platelet aggregation in other organism" RELATED [GOC:bf]
is_a: GO:0035806 ! modulation of blood coagulation in another organism
-is_a: GO:0044364 ! disruption of cells of another organism
is_a: GO:0090330 ! regulation of platelet aggregation
[Term]
@@ -212155,7 +212100,7 @@ synonym: "pore complex biogenesis in other organism" EXACT [GOC:bf]
synonym: "pore formation in membrane of other organism" EXACT []
synonym: "pore formation in other organism" EXACT [GOC:bf]
synonym: "pore-forming toxin activity" RELATED [GOC:bf]
-is_a: GO:0051673 ! membrane disruption in another organism
+is_a: GO:0051673 ! disruption of membrane integrity in another organism
[Term]
id: GO:0035916
@@ -212240,7 +212185,7 @@ name: flurbiprofen binding
namespace: molecular_function
def: "Binding to flurbiprofen." [GOC:BHF, GOC:rl]
synonym: "2-(2-fluoro-[1,1'-biphenyl-4-yl])propanoic acid binding" EXACT []
-is_a: GO:0043177 ! organic acid binding
+is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
[Term]
@@ -212274,7 +212219,7 @@ def: "The process in which a rRNA, ribosomal ribonucleic acid, is transported fr
synonym: "cytoplasmic RNA import into mitochondrion" NARROW [GOC:ans]
synonym: "nuclear-encoded RNA import into mitochondrion" NARROW [GOC:bf]
is_a: GO:0050658 ! RNA transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0035928
@@ -212363,8 +212308,7 @@ namespace: biological_process
def: "The regulated release of estradiol into the circulatory system." [GOC:sl, PMID:21632818]
synonym: "oestradiol secretion" EXACT []
is_a: GO:0015850 ! organic hydroxy compound transport
-is_a: GO:0046879 ! hormone secretion
-is_a: GO:0140353 ! lipid export from cell
+is_a: GO:0035929 ! steroid hormone secretion
[Term]
id: GO:0035939
@@ -212418,8 +212362,7 @@ def: "The regulated release of estrone into the circulatory system." [GOC:sl, PM
synonym: "3-hydroxy-1,3,5(10)-estratrien-17-one secretion" EXACT []
synonym: "folliculin secretion" EXACT []
is_a: GO:0015850 ! organic hydroxy compound transport
-is_a: GO:0046879 ! hormone secretion
-is_a: GO:0140353 ! lipid export from cell
+is_a: GO:0035929 ! steroid hormone secretion
[Term]
id: GO:0035944
@@ -212849,22 +212792,24 @@ relationship: part_of GO:0006516 ! glycoprotein catabolic process
[Term]
id: GO:0035978
-name: histone H2A-S139 phosphorylation
+name: obsolete histone H2A-S139 phosphorylation
namespace: biological_process
-def: "The modification of histone H2A by the addition of an phosphate group to a serine residue at position 139 of the histone." [GOC:yaf, PMID:16061642]
-comment: Residue 1 of histone H2AX is taken as the first residue following removal of the initiating Methionine (Met).
+def: "OBSOLETE. The modification of histone H2A by the addition of an phosphate group to a serine residue at position 139 of the histone." [GOC:yaf, PMID:16061642]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H2A.x phosphorylation at S139" NARROW [GOC:bf, PMID:16061642]
-is_a: GO:0035404 ! histone-serine phosphorylation
-is_a: GO:1990164 ! histone H2A phosphorylation
+is_obsolete: true
+consider: GO:0035979
[Term]
id: GO:0035979
-name: histone kinase activity (H2A-S139 specific)
+name: histone H2AXS139 kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to the serine-139 residue of the C-terminal tail of histone H2A." [GOC:yaf, PMID:16061642]
+def: "Catalysis of the reaction: histone H2AX-serine (position 139) + ATP = histone H2AX-phosphoserine (position 139) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 139 of histone variant H2AX." [GOC:yaf, PMID:11893489, PMID:16061642]
comment: Residue 1 of histone H2A is taken as the first residue following removal of the initiating Methionine (Met).
+synonym: "histone H2AS139 kinase activity" RELATED []
+synonym: "histone kinase activity (H2A-S139 specific)" RELATED []
synonym: "histone kinase activity (H2A.x-S139 specific)" NARROW [GOC:bf, PMID:16061642]
-is_a: GO:0035174 ! histone serine kinase activity
+is_a: GO:0141003 ! histone H2AX kinase activity
[Term]
id: GO:0035980
@@ -212893,7 +212838,6 @@ synonym: "age-dependent behavioural decline" EXACT [GOC:bf]
synonym: "age-related behavioral decline" EXACT [GOC:kmv]
synonym: "behavioral aging" EXACT [GOC:kmv]
is_obsolete: true
-replaced_by: GO:0090647
[Term]
id: GO:0035983
@@ -212930,7 +212874,7 @@ id: GO:0035986
name: obsolete senescence-associated heterochromatin focus assembly
namespace: biological_process
def: "OBSOLETE. The assembly of chromatin into senescence-associated heterochromatin foci (SAHF), transcriptionally-silent heterochromatin structures present in senescent cells, containing the condensed chromatin of one chromosome, and enriched for histone modifications. Formation of these chromatin structures is thought to repress expression of proliferation-promoting genes." [GOC:yaf, PMID:15621527, PMID:21248468]
-comment: This term was obsoleted because there is no evidence that this is a distinct process; this should be captured as an extension
+comment: This term was obsoleted because there is no evidence that this is a distinct process; this should be captured as an extension.
synonym: "SAHF formation" EXACT [GOC:yaf]
synonym: "senescence-associated heterochromatin foci formation" EXACT [GOC:yaf]
synonym: "senescence-associated heterochromatin focus formation" EXACT []
@@ -213040,7 +212984,6 @@ synonym: "7,8-dihydroneopterin 3'-triphosphate anabolism" EXACT [GOC:bf]
synonym: "7,8-dihydroneopterin 3'-triphosphate biosynthesis" EXACT [GOC:bf]
synonym: "7,8-dihydroneopterin 3'-triphosphate formation" EXACT [GOC:bf]
synonym: "7,8-dihydroneopterin 3'-triphosphate synthesis" EXACT [GOC:bf]
-xref: UniPathway:UPA00848
is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0042559 ! pteridine-containing compound biosynthetic process
is_a: GO:0051066 ! dihydrobiopterin metabolic process
@@ -213050,9 +212993,8 @@ is_a: GO:0090407 ! organophosphate biosynthetic process
id: GO:0035999
name: tetrahydrofolate interconversion
namespace: biological_process
-def: "The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules." [GOC:yaf, PMID:1825999, UniPathway:UPA00193]
+def: "The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules." [GOC:yaf, PMID:1825999]
xref: MetaCyc:PWY-2201
-xref: UniPathway:UPA00193
is_a: GO:0006730 ! one-carbon metabolic process
is_a: GO:0046653 ! tetrahydrofolate metabolic process
@@ -213142,6 +213084,8 @@ id: GO:0036009
name: protein-glutamine N-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + protein L-glutamine = S-adenosyl-L-homocysteine + protein N-methyl-L-glutamine." [GOC:imk, PMID:11847124]
+synonym: "protein glutamine N-methylase activity" EXACT []
+synonym: "protein glutamine N-methyltransferase activity" EXACT []
xref: Reactome:R-HSA-6800138 "N6AMT1:TRMT112 transfers CH3 group from AdoMet to ETF1 dimer"
is_a: GO:0008170 ! N-methyltransferase activity
is_a: GO:0008276 ! protein methyltransferase activity
@@ -213367,7 +213311,7 @@ namespace: biological_process
def: "The process in which the guanylyltransferase enzyme responsible for adding a 7-methylguanosine cap on pre-mRNA becomes associated with the RNA polymerase II holoenzyme complex and the 5' end of a transcript." [GOC:bf, GOC:rb, PMID:10594013]
synonym: "capping enzyme targeting to RNA polymerase II" EXACT [PMID:10594013]
synonym: "recruitment of guanylyltransferase to RNA polymerase II holoenzyme complex" EXACT [GOC:bf]
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
relationship: part_of GO:0006370 ! 7-methylguanosine mRNA capping
[Term]
@@ -213479,7 +213423,7 @@ is_a: GO:1901502 ! ether catabolic process
id: GO:0036041
name: long-chain fatty acid binding
namespace: molecular_function
-def: "Binding to a long-chain fatty acid. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [GOC:pm, PMID:12641450]
+def: "Binding to a long-chain fatty acid. A long-chain fatty acid is a fatty acid with an aliphatic tail of 13 to 21 carbons." [GOC:pm, PMID:12641450]
synonym: "long chain fatty acid binding" EXACT [PMID:12641450]
is_a: GO:0005504 ! fatty acid binding
@@ -213487,7 +213431,7 @@ is_a: GO:0005504 ! fatty acid binding
id: GO:0036042
name: long-chain fatty acyl-CoA binding
namespace: molecular_function
-def: "Binding to a long-chain fatty acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. Long-chain fatty-acyl-CoAs have chain lengths of C13 or more." [GOC:krc, GOC:pm]
+def: "Binding to a long-chain fatty acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. A long-chain fatty acid is a fatty acid with an aliphatic tail of 13 to 21 carbons." [GOC:krc, GOC:pm]
synonym: "long-chain fatty acyl-coenyme A binding" EXACT []
is_a: GO:0000062 ! fatty-acyl-CoA binding
@@ -213567,7 +213511,7 @@ name: protein localization to trailing edge
namespace: biological_process
def: "A process in which a protein is transported to, or maintained at, the trailing edge. The trailing edge is the area of a motile cell opposite to the direction of movement." [GOC:pf, GOC:pg]
synonym: "protein localisation to trailing edge" EXACT [GOC:mah]
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
[Term]
id: GO:0036052
@@ -213595,12 +213539,13 @@ synonym: "peptidyl-malonyllysine demalonylase activity" EXACT []
synonym: "protein lysine demalonylation activity" EXACT [PMID:21908771]
synonym: "protein malonyl lysine demalonylation activity" EXACT [GOC:bf]
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
+is_a: GO:0140096 ! catalytic activity, acting on a protein
[Term]
id: GO:0036055
name: protein-succinyllysine desuccinylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + N(6)-succinyl-L-lysyl-[protein] + NAD(+) = 2''-O-succinyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide." [GOC:sp, PMID:22076378]
+def: "Catalysis of the reaction: H2O + N(6)-succinyl-L-lysyl-[protein] + NAD+ = 2''-O-succinyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide." [GOC:sp, PMID:22076378]
comment: This reaction is the removal of a succinyl group (CO-CH2-CH2-CO) from a succinylated lysine residue of a protein or peptide.
synonym: "peptidyl-succinyllysine desuccinylase activity" EXACT []
synonym: "succinyl lysine desuccinylase activity" BROAD [GOC:bf]
@@ -213721,7 +213666,7 @@ is_a: GO:0015995 ! chlorophyll biosynthetic process
id: GO:0036068
name: light-independent chlorophyll biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors, which occur in the absence of light." [GOC:yaf, PMID:12242396, UniPathway:UPA00670]
+def: "The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors, which occur in the absence of light." [GOC:yaf, PMID:12242396]
synonym: "light independent chlorophyll biosynthetic process" EXACT [GOC:yaf]
synonym: "light-independent chlorophyll anabolism" EXACT [GOC:bf]
synonym: "light-independent chlorophyll biosynthesis" EXACT [GOC:bf]
@@ -213746,7 +213691,7 @@ is_a: GO:0036067 ! light-dependent chlorophyll biosynthetic process
id: GO:0036070
name: light-independent bacteriochlorophyll biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a bacteriochlorophyll, which occur in the absence of light. Bacteriochlorophylls are any of the chlorophylls of photosynthetic bacteria; they differ structurally from the chlorophylls of higher plants." [GOC:yaf, PMID:12242396, UniPathway:UPA00671]
+def: "The chemical reactions and pathways resulting in the formation of a bacteriochlorophyll, which occur in the absence of light. Bacteriochlorophylls are any of the chlorophylls of photosynthetic bacteria; they differ structurally from the chlorophylls of higher plants." [GOC:yaf, PMID:12242396]
synonym: "light independent bacteriochlorophyll biosynthetic process" EXACT [GOC:bf]
synonym: "light-independent bacteriochlorophyll anabolism" EXACT [GOC:bf]
synonym: "light-independent bacteriochlorophyll biosynthesis" EXACT [GOC:bf]
@@ -213826,19 +213771,21 @@ is_a: GO:0005338 ! nucleotide-sugar transmembrane transporter activity
[Term]
id: GO:0036081
-name: extracellular ammonia-gated ion channel activity
+name: extracellular ammonia-gated monoatomic ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a channel that opens when extracellular ammonia (NH3) has been bound by the channel complex or one of its constituent parts." [GOC:sart, PMID:19135896]
+synonym: "extracellular ammonia-gated ion channel activity" BROAD []
synonym: "ionotropic ammonia receptor activity" RELATED [PMID:19135896]
-is_a: GO:0005230 ! extracellular ligand-gated ion channel activity
+is_a: GO:0005230 ! extracellular ligand-gated monoatomic ion channel activity
[Term]
id: GO:0036082
-name: extracellular phenylacetaldehyde-gated ion channel activity
+name: extracellular phenylacetaldehyde-gated monoatomic ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a channel that opens when extracellular phenylacetaldehyde has been bound by the channel complex or one of its constituent parts." [GOC:sart, PMID:19135896]
+synonym: "extracellular phenylacetaldehyde-gated ion channel activity" BROAD []
synonym: "ionotropic phenylacetaldehyde receptor activity" RELATED [PMID:19135896]
-is_a: GO:0005230 ! extracellular ligand-gated ion channel activity
+is_a: GO:0005230 ! extracellular ligand-gated monoatomic ion channel activity
[Term]
id: GO:0036083
@@ -213868,6 +213815,7 @@ synonym: "GDP-fucose import into Golgi" EXACT [GOC:bf]
synonym: "GDP-fucose transport across Golgi membrane" EXACT [GOC:bf]
synonym: "GDP-fucose transport into Golgi lumen" EXACT [GOC:sart]
is_a: GO:0015783 ! GDP-fucose transmembrane transport
+is_a: GO:0140820 ! cytosol to Golgi apparatus transport
[Term]
id: GO:0036086
@@ -213882,7 +213830,7 @@ is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II p
id: GO:0036087
name: glutathione synthase complex
namespace: cellular_component
-def: "A protein complex composed of two or more polypeptide subunits, and which possesses glutathione synthase activity (catalysis of the reaction: L-gamma-glutamyl-L-cysteine + ATP + glycine = ADP + glutathione + 2 H(+) + phosphate). In eukaryotes, the complex is homodimeric, in E. coli glutathione synthase exists as a tetramer, and in S. pombe the complex exists as a homodimer or a heterotetramer." [GOC:al, PMID:12734194, PMID:14990577, PMID:1958212]
+def: "A protein complex composed of two or more polypeptide subunits, and which possesses glutathione synthase activity (catalysis of the reaction: L-gamma-glutamyl-L-cysteine + ATP + glycine = ADP + glutathione + 2 H+ + phosphate). In eukaryotes, the complex is homodimeric, in E. coli glutathione synthase exists as a tetramer, and in S. pombe the complex exists as a homodimer or a heterotetramer." [GOC:al, PMID:12734194, PMID:14990577, PMID:1958212]
synonym: "glutathione synthetase complex" EXACT [PMID:12734194, PMID:14990577, PMID:1958212]
is_a: GO:1902494 ! catalytic complex
@@ -214020,15 +213968,14 @@ is_a: GO:0046395 ! carboxylic acid catabolic process
id: GO:0036101
name: leukotriene B4 catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of leukotriene B4, a leukotriene composed of (6Z,8E,10E,14Z)-eicosatetraenoic acid having (5S)- and (12R)-hydroxy substituents." [GOC:yaf, PMID:9799565, UniPathway:UPA00883]
+def: "The chemical reactions and pathways resulting in the breakdown of leukotriene B4, a leukotriene composed of (6Z,8E,10E,14Z)-eicosatetraenoic acid having (5S)- and (12R)-hydroxy substituents." [GOC:yaf, PMID:9799565]
synonym: "leukotriene B4 breakdown" EXACT [GOC:bf]
synonym: "leukotriene B4 catabolism" EXACT [GOC:bf]
synonym: "leukotriene B4 degradation" EXACT [GOC:bf]
synonym: "LTB4 catabolism" EXACT []
-is_a: GO:0016042 ! lipid catabolic process
is_a: GO:0036100 ! leukotriene catabolic process
is_a: GO:0036102 ! leukotriene B4 metabolic process
-is_a: GO:0072329 ! monocarboxylic acid catabolic process
+is_a: GO:0042758 ! long-chain fatty acid catabolic process
is_a: GO:1901523 ! icosanoid catabolic process
is_a: GO:1901616 ! organic hydroxy compound catabolic process
@@ -214038,9 +213985,8 @@ name: leukotriene B4 metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving leukotriene B4, a leukotriene composed of (6Z,8E,10E,14Z)-eicosatetraenoic acid having (5S)- and (12R)-hydroxy substituents." [GOC:bf]
synonym: "LTB4 metabolism" EXACT []
-is_a: GO:0006629 ! lipid metabolic process
+is_a: GO:0001676 ! long-chain fatty acid metabolic process
is_a: GO:0006691 ! leukotriene metabolic process
-is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:1901568 ! fatty acid derivative metabolic process
is_a: GO:1901615 ! organic hydroxy compound metabolic process
@@ -214054,14 +214000,14 @@ is_a: GO:0006644 ! phospholipid metabolic process
is_a: GO:0006664 ! glycolipid metabolic process
is_a: GO:0043648 ! dicarboxylic acid metabolic process
is_a: GO:1901269 ! lipooligosaccharide metabolic process
+is_a: GO:1901568 ! fatty acid derivative metabolic process
[Term]
id: GO:0036104
name: Kdo2-lipid A biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of Kdo2-lipid A, a lipopolysaccharide (LPS) component." [GOC:yaf, UniPathway:UPA00360]
-synonym: "di[3-deoxy-D-manno-octulosonyl]-lipid A biosynthesis" EXACT [UniPathway:UPA00360]
-synonym: "KDO(2)-lipid A biosynthesis" EXACT [UniPathway:UPA00360]
+def: "The chemical reactions and pathways resulting in the formation of Kdo2-lipid A, a lipopolysaccharide (LPS) component." [GOC:yaf, PMID:21106097]
+synonym: "3-deoxy-d-manno-octulosonic acid-lipid A biosynthesis" EXACT [PMID:24838025]
synonym: "Kdo2-lipid A anabolism" EXACT [GOC:bf]
synonym: "Kdo2-lipid A biosynthesis" EXACT [GOC:bf]
synonym: "Kdo2-lipid A formation" EXACT [GOC:bf]
@@ -214071,6 +214017,7 @@ is_a: GO:0009247 ! glycolipid biosynthetic process
is_a: GO:0036103 ! Kdo2-lipid A metabolic process
is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
is_a: GO:1901271 ! lipooligosaccharide biosynthetic process
+is_a: GO:1901570 ! fatty acid derivative biosynthetic process
[Term]
id: GO:0036105
@@ -214107,7 +214054,7 @@ is_a: GO:0006721 ! terpenoid metabolic process
id: GO:0036108
name: 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate, a precursor of 4-amino-4-deoxy-L-arabinose (L-Ara4N)." [GOC:yaf, PMID:15695810, UniPathway:UPA00036]
+def: "The chemical reactions and pathways resulting in the formation of 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate, a precursor of 4-amino-4-deoxy-L-arabinose (L-Ara4N)." [GOC:yaf, PMID:15695810]
synonym: "4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate anabolism" EXACT [GOC:bf]
synonym: "4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate biosynthesis" EXACT [GOC:bf]
synonym: "4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate formation" EXACT [GOC:bf]
@@ -214150,7 +214097,7 @@ is_a: GO:0035337 ! fatty-acyl-CoA metabolic process
id: GO:0036112
name: medium-chain fatty-acyl-CoA metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving medium-chain fatty-acyl-CoAs, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. A medium-chain fatty acid is a fatty acid with a chain length of between C6 and C12." [GOC:pm]
+def: "The chemical reactions and pathways involving medium-chain fatty-acyl-CoAs, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. A medium-chain fatty acid is a fatty acid with an aliphatic tail of 6 to 12 carbons." [GOC:pm]
synonym: "medium-chain fatty acyl CoA metabolic process" EXACT [GOC:bf]
synonym: "medium-chain fatty acyl-CoA metabolism" EXACT [GOC:bf]
is_a: GO:0035337 ! fatty-acyl-CoA metabolic process
@@ -214170,7 +214117,7 @@ is_a: GO:0036115 ! fatty-acyl-CoA catabolic process
id: GO:0036114
name: medium-chain fatty-acyl-CoA catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of medium-chain fatty-acyl-CoAs, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a medium-chain fatty-acyl group. A medium-chain fatty acid is a fatty acid with a chain length of between C6 and C12." [GOC:pm]
+def: "The chemical reactions and pathways resulting in the breakdown of medium-chain fatty-acyl-CoAs, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a medium-chain fatty-acyl group. A medium-chain fatty acid is a fatty acid with an aliphatic tail of 6 to 12 carbons." [GOC:pm]
synonym: "medium-chain fatty-acyl-CoA breakdown" EXACT [GOC:bf]
synonym: "medium-chain fatty-acyl-CoA catabolism" EXACT [GOC:bf]
synonym: "medium-chain fatty-acyl-CoA degradation" EXACT [GOC:bf]
@@ -214227,7 +214174,6 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a platelet-derived growth factor stimulus." [GOC:yaf]
synonym: "response to PDGF stimulus" EXACT [GOC:bf]
synonym: "response to platelet-derived growth factor stimulus" EXACT [GOC:dos]
-is_a: GO:0009719 ! response to endogenous stimulus
is_a: GO:0070848 ! response to growth factor
[Term]
@@ -214238,7 +214184,6 @@ def: "Any process that results in a change in state or activity of a cell (in te
synonym: "cellular response to PDGF stimulus" EXACT [GOC:bf]
is_a: GO:0036119 ! response to platelet-derived growth factor
is_a: GO:0071363 ! cellular response to growth factor stimulus
-is_a: GO:0071495 ! cellular response to endogenous stimulus
[Term]
id: GO:0036121
@@ -214284,7 +214229,7 @@ name: fatty acid beta-oxidation multienzyme complex
namespace: cellular_component
def: "A multienzyme complex possessing three kinds of enzymes that catalyze the chain reactions in the fatty acid beta-oxidation cycle, enoyl-CoA hydratase (ECH), 3-hydroxyacyl-CoA dehydrogenase (HACD), and acetyl-CoA C-acyltransferase (KACT)." [GOC:imk, PMID:12115060, PMID:16472743]
comment: For fatty acid beta-oxidation multienzyme complexes located in the mitochondrial matrix, consider instead the term 'mitochondrial fatty acid beta-oxidation multienzyme complex ; GO:0016507'.
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0036126
@@ -214303,7 +214248,6 @@ namespace: molecular_function
def: "Binding to 3-sulfino-L-alanine (cysteine sulfinate)." [GOC:al, PMID:8346915]
synonym: "cysteine sulfinate binding" EXACT [GOC:al]
is_a: GO:0016597 ! amino acid binding
-is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0072341 ! modified amino acid binding
is_a: GO:1901681 ! sulfur compound binding
@@ -214341,7 +214285,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0036131
name: prostaglandin D2 11-ketoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: prostaglandin D2 + H+ + NADPH -> 11-epi-prostaglandin F2alpha + NADP+." [EC:1.1.1.188, GOC:mw, KEGG_REACTION:R02799, PMID:1504718, PMID:3862115]
+def: "Catalysis of the reaction: prostaglandin D2 + H+ + NADPH = 11-epi-prostaglandin F2alpha + NADP+." [EC:1.1.1.188, GOC:mw, KEGG_REACTION:R02799, PMID:1504718, PMID:3862115]
synonym: "PGD2 11-ketoreductase" EXACT [PMID:14996743]
synonym: "prostaglandin 11-keto reductase" EXACT [PMID:7248318]
xref: EC:1.1.1.188
@@ -214432,9 +214376,13 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
[Term]
id: GO:0036140
-name: peptidyl-asparagine 3-dioxygenase activity
+name: [protein]-asparagine 3-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: peptidyl L-asparagine + 2-oxoglutarate + O2 = peptidyl 3-hydroxy-L-asparagine + succinate + CO2." [GOC:reh, PMID:12215170]
+alt_id: GO:0102113
+def: "Catalysis of the reaction: peptidyl L-asparagine + 2-oxoglutarate + O2 = peptidyl 3-hydroxy-L-asparagine + succinate + CO2." [GOC:reh, PMID:12215170, RHEA:54260]
+synonym: "hypoxia-inducible factor-asparagine oxygenase activity" NARROW []
+synonym: "peptidyl-asparagine 3-dioxygenase activity" EXACT []
+xref: RHEA:54260
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -214921,7 +214869,6 @@ synonym: "zymosterol biosynthesis" EXACT [GOC:bf]
synonym: "zymosterol formation" EXACT [GOC:bf]
synonym: "zymosterol synthesis" EXACT [GOC:bf]
xref: MetaCyc:PWY-6074
-xref: UniPathway:UPA00770
is_a: GO:0016126 ! sterol biosynthetic process
is_a: GO:0036196 ! zymosterol metabolic process
is_a: GO:1902653 ! secondary alcohol biosynthetic process
@@ -214930,10 +214877,9 @@ is_a: GO:1902653 ! secondary alcohol biosynthetic process
id: GO:0036198
name: dTMP salvage
namespace: biological_process
-def: "Any process which produces dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate) without de novo synthesis." [GOC:yaf, UniPathway:UPA00578]
-synonym: "deoxythymidine monophosphate biosynthesis via salvage pathway" RELATED [GOC:yaf, PMID:5387459, UniPathway:UPA00578]
-synonym: "dTMP biosynthesis via salvage pathway" RELATED [GOC:yaf, PMID:5387459, UniPathway:UPA00578]
-xref: UniPathway:UPA00578
+def: "Any process which produces dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate) without de novo synthesis." [GOC:yaf, PMID:5387459]
+synonym: "deoxythymidine monophosphate biosynthesis via salvage pathway" RELATED [GOC:yaf, PMID:5387459]
+synonym: "dTMP biosynthesis via salvage pathway" RELATED [GOC:yaf, PMID:5387459]
is_a: GO:0006231 ! dTMP biosynthetic process
is_a: GO:0010139 ! pyrimidine deoxyribonucleotide salvage
@@ -215008,7 +214954,7 @@ namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of a histone protein by individual cells." [GOC:krc]
comment: This term was created even though it describes a process relating to a group of gene products, because histones are highly conserved proteins that are essential components of cellular chromatin in eukaryotic cells.
synonym: "histone protein catabolic process" EXACT [GOC:bf, GOC:jl]
-is_a: GO:0044257 ! cellular protein catabolic process
+is_a: GO:0030163 ! protein catabolic process
[Term]
id: GO:0036206
@@ -215073,8 +215019,15 @@ is_a: GO:0052027 ! modulation by symbiont of host signal transduction pathway
id: GO:0036211
name: protein modification process
namespace: biological_process
+alt_id: GO:0006464
def: "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:bf, GOC:jl]
-subset: goslim_generic
+subset: goslim_candida
+subset: goslim_chembl
+subset: goslim_pir
+subset: goslim_plant
+subset: prokaryote_subset
+synonym: "cellular protein modification process" EXACT []
+synonym: "process resulting in protein modification" EXACT []
synonym: "protein modification" EXACT [GOC:bf]
is_a: GO:0019538 ! protein metabolic process
is_a: GO:0043412 ! macromolecule modification
@@ -215103,7 +215056,7 @@ relationship: part_of GO:0061640 ! cytoskeleton-dependent cytokinesis
id: GO:0036214
name: contractile ring localization
namespace: biological_process
-def: "The process in which a contractile ring is assembled and/or maintained in a specific location." [GOC:mah, GOC:vw]
+def: "The process in which a contractile ring is positioned or maintained in a specific location." [GOC:mah, GOC:vw]
comment: This term can be used to annotate localization of either bacterial or fungal contractile rings.
is_a: GO:0032506 ! cytokinetic process
is_a: GO:0051179 ! localization
@@ -215136,61 +215089,65 @@ is_a: GO:0071345 ! cellular response to cytokine stimulus
id: GO:0036217
name: dGTP diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dGTP + H2O = dGMP + diphosphate." [GOC:dgf, PMID:17090528, PMID:22531138, RHEA:28362]
+def: "Catalysis of the reaction: dGTP + H2O = dGMP + H+ + diphosphate." [GOC:dgf, PMID:17090528, PMID:22531138, RHEA:28362]
synonym: "2'-deoxyguanosine 5'-triphosphate diphosphohydrolase" EXACT [KEGG_REACTION:R01855]
+synonym: "dGTP pyrophosphatase activity" EXACT []
xref: KEGG_REACTION:R01855
xref: RHEA:28362
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0036218
name: dTTP diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dTTP + H2O = dTMP + diphosphate." [GOC:dgf, PMID:22531138, RHEA:28534]
-xref: EC:3.6.1.9
+def: "Catalysis of the reaction: dTTP + H2O = dTMP + H+ + diphosphate." [GOC:dgf, PMID:22531138, RHEA:28534]
+synonym: "dTTP pyrophosphatase activity" EXACT []
xref: MetaCyc:RXN0-5107
xref: RHEA:28534
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0036219
name: GTP diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GTP + H2O = GMP + diphosphate." [GOC:dgf, PMID:22531138, RHEA:29391]
+def: "Catalysis of the reaction: GTP + H2O = GMP + H+ + diphosphate." [GOC:dgf, PMID:22531138, RHEA:29391]
synonym: "GTP diphosphohydrolase (diphosphate-forming); guanosine 5'-triphosphate pyrophosphohydrolase" EXACT [KEGG_REACTION:R00426]
synonym: "GTP diphosphohydrolase activity" EXACT [GOC:bf]
+synonym: "GTP pyrophosphatase activity" EXACT []
xref: KEGG_REACTION:R00426
xref: RHEA:29391
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0036220
name: ITP diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ITP + H2O = IMP + diphosphate." [GOC:dgf, PMID:17899088, PMID:22531138]
+def: "Catalysis of the reaction: ITP + H2O = IMP + H+ + diphosphate." [GOC:dgf, PMID:17899088, PMID:22531138, RHEA:29399]
synonym: "inosine-5'-triphosphate pyrophosphohydrolase activity" EXACT [KEGG_REACTION:R00720]
+synonym: "ITP pyrophosphatase activity" EXACT []
+xref: EC:3.6.1.66
xref: KEGG_REACTION:R00720
xref: MetaCyc:RXN0-6382
xref: Reactome:R-HSA-2509827 "ITPA hydrolyses ITP to IMP"
xref: RHEA:29399
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0036221
name: UTP diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: UTP + H2O = UMP + diphosphate." [GOC:dgf, PMID:17899088]
+def: "Catalysis of the reaction: UTP + H2O = UMP + H+ + diphosphate." [GOC:dgf, PMID:17899088, RHEA:29395]
synonym: "uridine triphosphate pyrophosphohydrolase activity" EXACT [KEGG_REACTION:R00662]
xref: KEGG_REACTION:R00662
xref: RHEA:29395
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0036222
name: XTP diphosphatase activity
namespace: molecular_function
alt_id: GO:0103024
-def: "Catalysis of the reaction: XTP + H2O <=> H+ + XDP + monophosphate." [GOC:pz, PMID:16216582, PMID:22531138, RHEA:28610]
+def: "Catalysis of the reaction: XTP + H2O = XMP + H+ + diphosphate." [GOC:pz, PMID:16216582, PMID:22531138, RHEA:28610]
comment: While XTP is not produced by cells, deamination of purine bases can result in accumulation of such nucleotides as ITP, dITP, XTP, and dXTP. XTPase contributes to the removal of these abnormal bases from the cellular pool of nucleotide triphosphates.
synonym: "hypoxanthine/xanthine dNTP pyrophosphatase" RELATED [EC:3.6.1.66]
synonym: "XTP pyrophosphohydrolase activity" EXACT [KEGG_REACTION:R02720]
@@ -215202,7 +215159,7 @@ xref: MetaCyc:RXN0-1603
xref: MetaCyc:RXN0-5074
xref: Reactome:R-HSA-2509831 "ITPA hydrolyses XTP to XMP"
xref: RHEA:28610
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0036223
@@ -215307,11 +215264,10 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0036239
name: taxoid 7beta-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: taxusin + O2 + NADPH + H+ = 7beta-hydroxytaxusin + NADP+ + H2O." [EC:1.14.13.147]
-xref: EC:1.14.13.147
+def: "Catalysis of the reaction: taxusin + [reduced NADPH-hemoprotein reductase] + O2 = 7beta-hydroxytaxusin + [oxidized NADPH-hemoprotein reductase] + H2O and 2alpha-hydroxytaxusin + [reduced NADPH-hemoprotein reductase] + O2 = 2alpha,7beta-dihydroxytaxusin + [oxidized NADPH-hemoprotein reductase] + H2O." [PMID:15157877, PMID:15178487]
+xref: EC:1.14.14.182
xref: KEGG_REACTION:R09868
xref: MetaCyc:RXN-12885
-xref: RHEA:31975
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
[Term]
@@ -215410,6 +215366,7 @@ def: "The directed movement of cadmium ions into the vacuole." [GOC:al]
synonym: "vacuolar cadmium import" RELATED [GOC:bf]
is_a: GO:0000041 ! transition metal ion transport
is_a: GO:0034486 ! vacuolar transmembrane transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -215431,30 +215388,29 @@ consider: GO:0071472
[Term]
id: GO:0036252
-name: positive regulation of transcription from RNA polymerase II promoter in response to menadione
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to menadione
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a menadione stimulus. Menadione (also called vitamin K3) is a naphthoquinone having a methyl substituent at the 2-position." [GOC:al]
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a menadione stimulus. Menadione (also called vitamin K3) is a naphthoquinone having a methyl substituent at the 2-position." [GOC:al]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "positive regulation of transcription from RNA polymerase II promoter in response to menadione stress" NARROW [GOC:al]
-is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress
-is_a: GO:1901522 ! positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus
-relationship: part_of GO:0036245 ! cellular response to menadione
+is_obsolete: true
+replaced_by: GO:0045944
[Term]
id: GO:0036253
-name: response to amiloride
+name: obsolete response to amiloride
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amiloride stimulus." [GOC:mah]
-is_a: GO:0010243 ! response to organonitrogen compound
-is_a: GO:0014070 ! response to organic cyclic compound
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amiloride stimulus." [GOC:mah]
+comment: This term is out of scope for GO.
+is_obsolete: true
[Term]
id: GO:0036254
-name: cellular response to amiloride
+name: obsolete cellular response to amiloride
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amiloride stimulus." [GOC:mah]
-is_a: GO:0036253 ! response to amiloride
-is_a: GO:0071407 ! cellular response to organic cyclic compound
-is_a: GO:0071417 ! cellular response to organonitrogen compound
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amiloride stimulus." [GOC:mah]
+comment: This term is out of scope for GO.
+is_obsolete: true
[Term]
id: GO:0036255
@@ -215462,6 +215418,7 @@ name: response to methylamine
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a methylamine stimulus." [GOC:mah]
is_a: GO:0014075 ! response to amine
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0036256
@@ -215470,6 +215427,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a methylamine stimulus." [GOC:mah]
is_a: GO:0036255 ! response to methylamine
is_a: GO:0071418 ! cellular response to amine stimulus
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0036257
@@ -215606,6 +215564,7 @@ synonym: "response to 2'-deoxy-2',2'-difluorocytidine" EXACT [CHEBI:175901]
is_a: GO:0010243 ! response to organonitrogen compound
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0036273
@@ -215661,11 +215620,13 @@ is_a: GO:0042221 ! response to chemical
[Term]
id: GO:0036278
-name: positive regulation of transcription from RNA polymerase II promoter in response to nitrogen starvation
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to nitrogen starvation
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a deprivation of nitrogen." [GOC:al, PMID:21118960]
-is_a: GO:0006995 ! cellular response to nitrogen starvation
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a deprivation of nitrogen." [GOC:al, PMID:21118960]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0006995
+consider: GO:0045944
[Term]
id: GO:0036279
@@ -215682,6 +215643,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a L-canavanine stimulus. L-canavanine is L-homoserine substituted at oxygen with a guanidino (carbamimidamido) group." [GOC:al]
is_a: GO:0071230 ! cellular response to amino acid stimulus
is_a: GO:1901354 ! response to L-canavanine
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0036283
@@ -215904,7 +215866,9 @@ relationship: part_of GO:0035050 ! embryonic heart tube development
id: GO:0036307
name: 23S rRNA (adenine(2030)-N(6))-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + adenine(2030) in 23S rRNA = S-adenosyl-L-homocysteine + rRNA containing N(6)-methyladenine(2030) in 23S rRNA." [GOC:imk, PMID:22847818]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + adenine(2030) in 23S rRNA = S-adenosyl-L-homocysteine + rRNA containing N(6)-methyladenine(2030) in 23S rRNA." [GOC:imk, PMID:22847818, RHEA:43736]
+xref: EC:2.1.1.266
+xref: RHEA:43736
is_a: GO:0008988 ! rRNA (adenine-N6-)-methyltransferase activity
[Term]
@@ -215934,7 +215898,6 @@ synonym: "annealing helicase activity" RELATED [PMID:22888405]
synonym: "ATP-dependent DNA annealing activity" RELATED [GOC:sp]
synonym: "DNA rewinding activity" RELATED [PMID:22888405]
synonym: "nucleoside-triphosphatase activity involved in DNA annealing" EXACT [GOC:bf]
-xref: Reactome:R-HSA-5686642 "RAD52 promotes single strand annealing at resected DNA DSBs"
is_a: GO:0140657 ! ATP-dependent activity
is_a: GO:1990814 ! DNA/DNA annealing activity
@@ -216057,7 +216020,7 @@ is_a: GO:0030072 ! peptide hormone secretion
id: GO:0036323
name: vascular endothelial growth factor receptor-1 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor-1 (VEGFR-1) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:uh, Wikipedia:FLT1, Wikipedia:VEGF_receptors]
+def: "The series of molecular signals initiated by a ligand binding to a vascular endothelial growth factor receptor-1 (VEGFR-1) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:uh, Wikipedia:FLT1, Wikipedia:VEGF_receptors]
synonym: "FLT1 signaling pathway" EXACT [GOC:uh, PR:000007563]
synonym: "VEGFR-1 signaling pathway" EXACT [PR:000007563, Reactome:R-HSA-194311, Wikipedia:VEGF_receptors]
synonym: "VEGFR1 signaling pathway" EXACT [Reactome:R-HSA-194311]
@@ -216067,7 +216030,7 @@ is_a: GO:0048010 ! vascular endothelial growth factor receptor signaling pathway
id: GO:0036324
name: vascular endothelial growth factor receptor-2 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor-2 (VEGFR-2) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:uh, PMID:12967471, Wikipedia:Kinase_insert_domain_receptor, Wikipedia:VEGF_receptors]
+def: "The series of molecular signals initiated by a ligand binding to a vascular endothelial growth factor receptor-2 (VEGFR-2) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:uh, PMID:12967471, Wikipedia:Kinase_insert_domain_receptor, Wikipedia:VEGF_receptors]
synonym: "FLK-1 signaling pathway" EXACT [PR:000002112]
synonym: "KDR signaling pathway" EXACT [GOC:uh, PR:000002112, Wikipedia:Kinase_insert_domain_receptor]
synonym: "VEGFR-2 signaling pathway" EXACT [PR:000002112, Reactome:R-HSA-194310, Wikipedia:Kinase_insert_domain_receptor, Wikipedia:VEGF_receptors]
@@ -216078,7 +216041,7 @@ is_a: GO:0048010 ! vascular endothelial growth factor receptor signaling pathway
id: GO:0036325
name: vascular endothelial growth factor receptor-3 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor-3 (VEGFR-3) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:uh, Wikipedia:VEGF_receptors, Wikipedia:VEGFR3]
+def: "The series of molecular signals initiated by a ligand binding to a vascular endothelial growth factor receptor-3 (VEGFR-3) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:uh, Wikipedia:VEGF_receptors, Wikipedia:VEGFR3]
synonym: "FLT4 signaling pathway" EXACT [GOC:uh, PR:000007565]
synonym: "VEGFR-3 signaling pathway" EXACT [Reactome:R-HSA-194308, Wikipedia:VEGF_receptors]
synonym: "VEGFR3 signaling pathway" EXACT [Reactome:R-HSA-194310, Wikipedia:VEGFR3]
@@ -216094,10 +216057,10 @@ is_a: GO:0061303 ! cornea development in camera-type eye
[Term]
id: GO:0036332
-name: placental growth factor-activated receptor activity
+name: placental growth factor receptor activity
namespace: molecular_function
-def: "Combining with placental growth factor (PlGF) and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:uh, PMID:12871269, PMID:7929268, Wikipedia:Placental_growth_factor]
-synonym: "placental growth factor receptor activity" EXACT [GOC:bf]
+def: "Combining with placental growth factor (PlGF) receptor ligand and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:uh, PMID:12871269, PMID:7929268, Wikipedia:Placental_growth_factor]
+synonym: "placental growth factor-activated receptor activity" EXACT []
synonym: "PlGF receptor activity" RELATED [PMID:12871269]
synonym: "PlGF-activated receptor activity" EXACT [GOC:uh, PMID:12871269]
is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity
@@ -216120,7 +216083,8 @@ is_a: GO:0048872 ! homeostasis of number of cells
id: GO:0036335
name: intestinal stem cell homeostasis
namespace: biological_process
-def: "Any biological process involved in the maintenance of the steady-state number of intestinal stem cells within a population of cells." [GOC:nhn, PMID:22042863]
+def: "Any biological process involved in the maintenance of the steady-state number of intestinal stem cells within a population of cells." [GOC:nhn, PMID:22042863, PMID:22608824]
+synonym: "intestinal crypt stem cell homeostasis" NARROW []
is_a: GO:0048872 ! homeostasis of number of cells
[Term]
@@ -216134,7 +216098,7 @@ is_a: GO:0071674 ! mononuclear cell migration
id: GO:0036337
name: Fas signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a ligand to the receptor Fas on the surface of the cell, and ending with regulation of a downstream cellular process, e.g. transcription. Fas is a death domain-containing member of the tumor necrosis factor receptor (TNFR) superfamily." [GOC:nhn, PMID:12040174, Wikipedia:Fas_receptor]
+def: "The series of molecular signals initiated by the binding of a ligand to a Fas receptor on the surface of the cell, and ending with the regulation of a downstream cellular process, e.g. transcription. Fas is a death domain-containing member of the tumor necrosis factor receptor (TNFR) superfamily." [GOC:nhn, PMID:12040174, Wikipedia:Fas_receptor]
synonym: "Apo-1 signaling pathway" EXACT [PMID:12040174]
synonym: "CD95 signaling pathway" EXACT [PMID:12040174]
synonym: "FAS ligand-Fas signaling pathway" NARROW [PMID:12040174]
@@ -216213,6 +216177,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a L-cysteine stimulus. L-cysteine is an optically active form of cysteine having L-configuration." [GOC:al]
is_a: GO:0071230 ! cellular response to amino acid stimulus
is_a: GO:1901367 ! response to L-cysteine
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0036348
@@ -216361,8 +216326,7 @@ synonym: "TGF-B activation" EXACT [GOC:sl]
synonym: "TGF-beta activation" EXACT [PR:000000046]
synonym: "TGFB activation" EXACT [GOC:sl]
synonym: "TGFbeta activation" EXACT [GOC:bf]
-is_a: GO:0032501 ! multicellular organismal process
-relationship: part_of GO:0071604 ! transforming growth factor beta production
+is_a: GO:0007267 ! cell-cell signaling
[Term]
id: GO:0036364
@@ -216489,6 +216453,7 @@ xref: Reactome:R-HSA-9026912 "GGT hydrolyses PCTR1 to PCTR2"
xref: Reactome:R-HSA-9026916 "GGT hydrolyses RCTR2 to RCTR3"
xref: Reactome:R-HSA-9026927 "GGT hydrolyses RCTR1 to RCTR2"
xref: Reactome:R-HSA-9035966 "Defective GGT1 does not hydrolyse GSH"
+xref: Reactome:R-HSA-9753634 "GGT dimers hydrolyse APAP-SG"
xref: RHEA:28807
is_a: GO:0008242 ! omega peptidase activity
is_a: GO:0070003 ! threonine-type peptidase activity
@@ -216514,7 +216479,6 @@ synonym: "sodium export" RELATED [GOC:mah]
synonym: "sodium ion export" RELATED []
synonym: "sodium ion export from cell" EXACT []
is_a: GO:0035725 ! sodium ion transmembrane transport
-is_a: GO:0070839 ! metal ion export
is_a: GO:0140115 ! export across plasma membrane
[Term]
@@ -216538,7 +216502,6 @@ synonym: "1alpha,25-dihydroxyvitamin D3 biosynthesis" BROAD [CHEBI:17823]
synonym: "calcitriol biosynthesis from calciol" EXACT [GOC:bf]
synonym: "vitamin D3 activation" EXACT [GOC:bf, PMID:20506379]
is_a: GO:0042368 ! vitamin D biosynthetic process
-is_a: GO:0044108 ! cellular alcohol biosynthetic process
is_a: GO:0046173 ! polyol biosynthetic process
is_a: GO:0070640 ! vitamin D3 metabolic process
@@ -216584,9 +216547,7 @@ is_a: GO:0016843 ! amine-lyase activity
id: GO:0036382
name: flavin reductase (NADH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: reduced flavin + NAD+ = flavin + NADH + H+." [EC:1.5.1.36, GOC:rs]
-synonym: "flavin:NADH oxidoreductase activity" RELATED [EC:1.5.1.36]
-synonym: "NADH-dependent flavin reductase activity" RELATED [EC:1.5.1.36]
+def: "Catalysis of the reaction: a reduced flavin + NAD+ = an oxidized flavin + 2 H+ + NADH." [GOC:rs, RHEA:31303]
xref: EC:1.5.1.36
xref: KEGG_REACTION:R09662
xref: MetaCyc:1.5.1.36-RXN
@@ -216606,29 +216567,35 @@ is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorp
[Term]
id: GO:0036384
-name: cytidine-diphosphatase activity
+name: CDP phosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction: CDP + H2O = CMP + phosphate." [GOC:al, RHEA:64880]
+synonym: "CDP diphosphatase activity" BROAD []
synonym: "CDPase activity" EXACT [GOC:al]
+synonym: "cytidine diphosphatase activity" EXACT []
+synonym: "cytidine-diphosphatase activity" EXACT []
xref: RHEA:64880
-is_a: GO:0017110 ! nucleoside-diphosphatase activity
+is_a: GO:0017110 ! nucleoside diphosphate phosphatase activity
[Term]
id: GO:0036385
-name: nucleoid DNA packaging
+name: obsolete nucleoid DNA packaging
namespace: biological_process
-def: "Any process in which DNA and associated proteins are formed into a compact, orderly structure within a nucleoid." [GOC:bf, GOC:bhm]
-is_a: GO:0006323 ! DNA packaging
+def: "OBSOLETE. Any process in which DNA and associated proteins are formed into a compact, orderly structure within a nucleoid." [GOC:bf, GOC:bhm]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
[Term]
id: GO:0036386
-name: bacterial nucleoid DNA packaging
+name: bacterial nucleoid packaging
namespace: biological_process
-def: "Compaction of DNA in a bacterial nucleoid into a compact structure. Often achieved by DNA supercoiling." [GOC:bf, GOC:bhm, PMID:17097674, PMID:17360520]
+def: "A process in which chromosomal DNA and associated proteins organize into a compact, orderly bacterial nucleoid. Often resulting in DNA supercoiling." [GOC:bf, GOC:bhm, PMID:17097674, PMID:17360520]
+subset: prokaryote_subset
+synonym: "bacterial nucleoid DNA packaging" EXACT []
synonym: "chromosomal compaction" BROAD [PMID:17097674]
synonym: "nucleoid compaction" BROAD [PMID:17097674]
synonym: "prokaryotic DNA condensation" BROAD [Wikipedia:DNA_condensation]
-is_a: GO:0036385 ! nucleoid DNA packaging
+is_a: GO:0051276 ! chromosome organization
[Term]
id: GO:0036387
@@ -216648,7 +216615,7 @@ def: "The aggregation, arrangement and bonding together of a set of components t
synonym: "pre-RC assembly" EXACT [Wikipedia:Pre-replication_complex]
synonym: "pre-replication complex assembly" RELATED [Wikipedia:Pre-replication_complex]
is_a: GO:0065004 ! protein-DNA complex assembly
-relationship: part_of GO:0006261 ! DNA-dependent DNA replication
+relationship: part_of GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:0036389
@@ -216793,7 +216760,7 @@ is_a: GO:0140657 ! ATP-dependent activity
id: GO:0036403
name: arachidonate 8(S)-lipoxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: arachidonate + O(2) = (5Z,8S,9E,11Z,14Z)-8-hydroperoxyicosa-5,9,11,14-tetraenoate." [GOC:lb, PMID:10625675, RHEA:38675]
+def: "Catalysis of the reaction: arachidonate + O2 = (5Z,8S,9E,11Z,14Z)-8-hydroperoxyicosa-5,9,11,14-tetraenoate." [GOC:lb, PMID:10625675, RHEA:38675]
comment: This activity produces the S-enantiomer of HPETE, 8(S)-HPETE. For the reaction producing the S-enantiomer, see GO:0047677.
synonym: "8(S)-lipoxygenase activity" BROAD [GOC:bf]
synonym: "8-lipoxygenase (S-type)" BROAD [KEGG_REACTION:R07053]
@@ -216813,22 +216780,24 @@ consider: GO:0004521
[Term]
id: GO:0036405
-name: anchored component of cell outer membrane
+name: obsolete anchored component of cell outer membrane
namespace: cellular_component
-def: "The component of the cell outer membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos, GOC:md]
+def: "OBSOLETE. The component of the cell outer membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos, GOC:md]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "anchored to cell outer membrane" NARROW []
-is_a: GO:0031225 ! anchored component of membrane
-is_a: GO:0031230 ! intrinsic component of cell outer membrane
+is_obsolete: true
+replaced_by: GO:0009279
[Term]
id: GO:0036406
-name: anchored component of periplasmic side of cell outer membrane
+name: obsolete anchored component of periplasmic side of cell outer membrane
namespace: cellular_component
-def: "The component of the cell outer membrane consisting of gene products and protein complexes that are tethered to the periplasmic side of membrane by only a covalently attached anchor, embedded in the periplasmic side of the membrane only." [GOC:dos, GOC:md]
+def: "OBSOLETE. The component of the cell outer membrane consisting of gene products and protein complexes that are tethered to the periplasmic side of membrane by only a covalently attached anchor, embedded in the periplasmic side of the membrane only." [GOC:dos, GOC:md]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "anchored to internal side of cell outer membrane" EXACT []
synonym: "anchored to periplasmic side of cell outer membrane" NARROW []
-is_a: GO:0031246 ! intrinsic component of periplasmic side of cell outer membrane
-is_a: GO:0036405 ! anchored component of cell outer membrane
+is_obsolete: true
+replaced_by: GO:0031241
[Term]
id: GO:0036407
@@ -216842,11 +216811,14 @@ is_a: GO:0009279 ! cell outer membrane
[Term]
id: GO:0036408
-name: histone acetyltransferase activity (H3-K14 specific)
+name: histone H3K14 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 14) = CoA + histone H3 N6-acetyl-L-lysine (position 14)." [GOC:vw, PMID:21289066]
+synonym: "histone acetylase activity (H3-K14 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H3-K14 specific)" EXACT []
+synonym: "histone H3-K14 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H3-K14 specific)" EXACT [GOC:bf]
-is_a: GO:0010484 ! H3 histone acetyltransferase activity
+is_a: GO:0010484 ! histone H3 acetyltransferase activity
[Term]
id: GO:0036409
@@ -216858,6 +216830,7 @@ synonym: "histone acetyltransferase complex (H3-K14 specific)" EXACT [GOC:bf]
synonym: "histone H3 Lys 14 (H3K14) acetyltransferase complex" EXACT [PMID:21289066]
synonym: "histone H3K14 acetyltransferase complex" EXACT [PMID:21289066]
is_a: GO:0070775 ! H3 histone acetyltransferase complex
+is_a: GO:0140513 ! nuclear protein-containing complex
[Term]
id: GO:0036410
@@ -216886,20 +216859,23 @@ is_a: GO:0008410 ! CoA-transferase activity
[Term]
id: GO:0036413
-name: histone H3-R26 citrullination
+name: obsolete histone H3-R26 citrullination
namespace: biological_process
-def: "The hydrolysis of peptidyl-arginine to form peptidyl-citrulline at position 26 in histone H3." [GOC:als, PMID:22853951]
+def: "OBSOLETE. The hydrolysis of peptidyl-arginine to form peptidyl-citrulline at position 26 in histone H3." [GOC:als, PMID:22853951]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H3 arginine 26 citrullination" EXACT [GOC:als]
-is_a: GO:0036414 ! histone citrullination
+is_obsolete: true
+consider: GO:0140798
[Term]
id: GO:0036414
-name: histone citrullination
+name: obsolete histone citrullination
namespace: biological_process
-def: "The hydrolysis of peptidyl-arginine to form peptidyl-citrulline on a histone protein." [GOC:als, PMID:22853951, PMID:23175390]
+def: "OBSOLETE. The hydrolysis of peptidyl-arginine to form peptidyl-citrulline on a histone protein." [GOC:als, PMID:22853951, PMID:23175390]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone deimination" EXACT [Wikipedia:Citrullination]
-is_a: GO:0016570 ! histone modification
-is_a: GO:0018101 ! protein citrullination
+is_obsolete: true
+consider: GO:0140794
[Term]
id: GO:0036415
@@ -216929,25 +216905,27 @@ is_a: GO:1902372 ! positive regulation of tRNA catabolic process
[Term]
id: GO:0036418
-name: intrinsic component of mycolate outer membrane
+name: obsolete intrinsic component of mycolate outer membrane
namespace: cellular_component
-def: "The component of the mycolate outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:md]
+def: "OBSOLETE. The component of the mycolate outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:md]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to MOM" EXACT [GOC:md]
synonym: "intrinsic to mycolate outer membrane" NARROW []
synonym: "intrinsic to mycomembrane" EXACT [GOC:das, GOC:md]
-is_a: GO:0031230 ! intrinsic component of cell outer membrane
-relationship: part_of GO:0036407 ! mycolate outer membrane
+is_obsolete: true
+replaced_by: GO:0036407
[Term]
id: GO:0036419
-name: integral component of mycolate outer membrane
+name: obsolete integral component of mycolate outer membrane
namespace: cellular_component
-def: "The component of the mycolate outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:md]
+def: "OBSOLETE. The component of the mycolate outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:md]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to MOM" EXACT [GOC:md]
synonym: "integral to mycolate outer membrane" NARROW []
synonym: "integral to mycomembrane" EXACT [GOC:das, GOC:md]
-is_a: GO:0036418 ! intrinsic component of mycolate outer membrane
-is_a: GO:0045203 ! integral component of cell outer membrane
+is_obsolete: true
+replaced_by: GO:0036407
[Term]
id: GO:0036420
@@ -216972,20 +216950,6 @@ is_a: GO:0031242 ! extrinsic component of external side of cell outer membrane
is_a: GO:0036420 ! extrinsic component of mycolate outer membrane
relationship: part_of GO:0098568 ! external side of mycolate outer membrane
-[Term]
-id: GO:0036422
-name: heptaprenyl diphosphate synthase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate." [RHEA:27794]
-synonym: "all-trans-heptaprenyl-diphosphate synthase activity" RELATED [EC:2.5.1.30]
-synonym: "HepPP synthase activity" RELATED [EC:2.5.1.30]
-synonym: "heptaprenyl pyrophosphate synthase activity" RELATED [EC:2.5.1.30]
-synonym: "heptaprenyl pyrophosphate synthetase activity" RELATED [EC:2.5.1.30]
-xref: EC:2.5.1.30
-xref: MetaCyc:TRANS-HEXAPRENYLTRANSTRANSFERASE-RXN
-xref: RHEA:27794
-is_a: GO:0004659 ! prenyltransferase activity
-
[Term]
id: GO:0036423
name: hexaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) activity
@@ -217021,7 +216985,7 @@ id: GO:0036425
name: obsolete D-phosphoserine phosphatase activity
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: O-phospho-D-serine + H2O = L-serine + phosphate, on a free amino acid." [GOC:curators]
-comment: This term was obsoleted because there is no evidence that this function exisis. This reaction corresponds to RHEA:24873 and KEGG_REACTION:R02853.
+comment: This term was obsoleted because there is no evidence that this function exists. This reaction corresponds to RHEA:24873 and KEGG_REACTION:R02853.
is_obsolete: true
consider: GO:0036424
@@ -217107,7 +217071,7 @@ is_a: GO:0009038 ! undecaprenol kinase activity
id: GO:0036434
name: nitronate monooxygenase (FMN-linked) activity
namespace: molecular_function
-def: "Catalysis of the reaction: ethylnitronate + FMNH(2) + O(2) = acetaldehyde + FMN + H(2)O + H(+) + nitrite." [RHEA:26458]
+def: "Catalysis of the reaction: ethylnitronate + FMNH(2) + O2 = acetaldehyde + FMN + H2O + H+ + nitrite." [RHEA:26458]
xref: KEGG_REACTION:R00025
xref: RHEA:26458
is_a: GO:0016703 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases)
@@ -217148,9 +217112,10 @@ id: GO:0036440
name: citrate synthase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA." [RHEA:16845]
+xref: EC:2.3.3.16
xref: KEGG_REACTION:R00351
xref: RHEA:16845
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0036441
@@ -217179,8 +217144,6 @@ synonym: "calcium ion transmembrane import into mitochondrion" EXACT []
synonym: "mitochondrial calcium ion import" BROAD [GOC:vw]
synonym: "mitochondrial calcium uptake" EXACT []
is_a: GO:0006851 ! mitochondrial calcium ion transmembrane transport
-is_a: GO:0060401 ! cytosolic calcium ion transport
-is_a: GO:0070509 ! calcium ion import
[Term]
id: GO:0036445
@@ -217253,7 +217216,7 @@ name: transitive RNA interference
namespace: biological_process
def: "An RNA interference where the silencing signal spreads along the target mRNA in a 5' or 3' direction, outside of the initial target sequence." [GOC:pf, PMID:11719187, PMID:12554873, PMID:23724097, PMID:24369430]
synonym: "transitive RNAi" EXACT [PMID:12554873]
-is_a: GO:0016246 ! RNA interference
+is_a: GO:0035194 ! ncRNA-mediated post-transcriptional gene silencing
[Term]
id: GO:0036454
@@ -217393,7 +217356,7 @@ is_a: GO:0004058 ! aromatic-L-amino-acid decarboxylase activity
id: GO:0036470
name: tyrosine 3-monooxygenase activator activity
namespace: molecular_function
-def: "Interacts with and increases tyrosine 3-monooxygenase (tyrosine hydroxylase) activity." [GOC:bf, GOC:PARL, PMID:19703902]
+def: "Binds to and increases the activity of tyrosine 3-monooxygenase (tyrosine hydroxylase)." [GOC:bf, GOC:PARL, PMID:19703902]
synonym: "TH activator activity" EXACT [PMID:19703902]
synonym: "tyrosine hydroxylase activator activity" EXACT [PMID:19703902]
is_a: GO:0008047 ! enzyme activator activity
@@ -217408,14 +217371,17 @@ is_a: GO:0110096 ! cellular response to aldehyde
[Term]
id: GO:0036472
-name: suppression by virus of host protein-protein interaction
+name: obsolete suppression by virus of host protein-protein interaction
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of interaction between host proteins." [GOC:bf, GOC:PARL, PMID:17297443]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of interaction between host proteins." [GOC:bf, GOC:PARL, PMID:17297443]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "suppression by virus of host protein binding" EXACT [GOC:bf]
synonym: "suppression by virus of host protein interaction" EXACT [GOC:bf]
synonym: "suppression by virus of host protein:protein binding" EXACT [GOC:bf]
synonym: "suppression by virus of host protein:protein interaction" EXACT [GOC:bf]
-is_a: GO:0039507 ! suppression by virus of host molecular function
+is_obsolete: true
+consider: GO:0098772
+consider: GO:0140311
[Term]
id: GO:0036473
@@ -217488,7 +217454,7 @@ is_a: GO:0004857 ! enzyme inhibitor activity
id: GO:0036480
name: neuron intrinsic apoptotic signaling pathway in response to oxidative stress
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a neuron. The pathway is induced in response to oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, and ends when the execution phase of apoptosis is triggered." [GOC:bf, GOC:PARL, PMID:23858059]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a neuron. The pathway is induced in response to oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, and ends when the execution phase of apoptosis is triggered." [GOC:bf, GOC:PARL, PMID:23858059]
synonym: "neuron apoptosis in response to oxidative stress" RELATED [GOC:bf]
synonym: "oxidative stress-induced neuron apoptosis" BROAD [GOC:bf]
synonym: "oxidative stress-induced neuronal apoptosis" BROAD [GOC:bf]
@@ -217500,7 +217466,7 @@ relationship: part_of GO:0051402 ! neuron apoptotic process
id: GO:0036481
name: intrinsic apoptotic signaling pathway in response to hydrogen peroxide
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to hydrogen peroxide (H2O2)." [GOC:bf, GOC:PARL]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to hydrogen peroxide (H2O2)." [GOC:bf, GOC:PARL]
synonym: "H2O2-induced intrinsic apoptotic signaling pathway" RELATED [GOC:bf]
synonym: "hydrogen peroxide-induced apoptosis" BROAD [GOC:bf]
synonym: "hydrogen peroxide-induced intrinsic apoptotic signaling pathway" EXACT [GOC:bf]
@@ -217512,7 +217478,7 @@ relationship: part_of GO:0010421 ! hydrogen peroxide-mediated programmed cell de
id: GO:0036482
name: neuron intrinsic apoptotic signaling pathway in response to hydrogen peroxide
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a neuron in response to hydrogen peroxide." [GOC:bf, GOC:PARL]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a neuron in response to hydrogen peroxide." [GOC:bf, GOC:PARL]
synonym: "H2O2-induced neuron intrinsic apoptotic signaling pathway" EXACT [GOC:bf]
synonym: "hydrogen peroxide-induced neuron apoptosis" BROAD [GOC:bf]
synonym: "hydrogen peroxide-induced neuronal apoptosis" BROAD [GOC:bf]
@@ -217526,7 +217492,7 @@ relationship: part_of GO:0036476 ! neuron death in response to hydrogen peroxide
id: GO:0036483
name: neuron intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a neuron. The pathway is induced in response to a stimulus indicating endoplasmic reticulum (ER) stress, and ends when the execution phase of apoptosis is triggered. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen." [GOC:bf, GOC:PARL, PMID:21113145]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a neuron. The pathway is induced in response to a stimulus indicating endoplasmic reticulum (ER) stress, and ends when the execution phase of apoptosis is triggered. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen." [GOC:bf, GOC:PARL, PMID:21113145]
synonym: "endoplasmic reticulum stress-induced neuron apoptosis" BROAD [GOC:bf]
synonym: "endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway" EXACT [GOC:bf]
synonym: "ER stress-induced neuron apoptosis" BROAD [GOC:bf]
@@ -217673,7 +217639,7 @@ is_a: GO:0036496 ! regulation of translational initiation by eIF2 alpha dephosph
id: GO:0036498
name: IRE1-mediated unfolded protein response
namespace: biological_process
-def: "A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB." [GOC:bf, GOC:PARL, PMID:22013210]
+def: "The series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB." [GOC:bf, GOC:PARL, PMID:22013210]
comment: Consider also annotating to 'eiF2alpha phosphorylation in response to endoplasmic reticulum stress ; GO:0036492' or its descendants.
synonym: "endoplasmic reticulum unfolded protein response; IRE1 signaling" EXACT [GOC:bf]
synonym: "ERN1-mediated unfolded protein response" RELATED [HGNC:3449]
@@ -217691,7 +217657,7 @@ is_a: GO:0030968 ! endoplasmic reticulum unfolded protein response
id: GO:0036499
name: PERK-mediated unfolded protein response
namespace: biological_process
-def: "A series of molecular signals mediated by the endoplasmic reticulum membrane stress sensor PERK (PKR-like ER kinase). Begins with activation of PERK in response to endoplasmic reticulum (ER) stress and ends with regulation of a downstream cellular process, e.g. transcription. The main substrate of PERK is the translation initiation factor eIF2alpha. Serine-phosphorylation of eIF2alpha by PERK inactivates eIF2alpha and inhibits general protein translation. In addition, eIF2alpha phosphorylation preferentially increases the translation of selective mRNAs such as ATF4 (activating transcription factor 4), which up regulates a subset of UPR genes required to restore folding capacity." [GOC:bf, GOC:PARL, PMID:22013210, PMID:27629041]
+def: "The series of molecular signals mediated by the endoplasmic reticulum membrane stress sensor PERK (PKR-like ER kinase). Begins with activation of PERK in response to endoplasmic reticulum (ER) stress and ends with regulation of a downstream cellular process, e.g. transcription. The main substrate of PERK is the translation initiation factor eIF2alpha. Serine-phosphorylation of eIF2alpha by PERK inactivates eIF2alpha and inhibits general protein translation. In addition, eIF2alpha phosphorylation preferentially increases the translation of selective mRNAs such as ATF4 (activating transcription factor 4), which up regulates a subset of UPR genes required to restore folding capacity." [GOC:bf, GOC:PARL, PMID:22013210, PMID:27629041]
synonym: "EIF2AK3-mediated unfolded protein response" RELATED [HGNC:3255]
synonym: "endoplasmic reticulum unfolded protein response; PERK signaling" EXACT [GOC:bf]
synonym: "eukaryotic translation initiation factor 2-alpha kinase 3-mediated unfolded protein response" RELATED [HGNC:3255]
@@ -217708,7 +217674,7 @@ is_a: GO:0140467 ! integrated stress response signaling
id: GO:0036500
name: ATF6-mediated unfolded protein response
namespace: biological_process
-def: "A series of molecular signals mediated by the endoplasmic reticulum membrane stress sensor ATF6 (activating transcription factor 6). Begins with activation of ATF6 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. Under conditions of endoplasmic reticulum stress, ATF6 translocates to the Golgi where it is processed by proteases to release a cytoplasmic domain (ATF6f), which operates as a transcriptional activator of many genes required to restore folding capacity." [GOC:bf, GOC:PARL, PMID:22013210]
+def: "The series of molecular signals mediated by the endoplasmic reticulum membrane stress sensor ATF6 (activating transcription factor 6). Begins with activation of ATF6 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. Under conditions of endoplasmic reticulum stress, ATF6 translocates to the Golgi where it is processed by proteases to release a cytoplasmic domain (ATF6f), which operates as a transcriptional activator of many genes required to restore folding capacity." [GOC:bf, GOC:PARL, PMID:22013210]
synonym: "activating transcription factor 6 signaling in unfolded protein response" EXACT [GOC:bf]
synonym: "ATF6 branch of UPR" EXACT [GOC:bf]
synonym: "ATF6 signal transduction pathway" BROAD [GOC:bf]
@@ -217981,8 +217947,8 @@ namespace: biological_process
def: "The removal of a sugar or dicarbonyl from a glycated protein." [GOC:bf, GOC:PARL, PMID:14568004, PMID:25416785]
comment: Glycation is a non enzymatic covalent addition of a sugar or dicarbonyl (methylglyoxal, glyoxal) to a protein. Deglycation repairs the glycated amino acids.
synonym: "glycated protein repair" RELATED [PMID:25416785]
-is_a: GO:0006464 ! cellular protein modification process
is_a: GO:0030091 ! protein repair
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0036526
@@ -218061,7 +218027,7 @@ relationship: part_of GO:0050886 ! endocrine process
id: GO:0038003
name: G protein-coupled opioid receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of an opioid receptor binding to one of its physiological ligands." [GOC:bf, PMID:20494127]
+def: "A G protein-coupled receptor signaling pathway initiated by an opioid binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:bf, PMID:20494127]
synonym: "opioid receptor signaling pathway" BROAD []
synonym: "opioid receptor signalling pathway" EXACT [GOC:mah]
xref: Wikipedia:Opioid_receptor
@@ -218094,7 +218060,7 @@ is_a: GO:0005042 ! netrin receptor activity
id: GO:0038007
name: netrin-activated signaling pathway
namespace: biological_process
-def: "A series of molecular events initiated by the binding of a netrin protein to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Netrins can act as chemoattractant signals for some cells and chemorepellent signals for others. Netrins also have roles outside of cell and axon guidance." [GOC:signaling, PMID:10399919, PMID:15960985, PMID:19785719, PMID:20108323]
+def: "The series of molecular signals initiated by the binding of a netrin protein to its receptor on the surface of the target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. Netrins can act as chemoattractant signals for some cells and chemorepellent signals for others. Netrins also have roles outside of cell and axon guidance." [GOC:signaling, PMID:10399919, PMID:15960985, PMID:19785719, PMID:20108323]
synonym: "netrin signaling pathway" EXACT [GOC:bf]
synonym: "netrin-activated signal transduction pathway" EXACT [GOC:bf]
synonym: "netrin-activated signalling pathway" EXACT [GOC:bf]
@@ -218280,15 +218246,20 @@ id: GO:0038024
name: cargo receptor activity
namespace: molecular_function
def: "Binding specifically to a substance (cargo) to deliver it to a transport vesicle. Cargo receptors span a membrane (either the plasma membrane or a vesicle membrane), binding simultaneously to cargo molecules and coat adaptors, to efficiently recruit soluble proteins to nascent vesicles." [PMID:15239958, PMID:27903609]
-comment: Notes: (1) this term and its child terms are intended for receptors that bind to and internalize molecules by receptor-mediated endocytosis. For receptors that are coupled to a signal transduction pathway, consider instead the term 'signaling receptor activity ; GO:0038023' and its children. (2) Cargo receptors transport substances by vesicular transport, not by transmembrane transport. For transmembrane transporters, consider instead the term 'transmembrane transporter activity ; GO:0022857.
+comment: Notes: (1) this term and its child terms are intended for receptors that bind to and internalize molecules by receptor-mediated endocytosis. For receptors that are coupled to a signal transduction pathway, consider instead the term 'signaling receptor activity ; GO:0038023' and its children. (2) Cargo receptors transport substances by vesicular transport, not by transmembrane transport. For transmembrane transporters, consider instead the term 'transmembrane transporter activity ; GO:0022857.
subset: goslim_drosophila
subset: goslim_generic
synonym: "endocytic receptor activity" NARROW [GOC:signaling, ISBN:0123645387, PMID:12671190]
synonym: "receptor activity" BROAD []
synonym: "receptor activity involved in receptor-mediated endocytosis" NARROW [GOC:bf]
synonym: "transport receptor activity" BROAD [GOC:signaling]
-xref: Reactome:R-HSA-3000122 "CD320 transports extracellular TCII:Cbl to endosome"
+xref: Reactome:R-HSA-3000103 "CUBN:AMN binds CBLIF:RCbl"
+xref: Reactome:R-HSA-3000112 "CD320-mediated TCN2:RCbl uptake and delivery to lysosome"
+xref: Reactome:R-HSA-3000122 "CD320 binds extracellular TCN2:RCbl"
+xref: Reactome:R-HSA-3000137 "CUBN:AMN-mediated CBLIF:RCbl uptake and delivery to lysosome"
xref: Reactome:R-HSA-350168 "LRP2-mediated uptake of extracellular CUBN:GC:25(OH)D"
+xref: Reactome:R-HSA-9759202 "LRP2-mediated TCN2:RCbl uptake and delivery to lysosome"
+xref: Reactome:R-HSA-9759209 "LRP2 binds extracellular TCN2:RCbl"
is_a: GO:0003674 ! molecular_function
[Term]
@@ -218303,7 +218274,7 @@ is_a: GO:0004888 ! transmembrane signaling receptor activity
id: GO:0038026
name: reelin-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of reelin (a secreted glycoprotein) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, PMID:12827279, PMID:20223215]
+def: "The series of molecular signals initiated by the binding of reelin (a secreted glycoprotein) to a receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, PMID:12827279, PMID:20223215]
synonym: "reeler-mediated signaling pathway" EXACT [GOC:bf, PR:000013879]
synonym: "reelin-mediated signal transduction pathway" EXACT [GOC:bf]
synonym: "reelin-mediated signalling pathway" EXACT [GOC:bf]
@@ -218313,7 +218284,7 @@ is_a: GO:0007166 ! cell surface receptor signaling pathway
id: GO:0038027
name: apolipoprotein A-I-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of apolipoprotein A-I to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:signaling, PMID:16443932]
+def: "The series of molecular signals initiated by apolipoprotein A-I binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:signaling, PMID:16443932]
synonym: "apolipoprotein A-I-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -218321,7 +218292,7 @@ is_a: GO:0007166 ! cell surface receptor signaling pathway
id: GO:0038028
name: insulin receptor signaling pathway via phosphatidylinositol 3-kinase
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of the insulin receptor binding to its physiological ligand, where the signal is passed on via the phosphatidylinositol 3-kinase cascade." [GOC:bf, GOC:signaling, PMID:19322168, PMID:20696212]
+def: "An insulin receptor signaling pathway in which the signal is transmitted via the phosphatidylinositol 3-kinase cascade." [GOC:bf, GOC:signaling, PMID:19322168, PMID:20696212]
synonym: "insulin receptor signaling pathway via phosphatidylinositol 3-kinase cascade" RELATED []
synonym: "insulin receptor signaling pathway via PI3K cascade" EXACT [GOC:bf]
synonym: "insulin receptor signaling via PI3K" EXACT [GOC:bf]
@@ -218332,7 +218303,7 @@ is_a: GO:0008286 ! insulin receptor signaling pathway
id: GO:0038029
name: epidermal growth factor receptor signaling pathway via MAPK cascade
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of an epidermal growth factor receptor binding to one of its physiological ligands, where the signal is passed on via the MAPKKK cascade." [GOC:bf, GOC:signaling, PMID:21167805]
+def: "An epidermal growth factor receptor signaling pathway in which the signal is transmitted via the MAPKKK cascade." [GOC:bf, GOC:signaling, PMID:21167805]
synonym: "EGFR signaling pathway via MAPKKK cascade" EXACT [GOC:bf]
synonym: "EGFR signaling via MAPKKK cascade" EXACT [GOC:bf]
synonym: "EGFR/MAPK signaling" EXACT [GOC:bf]
@@ -218344,7 +218315,7 @@ is_a: GO:0007173 ! epidermal growth factor receptor signaling pathway
id: GO:0038030
name: non-canonical Wnt signaling pathway via MAPK cascade
namespace: biological_process
-def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, where the signal is passed on via the MAPKKK cascade." [GOC:BHF, GOC:signaling, GOC:vk, PMID:17720811]
+def: "The series of molecular signals initiated by a Wnt protein binding to a frizzled family receptor on the surface of a target cell, where the signal is passed on via the MAPKKK cascade." [GOC:BHF, GOC:signaling, GOC:vk, PMID:17720811]
synonym: "non-canonical Wnt receptor signaling pathway via MAPK cascade" EXACT []
synonym: "non-canonical Wnt receptor signaling pathway via MAPK signaling" EXACT [GOC:bf]
synonym: "non-canonical Wnt receptor signaling pathway via MAPKKK cascade" EXACT [GOC:signaling]
@@ -218377,7 +218348,7 @@ is_a: GO:0045744 ! negative regulation of G protein-coupled receptor signaling p
id: GO:0038033
name: positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a VEGFR on the surface of a cell, which activates or increases the frequency, rate or extent of endothelial cell chemotaxis." [GOC:bf, GOC:BHF, GOC:rl, PMID:21245381]
+def: "The series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to its receptor on the surface of a cell, which activates or increases the frequency, rate or extent of endothelial cell chemotaxis." [GOC:bf, GOC:BHF, GOC:rl, PMID:21245381]
synonym: "positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signalling pathway" EXACT [GOC:mah]
synonym: "positive regulation of endothelial cell chemotaxis by VEGF/VEGFR signaling pathway" EXACT [GOC:bf]
synonym: "vascular endothelial growth factor receptor signaling pathway involved in endothelial cell chemotaxis" RELATED [GOC:bf]
@@ -218391,7 +218362,7 @@ is_a: GO:2001028 ! positive regulation of endothelial cell chemotaxis
id: GO:0038034
name: signal transduction in absence of ligand
namespace: biological_process
-def: "A series of molecular signals initiated by the absence of a ligand or the withdrawal of a ligand from a receptor." [GOC:al, GOC:ppm, GOC:pr, PMID:15044679]
+def: "The series of molecular signals initiated by the absence of a ligand or the withdrawal of a ligand from a receptor." [GOC:al, GOC:ppm, GOC:pr, PMID:15044679]
synonym: "addiction receptor signaling pathway" BROAD [PMID:15044679]
synonym: "basal signaling" NARROW [GOC:al]
synonym: "dependence receptor signaling pathway" BROAD [PMID:15044679]
@@ -218404,7 +218375,7 @@ is_a: GO:0007165 ! signal transduction
id: GO:0038035
name: G protein-coupled receptor signaling in absence of ligand
namespace: biological_process
-def: "A series of molecular signals beginning with a consequence of a G protein-coupled receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex, where the G protein-coupled receptor is not bound to an agonist." [GOC:al, PMID:12402500, PMID:17629961]
+def: "The series of molecular signals beginning with a consequence of a G protein-coupled receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex, where the G protein-coupled receptor is not bound to an agonist." [GOC:al, PMID:12402500, PMID:17629961]
comment: This term is intended for use by G protein-coupled receptors which signal at a low-level in the absence of agonist binding.
synonym: "basal G-protein coupled receptor signaling" NARROW [GOC:al]
synonym: "G-protein coupled receptor signaling in absence of agonist" EXACT [GOC:bf]
@@ -218472,7 +218443,7 @@ is_a: GO:2000272 ! negative regulation of signaling receptor activity
id: GO:0038043
name: interleukin-5-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-5 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-5 binding to its receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:signaling]
synonym: "IL-5-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-5-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -218494,6 +218465,7 @@ def: "Combining with an enkephalin, and transmitting the signal across the membr
synonym: "delta-opioid receptor activity" RELATED [GOC:bf]
synonym: "enkephalin receptor activity" BROAD []
is_a: GO:0004985 ! G protein-coupled opioid receptor activity
+is_a: GO:0008528 ! G protein-coupled peptide receptor activity
[Term]
id: GO:0038047
@@ -218510,6 +218482,7 @@ namespace: molecular_function
def: "Combining with a dynorphin peptide, and transmitting the signal across the membrane by activating an associated G-protein. Dynorphin is any opioid peptide that is generated by cleavage of the precursor protein prodynorphin." [GOC:bf, Wikipedia:Dynorphin]
synonym: "kappa-opioid receptor activity" RELATED [GOC:bf]
is_a: GO:0004985 ! G protein-coupled opioid receptor activity
+is_a: GO:0008528 ! G protein-coupled peptide receptor activity
[Term]
id: GO:0038053
@@ -218526,9 +218499,10 @@ id: GO:0038054
name: G protein-coupled estrogen receptor activity
namespace: molecular_function
def: "Combining with estrogen and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:signaling, PMID:17379646, PMID:20960099]
+synonym: "estrogen receptor activity" BROAD []
synonym: "G-protein coupled estrogen receptor activity" EXACT []
is_a: GO:0004930 ! G protein-coupled receptor activity
-is_a: GO:0030284 ! estrogen receptor activity
+is_a: GO:0030284 ! nuclear estrogen receptor activity
[Term]
id: GO:0038055
@@ -218576,7 +218550,7 @@ namespace: molecular_function
def: "Combining with a tumor necrosis factor ligand superfamily member 11 (TNFSF11) and transmitting the signal across the cell membrane to initiate a change in cell activity or function." [GOC:bf, GOC:cjm]
synonym: "RANKL receptor activity" EXACT [PR:000002107, Wikipedia:RANKL]
synonym: "tumor necrosis factor ligand superfamily member 11 receptor activity" EXACT [PR:000002107, Wikipedia:RANKL]
-is_a: GO:0005031 ! tumor necrosis factor-activated receptor activity
+is_a: GO:0005031 ! tumor necrosis factor receptor activity
[Term]
id: GO:0038059
@@ -218607,6 +218581,10 @@ id: GO:0038061
name: NIK/NF-kappaB signaling
namespace: biological_process
def: "The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52)." [GOC:bf, GOC:mg2, GOC:signaling, GOC:vs, PMID:11239468, PMID:15140882]
+synonym: "NIK-IKK cascade" RELATED [GOC:rph, PMID:10094049, PMID:10581243, PMID:9244310]
+synonym: "NIK-IKK kinase cascade" RELATED [GOC:rph, PMID:10094049, PMID:10581243, PMID:9244310]
+synonym: "NIK-IKK signaling pathway" RELATED [GOC:rph, PMID:10094049, PMID:10581243, PMID:9244310]
+synonym: "NIK-IKK-alpha cascade" RELATED [GOC:rph, PMID:10094049, PMID:10581243, PMID:9244310]
synonym: "NIK/NF-kappaB cascade" RELATED [GOC:signaling]
synonym: "NIK/NF-kappaB signal transduction" EXACT [GOC:signaling]
synonym: "non-canonical NF-KB signaling" BROAD [PMID:21173796]
@@ -218629,7 +218607,7 @@ is_a: GO:0038064 ! collagen receptor activity
id: GO:0038063
name: collagen-activated tyrosine kinase receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of collagen to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:uh, PMID:15888913, PMID:16626936]
+def: "The series of molecular signals initiated by collagen binding to its receptor on the surface of a target cell where the receptor possesses tyrosine kinase activity, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:uh, PMID:15888913, PMID:16626936]
synonym: "collagen-activated RTK signaling pathway" EXACT [PMID:21568710]
synonym: "collagen-activated tyrosine kinase receptor signalling pathway" EXACT [GOC:mah]
synonym: "DDR signaling pathway" NARROW [PMID:16626936]
@@ -218649,7 +218627,7 @@ is_a: GO:0004888 ! transmembrane signaling receptor activity
id: GO:0038065
name: collagen-activated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by collagen binding to a cell surface receptor, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:uh, PMID:21568710]
+def: "The series of molecular signals initiated by collagen binding to a cell surface receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:uh, PMID:21568710]
synonym: "collagen-activated signalling pathway" EXACT [GOC:mah]
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -218839,7 +218817,7 @@ is_a: GO:0046777 ! protein autophosphorylation
id: GO:0038084
name: vascular endothelial growth factor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:17470632]
+def: "The series of molecular signals initiated by vascular endothelial growth factor (VEGF) binding its receptor on the surface of the target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:17470632]
comment: In GO, a gene product with 'vascular endothelial growth factor-activated receptor activity ; GO:0005021' necessarily binds VEGF to transduce a signal. To represent cross-talk between ligands and receptors, signaling pathways in GO are starting to be named after the receptor and/or the signal. GO:0038084 is for annotation of any pathway in which the ligand VEGF binds and activates any cell surface receptor (VEGFR, PDGFR etc.). For annotation of signaling pathways where a VEGFR binds one of its physiological ligands (VEGF or an alternative growth factor), consider 'vascular endothelial growth factor receptor signaling pathway ; GO:0048010'.
synonym: "vascular endothelial growth factor signalling pathway" EXACT [GOC:bf]
synonym: "VEGF signaling" EXACT [GOC:bf]
@@ -218859,7 +218837,7 @@ is_a: GO:0019838 ! growth factor binding
id: GO:0038086
name: VEGF-activated platelet-derived growth factor receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a platelet-derived growth factor receptor (PDGFR) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:17470632]
+def: "The series of molecular signals initiated by vascular endothelial growth factor (VEGF) binding to a platelet-derived growth factor receptor (PDGFR) on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:17470632]
synonym: "vascular endothelial growth factor-activated platelet-derived growth factor receptor signaling pathway" EXACT [GOC:bf]
synonym: "VEGF-A/PDGFR signaling" NARROW [PMID:17470632]
synonym: "VEGF-activated PDGFR signalling pathway" EXACT [GOC:bf]
@@ -218872,7 +218850,7 @@ is_a: GO:0048008 ! platelet-derived growth factor receptor signaling pathway
id: GO:0038087
name: VEGF-activated platelet-derived growth factor receptor-alpha signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to an alpha-type platelet-derived growth factor receptor (PDGFR) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:17470632]
+def: "The series of molecular signals initiated by vascular endothelial growth factor (VEGF) binding to an alpha-type platelet-derived growth factor receptor (PDGFR) on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:17470632]
synonym: "vascular endothelial growth factor-activated platelet-derived growth factor receptor-alpha signaling pathway" EXACT [GOC:bf]
synonym: "VEGF-A/PDGFRalpha signaling" NARROW [PMID:17470632]
synonym: "VEGF-activated PDGFRalpha signalling pathway" EXACT [GOC:bf]
@@ -218885,7 +218863,7 @@ is_a: GO:0038086 ! VEGF-activated platelet-derived growth factor receptor signal
id: GO:0038088
name: VEGF-activated platelet-derived growth factor receptor-beta signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a beta-type platelet-derived growth factor receptor (PDGFR) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:17470632]
+def: "The series of molecular signals initiated by vascular endothelial growth factor (VEGF) binding to a beta-type platelet-derived growth factor receptor (PDGFR) on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:17470632]
synonym: "vascular endothelial growth factor-activated platelet-derived growth factor receptor-beta signaling pathway" EXACT [GOC:bf]
synonym: "VEGF-A/PDGFRbeta signaling" NARROW [PMID:17470632]
synonym: "VEGF-activated PDGFRbeta signalling pathway" EXACT [GOC:bf]
@@ -218898,7 +218876,7 @@ is_a: GO:0038086 ! VEGF-activated platelet-derived growth factor receptor signal
id: GO:0038089
name: positive regulation of cell migration by vascular endothelial growth factor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a receptor on the surface of a cell, which activates or increases the frequency, rate or extent of the orderly movement of a cell from one site to another." [GOC:bf, GOC:signaling]
+def: "The series of molecular signals initiated by vascular endothelial growth factor (VEGF) binding to its receptor on the surface of a cell, which activates or increases the frequency, rate or extent of the orderly movement of a cell from one site to another." [GOC:bf, GOC:signaling]
synonym: "positive regulation of cell migration by vascular endothelial growth factor signalling pathway" EXACT [GOC:mah]
synonym: "positive regulation of cell migration by VEGF signaling pathway" EXACT [GOC:bf]
synonym: "VEGF-A-induced cell migration" NARROW [PMID:17470632]
@@ -218910,7 +218888,7 @@ is_a: GO:0038084 ! vascular endothelial growth factor signaling pathway
id: GO:0038090
name: positive regulation of cell migration by VEGF-activated platelet derived growth factor receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a platelet-derived growth factor receptor (PDGFR) on the surface of a cell, which activates or increases the frequency, rate or extent of the orderly movement of a cell from one site to another." [GOC:bf, GOC:signaling, PMID:17470632]
+def: "The series of molecular signals initiated by vascular endothelial growth factor (VEGF) binding to a platelet-derived growth factor receptor (PDGFR) on the surface of a cell, which activates or increases the frequency, rate or extent of the orderly movement of a cell from one site to another." [GOC:bf, GOC:signaling, PMID:17470632]
synonym: "positive regulation of cell migration by VEGF-activated platelet derived growth factor receptor signalling pathway" EXACT [GOC:mah]
synonym: "positive regulation of cell migration by VEGF/PDGFR signaling pathway" EXACT [PMID:17470632]
synonym: "VEGF/PDGFR-induced cell migration" EXACT [PMID:17470632]
@@ -218921,7 +218899,7 @@ is_a: GO:0038089 ! positive regulation of cell migration by vascular endothelial
id: GO:0038091
name: positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a platelet-derived growth factor receptor (PDGFR) on the surface of a cell, which activates or increases the frequency, rate or extent of cell proliferation." [GOC:signaling, PMID:17470632]
+def: "The series of molecular signals initiated by vascular endothelial growth factor (VEGF) binding to a platelet-derived growth factor receptor (PDGFR) on the surface of a cell, which activates or increases the frequency, rate or extent of cell proliferation." [GOC:signaling, PMID:17470632]
synonym: "positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signalling pathway" EXACT [GOC:mah]
synonym: "positive regulation of cell proliferation by VEGF/PDGFR signaling pathway" EXACT [GOC:bf]
synonym: "VEGF-A-induced cell proliferation" NARROW [PMID:17470632]
@@ -218932,7 +218910,7 @@ is_a: GO:0038086 ! VEGF-activated platelet-derived growth factor receptor signal
id: GO:0038092
name: nodal signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a nodal protein to an activin receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:vk, PMID:17287255]
+def: "The series of molecular signals initiated by nodal protein binding to an activin receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:vk, PMID:17287255]
synonym: "nodal signaling" EXACT [GOC:bf]
synonym: "nodal signalling pathway" EXACT [GOC:mah]
is_a: GO:0032924 ! activin receptor signaling pathway
@@ -218941,7 +218919,7 @@ is_a: GO:0032924 ! activin receptor signaling pathway
id: GO:0038093
name: Fc receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the Fc portion of an immunoglobulin to an Fc receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region." [GOC:phg, Wikipedia:Fc_receptor]
+def: "The series of molecular signals initiated by the binding of the Fc portion of an immunoglobulin to an Fc receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region." [GOC:phg, Wikipedia:Fc_receptor]
synonym: "Fc receptor signalling pathway" EXACT [GOC:bf]
is_a: GO:0002768 ! immune response-regulating cell surface receptor signaling pathway
@@ -218949,7 +218927,7 @@ is_a: GO:0002768 ! immune response-regulating cell surface receptor signaling pa
id: GO:0038094
name: Fc-gamma receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin G (IgG) to an Fc-gamma receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region." [GOC:phg, PMID:11244038]
+def: "The series of molecular signals initiated by the binding of the Fc portion of immunoglobulin G (IgG) to an Fc-gamma receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region." [GOC:phg, PMID:11244038]
synonym: "Fc-gamma receptor signalling pathway" EXACT [GOC:bf]
is_a: GO:0038093 ! Fc receptor signaling pathway
@@ -218957,7 +218935,7 @@ is_a: GO:0038093 ! Fc receptor signaling pathway
id: GO:0038095
name: Fc-epsilon receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region." [GOC:phg, PMID:12413516, PMID:15048725]
+def: "The series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region." [GOC:phg, PMID:12413516, PMID:15048725]
synonym: "Fc-epsilon receptor signalling pathway" EXACT [GOC:bf]
is_a: GO:0038093 ! Fc receptor signaling pathway
@@ -219073,17 +219051,17 @@ is_a: GO:0042562 ! hormone binding
id: GO:0038107
name: nodal signaling pathway involved in determination of left/right asymmetry
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a nodal protein to an activin receptor on the surface of a target cell, which contributes to the establishment of an organism's body plan or part of an organism with respect to the left and right halves." [GOC:BHF, GOC:vk, PMID:12857784, PMID:17287255, PMID:20413706]
+def: "The series of molecular signals initiated by a nodal protein binding of to an activin receptor on the surface of a target cell, which contributes to the establishment of an organism's body plan or part of an organism with respect to the left and right halves." [GOC:BHF, GOC:vk, PMID:12857784, PMID:17287255, PMID:20413706]
synonym: "nodal signalling pathway involved in determination of left/right asymmetry" EXACT [GOC:mah]
synonym: "regulation of transcription from RNA polymerase II promoter by nodal signaling pathway, involved in determination of left/right symmetry" EXACT [GOC:bf]
is_a: GO:0038092 ! nodal signaling pathway
-is_a: GO:1900094 ! regulation of transcription from RNA polymerase II promoter involved in determination of left/right symmetry
+relationship: part_of GO:0007368 ! determination of left/right symmetry
[Term]
id: GO:0038108
name: negative regulation of appetite by leptin-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of leptin to a receptor on the surface of a cell, which reduces appetite, the desire or physical craving for food." [GOC:BHF, GOC:vk, PMID:19150989]
+def: "The series of molecular signals initiated by leptin binding to its receptor on the surface of a cell, which reduces appetite, the desire or physical craving for food." [GOC:BHF, GOC:vk, PMID:19150989]
synonym: "inhibition of appetite by leptin signaling" EXACT [GOC:bf]
synonym: "negative regulation of appetite by leptin-mediated signalling pathway" EXACT [GOC:mah]
synonym: "reduction of appetite by leptin-mediated signaling" EXACT [GOC:bf]
@@ -219095,7 +219073,7 @@ is_a: GO:0033210 ! leptin-mediated signaling pathway
id: GO:0038109
name: Kit signaling pathway
namespace: biological_process
-def: "A series of molecular signals that starts with the binding of stem cell factor to the tyrosine kinase receptor KIT on the surface of a cell, and ends with regulation of a downstream cellular process, e.g. transcription. Stem cell factor (KIT ligand) binding to the receptor Kit mediates receptor dimerization, activation of its intrinsic tyrosine kinase activity and autophosphorylation. The activated receptor then phosphorylates various substrates, thereby activating distinct signaling cascades within the cell that trigger a change in state or activity of the cell." [GOC:nhn, GOC:signaling, PMID:16129412]
+def: "The series of molecular signals initiated by the binding of stem cell factor to the tyrosine kinase receptor KIT on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Stem cell factor (KIT ligand) binding to the receptor Kit mediates receptor dimerization, activation of its intrinsic tyrosine kinase activity and autophosphorylation. The activated receptor then phosphorylates various substrates, thereby activating distinct signaling cascades within the cell that trigger a change in state or activity of the cell." [GOC:nhn, GOC:signaling, PMID:16129412]
synonym: "Kit signalling pathway" EXACT [GOC:mah]
synonym: "SCF signaling pathway" EXACT [PMID:18787413]
synonym: "stem cell factor receptor signaling pathway" EXACT [PMID:16129412]
@@ -219108,7 +219086,7 @@ relationship: part_of GO:0036216 ! cellular response to stem cell factor stimulu
id: GO:0038110
name: interleukin-2-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-2 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-2 binding to its receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "IL-2-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-2-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -219118,7 +219096,7 @@ relationship: part_of GO:0071352 ! cellular response to interleukin-2
id: GO:0038111
name: interleukin-7-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-7 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-7 binding to its receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "IL-7-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-7-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -219128,7 +219106,7 @@ relationship: part_of GO:0098761 ! cellular response to interleukin-7
id: GO:0038112
name: interleukin-8-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-8 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-8 binding to its receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "IL-8-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-8-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -219138,7 +219116,7 @@ relationship: part_of GO:0098759 ! cellular response to interleukin-8
id: GO:0038113
name: interleukin-9-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-9 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-9 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "IL-9-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-9-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -219148,7 +219126,7 @@ relationship: part_of GO:0071355 ! cellular response to interleukin-9
id: GO:0038114
name: interleukin-21-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-21 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-21 binding to a receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "IL-21-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-21-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -219158,7 +219136,7 @@ relationship: part_of GO:0098757 ! cellular response to interleukin-21
id: GO:0038115
name: chemokine (C-C motif) ligand 19 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the C-C chemokine CCL19 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:15059845]
+def: "The series of molecular signals initiated by the binding of the C-C chemokine CCL19 to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:15059845]
comment: The C-C chemokine CCL19 s a known agonist of the chemokine receptor type 7 (CCR7). Consider instead annotating to the child term 'CCL19-activated CCR7 signaling pathway ; GO:0038119'.
synonym: "C-C chemokine receptor type 7 signaling pathway" RELATED [PMID:15059845]
synonym: "CCL19-mediated signaling pathway" EXACT [PMID:15059845]
@@ -219169,7 +219147,7 @@ is_a: GO:0070098 ! chemokine-mediated signaling pathway
id: GO:0038116
name: chemokine (C-C motif) ligand 21 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the C-C chemokine CCL21 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:15059845]
+def: "The series of molecular signals initiated by the binding of the C-C chemokine CCL21 to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:15059845]
comment: The C-C chemokine CCL21 s a known agonist of the chemokine receptor type 7 (CCR7). Consider instead annotating to the child term 'CCL21-activated CCR7 signaling pathway ; GO:0038120'.
synonym: "C-C chemokine receptor type 7 signaling pathway" RELATED [PMID:15059845, PR:000001203]
synonym: "CCL21-mediated signaling pathway" EXACT [PMID:15059845]
@@ -219188,7 +219166,7 @@ is_a: GO:0016493 ! C-C chemokine receptor activity
id: GO:0038118
name: C-C chemokine receptor CCR7 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by a the C-C chemokine type 7 receptor on the surface of a cell binding to one of it's physiological ligands, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:15059845, PMID:15778365]
+def: "The series of molecular signals initiated by a the C-C chemokine type 7 receptor on the surface of a cell binding to one of it's physiological ligands, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:15059845, PMID:15778365]
comment: This term was created to show the binding of cytokines to multiple receptor types, and vice-versa. Known agonists of chemokine receptor type 7 (CCR7) are C-C chemokines CCL19 and CCL21. Consider instead annotating to one of the child terms 'CCL19-activated CCR7 signaling pathway ; GO:0038119' and/or 'CCL21-activated CCR7 signaling pathway ; GO:0038120'.
synonym: "C-C chemokine receptor CCR7 signalling pathway" EXACT [GOC:mah]
synonym: "CCR7 signaling pathway" RELATED []
@@ -219198,7 +219176,7 @@ is_a: GO:0070098 ! chemokine-mediated signaling pathway
id: GO:0038119
name: CCL19-activated CCR7 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the C-C chemokine CCL19 to a C-C chemokine type 7 receptor (CCR7) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:15059845]
+def: "The series of molecular signals initiated by the binding of the C-C chemokine CCL19 to a C-C chemokine type 7 receptor (CCR7) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:15059845]
synonym: "CCL19-activated CCR7 signalling pathway" EXACT [GOC:mah]
is_a: GO:0038115 ! chemokine (C-C motif) ligand 19 signaling pathway
is_a: GO:0038118 ! C-C chemokine receptor CCR7 signaling pathway
@@ -219207,7 +219185,7 @@ is_a: GO:0038118 ! C-C chemokine receptor CCR7 signaling pathway
id: GO:0038120
name: CCL21-activated CCR7 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the C-C chemokine CCL21 to a C-C chemokine type 7 receptor (CCR7) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:15059845]
+def: "The series of molecular signals initiated by the binding of the C-C chemokine CCL21 to a C-C chemokine type 7 receptor (CCR7) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:15059845]
synonym: "CCL21-activated CCR7 signalling pathway" EXACT [GOC:mah]
is_a: GO:0038116 ! chemokine (C-C motif) ligand 21 signaling pathway
is_a: GO:0038118 ! C-C chemokine receptor CCR7 signaling pathway
@@ -219234,7 +219212,7 @@ is_a: GO:0016493 ! C-C chemokine receptor activity
id: GO:0038123
name: toll-like receptor TLR1:TLR2 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a heterodimeric TLR1:TLR2 complex to one of it's physiological ligands, followed by transmission of the signal by the activated receptor, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:17318230]
+def: "The series of molecular signals initiated by a ligand binding of a heterodimeric TLR1:TLR2 complex, followed by transmission of the signal by the activated receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:17318230]
synonym: "TLR2:TLR1 signaling pathway" EXACT [GOC:bf]
synonym: "toll-like receptor TLR1:TLR2 signalling pathway" EXACT [GOC:mah]
is_a: GO:0002224 ! toll-like receptor signaling pathway
@@ -219243,7 +219221,7 @@ is_a: GO:0002224 ! toll-like receptor signaling pathway
id: GO:0038124
name: toll-like receptor TLR6:TLR2 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a heterodimeric TLR6:TLR2 complex to one of it's physiological ligands, followed by transmission of the signal by the activated receptor, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:17318230]
+def: "The series of molecular signals initiated by a ligand binding of a heterodimeric TLR6:TLR2 complex, followed by transmission of the signal by the activated receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:17318230]
synonym: "TLR2:TLR6 signaling pathway" EXACT [GOC:bf]
synonym: "toll-like receptor TLR6:TLR2 signalling pathway" EXACT [GOC:mah]
is_a: GO:0002224 ! toll-like receptor signaling pathway
@@ -219252,7 +219230,7 @@ is_a: GO:0002224 ! toll-like receptor signaling pathway
id: GO:0038127
name: ERBB signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptor tyrosine kinases on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:jc, PMID:16460914, Wikipedia:ErbB]
+def: "The series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptor tyrosine kinases on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:jc, PMID:16460914, Wikipedia:ErbB]
synonym: "EGF receptor family signaling pathway" EXACT [PMID:11597398]
synonym: "EGFR family signaling pathway" RELATED [PMID:11597398]
synonym: "ErbB signaling" EXACT [PMID:20933094, Wikipedia:ErbB]
@@ -219263,7 +219241,7 @@ is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling path
id: GO:0038128
name: ERBB2 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair." [GOC:jc, PMID:16460914, Reactome:R-HSA-1227986]
+def: "The series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB2 on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair." [GOC:jc, PMID:16460914, Reactome:R-HSA-1227986]
synonym: "ERBB2 signalling pathway" EXACT [GOC:mah]
synonym: "HER2 signaling pathway" EXACT [PR:000002082]
synonym: "NEU signaling" EXACT [Reactome:R-HSA-1227986]
@@ -219274,7 +219252,7 @@ is_a: GO:0038127 ! ERBB signaling pathway
id: GO:0038129
name: ERBB3 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB3 on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB3 receptors have impaired kinase activity and rely on the kinase activity of the heterodimer partner for activation and signal transmission." [GOC:jc, PMID:16460914, Reactome:R-HSA-1247497]
+def: "The series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB3 on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription. ERBB3 receptors have impaired kinase activity and rely on the kinase activity of the heterodimer partner for activation and signal transmission." [GOC:jc, PMID:16460914, Reactome:R-HSA-1247497]
synonym: "ERBB3 signalling pathway" EXACT [GOC:mah]
synonym: "HER3 signaling pathway" EXACT [PR:000007159]
synonym: "receptor tyrosine-protein kinase erbB-3 signaling pathway" EXACT [PR:000007159]
@@ -219284,7 +219262,7 @@ is_a: GO:0038127 ! ERBB signaling pathway
id: GO:0038130
name: ERBB4 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB4 on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:jc, PMID:16460914, Reactome:R-HSA-1236394]
+def: "The series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB4 on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:jc, PMID:16460914, Reactome:R-HSA-1236394]
synonym: "ERBB4 signalling pathway" EXACT [GOC:mah]
synonym: "HER4 signaling pathway" EXACT [PR:000007160]
synonym: "receptor tyrosine-protein kinase erbB-4 signaling pathway" EXACT [PR:000007160]
@@ -219312,7 +219290,7 @@ is_a: GO:0019838 ! growth factor binding
id: GO:0038133
name: ERBB2-ERBB3 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by binding of a ligand to a ERBB3 receptor on the surface of a cell, followed by transmission of the signal by a heterodimeric complex of ERBB2 and ERBB3. ERBB2, which does not bind any known ligand, is activated through formation of a heterodimer with another ligand-activated ERBB family member such as ERBB3. ERBB3 also has impaired kinase activity and relies on ERBB2 for activation and signal transmission." [GOC:signaling, PMID:16460914, Reactome:R-HSA-1963589]
+def: "The series of molecular signals initiated by binding of a ligand to a ERBB3 receptor on the surface of a cell, followed by transmission of the signal by a heterodimeric complex of ERBB2 and ERBB3. ERBB2, which does not bind any known ligand, is activated through formation of a heterodimer with another ligand-activated ERBB family member such as ERBB3. ERBB3 also has impaired kinase activity and relies on ERBB2 for activation and signal transmission." [GOC:signaling, PMID:16460914, Reactome:R-HSA-1963589]
synonym: "ERBB2-ERBB3 signalling pathway" EXACT [GOC:mah]
synonym: "HER2-HER3 signaling pathway" EXACT [PR:000002082, PR:000007159]
is_a: GO:0038128 ! ERBB2 signaling pathway
@@ -219322,7 +219300,7 @@ is_a: GO:0038129 ! ERBB3 signaling pathway
id: GO:0038134
name: ERBB2-EGFR signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by binding of a ligand to an epidermal growth factor receptor (EGFR/ERBB1) on the surface of a cell, followed by transmission of the signal by a heterodimeric complex of ERBB2 and EGFR. ERBB2, which does not bind any known ligand, is activated through formation of a heterodimer with another ligand-activated ERBB family member such as EGFR." [GOC:signaling, PMID:16460914, Reactome:R-HSA-1963589]
+def: "The series of molecular signals initiated by binding of a ligand to an epidermal growth factor receptor (EGFR/ERBB1) on the surface of a cell, followed by transmission of the signal by a heterodimeric complex of ERBB2 and EGFR. ERBB2, which does not bind any known ligand, is activated through formation of a heterodimer with another ligand-activated ERBB family member such as EGFR." [GOC:signaling, PMID:16460914, Reactome:R-HSA-1963589]
synonym: "EGFR-HER2 signaling pathway" EXACT [PR:000002082, PR:000006933]
synonym: "ERBB2-EGFR signalling pathway" EXACT [GOC:mah]
is_a: GO:0007173 ! epidermal growth factor receptor signaling pathway
@@ -219332,7 +219310,7 @@ is_a: GO:0038128 ! ERBB2 signaling pathway
id: GO:0038135
name: ERBB2-ERBB4 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by binding of a ligand to a ERBB4 receptor on the surface of a cell, followed by transmission of the signal by a heterodimeric complex of ERBB2 and ERBB4. ERBB2, which does not bind any known ligand, is activated through formation of a heterodimer with another ligand-activated ERBB family member such as ERBB4." [GOC:signaling, PMID:16460914, Reactome:R-HSA-1963589]
+def: "The series of molecular signals initiated by binding of a ligand to a ERBB4 receptor on the surface of a cell, followed by transmission of the signal by a heterodimeric complex of ERBB2 and ERBB4. ERBB2, which does not bind any known ligand, is activated through formation of a heterodimer with another ligand-activated ERBB family member such as ERBB4." [GOC:signaling, PMID:16460914, Reactome:R-HSA-1963589]
synonym: "ERBB2-ERBB4 signalling pathway" EXACT [GOC:mah]
synonym: "HER2-HER4 signaling pathway" EXACT [PR:000002082, PR:000007160]
is_a: GO:0038128 ! ERBB2 signaling pathway
@@ -219342,7 +219320,7 @@ is_a: GO:0038130 ! ERBB4 signaling pathway
id: GO:0038136
name: ERBB3-ERBB4 signaling pathway
namespace: biological_process
-def: "A series of molecular signals transmitted by a heterodimeric complex of the tyrosine kinase receptors ERBB3 and ERBB4. The pathway begins with binding of a ligand to either cell surface receptor, or the dimeric receptor complex, and ends with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:16460914, Reactome:R-HSA-1977958]
+def: "The series of molecular signals transmitted by a heterodimeric complex of the tyrosine kinase receptors ERBB3 and ERBB4. The pathway begins with binding of a ligand to either cell surface receptor, or the dimeric receptor complex, and ends with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:16460914, Reactome:R-HSA-1977958]
synonym: "ERBB3-ERBB4 signalling pathway" EXACT [GOC:mah]
synonym: "HER3-HER4 signaling pathway" EXACT [PR:000007159, PR:000007160]
is_a: GO:0038129 ! ERBB3 signaling pathway
@@ -219352,7 +219330,7 @@ is_a: GO:0038130 ! ERBB4 signaling pathway
id: GO:0038137
name: ERBB4-EGFR signaling pathway
namespace: biological_process
-def: "A series of molecular signals transmitted by a heterodimeric complex of the tyrosine kinase receptors EGFR (epidermal growth factor receptor/ERBB1) and ERBB4. The pathway begins with binding of a ligand to either cell surface receptor, or the dimeric receptor complex, and ends with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:16460914, Reactome:R-HSA-1977959]
+def: "The series of molecular signals transmitted by a heterodimeric complex of the tyrosine kinase receptors EGFR (epidermal growth factor receptor/ERBB1) and ERBB4. The pathway begins with binding of a ligand to either cell surface receptor, or the dimeric receptor complex, and ends with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:16460914, Reactome:R-HSA-1977959]
synonym: "ERBB1-ERBB4 signaling pathway" EXACT [PR:000006933, PR:000007160]
synonym: "ERBB4-EGFR signalling pathway" EXACT [GOC:mah]
synonym: "HER1-HER4 signaling pathway" EXACT [PR:000006933, PR:000007160]
@@ -219363,7 +219341,7 @@ is_a: GO:0038130 ! ERBB4 signaling pathway
id: GO:0038138
name: ERBB4-ERBB4 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB4, followed by ligand-induced homodimerization of ERBB4 and transmission of the signal into the cell by the homodimeric ERBB4 complex. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:16460914, Reactome:R-HSA-1250220]
+def: "The series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor ERBB4, followed by ligand-induced homodimerization of ERBB4 and transmission of the signal into the cell by the homodimeric ERBB4 complex. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, PMID:16460914, Reactome:R-HSA-1250220]
synonym: "ERBB4 homodimeric signaling pathway" EXACT [PMID:16460914]
synonym: "ERBB4-ERBB4 signalling pathway" EXACT [GOC:mah]
synonym: "HER4-HER4 signaling pathway" EXACT [PR:000007160]
@@ -219426,7 +219404,7 @@ is_a: GO:0098802 ! plasma membrane signaling receptor complex
id: GO:0038145
name: macrophage colony-stimulating factor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the cytokine macrophage colony-stimulating factor (M-CSF) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, GOC:uh, PMID:12138890, Wikipedia:Macrophage_colony-stimulating_factor]
+def: "The series of molecular signals initiated by the binding of the cytokine macrophage colony-stimulating factor (M-CSF) to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, GOC:uh, PMID:12138890, Wikipedia:Macrophage_colony-stimulating_factor]
synonym: "M-CSF signaling pathway" EXACT [PMID:12138890]
synonym: "macrophage colony-stimulating factor signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -219436,7 +219414,7 @@ relationship: part_of GO:0036006 ! cellular response to macrophage colony-stimul
id: GO:0038146
name: chemokine (C-X-C motif) ligand 12 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the chemokine CXCL12 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, Wikipedia:Stromal_cell-derived_factor-1]
+def: "The series of molecular signals initiated by the binding of the chemokine CXCL12 to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, Wikipedia:Stromal_cell-derived_factor-1]
synonym: "CXCL12 signaling pathway" EXACT [GOC:bf]
synonym: "CXCL12-activated CXCR7 signaling pathway" NARROW [GOC:bf]
synonym: "SDF1 signaling pathway" EXACT [HGNC:10672, PMID:22204316, PR:000006066]
@@ -219459,7 +219437,7 @@ is_a: GO:0016494 ! C-X-C chemokine receptor activity
id: GO:0038148
name: chemokine (C-C motif) ligand 2 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the C-C chemokine CCL2 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, Wikipedia:CCL2]
+def: "The series of molecular signals initiated by the binding of the C-C chemokine CCL2 to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, Wikipedia:CCL2]
synonym: "CCL2 signaling pathway" EXACT [GOC:bf]
is_a: GO:0070098 ! chemokine-mediated signaling pathway
@@ -219475,7 +219453,7 @@ is_a: GO:0016493 ! C-C chemokine receptor activity
id: GO:0038150
name: C-C chemokine receptor CCR2 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by a the C-C chemokine type 2 receptor (CCR2) on the surface of a cell binding to one of it's physiological ligands, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by a the C-C chemokine type 2 receptor (CCR2) on the surface of a cell binding to one of it's physiological ligands, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "C-C chemokine receptor type 2 signaling pathway" EXACT [PR:000001199]
is_a: GO:0070098 ! chemokine-mediated signaling pathway
@@ -219483,7 +219461,7 @@ is_a: GO:0070098 ! chemokine-mediated signaling pathway
id: GO:0038151
name: CCL2-activated CCR2 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the C-C chemokine CCL2 to a C-C chemokine type 2 receptor (CCR2) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by the binding of the C-C chemokine CCL2 to a C-C chemokine type 2 receptor (CCR2) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "CCL2/CCR2 signaling pathway" EXACT [GOC:bf]
is_a: GO:0038148 ! chemokine (C-C motif) ligand 2 signaling pathway
is_a: GO:0038150 ! C-C chemokine receptor CCR2 signaling pathway
@@ -219492,7 +219470,7 @@ is_a: GO:0038150 ! C-C chemokine receptor CCR2 signaling pathway
id: GO:0038152
name: C-C chemokine receptor CCR4 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by a the C-C chemokine type 2 receptor (CCR4) on the surface of a cell binding to one of it's physiological ligands, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by a the C-C chemokine type 2 receptor (CCR4) on the surface of a cell binding to one of it's physiological ligands, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "C-C chemokine receptor type 4 signaling pathway" EXACT [PR:000001200]
synonym: "chemokine receptor CCR4 signaling pathway" EXACT [GOC:bf]
is_a: GO:0070098 ! chemokine-mediated signaling pathway
@@ -219501,7 +219479,7 @@ is_a: GO:0070098 ! chemokine-mediated signaling pathway
id: GO:0038153
name: CCL2-activated CCR4 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the C-C chemokine CCL2 to a C-C chemokine type 4 receptor (CCR4) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by the binding of the C-C chemokine CCL2 to a C-C chemokine type 4 receptor (CCR4) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "CCL2/CCR4 signaling pathway" RELATED [GOC:bf]
is_a: GO:0038148 ! chemokine (C-C motif) ligand 2 signaling pathway
is_a: GO:0038152 ! C-C chemokine receptor CCR4 signaling pathway
@@ -219510,7 +219488,7 @@ is_a: GO:0038152 ! C-C chemokine receptor CCR4 signaling pathway
id: GO:0038154
name: interleukin-11-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-11 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by the binding of interleukin-11 to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "IL-11-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-11-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -219519,7 +219497,7 @@ is_a: GO:0019221 ! cytokine-mediated signaling pathway
id: GO:0038155
name: interleukin-23-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-23 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-23 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "IL-23-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-23-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -219528,7 +219506,7 @@ is_a: GO:0019221 ! cytokine-mediated signaling pathway
id: GO:0038156
name: interleukin-3-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-3 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-3 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "IL-3-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-3-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -219537,7 +219515,7 @@ is_a: GO:0019221 ! cytokine-mediated signaling pathway
id: GO:0038157
name: granulocyte-macrophage colony-stimulating factor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the cytokine granulocyte macrophage colony-stimulating factor (GM-CSF) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. GM-CSF binds to a heterodimer receptor (CSF2R) consisting of an alpha ligand-binding subunit, and a common beta subunit that is shared with other cytokine receptors." [GOC:nhn, GOC:signaling, PMID:17027509]
+def: "The series of molecular signals initiated by the binding of the cytokine granulocyte macrophage colony-stimulating factor (GM-CSF) to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. GM-CSF binds to a heterodimer receptor (CSF2R) consisting of an alpha ligand-binding subunit, and a common beta subunit that is shared with other cytokine receptors." [GOC:nhn, GOC:signaling, PMID:17027509]
synonym: "CSF2 signaling pathway" EXACT [PR:000005931]
synonym: "GM-CSF receptor signaling pathway" EXACT [GOC:nhn]
synonym: "GM-CSF signaling pathway" EXACT [PR:000005931]
@@ -219549,7 +219527,7 @@ is_a: GO:0019221 ! cytokine-mediated signaling pathway
id: GO:0038158
name: granulocyte colony-stimulating factor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the cytokine granulocyte colony-stimulating factor (G-CSF) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. G-CSF binds to the receptor (CSF3R)." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by the binding of the cytokine granulocyte colony-stimulating factor (G-CSF) to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. G-CSF binds to the receptor (CSF3R)." [GOC:nhn, GOC:signaling]
synonym: "CSF3 signaling pathway" EXACT [PR:000005932]
synonym: "G-CSF receptor signaling pathway" EXACT [GOC:nhn]
synonym: "G-CSF signaling pathway" EXACT [PR:000005932]
@@ -219561,7 +219539,7 @@ is_a: GO:0019221 ! cytokine-mediated signaling pathway
id: GO:0038159
name: C-X-C chemokine receptor CXCR4 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by a the C-X-C chemokine type 4 receptor on the surface of a cell binding to one of it's physiological ligands, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
+def: "The series of molecular signals initiated by a the C-X-C chemokine type 4 receptor on the surface of a cell binding to one of it's physiological ligands, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling]
synonym: "CXCR4 signaling pathway" EXACT [PR:000001208]
is_a: GO:0070098 ! chemokine-mediated signaling pathway
@@ -219569,7 +219547,7 @@ is_a: GO:0070098 ! chemokine-mediated signaling pathway
id: GO:0038160
name: CXCL12-activated CXCR4 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the C-X-C chemokine CXCL12 to a C-X-C chemokine type 4 receptor (CXCR4) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn]
+def: "The series of molecular signals initiated by the binding of the C-X-C chemokine CXCL12 to a C-X-C chemokine type 4 receptor (CXCR4) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn]
synonym: "CXCL12-activated CXCR4 signalling pathway" EXACT [GOC:bf]
is_a: GO:0038146 ! chemokine (C-X-C motif) ligand 12 signaling pathway
is_a: GO:0038159 ! C-X-C chemokine receptor CXCR4 signaling pathway
@@ -219578,7 +219556,7 @@ is_a: GO:0038159 ! C-X-C chemokine receptor CXCR4 signaling pathway
id: GO:0038161
name: prolactin signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of the peptide hormone prolactin to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:21664429]
+def: "The series of molecular signals initiated by the binding of the peptide hormone prolactin to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:21664429]
synonym: "PRL signaling pathway" EXACT [PMID:21664429, PR:000013246]
synonym: "prolactin-mediated signaling pathway" EXACT [GOC:bf]
is_a: GO:0009755 ! hormone-mediated signaling pathway
@@ -219588,7 +219566,7 @@ is_a: GO:0019221 ! cytokine-mediated signaling pathway
id: GO:0038162
name: erythropoietin-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of erythropoietin (EPO) to the erythropoietin receptor (EPO-R) on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, PMID:12489509]
+def: "The series of molecular signals initiated by erythropoietin (EPO) binding to the erythropoietin receptor (EPO-R) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, PMID:12489509]
synonym: "EPO-R signaling pathway" EXACT [PMID:12489509]
synonym: "erythropoietin receptor signaling pathway" EXACT [PMID:12489509]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -219598,7 +219576,7 @@ relationship: part_of GO:0036018 ! cellular response to erythropoietin
id: GO:0038163
name: thrombopoietin-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a thrombopoietin to the thrombopoietin receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:19630807]
+def: "The series of molecular signals initiated by thrombopoietin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, GOC:signaling, PMID:19630807]
synonym: "THPO signaling pathway" EXACT [PR:000016318]
synonym: "THPO/MPL signaling pathway" EXACT [PMID:18371409]
synonym: "thrombopoietin receptor signaling pathway" EXACT [GOC:nhn, PR:000001939]
@@ -219615,7 +219593,7 @@ is_a: GO:0004896 ! cytokine receptor activity
id: GO:0038165
name: oncostatin-M-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of oncostatin-M (OSM) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. OSM can signal via at least two different receptors (a specific receptor and a LIF receptor) to activate different downstream signal transduction pathways." [GOC:nhn, GOC:signaling, PMID:10579456, PMID:12811586]
+def: "The series of molecular signals initiated by oncostatin-M (OSM) binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. OSM can signal via at least two different receptors (a specific receptor and a LIF receptor) to activate different downstream signal transduction pathways." [GOC:nhn, GOC:signaling, PMID:10579456, PMID:12811586]
synonym: "oncostatin-M signaling pathway" EXACT [GOC:bf]
synonym: "OSM signaling pathway" EXACT [PMID:10579456, PR:000012059]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -219624,7 +219602,7 @@ is_a: GO:0019221 ! cytokine-mediated signaling pathway
id: GO:0038166
name: angiotensin-activated signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of angiotensin II binding to an angiotensin receptor on the surface of the cell, and proceeding with the activated receptor transmitting the signal to a heterotrimeric G-protein complex to initiate a change in cell activity. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:nhn, GOC:signaling, PMID:10977869]
+def: "A G protein-coupled receptor signaling pathway initiated by angiotensin II binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:nhn, GOC:signaling, PMID:10977869]
synonym: "angiotensin II-mediated signaling pathway" EXACT [GOC:bf]
synonym: "angiotensin receptor signaling pathway" EXACT [GOC:bf, GOC:mtg_cardiac_conduct_nov11]
synonym: "angiotensin-mediated signaling pathway" RELATED []
@@ -219635,7 +219613,7 @@ relationship: part_of GO:1904385 ! cellular response to angiotensin
id: GO:0038167
name: epidermal growth factor receptor signaling pathway via positive regulation of NF-kappaB transcription factor activity
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of an epidermal growth factor receptor binding to one of its physiological ligands, where the signal is passed on within the cell via activation of the transcription factor NF-kappaB." [GOC:signaling, GOC:uh, PMID:21229383, PMID:21518868, PMID:22132240]
+def: "An epidermal growth factor receptor signaling pathway in which the signal transmitted via the activation of the transcription factor NF-kappaB." [GOC:signaling, GOC:uh, PMID:21229383, PMID:21518868, PMID:22132240]
synonym: "EGFR signaling pathway via activation of NF-kappaB" EXACT [GOC:bf]
synonym: "epidermal growth factor receptor signalling pathway via positive regulation of NF-kappaB transcription factor activity" EXACT []
is_a: GO:0007173 ! epidermal growth factor receptor signaling pathway
@@ -219644,7 +219622,7 @@ is_a: GO:0007173 ! epidermal growth factor receptor signaling pathway
id: GO:0038168
name: epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of an epidermal growth factor receptor binding to one of its physiological ligands, where the signal is passed on within the cell via I-kappaB-kinase (IKK)-dependent activation of the transcription factor NF-kappaB." [GOC:bf, PMID:22132240]
+def: "An epidermal growth factor receptor signaling pathway in which the signal transmitted via I-kappaB-kinase (IKK)-dependent activation of the transcription factor NF-kappaB." [GOC:bf, PMID:22132240]
synonym: "EGFR signaling pathway via IKK-dependent activation of NF-kappaB" EXACT [GOC:bf]
synonym: "EGFR signaling pathway via IKK/NF-kappaB cascade" EXACT [GOC:bf]
is_a: GO:0038167 ! epidermal growth factor receptor signaling pathway via positive regulation of NF-kappaB transcription factor activity
@@ -219653,7 +219631,7 @@ is_a: GO:0038167 ! epidermal growth factor receptor signaling pathway via positi
id: GO:0038169
name: somatostatin receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a somatostatin receptor (SSTR) binding to one of its physiological ligands and transmitting the signal to a heterotrimeric G-protein complex. The pathway ends with regulation of a downstream cellular process, e.g. transcription." [GOC:jc, PMID:18006219, PMID:8769369]
+def: "A G protein-coupled receptor signaling pathway initiated by somatostatin binding to the somatostatin receptor (SSTR) on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:jc, PMID:18006219, PMID:8769369]
comment: In addition to somatostatin (SST), the somatostatin receptors (SSTRs) can also be activated by the agonist cortistatin (CST). For signal transduction specifically initiated by the ligand somatostatin, consider instead annotating to the child term 'somatostatin signaling pathway ; GO:0038170'.
synonym: "SST receptor signaling pathway" EXACT [GOC:bf]
synonym: "SSTR signaling pathway" RELATED [GOC:bf]
@@ -219663,7 +219641,7 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
id: GO:0038170
name: somatostatin signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of the peptide somatostatin (SST) binding to a somatostatin receptor (SSTR). The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:nhn, GOC:signaling, PMID:18006219, Wikipedia:Somatostatin]
+def: "A G protein-coupled receptor signaling pathway initiated by somatostatin binding to a somatostatin receptor (SSTR), and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:nhn, GOC:signaling, PMID:18006219, Wikipedia:Somatostatin]
synonym: "somatostatin signalling pathway" EXACT [GOC:bf]
synonym: "somatostatin-activated somatostatin receptor signaling pathway" EXACT [GOC:bf]
synonym: "somatostatin-mediated signaling pathway" EXACT [GOC:bf]
@@ -219677,7 +219655,7 @@ is_a: GO:0038169 ! somatostatin receptor signaling pathway
id: GO:0038171
name: cannabinoid signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a cannabinoid binding to a cell surface receptor. The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription. Cannabinoids are a class of diverse chemical compounds that include the endocannabinoids and the phytocannabinoids." [GOC:bf, GOC:jc, GOC:signaling, Wikipedia:Cannabinoid]
+def: "A G protein-coupled receptor signaling pathway initiated by a cannabinoid binding to its receptor on the cell surface, and ending with the regulation of a downstream cellular process, e.g. transcription. Cannabinoids are a class of diverse chemical compounds that include the endocannabinoids and the phytocannabinoids." [GOC:bf, GOC:jc, GOC:signaling, Wikipedia:Cannabinoid]
synonym: "cannabinoid receptor signaling pathway" EXACT [GOC:bf]
synonym: "cannabinoid-activated signaling pathway" EXACT [GOC:bf]
synonym: "cannabinoid-mediated signaling pathway" EXACT [GOC:bf]
@@ -219687,7 +219665,7 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
id: GO:0038172
name: interleukin-33-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-33 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:jc, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-33 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:jc, GOC:signaling]
synonym: "IL-33-mediated signaling pathway" EXACT [GOC:bf]
synonym: "IL33 signaling pathway" EXACT [PR:000001389]
synonym: "interleukin-33 signaling pathway" RELATED [GOC:jc]
@@ -219698,7 +219676,7 @@ is_a: GO:0019221 ! cytokine-mediated signaling pathway
id: GO:0038173
name: interleukin-17A-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-17A to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:jc, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-17A binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:jc, GOC:signaling]
synonym: "IL-17A-mediated signaling pathway" EXACT [GOC:bf]
synonym: "IL17A signaling pathway" EXACT [PR:000001138, Wikipedia:IL17A]
synonym: "interleukin-17A signaling pathway" RELATED [GOC:jc]
@@ -219744,7 +219722,7 @@ is_a: GO:0048018 ! receptor ligand activity
id: GO:0038178
name: complement component C5a signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of a the C5a component of the complement pathway binding to a complement receptor, and ending with regulation of a downstream cellular process. C5a is a peptide derived from the C5 complement factor." [GOC:jc, PMID:15313431, Wikipedia:Complement_component_5a]
+def: "A G protein-coupled receptor signaling pathway initiated by a C5a component of the complement pathway binding to a complement receptor, and ending with regulation of a downstream cellular process. C5a is a peptide derived from the C5 complement factor." [GOC:jc, PMID:15313431, Wikipedia:Complement_component_5a]
synonym: "complement component C5a-induced signaling pathway" EXACT [GOC:jc]
is_a: GO:0002430 ! complement receptor mediated signaling pathway
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -219753,7 +219731,7 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
id: GO:0038179
name: neurotrophin signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a neurotrophin to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Neurotrophins are a family of secreted growth factors that induce the survival, development, and function of neurons." [GOC:bf, GOC:jc, GOC:signaling, PMID:17466268, Wikipedia:Neurotrophin]
+def: "The series of molecular signals initiated by neurotrophin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. Neurotrophins are a family of secreted growth factors that induce the survival, development, and function of neurons." [GOC:bf, GOC:jc, GOC:signaling, PMID:17466268, Wikipedia:Neurotrophin]
comment: There are two classes of receptors for neurotrophins: p75 and the Trk family of tyrosine kinase receptors.
synonym: "neurotrophin receptor signaling pathway" EXACT [PMID:22333586]
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -219763,7 +219741,7 @@ relationship: part_of GO:0071363 ! cellular response to growth factor stimulus
id: GO:0038180
name: nerve growth factor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of nerve growth factor (NGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, PMID:11520933]
+def: "The series of molecular signals initiated by nerve growth factor (NGF) binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, PMID:11520933]
comment: Nerve growth factor (NGF) binds at least two classes of receptors: the p75 LNGFR (low-affinity nerve growth factor receptor) and TrkA, a transmembrane tyrosine kinase.
synonym: "nerve growth factor signalling pathway" EXACT [GOC:bf]
synonym: "NGF signaling pathway" EXACT [PR:000011194, Wikipedia:Nerve_growth_factor]
@@ -219794,14 +219772,14 @@ is_a: GO:0038181 ! bile acid receptor activity
id: GO:0038183
name: bile acid signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a bile acid to a receptor, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:signaling, PMID:12016314]
+def: "The series of molecular signals initiated by bile acid binding to its receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:signaling, PMID:12016314]
is_a: GO:0007165 ! signal transduction
[Term]
id: GO:0038184
name: cell surface bile acid receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by binding of a bile acid to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, PMID:12419312, PMID:19442546]
+def: "The series of molecular signals initiated by binding of a bile acid to a receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, PMID:12419312, PMID:19442546]
synonym: "membrane bile acid receptor signaling pathway" RELATED [GOC:bf]
is_a: GO:0007166 ! cell surface receptor signaling pathway
is_a: GO:0038183 ! bile acid signaling pathway
@@ -219810,7 +219788,7 @@ is_a: GO:0038183 ! bile acid signaling pathway
id: GO:0038185
name: intracellular bile acid receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by a bile acid binding to an receptor located within a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, PMID:10334992]
+def: "The series of molecular signals initiated by a bile acid binding to an receptor located within a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, PMID:10334992]
synonym: "nuclear bile acid receptor signaling pathway" RELATED []
is_a: GO:0030522 ! intracellular receptor signaling pathway
is_a: GO:0038183 ! bile acid signaling pathway
@@ -219844,7 +219822,7 @@ is_a: GO:0038023 ! signaling receptor activity
id: GO:0038188
name: cholecystokinin signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of cholecystokinin binding to a receptor on the surface of the cell, and proceeding with the activated receptor transmitting the signal to a heterotrimeric G-protein complex to initiate a change in cell activity. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:jc, PMID:11181948]
+def: "A G protein-coupled receptor signaling pathway initiated by cholecystokinin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:jc, PMID:11181948]
synonym: "CCK signaling" EXACT [PMID:11181948, Wikipedia:Cholecystokinin]
synonym: "cholecystokinin receptor signaling pathway" RELATED [GOC:bf]
xref: Wikipedia:Cholecystokinin
@@ -219854,7 +219832,7 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
id: GO:0038189
name: neuropilin signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a neuropilin protein on the surface of a target cell, followed by transmission of the signal, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, PMID:12852851]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a neuropilin protein on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, PMID:12852851]
synonym: "Npn signaling" EXACT [PMID:12852851]
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -219862,9 +219840,9 @@ is_a: GO:0007166 ! cell surface receptor signaling pathway
id: GO:0038190
name: VEGF-activated neuropilin signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of vascular endothelial growth factor (VEGF) to a neuropilin protein on the surface of a target cell, followed by transmission of the signal, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:rl, PMID:12852851]
-synonym: "vascular endothelial growth factor-activated neuropilin signaling pathway" RELATED [GOC:bf]
-synonym: "VEGF-Npn-1 signaling" NARROW [PMID:12852851]
+def: "The series of molecular signals initiated by vascular endothelial growth factor (VEGF) binding to a neuropilin protein on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:rl, PMID:12852851]
+synonym: "vascular endothelial growth factor-activated neuropilin signaling pathway" EXACT [GOC:bf]
+synonym: "VEGF-Npn-1 signaling" EXACT [PMID:12852851]
is_a: GO:0038084 ! vascular endothelial growth factor signaling pathway
is_a: GO:0038189 ! neuropilin signaling pathway
@@ -219882,7 +219860,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0038192
name: gastric inhibitory peptide signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a gastric inhibitory peptide (GIP) binding to a cell surface receptor. The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, PMID:15955806]
+def: "A G protein-coupled receptor signaling pathway initiated by gastric inhibitory peptide (GIP) binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, PMID:15955806]
synonym: "gastric inhibitory polypeptide receptor signaling pathway" EXACT [GOC:nhn]
synonym: "GIP signaling" EXACT [PMID:19251046]
synonym: "glucose-dependent insulinotropic polypeptide signaling" EXACT [PMID:19251046]
@@ -219892,7 +219870,7 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
id: GO:0038193
name: thromboxane A2 signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of thromboxane A2 binding to a cell surface receptor. The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, PMID:15893915]
+def: "A G protein-coupled receptor signaling pathway initiated by thromboxane A2 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:nhn, PMID:15893915]
synonym: "TXA(2) receptor signaling" EXACT [PMID:15893915]
synonym: "TXA2 signaling" EXACT [PMID:15242977]
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -219901,7 +219879,7 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
id: GO:0038194
name: thyroid-stimulating hormone signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of thyroid-stimulating hormone (thyrotropin) binding to a cell surface receptor. The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription." [GOC:gap, PMID:10809230]
+def: "A G protein-coupled receptor signaling pathway initiated by thyroid-stimulating hormone (thyrotropin) binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:gap, PMID:10809230]
synonym: "thyrotropin signaling pathway" EXACT [GOC:gap, PMID:10809230]
synonym: "TSH signaling pathway" EXACT [PMID:10809230]
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -219910,18 +219888,19 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
id: GO:0038195
name: urokinase plasminogen activator signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of urokinase plasminogen activator to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:gap, PMID:9417082]
+def: "The series of molecular signals initiated by urokinase plasminogen activator binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:gap, PMID:9417082]
synonym: "uPA signaling pathway" EXACT [PMID:9417082]
is_a: GO:0007166 ! cell surface receptor signaling pathway
[Term]
id: GO:0038196
-name: type III interferon signaling pathway
+name: type III interferon-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a type III interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon lambda is the only member of the type III interferon found so far." [GOC:pg, GOC:signaling]
-synonym: "interferon lambda signaling pathway" NARROW [PR:000001362]
+def: "The series of molecular signals initiated by type III interferon binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. Interferon lambda is the only member of the type III interferon found so far." [GOC:signaling, PMID:32464097]
+synonym: "interferon lambda signaling pathway" NARROW []
+synonym: "type III interferon signaling pathway" EXACT []
synonym: "type III interferon-activated signaling pathway" EXACT [GOC:signaling]
-is_a: GO:0019221 ! cytokine-mediated signaling pathway
+is_a: GO:0140888 ! interferon-mediated signaling pathway
relationship: part_of GO:0071358 ! cellular response to type III interferon
[Term]
@@ -219931,7 +219910,6 @@ namespace: cellular_component
def: "A heterodimeric protein complex that binds a type I interferon and transmits the signal across the membrane into the cell. Consists of an alpha subunit (IFNAR1) and a beta subunit (IFNAR2)." [GOC:cjm, GOC:signaling, PMID:17502368]
synonym: "interferon-alpha/beta receptor complex" NARROW [GOC:bf]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0038198
@@ -220188,15 +220166,14 @@ is_a: GO:0046775 ! suppression by virus of host cytokine production
id: GO:0039502
name: suppression by virus of host type I interferon-mediated signaling pathway
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." [GOC:add, GOC:bf, GOC:sp, UniProtKB-KW:KW-1114, VZ:883]
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." [GOC:add, GOC:bf, GOC:sp, PMID:19802576, PMID:26712804, PMID:32464097, PMID:32733001, PMID:33097660]
synonym: "inhibition of host interferon signaling pathway by virus" RELATED [UniProtKB-KW:KW-1114]
synonym: "negative regulation by virus of host type I interferon-mediated signaling pathway" EXACT [GOC:bf]
synonym: "suppression by virus of host type I IFN-mediated signaling pathway" EXACT [GOC:bf]
synonym: "suppression by virus of host type I interferon-mediated signalling pathway" EXACT [GOC:bf]
xref: VZ:883 "Inhibition of host IFN-mediated response initiation by virus"
-is_a: GO:0039503 ! suppression by virus of host innate immune response
is_a: GO:0060339 ! negative regulation of type I interferon-mediated signaling pathway
-is_a: GO:0075114 ! suppression by symbiont of host transmembrane receptor-mediated signal transduction
+is_a: GO:0140886 ! suppression by virus of host interferon-mediated signaling pathway
[Term]
id: GO:0039503
@@ -220207,7 +220184,7 @@ synonym: "inhibition of host innate immune response by virus" EXACT [UniProtKB-K
synonym: "negative regulation by virus of host innate immune response" EXACT [GOC:bf]
synonym: "negative regulation by virus of host innate immunity" EXACT [GOC:bf]
synonym: "suppression by virus of host innate immunity" EXACT [GOC:pg]
-is_a: GO:0030683 ! mitigation of host immune response by virus
+is_a: GO:0019049 ! mitigation of host antiviral defense response
is_a: GO:0050776 ! regulation of immune response
is_a: GO:0050794 ! regulation of cellular process
is_a: GO:0052170 ! suppression by symbiont of host innate immune response
@@ -220222,7 +220199,7 @@ synonym: "inhibition of host adaptive immune response by virus" EXACT [UniProtKB
synonym: "negative regulation by virus of host adaptive immune response" EXACT [GOC:bf]
synonym: "negative regulation by virus of host adaptive immunity" EXACT [GOC:bf]
synonym: "suppression by virus of host acquired immune response" EXACT [ISBN:068340007X]
-is_a: GO:0030683 ! mitigation of host immune response by virus
+is_a: GO:0019049 ! mitigation of host antiviral defense response
is_a: GO:0052562 ! suppression by symbiont of host immune response
is_a: GO:0075528 ! modulation by virus of host immune response
relationship: negatively_regulates GO:0002250 ! adaptive immune response
@@ -220245,7 +220222,7 @@ name: modulation by virus of host molecular function
namespace: biological_process
def: "The process in which a virus effects a change in the function of a host protein via a direct interaction." [GOC:bf, GOC:sp]
synonym: "modification by virus of host protein function" EXACT [GOC:bf]
-is_a: GO:0019048 ! modulation by virus of host process
+is_a: GO:0019054 ! modulation by virus of host cellular process
is_a: GO:0052055 ! modulation by symbiont of host molecular function
[Term]
@@ -220259,34 +220236,38 @@ synonym: "inhibition by virus of host protein function" NARROW [GOC:bf]
synonym: "inhibition of host protein function" NARROW [GOC:bf]
synonym: "negative regulation by virus of host molecular function" EXACT [GOC:bf]
synonym: "negative regulation by virus of host protein function" EXACT [GOC:bf]
+is_a: GO:0039506 ! modulation by virus of host molecular function
is_a: GO:0039516 ! modulation by virus of host catalytic activity
is_a: GO:0052053 ! negative regulation by symbiont of host catalytic activity
[Term]
id: GO:0039508
-name: suppression by virus of host receptor activity
+name: obsolete suppression by virus of host receptor activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the functional activity of a host receptor." [GOC:bf, GOC:sp]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the functional activity of a host receptor." [GOC:bf, GOC:sp]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down-regulation by virus of host receptor activity" EXACT [GOC:bf]
synonym: "downregulation by virus of host receptor activity" EXACT [GOC:bf]
synonym: "inhibition by virus of host receptor activity" NARROW [GOC:bf]
synonym: "negative regulation by virus of host receptor activity" EXACT [GOC:bf]
synonym: "suppression by virus of host receptor function" EXACT [GOC:bf]
synonym: "viral inhibition of host receptor" EXACT [GOC:bf]
-is_a: GO:0039507 ! suppression by virus of host molecular function
+is_obsolete: true
[Term]
id: GO:0039509
-name: suppression by virus of host pattern recognition receptor activity
+name: obsolete suppression by virus of host pattern recognition receptor activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the functional activity of a host pattern recognition receptor. A pattern recognition receptor combines with a molecular pattern based on a repeating or polymeric structure, such as a polysaccharide or peptidoglycan, to initiate a change in cell activity." [GOC:bf, GOC:sp]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the functional activity of a host pattern recognition receptor. A pattern recognition receptor combines with a molecular pattern based on a repeating or polymeric structure, such as a polysaccharide or peptidoglycan, to initiate a change in cell activity." [GOC:bf, GOC:sp]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation by virus of host pattern recognition receptor activity" EXACT [GOC:bf]
synonym: "down-regulation by virus of host pattern recognition receptor activity" EXACT [GOC:bf]
synonym: "inhibition by virus of host pattern recognition receptor activity" NARROW [GOC:rf]
synonym: "negative regulation by virus of host pattern recognition receptor activity" EXACT [GOC:bf]
synonym: "suppression by virus of host pattern recognition receptor function" EXACT [GOC:bf]
synonym: "viral inhibition of host pattern recognition receptor activity" NARROW [GOC:bf]
-is_a: GO:0039508 ! suppression by virus of host receptor activity
+is_obsolete: true
+consider: GO:0039537
[Term]
id: GO:0039510
@@ -220302,27 +220283,30 @@ is_obsolete: true
[Term]
id: GO:0039511
-name: suppression by virus of host interferon receptor activity
+name: obsolete suppression by virus of host interferon receptor activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the functional activity of a host interferon receptor." [GOC:bf, GOC:sp, UniProtKB-KW:KW-1091, VZ:843]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the functional activity of a host interferon receptor." [GOC:bf, GOC:sp, UniProtKB-KW:KW-1091, VZ:843]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down-regulation by virus of host interferon receptor activity" EXACT [GOC:bf]
synonym: "downregulation by virus of host interferon receptor activity" EXACT [GOC:bf]
synonym: "inhibition by virus of host interferon receptor activity" NARROW [GOC:bf]
synonym: "inhibition of host interferon receptors by virus" EXACT [UniProtKB-KW:KW-1091]
synonym: "negative regulation by virus of host interferon receptor activity" EXACT [GOC:bf]
xref: VZ:843 "Inhibition of host interferon receptors by virus"
-is_a: GO:0039508 ! suppression by virus of host receptor activity
+is_obsolete: true
+consider: GO:0140886
[Term]
id: GO:0039512
-name: suppression by virus of host protein tyrosine kinase activity
+name: obsolete suppression by virus of host protein tyrosine kinase activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host protein tyrosine kinase activity." [GOC:bf, GOC:sp]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host protein tyrosine kinase activity." [GOC:bf, GOC:sp]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
synonym: "down-regulation by virus of host protein tyrosine kinase activity" EXACT [GOC:bf]
synonym: "downregulation by virus of host protein tyrosine kinase activity" EXACT [GOC:bf]
synonym: "inhibition by virus of host protein tyrosine kinase activity" NARROW [GOC:bf]
synonym: "negative regulation by virus of host protein tyrosine kinase activity" EXACT [GOC:bf]
-is_a: GO:0039584 ! suppression by virus of host protein kinase activity
+is_obsolete: true
[Term]
id: GO:0039513
@@ -220354,29 +220338,31 @@ def: "The process in which a virus effects a change in host enzyme activity." [G
synonym: "modulation of catalytic activity of host by virus" EXACT [GOC:bf]
synonym: "regulation by virus of host catalytic activity" EXACT [GOC:bf]
synonym: "regulation of host catalytic activity by virus" EXACT [GOC:bf]
-is_a: GO:0039506 ! modulation by virus of host molecular function
+is_a: GO:0019048 ! modulation by virus of host process
is_a: GO:0052148 ! modulation by symbiont of host catalytic activity
[Term]
id: GO:0039517
-name: modulation by virus of host protein serine/threonine phosphatase activity
+name: obsolete modulation by virus of host protein serine/threonine phosphatase activity
namespace: biological_process
-def: "The process in which a virus effects a change in host protein serine/threonine phosphatase activity." [GOC:bf, GOC:sp]
+def: "OBSOLETE. The process in which a virus effects a change in host protein serine/threonine phosphatase activity." [GOC:bf, GOC:sp]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
synonym: "modulation by virus of protein serine/threonine phosphatase activity in host" EXACT [GOC:bf]
synonym: "regulation by virus of host protein serine/threonine phosphatase activity" EXACT [GOC:bf]
-is_a: GO:0019054 ! modulation by virus of host cellular process
-is_a: GO:0039516 ! modulation by virus of host catalytic activity
+is_obsolete: true
[Term]
id: GO:0039518
-name: suppression by virus of host cytokine activity
+name: obsolete suppression by virus of host cytokine activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host cytokine activity." [GOC:bf, GOC:sp]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host cytokine activity." [GOC:bf, GOC:sp]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down-regulation by virus of host cytokine activity" EXACT [GOC:bf]
synonym: "downregulation by virus of host cytokine activity" EXACT [GOC:bf]
synonym: "inhibition by virus of host cytokine activity" NARROW [GOC:bf]
synonym: "negative regulation by virus of host cytokine activity" EXACT [GOC:bf]
-is_a: GO:0039507 ! suppression by virus of host molecular function
+is_obsolete: true
+consider: GO:0052170
[Term]
id: GO:0039519
@@ -220394,13 +220380,16 @@ is_a: GO:1904092 ! regulation of autophagic cell death
id: GO:0039520
name: induction by virus of host autophagy
namespace: biological_process
+alt_id: GO:0075044
def: "Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host." [GOC:bf, GOC:sp, UniProtKB-KW:KW-1072, VZ:846]
synonym: "activation of host autophagy by virus" EXACT [UniProtKB-KW:KW-1072]
+synonym: "autophagy of host cells involved in interaction with symbiont" RELATED []
+synonym: "positive regulation by symbiont of host autophagotic process" RELATED []
+synonym: "positive regulation by symbiont of host autophagy" EXACT []
synonym: "positive regulation by virus of host autophagy" BROAD [GOC:bf]
xref: VZ:846 "Activation of host autophagy by virus"
is_a: GO:0010508 ! positive regulation of autophagy
is_a: GO:0039519 ! modulation by virus of host autophagy
-is_a: GO:0075044 ! positive regulation by symbiont of host autophagy
[Term]
id: GO:0039521
@@ -220410,10 +220399,8 @@ def: "Any process in which a virus stops, prevents, or reduces the frequency, ra
synonym: "inhibition by virus of host autophagy" EXACT [GOC:bf]
synonym: "inhibition of host autophagy by virus" EXACT [UniProtKB-KW:KW-1083]
synonym: "negative regulation by virus of host autophagy" BROAD [GOC:bf]
-xref: VZ:845 "Inhibition of host autophagy by virus"
-is_a: GO:0010507 ! negative regulation of autophagy
-is_a: GO:0039519 ! modulation by virus of host autophagy
-is_a: GO:0140321 ! negative regulation by symbiont of host autophagy
+is_a: GO:0019054 ! modulation by virus of host cellular process
+is_a: GO:0140321 ! suppression of host autophagy
[Term]
id: GO:0039522
@@ -220457,7 +220444,7 @@ is_a: GO:0050686 ! negative regulation of mRNA processing
id: GO:0039525
name: modulation by virus of host chromatin organization
namespace: biological_process
-def: "Any process in which a virus effects a change in the organization of chromatin in the host." [GOC:bf, GOC:sp, UniProtKB-KW:KW-1122]
+def: "Any process in which a virus effects a change in the organization of chromatin in the host." [GOC:bf, GOC:sp, PMID:11483770, PMID:16687403]
synonym: "modulation by virus of host chromatin organisation" EXACT [GOC:mah]
synonym: "modulation of host chromatin by virus" EXACT [UniProtKB-KW:KW-1122]
synonym: "modulation of host chromatin structure by virus" EXACT [GOC:bf]
@@ -220481,78 +220468,65 @@ is_a: GO:0052150 ! modulation by symbiont of host apoptotic process
id: GO:0039527
name: suppression by virus of host TRAF-mediated signal transduction
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of TRAF-mediated signal transduction in the host." [GOC:bf, GOC:sp]
+alt_id: GO:0039547
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of TRAF-mediated signal transduction in the host." [GOC:bf, GOC:sp, PMID:20335533, PMID:27387501, PMID:28522607, PMID:31311877, PMID:33372174]
+comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response.
synonym: "inhibition of host TRAF-mediated signal transduction by virus" EXACT [GOC:bf]
+synonym: "inhibition of host TRAFs by virus" NARROW []
synonym: "negative regulation by virus of host TRAF-mediated signal transduction" BROAD [GOC:bf]
+synonym: "suppression by virus of host TRAF activity" EXACT []
synonym: "suppression by virus of host tumor necrosis factor receptor-associated factor signaling" EXACT [GOC:bf]
is_a: GO:0052029 ! suppression by symbiont of host signal transduction pathway
-[Term]
-id: GO:0039528
-name: cytoplasmic pattern recognition receptor signaling pathway in response to virus
-namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of a virus or viral RNA binding to a pattern recognition receptor (PRR) located in the cytoplasm. Cytosolic PRRs such as RIG-I (DDX58) and MDA-5 (IFIH1) detect RNA synthesized during active viral replication and trigger a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines." [GOC:bf, PMID:17328678, PMID:18272355, PMID:19531363]
-comment: This term should be used for annotation when it is not known which cytoplasmic pattern recognition receptor (PRR) has detected the viral RNA. If the PRR is known, consider instead the child terms. The RIG-like family is composed of at least RIG-I (retinoic acid inducible gene I; also known as DDX58), melanoma differentiation-associated gene 5 (MDA5; also known as helicard or IFIH1) and LGP2.
-synonym: "cytoplasmic caspase-recruiting domain (CARD) helicase signaling pathway" NARROW [PMID:17328678]
-synonym: "cytoplasmic pattern recognition receptor signalling pathway in response to virus" EXACT [GOC:mah]
-synonym: "RIG-I-like receptor (RLR) signaling pathway" NARROW [PMID:21626883]
-synonym: "RIG-I/MDA5 signaling pathway" NARROW [PMID:21187438]
-synonym: "RIG-like helicase signaling pathway" NARROW [PMID:18272355]
-synonym: "RIG-like receptor signaling pathway" NARROW [PMID:19531363]
-synonym: "RLH signaling pathway" NARROW [PMID:18272355]
-synonym: "RLR signaling pathway" NARROW [PMID:19531363]
-synonym: "virus-induced cytoplasmic pattern recognition receptor signaling pathway" EXACT [GOC:bf]
-is_a: GO:0002753 ! cytoplasmic pattern recognition receptor signaling pathway
-is_a: GO:0098586 ! cellular response to virus
-relationship: part_of GO:0051607 ! defense response to virus
-
[Term]
id: GO:0039529
name: RIG-I signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) RIG-1 (also known as DDX58) binding to viral RNA. RIG-I detects RNA synthesized during active viral replication and triggers a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines." [GOC:bf, PMID:17328678, PMID:19620789, PMID:21435580]
-comment: The apoptosis effect triggered by the RIG-I signaling pathway is inconclusive and may represent an in-vitro phenomenon. Therefore, in GO the term 'RIG-I signaling pathway ; GO:0039529' is positioned under 'regulation of cytokine production' as this is its primary effect.
+def: "The series of molecular signals initiated by the binding ssRNA or dsRNA from another organism to the cytoplasmic pattern recognition receptor (PRR) RIG-1 (also known as DDX58). RIG-I detects RNA synthesized during viral replication or shed by non-viral pathogens, and triggers a signaling pathway to protect the host against infection, for example by inducing the expression of cytokines." [GOC:bf, PMID:17328678, PMID:19620789, PMID:21435580, PMID:25579795]
synonym: "DDX58 signaling pathway" EXACT [HGNC:19102]
synonym: "retinoic acid inducible gene I signaling pathway" EXACT [HGNC:19102]
synonym: "RIG-I signalling pathway" EXACT [GOC:mah]
-is_a: GO:0039528 ! cytoplasmic pattern recognition receptor signaling pathway in response to virus
+synonym: "RIG-I-like receptor (RLR) signaling pathway" EXACT []
+synonym: "RIG-like helicase signaling pathway" EXACT []
+synonym: "RIG-like receptor signaling pathway" EXACT []
+synonym: "RLH signaling pathway" EXACT []
+synonym: "RLR signaling pathway" EXACT []
+is_a: GO:0002753 ! cytosolic pattern recognition receptor signaling pathway
[Term]
id: GO:0039530
name: MDA-5 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) MDA-5 (also known as IFIH1) binding to viral RNA. MDA-5 detects RNA synthesized during active viral replication and triggers a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines." [GOC:bf, PMID:19620789]
+def: "The series of molecular signals initiated by the binding of dsRNA from another organism to the cytoplasmic pattern recognition receptor (PRR) MDA-5 (also known as IFIH1). MDA-5 detects RNA synthesized during viral replication or shed by non-viral pathogens, and triggers a signaling pathway to protect the host against infection, for example by inducing the expression of cytokines." [GOC:bf, PMID:19620789, PMID:33087405]
synonym: "IFIH1 signaling pathway" EXACT [HGNC:18873]
synonym: "MDA-5 signalling pathway" EXACT [GOC:mah]
synonym: "MDA5 signaling pathway" NARROW [PMID:17328678]
synonym: "melanoma differentiation-associated gene 5 signaling pathway" EXACT [HGNC:18873]
-is_a: GO:0039528 ! cytoplasmic pattern recognition receptor signaling pathway in response to virus
+is_a: GO:0002753 ! cytosolic pattern recognition receptor signaling pathway
[Term]
id: GO:0039531
name: regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the series of molecular signals generated as a consequence of a virus or viral RNA binding to a pattern recognition receptor (PRR) located in the cytoplasm." [GOC:bf, GOC:jl]
+def: "Any process that modulates the frequency, rate or extent of a cytoplasmic pattern recognition receptor signaling pathway in response to a virus." [GOC:bf, GOC:jl]
synonym: "regulation of MAV signaling" RELATED [GOC:bf, GOC:sp]
synonym: "regulation of viral-induced cytoplasmic pattern recognition receptor signalling pathway" EXACT [GOC:mah]
-is_a: GO:0002831 ! regulation of response to biotic stimulus
-is_a: GO:0032101 ! regulation of response to external stimulus
is_a: GO:0062207 ! regulation of pattern recognition receptor signaling pathway
-is_a: GO:1902531 ! regulation of intracellular signal transduction
-relationship: regulates GO:0039528 ! cytoplasmic pattern recognition receptor signaling pathway in response to virus
+relationship: regulates GO:0002753 ! cytosolic pattern recognition receptor signaling pathway
[Term]
id: GO:0039532
name: negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the series of molecular signals generated as a consequence of a virus or viral RNA binding to a pattern recognition receptor (PRR) located in the cytoplasm." [GOC:bf, GOC:jl]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the series of a cytoplasmic pattern recognition receptor signaling pathway in response to a virus." [GOC:bf, GOC:jl]
synonym: "negative regulation of cytoplasmic pattern recognition receptor signaling pathway in response to virus" EXACT [GOC:bf]
synonym: "negative regulation of MAVS signaling" RELATED [GOC:bf]
synonym: "negative regulation of viral-induced cytoplasmic pattern recognition receptor signalling pathway" EXACT [GOC:mah]
+is_a: GO:0002683 ! negative regulation of immune system process
+is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:0039531 ! regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
is_a: GO:0050687 ! negative regulation of defense response to virus
-is_a: GO:1902532 ! negative regulation of intracellular signal transduction
-relationship: negatively_regulates GO:0039528 ! cytoplasmic pattern recognition receptor signaling pathway in response to virus
+relationship: negatively_regulates GO:0002753 ! cytosolic pattern recognition receptor signaling pathway
[Term]
id: GO:0039533
@@ -220570,7 +220544,7 @@ relationship: regulates GO:0039530 ! MDA-5 signaling pathway
id: GO:0039534
name: negative regulation of MDA-5 signaling pathway
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) MDA-5 (also known as IFIH1) binding to viral RNA." [GOC:bf, GOC:jl]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the series of the MDA-5 signaling pathway." [GOC:bf, GOC:jl]
synonym: "negative regulation of IFIH1 signaling pathway" EXACT [HGNC:18873]
synonym: "negative regulation of MDA-5 signalling pathway" EXACT [GOC:mah]
synonym: "negative regulation of MDA5 signaling pathway" EXACT [PMID:17328678]
@@ -220583,7 +220557,7 @@ relationship: negatively_regulates GO:0039530 ! MDA-5 signaling pathway
id: GO:0039535
name: regulation of RIG-I signaling pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) RIG-1 (also known as DDX58) binding to viral RNA." [GOC:bf, GOC:jl]
+def: "Any process that modulates the frequency, rate or extent of the RIG-I signaling pathway." [GOC:bf, GOC:jl]
synonym: "regulation of DDX58 signaling pathway" EXACT [HGNC:19102]
synonym: "regulation of retinoic acid inducible gene I signaling pathway" EXACT [HGNC:19102]
synonym: "regulation of RIG-I signalling pathway" EXACT [GOC:mah]
@@ -220594,7 +220568,7 @@ relationship: regulates GO:0039529 ! RIG-I signaling pathway
id: GO:0039536
name: negative regulation of RIG-I signaling pathway
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) RIG-1 (also known as DDX58) binding to viral RNA." [GOC:bf, GOC:jl]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the RIG-I signaling pathway." [GOC:bf, GOC:jl]
synonym: "negative regulation of DDX58 signaling pathway" EXACT [HGNC:19102]
synonym: "negative regulation of retinoic acid inducible gene I signaling pathway" EXACT [HGNC:19102]
synonym: "negative regulation of RIG-I signalling pathway" EXACT [GOC:mah]
@@ -220606,7 +220580,7 @@ relationship: negatively_regulates GO:0039529 ! RIG-I signaling pathway
id: GO:0039537
name: suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the series of molecular signals generated as a consequence of a virus or viral RNA binding to a pattern recognition receptor (PRR) located in the cytoplasm. This is a mechanism by which the virus evades the host innate immune response." [GOC:bf, GOC:jl]
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the host viral-induced cytoplasmic pattern recognition receptor signaling pathway. This is a mechanism by which the virus evades the host innate immune response." [GOC:bf, GOC:jl]
synonym: "suppression by virus of host cytoplasmic pattern recognition receptor signaling pathway in response to virus" EXACT [GOC:bf]
synonym: "suppression by virus of host RIG-I-like receptor (RLR) signaling pathway" RELATED [GOC:bf]
synonym: "suppression by virus of host RIG-I/MDA5 signaling pathway" RELATED [GOC:bf]
@@ -220693,16 +220667,6 @@ comment: The reason for obsoleting this term is that it is too specific. The exa
synonym: "viral protease cleavage of MAVS" EXACT [PMID:22238314]
is_obsolete: true
-[Term]
-id: GO:0039547
-name: suppression by virus of host TRAF activity
-namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the activity of a host TRAF (tumor necrosis factor receptor-associated factor) protein. TRAFs are intracellular signal transducers that lie downstream of receptors including RIG-I, MDA-5 and Toll-like receptors (TLR) and transfer the signal to other intracellular signaling components." [GOC:bf, UniProtKB-KW:KW-1110, VZ:715]
-comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response.
-synonym: "inhibition of host TRAFs by virus" EXACT [UniProtKB-KW:KW-1110]
-is_a: GO:0039507 ! suppression by virus of host molecular function
-relationship: part_of GO:0039527 ! suppression by virus of host TRAF-mediated signal transduction
-
[Term]
id: GO:0039548
name: suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity
@@ -220754,16 +220718,18 @@ is_a: GO:0005102 ! signaling receptor binding
[Term]
id: GO:0039553
-name: suppression by virus of host chemokine activity
+name: obsolete suppression by virus of host chemokine activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host chemokine activity." [GOC:bf, GOC:sp, UniProtKB-KW:KW-1086, VZ:813]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host chemokine activity." [GOC:bf, GOC:sp, UniProtKB-KW:KW-1086, VZ:813]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down-regulation by virus of host chemokine activity" EXACT [GOC:bf]
synonym: "downregulation by virus of host chemokine activity" EXACT [GOC:bf]
synonym: "inhibition by virus of host chemokine activity" NARROW [GOC:bf]
synonym: "inhibition of host chemokines by virus" NARROW [UniProtKB-KW:KW-1086]
synonym: "negative regulation by virus of host chemokine activity" EXACT [GOC:bf]
xref: VZ:813 "Inhibition of host chemokines by virus"
-is_a: GO:0039518 ! suppression by virus of host cytokine activity
+is_obsolete: true
+consider: GO:0052170
[Term]
id: GO:0039554
@@ -220972,10 +220938,9 @@ synonym: "inhibition of host complement activation by virus" EXACT [GOC:bf]
synonym: "inhibition of host complement cascade by virus" EXACT [GOC:bf]
synonym: "inhibition of host complement factors by virus" BROAD [UniProtKB-KW:KW-1087]
xref: VZ:811 "Inhibition of host complement factors by virus"
-is_a: GO:0030683 ! mitigation of host immune response by virus
-is_a: GO:0045916 ! negative regulation of complement activation
-is_a: GO:0050794 ! regulation of cellular process
+is_a: GO:0019049 ! mitigation of host antiviral defense response
is_a: GO:0075528 ! modulation by virus of host immune response
+relationship: negatively_regulates GO:0006956 ! complement activation
[Term]
id: GO:0039574
@@ -221025,7 +220990,7 @@ is_obsolete: true
id: GO:0039578
name: obsolete suppression by virus of host JAK1 activity via JAK1 binding
namespace: biological_process
-def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host JAK1 (Janus Kinase 1) activity by interacting directly and selectively with JAK1. For example, the polyoma virus T antigen binds to JAK1 and renders it inactive." [PMID:9448289]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host JAK1 (Janus Kinase 1) activity by interacting directly and selectively with JAK1. For example, the polyoma virus T antigen binds to JAK1 and renders it inactive." [PMID:9448289]
comment: The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
is_obsolete: true
@@ -221041,7 +221006,7 @@ is_a: GO:0039503 ! suppression by virus of host innate immune response
id: GO:0039580
name: suppression by virus of host PKR signaling
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host PKR (Protein Kinase regulated by RNA) signaling. Host PKR signaling includes targets such as the translation initiation factor eIF2alpha, inhibiting protein synthesis as an antiviral response." [PMID:15207627]
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host PKR (Protein Kinase regulated by RNA) signaling. Host PKR signaling includes targets such as the translation initiation factor eIF2alpha, inhibiting protein synthesis as an antiviral response." [PMID:15207627]
synonym: "suppression by virus of host EIF2AK2 activity" NARROW []
synonym: "suppression by virus of host PKR activity" NARROW []
is_a: GO:0019057 ! modulation by virus of host translation
@@ -221079,12 +221044,11 @@ is_obsolete: true
[Term]
id: GO:0039584
-name: suppression by virus of host protein kinase activity
+name: obsolete suppression by virus of host protein kinase activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host protein kinase activity." [GOC:bf]
-is_a: GO:0039513 ! suppression by virus of host catalytic activity
-is_a: GO:0039613 ! suppression by virus of host protein phosphorylation
-is_a: GO:0043086 ! negative regulation of catalytic activity
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host protein kinase activity." [GOC:bf]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
+is_obsolete: true
[Term]
id: GO:0039585
@@ -221101,13 +221065,14 @@ is_a: GO:0140467 ! integrated stress response signaling
[Term]
id: GO:0039586
-name: modulation by virus of host PP1 activity
+name: obsolete modulation by virus of host PP1 activity
namespace: biological_process
-def: "The process in which a virus effects a change in host protein phosphatase-1 (PP1) activity, a serine/threonine phosphatase. Different viruses modulate host PP1 activity to remove phosphates from various cellular substrates and downregulate the host's antiviral response." [UniProtKB-KW:KW-1126, VZ:803]
+def: "OBSOLETE. The process in which a virus effects a change in host protein phosphatase-1 (PP1) activity, a serine/threonine phosphatase. Different viruses modulate host PP1 activity to remove phosphates from various cellular substrates and downregulate the host's antiviral response." [UniProtKB-KW:KW-1126, VZ:803]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
synonym: "modulation of host PP1 activity by virus" EXACT [UniProtKB-KW:KW-1126]
synonym: "regulation by virus of host PP1 activity" EXACT [GOC:bf]
xref: VZ:803 "Modulation of host PP1 activity by virus"
-is_a: GO:0039517 ! modulation by virus of host protein serine/threonine phosphatase activity
+is_obsolete: true
[Term]
id: GO:0039587
@@ -221115,7 +221080,7 @@ name: suppression by virus of host tetherin activity
namespace: biological_process
def: "Any process in which a virus stops, prevents, or reduces the activity of host tetherin activity. Tetherin (also known as BST2) is an alpha interferon-inducible cellular factor that impairs the release of many enveloped viruses. By blocking tetherin activity, many viruses circumvent its antiviral effects." [PMID:22493439]
synonym: "inhibition of host BST2/Tetherin by virus" EXACT []
-is_a: GO:0019049 ! mitigation of host defenses by virus
+is_a: GO:0019049 ! mitigation of host antiviral defense response
[Term]
id: GO:0039588
@@ -221161,7 +221126,7 @@ name: endoribonuclease activity involved in viral induction of host mRNA catabol
namespace: molecular_function
def: "Any endoribonuclease activity that contributes to the viral-induced catabolism of host mRNA." [GOC:bf, PMID:22046136]
comment: GO:0039594 can be used to annotate a host or viral endoribonuclease activity that cleaves host mRNA in response to a viral infection.
-is_a: GO:0004521 ! endoribonuclease activity
+is_a: GO:0004521 ! RNA endonuclease activity
[Term]
id: GO:0039595
@@ -221174,17 +221139,16 @@ synonym: "promotion of host mRNA degradation" EXACT []
synonym: "viral induction of host mRNA decay" EXACT [GOC:bf]
synonym: "virus-mediated mRNA decay" EXACT [VZ:901]
xref: VZ:901 "Virus-mediated host mRNA decay"
-is_a: GO:0019054 ! modulation by virus of host cellular process
is_a: GO:0039656 ! modulation by virus of host gene expression
is_a: GO:0061014 ! positive regulation of mRNA catabolic process
[Term]
id: GO:0039596
-name: modulation by virus of host protein dephosphorylation
+name: obsolete modulation by virus of host protein dephosphorylation
namespace: biological_process
-def: "Any viral process that modulates the frequency, rate or extent of dephosphorylation of a host protein." [GOC:bf]
-is_a: GO:0019054 ! modulation by virus of host cellular process
-is_a: GO:0035304 ! regulation of protein dephosphorylation
+def: "OBSOLETE. Any viral process that modulates the frequency, rate or extent of dephosphorylation of a host protein." [GOC:bf]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
+is_obsolete: true
[Term]
id: GO:0039597
@@ -221206,25 +221170,6 @@ synonym: "induction by virus of host nuclear polyadenylation-dependent mRNA cata
synonym: "virus-mediated host mRNA decay by hyperadenylation" NARROW [GOC:sp]
is_obsolete: true
-[Term]
-id: GO:0039599
-name: cleavage by virus of host mRNA
-namespace: biological_process
-def: "Any process in which a host pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner by a viral endoribonuclease." [PMID:22046136]
-synonym: "host mRNA cleavage by viral endoribonuclease" EXACT [GOC:bf]
-synonym: "viral endoribonuclease activity involved in degradation of host mRNA" RELATED [GOC:bf]
-is_a: GO:0019048 ! modulation by virus of host process
-
-[Term]
-id: GO:0039600
-name: induction by virus of host endonucleolytic cleavage-dependent mRNA catabolic process
-namespace: biological_process
-def: "The process in which a virus increases the frequency, rate or extent of the breakdown of host nuclear-transcribed mRNAs that begins with endonucleolytic cleavage (by either a host or a viral RNAse) to generate unprotected ends." [GOC:bf, PMID:22174690]
-comment: Some viruses utilize a host RNase to induce endonucleolytic cleavage of template mRNAs (e.g. the NSP1 protein of SARS coronavirus); for these consider instead annotating to the child term 'induction by virus of host endoribonuclease activity ; GO:0039597'. Other viral proteins act as endonucleases themselves to cleave mRNA and then rely on the host degradation machinery to clear the resulting fragments (e.g. gamma herpesvirus SOX protein); for these cases consider instead annotating to the child term 'endoribonuclease activity involved in viral induction of host mRNA catabolic process ; GO:0039594'.
-synonym: "induction by virus of host endonucleolytic cleavage-dependent mRNA decay" EXACT [GOC:bf]
-synonym: "induction by virus of host nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay" EXACT [GOC:bf]
-is_a: GO:0039595 ! induction by virus of catabolism of host mRNA
-
[Term]
id: GO:0039602
name: suppression by virus of host transcription initiation from RNA polymerase II promoter
@@ -221248,12 +221193,20 @@ is_obsolete: true
id: GO:0039604
name: suppression by virus of host translation
namespace: biological_process
-def: "Any process in which a virus prevents or reduces the frequency, rate or extent of translation of host mRNA." [UniProtKB-KW:KW-1193, VZ:1579]
+alt_id: GO:0039599
+alt_id: GO:0039600
+def: "Any process in which a virus prevents or reduces the frequency, rate or extent of translation of host mRNA, for example by cleavage of the host mRNAs." [PMID:22046136, PMID:22174690]
+synonym: "cleavage by virus of host mRNA" NARROW []
+synonym: "host mRNA cleavage by viral endoribonuclease" NARROW [GOC:bf]
synonym: "host translation shutoff by virus" EXACT [UniProtKB-KW:KW-1193, VZ:1579]
+synonym: "induction by virus of host endonucleolytic cleavage-dependent mRNA catabolic process" NARROW []
+synonym: "induction by virus of host endonucleolytic cleavage-dependent mRNA decay" NARROW [GOC:bf]
+synonym: "viral endoribonuclease activity involved in degradation of host mRNA" NARROW [GOC:bf]
synonym: "viral inhibition of cellular protein synthesis" EXACT [VZ:1579]
synonym: "viral shutoff of host protein synthesis" EXACT [PMID:8643618]
xref: VZ:1579 "Translation shutoff"
is_a: GO:0019057 ! modulation by virus of host translation
+is_a: GO:0039595 ! induction by virus of catabolism of host mRNA
is_a: GO:0039657 ! suppression by virus of host gene expression
[Term]
@@ -221293,41 +221246,41 @@ is_obsolete: true
[Term]
id: GO:0039611
-name: suppression by virus of host translation initiation factor activity
+name: obsolete suppression by virus of host translation initiation factor activity
namespace: biological_process
-def: "Any process in which a virus prevents or reduces the frequency, rate or extent of activity of a host translation initiation factor." [GOC:bf, UniProtKB-KW:KW-1075]
+def: "OBSOLETE. Any process in which a virus prevents or reduces the frequency, rate or extent of activity of a host translation initiation factor." [GOC:bf, UniProtKB-KW:KW-1075]
+comment: This term has been obsoleted because it represents a molecular function as a biological process.
synonym: "inactivation of eIF2 activity" NARROW [PMID:12239292]
synonym: "inhibition of activity of host translation initiation factor" EXACT [PMID:12239292]
synonym: "Inhibition of host translation factors by virus" BROAD [UniProtKB-KW:KW-1075]
synonym: "suppression by virus of host EIF-4E activity" EXACT [GOC:bf]
-is_a: GO:0039507 ! suppression by virus of host molecular function
-is_a: GO:0039606 ! suppression by virus of host translation initiation
-is_a: GO:0043086 ! negative regulation of catalytic activity
+is_obsolete: true
+replaced_by: GO:0039606
[Term]
id: GO:0039612
-name: modulation by virus of host protein phosphorylation
+name: obsolete modulation by virus of host protein phosphorylation
namespace: biological_process
-def: "Any viral process that modulates the frequency, rate or extent of phosphorylation of viral or host proteins in a host." [GOC:bf]
-is_a: GO:0001932 ! regulation of protein phosphorylation
-is_a: GO:0019054 ! modulation by virus of host cellular process
+def: "OBSOLETE. Any viral process that modulates the frequency, rate or extent of phosphorylation of viral or host proteins in a host." [GOC:bf]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
+is_obsolete: true
[Term]
id: GO:0039613
-name: suppression by virus of host protein phosphorylation
+name: obsolete suppression by virus of host protein phosphorylation
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of phosphorylation of viral or host proteins in a host." [GOC:bf]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of phosphorylation of viral or host proteins in a host." [GOC:bf]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
synonym: "viral inhibition of host protein phosphorylation" EXACT [GOC:bf]
-is_a: GO:0001933 ! negative regulation of protein phosphorylation
-is_a: GO:0039612 ! modulation by virus of host protein phosphorylation
+is_obsolete: true
[Term]
id: GO:0039614
-name: induction by virus of host protein phosphorylation
+name: obsolete induction by virus of host protein phosphorylation
namespace: biological_process
-def: "Any process in which a virus activates or increases the frequency, rate or extent of phosphorylation of viral or host proteins in a host." [GOC:bf]
-is_a: GO:0001934 ! positive regulation of protein phosphorylation
-is_a: GO:0039612 ! modulation by virus of host protein phosphorylation
+def: "OBSOLETE. Any process in which a virus activates or increases the frequency, rate or extent of phosphorylation of viral or host proteins in a host." [GOC:bf]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
+is_obsolete: true
[Term]
id: GO:0039615
@@ -221463,30 +221416,34 @@ is_a: GO:0008186 ! ATP-dependent activity, acting on RNA
[Term]
id: GO:0039631
-name: DNA translocase activity involved in viral DNA genome packaging
+name: obsolete DNA translocase activity involved in viral DNA genome packaging
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule, that contributes to the packing of viral DNA into a capsid." [GOC:bm, PMID:17501915]
+def: "OBSOLETE. Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule, that contributes to the packing of viral DNA into a capsid." [GOC:bm, PMID:17501915]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
synonym: "viral DNA packaging activity" RELATED [GOC:bm]
synonym: "viral DNA packaging motor activity" RELATED [PMID:17501915]
-is_a: GO:0015616 ! DNA translocase activity
+is_obsolete: true
[Term]
id: GO:0039632
-name: RNA translocase activity involved in viral RNA genome packaging
+name: obsolete RNA translocase activity involved in viral RNA genome packaging
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded RNA molecule, which contributes to the packaging of viral RNA into a nucleocapsid." [GOC:bm, PMID:22297533]
+def: "OBSOLETE. Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded RNA molecule, which contributes to the packaging of viral RNA into a nucleocapsid." [GOC:bm, PMID:22297533]
+comment: This term was obsoleted because it represents both a molecular function and a biological process.
synonym: "RNA packaging ATPase activity" EXACT [PMID:22297533]
synonym: "viral RNA packaging activity" RELATED [GOC:bm]
-is_a: GO:0039630 ! RNA translocase activity
+is_obsolete: true
+replaced_by: GO:0039630
[Term]
id: GO:0039633
-name: killing by virus of host cell
+name: obsolete killing by virus of host cell
namespace: biological_process
-def: "Any process mediated by a virus that results in the death of a cell in the host organism." [GOC:bf, GOC:bm, GOC:jl]
+def: "OBSOLETE. Any process mediated by a virus that results in the death of a cell in the host organism." [GOC:bf, GOC:bm, GOC:jl]
+comment: This term was obsoleted because it was redundant with other terms.
synonym: "killing by phage of host cells" NARROW [GOC:bm]
synonym: "killing by virus of host cells" EXACT []
-is_a: GO:0001907 ! killing by symbiont of host cells
+is_obsolete: true
[Term]
id: GO:0039634
@@ -221496,8 +221453,8 @@ def: "The viral-killing of a host cell by a pre-existing virus in response to a
synonym: "killing by virus of host cells during superinfection exclusion" EXACT []
synonym: "killing by virus of host cells involved in superinfection exclusion" EXACT [GOC:bf]
synonym: "Rex exclusion" NARROW []
+is_a: GO:0001907 ! killing by symbiont of host cells
is_a: GO:0009615 ! response to virus
-is_a: GO:0039633 ! killing by virus of host cell
[Term]
id: GO:0039635
@@ -221538,16 +221495,16 @@ namespace: biological_process
def: "The prevention or delay of host cell lysis by a pre-existing virus in response to a subsequent infection of the host cell by second virus." [GOC:bm, GOC:jl, PMID:22389108, PMID:9560373]
synonym: "lysis inhibition" BROAD [GOC:bm, PMID:22389108]
synonym: "suppression by virus of host cell lysis in response to superinfecting virus" EXACT [GOC:bf]
-is_a: GO:0001899 ! negative regulation of cytolysis by symbiont of host cells
is_a: GO:0098586 ! cellular response to virus
[Term]
id: GO:0039640
-name: viral release by cytolysis via suppression of host peptidoglycan biosynthetic process
+name: viral release via suppression of host peptidoglycan biosynthetic process
namespace: biological_process
-def: "The killing by a virus of host cell by cytolysis, caused by a virus stopping, preventing, or reducing peptidoglycan biosynthesis in the host organism. Peptidoglycans are any of a class of glycoconjugates found in bacterial cell walls." [GOC:bf, GOC:bm, PMID:28894177]
+def: "The dissemination of mature viral particles from a host cell, caused by a virus stopping, preventing, or reducing peptidoglycan biosynthesis in the host organism. Peptidoglycans are any of a class of glycoconjugates found in bacterial cell walls." [GOC:bf, GOC:bm, PMID:28894177]
synonym: "cytolysis by virus via suppression of host peptidoglycan biosynthetic process" RELATED []
synonym: "viral exit by cytolysis via suppression of host peptidoglycan biosynthetic process" EXACT []
+synonym: "viral release by cytolysis via suppression of host peptidoglycan biosynthetic process" EXACT []
is_a: GO:0044659 ! viral release from host cell by cytolysis
[Term]
@@ -221580,8 +221537,7 @@ namespace: biological_process
def: "Any process in which a virus stops, prevents, or reduces a host NF-kappaB cascade." [PMID:10920188, PMID:25275128]
synonym: "inhibition of host NF-kappa-B by virus" EXACT []
synonym: "suppression by virus of host NF-kappaB transcription factor activity" RELATED []
-is_a: GO:0019049 ! mitigation of host defenses by virus
-is_a: GO:0019054 ! modulation by virus of host cellular process
+is_a: GO:0019049 ! mitigation of host antiviral defense response
[Term]
id: GO:0039645
@@ -221614,39 +221570,22 @@ consider: GO:0039604
[Term]
id: GO:0039648
-name: modulation by virus of host protein ubiquitination
+name: modulation by symbiont of host protein ubiquitination
namespace: biological_process
-def: "Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein." [UniProtKB-KW:KW-1130]
-synonym: "modulation of host ubiquitin pathway by virus" RELATED [UniProtKB-KW:KW-1130]
+def: "Any process by which a symbiont increases or decreases ubiquitination of target proteins of a host organism." [PMID:25166298, PMID:26483404, PMID:26712804]
+synonym: "modulation of host ubiquitin pathway by virus" RELATED []
is_a: GO:0019054 ! modulation by virus of host cellular process
relationship: regulates GO:0016567 ! protein ubiquitination
[Term]
id: GO:0039649
-name: modulation by virus of host ubiquitin-protein ligase activity
+name: obsolete modulation by virus of host ubiquitin-protein ligase activity
namespace: biological_process
-def: "The process in which a virus effects a change in host ubiquitin-protein ligase activity. Ubiquitin-protein ligase activity catalyzes the reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine." [UniProtKB-KW:KW-1123]
+def: "OBSOLETE. The process in which a virus effects a change in host ubiquitin-protein ligase activity. Ubiquitin-protein ligase activity catalyzes the reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine." [UniProtKB-KW:KW-1123]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "modulation of host E3 ubiquitin ligases by virus" NARROW [UniProtKB-KW:KW-1123]
-is_a: GO:0039516 ! modulation by virus of host catalytic activity
-
-[Term]
-id: GO:0039650
-name: suppression by virus of host cysteine-type endopeptidase activity involved in apoptotic process
-namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host caspase activity. Caspases are cysteine-type endopeptidases which contribute to the apoptotic process." [UniProtKB-KW:KW-1085, VZ:912]
-synonym: "inhibition of host caspases by virus" NARROW [UniProtKB-KW:KW-1085, VZ:912]
-is_a: GO:0019050 ! suppression by virus of host apoptotic process
-is_a: GO:0039513 ! suppression by virus of host catalytic activity
-is_a: GO:0043086 ! negative regulation of catalytic activity
-
-[Term]
-id: GO:0039651
-name: induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process
-namespace: biological_process
-def: "Any process in which a virus increases the frequency, rate or extent of host cysteine-type endopeptidase activity (also called caspase activity) which contributes to the apoptotic process." [GOC:mtg_apoptosis, UniProtKB-KW:KW-1073]
-synonym: "activation of host caspases by virus" NARROW [UniProtKB-KW:KW-1073]
-synonym: "induction by virus of host caspase activity" NARROW [GOC:bf, GOC:jl]
-is_a: GO:0019051 ! induction by virus of host apoptotic process
+is_obsolete: true
+replaced_by: GO:0039648
[Term]
id: GO:0039652
@@ -221669,7 +221608,6 @@ synonym: "suppression by virus of host DNA-dependent transcription" EXACT [GOC:b
xref: VZ:1577 "Host transcription shutoff by virus"
is_a: GO:0019056 ! modulation by virus of host transcription
is_a: GO:0039657 ! suppression by virus of host gene expression
-is_a: GO:0050794 ! regulation of cellular process
[Term]
id: GO:0039654
@@ -221705,7 +221643,7 @@ name: modulation by virus of host gene expression
namespace: biological_process
def: "The process in which a virus effects a change in gene expression in its host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form." [GOC:bf]
synonym: "regulation by virus of host gene expression" RELATED [GOC:bf]
-is_a: GO:0019048 ! modulation by virus of host process
+is_a: GO:0019054 ! modulation by virus of host cellular process
relationship: regulates GO:0010467 ! gene expression
[Term]
@@ -221717,6 +221655,7 @@ synonym: "host gene expression shutoff by virus" EXACT [UniProtKB-KW:KW-1190, VZ
xref: VZ:1582 "Host gene expression shutoff by virus"
is_a: GO:0010629 ! negative regulation of gene expression
is_a: GO:0039656 ! modulation by virus of host gene expression
+is_a: GO:0050794 ! regulation of cellular process
[Term]
id: GO:0039658
@@ -221854,7 +221793,7 @@ synonym: "modulation of host NK-cell activity by virus" RELATED [UniProtKB-KW:KW
synonym: "protection by virus against host NK cell cytotoxicity" EXACT [PMID:12782710]
synonym: "suppression by virus of host natural killer cell function" EXACT [PMID:15640804]
synonym: "viral immunoevasion of host NK cell" EXACT [GOC:bf]
-is_a: GO:0030683 ! mitigation of host immune response by virus
+is_a: GO:0019049 ! mitigation of host antiviral defense response
[Term]
id: GO:0039672
@@ -221862,7 +221801,6 @@ name: suppression by virus of host natural killer cell activation
namespace: biological_process
def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of natural killer cell activation in the host." [GOC:bf, GOC:jl]
synonym: "suppression by virus of host NK-cell activation" EXACT [GOC:bf, GOC:jl]
-is_a: GO:0019054 ! modulation by virus of host cellular process
is_a: GO:0032815 ! negative regulation of natural killer cell activation
is_a: GO:0039671 ! evasion by virus of host natural killer cell activity
@@ -221874,7 +221812,7 @@ def: "Any process by which a virus avoids the effects mediated by the host organ
synonym: "evasion by virus of host dendritic cell response" EXACT []
synonym: "impairing dendritic cell function by virus" EXACT [UniProtKB-KW:KW-1118]
synonym: "modulation of host dendritic cell activity by virus" BROAD [UniProtKB-KW:KW-1118]
-is_a: GO:0030683 ! mitigation of host immune response by virus
+is_a: GO:0019049 ! mitigation of host antiviral defense response
[Term]
id: GO:0039674
@@ -222042,6 +221980,7 @@ synonym: "DNA-dependent viral DNA replication" EXACT [GOC:bf, GOC:jl]
synonym: "viral DNA replication" EXACT [GOC:bf, GOC:jl]
synonym: "viral DNA-dependent DNA replication" EXACT []
is_a: GO:0019079 ! viral genome replication
+is_a: GO:0071897 ! DNA biosynthetic process
[Term]
id: GO:0039694
@@ -222049,6 +221988,7 @@ name: viral RNA genome replication
namespace: biological_process
def: "The replication of a viral RNA genome." [GOC:bf, GOC:jl]
is_a: GO:0019079 ! viral genome replication
+is_a: GO:0032774 ! RNA biosynthetic process
[Term]
id: GO:0039695
@@ -222086,9 +222026,9 @@ is_a: GO:0043631 ! RNA polyadenylation
id: GO:0039699
name: viral mRNA cap methylation
namespace: biological_process
-def: "Methylation of the 2'-O-ribose of the first or second transcribed nucleotide of a viral mRNA. Methylation allows evasion of the host innate immune response, which degrades cap0 (non-methylated) mRNAs." [UniProtKB-KW:KW-1196]
-synonym: "IFIT mRNA restriction evasion by virus" EXACT [UniProtKB-KW:KW-1196]
-is_a: GO:0039503 ! suppression by virus of host innate immune response
+def: "An innate immune response evasion mechanism in which a virus methylates the 2'-O-ribose of the first or second transcribed nucleotide of its mRNAs. Methylation allows evasion of the host innate immune response, which degrades cap0 (non-methylated) mRNAs." [PMID:35215972]
+synonym: "IFIT mRNA restriction evasion by virus" EXACT [PMID:35215972]
+is_a: GO:0019049 ! mitigation of host antiviral defense response
[Term]
id: GO:0039700
@@ -222599,12 +222539,13 @@ relationship: regulates GO:0040025 ! vulval development
[Term]
id: GO:0040029
-name: regulation of gene expression, epigenetic
+name: epigenetic regulation of gene expression
namespace: biological_process
-def: "A process that modulates the frequency, rate or extent of gene expression by remodelling of chromatin by either modifying the chromatin fiber, the nucleosomal histones, or the DNA. Once established, this regulation may be maintained over many cell divisions. It can also be heritable in the absence of the instigating signal." [PMID:10521337, PMID:11498582, PMID:22243696, PMID:34414474]
+def: "A process that modulates the frequency, rate or extent of gene expression through chromatin remodelling either by modifying higher order chromatin fiber structure, nucleosomal histones, or the DNA. Once established, this regulation may be maintained over many cell divisions. It can also be heritable in the absence of the instigating signal." [PMID:10521337, PMID:11498582, PMID:22243696, PMID:34414474]
subset: goslim_plant
+synonym: "regulation of gene expression, epigenetic" EXACT []
+is_a: GO:0006338 ! chromatin remodeling
is_a: GO:0010468 ! regulation of gene expression
-relationship: part_of GO:0006325 ! chromatin organization
[Term]
id: GO:0040030
@@ -222634,16 +222575,16 @@ is_a: GO:0010171 ! body morphogenesis
[Term]
id: GO:0040033
-name: RNA-mediated gene silencing by inhibition of translation
-namespace: biological_process
-def: "Any process, mediated by small non-coding RNAs, that stops, prevents or reduces the rate that mRNAs are effectively translated into protein." [GOC:dph, GOC:ems, GOC:tb]
-synonym: "down regulation of mRNA translation, ncRNA-mediated" EXACT []
-synonym: "down-regulation of mRNA translation, ncRNA-mediated" EXACT []
-synonym: "downregulation of mRNA translation, ncRNA-mediated" EXACT []
-synonym: "inhibition of mRNA translation, ncRNA-mediated" NARROW []
-synonym: "negative regulation of translation, ncRNA-mediated" EXACT []
-is_a: GO:0017148 ! negative regulation of translation
-is_a: GO:0035194 ! post-transcriptional gene silencing by RNA
+name: sRNA-mediated gene silencing
+namespace: biological_process
+def: "A post-transcriptional gene silencing pathway mediated by the action of small regulatory non-coding RNAs (sRNAs). sRNAs are 20-500 nucleotides in length and found in bacteria." [PMID:12460531, PMID:2468565, PMID:33963446]
+comment: It is postulated that there 3 mechanisms of sRNA-mediated gene silencing: (i) translation inhibition, (ii) RNA destabilization, and (iii) transcription termination loop formation (as this is common when looking at riboswitches). sRNA mediated gene silencing is sometimes referred to as 'regulation of riboswitch'.
+subset: prokaryote_subset
+synonym: "downregulation of mRNA translation, ncRNA-mediated" BROAD []
+synonym: "inhibition of mRNA translation, ncRNA-mediated" BROAD []
+synonym: "RNA-mediated gene silencing by inhibition of translation" BROAD []
+synonym: "small RNA-mediated gene silencing" EXACT []
+is_a: GO:0035194 ! ncRNA-mediated post-transcriptional gene silencing
[Term]
id: GO:0040034
@@ -222657,11 +222598,12 @@ is_a: GO:0050793 ! regulation of developmental process
[Term]
id: GO:0040035
-name: hermaphrodite genitalia development
+name: obsolete hermaphrodite genitalia development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the hermaphrodite genitalia over time, from formation to the mature structures." [GOC:ems, ISBN:0140512888]
-is_a: GO:0008406 ! gonad development
-is_a: GO:0048806 ! genitalia development
+def: "OBSOLETE. The process whose specific outcome is the progression of the hermaphrodite genitalia over time, from formation to the mature structures." [GOC:ems, ISBN:0140512888]
+comment: The reason for obsoletion is that this term maybe redundant with female genitalia development.
+is_obsolete: true
+consider: GO:0030540
[Term]
id: GO:0040036
@@ -222729,7 +222671,6 @@ synonym: "translocation of peptides or proteins into other organism during symbi
synonym: "translocation of peptides or proteins into other organism involved in symbiotic interaction" BROAD []
synonym: "transport of peptides or proteins into host" EXACT []
synonym: "transport of peptides or proteins into other organism during symbiotic interaction" BROAD []
-is_a: GO:0015031 ! protein transport
is_a: GO:0044417 ! translocation of molecules into host
[Term]
@@ -222898,7 +222839,6 @@ def: "A protein complex that binds interleukin-12 and that consists of, at a min
synonym: "IL-12 receptor complex" EXACT [GOC:add]
synonym: "IL12RB1-IL12RB2 complex" NARROW [CORUM:2026]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0042023
@@ -222955,7 +222895,7 @@ name: ATPase inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents or reduces an ATP hydrolysis activity." [GOC:jl]
synonym: "adenosinetriphosphatase inhibitor" EXACT []
-is_a: GO:0140678 ! molecular function inhibitor activity
+is_a: GO:0060590 ! ATPase regulator activity
[Term]
id: GO:0042031
@@ -222971,14 +222911,12 @@ replaced_by: GO:0060422
[Term]
id: GO:0042034
-name: peptidyl-L-lysine methyl ester biosynthetic process from peptidyl-lysine
+name: obsolete peptidyl-L-lysine methyl ester biosynthetic process from peptidyl-lysine
namespace: biological_process
-def: "The modification of a C-terminal peptidyl-lysine to form peptidyl-L-lysine methyl ester." [RESID:AA0318]
+def: "OBSOLETE. The modification of a C-terminal peptidyl-lysine to form peptidyl-L-lysine methyl ester." [RESID:AA0318]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-lysine esterification" EXACT []
-xref: RESID:AA0318
-is_a: GO:0006481 ! C-terminal protein methylation
-is_a: GO:0018205 ! peptidyl-lysine modification
-is_a: GO:0018350 ! protein esterification
+is_obsolete: true
[Term]
id: GO:0042037
@@ -223013,7 +222951,7 @@ id: GO:0042040
name: metal incorporation into metallo-molybdopterin complex
namespace: biological_process
def: "The incorporation of a metal into a metallo-molybdopterin complex." [GOC:ai]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0042042
@@ -223068,11 +223006,8 @@ synonym: "W-molybdopterin cofactor anabolism" EXACT []
synonym: "W-molybdopterin cofactor biosynthesis" EXACT []
synonym: "W-molybdopterin cofactor formation" EXACT []
synonym: "W-molybdopterin cofactor synthesis" EXACT []
-is_a: GO:0018130 ! heterocycle biosynthetic process
+is_a: GO:0032324 ! molybdopterin cofactor biosynthetic process
is_a: GO:0042046 ! W-molybdopterin cofactor metabolic process
-is_a: GO:0090407 ! organophosphate biosynthetic process
-is_a: GO:1901362 ! organic cyclic compound biosynthetic process
-is_a: GO:1901566 ! organonitrogen compound biosynthetic process
[Term]
id: GO:0042048
@@ -223089,11 +223024,12 @@ is_a: GO:0007635 ! chemosensory behavior
[Term]
id: GO:0042049
-name: cellular acyl-CoA homeostasis
+name: intracellular acyl-CoA homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of acyl-CoA within a cell or between a cell and its external environment." [GOC:ai, GOC:dph, GOC:tb]
+def: "A homeostatic process involved in the maintenance of a steady state level of acyl-CoA within a cell." [GOC:ai, GOC:dph, GOC:tb]
synonym: "cell acyl-CoA homeostasis" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0055082 ! cellular chemical homeostasis
+synonym: "cellular acyl-CoA homeostasis" EXACT []
+is_a: GO:0140979 ! intracellular nucleotide homeostasis
[Term]
id: GO:0042051
@@ -223126,10 +223062,11 @@ relationship: regulates GO:0042417 ! dopamine metabolic process
id: GO:0042054
name: histone methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or lysine residue." [GOC:curators]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or a lysine residue." [GOC:curators]
synonym: "histone methylase activity" EXACT [GOC:mah]
-xref: EC:2.1.1.354
+synonym: "histone N-methyltransferase activity" EXACT []
is_a: GO:0008276 ! protein methyltransferase activity
+is_a: GO:0140993 ! histone modifying activity
[Term]
id: GO:0042056
@@ -223259,7 +223196,8 @@ name: regulation of catecholamine metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catecholamines." [GOC:go_curators]
synonym: "regulation of catecholamine metabolism" EXACT []
-is_a: GO:0033238 ! regulation of cellular amine metabolic process
+is_a: GO:0031323 ! regulation of cellular metabolic process
+is_a: GO:0033238 ! regulation of amine metabolic process
is_a: GO:0080090 ! regulation of primary metabolic process
relationship: regulates GO:0006584 ! catecholamine metabolic process
@@ -223278,6 +223216,7 @@ synonym: "oocyte axis determination, maintenance of oocyte nucleus localization"
synonym: "oocyte axis determination, maintenance of oocyte nucleus position" BROAD []
synonym: "oocyte axis determination, oocyte nucleus anchoring" BROAD []
synonym: "oocyte nucleus anchoring during oocyte axis determination" BROAD []
+is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
is_a: GO:0051658 ! maintenance of nucleus location
is_a: GO:0051663 ! oocyte nucleus localization involved in oocyte dorsal/ventral axis specification
@@ -223660,8 +223599,8 @@ def: "The chemical reactions and pathways involving alginic acid, a hydrophilic
synonym: "alginate metabolic process" EXACT []
synonym: "alginate metabolism" EXACT []
synonym: "alginic acid metabolism" EXACT []
+is_a: GO:0005976 ! polysaccharide metabolic process
is_a: GO:0019752 ! carboxylic acid metabolic process
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
[Term]
id: GO:0042121
@@ -223674,7 +223613,7 @@ synonym: "alginic acid anabolism" EXACT []
synonym: "alginic acid biosynthesis" EXACT []
synonym: "alginic acid formation" EXACT []
synonym: "alginic acid synthesis" EXACT []
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
+is_a: GO:0000271 ! polysaccharide biosynthetic process
is_a: GO:0042120 ! alginic acid metabolic process
is_a: GO:0046394 ! carboxylic acid biosynthetic process
@@ -223688,8 +223627,8 @@ synonym: "alginate catabolism" EXACT []
synonym: "alginic acid breakdown" EXACT []
synonym: "alginic acid catabolism" EXACT []
synonym: "alginic acid degradation" EXACT []
+is_a: GO:0000272 ! polysaccharide catabolic process
is_a: GO:0042120 ! alginic acid metabolic process
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
is_a: GO:0046395 ! carboxylic acid catabolic process
[Term]
@@ -223775,10 +223714,12 @@ relationship: negatively_regulates GO:0042098 ! T cell proliferation
id: GO:0042131
name: thiamine phosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: thiamine phosphate + H2O = thiamine + phosphate." [PMID:197075]
+def: "Catalysis of the reaction: thiamine phosphate + H2O = thiamine + phosphate." [PMID:197075, RHEA:47948]
synonym: "thiamin monophosphate phosphatase" EXACT []
synonym: "thiamin phosphate phosphatase activity" EXACT []
synonym: "ThMPase" EXACT []
+xref: EC:3.1.3.100
+xref: RHEA:47948
is_a: GO:0003993 ! acid phosphatase activity
[Term]
@@ -223804,7 +223745,7 @@ synonym: "hexose diphosphatase activity" RELATED [EC:3.1.3.11]
synonym: "hexosediphosphatase activity" BROAD [EC:3.1.3.11]
xref: EC:3.1.3.11
xref: MetaCyc:F16BDEPHOS-RXN
-xref: Reactome:R-HSA-70479 "D-fructose 1,6-bisphosphate + H2O => D-fructose 6-phosphate + orthophosphate"
+xref: Reactome:R-HSA-70479 "FBP tetramers hydrolyze F1,6PP to Fru(6)P"
xref: RHEA:11064
is_a: GO:0050308 ! sugar-phosphatase activity
@@ -224015,7 +223956,7 @@ synonym: "lipoprotein anabolism" EXACT []
synonym: "lipoprotein biosynthesis" EXACT []
synonym: "lipoprotein formation" EXACT []
synonym: "lipoprotein synthesis" EXACT []
-is_a: GO:0034645 ! cellular macromolecule biosynthetic process
+is_a: GO:0009059 ! macromolecule biosynthetic process
is_a: GO:0042157 ! lipoprotein metabolic process
is_a: GO:1901566 ! organonitrogen compound biosynthetic process
@@ -224090,6 +224031,7 @@ namespace: molecular_function
def: "Binding to acetylcholine, an acetic acid ester of the organic base choline that functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions." [GOC:ai]
is_a: GO:0042165 ! neurotransmitter binding
is_a: GO:0043169 ! cation binding
+is_a: GO:0050997 ! quaternary ammonium group binding
[Term]
id: GO:0042167
@@ -224145,7 +224087,6 @@ name: regulation of sporulation resulting in formation of a cellular spore
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of spore formation." [GOC:jl]
is_a: GO:0043937 ! regulation of sporulation
-is_a: GO:0045595 ! regulation of cell differentiation
relationship: regulates GO:0030435 ! sporulation resulting in formation of a cellular spore
[Term]
@@ -224159,7 +224100,6 @@ synonym: "downregulation of sporulation" EXACT []
synonym: "inhibition of sporulation" NARROW []
is_a: GO:0042173 ! regulation of sporulation resulting in formation of a cellular spore
is_a: GO:0043939 ! negative regulation of sporulation
-is_a: GO:0045596 ! negative regulation of cell differentiation
relationship: negatively_regulates GO:0030435 ! sporulation resulting in formation of a cellular spore
[Term]
@@ -224181,7 +224121,18 @@ relationship: part_of GO:0012505 ! endomembrane system
id: GO:0042176
name: regulation of protein catabolic process
namespace: biological_process
+alt_id: GO:1903362
+alt_id: GO:2000598
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators, GOC:jl]
+synonym: "regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
+synonym: "regulation of cellular protein catabolic process" EXACT []
+synonym: "regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
+synonym: "regulation of cellular protein degradation" EXACT [GOC:TermGenie]
+synonym: "regulation of cyclin breakdown" NARROW [GOC:obol]
+synonym: "regulation of cyclin catabolic process" NARROW []
+synonym: "regulation of cyclin catabolism" NARROW [GOC:obol]
+synonym: "regulation of cyclin degradation" NARROW [GOC:obol]
+synonym: "regulation of degradation of cyclin" NARROW [GOC:obol]
synonym: "regulation of protein breakdown" EXACT []
synonym: "regulation of protein catabolism" EXACT []
synonym: "regulation of protein degradation" EXACT []
@@ -224193,11 +224144,33 @@ relationship: regulates GO:0030163 ! protein catabolic process
id: GO:0042177
name: negative regulation of protein catabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators, GOC:jl, PMID:10207076]
+alt_id: GO:1903363
+alt_id: GO:2000599
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process." [GO_REF:0000058, GOC:kmv, GOC:obol, GOC:TermGenie, PMID:24785082]
+synonym: "down regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
+synonym: "down regulation of cellular protein catabolic process" EXACT [GOC:TermGenie]
+synonym: "down regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
+synonym: "down regulation of cellular protein degradation" EXACT [GOC:TermGenie]
synonym: "down regulation of protein catabolic process" EXACT []
+synonym: "down-regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
+synonym: "down-regulation of cellular protein catabolic process" EXACT [GOC:TermGenie]
+synonym: "down-regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
+synonym: "down-regulation of cellular protein degradation" EXACT [GOC:TermGenie]
synonym: "down-regulation of protein catabolic process" EXACT []
+synonym: "downregulation of cellular protein breakdown" EXACT [GOC:TermGenie]
+synonym: "downregulation of cellular protein catabolic process" EXACT [GOC:TermGenie]
+synonym: "downregulation of cellular protein catabolism" EXACT [GOC:TermGenie]
+synonym: "downregulation of cellular protein degradation" EXACT [GOC:TermGenie]
synonym: "downregulation of protein catabolic process" EXACT []
+synonym: "inhibition of cellular protein breakdown" NARROW [GOC:TermGenie]
+synonym: "inhibition of cellular protein catabolic process" NARROW [GOC:TermGenie]
+synonym: "inhibition of cellular protein catabolism" NARROW [GOC:TermGenie]
+synonym: "inhibition of cellular protein degradation" NARROW [GOC:TermGenie]
synonym: "inhibition of protein catabolic process" NARROW []
+synonym: "negative regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
+synonym: "negative regulation of cellular protein catabolic process" EXACT []
+synonym: "negative regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
+synonym: "negative regulation of cellular protein degradation" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein breakdown" EXACT []
synonym: "negative regulation of protein catabolism" EXACT []
synonym: "negative regulation of protein degradation" EXACT []
@@ -224213,6 +224186,7 @@ namespace: biological_process
alt_id: GO:0042737
alt_id: GO:0042738
def: "The chemical reactions and pathways resulting in the breakdown of a xenobiotic compound, a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:jl, GOC:krc]
+subset: prokaryote_subset
synonym: "drug breakdown" RELATED []
synonym: "drug catabolic process" RELATED []
synonym: "drug catabolism" RELATED []
@@ -224715,7 +224689,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of 1-aminoc
synonym: "1-aminocyclopropane-1-carboxylate breakdown" EXACT []
synonym: "1-aminocyclopropane-1-carboxylate catabolism" EXACT []
synonym: "1-aminocyclopropane-1-carboxylate degradation" EXACT []
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0018871 ! 1-aminocyclopropane-1-carboxylate metabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
@@ -224757,6 +224731,7 @@ def: "Any process that results in a change in state or activity of a cell or an
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0043279 ! response to alkaloid
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0042221
@@ -224765,7 +224740,6 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus." [GOC:jl]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_manually_annotate
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_drosophila
subset: goslim_metagenomics
@@ -224876,13 +224850,13 @@ name: ribosome biogenesis
namespace: biological_process
alt_id: GO:0007046
def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis." [GOC:ma, PMID:26404467, Wikipedia:Ribosome_biogenesis]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
+subset: prokaryote_subset
synonym: "ribosome biogenesis and assembly" EXACT []
is_a: GO:0022613 ! ribonucleoprotein complex biogenesis
@@ -224891,7 +224865,7 @@ id: GO:0042255
name: ribosome assembly
namespace: biological_process
alt_id: GO:0042257
-def: "The aggregation, arrangement and bonding together of the mature ribosome and of its subunits." [GOC:ma]
+def: "The aggregation, arrangement and bonding together of the mature ribosome and of its subunits." [GOC:ma, PMID:30467428]
subset: goslim_yeast
synonym: "ribosomal subunit assembly" NARROW [GOC:mah, GOC:vw]
is_a: GO:0140694 ! non-membrane-bounded organelle assembly
@@ -224899,9 +224873,10 @@ relationship: part_of GO:0042254 ! ribosome biogenesis
[Term]
id: GO:0042256
-name: mature ribosome assembly
+name: cytosolic ribosome assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of the large and small ribosomal subunits into a functional ribosome." [GOC:ma]
+def: "The aggregation, arrangement and bonding together of the large and small ribosomal subunits into a functional cytosolic ribosome. Distinct stages of this process take place first in the nucleolus, then in the nucleus and finally in the cytosol." [GOC:ma, PMID:30467428]
+synonym: "mature ribosome assembly" EXACT []
is_a: GO:0042255 ! ribosome assembly
[Term]
@@ -224915,14 +224890,14 @@ is_a: GO:0018315 ! molybdenum incorporation into molybdenum-molybdopterin comple
[Term]
id: GO:0042259
-name: peptidyl-L-beta-methylthioasparagine biosynthetic process from peptidyl-asparagine
+name: obsolete peptidyl-L-beta-methylthioasparagine biosynthetic process from peptidyl-asparagine
namespace: biological_process
-def: "The modification of peptidyl-asparagine to form peptidyl-L-beta-methylthioasparagine, typical of bacterial ribosomal protein S12." [GOC:jsg, RESID:AA0320]
+def: "OBSOLETE. The modification of peptidyl-asparagine to form peptidyl-L-beta-methylthioasparagine, typical of bacterial ribosomal protein S12." [GOC:jsg, RESID:AA0320]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-L-beta-methylthioasparagine anabolism from peptidyl-asparagine" EXACT []
synonym: "peptidyl-L-beta-methylthioasparagine formation from peptidyl-asparagine" EXACT []
synonym: "peptidyl-L-beta-methylthioasparagine synthesis from peptidyl-asparagine" EXACT []
-xref: RESID:AA0320
-is_a: GO:0018196 ! peptidyl-asparagine modification
+is_obsolete: true
[Term]
id: GO:0042262
@@ -224953,12 +224928,12 @@ is_a: GO:0018197 ! peptidyl-aspartic acid modification
[Term]
id: GO:0042265
-name: peptidyl-asparagine hydroxylation
+name: obsolete peptidyl-asparagine hydroxylation
namespace: biological_process
-def: "The hydroxylation of peptidyl-asparagine to form peptidyl-hydroxyasparagine." [GOC:mah]
+def: "OBSOLETE. The hydroxylation of peptidyl-asparagine to form peptidyl-hydroxyasparagine." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-aspartic acid/asparagine hydroxylation" BROAD []
-is_a: GO:0018126 ! protein hydroxylation
-is_a: GO:0018196 ! peptidyl-asparagine modification
+is_obsolete: true
[Term]
id: GO:0042267
@@ -225356,7 +225331,6 @@ synonym: "regulation of protein-nucleus import" EXACT []
is_a: GO:0033157 ! regulation of intracellular protein transport
is_a: GO:0046822 ! regulation of nucleocytoplasmic transport
is_a: GO:1900180 ! regulation of protein localization to nucleus
-is_a: GO:1904589 ! regulation of protein import
relationship: regulates GO:0006606 ! protein import into nucleus
[Term]
@@ -225376,7 +225350,6 @@ is_a: GO:0042306 ! regulation of protein import into nucleus
is_a: GO:0046824 ! positive regulation of nucleocytoplasmic transport
is_a: GO:0090316 ! positive regulation of intracellular protein transport
is_a: GO:1900182 ! positive regulation of protein localization to nucleus
-is_a: GO:1904591 ! positive regulation of protein import
relationship: positively_regulates GO:0006606 ! protein import into nucleus
[Term]
@@ -225395,7 +225368,6 @@ is_a: GO:0042306 ! regulation of protein import into nucleus
is_a: GO:0046823 ! negative regulation of nucleocytoplasmic transport
is_a: GO:0090317 ! negative regulation of intracellular protein transport
is_a: GO:1900181 ! negative regulation of protein localization to nucleus
-is_a: GO:1904590 ! negative regulation of protein import
relationship: negatively_regulates GO:0006606 ! protein import into nucleus
[Term]
@@ -225539,7 +225511,6 @@ synonym: "negative regulation of sleep" EXACT []
is_a: GO:0042754 ! negative regulation of circadian rhythm
is_a: GO:0045187 ! regulation of circadian sleep/wake cycle, sleep
is_a: GO:0048521 ! negative regulation of behavior
-is_a: GO:0051241 ! negative regulation of multicellular organismal process
relationship: negatively_regulates GO:0050802 ! circadian sleep/wake cycle, sleep
[Term]
@@ -225572,11 +225543,11 @@ relationship: negatively_regulates GO:0042748 ! circadian sleep/wake cycle, non-
[Term]
id: GO:0042324
-name: hypocretin receptor binding
+name: orexin receptor binding
namespace: molecular_function
-def: "Binding to a hypocretin receptor." [GOC:ceb, PMID:11988773]
+def: "Binding to an orexin receptor." [GOC:ceb, PMID:11988773]
+synonym: "hypocretin receptor binding" EXACT []
synonym: "hypocretin receptor ligand" NARROW []
-synonym: "orexin receptor binding" EXACT []
synonym: "orexin receptor ligand" NARROW []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -226060,7 +226031,7 @@ synonym: "vitamin H catabolic process" EXACT []
synonym: "vitamin H catabolism" EXACT []
is_a: GO:0006768 ! biotin metabolic process
is_a: GO:0042365 ! water-soluble vitamin catabolic process
-is_a: GO:0043605 ! cellular amide catabolic process
+is_a: GO:0043605 ! amide catabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
is_a: GO:0046700 ! heterocycle catabolic process
is_a: GO:0072329 ! monocarboxylic acid catabolic process
@@ -226283,7 +226254,7 @@ is_a: GO:0042386 ! hemocyte differentiation
id: GO:0042388
name: gibberellic acid mediated signaling pathway, G-alpha-dependent
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of gibberellic acid and dependent on the coupling of the alpha subunit of G proteins to the hormone receptors." [GOC:pj, PMID:11027362]
+def: "The series of molecular signals mediated by the detection of gibberellic acid and dependent on the coupling of the alpha subunit of G proteins to the hormone receptors." [GOC:pj, PMID:11027362]
synonym: "gibberellic acid mediated signalling, G-alpha-dependent" EXACT []
is_a: GO:0009740 ! gibberellic acid mediated signaling pathway
@@ -226298,7 +226269,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0042390
name: gibberellic acid mediated signaling pathway, G-alpha-independent
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of gibberellic acid and not dependent on the coupling of the alpha subunit of G proteins to the hormone receptors." [GOC:pj, PMID:11027362]
+def: "The series of molecular signals mediated by the detection of gibberellic acid and not dependent on the coupling of the alpha subunit of G proteins to the hormone receptors." [GOC:pj, PMID:11027362]
synonym: "gibberellic acid mediated signalling, G-alpha-independent" EXACT []
is_a: GO:0009740 ! gibberellic acid mediated signaling pathway
@@ -226328,11 +226299,12 @@ is_a: GO:0042577 ! lipid phosphatase activity
id: GO:0042393
name: histone binding
namespace: molecular_function
-def: "Binding to a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity." [GOC:jl]
+def: "Binding to a histone, any of a group of water-soluble proteins found in association with the DNA of eukaryotic or archaeal chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in gene regulation and DNA replication. They may be chemically modified (methylated, acetlyated and others) to regulate gene transcription." [GOC:jl, PMID:16209651, PMID:30212449, PMID:9305837]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "histone-specific chaperone activity" RELATED []
is_a: GO:0005515 ! protein binding
@@ -226425,14 +226397,15 @@ is_a: GO:1901565 ! organonitrogen compound catabolic process
[Term]
id: GO:0042401
-name: cellular biogenic amine biosynthetic process
+name: biogenic amine biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways occurring at the level of individual cells resulting in the formation of any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters." [GOC:jl, ISBN:0395825172]
synonym: "biogenic amine anabolism" EXACT []
synonym: "biogenic amine biosynthesis" EXACT []
synonym: "biogenic amine formation" EXACT []
synonym: "biogenic amine synthesis" EXACT []
-is_a: GO:0006576 ! cellular biogenic amine metabolic process
+synonym: "cellular biogenic amine biosynthetic process" EXACT []
+is_a: GO:0006576 ! biogenic amine metabolic process
is_a: GO:0009309 ! amine biosynthetic process
[Term]
@@ -226443,7 +226416,6 @@ def: "The chemical reactions and pathways occurring at the level of individual c
synonym: "biogenic amine breakdown" EXACT []
synonym: "biogenic amine catabolism" EXACT []
synonym: "biogenic amine degradation" EXACT []
-is_a: GO:0006576 ! cellular biogenic amine metabolic process
is_a: GO:0009310 ! amine catabolic process
[Term]
@@ -226524,7 +226496,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0042410
name: 6-carboxyhexanoate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + CoA + pimelate = AMP + diphosphate + H(+) + pimelyl-CoA." [EC:6.2.1.14, RHEA:14781]
+def: "Catalysis of the reaction: ATP + CoA + pimelate = AMP + diphosphate + H+ + pimelyl-CoA." [EC:6.2.1.14, RHEA:14781]
synonym: "6-carboxyhexanoate:CoA ligase (AMP-forming)" RELATED [EC:6.2.1.14]
synonym: "6-carboxyhexanoyl-CoA synthetase activity" RELATED [EC:6.2.1.14]
synonym: "pimeloyl-CoA synthetase activity" RELATED [EC:6.2.1.14]
@@ -226545,9 +226517,7 @@ synonym: "taurine anabolism" EXACT []
synonym: "taurine biosynthesis" EXACT []
synonym: "taurine formation" EXACT []
synonym: "taurine synthesis" EXACT []
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0019530 ! taurine metabolic process
-is_a: GO:0044272 ! sulfur compound biosynthetic process
is_a: GO:0046305 ! alkanesulfonate biosynthetic process
is_a: GO:1901566 ! organonitrogen compound biosynthetic process
@@ -226688,7 +226658,7 @@ synonym: "catecholamine synthesis" EXACT []
xref: Wikipedia:Catecholamines
is_a: GO:0006584 ! catecholamine metabolic process
is_a: GO:0009713 ! catechol-containing compound biosynthetic process
-is_a: GO:0042401 ! cellular biogenic amine biosynthetic process
+is_a: GO:0042401 ! biogenic amine biosynthetic process
[Term]
id: GO:0042424
@@ -226713,7 +226683,7 @@ synonym: "choline formation" EXACT []
synonym: "choline synthesis" EXACT []
xref: MetaCyc:PWY-4762
is_a: GO:0019695 ! choline metabolic process
-is_a: GO:0042401 ! cellular biogenic amine biosynthetic process
+is_a: GO:0042401 ! biogenic amine biosynthetic process
[Term]
id: GO:0042426
@@ -226889,7 +226859,7 @@ synonym: "ethanolamine and derivative metabolic process" EXACT []
synonym: "ethanolamine and derivative metabolism" EXACT []
synonym: "ethanolamine-containing compound metabolism" EXACT [GOC:mah]
is_a: GO:0006066 ! alcohol metabolic process
-is_a: GO:0006576 ! cellular biogenic amine metabolic process
+is_a: GO:0006576 ! biogenic amine metabolic process
[Term]
id: GO:0042440
@@ -226929,7 +226899,7 @@ name: phenylethylamine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving phenylethylamine, an amine with pharmacological properties similar to those of amphetamine, occurs naturally as a neurotransmitter in the brain, and is present in chocolate and oil of bitter almonds." [GOC:jl, ISBN:0395825172]
synonym: "phenylethylamine metabolism" EXACT []
-is_a: GO:0006576 ! cellular biogenic amine metabolic process
+is_a: GO:0006576 ! biogenic amine metabolic process
is_a: GO:1901160 ! primary amino compound metabolic process
[Term]
@@ -226941,7 +226911,7 @@ synonym: "phenylethylamine anabolism" EXACT []
synonym: "phenylethylamine biosynthesis" EXACT []
synonym: "phenylethylamine formation" EXACT []
synonym: "phenylethylamine synthesis" EXACT []
-is_a: GO:0042401 ! cellular biogenic amine biosynthetic process
+is_a: GO:0042401 ! biogenic amine biosynthetic process
is_a: GO:0042443 ! phenylethylamine metabolic process
is_a: GO:1901162 ! primary amino compound biosynthetic process
@@ -226949,8 +226919,10 @@ is_a: GO:1901162 ! primary amino compound biosynthetic process
id: GO:0042445
name: hormone metabolic process
namespace: biological_process
+alt_id: GO:0034754
def: "The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." [GOC:jl]
subset: goslim_pir
+synonym: "cellular hormone metabolic process" RELATED []
synonym: "hormone metabolism" EXACT []
is_a: GO:0008152 ! metabolic process
is_a: GO:0010817 ! regulation of hormone levels
@@ -227122,7 +227094,8 @@ relationship: part_of GO:0042705 ! ocellus photoreceptor cell differentiation
id: GO:0042464
name: dosage compensation by hypoactivation of X chromosome
namespace: biological_process
-def: "Compensating for the two-fold variation in X:autosome chromosome ratios between sexes by an inactivation of a proportion of genes on both of the X chromosomes of the XX sex, leading to a decrease, of half, of the levels of gene expression from these chromosomes. An example of this process is found in Caenorhabditis elegans." [GOC:jl, GOC:mr, PMID:11102361, PMID:20622855, Wikipedia:XY_sex-determination_system]
+def: "Compensating for the two-fold variation in X:autosome chromosome ratios between sexes by an inactivation of a proportion of genes on both of the X chromosomes of the XX sex, leading to a decrease, of half, of the levels of gene expression from these chromosomes. An example of this process is found in Caenorhabditis elegans." [GOC:jl, GOC:mr, PMID:11102361]
+xref: Wikipedia:XY_sex-determination_system
is_a: GO:0007549 ! dosage compensation
[Term]
@@ -227468,6 +227441,7 @@ def: "Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide
comment: Note that although GO generally avoids the use of localization information in terms, in this case an exception was made. This is because the fact that the cleavage occurs within the membrane is integral to its function, as it is the only thing that distinguishes this group from other aspartic endopeptidases.
xref: EC:3.4.23.-
xref: Reactome:R-HSA-8863101 "SPPL2a/b cleaves TNF(1-76)"
+xref: Reactome:R-HSA-9708457 "HM13 cleaves HMOX1 dimer"
is_a: GO:0004190 ! aspartic-type endopeptidase activity
[Term]
@@ -227667,7 +227641,6 @@ synonym: "hemoglobin degradation" EXACT []
synonym: "hemoglobin hydrolysis" NARROW []
is_a: GO:0020027 ! hemoglobin metabolic process
is_a: GO:0030163 ! protein catabolic process
-is_a: GO:0044265 ! cellular macromolecule catabolic process
[Term]
id: GO:0042541
@@ -227680,8 +227653,8 @@ synonym: "hemoglobin anabolism" EXACT []
synonym: "hemoglobin biosynthesis" EXACT []
synonym: "hemoglobin formation" EXACT []
synonym: "hemoglobin synthesis" EXACT []
+is_a: GO:0009059 ! macromolecule biosynthetic process
is_a: GO:0020027 ! hemoglobin metabolic process
-is_a: GO:0034645 ! cellular macromolecule biosynthetic process
is_a: GO:1901566 ! organonitrogen compound biosynthetic process
[Term]
@@ -227690,6 +227663,7 @@ name: response to hydrogen peroxide
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus." [GOC:jl]
is_a: GO:0000302 ! response to reactive oxygen species
+is_a: GO:0010033 ! response to organic substance
is_a: GO:0010035 ! response to inorganic substance
[Term]
@@ -227958,7 +227932,7 @@ synonym: "vitamin A1 metabolism" EXACT []
xref: Wikipedia:Retinol
is_a: GO:0001523 ! retinoid metabolic process
is_a: GO:0034308 ! primary alcohol metabolic process
-is_a: GO:0034754 ! cellular hormone metabolic process
+is_a: GO:0042445 ! hormone metabolic process
is_a: GO:0120254 ! olefinic compound metabolic process
[Term]
@@ -227971,7 +227945,7 @@ synonym: "vitamin A1 acid metabolic process" EXACT []
synonym: "vitamin A1 acid metabolism" EXACT []
is_a: GO:0001523 ! retinoid metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
-is_a: GO:0034754 ! cellular hormone metabolic process
+is_a: GO:0042445 ! hormone metabolic process
[Term]
id: GO:0042574
@@ -228147,7 +228121,7 @@ synonym: "inhibition of homeostatic process" NARROW []
synonym: "negative regulation of homeostatic process" RELATED []
synonym: "positive regulation of homeostatic process" RELATED []
synonym: "regulation of homeostatic process" RELATED []
-is_a: GO:0065008 ! regulation of biological quality
+is_a: GO:0008150 ! biological_process
[Term]
id: GO:0042593
@@ -228190,6 +228164,7 @@ alt_id: GO:0005620
def: "The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria)." [GOC:go_curators, GOC:md]
subset: goslim_metagenomics
subset: goslim_pir
+subset: prokaryote_subset
synonym: "periplasm" EXACT []
is_a: GO:0110165 ! cellular anatomical entity
@@ -228235,7 +228210,7 @@ is_a: GO:0042763 ! intracellular immature spore
id: GO:0042602
name: riboflavin reductase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: reduced riboflavin + NADP+ = riboflavin + NADPH + 2 H+." [EC:1.5.1.30]
+def: "Catalysis of the reaction: reduced riboflavin + NADP+ = riboflavin + NADPH + 2 H+." [RHEA:19377]
synonym: "flavin reductase activity" RELATED [EC:1.5.1.30]
synonym: "FMN reductase (NADPH) activity" RELATED [EC:1.5.1.30]
synonym: "NADPH dehydrogenase (riboflavin) activity" RELATED [EC:1.5.1.30]
@@ -228244,15 +228219,12 @@ synonym: "NADPH-FMN reductase activity" RELATED [EC:1.5.1.30]
synonym: "NADPH-riboflavin oxidoreductase activity" EXACT []
synonym: "NADPH-riboflavin reductase activity" RELATED [EC:1.5.1.30]
synonym: "NADPH-specific FMN reductase activity" RELATED [EC:1.5.1.30]
-synonym: "NADPH2 dehydrogenase (riboflavin)" RELATED [EC:1.5.1.30]
-synonym: "NADPH2:riboflavin oxidoreductase activity" RELATED [EC:1.5.1.30]
synonym: "NADPH:riboflavin oxidoreductase activity" RELATED [EC:1.5.1.30]
synonym: "reduced-riboflavin:NADP+ oxidoreductase activity" RELATED [EC:1.5.1.30]
synonym: "riboflavin mononucleotide (reduced nicotinamide adenine dinucleotide phosphate) reductase activity" RELATED [EC:1.5.1.30]
synonym: "riboflavin mononucleotide reductase activity" BROAD [EC:1.5.1.30]
synonym: "riboflavine mononucleotide reductase activity" BROAD [EC:1.5.1.30]
xref: EC:1.5.1.30
-xref: EC:1.5.1.41
xref: KEGG_REACTION:R05707
xref: MetaCyc:NADPH-DEHYDROGENASE-FLAVIN-RXN
xref: RHEA:19377
@@ -228349,30 +228321,23 @@ synonym: "CD40 receptor activity" RELATED []
synonym: "CD40L binding" EXACT []
is_a: GO:0005102 ! signaling receptor binding
-[Term]
-id: GO:0042616
-name: paclitaxel metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving paclitaxel, a tetracyclic diterpenoid isolated originally from the bark of the Pacific yew tree, Taxus brevifolia." [GOC:jl, GOC:krc]
-synonym: "paclitaxel metabolism" EXACT []
-synonym: "taxol metabolic process" NARROW []
-synonym: "taxol metabolism" NARROW []
-is_a: GO:0016101 ! diterpenoid metabolic process
-is_a: GO:0034641 ! cellular nitrogen compound metabolic process
-
[Term]
id: GO:0042617
name: paclitaxel biosynthetic process
namespace: biological_process
+alt_id: GO:0042616
def: "The chemical reactions and pathways resulting in the formation of paclitaxel, a tetracyclic diterpenoid isolated originally from the bark of the Pacific yew tree, Taxus brevifolia." [GOC:jl, GOC:krc]
synonym: "paclitaxel anabolism" EXACT []
synonym: "paclitaxel biosynthesis" EXACT []
synonym: "paclitaxel formation" EXACT []
+synonym: "paclitaxel metabolic process" BROAD []
+synonym: "paclitaxel metabolism" BROAD []
synonym: "paclitaxel synthesis" EXACT []
synonym: "taxol biosynthesis" NARROW []
synonym: "taxol biosynthetic process" NARROW []
+synonym: "taxol metabolic process" BROAD []
+synonym: "taxol metabolism" BROAD []
is_a: GO:0016102 ! diterpenoid biosynthetic process
-is_a: GO:0042616 ! paclitaxel metabolic process
[Term]
id: GO:0042618
@@ -228469,6 +228434,16 @@ xref: Reactome:R-HSA-2161506 "abacavir [cytosol] + ATP + H2O => abacavir[extrace
xref: Reactome:R-HSA-2161538 "abacavir [cytosol] + ATP + H2O => abacavir[extracellular] + ADP + phosphate"
xref: Reactome:R-HSA-9033499 "PEX1:PEX6:PEX26:ZFAND6 dissociates Ub:PEX5L and PEX7 from PEX14:PEX13:PEX2:PEX10:PEX12 and translocates PEX5L and PEX7 from the peroxisomal membrane to the cytosol"
xref: Reactome:R-HSA-9033505 "PEX1:PEX6:PEX26:ZFAND6:Ub:PEX5S,L:PEX14:PEX13:PEX2:PEX10:PEX12 dissociates yielding cytosolic Ub:PEX5S,L and membrane PEX14:PEX13:PEX2:PEX10:PEX12"
+xref: Reactome:R-HSA-9659680 "ABCB1 transports xenobiotics out of the cell"
+xref: Reactome:R-HSA-9750546 "ABCC4 transports TPMP substrates from cytosol to extracellular region"
+xref: Reactome:R-HSA-9750617 "ABCC5 transports TPMP substrates from cytosol to extracellular region"
+xref: Reactome:R-HSA-9753278 "ABCC2,ABCG2 transport APAP-GlcA, APAP-SO3"
+xref: Reactome:R-HSA-9753283 "ABCC3,ABCC4 transport APAP-GlcA, APAP-SO3"
+xref: Reactome:R-HSA-9753284 "ABCC1,4,5 transport APAP-Cys,APAP-Mer from cytosol to extracellular region"
+xref: Reactome:R-HSA-9759454 "ABCB1 transports PREDN,PREDL out of kidney cells"
+xref: Reactome:R-HSA-9759461 "ABCB1 transports PREDN,PREDL out of hepatic cells"
+xref: Reactome:R-HSA-9794120 "ABCG2 transports Cipro from intestinal cell to extracellular space"
+xref: Reactome:R-HSA-9794572 "ABCG2 transports Cipro from hepatic cell to extracellular space"
is_a: GO:0015399 ! primary active transmembrane transporter activity
is_a: GO:0140657 ! ATP-dependent activity
@@ -229114,7 +229089,7 @@ comment: Note that this term should not be used for direct annotation. If you ar
subset: gocheck_do_not_annotate
xref: Wikipedia:Menopause
is_a: GO:0022601 ! menstrual cycle phase
-relationship: part_of GO:0010259 ! multicellular organism aging
+is_a: GO:1990636 ! reproductive senescence
[Term]
id: GO:0042698
@@ -229128,7 +229103,7 @@ is_a: GO:0048609 ! multicellular organismal reproductive process
id: GO:0042699
name: follicle-stimulating hormone signaling pathway
namespace: biological_process
-def: "The series of molecular signals mediated by follicle-stimulating hormone." [GOC:dph]
+def: "A G protein-coupled receptor signaling pathway initiated by follicle-stimulating hormone binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:dph]
synonym: "follicle stimulating hormone signaling pathway" EXACT []
synonym: "follicle stimulating hormone signalling pathway" EXACT []
synonym: "follicle-stimulating hormone signalling pathway" EXACT []
@@ -229141,7 +229116,7 @@ relationship: part_of GO:0001541 ! ovarian follicle development
id: GO:0042700
name: luteinizing hormone signaling pathway
namespace: biological_process
-def: "The series of molecular signals mediated by luteinizing hormone." [GOC:dph]
+def: "A G protein-coupled receptor signaling pathway initiated by luteinizing hormone binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:dph]
synonym: "luteinizing hormone signalling pathway" EXACT []
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -229161,7 +229136,7 @@ name: uterine wall growth
namespace: biological_process
def: "The regrowth of the endometrium and blood vessels in the uterus following menstruation, resulting from a rise in progesterone levels." [GOC:jl]
is_a: GO:0022602 ! ovulation cycle process
-is_a: GO:0040007 ! growth
+is_a: GO:0048589 ! developmental growth
relationship: part_of GO:0001553 ! luteinization
[Term]
@@ -229220,7 +229195,6 @@ name: succinate-CoA ligase complex
namespace: cellular_component
def: "A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP or GTP." [GOC:jl, PMID:10671455]
is_a: GO:0045239 ! tricarboxylic acid cycle enzyme complex
-is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0042710
@@ -229319,6 +229293,7 @@ def: "Protease complex of the mitochondrial inner membrane, consisting of at lea
synonym: "IMP" NARROW []
synonym: "mitochondrion inner membrane peptidase complex" EXACT []
is_a: GO:0098800 ! inner mitochondrial membrane protein complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0042721
@@ -229512,9 +229487,10 @@ relationship: part_of GO:0098793 ! presynapse
[Term]
id: GO:0042735
-name: protein body
+name: endosperm protein body
namespace: cellular_component
def: "A membrane-bounded plant organelle found in the developing endosperm, contains storage proteins." [GOC:jl, PMID:7704047]
+synonym: "https://github.com/geneontology/go-ontology/issues/24425" EXACT []
is_a: GO:0043231 ! intracellular membrane-bounded organelle
relationship: part_of GO:0005737 ! cytoplasm
@@ -229522,7 +229498,7 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0042736
name: NADH kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + NADH = ADP + 2 H(+) + NADPH." [EC:2.7.1.86, RHEA:12260]
+def: "Catalysis of the reaction: ATP + NADH = ADP + 2 H+ + NADPH." [EC:2.7.1.86, RHEA:12260]
synonym: "ATP:NADH 2'-phosphotransferase activity" RELATED [EC:2.7.1.86]
synonym: "DPNH kinase activity" RELATED [EC:2.7.1.86]
synonym: "reduced diphosphopyridine nucleotide kinase activity" RELATED [EC:2.7.1.86]
@@ -229591,6 +229567,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving hydrogen peroxide (H2O2), a potentially harmful byproduct of aerobic cellular respiration which can cause damage to DNA." [GOC:jl, PMID:21734470]
synonym: "H2O2 metabolic process" EXACT [GOC:mah]
synonym: "hydrogen peroxide metabolism" EXACT []
+is_a: GO:0071704 ! organic substance metabolic process
is_a: GO:0072593 ! reactive oxygen species metabolic process
[Term]
@@ -229609,6 +229586,7 @@ synonym: "hydrogen peroxide removal" RELATED []
synonym: "hydrogen peroxide scavenging" RELATED [GOC:vw]
is_a: GO:0042743 ! hydrogen peroxide metabolic process
is_a: GO:0044248 ! cellular catabolic process
+is_a: GO:1901575 ! organic substance catabolic process
[Term]
id: GO:0042745
@@ -229647,7 +229625,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the circadian sleep/wake cycle." [GOC:jl]
is_a: GO:0042752 ! regulation of circadian rhythm
is_a: GO:0050795 ! regulation of behavior
-is_a: GO:0051239 ! regulation of multicellular organismal process
relationship: regulates GO:0042745 ! circadian sleep/wake cycle
[Term]
@@ -229729,7 +229706,7 @@ is_a: GO:0030424 ! axon
id: GO:0042758
name: long-chain fatty acid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of long-chain fatty acids, a fatty acid with a chain length between C13 and C22." [PMID:20043225]
+def: "The chemical reactions and pathways resulting in the breakdown of a long-chain fatty acid, a fatty acid with an aliphatic tail of 13 to 21 carbons." [PMID:20043225]
synonym: "long-chain fatty acid breakdown" EXACT []
synonym: "long-chain fatty acid catabolism" EXACT []
synonym: "long-chain fatty acid degradation" EXACT []
@@ -229740,7 +229717,7 @@ is_a: GO:0009062 ! fatty acid catabolic process
id: GO:0042759
name: long-chain fatty acid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of long-chain fatty acids, any fatty acid with a chain length between C13 and C22." [PMID:18390550]
+def: "The chemical reactions and pathways resulting in the formation of a long-chain fatty acid, a fatty acid with an aliphatic tail of 13 to 21 carbons." [PMID:18390550]
synonym: "long-chain fatty acid anabolism" EXACT []
synonym: "long-chain fatty acid biosynthesis" EXACT []
synonym: "long-chain fatty acid formation" EXACT []
@@ -229752,7 +229729,7 @@ is_a: GO:0006633 ! fatty acid biosynthetic process
id: GO:0042760
name: very long-chain fatty acid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a fatty acid which has a chain length greater than C22." [PMID:7744868]
+def: "The chemical reactions and pathways resulting in the breakdown of a very long chain fatty acid, a fatty acid with an aliphatic tail of 22 or more carbons." [PMID:7744868]
synonym: "very-long-chain fatty acid breakdown" EXACT []
synonym: "very-long-chain fatty acid catabolic process" EXACT []
synonym: "very-long-chain fatty acid catabolism" EXACT []
@@ -229764,7 +229741,7 @@ is_a: GO:0009062 ! fatty acid catabolic process
id: GO:0042761
name: very long-chain fatty acid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a fatty acid which has a chain length greater than C22." [PMID:7744868]
+def: "The chemical reactions and pathways resulting in the formation of a very long chain fatty acid, a fatty acid with an aliphatic tail of 22 or more carbons." [PMID:7744868]
synonym: "very-long-chain fatty acid anabolism" EXACT []
synonym: "very-long-chain fatty acid biosynthesis" EXACT []
synonym: "very-long-chain fatty acid biosynthetic process" EXACT []
@@ -229810,15 +229787,19 @@ synonym: "GPIT complex" EXACT []
is_a: GO:0008303 ! caspase complex
is_a: GO:0098796 ! membrane protein complex
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
-relationship: part_of GO:0030176 ! integral component of endoplasmic reticulum membrane
+relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
[Term]
id: GO:0042766
-name: nucleosome mobilization
+name: obsolete nucleosome mobilization
namespace: biological_process
-def: "The movement of nucleosomes along a DNA fragment." [PMID:12006495]
+def: "OBSOLETE. The movement of nucleosomes along a DNA fragment." [PMID:12006495]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "nucleosome sliding" EXACT [GOC:dph]
-is_a: GO:0034728 ! nucleosome organization
+is_obsolete: true
+consider: GO:0140658
+consider: GO:0140750
+consider: GO:0140751
[Term]
id: GO:0042767
@@ -229853,17 +229834,19 @@ consider: GO:0140664
id: GO:0042770
name: signal transduction in response to DNA damage
namespace: biological_process
+alt_id: GO:0006975
def: "A cascade of processes induced by the detection of DNA damage within a cell." [GOC:go_curators]
+synonym: "DNA damage induced protein phosphorylation" NARROW []
synonym: "DNA damage response, signal transduction" EXACT []
synonym: "response to DNA damage stimulus by intracellular signaling cascade" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0006974 ! cellular response to DNA damage stimulus
+is_a: GO:0006974 ! DNA damage response
is_a: GO:0035556 ! intracellular signal transduction
[Term]
id: GO:0042771
name: intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage, and ends when the execution phase of apoptosis is triggered." [GOC:go_curators, GOC:mtg_apoptosis]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage, and ends when the execution phase of apoptosis is triggered." [GOC:go_curators, GOC:mtg_apoptosis]
synonym: "DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis" RELATED []
is_a: GO:0008630 ! intrinsic apoptotic signaling pathway in response to DNA damage
is_a: GO:0072332 ! intrinsic apoptotic signaling pathway by p53 class mediator
@@ -229901,22 +229884,22 @@ is_a: GO:0042773 ! ATP synthesis coupled electron transport
[Term]
id: GO:0042776
-name: mitochondrial ATP synthesis coupled proton transport
+name: proton motive force-driven mitochondrial ATP synthesis
namespace: biological_process
def: "The transport of protons across a mitochondrial membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis." [GOC:mtg_sensu, ISBN:0716731363]
+synonym: "mitochondrial ATP synthesis coupled proton transport" EXACT []
synonym: "mitochondrial proton transport" BROAD []
-is_a: GO:0006839 ! mitochondrial transport
-is_a: GO:0015986 ! ATP synthesis coupled proton transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
+is_a: GO:0015986 ! proton motive force-driven ATP synthesis
relationship: part_of GO:0006119 ! oxidative phosphorylation
[Term]
id: GO:0042777
-name: plasma membrane ATP synthesis coupled proton transport
+name: proton motive force-driven plasma membrane ATP synthesis
namespace: biological_process
def: "The transport of protons across the plasma membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis." [GOC:mtg_sensu, ISBN:0716731363]
synonym: "ATP synthesis coupled proton transport" BROAD []
-is_a: GO:0015986 ! ATP synthesis coupled proton transport
+synonym: "plasma membrane ATP synthesis coupled proton transport" EXACT []
+is_a: GO:0015986 ! proton motive force-driven ATP synthesis
[Term]
id: GO:0042778
@@ -229942,7 +229925,7 @@ namespace: biological_process
def: "The process in which the 3' end of a pre-tRNA molecule is converted to that of a mature tRNA." [GOC:go_curators]
synonym: "tRNA 3' processing" EXACT []
is_a: GO:0008033 ! tRNA processing
-is_a: GO:0043628 ! ncRNA 3'-end processing
+is_a: GO:0031123 ! RNA 3'-end processing
[Term]
id: GO:0042781
@@ -229959,7 +229942,7 @@ synonym: "tRNA 3' endonuclease activity" EXACT []
synonym: "tRNAse Z" RELATED [EC:3.1.26.11]
xref: EC:3.1.26.11
xref: MetaCyc:3.1.26.11-RXN
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
[Term]
@@ -229975,17 +229958,21 @@ def: "A process by which an organism avoids the effects of the host organism's i
synonym: "active evasion of host immune response" RELATED []
synonym: "active evasion of immune response of other organism involved in symbiotic interaction" BROAD []
synonym: "active immune evasion" BROAD []
+synonym: "evasion by virus of host immune response" RELATED []
synonym: "evasion or tolerance of host immune response" BROAD []
synonym: "immune evasion" EXACT []
+synonym: "mitigation by virus of host immune response" RELATED []
synonym: "mitigation of host immune response" RELATED []
+synonym: "mitigation of host immune response by virus" RELATED []
synonym: "passive evasion of host immune response" RELATED []
synonym: "passive evasion of immune response of other organism involved in symbiotic interaction" RELATED []
synonym: "passive immune evasion" RELATED []
+synonym: "suppression by virus of host immune response" RELATED []
is_a: GO:0052572 ! response to host immune response
[Term]
id: GO:0042784
-name: evasion of host immune response via regulation of host complement system
+name: evasion of host immune response via modulation of host complement system
namespace: biological_process
alt_id: GO:0051811
def: "Any mechanism of active immune avoidance which works by regulating the host complement system, e.g. by possessing complement receptors which mediate attachment to, then infection of, host macrophages, which are eventually destroyed. The host is defined as the larger of the organisms involved in a symbiotic interaction." [http://www.brown.edu/Courses/Bio_160/Projects1999/ies/ces.html]
@@ -229993,23 +229980,25 @@ synonym: "active evasion of host immune response via regulation of host compleme
synonym: "active evasion of immune response of other organism via regulation of complement system of other organism involved in symbiotic interaction" BROAD []
synonym: "active immune evasion via modulation of host complement system" EXACT []
synonym: "active immune evasion via regulation of host complement system" EXACT []
+synonym: "evasion of host immune response via regulation of host complement system" EXACT []
is_a: GO:0042783 ! evasion of host immune response
[Term]
id: GO:0042785
-name: evasion of host immune response via regulation of host cytokine network
+name: evasion of host immune response via modulation of host cytokine network
namespace: biological_process
alt_id: GO:0051812
-def: "Any mechanism of active immune avoidance which works by regulating host cytokine networks, e.g. by secreting proteins that mimic cytokine receptors that act to sequester host cytokines and inhibit action. The host is defined as the larger of the organisms involved in a symbiotic interaction." [http://www.brown.edu/Courses/Bio_160/Projects1999/ies/cytok.html#Manipulation]
+def: "Any mechanism of active immune avoidance which works by regulating host cytokine networks, e.g. by secreting proteins that mimic cytokine receptors that act to sequester host cytokines and inhibit action. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:10620615, PMID:9275219, PMID:9600978]
synonym: "active evasion of host immune response via regulation of host cytokine network" RELATED []
synonym: "active evasion of immune response of other organism via regulation of cytokine network of other organism involved in symbiotic interaction" BROAD []
synonym: "active immune evasion via modulation of host cytokine network" EXACT []
synonym: "active immune evasion via regulation of host cytokine network" EXACT []
+synonym: "evasion of host immune response via regulation of host cytokine network" EXACT []
is_a: GO:0042783 ! evasion of host immune response
[Term]
id: GO:0042786
-name: evasion of host immune response via regulation of host antigen processing and presentation
+name: evasion of host immune response via modulation of host antigen processing and presentation
namespace: biological_process
alt_id: GO:0051813
def: "Any mechanism of active immune avoidance which works by regulating the host's antigen processing or presentation pathways, e.g. by blocking any stage in MHC class II presentation. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:12439615]
@@ -230019,6 +230008,7 @@ synonym: "active evasion of immune response of other organism via regulation of
synonym: "active immune evasion via modulation of antigen processing and presentation" EXACT []
synonym: "active immune evasion via modulation of antigen processing/presentation" EXACT []
synonym: "active immune evasion via regulation of antigen processing and presentation" EXACT []
+synonym: "evasion of host immune response via regulation of host antigen processing and presentation" EXACT []
is_a: GO:0042783 ! evasion of host immune response
[Term]
@@ -230063,12 +230053,13 @@ is_a: GO:0009303 ! rRNA transcription
[Term]
id: GO:0042792
-name: mitochondrial rRNA transcription
+name: obsolete mitochondrial rRNA transcription
namespace: biological_process
-def: "The synthesis of ribosomal RNA (rRNA) from a mitochondrial DNA template." [GOC:jl, ISBN:0321000382]
+def: "OBSOLETE. The synthesis of ribosomal RNA (rRNA) from a mitochondrial DNA template." [GOC:jl, PMID:23632312]
+comment: This term was obsoleted because it is the same as its parent, 'mitochondrial transcription', since there is no specific pathway or factors for rRNA transcription.
synonym: "rRNA transcription from mitochondrial promoter" EXACT []
-is_a: GO:0006390 ! mitochondrial transcription
-is_a: GO:0009303 ! rRNA transcription
+is_obsolete: true
+replaced_by: GO:0006390
[Term]
id: GO:0042793
@@ -230076,7 +230067,7 @@ name: plastid transcription
namespace: biological_process
def: "The synthesis of RNA from a plastid DNA template, usually by a specific plastid RNA polymerase." [GOC:jl, ISBN:0321000382]
synonym: "transcription from plastid promoter" EXACT []
-is_a: GO:0006351 ! transcription, DNA-templated
+is_a: GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0042794
@@ -230134,26 +230125,34 @@ consider: GO:0045116
[Term]
id: GO:0042799
-name: histone methyltransferase activity (H4-K20 specific)
+name: histone H4K20 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H4 L-lysine (position 20) = S-adenosyl-L-homocysteine + histone H4 N6-methyl-L-lysine (position 20). This reaction is the addition of a methyl group onto lysine at position 20 of the histone H4 protein." [PMID:12086618]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H4 L-lysine (position 20) = S-adenosyl-L-homocysteine + histone H4 N6-methyl-L-lysine (position 20). This reaction is the addition of a methyl group to the lysine residue at position 20 of the histone H4 protein." [PMID:12086618]
comment: Note that in some species, the methyl group may be added to a lysine in a slightly different position of the histone H4 protein, but that this term still applies.
synonym: "histone H4 lysine 20-specific methyltransferase activity" EXACT []
+synonym: "histone H4K20 methylase activity" BROAD []
+synonym: "histone H4K20 methylation" EXACT []
synonym: "histone lysine N-methyltransferase activity (H4-K20 specific)" EXACT []
-synonym: "histone methylase activity (H4-K20 specific)" EXACT [GOC:mah]
+synonym: "histone methylase activity (H4-K20 specific)" EXACT []
+synonym: "histone methyltransferase activity (H4-K20 specific)" EXACT []
+synonym: "histone-H4K20 methyltransferase activity" EXACT []
xref: Reactome:R-HSA-2301205 "SETD8 monomethylates histone H4"
xref: Reactome:R-HSA-5682965 "WHSC1 dimethylates histone H4 on lysine K21 at DSBs"
-is_a: GO:0018024 ! histone-lysine N-methyltransferase activity
+is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
+is_a: GO:0140939 ! histone H4 methyltransferase activity
[Term]
id: GO:0042800
-name: histone methyltransferase activity (H3-K4 specific)
+name: histone H3K4 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein." [PMID:12086618]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of up to three methyl groups to the lysine residue at position 4 of the histone H3 protein." [PMID:12086618]
comment: Note that in some species, the methyl group may be added to a lysine in a slightly different position of the histone H3 protein, but that this term still applies.
synonym: "histone H3 lysine 4-specific methyltransferase activity" EXACT []
+synonym: "histone H3K4 methylase activity" EXACT []
synonym: "histone lysine N-methyltransferase activity (H3-K4 specific)" EXACT []
synonym: "histone methylase activity (H3-K4 specific)" EXACT [GOC:mah]
+synonym: "histone methyltransferase activity (H3-K4 specific)" EXACT []
+synonym: "histone-H3K4 methyltransferase activity" EXACT []
xref: Reactome:R-HSA-1214188 "PRDM9 trimethylates histone H3"
xref: Reactome:R-HSA-3364026 "SET1 complex trimethylates H3K4 at the MYC gene"
xref: Reactome:R-HSA-8865498 "KMT2A trimethylates nucleosomes at the SPI1 gene locus producing H3K4Me3 mark"
@@ -230161,7 +230160,8 @@ xref: Reactome:R-HSA-8936481 "Core MLL complex methylates H3K4Me2-Nucleosome at
xref: Reactome:R-HSA-8936621 "Core MLL complex methylates H3K4Me2-Nucleosome at the GP1BA gene promoter"
xref: Reactome:R-HSA-8937016 "Core MLL complex methylates H3K4Me2-Nucleosome at the THBS1 gene promoter"
xref: Reactome:R-HSA-8937050 "Core MLL complex methylates H3K4Me2-Nucleosome at the MIR27A gene promoter"
-is_a: GO:0018024 ! histone-lysine N-methyltransferase activity
+is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
+is_a: GO:0140938 ! histone H3 methyltransferase activity
[Term]
id: GO:0042801
@@ -230238,11 +230238,12 @@ replaced_by: GO:0019901
[Term]
id: GO:0042809
-name: vitamin D receptor binding
+name: nuclear vitamin D receptor binding
namespace: molecular_function
-def: "Binding to a vitamin D receptor, a nuclear receptor that mediates the action of vitamin D by binding DNA and controlling the transcription of hormone-sensitive genes." [GOC:jl, PMID:12637589]
+def: "Binding to a nuclear vitamin D receptor, a nuclear receptor that mediates the action of vitamin D by binding DNA and controlling the transcription of hormone-sensitive genes." [GOC:jl, PMID:12637589]
synonym: "calciferol receptor binding" NARROW []
synonym: "VDR binding" EXACT []
+synonym: "vitamin D receptor binding" BROAD []
is_a: GO:0016922 ! nuclear receptor binding
[Term]
@@ -230286,13 +230287,13 @@ is_a: GO:0044248 ! cellular catabolic process
[Term]
id: GO:0042813
-name: Wnt-activated receptor activity
+name: Wnt receptor activity
namespace: molecular_function
def: "Combining with a Wnt protein and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:go_curators]
subset: goslim_chembl
synonym: "frizzled receptor activity" RELATED []
synonym: "frizzled-2 receptor activity" RELATED []
-synonym: "Wnt receptor activity" EXACT [GOC:bf, GOC:signaling]
+synonym: "Wnt-activated receptor activity" EXACT []
is_a: GO:0004888 ! transmembrane signaling receptor activity
[Term]
@@ -230351,7 +230352,7 @@ id: GO:0042819
name: vitamin B6 biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of any of the vitamin B6 compounds; pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate." [GOC:jl, http://www.indstate.edu/thcme/mwking/vitamins.html]
-synonym: "pyridoxine-5'-phosphate biosynthesis" RELATED [GOC:yaf, UniPathway:UPA00244]
+synonym: "pyridoxine-5'-phosphate biosynthesis" RELATED [GOC:yaf, PMID:12271461]
synonym: "vitamin B6 anabolism" EXACT []
synonym: "vitamin B6 biosynthesis" EXACT []
synonym: "vitamin B6 formation" EXACT []
@@ -230432,7 +230433,7 @@ synonym: "peptide-loading complex" EXACT [GOC:bhm]
synonym: "PLC" RELATED [GOC:bhm]
is_a: GO:0098796 ! membrane protein complex
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
-relationship: part_of GO:0030176 ! integral component of endoplasmic reticulum membrane
+relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
[Term]
id: GO:0042825
@@ -230500,6 +230501,7 @@ def: "The chemical reactions and pathways involving D-glucarate, the D-enantiome
synonym: "D-glucarate metabolism" EXACT []
synonym: "saccharate metabolic process" EXACT []
synonym: "saccharate metabolism" EXACT []
+is_a: GO:0005975 ! carbohydrate metabolic process
is_a: GO:0019392 ! glucarate metabolic process
[Term]
@@ -230527,6 +230529,7 @@ synonym: "D-glucarate catabolism" EXACT []
synonym: "D-glucarate degradation" EXACT []
synonym: "saccharate catabolic process" EXACT []
synonym: "saccharate catabolism" EXACT []
+is_a: GO:0016052 ! carbohydrate catabolic process
is_a: GO:0019394 ! glucarate catabolic process
is_a: GO:0042836 ! D-glucarate metabolic process
@@ -230754,10 +230757,10 @@ name: chrysobactin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving the siderophore chrysobactin (alpha-N-(2,3-dihydroxybenzoyl)-D-lysyl-L-serine)." [GOC:jl, PMID:8837459]
synonym: "chrysobactin metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0006518 ! peptide metabolic process
is_a: GO:0009237 ! siderophore metabolic process
is_a: GO:0009712 ! catechol-containing compound metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0034308 ! primary alcohol metabolic process
is_a: GO:1901160 ! primary amino compound metabolic process
@@ -230775,10 +230778,10 @@ synonym: "chrysobactin biosynthetic process, peptide modification" NARROW []
synonym: "chrysobactin formation" EXACT []
synonym: "chrysobactin synthesis" EXACT []
is_a: GO:0009713 ! catechol-containing compound biosynthetic process
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0019290 ! siderophore biosynthetic process
is_a: GO:0034309 ! primary alcohol biosynthetic process
is_a: GO:0042857 ! chrysobactin metabolic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:1901162 ! primary amino compound biosynthetic process
[Term]
@@ -230789,12 +230792,12 @@ def: "The chemical reactions and pathways resulting in the breakdown of the side
synonym: "chrysobactin breakdown" EXACT []
synonym: "chrysobactin catabolism" EXACT []
synonym: "chrysobactin degradation" EXACT []
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0019614 ! catechol-containing compound catabolic process
is_a: GO:0034310 ! primary alcohol catabolic process
is_a: GO:0042857 ! chrysobactin metabolic process
is_a: GO:0043171 ! peptide catabolic process
is_a: GO:0046215 ! siderophore catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:1901161 ! primary amino compound catabolic process
[Term]
@@ -230805,7 +230808,7 @@ def: "The chemical reactions and pathways involving achromobactin, a citrate sid
synonym: "achromobactin metabolism" EXACT []
is_a: GO:0009237 ! siderophore metabolic process
is_a: GO:0019752 ! carboxylic acid metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
is_a: GO:1901615 ! organic hydroxy compound metabolic process
@@ -230845,10 +230848,10 @@ name: pyochelin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving the siderochrome pyochelin (2-(2-o-hydroxyphenyl-2-thiazolin-4-yl)-3-methylthiazolidine-4-carboxylic acid)." [GOC:jl, PMID:6794030]
synonym: "pyochelin metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0006790 ! sulfur compound metabolic process
is_a: GO:0009237 ! siderophore metabolic process
is_a: GO:0018958 ! phenol-containing compound metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
@@ -230865,12 +230868,12 @@ synonym: "pyochelin biosynthetic process, peptide formation" NARROW []
synonym: "pyochelin biosynthetic process, peptide modification" NARROW []
synonym: "pyochelin formation" EXACT []
synonym: "pyochelin synthesis" EXACT []
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0019290 ! siderophore biosynthetic process
is_a: GO:0042863 ! pyochelin metabolic process
is_a: GO:0044272 ! sulfur compound biosynthetic process
is_a: GO:0046189 ! phenol-containing compound biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
[Term]
id: GO:0042865
@@ -230880,11 +230883,11 @@ def: "The chemical reactions and pathways resulting in the breakdown of the side
synonym: "pyochelin breakdown" EXACT []
synonym: "pyochelin catabolism" EXACT []
synonym: "pyochelin degradation" EXACT []
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0019336 ! phenol-containing compound catabolic process
is_a: GO:0042863 ! pyochelin metabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
is_a: GO:0046215 ! siderophore catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:0046700 ! heterocycle catabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
@@ -230926,7 +230929,7 @@ namespace: biological_process
def: "The process in which aldarate is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:go_curators]
synonym: "aldarate transport" RELATED []
is_a: GO:0006835 ! dicarboxylic acid transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:0042870
@@ -230936,7 +230939,6 @@ def: "The process in which D-glucarate, the D-enantiomer of glucarate, is transp
synonym: "D-glucarate transport" RELATED []
is_a: GO:0034219 ! carbohydrate transmembrane transport
is_a: GO:0042869 ! aldarate transmembrane transport
-is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:0042873
@@ -230945,7 +230947,7 @@ namespace: biological_process
def: "The process in which aldonate is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:jl]
synonym: "aldonate transport" RELATED []
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:0042874
@@ -230963,14 +230965,13 @@ def: "The process in which D-galactonate, the D-enantiomer of galactonate, is tr
synonym: "D-galactonate transport" RELATED []
is_a: GO:0034219 ! carbohydrate transmembrane transport
is_a: GO:0042873 ! aldonate transmembrane transport
-is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:0042876
name: aldarate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of aldarate from one side of a membrane to the other." [GOC:go_curators, PMID:15034926]
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
[Term]
id: GO:0042878
@@ -230986,7 +230987,7 @@ id: GO:0042879
name: aldonate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of aldonate from one side of a membrane to the other." [GOC:jl, GOC:mtg_transport, ISBN:0815340729]
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
[Term]
id: GO:0042880
@@ -231019,9 +231020,7 @@ namespace: biological_process
def: "The directed movement of cysteine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, ISBN:0198506732]
synonym: "L-cysteine transport" NARROW []
is_a: GO:0000101 ! sulfur amino acid transport
-is_a: GO:0006812 ! cation transport
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0042884
@@ -231062,25 +231061,25 @@ is_a: GO:0046915 ! transition metal ion transmembrane transporter activity
[Term]
id: GO:0042889
-name: 3-phenylpropionic acid transport
+name: obsolete 3-phenylpropionic acid transport
namespace: biological_process
-def: "The directed movement of 3-phenylpropionic acid into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl]
+def: "OBSOLETE. The directed movement of 3-phenylpropionic acid into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl]
+comment: The reason for obsoletion is that there is no evidence that this process exists.
synonym: "3-phenylpropionate transport" EXACT []
synonym: "HCA transport" EXACT []
synonym: "hydrocinnamic acid transport" EXACT []
-is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
+is_obsolete: true
[Term]
id: GO:0042890
-name: 3-phenylpropionic acid transmembrane transporter activity
+name: obsolete 3-phenylpropionic acid transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of 3-phenylpropionic acid from one side of a membrane to the other." [GOC:jl]
+def: "OBSOLETE. Enables the transfer of 3-phenylpropionic acid from one side of a membrane to the other." [GOC:jl]
+comment: The reason for obsoletion is that there is no evidence that this function exists.
synonym: "3-phenylpropionate acid transporter activity" EXACT []
synonym: "HCA transporter activity" EXACT []
synonym: "hydrocinnamic acid transporter activity" EXACT []
-is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_obsolete: true
[Term]
id: GO:0042891
@@ -231096,9 +231095,8 @@ name: chloramphenicol transmembrane transport
namespace: biological_process
def: "The directed movement of chloramphenicol, a broad-spectrum antibiotic that inhibits bacterial protein synthesis, across a lipid bilayer, from one side of a membrane to the other." [PMID:29150447]
synonym: "chloramphenicol transport" BROAD []
-is_a: GO:0015791 ! polyol transport
+is_a: GO:0015791 ! polyol transmembrane transport
is_a: GO:0042886 ! amide transport
-is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0042893
@@ -231190,7 +231188,7 @@ namespace: molecular_function
def: "Catalysis of the reaction: N-acetyl(alpha-tubulin) + H2O = alpha-tubulin + acetate." [PMID:12024216, PMID:12486003]
xref: Reactome:R-HSA-5618331 "HDAC6 deacetylates microtubules"
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
-is_a: GO:0033558 ! protein deacetylase activity
+is_a: GO:0033558 ! protein lysine deacetylase activity
[Term]
id: GO:0042904
@@ -231239,11 +231237,11 @@ is_a: GO:0006810 ! transport
[Term]
id: GO:0042909
-name: acridine transport
+name: obsolete acridine transport
namespace: biological_process
-def: "The directed movement of acridine (10-azaanthracene), a heterocyclic ring compound found in crude coal-tar anthracene, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, Wikipedia:Acridine]
-is_a: GO:0071702 ! organic substance transport
-is_a: GO:0071705 ! nitrogen compound transport
+def: "OBSOLETE. The directed movement of acridine (10-azaanthracene), a heterocyclic ring compound found in crude coal-tar anthracene, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, Wikipedia:Acridine]
+comment: This term is out of scope for GO.
+is_obsolete: true
[Term]
id: GO:0042910
@@ -231266,11 +231264,12 @@ is_a: GO:0022857 ! transmembrane transporter activity
[Term]
id: GO:0042911
-name: acridine transmembrane transporter activity
+name: obsolete acridine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the directed movement of acridine (10-azaanthracene), a heterocyclic ring compound found in crude coal-tar anthracene from one side of a membrane to the other." [GOC:jl]
+def: "OBSOLETE. Enables the directed movement of acridine (10-azaanthracene), a heterocyclic ring compound found in crude coal-tar anthracene from one side of a membrane to the other." [GOC:jl]
+comment: The reason for obsoletion is that these terms are beyond the scope of GO.
synonym: "acridine transporter activity" RELATED []
-is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
+is_obsolete: true
[Term]
id: GO:0042912
@@ -231307,6 +231306,8 @@ namespace: biological_process
def: "The directed movement of an alkanesulfonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Alkanesulfonates are organic esters or salts of sulfonic acid containing an aliphatic hydrocarbon radical." [GOC:jl]
synonym: "alkanesulphonate transport" EXACT []
is_a: GO:0015711 ! organic anion transport
+is_a: GO:0015849 ! organic acid transport
+is_a: GO:0072348 ! sulfur compound transport
[Term]
id: GO:0042919
@@ -231314,25 +231315,23 @@ name: benzoate transport
namespace: biological_process
def: "The directed movement of benzoate, the anion of benzoic acid (benzenecarboxylic acid) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, ISBN:0721662544]
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
[Term]
id: GO:0042920
name: 3-hydroxyphenylpropionic acid transmembrane transport
namespace: biological_process
-def: "The directed movement of 3-hydroxyphenylpropionic acid across a lipid bilayer, from one side of a membrane to the other." [GOC:go_curators]
+def: "The directed movement of 3-hydroxyphenylpropionic acid across a lipid bilayer, from one side of a membrane to the other." [GOC:go_curators, PMID:9098055]
synonym: "3-(3-hydroxyphenyl)propionic acid transport" EXACT []
synonym: "3-hydroxyphenylpropionic acid transport" BROAD []
synonym: "m-hydroxyphenylpropionic acid transport" EXACT []
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
[Term]
id: GO:0042921
name: glucocorticoid receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of a glucocorticoid binding to its receptor." [GOC:mah]
+def: "The series of molecular signals initiated by glucocorticoid binding to its receptor." [GOC:mah]
synonym: "glucocorticoid receptor signalling pathway" EXACT []
is_a: GO:0031958 ! corticosteroid receptor signaling pathway
@@ -231365,20 +231364,19 @@ namespace: molecular_function
def: "Enables the directed movement of benzoate, the anion of benzoic acid (benzenecarboxylic acid) from one side of a membrane to the other." [GOC:jl, ISBN:0721662544]
synonym: "benzoate transporter activity" RELATED []
xref: RHEA:32811
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0042926
name: 3-hydroxyphenylpropionic acid transmembrane transporter activity
namespace: molecular_function
-def: "Enables the directed movement of 3-hydroxyphenylpropionic acid from one side of a membrane to the other." [GOC:jl]
+def: "Enables the directed movement of 3-hydroxyphenylpropionic acid from one side of a membrane to the other." [GOC:jl, PMID:9098055]
synonym: "3-(3-hydroxyphenyl)propionic acid transporter activity" EXACT []
synonym: "3-hydroxyphenylpropionic acid transporter activity" RELATED []
synonym: "m-hydroxyphenylpropionic acid transporter activity" EXACT []
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
[Term]
@@ -231396,7 +231394,7 @@ name: ferrichrome transmembrane transporter activity
namespace: molecular_function
def: "Enables the directed movement of a ferrichrome from one side of a membrane to the other. Ferrichromes are any of a group of growth-promoting Fe(III) chelates formed by various genera of microfungi. They are homodetic cyclic hexapeptides made up of a tripeptide of glycine (or other small neutral amino acids) and a tripeptide of an N'acyl-N4-hydroxy-L-ornithine." [GOC:jl, ISBN:0198506732]
synonym: "ferrichrome transporter activity" RELATED []
-is_a: GO:0015343 ! siderophore transmembrane transporter activity
+is_a: GO:0015343 ! siderophore-iron transmembrane transporter activity
is_a: GO:0015603 ! iron chelate transmembrane transporter activity
is_a: GO:1904680 ! peptide transmembrane transporter activity
@@ -231418,7 +231416,7 @@ def: "Enables the directed movement of the siderochrome enterochelin, a cyclic t
synonym: "enterobactin transporter activity" RELATED []
synonym: "enterochelin transporter activity" EXACT []
is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015343 ! siderophore transmembrane transporter activity
+is_a: GO:0015343 ! siderophore-iron transmembrane transporter activity
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
[Term]
@@ -231426,10 +231424,10 @@ id: GO:0042932
name: chrysobactin transport
namespace: biological_process
def: "The directed movement of the siderophore chrysobactin (alpha-N-(2,3-dihydroxybenzoyl)-D-lysyl-L-serine) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, PMID:8837459]
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0015891 ! siderophore transport
is_a: GO:0042938 ! dipeptide transport
+is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0042933
@@ -231438,7 +231436,7 @@ namespace: molecular_function
def: "Enables the directed movement of the siderophore chrysobactin (alpha-N-(2,3-dihydroxybenzoyl)-D-lysyl-L-serine) from one side of a membrane to the other." [GOC:jl, PMID:8837459]
synonym: "chrysobactin transporter activity" RELATED []
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0015343 ! siderophore transmembrane transporter activity
+is_a: GO:0015343 ! siderophore-iron transmembrane transporter activity
is_a: GO:0015665 ! alcohol transmembrane transporter activity
is_a: GO:0071916 ! dipeptide transmembrane transporter activity
@@ -231448,8 +231446,7 @@ name: achromobactin transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of achromobactin, a citrate siderophore, from one side of a membrane to the other." [GOC:jl]
synonym: "achromobactin transporter activity" RELATED []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015343 ! siderophore transmembrane transporter activity
+is_a: GO:0015343 ! siderophore-iron transmembrane transporter activity
is_a: GO:0042887 ! amide transmembrane transporter activity
is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
@@ -231459,7 +231456,6 @@ id: GO:0042935
name: achromobactin transport
namespace: biological_process
def: "The directed movement of achromobactin, a citrate siderophore, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, PMID:10928541]
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0015891 ! siderophore transport
is_a: GO:0042886 ! amide transport
@@ -231493,7 +231489,6 @@ name: D-amino acid transport
namespace: biological_process
def: "The directed movement of the D-enantiomer of an amino acid into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, GOC:jsg, GOC:mah]
is_a: GO:0006865 ! amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0042941
@@ -231517,7 +231512,6 @@ name: D-amino acid transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of D-amino acids from one side of a membrane to the other. D-amino acids are the D-enantiomers of amino acids." [GOC:jl, GOC:jsg, GOC:mah, GOC:mtg_transport, ISBN:0815340729]
synonym: "D-amino acid transporter activity" BROAD []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015171 ! amino acid transmembrane transporter activity
[Term]
@@ -231616,9 +231610,10 @@ is_a: GO:0015774 ! polysaccharide transport
[Term]
id: GO:0042956
-name: maltodextrin transport
+name: maltodextrin transmembrane transport
namespace: biological_process
-def: "The directed movement of maltodextrin, any polysaccharide of glucose residues in beta-(1,4) linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl]
+def: "The directed movement of maltodextrin, any polysaccharide of glucose residues in beta-(1,4) linkage, across a membrane." [GOC:jl]
+synonym: "maltodextrin transport" BROAD []
is_a: GO:0015774 ! polysaccharide transport
[Term]
@@ -231642,8 +231637,10 @@ namespace: molecular_function
def: "Enables the directed movement of alkanesulfonate from one side of a membrane to the other." [GOC:jl]
synonym: "alkanesulfonate transporter activity" RELATED []
synonym: "alkanesulphonate transporter activity" EXACT []
+is_a: GO:0005342 ! organic acid transmembrane transporter activity
is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
+is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
[Term]
id: GO:0042960
@@ -231653,7 +231650,6 @@ def: "Enables the transfer of antimonite from one side of a membrane to the othe
synonym: "antimonite porter activity" RELATED []
is_a: GO:0015104 ! antimonite transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0042961
@@ -231672,7 +231668,9 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + acridine(in) = H+(in) + acridine(out)." [PMID:10735876]
synonym: "acridine efflux pump activity" RELATED []
synonym: "acridine:hydrogen antiporter activity" EXACT []
-is_a: GO:0015299 ! solute:proton antiporter activity
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0042964
@@ -231734,7 +231732,6 @@ name: homoserine transport
namespace: biological_process
def: "The directed movement of homoserine, alpha-amino-gamma-hydroxybutyric acid, an intermediate in the biosynthesis of cystathionine, threonine and methionine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators, ISBN:0198506732]
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0042969
@@ -231750,7 +231747,7 @@ name: homoserine transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of homoserine from one side of a membrane to the other. Homoserine is alpha-amino-gamma-hydroxybutyric acid, an intermediate in the biosynthesis of cystathionine, threonine and methionine." [GOC:go_curators, ISBN:0198506732]
synonym: "homoserine transporter activity" BROAD []
-is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
[Term]
@@ -231805,10 +231802,11 @@ is_a: GO:0008422 ! beta-glucosidase activity
[Term]
id: GO:0042974
-name: retinoic acid receptor binding
+name: nuclear retinoic acid receptor binding
namespace: molecular_function
-def: "Binding to a retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily." [GOC:jl, PMID:12476796]
+def: "Binding to a nuclear retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily." [GOC:jl, PMID:12476796]
synonym: "RAR binding" EXACT []
+synonym: "retinoic acid receptor binding" BROAD []
is_a: GO:0016922 ! nuclear receptor binding
[Term]
@@ -232075,6 +232073,7 @@ subset: goslim_agr
subset: goslim_flybase_ribbon
subset: goslim_mouse
subset: goslim_pir
+subset: prokaryote_subset
synonym: "cell process" BROAD []
synonym: "cellular process" BROAD []
synonym: "cellular projection" EXACT []
@@ -232121,19 +232120,21 @@ relationship: positively_regulates GO:0043001 ! Golgi to plasma membrane protein
[Term]
id: GO:0042999
-name: regulation of Golgi to plasma membrane CFTR protein transport
+name: obsolete regulation of Golgi to plasma membrane CFTR protein transport
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transport of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein from the Golgi to the plasma membrane." [GOC:jl]
-is_a: GO:0042996 ! regulation of Golgi to plasma membrane protein transport
-relationship: regulates GO:0043000 ! Golgi to plasma membrane CFTR protein transport
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transport of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein from the Golgi to the plasma membrane." [GOC:jl]
+comment: This term was made obsolete because it involved a specific gene product.
+is_obsolete: true
[Term]
id: GO:0043000
-name: Golgi to plasma membrane CFTR protein transport
+name: obsolete Golgi to plasma membrane CFTR protein transport
namespace: biological_process
-def: "The directed movement of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein from the Golgi to the plasma membrane." [GOC:jl]
+def: "OBSOLETE. The directed movement of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein from the Golgi to the plasma membrane." [GOC:jl]
+comment: This term was made obsolete because it involved a specific gene product.
synonym: "Golgi to plasma membrane cystic fibrosis transmembrane conductance regulator protein transport" EXACT []
-is_a: GO:0043001 ! Golgi to plasma membrane protein transport
+is_obsolete: true
+replaced_by: GO:0043001
[Term]
id: GO:0043001
@@ -232146,36 +232147,35 @@ is_a: GO:0061951 ! establishment of protein localization to plasma membrane
[Term]
id: GO:0043002
-name: negative regulation of Golgi to plasma membrane CFTR protein transport
+name: obsolete negative regulation of Golgi to plasma membrane CFTR protein transport
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transport of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein from the Golgi to the plasma membrane." [GOC:jl]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transport of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein from the Golgi to the plasma membrane." [GOC:jl]
+comment: This term was made obsolete because it involved a specific gene product.
synonym: "down regulation of Golgi to plasma membrane CFTR protein transport" EXACT []
synonym: "down-regulation of Golgi to plasma membrane CFTR protein transport" EXACT []
synonym: "downregulation of Golgi to plasma membrane CFTR protein transport" EXACT []
synonym: "inhibition of Golgi to plasma membrane CFTR protein transport" NARROW []
-is_a: GO:0042997 ! negative regulation of Golgi to plasma membrane protein transport
-is_a: GO:0042999 ! regulation of Golgi to plasma membrane CFTR protein transport
-relationship: negatively_regulates GO:0043000 ! Golgi to plasma membrane CFTR protein transport
+is_obsolete: true
[Term]
id: GO:0043003
-name: positive regulation of Golgi to plasma membrane CFTR protein transport
+name: obsolete positive regulation of Golgi to plasma membrane CFTR protein transport
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of transport of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein from the Golgi to the plasma membrane." [GOC:jl]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transport of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein from the Golgi to the plasma membrane." [GOC:jl]
+comment: This term was made obsolete because it involved a specific gene product.
synonym: "activation of Golgi to plasma membrane CFTR protein transport" NARROW []
synonym: "stimulation of Golgi to plasma membrane CFTR protein transport" NARROW []
synonym: "up regulation of Golgi to plasma membrane CFTR protein transport" EXACT []
synonym: "up-regulation of Golgi to plasma membrane CFTR protein transport" EXACT []
synonym: "upregulation of Golgi to plasma membrane CFTR protein transport" EXACT []
-is_a: GO:0042998 ! positive regulation of Golgi to plasma membrane protein transport
-is_a: GO:0042999 ! regulation of Golgi to plasma membrane CFTR protein transport
-relationship: positively_regulates GO:0043000 ! Golgi to plasma membrane CFTR protein transport
+is_obsolete: true
[Term]
id: GO:0043004
-name: cytoplasmic sequestering of CFTR protein
+name: obsolete cytoplasmic sequestering of CFTR protein
namespace: biological_process
-def: "The selective interaction of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein with specific molecules in the cytoplasm, thereby inhibiting its transport to the cell membrane." [GOC:jl]
+def: "OBSOLETE. The selective interaction of Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein with specific molecules in the cytoplasm, thereby inhibiting its transport to the cell membrane." [GOC:jl]
+comment: This term was made obsolete because it involved a specific gene product.
synonym: "cytoplasmic retention of CFTR (cystic fibrosis transmembrane conductance regulator) protein" EXACT []
synonym: "cytoplasmic sequestering of cystic fibrosis transmembrane conductance regulator protein" EXACT []
synonym: "cytoplasmic sequestration of CFTR (cystic fibrosis transmembrane conductance regulator protein)" EXACT []
@@ -232185,8 +232185,7 @@ synonym: "retention of CFTR (cystic fibrosis transmembrane conductance regulator
synonym: "sequestering of CFTR (cystic fibrosis transmembrane conductance regulator protein) in cytoplasm" EXACT []
synonym: "sequestration of CFTR (cystic fibrosis transmembrane conductance regulator protein) in cytoplasm" EXACT []
synonym: "storage of CFTR (cystic fibrosis transmembrane conductance regulator) protein in cytoplasm" EXACT []
-is_a: GO:0043002 ! negative regulation of Golgi to plasma membrane CFTR protein transport
-is_a: GO:0051220 ! cytoplasmic sequestering of protein
+is_obsolete: true
[Term]
id: GO:0043005
@@ -232204,14 +232203,14 @@ is_a: GO:0120025 ! plasma membrane bounded cell projection
[Term]
id: GO:0043006
-name: activation of phospholipase A2 activity by calcium-mediated signaling
+name: obsolete activation of phospholipase A2 activity by calcium-mediated signaling
namespace: biological_process
-def: "A series of molecular signals that leads to the upregulation of calcium-dependent phospholipase A2 activity in response to the signal." [GOC:dph, GOC:jl, GOC:tb]
+def: "OBSOLETE. The series of molecular signals that leads to the upregulation of calcium-dependent phospholipase A2 activity in response to the signal." [GOC:dph, GOC:jl, GOC:tb]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of phospholipase A2 activity by calcium-mediated signalling" EXACT [GOC:mah]
synonym: "calcium-dependent activation of phospholipase A2" EXACT [GOC:dph, GOC:tb]
synonym: "calcium-dependent phospholipase A2 activation" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0019722 ! calcium-mediated signaling
-is_a: GO:0032431 ! activation of phospholipase A2 activity
+is_obsolete: true
[Term]
id: GO:0043007
@@ -232309,7 +232308,6 @@ synonym: "flavocytochrome b558" NARROW []
synonym: "respiratory-burst oxidase" RELATED []
is_a: GO:0098797 ! plasma membrane protein complex
is_a: GO:1990204 ! oxidoreductase complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0043021
@@ -232336,14 +232334,14 @@ id: GO:0043023
name: ribosomal large subunit binding
namespace: molecular_function
def: "Binding to a large ribosomal subunit." [GOC:go_curators]
-is_a: GO:0043021 ! ribonucleoprotein complex binding
+is_a: GO:0043022 ! ribosome binding
[Term]
id: GO:0043024
name: ribosomal small subunit binding
namespace: molecular_function
def: "Binding to a small ribosomal subunit." [GOC:go_curators]
-is_a: GO:0043021 ! ribonucleoprotein complex binding
+is_a: GO:0043022 ! ribosome binding
[Term]
id: GO:0043025
@@ -232365,7 +232363,6 @@ name: cysteine-type endopeptidase inhibitor activity involved in apoptotic proce
namespace: molecular_function
def: "Binds to and stops, prevents or reduces the activity of a cysteine-type endopeptidase involved in the apoptotic process." [GOC:jl, GOC:mtg_apoptosis, PMID:14744432, Wikipedia:Caspase]
synonym: "caspase inhibitor activity" BROAD []
-is_a: GO:0004869 ! cysteine-type endopeptidase inhibitor activity
is_a: GO:0043028 ! cysteine-type endopeptidase regulator activity involved in apoptotic process
[Term]
@@ -232464,13 +232461,13 @@ id: GO:0043038
name: amino acid activation
namespace: biological_process
def: "The modification of an amino acid to an active form, for incorporation into a peptide, protein or other macromolecule." [GOC:jl]
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
[Term]
id: GO:0043039
name: tRNA aminoacylation
namespace: biological_process
-def: "The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules." [GOC:ma, GOC:mah, MetaCyc:Aminoacyl-tRNAs]
+def: "The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules." [GOC:ma, GOC:mah, MetaCyc:Aminoacyl-tRNAs]
synonym: "aminoacyl-tRNA biosynthesis" EXACT [GOC:mah]
synonym: "aminoacyl-tRNA biosynthetic process" EXACT [GOC:mah]
synonym: "tRNA charging" EXACT []
@@ -232527,7 +232524,7 @@ namespace: biological_process
def: "The covalent transfer of a methyl group to C-5 of cytosine that contributes to the epigenetic regulation of embryonic gene expression." [GOC:go_curators, PMID:12138111]
synonym: "de novo DNA methylation" RELATED []
is_a: GO:0006306 ! DNA methylation
-is_a: GO:1901538 ! changes to DNA methylation involved in embryo development
+relationship: part_of GO:0009790 ! embryo development
[Term]
id: GO:0043046
@@ -232672,6 +232669,7 @@ name: extracellular structure organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite." [GOC:ai, GOC:dph, GOC:jl, GOC:mah]
subset: goslim_pir
+subset: prokaryote_subset
synonym: "extracellular structure organisation" EXACT []
synonym: "extracellular structure organization and biogenesis" EXACT [GOC:dph, GOC:jl, GOC:mah]
is_a: GO:0016043 ! cellular component organization
@@ -233016,7 +233014,7 @@ id: GO:0043102
name: amino acid salvage
namespace: biological_process
def: "Any process which produces an amino acid from derivatives of it, without de novo synthesis." [GOC:jl]
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
+is_a: GO:0008652 ! amino acid biosynthetic process
is_a: GO:0043094 ! cellular metabolic compound salvage
[Term]
@@ -233092,8 +233090,8 @@ comment: See also the biological process term 'site-specific replication termina
synonym: "negative regulation of DNA replication at replication fork barrier" EXACT [GOC:dph, GOC:tb]
synonym: "replication fork blocking" EXACT []
synonym: "replication fork stalling" EXACT []
-is_a: GO:0045005 ! DNA-dependent DNA replication maintenance of fidelity
-is_a: GO:2000104 ! negative regulation of DNA-dependent DNA replication
+is_a: GO:0045005 ! DNA-templated DNA replication maintenance of fidelity
+is_a: GO:2000104 ! negative regulation of DNA-templated DNA replication
[Term]
id: GO:0043112
@@ -233101,7 +233099,7 @@ name: receptor metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:jl]
synonym: "receptor metabolism" EXACT []
-is_a: GO:0044260 ! cellular macromolecule metabolic process
+is_a: GO:0043170 ! macromolecule metabolic process
[Term]
id: GO:0043113
@@ -233123,7 +233121,7 @@ relationship: part_of GO:0008015 ! blood circulation
id: GO:0043115
name: precorrin-2 dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD(+) + precorrin-2 = 2 H(+) + NADH + sirohydrochlorin." [EC:1.3.1.76, RHEA:15613]
+def: "Catalysis of the reaction: NAD+ + precorrin-2 = 2 H+ + NADH + sirohydrochlorin." [EC:1.3.1.76, RHEA:15613]
synonym: "1,3-dimethyluroporphyrinogen III dehydrogenase activity" EXACT []
synonym: "CysG" RELATED [EC:1.3.1.76]
synonym: "dihydrosirohydrochlorin dehydrogenase activity" EXACT []
@@ -233281,8 +233279,12 @@ is_a: GO:0090218 ! positive regulation of lipid kinase activity
id: GO:0043129
name: surfactant homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of a steady-state level of the surface-active lipoprotein mixture which coats the alveoli." [PMID:9751757]
-is_a: GO:0048875 ! chemical homeostasis within a tissue
+alt_id: GO:0050828
+def: "Any process involved in the maintenance of a steady-state level of a surface-active agent that maintains the surface tension of a liquid." [PMID:23708874, PMID:9751757]
+synonym: "regulation of liquid surface tension" RELATED []
+synonym: "regulation of surface tension of a liquid" RELATED []
+synonym: "surfactant activity" RELATED []
+is_a: GO:0140962 ! multicellular organismal-level chemical homeostasis
[Term]
id: GO:0043130
@@ -233315,7 +233317,7 @@ synonym: "oxidized NAD transport" EXACT []
synonym: "oxidized nicotinamide adenine dinucleotide transport" EXACT []
synonym: "reduced NAD transport" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide transport" EXACT []
-is_a: GO:0006862 ! nucleotide transport
+is_a: GO:0051503 ! adenine nucleotide transport
[Term]
id: GO:0043133
@@ -233366,10 +233368,11 @@ id: GO:0043138
name: 3'-5' DNA helicase activity
namespace: molecular_function
alt_id: GO:0043140
-def: "Unwinding a DNA helix in the direction 5' to 3', driven by ATP hydrolysis." [GOC:jl]
+def: "Unwinding a DNA helix in the direction 5' to 3', driven by ATP hydrolysis." [EC:5.6.2.4, GOC:jl]
synonym: "3' to 5' DNA helicase activity" EXACT []
synonym: "ATP-dependent 3' to 5' DNA helicase activity" EXACT []
synonym: "ATP-dependent 3'-5' DNA helicase activity" EXACT []
+xref: EC:5.6.2.4
xref: Reactome:R-HSA-167097 "HIV Promoter Opening: First Transition"
xref: Reactome:R-HSA-174438 "Formation of the Flap Intermediate on the C-strand"
xref: Reactome:R-HSA-75949 "RNA Polymerase II Promoter Opening: First Transition"
@@ -233386,11 +233389,12 @@ name: 5'-3' DNA helicase activity
namespace: molecular_function
alt_id: GO:0008722
alt_id: GO:0043141
-def: "Unwinding a DNA helix in the 5' to 3' direction, driven by ATP hydrolysis." [GOC:jl]
+def: "Unwinding a DNA helix in the 5' to 3' direction, driven by ATP hydrolysis." [EC:5.6.2.3, GOC:jl]
synonym: "5' to 3' DNA helicase activity" EXACT []
synonym: "ATP-dependent 5' to 3' DNA helicase activity" EXACT []
synonym: "ATP-dependent 5'-3' DNA helicase activity" EXACT []
synonym: "DNA helicase IV activity" NARROW []
+xref: EC:5.6.2.3
xref: Reactome:R-HSA-6782131 "ERCC2-facilitated RNA Pol II backtracking in TC-NER"
is_a: GO:0003678 ! DNA helicase activity
@@ -233405,7 +233409,7 @@ synonym: "regulation of translation by machinery localisation" EXACT [GOC:mah]
synonym: "translational machinery localization" EXACT [GOC:dph, GOC:tb]
synonym: "translational protein localization" EXACT []
is_a: GO:0006417 ! regulation of translation
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
relationship: part_of GO:0006412 ! translation
[Term]
@@ -233521,13 +233525,13 @@ is_a: GO:0009651 ! response to salt stress
[Term]
id: GO:0043158
-name: heterocyst differentiation
+name: heterocyst development
namespace: biological_process
-def: "The process in which a relatively unspecialized cell acquires specialized features of a heterocyst, a differentiated cell in certain cyanobacteria whose purpose is to fix nitrogen." [GOC:jl]
-synonym: "heterocyst biosynthesis" EXACT []
-synonym: "heterocyst cell differentiation" EXACT []
+def: "The cellular developmental process by which a cell becomes a heterocyst, a cell that carries out nitrogen fixation. This process involves changes to the cell wall, expression of nitrogenase and other proteins involved in nitrogen fixation, and degradation of photosystem II, which produces oxygen. This process is known to occur in some cyanobacteria." [PMID:11121783, PMID:35744626]
+synonym: "heterocyst cell differentiation" RELATED []
+synonym: "heterocyst differentiation" RELATED []
synonym: "heterocyst formation" EXACT []
-is_a: GO:0030154 ! cell differentiation
+is_a: GO:0048869 ! cellular developmental process
[Term]
id: GO:0043159
@@ -233635,6 +233639,7 @@ is_a: GO:0043167 ! ion binding
id: GO:0043170
name: macromolecule metabolic process
namespace: biological_process
+alt_id: GO:0034960
alt_id: GO:0043283
alt_id: GO:0044259
def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:mah]
@@ -233758,7 +233763,7 @@ synonym: "vacuolar sequestration of sodium ion (Na+)" EXACT []
synonym: "vacuolar sodium ion (Na+) retention" EXACT []
synonym: "vacuolar sodium ion (Na+) storage" EXACT []
is_a: GO:0043181 ! vacuolar sequestering
-relationship: part_of GO:0006883 ! cellular sodium ion homeostasis
+relationship: part_of GO:0006883 ! intracellular sodium ion homeostasis
[Term]
id: GO:0043183
@@ -233871,7 +233876,7 @@ relationship: part_of GO:0044304 ! main axon
id: GO:0043197
name: dendritic spine
namespace: cellular_component
-def: "A small, membranous protrusion from a dendrite that forms a postsynaptic compartment, typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable:they can be thin, stubby, mushroom, or branched, with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity." [GOC:nln]
+def: "A small, membranous protrusion from a dendrite that forms a postsynaptic compartment, typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable:they can be thin, stubby, mushroom, or branched, with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity." [GOC:nln]
subset: goslim_synapse
synonym: "branched dendritic spine" NARROW [NIF_Subcellular:sao965204139]
synonym: "dendrite spine" EXACT []
@@ -233984,6 +233989,8 @@ name: alkanesulfonate binding
namespace: molecular_function
def: "Binding to alkanesulfonates, the anion of alkanesulfonic acids, sulfonic acid derivatives containing an aliphatic hydrocarbon group." [GOC:mlg]
is_a: GO:0043168 ! anion binding
+is_a: GO:0043177 ! organic acid binding
+is_a: GO:1901681 ! sulfur compound binding
[Term]
id: GO:0043211
@@ -234132,7 +234139,6 @@ synonym: "ATPase-coupled anion transmembrane transporter activity" EXACT []
xref: Reactome:R-HSA-1454916 "The ABCC family mediates organic anion transport"
xref: Reactome:R-HSA-5690340 "Defective ABCC6 does not transport organic anion from cytosol to extracellular region"
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0042626 ! ATPase-coupled transmembrane transporter activity
[Term]
@@ -234143,6 +234149,7 @@ def: "Organized structure of distinctive morphology and function. Includes the n
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
+subset: prokaryote_subset
xref: NIF_Subcellular:sao1539965131
xref: Wikipedia:Organelle
is_a: GO:0110165 ! cellular anatomical entity
@@ -234161,6 +234168,7 @@ id: GO:0043228
name: non-membrane-bounded organelle
namespace: cellular_component
def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators]
+subset: goslim_mouse
synonym: "biological condensate" NARROW []
synonym: "non-membrane-enclosed organelle" EXACT []
xref: NIF_Subcellular:sao1456184038
@@ -234199,7 +234207,6 @@ id: GO:0043232
name: intracellular non-membrane-bounded organelle
namespace: cellular_component
def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators]
-subset: goslim_mouse
subset: goslim_pir
synonym: "intracellular non-membrane-enclosed organelle" EXACT []
is_a: GO:0043228 ! non-membrane-bounded organelle
@@ -234210,6 +234217,7 @@ id: GO:0043233
name: organelle lumen
namespace: cellular_component
def: "The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen." [GOC:jl, GOC:mah]
+subset: goslim_mouse
is_a: GO:0031974 ! membrane-enclosed lumen
relationship: part_of GO:0043226 ! organelle
@@ -234312,7 +234320,7 @@ namespace: biological_process
def: "Any process that occur in response to the presence of critically short or damaged telomeres." [GOC:BHF, GOC:BHF_telomere, GOC:jbu, PMID:15279784]
synonym: "DNA damage response, telomere maintenance" EXACT []
is_a: GO:0000723 ! telomere maintenance
-is_a: GO:0006974 ! cellular response to DNA damage stimulus
+is_a: GO:0006974 ! DNA damage response
[Term]
id: GO:0043248
@@ -234437,17 +234445,19 @@ is_a: GO:0043256 ! laminin complex
[Term]
id: GO:0043262
-name: adenosine-diphosphatase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: ADP + H2O = AMP + phosphate." [EC:3.6.1.5, PMID:1470606]
-synonym: "adenosine diphosphatase activity" EXACT []
-synonym: "ADPase" BROAD [EC:3.6.1.5]
-synonym: "ADPase activity" RELATED [EC:3.6.1.5]
-synonym: "ATP diphosphohydrolase activity" RELATED [EC:3.6.1.5]
-synonym: "ATP-diphosphatase activity" RELATED [EC:3.6.1.5]
+name: ADP phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: ADP + H2O = AMP + phosphate." [PMID:1470606, RHEA:61436]
+synonym: "adenosine diphosphatase activity" RELATED []
+synonym: "adenosine-diphosphatase activity" EXACT []
+synonym: "ADP diphosphatase activity" BROAD []
+synonym: "ADPase" BROAD []
+synonym: "ADPase activity" RELATED []
+synonym: "ATP diphosphohydrolase activity" RELATED []
+synonym: "ATP-diphosphatase activity" RELATED []
xref: MetaCyc:APYRASE-RXN
xref: RHEA:61436
-is_a: GO:0017110 ! nucleoside-diphosphatase activity
+is_a: GO:0017110 ! nucleoside diphosphate phosphatase activity
[Term]
id: GO:0043263
@@ -234505,7 +234515,7 @@ synonym: "regulation of K+ conductance" NARROW []
synonym: "regulation of potassium conductance" NARROW []
synonym: "transmembrane conductance regulator activity" RELATED []
is_a: GO:0043266 ! regulation of potassium ion transport
-is_a: GO:0043271 ! negative regulation of ion transport
+is_a: GO:0043271 ! negative regulation of monoatomic ion transport
relationship: negatively_regulates GO:0006813 ! potassium ion transport
[Term]
@@ -234524,20 +234534,21 @@ synonym: "up regulation of potassium ion transport" EXACT []
synonym: "up-regulation of potassium ion transport" EXACT []
synonym: "upregulation of potassium ion transport" EXACT []
is_a: GO:0043266 ! regulation of potassium ion transport
-is_a: GO:0043270 ! positive regulation of ion transport
+is_a: GO:0043270 ! positive regulation of monoatomic ion transport
relationship: positively_regulates GO:0006813 ! potassium ion transport
[Term]
id: GO:0043269
-name: regulation of ion transport
+name: regulation of monoatomic ion transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl]
+synonym: "regulation of ion transport" BROAD []
is_a: GO:0051049 ! regulation of transport
-relationship: regulates GO:0006811 ! ion transport
+relationship: regulates GO:0006811 ! monoatomic ion transport
[Term]
id: GO:0043270
-name: positive regulation of ion transport
+name: positive regulation of monoatomic ion transport
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl]
synonym: "activation of ion transport" NARROW []
@@ -234545,22 +234556,23 @@ synonym: "stimulation of ion transport" NARROW []
synonym: "up regulation of ion transport" EXACT []
synonym: "up-regulation of ion transport" EXACT []
synonym: "upregulation of ion transport" EXACT []
-is_a: GO:0043269 ! regulation of ion transport
+is_a: GO:0043269 ! regulation of monoatomic ion transport
is_a: GO:0051050 ! positive regulation of transport
-relationship: positively_regulates GO:0006811 ! ion transport
+relationship: positively_regulates GO:0006811 ! monoatomic ion transport
[Term]
id: GO:0043271
-name: negative regulation of ion transport
+name: negative regulation of monoatomic ion transport
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl]
synonym: "down regulation of ion transport" EXACT []
synonym: "down-regulation of ion transport" EXACT []
synonym: "downregulation of ion transport" EXACT []
synonym: "inhibition of ion transport" NARROW []
-is_a: GO:0043269 ! regulation of ion transport
+synonym: "negative regulation of ion transport" BROAD []
+is_a: GO:0043269 ! regulation of monoatomic ion transport
is_a: GO:0051051 ! negative regulation of transport
-relationship: negatively_regulates GO:0006811 ! ion transport
+relationship: negatively_regulates GO:0006811 ! monoatomic ion transport
[Term]
id: GO:0043272
@@ -234580,11 +234592,12 @@ name: CTPase activity
namespace: molecular_function
alt_id: GO:0061747
alt_id: GO:0061748
-def: "Catalysis of the reaction: CTP + H2O = CDP + phosphate. May or may not be coupled to another reaction." [GOC:go_curators]
+def: "Catalysis of the reaction: CTP + H2O = CDP + H+ + phosphate. May or may not be coupled to another reaction." [RHEA:29387]
synonym: "CTPase activity, coupled" RELATED []
synonym: "cytidine triphosphatase activity" EXACT []
synonym: "single-stranded DNA-dependent CTPase activity" NARROW []
-is_a: GO:0017111 ! nucleoside-triphosphatase activity
+xref: RHEA:29387
+is_a: GO:0017111 ! ribonucleoside triphosphate phosphatase activity
[Term]
id: GO:0043274
@@ -234652,6 +234665,7 @@ name: response to morphine
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a morphine stimulus. Morphine is an opioid alkaloid, isolated from opium, with a complex ring structure." [GOC:ef, GOC:jl]
is_a: GO:0014072 ! response to isoquinoline alkaloid
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0043279
@@ -234790,9 +234804,6 @@ name: glutathione binding
namespace: molecular_function
def: "Binding to glutathione; a tripeptide composed of the three amino acids cysteine, glutamic acid and glycine." [GOC:bf, ISBN:0198506732]
is_a: GO:0043168 ! anion binding
-is_a: GO:0072341 ! modified amino acid binding
-is_a: GO:1900750 ! oligopeptide binding
-is_a: GO:1901681 ! sulfur compound binding
[Term]
id: GO:0043296
@@ -234891,7 +234902,6 @@ synonym: "regulation of mast cell granule exocytosis" EXACT []
is_a: GO:0002886 ! regulation of myeloid leukocyte mediated immunity
is_a: GO:0033006 ! regulation of mast cell activation involved in immune response
is_a: GO:0043300 ! regulation of leukocyte degranulation
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0043303 ! mast cell degranulation
[Term]
@@ -235330,11 +235340,13 @@ is_a: GO:0140097 ! catalytic activity, acting on DNA
[Term]
id: GO:0043337
-name: CDP-diacylglycerol-phosphatidylglycerol phosphatidyltransferase activity
+name: cardiolipin synthase (CMP-forming)
namespace: molecular_function
def: "Catalysis of the reaction: CDP-diacylglycerol + phosphatidylglycerol = CMP + diphosphatidylglycerol." [GOC:jl]
synonym: "cardiolipin synthase" BROAD []
synonym: "cardiolipin synthetase" BROAD []
+synonym: "CDP-diacylglycerol-phosphatidylglycerol phosphatidyltransferase activity" EXACT []
+xref: EC:2.7.8.41
xref: MetaCyc:RXN-8141
xref: Reactome:R-HSA-1483063 "PG and CDP-DAG are converted to CL by CRLS1"
xref: RHEA:32931
@@ -235713,7 +235725,6 @@ synonym: "pre-T-cell receptor complex" EXACT []
synonym: "pre-T-lymphocyte receptor complex" EXACT []
synonym: "pre-TCR complex" EXACT []
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0043385
@@ -235845,7 +235856,7 @@ is_a: GO:0035933 ! glucocorticoid secretion
id: GO:0043401
name: steroid hormone mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals mediated by a steroid hormone binding to a receptor." [PMID:12606724]
+def: "The series of molecular signals mediated by a steroid hormone binding to a receptor." [PMID:12606724]
synonym: "steroid hormone mediated signalling" EXACT []
is_a: GO:0009755 ! hormone-mediated signaling pathway
relationship: part_of GO:0071383 ! cellular response to steroid hormone stimulus
@@ -235854,7 +235865,7 @@ relationship: part_of GO:0071383 ! cellular response to steroid hormone stimulus
id: GO:0043402
name: glucocorticoid mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of a glucocorticoid hormone." [PMID:15240347]
+def: "The series of molecular signals mediated by the detection of a glucocorticoid hormone." [PMID:15240347]
synonym: "glucocorticoid mediated signalling" EXACT []
is_a: GO:0043401 ! steroid hormone mediated signaling pathway
relationship: part_of GO:0071385 ! cellular response to glucocorticoid stimulus
@@ -236015,7 +236026,6 @@ namespace: biological_process
def: "The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule." [GOC:go_curators]
is_a: GO:0032259 ! methylation
is_a: GO:0043412 ! macromolecule modification
-is_a: GO:0044260 ! cellular macromolecule metabolic process
[Term]
id: GO:0043415
@@ -236064,7 +236074,7 @@ synonym: "homocysteine breakdown" EXACT []
synonym: "homocysteine catabolism" EXACT []
synonym: "homocysteine degradation" EXACT []
is_a: GO:0000098 ! sulfur amino acid catabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0050667 ! homocysteine metabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
@@ -236078,7 +236088,7 @@ synonym: "urea catabolism" EXACT []
synonym: "urea decomposition" EXACT []
synonym: "urea degradation" EXACT []
is_a: GO:0019627 ! urea metabolic process
-is_a: GO:0043605 ! cellular amide catabolic process
+is_a: GO:0043605 ! amide catabolic process
is_a: GO:0044282 ! small molecule catabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
@@ -236096,7 +236106,7 @@ synonym: "anthranilic acid metabolism" NARROW []
synonym: "ortho-aminobenzoic acid metabolic process" NARROW []
synonym: "ortho-aminobenzoic acid metabolism" NARROW []
xref: UM-BBD_pathwayID:abz2
-is_a: GO:0009072 ! aromatic amino acid family metabolic process
+is_a: GO:0009072 ! aromatic amino acid metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:0042537 ! benzene-containing compound metabolic process
@@ -236327,9 +236337,10 @@ is_a: GO:0046952 ! ketone body catabolic process
[Term]
id: GO:0043443
-name: acetone metabolic process
+name: obsolete acetone metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving acetone, propan-2-one." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways involving acetone, propan-2-one." [GOC:jl]
+comment: This term was obsoleted because it is not a biological process as defined by GO.
synonym: "2-propanone metabolic process" EXACT []
synonym: "2-propanone metabolism" EXACT []
synonym: "acetone metabolism" EXACT []
@@ -236337,14 +236348,15 @@ synonym: "dimethyl ketone metabolic process" EXACT []
synonym: "dimethyl ketone metabolism" EXACT []
synonym: "propan-2-one metabolic process" EXACT []
synonym: "propan-2-one metabolism" EXACT []
-is_a: GO:0042180 ! cellular ketone metabolic process
-is_a: GO:1902224 ! ketone body metabolic process
+is_obsolete: true
+consider: GO:0140977
[Term]
id: GO:0043444
-name: acetone catabolic process
+name: obsolete acetone catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of acetone, propan-2-one." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of acetone, propan-2-one." [GOC:jl]
+comment: This term was obsoleted because it is not a biological process as defined by GO.
synonym: "2-propanone catabolic process" EXACT []
synonym: "2-propanone catabolism" EXACT []
synonym: "acetone breakdown" EXACT []
@@ -236354,15 +236366,15 @@ synonym: "dimethyl ketone catabolic process" EXACT []
synonym: "dimethyl ketone catabolism" EXACT []
synonym: "propan-2-one catabolic process" EXACT []
synonym: "propan-2-one catabolism" EXACT []
-is_a: GO:0042182 ! ketone catabolic process
-is_a: GO:0043443 ! acetone metabolic process
-is_a: GO:0046952 ! ketone body catabolic process
+is_obsolete: true
+consider: GO:0140977
[Term]
id: GO:0043445
-name: acetone biosynthetic process
+name: obsolete acetone biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of acetone, propan-2-one." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of acetone, propan-2-one." [GOC:jl]
+comment: This term was obsoleted because it is not a biological process as defined by GO.
synonym: "2-propanone biosynthesis" EXACT []
synonym: "2-propanone biosynthetic process" EXACT []
synonym: "acetone anabolism" EXACT []
@@ -236373,9 +236385,7 @@ synonym: "dimethyl ketone biosynthesis" EXACT []
synonym: "dimethyl ketone biosynthetic process" EXACT []
synonym: "propan-2-one biosynthesis" EXACT []
synonym: "propan-2-one biosynthetic process" EXACT []
-is_a: GO:0042181 ! ketone biosynthetic process
-is_a: GO:0043443 ! acetone metabolic process
-is_a: GO:0046951 ! ketone body biosynthetic process
+is_obsolete: true
[Term]
id: GO:0043446
@@ -236482,7 +236492,6 @@ synonym: "alkyne breakdown" EXACT []
synonym: "alkyne catabolism" EXACT []
synonym: "alkyne degradation" EXACT []
is_a: GO:0043452 ! cellular alkyne metabolic process
-is_a: GO:0044248 ! cellular catabolic process
is_a: GO:0120248 ! acetylenic compound catabolic process
is_a: GO:0120253 ! hydrocarbon catabolic process
@@ -236503,10 +236512,9 @@ def: "Any process that modulates the frequency, rate or extent of the pentose-ph
synonym: "regulation of pentose phosphate pathway" EXACT []
synonym: "regulation of pentose phosphate shunt" EXACT []
synonym: "regulation of pentose-phosphate pathway" EXACT []
-is_a: GO:0019220 ! regulation of phosphate metabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0043467 ! regulation of generation of precursor metabolites and energy
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
is_a: GO:1902031 ! regulation of NADP metabolic process
relationship: regulates GO:0006098 ! pentose-phosphate shunt
@@ -236518,17 +236526,6 @@ def: "Any process that modulates the frequency, rate or extent of cellular respi
is_a: GO:0043467 ! regulation of generation of precursor metabolites and energy
relationship: regulates GO:0045333 ! cellular respiration
-[Term]
-id: GO:0043458
-name: ethanol biosynthetic process involved in glucose fermentation to ethanol
-namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of ethanol, CH3-CH2-OH, as part of the process of glucose catabolism to ethanol, CO2 and ATP." [GOC:dph, GOC:jl, GOC:tb]
-synonym: "ethanol anabolism during fermentation" RELATED []
-synonym: "ethanol formation during fermentation" RELATED []
-synonym: "ethanol synthesis during fermentation" RELATED []
-is_a: GO:0006115 ! ethanol biosynthetic process
-relationship: part_of GO:0019655 ! glycolytic fermentation to ethanol
-
[Term]
id: GO:0043459
name: obsolete response to short exposure to lithium ion
@@ -236572,7 +236569,7 @@ def: "Any process that modulates the frequency, rate or extent of the chemical r
synonym: "regulation of rhamnose breakdown" EXACT []
synonym: "regulation of rhamnose catabolism" EXACT []
synonym: "regulation of rhamnose degradation" EXACT []
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
relationship: regulates GO:0019301 ! rhamnose catabolic process
@@ -236619,7 +236616,7 @@ id: GO:0043468
name: regulation of fucose catabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of fucose." [GOC:mlg]
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
relationship: regulates GO:0019317 ! fucose catabolic process
@@ -236628,7 +236625,7 @@ id: GO:0043469
name: regulation of D-xylose catabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of xylose." [GOC:mlg]
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
relationship: regulates GO:0042843 ! D-xylose catabolic process
@@ -236643,14 +236640,12 @@ relationship: regulates GO:0016052 ! carbohydrate catabolic process
[Term]
id: GO:0043471
-name: regulation of cellular carbohydrate catabolic process
+name: obsolete regulation of cellular carbohydrate catabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates, carried out by individual cells." [GOC:jl]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
-is_a: GO:0031329 ! regulation of cellular catabolic process
-is_a: GO:0043470 ! regulation of carbohydrate catabolic process
-is_a: GO:0060255 ! regulation of macromolecule metabolic process
-relationship: regulates GO:0044275 ! cellular carbohydrate catabolic process
+def: "OBSOLETE. Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates, carried out by individual cells." [GOC:jl]
+comment: This term was obsoleted because it is not different from its parent, regulation of carbohydrate catabolic process ; GO:0043470.
+is_obsolete: true
+replaced_by: GO:0043470
[Term]
id: GO:0043472
@@ -236778,20 +236773,22 @@ relationship: part_of GO:0048757 ! pigment granule maturation
[Term]
id: GO:0043486
-name: histone exchange
+name: obsolete histone exchange
namespace: biological_process
-def: "The replacement, within chromatin, of resident histones or histone subunits with alternative, sometimes variant, histones or subunits." [GOC:jl, PMID:11735001, PMID:15066277]
-comment: Note that this term also includes the exchange of sperm-specific histones or protamines with histones, occurring during spermatogenesis and fertilization.
+def: "OBSOLETE. The replacement, within chromatin, of resident histones or histone subunits with alternative, sometimes variant, histones or subunits." [GOC:jl, PMID:11735001, PMID:15066277]
+comment: This term was obsoleted because it represents a molecular function, histone chaperone activity.
synonym: "histone chaperone" RELATED [GOC:vw]
synonym: "histone replacement" EXACT []
-is_a: GO:0034728 ! nucleosome organization
+is_obsolete: true
+consider: GO:0006338
+consider: GO:0140713
[Term]
id: GO:0043487
name: regulation of RNA stability
namespace: biological_process
def: "Any process that modulates the propensity of RNA molecules to degradation. Includes processes that both stabilize and destabilize RNAs." [GOC:jl]
-is_a: GO:0010608 ! posttranscriptional regulation of gene expression
+is_a: GO:0010608 ! post-transcriptional regulation of gene expression
is_a: GO:0031329 ! regulation of cellular catabolic process
is_a: GO:0051252 ! regulation of RNA metabolic process
is_a: GO:0065008 ! regulation of biological quality
@@ -236847,7 +236844,7 @@ is_a: GO:0035556 ! intracellular signal transduction
id: GO:0043493
name: viral terminase complex
namespace: cellular_component
-def: "A complex of a large and small subunit which catalyze the packaging of DNA into viral heads. Note that not all viral terminases have this structure, some exist as single polypeptides." [GOC:bf, GOC:bm, GOC:jl, GOC:mlg]
+def: "A complex of a large and small subunit which catalyze the packaging of DNA into viral heads. Note that not all viral terminases have this structure, some exist as single polypeptides." [GOC:bf, GOC:bm, GOC:jl, GOC:mlg, PMID:18687036]
synonym: "phage terminase complex" NARROW [GOC:bm]
synonym: "virus terminase complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
@@ -236862,8 +236859,8 @@ synonym: "CLRC ubiquitin ligase complex" EXACT []
synonym: "Rik1 E3 ubiquitin ligase complex" EXACT []
synonym: "Rik1-E3 ubiquitin ligase complex" EXACT []
is_a: GO:0000152 ! nuclear ubiquitin ligase complex
-is_a: GO:0031465 ! Cul4B-RING E3 ubiquitin ligase complex
is_a: GO:0035097 ! histone methyltransferase complex
+is_a: GO:0080008 ! Cul4-RING E3 ubiquitin ligase complex
[Term]
id: GO:0043495
@@ -236871,6 +236868,7 @@ name: protein-membrane adaptor activity
namespace: molecular_function
def: "The binding activity of a molecule that brings together a protein or a protein complex with a membrane, or bringing together two membranes, either via membrane lipid binding or by interacting with a membrane protein, to establish or maintain the localization of the protein, protein complex or organelle." [GOC:go_curators]
synonym: "anchoring" RELATED []
+synonym: "membrane-membrane adaptor activity" NARROW []
synonym: "protein membrane adaptor" EXACT []
synonym: "protein membrane adaptor activity" EXACT []
synonym: "protein membrane anchor" RELATED []
@@ -237088,8 +237086,8 @@ name: regulation of DNA damage response, signal transduction by p53 class mediat
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage." [GOC:jl]
synonym: "regulation of p53 induced by DNA damage response" EXACT []
+is_a: GO:0080135 ! regulation of cellular response to stress
is_a: GO:1901796 ! regulation of signal transduction by p53 class mediator
-is_a: GO:2001020 ! regulation of response to DNA damage stimulus
relationship: regulates GO:0030330 ! DNA damage response, signal transduction by p53 class mediator
[Term]
@@ -237105,7 +237103,6 @@ synonym: "up-regulation of DNA damage response, signal transduction by p53 class
synonym: "upregulation of DNA damage response, signal transduction by p53 class mediator" EXACT []
is_a: GO:0043516 ! regulation of DNA damage response, signal transduction by p53 class mediator
is_a: GO:1901798 ! positive regulation of signal transduction by p53 class mediator
-is_a: GO:2001022 ! positive regulation of response to DNA damage stimulus
relationship: positively_regulates GO:0030330 ! DNA damage response, signal transduction by p53 class mediator
[Term]
@@ -237120,7 +237117,6 @@ synonym: "inhibition of DNA damage response, signal transduction by p53 class me
synonym: "negative regulation of p53 induced by DNA damage response" EXACT []
is_a: GO:0043516 ! regulation of DNA damage response, signal transduction by p53 class mediator
is_a: GO:1901797 ! negative regulation of signal transduction by p53 class mediator
-is_a: GO:2001021 ! negative regulation of response to DNA damage stimulus
relationship: negatively_regulates GO:0030330 ! DNA damage response, signal transduction by p53 class mediator
[Term]
@@ -237359,6 +237355,7 @@ def: "A multienzyme, heterooligomeric complex involved in dolichyl-linked oligos
comment: See also the molecular function term 'N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity ; GO:0004577'.
is_a: GO:0098796 ! membrane protein complex
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
[Term]
@@ -237375,7 +237372,7 @@ namespace: biological_process
def: "The addition of an acyl group, any group or radical of the form RCO- where R is an organic group, to a protein amino acid." [GOC:jl]
subset: goslim_yeast
synonym: "protein amino acid acylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0043544
@@ -237857,6 +237854,7 @@ id: GO:0043590
name: bacterial nucleoid
namespace: cellular_component
def: "The region of a bacterial cell to which the DNA is confined." [GOC:jl]
+subset: prokaryote_subset
is_a: GO:0009295 ! nucleoid
is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
@@ -237973,28 +237971,30 @@ is_a: GO:0044270 ! cellular nitrogen compound catabolic process
[Term]
id: GO:0043603
-name: cellular amide metabolic process
+name: amide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells." [GOC:curators]
subset: goslim_pir
synonym: "amide metabolism" EXACT []
-is_a: GO:0034641 ! cellular nitrogen compound metabolic process
+synonym: "cellular amide metabolic process" EXACT []
+is_a: GO:0006807 ! nitrogen compound metabolic process
[Term]
id: GO:0043604
name: amide biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [GOC:curators]
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0044271 ! cellular nitrogen compound biosynthetic process
[Term]
id: GO:0043605
-name: cellular amide catabolic process
+name: amide catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [GOC:curators]
-is_a: GO:0043603 ! cellular amide metabolic process
-is_a: GO:0044270 ! cellular nitrogen compound catabolic process
+synonym: "cellular amide catabolic process" EXACT []
+is_a: GO:0009056 ! catabolic process
+is_a: GO:0043603 ! amide metabolic process
[Term]
id: GO:0043606
@@ -238002,7 +238002,7 @@ name: formamide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving formamide, the simplest amide, HCONH2, derived from formic acid." [GOC:jl]
synonym: "formamide metabolism" EXACT []
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
@@ -238019,7 +238019,7 @@ id: GO:0043608
name: formamide catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of formamide, the simplest amide, HCONH2, derived from formic acid." [GOC:jl]
-is_a: GO:0043605 ! cellular amide catabolic process
+is_a: GO:0043605 ! amide catabolic process
is_a: GO:0043606 ! formamide metabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
@@ -238028,7 +238028,7 @@ id: GO:0043609
name: regulation of carbon utilization
namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of carbon utilization." [GOC:jl]
-is_a: GO:0050789 ! regulation of biological process
+is_a: GO:0032107 ! regulation of response to nutrient levels
relationship: regulates GO:0015976 ! carbon utilization
[Term]
@@ -238037,7 +238037,7 @@ name: regulation of carbohydrate utilization
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of carbohydrate utilization." [GOC:jl]
synonym: "regulation of sugar utilization" NARROW [GOC:mcc2]
-is_a: GO:0050789 ! regulation of biological process
+is_a: GO:0032107 ! regulation of response to nutrient levels
relationship: regulates GO:0009758 ! carbohydrate utilization
[Term]
@@ -238133,7 +238133,7 @@ name: regulation of DNA-templated transcription in response to stress
namespace: biological_process
def: "Modulation of the frequency, rate or extent of transcription from a DNA template as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:jl, GOC:txnOH]
synonym: "regulation of DNA-dependent transcription in response to stress" EXACT [GOC:txnOH]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
is_a: GO:0033554 ! cellular response to stress
[Term]
@@ -238185,18 +238185,20 @@ id: GO:0043627
name: response to estrogen
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics." [GOC:jl, ISBN:0198506732]
+synonym: "response to 17alpha-ethynylestradiol" RELATED []
synonym: "response to estrogen stimulus" EXACT [GOC:dos]
synonym: "response to oestrogen stimulus" EXACT []
is_a: GO:0009725 ! response to hormone
[Term]
id: GO:0043628
-name: ncRNA 3'-end processing
+name: regulatory ncRNA 3'-end processing
namespace: biological_process
-def: "Any process involved in forming the mature 3' end of a non-coding RNA molecule." [GOC:jl]
-synonym: "ncRNA 3' end processing" EXACT []
+def: "Any process involved in forming the mature 3' end of a regulatory non-coding RNA molecule." [GOC:jl]
+synonym: "ncRNA 3' end processing" BROAD []
+synonym: "ncRNA 3'-end processing" BROAD []
+synonym: "small regulatory ncRNA 3'-end processing" NARROW []
is_a: GO:0031123 ! RNA 3'-end processing
-is_a: GO:0034470 ! ncRNA processing
[Term]
id: GO:0043629
@@ -238229,7 +238231,7 @@ id: GO:0043632
name: modification-dependent macromolecule catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, initiated by covalent modification of the target molecule." [GOC:jl]
-is_a: GO:0044265 ! cellular macromolecule catabolic process
+is_a: GO:0009057 ! macromolecule catabolic process
[Term]
id: GO:0043633
@@ -238328,7 +238330,7 @@ is_a: GO:0016137 ! glycoside metabolic process
is_a: GO:0016999 ! antibiotic metabolic process
is_a: GO:0018904 ! ether metabolic process
is_a: GO:0018958 ! phenol-containing compound metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
@@ -238734,7 +238736,9 @@ xref: Reactome:R-HSA-936895 "ATP7B transports cytosolic Cu2+ to Golgi lumen"
xref: RHEA:10376
is_a: GO:0005375 ! copper ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
+is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0043683
@@ -238780,7 +238784,7 @@ synonym: "co-translational modification" EXACT []
synonym: "cotranslational amino acid modification" EXACT []
synonym: "cotranslational modification" EXACT []
synonym: "cotranslational protein modification" EXACT []
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0043687
@@ -238795,7 +238799,7 @@ synonym: "posttranslational modification" EXACT []
synonym: "posttranslational protein modification" EXACT []
synonym: "PTM" EXACT []
xref: Wikipedia:Posttranslational_modification
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0043688
@@ -238994,12 +238998,12 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0043714
name: (R)-citramalate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: pyruvate + acetyl-CoA + H2O = (R)-citramalate + CoA." [GOC:jl, PMID:9864346]
+def: "Catalysis of the reaction: pyruvate + acetyl-CoA + H2O = (R)-citramalate + CoA." [GOC:jl, PMID:9864346, RHEA:19045]
synonym: "citramalate synthase" BROAD []
-xref: EC:2.3.1.182
+xref: EC:2.3.3.21
xref: MetaCyc:RXN-7743
xref: RHEA:19045
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
id: GO:0043715
@@ -239042,7 +239046,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0043718
name: 2-hydroxymethylglutarate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-(hydroxymethyl)glutarate + NAD(+) = 2-formylglutarate + H(+) + NADH." [EC:1.1.1.291, RHEA:15505]
+def: "Catalysis of the reaction: 2-(hydroxymethyl)glutarate + NAD+ = 2-formylglutarate + H+ + NADH." [EC:1.1.1.291, RHEA:15505]
synonym: "(S)-2-hydroxymethylglutarate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.291]
synonym: "HgD" EXACT []
xref: EC:1.1.1.291
@@ -239090,7 +239094,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0043722
name: 4-hydroxyphenylacetate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (4-hydroxyphenyl)acetate + H(+) = 4-cresol + CO(2)." [EC:4.1.1.83, RHEA:22732]
+def: "Catalysis of the reaction: (4-hydroxyphenyl)acetate + H+ = 4-cresol + CO2." [EC:4.1.1.83, RHEA:22732]
synonym: "4-(hydroxyphenyl)acetate carboxy-lyase (4-methylphenol-forming)" RELATED [EC:4.1.1.83]
synonym: "4-Hpd activity" RELATED [EC:4.1.1.83]
synonym: "4-hydroxyphenylacetate carboxy-lyase activity" RELATED [EC:4.1.1.83]
@@ -239152,8 +239156,10 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0043729
name: 2-amino-5-formylamino-6-(5-phosphoribosylamino)pyrimidin-4(3H)-one formate-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-amino-5-formylamino-6-(5-phosphoribosylamino)pyrimidin-4(3H)-one + H2O = 2,5-diamino-6-(5-phosphoribosylamino)pyrimidin-4(3H)-one + formate." [GOC:jl]
-is_a: GO:0016829 ! lyase activity
+def: "Catalysis of the reaction: 2-amino-5-formylamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + H2O = 2,5-diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + formate + H+." [RHEA:27282]
+xref: EC:3.5.1.102
+xref: RHEA:27282
+is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
[Term]
id: GO:0043730
@@ -239176,7 +239182,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0043732
name: 6-hydroxynicotinate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-hydroxynicotinate + H(2)O + O(2) = 2,6-dihydroxynicotinate + H(2)O(2)." [EC:1.17.3.3, RHEA:22808]
+def: "Catalysis of the reaction: 6-hydroxynicotinate + H2O + O2 = 2,6-dihydroxynicotinate + H2O2." [EC:1.17.3.3, RHEA:22808]
synonym: "6-hydroxynicotinate hydroxylase activity" RELATED [EC:1.17.3.3]
synonym: "6-hydroxynicotinate:O2 oxidoreductase activity" RELATED [EC:1.17.3.3]
synonym: "6-hydroxynicotinic acid dehydrogenase activity" RELATED [EC:1.17.3.3]
@@ -239252,10 +239258,11 @@ is_a: GO:0016491 ! oxidoreductase activity
id: GO:0043739
name: G/U mismatch-specific uracil-DNA glycosylase activity
namespace: molecular_function
-def: "Catalysis of the removal of uracil from a U*G mispair by the cleavage the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free uracil and leaves an apyrimidinic (AP) site." [PMID:24739389]
+def: "Hydrolyzes mismatched double-stranded DNA and polynucleotides, releasing free uracil and leaving an apyrimidinic (AP) site." [EC:3.2.2.28, PMID:24739389]
synonym: "GU mismatch-specific uracil-DNA glycosylase activity" EXACT []
synonym: "MUG" EXACT []
synonym: "uracil mismatch repair protein" BROAD []
+xref: EC:3.2.2.28
is_a: GO:0004844 ! uracil DNA N-glycosylase activity
is_a: GO:0008263 ! pyrimidine-specific mismatch base pair DNA N-glycosylase activity
@@ -239263,7 +239270,7 @@ is_a: GO:0008263 ! pyrimidine-specific mismatch base pair DNA N-glycosylase acti
id: GO:0043740
name: GTP cyclohydrolase IIa activity
namespace: molecular_function
-def: "Catalysis of the reaction: GTP + 3 H(2)O = 2-amino-5-formylamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + 3 H(+) + 2 phosphate." [EC:3.5.4.29, RHEA:22468]
+def: "Catalysis of the reaction: GTP + 3 H2O = 2-amino-5-formylamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + 3 H+ + 2 phosphate." [EC:3.5.4.29, RHEA:22468]
synonym: "GTP 8,9-dihydrolase (phosphate-forming)" RELATED [EC:3.5.4.29]
synonym: "GTP 8,9-hydrolase (phosphate-forming)" EXACT []
synonym: "GTP cyclohydrolase III activity" NARROW [EC:3.5.4.29]
@@ -239398,9 +239405,12 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0043754
name: dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-methylpropanoyl-CoA + enzyme N6-(dihydrolipoyl)lysine = CoA + enzyme N6-(S-[2-methylpropanoyl]dihydrolipoyl)lysine." [EC:2.3.1.168]
+alt_id: GO:0004147
+def: "Catalysis of the reaction: 2-methylpropanoyl-CoA + enzyme N6-(dihydrolipoyl)lysine = CoA + enzyme N6-(S-[2-methylpropanoyl]dihydrolipoyl)lysine." [RHEA:18865]
synonym: "2-methylpropanoyl-CoA:enzyme-6-N-(dihydrolipoyl)lysine:S-(2-methylpropanoyl)transferase activity" RELATED [EC:2.3.1.168]
synonym: "2-methylpropanoyl-CoA:enzyme-N6-(dihydrolipoyl)lysine:S-(2-methylpropanoyl)transferase activity" RELATED [EC:2.3.1.168]
+synonym: "dihydrolipoamide branched chain acyltransferase activity" EXACT []
+synonym: "dihydrolipoamide branched chain transacylase activity" EXACT []
synonym: "dihydrolipoyl transacylase activity" RELATED [EC:2.3.1.168]
synonym: "enzyme-dihydrolipoyllysine:2-methylpropanoyl-CoA S-(2-methylpropanoyl)transferase activity" EXACT []
xref: EC:2.3.1.168
@@ -239413,7 +239423,7 @@ id: GO:0043755
name: alpha-ribazole phosphatase activity
namespace: molecular_function
alt_id: GO:0019175
-def: "Catalysis of the reaction: alpha-ribazole 5'-phosphate + H(2)O = alpha-ribazole + phosphate." [EC:3.1.3.73, RHEA:24456]
+def: "Catalysis of the reaction: alpha-ribazole 5'-phosphate + H2O = alpha-ribazole + phosphate." [EC:3.1.3.73, RHEA:24456]
synonym: "alpha-ribazole-5'-P phosphatase activity" EXACT []
synonym: "alpha-ribazole-5'-phosphate phosphohydrolase activity" EXACT []
synonym: "CobC" RELATED []
@@ -239427,7 +239437,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0043756
name: adenosylcobinamide hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: adenosylcobinamide + H(2)O = (R)-1-aminopropan-2-ol + adenosylcobyrate." [EC:3.5.1.90, RHEA:23504]
+def: "Catalysis of the reaction: adenosylcobinamide + H2O = (R)-1-aminopropan-2-ol + adenosylcobyrate." [EC:3.5.1.90, RHEA:23504]
synonym: "adenosylcobinamide amidohydrolase activity" RELATED [EC:3.5.1.90]
synonym: "AdoCbi amidohydrolase activity" RELATED [EC:3.5.1.90]
synonym: "AdoCbi hydrolase activity" RELATED [EC:3.5.1.90]
@@ -239472,7 +239482,7 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0043759
name: methylbutanoate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + 2-methylbutanoate + CoA = AMP + diphosphate + 2-methylbutanoyl-CoA." [RHEA:46180]
+def: "Catalysis of the reaction: ATP + 2-methylbutanoate + CoA = AMP + diphosphate + 2-methylbutanoyl-CoA." [RHEA:46180]
synonym: "branched chain acyl CoA synthetase (ADP-forming) activity" EXACT []
synonym: "branched chain acyl-CoA synthetase (ADP-forming) activity" EXACT []
synonym: "branched-chain acyl CoA synthetase (ADP-forming) activity" EXACT []
@@ -239518,7 +239528,7 @@ synonym: "DNA mismatch endonuclease" BROAD []
synonym: "V.EcoKDcm" RELATED []
synonym: "very short patch repair protein" RELATED []
synonym: "Vsr mismatch endonuclease" RELATED []
-is_a: GO:0004520 ! endodeoxyribonuclease activity
+is_a: GO:0004520 ! DNA endonuclease activity
[Term]
id: GO:0043766
@@ -239582,7 +239592,10 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0043771
name: cytidine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + cytidine = ADP + CMP." [PMID:211379]
+def: "Catalysis of the reaction: ATP + cytidine = ADP + CMP." [PMID:211379, RHEA:24674]
+synonym: "uridine-cytidine kinase activity" NARROW [EC:2.7.1.48]
+xref: EC:2.7.1.213
+xref: RHEA:24674
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
is_a: GO:0019206 ! nucleoside kinase activity
@@ -239657,11 +239670,12 @@ is_a: GO:0016867 ! intramolecular transferase activity, transferring acyl groups
id: GO:0043779
name: cobalt-precorrin-5A acetaldehyde-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cobalt-precorrin 5A + H2O = cobalt-precorrin 5B + acetaldehyde." [MetaCyc:RXN-8763]
+def: "Catalysis of the reaction: cobalt-precorrin 5A + H2O = cobalt-precorrin 5B + acetaldehyde + H+." [RHEA:26281]
synonym: "cobalt-precorrin 5A acetaldehyde-lyase activity" EXACT []
+xref: EC:3.7.1.12
xref: MetaCyc:RXN-8763
xref: RHEA:26281
-is_a: GO:0016829 ! lyase activity
+is_a: GO:0016823 ! hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances
[Term]
id: GO:0043780
@@ -239710,18 +239724,6 @@ synonym: "oxidoreductase activity, reducing metal ions, flavin as acceptor" RELA
xref: EC:1.16.8.-
is_a: GO:0016722 ! oxidoreductase activity, acting on metal ions
-[Term]
-id: GO:0043784
-name: cob(II)yrinic acid a,c-diamide reductase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 2 cob(I)yrinate a,c diamide + FMN + 3 H(+) = 2 cob(II)yrinate a,c diamide + FMNH(2)." [EC:1.16.8.1, RHEA:24300]
-synonym: "cob(II)yrinic acid-a,c-diamide:FMN oxidoreductase activity" EXACT []
-xref: EC:1.16.8.1
-xref: KEGG_REACTION:R05218
-xref: MetaCyc:R343-RXN
-xref: RHEA:24300
-is_a: GO:0043783 ! oxidoreductase activity, acting on metal ions, flavin as acceptor
-
[Term]
id: GO:0043785
name: cinnamoyl-CoA:phenyllactate CoA-transferase activity
@@ -239740,7 +239742,6 @@ id: GO:0043786
name: cinnamate reductase activity
namespace: molecular_function
def: "Catalysis of the reaction: 3-phenylpropanoate + NAD+ = (E)-cinnamate + NADH + H+." [PMID:10849007]
-xref: EC:1.3.1.-
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
[Term]
@@ -239764,7 +239765,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0043792
name: enamidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,4,5,6-tetrahydro-6-oxonicotinate + 2 H(2)O = 2-formylglutarate + NH(4)(+)." [EC:3.5.2.18, RHEA:17209]
+def: "Catalysis of the reaction: 1,4,5,6-tetrahydro-6-oxonicotinate + 2 H2O = 2-formylglutarate + NH4." [EC:3.5.2.18, RHEA:17209]
synonym: "6-oxo-1,4,5,6-tetrahydronicotinate amidohydrolase activity" EXACT []
xref: EC:3.5.2.18
xref: KEGG_REACTION:R07984
@@ -239794,7 +239795,7 @@ is_a: GO:0016903 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0043795
name: glyceraldehyde oxidoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: A + D-glyceraldehyde + H2O = (R)-glycerate + AH2 + H(+)." [PMID:10095793, RHEA:36047]
+def: "Catalysis of the reaction: A + D-glyceraldehyde + H2O = (R)-glycerate + AH2 + H+." [PMID:10095793, RHEA:36047]
xref: EC:1.2.99.8
xref: RHEA:36047
is_a: GO:0016903 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors
@@ -239806,7 +239807,7 @@ namespace: molecular_function
def: "Catalysis of the reaction: D-glyceraldehyde + H2O + NADP+ = D-glycerate + NADPH + H+." [EC:1.2.1.89]
xref: EC:1.2.1.89
xref: RHEA:40163
-is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
+is_a: GO:0033721 ! aldehyde dehydrogenase (NADP+) activity
[Term]
id: GO:0043797
@@ -239846,7 +239847,7 @@ xref: MetaCyc:1.4.3.19-RXN
xref: MetaCyc:RXN-8672
xref: MetaCyc:RXN-8673
xref: MetaCyc:RXN-8674
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+is_a: GO:0052595 ! aliphatic amine oxidase activity
[Term]
id: GO:0043800
@@ -239873,7 +239874,7 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0043802
name: hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 L-glutamine + 2 ATP + 2 H(2)O + hydrogenobyrinate = 2 L-glutamate + 2 ADP + 4 H(+) + hydrogenobyrinate a,c-diamide + 2 phosphate." [EC:6.3.5.9, RHEA:12544]
+def: "Catalysis of the reaction: 2 L-glutamine + 2 ATP + 2 H2O + hydrogenobyrinate = 2 L-glutamate + 2 ADP + 4 H+ + hydrogenobyrinate a,c-diamide + 2 phosphate." [EC:6.3.5.9, RHEA:12544]
synonym: "CobB" RELATED []
synonym: "hydrogenobyrinic acid a,c diamide synthase (glutamine-hydrolysing) activity" EXACT []
synonym: "hydrogenobyrinic-acid:L-glutamine amido-ligase (AMP-forming)" EXACT []
@@ -239887,7 +239888,7 @@ is_a: GO:0016884 ! carbon-nitrogen ligase activity, with glutamine as amido-N-do
id: GO:0043803
name: hydroxyneurosporene-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: demethylspheroidene + S-adenosyl-L-methionine = H(+) + S-adenosyl-L-homocysteine + spheroidene." [PMID:12664193, PMID:12770713, PMID:7358679, RHEA:30903]
+def: "Catalysis of the reaction: demethylspheroidene + S-adenosyl-L-methionine = H+ + S-adenosyl-L-homocysteine + spheroidene." [PMID:12664193, PMID:12770713, PMID:7358679, RHEA:30903]
synonym: "1-HO-carotenoid methylase" RELATED [EC:2.1.1.210]
synonym: "1-hydroxycarotenoid methylase" RELATED [EC:2.1.1.210]
synonym: "1-hydroxycarotenoid O-methylase" RELATED [EC:2.1.1.210]
@@ -239973,15 +239974,18 @@ is_a: GO:0016410 ! N-acyltransferase activity
id: GO:0043811
name: phosphate:acyl-[acyl carrier protein] acyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-[acyl-carrier protein] + orthophosphate = acyl phosphate + [acyl-carrier protein]." [IMG:01871]
+def: "Catalysis of the reaction: a fatty acyl-[acyl-carrier protein] + orthophosphate = acyl phosphate + [acyl-carrier protein]." [RHEA:42292]
+xref: EC:2.3.1.274
+xref: RHEA:42292
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
id: GO:0043812
name: phosphatidylinositol-4-phosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phosphatidylinositol-4-phosphate + H2O = phosphatidylinositol + orthophosphate." [PMID:10224048]
+def: "Catalysis of the reaction: phosphatidyl-1D-myo-inositol-4-phosphate + H2O = phosphatidyl-1D-myo-inositol + phosphate." [PMID:10224048, RHEA:55652]
synonym: "phosphatidylinositol 4-phosphate phosphatase activity" EXACT []
+xref: RHEA:55652
is_a: GO:0034596 ! phosphatidylinositol phosphate 4-phosphatase activity
is_a: GO:0052744 ! phosphatidylinositol monophosphate phosphatase activity
@@ -239989,12 +239993,13 @@ is_a: GO:0052744 ! phosphatidylinositol monophosphate phosphatase activity
id: GO:0043813
name: phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phosphatidylinositol-3,5-bisphosphate + H2O = phosphatidylinositol-3-phosphate + orthophosphate." [PMID:10806194, PMID:16607019]
+def: "Catalysis of the reaction: phosphatidylinositol-3,5-bisphosphate + H2O = phosphatidylinositol-3-phosphate + orthophosphate." [PMID:10806194, PMID:16607019, RHEA:32955]
synonym: "phosphatidylinositol 3,5-bisphosphate 5-phosphatase activity" EXACT []
xref: Reactome:R-HSA-1675836 "PI(3,5)P2 is dephosphorylated to PI3P by SYNJ at the plasma membrane"
xref: Reactome:R-HSA-1676005 "PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the Golgi membrane"
xref: Reactome:R-HSA-1676020 "PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the late endosome membrane"
xref: Reactome:R-HSA-1676174 "PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the early endosome membrane"
+xref: RHEA:32955
is_a: GO:0034595 ! phosphatidylinositol phosphate 5-phosphatase activity
is_a: GO:0106018 ! phosphatidylinositol-3,5-bisphosphate phosphatase activity
@@ -240002,10 +240007,9 @@ is_a: GO:0106018 ! phosphatidylinositol-3,5-bisphosphate phosphatase activity
id: GO:0043814
name: phospholactate guanylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-phospho-(S)-lactate + GTP = lactyl-2-diphospho-5'-guanosine + diphosphate." [PMID:18260642]
+def: "Catalysis of the reaction: 2-phospho-(S)-lactate + GTP = lactyl-2-diphospho-5'-guanosine + diphosphate." [PMID:18260642, RHEA:63424]
xref: EC:2.7.7.68
-xref: MetaCyc:RXN-8077
-xref: RHEA:30519
+xref: RHEA:63424
is_a: GO:0070568 ! guanylyltransferase activity
[Term]
@@ -240054,7 +240058,7 @@ is_a: GO:0016846 ! carbon-sulfur lyase activity
id: GO:0043818
name: precorrin-3B synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADH + O(2) + precorrin-3A = H(2)O + NAD(+) + precorrin-3B." [EC:1.14.13.83, RHEA:17293]
+def: "Catalysis of the reaction: H+ + NADH + O2 + precorrin-3A = H2O + NAD+ + precorrin-3B." [EC:1.14.13.83, RHEA:17293]
synonym: "CobG" RELATED []
synonym: "precorrin-3A,NADH:oxygen oxidoreductase (20-hydroxylating)" EXACT []
synonym: "precorrin-3X synthase activity" RELATED [EC:1.14.13.83]
@@ -240068,7 +240072,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0043819
name: precorrin-6A synthase (deacetylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + H(2)O + precorrin-5 = S-adenosyl-L-homocysteine + acetate + 2 H(+) + precorrin-6X." [EC:2.1.1.152, RHEA:18261]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + H2O + precorrin-5 = S-adenosyl-L-homocysteine + acetate + 2 H+ + precorrin-6X." [EC:2.1.1.152, RHEA:18261]
synonym: "CobF" RELATED []
synonym: "precorrin-6X synthase (deacetylating) activity" RELATED [EC:2.1.1.152]
synonym: "S-adenosyl-L-methionine:precorrin-5 C1-methyltransferase (deacetylating)" EXACT []
@@ -240107,7 +240111,7 @@ synonym: "5S ribosomal RNA maturation endonuclease activity" EXACT []
synonym: "RNase M5 activity" RELATED [EC:3.1.26.8]
xref: EC:3.1.26.8
xref: MetaCyc:3.1.26.8-RXN
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0043823
@@ -240117,13 +240121,13 @@ def: "Catalysis of the reaction: spheroidene + O2 = spheroidenone + H2O." [PMID:
xref: EC:1.14.15.9
xref: MetaCyc:RXN-10670
xref: RHEA:33027
-is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+is_a: GO:0016713 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0043824
name: succinylglutamate-semialdehyde dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-succinyl-L-glutamate 5-semialdehyde + H(2)O + NAD(+) = N-succinyl-L-glutamate + 2 H(+) + NADH." [EC:1.2.1.71, RHEA:10812]
+def: "Catalysis of the reaction: N-succinyl-L-glutamate 5-semialdehyde + H2O + NAD+ = N-succinyl-L-glutamate + 2 H+ + NADH." [EC:1.2.1.71, RHEA:10812]
synonym: "AruD" RELATED []
synonym: "AstD" RELATED []
synonym: "N-succinyl-L-glutamate 5-semialdehyde:NAD+ oxidoreductase activity" RELATED [EC:1.2.1.71]
@@ -240193,10 +240197,12 @@ is_a: GO:0140101 ! catalytic activity, acting on a tRNA
id: GO:0043829
name: tRNA-specific adenosine-37 deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: adenosine-37 + H2O = inosine-37 + NH3, in a tRNA-Ala molecule." [PMID:8915538, PMID:9707437]
+def: "Catalysis of the reaction: adenosine-37 + H2O = inosine-37 + NH3, in a tRNA-Ala molecule." [PMID:8915538, PMID:9707437, RHEA:50968]
synonym: "TAD1" RELATED []
synonym: "tRNA(Ala)-A37 deaminase activity" EXACT []
synonym: "tRNA-specific adenosine deaminase 1" EXACT []
+xref: EC:3.5.4.34
+xref: RHEA:50968
is_a: GO:0008251 ! tRNA-specific adenosine deaminase activity
[Term]
@@ -240211,7 +240217,7 @@ is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
id: GO:0043831
name: thiosulfate dehydrogenase (quinone) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-decylubiquinone + 2 thiosulfate = 6-decylubiquinol + tetrathionate." [EC:1.8.5.2, RHEA:10936]
+def: "Catalysis of the reaction: 6-decylubiquinone + 2 thiosulfate = 6-decylubiquinol + tetrathionate." [RHEA:10936]
synonym: "DoxA" RELATED []
synonym: "DoxD" RELATED []
synonym: "thiosulfate oxidoreductase, tetrathionate-forming activity" RELATED [EC:1.8.5.2]
@@ -240228,19 +240234,21 @@ is_a: GO:0016672 ! oxidoreductase activity, acting on a sulfur group of donors,
[Term]
id: GO:0043833
-name: methylamine-specific methylcobalamin:coenzyme M methyltransferase activity
+name: [methyl-Co(III) methylamine-specific corrinoid protein]:coenzyme M methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a methylated methylamine corrinoid protein + coenzyme M = a methylamine corrinoid protein + methyl-CoM. This reaction is the transfer of the methyl group from the methylated corrinoid cofactor of a methylamine corrinoid protein to coenzyme M." [MetaCyc:RXN-8099]
+def: "Catalysis of the reaction: [methyl-Co(III) methylamine-specific corrinoid protein] + coenzyme M = [Co(I) methylamine-specific corrinoid protein] + H+ + methyl-coenzyme M. This reaction is the transfer of the methyl group from the methylated corrinoid cofactor of a methylamine corrinoid protein to coenzyme M." [RHEA:18773]
comment: This function is the second step in the pathway of methanogenesis from monomethylamine, dimethylamine and trimethylamine.
+synonym: "methylamine-specific methylcobalamin:coenzyme M methyltransferase activity" EXACT []
synonym: "methylamine-specific methylcobalamin:CoM methyltransferase activity" EXACT []
-synonym: "methylcobamide:coenzyme M methyltransferase activity" EXACT []
-synonym: "methylcobamide:CoM methyltransferase activity" EXACT []
-synonym: "methylcobamide:CoM methyltransferase II isozyme A" RELATED []
+synonym: "methylcobamide:coenzyme M methyltransferase activity" BROAD []
+synonym: "methylcobamide:CoM methyltransferase activity" BROAD []
synonym: "monomethylamine-specific methylcobalamin:coenzyme M methyltransferase activity" NARROW []
+synonym: "MT2-A" BROAD [EC:2.1.1.247]
xref: EC:2.1.1.247
xref: MetaCyc:RXN-8099
xref: MetaCyc:RXN-8101
xref: MetaCyc:RXN-8103
+xref: RHEA:18773
is_a: GO:0008168 ! methyltransferase activity
[Term]
@@ -240440,22 +240448,6 @@ def: "A heterotrimeric complex composed of the subunits RecF, RecO and RecR. Med
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0005694 ! chromosome
-[Term]
-id: GO:0043851
-name: methanol-specific methylcobalamin:coenzyme M methyltransferase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: a methylated methanol corrinoid protein + coenzyme M = a methanol corrinoid protein + methyl-CoM. This reaction is the transfer of the methyl group from the methylated corrinoid cofactor of a methylamine corrinoid protein to coenzyme M." [IMG:01315, MetaCyc:RXN-8096]
-comment: This function is the second step in the pathway of methanogenesis from methanol.
-synonym: "methanol-specific methylcobalamin: coenzyme M methyltransferase activity" EXACT []
-synonym: "methanol-specific methylcobalamin:CoM methyltransferase activity" EXACT []
-synonym: "methyltransferase 2" BROAD []
-synonym: "MT2" BROAD []
-synonym: "MtaA" RELATED []
-synonym: "MtaC protein: coenzyme M methyltransferase activity" EXACT []
-synonym: "MtaC protein:coenzyme M methyltransferase activity" EXACT []
-xref: MetaCyc:RXN-8096
-is_a: GO:0008168 ! methyltransferase activity
-
[Term]
id: GO:0043852
name: monomethylamine methyltransferase activity
@@ -240485,26 +240477,28 @@ is_a: GO:0034708 ! methyltransferase complex
[Term]
id: GO:0043854
-name: cyclic nucleotide-gated mechanosensitive ion channel activity
+name: cyclic nucleotide-gated mechanosensitive monoatomic ion channel activity
namespace: molecular_function
-def: "Enables the transmembrane transfer of an ion by a channel that opens in response to a mechanical stress and when a cyclic nucleotide has been bound by the channel complex or one of its constituent parts." [GOC:jl, PMID:22206667]
+def: "Enables the transmembrane transfer of an monoatomic ion by a channel that opens in response to a mechanical stress and when a cyclic nucleotide has been bound by the channel complex or one of its constituent parts." [GOC:jl, PMID:22206667]
synonym: "cyclic nucleotide gated mechanosensitive ion channel activity" EXACT []
synonym: "cyclic nucleotide regulated mechanosensitive ion channel" EXACT []
+synonym: "cyclic nucleotide-gated mechanosensitive ion channel activity" BROAD []
synonym: "cyclic nucleotide-regulated mechanosensitive ion channel" EXACT []
synonym: "cyclic nucleotide-regulated small mechanosensitive ion channel" RELATED []
synonym: "MscS" RELATED []
synonym: "small conductance mechanosensitive ion channel" EXACT []
-is_a: GO:0008381 ! mechanosensitive ion channel activity
+is_a: GO:0008381 ! mechanosensitive monoatomic ion channel activity
[Term]
id: GO:0043855
-name: cyclic nucleotide-gated ion channel activity
+name: cyclic nucleotide-gated monoatomic ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a channel that opens when a cyclic nucleotide has been bound by the channel complex or one of its constituent parts." [GOC:jl]
synonym: "cyclic nucleotide activated ion channel activity" EXACT []
synonym: "cyclic nucleotide gated ion channel activity" EXACT []
synonym: "cyclic nucleotide-activated ion channel activity" EXACT []
-is_a: GO:0015276 ! ligand-gated ion channel activity
+synonym: "cyclic nucleotide-gated ion channel activity" BROAD []
+is_a: GO:0015276 ! ligand-gated monoatomic ion channel activity
[Term]
id: GO:0043856
@@ -240518,7 +240512,7 @@ is_a: GO:0140110 ! transcription regulator activity
id: GO:0043857
name: N-acetylornithine carbamoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(2)-acetyl-L-ornithine + carbamoyl phosphate = N(2)-acetyl-L-citrulline + H(+) + phosphate." [EC:2.1.3.9, RHEA:18609]
+def: "Catalysis of the reaction: N(2)-acetyl-L-ornithine + carbamoyl phosphate = N(2)-acetyl-L-citrulline + H+ + phosphate." [EC:2.1.3.9, RHEA:18609]
synonym: "acetylornithine transcarbamylase activity" EXACT []
synonym: "AOTC" RELATED []
synonym: "carbamoyl-phosphate:2-N-acetyl-L-ornithine carbamoyltransferase activity" RELATED [EC:2.1.3.9]
@@ -240534,14 +240528,13 @@ is_a: GO:0016743 ! carboxyl- or carbamoyltransferase activity
id: GO:0043858
name: arginine:ornithine antiporter activity
namespace: molecular_function
-def: "Catalysis of the reaction: arginine(out) + ornithine(in) = arginine(in) + ornithine(out)." [GOC:jl, PMID:17110979]
+def: "Catalysis of the reaction: arginine(out) + ornithine(in) = arginine(in) + ornithine(out)." [GOC:jl, PMID:17110979, RHEA:34991]
synonym: "ArcD" RELATED []
synonym: "arginine-ornithine antiporter activity" EXACT []
synonym: "arginine/ornithine antiporter activity" EXACT []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+xref: RHEA:34991
is_a: GO:0015171 ! amino acid transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
-is_a: GO:0015491 ! cation:cation antiporter activity
+is_a: GO:0015297 ! antiporter activity
[Term]
id: GO:0043859
@@ -240569,8 +240562,8 @@ namespace: molecular_function
def: "Catalysis of the reaction: agmatine(out) + putrescine(in) = agmatine(in) + putrescine(out)." [GOC:jl, PMID:17028272]
synonym: "agmatine-putrescine antiporter activity" EXACT []
synonym: "agmatine/putrescine antiporter activity" EXACT []
+is_a: GO:0015297 ! antiporter activity
is_a: GO:0015489 ! putrescine transmembrane transporter activity
-is_a: GO:0015491 ! cation:cation antiporter activity
[Term]
id: GO:0043862
@@ -240581,10 +240574,9 @@ synonym: "AdiC" RELATED []
synonym: "arginine-agmatine antiporter activity" EXACT []
synonym: "arginine-agmatine exchange transporter activity" EXACT []
synonym: "arginine/agmatine antiporter activity" EXACT []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015101 ! organic cation transmembrane transporter activity
is_a: GO:0015171 ! amino acid transmembrane transporter activity
-is_a: GO:0015491 ! cation:cation antiporter activity
+is_a: GO:0015297 ! antiporter activity
[Term]
id: GO:0043863
@@ -240625,8 +240617,6 @@ synonym: "methionine importer activity" NARROW []
synonym: "methionine importing activity" NARROW []
synonym: "methionine-importing activity" NARROW []
is_a: GO:0000099 ! sulfur amino acid transmembrane transporter activity
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
[Term]
id: GO:0043866
@@ -240689,10 +240679,10 @@ synonym: "cadaverine transmembrane transporter activity" NARROW []
synonym: "cadaverine:lysine antiporter activity" EXACT []
synonym: "lysine-cadaverine antiporter activity" EXACT []
synonym: "lysine/cadaverine antiporter activity" EXACT []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015101 ! organic cation transmembrane transporter activity
is_a: GO:0015171 ! amino acid transmembrane transporter activity
-is_a: GO:0015491 ! cation:cation antiporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0043873
@@ -240724,12 +240714,13 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0043875
name: 2-ketobutyrate formate-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxobutanoate + coenzyme A = propionyl-CoA + formate." [MetaCyc:KETOBUTFORMLY-RXN, PMID:9484901]
+def: "Catalysis of the reaction: 2-oxobutanoate + coenzyme A = propionyl-CoA + formate." [PMID:9484901, RHEA:28054]
comment: This function is part of an anaerobic pathway for the catabolism of L-threonine.
synonym: "keto-acid formate acetyltransferase" BROAD []
synonym: "KFL" EXACT []
synonym: "TdcE" RELATED []
xref: MetaCyc:KETOBUTFORMLY-RXN
+xref: RHEA:28054
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
@@ -240782,8 +240773,8 @@ synonym: "glycolic acid transmembrane transporter activity" EXACT []
synonym: "hydroxyacetic acid transmembrane transporter activity" EXACT []
xref: RHEA:29447
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015665 ! alcohol transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0043880
@@ -240867,9 +240858,10 @@ is_a: GO:0016625 ! oxidoreductase activity, acting on the aldehyde or oxo group
[Term]
id: GO:0043886
-name: structural constituent of carboxysome
+name: structural constituent of carboxysome shell
namespace: molecular_function
-def: "The action of a molecule that contributes to the structural integrity of a carboxysome, an organelle found in all cyanobacteria and some chemoautotrophs, consisting of a proteinaceous coat and enzymes for the fixation of CO(2)." [GOC:jl, PMID:28934381]
+def: "The action of a molecule that contributes to the structural integrity of a carboxysome shell, an organelle found in all cyanobacteria and some chemoautotrophs, consisting of a proteinaceous coat and enzymes for the fixation of CO2." [GOC:jl, PMID:28934381]
+synonym: "structural constituent of carboxysome" RELATED []
is_a: GO:0005198 ! structural molecule activity
[Term]
@@ -240894,7 +240886,7 @@ synonym: "sodium/melibiose symporter activity" EXACT []
synonym: "sodium:melibiose symporter activity" EXACT []
synonym: "thiomethylgalactoside permease II" RELATED []
is_a: GO:0015370 ! solute:sodium symporter activity
-is_a: GO:0015487 ! melibiose:cation symporter activity
+is_a: GO:0015487 ! melibiose:monoatomic cation symporter activity
[Term]
id: GO:0043888
@@ -240971,18 +240963,19 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
[Term]
id: GO:0043893
-name: acetate:cation symporter activity
+name: acetate:monoatomic cation symporter activity
namespace: molecular_function
def: "Enables the transfer of acetate from one side of a membrane to the other according to the reaction: acetate(out) + cation(out) = acetate(in) + cation(in)." [GOC:jl, PMID:14563880]
synonym: "acetate permease" BROAD []
synonym: "acetate-cation symporter activity" EXACT []
synonym: "acetate/cation symporter activity" EXACT []
+synonym: "acetate:cation symporter activity" BROAD []
synonym: "ActP" RELATED []
synonym: "cation-acetate symporter activity" EXACT []
synonym: "cation/acetate symporter activity" EXACT []
synonym: "cation:acetate symporter activity" EXACT []
is_a: GO:0015123 ! acetate transmembrane transporter activity
-is_a: GO:0015294 ! solute:cation symporter activity
+is_a: GO:0015294 ! solute:monoatomic cation symporter activity
is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
[Term]
@@ -241118,7 +241111,6 @@ name: Ser-tRNA(Thr) hydrolase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of misacylated Ser-tRNA(Thr)." [GOC:jl, PMID:15240874]
synonym: "Ser-tRNAThr hydrolase activity" EXACT []
-xref: EC:3.1.1.-
is_a: GO:0052689 ! carboxylic ester hydrolase activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
@@ -241128,7 +241120,6 @@ name: Ala-tRNA(Pro) hydrolase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of misacylated Ala-tRNA(Pro)." [GOC:jl, PMID:14663147]
synonym: "Ala-tRNAPro hydrolase activity" EXACT []
-xref: EC:3.1.1.-
is_a: GO:0002161 ! aminoacyl-tRNA editing activity
[Term]
@@ -241138,7 +241129,6 @@ namespace: molecular_function
def: "Catalysis of the hydrolysis of misacylated Cys-tRNA(Pro)." [GOC:jl, PMID:15886196]
synonym: "Cys-tRNA(Pro) deacetylase activity" EXACT []
synonym: "Cys-tRNAPro hydrolase activity" EXACT []
-xref: EC:3.1.1.-
is_a: GO:0002161 ! aminoacyl-tRNA editing activity
[Term]
@@ -241147,7 +241137,6 @@ name: Ser(Gly)-tRNA(Ala) hydrolase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of misacylated Ser-tRNA(Ala) and Gly-tRNA(Ala)." [GOC:jl, PMID:14663147]
synonym: "Ser(Gly)-tRNAAla hydrolase activity" EXACT []
-xref: EC:3.1.1.-
is_a: GO:0052689 ! carboxylic ester hydrolase activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
@@ -241309,17 +241298,19 @@ namespace: molecular_function
def: "Binding to suramin, a naphthalenesulfonic acid compound which is used in the treatment of diseases caused by trypanosomes and worms." [GOC:jl, Wikipedia:Suramin]
synonym: "Germanin binding" EXACT []
is_a: GO:0033218 ! amide binding
+is_a: GO:0043168 ! anion binding
is_a: GO:0043177 ! organic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901681 ! sulfur compound binding
[Term]
id: GO:0043927
-name: exonucleolytic nuclear-transcribed mRNA catabolic process involved in endonucleolytic cleavage-dependent decay
+name: obsolete exonucleolytic nuclear-transcribed mRNA catabolic process involved in endonucleolytic cleavage-dependent decay
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 5'-cap." [GOC:mtg_mpo]
-is_a: GO:0000291 ! nuclear-transcribed mRNA catabolic process, exonucleolytic
-relationship: part_of GO:0000294 ! nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 5'-cap." [GOC:mtg_mpo]
+comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
+is_obsolete: true
+replaced_by: GO:0000956
[Term]
id: GO:0043928
@@ -241402,7 +241393,6 @@ namespace: biological_process
def: "The formation of spores derived from the products of meiosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction." [GOC:pamgo_curators]
is_a: GO:0030435 ! sporulation resulting in formation of a cellular spore
is_a: GO:0034293 ! sexual sporulation
-is_a: GO:1903046 ! meiotic cell cycle process
[Term]
id: GO:0043936
@@ -241445,7 +241435,6 @@ id: GO:0043940
name: regulation of sexual sporulation resulting in formation of a cellular spore
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the formation of cellular spores derived from the products of meiosis." [GOC:pamgo_curators]
-is_a: GO:0010564 ! regulation of cell cycle process
is_a: GO:0034306 ! regulation of sexual sporulation
is_a: GO:0042173 ! regulation of sporulation resulting in formation of a cellular spore
relationship: regulates GO:0043935 ! sexual sporulation resulting in formation of a cellular spore
@@ -241458,7 +241447,6 @@ def: "Any process that activates, maintains or increases the frequency, rate or
is_a: GO:0043940 ! regulation of sexual sporulation resulting in formation of a cellular spore
is_a: GO:0045881 ! positive regulation of sporulation resulting in formation of a cellular spore
is_a: GO:0051446 ! positive regulation of meiotic cell cycle
-is_a: GO:0090068 ! positive regulation of cell cycle process
relationship: positively_regulates GO:0043935 ! sexual sporulation resulting in formation of a cellular spore
[Term]
@@ -241466,7 +241454,6 @@ id: GO:0043942
name: negative regulation of sexual sporulation resulting in formation of a cellular spore
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the formation of cellular spores derived from the products of meiosis." [GOC:pamgo_curators]
-is_a: GO:0010948 ! negative regulation of cell cycle process
is_a: GO:0042174 ! negative regulation of sporulation resulting in formation of a cellular spore
is_a: GO:0043940 ! regulation of sexual sporulation resulting in formation of a cellular spore
is_a: GO:0051447 ! negative regulation of meiotic cell cycle
@@ -241549,7 +241536,7 @@ is_obsolete: true
id: GO:0043949
name: regulation of cAMP-mediated signaling
namespace: biological_process
-def: "Any process which modulates the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response." [GOC:jl]
+def: "Any process which modulates the frequency, rate or extent of cAMP-mediated signaling." [GOC:jl]
synonym: "regulation of cAMP-mediated signalling" EXACT []
is_a: GO:1902531 ! regulation of intracellular signal transduction
relationship: regulates GO:0019933 ! cAMP-mediated signaling
@@ -241558,7 +241545,7 @@ relationship: regulates GO:0019933 ! cAMP-mediated signaling
id: GO:0043950
name: positive regulation of cAMP-mediated signaling
namespace: biological_process
-def: "Any process which activates, maintains or increases the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response." [GOC:jl]
+def: "Any process which activates, maintains or increases the frequency, rate or extent of cAMP-mediated signaling." [GOC:jl]
synonym: "positive regulation of cAMP-mediated signalling" EXACT []
is_a: GO:0043949 ! regulation of cAMP-mediated signaling
is_a: GO:1902533 ! positive regulation of intracellular signal transduction
@@ -241568,7 +241555,7 @@ relationship: positively_regulates GO:0019933 ! cAMP-mediated signaling
id: GO:0043951
name: negative regulation of cAMP-mediated signaling
namespace: biological_process
-def: "Any process which stops, prevents, or reduces the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response." [GOC:jl]
+def: "Any process which stops, prevents, or reduces the frequency, rate or extent of cAMP-mediated signaling." [GOC:jl]
synonym: "negative regulation of cAMP-mediated signalling" EXACT []
is_a: GO:0043949 ! regulation of cAMP-mediated signaling
is_a: GO:1902532 ! negative regulation of intracellular signal transduction
@@ -241626,7 +241613,7 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0043956
name: 3-hydroxypropionyl-CoA dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxypropionyl-CoA = acrylyl-CoA + H2O." [GOC:jl, PMID:11821399]
+def: "Catalysis of the reaction: 3-hydroxypropionyl-CoA = acryloyl-CoA + H2O." [GOC:jl, PMID:11821399]
comment: Note that this function is one of the activities of the trifunctional enzyme propionyl-coenzyme A synthase. See PMID:11821399.
synonym: "3-hydroxy propionyl-CoA dehydratase activity" EXACT []
synonym: "acetyl-coenzyme A synthetase" BROAD []
@@ -241637,7 +241624,7 @@ synonym: "enoyl-CoA hydratase/isomerase" BROAD []
xref: EC:4.2.1.116
xref: MetaCyc:RXN-6383
xref: RHEA:26518
-is_a: GO:0016836 ! hydro-lyase activity
+is_a: GO:0004300 ! enoyl-CoA hydratase activity
[Term]
id: GO:0043957
@@ -241660,14 +241647,15 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
[Term]
id: GO:0043958
-name: acryloyl-CoA reductase activity
+name: acryloyl-CoA reductase (NADH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: acryloyl-CoA + NADH + H+ + a reduced electron-transfer flavoprotein = propionyl-CoA + NAD+ + an oxidized electron-transfer flavoprotein." [GOC:jl, PMID:12603323]
+def: "Catalysis of the reaction: propanoyl-CoA + NAD+ = acryloyl-CoA + H+ + NADH." [GOC:jl, PMID:12603323]
comment: Note that this function is part of the process of L-alanine fermentation to propionate.
-synonym: "acryloyl-coenzyme A reductase activity" EXACT []
+synonym: "acryloyl-CoA reductase activity" BROAD []
+synonym: "acryloyl-coenzyme A reductase activity" BROAD []
synonym: "acrylyl-CoA reductase (NADH)" EXACT []
-synonym: "propionyl-CoA dehydrogenase" EXACT []
-xref: EC:1.3.99.3
+synonym: "propionyl-CoA dehydrogenase" BROAD []
+xref: EC:1.3.1.95
xref: MetaCyc:RXN-8568
xref: RHEA:34471
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
@@ -241810,21 +241798,25 @@ is_a: GO:0043966 ! histone H3 acetylation
[Term]
id: GO:0043975
-name: histone H3-K36 acetylation
+name: obsolete histone H3-K36 acetylation
namespace: biological_process
-def: "The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 36 of the histone." [GOC:jl]
+def: "OBSOLETE. The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 36 of the histone." [GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H3 acetylation at K36" EXACT []
synonym: "histone H3K36 acetylation" EXACT []
-is_a: GO:0043966 ! histone H3 acetylation
+is_obsolete: true
+consider: GO:0044018
[Term]
id: GO:0043976
-name: histone H3-K79 acetylation
+name: obsolete histone H3-K79 acetylation
namespace: biological_process
-def: "The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 79 of the histone." [GOC:jl]
+def: "OBSOLETE. The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 79 of the histone." [GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H3 acetylation at K79" EXACT []
synonym: "histone H3K79 acetylation" EXACT []
-is_a: GO:0043966 ! histone H3 acetylation
+is_obsolete: true
+consider: GO:0031151
[Term]
id: GO:0043977
@@ -241836,11 +241828,13 @@ is_a: GO:0043968 ! histone H2A acetylation
[Term]
id: GO:0043978
-name: histone H2A-K9 acetylation
+name: obsolete histone H2A-K9 acetylation
namespace: biological_process
-def: "The modification of histone H2A by the addition of an acetyl group to a lysine residue at position 9 of the histone." [GOC:jl]
+def: "OBSOLETE. The modification of histone H2A by the addition of an acetyl group to a lysine residue at position 9 of the histone." [GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H2A acetylation at K9" EXACT []
-is_a: GO:0043968 ! histone H2A acetylation
+is_obsolete: true
+consider: GO:0044012
[Term]
id: GO:0043979
@@ -241902,126 +241896,159 @@ is_a: GO:0034969 ! histone arginine methylation
[Term]
id: GO:0043987
-name: histone H3-S10 phosphorylation
+name: obsolete histone H3-S10 phosphorylation
namespace: biological_process
alt_id: GO:0043986
-def: "The modification of histone H3 by the addition of an phosphate group to a serine residue at position 10 of the histone." [GOC:jl]
+def: "OBSOLETE. The modification of histone H3 by the addition of an phosphate group to a serine residue at position 10 of the histone." [GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H3 phosphorylation at S10" EXACT []
synonym: "histone H3S10 phosphorylation" EXACT []
-is_a: GO:0035404 ! histone-serine phosphorylation
+is_obsolete: true
+consider: GO:0035175
[Term]
id: GO:0043988
-name: histone H3-S28 phosphorylation
+name: obsolete histone H3-S28 phosphorylation
namespace: biological_process
-def: "The modification of histone H3 by the addition of an phosphate group to a serine residue at position 28 of the histone." [GOC:jl]
+def: "OBSOLETE. The modification of histone H3 by the addition of an phosphate group to a serine residue at position 28 of the histone." [GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H3 phosphorylation at S28" EXACT []
synonym: "histone H3S28 phosphorylation" EXACT []
-is_a: GO:0035404 ! histone-serine phosphorylation
+is_obsolete: true
+consider: GO:0044022
[Term]
id: GO:0043989
-name: histone H4-S1 phosphorylation
+name: obsolete histone H4-S1 phosphorylation
namespace: biological_process
-def: "The modification of histone H4 by the addition of an phosphate group to a serine residue at position 1 of the histone." [GOC:jl]
+def: "OBSOLETE. The modification of histone H4 by the addition of an phosphate group to a serine residue at position 1 of the histone." [GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H4 phosphorylation at S1" EXACT []
synonym: "histone H4S1 phosphorylation" EXACT []
-is_a: GO:0035404 ! histone-serine phosphorylation
+is_obsolete: true
+consider: GO:0044023
[Term]
id: GO:0043990
-name: histone H2A-S1 phosphorylation
+name: obsolete histone H2A-S1 phosphorylation
namespace: biological_process
-def: "The modification of histone H2A by the addition of an phosphate group to a serine residue at position 1 of the histone." [GOC:jl]
+def: "OBSOLETE. The modification of histone H2A by the addition of an phosphate group to a serine residue at position 1 of the histone." [GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H2A phosphorylation at S1" EXACT []
synonym: "histone H2AS1 phosphorylation" EXACT []
-is_a: GO:0035404 ! histone-serine phosphorylation
-is_a: GO:1990164 ! histone H2A phosphorylation
+is_obsolete: true
+consider: GO:0044024
[Term]
id: GO:0043991
-name: histone H2B-S14 phosphorylation
+name: obsolete histone H2B-S14 phosphorylation
namespace: biological_process
-def: "The modification of histone H2B by the addition of an phosphate group to a serine residue at position 14 of the histone." [GOC:jl]
+def: "OBSOLETE. The modification of histone H2B by the addition of an phosphate group to a serine residue at position 14 of the histone." [GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H2B phosphorylation at S14" EXACT []
synonym: "histone H2BS14 phosphorylation" EXACT []
-is_a: GO:0035404 ! histone-serine phosphorylation
+is_obsolete: true
+consider: GO:0044025
[Term]
id: GO:0043992
-name: histone acetyltransferase activity (H3-K9 specific)
+name: histone H3K9 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 9) = CoA + histone H3 N6-acetyl-L-lysine (position 9)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H3-K9 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H3-K9 specific)" EXACT []
+synonym: "histone H3-K9 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H3-K9 specific)" EXACT []
-is_a: GO:0010484 ! H3 histone acetyltransferase activity
+is_a: GO:0010484 ! histone H3 acetyltransferase activity
[Term]
id: GO:0043993
-name: histone acetyltransferase activity (H3-K18 specific)
+name: histone H3K18 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 18) = CoA + histone H3 N6-acetyl-L-lysine (position 18)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H3-K18 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H3-K18 specific)" EXACT []
+synonym: "histone H3-K18 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H3-K18 specific)" EXACT []
-is_a: GO:0010484 ! H3 histone acetyltransferase activity
+is_a: GO:0010484 ! histone H3 acetyltransferase activity
[Term]
id: GO:0043994
-name: histone acetyltransferase activity (H3-K23 specific)
+name: histone H3K23 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 23) = CoA + histone H3 N6-acetyl-L-lysine (position 23)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H3-K23 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H3-K23 specific)" EXACT []
+synonym: "histone H3-K23 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H3-K23 specific)" EXACT []
-is_a: GO:0010484 ! H3 histone acetyltransferase activity
+is_a: GO:0010484 ! histone H3 acetyltransferase activity
[Term]
id: GO:0043995
-name: histone acetyltransferase activity (H4-K5 specific)
+name: histone H4K5 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 5) = CoA + histone H4 N6-acetyl-L-lysine (position 5)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H4-K5 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H4-K5 specific)" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H4-K5 specific)" EXACT []
-is_a: GO:0010485 ! H4 histone acetyltransferase activity
+is_a: GO:0010485 ! histone H4 acetyltransferase activity
[Term]
id: GO:0043996
-name: histone acetyltransferase activity (H4-K8 specific)
+name: histone H4K8 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 8) = CoA + histone H4 N6-acetyl-L-lysine (position 8)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H4-K8 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H4-K8 specific)" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H4-K8 specific)" EXACT []
-is_a: GO:0010485 ! H4 histone acetyltransferase activity
+is_a: GO:0010485 ! histone H4 acetyltransferase activity
[Term]
id: GO:0043997
-name: histone acetyltransferase activity (H4-K12 specific)
+name: histone H4K12 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 12) = CoA + histone H4 N6-acetyl-L-lysine (position 12)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H4-K12 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H4-K12 specific)" EXACT []
+synonym: "histone H4-K12 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H4-K12 specific)" EXACT []
-is_a: GO:0010485 ! H4 histone acetyltransferase activity
+is_a: GO:0010485 ! histone H4 acetyltransferase activity
[Term]
id: GO:0043998
-name: H2A histone acetyltransferase activity
+name: histone H2A acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H2A L-lysine = CoA + histone H2A N6-acetyl-L-lysine." [EC:2.3.1.48]
+synonym: "H2A histone acetylase activity" EXACT []
+synonym: "H2A histone acetyltransferase activity" EXACT []
synonym: "H2A histone lysine N-acetyltransferase activity" EXACT []
is_a: GO:0004402 ! histone acetyltransferase activity
[Term]
id: GO:0043999
-name: histone acetyltransferase activity (H2A-K5 specific)
+name: histone H2AK5 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H2A L-lysine (position 5) = CoA + histone H2A N6-acetyl-L-lysine (position 5)." [EC:2.3.1.48]
+comment: Note that in yeast, this is corresponds to H2AK4.
+synonym: "histone acetylase activity (H2A-K5 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H2A-K5 specific)" EXACT []
+synonym: "histone H2A-K5 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H2A-K5 specific)" EXACT []
-is_a: GO:0043998 ! H2A histone acetyltransferase activity
+is_a: GO:0043998 ! histone H2A acetyltransferase activity
[Term]
id: GO:0044000
name: movement in host
namespace: biological_process
+alt_id: GO:0052126
def: "The process in which an organism or its progeny spreads from one location to another within its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:cc]
+synonym: "movement in host environment" RELATED []
synonym: "movement of symbiont in host" EXACT []
synonym: "movement of symbiont within host" EXACT []
synonym: "movement within host" EXACT []
synonym: "symbiont movement in host" EXACT []
synonym: "symbiont movement within host" RELATED []
-is_a: GO:0052126 ! movement in host environment
+is_a: GO:0051701 ! biological process involved in interaction with host
[Term]
id: GO:0044001
@@ -242051,6 +242078,7 @@ synonym: "modification by symbiont of host morphology or physiology" RELATED []
synonym: "modulation by symbiont of host system process" NARROW []
synonym: "pathogenesis" RELATED []
synonym: "regulation by symbiont of host system process" NARROW []
+is_a: GO:0035821 ! modulation of process of another organism
is_a: GO:0051701 ! biological process involved in interaction with host
[Term]
@@ -242103,142 +242131,183 @@ is_a: GO:0090609 ! single-species submerged biofilm formation
[Term]
id: GO:0044012
-name: histone acetyltransferase activity (H2A-K9 specific)
+name: histone H2AK9 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H2A L-lysine (position 9) = CoA + histone H2A N6-acetyl-L-lysine (position 9)." [EC:2.3.1.48]
+comment: Note that in yeast, this is corresponds to H2AK7.
+synonym: "histone acetylase activity (H2A-K9 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H2A-K9 specific)" EXACT []
+synonym: "histone H2A-K9 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H2A-K9 specific)" EXACT []
-is_a: GO:0043998 ! H2A histone acetyltransferase activity
+is_a: GO:0043998 ! histone H2A acetyltransferase activity
[Term]
id: GO:0044013
-name: H2B histone acetyltransferase activity
+name: histone H2B acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H2B L-lysine = CoA + histone H2B N6-acetyl-L-lysine." [EC:2.3.1.48]
+synonym: "H2B histone acetylase activity" EXACT []
+synonym: "H2B histone acetyltransferase activity" EXACT []
synonym: "H2B histone lysine N-acetyltransferase activity" EXACT []
is_a: GO:0004402 ! histone acetyltransferase activity
[Term]
id: GO:0044014
-name: histone acetyltransferase activity (H2B-K5 specific)
+name: histone H2BK5 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H2B L-lysine (position 5) = CoA + histone H2B N6-acetyl-L-lysine (position 5)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H2B-K5 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H2B-K5 specific)" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H2B-K5 specific)" EXACT []
-is_a: GO:0044013 ! H2B histone acetyltransferase activity
+is_a: GO:0044013 ! histone H2B acetyltransferase activity
[Term]
id: GO:0044015
-name: histone acetyltransferase activity (H2B-K12 specific)
+name: histone H2BK12 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H2B L-lysine (position 12) = CoA + histone H2B N6-acetyl-L-lysine (position 12)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H2B-K12 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H2B-K12 specific)" EXACT []
+synonym: "histone H2B-K12 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H2B-K12 specific)" EXACT []
-is_a: GO:0044013 ! H2B histone acetyltransferase activity
+is_a: GO:0044013 ! histone H2B acetyltransferase activity
[Term]
id: GO:0044016
-name: histone acetyltransferase activity (H3-K4 specific)
+name: histone H3K4 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 4) = CoA + histone H3 N6-acetyl-L-lysine (position 4)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H3-K4 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H3-K4 specific)" EXACT []
+synonym: "histone H3-K4 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H3-K4 specific)" EXACT []
-is_a: GO:0010484 ! H3 histone acetyltransferase activity
+is_a: GO:0010484 ! histone H3 acetyltransferase activity
[Term]
id: GO:0044017
-name: histone acetyltransferase activity (H3-K27 specific)
+name: histone H3K27 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 27) = CoA + histone H3 N6-acetyl-L-lysine (position 27)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H3-K27 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H3-K27 specific)" EXACT []
+synonym: "histone H3-K27 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H3-K27 specific)" EXACT []
-is_a: GO:0010484 ! H3 histone acetyltransferase activity
+is_a: GO:0010484 ! histone H3 acetyltransferase activity
[Term]
id: GO:0044018
-name: histone acetyltransferase activity (H3-K36 specific)
+name: histone H3K36 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 36) = CoA + histone H3 N6-acetyl-L-lysine (position 36)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H3-K36 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H3-K36 specific)" EXACT []
+synonym: "histone H3-K36 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H3-K36 specific)" EXACT []
-is_a: GO:0010484 ! H3 histone acetyltransferase activity
+is_a: GO:0010484 ! histone H3 acetyltransferase activity
[Term]
id: GO:0044019
-name: histone acetyltransferase activity (H3-K72 specific)
+name: histone H3K72 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 72) = CoA + histone H3 N6-acetyl-L-lysine (position 72)." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H3-K72 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H3-K72 specific)" EXACT []
+synonym: "histone H3-K72 acetyltransferase activity" EXACT []
synonym: "histone lysine N-acetyltransferase activity (H3-K72 specific)" EXACT []
-is_a: GO:0010484 ! H3 histone acetyltransferase activity
+is_a: GO:0010484 ! histone H3 acetyltransferase activity
[Term]
id: GO:0044020
-name: histone methyltransferase activity (H4-R3 specific)
+name: histone H4R3 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone H4)-arginine (position 3) = S-adenosyl-L-homocysteine + (histone H4)-N-methyl-arginine (position 3). This reaction is the addition of a methyl group to arginine at position 3 of histone H4." [GOC:mah, PMID:17898714]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone H4)-arginine (position 3) = S-adenosyl-L-homocysteine + (histone H4)-N-methyl-arginine (position 3). This reaction is the addition of a methyl group to the arginine residue at position 3 of histone H4, producing histone H4R3me." [GOC:mah, PMID:17898714]
+synonym: "histone H4KR3 methylation" EXACT []
+synonym: "histone H4R3 arginine methylase activity" EXACT []
synonym: "histone methylase activity (H4-R3 specific)" EXACT [GOC:mah]
+synonym: "histone methyltransferase activity (H4-R3 specific)" EXACT []
synonym: "histone-arginine N-methyltransferase activity (H4-R3 specific)" EXACT []
-is_a: GO:0008469 ! histone-arginine N-methyltransferase activity
+is_a: GO:0016274 ! protein-arginine N-methyltransferase activity
+is_a: GO:0140939 ! histone H4 methyltransferase activity
[Term]
id: GO:0044022
-name: histone kinase activity (H3-S28 specific)
+name: histone H3S28 kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to the serine-28 residue of the N-terminal tail of histone H3." [GOC:jl]
+def: "Catalysis of the reaction: histone H3-serine (position 28) + ATP = histone H3-phosphoserine (position 28) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 28 of histone H3." [GOC:jl]
+synonym: "histone kinase activity (H3-S28 specific)" EXACT []
synonym: "histone serine kinase activity (H3-S28 specific)" EXACT []
synonym: "histone-serine kinase activity (H3-S28 specific)" EXACT []
-is_a: GO:0035174 ! histone serine kinase activity
+is_a: GO:0140996 ! histone H3 kinase activity
[Term]
id: GO:0044023
-name: histone kinase activity (H4-S1 specific)
+name: histone H4S1 kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to the serine-1 residue of the N-terminal tail of histone H4." [GOC:jl]
+def: "Catalysis of the reaction: histone H4-serine (position 1) + ATP = histone H4-phosphoserine (position 1) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 1 of histone H4." [GOC:jl]
+synonym: "histone kinase activity (H4-S1 specific)" EXACT []
synonym: "histone serine kinase activity (H4-S1 specific)" EXACT []
synonym: "histone-serine kinase activity (H4-S1 specific)" EXACT []
-is_a: GO:0035174 ! histone serine kinase activity
+is_a: GO:0140997 ! histone H4 kinase activity
[Term]
id: GO:0044024
-name: histone kinase activity (H2A-S1 specific)
+name: histone H2AS1 kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to the serine-1 residue of the N-terminal tail of histone H2A." [GOC:jl]
+def: "Catalysis of the reaction: histone H2A-serine (position 1) + ATP = histone H2A-phosphoserine (position 1) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 1 of histone H2A." [GOC:jl]
+synonym: "histone kinase activity (H2A-S1 specific)" EXACT []
synonym: "histone serine kinase activity (H2A-S1 specific)" EXACT []
synonym: "histone-serine kinase activity (H2A-S1 specific)" EXACT []
-is_a: GO:0035174 ! histone serine kinase activity
+is_a: GO:0140995 ! histone H2A kinase activity
[Term]
id: GO:0044025
-name: histone kinase activity (H2B-S14 specific)
+name: histone H2BS14 kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to the serine-14 or an equivalent residue of the N-terminal tail of histone H2B." [GOC:jl]
+def: "Catalysis of the reaction: histone H2B-serine (position 14) + ATP = histone H2B-phosphoserine (position 14) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 14 of histone H2B." [GOC:jl]
+synonym: "histone kinase activity (H2B-S14 specific)" EXACT []
synonym: "histone serine kinase activity (H2B-S14 specific)" EXACT []
synonym: "histone-serine kinase activity (H2B-S14 specific)" EXACT []
-is_a: GO:0035174 ! histone serine kinase activity
+is_a: GO:0140998 ! histone H2B kinase activity
[Term]
id: GO:0044026
-name: DNA hypermethylation
+name: obsolete DNA hypermethylation
namespace: biological_process
-def: "An increase in the epigenetic methylation of cytosine and adenosine residues in DNA." [GOC:jl, http://en.wiktionary.org/]
-is_a: GO:0044030 ! regulation of DNA methylation
+def: "OBSOLETE. An increase in the epigenetic methylation of cytosine and adenosine residues in DNA." [GOC:jl, http://en.wiktionary.org/]
+comment: The reason for obsoletion is this is a readout.
+is_obsolete: true
+consider: GO:0040029
[Term]
id: GO:0044027
-name: hypermethylation of CpG island
+name: negative regulation of gene expression via CpG island methylation
namespace: biological_process
-def: "An increase in the epigenetic methylation of cytosine and adenosine residues in a CpG island in DNA. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes." [GOC:jl, Wikipedia:Cpg_island]
+def: "An epigenetic gene regulation mechanism that negatively regulates gene expression by methylation of cytosine residues in chromosomal CpG islands. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes." [GOC:jl, PMID:11898023, Wikipedia:Cpg_island]
synonym: "DNA hypermethylation of CpG island" EXACT []
-is_a: GO:0044026 ! DNA hypermethylation
+synonym: "epigenetic regulation of gene expression via CpG island hypermethylation" EXACT []
+synonym: "hypermethylation of CpG island" EXACT []
+synonym: "maintenance of DNA methylation" BROAD []
+synonym: "negative regulation of gene expression via chromosomal DNA cytosine methylation" EXACT []
+synonym: "negative regulation of gene expression via CpG island hypermethylation" EXACT []
+is_a: GO:0045814 ! negative regulation of gene expression, epigenetic
[Term]
id: GO:0044028
-name: DNA hypomethylation
+name: obsolete DNA hypomethylation
namespace: biological_process
-def: "An decrease in the epigenetic methylation of cytosine and adenosine residues in DNA." [GOC:jl, http://en.wiktionary.org/hypomethylation]
-is_a: GO:0044030 ! regulation of DNA methylation
+def: "OBSOLETE. An decrease in the epigenetic methylation of cytosine and adenosine residues in DNA." [GOC:jl, http://en.wiktionary.org/hypomethylation]
+comment: The reason for obsoletion is that this is a readout.
+is_obsolete: true
+consider: GO:0040029
[Term]
id: GO:0044029
-name: hypomethylation of CpG island
+name: positive regulation of gene expression via CpG island demethylation
namespace: biological_process
-def: "An decrease in the epigenetic methylation of cytosine and adenosine residues in a CpG island in DNA. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes." [GOC:jl, Wikipedia:Cpg_island]
+def: "An epigenetic gene regulation mechanism that positively regulates gene expression by demethylation of cytosine residues in chromosomal CpG islands. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes." [GOC:jl, Wikipedia:Cpg_island]
synonym: "DNA hypomethylation of CpG island" EXACT []
-is_a: GO:0044028 ! DNA hypomethylation
+synonym: "hypomethylation of CpG island" EXACT []
+is_a: GO:0045815 ! transcription initiation-coupled chromatin remodeling
[Term]
id: GO:0044030
@@ -242307,7 +242376,7 @@ alt_id: GO:0010382
def: "The chemical reactions and pathways involving macromolecules forming, or destined to form, part of the cell wall. A cell wall is a rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis." [GOC:jl, GOC:mah]
synonym: "cellular cell wall macromolecule metabolic process" EXACT []
synonym: "cellular cell wall macromolecule metabolism" EXACT []
-is_a: GO:0044260 ! cellular macromolecule metabolic process
+is_a: GO:0043170 ! macromolecule metabolic process
relationship: part_of GO:0071554 ! cell wall organization or biogenesis
[Term]
@@ -242329,8 +242398,7 @@ synonym: "cell wall macromolecule biosynthesis" EXACT [GOC:mah]
synonym: "cell wall macromolecule biosynthetic process at cellular level" EXACT [GOC:mah]
synonym: "cell wall macromolecule synthesis" EXACT [GOC:mah]
synonym: "cellular cell wall macromolecule biosynthetic process" EXACT [GOC:mah]
-is_a: GO:0044036 ! cell wall macromolecule metabolic process
-is_a: GO:0070589 ! cellular component macromolecule biosynthetic process
+is_a: GO:0009059 ! macromolecule biosynthetic process
relationship: part_of GO:0042546 ! cell wall biogenesis
[Term]
@@ -242460,12 +242528,12 @@ is_a: GO:0042000 ! translocation of peptides or proteins into host
[Term]
id: GO:0044056
-name: modulation by symbiont of host digestive system process
+name: obsolete modulation by symbiont of host digestive system process
namespace: biological_process
-def: "The alteration by a symbiont organism of the functioning of a digestive system process, a physical, chemical, or biochemical process carried out by the host organism to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." [MITRE:tk]
+def: "OBSOLETE. The alteration by a symbiont organism of the functioning of a digestive system process, a physical, chemical, or biochemical process carried out by the host organism to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." [MITRE:tk]
+comment: This term was obsoleted because it is not sufficiently precise.
synonym: "regulation by symbiont of host digestive system process" EXACT []
-is_a: GO:0044003 ! modulation by symbiont of host process
-relationship: regulates GO:0022600 ! digestive system process
+is_obsolete: true
[Term]
id: GO:0044057
@@ -242485,12 +242553,12 @@ relationship: regulates GO:0022600 ! digestive system process
[Term]
id: GO:0044059
-name: modulation by symbiont of host endocrine process
+name: obsolete modulation by symbiont of host endocrine process
namespace: biological_process
-def: "The alteration by a symbiont organism of the functioning of a endocrine process, any of the hormonal, neural, and secretory processes that release products into the blood or lymph, in the host organism." [MITRE:tk]
+def: "OBSOLETE. The alteration by a symbiont organism of the functioning of a endocrine process, any of the hormonal, neural, and secretory processes that release products into the blood or lymph, in the host organism." [MITRE:tk]
+comment: This term was obsoleted because it is not sufficiently precise.
synonym: "regulation by symbiont of host endocrine process" EXACT []
-is_a: GO:0044003 ! modulation by symbiont of host process
-is_a: GO:0044060 ! regulation of endocrine process
+is_obsolete: true
[Term]
id: GO:0044060
@@ -242521,22 +242589,22 @@ relationship: regulates GO:0007588 ! excretion
[Term]
id: GO:0044063
-name: modulation by symbiont of host nervous system process
+name: obsolete modulation by symbiont of host nervous system process
namespace: biological_process
-def: "The alteration by a symbiont organism of the functioning of a host neurophysiological process, an organ system process carried out by any of the organs or tissues of neurological system." [MITRE:tk]
+def: "OBSOLETE. The alteration by a symbiont organism of the functioning of a host neurophysiological process, an organ system process carried out by any of the organs or tissues of neurological system." [MITRE:tk]
+comment: This term was obsoleted because it is not sufficiently precise.
synonym: "modulation by symbiont of host neurological system process" EXACT []
synonym: "regulation by symbiont of host neurological system process" EXACT []
-is_a: GO:0044003 ! modulation by symbiont of host process
-relationship: regulates GO:0050877 ! nervous system process
+is_obsolete: true
[Term]
id: GO:0044064
-name: modulation by symbiont of host respiratory system process
+name: obsolete modulation by symbiont of host respiratory system process
namespace: biological_process
-def: "The alteration by a symbiont organism of the functioning of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system." [MITRE:tk]
+def: "OBSOLETE. The alteration by a symbiont organism of the functioning of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system." [MITRE:tk]
+comment: This term was obsoleted because it is not sufficiently precise.
synonym: "regulation by symbiont of host respiratory system process" EXACT []
-is_a: GO:0044003 ! modulation by symbiont of host process
-relationship: regulates GO:0003016 ! respiratory system process
+is_obsolete: true
[Term]
id: GO:0044065
@@ -242559,9 +242627,10 @@ is_a: GO:0052043 ! modification by symbiont of host cellular component
[Term]
id: GO:0044067
-name: modification by symbiont of host intercellular junctions
+name: modification by symbiont of host cell-cell junction
namespace: biological_process
-def: "The process in which a symbiont organism effects a change in the structure or function of its host intercellular junction, a specialized region of connection between two cells." [MITRE:tk]
+def: "The process in which a symbiont organism effects a change in the structure or function of its host intercellular junction, a specialized region of connection between two cells. Intercellular junction include tight junctions and adherens junctions." [MITRE:tk]
+synonym: "modification by symbiont of host intercellular junctions" EXACT []
synonym: "modification of host intercellular junctions by symbiont" EXACT []
is_a: GO:0052043 ! modification by symbiont of host cellular component
@@ -242583,15 +242652,16 @@ namespace: biological_process
def: "The process in which a symbiont organism modulates the anion transport, the directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, of its host organism." [MITRE:tk]
synonym: "modification of host anion transport by symbiont" EXACT []
is_a: GO:0044068 ! modulation by symbiont of host cellular process
-relationship: regulates GO:0006820 ! anion transport
+relationship: regulates GO:0006820 ! monoatomic anion transport
[Term]
id: GO:0044070
-name: regulation of anion transport
+name: regulation of monoatomic anion transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the directed movement of anions, atoms or small molecules with a net negative charge into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl]
-is_a: GO:0043269 ! regulation of ion transport
-relationship: regulates GO:0006820 ! anion transport
+synonym: "regulation of anion transport" BROAD []
+is_a: GO:0043269 ! regulation of monoatomic ion transport
+relationship: regulates GO:0006820 ! monoatomic anion transport
[Term]
id: GO:0044071
@@ -242689,7 +242759,7 @@ relationship: regulates GO:0007269 ! neurotransmitter secretion
id: GO:0044080
name: modulation by symbiont of host cGMP-mediated signal transduction
namespace: biological_process
-def: "Any process in which a symbiont organism modulates the rate, frequency or extent of cGMP-mediated signaling in its host organism. cGMP-mediated signaling is a series of molecular signals in which a cell uses cyclic GMP to convert an extracellular signal into a response." [MITRE:tk]
+def: "Any process in which a symbiont organism modulates the rate, frequency or extent of cGMP-mediated signaling in its host organism." [MITRE:tk]
synonym: "modulation by symbiont of host cGMP-mediated signal transduction pathway" EXACT []
synonym: "modulation by symbiont of host cGMP-mediated signaling" EXACT []
synonym: "modulation by symbiont of host cGMP-mediated signalling" EXACT []
@@ -242702,7 +242772,7 @@ is_a: GO:0052027 ! modulation by symbiont of host signal transduction pathway
id: GO:0044081
name: modulation by symbiont of host nitric oxide-mediated signal transduction
namespace: biological_process
-def: "Any process in which a symbiont organism modulates the rate, frequency or extent of nitric oxide mediated signal transduction in its host organism. Nitric oxide mediated signal transduction is a series of molecular signals mediated by the detection of nitric oxide (NO)." [MITRE:tk]
+def: "Any process in which a symbiont organism modulates the rate, frequency or extent of nitric oxide mediated signal transduction in its host organism." [MITRE:tk]
synonym: "modulation by symbiont of host nitric oxide mediated signal transduction" EXACT []
synonym: "modulation of host nitric oxide-mediated signal transduction by symbiont" EXACT []
synonym: "modulation of host nitric oxide-mediated signaling by symbiont" EXACT []
@@ -242914,39 +242984,32 @@ namespace: molecular_function
def: "Catalysis of the reaction: xylitol + NAD+ = L-xylulose + NADH + H+." [PMID:14736891]
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
-[Term]
-id: GO:0044106
-name: cellular amine metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group, as carried out by individual cells. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom." [GOC:jl]
-is_a: GO:0009308 ! amine metabolic process
-is_a: GO:0034641 ! cellular nitrogen compound metabolic process
-
[Term]
id: GO:0044107
-name: cellular alcohol metabolic process
+name: obsolete cellular alcohol metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom, as carried out by individual cells." [GOC:jl]
-is_a: GO:0006066 ! alcohol metabolic process
-is_a: GO:0044237 ! cellular metabolic process
+def: "OBSOLETE. The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom, as carried out by individual cells." [GOC:jl]
+comment: This term was obsoleted because it is an unnecessary grouping classes.
+is_obsolete: true
+replaced_by: GO:0006066
[Term]
id: GO:0044108
-name: cellular alcohol biosynthetic process
+name: obsolete cellular alcohol biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom, carried out at the level of an individual cell." [GOC:jl]
-is_a: GO:0044107 ! cellular alcohol metabolic process
-is_a: GO:0044249 ! cellular biosynthetic process
-is_a: GO:0046165 ! alcohol biosynthetic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom, carried out at the level of an individual cell." [GOC:jl]
+comment: This term was obsoleted because it is an unnecessary grouping classes.
+is_obsolete: true
+replaced_by: GO:0046165
[Term]
id: GO:0044109
-name: cellular alcohol catabolic process
+name: obsolete cellular alcohol catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom, occurring at the level of the individual cell." [GOC:jl]
-is_a: GO:0044107 ! cellular alcohol metabolic process
-is_a: GO:0044248 ! cellular catabolic process
-is_a: GO:0046164 ! alcohol catabolic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom, occurring at the level of the individual cell." [GOC:jl]
+comment: This term was obsoleted because it is an unnecessary grouping classes.
+is_obsolete: true
+replaced_by: GO:0046164
[Term]
id: GO:0044110
@@ -243285,7 +243348,7 @@ id: GO:0044159
name: host thylakoid
namespace: cellular_component
def: "A membranous cellular structure within the host cell that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the host plasma membrane. In eukaryotic host cells they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation." [GOC:rph]
-is_a: GO:0033655 ! host cell cytoplasm part
+is_a: GO:0033647 ! host intracellular organelle
[Term]
id: GO:0044160
@@ -243317,7 +243380,7 @@ relationship: part_of GO:0044161 ! host cell cytoplasmic vesicle
id: GO:0044163
name: host cytoskeleton
namespace: cellular_component
-def: "Any of the various filamentous elements that form the internal framework of host cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the host cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the host cell. The various elements of the host cytoskeleton not only serve in the maintenance of host cellular shape but also have roles in other host cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles." [GOC:rph]
+def: "A cellular structure that forms the internal framework of eukaryotic and prokaryotic host cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles." [GOC:rph]
is_a: GO:0033647 ! host intracellular organelle
[Term]
@@ -243459,8 +243522,11 @@ relationship: part_of GO:0044177 ! host cell Golgi apparatus
id: GO:0044179
name: hemolysis in another organism
namespace: biological_process
-def: "The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another." [GOC:jl]
+alt_id: GO:1990142
+def: "The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another." [GOC:jl, PMID:21590705]
subset: goslim_chembl
+synonym: "envenomation resulting in hemolysis in another organism" NARROW []
+synonym: "envenomation resulting in hemolysis in other organism" NARROW []
synonym: "hemolysis in other organism" EXACT []
synonym: "hemolysis of cells in other organism" EXACT [GOC:bf]
synonym: "hemolysis of erythrocytes in other organism" EXACT []
@@ -243498,6 +243564,7 @@ def: "Binding to a protein or a protein-containing complex to assist the protein
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
+subset: prokaryote_subset
synonym: "chaperone activity" BROAD []
synonym: "protein binding involved in protein folding" EXACT []
xref: Reactome:R-HSA-9018785 "RHOBTB2 binds GTP"
@@ -243677,7 +243744,7 @@ is_a: GO:0044094 ! host cell nuclear part
id: GO:0044205
name: 'de novo' UMP biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen." [GOC:ecd, GOC:jl]
+def: "The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD+ or oxygen." [GOC:ecd, GOC:jl]
synonym: "'de novo' UMP biosynthesis" EXACT []
is_a: GO:0006222 ! UMP biosynthetic process
@@ -243738,14 +243805,14 @@ is_a: GO:0010138 ! pyrimidine ribonucleotide salvage
[Term]
id: GO:0044214
-name: spanning component of plasma membrane
+name: obsolete spanning component of plasma membrane
namespace: cellular_component
-def: "The component of the plasma membrane consisting of gene products and protein complexes that have some part that spans both leaflets of the membrane." [GOC:ecd]
-comment: Proteins that span the membrane but have the bulk on one side of the membrane may be additionally annotated with a term of the form integral to X side of the plasma membrane.
+def: "OBSOLETE. The component of the plasma membrane consisting of gene products and protein complexes that have some part that spans both leaflets of the membrane." [GOC:ecd]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "fully spanning plasma membrane" EXACT []
synonym: "transmembrane" RELATED [GOC:mah]
-is_a: GO:0005887 ! integral component of plasma membrane
-is_a: GO:0089717 ! spanning component of membrane
+is_obsolete: true
+replaced_by: GO:0005886
[Term]
id: GO:0044215
@@ -243922,6 +243989,7 @@ id: GO:0044237
name: cellular metabolic process
namespace: biological_process
def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators]
+comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
subset: gocheck_do_not_annotate
synonym: "cellular metabolism" EXACT []
synonym: "intermediary metabolism" RELATED [GOC:mah]
@@ -243977,15 +244045,15 @@ is_a: GO:0007586 ! digestion
[Term]
id: GO:0044247
-name: cellular polysaccharide catabolic process
+name: obsolete cellular polysaccharide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, as carried out by individual cells." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, as carried out by individual cells." [GOC:jl]
+comment: This term was obsoleted because it is not different from its parent, polysaccharide catabolic process ; GO:0000272.
synonym: "cellular polysaccharide breakdown" EXACT []
synonym: "cellular polysaccharide catabolism" EXACT []
synonym: "cellular polysaccharide degradation" EXACT []
-is_a: GO:0000272 ! polysaccharide catabolic process
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
-is_a: GO:0044275 ! cellular carbohydrate catabolic process
+is_obsolete: true
+replaced_by: GO:0000272
[Term]
id: GO:0044248
@@ -244051,18 +244119,6 @@ namespace: biological_process
def: "The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested proteins into components that may be easily absorbed and directed into metabolism." [GOC:go_curators]
is_a: GO:0007586 ! digestion
-[Term]
-id: GO:0044257
-name: cellular protein catabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a protein by individual cells." [GOC:jl]
-synonym: "cellular protein breakdown" EXACT []
-synonym: "cellular protein catabolism" EXACT []
-synonym: "cellular protein degradation" EXACT []
-is_a: GO:0030163 ! protein catabolic process
-is_a: GO:0044265 ! cellular macromolecule catabolic process
-is_a: GO:0044267 ! cellular protein metabolic process
-
[Term]
id: GO:0044258
name: intestinal lipid catabolic process
@@ -244075,61 +244131,53 @@ is_a: GO:0016042 ! lipid catabolic process
[Term]
id: GO:0044260
-name: cellular macromolecule metabolic process
+name: obsolete cellular macromolecule metabolic process
namespace: biological_process
-alt_id: GO:0034960
-def: "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells." [GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells." [GOC:mah]
+comment: This term was obsoleted because it is not different from its parent, macromolecule metabolic process ; GO:0043170.
synonym: "cellular biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09]
synonym: "cellular macromolecule metabolism" EXACT []
-is_a: GO:0043170 ! macromolecule metabolic process
-is_a: GO:0044237 ! cellular metabolic process
+is_obsolete: true
+replaced_by: GO:0043170
[Term]
id: GO:0044262
-name: cellular carbohydrate metabolic process
+name: obsolete cellular carbohydrate metabolic process
namespace: biological_process
alt_id: GO:0006092
-def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:jl]
+comment: This term was obsoleted because it is not different from its parent, carbohydrate metabolic process ; GO:0005975.
synonym: "cellular carbohydrate metabolism" EXACT []
synonym: "main pathways of carbohydrate metabolic process" NARROW []
synonym: "main pathways of carbohydrate metabolism" NARROW []
-is_a: GO:0005975 ! carbohydrate metabolic process
-is_a: GO:0044237 ! cellular metabolic process
+is_obsolete: true
+replaced_by: GO:0005975
[Term]
id: GO:0044264
-name: cellular polysaccharide metabolic process
+name: obsolete cellular polysaccharide metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving polysaccharides, polymers of more than 10 monosaccharide residues joined by glycosidic linkages, as carried out by individual cells." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways involving polysaccharides, polymers of more than 10 monosaccharide residues joined by glycosidic linkages, as carried out by individual cells." [GOC:jl]
+comment: This term was obsoleted because it is not different from its parent, polysaccharide metabolic process ; GO:0005976.
synonym: "cellular glycan metabolic process" EXACT []
synonym: "cellular glycan metabolism" EXACT []
synonym: "cellular polysaccharide metabolism" EXACT []
-is_a: GO:0005976 ! polysaccharide metabolic process
-is_a: GO:0044260 ! cellular macromolecule metabolic process
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
+is_obsolete: true
+replaced_by: GO:0005976
[Term]
id: GO:0044265
-name: cellular macromolecule catabolic process
+name: obsolete cellular macromolecule catabolic process
namespace: biological_process
alt_id: GO:0034962
-def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells." [GOC:jl]
+comment: This term was obsoleted because it is not different from its parent, macromolecule catabolic process ; GO:0009057.
synonym: "cellular biopolymer catabolic process" EXACT [GOC:mtg_chebi_dec09]
synonym: "cellular macromolecule breakdown" EXACT []
synonym: "cellular macromolecule catabolism" EXACT []
synonym: "cellular macromolecule degradation" EXACT []
-is_a: GO:0009057 ! macromolecule catabolic process
-is_a: GO:0044248 ! cellular catabolic process
-is_a: GO:0044260 ! cellular macromolecule metabolic process
-
-[Term]
-id: GO:0044267
-name: cellular protein metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification." [GOC:jl]
-synonym: "cellular protein metabolism" EXACT []
-is_a: GO:0019538 ! protein metabolic process
-is_a: GO:0044260 ! cellular macromolecule metabolic process
+is_obsolete: true
+replaced_by: GO:0009057
[Term]
id: GO:0044269
@@ -244195,15 +244243,15 @@ is_a: GO:0044248 ! cellular catabolic process
[Term]
id: GO:0044275
-name: cellular carbohydrate catabolic process
+name: obsolete cellular carbohydrate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells." [GOC:jl]
+comment: This term was obsoleted because it is not different from its parent, carbohydrate catabolic process ; GO:0016052.
synonym: "cellular carbohydrate breakdown" EXACT []
synonym: "cellular carbohydrate catabolism" EXACT []
synonym: "cellular carbohydrate degradation" EXACT []
-is_a: GO:0016052 ! carbohydrate catabolic process
-is_a: GO:0044248 ! cellular catabolic process
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
+is_obsolete: true
+replaced_by: GO:0016052
[Term]
id: GO:0044277
@@ -244219,9 +244267,9 @@ is_a: GO:0071555 ! cell wall organization
id: GO:0044278
name: cell wall disruption in another organism
namespace: biological_process
-def: "A process carried out by an organism that results in the breakdown of the cell wall of a second organism." [GOC:jl]
+def: "The disruption of the cell wall of another organism, leading to damage or temporary subversion of the cell wall." [GOC:jl]
synonym: "cell wall disruption in other organism" EXACT []
-is_a: GO:0035821 ! modulation of process of another organism
+is_a: GO:0140975 ! disruption of cellular component of another organism
[Term]
id: GO:0044280
@@ -244260,6 +244308,7 @@ name: small molecule biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw]
comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
+subset: prokaryote_subset
synonym: "small molecule biosynthesis" EXACT []
is_a: GO:0009058 ! biosynthetic process
is_a: GO:0044281 ! small molecule metabolic process
@@ -244617,11 +244666,11 @@ is_a: GO:0000978 ! RNA polymerase II cis-regulatory region sequence-specific DNA
[Term]
id: GO:0044324
-name: regulation of transcription involved in anterior/posterior axis specification
+name: obsolete regulation of transcription involved in anterior/posterior axis specification
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transcription that contributes to the specification of the anterior/posterior axis." [GOC:jl]
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-relationship: part_of GO:0009948 ! anterior/posterior axis specification
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription that contributes to the specification of the anterior/posterior axis." [GOC:jl]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0044325
@@ -244831,7 +244880,6 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an fibroblast growth factor stimulus." [GOC:jl, GOC:yaf]
synonym: "cellular response to FGF stimulus" EXACT []
is_a: GO:0071363 ! cellular response to growth factor stimulus
-is_a: GO:0071495 ! cellular response to endogenous stimulus
is_a: GO:0071774 ! response to fibroblast growth factor
[Term]
@@ -244859,6 +244907,7 @@ namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of cell wall polysaccharides." [GOC:mengo_curators]
synonym: "cell wall polysaccharide breakdown" EXACT [GOC:mah]
is_a: GO:0000272 ! polysaccharide catabolic process
+is_a: GO:0010383 ! cell wall polysaccharide metabolic process
is_a: GO:0016998 ! cell wall macromolecule catabolic process
[Term]
@@ -244994,7 +245043,7 @@ name: disruption of cells of another organism
namespace: biological_process
def: "A process in which an organism has a negative effect on the functioning of the second organism's cells." [GOC:jl]
synonym: "disruption of cells of other organism" EXACT []
-is_a: GO:0035821 ! modulation of process of another organism
+is_a: GO:0140975 ! disruption of cellular component of another organism
[Term]
id: GO:0044365
@@ -245116,19 +245165,21 @@ is_a: GO:0033644 ! host cell membrane
[Term]
id: GO:0044385
-name: integral to membrane of host cell
+name: obsolete integral to membrane of host cell
namespace: cellular_component
-def: "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. Occurring in a host cell." [GOC:jl]
-is_a: GO:0033643 ! host cell part
-relationship: part_of GO:0033644 ! host cell membrane
+def: "OBSOLETE. Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. Occurring in a host cell." [GOC:jl]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0033644
[Term]
id: GO:0044386
-name: integral to host endoplasmic reticulum membrane
+name: obsolete integral to host endoplasmic reticulum membrane
namespace: cellular_component
-def: "Penetrating at least one phospholipid bilayer of an endoplasmic reticulum membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. Occurring in a host cell." [GOC:jl]
-is_a: GO:0044385 ! integral to membrane of host cell
-relationship: part_of GO:0044167 ! host cell endoplasmic reticulum membrane
+def: "OBSOLETE. Penetrating at least one phospholipid bilayer of an endoplasmic reticulum membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. Occurring in a host cell." [GOC:jl]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0044167
[Term]
id: GO:0044387
@@ -245211,6 +245262,7 @@ namespace: biological_process
def: "A process that is carried out at the cellular level and results in the assembly, arrangement of constituent parts, or disassembly of an actin cortical patch, a discrete actin-containing structure found at the plasma membrane in cells, at sites of endocytosis." [GOC:jl]
synonym: "actin cortical patch organisation" EXACT [GOC:mah]
is_a: GO:0016043 ! cellular component organization
+relationship: part_of GO:0030866 ! cortical actin cytoskeleton organization
[Term]
id: GO:0044397
@@ -245293,15 +245345,12 @@ name: adhesion of symbiont to host
namespace: biological_process
alt_id: GO:0051825
alt_id: GO:0051856
-def: "The attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:bf, GOC:cc, GOC:dos, GOC:jl]
-comment: This term can be used to annotate both symbiont and host organisms. Consider also annotating to biological process involved in interaction with symbiont ; GO:0051702.
-synonym: "adhesion to host" NARROW []
+def: "The attachment of a symbiont to its host via either adhesion molecules, general stickiness, or other mechanisms. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:bf, GOC:cc, GOC:dos, GOC:jl]
+synonym: "adhesion to host" RELATED []
synonym: "adhesion to other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "adhesion to other organism involved in symbiotic interaction" EXACT []
-synonym: "adhesion to symbiont" NARROW []
synonym: "host adhesion" NARROW []
-is_a: GO:0022610 ! biological adhesion
-is_a: GO:0044403 ! biological process involved in symbiotic interaction
+is_a: GO:0051701 ! biological process involved in interaction with host
[Term]
id: GO:0044407
@@ -245356,7 +245405,7 @@ synonym: "other organism invasion" RELATED []
synonym: "penetration into host" EXACT [GOC:vw]
synonym: "penetration into host via a specialized structure" NARROW [GOC:vw]
synonym: "penetration into host via a specialized structure during symbiotic interaction" NARROW [GOC:vw]
-is_a: GO:0052126 ! movement in host environment
+is_a: GO:0044000 ! movement in host
[Term]
id: GO:0044410
@@ -245966,7 +246015,6 @@ synonym: "cellular subcomponent" EXACT [NIF_Subcellular:sao628508602]
synonym: "protoplast" RELATED [GOC:mah]
xref: NIF_Subcellular:sao628508602
is_obsolete: true
-consider: CL:0000000
[Term]
id: GO:0044465
@@ -246108,11 +246156,12 @@ is_a: GO:0044479 ! envenomation resulting in modulation of mast cell degranulati
[Term]
id: GO:0044481
-name: envenomation resulting in proteolysis in another organism
+name: obsolete envenomation resulting in proteolysis in another organism
namespace: biological_process
-def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant hydrolysis of proteins in of the bitten organism." [GOC:fj, GOC:jl, PMID:15922779]
+def: "OBSOLETE. A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant hydrolysis of proteins in of the bitten organism." [GOC:fj, GOC:jl, PMID:15922779]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in proteolysis in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
+is_obsolete: true
[Term]
id: GO:0044482
@@ -246236,7 +246285,7 @@ namespace: biological_process
def: "A process by which one organism modulates the force with which blood travels through the circulatory system of another organism." [GOC:fj, GOC:jl, PMID:19837656]
synonym: "modulation of blood pressure in other organism" EXACT []
synonym: "regulation of blood pressure in other organism" EXACT []
-is_a: GO:0008217 ! regulation of blood pressure
+is_a: GO:0044553 ! modulation of biological quality in another organism
[Term]
id: GO:0044496
@@ -246481,7 +246530,7 @@ id: GO:0044524
name: protein sulfhydration
namespace: biological_process
def: "The modification of a protein amino acid by the addition of sulfur." [GOC:jl, GOC:jsg, PMID:19903941, PMID:22169477, PMID:8161529]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0044525
@@ -246561,7 +246610,6 @@ def: "Catalysis of the reaction: very-long-chain fatty acyl-CoA (C22 - C24) + O2
synonym: "very long chain fatty-acyl-CoA oxidase activity" EXACT []
synonym: "very-long-chain acyl-CoA oxidase activity" EXACT []
synonym: "VLC fatty-acyl-CoA oxidase activity" EXACT []
-xref: EC:1.3.3.-
is_a: GO:0003997 ! acyl-CoA oxidase activity
[Term]
@@ -246592,7 +246640,7 @@ is_a: GO:0033643 ! host cell part
id: GO:0044539
name: long-chain fatty acid import into cell
namespace: biological_process
-def: "The directed movement of a long-chain fatty acid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [GOC:jl, GOC:pm, PMID:22022213]
+def: "The directed movement of a long-chain fatty acid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis. A long-chain fatty acid is a fatty acid with an aliphatic tail of 13 to 21 carbons." [GOC:jl, GOC:pm, PMID:22022213]
synonym: "long-chain fatty acid import" RELATED []
synonym: "long-chain fatty acid uptake" EXACT []
is_a: GO:0015909 ! long-chain fatty acid transport
@@ -246602,7 +246650,7 @@ is_a: GO:0140354 ! lipid import into cell
id: GO:0044540
name: L-cystine L-cysteine-lyase (deaminating)
namespace: molecular_function
-def: "Catalysis of the reaction: L-cystine + H2O <=> pyruvate + NH3 + thiocysteine. Thiocysteine is also known as cysteine persulfide." [GOC:jl, RHEA:24927]
+def: "Catalysis of the reaction: L-cystine + H2O = pyruvate + NH3 + thiocysteine. Thiocysteine is also known as cysteine persulfide." [GOC:jl, RHEA:24927]
xref: EC:4.4.1.1
xref: KEGG_REACTION:R02408
xref: RHEA:24927
@@ -246627,11 +246675,12 @@ is_a: GO:0044541 ! zymogen activation in another organism
[Term]
id: GO:0044543
-name: envenomation resulting in zymogen activation in another organism
+name: obsolete envenomation resulting in zymogen activation in another organism
namespace: biological_process
-def: "The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the proteolytic processing of an inactive enzyme to an active form." [GOC:fj, GOC:jl]
+def: "OBSOLETE. The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the proteolytic processing of an inactive enzyme to an active form." [GOC:fj, GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in zymogen activation in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
+is_obsolete: true
[Term]
id: GO:0044544
@@ -246656,7 +246705,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form the NLRP3 inflammasome complex, occurring at the level of an individual cell." [GOC:jl, PMID:21048113]
synonym: "NALP3 inflammasome complex assembly" EXACT []
synonym: "NLRP3 inflammasome activation" RELATED []
-is_a: GO:0140632 ! inflammasome complex assembly
+is_a: GO:0140632 ! canonical inflammasome complex assembly
[Term]
id: GO:0044547
@@ -246693,6 +246742,7 @@ id: GO:0044550
name: secondary metabolite biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of secondary metabolites, the compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon." [GOC:jl]
+subset: prokaryote_subset
synonym: "secondary metabolite biosynthesis" EXACT []
is_a: GO:0009058 ! biosynthetic process
is_a: GO:0019748 ! secondary metabolic process
@@ -246826,7 +246876,7 @@ id: GO:0044565
name: dendritic cell proliferation
namespace: biological_process
def: "The expansion of a dendritic cell population by cell division. A dendritic cell is a cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation." [CL:0000451, PMID:18469816]
-is_a: GO:0046651 ! lymphocyte proliferation
+is_a: GO:0032943 ! mononuclear cell proliferation
[Term]
id: GO:0044566
@@ -247068,8 +247118,7 @@ id: GO:0044594
name: 17-beta-hydroxysteroid dehydrogenase (NAD+) activity
namespace: molecular_function
def: "Catalysis of the reaction: a 17-beta-hydroxysteroid + NAD+ = a 17-oxosteroid + NADH + H+." [PMID:17074428]
-xref: RHEA:24612
-is_a: GO:0004303 ! estradiol 17-beta-dehydrogenase activity
+is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0044595
@@ -247131,6 +247180,7 @@ id: GO:0044600
name: protein guanylyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: GTP + protein = diphosphate + guanylyl-protein; mediates the addition of an guanylyl (guanosine 5'-monophosphate; GMP group) to specific residues of target proteins." [GOC:sp, PMID:20651120]
+xref: Reactome:R-HSA-9765952 "nsp12 guanylates nsp7"
is_a: GO:0070568 ! guanylyltransferase activity
[Term]
@@ -247138,7 +247188,7 @@ id: GO:0044601
name: protein denucleotidylation
namespace: biological_process
def: "The removal of a nucleotide from a protein amino acid." [GOC:sp, PMID:21734656]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0044602
@@ -247200,13 +247250,12 @@ is_obsolete: true
[Term]
id: GO:0044608
-name: peptidyl-L-threonine methyl ester biosynthetic process from peptidyl-threonine
+name: obsolete peptidyl-L-threonine methyl ester biosynthetic process from peptidyl-threonine
namespace: biological_process
-def: "The modification of a C-terminal peptidyl-threonine to form peptidyl-L-threonine methyl ester." [RESID:AA0507]
+def: "OBSOLETE. The modification of a C-terminal peptidyl-threonine to form peptidyl-L-threonine methyl ester." [RESID:AA0507]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-threonine esterification" EXACT []
-xref: RESID:AA0507
-is_a: GO:0006481 ! C-terminal protein methylation
-is_a: GO:0018350 ! protein esterification
+is_obsolete: true
[Term]
id: GO:0044609
@@ -247324,7 +247373,11 @@ is_a: GO:0051192 ! prosthetic group binding
id: GO:0044621
name: modulation of cell migration in another organism
namespace: biological_process
+alt_id: GO:0044624
def: "The process in which an organism effects a change in the process of cell migration in a second organism." [GOC:jl]
+synonym: "envenomation resulting in modulation of cell migration in another organism" NARROW []
+synonym: "envenomation resulting in modulation of cell migration in other organism" NARROW []
+synonym: "envenomation resulting in regulation of cell migration in other organism" NARROW []
synonym: "modulation of cell migration in other organism" EXACT []
synonym: "regulation of cell migration in other organism" EXACT []
is_a: GO:0030334 ! regulation of cell migration
@@ -247334,7 +247387,10 @@ is_a: GO:0035821 ! modulation of process of another organism
id: GO:0044622
name: negative regulation of cell migration in another organism
namespace: biological_process
+alt_id: GO:0044625
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration in a second organism." [GOC:jl]
+synonym: "envenomation resulting in negative regulation of cell migration in another organism" NARROW []
+synonym: "envenomation resulting in negative regulation of cell migration in other organism" NARROW []
synonym: "negative regulation of cell migration in other organism" EXACT []
is_a: GO:0030336 ! negative regulation of cell migration
is_a: GO:0044621 ! modulation of cell migration in another organism
@@ -247343,36 +247399,14 @@ is_a: GO:0044621 ! modulation of cell migration in another organism
id: GO:0044623
name: positive regulation of cell migration in another organism
namespace: biological_process
+alt_id: GO:0044626
def: "Any process that activates or increases the frequency, rate or extent of cell migration in a second organism." [GOC:jl]
+synonym: "envenomation resulting in positive regulation of cell migration in another organism" NARROW []
+synonym: "envenomation resulting in positive regulation of cell migration in other organism" NARROW []
synonym: "positive regulation of cell migration in other organism" EXACT []
is_a: GO:0030335 ! positive regulation of cell migration
is_a: GO:0044621 ! modulation of cell migration in another organism
-[Term]
-id: GO:0044624
-name: envenomation resulting in modulation of cell migration in another organism
-namespace: biological_process
-def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the modulation of cell migration in the bitten organism." [GOC:jl, PMID:19932752]
-synonym: "envenomation resulting in modulation of cell migration in other organism" EXACT []
-synonym: "envenomation resulting in regulation of cell migration in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
-
-[Term]
-id: GO:0044625
-name: envenomation resulting in negative regulation of cell migration in another organism
-namespace: biological_process
-def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the negative regulation of cell migration in the bitten organism." [GOC:jl, PMID:19932752]
-synonym: "envenomation resulting in negative regulation of cell migration in other organism" EXACT []
-is_a: GO:0044624 ! envenomation resulting in modulation of cell migration in another organism
-
-[Term]
-id: GO:0044626
-name: envenomation resulting in positive regulation of cell migration in another organism
-namespace: biological_process
-def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the positive regulation of cell migration in the bitten organism." [GOC:jl, PMID:19932752]
-synonym: "envenomation resulting in positive regulation of cell migration in other organism" EXACT []
-is_a: GO:0044624 ! envenomation resulting in modulation of cell migration in another organism
-
[Term]
id: GO:0044627
name: modulation of complement activation, classical pathway in another organism
@@ -247567,14 +247601,6 @@ def: "The modification of histone H3 by addition of two methyl groups to lysine
is_a: GO:0018027 ! peptidyl-lysine dimethylation
is_a: GO:0051568 ! histone H3-K4 methylation
-[Term]
-id: GO:0044649
-name: envenomation resulting in cytolysis in another organism
-namespace: biological_process
-def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with cytolysis in the bitten organism." [GOC:fj, GOC:jl, PMID:22484288]
-synonym: "envenomation resulting in cytolysis in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
-
[Term]
id: GO:0044650
name: adhesion of symbiont to host cell
@@ -247601,7 +247627,6 @@ id: GO:0044653
name: dextrin alpha-glucosidase activity
namespace: molecular_function
def: "Catalysis of the reaction: dextrin + H2O = alpha-D-glucose." [PMID:18556189]
-xref: EC:3.2.1.-
is_a: GO:0090599 ! alpha-glucosidase activity
[Term]
@@ -247609,7 +247634,6 @@ id: GO:0044654
name: starch alpha-glucosidase activity
namespace: molecular_function
def: "Catalysis of the reaction: starch + H2O = alpha-D-glucose." [PMID:18556189]
-xref: EC:3.2.1.-
is_a: GO:0090599 ! alpha-glucosidase activity
[Term]
@@ -247630,7 +247654,7 @@ def: "Any process that modulates the volume of a post-lysosomal vacuole, a membr
synonym: "regulation of post-lysosome size" EXACT [GOC:dph]
synonym: "regulation of postlysosomal vacuole size" EXACT []
synonym: "regulation of postlysosome vacuole size" EXACT []
-is_a: GO:0032535 ! regulation of cellular component size
+is_a: GO:0097494 ! regulation of vesicle size
[Term]
id: GO:0044657
@@ -247653,7 +247677,7 @@ name: viral release from host cell by cytolysis
namespace: biological_process
alt_id: GO:0019077
alt_id: GO:0046756
-def: "The killing by a virus of a cell by means of the rupture of cell membranes and the loss of cytoplasm." [GOC:jl, PMID:26728778]
+def: "The dissemination of mature viral particles from a host cell by the rupture of cell membranes and the loss of cytoplasm." [GOC:jl, PMID:26728778]
synonym: "cytolysis by virus of host cell" RELATED []
synonym: "lytic viral life cycle" RELATED []
synonym: "lytic viral release" EXACT []
@@ -247661,28 +247685,20 @@ synonym: "viral exit from host cell by cytolysis" EXACT []
synonym: "viral release by cell lysis" EXACT []
synonym: "viral release by host cell lysis" EXACT []
xref: VZ:1077 "Cell lysis"
+is_a: GO:0001897 ! cytolysis by symbiont of host cells
is_a: GO:0019076 ! viral release from host cell
-is_a: GO:0039633 ! killing by virus of host cell
+is_a: GO:0051673 ! disruption of membrane integrity in another organism
[Term]
id: GO:0044660
-name: viral release by cytolysis via pore formation in host cell membrane
+name: viral release via pore formation in host cell membrane
namespace: biological_process
-def: "The killing by a virus of a cell in its host organism by cytolysis, caused by the formation by the virus of pores in its host cell membrane." [GOC:jl]
+def: "The dissemination of mature viral particles from a host cell via the formation by the virus of pores in its host cell membrane." [GOC:jl]
synonym: "cytolysis by virus via pore formation in host cell membrane" RELATED []
synonym: "viral exit by cytolysis via pore formation in host cell membrane" EXACT []
+synonym: "viral release by cytolysis via pore formation in host cell membrane" EXACT []
is_a: GO:0044659 ! viral release from host cell by cytolysis
-[Term]
-id: GO:0044662
-name: disruption by virus of host cell membrane
-namespace: biological_process
-def: "A process by which a virus has a negative effect on the functioning of a host cellular membrane." [GOC:jl]
-synonym: "disruption by organism of host cell membrane" EXACT []
-is_a: GO:0019048 ! modulation by virus of host process
-is_a: GO:0051673 ! membrane disruption in another organism
-is_a: GO:0052025 ! modification by symbiont of host cell membrane
-
[Term]
id: GO:0044663
name: establishment or maintenance of cell type involved in phenotypic switching
@@ -247724,7 +247740,7 @@ synonym: "(R)-carnitine:gamma-butyrobetaine antiporter activity" EXACT []
synonym: "L-carnitine:4-(trimethylammonio)butanoate antiporter activity" EXACT []
synonym: "L-carnitine:gamma-butyrobetaine antiporter activity" EXACT []
xref: RHEA:29427
-is_a: GO:0015491 ! cation:cation antiporter activity
+is_a: GO:0015297 ! antiporter activity
is_a: GO:1901235 ! (R)-carnitine transmembrane transporter activity
is_a: GO:1901236 ! 4-(trimethylammonio)butanoate transmembrane transporter activity
@@ -247764,7 +247780,7 @@ synonym: "CO dehydrogenase complex" BROAD []
synonym: "CO dehydrogenase/acetyl-CoA synthase complex" EXACT []
synonym: "CODH" BROAD []
synonym: "CODH/ACS complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0044673
@@ -247786,14 +247802,14 @@ id: GO:0044675
name: formyl-methanofuran dehydrogenase (tungsten enzyme) complex
namespace: cellular_component
def: "A protein complex consisting of four polypeptides which also contains tungsten, a molybdopterin guanine dinucleotide, and iron-sulfur clusters. This protein complex catalyzes the reversible conversion of CO2 and methanofuran to formylmethanofuran during methanogenesis." [GOC:mengo_curators, PMID:8125106, PMID:8575452]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0044676
name: formyl-methanofuran dehydrogenase (molybdenum enzyme) complex
namespace: cellular_component
def: "A protein complex consisting of three polypeptides which also contains molybdenum, a molybdopterin guanine dinucleotide and iron-sulfur clusters. This protein complex catalyzes the reversible conversion of CO2 and methanofuran to formylmethanofuran during methanogenesis." [GOC:mengo_curators, PMID:1915887, PMID:8954165]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0044677
@@ -247804,7 +247820,7 @@ synonym: "5-methyl-5,6,7,8-tetrahydromethanopterin:2-mercaptoethane sulfonate 2-
synonym: "coenzyme M methyltransferase complex" BROAD []
synonym: "methyl-H4MPT" BROAD []
synonym: "N5-methyltetrahydromethanopterin-coenzyme M methyltransferase complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0044678
@@ -247843,7 +247859,7 @@ is_a: GO:1902494 ! catalytic complex
id: GO:0044682
name: archaeal-specific GTP cyclohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GTP + H2O <=> 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate + diphosphate +formate + H+. This activity is part of the biosynthesis of methanopterin in Archaea, and requires Fe2+." [GOC:mengo_curators, PMID:17497938]
+def: "Catalysis of the reaction: GTP + H2O = 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate + diphosphate +formate + H+. This activity is part of the biosynthesis of methanopterin in Archaea, and requires Fe2+." [GOC:mengo_curators, PMID:17497938]
synonym: "Fe(2+)-dependent archaeal-specific GTP cyclohydrolase activity" EXACT []
synonym: "MptA activity" NARROW []
is_a: GO:0003933 ! GTP cyclohydrolase activity
@@ -247972,7 +247988,7 @@ def: "The process by which a virus causes the death of daughter cells which do n
comment: Note that this process occurs after the cell division partitioning event.
synonym: "killing by virus of host cell by PSK" EXACT []
synonym: "killing by virus of host cell by toxin-antitoxin system" EXACT []
-is_a: GO:0039633 ! killing by virus of host cell
+is_a: GO:0001907 ! killing by symbiont of host cells
[Term]
id: GO:0044697
@@ -248019,10 +248035,10 @@ name: 8-oxo-dGDP phosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction 8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate." [GOC:pde, PMID:22556419, RHEA:32063]
xref: EC:3.6.1.58
-xref: Reactome:R-HSA-2395873 "NUDT18 hydrolyses 8-oxo-GDP to 8-oxo-GMP"
+xref: Reactome:R-HSA-2395876 "NUDT15 hydrolyses 8-oxo-dGDP to 8-oxo-dGMP"
xref: Reactome:R-HSA-2395879 "NUDT18 hydrolyses 8-oxo-dGDP to 8-oxo-dGMP"
xref: RHEA:32063
-is_a: GO:0017110 ! nucleoside-diphosphatase activity
+is_a: GO:0017110 ! nucleoside diphosphate phosphatase activity
[Term]
id: GO:0044716
@@ -248030,16 +248046,17 @@ name: 8-oxo-GDP phosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction 8-oxo-GDP + H2O = 8-oxo-GMP + phosphate." [GOC:pde, PMID:22556419, RHEA:62356]
xref: EC:3.6.1.58
+xref: Reactome:R-HSA-2395873 "NUDT18 hydrolyses 8-oxo-GDP to 8-oxo-GMP"
xref: RHEA:62356
-is_a: GO:0017110 ! nucleoside-diphosphatase activity
+is_a: GO:0017110 ! nucleoside diphosphate phosphatase activity
[Term]
id: GO:0044717
name: 8-hydroxy-dADP phosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction: 8-hydroxy-dADP + H2O = 8-hydroxy-dAMP + phosphate." [GOC:pde, PMID:22556419]
-xref: Reactome:R-HSA-2395965 "NUDT18 hydrolyses 8-OH-dADP to 8-OH-dAMP"
-is_a: GO:0017110 ! nucleoside-diphosphatase activity
+xref: Reactome:R-HSA-2395965 "NUDT18 hydrolyses 8-oxo-dADP to 8-oxo-dAMP"
+is_a: GO:0017110 ! nucleoside diphosphate phosphatase activity
[Term]
id: GO:0044718
@@ -248091,10 +248108,11 @@ is_a: GO:0043045 ! DNA methylation involved in embryo development
[Term]
id: GO:0044726
-name: protection of DNA demethylation of female pronucleus
+name: maintenance of DNA methylation at imprinted genes
namespace: biological_process
def: "The protection of the maternal genome from DNA demethylation in the zygote following fertilization." [GOC:sp, PMID:22868271]
-is_a: GO:0044030 ! regulation of DNA methylation
+synonym: "protection of DNA demethylation of female pronucleus" NARROW []
+is_a: GO:0045814 ! negative regulation of gene expression, epigenetic
relationship: part_of GO:0044725 ! chromatin reprogramming in the zygote
[Term]
@@ -248107,11 +248125,12 @@ relationship: part_of GO:0044725 ! chromatin reprogramming in the zygote
[Term]
id: GO:0044728
-name: DNA methylation or demethylation
+name: obsolete DNA methylation or demethylation
namespace: biological_process
-def: "The process of adding or removing a methyl group from one or more nucleotides within an DNA molecule." [GOC:jl]
+def: "OBSOLETE. The process of adding or removing a methyl group from one or more nucleotides within an DNA molecule." [GOC:jl]
+comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "changes in DNA methylation" RELATED []
-is_a: GO:0006304 ! DNA modification
+is_obsolete: true
[Term]
id: GO:0044729
@@ -248246,21 +248265,21 @@ id: GO:0044743
name: protein transmembrane import into intracellular organelle
namespace: biological_process
def: "The directed movement of proteins into an intracellular organelle, across a membrane." [GOC:jl]
-is_a: GO:0017038 ! protein import
is_a: GO:0071806 ! protein transmembrane transport
is_a: GO:0072594 ! establishment of protein localization to organelle
[Term]
id: GO:0044747
-name: mature miRNA 3'-end processing
+name: pre-miRNA 3'-end processing
namespace: biological_process
def: "Any process involved in forming distinct miRNA isoforms from a mature miRNA that differ at their 3'-ends." [PMID:22055292, PMID:22055293]
+synonym: "mature miRNA 3'-end processing" RELATED []
synonym: "miRNA 3' end terminal trimming" BROAD []
synonym: "miRNA 3'-end processing" BROAD []
synonym: "miRNA trimming" BROAD []
-is_a: GO:0010586 ! miRNA metabolic process
-is_a: GO:0043628 ! ncRNA 3'-end processing
-relationship: part_of GO:0035196 ! production of miRNAs involved in gene silencing by miRNA
+is_a: GO:0031054 ! pre-miRNA processing
+is_a: GO:0043628 ! regulatory ncRNA 3'-end processing
+relationship: part_of GO:0035196 ! miRNA processing
[Term]
id: GO:0044748
@@ -248268,7 +248287,7 @@ name: 3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing
namespace: molecular_function
def: "Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule that contributes to forming distinct miRNA isoforms from a mature miRNA." [GOC:sart]
synonym: "exonucleolytic trimming to generate 3' end of miRNA" BROAD []
-is_a: GO:0000175 ! 3'-5'-exoribonuclease activity
+is_a: GO:0000175 ! 3'-5'-RNA exonuclease activity
[Term]
id: GO:0044750
@@ -248358,10 +248377,11 @@ is_a: GO:0046929 ! negative regulation of neurotransmitter secretion
[Term]
id: GO:0044764
-name: multi-organism cellular process
+name: obsolete multi-organism cellular process
namespace: biological_process
-def: "Any process that is carried out at the cellular level which involves another organism of the same or different species." [GOC:jl]
-is_a: GO:0009987 ! cellular process
+def: "OBSOLETE. Any process that is carried out at the cellular level which involves another organism of the same or different species." [GOC:jl]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
+is_obsolete: true
[Term]
id: GO:0044766
@@ -248371,25 +248391,6 @@ def: "OBSOLETE. The directed movement of substances (such as macromolecules, sma
comment: This term was obsoleted because there is no evidence that this process exists.
is_obsolete: true
-[Term]
-id: GO:0044768
-name: NMS complex assembly
-namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form an NMS complex. The NMS complex results from the association of two subcomplexes (known as MIND and Ndc80 in Schizosaccharomyces) and is required for kinetochore assembly." [GOC:vw, PMID:22561345]
-synonym: "KMN complex interaction involved in chromosome segregation" EXACT []
-synonym: "KMN kinetochore network assembly" EXACT []
-synonym: "KMN kinetochore network formation" EXACT []
-synonym: "KMN network assembly involved in chromosome segregation" EXACT []
-synonym: "KNL-1-Mis12-Ndc80 assembly" EXACT []
-synonym: "KNL-1-Mis12-Ndc80 formation" EXACT []
-synonym: "Ndc80-MIND-Spc7 complex assembly" EXACT []
-synonym: "Ndc80-MIND-Spc7 complex formation" EXACT []
-synonym: "NMS complex assembly involved in kinetochore assembly" EXACT []
-synonym: "NMS complex association involved in chromosome segregation" EXACT []
-synonym: "NMS complex formation" EXACT []
-is_a: GO:0065003 ! protein-containing complex assembly
-relationship: part_of GO:0051382 ! kinetochore assembly
-
[Term]
id: GO:0044769
name: ATPase activity, coupled to transmembrane movement of ions, rotational mechanism
@@ -248568,7 +248569,7 @@ id: GO:0044786
name: cell cycle DNA replication
namespace: biological_process
def: "The DNA-dependent DNA replication that takes place as part of the cell cycle." [GOC:mtg_cell_cycle]
-is_a: GO:0006261 ! DNA-dependent DNA replication
+is_a: GO:0006261 ! DNA-templated DNA replication
is_a: GO:0022402 ! cell cycle process
[Term]
@@ -248678,7 +248679,6 @@ synonym: "nitrate reductase A" EXACT []
is_a: GO:0009325 ! nitrate reductase complex
is_a: GO:0098797 ! plasma membrane protein complex
is_a: GO:0098803 ! respiratory chain complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
relationship: part_of GO:0070470 ! plasma membrane respirasome
[Term]
@@ -248691,10 +248691,11 @@ is_obsolete: true
[Term]
id: GO:0044803
-name: multi-organism membrane organization
+name: obsolete multi-organism membrane organization
namespace: biological_process
-def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane, involving more than one organism." [GOC:jl]
-is_a: GO:0061024 ! membrane organization
+def: "OBSOLETE. A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane, involving more than one organism." [GOC:jl]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0044804
@@ -248764,6 +248765,7 @@ id: GO:0044813
name: glycolytic fermentation via PFOR pathway
namespace: biological_process
def: "The glycolytic fermentation beginning with the anaerobic conversion of glucose to pyruvate by the glycolytic pathway, continuing with pyruvate:ferredoxin oxidoreductase (PFOR) activity. This pathway is found in strict anaerobes such as Clostridia species." [GOC:mengo_curators, PMID:20395274, PMID:20692761]
+xref: MetaCyc:CENTFERM-PWY
is_a: GO:0019660 ! glycolytic fermentation
[Term]
@@ -248775,10 +248777,11 @@ is_a: GO:0019660 ! glycolytic fermentation
[Term]
id: GO:0044815
-name: DNA packaging complex
+name: obsolete DNA packaging complex
namespace: cellular_component
-def: "A protein complex that plays a role in the process of DNA packaging." [GOC:jl]
-is_a: GO:0032991 ! protein-containing complex
+def: "OBSOLETE. A protein complex that plays a role in the process of DNA packaging." [GOC:jl]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term.
+is_obsolete: true
[Term]
id: GO:0044816
@@ -248843,7 +248846,7 @@ def: "The catalysis of the removal of two di- or tri-nucleotides from each 3' en
comment: This reaction may serve to remove heterogeneous extra bases from the viral DNA end, and to stabilize the integrase-DNA complex. The chemistry of cleavage is a simple hydrolysis by single-step transesterification.
synonym: "3' processing reaction" EXACT []
synonym: "3'-processing activity" EXACT []
-is_a: GO:0004520 ! endodeoxyribonuclease activity
+is_a: GO:0004520 ! DNA endonuclease activity
relationship: part_of GO:0044823 ! retroviral integrase activity
[Term]
@@ -248887,7 +248890,7 @@ relationship: negatively_regulates GO:0019079 ! viral genome replication
id: GO:0044829
name: positive regulation by host of viral genome replication
namespace: biological_process
-def: "A process in which a host organism activates or increases the frequency, rate or extent of viral genome replication." [GOC:jl]
+def: "A process in which a host organism activates or increases the frequency, rate or extent of viral genome replication." [GOC:jl]
is_a: GO:0044794 ! positive regulation by host of viral process
is_a: GO:0044827 ! modulation by host of viral genome replication
relationship: positively_regulates GO:0019079 ! viral genome replication
@@ -248906,7 +248909,6 @@ id: GO:0044831
name: modulation by virus of host cytokine production
namespace: biological_process
def: "Any process in which a virus modulates the frequency, rate or extent of cytokine production in its host organism." [GOC:jl]
-is_a: GO:0039656 ! modulation by virus of host gene expression
is_a: GO:0075528 ! modulation by virus of host immune response
relationship: regulates GO:0001816 ! cytokine production
@@ -248920,7 +248922,6 @@ is_a: GO:0001819 ! positive regulation of cytokine production
is_a: GO:0044416 ! induction by symbiont of host defense response
is_a: GO:0044831 ! modulation by virus of host cytokine production
is_a: GO:0050776 ! regulation of immune response
-is_a: GO:0050794 ! regulation of cellular process
[Term]
id: GO:0044833
@@ -249092,12 +249093,12 @@ is_a: GO:0044848 ! biological phase
[Term]
id: GO:0044852
-name: nonrepetitive DNA condensation
+name: obsolete nonrepetitive DNA condensation
namespace: biological_process
-def: "The process in which chromatin structure of nonrepetitive regions of DNA is compacted prior to and during mitosis in eukaryotic cells." [GOC:jl, PMID:10811823]
+def: "OBSOLETE. The process in which chromatin structure of nonrepetitive regions of DNA is compacted prior to and during mitosis in eukaryotic cells." [GOC:jl, PMID:10811823]
+comment: This term was obsoleted because is is defined in a negative manner.
synonym: "nonrepetitive DNA packaging" EXACT []
-is_a: GO:0006323 ! DNA packaging
-relationship: part_of GO:0030261 ! chromosome condensation
+is_obsolete: true
[Term]
id: GO:0044853
@@ -249282,7 +249283,7 @@ is_a: GO:0044873 ! lipoprotein localization to membrane
id: GO:0044875
name: gamma-glutamyl hercynylcysteine sulfoxide synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: gamma-glutamyl cysteine + hercynine + O2 <=> gamma-glutamyl-hercynyl cysteine sulfoxide + H2O." [GOC:jl, PMID:24828577, RHEA:42672]
+def: "Catalysis of the reaction: gamma-glutamyl cysteine + hercynine + O2 = gamma-glutamyl-hercynyl cysteine sulfoxide + H2O." [GOC:jl, PMID:24828577, RHEA:42672]
synonym: "gamma-glutamyl hercynylcysteine S-oxide synthase" EXACT [GOC:dph]
synonym: "gamma-glutamyl hercynylcysteine sulfoxide synthase" EXACT []
xref: EC:1.14.99.50
@@ -249293,7 +249294,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0044876
name: hercynylselenocysteine synthase
namespace: molecular_function
-def: "Catalysis of the reaction: 2 L-selenocysteine + 2 hercynine + O2 <=> 2 H2O + 2 hercynylselenocysteine." [GOC:jl, PMID:24828577, RHEA:42680]
+def: "Catalysis of the reaction: 2 L-selenocysteine + 2 hercynine + O2 = 2 H2O + 2 hercynylselenocysteine." [GOC:jl, PMID:24828577, RHEA:42680]
xref: MetaCyc:RXN-15803
xref: RHEA:42680
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
@@ -249367,17 +249368,18 @@ name: DNA replication proofreading
namespace: biological_process
def: "Correction of replication errors by DNA polymerase using a 3'-5' exonuclease activity." [GOC:ai]
is_a: GO:0006281 ! DNA repair
-is_a: GO:0045005 ! DNA-dependent DNA replication maintenance of fidelity
+is_a: GO:0045005 ! DNA-templated DNA replication maintenance of fidelity
[Term]
id: GO:0045005
-name: DNA-dependent DNA replication maintenance of fidelity
+name: DNA-templated DNA replication maintenance of fidelity
namespace: biological_process
def: "A DNA metabolic process that prevents or corrects errors to ensure that DNA is replicated accurately. Errors can be corrected either by intrinsic DNA polymerase proofreading activity or via mismatch repair." [GOC:mah, GOC:vw]
+synonym: "DNA-dependent DNA replication maintenance of fidelity" EXACT []
synonym: "maintenance of fidelity during DNA-dependent DNA replication" RELATED [GOC:dph, GOC:tb]
synonym: "maintenance of fidelity involved in DNA-dependent DNA replication" EXACT []
is_a: GO:0006259 ! DNA metabolic process
-relationship: part_of GO:0006261 ! DNA-dependent DNA replication
+relationship: part_of GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:0045006
@@ -249439,7 +249441,7 @@ namespace: biological_process
def: "A transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances." [GOC:mah, ISBN:0198506732, PMID:11018147, PMID:18359269, PMID:9618445]
synonym: "carbon catabolite repression" RELATED [GOC:dph]
synonym: "negative regulation of transcription by carbon catabolites" EXACT [GOC:mah]
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
is_a: GO:0045990 ! carbon catabolite regulation of transcription
is_a: GO:0061985 ! carbon catabolite repression
@@ -249473,7 +249475,6 @@ alt_id: GO:1990614
def: "The process in which a magnesium ion (Mg2+) is transported across a mitochondrial membrane, into or out of the mitochondrion." [GOC:ai, PMID:11254124]
synonym: "mitochondrial magnesium ion transport" RELATED []
is_a: GO:1903830 ! magnesium ion transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0045017
@@ -249678,7 +249679,6 @@ namespace: biological_process
def: "The targeting and import of proteins into the chloroplast stroma. Import depends on ATP hydrolysis catalyzed by stromal chaperones. Chloroplast stromal proteins, such as the S subunit of rubisco, have a N-terminal stromal-import sequence of about 44 amino acids which is cleaved from the protein precursor after import." [ISBN:0716731363]
synonym: "chloroplast stroma protein import" EXACT []
synonym: "protein transport into chloroplast stroma" EXACT []
-is_a: GO:0017038 ! protein import
is_a: GO:0045036 ! protein targeting to chloroplast
is_a: GO:0065002 ! intracellular protein transmembrane transport
@@ -249690,6 +249690,7 @@ def: "The import of proteins into the chloroplast thylakoid membranes. Proteins
synonym: "chloroplast thylakoid membrane protein import" EXACT []
synonym: "protein transport into chloroplast thylakoid membrane" EXACT []
is_a: GO:0006612 ! protein targeting to membrane
+is_a: GO:0017038 ! protein import
is_a: GO:0044743 ! protein transmembrane import into intracellular organelle
is_a: GO:0045036 ! protein targeting to chloroplast
is_a: GO:0065002 ! intracellular protein transmembrane transport
@@ -249715,7 +249716,6 @@ synonym: "mitochondrial outer membrane protein import" EXACT []
synonym: "protein import into mitochondrial outer membrane" EXACT []
synonym: "protein transport into mitochondrial outer membrane" EXACT []
is_a: GO:0007008 ! outer mitochondrial membrane organization
-is_a: GO:0017038 ! protein import
is_a: GO:0051204 ! protein insertion into mitochondrial membrane
relationship: part_of GO:0006626 ! protein targeting to mitochondrion
@@ -249732,7 +249732,6 @@ synonym: "protein import into mitochondrial intermembrane space, direct" NARROW
synonym: "protein import into mitochondrial intermembrane space, nonconservative" NARROW [GOC:mcc]
synonym: "protein transport into mitochondrial IMS" EXACT []
synonym: "protein transport into mitochondrial intermembrane space" EXACT []
-is_a: GO:0006839 ! mitochondrial transport
is_a: GO:0044743 ! protein transmembrane import into intracellular organelle
is_a: GO:0065002 ! intracellular protein transmembrane transport
is_a: GO:0072655 ! establishment of protein localization to mitochondrion
@@ -249777,7 +249776,6 @@ synonym: "protein transport into peroxisome membrane" EXACT []
is_a: GO:0006612 ! protein targeting to membrane
is_a: GO:0006625 ! protein targeting to peroxisome
is_a: GO:0015919 ! peroxisomal membrane transport
-is_a: GO:0017038 ! protein import
[Term]
id: GO:0045047
@@ -250105,6 +250103,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of single stranded viral RNA replication via double stranded DNA intermediate." [GOC:go_curators]
synonym: "regulation of retroviral genome replication" EXACT [GOC:bf, GOC:jl]
is_a: GO:0045069 ! regulation of viral genome replication
+is_a: GO:2001141 ! regulation of RNA biosynthetic process
relationship: regulates GO:0039692 ! single stranded viral RNA replication via double stranded DNA intermediate
[Term]
@@ -250114,7 +250113,6 @@ namespace: cellular_component
def: "A protein complex that binds interleukin-18; comprises an alpha and a beta subunit." [GOC:mah, PMID:12759435]
synonym: "IL-18 receptor complex" EXACT [GOC:add]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0045093
@@ -250366,7 +250364,9 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + azole(in) = H+(in) + azole(out). Azoles are heterocyclic compounds found in many biologically important substances." [GOC:ai, ISBN:3527307206, Wikipedia:Azole]
synonym: "azole:hydrogen antiporter activity" EXACT []
synonym: "bicyclomycin/sulfathiazole:hydrogen antiporter activity" NARROW []
-is_a: GO:0015299 ! solute:proton antiporter activity
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
is_a: GO:1901474 ! azole transmembrane transporter activity
[Term]
@@ -250420,7 +250420,6 @@ name: regulation of bone resorption
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of bone tissue loss (resorption)." [GOC:ai]
is_a: GO:0046850 ! regulation of bone remodeling
-is_a: GO:0065008 ! regulation of biological quality
relationship: regulates GO:0045453 ! bone resorption
[Term]
@@ -250434,7 +250433,7 @@ is_a: GO:0004930 ! G protein-coupled receptor activity
id: GO:0045127
name: N-acetylglucosamine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-acetyl-D-glucosamine + ATP = N-acetyl-D-glucosamine 6-phosphate + ADP + 2 H(+)." [EC:2.7.1.59, RHEA:17417]
+def: "Catalysis of the reaction: N-acetyl-D-glucosamine + ATP = N-acetyl-D-glucosamine 6-phosphate + ADP + 2 H+." [EC:2.7.1.59, RHEA:17417]
synonym: "2-acetylamino-2-deoxy-D-glucose kinase activity" RELATED [EC:2.7.1.59]
synonym: "acetylaminodeoxyglucokinase activity" RELATED [EC:2.7.1.59]
synonym: "acetylglucosamine kinase (phosphorylating)" RELATED [EC:2.7.1.59]
@@ -250507,7 +250506,7 @@ relationship: part_of GO:0140013 ! meiotic nuclear division
id: GO:0045133
name: 2,3-dihydroxybenzoate 3,4-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,3-dihydroxybenzoate + O(2) = 2-hydroxy-3-(3-oxoprop-1-enyl)but-2-enedioate + H(+)." [EC:1.13.11.14, RHEA:18477]
+def: "Catalysis of the reaction: 2,3-dihydroxybenzoate + O2 = 2-hydroxy-3-(3-oxoprop-1-enyl)but-2-enedioate + H+." [EC:1.13.11.14, RHEA:18477]
synonym: "2,3-dihydroxybenzoate 1,2-dioxygenase activity" RELATED [EC:1.13.11.14]
synonym: "2,3-dihydroxybenzoate oxygenase activity" RELATED [EC:1.13.11.14]
synonym: "2,3-dihydroxybenzoate:oxygen 3,4-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.14]
@@ -250521,18 +250520,18 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
[Term]
id: GO:0045134
-name: uridine-diphosphatase activity
+name: UDP phosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction: UDP + H2O = UMP + phosphate." [RHEA:64876]
synonym: "UDP phosphohydrolase activity" EXACT [KEGG_REACTION:R00155]
-synonym: "UDPase activity" RELATED [EC:3.6.1.6]
-synonym: "uridine 5'-diphosphatase activity" RELATED [EC:3.6.1.6]
-synonym: "uridine diphosphatase activity" RELATED [EC:3.6.1.6]
-xref: EC:3.6.1.6
+synonym: "UDPase activity" RELATED []
+synonym: "uridine 5'-diphosphatase activity" RELATED []
+synonym: "uridine diphosphatase activity" RELATED []
+synonym: "uridine-diphosphatase activity" EXACT []
xref: KEGG_REACTION:R00155
xref: MetaCyc:RXN-12197
xref: RHEA:64876
-is_a: GO:0017110 ! nucleoside-diphosphatase activity
+is_a: GO:0017110 ! nucleoside diphosphate phosphatase activity
[Term]
id: GO:0045135
@@ -250636,13 +250635,13 @@ relationship: part_of GO:0007135 ! meiosis II
[Term]
id: GO:0045145
-name: single-stranded DNA 5'-3' exodeoxyribonuclease activity
+name: single-stranded DNA 5'-3' DNA exonuclease activity
namespace: molecular_function
def: "Catalysis of the sequential cleavage of nucleotides (such as mononucleotides or dinucleotides) from a free 5' terminus of a single-stranded DNA molecule." [GOC:ai, GOC:elh, PMID:20086101]
synonym: "single-stranded DNA specific 5'-3' exodeoxyribonuclease activity" RELATED []
synonym: "ssDNA-specific 5'-3' exodeoxyribonuclease activity" RELATED [GOC:mah]
is_a: GO:0008297 ! single-stranded DNA exodeoxyribonuclease activity
-is_a: GO:0035312 ! 5'-3' exodeoxyribonuclease activity
+is_a: GO:0035312 ! 5'-3' DNA exonuclease activity
[Term]
id: GO:0045146
@@ -250820,7 +250819,7 @@ consider: GO:0046659
id: GO:0045165
name: cell fate commitment
namespace: biological_process
-def: "The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field." [ISBN:0716731185]
+def: "The cellular developmental process by which a cell establishes the intrinsic character of a cell or tissue region irreversibly committing it to a particular fate." [ISBN:0716731185]
comment: Note that this term was 'cell fate determination' but the term name was changed to better match its existing definition and the child term 'cell fate determination; GO:0001709' was also created.
is_a: GO:0048869 ! cellular developmental process
relationship: part_of GO:0030154 ! cell differentiation
@@ -250874,7 +250873,6 @@ name: intercellular bridge
namespace: cellular_component
def: "A direct connection between the cytoplasm of two cells that is formed following the completion of cleavage furrow ingression during cell division. They are usually present only briefly prior to completion of cytokinesis. However, in some cases, such as the bridges between germ cells during their development, they become stabilised." [PMID:9635420]
is_a: GO:0110165 ! cellular anatomical entity
-relationship: part_of GO:0005576 ! extracellular region
[Term]
id: GO:0045172
@@ -250982,12 +250980,12 @@ id: GO:0045182
name: translation regulator activity
namespace: molecular_function
def: "Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
+subset: prokaryote_subset
synonym: "translation factor activity" EXACT []
is_a: GO:0003674 ! molecular_function
@@ -251216,14 +251214,15 @@ is_a: GO:0030054 ! cell junction
[Term]
id: GO:0045203
-name: integral component of cell outer membrane
+name: obsolete integral component of cell outer membrane
namespace: cellular_component
-def: "The component of the cell outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:go_curators, GOC:mtg_sensu]
+def: "OBSOLETE. The component of the cell outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:go_curators, GOC:mtg_sensu]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to cell outer membrane" NARROW []
synonym: "integral to external membrane" RELATED []
synonym: "integral to outer membrane" RELATED []
-is_a: GO:0016021 ! integral component of membrane
-is_a: GO:0031230 ! intrinsic component of cell outer membrane
+is_obsolete: true
+replaced_by: GO:0009279
[Term]
id: GO:0045204
@@ -251490,7 +251489,7 @@ synonym: "extracellular polysaccharide anabolism" EXACT []
synonym: "extracellular polysaccharide biosynthesis" EXACT []
synonym: "extracellular polysaccharide formation" EXACT []
synonym: "extracellular polysaccharide synthesis" EXACT []
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
+is_a: GO:0000271 ! polysaccharide biosynthetic process
is_a: GO:0046379 ! extracellular polysaccharide metabolic process
[Term]
@@ -251616,7 +251615,7 @@ namespace: cellular_component
def: "Any of the heteromeric enzymes that act in the TCA cycle." [GOC:mah]
subset: goslim_pir
synonym: "TCA cycle enzyme complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005737 ! cytoplasm
[Term]
@@ -251725,7 +251724,7 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0045252
name: oxoglutarate dehydrogenase complex
namespace: cellular_component
-def: "A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2)." [MetaCyc:CPLX66-42, PMID:10848975]
+def: "A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2)." [MetaCyc:CPLX66-42, PMID:10848975]
subset: goslim_pir
synonym: "dihydrolipoamide S-succinyltransferase complex" EXACT []
is_a: GO:0045240 ! dihydrolipoyl dehydrogenase complex
@@ -251936,7 +251935,7 @@ def: "A part of the respiratory chain, containing the four polypeptide subunits
subset: goslim_pir
synonym: "electron transport complex II" RELATED []
is_a: GO:0098803 ! respiratory chain complex
-relationship: part_of GO:0005622 ! intracellular anatomical structure
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0045274
@@ -252019,6 +252018,7 @@ namespace: cellular_component
def: "A multimeric complex which consists of flavoprotein (subunit A ; InterPro:IPR003952), iron-sulfur protein (subunit B) and membrane-bound cytochrome b560 (subunit C; InterPro:IPR000701). In some Archaea, the membrane-bound subunits (C or C and D) do not necessarily contain heme. Membrane-bound subunits can bind or react with quinones." [GOC:kd, InterPro:IPR000701]
is_a: GO:0098803 ! respiratory chain complex
is_a: GO:1990204 ! oxidoreductase complex
+relationship: part_of GO:0005622 ! intracellular anatomical structure
relationship: part_of GO:0045273 ! respiratory chain complex II
[Term]
@@ -252038,6 +252038,7 @@ namespace: cellular_component
def: "A membrane-bound flavoenzyme complex consisting of four subunits, A, B, C, and D. A and B comprise the membrane-extrinsic catalytic domain and C (InterPro:IPR003510; InterPro:IPR004224) and D (InterPro:IPR003418) link the catalytic centers to the electron-transport chain. This family consists of the 13 kDa hydrophobic subunit D. This component may be required to anchor the catalytic components of the fumarate reductase complex to the cytoplasmic membrane. Fumarate reductase couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, in a reaction opposite to that catalyzed by the related complex II of the respiratory chain (succinate dehydrogenase-(ubiquinone))." [InterPro:IPR003418, InterPro:IPR004224]
comment: See also the molecular function term 'succinate dehydrogenase (ubiquinone) activity ; GO:0008177'.
is_a: GO:0098803 ! respiratory chain complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0045273 ! respiratory chain complex II
[Term]
@@ -252096,7 +252097,7 @@ namespace: cellular_component
def: "A protein complex that posttranscriptionally catalyzes insertion, deletion or substitution of nucleotides at multiple sites within nascent mRNA transcripts to produce mature mRNAs in eukaryotes." [http://www.ejbiotechnology.info/content/vol1/issue1/full/4/, PMID:11564867, PMID:12139607, PMID:24316715]
subset: goslim_pir
synonym: "editosome" EXACT []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0045294
@@ -252158,7 +252159,6 @@ synonym: "stearyl acyl carrier protein desaturase activity" RELATED [EC:1.14.19.
synonym: "stearyl-ACP desaturase activity" RELATED [EC:1.14.19.2]
xref: EC:1.14.19.2
xref: MetaCyc:1.14.19.2-RXN
-xref: MetaCyc:PWY-5147
is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
[Term]
@@ -252387,7 +252387,6 @@ namespace: cellular_component
def: "A protein complex that binds interleukin-1; comprises an alpha and a beta subunit." [GOC:mah, InterPro:IPR004075]
synonym: "IL-1 receptor complex" EXACT [GOC:add]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0045324
@@ -252483,7 +252482,6 @@ id: GO:0045333
name: cellular respiration
namespace: biological_process
def: "The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration)." [GOC:das, ISBN:0140513590, ISBN:0198506732]
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
subset: goslim_yeast
@@ -252825,7 +252823,7 @@ is_a: GO:0016860 ! intramolecular oxidoreductase activity
id: GO:0045437
name: uridine nucleosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + uridine = ribofuranose + uracil." [EC:3.2.2.3, RHEA:15577]
+def: "Catalysis of the reaction: H2O + uridine = ribofuranose + uracil." [EC:3.2.2.3, RHEA:15577]
synonym: "uridine hydrolase activity" EXACT []
synonym: "uridine ribohydrolase activity" RELATED [EC:3.2.2.3]
xref: EC:3.2.2.3
@@ -252859,7 +252857,7 @@ is_a: GO:0016855 ! racemase and epimerase activity, acting on amino acids and de
id: GO:0045442
name: deacetoxycephalosporin-C hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + deacetoxycephalosporin C + O(2) = CO(2) + deacetylcephalosporin C + succinate." [EC:1.14.11.26, RHEA:16805]
+def: "Catalysis of the reaction: 2-oxoglutarate + deacetoxycephalosporin C + O2 = CO2 + deacetylcephalosporin C + succinate." [EC:1.14.11.26, RHEA:16805]
synonym: "3'-methylcephem hydroxylase activity" RELATED [EC:1.14.11.26]
synonym: "beta-lactam hydroxylase activity" EXACT []
synonym: "DACS" RELATED [EC:1.14.11.26]
@@ -252963,7 +252961,6 @@ synonym: "regulation of cell redox homeostasis" RELATED []
synonym: "regulation of redox homeostasis" BROAD []
xref: Wikipedia:Redox
is_a: GO:0019725 ! cellular homeostasis
-is_a: GO:0050794 ! regulation of cellular process
[Term]
id: GO:0045455
@@ -252972,8 +252969,8 @@ namespace: biological_process
def: "The chemical reactions and pathways involving ecdysteroids, a group of polyhydroxylated ketosteroids ubiquitous in insects and other arthropods, in which they initiate post-embryonic development, including the metamorphosis of immature forms and the development of the reproductive system and the maturation of oocytes in adult females." [ISBN:0198506732]
synonym: "ecdysteroid metabolism" EXACT []
is_a: GO:0008202 ! steroid metabolic process
-is_a: GO:0034754 ! cellular hormone metabolic process
is_a: GO:0042180 ! cellular ketone metabolic process
+is_a: GO:0042445 ! hormone metabolic process
relationship: part_of GO:0002165 ! instar larval or pupal development
[Term]
@@ -252985,9 +252982,10 @@ synonym: "ecdysteroid anabolism" EXACT []
synonym: "ecdysteroid biosynthesis" EXACT []
synonym: "ecdysteroid formation" EXACT []
synonym: "ecdysteroid synthesis" EXACT []
+is_a: GO:0006694 ! steroid biosynthetic process
is_a: GO:0042181 ! ketone biosynthetic process
+is_a: GO:0042446 ! hormone biosynthetic process
is_a: GO:0045455 ! ecdysteroid metabolic process
-is_a: GO:0120178 ! steroid hormone biosynthetic process
[Term]
id: GO:0045457
@@ -253224,7 +253222,7 @@ is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0045481
name: 6-endo-hydroxycineole dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-endo-hydroxycineole + NAD(+) = 6-oxocineole + H(+) + NADH." [EC:1.1.1.241, RHEA:11736]
+def: "Catalysis of the reaction: 6-endo-hydroxycineole + NAD+ = 6-oxocineole + H+ + NADH." [EC:1.1.1.241, RHEA:11736]
synonym: "6-endo-hydroxycineole:NAD+ 6-oxidoreductase activity" RELATED [EC:1.1.1.241]
xref: EC:1.1.1.241
xref: KEGG_REACTION:R02994
@@ -253320,8 +253318,8 @@ synonym: "gibberellic acid catabolism" NARROW []
synonym: "gibberellic acid degradation" NARROW []
synonym: "gibberellin catabolism" EXACT []
is_a: GO:0009685 ! gibberellin metabolic process
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0016103 ! diterpenoid catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
[Term]
id: GO:0045488
@@ -253382,8 +253380,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of xylan, a
synonym: "xylan breakdown" EXACT []
synonym: "xylan catabolism" EXACT []
synonym: "xylan degradation" EXACT []
-is_a: GO:0044347 ! cell wall polysaccharide catabolic process
is_a: GO:0045491 ! xylan metabolic process
+is_a: GO:2000895 ! hemicellulose catabolic process
[Term]
id: GO:0045494
@@ -253436,7 +253434,7 @@ is_a: GO:0048018 ! receptor ligand activity
id: GO:0045500
name: sevenless signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to sevenless (sev; a receptor tyrosine kinase) on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:signaling, PMID:10771085]
+def: "The series of molecular signals initiated by an extracellular ligand binding to sevenless (sev; a receptor tyrosine kinase) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:signaling, PMID:10771085]
synonym: "sev receptor signaling pathway" EXACT []
synonym: "sev signaling pathway" EXACT []
synonym: "sevenless signalling pathway" EXACT []
@@ -253690,14 +253688,12 @@ relationship: positively_regulates GO:0006695 ! cholesterol biosynthetic process
id: GO:0045543
name: gibberellin 2-beta-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a gibberellin + 2-oxoglutarate + O2 = a 2-beta-hydroxygibberellin + succinate + CO2." [EC:1.14.11.13, GOC:kad]
-synonym: "(gibberellin-1),2-oxoglutarate:oxygen oxidoreductase (2beta-hydroxylating)" NARROW [EC:1.14.11.13]
+def: "Catalysis of the reaction: a gibberellin + 2-oxoglutarate + O2 = a 2-beta-hydroxygibberellin + succinate + CO2." [GOC:kad, RHEA:15005]
synonym: "gibberellin 2-beta-hydroxylase activity" RELATED [EC:1.14.11.13]
synonym: "gibberellin 2-oxidase activity" EXACT []
synonym: "gibberellin 2beta-dioxygenase activity" RELATED [EC:1.14.11.13]
synonym: "gibberellin 2beta-hydroxylase activity" RELATED [EC:1.14.11.13]
xref: EC:1.14.11.13
-xref: MetaCyc:PWY-102
xref: RHEA:15005
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
@@ -253720,13 +253716,15 @@ id: GO:0045547
name: dehydrodolichyl diphosphate synthase activity
namespace: molecular_function
def: "Catalysis of the condensation of isopentenyl diphosphate and farnesyl diphosphate in the cis-configuration to form dehydrodolichyl diphosphate." [PMID:9858571]
+xref: EC:2.5.1.87
+xref: RHEA:53008
is_a: GO:0004659 ! prenyltransferase activity
[Term]
id: GO:0045548
name: phenylalanine ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-phenylalanine = NH(4)(+) + trans-cinnamate." [RHEA:21384]
+def: "Catalysis of the reaction: L-phenylalanine = NH4 + trans-cinnamate." [RHEA:21384]
synonym: "L-phenylalanine ammonia-lyase activity" RELATED [EC:4.3.1.24]
synonym: "PAL activity" BROAD [EC:4.3.1.24]
synonym: "phe ammonia-lyase activity" RELATED [EC:4.3.1.24]
@@ -253975,7 +253973,7 @@ id: GO:0045570
name: regulation of imaginal disc growth
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the growth of the imaginal disc." [GOC:go_curators]
-is_a: GO:0046620 ! regulation of organ growth
+is_a: GO:0048638 ! regulation of developmental growth
relationship: regulates GO:0007446 ! imaginal disc growth
[Term]
@@ -253988,7 +253986,7 @@ synonym: "down-regulation of imaginal disc growth" EXACT []
synonym: "downregulation of imaginal disc growth" EXACT []
synonym: "inhibition of imaginal disc growth" NARROW []
is_a: GO:0045570 ! regulation of imaginal disc growth
-is_a: GO:0046621 ! negative regulation of organ growth
+is_a: GO:0048640 ! negative regulation of developmental growth
relationship: negatively_regulates GO:0007446 ! imaginal disc growth
[Term]
@@ -254002,7 +254000,7 @@ synonym: "up regulation of imaginal disc growth" EXACT []
synonym: "up-regulation of imaginal disc growth" EXACT []
synonym: "upregulation of imaginal disc growth" EXACT []
is_a: GO:0045570 ! regulation of imaginal disc growth
-is_a: GO:0046622 ! positive regulation of organ growth
+is_a: GO:0048639 ! positive regulation of developmental growth
relationship: positively_regulates GO:0007446 ! imaginal disc growth
[Term]
@@ -254910,7 +254908,6 @@ id: GO:0045637
name: regulation of myeloid cell differentiation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of myeloid cell differentiation." [GOC:go_curators]
-is_a: GO:0045595 ! regulation of cell differentiation
is_a: GO:1903706 ! regulation of hemopoiesis
relationship: regulates GO:0030099 ! myeloid cell differentiation
@@ -254982,7 +254979,6 @@ name: regulation of eosinophil differentiation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of eosinophil differentiation." [GOC:go_curators]
is_a: GO:0030852 ! regulation of granulocyte differentiation
-is_a: GO:0060284 ! regulation of cell development
relationship: regulates GO:0030222 ! eosinophil differentiation
[Term]
@@ -254994,7 +254990,6 @@ synonym: "down regulation of eosinophil differentiation" EXACT []
synonym: "down-regulation of eosinophil differentiation" EXACT []
synonym: "downregulation of eosinophil differentiation" EXACT []
synonym: "inhibition of eosinophil differentiation" NARROW []
-is_a: GO:0010721 ! negative regulation of cell development
is_a: GO:0030853 ! negative regulation of granulocyte differentiation
is_a: GO:0045643 ! regulation of eosinophil differentiation
relationship: negatively_regulates GO:0030222 ! eosinophil differentiation
@@ -255009,7 +255004,6 @@ synonym: "stimulation of eosinophil differentiation" NARROW []
synonym: "up regulation of eosinophil differentiation" EXACT []
synonym: "up-regulation of eosinophil differentiation" EXACT []
synonym: "upregulation of eosinophil differentiation" EXACT []
-is_a: GO:0010720 ! positive regulation of cell development
is_a: GO:0030854 ! positive regulation of granulocyte differentiation
is_a: GO:0045643 ! regulation of eosinophil differentiation
relationship: positively_regulates GO:0030222 ! eosinophil differentiation
@@ -255931,8 +255925,8 @@ synonym: "negative regulation of glycogen biosynthesis" EXACT []
synonym: "negative regulation of glycogen formation" EXACT []
synonym: "negative regulation of glycogen synthesis" EXACT []
is_a: GO:0005979 ! regulation of glycogen biosynthetic process
+is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process
is_a: GO:0070874 ! negative regulation of glycogen metabolic process
-is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process
relationship: negatively_regulates GO:0005978 ! glycogen biosynthetic process
[Term]
@@ -255963,8 +255957,8 @@ synonym: "down-regulation of gluconeogenesis" EXACT []
synonym: "downregulation of gluconeogenesis" EXACT []
synonym: "inhibition of gluconeogenesis" NARROW []
is_a: GO:0006111 ! regulation of gluconeogenesis
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
relationship: negatively_regulates GO:0006094 ! gluconeogenesis
@@ -256079,8 +256073,8 @@ is_a: GO:0006417 ! regulation of translation
is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process
is_a: GO:0010628 ! positive regulation of gene expression
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0032270 ! positive regulation of cellular protein metabolic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
+is_a: GO:0051247 ! positive regulation of protein metabolic process
relationship: positively_regulates GO:0006412 ! translation
[Term]
@@ -256117,14 +256111,41 @@ is_a: GO:0008152 ! metabolic process
id: GO:0045732
name: positive regulation of protein catabolic process
namespace: biological_process
+alt_id: GO:1903364
+alt_id: GO:2000600
def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators]
+synonym: "activation of cellular protein breakdown" NARROW [GOC:TermGenie]
+synonym: "activation of cellular protein catabolic process" NARROW [GOC:TermGenie]
+synonym: "activation of cellular protein catabolism" NARROW [GOC:TermGenie]
+synonym: "activation of cellular protein degradation" NARROW [GOC:TermGenie]
synonym: "activation of protein catabolic process" NARROW []
+synonym: "positive regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
+synonym: "positive regulation of cellular protein catabolic process" EXACT []
+synonym: "positive regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
+synonym: "positive regulation of cellular protein degradation" EXACT [GOC:TermGenie]
+synonym: "positive regulation of cyclin breakdown" NARROW [GOC:obol]
+synonym: "positive regulation of cyclin catabolic process" NARROW []
+synonym: "positive regulation of cyclin catabolism" NARROW [GOC:obol]
+synonym: "positive regulation of cyclin degradation" NARROW [GOC:obol]
+synonym: "positive regulation of degradation of cyclin" NARROW [GOC:obol]
synonym: "positive regulation of protein breakdown" EXACT []
synonym: "positive regulation of protein catabolism" EXACT []
synonym: "positive regulation of protein degradation" EXACT []
synonym: "stimulation of protein catabolic process" NARROW []
+synonym: "up regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
+synonym: "up regulation of cellular protein catabolic process" EXACT [GOC:TermGenie]
+synonym: "up regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
+synonym: "up regulation of cellular protein degradation" EXACT [GOC:TermGenie]
synonym: "up regulation of protein catabolic process" EXACT []
+synonym: "up-regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
+synonym: "up-regulation of cellular protein catabolic process" EXACT [GOC:TermGenie]
+synonym: "up-regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
+synonym: "up-regulation of cellular protein degradation" EXACT [GOC:TermGenie]
synonym: "up-regulation of protein catabolic process" EXACT []
+synonym: "upregulation of cellular protein breakdown" EXACT [GOC:TermGenie]
+synonym: "upregulation of cellular protein catabolic process" EXACT [GOC:TermGenie]
+synonym: "upregulation of cellular protein catabolism" EXACT [GOC:TermGenie]
+synonym: "upregulation of cellular protein degradation" EXACT [GOC:TermGenie]
synonym: "upregulation of protein catabolic process" EXACT []
is_a: GO:0009896 ! positive regulation of catabolic process
is_a: GO:0042176 ! regulation of protein catabolic process
@@ -256154,6 +256175,7 @@ synonym: "regulation of acetate catabolism" EXACT []
synonym: "regulation of acetate degradation" EXACT []
is_a: GO:0010565 ! regulation of cellular ketone metabolic process
is_a: GO:0031329 ! regulation of cellular catabolic process
+is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
relationship: regulates GO:0045733 ! acetate catabolic process
[Term]
@@ -256164,6 +256186,7 @@ def: "Functions in the storage of nutritious substrates." [GOC:ai]
comment: Note that this term can be used in place of the obsolete terms 'storage protein ; GO:0005187' and 'storage protein of fat body (sensu Insecta) ; GO:0008041'.
subset: goslim_generic
subset: goslim_pir
+subset: prokaryote_subset
synonym: "storage protein" RELATED []
synonym: "storage protein of fat body" RELATED []
synonym: "yolk protein" RELATED []
@@ -256206,8 +256229,8 @@ synonym: "down-regulation of DNA repair" EXACT []
synonym: "downregulation of DNA repair" EXACT []
synonym: "inhibition of DNA repair" NARROW []
is_a: GO:0006282 ! regulation of DNA repair
+is_a: GO:0048585 ! negative regulation of response to stimulus
is_a: GO:0051053 ! negative regulation of DNA metabolic process
-is_a: GO:2001021 ! negative regulation of response to DNA damage stimulus
relationship: negatively_regulates GO:0006281 ! DNA repair
[Term]
@@ -256221,8 +256244,8 @@ synonym: "up regulation of DNA repair" EXACT []
synonym: "up-regulation of DNA repair" EXACT []
synonym: "upregulation of DNA repair" EXACT []
is_a: GO:0006282 ! regulation of DNA repair
+is_a: GO:0048584 ! positive regulation of response to stimulus
is_a: GO:0051054 ! positive regulation of DNA metabolic process
-is_a: GO:2001022 ! positive regulation of response to DNA damage stimulus
relationship: positively_regulates GO:0006281 ! DNA repair
[Term]
@@ -256236,8 +256259,7 @@ synonym: "up regulation of DNA replication" EXACT []
synonym: "up-regulation of DNA replication" EXACT []
synonym: "upregulation of DNA replication" EXACT []
is_a: GO:0006275 ! regulation of DNA replication
-is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
+is_a: GO:0051054 ! positive regulation of DNA metabolic process
relationship: positively_regulates GO:0006260 ! DNA replication
[Term]
@@ -256454,6 +256476,7 @@ synonym: "negative regulation of acetate catabolism" EXACT []
synonym: "negative regulation of acetate degradation" EXACT []
is_a: GO:0031330 ! negative regulation of cellular catabolic process
is_a: GO:0045734 ! regulation of acetate catabolic process
+is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
relationship: negatively_regulates GO:0045733 ! acetate catabolic process
@@ -256472,6 +256495,7 @@ synonym: "up-regulation of acetate catabolic process" EXACT []
synonym: "upregulation of acetate catabolic process" EXACT []
is_a: GO:0031331 ! positive regulation of cellular catabolic process
is_a: GO:0045734 ! regulation of acetate catabolic process
+is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
relationship: positively_regulates GO:0045733 ! acetate catabolic process
@@ -256592,25 +256616,28 @@ synonym: "downregulation of amino acid metabolic process" EXACT []
synonym: "inhibition of amino acid metabolic process" NARROW []
synonym: "negative regulation of amino acid metabolism" EXACT []
is_a: GO:0006521 ! regulation of cellular amino acid metabolic process
-is_a: GO:0033239 ! negative regulation of cellular amine metabolic process
+is_a: GO:0031324 ! negative regulation of cellular metabolic process
+is_a: GO:0033239 ! negative regulation of amine metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
-relationship: negatively_regulates GO:0006520 ! cellular amino acid metabolic process
+relationship: negatively_regulates GO:0006520 ! amino acid metabolic process
[Term]
id: GO:0045764
-name: positive regulation of cellular amino acid metabolic process
+name: positive regulation of amino acid metabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid." [GOC:go_curators]
synonym: "activation of amino acid metabolic process" NARROW []
synonym: "positive regulation of amino acid metabolism" EXACT []
+synonym: "positive regulation of cellular amino acid metabolic process" EXACT []
synonym: "stimulation of amino acid metabolic process" NARROW []
synonym: "up regulation of amino acid metabolic process" EXACT []
synonym: "up-regulation of amino acid metabolic process" EXACT []
synonym: "upregulation of amino acid metabolic process" EXACT []
is_a: GO:0006521 ! regulation of cellular amino acid metabolic process
-is_a: GO:0033240 ! positive regulation of cellular amine metabolic process
+is_a: GO:0031325 ! positive regulation of cellular metabolic process
+is_a: GO:0033240 ! positive regulation of amine metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
-relationship: positively_regulates GO:0006520 ! cellular amino acid metabolic process
+relationship: positively_regulates GO:0006520 ! amino acid metabolic process
[Term]
id: GO:0045765
@@ -256824,7 +256851,7 @@ synonym: "up regulation of bone resorption" EXACT []
synonym: "up-regulation of bone resorption" EXACT []
synonym: "upregulation of bone resorption" EXACT []
is_a: GO:0045124 ! regulation of bone resorption
-is_a: GO:0048518 ! positive regulation of biological process
+is_a: GO:0051240 ! positive regulation of multicellular organismal process
relationship: positively_regulates GO:0045453 ! bone resorption
[Term]
@@ -256993,35 +257020,6 @@ is_a: GO:0032376 ! positive regulation of cholesterol transport
is_a: GO:1904731 ! positive regulation of intestinal lipid absorption
relationship: positively_regulates GO:0030299 ! intestinal cholesterol absorption
-[Term]
-id: GO:0045798
-name: negative regulation of chromatin assembly or disassembly
-namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin assembly or disassembly." [GOC:go_curators]
-synonym: "down regulation of chromatin assembly or disassembly" EXACT []
-synonym: "down-regulation of chromatin assembly or disassembly" EXACT []
-synonym: "downregulation of chromatin assembly or disassembly" EXACT []
-synonym: "inhibition of chromatin assembly or disassembly" NARROW []
-synonym: "negative regulation of chromatin assembly/disassembly" EXACT []
-is_a: GO:0001672 ! regulation of chromatin assembly or disassembly
-is_a: GO:1905268 ! negative regulation of chromatin organization
-relationship: negatively_regulates GO:0006333 ! chromatin assembly or disassembly
-
-[Term]
-id: GO:0045799
-name: positive regulation of chromatin assembly or disassembly
-namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of chromatin assembly or disassembly." [GOC:go_curators]
-synonym: "activation of chromatin assembly or disassembly" NARROW []
-synonym: "positive regulation of chromatin assembly/disassembly" EXACT []
-synonym: "stimulation of chromatin assembly or disassembly" NARROW []
-synonym: "up regulation of chromatin assembly or disassembly" EXACT []
-synonym: "up-regulation of chromatin assembly or disassembly" EXACT []
-synonym: "upregulation of chromatin assembly or disassembly" EXACT []
-is_a: GO:0001672 ! regulation of chromatin assembly or disassembly
-is_a: GO:1905269 ! positive regulation of chromatin organization
-relationship: positively_regulates GO:0006333 ! chromatin assembly or disassembly
-
[Term]
id: GO:0045800
name: negative regulation of chitin-based cuticle tanning
@@ -257202,24 +257200,26 @@ relationship: positively_regulates GO:0007223 ! Wnt signaling pathway, calcium m
id: GO:0045814
name: negative regulation of gene expression, epigenetic
namespace: biological_process
-def: "An epigenetic process that stops, prevents or reduces the rate of gene expression by remodelling of chromatin by either modifying the chromatin fiber, the nucleosomal histones, or the DNA." [PMID:22243696]
+def: "An epigenetic process that silences gene expression at specific genomic regions through chromatin remodelling either by modifying higher order chromatin fiber structure, nucleosomal histones, or the DNA." [PMID:22243696]
synonym: "down regulation of gene expression, epigenetic" EXACT []
synonym: "down-regulation of gene expression, epigenetic" EXACT []
synonym: "downregulation of gene expression, epigenetic" EXACT []
synonym: "gene silencing" RELATED []
synonym: "inhibition of gene expression, epigenetic" NARROW []
is_a: GO:0010629 ! negative regulation of gene expression
-is_a: GO:0040029 ! regulation of gene expression, epigenetic
+is_a: GO:0040029 ! epigenetic regulation of gene expression
[Term]
id: GO:0045815
-name: epigenetic maintenance of chromatin in transcription-competent conformation
+name: transcription initiation-coupled chromatin remodeling
namespace: biological_process
alt_id: GO:0048096
-def: "An epigenetic process that capacitates gene expression by remodelling of chromatin by either modifying the chromatin fiber, the nucleosomal histones, or the DNA." [PMID:34414474]
-comment: This regulation is exemplified by members of the trithorax group, which maintain the active state of homeotic gene transcription. Do not confuse with GO:0140673 ; co-transcriptional chromatin reassembly, which describes the reforming of chromatin after RNA polymerase II passage.
+def: "An epigenetic mechanism of regulation of gene expression that involves chromatin remodeling to capacitate gene expression by either modifying the chromatin fiber, the nucleosomal histones, or the DNA." [PMID:34414474]
+comment: This regulation is exemplified by members of the trithorax group, which maintain the active state of homeotic gene transcription. Do not confuse with GO:0140673 ; transcriptional elongation-coupled chromatin remodeling, which describes the reforming of chromatin after RNA polymerase II passage.
synonym: "activation of gene expression, epigenetic" RELATED []
synonym: "chromatin-mediated maintenance of transcription" EXACT []
+synonym: "DNA replication-independent chromatin organization" RELATED []
+synonym: "epigenetic maintenance of chromatin in transcription-competent conformation" EXACT []
synonym: "euchromatin assembly" RELATED []
synonym: "euchromatin organisation" RELATED []
synonym: "euchromatin organization" RELATED []
@@ -257227,11 +257227,14 @@ synonym: "long-term maintenance of gene activation" RELATED []
synonym: "maintenance of chromatin in transcription-competent conformation" EXACT []
synonym: "positive regulation of gene expression, epigenetic" EXACT []
synonym: "stimulation of gene expression, epigenetic" RELATED []
+synonym: "transciptional initiation-coupled chromatin remodeling" EXACT []
+synonym: "transcription initiation coupled chromatin remodeling" EXACT []
+synonym: "transcriptional initiation-coupled chromatin remodeling" EXACT []
synonym: "up regulation of gene expression, epigenetic" EXACT []
synonym: "up-regulation of gene expression, epigenetic" EXACT []
synonym: "upregulation of gene expression, epigenetic" EXACT []
is_a: GO:0010628 ! positive regulation of gene expression
-is_a: GO:0040029 ! regulation of gene expression, epigenetic
+is_a: GO:0040029 ! epigenetic regulation of gene expression
[Term]
id: GO:0045818
@@ -257281,10 +257284,9 @@ synonym: "downregulation of glycolysis" EXACT []
synonym: "inhibition of glycolysis" NARROW []
is_a: GO:0006110 ! regulation of glycolytic process
is_a: GO:0009895 ! negative regulation of catabolic process
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
-is_a: GO:0042326 ! negative regulation of phosphorylation
-is_a: GO:1900543 ! negative regulation of purine nucleotide metabolic process
-is_a: GO:1903579 ! negative regulation of ATP metabolic process
+is_a: GO:0031324 ! negative regulation of cellular metabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
+is_a: GO:0062014 ! negative regulation of small molecule metabolic process
relationship: negatively_regulates GO:0006096 ! glycolytic process
[Term]
@@ -257299,10 +257301,8 @@ synonym: "up-regulation of glycolysis" EXACT []
synonym: "upregulation of glycolysis" EXACT []
is_a: GO:0006110 ! regulation of glycolytic process
is_a: GO:0031331 ! positive regulation of cellular catabolic process
-is_a: GO:0042327 ! positive regulation of phosphorylation
is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
-is_a: GO:1900544 ! positive regulation of purine nucleotide metabolic process
-is_a: GO:1903580 ! positive regulation of ATP metabolic process
+is_a: GO:0062013 ! positive regulation of small molecule metabolic process
relationship: positively_regulates GO:0006096 ! glycolytic process
[Term]
@@ -257421,7 +257421,6 @@ is_a: GO:0045191 ! regulation of isotype switching
is_a: GO:0045910 ! negative regulation of DNA recombination
is_a: GO:0050869 ! negative regulation of B cell activation
is_a: GO:0051093 ! negative regulation of developmental process
-is_a: GO:0051241 ! negative regulation of multicellular organismal process
relationship: negatively_regulates GO:0045190 ! isotype switching
[Term]
@@ -257443,7 +257442,6 @@ is_a: GO:0045191 ! regulation of isotype switching
is_a: GO:0045911 ! positive regulation of DNA recombination
is_a: GO:0050871 ! positive regulation of B cell activation
is_a: GO:0051094 ! positive regulation of developmental process
-is_a: GO:0051240 ! positive regulation of multicellular organismal process
relationship: positively_regulates GO:0045190 ! isotype switching
[Term]
@@ -257663,7 +257661,7 @@ synonym: "down-regulation of nitrogen utilization" EXACT []
synonym: "downregulation of nitrogen utilization" EXACT []
synonym: "inhibition of nitrogen utilization" NARROW []
is_a: GO:0006808 ! regulation of nitrogen utilization
-is_a: GO:0048519 ! negative regulation of biological process
+is_a: GO:0032108 ! negative regulation of response to nutrient levels
relationship: negatively_regulates GO:0019740 ! nitrogen utilization
[Term]
@@ -257677,7 +257675,7 @@ synonym: "up regulation of nitrogen utilization" EXACT []
synonym: "up-regulation of nitrogen utilization" EXACT []
synonym: "upregulation of nitrogen utilization" EXACT []
is_a: GO:0006808 ! regulation of nitrogen utilization
-is_a: GO:0048518 ! positive regulation of biological process
+is_a: GO:0032109 ! positive regulation of response to nutrient levels
relationship: positively_regulates GO:0019740 ! nitrogen utilization
[Term]
@@ -257850,7 +257848,7 @@ synonym: "downregulation of proteolysis" EXACT []
synonym: "inhibition of proteolysis" NARROW []
synonym: "negative regulation of peptidolysis" EXACT []
is_a: GO:0030162 ! regulation of proteolysis
-is_a: GO:0032269 ! negative regulation of cellular protein metabolic process
+is_a: GO:0051248 ! negative regulation of protein metabolic process
relationship: negatively_regulates GO:0006508 ! proteolysis
[Term]
@@ -257865,7 +257863,7 @@ synonym: "up regulation of proteolysis" EXACT []
synonym: "up-regulation of proteolysis" EXACT []
synonym: "upregulation of proteolysis" EXACT []
is_a: GO:0030162 ! regulation of proteolysis
-is_a: GO:0032270 ! positive regulation of cellular protein metabolic process
+is_a: GO:0051247 ! positive regulation of protein metabolic process
relationship: positively_regulates GO:0006508 ! proteolysis
[Term]
@@ -257932,6 +257930,7 @@ synonym: "negative regulation of retroviral genome replication" EXACT [GOC:bf, G
synonym: "regulation of retroviral genome replication" RELATED []
is_a: GO:0045071 ! negative regulation of viral genome replication
is_a: GO:0045091 ! regulation of single stranded viral RNA replication via double stranded DNA intermediate
+is_a: GO:1902679 ! negative regulation of RNA biosynthetic process
relationship: negatively_regulates GO:0039692 ! single stranded viral RNA replication via double stranded DNA intermediate
[Term]
@@ -257947,6 +257946,7 @@ synonym: "up-regulation of retroviral genome replication" EXACT []
synonym: "upregulation of retroviral genome replication" EXACT []
is_a: GO:0045070 ! positive regulation of viral genome replication
is_a: GO:0045091 ! regulation of single stranded viral RNA replication via double stranded DNA intermediate
+is_a: GO:1902680 ! positive regulation of RNA biosynthetic process
relationship: positively_regulates GO:0039692 ! single stranded viral RNA replication via double stranded DNA intermediate
[Term]
@@ -258092,7 +258092,6 @@ synonym: "up-regulation of sporulation" EXACT []
synonym: "upregulation of sporulation" EXACT []
is_a: GO:0042173 ! regulation of sporulation resulting in formation of a cellular spore
is_a: GO:0043938 ! positive regulation of sporulation
-is_a: GO:0045597 ! positive regulation of cell differentiation
relationship: positively_regulates GO:0030435 ! sporulation resulting in formation of a cellular spore
[Term]
@@ -258106,7 +258105,7 @@ synonym: "downregulation of sulfur utilization" EXACT []
synonym: "inhibition of sulfur utilization" NARROW []
synonym: "negative regulation of sulphur utilization" EXACT []
is_a: GO:0006792 ! regulation of sulfur utilization
-is_a: GO:0048519 ! negative regulation of biological process
+is_a: GO:0032108 ! negative regulation of response to nutrient levels
relationship: negatively_regulates GO:0006791 ! sulfur utilization
[Term]
@@ -258121,7 +258120,7 @@ synonym: "up regulation of sulfur utilization" EXACT []
synonym: "up-regulation of sulfur utilization" EXACT []
synonym: "upregulation of sulfur utilization" EXACT []
is_a: GO:0006792 ! regulation of sulfur utilization
-is_a: GO:0048518 ! positive regulation of biological process
+is_a: GO:0032109 ! positive regulation of response to nutrient levels
relationship: positively_regulates GO:0006791 ! sulfur utilization
[Term]
@@ -258226,7 +258225,7 @@ consider: GO:0000122
[Term]
id: GO:0045892
-name: negative regulation of transcription, DNA-templated
+name: negative regulation of DNA-templated transcription
namespace: biological_process
alt_id: GO:0016481
alt_id: GO:0032582
@@ -258243,14 +258242,15 @@ synonym: "inhibition of transcription, DNA-dependent" NARROW []
synonym: "negative regulation of cellular transcription, DNA-dependent" EXACT []
synonym: "negative regulation of gene-specific transcription" RELATED []
synonym: "negative regulation of transcription, DNA-dependent" EXACT [GOC:txnOH]
+synonym: "negative regulation of transcription, DNA-templated" EXACT []
synonym: "transcription repressor activity" RELATED []
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
is_a: GO:1903507 ! negative regulation of nucleic acid-templated transcription
-relationship: negatively_regulates GO:0006351 ! transcription, DNA-templated
+relationship: negatively_regulates GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0045893
-name: positive regulation of transcription, DNA-templated
+name: positive regulation of DNA-templated transcription
namespace: biological_process
alt_id: GO:0043193
alt_id: GO:0045941
@@ -258261,6 +258261,7 @@ synonym: "activation of transcription, DNA-dependent" NARROW []
synonym: "positive regulation of cellular transcription, DNA-dependent" EXACT []
synonym: "positive regulation of gene-specific transcription" RELATED []
synonym: "positive regulation of transcription, DNA-dependent" EXACT [GOC:txnOH]
+synonym: "positive regulation of transcription, DNA-templated" EXACT []
synonym: "stimulation of gene-specific transcription" NARROW []
synonym: "stimulation of transcription, DNA-dependent" NARROW []
synonym: "transcription activator activity" RELATED []
@@ -258270,9 +258271,9 @@ synonym: "up-regulation of gene-specific transcription" RELATED []
synonym: "up-regulation of transcription, DNA-dependent" EXACT []
synonym: "upregulation of gene-specific transcription" RELATED []
synonym: "upregulation of transcription, DNA-dependent" EXACT []
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
is_a: GO:1903508 ! positive regulation of nucleic acid-templated transcription
-relationship: positively_regulates GO:0006351 ! transcription, DNA-templated
+relationship: positively_regulates GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0045894
@@ -258285,7 +258286,7 @@ synonym: "downregulation of transcription, mating-type specific" EXACT []
synonym: "inhibition of transcription, mating-type specific" NARROW []
synonym: "negative regulation of mating-type specific transcription, DNA-dependent" EXACT [GOC:txnOH]
is_a: GO:0007532 ! regulation of mating-type specific transcription, DNA-templated
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
[Term]
id: GO:0045895
@@ -258299,7 +258300,7 @@ synonym: "up regulation of transcription, mating-type specific" EXACT []
synonym: "up-regulation of transcription, mating-type specific" EXACT []
synonym: "upregulation of transcription, mating-type specific" EXACT []
is_a: GO:0007532 ! regulation of mating-type specific transcription, DNA-templated
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
[Term]
id: GO:0045896
@@ -258340,7 +258341,7 @@ synonym: "regulation of RNA polymerase II transcriptional pre-initiation complex
synonym: "regulation of RNA polymerase II transcriptional preinitiation complex assembly" EXACT []
synonym: "regulation of RNA polymerase II transcriptional preinitiation complex formation" RELATED []
is_a: GO:0043254 ! regulation of protein-containing complex assembly
-is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter
+is_a: GO:0060260 ! regulation of transcription initiation by RNA polymerase II
relationship: regulates GO:0051123 ! RNA polymerase II preinitiation complex assembly
[Term]
@@ -258359,7 +258360,7 @@ synonym: "up-regulation of RNA polymerase II transcriptional preinitiation compl
synonym: "upregulation of RNA polymerase II transcriptional preinitiation complex assembly" EXACT []
is_a: GO:0031334 ! positive regulation of protein-containing complex assembly
is_a: GO:0045898 ! regulation of RNA polymerase II transcription preinitiation complex assembly
-is_a: GO:0060261 ! positive regulation of transcription initiation from RNA polymerase II promoter
+is_a: GO:0060261 ! positive regulation of transcription initiation by RNA polymerase II
relationship: positively_regulates GO:0051123 ! RNA polymerase II preinitiation complex assembly
[Term]
@@ -258536,7 +258537,8 @@ synonym: "down-regulation of catecholamine metabolic process" EXACT []
synonym: "downregulation of catecholamine metabolic process" EXACT []
synonym: "inhibition of catecholamine metabolic process" NARROW []
synonym: "negative regulation of catecholamine metabolism" EXACT []
-is_a: GO:0033239 ! negative regulation of cellular amine metabolic process
+is_a: GO:0031324 ! negative regulation of cellular metabolic process
+is_a: GO:0033239 ! negative regulation of amine metabolic process
is_a: GO:0042069 ! regulation of catecholamine metabolic process
relationship: negatively_regulates GO:0006584 ! catecholamine metabolic process
@@ -258551,7 +258553,8 @@ synonym: "stimulation of catecholamine metabolic process" NARROW []
synonym: "up regulation of catecholamine metabolic process" EXACT []
synonym: "up-regulation of catecholamine metabolic process" EXACT []
synonym: "upregulation of catecholamine metabolic process" EXACT []
-is_a: GO:0033240 ! positive regulation of cellular amine metabolic process
+is_a: GO:0031325 ! positive regulation of cellular metabolic process
+is_a: GO:0033240 ! positive regulation of amine metabolic process
is_a: GO:0042069 ! regulation of catecholamine metabolic process
relationship: positively_regulates GO:0006584 ! catecholamine metabolic process
@@ -258887,7 +258890,6 @@ synonym: "upregulation of circadian sleep/wake cycle, sleep" EXACT []
is_a: GO:0042753 ! positive regulation of circadian rhythm
is_a: GO:0045187 ! regulation of circadian sleep/wake cycle, sleep
is_a: GO:0048520 ! positive regulation of behavior
-is_a: GO:0051240 ! positive regulation of multicellular organismal process
relationship: positively_regulates GO:0050802 ! circadian sleep/wake cycle, sleep
[Term]
@@ -258929,7 +258931,7 @@ synonym: "down-regulation of phosphorus utilization" EXACT []
synonym: "downregulation of phosphorus utilization" EXACT []
synonym: "inhibition of phosphorus utilization" NARROW []
is_a: GO:0006795 ! regulation of phosphorus utilization
-is_a: GO:0048519 ! negative regulation of biological process
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
relationship: negatively_regulates GO:0006794 ! phosphorus utilization
[Term]
@@ -258945,7 +258947,7 @@ synonym: "up regulation of transcription from RNA polymerase I promoter" EXACT [
synonym: "up-regulation of transcription from RNA polymerase I promoter" EXACT []
synonym: "upregulation of transcription from RNA polymerase I promoter" EXACT []
is_a: GO:0006356 ! regulation of transcription by RNA polymerase I
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
relationship: positively_regulates GO:0006360 ! transcription by RNA polymerase I
[Term]
@@ -258971,7 +258973,7 @@ synonym: "up-regulation of transcription from RNA polymerase II promoter" EXACT
synonym: "upregulation of global transcription from RNA polymerase II promoter" RELATED []
synonym: "upregulation of transcription from RNA polymerase II promoter" EXACT []
is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
relationship: positively_regulates GO:0006366 ! transcription by RNA polymerase II
[Term]
@@ -258987,7 +258989,7 @@ synonym: "up regulation of transcription from RNA polymerase III promoter" EXACT
synonym: "up-regulation of transcription from RNA polymerase III promoter" EXACT []
synonym: "upregulation of transcription from RNA polymerase III promoter" EXACT []
is_a: GO:0006359 ! regulation of transcription by RNA polymerase III
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
relationship: positively_regulates GO:0006383 ! transcription by RNA polymerase III
[Term]
@@ -259028,7 +259030,7 @@ synonym: "up regulation of phosphorus utilization" EXACT []
synonym: "up-regulation of phosphorus utilization" EXACT []
synonym: "upregulation of phosphorus utilization" EXACT []
is_a: GO:0006795 ! regulation of phosphorus utilization
-is_a: GO:0048518 ! positive regulation of biological process
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
relationship: positively_regulates GO:0006794 ! phosphorus utilization
[Term]
@@ -259655,7 +259657,7 @@ name: carbon catabolite regulation of transcription
namespace: biological_process
def: "A transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources." [GOC:go_curators, GOC:mah, PMID:18359269, PMID:9618445]
synonym: "regulation of transcription by carbon catabolites" EXACT [GOC:mah]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
is_a: GO:0031670 ! cellular response to nutrient
[Term]
@@ -259664,7 +259666,7 @@ name: carbon catabolite activation of transcription
namespace: biological_process
def: "A transcription regulation process in which the presence of one carbon source leads to an increase in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources." [GOC:mah, PMID:10559153]
synonym: "positive regulation of transcription by carbon catabolites" EXACT [GOC:mah]
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
is_a: GO:0045990 ! carbon catabolite regulation of transcription
[Term]
@@ -259716,15 +259718,15 @@ relationship: regulates GO:0009790 ! embryo development
[Term]
id: GO:0045996
-name: negative regulation of transcription by pheromones
+name: obsolete negative regulation of transcription by pheromones
namespace: biological_process
-def: "Any process involving pheromones that stops, prevents or reduces the rate of transcription." [GOC:go_curators]
+def: "OBSOLETE. Any process involving pheromones that stops, prevents or reduces the rate of transcription." [GOC:go_curators]
+comment: This term has been obsoleted because it represents a GO-CAM model.
synonym: "down regulation of transcription by pheromones" EXACT []
synonym: "down-regulation of transcription by pheromones" EXACT []
synonym: "downregulation of transcription by pheromones" EXACT []
synonym: "inhibition of transcription by pheromones" NARROW []
-is_a: GO:0009373 ! regulation of transcription by pheromones
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_obsolete: true
[Term]
id: GO:0045997
@@ -259983,7 +259985,7 @@ id: GO:0046015
name: regulation of transcription by glucose
namespace: biological_process
def: "Any process involving glucose that modulates the frequency, rate or extent or transcription." [GOC:go_curators]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
[Term]
id: GO:0046016
@@ -260031,26 +260033,25 @@ consider: GO:0045943
[Term]
id: GO:0046019
-name: regulation of transcription from RNA polymerase II promoter by pheromones
+name: obsolete regulation of transcription from RNA polymerase II promoter by pheromones
namespace: biological_process
-def: "Any process involving pheromones that modulates the frequency, rate or extent or transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH]
+def: "OBSOLETE. Any process involving pheromones that modulates the frequency, rate or extent or transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH]
+comment: This term has been obsoleted because it represents a GO-CAM model.
synonym: "regulation of transcription from Pol II promoter by pheromones" EXACT []
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-is_a: GO:0009373 ! regulation of transcription by pheromones
+is_obsolete: true
[Term]
id: GO:0046020
-name: negative regulation of transcription from RNA polymerase II promoter by pheromones
+name: obsolete negative regulation of transcription from RNA polymerase II promoter by pheromones
namespace: biological_process
-def: "Any process involving pheromones that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:go_curators]
+def: "OBSOLETE. Any process involving pheromones that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:go_curators]
+comment: This term has been obsoleted because it represents a GO-CAM model.
synonym: "down regulation of transcription from RNA polymerase II promoter by pheromones" EXACT []
synonym: "down-regulation of transcription from RNA polymerase II promoter by pheromones" EXACT []
synonym: "downregulation of transcription from RNA polymerase II promoter by pheromones" EXACT []
synonym: "inhibition of transcription from RNA polymerase II promoter by pheromones" NARROW []
synonym: "negative regulation of transcription from Pol II promoter by pheromones" EXACT []
-is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:0045996 ! negative regulation of transcription by pheromones
-is_a: GO:0046019 ! regulation of transcription from RNA polymerase II promoter by pheromones
+is_obsolete: true
[Term]
id: GO:0046021
@@ -260163,7 +260164,7 @@ is_a: GO:0009055 ! electron transfer activity
id: GO:0046029
name: mannitol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-mannitol + NAD(+) = D-mannose + H(+) + NADH." [EC:1.1.1.255, RHEA:15029]
+def: "Catalysis of the reaction: D-mannitol + NAD+ = D-mannose + H+ + NADH." [EC:1.1.1.255, RHEA:15029]
synonym: "mannitol:NAD+ 1-oxidoreductase activity" RELATED [EC:1.1.1.255]
synonym: "MTD activity" RELATED [EC:1.1.1.255]
synonym: "NAD-dependent mannitol dehydrogenase activity" BROAD [EC:1.1.1.255]
@@ -260179,7 +260180,6 @@ id: GO:0046030
name: inositol trisphosphate phosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction: myo-inositol trisphosphate + H2O = myo-inositol bisphosphate + phosphate." [GOC:bf]
-synonym: "inositol-1,4,5-trisphosphate phosphatase" NARROW []
synonym: "IP(3) phosphatase activity" EXACT []
synonym: "IP3 phosphatase activity" EXACT []
is_a: GO:0052745 ! inositol phosphate phosphatase activity
@@ -260221,7 +260221,8 @@ name: ATP metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator." [GOC:go_curators]
synonym: "ATP metabolism" EXACT []
-is_a: GO:0008152 ! metabolic process
+is_a: GO:0009150 ! purine ribonucleotide metabolic process
+is_a: GO:0009205 ! purine ribonucleoside triphosphate metabolic process
[Term]
id: GO:0046035
@@ -260475,7 +260476,7 @@ synonym: "cAMP metabolism" EXACT []
synonym: "cyclic AMP metabolic process" EXACT []
synonym: "cyclic AMP metabolism" EXACT []
is_a: GO:0009150 ! purine ribonucleotide metabolic process
-is_a: GO:0009187 ! cyclic nucleotide metabolic process
+is_a: GO:0052652 ! cyclic purine nucleotide metabolic process
[Term]
id: GO:0046059
@@ -260578,7 +260579,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving cyclic GMP, guanosine 3',5'-phosphate." [GOC:go_curators]
synonym: "cGMP metabolism" EXACT []
is_a: GO:0009150 ! purine ribonucleotide metabolic process
-is_a: GO:0009187 ! cyclic nucleotide metabolic process
+is_a: GO:0052652 ! cyclic purine nucleotide metabolic process
[Term]
id: GO:0046069
@@ -261395,7 +261396,6 @@ def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate
comment: This term was made obsolete because it was replaced by more specific terms.
synonym: "negative regulation of coenzyme and prosthetic group metabolic process" EXACT []
is_obsolete: true
-consider: GO:0051201
[Term]
id: GO:0046143
@@ -261405,27 +261405,27 @@ def: "OBSOLETE. Any process that activates or increases the frequency, rate or e
comment: This term was made obsolete because it was replaced by more specific terms.
synonym: "positive regulation of coenzyme and prosthetic group metabolic process" EXACT []
is_obsolete: true
-consider: GO:0051200
[Term]
id: GO:0046144
-name: D-alanine family amino acid metabolic process
+name: obsolete D-alanine family amino acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving D-alanine and related amino acids." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways involving D-alanine and related amino acids." [GOC:ai]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "D-alanine family amino acid metabolism" EXACT []
-is_a: GO:0006522 ! alanine metabolic process
+is_obsolete: true
[Term]
id: GO:0046145
-name: D-alanine family amino acid biosynthetic process
+name: obsolete D-alanine family amino acid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of D-alanine and related amino acids." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of D-alanine and related amino acids." [GOC:ai]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "D-alanine family amino acid anabolism" EXACT []
synonym: "D-alanine family amino acid biosynthesis" EXACT []
synonym: "D-alanine family amino acid formation" EXACT []
synonym: "D-alanine family amino acid synthesis" EXACT []
-is_a: GO:0006523 ! alanine biosynthetic process
-is_a: GO:0046144 ! D-alanine family amino acid metabolic process
+is_obsolete: true
[Term]
id: GO:0046146
@@ -261527,8 +261527,8 @@ name: rhodopsin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving rhodopsin, a brilliant purplish-red, light-sensitive visual pigment found in the rod cells of the retinas." [ISBN:0198506732]
synonym: "rhodopsin metabolism" EXACT []
+is_a: GO:0019538 ! protein metabolic process
is_a: GO:0042441 ! eye pigment metabolic process
-is_a: GO:0044267 ! cellular protein metabolic process
[Term]
id: GO:0046155
@@ -261538,9 +261538,11 @@ def: "The chemical reactions and pathways resulting in the breakdown of rhodopsi
synonym: "rhodopsin breakdown" EXACT []
synonym: "rhodopsin catabolism" EXACT []
synonym: "rhodopsin degradation" EXACT []
-is_a: GO:0044257 ! cellular protein catabolic process
+is_a: GO:0016124 ! xanthophyll catabolic process
+is_a: GO:0030163 ! protein catabolic process
is_a: GO:0046151 ! eye pigment catabolic process
-is_a: GO:0046154 ! rhodopsin metabolic process
+is_a: GO:0046164 ! alcohol catabolic process
+is_a: GO:1902644 ! tertiary alcohol metabolic process
[Term]
id: GO:0046156
@@ -261781,7 +261783,6 @@ synonym: "aldonic acid biosynthesis" EXACT []
synonym: "aldonic acid formation" EXACT []
synonym: "aldonic acid synthesis" EXACT []
is_a: GO:0019520 ! aldonic acid metabolic process
-is_a: GO:0034637 ! cellular carbohydrate biosynthetic process
is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
[Term]
@@ -261793,7 +261794,6 @@ synonym: "aldonic acid breakdown" EXACT []
synonym: "aldonic acid catabolism" EXACT []
synonym: "aldonic acid degradation" EXACT []
is_a: GO:0019520 ! aldonic acid metabolic process
-is_a: GO:0044275 ! cellular carbohydrate catabolic process
is_a: GO:0072329 ! monocarboxylic acid catabolic process
[Term]
@@ -261805,6 +261805,7 @@ synonym: "D-gluconate breakdown" EXACT []
synonym: "D-gluconate catabolism" EXACT []
synonym: "D-gluconate degradation" EXACT []
xref: MetaCyc:GLUCONSUPER-PWY
+is_a: GO:0009313 ! oligosaccharide catabolic process
is_a: GO:0019521 ! D-gluconate metabolic process
is_a: GO:0046176 ! aldonic acid catabolic process
@@ -261817,6 +261818,7 @@ synonym: "D-gluconate anabolism" EXACT []
synonym: "D-gluconate biosynthesis" EXACT []
synonym: "D-gluconate formation" EXACT []
synonym: "D-gluconate synthesis" EXACT []
+is_a: GO:0009312 ! oligosaccharide biosynthetic process
is_a: GO:0019521 ! D-gluconate metabolic process
is_a: GO:0046175 ! aldonic acid biosynthetic process
@@ -261864,6 +261866,7 @@ synonym: "L-idonate anabolism" EXACT []
synonym: "L-idonate biosynthesis" EXACT []
synonym: "L-idonate formation" EXACT []
synonym: "L-idonate synthesis" EXACT []
+is_a: GO:0016051 ! carbohydrate biosynthetic process
is_a: GO:0019523 ! L-idonate metabolic process
is_a: GO:0046175 ! aldonic acid biosynthetic process
@@ -261875,6 +261878,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of L-idonat
synonym: "L-idonate breakdown" EXACT []
synonym: "L-idonate catabolism" EXACT []
synonym: "L-idonate degradation" EXACT []
+is_a: GO:0016052 ! carbohydrate catabolic process
is_a: GO:0019523 ! L-idonate metabolic process
is_a: GO:0046176 ! aldonic acid catabolic process
@@ -262115,7 +262119,7 @@ synonym: "cyanide formation" EXACT []
synonym: "cyanide synthesis" EXACT []
is_a: GO:0019499 ! cyanide metabolic process
is_a: GO:0044271 ! cellular nitrogen compound biosynthetic process
-is_a: GO:1901576 ! organic substance biosynthetic process
+is_a: GO:1901566 ! organonitrogen compound biosynthetic process
[Term]
id: GO:0046203
@@ -262285,15 +262289,14 @@ is_a: GO:0052314 ! phytoalexin metabolic process
[Term]
id: GO:0046218
-name: indolalkylamine catabolic process
+name: obsolete indolalkylamine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group." [GOC:curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group." [GOC:curators]
+comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "indolalkylamine breakdown" EXACT []
synonym: "indolalkylamine catabolism" EXACT []
synonym: "indolalkylamine degradation" EXACT []
-is_a: GO:0006586 ! indolalkylamine metabolic process
-is_a: GO:0042402 ! cellular biogenic amine catabolic process
-is_a: GO:0042436 ! indole-containing compound catabolic process
+is_obsolete: true
[Term]
id: GO:0046219
@@ -262305,7 +262308,7 @@ synonym: "indolalkylamine biosynthesis" EXACT []
synonym: "indolalkylamine formation" EXACT []
synonym: "indolalkylamine synthesis" EXACT []
is_a: GO:0006586 ! indolalkylamine metabolic process
-is_a: GO:0042401 ! cellular biogenic amine biosynthetic process
+is_a: GO:0042401 ! biogenic amine biosynthetic process
is_a: GO:0042435 ! indole-containing compound biosynthetic process
[Term]
@@ -262944,20 +262947,18 @@ synonym: "triethanolamine biosynthetic process" EXACT []
synonym: "triethanolamine formation" EXACT []
synonym: "triethanolamine synthesis" EXACT []
is_obsolete: true
-replaced_by: GO:0018981
[Term]
id: GO:0046267
-name: triethanolamine catabolic process
+name: obsolete triethanolamine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of triethanolamine, a combustible, hygroscopic, colorless liquid commonly used in dry-cleaning solutions, cosmetics, detergents, textile processing, wool scouring, and as a corrosion inhibitor and pharmaceutical alkalizing agent." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of triethanolamine, a combustible, hygroscopic, colorless liquid commonly used in dry-cleaning solutions, cosmetics, detergents, textile processing, wool scouring, and as a corrosion inhibitor and pharmaceutical alkalizing agent." [GOC:ai]
+comment: Triethanolamine is not a natural compound.
synonym: "triethanolamine breakdown" EXACT []
synonym: "triethanolamine catabolism" EXACT []
synonym: "triethanolamine degradation" EXACT []
-is_a: GO:0018981 ! triethanolamine metabolic process
-is_a: GO:0042178 ! xenobiotic catabolic process
-is_a: GO:0046174 ! polyol catabolic process
-is_a: GO:1901565 ! organonitrogen compound catabolic process
+is_obsolete: true
+consider: GO:0042178
[Term]
id: GO:0046268
@@ -263383,6 +263384,7 @@ is_a: GO:0019439 ! aromatic compound catabolic process
is_a: GO:0072329 ! monocarboxylic acid catabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
is_a: GO:1901502 ! ether catabolic process
+is_a: GO:1901565 ! organonitrogen compound catabolic process
[Term]
id: GO:0046301
@@ -263449,8 +263451,9 @@ synonym: "alkanesulfonate formation" EXACT []
synonym: "alkanesulfonate synthesis" EXACT []
synonym: "alkanesulphonate biosynthesis" EXACT []
synonym: "alkanesulphonate biosynthetic process" EXACT []
+is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0019694 ! alkanesulfonate metabolic process
-is_a: GO:1901576 ! organic substance biosynthetic process
+is_a: GO:0044272 ! sulfur compound biosynthetic process
[Term]
id: GO:0046306
@@ -263462,8 +263465,9 @@ synonym: "alkanesulfonate catabolism" EXACT []
synonym: "alkanesulfonate degradation" EXACT []
synonym: "alkanesulphonate catabolic process" EXACT []
synonym: "alkanesulphonate catabolism" EXACT []
+is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0019694 ! alkanesulfonate metabolic process
-is_a: GO:1901575 ! organic substance catabolic process
+is_a: GO:0044273 ! sulfur compound catabolic process
[Term]
id: GO:0046307
@@ -263490,28 +263494,27 @@ is_a: GO:1901575 ! organic substance catabolic process
[Term]
id: GO:0046309
-name: 1,3-dichloro-2-propanol biosynthetic process
+name: obsolete 1,3-dichloro-2-propanol biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 1,3-dichloro-2-propanol (DCP), a halohydrin suspected of being carcinogenic, mutagenic and genotoxic." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of 1,3-dichloro-2-propanol (DCP), a halohydrin suspected of being carcinogenic, mutagenic and genotoxic." [GOC:ai]
+comment: 1,3-dichloro-2-propanol is not a natural compound.
synonym: "1,3-dichloro-2-propanol anabolism" EXACT []
synonym: "1,3-dichloro-2-propanol biosynthesis" EXACT []
synonym: "1,3-dichloro-2-propanol formation" EXACT []
synonym: "1,3-dichloro-2-propanol synthesis" EXACT []
-is_a: GO:0018902 ! 1,3-dichloro-2-propanol metabolic process
-is_a: GO:0044108 ! cellular alcohol biosynthetic process
-is_a: GO:1902653 ! secondary alcohol biosynthetic process
+is_obsolete: true
[Term]
id: GO:0046310
-name: 1,3-dichloro-2-propanol catabolic process
+name: obsolete 1,3-dichloro-2-propanol catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 1,3-dichloro-2-propanol (DCP), a halohydrin suspected of being carcinogenic, mutagenic and genotoxic." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of 1,3-dichloro-2-propanol (DCP), a halohydrin suspected of being carcinogenic, mutagenic and genotoxic." [GOC:ai]
+comment: 1,3-dichloro-2-propanol is not a natural compound.
synonym: "1,3-dichloro-2-propanol breakdown" EXACT []
synonym: "1,3-dichloro-2-propanol catabolism" EXACT []
synonym: "1,3-dichloro-2-propanol degradation" EXACT []
-is_a: GO:0018902 ! 1,3-dichloro-2-propanol metabolic process
-is_a: GO:0042178 ! xenobiotic catabolic process
-is_a: GO:0044109 ! cellular alcohol catabolic process
+is_obsolete: true
+consider: GO:0042178
[Term]
id: GO:0046311
@@ -263547,7 +263550,7 @@ synonym: "phosphoarginine breakdown" EXACT []
synonym: "phosphoarginine catabolism" EXACT []
synonym: "phosphoarginine degradation" EXACT []
is_a: GO:0006604 ! phosphoarginine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0042397 ! phosphagen catabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
@@ -263578,7 +263581,7 @@ is_a: GO:0042397 ! phosphagen catabolic process
id: GO:0046316
name: gluconokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-gluconate + ATP = 6-phospho-D-gluconate + ADP + 2 H(+)." [EC:2.7.1.12, RHEA:19433]
+def: "Catalysis of the reaction: D-gluconate + ATP = 6-phospho-D-gluconate + ADP + 2 H+." [EC:2.7.1.12, RHEA:19433]
synonym: "ATP:D-gluconate 6-phosphotransferase activity" RELATED [EC:2.7.1.12]
synonym: "gluconate kinase activity" RELATED [EC:2.7.1.12]
synonym: "gluconokinase (phosphorylating)" RELATED [EC:2.7.1.12]
@@ -263816,7 +263819,7 @@ synonym: "ethanolamine formation" EXACT []
synonym: "ethanolamine synthesis" EXACT []
is_a: GO:0006580 ! ethanolamine metabolic process
is_a: GO:0034309 ! primary alcohol biosynthetic process
-is_a: GO:0042401 ! cellular biogenic amine biosynthetic process
+is_a: GO:0042401 ! biogenic amine biosynthetic process
is_a: GO:1901162 ! primary amino compound biosynthetic process
[Term]
@@ -263897,6 +263900,8 @@ name: streptomycin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving streptomycin, a commonly used antibiotic in cell culture media. It acts only on prokaryotes and blocks transition from initiation complex to chain elongating ribosome." [PMID:2111804]
synonym: "streptomycin metabolism" EXACT []
+is_a: GO:0006790 ! sulfur compound metabolic process
+is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0019751 ! polyol metabolic process
is_a: GO:0030647 ! aminoglycoside antibiotic metabolic process
@@ -263997,7 +264002,6 @@ synonym: "disaccharide formation" EXACT []
synonym: "disaccharide synthesis" EXACT []
is_a: GO:0005984 ! disaccharide metabolic process
is_a: GO:0009312 ! oligosaccharide biosynthetic process
-is_a: GO:0034637 ! cellular carbohydrate biosynthetic process
[Term]
id: GO:0046352
@@ -264009,7 +264013,6 @@ synonym: "disaccharide catabolism" EXACT []
synonym: "disaccharide degradation" EXACT []
is_a: GO:0005984 ! disaccharide metabolic process
is_a: GO:0009313 ! oligosaccharide catabolic process
-is_a: GO:0044275 ! cellular carbohydrate catabolic process
[Term]
id: GO:0046353
@@ -264055,7 +264058,6 @@ synonym: "mannan breakdown" EXACT []
synonym: "mannan catabolism" EXACT []
synonym: "mannan degradation" EXACT []
is_a: GO:0010412 ! mannan metabolic process
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
is_a: GO:0044347 ! cell wall polysaccharide catabolic process
[Term]
@@ -264291,7 +264293,7 @@ name: K antigen metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving K antigen, a capsular polysaccharide antigen carried on the surface of bacterial capsules that masks somatic (O) antigens." [ISBN:0198506732]
synonym: "K antigen metabolism" EXACT []
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
+is_a: GO:0005976 ! polysaccharide metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
[Term]
@@ -264311,7 +264313,7 @@ name: colanic acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving colanic acid, a capsular bacterial polysaccharide composed of glucose, galactose, fucose and glucuronic acid residues." [GOC:ai, http://www.science.siu.edu/microbiology/micr425/425Notes/02-CellEnv.html]
synonym: "colanic acid metabolism" EXACT []
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
+is_a: GO:0043170 ! macromolecule metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
[Term]
@@ -264320,7 +264322,7 @@ name: enterobacterial common antigen metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving enterobacterial common antigen, an acidic polysaccharide containing N-acetyl-D-glucosamine, N-acetyl-D-mannosaminouronic acid, and 4-acetamido-4,6-dideoxy-D-galactose. A major component of the cell wall outer membrane of Gram-negative bacteria." [GOC:ma]
synonym: "enterobacterial common antigen metabolism" EXACT []
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
+is_a: GO:0005976 ! polysaccharide metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
[Term]
@@ -264329,7 +264331,7 @@ name: extracellular polysaccharide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving polysaccharides used in extracellular structures." [GOC:ai]
synonym: "extracellular polysaccharide metabolism" EXACT []
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
+is_a: GO:0005976 ! polysaccharide metabolic process
[Term]
id: GO:0046380
@@ -264558,7 +264560,7 @@ name: O antigen metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide." [ISBN:0198506732]
synonym: "O antigen metabolism" EXACT []
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
+is_a: GO:0005976 ! polysaccharide metabolic process
[Term]
id: GO:0046403
@@ -264574,24 +264576,19 @@ xref: EC:3.1.3.32
xref: MetaCyc:POLYNUCLEOTIDE-3-PHOSPHATASE-RXN
xref: Reactome:R-HSA-5649705 "PNKP hydrolyzes the terminal 3'Pi at the NEIL1,NEIL2-generated single strand break (SSB)"
xref: RHEA:14113
-is_a: GO:0098518 ! polynucleotide phosphatase activity
+is_a: GO:0016791 ! phosphatase activity
[Term]
id: GO:0046404
-name: polydeoxyribonucleotide 5'-hydroxyl-kinase activity
+name: ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA." [RHEA:15669]
-synonym: "ATP-dependent DNA 5'-hydroxyl-kinase activity" EXACT []
synonym: "ATP-dependent DNA kinase activity" EXACT []
-synonym: "ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity" RELATED []
-synonym: "ATP-dependent polynucleotide 5'-hydroxyl-kinase activity" BROAD []
-synonym: "ATP:5'-dephosphopolydeoxyribonucleotide 5'-phosphotransferase activity" EXACT []
-xref: EC:2.7.1.78
+synonym: "polydeoxyribonucleotide 5'-hydroxyl-kinase activity" BROAD []
xref: KEGG_REACTION:R03840
xref: MetaCyc:POLYNUCLEOTIDE-5-HYDROXYL-KINASE-RXN
xref: RHEA:15669
-is_a: GO:0051733 ! polydeoxyribonucleotide kinase activity
-is_a: GO:0051734 ! polynucleotide kinase activity
+is_a: GO:0051734 ! ATP-dependent polynucleotide 5'-hydroxyl-kinase activity
[Term]
id: GO:0046405
@@ -264610,7 +264607,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0046406
name: magnesium protoporphyrin IX methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + magnesium protoporphyrin IX = S-adenosyl-L-homocysteine + H(+) + magnesium protoporphyrin IX 13-monomethyl ester." [EC:2.1.1.11, RHEA:17809]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + magnesium protoporphyrin IX = S-adenosyl-L-homocysteine + H+ + magnesium protoporphyrin IX 13-monomethyl ester." [EC:2.1.1.11, RHEA:17809]
synonym: "(-)-S-adenosyl-L-methionine:magnesium-protoporphyrin IX methyltransferase activity" RELATED [EC:2.1.1.11]
synonym: "magnesium-protoporphyrin O-methyltransferase activity" EXACT []
synonym: "Mg-protoporphyrin IX methyltransferase activity" RELATED [EC:2.1.1.11]
@@ -264631,7 +264628,7 @@ id: GO:0046408
name: chlorophyll synthetase activity
namespace: molecular_function
alt_id: GO:0043787
-def: "Catalysis of the reaction: chlorophyllide a + 2 H(+) + phytyl diphosphate = chlorophyll a + diphosphate." [EC:2.5.1.62, RHEA:17317]
+def: "Catalysis of the reaction: chlorophyllide a + 2 H+ + phytyl diphosphate = chlorophyll a + diphosphate." [EC:2.5.1.62, RHEA:17317]
synonym: "chlorophyll synthase activity" EXACT []
synonym: "chlorophyllide-a:phytyl-diphosphate phytyltransferase activity" EXACT []
xref: EC:2.5.1.62
@@ -264667,7 +264664,6 @@ def: "The process in which 2-keto-3-deoxygluconate is transported across a lipid
synonym: "2-keto-3-deoxygluconate transport" RELATED []
is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0015749 ! monosaccharide transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -264710,7 +264706,8 @@ name: urate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving urate, the anion of uric acid, 2,6,8-trioxypurine, the end product of purine metabolism in certain mammals and the main excretory product in uricotelic animals." [ISBN:0198506732]
synonym: "urate metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
+is_a: GO:0044281 ! small molecule metabolic process
+is_a: GO:0072521 ! purine-containing compound metabolic process
[Term]
id: GO:0046416
@@ -264734,7 +264731,7 @@ name: nopaline metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving nopaline, (N-(I-carboxy-4-guanidinobutyl)glutamic acid), a rare amino-acid derivative." [GOC:ai]
synonym: "nopaline metabolism" EXACT []
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
is_a: GO:0006575 ! cellular modified amino acid metabolic process
[Term]
@@ -264932,7 +264929,7 @@ name: D-alanine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving D-alanine, the D-enantiomer of the amino acid alanine, i.e. (2R)-2-aminopropanoic acid." [GOC:ai, GOC:jsg]
synonym: "D-alanine metabolism" EXACT []
-is_a: GO:0046144 ! D-alanine family amino acid metabolic process
+is_a: GO:0006522 ! alanine metabolic process
is_a: GO:0046416 ! D-amino acid metabolic process
[Term]
@@ -264963,6 +264960,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving L-cysteine, the L-enantiomer of 2-amino-3-mercaptopropanoic acid, i.e. (2R)-2-amino-3-mercaptopropanoic acid." [GOC:ai, GOC:jsg, GOC:mah]
synonym: "L-cysteine metabolism" EXACT []
is_a: GO:0006534 ! cysteine metabolic process
+is_a: GO:0006575 ! cellular modified amino acid metabolic process
[Term]
id: GO:0046440
@@ -265011,6 +265009,7 @@ synonym: "FMN metabolism" EXACT []
is_a: GO:0009161 ! ribonucleoside monophosphate metabolic process
is_a: GO:0009259 ! ribonucleotide metabolic process
is_a: GO:0042726 ! flavin-containing compound metabolic process
+is_a: GO:0052648 ! ribitol phosphate metabolic process
[Term]
id: GO:0046445
@@ -265033,7 +265032,7 @@ is_a: GO:0072521 ! purine-containing compound metabolic process
id: GO:0046447
name: terpenoid indole alkaloid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving terpenoid indole alkaloids, compounds formed from the condensation of tryptamine (derived from tryptophan) and secologanin (derived from geranyl pyrophosphate)." [GOC:ai, http://rycomusa.com/aspp2000/public/P29/0525.html]
+def: "The chemical reactions and pathways involving terpenoid indole alkaloids, compounds formed from the condensation of tryptamine (derived from tryptophan) and secologanin (derived from geranyl pyrophosphate)." [GOC:ai]
synonym: "terpenoid indole alkaloid metabolism" EXACT []
is_a: GO:0035834 ! indole alkaloid metabolic process
@@ -265053,9 +265052,7 @@ name: creatinine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving creatinine, 2-amino-1,5-dihydro-1-methyl-4H-imidazol-4-one, an end product of creatine metabolism and a normal constituent of urine." [ISBN:0198506732]
synonym: "creatinine metabolism" EXACT []
-is_a: GO:0072338 ! cellular lactam metabolic process
-is_a: GO:1901360 ! organic cyclic compound metabolic process
-is_a: GO:1901564 ! organonitrogen compound metabolic process
+is_a: GO:0072338 ! lactam metabolic process
[Term]
id: GO:0046450
@@ -265066,7 +265063,7 @@ synonym: "desthiobiotin metabolic process" EXACT []
synonym: "desthiobiotin metabolism" EXACT []
synonym: "dethiobiotin metabolism" EXACT []
is_a: GO:0032787 ! monocarboxylic acid metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
@@ -265165,7 +265162,7 @@ is_a: GO:0006081 ! cellular aldehyde metabolic process
id: GO:0046459
name: short-chain fatty acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving fatty acids with a chain length of less than C6." [Wikipedia:Fatty_acid_metabolism]
+def: "The chemical reactions and pathways involving a fatty acid with an aliphatic tail of less than 6 carbons." [Wikipedia:Fatty_acid_metabolism]
synonym: "short-chain fatty acid metabolism" EXACT []
is_a: GO:0006631 ! fatty acid metabolic process
@@ -265404,7 +265401,7 @@ is_a: GO:0008378 ! galactosyltransferase activity
id: GO:0046481
name: digalactosyldiacylglycerol synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,2-diacyl-3-beta-D-galactosyl-sn-glycerol + UDP-D-galactose = 3-[alpha-D-galactosyl-(1->6)-beta-D-galactosyl]-1,2-diacyl-sn-glycerol + H(+) + UDP." [EC:2.4.1.241, RHEA:10520]
+def: "Catalysis of the reaction: 1,2-diacyl-3-beta-D-galactosyl-sn-glycerol + UDP-D-galactose = 3-[alpha-D-galactosyl-(1->6)-beta-D-galactosyl]-1,2-diacyl-sn-glycerol + H+ + UDP." [EC:2.4.1.241, RHEA:10520]
synonym: "DGD1" NARROW []
synonym: "DGD2" NARROW []
synonym: "DGDG synthase activity" BROAD [EC:2.4.1.241]
@@ -265433,7 +265430,7 @@ synonym: "PABA metabolism" EXACT []
synonym: "para-aminobenzoic acid metabolism" EXACT []
synonym: "vitamin Bx metabolic process" EXACT []
synonym: "vitamin Bx metabolism" EXACT []
-is_a: GO:0009072 ! aromatic amino acid family metabolic process
+is_a: GO:0009072 ! aromatic amino acid metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:0042537 ! benzene-containing compound metabolic process
@@ -265544,9 +265541,9 @@ name: rhizobactin 1021 metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving rhizobactin 1021, (E)-4-((3-(acetylhydroxyamino)propyl)-amino)-2-hydroxy-(2-(2-(3-(hydroxy(1-oxo-2-decenyl)amino)propyl)amino)-2-oxoethyl)-4-oxobutanoic acid, a siderophore produced by Sinorhizobium meliloti." [MetaCyc:PWY-761, PMID:11274118]
synonym: "rhizobactin 1021 metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0009237 ! siderophore metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
is_a: GO:1902644 ! tertiary alcohol metabolic process
@@ -265679,7 +265676,7 @@ is_a: GO:0046505 ! sulfolipid metabolic process
id: GO:0046507
name: UDPsulfoquinovose synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: sulfite + UDP-D-glucose = H(2)O + UDP-6-sulfoquinovose." [EC:3.13.1.1, RHEA:13197]
+def: "Catalysis of the reaction: sulfite + UDP-D-glucose = H2O + UDP-6-sulfoquinovose." [EC:3.13.1.1, RHEA:13197]
synonym: "sulfite:UDP-glucose sulfotransferase activity" EXACT []
synonym: "UDP-6-sulfo-6-deoxyglucose sulfohydrolase activity" RELATED [EC:3.13.1.1]
synonym: "UDP-sulfoquinovose synthase activity" RELATED [EC:3.13.1.1]
@@ -265703,7 +265700,7 @@ is_a: GO:0016787 ! hydrolase activity
id: GO:0046509
name: 1,2-diacylglycerol 3-beta-galactosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,2-diacyl-sn-glycerol + UDP-D-galactose = 1,2-diacyl-3-beta-D-galactosyl-sn-glycerol + H(+) + UDP." [EC:2.4.1.46, RHEA:14945]
+def: "Catalysis of the reaction: 1,2-diacyl-sn-glycerol + UDP-D-galactose = 1,2-diacyl-3-beta-D-galactosyl-sn-glycerol + H+ + UDP." [EC:2.4.1.46, RHEA:14945]
synonym: "1-beta-MGDG activity" RELATED [EC:2.4.1.46]
synonym: "1beta-MGDG" RELATED [EC:2.4.1.46]
synonym: "MGDG synthase activity" EXACT []
@@ -265853,7 +265850,7 @@ is_a: GO:0046519 ! sphingoid metabolic process
id: GO:0046522
name: S-methyl-5-thioribose kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-methyl-5-thio-D-ribose + ATP = S-methyl-5-thio-alpha-D-ribose 1-phosphate + ADP + 2 H(+)." [EC:2.7.1.100, RHEA:22312]
+def: "Catalysis of the reaction: S-methyl-5-thio-D-ribose + ATP = S-methyl-5-thio-alpha-D-ribose 1-phosphate + ADP + 2 H+." [EC:2.7.1.100, RHEA:22312]
synonym: "5-methylthioribose kinase (phosphorylating)" RELATED [EC:2.7.1.100]
synonym: "5-methylthioribose kinase activity" EXACT []
synonym: "ATP:S-methyl-5-thio-D-ribose 1-phosphotransferase activity" RELATED [EC:2.7.1.100]
@@ -265934,7 +265931,7 @@ is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
id: GO:0046526
name: D-xylulose reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD(+) + xylitol = D-xylulose + H(+) + NADH." [EC:1.1.1.9, RHEA:20433]
+def: "Catalysis of the reaction: NAD+ + xylitol = D-xylulose + H+ + NADH." [EC:1.1.1.9, RHEA:20433]
synonym: "xylitol dehydrogenase activity" RELATED [EC:1.1.1.9]
xref: EC:1.1.1.9
xref: KEGG_REACTION:R01896
@@ -266056,24 +266053,25 @@ relationship: part_of GO:0000803 ! sex chromosome
id: GO:0046537
name: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D glycerate; this reaction does not require the cofactor 2,3-bisphosphoglycerate." [EC:5.4.2.1]
-synonym: "PGAM-i" RELATED [EC:5.4.2.1]
+def: "Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D glycerate; this reaction does not require the cofactor 2,3-bisphosphoglycerate." [EC:5.4.2.12]
+xref: EC:5.4.2.12
is_a: GO:0004619 ! phosphoglycerate mutase activity
[Term]
id: GO:0046538
name: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate; this reaction requires the cofactor 2,3-bisphosphoglycerate." [EC:5.4.2.1]
-synonym: "glycerate phosphomutase (diphosphoglycerate cofactor) activity" RELATED [EC:5.4.2.1]
-synonym: "PGAM-d" RELATED [EC:5.4.2.1]
+def: "Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate; this reaction mechanism uses 2,3-bisphosphoglycerate as a phosphate donor." [EC:5.4.2.11]
+synonym: "glycerate phosphomutase (diphosphoglycerate cofactor) activity" RELATED [EC:5.4.2.11]
+xref: EC:5.4.2.11
+xref: KEGG_REACTION:R01516
is_a: GO:0004619 ! phosphoglycerate mutase activity
[Term]
id: GO:0046539
name: histamine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + histamine = N(tau)-methylhistamine + S-adenosyl-L-homocysteine + H(+)." [EC:2.1.1.8, RHEA:19301]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + histamine = N(tau)-methylhistamine + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.8, RHEA:19301]
synonym: "histamine 1-methyltransferase activity" RELATED [EC:2.1.1.8]
synonym: "histamine methyltransferase activity" RELATED [EC:2.1.1.8]
synonym: "histamine-methylating enzyme" RELATED [EC:2.1.1.8]
@@ -266178,17 +266176,14 @@ relationship: part_of GO:0042670 ! retinal cone cell differentiation
[Term]
id: GO:0046550
-name: (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine biosynthetic process from asparagine
+name: obsolete (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine biosynthetic process from asparagine
namespace: biological_process
-def: "The modification of asparagine to (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine as found in microcin C7 produced from the mccA gene in E. coli plasmid pMccC7." [RESID:AA0328]
+def: "OBSOLETE. The modification of asparagine to (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine as found in microcin C7 produced from the mccA gene in E. coli plasmid pMccC7." [RESID:AA0328]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "(3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine anabolism from asparagine" EXACT []
synonym: "(3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine formation from asparagine" EXACT []
synonym: "(3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine synthesis from asparagine" EXACT []
-xref: RESID:AA0328
-is_a: GO:0006528 ! asparagine metabolic process
-is_a: GO:0009165 ! nucleotide biosynthetic process
-is_a: GO:0018196 ! peptidyl-asparagine modification
-is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
+is_obsolete: true
[Term]
id: GO:0046551
@@ -266210,7 +266205,7 @@ relationship: part_of GO:0046530 ! photoreceptor cell differentiation
id: GO:0046553
name: D-malate dehydrogenase (decarboxylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-malate + NAD(+) = CO(2) + NADH + pyruvate." [EC:1.1.1.83, RHEA:18365]
+def: "Catalysis of the reaction: (R)-malate + NAD+ = CO2 + NADH + pyruvate." [EC:1.1.1.83, RHEA:18365]
synonym: "(R)-malate:NAD+ oxidoreductase (decarboxylating)" RELATED [EC:1.1.1.83]
synonym: "bifunctional L(+)-tartrate dehydrogenase-D(+)-malate (decarboxylating)" RELATED [EC:1.1.1.83]
synonym: "D-malate dehydrogenase activity" RELATED [EC:1.1.1.83]
@@ -266391,7 +266386,7 @@ is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0046564
name: oxalate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + oxalate = CO(2) + formate." [EC:4.1.1.2, RHEA:16509]
+def: "Catalysis of the reaction: H+ + oxalate = CO2 + formate." [EC:4.1.1.2, RHEA:16509]
synonym: "oxalate carboxy-lyase (formate-forming)" RELATED [EC:4.1.1.2]
synonym: "oxalate carboxy-lyase activity" RELATED [EC:4.1.1.2]
xref: EC:4.1.1.2
@@ -266456,7 +266451,7 @@ id: GO:0046570
name: methylthioribulose 1-phosphate dehydratase activity
namespace: molecular_function
alt_id: GO:0043809
-def: "Catalysis of the reaction: S-methyl-5-thio-D-ribulose 1-phosphate = 5-(methylthio)-2,3-dioxopentyl phosphate + H(2)O." [EC:4.2.1.109, RHEA:15549]
+def: "Catalysis of the reaction: S-methyl-5-thio-D-ribulose 1-phosphate = 5-(methylthio)-2,3-dioxopentyl phosphate + H2O." [EC:4.2.1.109, RHEA:15549]
synonym: "1-PMT-ribulose dehydratase activity" RELATED [EC:4.2.1.109]
synonym: "5-methylthioribulose-1-phosphate 4-dehydratase activity" EXACT [MetaCyc:R145-RXN]
synonym: "methylthioribulose-1-phosphate dehydratase activity" EXACT []
@@ -266576,11 +266571,12 @@ is_a: GO:0005911 ! cell-cell junction
[Term]
id: GO:0046583
-name: cation efflux transmembrane transporter activity
+name: monoatomic cation efflux transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of a cation or cations from the inside of the cell to the outside of the cell across a membrane." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
synonym: "cation efflux permease activity" EXACT []
-is_a: GO:0008324 ! cation transmembrane transporter activity
+synonym: "cation efflux transmembrane transporter activity" BROAD []
+is_a: GO:0008324 ! monoatomic cation transmembrane transporter activity
is_a: GO:0015562 ! efflux transmembrane transporter activity
[Term]
@@ -266591,6 +266587,7 @@ def: "The chemical reactions and pathways involving enniatins, any of various cy
synonym: "enniatin metabolism" EXACT []
is_a: GO:0016999 ! antibiotic metabolic process
is_a: GO:0050761 ! depsipeptide metabolic process
+is_a: GO:0072338 ! lactam metabolic process
is_a: GO:1901334 ! lactone metabolic process
[Term]
@@ -266605,6 +266602,7 @@ synonym: "enniatin synthesis" EXACT []
is_a: GO:0017000 ! antibiotic biosynthetic process
is_a: GO:0046584 ! enniatin metabolic process
is_a: GO:0050763 ! depsipeptide biosynthetic process
+is_a: GO:0072339 ! lactam biosynthetic process
is_a: GO:1901336 ! lactone biosynthetic process
[Term]
@@ -266669,7 +266667,7 @@ synonym: "RNase T1" RELATED [EC:4.6.1.24]
synonym: "RNase T1 activity" EXACT []
xref: EC:4.6.1.24
xref: MetaCyc:3.1.27.3-RXN
-is_a: GO:0004540 ! ribonuclease activity
+is_a: GO:0004540 ! RNA nuclease activity
[Term]
id: GO:0046590
@@ -266955,16 +266953,17 @@ def: "OBSOLETE. The process of nucleolar expansion, as seen in Saccharomyces." [
comment: This term was made obsolete because it does not describe a biological process.
synonym: "nucleolar size increase (sensu Saccharomyces)" EXACT []
is_obsolete: true
-consider: GO:0007571
-consider: GO:0007576
[Term]
id: GO:0046618
-name: xenobiotic export
+name: xenobiotic export from cell
namespace: biological_process
-def: "The directed movement of a xenobiotic, a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:go_curators, GOC:krc]
+def: "The directed movement of a xenobiotic from a cell, into the extracellular region. A xenobiotic is a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:go_curators, GOC:krc]
synonym: "drug export" RELATED []
+synonym: "xenobiotic export" RELATED []
is_a: GO:0042908 ! xenobiotic transport
+is_a: GO:0055085 ! transmembrane transport
+is_a: GO:0140352 ! export from cell
[Term]
id: GO:0046619
@@ -267412,7 +267411,7 @@ synonym: "vitamin M metabolic process" EXACT []
synonym: "vitamin M metabolism" EXACT []
is_a: GO:0006760 ! folic acid-containing compound metabolic process
is_a: GO:0006767 ! water-soluble vitamin metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0043648 ! dicarboxylic acid metabolic process
[Term]
@@ -267459,13 +267458,14 @@ is_a: GO:0046655 ! folic acid metabolic process
[Term]
id: GO:0046658
-name: anchored component of plasma membrane
+name: obsolete anchored component of plasma membrane
namespace: cellular_component
-def: "The component of the plasma membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group, that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the plasma membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group, that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "anchored to plasma membrane" NARROW []
synonym: "plasma membrane, GPI-anchored" NARROW []
-is_a: GO:0031225 ! anchored component of membrane
-is_a: GO:0031226 ! intrinsic component of plasma membrane
+is_obsolete: true
+replaced_by: GO:0005886
[Term]
id: GO:0046659
@@ -267493,15 +267493,15 @@ relationship: part_of GO:0007275 ! multicellular organism development
[Term]
id: GO:0046662
-name: regulation of oviposition
+name: regulation of egg-laying behavior
namespace: biological_process
alt_id: GO:0048042
def: "Any process that modulates the frequency, rate or extent of the deposition of eggs, either fertilized or not, upon a surface or into a medium." [GOC:dph, GOC:tb, PMID:11932766]
+synonym: "regulation of oviposition" EXACT []
synonym: "regulation of post-mating oviposition" NARROW []
is_a: GO:0050795 ! regulation of behavior
-is_a: GO:0051239 ! regulation of multicellular organismal process
is_a: GO:2000241 ! regulation of reproductive process
-relationship: regulates GO:0018991 ! oviposition
+relationship: regulates GO:0018991 ! egg-laying behavior
[Term]
id: GO:0046663
@@ -267668,6 +267668,8 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a streptomycin stimulus. Streptomycin is a commonly used antibiotic in cell culture media which acts only on prokaryotes and blocks transition from initiation complex to chain elongating ribosome." [GOC:curators]
synonym: "streptomycin susceptibility/resistance" RELATED []
is_a: GO:0046677 ! response to antibiotic
+is_a: GO:1901698 ! response to nitrogen compound
+is_a: GO:1902074 ! response to salt
is_a: GO:1903416 ! response to glycoside
[Term]
@@ -267745,6 +267747,7 @@ def: "Any process that results in a change in state or activity of a cell or an
synonym: "chromate sensitivity/resistance" RELATED []
is_a: GO:0010035 ! response to inorganic substance
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0046688
@@ -267835,7 +267838,6 @@ comment: Note that this term should not be used to refer to CD14 alone, but the
synonym: "LPS receptor complex" EXACT []
is_a: GO:0043235 ! receptor complex
is_a: GO:0098796 ! membrane protein complex
-relationship: part_of GO:0016021 ! integral component of membrane
[Term]
id: GO:0046697
@@ -268019,7 +268021,7 @@ synonym: "boron uptake transmembrane transporter activity" RELATED []
synonym: "efflux-type borate transporter" NARROW []
synonym: "efflux-type boron transporter" RELATED []
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0022804 ! active transmembrane transporter activity
[Term]
id: GO:0046716
@@ -268029,7 +268031,6 @@ def: "The cellular homeostatic process that preserves a muscle cell in a stable
synonym: "muscle fiber maintenance" NARROW [GOC:dph, GOC:tb]
synonym: "muscle homeostasis" RELATED [GOC:dph]
is_a: GO:0019725 ! cellular homeostasis
-is_a: GO:0060249 ! anatomical structure homeostasis
[Term]
id: GO:0046717
@@ -268062,8 +268063,8 @@ name: regulation by virus of viral protein levels in host cell
namespace: biological_process
def: "Any virus-mediated process that modulates the levels of viral proteins in a cell." [GOC:ai]
synonym: "regulation of viral protein levels" EXACT []
-is_a: GO:0048878 ! chemical homeostasis
is_a: GO:0050792 ! regulation of viral process
+is_a: GO:0065008 ! regulation of biological quality
[Term]
id: GO:0046720
@@ -268157,14 +268158,15 @@ is_a: GO:0044423 ! virion component
[Term]
id: GO:0046730
-name: induction by virus of host immune response
+name: obsolete induction by virus of host immune response
namespace: biological_process
alt_id: GO:0046731
alt_id: GO:0046732
alt_id: GO:0046733
alt_id: GO:0046734
alt_id: GO:0046735
-def: "The induction by a virus of an immune response in the host organism." [GOC:jl]
+def: "OBSOLETE. The induction by a virus of an immune response in the host organism." [GOC:jl]
+comment: This term was obsoleted because there is no evidence that this is different from the normal host immunity.
synonym: "activation of host immune response by virus" EXACT []
synonym: "active induction of host immune response by virus" RELATED []
synonym: "active viral induction of host immune response" RELATED []
@@ -268183,37 +268185,41 @@ synonym: "passive viral induction of cell-mediated immune response in host" NARR
synonym: "passive viral induction of host immune response" NARROW []
synonym: "passive viral induction of humoral immune response in host" NARROW []
synonym: "passive viral induction of innate immune response in host" NARROW []
-is_a: GO:0044416 ! induction by symbiont of host defense response
-is_a: GO:0050778 ! positive regulation of immune response
-is_a: GO:0050794 ! regulation of cellular process
-is_a: GO:0075528 ! modulation by virus of host immune response
+is_obsolete: true
+replaced_by: GO:0006955
[Term]
id: GO:0046736
-name: induction of humoral immune response in host by virus
+name: obsolete induction of humoral immune response in host by virus
namespace: biological_process
-def: "The intentional, virally-encoded stimulation of a host humoral defense response to viral infection." [GOC:jl]
+def: "OBSOLETE. The intentional, virally-encoded stimulation of a host humoral defense response to viral infection." [GOC:jl]
+comment: This term was obsoleted because there is no evidence that this is different from the normal host immunity.
synonym: "active induction of humoral immune response in host by virus" RELATED []
synonym: "active viral induction of humoral immune response in host" EXACT []
-is_a: GO:0046730 ! induction by virus of host immune response
+is_obsolete: true
+consider: GO:0061844
[Term]
id: GO:0046737
-name: induction of cell-mediated immune response in host by virus
+name: obsolete induction of cell-mediated immune response in host by virus
namespace: biological_process
-def: "The intentional, virally-encoded stimulation of a cell-mediated host defense response to viral infection." [GOC:jl]
+def: "OBSOLETE. The intentional, virally-encoded stimulation of a cell-mediated host defense response to viral infection." [GOC:jl]
+comment: This term was obsoleted because there is no evidence that this is different from the normal host immunity.
synonym: "active induction of cell-mediated immune response in host by virus" RELATED []
synonym: "active viral induction of cell-mediated immune response in host" EXACT []
-is_a: GO:0046730 ! induction by virus of host immune response
+is_obsolete: true
+consider: GO:0001788
[Term]
id: GO:0046738
-name: induction of innate immune response in host by virus
+name: obsolete induction of innate immune response in host by virus
namespace: biological_process
-def: "The intentional, virally-encoded stimulation of an innate host defense response to viral infection." [GOC:jl]
+def: "OBSOLETE. The intentional, virally-encoded stimulation of an innate host defense response to viral infection." [GOC:jl]
+comment: This term was obsoleted because there is no evidence that this is different from the normal host immunity.
synonym: "active induction of innate immune response in host by virus" RELATED []
synonym: "active viral induction of innate immune response in host" EXACT []
-is_a: GO:0046730 ! induction by virus of host immune response
+is_obsolete: true
+consider: GO:0140374
[Term]
id: GO:0046739
@@ -268223,7 +268229,7 @@ def: "The transport of a virus between cells in a multicellular organism. The ce
synonym: "spread of virus in multicellular host" RELATED [GOC:bf, GOC:jl]
synonym: "spread of virus within multicellular host" EXACT []
synonym: "viral spread within multicellular host" EXACT []
-is_a: GO:0044000 ! movement in host
+is_a: GO:0044001 ! migration in host
is_a: GO:0046794 ! transport of virus
[Term]
@@ -268296,31 +268302,31 @@ is_a: GO:0016032 ! viral process
[Term]
id: GO:0046752
-name: viral capsid precursor transport to host cell nucleus
+name: obsolete viral capsid precursor transport to host cell nucleus
namespace: biological_process
-def: "Any process in which viral capsid precursors are transported to a specific location in the nucleus, thus accumulating the necessary components for assembly of a capsid." [ISBN:0781718325]
+def: "OBSOLETE. Any process in which viral capsid precursors are transported to a specific location in the nucleus, thus accumulating the necessary components for assembly of a capsid." [ISBN:0781718325]
+comment: This term was obsoleted because it encompasses the target of the transport process.
synonym: "establishment and maintenance of viral capsid precursor localization in nucleus" BROAD []
synonym: "localization of viral capsid precursors in nucleus" BROAD []
synonym: "nuclear localization of viral capsid precursors" BROAD []
synonym: "viral capsid precursor localisation in host cell nucleus" BROAD [GOC:mah]
synonym: "viral capsid precursor localization in host cell nucleus" BROAD []
synonym: "viral capsid precursor localization to host cell nucleus" BROAD [GOC:bf, GOC:jl]
-is_a: GO:0030581 ! symbiont intracellular protein transport in host
-is_a: GO:0042000 ! translocation of peptides or proteins into host
-relationship: part_of GO:0039708 ! nuclear capsid assembly
+is_obsolete: true
[Term]
id: GO:0046753
name: non-lytic viral release
namespace: biological_process
-def: "The exit of a viral particle from a cell that does not involve cell lysis." [GOC:bf, GOC:jl, ISBN:0072370319]
+def: "The exit of a viral particle from a host cell that does not involve cell lysis." [GOC:bf, GOC:jl, ISBN:0072370319]
is_a: GO:0019076 ! viral release from host cell
[Term]
id: GO:0046754
name: viral exocytosis
namespace: biological_process
-def: "The exit of enveloped or unenveloped virion particles from the host cell by exocytosis, without causing cell lysis." [ISBN:0072370319]
+def: "The exit of a fully formed virion particles from the host cell by exocytosis via a host vesicle." [ISBN:0072370319, PMID:33157038]
+synonym: "viral egress by exocytosis" EXACT []
is_a: GO:0046753 ! non-lytic viral release
[Term]
@@ -268392,7 +268398,7 @@ name: viral budding from plasma membrane
namespace: biological_process
alt_id: GO:0046766
alt_id: GO:0046767
-def: "A viral budding that starts with formation of a membrane curvature in the host plasma membrane." [GOC:bf, ISBN:0072370319, PMID:9394621, VZ:1947]
+def: "A viral budding that starts with formation of a curvature in the host plasma membrane around which the virion particle assembles." [GOC:bf, ISBN:0072370319, PMID:9394621, VZ:1947]
synonym: "plasma membrane viral budding" EXACT []
synonym: "plasma membrane viral budding during viral capsid envelopment" RELATED []
synonym: "viral budding from plasma membrane by viral capsid envelopment" RELATED []
@@ -268484,7 +268490,7 @@ namespace: biological_process
def: "Any viral process that results in the inhibition of interferon activity within the host cell." [PMID:10859382]
synonym: "negative regulation by virus of intracellular interferon activity" EXACT []
synonym: "suppression by virus of intracellular interferon activity in host" EXACT []
-is_a: GO:0030683 ! mitigation of host immune response by virus
+is_a: GO:0019049 ! mitigation of host antiviral defense response
is_a: GO:0075528 ! modulation by virus of host immune response
[Term]
@@ -268497,7 +268503,6 @@ is_a: GO:0001818 ! negative regulation of cytokine production
is_a: GO:0044414 ! suppression of host defenses by symbiont
is_a: GO:0044831 ! modulation by virus of host cytokine production
is_a: GO:0050776 ! regulation of immune response
-is_a: GO:0050794 ! regulation of cellular process
[Term]
id: GO:0046776
@@ -268529,7 +268534,6 @@ namespace: biological_process
def: "Any viral process that interferes with the processing of mRNA in the host cell." [ISBN:0781718325]
synonym: "viral perturbation of host mRNA processing" EXACT []
is_a: GO:0010468 ! regulation of gene expression
-is_a: GO:0019054 ! modulation by virus of host cellular process
is_a: GO:0039656 ! modulation by virus of host gene expression
is_a: GO:0050684 ! regulation of mRNA processing
@@ -268650,14 +268654,13 @@ is_a: GO:0019055 ! modification by virus of host cell cycle regulation
[Term]
id: GO:0046793
-name: induction by virus of phosphorylation of host RNA polymerase II
+name: obsolete induction by virus of phosphorylation of host RNA polymerase II
namespace: biological_process
-def: "Any process in which a virus activates the frequency, rate or extent of phosphorylation of host RNA polymerase II." [PMID:7637000]
+def: "OBSOLETE. Any process in which a virus activates the frequency, rate or extent of phosphorylation of host RNA polymerase II." [PMID:7637000]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
synonym: "induction by virus of modification of host RNA polymerase II" BROAD [GOC:bf, GOC:jl]
synonym: "virus-induced modification of host RNA polymerase II" EXACT []
-is_a: GO:0010468 ! regulation of gene expression
-is_a: GO:0019056 ! modulation by virus of host transcription
-is_a: GO:0039614 ! induction by virus of host protein phosphorylation
+is_obsolete: true
[Term]
id: GO:0046794
@@ -268824,11 +268827,12 @@ is_a: GO:0019062 ! virion attachment to host cell
[Term]
id: GO:0046815
-name: genome retention in viral capsid
+name: obsolete genome retention in viral capsid
namespace: biological_process
-def: "Any process in which the viral genome is retained within the capsid during genome cleavage and packaging." [PMID:9696839]
-is_a: GO:0016032 ! viral process
-relationship: part_of GO:0019079 ! viral genome replication
+def: "OBSOLETE. Any process in which the viral genome is retained within the capsid during genome cleavage and packaging." [PMID:9696839]
+comment: This term was obsoleted because it represents an assay.
+is_obsolete: true
+consider: GO:0019072
[Term]
id: GO:0046816
@@ -269087,8 +269091,8 @@ id: GO:0046835
name: carbohydrate phosphorylation
namespace: biological_process
def: "The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y." [ISBN:0198506732]
+is_a: GO:0005975 ! carbohydrate metabolic process
is_a: GO:0016310 ! phosphorylation
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
[Term]
id: GO:0046836
@@ -269100,11 +269104,11 @@ is_a: GO:1901264 ! carbohydrate derivative transport
[Term]
id: GO:0046838
-name: phosphorylated carbohydrate dephosphorylation
+name: obsolete phosphorylated carbohydrate dephosphorylation
namespace: biological_process
-def: "The process of removing a phosphate group from a phosphorylated carbohydrate, any organic compound based on the general formula Cx(H2O)y with a phosphate group attached to it." [ISBN:0198506732]
-is_a: GO:0016311 ! dephosphorylation
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
+def: "OBSOLETE. The process of removing a phosphate group from a phosphorylated carbohydrate, any organic compound based on the general formula Cx(H2O)y with a phosphate group attached to it." [ISBN:0198506732]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0046839
@@ -269140,7 +269144,7 @@ namespace: biological_process
def: "Establishment of the dorsal filaments, elaborate specializations of the chorion that protrude from the anterior end of the egg and facilitate embryonic respiration." [ISBN:0879694238]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
-relationship: part_of GO:0007306 ! eggshell chorion assembly
+relationship: part_of GO:0007306 ! egg chorion assembly
[Term]
id: GO:0046844
@@ -269149,7 +269153,7 @@ namespace: biological_process
def: "Establishment of the micropyle, a single cone-shaped specialization of the chorion that allows sperm entry into the egg prior to fertilization." [ISBN:0879694238]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
-relationship: part_of GO:0007306 ! eggshell chorion assembly
+relationship: part_of GO:0007306 ! egg chorion assembly
[Term]
id: GO:0046845
@@ -269234,7 +269238,6 @@ synonym: "myo-inositol and derivative phosphorylation" RELATED []
synonym: "myo-inositol or phosphatidyl-myo-inositol phosphorylation" NARROW []
is_obsolete: true
consider: GO:0046854
-consider: GO:0052746
[Term]
id: GO:0046854
@@ -269252,12 +269255,14 @@ is_a: GO:0006661 ! phosphatidylinositol biosynthetic process
[Term]
id: GO:0046855
-name: inositol phosphate dephosphorylation
+name: obsolete inositol phosphate dephosphorylation
namespace: biological_process
-def: "The process of removing a phosphate group from any mono- or polyphosphorylated inositol." [ISBN:0198506732]
+def: "OBSOLETE. The process of removing a phosphate group from any mono- or polyphosphorylated inositol." [ISBN:0198506732]
+comment: This term was obsoleted because it represents a molecular function.
+synonym: "https://github.com/geneontology/go-ontology/issues/24269" BROAD []
synonym: "myo-inositol phosphate dephosphorylation" NARROW []
-is_a: GO:0046838 ! phosphorylated carbohydrate dephosphorylation
-is_a: GO:0071545 ! inositol phosphate catabolic process
+is_obsolete: true
+consider: GO:0043647
[Term]
id: GO:0046856
@@ -269329,7 +269334,7 @@ id: GO:0046863
name: ribulose-1,5-bisphosphate carboxylase/oxygenase activator activity
namespace: molecular_function
alt_id: GO:0018236
-def: "Increases the activity of rubisco by the removal of otherwise inhibitory sugar phosphates: RuBP, and in some plants, 2-carboxyarabinitol 1-phosphate." [PMID:10430961, PMID:10965036, PMID:2404515]
+def: "Binds to and iincreases the activity of rubisco by the removal of otherwise inhibitory sugar phosphates: RuBP, and in some plants, 2-carboxyarabinitol 1-phosphate." [PMID:10430961, PMID:10965036, PMID:2404515]
comment: See also the molecular function term 'ribulose-bisphosphate carboxylase activity ; GO:0016984'.
synonym: "ribulose-1,5-bisphosphate carboxylase/oxygenase activase activity" EXACT [GOC:dph, GOC:tb]
synonym: "ribulose-bisphosphate carboxylase activase activity" EXACT []
@@ -269426,6 +269431,7 @@ synonym: "heavy metal ion:hydrogen symporter activity" NARROW []
synonym: "heavy metal-exporting ATPase activity" NARROW []
synonym: "high affinity metal ion uptake transporter activity" NARROW []
synonym: "low affinity metal ion uptake transporter activity" NARROW []
+is_a: GO:0008324 ! monoatomic cation transmembrane transporter activity
is_a: GO:0022890 ! inorganic cation transmembrane transporter activity
[Term]
@@ -269797,7 +269803,7 @@ id: GO:0046904
name: calcium oxalate binding
namespace: molecular_function
def: "Binding to calcium oxalate, CaC2O4, a salt of oxalic acid. In animals, it may be excreted in urine or retained in the form of urinary calculi." [ISBN:0721662544]
-is_a: GO:0005488 ! binding
+is_a: GO:0031406 ! carboxylic acid binding
[Term]
id: GO:0046905
@@ -269872,9 +269878,10 @@ is_a: GO:0046872 ! metal ion binding
[Term]
id: GO:0046912
-name: acyltransferase, acyl groups converted into alkyl on transfer
+name: acyltransferase activity, acyl groups converted into alkyl on transfer
namespace: molecular_function
def: "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer." [GOC:jl]
+synonym: "acyltransferase, acyl groups converted into alkyl on transfer" EXACT []
synonym: "transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer" EXACT []
xref: EC:2.3.3.-
is_a: GO:0016746 ! acyltransferase activity
@@ -269895,11 +269902,13 @@ is_a: GO:0046873 ! metal ion transmembrane transporter activity
[Term]
id: GO:0046916
-name: cellular transition metal ion homeostasis
+name: obsolete intracellular transition metal ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of transition metal ions at the level of a cell. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver." [GOC:mah, ISBN:0198506732]
-is_a: GO:0006875 ! cellular metal ion homeostasis
-is_a: GO:0055076 ! transition metal ion homeostasis
+def: "OBSOLETE. A homeostatic process involved in the maintenance of a steady state level of transition metal ions within a cell. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver." [GOC:mah, ISBN:0198506732]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+synonym: "cellular transition metal ion homeostasis" EXACT []
+is_obsolete: true
+replaced_by: GO:0030003
[Term]
id: GO:0046917
@@ -270039,7 +270048,6 @@ synonym: "down-regulation of neurotransmitter secretion" EXACT []
synonym: "downregulation of neurotransmitter secretion" EXACT []
synonym: "inhibition of neurotransmitter secretion" NARROW []
is_a: GO:0046928 ! regulation of neurotransmitter secretion
-is_a: GO:0050805 ! negative regulation of synaptic transmission
is_a: GO:0051589 ! negative regulation of neurotransmitter transport
is_a: GO:1903531 ! negative regulation of secretion by cell
relationship: negatively_regulates GO:0007269 ! neurotransmitter secretion
@@ -270053,7 +270061,6 @@ synonym: "channel-forming toxin activity" RELATED []
synonym: "pore" EXACT []
synonym: "pore-forming toxin activity" RELATED []
is_a: GO:0098796 ! membrane protein complex
-relationship: part_of GO:0016021 ! integral component of membrane
[Term]
id: GO:0046931
@@ -270103,7 +270110,7 @@ is_a: GO:0016874 ! ligase activity
id: GO:0046934
name: phosphatidylinositol-4,5-bisphosphate 3-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+)." [EC:2.7.1.153, RHEA:21292]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H+." [EC:2.7.1.153, RHEA:21292]
synonym: "ATP:1-phosphatidyl-1D-myo-inositol-4,5-bisphosphate 3-phosphotransferase activity" RELATED [EC:2.7.1.153]
synonym: "phosphatidylinositol 3-kinase activity, class I" NARROW []
synonym: "phosphatidylinositol 3-kinase activity, class II" NARROW []
@@ -270123,6 +270130,7 @@ xref: Reactome:R-HSA-1839091 "Cytosolic FGFR1 fusion protein-associated PI3K pho
xref: Reactome:R-HSA-1839107 "BCR-FGFR1-associated PI3K phosphorylates PIP2 to PIP3."
xref: Reactome:R-HSA-186800 "PI3K catalyses the phosphorylation of PIP2 to PIP3"
xref: Reactome:R-HSA-198266 "PI3K produces PIP3 and other phosphatidyl inositides"
+xref: Reactome:R-HSA-201510 "PI3K synthesizes PIP3 downstream of ALK"
xref: Reactome:R-HSA-202365 "PI3K bound to TRAT1 phosphorylates PIP2 to PIP3"
xref: Reactome:R-HSA-2029271 "PI3K phosphorylates PIP2 to PIP3"
xref: Reactome:R-HSA-2076220 "CD19 Signalosome phosphorylates PI(4,5)P2 forming PI(3,4,5)P3"
@@ -270144,11 +270152,10 @@ xref: Reactome:R-HSA-5654709 "FGFR3- and PTPN11-associated PI3K phosphorylates P
xref: Reactome:R-HSA-5654714 "FGFR4- and PTPN11-associated PI3K phosphorylates PIP2 to PIP3"
xref: Reactome:R-HSA-5654717 "FGFR4-associated PI3K phosphorylates PIP2 to PIP3"
xref: Reactome:R-HSA-5655235 "Activated FGFR4 mutant-associated PI3K phosphorylates PIP2 to PIP3"
-xref: Reactome:R-HSA-5655289 "Activated FGFR3 mutant-associated PI3K phosphorylates PIP2 to PIP3"
+xref: Reactome:R-HSA-5655289 "Activated FGFR3 point, translocation and fusion mutant-associated PI3K phosphorylates PIP2 to PIP3"
xref: Reactome:R-HSA-5655290 "Activated FGFR1 mutant-associated PI3K phosphorylates PIP2 to PIP3"
xref: Reactome:R-HSA-5655323 "Activated FGFR2 mutant-associated PI3K phosphorylates PIP2 to PIP3"
xref: Reactome:R-HSA-8852019 "MET bound PI3K generates PIP3"
-xref: Reactome:R-HSA-8853323 "Activated FGFR3 fusion-associated PI3K phosphorylates PIP2 to PIP3"
xref: Reactome:R-HSA-9021627 "EPOR-associated PI3K phosphorylates PIP2 to PIP3"
xref: Reactome:R-HSA-9603445 "Activated NTRK3 stimulates PI3K activity"
xref: Reactome:R-HSA-9664664 "PI3K bound to phosphorylated heterodimers of ERBB2 KD mutants and ERBB3 converts PIP2 to PIP3"
@@ -270156,6 +270163,7 @@ xref: Reactome:R-HSA-9664940 "PI3K bound to phosphorylated heterodimers of ERBB2
xref: Reactome:R-HSA-9665407 "PI3K bound to phosphorylated heterodimers of ERBB2 ECD mutants and EGFR converts PIP2 to PIP3"
xref: Reactome:R-HSA-9672162 "PI3K catalyses the phosphorylation of PIP2 to PIP3 downstream of PDGFRA extracellular domain dimers"
xref: Reactome:R-HSA-9672177 "PI3K catalyses the phosphorylation of PIP2 to PIP3 downstream of mutant PDGFR"
+xref: Reactome:R-HSA-9712084 "PI3K synthesizes PIP3 downstream of ALK mutants"
xref: RHEA:21292
is_a: GO:0035004 ! phosphatidylinositol 3-kinase activity
is_a: GO:0052813 ! phosphatidylinositol bisphosphate kinase activity
@@ -270176,8 +270184,10 @@ name: 2'-deoxyadenosine deaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2'-deoxyadenosine + H2O = deoxyinosine + NH3." [GOC:ai, RHEA:28190]
synonym: "deoxyadenosine deaminase reaction" EXACT []
+xref: EC:3.5.4.4
xref: MetaCyc:ADDALT-RXN
xref: RHEA:28190
+is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
is_a: GO:0019239 ! deaminase activity
[Term]
@@ -270207,10 +270217,11 @@ is_a: GO:0046937 ! phytochelatin metabolic process
[Term]
id: GO:0046939
-name: nucleotide phosphorylation
+name: obsolete nucleotide phosphorylation
namespace: biological_process
-def: "The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside." [GOC:ai]
-is_a: GO:0016310 ! phosphorylation
+def: "OBSOLETE. The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside." [GOC:ai]
+comment: The reason for obsoletion is that this term represents a single step MF.
+is_obsolete: true
[Term]
id: GO:0046940
@@ -270233,6 +270244,7 @@ name: carboxylic acid transport
namespace: biological_process
def: "The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC:ai]
is_a: GO:0015711 ! organic anion transport
+is_a: GO:0015849 ! organic acid transport
[Term]
id: GO:0046943
@@ -270241,6 +270253,7 @@ namespace: molecular_function
def: "Enables the transfer of carboxylic acids from one side of a membrane to the other. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC:ai]
xref: Reactome:R-HSA-390347 "Exchange of isocitrate and 2-oxoglutarate across the peroxisomal membrane"
is_a: GO:0005342 ! organic acid transmembrane transporter activity
+is_a: GO:0008514 ! organic anion transmembrane transporter activity
[Term]
id: GO:0046944
@@ -270248,7 +270261,7 @@ name: protein carbamoylation
namespace: biological_process
def: "The addition of a carbamoyl group to a protein amino acid. A carbamoyl group is the acyl group -CO-NH2." [GOC:ai]
synonym: "protein amino acid carbamoylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0046945
@@ -270291,7 +270304,6 @@ def: "The chemical reactions and pathways resulting in the breakdown of hydroxyl
synonym: "hydroxylysine breakdown" EXACT []
synonym: "hydroxylysine catabolism" EXACT []
synonym: "hydroxylysine degradation" EXACT []
-is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009068 ! aspartate family amino acid catabolic process
is_a: GO:0042219 ! cellular modified amino acid catabolic process
is_a: GO:0046946 ! hydroxylysine metabolic process
@@ -270415,7 +270427,7 @@ synonym: "F(o)F(1)-ATPase activity" NARROW [EC:7.1.2.2]
synonym: "F0F1-ATPase" NARROW [EC:7.1.2.2]
synonym: "F1-ATPase" NARROW []
synonym: "FoF1-ATPase" NARROW [EC:7.1.2.2]
-synonym: "H(+)-transporting ATP synthase activity" NARROW [EC:7.1.2.2]
+synonym: "H+-transporting ATP synthase activity" NARROW [EC:7.1.2.2]
synonym: "H+-transporting ATPase activity" NARROW [EC:7.1.2.2]
synonym: "hydrogen ion translocating A-type ATPase activity" NARROW []
synonym: "hydrogen ion translocating F-type ATPase activity" NARROW []
@@ -270425,7 +270437,7 @@ synonym: "hydrogen ion transporting two-sector ATPase activity" NARROW []
synonym: "mitochondrial ATPase activity" NARROW [EC:7.1.2.2]
xref: RHEA:57721
is_a: GO:0009678 ! pyrophosphate hydrolysis-driven proton transmembrane transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
is_a: GO:0044769 ! ATPase activity, coupled to transmembrane movement of ions, rotational mechanism
[Term]
@@ -270433,7 +270445,7 @@ id: GO:0046962
name: sodium-transporting ATPase activity, rotational mechanism
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na+(in) -> ADP + phosphate + Na+(out), by a rotational mechanism." [PMID:30791207, RHEA:58157]
-comment: Found in some halophilic or alkalophilic bacteria that functions in maintaining sodium homeostasis; similar to EC:7.1.2.2 but pumps Na(+) rather than H(+). (Source: EC:7.2.2.1)
+comment: Found in some halophilic or alkalophilic bacteria that functions in maintaining sodium homeostasis; similar to EC:7.1.2.2 but pumps Na+ rather than H+. (Source: EC:7.2.2.1)
synonym: "ATP phosphohydrolase (Na+-transporting) activity" RELATED []
synonym: "ATP synthase, sodium ion specific activity" RELATED [EC:7.2.2.1]
synonym: "Na(+)-translocating ATPase activity" BROAD []
@@ -270452,7 +270464,7 @@ xref: MetaCyc:3.6.3.15-RXN
xref: RHEA:58156
xref: RHEA:58157
is_a: GO:0015081 ! sodium ion transmembrane transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
is_a: GO:0044769 ! ATPase activity, coupled to transmembrane movement of ions, rotational mechanism
[Term]
@@ -270484,18 +270496,20 @@ is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
[Term]
id: GO:0046965
-name: retinoid X receptor binding
+name: nuclear retinoid X receptor binding
namespace: molecular_function
-def: "Binding to a retinoid X receptor." [GOC:ai]
+def: "Binding to a nuclear retinoid X receptor." [GOC:ai]
+synonym: "retinoid X receptor binding" BROAD []
synonym: "RXR binding" EXACT []
-is_a: GO:0042974 ! retinoic acid receptor binding
+is_a: GO:0042974 ! nuclear retinoic acid receptor binding
[Term]
id: GO:0046966
-name: thyroid hormone receptor binding
+name: nuclear thyroid hormone receptor binding
namespace: molecular_function
-def: "Binding to a thyroid hormone receptor." [GOC:ai]
+def: "Binding to a nuclear thyroid hormone receptor." [GOC:ai]
synonym: "ligand-dependent thyroid hormone receptor interactor activity" NARROW []
+synonym: "thyroid hormone receptor binding" BROAD []
is_a: GO:0016922 ! nuclear receptor binding
[Term]
@@ -270517,28 +270531,34 @@ relationship: part_of GO:0048002 ! antigen processing and presentation of peptid
[Term]
id: GO:0046969
-name: NAD-dependent histone deacetylase activity (H3-K9 specific)
+name: NAD-dependent histone H3K9 deacetylase activity
namespace: molecular_function
def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 9) + H2O = histone H3 L-lysine (position 9) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 9 of the histone H3 protein." [PMID:28450737]
+synonym: "NAD-dependent H3-K9 histone deacetylase activity" EXACT []
+synonym: "NAD-dependent histone deacetylase activity (H3-K9 specific)" EXACT []
xref: Reactome:R-HSA-9604829 "SIRT6 deacetylates histones at NOTCH1 and NOTCH4 gene promoters"
is_a: GO:0017136 ! NAD-dependent histone deacetylase activity
-is_a: GO:0032129 ! histone deacetylase activity (H3-K9 specific)
+is_a: GO:0032129 ! histone H3K9 deacetylase activity
[Term]
id: GO:0046970
-name: NAD-dependent histone deacetylase activity (H4-K16 specific)
+name: NAD-dependent histone H4K16 deacetylase activity
namespace: molecular_function
def: "Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein." [GOC:vw, PMID:28450737]
-is_a: GO:0034739 ! histone deacetylase activity (H4-K16 specific)
-is_a: GO:0046969 ! NAD-dependent histone deacetylase activity (H3-K9 specific)
+synonym: "NAD-dependent histone deacetylase activity (H4-K16 specific)" EXACT []
+synonym: "NAD-dependent histone H4-K16 deacetylase activity" EXACT []
+is_a: GO:0017136 ! NAD-dependent histone deacetylase activity
+is_a: GO:0034739 ! histone H4K16 deacetylase activity
[Term]
id: GO:0046972
-name: histone acetyltransferase activity (H4-K16 specific)
+name: histone H4K16 acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 16) = CoA + histone H4 N6-acetyl-L-lysine (position 16). This reaction represents the addition of an acetyl group to the lysine at position 16 of histone H4." [EC:2.3.1.48]
+synonym: "histone acetylase activity (H4-K16 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H4-K16 specific)" EXACT []
synonym: "histone lysine acetyltransferase activity (H4-K16 specific)" EXACT []
-is_a: GO:0010485 ! H4 histone acetyltransferase activity
+is_a: GO:0010485 ! histone H4 acetyltransferase activity
[Term]
id: GO:0046973
@@ -270552,33 +270572,47 @@ consider: GO:0042800
[Term]
id: GO:0046974
-name: histone methyltransferase activity (H3-K9 specific)
+name: histone H3K9 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 9) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 9). This reaction is the addition of a methyl group onto lysine at position 9 of the histone H3 protein." [GOC:ai]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 9) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 9). This reaction is the addition of up to three methyl groups to the lysine residue at position 9 of the histone H3 protein." [GOC:ai]
+synonym: "histone H3K9 methylase activity" EXACT []
synonym: "histone lysine N-methyltransferase activity (H3-K9 specific)" EXACT []
synonym: "histone methylase activity (H3-K9 specific)" EXACT [GOC:mah]
+synonym: "histone methyltransferase activity (H3-K9 specific)" EXACT []
+synonym: "histone-H3K9 methyltransferase activity" EXACT []
xref: Reactome:R-HSA-427336 "TTF1:rRNA promoter:ERCC6:EHMT2 complex dimethylates histone H3 at lysine-9."
xref: Reactome:R-HSA-427527 "eNoSC dimethylates histone H3 at lysine-9"
-is_a: GO:0018024 ! histone-lysine N-methyltransferase activity
+is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
+is_a: GO:0140938 ! histone H3 methyltransferase activity
[Term]
id: GO:0046975
-name: histone methyltransferase activity (H3-K36 specific)
+name: histone H3K36 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 36) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 36). This reaction is the addition of a methyl group onto lysine at position 36 of the histone H3 protein." [GOC:ai]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 36) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 36). This reaction is the addition of a methyl group to the lysine residue at position 36 of the histone H3 protein." [GOC:ai]
+synonym: "histone H3K36 methylase activity" EXACT []
synonym: "histone lysine N-methyltransferase activity (H3-K36 specific)" EXACT []
synonym: "histone methylase activity (H3-K36 specific)" EXACT [GOC:mah]
-is_a: GO:0018024 ! histone-lysine N-methyltransferase activity
+synonym: "histone methyltransferase activity (H3-K36 specific)" EXACT []
+synonym: "histone-H3K36 methyltransferase activity" EXACT []
+is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
+is_a: GO:0140938 ! histone H3 methyltransferase activity
[Term]
id: GO:0046976
-name: histone methyltransferase activity (H3-K27 specific)
+name: histone H3K27 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 27) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 27). This reaction is the addition of a methyl group onto lysine at position 27 of the histone H3 protein." [GOC:ai]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 27) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 27). This reaction is the addition of a methyl group to the lysine residue at position 27 of the histone H3 protein." [GOC:ai]
+synonym: "histone H3K27 methylase activity" EXACT []
synonym: "histone lysine N-methyltransferase activity (H3-K27 specific)" EXACT []
synonym: "histone methylase activity (H3-K27 specific)" EXACT [GOC:mah]
+synonym: "histone methylase activity (H3-K56 specific)" EXACT []
+synonym: "histone methyltransferase activity (H3-K27 specific)" EXACT []
+synonym: "histone-H3K27 methyltransferase activity" EXACT []
+xref: EC:2.1.1.356
xref: Reactome:R-HSA-3240295 "PRC2-EZH2 trimethylates nucleosomes associated with CDKN2A promoter"
-is_a: GO:0018024 ! histone-lysine N-methyltransferase activity
+is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
+is_a: GO:0140938 ! histone H3 methyltransferase activity
[Term]
id: GO:0046977
@@ -270644,8 +270678,8 @@ synonym: "regulation of hemoglobin anabolism" EXACT []
synonym: "regulation of hemoglobin biosynthesis" EXACT []
synonym: "regulation of hemoglobin formation" EXACT []
synonym: "regulation of hemoglobin synthesis" EXACT []
+is_a: GO:0010556 ! regulation of macromolecule biosynthetic process
is_a: GO:0051246 ! regulation of protein metabolic process
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
relationship: regulates GO:0042541 ! hemoglobin biosynthetic process
[Term]
@@ -270665,7 +270699,6 @@ synonym: "up regulation of hemoglobin biosynthetic process" EXACT []
synonym: "up-regulation of hemoglobin biosynthetic process" EXACT []
synonym: "upregulation of hemoglobin biosynthetic process" EXACT []
is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:0046984 ! regulation of hemoglobin biosynthetic process
is_a: GO:0051247 ! positive regulation of protein metabolic process
relationship: positively_regulates GO:0042541 ! hemoglobin biosynthetic process
@@ -270685,9 +270718,9 @@ synonym: "negative regulation of hemoglobin anabolism" EXACT []
synonym: "negative regulation of hemoglobin biosynthesis" EXACT []
synonym: "negative regulation of hemoglobin formation" EXACT []
synonym: "negative regulation of hemoglobin synthesis" EXACT []
+is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process
is_a: GO:0046984 ! regulation of hemoglobin biosynthetic process
is_a: GO:0051248 ! negative regulation of protein metabolic process
-is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process
relationship: negatively_regulates GO:0042541 ! hemoglobin biosynthetic process
[Term]
@@ -270780,7 +270813,7 @@ is_a: GO:0016645 ! oxidoreductase activity, acting on the CH-NH group of donors
id: GO:0046998
name: (S)-usnate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (6R)-2-acetyl-6-(3-acetyl-2,4,6-trihydroxy-5-methylphenyl)-3-hydroxy-6-methylcyclohexa-2,4-dien-1-one + NAD(+) = (S)-usnate + 2 H(+) + NADH." [EC:1.1.1.199, RHEA:21876]
+def: "Catalysis of the reaction: (6R)-2-acetyl-6-(3-acetyl-2,4,6-trihydroxy-5-methylphenyl)-3-hydroxy-6-methylcyclohexa-2,4-dien-1-one + NAD+ = (S)-usnate + 2 H+ + NADH." [EC:1.1.1.199, RHEA:21876]
synonym: "L-usnic acid dehydrogenase activity" RELATED [EC:1.1.1.199]
synonym: "reduced-(S)-usnate:NAD+ oxidoreductase (ether-bond-forming)" RELATED [EC:1.1.1.199]
xref: EC:1.1.1.199
@@ -270791,17 +270824,17 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
[Term]
id: GO:0046999
-name: regulation of conjugation
+name: obsolete regulation of conjugation
namespace: biological_process
-def: "Any process that modulates the rate or frequency of conjugation, the union or introduction of genetic information from compatible mating types that results in a genetically different individual." [GOC:ai]
-is_a: GO:0050794 ! regulation of cellular process
-relationship: regulates GO:0000746 ! conjugation
+def: "OBSOLETE. Any process that modulates the rate or frequency of conjugation, the union or introduction of genetic information from compatible mating types that results in a genetically different individual." [GOC:ai]
+comment: This term was obsoleted because its target (conjugation) was not clearly defined.
+is_obsolete: true
[Term]
id: GO:0047000
name: 2-dehydro-3-deoxy-D-gluconate 6-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate + NADP(+) = (4S,5S)-4,5-dihydroxy-2,6-dioxohexanoate + H(+) + NADPH." [EC:1.1.1.126, RHEA:15109]
+def: "Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate + NADP+ = (4S,5S)-4,5-dihydroxy-2,6-dioxohexanoate + H+ + NADPH." [EC:1.1.1.126, RHEA:15109]
synonym: "2-dehydro-3-deoxy-D-gluconate:NADP+ 6-oxidoreductase activity" RELATED [EC:1.1.1.126]
synonym: "2-keto-3-deoxy-D-gluconate dehydrogenase activity" RELATED [EC:1.1.1.126]
xref: EC:1.1.1.126
@@ -270829,7 +270862,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047002
name: L-arabinitol 2-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arabinitol + NAD(+) = L-ribulose + H(+) + NADH." [EC:1.1.1.13, RHEA:21356]
+def: "Catalysis of the reaction: L-arabinitol + NAD+ = L-ribulose + H+ + NADH." [EC:1.1.1.13, RHEA:21356]
synonym: "L-arabinitol 2-dehydrogenase (ribulose forming) activity" EXACT []
xref: EC:1.1.1.13
xref: KEGG_REACTION:R02441
@@ -270841,7 +270874,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047003
name: dTDP-6-deoxy-L-talose 4-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dTDP-6-deoxy-L-talose + NADP(+) = dTDP-4-dehydro-6-deoxy-L-mannose + H(+) + NADPH." [EC:1.1.1.134, RHEA:23648]
+def: "Catalysis of the reaction: dTDP-6-deoxy-L-talose + NADP+ = dTDP-4-dehydro-6-deoxy-L-mannose + H+ + NADPH." [EC:1.1.1.134, RHEA:23648]
synonym: "dTDP-6-deoxy-L-talose dehydrogenase (4-reductase)" RELATED [EC:1.1.1.134]
synonym: "dTDP-6-deoxy-L-talose:NADP+ 4-oxidoreductase activity" RELATED [EC:1.1.1.134]
synonym: "TDP-6-deoxy-L-talose dehydrogenase activity" RELATED [EC:1.1.1.134]
@@ -270856,7 +270889,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047004
name: UDP-N-acetylglucosamine 6-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + 2 NAD(+) + UDP-N-acetyl-alpha-D-glucosamine = 3 H(+) + 2 NADH + UDP-N-acetyl-2-amino-2-deoxy-D-glucuronate." [EC:1.1.1.136, RHEA:13325]
+def: "Catalysis of the reaction: H2O + 2 NAD+ + UDP-N-acetyl-alpha-D-glucosamine = 3 H+ + 2 NADH + UDP-N-acetyl-2-amino-2-deoxy-D-glucuronate." [EC:1.1.1.136, RHEA:13325]
synonym: "UDP-2-acetamido-2-deoxy-D-glucose:NAD oxidoreductase activity" RELATED [EC:1.1.1.136]
synonym: "UDP-GLcNAc dehydrogenase activity" RELATED [EC:1.1.1.136]
synonym: "UDP-N-acetyl-D-glucosamine:NAD+ 6-oxidoreductase activity" RELATED [EC:1.1.1.136]
@@ -270898,7 +270931,7 @@ is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of
id: GO:0047007
name: pregnan-21-ol dehydrogenase (NAD+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD(+) + pregnan-21-ol = H(+) + NADH + pregnan-21-al." [EC:1.1.1.150, RHEA:11448]
+def: "Catalysis of the reaction: NAD+ + pregnan-21-ol = H+ + NADH + pregnan-21-al." [EC:1.1.1.150, RHEA:11448]
synonym: "21-hydroxysteroid dehydrogenase (NAD+) activity" BROAD [EC:1.1.1.50]
synonym: "21-hydroxysteroid:NAD+ 21-oxidoreductase activity" BROAD [EC:1.1.1.150]
xref: EC:1.1.1.150
@@ -270911,7 +270944,7 @@ is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of
id: GO:0047008
name: pregnan-21-ol dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + pregnan-21-ol = H(+) + NADPH + pregnan-21-al." [EC:1.1.1.151, RHEA:23712]
+def: "Catalysis of the reaction: NADP+ + pregnan-21-ol = H+ + NADPH + pregnan-21-al." [EC:1.1.1.151, RHEA:23712]
synonym: "21-hydroxy steroid (nicotinamide adenine dinucleotide phosphate) dehydrogenase activity" BROAD [EC:1.1.1.151]
synonym: "21-hydroxy steroid dehydrogenase (nicotinamide adenine dinucleotide phosphate) activity" BROAD [EC:1.1.1.151]
synonym: "21-hydroxy steroid dehydrogenase activity" BROAD [EC:1.1.1.151]
@@ -270943,7 +270976,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047010
name: hydroxycyclohexanecarboxylate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (1S,3R,4S)-3,4-dihydroxycyclohexane-1-carboxylate + NAD(+) = (1S,4S)-4-hydroxy-3-oxocyclohexane-1-carboxylate + H(+) + NADH." [EC:1.1.1.166, RHEA:10516]
+def: "Catalysis of the reaction: (1S,3R,4S)-3,4-dihydroxycyclohexane-1-carboxylate + NAD+ = (1S,4S)-4-hydroxy-3-oxocyclohexane-1-carboxylate + H+ + NADH." [EC:1.1.1.166, RHEA:10516]
synonym: "(-)t-3,t-4-dihydroxycyclohexane-c-1-carboxylate-NAD oxidoreductase activity" RELATED [EC:1.1.1.166]
synonym: "(1S,3R,4S)-3,4-dihydroxycyclohexane-1-carboxylate:NAD+ 3-oxidoreductase activity" RELATED [EC:1.1.1.166]
synonym: "dihydroxycyclohexanecarboxylate dehydrogenase activity" RELATED [EC:1.1.1.166]
@@ -270985,7 +271018,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047013
name: cholate 12-alpha dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cholate + NADP(+) = 3alpha,7alpha-dihydroxy-12-oxo-5beta-cholanate + H(+) + NADPH." [EC:1.1.1.176, RHEA:14129]
+def: "Catalysis of the reaction: cholate + NADP+ = 3alpha,7alpha-dihydroxy-12-oxo-5beta-cholanate + H+ + NADPH." [EC:1.1.1.176, RHEA:14129]
synonym: "12-alpha-hydroxysteroid dehydrogenase activity" BROAD [EC:1.1.1.176]
synonym: "12alpha-hydroxy steroid dehydrogenase activity" BROAD [EC:1.1.1.176]
synonym: "12alpha-hydroxysteroid dehydrogenase activity" BROAD [EC:1.1.1.176]
@@ -271002,7 +271035,7 @@ is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of
id: GO:0047014
name: glycerol-3-phosphate 1-dehydrogenase [NADP+] activity
namespace: molecular_function
-def: "Catalysis of the reaction: sn-glycerol 3-phosphate + NADP(+) = D-glyceraldehyde 3-phosphate + H(+) + NADPH." [EC:1.1.1.177, RHEA:19773]
+def: "Catalysis of the reaction: sn-glycerol 3-phosphate + NADP+ = D-glyceraldehyde 3-phosphate + H+ + NADPH." [EC:1.1.1.177, RHEA:19773]
synonym: "glycerin-3-phosphate dehydrogenase activity" RELATED [EC:1.1.1.177]
synonym: "glycerol phosphate (nicotinamide adenine dinucleotide phosphate) dehydrogenase activity" RELATED [EC:1.1.1.177]
synonym: "L-glycerol 3-phosphate:NADP oxidoreductase activity" RELATED [EC:1.1.1.177]
@@ -271076,7 +271109,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047018
name: indole-3-acetaldehyde reductase (NADH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: indole-3-ethanol + NAD(+) = (indol-3-yl)acetaldehyde + H(+) + NADH." [EC:1.1.1.190, RHEA:14873]
+def: "Catalysis of the reaction: indole-3-ethanol + NAD+ = (indol-3-yl)acetaldehyde + H+ + NADH." [EC:1.1.1.190, RHEA:14873]
synonym: "(indol-3-yl)ethanol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.190]
synonym: "indole-3-ethanol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.190]
synonym: "indoleacetaldehyde reductase activity" RELATED [EC:1.1.1.190]
@@ -271090,7 +271123,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047019
name: indole-3-acetaldehyde reductase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: indole-3-ethanol + NADP(+) = (indol-3-yl)acetaldehyde + H(+) + NADPH." [EC:1.1.1.191, RHEA:17037]
+def: "Catalysis of the reaction: indole-3-ethanol + NADP+ = (indol-3-yl)acetaldehyde + H+ + NADPH." [EC:1.1.1.191, RHEA:17037]
synonym: "(indol-3-yl)ethanol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.191]
synonym: "indole-3-ethanol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.191]
synonym: "indoleacetaldehyde (reduced nicotinamide adenine dinucleotide phosphate) reductase activity" RELATED [EC:1.1.1.191]
@@ -271128,7 +271161,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047021
name: 15-hydroxyprostaglandin dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + prostaglandin E(1) = 15-dehydro-prostaglandin E1 + H(+) + NADPH." [EC:1.1.1.197, RHEA:11636]
+def: "Catalysis of the reaction: NADP+ + prostaglandin E(1) = 15-dehydro-prostaglandin E1 + H+ + NADPH." [EC:1.1.1.197, RHEA:11636]
synonym: "(13E)-(15S)-11alpha,15-dihydroxy-9-oxoprost-13-enoate:NADP+ 15-oxidoreductase activity" RELATED [EC:1.1.1.197]
synonym: "NADP-dependent 15-hydroxyprostaglandin dehydrogenase" BROAD [EC:1.1.1.197]
synonym: "NADP-linked 15-hydroxyprostaglandin dehydrogenase" BROAD [EC:1.1.1.197]
@@ -271172,7 +271205,7 @@ is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of
id: GO:0047024
name: 5alpha-androstane-3beta,17beta-diol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5alpha-androstane-3beta,17beta-diol + NADP(+) = 17beta-hydroxy-5alpha-androstan-3-one + H(+) + NADPH." [EC:1.1.1.210, RHEA:16297]
+def: "Catalysis of the reaction: 5alpha-androstane-3beta,17beta-diol + NADP+ = 17beta-hydroxy-5alpha-androstan-3-one + H+ + NADPH." [EC:1.1.1.210, RHEA:16297]
synonym: "3-beta(or 20-alpha)-hydroxysteroid dehydrogenase activity" BROAD [EC:1.1.1.210]
synonym: "3-beta-HSD activity" RELATED [EC:1.1.1.210]
synonym: "3beta(or 20alpha)-hydroxysteroid dehydrogenase activity" BROAD [EC:1.1.1.210]
@@ -271218,7 +271251,7 @@ is_a: GO:0047023 ! androsterone dehydrogenase activity
id: GO:0047027
name: benzyl-2-methyl-hydroxybutyrate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: benzyl (2R,3S)-2-methyl-3-hydroxybutanoate + NADP(+) = benzyl 2-methyl-3-oxobutanoate + H(+) + NADPH." [EC:1.1.1.217, RHEA:16405]
+def: "Catalysis of the reaction: benzyl (2R,3S)-2-methyl-3-hydroxybutanoate + NADP+ = benzyl 2-methyl-3-oxobutanoate + H+ + NADPH." [EC:1.1.1.217, RHEA:16405]
synonym: "benzyl 2-methyl-3-hydroxybutyrate dehydrogenase activity" RELATED [EC:1.1.1.217]
synonym: "benzyl-(2R,3S)-2-methyl-3-hydroxybutanoate:NADP+ 3-oxidoreductase activity" RELATED [EC:1.1.1.217]
xref: EC:1.1.1.217
@@ -271260,7 +271293,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047030
name: 4-hydroxycyclohexanecarboxylate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: trans-4-hydroxycyclohexanecarboxylate + NAD(+) = 4-oxocyclohexanecarboxylate + H(+) + NADH." [EC:1.1.1.226, RHEA:17429]
+def: "Catalysis of the reaction: trans-4-hydroxycyclohexanecarboxylate + NAD+ = 4-oxocyclohexanecarboxylate + H+ + NADH." [EC:1.1.1.226, RHEA:17429]
synonym: "trans-4-hydroxycyclohexanecarboxylate dehydrogenase activity" RELATED [EC:1.1.1.226]
synonym: "trans-4-hydroxycyclohexanecarboxylate:NAD+ 4-oxidoreductase activity" RELATED [EC:1.1.1.226]
xref: EC:1.1.1.226
@@ -271273,7 +271306,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047031
name: diethyl 2-methyl-3-oxosuccinate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: diethyl (2R,3R)-2-methyl-3-hydroxysuccinate + NADP(+) = diethyl 2-methyl-3-oxosuccinate + H(+) + NADPH." [EC:1.1.1.229, RHEA:21008]
+def: "Catalysis of the reaction: diethyl (2R,3R)-2-methyl-3-hydroxysuccinate + NADP+ = diethyl 2-methyl-3-oxosuccinate + H+ + NADPH." [EC:1.1.1.229, RHEA:21008]
synonym: "diethyl-(2R,3R)-2-methyl-3-hydroxysuccinate:NADP+ 3-oxidoreductase activity" RELATED [EC:1.1.1.229]
xref: EC:1.1.1.229
xref: KEGG_REACTION:R04387
@@ -271285,7 +271318,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047032
name: 3-alpha-hydroxyglycyrrhetinate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3alpha-hydroxyglycyrrhetinate + NADP(+) = 3-oxoglycyrrhetinate + H(+) + NADPH." [EC:1.1.1.230, RHEA:20816]
+def: "Catalysis of the reaction: 3alpha-hydroxyglycyrrhetinate + NADP+ = 3-oxoglycyrrhetinate + H+ + NADPH." [EC:1.1.1.230, RHEA:20816]
synonym: "3alpha-hydroxyglycyrrhetinate dehydrogenase activity" RELATED [EC:1.1.1.230]
synonym: "3alpha-hydroxyglycyrrhetinate:NADP+ 3-oxidoreductase activity" RELATED [EC:1.1.1.230]
xref: EC:1.1.1.230
@@ -271298,7 +271331,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047033
name: 15-hydroxyprostaglandin-I dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + prostaglandin I(2) = 15-dehydro-prostaglandin I(2) + H(+) + NADPH." [EC:1.1.1.231, RHEA:21420]
+def: "Catalysis of the reaction: NADP+ + prostaglandin I(2) = 15-dehydro-prostaglandin I(2) + H+ + NADPH." [EC:1.1.1.231, RHEA:21420]
synonym: "(5Z,13E)-(15S)-6,9alpha-epoxy-11alpha,15-dihydroxyprosta-5,13-dienoate:NADP+ 15-oxidoreductase activity" RELATED [EC:1.1.1.231]
synonym: "NADP+-dependent PGI2-specific 15-hydroxyprostaglandin dehydrogenase activity" RELATED [EC:1.1.1.231]
synonym: "NADP-linked 15-hydroxyprostaglandin (prostacyclin) dehydrogenase activity" RELATED [EC:1.1.1.231]
@@ -271352,7 +271385,7 @@ is_a: GO:0030283 ! testosterone dehydrogenase [NAD(P)] activity
id: GO:0047036
name: codeinone reductase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: codeine + NADP(+) = codeinone + H(+) + NADPH." [EC:1.1.1.247, RHEA:19209]
+def: "Catalysis of the reaction: codeine + NADP+ = codeinone + H+ + NADPH." [EC:1.1.1.247, RHEA:19209]
synonym: "codeine:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.247]
xref: EC:1.1.1.247
xref: KEGG_REACTION:R05124
@@ -271364,7 +271397,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047037
name: salutaridine reductase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (7S)-salutaridinol + NADP(+) = H(+) + NADPH + salutaridine." [EC:1.1.1.248, RHEA:10108]
+def: "Catalysis of the reaction: (7S)-salutaridinol + NADP+ = H+ + NADPH + salutaridine." [EC:1.1.1.248, RHEA:10108]
synonym: "salutaridinol:NADP+ 7-oxidoreductase activity" RELATED [EC:1.1.1.248]
xref: EC:1.1.1.248
xref: KEGG_REACTION:R04697
@@ -271376,7 +271409,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047038
name: D-arabinitol 2-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-arabinitol + NAD(+) = D-ribulose + H(+) + NADH." [EC:1.1.1.250, RHEA:17389]
+def: "Catalysis of the reaction: D-arabinitol + NAD+ = D-ribulose + H+ + NADH." [EC:1.1.1.250, RHEA:17389]
synonym: "D-arabinitol 2-dehydrogenase (ribulose-forming) activity" RELATED [EC:1.1.1.250]
synonym: "D-arabinitol:NAD+ 2-oxidoreductase (D-ribulose-forming)" RELATED [EC:1.1.1.250]
xref: EC:1.1.1.250
@@ -271401,7 +271434,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047040
name: pteridine reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5,6,7,8-tetrahydrobiopterin + 2 NADP(+) = biopterin + 2 H(+) + 2 NADPH." [EC:1.5.1.33, RHEA:19509]
+def: "Catalysis of the reaction: 5,6,7,8-tetrahydrobiopterin + 2 NADP+ = biopterin + 2 H+ + 2 NADPH." [EC:1.5.1.33, RHEA:19509]
comment: Note that this function was formerly EC:1.1.1.253.
synonym: "5,6,7,8-tetrahydrobiopterin:NADP+ oxidoreductase activity" RELATED [EC:1.5.1.33]
synonym: "dihydrobiopterin reduction" RELATED []
@@ -271418,7 +271451,7 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0047041
name: (S)-carnitine 3-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-carnitine + NAD(+) = 3-dehydrocarnitine + H(+) + NADH." [EC:1.1.1.254, RHEA:11556]
+def: "Catalysis of the reaction: (S)-carnitine + NAD+ = 3-dehydrocarnitine + H+ + NADH." [EC:1.1.1.254, RHEA:11556]
synonym: "(S)-carnitine:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.254]
synonym: "D-carnitine dehydrogenase activity" RELATED [EC:1.1.1.254]
xref: EC:1.1.1.254
@@ -271449,7 +271482,7 @@ is_a: GO:0047023 ! androsterone dehydrogenase activity
id: GO:0047043
name: 3-alpha-hydroxycholanate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: lithocholate + NAD(+) = 3-oxo-5beta-cholanate + H(+) + NADH." [EC:1.1.1.52, RHEA:19585]
+def: "Catalysis of the reaction: lithocholate + NAD+ = 3-oxo-5beta-cholanate + H+ + NADH." [EC:1.1.1.52, RHEA:19585]
synonym: "3alpha-hydroxy-5beta-cholanate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.52]
synonym: "3alpha-hydroxycholanate dehydrogenase activity" RELATED [EC:1.1.1.52]
synonym: "alpha-hydroxy-cholanate dehydrogenase activity" RELATED [EC:1.1.1.52]
@@ -271530,7 +271563,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047048
name: 3-hydroxybenzyl-alcohol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxybenzyl alcohol + NADP(+) = 3-hydroxybenzaldehyde + H(+) + NADPH." [EC:1.1.1.97, RHEA:22340]
+def: "Catalysis of the reaction: 3-hydroxybenzyl alcohol + NADP+ = 3-hydroxybenzaldehyde + H+ + NADPH." [EC:1.1.1.97, RHEA:22340]
synonym: "3-hydroxybenzyl-alcohol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.97]
synonym: "m-hydroxybenzyl alcohol (NADP) dehydrogenase activity" RELATED [EC:1.1.1.97]
synonym: "m-hydroxybenzyl alcohol dehydrogenase activity" RELATED [EC:1.1.1.97]
@@ -271545,7 +271578,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047049
name: (R)-2-hydroxy-fatty acid dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-2-hydroxystearate + NAD(+) = 2-oxostearate + H(+) + NADH." [EC:1.1.1.98, RHEA:15949]
+def: "Catalysis of the reaction: (R)-2-hydroxystearate + NAD+ = 2-oxostearate + H+ + NADH." [EC:1.1.1.98, RHEA:15949]
synonym: "(R)-2-hydroxy-fatty-acid dehydrogenase activity" EXACT []
synonym: "(R)-2-hydroxystearate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.98]
synonym: "2-hydroxy fatty acid oxidase" BROAD [EC:1.1.1.98]
@@ -271560,7 +271593,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047050
name: (S)-2-hydroxy-fatty acid dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-2-hydroxystearate + NAD(+) = 2-oxostearate + H(+) + NADH." [EC:1.1.1.99, RHEA:11384]
+def: "Catalysis of the reaction: (S)-2-hydroxystearate + NAD+ = 2-oxostearate + H+ + NADH." [EC:1.1.1.99, RHEA:11384]
synonym: "(S)-2-hydroxy-fatty-acid dehydrogenase activity" EXACT []
synonym: "(S)-2-hydroxystearate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.99]
synonym: "2-hydroxy fatty acid oxidase" BROAD [EC:1.1.1.99]
@@ -271613,7 +271646,7 @@ is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidat
id: GO:0047054
name: berbamunine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-N-methylcoclaurine + (R)-N-methylcoclaurine + [reduced NADPH--hemoprotein reductase] + O2 <=> berbamunine + [oxidized NADPH--hemoprotein reductase] + 2 H2O." [RHEA:23576]
+def: "Catalysis of the reaction: (S)-N-methylcoclaurine + (R)-N-methylcoclaurine + [reduced NADPH--hemoprotein reductase] + O2 = berbamunine + [oxidized NADPH--hemoprotein reductase] + 2 H2O." [RHEA:23576]
synonym: "heme-thiolate" RELATED [EC:1.14.19.66]
xref: EC:1.14.19.66
xref: MetaCyc:1.1.3.34-RXN
@@ -271658,7 +271691,7 @@ xref: MetaCyc:1.1.4.1-RXN
xref: Reactome:R-HSA-159790 "VKORC1 reduces vitamin K epoxide to MK4 (vitamin K hydroquinone)"
xref: Reactome:R-HSA-6806647 "VKORC1L1 reduces vitamin K epoxide to MK4 (vitamin K hydroquinone)"
xref: RHEA:57744
-is_a: GO:0016900 ! oxidoreductase activity, acting on the CH-OH group of donors, disulfide as acceptor
+is_a: GO:0016728 ! oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor
[Term]
id: GO:0047058
@@ -271670,7 +271703,7 @@ synonym: "vitamin K 2,3-epoxide reductase activity" RELATED [EC:1.17.4.5]
xref: EC:1.17.4.5
xref: MetaCyc:1.1.4.2-RXN
xref: RHEA:21560
-is_a: GO:0016900 ! oxidoreductase activity, acting on the CH-OH group of donors, disulfide as acceptor
+is_a: GO:0016728 ! oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor
[Term]
id: GO:0047059
@@ -271719,7 +271752,7 @@ is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
id: GO:0047062
name: trans-acenaphthene-1,2-diol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (+-)-trans-acenaphthene-1,2-diol + 2 NADP(+) = acenaphthene-1,2-dione + 2 H(+) + 2 NADPH." [EC:1.10.1.1, RHEA:22184]
+def: "Catalysis of the reaction: (+-)-trans-acenaphthene-1,2-diol + 2 NADP+ = acenaphthene-1,2-dione + 2 H+ + 2 NADPH." [EC:1.10.1.1, RHEA:22184]
synonym: "(+-)-trans-acenaphthene-1,2-diol:NADP+ oxidoreductase activity" RELATED [EC:1.10.1.1]
synonym: "trans-1,2-acenaphthenediol dehydrogenase activity" RELATED [EC:1.10.1.1]
xref: EC:1.10.1.1
@@ -271743,7 +271776,7 @@ is_obsolete: true
id: GO:0047064
name: sulochrin oxidase [(+)-bisdechlorogeodin-forming] activity
namespace: molecular_function
-def: "Catalysis of the reaction: O(2) + 2 sulochrin = 2 (2S)-bisdechlorogeodin + 2 H(2)O." [EC:1.21.3.4, RHEA:24092]
+def: "Catalysis of the reaction: O2 + 2 sulochrin = 2 (2S)-bisdechlorogeodin + 2 H2O." [EC:1.21.3.4, RHEA:24092]
synonym: "sulochrin oxidase activity" RELATED [EC:1.21.3.4]
synonym: "sulochrin:oxygen oxidoreductase (cyclizing, (+)-specific)" RELATED [EC:1.21.3.4]
xref: EC:1.21.3.4
@@ -271756,7 +271789,7 @@ is_a: GO:0046993 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y
id: GO:0047065
name: sulochrin oxidase [(-)-bisdechlorogeodin-forming] activity
namespace: molecular_function
-def: "Catalysis of the reaction: O(2) + 2 sulochrin = 2 (2R)-bisdechlorogeodin + 2 H(2)O." [EC:1.21.3.5, RHEA:22616]
+def: "Catalysis of the reaction: O2 + 2 sulochrin = 2 (2R)-bisdechlorogeodin + 2 H2O." [EC:1.21.3.5, RHEA:22616]
synonym: "sulochrin oxidase activity" BROAD [EC:1.21.3.5]
synonym: "sulochrin:oxygen oxidoreductase (cyclizing, (-)-specific)" RELATED [EC:1.21.3.5]
xref: EC:1.21.3.5
@@ -271769,13 +271802,10 @@ is_a: GO:0046993 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y
id: GO:0047066
name: phospholipid-hydroperoxide glutathione peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a lipid hydroperoxide + 2 reduced glutathione = 2 H2O + lipid + 2 oxidized glutathione." [EC:1.11.1.12, MetaCyc:1.11.1.12-RXN]
-synonym: "glutathione:lipid-hydroperoxide oxidoreductase activity" RELATED [EC:1.11.1.12]
-synonym: "hydroperoxide glutathione peroxidase activity" RELATED [EC:1.11.1.12]
+def: "Catalysis of the reaction: a hydroperoxy polyunsaturated fatty acid + 2 glutathione = a hydroxy polyunsaturated fatty acid + glutathione disulfide + H2O." [PMID:3978121, PMID:8617728, RHEA:19057]
+synonym: "hydroperoxide glutathione peroxidase activity" RELATED []
synonym: "peroxidation-inhibiting protein activity" RELATED [EC:1.11.1.12]
-synonym: "peroxidation-inhibiting protein: peroxidase, glutathione (phospholipid hydroperoxide-reducing)" RELATED [EC:1.11.1.12]
-synonym: "PHGPX" RELATED [EC:1.11.1.12]
-synonym: "phospholipid hydroperoxide glutathione peroxidase activity" RELATED [EC:1.11.1.12]
+synonym: "phospholipid hydroperoxide glutathione peroxidase activity" RELATED []
xref: EC:1.11.1.12
xref: MetaCyc:1.11.1.12-RXN
xref: Reactome:R-HSA-9018868 "GPX4-2 reduces 18(S)-HpEPE to 18(S)-HEPE"
@@ -271783,7 +271813,7 @@ xref: Reactome:R-HSA-9018895 "GPX4-2 reduces 18(R)-HpEPE to 18(R)-HEPE"
xref: Reactome:R-HSA-9020271 "GPX4-2 reduces 17(R)-Hp-DHA to 17(R)-HDHA"
xref: Reactome:R-HSA-9020273 "GPX4-2 reduces 17(S)-Hp-DHA to 17(S)-HDHA"
xref: RHEA:19057
-is_a: GO:0016684 ! oxidoreductase activity, acting on peroxide as acceptor
+is_a: GO:0004601 ! peroxidase activity
[Term]
id: GO:0047067
@@ -271805,7 +271835,7 @@ id: GO:0047068
name: N5,N10-methenyltetrahydromethanopterin hydrogenase activity
namespace: molecular_function
alt_id: GO:0016947
-def: "Catalysis of the reaction: 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H(2) = 5,10-methylenetetrahydromethanopterin + H(+)." [EC:1.12.98.2, RHEA:20017]
+def: "Catalysis of the reaction: 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H(2) = 5,10-methylenetetrahydromethanopterin + H+." [EC:1.12.98.2, RHEA:20017]
synonym: "5,10-methenyltetrahydromethanopterin hydrogenase activity" RELATED [EC:1.12.98.2]
synonym: "H(2)-dependent methylene-H(4)MPT dehydrogenase activity" RELATED [EC:1.12.98.2]
synonym: "H(2)-forming N(5),N(10)-methylenetetrahydromethanopterin dehydrogenase activity" RELATED [EC:1.12.98.2]
@@ -271827,7 +271857,7 @@ is_a: GO:0046995 ! oxidoreductase activity, acting on hydrogen as donor, with ot
id: GO:0047069
name: 7,8-dihydroxykynurenate 8,8a-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7,8-dihydroxykynurenate + O(2) = 5-(3-carboxylato-3-oxoprop-1-en-1-yl)-4,6-dihydroxypyridine-2-carboxylate + H(+)." [EC:1.13.11.10, RHEA:23400]
+def: "Catalysis of the reaction: 7,8-dihydroxykynurenate + O2 = 5-(3-carboxylato-3-oxoprop-1-en-1-yl)-4,6-dihydroxypyridine-2-carboxylate + H+." [EC:1.13.11.10, RHEA:23400]
synonym: "7,8-dihydroxykynurenate 8,8alpha-dioxygenase activity" RELATED [EC:1.13.11.10]
synonym: "7,8-dihydroxykynurenate oxygenase activity" RELATED [EC:1.13.11.10]
synonym: "7,8-dihydroxykynurenate:oxygen 8,8a-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.10]
@@ -271857,7 +271887,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0047071
name: 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione 4,5-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione + O(2) = 3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta-1(10),2-dien-4-oate + H(+)." [EC:1.13.11.25, RHEA:21352]
+def: "Catalysis of the reaction: 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione + O2 = 3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta-1(10),2-dien-4-oate + H+." [EC:1.13.11.25, RHEA:21352]
synonym: "3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione:oxygen 4,5-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.25]
synonym: "3-alkylcatechol 2,3-dioxygenase activity" RELATED [EC:1.13.11.25]
synonym: "steroid 4,5-dioxygenase activity" BROAD [EC:1.13.11.25]
@@ -271872,7 +271902,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0047072
name: 2,3-dihydroxybenzoate 2,3-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,3-dihydroxybenzoate + O(2) = 2-carboxy-cis,cis-muconate + 2 H(+)." [EC:1.13.11.28, RHEA:15369]
+def: "Catalysis of the reaction: 2,3-dihydroxybenzoate + O2 = 2-carboxy-cis,cis-muconate + 2 H+." [EC:1.13.11.28, RHEA:15369]
synonym: "2,3-dihydroxybenzoate 2,3-oxygenase activity" RELATED [EC:1.13.11.28]
synonym: "2,3-dihydroxybenzoate:oxygen 2,3-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.28]
xref: EC:1.13.11.28
@@ -271885,7 +271915,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0047073
name: 2,4'-dihydroxyacetophenone dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,4'-dihydroxyacetophenone + O(2) = 4-hydroxybenzoate + formate + 2 H(+)." [EC:1.13.11.41, RHEA:24416]
+def: "Catalysis of the reaction: 2,4'-dihydroxyacetophenone + O2 = 4-hydroxybenzoate + formate + 2 H+." [EC:1.13.11.41, RHEA:24416]
synonym: "(4-hydroxybenzoyl)methanol oxygenase activity" RELATED [EC:1.13.11.41]
synonym: "2,4'-dihydroxyacetophenone oxidoreductase (C-C-bond-cleaving)" RELATED [EC:1.13.11.41]
xref: EC:1.13.11.41
@@ -271959,7 +271989,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0047079
name: deoxyuridine 1'-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2'-deoxyuridine + 2-oxoglutarate + O(2) = 2-deoxy-D-ribono-1,4-lactone + CO(2) + succinate + uracil." [EC:1.14.11.10, RHEA:23316]
+def: "Catalysis of the reaction: 2'-deoxyuridine + 2-oxoglutarate + O2 = 2-deoxy-D-ribono-1,4-lactone + CO2 + succinate + uracil." [EC:1.14.11.10, RHEA:23316]
synonym: "2'-deoxyuridine,2-oxoglutarate:oxygen oxidoreductase (1'-hydroxylating)" RELATED [EC:1.14.11.10]
synonym: "pyrimidine-deoxynucleoside 1'-dioxygenase activity" BROAD [EC:1.14.11.10]
synonym: "pyrimidine-deoxynucleoside,2-oxoglutarate 1'-dioxygenase activity" BROAD [EC:1.14.11.10]
@@ -271973,7 +272003,7 @@ is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
id: GO:0047080
name: deoxyuridine 2'-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2'-deoxyuridine + 2-oxoglutarate + O(2) = CO(2) + succinate + uridine." [EC:1.14.11.3, RHEA:21076]
+def: "Catalysis of the reaction: 2'-deoxyuridine + 2-oxoglutarate + O2 = CO2 + succinate + uridine." [EC:1.14.11.3, RHEA:21076]
synonym: "2'-deoxyuridine,2-oxoglutarate:oxygen oxidoreductase (2'-hydroxylating)" RELATED [EC:1.14.11.3]
synonym: "deoxyuridine 2'-hydroxylase activity" RELATED [EC:1.14.11.3]
synonym: "pyrimidine deoxyribonucleoside 2'-hydroxylase activity" BROAD [EC:1.14.11.3]
@@ -272008,7 +272038,7 @@ is_a: GO:0016708 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047082
name: 3,9-dihydroxypterocarpan 6a-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (6aR,11aR)-3,9-dihydroxypterocarpan + H(+) + NADPH + O(2) = (6aS,11aS)-3,6a,9-trihydroxypterocarpan + H(2)O + NADP(+). (6aS,11aS)-3,6a,9-trihydroxypterocarpan is also known as (-)-glycinol." [EC:1.14.14.93, RHEA:15321]
+def: "Catalysis of the reaction: (6aR,11aR)-3,9-dihydroxypterocarpan + H+ + NADPH + O2 = (6aS,11aS)-3,6a,9-trihydroxypterocarpan + H2O + NADP+. (6aS,11aS)-3,6a,9-trihydroxypterocarpan is also known as (-)-glycinol." [EC:1.14.14.93, RHEA:15321]
synonym: "(6aR,11aR)-3,9-dihydroxypterocarpan,NADPH:oxygen oxidoreductase (6a-hydroxylating)" RELATED [EC:1.14.14.93]
synonym: "3,9-dihydroxypterocarpan 6a-hydroxylase activity" EXACT []
synonym: "3,9-dihydroxypterocarpan 6alpha-monooxygenase" RELATED []
@@ -272049,13 +272079,13 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047085
name: hydroxyphenylacetonitrile 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-hydroxyphenylacetonitrile + H(+) + NADPH + O(2) = 4-hydroxymandelonitrile + H(2)O + NADP(+)." [RHEA:23740]
+def: "Catalysis of the reaction: 4-hydroxyphenylacetonitrile + H+ + NADPH + O2 = 4-hydroxymandelonitrile + H2O + NADP+." [RHEA:50732]
synonym: "4-hydroxyphenylacetonitrile hydroxylase activity" EXACT []
synonym: "4-hydroxyphenylacetonitrile monooxygenase activity" EXACT []
synonym: "4-hydroxyphenylacetonitrile,NADPH:oxygen oxidoreductase (2-hydroxylating)" EXACT []
xref: KEGG_REACTION:R02708
xref: MetaCyc:1.14.13.42-RXN
-xref: RHEA:23740
+xref: RHEA:50732
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
[Term]
@@ -272076,7 +272106,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047087
name: protopine 6-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADPH + O(2) + protopine = 6-hydroxyprotopine + H(2)O + NADP(+)." [EC:1.14.14.98, RHEA:22644]
+def: "Catalysis of the reaction: H+ + NADPH + O2 + protopine = 6-hydroxyprotopine + H2O + NADP+." [EC:1.14.14.98, RHEA:22644]
synonym: "protopine 6-hydroxylase activity" EXACT []
synonym: "protopine,NADPH:oxygen oxidoreductase (6-hydroxylating)" RELATED [EC:1.14.14.98]
xref: EC:1.14.14.98
@@ -272089,7 +272119,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047088
name: dihydrosanguinarine 10-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dihydrosanguinarine + H(+) + NADPH + O(2) = 10-hydroxydihydrosanguinarine + H(2)O + NADP(+)." [EC:1.14.14.100, RHEA:10528]
+def: "Catalysis of the reaction: dihydrosanguinarine + H+ + NADPH + O2 = 10-hydroxydihydrosanguinarine + H2O + NADP+." [EC:1.14.14.100, RHEA:10528]
synonym: "dihydrosanguinarine 10-hydroxylase activity" EXACT []
synonym: "dihydrosanguinarine,NADPH:oxygen oxidoreductase (10-hydroxylating)" RELATED [EC:1.14.14.100]
xref: EC:1.14.14.100
@@ -272102,7 +272132,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047089
name: dihydrochelirubine 12-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dihydrochelirubine + H(+) + NADPH + O(2) = 12-hydroxydihydrochelirubine + H(2)O + NADP(+)." [EC:1.14.14.101, RHEA:10156]
+def: "Catalysis of the reaction: dihydrochelirubine + H+ + NADPH + O2 = 12-hydroxydihydrochelirubine + H2O + NADP+." [EC:1.14.14.101, RHEA:10156]
synonym: "dihydrochelirubine 12-hydroxylase activity" EXACT []
synonym: "dihydrochelirubine,NADPH:oxygen oxidoreductase (12-hydroxylating)" RELATED [EC:1.14.14.101]
xref: EC:1.14.14.101
@@ -272115,7 +272145,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047090
name: benzoyl-CoA 3-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: benzoyl-CoA + H(+) + NADPH + O(2) = 3-hydroxybenzoyl-CoA + H(2)O + NADP(+)." [EC:1.14.13.58, RHEA:23216]
+def: "Catalysis of the reaction: benzoyl-CoA + H+ + NADPH + O2 = 3-hydroxybenzoyl-CoA + H2O + NADP+." [EC:1.14.13.58, RHEA:23216]
synonym: "benzoyl-CoA 3-hydroxylase activity" EXACT []
synonym: "benzoyl-CoA,NADPH:oxygen oxidoreductase (3-hydroxylating)" RELATED [EC:1.14.13.58]
xref: EC:1.14.13.58
@@ -272129,7 +272159,7 @@ id: GO:0047091
name: L-lysine 6-monooxygenase (NADPH) activity
namespace: molecular_function
alt_id: GO:0008739
-def: "Catalysis of the reaction: L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + H(2)O + NADP(+)." [EC:1.14.13.59, RHEA:23228]
+def: "Catalysis of the reaction: L-lysine + NADPH + O2 = N(6)-hydroxy-L-lysine + H2O + NADP+." [EC:1.14.13.59, RHEA:23228]
comment: Note that EC:1.13.12.10 was merged into this term.
synonym: "L-lysine 6-monooxygenase activity" EXACT []
synonym: "L-lysine,NADPH:oxygen oxidoreductase (6-hydroxylating)" RELATED [EC:1.14.13.59]
@@ -272161,7 +272191,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047093
name: 4-hydroxyquinoline 3-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADH + O(2) + quinolin-4-ol = H(2)O + NAD(+) + quinoline-3,4-diol." [EC:1.14.13.62, RHEA:19325]
+def: "Catalysis of the reaction: H+ + NADH + O2 + quinolin-4-ol = H2O + NAD+ + quinoline-3,4-diol." [EC:1.14.13.62, RHEA:19325]
synonym: "1-H-4-oxoquinoline 3-monooxygenase activity" RELATED [EC:1.14.13.62]
synonym: "quinolin-4(1H)-one 3-monooxygenase activity" RELATED [EC:1.14.13.62]
synonym: "quinolin-4(1H)-one,NADH:oxygen oxidoreductase (3-oxygenating)" RELATED [EC:1.14.13.62]
@@ -272186,7 +272216,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047095
name: 2-hydroxycyclohexanone 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-hydroxycyclohexan-1-one + NADPH + O(2) = 6-oxohexanoate + H(2)O + NADP(+)." [EC:1.14.13.66, RHEA:33283]
+def: "Catalysis of the reaction: 2-hydroxycyclohexan-1-one + NADPH + O2 = 6-oxohexanoate + H2O + NADP+." [EC:1.14.13.66, RHEA:33283]
synonym: "2-hydroxycyclohexan-1-one,NADPH:oxygen 2-oxidoreductase (1,2-lactonizing)" RELATED [EC:1.14.13.66]
xref: EC:1.14.13.66
xref: KEGG_REACTION:R03281
@@ -272198,7 +272228,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047096
name: androst-4-ene-3,17-dione monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + androst-4-ene-3,17-dione + O(2) = A + H(2)O + testololactone." [EC:1.14.99.12, RHEA:22696]
+def: "Catalysis of the reaction: AH(2) + androst-4-ene-3,17-dione + O2 = A + H2O + testololactone." [EC:1.14.99.12, RHEA:22696]
synonym: "4-androstene-3,17-dione monooxygenase activity" EXACT []
synonym: "androst-4-ene-3,17-dione 17-oxidoreductase activity" RELATED [EC:1.14.99.12]
synonym: "androst-4-ene-3,17-dione hydroxylase activity" RELATED [EC:1.14.99.12]
@@ -272216,7 +272246,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047097
name: phylloquinone monooxygenase (2,3-epoxidizing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + O(2) + phylloquinone = 2,3-epoxyphylloquinone + A + H(2)O." [EC:1.14.99.20, RHEA:16745]
+def: "Catalysis of the reaction: AH(2) + O2 + phylloquinone = 2,3-epoxyphylloquinone + A + H2O." [EC:1.14.99.20, RHEA:16745]
synonym: "phylloquinone epoxidase activity" RELATED [EC:1.14.99.20]
synonym: "phylloquinone,hydrogen-donor:oxygen oxidoreductase (2,3-epoxidizing)" RELATED [EC:1.14.99.20]
synonym: "vitamin K 2,3-epoxidase activity" RELATED [EC:1.14.99.20]
@@ -272331,7 +272361,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0047104
name: hexadecanal dehydrogenase (acylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: CoA + NAD(+) + palmitaldehyde = H(+) + NADH + palmitoyl-CoA." [EC:1.2.1.42, RHEA:19705]
+def: "Catalysis of the reaction: CoA + NAD+ + palmitaldehyde = H+ + NADH + palmitoyl-CoA." [EC:1.2.1.42, RHEA:19705]
synonym: "fatty acyl-CoA reductase activity" BROAD [EC:1.2.1.42]
synonym: "hexadecanal:NAD+ oxidoreductase (CoA-acylating)" RELATED [EC:1.2.1.42]
xref: EC:1.2.1.42
@@ -272351,6 +272381,7 @@ synonym: "4-trimethylaminobutyraldehyde dehydrogenase activity" RELATED [EC:1.2.
synonym: "4-trimethylammoniobutanal:NAD+ 1-oxidoreductase activity" RELATED [EC:1.2.1.47]
xref: EC:1.2.1.47
xref: MetaCyc:1.2.1.47-RXN
+xref: Reactome:R-HSA-71260 "ALDH9A1 tetramer dehydrogenates TEABL to form TEABT"
xref: RHEA:17985
is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
@@ -272370,7 +272401,7 @@ is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
id: GO:0047107
name: gamma-guanidinobutyraldehyde dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-guanidinobutanal + H(2)O + NAD(+) = 4-guanidinobutanoate + 2 H(+) + NADH." [EC:1.2.1.54, RHEA:14381]
+def: "Catalysis of the reaction: 4-guanidinobutanal + H2O + NAD+ = 4-guanidinobutanoate + 2 H+ + NADH." [EC:1.2.1.54, RHEA:14381]
synonym: "4-guanidinobutanal:NAD+ 1-oxidoreductase activity" RELATED [EC:1.2.1.54]
synonym: "4-guanidinobutyraldehyde dehydrogenase activity" RELATED [EC:1.2.1.54]
synonym: "alpha-guanidinobutyraldehyde dehydrogenase activity" RELATED [EC:1.2.1.54]
@@ -272385,7 +272416,7 @@ is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
id: GO:0047108
name: (R)-3-hydroxyacid-ester dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ethyl (R)-3-hydroxyhexanoate + NADP(+) = ethyl 3-oxohexanoate + H(+) + NADPH." [EC:1.1.1.279, RHEA:24352]
+def: "Catalysis of the reaction: ethyl (R)-3-hydroxyhexanoate + NADP+ = ethyl 3-oxohexanoate + H+ + NADPH." [EC:1.1.1.279, RHEA:24352]
comment: Note that this term was EC:1.2.1.55.
synonym: "(R)-3-hydroxyacid ester dehydrogenase activity" EXACT []
synonym: "3-oxo ester (R)-reductase activity" RELATED [EC:1.1.1.279]
@@ -272400,7 +272431,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047109
name: (S)-3-hydroxyacid-ester dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ethyl (S)-3-hydroxyhexanoate + NADP(+) = ethyl 3-oxohexanoate + H(+) + NADPH." [EC:1.1.1.280, RHEA:18269]
+def: "Catalysis of the reaction: ethyl (S)-3-hydroxyhexanoate + NADP+ = ethyl 3-oxohexanoate + H+ + NADPH." [EC:1.1.1.280, RHEA:18269]
comment: Note that this term was EC:1.2.1.56.
synonym: "(S)-3-hydroxyacid ester dehydrogenase activity" EXACT []
synonym: "3-oxo ester (S)-reductase activity" RELATED [EC:1.1.1.280]
@@ -272415,7 +272446,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047110
name: phenylglyoxylate dehydrogenase (acylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: CoA + NAD(+) + phenylglyoxylate = benzoyl-CoA + CO(2) + NADH." [EC:1.2.1.58, RHEA:10372]
+def: "Catalysis of the reaction: CoA + NAD+ + phenylglyoxylate = benzoyl-CoA + CO2 + NADH." [EC:1.2.1.58, RHEA:10372]
synonym: "phenylglyoxylate:NAD+ oxidoreductase activity" RELATED [EC:1.2.1.58]
xref: EC:1.2.1.58
xref: KEGG_REACTION:R02450
@@ -272439,7 +272470,7 @@ is_a: GO:0016622 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0047112
name: pyruvate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + O(2) + phosphate + pyruvate = acetyl phosphate + CO(2) + H(2)O(2)." [EC:1.2.3.3, RHEA:20848]
+def: "Catalysis of the reaction: H+ + O2 + phosphate + pyruvate = acetyl phosphate + CO2 + H2O2." [EC:1.2.3.3, RHEA:20848]
synonym: "phosphate-dependent pyruvate oxidase activity" RELATED [EC:1.2.3.3]
synonym: "pyruvate:oxygen 2-oxidoreductase (phosphorylating)" RELATED [EC:1.2.3.3]
synonym: "pyruvic oxidase activity" RELATED [EC:1.2.3.3]
@@ -272466,7 +272497,7 @@ is_a: GO:0016903 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0047114
name: kynurenate-7,8-dihydrodiol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7,8-dihydro-7,8-dihydroxykynurenate + NAD(+) = 7,8-dihydroxykynurenate + H(+) + NADH." [EC:1.3.1.18, RHEA:22248]
+def: "Catalysis of the reaction: 7,8-dihydro-7,8-dihydroxykynurenate + NAD+ = 7,8-dihydroxykynurenate + H+ + NADH." [EC:1.3.1.18, RHEA:22248]
synonym: "7,8-dihydro-7,8-dihydroxykynurenate dehydrogenase activity" RELATED [EC:1.3.1.18]
synonym: "7,8-dihydro-7,8-dihydroxykynurenate:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.18]
synonym: "7,8-dihydroxykynurenic acid 7,8-diol dehydrogenase activity" RELATED [EC:1.3.1.18]
@@ -272526,7 +272557,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047118
name: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,6-dioxo-6-phenylhexanoate + NADP(+) = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate + H(+) + NADPH." [EC:1.3.1.40, RHEA:24268]
+def: "Catalysis of the reaction: 2,6-dioxo-6-phenylhexanoate + NADP+ = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate + H+ + NADPH." [EC:1.3.1.40, RHEA:24268]
synonym: "2,6-dioxo-6-phenylhexanoate:NADP+ delta2-oxidoreductase activity" RELATED [EC:1.3.1.40]
synonym: "2-hydroxy-6-oxo-phenylhexa-2,4-dienoate (reduced nicotinamide adenine dinucleotide phosphate) reductase activity" RELATED [EC:1.3.1.40]
xref: EC:1.3.1.40
@@ -272535,24 +272566,12 @@ xref: MetaCyc:1.3.1.40-RXN
xref: RHEA:24268
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
-[Term]
-id: GO:0047119
-name: 2-methyl-branched-chain-enoyl-CoA reductase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 2-methylbutanoyl-CoA + NAD(+) = 2-methylbut-2-enoyl-CoA + H(+) + NADH." [PMID:10989435, PMID:6401712, RHEA:43780]
-synonym: "2-methyl-branched-chain-acyl-CoA:NAD+ 2-oxidoreductase activity" RELATED [EC:1.3.1.52]
-xref: EC:1.3.8.5
-xref: KEGG_REACTION:R03169
-xref: MetaCyc:1.3.1.52-RXN
-xref: RHEA:43780
-is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
-
[Term]
id: GO:0047120
name: (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate dehydrogenase activity
namespace: molecular_function
alt_id: GO:0018514
-def: "Catalysis of the reaction: (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate + NAD(+) = 3,4-dihydroxybenzoate + CO(2) + NADH." [EC:1.3.1.53, RHEA:10744]
+def: "Catalysis of the reaction: (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate + NAD+ = 3,4-dihydroxybenzoate + CO2 + NADH." [EC:1.3.1.53, RHEA:10744]
synonym: "(1R,2S)-dihydroxy-3,5-cyclohexadiene-1,4-dicarboxylate dehydrogenase activity" RELATED [EC:1.3.1.53]
synonym: "(3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.53]
synonym: "cis-4,5-dihydroxycyclohexa-1(6),2-diene-1,4-dicarboxylate:NAD+ oxidoreductase (decarboxylating)" RELATED [EC:1.3.1.53]
@@ -272569,7 +272588,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047121
name: isoquinoline 1-oxidoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: A + H(2)O + isoquinoline = AH(2) + isoquinolin-1(2H)-one." [EC:1.3.99.16, RHEA:11588]
+def: "Catalysis of the reaction: A + H2O + isoquinoline = AH(2) + isoquinolin-1(2H)-one." [EC:1.3.99.16, RHEA:11588]
synonym: "isoquinoline:acceptor 1-oxidoreductase (hydroxylating)" RELATED [EC:1.3.99.16]
xref: EC:1.3.99.16
xref: KEGG_REACTION:R05151
@@ -272581,7 +272600,7 @@ is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
id: GO:0047122
name: quinaldate 4-oxidoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: A + H(2)O + quinaldate = AH(2) + kynurenate." [EC:1.3.99.18, RHEA:16697]
+def: "Catalysis of the reaction: A + H2O + quinaldate = AH(2) + kynurenate." [EC:1.3.99.18, RHEA:16697]
synonym: "quinaldic acid 4-oxidoreductase activity" RELATED [EC:1.3.99.18]
synonym: "quinoline-2-carboxylate:acceptor 4-oxidoreductase (hydroxylating)" RELATED [EC:1.3.99.18]
xref: EC:1.3.99.18
@@ -272594,7 +272613,7 @@ is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
id: GO:0047123
name: quinoline-4-carboxylate 2-oxidoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: A + H(2)O + quinoline-4-carboxylate = 2-oxo-1,2-dihydroquinoline-4-carboxylate + AH(2)." [EC:1.3.99.19, RHEA:14949]
+def: "Catalysis of the reaction: A + H2O + quinoline-4-carboxylate = 2-oxo-1,2-dihydroquinoline-4-carboxylate + AH(2)." [EC:1.3.99.19, RHEA:14949]
synonym: "quinoline-4-carboxylate:acceptor 2-oxidoreductase (hydroxylating)" RELATED [EC:1.3.99.19]
synonym: "quinoline-4-carboxylic acid 2-oxidoreductase activity" RELATED [EC:1.3.99.19]
xref: EC:1.3.99.19
@@ -272607,7 +272626,7 @@ is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
id: GO:0047124
name: L-erythro-3,5-diaminohexanoate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (3S,5S)-3,5-diaminohexanoate + H(2)O + NAD(+) = (S)-5-amino-3-oxo-hexanoate + H(+) + NADH + NH(4)(+)." [EC:1.4.1.11, RHEA:19633]
+def: "Catalysis of the reaction: (3S,5S)-3,5-diaminohexanoate + H2O + NAD+ = (S)-5-amino-3-oxo-hexanoate + H+ + NADH + NH4." [EC:1.4.1.11, RHEA:19633]
synonym: "L-3,5-diaminohexanoate dehydrogenase activity" RELATED [EC:1.4.1.11]
synonym: "L-erythro-3,5-diaminohexanoate:NAD+ oxidoreductase (deaminating)" RELATED [EC:1.4.1.11]
xref: EC:1.4.1.11
@@ -272636,7 +272655,7 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0047126
name: N5-(carboxyethyl)ornithine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(5)-[1(S)-1-carboxyethyl]-L-ornithine + H(2)O + NADP(+) = L-ornithine + H(+) + NADPH + pyruvate." [EC:1.5.1.24, RHEA:18661]
+def: "Catalysis of the reaction: N(5)-[1(S)-1-carboxyethyl]-L-ornithine + H2O + NADP+ = L-ornithine + H+ + NADPH + pyruvate." [EC:1.5.1.24, RHEA:18661]
synonym: "5-N-(L-1-carboxyethyl)-L-ornithine:NADP+ oxidoreductase (L-ornithine-forming)" RELATED [EC:1.5.1.24]
synonym: "N5-(L-1-carboxyethyl)-L-ornithine:NADP+ oxidoreductase (L-ornithine-forming)" RELATED [EC:1.5.1.24]
xref: EC:1.5.1.24
@@ -272662,7 +272681,7 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0047128
name: 1,2-dehydroreticulinium reductase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-reticuline + NADP(+) = 1,2-dehydroreticuline + H(+) + NADPH." [EC:1.5.1.27, RHEA:17569]
+def: "Catalysis of the reaction: (R)-reticuline + NADP+ = 1,2-dehydroreticuline + H+ + NADPH." [EC:1.5.1.27, RHEA:17569]
synonym: "(R)-reticuline:NADP+ oxidoreductase activity" RELATED [EC:1.5.1.27]
synonym: "1,2-dehydroreticulinium ion reductase activity" RELATED [EC:1.5.1.27]
xref: EC:1.5.1.27
@@ -272675,7 +272694,7 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0047129
name: opine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2S)-2-[(R)-1-carboxyethylamino]pentanoate + H(2)O + NAD(+) = L-2-aminopentanoate + H(+) + NADH + pyruvate." [EC:1.5.1.28, RHEA:21592]
+def: "Catalysis of the reaction: (2S)-2-[(R)-1-carboxyethylamino]pentanoate + H2O + NAD+ = L-2-aminopentanoate + H+ + NADH + pyruvate." [EC:1.5.1.28, RHEA:21592]
synonym: "(2S)-2-{[1-(R)-carboxyethyl]amino}pentanoate dehydrogenase (NAD, L-aminopentanoate-forming)" RELATED [EC:1.5.1.28]
synonym: "(2S)-2-{[1-(R)-carboxyethyl]amino}pentanoate:NAD+ oxidoreductase (L-aminopentanoate-forming)" RELATED [EC:1.5.1.28]
xref: EC:1.5.1.28
@@ -272689,7 +272708,7 @@ id: GO:0047130
name: saccharopine dehydrogenase (NADP+, L-lysine-forming) activity
namespace: molecular_function
alt_id: GO:0010010
-def: "Catalysis of the reaction: L-saccharopine + H(2)O + NADP(+) = 2-oxoglutarate + L-lysine + H(+) + NADPH." [EC:1.5.1.8, RHEA:19373]
+def: "Catalysis of the reaction: L-saccharopine + H2O + NADP+ = 2-oxoglutarate + L-lysine + H+ + NADPH." [EC:1.5.1.8, RHEA:19373]
synonym: "6-N-(L-1,3-dicarboxypropyl)-L-lysine:NADP+ oxidoreductase (L-lysine-forming)" RELATED [EC:1.5.1.8]
synonym: "L-lysine-alpha-ketoglutarate reductase activity" RELATED [EC:1.5.1.8]
synonym: "lysine:alpha-ketoglutarate:TPNH oxidoreductase (epsilon-N-[gultaryl-2]-L-lysine forming)" RELATED [EC:1.5.1.8]
@@ -272706,7 +272725,7 @@ is_a: GO:0004753 ! saccharopine dehydrogenase activity
id: GO:0047131
name: saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-saccharopine + H(2)O + NAD(+) = L-glutamate + allysine + H(+) + NADH." [EC:1.5.1.9, RHEA:24520]
+def: "Catalysis of the reaction: L-saccharopine + H2O + NAD+ = L-glutamate + allysine + H+ + NADH." [EC:1.5.1.9, RHEA:24520]
synonym: "6-N-(L-1,3-dicarboxypropyl)-L-lysine:NAD+ oxidoreductase (L-glutamate-forming)" RELATED [EC:1.5.1.9]
synonym: "aminoadipic semialdehyde synthase activity" RELATED [EC:1.5.1.9]
synonym: "dehydrogenase, saccharopine (nicotinamide adenine dinucleotide, glutamate-forming)" RELATED [EC:1.5.1.9]
@@ -272766,7 +272785,7 @@ is_a: GO:0016668 ! oxidoreductase activity, acting on a sulfur group of donors,
id: GO:0047135
name: bis-gamma-glutamylcystine reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 L-gamma-glutamyl-L-cysteine + NADP(+) = bis-gamma-glutamylcystine + H(+) + NADPH." [EC:1.8.1.13, RHEA:11980]
+def: "Catalysis of the reaction: 2 L-gamma-glutamyl-L-cysteine + NADP+ = bis-gamma-glutamylcystine + H+ + NADPH." [EC:1.8.1.13, RHEA:11980]
synonym: "bis-g-glutamylcystine reductase (NADPH) activity" EXACT []
synonym: "Bis-gamma-glutamylcystine reductase (NADPH)" RELATED [EC:1.8.1.13]
synonym: "bis-gamma-glutamylcystine reductase (NADPH) activity" RELATED [EC:1.8.1.13]
@@ -272783,7 +272802,7 @@ is_a: GO:0016668 ! oxidoreductase activity, acting on a sulfur group of donors,
id: GO:0047136
name: 4-(dimethylamino)phenylazoxybenzene reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-(dimethylamino)azobenzene + H(2)O + NADP(+) = 4-(dimethylamino)phenylazoxybenzene + H(+) + NADPH." [EC:1.7.1.11, RHEA:19789]
+def: "Catalysis of the reaction: 4-(dimethylamino)azobenzene + H2O + NADP+ = 4-(dimethylamino)phenylazoxybenzene + H+ + NADPH." [EC:1.7.1.11, RHEA:19789]
synonym: "4-(dimethylamino)phenylazobenzene:NADP+ oxidoreductase activity" RELATED [EC:1.7.1.11]
synonym: "dimethylaminoazobenzene N-oxide reductase activity" RELATED [EC:1.7.1.11]
synonym: "N,N-dimethyl-p-aminoazobenzene oxide reductase activity" RELATED [EC:1.7.1.11]
@@ -272889,7 +272908,7 @@ is_a: GO:0016671 ! oxidoreductase activity, acting on a sulfur group of donors,
id: GO:0047143
name: chlorate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + chlorate = A + chlorite + H(2)O + H(+)." [EC:1.97.1.1, RHEA:16349]
+def: "Catalysis of the reaction: AH(2) + chlorate = A + chlorite + H2O + H+." [EC:1.97.1.1, RHEA:16349]
synonym: "chlorate reductase C" RELATED [EC:1.97.1.1]
synonym: "chlorite:acceptor oxidoreductase activity" RELATED [EC:1.97.1.1]
xref: EC:1.97.1.1
@@ -272950,7 +272969,7 @@ is_a: GO:0008171 ! O-methyltransferase activity
id: GO:0047147
name: trimethylsulfonium-tetrahydrofolate N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (6S)-5,6,7,8-tetrahydrofolate + trimethylsulfonium = (6S)-5-methyl-5,6,7,8-tetrahydrofolate + dimethyl sulfide + H(+)." [EC:2.1.1.19, RHEA:13693]
+def: "Catalysis of the reaction: (6S)-5,6,7,8-tetrahydrofolate + trimethylsulfonium = (6S)-5-methyl-5,6,7,8-tetrahydrofolate + dimethyl sulfide + H+." [EC:2.1.1.19, RHEA:13693]
synonym: "trimethylsulfonium-tetrahydrofolate methyltransferase activity" RELATED [EC:2.1.1.19]
synonym: "trimethylsulfonium:tetrahydrofolate N-methyltransferase activity" RELATED [EC:2.1.1.19]
synonym: "trimethylsulphonium-tetrahydrofolate N-methyltransferase activity" EXACT []
@@ -272964,7 +272983,7 @@ is_a: GO:0008170 ! N-methyltransferase activity
id: GO:0047148
name: methylamine-glutamate N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-glutamate + methylammonium = N-methyl-L-glutamate + NH(4)(+)." [EC:2.1.1.21, RHEA:15837]
+def: "Catalysis of the reaction: L-glutamate + methylammonium = N-methyl-L-glutamate + NH4." [EC:2.1.1.21, RHEA:15837]
synonym: "methylamine-glutamate methyltransferase activity" RELATED [EC:2.1.1.21]
synonym: "methylamine:L-glutamate N-methyltransferase activity" RELATED [EC:2.1.1.21]
synonym: "N-methylglutamate synthase activity" RELATED [EC:2.1.1.21]
@@ -272978,7 +272997,7 @@ is_a: GO:0008170 ! N-methyltransferase activity
id: GO:0047149
name: thetin-homocysteine S-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-homocysteine + dimethylsulfonioacetate = (methylthio)acetate + L-methionine + H(+)." [EC:2.1.1.3, RHEA:22788]
+def: "Catalysis of the reaction: L-homocysteine + dimethylsulfonioacetate = (methylthio)acetate + L-methionine + H+." [EC:2.1.1.3, RHEA:22788]
synonym: "dimethylsulfonioacetate:L-homocysteine S-methyltransferase activity" RELATED [EC:2.1.1.3]
synonym: "dimethylthetin-homocysteine methyltransferase activity" RELATED [EC:2.1.1.3]
synonym: "thetin-homocysteine methylpherase activity" RELATED [EC:2.1.1.3]
@@ -273044,7 +273063,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0047153
name: deoxycytidylate 5-hydroxymethyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dCMP + H(2)O = (6S)-5,6,7,8-tetrahydrofolate + 5-hydroxymethyldeoxycytidylate." [EC:2.1.2.8, RHEA:11280]
+def: "Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dCMP + H2O = (6S)-5,6,7,8-tetrahydrofolate + 5-hydroxymethyldeoxycytidylate." [EC:2.1.2.8, RHEA:11280]
synonym: "5,10-methylenetetrahydrofolate:deoxycytidylate 5-hydroxymethyltransferase activity" RELATED [EC:2.1.2.8]
synonym: "d-cytidine 5'-monophosphate hydroxymethylase activity" RELATED [EC:2.1.2.8]
synonym: "dCMP hydroxymethylase activity" RELATED [EC:2.1.2.8]
@@ -273335,7 +273354,7 @@ is_a: GO:0008374 ! O-acyltransferase activity
id: GO:0047174
name: putrescine N-hydroxycinnamoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: caffeoyl-CoA + putrescine = N-caffeoylputrescine + CoA + H(+)." [EC:2.3.1.138, RHEA:12436]
+def: "Catalysis of the reaction: caffeoyl-CoA + putrescine = N-caffeoylputrescine + CoA + H+." [EC:2.3.1.138, RHEA:12436]
synonym: "caffeoyl-CoA putrescine N-caffeoyl transferase activity" RELATED [EC:2.3.1.138]
synonym: "caffeoyl-CoA:putrescine N-(3,4-dihydroxycinnamoyl)transferase activity" RELATED [EC:2.3.1.138]
synonym: "hydroxycinnamoyl-CoA:putrescine hydroxycinnamoyltransferase activity" RELATED [EC:2.3.1.138]
@@ -273545,7 +273564,7 @@ is_a: GO:0016413 ! O-acetyltransferase activity
id: GO:0047189
name: 2,3-diaminopropionate N-oxalyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-amino-L-alanine + oxalyl-CoA = N(3)-oxalyl-L-2,3-diaminopropanoate + CoA." [EC:2.3.1.58, RHEA:13465]
+def: "Catalysis of the reaction: 3-amino-L-alanine + oxalyl-CoA = N(3)-oxalyl-L-2,3-diaminopropanoate + CoA." [RHEA:13465]
synonym: "ODAP synthase activity" RELATED [EC:2.3.1.58]
synonym: "oxalyl-CoA:L-2,3-diaminopropanoate 3-N-oxalyltransferase activity" RELATED [EC:2.3.1.58]
synonym: "oxalyl-CoA:L-2,3-diaminopropanoate N3-oxalyltransferase activity" RELATED [EC:2.3.1.58]
@@ -273681,7 +273700,7 @@ is_a: GO:0008374 ! O-acyltransferase activity
id: GO:0047198
name: cysteine-S-conjugate N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-substituted L-cysteine + acetyl-CoA = S-substituted N-acetyl-L-cysteine + CoA + H(+)." [EC:2.3.1.80, RHEA:19213]
+def: "Catalysis of the reaction: S-substituted L-cysteine + acetyl-CoA = S-substituted N-acetyl-L-cysteine + CoA + H+." [EC:2.3.1.80, RHEA:19213]
synonym: "acetyl-CoA:S-substituted L-cysteine N-acetyltransferase activity" RELATED [EC:2.3.1.80]
xref: EC:2.3.1.80
xref: KEGG_REACTION:R04950
@@ -273706,7 +273725,7 @@ is_a: GO:0008374 ! O-acyltransferase activity
id: GO:0047200
name: tetrahydrodipicolinate N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + acetyl-CoA + H(2)O = L-2-acetamido-6-oxopimelate + CoA." [EC:2.3.1.89, RHEA:13085]
+def: "Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + acetyl-CoA + H2O = L-2-acetamido-6-oxopimelate + CoA." [EC:2.3.1.89, RHEA:13085]
synonym: "acetyl-CoA:(S)-2,3,4,5-tetrahydrodipicolinate-2,6-dicarboxylate N2-acetyltransferase activity" RELATED [EC:2.3.1.89]
synonym: "acetyl-CoA:(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate 2-N-acetyltransferase activity" RELATED [EC:2.3.1.89]
synonym: "acetyl-CoA:L-2,3,4,5-tetrahydrodipicolinate N2-acetyltransferase activity" RELATED [EC:2.3.1.89]
@@ -273747,7 +273766,7 @@ is_a: GO:0016753 ! O-sinapoyltransferase activity
id: GO:0047203
name: 13-hydroxylupinine O-tigloyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 13-hydroxylupanine + 2-methylcrotonoyl-CoA = 13-(2-methylcrotonoyloxy)lupanine + CoA." [EC:2.3.1.93, RHEA:12360]
+def: "Catalysis of the reaction: 13-hydroxylupanine + 2-methylcrotonoyl-CoA = 13-(2-methylcrotonoyloxy)lupanine + CoA." [RHEA:12360]
synonym: "(E)-2-methylcrotonoyl-CoA:13-hydroxylupinine O-2-methylcrotonoyltransferase activity" RELATED [EC:2.3.1.93]
synonym: "13-hydroxylupanine acyltransferase activity" RELATED [EC:2.3.1.93]
synonym: "tigloyl-CoA:13-hydroxylupanine O-tigloyltransferase activity" RELATED [EC:2.3.1.93]
@@ -273822,7 +273841,7 @@ is_a: GO:0050738 ! fructosyltransferase activity
id: GO:0047208
name: o-dihydroxycoumarin 7-O-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7,8-dihydroxycoumarin + UDP-D-glucose = daphnin + H(+) + UDP." [EC:2.4.1.104, RHEA:14325]
+def: "Catalysis of the reaction: 7,8-dihydroxycoumarin + UDP-D-glucose = daphnin + H+ + UDP." [EC:2.4.1.104, RHEA:14325]
synonym: "UDP-glucose:7,8-dihydroxycoumarin 7-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.104]
synonym: "UDP-glucose:o-dihydroxycoumarin glucosyltransferase activity" RELATED [EC:2.4.1.104]
synonym: "UDPglucose:7,8-dihydroxycoumarin 7-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.104]
@@ -273866,7 +273885,7 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
id: GO:0047212
name: 2-coumarate O-beta-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: trans-2-coumarate + UDP-D-glucose = trans-beta-D-glucosyl-2-hydroxycinnamate + H(+) + UDP." [EC:2.4.1.114, RHEA:10236]
+def: "Catalysis of the reaction: trans-2-coumarate + UDP-D-glucose = trans-beta-D-glucosyl-2-hydroxycinnamate + H+ + UDP." [EC:2.4.1.114, RHEA:10236]
synonym: "UDP-glucose:trans-2-hydroxycinnamate O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.114]
synonym: "UDPG:o-coumaric acid O-glucosyltransferase activity" RELATED [EC:2.4.1.114]
synonym: "UDPglucose:trans-2-hydroxycinnamate O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.114]
@@ -273980,7 +273999,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0047219
name: monoterpenol beta-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (-)-menthol + UDP-D-glucose = (-)-menthyl beta-D-glucoside + H(+) + UDP." [EC:2.4.1.127, RHEA:11520]
+def: "Catalysis of the reaction: (-)-menthol + UDP-D-glucose = (-)-menthyl beta-D-glucoside + H+ + UDP." [EC:2.4.1.127, RHEA:11520]
synonym: "UDP-glucose:(-)-menthol O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.127]
synonym: "UDPglucose:(-)-menthol O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.127]
synonym: "UDPglucose:monoterpenol glucosyltransferase activity" RELATED [EC:2.4.1.127]
@@ -274012,7 +274031,7 @@ is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
id: GO:0047221
name: sn-glycerol-3-phosphate 2-alpha-galactosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: sn-glycerol 3-phosphate + UDP-D-galactose = 2-(alpha-D-galactosyl)-sn-glycerol 3-phosphate + H(+) + UDP." [EC:2.4.1.137, RHEA:14285]
+def: "Catalysis of the reaction: sn-glycerol 3-phosphate + UDP-D-galactose = 2-(alpha-D-galactosyl)-sn-glycerol 3-phosphate + H+ + UDP." [EC:2.4.1.137, RHEA:14285]
synonym: "floridoside phosphate synthase activity" RELATED [EC:2.4.1.137]
synonym: "floridoside phosphate synthetase activity" RELATED [EC:2.4.1.137]
synonym: "floridoside-phosphate synthase activity" RELATED [EC:2.4.1.137]
@@ -274093,7 +274112,7 @@ is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
id: GO:0047227
name: indolylacetyl-myo-inositol galactosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1L-1-O-(indol-3-yl)acetyl-myo-inositol + UDP-D-galactose = 5-O-(indol-3-ylacetyl)-myo-inositol D-galactoside + H(+) + UDP." [EC:2.4.1.156, RHEA:21148]
+def: "Catalysis of the reaction: 1L-1-O-(indol-3-yl)acetyl-myo-inositol + UDP-D-galactose = 5-O-(indol-3-ylacetyl)-myo-inositol D-galactoside + H+ + UDP." [EC:2.4.1.156, RHEA:21148]
synonym: "indol-3-ylacetyl-myo-inositol galactoside synthase activity" RELATED [EC:2.4.1.156]
synonym: "UDP-galactose:(indol-3-yl)acetyl-myo-inositol 5-O-D-galactosyltransferase activity" RELATED [EC:2.4.1.156]
synonym: "UDP-galactose:indol-3-ylacetyl-myo-inositol 5-O-D-galactosyltransferase activity" RELATED [EC:2.4.1.156]
@@ -274153,7 +274172,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0047231
name: pyridoxine 5'-O-beta-D-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: pyridoxine + UDP-D-glucose = 5'-O-beta-D-glucosylpyridoxine + H(+) + UDP." [EC:2.4.1.160, RHEA:20177]
+def: "Catalysis of the reaction: pyridoxine + UDP-D-glucose = 5'-O-beta-D-glucosylpyridoxine + H+ + UDP." [EC:2.4.1.160, RHEA:20177]
synonym: "UDP-glucose-pyridoxine glucosyltransferase activity" RELATED [EC:2.4.1.160]
synonym: "UDP-glucose:pyridoxine 5'-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.160]
synonym: "UDP-glucose:pyridoxine 5'-O-beta-glucosyltransferase activity" RELATED [EC:2.4.1.160]
@@ -274273,7 +274292,7 @@ is_a: GO:0008376 ! acetylgalactosaminyltransferase activity
id: GO:0047239
name: hydroxymandelonitrile glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-hydroxymandelonitrile + UDP-D-glucose = H(+) + taxiphyllin + UDP." [EC:2.4.1.178, RHEA:15961]
+def: "Catalysis of the reaction: 4-hydroxymandelonitrile + UDP-D-glucose = H+ + taxiphyllin + UDP." [EC:2.4.1.178, RHEA:15961]
synonym: "cyanohydrin glucosyltransferase activity" RELATED [EC:2.4.1.178]
synonym: "UDP-glucose:4-hydroxymandelonitrile glucosyltransferase activity" RELATED [EC:2.4.1.178]
synonym: "UDPglucose:4-hydroxymandelonitrile glucosyltransferase activity" RELATED [EC:2.4.1.178]
@@ -274287,7 +274306,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0047240
name: lactosylceramide beta-1,3-galactosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-galactosyl-(1->4)-beta-D-glucosyl-R + UDP-D-galactose = D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-R + H(+) + UDP." [EC:2.4.1.179, RHEA:18413]
+def: "Catalysis of the reaction: D-galactosyl-(1->4)-beta-D-glucosyl-R + UDP-D-galactose = D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-R + H+ + UDP." [EC:2.4.1.179, RHEA:18413]
synonym: "UDP-galactose:D-galactosyl-1,4-beta-D-glucosyl-R beta-1,3-galactosyltransferase activity" RELATED [EC:2.4.1.179]
synonym: "UDPgalactose:D-galactosyl-1,4-beta-D-glucosyl-R beta-1,3-galactosyltransferase activity" RELATED [EC:2.4.1.179]
synonym: "uridine diphosphogalactose-lactosylceramide beta1->3-galactosyltransferase activity" RELATED [EC:2.4.1.179]
@@ -274373,7 +274392,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0047246
name: luteolin-7-O-glucuronide 7-O-glucuronosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: luteolin 7-O-beta-D-glucosiduronate + UDP-alpha-D-glucuronate = H(+) + luteolin 7-O-[(beta-D-glucosiduronate)-(1->2)-(beta-D-glucosiduronate)] + UDP." [EC:2.4.1.190, RHEA:14149]
+def: "Catalysis of the reaction: luteolin 7-O-beta-D-glucosiduronate + UDP-alpha-D-glucuronate = H+ + luteolin 7-O-[(beta-D-glucosiduronate)-(1->2)-(beta-D-glucosiduronate)] + UDP." [EC:2.4.1.190, RHEA:14149]
synonym: "LMT activity" RELATED [EC:2.4.1.190]
synonym: "luteolin-7-O-glucuronide 2''-O-glucuronosyltransferase activity" RELATED [EC:2.4.1.190]
synonym: "UDP-glucuronate:luteolin 7-O-glucuronide-glucuronosyltransferase activity" RELATED [EC:2.4.1.190]
@@ -274389,7 +274408,7 @@ is_a: GO:0015020 ! glucuronosyltransferase activity
id: GO:0047247
name: luteolin-7-O-diglucuronide 4'-O-glucuronosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: luteolin 7-O-[(beta-D-glucosiduronate)-(1->2)-(beta-D-glucosiduronate)] + UDP-alpha-D-glucuronate = H(+) + luteolin 7-O-[(beta-D-glucosiduronate)-(1->2)-(beta-D-glucosiduronate)] 4'-O-beta-D-glucosiduronate + UDP." [EC:2.4.1.191, RHEA:22116]
+def: "Catalysis of the reaction: luteolin 7-O-[(beta-D-glucosiduronate)-(1->2)-(beta-D-glucosiduronate)] + UDP-alpha-D-glucuronate = H+ + luteolin 7-O-[(beta-D-glucosiduronate)-(1->2)-(beta-D-glucosiduronate)] 4'-O-beta-D-glucosiduronate + UDP." [EC:2.4.1.191, RHEA:22116]
synonym: "LDT" RELATED [EC:2.4.1.191]
synonym: "UDP-glucuronate:luteolin 7-O-diglucuronide-glucuronosyltransferase activity" RELATED [EC:2.4.1.191]
synonym: "UDP-glucuronate:luteolin-7-O-beta-D-diglucuronide 4'-O-glucuronosyltransferase activity" RELATED [EC:2.4.1.191]
@@ -274406,7 +274425,7 @@ is_a: GO:0015020 ! glucuronosyltransferase activity
id: GO:0047248
name: nuatigenin 3-beta-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: nuatigenin + UDP-D-glucose = H(+) + nuatigenin 3-beta-D-glucopyranoside + UDP." [EC:2.4.1.192, RHEA:19329]
+def: "Catalysis of the reaction: nuatigenin + UDP-D-glucose = H+ + nuatigenin 3-beta-D-glucopyranoside + UDP." [EC:2.4.1.192, RHEA:19329]
synonym: "nuatigenin 3beta-glucosyltransferase activity" RELATED [EC:2.4.1.192]
synonym: "UDP-glucose:(20S,22S,25S)-22,25-epoxyfurost-5-ene-3beta,26-diol 3-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.192]
synonym: "UDPglucose:(20S,22S,25S)-22,25-epoxyfurost-5-ene-3beta,26-diol 3-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.192]
@@ -274421,7 +274440,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0047249
name: sarsapogenin 3-beta-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (25S)-5beta-spirostan-3beta-ol + UDP-D-glucose = (25S)-5beta-spirostan-3beta-yl beta-D-glucoside + H(+) + UDP." [EC:2.4.1.193, RHEA:14461]
+def: "Catalysis of the reaction: (25S)-5beta-spirostan-3beta-ol + UDP-D-glucose = (25S)-5beta-spirostan-3beta-yl beta-D-glucoside + H+ + UDP." [EC:2.4.1.193, RHEA:14461]
synonym: "sarsapogenin 3beta-glucosyltransferase activity" RELATED [EC:2.4.1.193]
synonym: "UDP-glucose:(25S)-5beta-spirostan-3beta-ol 3-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.193]
synonym: "UDPglucose:(25S)-5beta-spirostan-3beta-ol 3-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.193]
@@ -274436,7 +274455,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0047250
name: 4-hydroxybenzoate 4-O-beta-D-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-hydroxybenzoate + UDP-D-glucose = 4-(beta-D-glucosyloxy)benzoate + H(+) + UDP." [EC:2.4.1.194, RHEA:15153]
+def: "Catalysis of the reaction: 4-hydroxybenzoate + UDP-D-glucose = 4-(beta-D-glucosyloxy)benzoate + H+ + UDP." [EC:2.4.1.194, RHEA:15153]
synonym: "HBA glucosyltransferase activity" RELATED [EC:2.4.1.194]
synonym: "p-hydroxybenzoate glucosyltransferase activity" RELATED [EC:2.4.1.194]
synonym: "PHB glucosyltransferase activity" RELATED [EC:2.4.1.194]
@@ -274562,7 +274581,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0047258
name: sphingosine beta-galactosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: sphingosine + UDP-D-galactose = H(+) + psychosine + UDP." [EC:2.4.1.23, RHEA:19485]
+def: "Catalysis of the reaction: sphingosine + UDP-D-galactose = H+ + psychosine + UDP." [EC:2.4.1.23, RHEA:19485]
synonym: "galactosyl-sphingosine transferase activity" RELATED [EC:2.4.1.23]
synonym: "psychosine-UDP galactosyltransferase activity" RELATED [EC:2.4.1.23]
synonym: "psychosine-uridine diphosphate galactosyltransferase activity" RELATED [EC:2.4.1.23]
@@ -274609,7 +274628,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0047261
name: steroid N-acetylglucosaminyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: estradiol-17alpha 3-D-glucuronoside + UDP-N-acetyl-alpha-D-glucosamine = 17alpha-(N-acetyl-D-glucosaminyl)-estradiol 3-D-glucuronoside + H(+) + UDP." [EC:2.4.1.39, RHEA:14153]
+def: "Catalysis of the reaction: estradiol-17alpha 3-D-glucuronoside + UDP-N-acetyl-alpha-D-glucosamine = 17alpha-(N-acetyl-D-glucosaminyl)-estradiol 3-D-glucuronoside + H+ + UDP." [EC:2.4.1.39, RHEA:14153]
synonym: "hydroxy steroid acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.39]
synonym: "steroid acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.39]
synonym: "UDP-N-acetyl-D-glucosamine:estradiol-17alpha-3-D-glucuronoside 17alpha-N-acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.39]
@@ -274883,7 +274902,7 @@ is_a: GO:0015020 ! glucuronosyltransferase activity
id: GO:0047279
name: sn-glycerol-3-phosphate 1-galactosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: sn-glycerol 3-phosphate + UDP-D-galactose = 1-O-alpha-D-galactosyl-sn-glycerol 3-phosphate + H(+) + UDP." [EC:2.4.1.96, RHEA:20341]
+def: "Catalysis of the reaction: sn-glycerol 3-phosphate + UDP-D-galactose = 1-O-alpha-D-galactosyl-sn-glycerol 3-phosphate + H+ + UDP." [EC:2.4.1.96, RHEA:20341]
synonym: "glycerol 3-phosphate 1alpha-galactosyltransferase activity" RELATED [EC:2.4.1.96]
synonym: "isofloridoside-phosphate synthase activity" RELATED [EC:2.4.1.96]
synonym: "UDP-Gal:sn-glycero-3-phosphoric acid 1-alpha-galactosyl-transferase activity" RELATED [EC:2.4.1.96]
@@ -274901,7 +274920,7 @@ is_a: GO:0035250 ! UDP-galactosyltransferase activity
id: GO:0047280
name: nicotinamide phosphoribosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: diphosphate + nicotinamide mononucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + H(+) + nicotinamide." [RHEA:16149]
+def: "Catalysis of the reaction: diphosphate + nicotinamide mononucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + H+ + nicotinamide." [RHEA:16149]
synonym: "nicotinamide mononucleotide pyrophosphorylase activity" RELATED [EC:2.4.2.12]
synonym: "nicotinamide mononucleotide synthetase activity" RELATED [EC:2.4.2.12]
synonym: "nicotinamide-nucleotide:diphosphate phospho-alpha-D-ribosyltransferase activity" RELATED [EC:2.4.2.12]
@@ -274934,7 +274953,7 @@ is_a: GO:0016763 ! pentosyltransferase activity
id: GO:0047282
name: dTDP-dihydrostreptose-streptidine-6-phosphate dihydrostreptosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dTDP-L-dihydrostreptose + streptidine 6-phosphate = O-(1->4)-alpha-L-dihydrostreptosyl-streptidine 6-phosphate + dTDP + H(+)." [EC:2.4.2.27, RHEA:24392]
+def: "Catalysis of the reaction: dTDP-L-dihydrostreptose + streptidine 6-phosphate = O-(1->4)-alpha-L-dihydrostreptosyl-streptidine 6-phosphate + dTDP + H+." [EC:2.4.2.27, RHEA:24392]
synonym: "dTDP-L-dihydrostreptose:streptidine-6-phosphate dihydrostreptosyltransferase activity" RELATED [EC:2.4.2.27]
synonym: "dTDPdihydrostreptose-streptidine-6-phosphate dihydrostreptosyltransferase activity" RELATED [EC:2.4.2.27]
synonym: "thymidine diphosphodihydrostreptose-streptidine 6-phosphate dihydrostreptosyltransferase activity" RELATED [EC:2.4.2.27]
@@ -275022,7 +275041,7 @@ is_a: GO:0008373 ! sialyltransferase activity
id: GO:0047289
name: galactosyldiacylglycerol alpha-2,3-sialyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,2-diacyl-3-beta-D-galactosyl-sn-glycerol + CMP-N-acetyl-beta-neuraminate = 1,2-diacyl-3-[3-(alpha-D-N-acetylneuraminyl)-beta-D-galactosyl]-sn-glycerol + CMP + H(+)." [EC:2.4.99.5, RHEA:11664]
+def: "Catalysis of the reaction: 1,2-diacyl-3-beta-D-galactosyl-sn-glycerol + CMP-N-acetyl-beta-neuraminate = 1,2-diacyl-3-[3-(alpha-D-N-acetylneuraminyl)-beta-D-galactosyl]-sn-glycerol + CMP + H+." [EC:2.4.99.5, RHEA:11664]
synonym: "CMP-N-acetylneuraminate:1,2-diacyl-3-beta-D-galactosyl-sn-glycerol N-acetylneuraminyltransferase activity" RELATED [EC:2.4.99.5]
xref: EC:2.4.99.5
xref: KEGG_REACTION:R03468
@@ -275048,7 +275067,7 @@ synonym: "ST6GALNAC activity" RELATED [EC:2.4.99.7]
xref: EC:2.4.99.7
xref: KEGG_REACTION:R04635
xref: MetaCyc:2.4.99.7-RXN
-xref: Reactome:R-HSA-981809 "ST6GALNAC3/4 can add a sialic acid to the sialyl T antigen to form the disialyl T antigen"
+xref: Reactome:R-HSA-981809 "ST6GALNAC3/4 transfers sialic acid to the sialyl T antigen to form the disialyl T antigen"
xref: RHEA:53896
is_a: GO:0008373 ! sialyltransferase activity
@@ -275672,7 +275691,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0047331
name: diphosphate-glycerol phosphotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycerol + diphosphate = glycerol 1-phosphate + H(+) + phosphate." [EC:2.7.1.79, RHEA:13689]
+def: "Catalysis of the reaction: glycerol + diphosphate = glycerol 1-phosphate + H+ + phosphate." [EC:2.7.1.79, RHEA:13689]
synonym: "diphosphate:glycerol 1-phosphotransferase activity" RELATED [EC:2.7.1.79]
synonym: "PPi-glycerol phosphotransferase activity" RELATED [EC:2.7.1.79]
synonym: "pyrophosphate--glycerol phosphotransferase activity" RELATED [EC:2.7.1.79]
@@ -275687,7 +275706,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0047332
name: diphosphate-serine phosphotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-serine + diphosphate = O-phospho-L-serine + H(+) + phosphate." [EC:2.7.1.80, RHEA:23764]
+def: "Catalysis of the reaction: L-serine + diphosphate = O-phospho-L-serine + H+ + phosphate." [EC:2.7.1.80, RHEA:23764]
synonym: "diphosphate:L-serine O-phosphotransferase activity" RELATED [EC:2.7.1.80]
synonym: "pyrophosphate--serine phosphotransferase activity" RELATED [EC:2.7.1.80]
synonym: "pyrophosphate-L-serine phosphotransferase activity" RELATED [EC:2.7.1.80]
@@ -275702,7 +275721,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0047333
name: dihydrostreptomycin-6-phosphate 3'-alpha-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + dihydrostreptomycin 6-phosphate = ADP + dihydrostreptomycin 3'alpha,6-bisphosphate + 2 H(+)." [EC:2.7.1.88, RHEA:16281]
+def: "Catalysis of the reaction: ATP + dihydrostreptomycin 6-phosphate = ADP + dihydrostreptomycin 3'alpha,6-bisphosphate + 2 H+." [EC:2.7.1.88, RHEA:16281]
synonym: "ATP:dihydrostreptomycin-6-P 3'alpha-phosphotransferase activity" RELATED [EC:2.7.1.88]
synonym: "ATP:dihydrostreptomycin-6-phosphate 3'alpha-phosphotransferase activity" RELATED [EC:2.7.1.88]
synonym: "dihydrostreptomycin 6-phosphate kinase (phosphorylating)" RELATED [EC:2.7.1.88]
@@ -275750,7 +275769,7 @@ is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
id: GO:0047336
name: 5-methyldeoxycytidine-5'-phosphate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2'-deoxy-5-methyl-5'-cytidylate + ATP = 5-methyldeoxycytidine diphosphate + ADP + H(+)." [EC:2.7.4.19, RHEA:11396]
+def: "Catalysis of the reaction: 2'-deoxy-5-methyl-5'-cytidylate + ATP = 5-methyldeoxycytidine diphosphate + ADP + H+." [EC:2.7.4.19, RHEA:11396]
synonym: "ATP:5-methyldeoxycytidine-5'-phosphate phosphotransferase activity" RELATED [EC:2.7.4.19]
xref: EC:2.7.4.19
xref: KEGG_REACTION:R04235
@@ -275817,7 +275836,7 @@ is_a: GO:0016779 ! nucleotidyltransferase activity
id: GO:0047341
name: fucose-1-phosphate guanylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: beta-L-fucose 1-phosphate + GTP = diphosphate + GDP-L-fucose." [EC:2.7.7.30, RHEA:13549]
+def: "Catalysis of the reaction: beta-L-fucose 1-phosphate + GTP + H+ = diphosphate + GDP-beta-L-fucose." [RHEA:13549]
synonym: "GDP fucose pyrophosphorylase activity" RELATED [EC:2.7.7.30]
synonym: "GDP-fucose diphosphorylase activity" RELATED [EC:2.7.7.30]
synonym: "GDP-fucose pyrophosphorylase activity" RELATED [EC:2.7.7.30]
@@ -275875,7 +275894,7 @@ is_a: GO:0070567 ! cytidylyltransferase activity
id: GO:0047344
name: glucose-1-phosphate guanylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: alpha-D-glucose 1-phosphate + GTP = diphosphate + GDP-D-glucose." [EC:2.7.7.34, RHEA:10708]
+def: "Catalysis of the reaction: alpha-D-glucose 1-phosphate + GTP = diphosphate + GDP-D-glucose." [RHEA:10708]
synonym: "GDP glucose pyrophosphorylase activity" RELATED [EC:2.7.7.34]
synonym: "GDP-glucose diphosphorylase activity" RELATED [EC:2.7.7.34]
synonym: "GDP-glucose pyrophosphorylase activity" RELATED [EC:2.7.7.34]
@@ -275892,7 +275911,7 @@ is_a: GO:0070568 ! guanylyltransferase activity
id: GO:0047345
name: ribose-5-phosphate adenylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-ribose 5-phosphate + ADP + H(+) = ADP-ribose + phosphate." [EC:2.7.7.35, RHEA:14529]
+def: "Catalysis of the reaction: D-ribose 5-phosphate + ADP + H+ = ADP-ribose + phosphate." [EC:2.7.7.35, RHEA:14529]
synonym: "adenosine diphosphoribose phosphorylase activity" RELATED [EC:2.7.7.35]
synonym: "ADP ribose phosphorylase activity" RELATED [EC:2.7.7.35]
synonym: "ADP-ribose phosphorylase activity" RELATED [EC:2.7.7.35]
@@ -275999,10 +276018,11 @@ is_a: GO:0070569 ! uridylyltransferase activity
[Term]
id: GO:0047351
-name: guanosine-triphosphate guanylyltransferase activity
+name: GTP guanylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 GTP = P(1),P(4)-bis(5'-guanosyl) tetraphosphate + diphosphate + H(+)." [EC:2.7.7.45, RHEA:18153]
+def: "Catalysis of the reaction: 2 GTP + H+ = P(1),P(4)-bis(5'-guanosyl) tetraphosphate + diphosphate + H+." [RHEA:18153]
synonym: "GTP:GTP guanylyltransferase activity" BROAD []
+synonym: "guanosine-triphosphate guanylyltransferase activity" EXACT []
xref: EC:2.7.7.45
xref: KEGG_REACTION:R00012
xref: MetaCyc:2.7.7.45-RXN
@@ -276013,7 +276033,7 @@ is_a: GO:0070568 ! guanylyltransferase activity
id: GO:0047352
name: adenylylsulfate-ammonia adenylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5'-adenylyl sulfate + NH(4)(+) = adenosine 5'-phosphoramidate + 2 H(+) + sulfate." [EC:2.7.7.51, RHEA:19197]
+def: "Catalysis of the reaction: 5'-adenylyl sulfate + NH4 = adenosine 5'-phosphoramidate + 2 H+ + sulfate." [EC:2.7.7.51, RHEA:19197]
synonym: "adenylylsulfate:ammonia adenylyltransferase activity" RELATED [EC:2.7.7.51]
synonym: "adenylylsulphate-ammonia adenylyltransferase activity" EXACT []
synonym: "APSAT" RELATED [EC:2.7.7.51]
@@ -276042,7 +276062,7 @@ is_a: GO:0070567 ! cytidylyltransferase activity
id: GO:0047354
name: sphingosine cholinephosphotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: CDP-choline + sphingosine = CMP + H(+) + sphingosyl-phosphocholine." [EC:2.7.8.10, RHEA:21224]
+def: "Catalysis of the reaction: CDP-choline + sphingosine = CMP + H+ + sphingosyl-phosphocholine." [EC:2.7.8.10, RHEA:21224]
synonym: "CDP-choline-sphingosine cholinephosphotransferase activity" RELATED [EC:2.7.8.10]
synonym: "CDP-choline:sphingosine cholinephosphotransferase activity" RELATED [EC:2.7.8.10]
synonym: "cytidine diphosphocholine-sphingosine cholinephosphotransferase activity" RELATED [EC:2.7.8.10]
@@ -276094,7 +276114,7 @@ is_a: GO:0016780 ! phosphotransferase activity, for other substituted phosphate
id: GO:0047357
name: UDP-galactose-UDP-N-acetylglucosamine galactose phosphotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: UDP-N-acetyl-alpha-D-glucosamine + UDP-D-galactose = H(+) + UDP-N-acetyl-6-(D-galactose-1-phospho)-D-glucosamine + UMP." [EC:2.7.8.18, RHEA:22440]
+def: "Catalysis of the reaction: UDP-N-acetyl-alpha-D-glucosamine + UDP-D-galactose = H+ + UDP-N-acetyl-6-(D-galactose-1-phospho)-D-glucosamine + UMP." [EC:2.7.8.18, RHEA:22440]
synonym: "galactose-1-phosphotransferase activity" RELATED [EC:2.7.8.18]
synonym: "galactosyl phosphotransferase activity" RELATED [EC:2.7.8.18]
synonym: "UDP-galactose:UDP-N-acetyl-D-glucosamine galactose phosphotransferase activity" RELATED [EC:2.7.8.18]
@@ -276193,7 +276213,7 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0047364
name: desulfoglucosinolate sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + desulfoglucotropeolin = adenosine 3',5'-diphosphate + glucotropeolin + H(+)." [EC:2.8.2.24, RHEA:20281]
+def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + desulfoglucotropeolin = adenosine 3',5'-diphosphate + glucotropeolin + H+." [EC:2.8.2.24, RHEA:20281]
synonym: "3'-phosphoadenosine-5'-phosphosulfate:desulfoglucosinolate sulfotransferase activity" RELATED [EC:2.8.2.24]
synonym: "3'-phosphoadenylyl-sulfate:desulfoglucosinolate sulfotransferase activity" RELATED [EC:2.8.2.24]
synonym: "desulphoglucosinolate sulphotransferase activity" EXACT []
@@ -276208,7 +276228,7 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0047365
name: quercetin-3-sulfate 3'-sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + quercetin 3-sulfate = adenosine 3',5'-diphosphate + H(+) + quercetin 3,3'-disulfate." [EC:2.8.2.26, RHEA:22504]
+def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + quercetin 3-sulfate = adenosine 3',5'-diphosphate + H+ + quercetin 3,3'-disulfate." [EC:2.8.2.26, RHEA:22504]
synonym: "3'-phosphoadenylyl-sulfate:quercetin-3-sulfate 3'-sulfotransferase activity" RELATED [EC:2.8.2.26]
synonym: "3'-sulfotransferase activity" RELATED [EC:2.8.2.26]
synonym: "flavonol 3'-sulfotransferase activity" RELATED [EC:2.8.2.26]
@@ -276224,7 +276244,7 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0047366
name: quercetin-3-sulfate 4'-sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + quercetin 3-sulfate = adenosine 3',5'-diphosphate + H(+) + quercetin 3,4'-disulfate." [EC:2.8.2.27, RHEA:17205]
+def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + quercetin 3-sulfate = adenosine 3',5'-diphosphate + H+ + quercetin 3,4'-disulfate." [EC:2.8.2.27, RHEA:17205]
synonym: "3'-phosphoadenylyl-sulfate:quercetin-3-sulfate 4'-sulfotransferase activity" RELATED [EC:2.8.2.27]
synonym: "flavonol 4'-sulfotransferase activity" RELATED [EC:2.8.2.27]
synonym: "PAPS:flavonol 3-sulfate 4'-sulfotransferase activity" RELATED [EC:2.8.2.27]
@@ -276254,7 +276274,7 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0047368
name: UDP-N-acetylgalactosamine-4-sulfate sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + UDP-N-acetyl-D-galactosamine 4-sulfate = adenosine 3',5'-diphosphate + H(+) + UDP-N-acetyl-D-galactosamine 4,6-disulfate." [EC:2.8.2.7, RHEA:14337]
+def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + UDP-N-acetyl-D-galactosamine 4-sulfate = adenosine 3',5'-diphosphate + H+ + UDP-N-acetyl-D-galactosamine 4,6-disulfate." [EC:2.8.2.7, RHEA:14337]
synonym: "3'-phosphoadenylyl-sulfate:UDP-N-acetyl-D-galactosamine-4-sulfate 6-sulfotransferase activity" RELATED [EC:2.8.2.7]
synonym: "UDP-N-acetylgalactosamine-4-sulphate sulphotransferase activity" EXACT []
synonym: "uridine diphospho-N-acetylgalactosamine 4-sulfate sulfotransferase activity" RELATED [EC:2.8.2.7]
@@ -276340,7 +276360,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0047373
name: acetoxybutynylbithiophene deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-(4-acetoxybut-1-ynyl)-2,2'-bithiophene + H(2)O = 5-(4-hydroxy-but-1-ynyl)-2,2'-bithiophene + acetate + H(+)." [EC:3.1.1.54, RHEA:11548]
+def: "Catalysis of the reaction: 5-(4-acetoxybut-1-ynyl)-2,2'-bithiophene + H2O = 5-(4-hydroxy-but-1-ynyl)-2,2'-bithiophene + acetate + H+." [EC:3.1.1.54, RHEA:11548]
synonym: "5-(4-acetoxy-1-butynyl)-2,2'-bithiophene:acetate esterase activity" RELATED [EC:3.1.1.54]
synonym: "5-(4-acetoxybut-1-ynyl)-2,2'-bithiophene O-acetylhydrolase activity" RELATED [EC:3.1.1.54]
synonym: "acetoxybutynylbithiophene esterase activity" RELATED [EC:3.1.1.54]
@@ -276355,7 +276375,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0047374
name: methylumbelliferyl-acetate deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-methylumbelliferyl acetate + H(2)O = 4-methylumbelliferone + acetate + H(+)." [EC:3.1.1.56, RHEA:12208]
+def: "Catalysis of the reaction: 4-methylumbelliferyl acetate + H2O = 4-methylumbelliferone + acetate + H+." [EC:3.1.1.56, RHEA:12208]
synonym: "4-methylumbelliferyl-acetate acylhydrolase activity" RELATED [EC:3.1.1.56]
synonym: "esterase D activity" RELATED [EC:3.1.1.56]
xref: EC:3.1.1.56
@@ -276384,21 +276404,21 @@ id: GO:0047376
name: all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity
namespace: molecular_function
def: "Catalysis of the reaction: all-trans-retinyl palmitate + H2O = all-trans-retinol + H+ + palmitate." [RHEA:13933]
-synonym: "all-trans-retinyl-palmitate acylhydrolase activity" BROAD [EC:3.1.1.64]
-synonym: "all-trans-retinyl-palmitate hydrolase activity" BROAD [EC:3.1.1.64]
+synonym: "all-trans-retinyl-palmitate acylhydrolase activity" BROAD []
+synonym: "all-trans-retinyl-palmitate hydrolase activity" BROAD []
synonym: "retinyl-palmitate palmitohydrolase activity" BROAD [KEGG_REACTION:R02368]
xref: KEGG_REACTION:R02368
xref: MetaCyc:3.1.1.64-RXN
xref: Reactome:R-HSA-2404140 "NREH hydrolyses atREs to atROL and FAs"
xref: Reactome:R-HSA-2429643 "NREH hydrolyses atREs (HSPG:apoE) to atROL and FAs"
xref: RHEA:13933
-is_a: GO:0052689 ! carboxylic ester hydrolase activity
+is_a: GO:0050253 ! retinyl-palmitate esterase activity
[Term]
id: GO:0047377
name: 5-(3,4-diacetoxybut-1-ynyl)-2,2'-bithiophene deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-(3,4-diacetoxybut-1-ynyl)-2,2'-bithiophene + H(2)O = 5-(3-hydroxy-4-acetoxybut-1-ynyl)-2,2'-bithiophene + acetate + H(+)." [EC:3.1.1.66, RHEA:16313]
+def: "Catalysis of the reaction: 5-(3,4-diacetoxybut-1-ynyl)-2,2'-bithiophene + H2O = 5-(3-hydroxy-4-acetoxybut-1-ynyl)-2,2'-bithiophene + acetate + H+." [EC:3.1.1.66, RHEA:16313]
synonym: "3,4-diacetoxybutinylbithiophene:4-acetate esterase activity" RELATED [EC:3.1.1.66]
synonym: "5-(3,4-diacetoxybut-1-ynyl)-2,2'-bithiophene acetylhydrolase activity" RELATED [EC:3.1.1.66]
synonym: "diacetoxybutynylbithiophene acetate esterase activity" RELATED [EC:3.1.1.66]
@@ -276413,7 +276433,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0047378
name: acetylalkylglycerol acetylhydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-acetyl-1-alkyl-sn-glycerol + H(2)O = 1-alkyl-sn-glycerol + acetate + H(+)." [EC:3.1.1.71, RHEA:11552]
+def: "Catalysis of the reaction: 2-acetyl-1-alkyl-sn-glycerol + H2O = 1-alkyl-sn-glycerol + acetate + H+." [EC:3.1.1.71, RHEA:11552]
synonym: "2-acetyl-1-alkyl-sn-glycerol acetylhydrolase activity" RELATED [EC:3.1.1.71]
synonym: "alkylacetylglycerol acetylhydrolase activity" RELATED [EC:3.1.1.71]
xref: EC:3.1.1.71
@@ -276478,7 +276498,7 @@ is_a: GO:0016297 ! acyl-[acyl-carrier-protein] hydrolase activity
id: GO:0047382
name: methylphosphothioglycerate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-methyl-3-phospho-1-thio-D-glycerate + H(2)O = S-methyl-1-thio-D-glycerate + phosphate." [EC:3.1.3.14, RHEA:16081]
+def: "Catalysis of the reaction: S-methyl-3-phospho-1-thio-D-glycerate + H2O = S-methyl-1-thio-D-glycerate + phosphate." [EC:3.1.3.14, RHEA:16081]
synonym: "methylthiophosphoglycerate phosphatase activity" RELATED [EC:3.1.3.14]
synonym: "S-methyl-3-phospho-1-thio-D-glycerate phosphohydrolase activity" RELATED [EC:3.1.3.14]
xref: EC:3.1.3.14
@@ -276491,7 +276511,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0047383
name: guanidinodeoxy-scyllo-inositol-4-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-guanidino-1-deoxy-scyllo-inositol 4-phosphate + H(2)O = 1-guanidino-1-deoxy-scyllo-inositol + phosphate." [EC:3.1.3.40, RHEA:15777]
+def: "Catalysis of the reaction: 1-guanidino-1-deoxy-scyllo-inositol 4-phosphate + H2O = 1-guanidino-1-deoxy-scyllo-inositol + phosphate." [EC:3.1.3.40, RHEA:15777]
synonym: "1-guanidino-1-deoxy-scyllo-inositol-4-P phosphohydrolase activity" RELATED [EC:3.1.3.40]
synonym: "1-guanidino-1-deoxy-scyllo-inositol-4-phosphate 4-phosphohydrolase activity" RELATED [EC:3.1.3.40]
synonym: "1-guanidino-scyllo-inositol 4-phosphatase activity" RELATED [EC:3.1.3.40]
@@ -276531,7 +276551,7 @@ is_a: GO:0004721 ! phosphoprotein phosphatase activity
id: GO:0047386
name: fructose-2,6-bisphosphate 6-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: beta-D-fructose 2,6-bisphosphate + H(2)O = beta-D-fructofuranose 2-phosphate + phosphate." [EC:3.1.3.54, RHEA:13333]
+def: "Catalysis of the reaction: beta-D-fructose 2,6-bisphosphate + H2O = beta-D-fructofuranose 2-phosphate + phosphate." [EC:3.1.3.54, RHEA:13333]
synonym: "beta-D-fructose-2,6-bisphosphate 6-phosphohydrolase activity" RELATED [EC:3.1.3.54]
synonym: "D-fructose-2,6-bisphosphate 6-phosphohydrolase activity" RELATED [EC:3.1.3.54]
synonym: "fructose 2,6-bisphosphate-6-phosphohydrolase activity" RELATED [EC:3.1.3.54]
@@ -276546,7 +276566,7 @@ is_a: GO:0050308 ! sugar-phosphatase activity
id: GO:0047387
name: serine-ethanolaminephosphate phosphodiesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + serine phosphoethanolamine = H(+) + phosphoethanolamine + serine." [EC:3.1.4.13, RHEA:17113]
+def: "Catalysis of the reaction: H2O + serine phosphoethanolamine = H+ + phosphoethanolamine + serine." [EC:3.1.4.13, RHEA:17113]
synonym: "SEP diesterase activity" RELATED [EC:3.1.4.13]
synonym: "serine ethanolamine phosphodiester phosphodiesterase activity" RELATED [EC:3.1.4.13]
synonym: "serine-phosphoethanolamine ethanolaminephosphohydrolase activity" RELATED [EC:3.1.4.13]
@@ -276595,7 +276615,7 @@ is_a: GO:0008081 ! phosphoric diester hydrolase activity
id: GO:0047390
name: glycerophosphocholine cholinephosphodiesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: sn-glycero-3-phosphocholine + H(2)O = choline phosphate + glycerol + H(+)." [EC:3.1.4.38, RHEA:19545]
+def: "Catalysis of the reaction: sn-glycero-3-phosphocholine + H2O = choline phosphate + glycerol + H+." [EC:3.1.4.38, RHEA:19545]
synonym: "L-3-glycerylphosphinicocholine cholinephosphohydrolase activity" RELATED [EC:3.1.4.38]
synonym: "sn-glycero-3-phosphocholine cholinephosphohydrolase activity" RELATED [EC:3.1.4.38]
xref: EC:3.1.4.38
@@ -276639,7 +276659,7 @@ is_a: GO:0008081 ! phosphoric diester hydrolase activity
id: GO:0047393
name: glycerol-1,2-cyclic-phosphate 2-phosphodiesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycerol 1,2-cyclic phosphate + H(2)O = glycerol 1-phosphate + H(+)." [EC:3.1.4.42, RHEA:16493]
+def: "Catalysis of the reaction: glycerol 1,2-cyclic phosphate + H2O = glycerol 1-phosphate + H+." [EC:3.1.4.42, RHEA:16493]
synonym: "rac-glycerol 1:2-cyclic phosphate 2-phosphodiesterase activity" RELATED [EC:3.1.4.42]
synonym: "rac-glycerol-1,2-cyclic-phosphate 2-glycerophosphohydrolase activity" RELATED [EC:3.1.4.42]
xref: EC:3.1.4.42
@@ -276669,7 +276689,7 @@ is_a: GO:0008081 ! phosphoric diester hydrolase activity
id: GO:0047395
name: glycerophosphoinositol glycerophosphodiesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-(sn-glycero-3-phospho)-1D-myo-inositol + H(2)O = sn-glycerol 3-phosphate + myo-inositol + H(+)." [EC:3.1.4.44, RHEA:16501]
+def: "Catalysis of the reaction: 1-(sn-glycero-3-phospho)-1D-myo-inositol + H2O = sn-glycerol 3-phosphate + myo-inositol + H+." [EC:3.1.4.44, RHEA:16501]
synonym: "1-(sn-glycero-3-phospho)-1D-myo-inositol glycerophosphohydrolase activity" RELATED [EC:3.1.4.44]
synonym: "sn-glycero(3)phosphoinositol glycerophosphohydrolase activity" RELATED [EC:3.1.4.44]
synonym: "sn-glycero-3-phospho-1-inositol glycerophosphohydrolase activity" RELATED [EC:3.1.4.44]
@@ -276743,7 +276763,7 @@ is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
id: GO:0047400
name: phosphonoacetate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + phosphonoacetate = acetate + H(+) + phosphate." [EC:3.11.1.2, RHEA:16749]
+def: "Catalysis of the reaction: H2O + phosphonoacetate = acetate + H+ + phosphate." [EC:3.11.1.2, RHEA:16749]
synonym: "phosphonoacetate phosphonohydrolase activity" RELATED [EC:3.11.1.2]
xref: EC:3.11.1.2
xref: KEGG_REACTION:R00318
@@ -276755,7 +276775,7 @@ is_a: GO:0016827 ! hydrolase activity, acting on acid carbon-phosphorus bonds
id: GO:0047401
name: trithionate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + trithionate = H(+) + sulfate + thiosulfate." [EC:3.12.1.1, RHEA:21884]
+def: "Catalysis of the reaction: H2O + trithionate = H+ + sulfate + thiosulfate." [EC:3.12.1.1, RHEA:21884]
synonym: "trithionate thiosulfohydrolase activity" RELATED [EC:3.12.1.1]
xref: EC:3.12.1.1
xref: KEGG_REACTION:R01930
@@ -276816,7 +276836,7 @@ is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
id: GO:0047406
name: beta-aspartyl-N-acetylglucosaminidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(4)-(beta-N-acetyl-D-glucosaminyl)-L-asparagine + H(2)O = N-acetyl-D-glucosamine + L-asparagine." [EC:3.2.2.11, RHEA:12324]
+def: "Catalysis of the reaction: N(4)-(beta-N-acetyl-D-glucosaminyl)-L-asparagine + H2O = N-acetyl-D-glucosamine + L-asparagine." [EC:3.2.2.11, RHEA:12324]
synonym: "1-beta-aspartyl-N-acetyl-D-glucosaminylamine L-asparaginohydrolase activity" RELATED [EC:3.2.2.11]
synonym: "beta-aspartylacetylglucosaminidase activity" RELATED [EC:3.2.2.11]
xref: EC:3.2.2.11
@@ -276903,7 +276923,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047413
name: N(alpha)-benzyloxycarbonylleucine hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-benzyloxycarbonyl-L-leucine + H(2)O + H(+) = L-leucine + benzyl alcohol + CO(2)." [EC:3.5.1.64, RHEA:18901]
+def: "Catalysis of the reaction: N-benzyloxycarbonyl-L-leucine + H2O + H+ = L-leucine + benzyl alcohol + CO2." [EC:3.5.1.64, RHEA:18901]
synonym: "alpha-N-benzyloxycarbonyl-L-leucine urethanehydrolase activity" RELATED [EC:3.5.1.64]
synonym: "benzyloxycarbonylleucine hydrolase activity" RELATED [EC:3.5.1.64]
synonym: "nalpha-benzyloxycarbonyl amino acid urethane hydrolase IV" RELATED [EC:3.5.1.64]
@@ -276919,7 +276939,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047414
name: 2-(hydroxymethyl)-3-(acetamidomethylene)succinate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2Z)-2-(acetamidomethylene)-3-(hydroxymethyl)succinate + 2 H(2)O + H(+) = 2-(hydroxymethyl)-4-oxobutanoate + acetate + CO(2) + NH(4)(+)." [EC:3.5.1.66, RHEA:17677]
+def: "Catalysis of the reaction: (2Z)-2-(acetamidomethylene)-3-(hydroxymethyl)succinate + 2 H2O + H+ = 2-(hydroxymethyl)-4-oxobutanoate + acetate + CO2 + NH4." [EC:3.5.1.66, RHEA:17677]
synonym: "2-(hydroxymethyl)-3-(acetamidomethylene)succinate amidohydrolase (deaminating, decarboxylating)" RELATED [EC:3.5.1.66]
synonym: "alpha-hydroxymethyl-alpha'-(N-acetylaminomethylene)succinic acid hydrolase activity" RELATED [EC:3.5.1.66]
synonym: "compound B hydrolase activity" RELATED [EC:3.5.1.66]
@@ -276934,7 +276954,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047415
name: D-benzoylarginine-4-nitroanilide amidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(2)-benzoyl-D-arginine-4-nitroanilide + H(2)O = 4-nitroaniline + N(2)-benzoyl-D-arginine + H(+)." [EC:3.5.1.72, RHEA:14421]
+def: "Catalysis of the reaction: N(2)-benzoyl-D-arginine-4-nitroanilide + H2O = 4-nitroaniline + N(2)-benzoyl-D-arginine + H+." [EC:3.5.1.72, RHEA:14421]
synonym: "benzoyl-D-arginine arylamidase activity" RELATED [EC:3.5.1.72]
synonym: "D-BAPA-ase activity" RELATED [EC:3.5.1.72]
synonym: "N-benzoyl-D-arginine-4-nitroanilide amidohydrolase activity" RELATED [EC:3.5.1.72]
@@ -277006,7 +277026,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047421
name: N-acyl-D-glutamate deacylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-acyl-D-glutamate + H(2)O = D-glutamate + a carboxylate." [EC:3.5.1.82, RHEA:12833]
+def: "Catalysis of the reaction: N-acyl-D-glutamate + H2O = D-glutamate + a carboxylate." [EC:3.5.1.82, RHEA:12833]
synonym: "N-acyl-D-glutamate amidohydrolase activity" RELATED [EC:3.5.1.82]
xref: EC:3.5.1.82
xref: KEGG_REACTION:R01581
@@ -277018,7 +277038,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047422
name: N-acyl-D-aspartate deacylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-acyl-D-aspartate + H(2)O = D-aspartate + a carboxylate." [EC:3.5.1.83, RHEA:18285]
+def: "Catalysis of the reaction: N-acyl-D-aspartate + H2O = D-aspartate + a carboxylate." [EC:3.5.1.83, RHEA:18285]
synonym: "N-acyl-D-aspartate amidohydrolase activity" RELATED [EC:3.5.1.83]
xref: EC:3.5.1.83
xref: KEGG_REACTION:R02182
@@ -277030,7 +277050,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047423
name: N-methylhydantoinase (ATP-hydrolyzing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-methylhydantoin + ATP + 2 H(2)O = N-carbamoylsarcosine + ADP + 3 H(+) + phosphate." [EC:3.5.2.14, RHEA:11720]
+def: "Catalysis of the reaction: N-methylhydantoin + ATP + 2 H2O = N-carbamoylsarcosine + ADP + 3 H+ + phosphate." [EC:3.5.2.14, RHEA:11720]
synonym: "methylhydantoin amidase activity" RELATED [EC:3.5.2.14]
synonym: "N-methylhydantoin amidohydrolase activity" RELATED [EC:3.5.2.14]
synonym: "N-methylhydantoin hydrolase activity" RELATED [EC:3.5.2.14]
@@ -277061,7 +277081,7 @@ is_a: GO:0019239 ! deaminase activity
id: GO:0047425
name: 1-pyrroline-4-hydroxy-2-carboxylate deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-hydroxy-1-pyrroline-2-carboxylate + H(2)O + H(+) = 2,5-dioxopentanoate + NH(4)(+)." [EC:3.5.4.22, RHEA:10560]
+def: "Catalysis of the reaction: 4-hydroxy-1-pyrroline-2-carboxylate + H2O + H+ = 2,5-dioxopentanoate + NH4." [EC:3.5.4.22, RHEA:10560]
synonym: "1-pyrroline-4-hydroxy-2-carboxylate aminohydrolase (decyclizing)" RELATED [EC:3.5.4.22]
synonym: "HPC deaminase activity" RELATED [EC:3.5.4.22]
xref: EC:3.5.4.22
@@ -277086,7 +277106,7 @@ is_a: GO:0000257 ! nitrilase activity
id: GO:0047427
name: cyanoalanine nitrilase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-cyano-L-alanine + 2 H(2)O + H(+) = L-aspartate + NH(4)(+)." [EC:3.5.5.4, RHEA:11188]
+def: "Catalysis of the reaction: 3-cyano-L-alanine + 2 H2O + H+ = L-aspartate + NH4." [EC:3.5.5.4, RHEA:11188]
synonym: "3-cyano-L-alanine aminohydrolase activity" RELATED [EC:3.5.5.4]
synonym: "beta-cyanoalanine nitrilase activity" RELATED [EC:3.5.5.4]
xref: EC:3.5.5.4
@@ -277108,13 +277128,15 @@ is_a: GO:0000257 ! nitrilase activity
[Term]
id: GO:0047429
-name: nucleoside-triphosphate diphosphatase activity
+name: nucleoside triphosphate diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + a nucleoside triphosphate = diphosphate + a nucleotide." [MetaCyc:3.6.1.19-RXN]
-synonym: "nucleoside-triphosphate diphosphohydrolase activity" RELATED [EC:3.6.1.9]
-synonym: "nucleoside-triphosphate pyrophosphatase activity" RELATED [EC:3.6.1.9]
+def: "Catalysis of the reaction: a nucleoside triphosphate + H2O = a nucleotide + H+ + diphosphate." [EC:3.6.1.9]
+synonym: "nucleoside-triphosphate diphosphatase activity" EXACT []
+synonym: "nucleoside-triphosphate diphosphohydrolase activity" EXACT [EC:3.6.1.9]
+synonym: "nucleoside-triphosphate pyrophosphatase activity" EXACT [EC:3.6.1.9]
xref: EC:3.6.1.9
xref: MetaCyc:3.6.1.19-RXN
+xref: Reactome:R-HSA-9755030 "ITPA dimer dephosphorylates RBV-TP to RBV-MP"
is_a: GO:0016462 ! pyrophosphatase activity
[Term]
@@ -277133,7 +277155,7 @@ is_a: GO:0016462 ! pyrophosphatase activity
id: GO:0047431
name: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-hydroxy-6-methylpyridine-3,4-dicarboxylate + H(+) = 5-hydroxy-6-methylpyridine-3-carboxylate + CO(2)." [EC:4.1.1.51, RHEA:13669]
+def: "Catalysis of the reaction: 5-hydroxy-6-methylpyridine-3,4-dicarboxylate + H+ = 5-hydroxy-6-methylpyridine-3-carboxylate + CO2." [EC:4.1.1.51, RHEA:13669]
synonym: "3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-carboxy-lyase (3-hydroxy-2-methylpyridine-5-carboxylate-forming)" RELATED [EC:4.1.1.51]
synonym: "3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-carboxy-lyase activity" RELATED [EC:4.1.1.51]
xref: EC:4.1.1.51
@@ -277146,7 +277168,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0047432
name: 2,2-dialkylglycine decarboxylase (pyruvate) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,2-dialkylglycine + H(+) + pyruvate = L-alanine + CO(2) + dialkyl ketone." [EC:4.1.1.64, RHEA:16073]
+def: "Catalysis of the reaction: 2,2-dialkylglycine + H+ + pyruvate = L-alanine + CO2 + dialkyl ketone." [EC:4.1.1.64, RHEA:16073]
synonym: "2,2-dialkyl-2-amino acid-pyruvate aminotransferase activity" RELATED [EC:4.1.1.64]
synonym: "2,2-dialkylglycine carboxy-lyase (amino-transferring)" RELATED [EC:4.1.1.64]
synonym: "2,2-dialkylglycine carboxy-lyase (amino-transferring; L-alanine-forming)" RELATED [EC:4.1.1.64]
@@ -277164,7 +277186,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0047433
name: branched-chain-2-oxoacid decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-3-methyl-2-oxopentanoate + H(+) = 2-methylbutanal + CO(2)." [EC:4.1.1.72, RHEA:21108]
+def: "Catalysis of the reaction: (S)-3-methyl-2-oxopentanoate + H+ = 2-methylbutanal + CO2." [EC:4.1.1.72, RHEA:21108]
synonym: "(3S)-3-methyl-2-oxopentanoate carboxy-lyase (2-methylbutanal-forming)" RELATED [EC:4.1.1.72]
synonym: "(3S)-3-methyl-2-oxopentanoate carboxy-lyase activity" RELATED [EC:4.1.1.72]
synonym: "BCKA" RELATED [EC:4.1.1.72]
@@ -277195,7 +277217,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0047435
name: 5-guanidino-2-oxopentanoate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-guanidino-2-oxopentanoate + H(+) = 4-guanidinobutanal + CO(2)." [EC:4.1.1.75, RHEA:11340]
+def: "Catalysis of the reaction: 5-guanidino-2-oxopentanoate + H+ = 4-guanidinobutanal + CO2." [EC:4.1.1.75, RHEA:11340]
synonym: "2-oxo-5-guanidinopentanoate carboxy-lyase (4-guanidinobutanal-forming)" RELATED [EC:4.1.1.75]
synonym: "2-oxo-5-guanidinopentanoate carboxy-lyase activity" RELATED [EC:4.1.1.75]
synonym: "2-oxo-5-guanidinopentanoate decarboxylase activity" RELATED [EC:4.1.1.75]
@@ -277211,7 +277233,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0047436
name: arylmalonate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-aryl-2-methylmalonate + H(+) = 2-arylpropionate + CO(2)." [EC:4.1.1.76, RHEA:20513]
+def: "Catalysis of the reaction: 2-aryl-2-methylmalonate + H+ = 2-arylpropionate + CO2." [EC:4.1.1.76, RHEA:20513]
synonym: "2-aryl-2-methylmalonate carboxy-lyase (2-arylpropanoate-forming)" RELATED [EC:4.1.1.76]
synonym: "2-aryl-2-methylmalonate carboxy-lyase activity" RELATED [EC:4.1.1.76]
synonym: "AMDASE" RELATED [EC:4.1.1.76]
@@ -277351,7 +277373,7 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0047445
name: 3-hydroxy-3-isohexenylglutaryl-CoA lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA + 4 H(+) = 7-methyl-3-oxooct-6-enoyl-CoA + acetate." [EC:4.1.3.26, RHEA:23084]
+def: "Catalysis of the reaction: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA + 4 H+ = 7-methyl-3-oxooct-6-enoyl-CoA + acetate." [EC:4.1.3.26, RHEA:23084]
synonym: "3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA acetate-lyase (7-methyl-3-oxooct-6-enoyl-CoA-forming)" RELATED [EC:4.1.3.26]
synonym: "3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA acetate-lyase activity" RELATED [EC:4.1.3.26]
synonym: "3-hydroxy-3-isohexenylglutaryl coenzyme A lyase activity" RELATED [EC:4.1.3.26]
@@ -277399,7 +277421,7 @@ is_a: GO:0016841 ! ammonia-lyase activity
id: GO:0047448
name: 5-dehydro-4-deoxyglucarate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-dehydro-4-deoxy-D-glucarate + H(+) = 2,5-dioxopentanoate + CO(2) + H(2)O." [EC:4.2.1.41, RHEA:24608]
+def: "Catalysis of the reaction: 5-dehydro-4-deoxy-D-glucarate + H+ = 2,5-dioxopentanoate + CO2 + H2O." [EC:4.2.1.41, RHEA:24608]
synonym: "5-dehydro-4-deoxy-D-glucarate hydro-lyase (decarboxylating)" RELATED [EC:4.2.1.41]
synonym: "5-dehydro-4-deoxy-D-glucarate hydro-lyase (decarboxylating; 2,5-dioxopentanoate-forming)" RELATED [EC:4.2.1.41]
synonym: "5-keto-4-deoxy-glucarate dehydratase activity" RELATED [EC:4.2.1.41]
@@ -277415,7 +277437,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047449
name: 2-dehydro-3-deoxy-L-arabinonate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-dehydro-3-deoxy-L-arabinonate = 2,5-dioxopentanoate + H(2)O." [EC:4.2.1.43, RHEA:17201]
+def: "Catalysis of the reaction: 2-dehydro-3-deoxy-L-arabinonate = 2,5-dioxopentanoate + H2O." [EC:4.2.1.43, RHEA:17201]
synonym: "2-dehydro-3-deoxy-L-arabinonate hydro-lyase (2,5-dioxopentanoate-forming)" RELATED [EC:4.2.1.43]
synonym: "2-dehydro-3-deoxy-L-arabinonate hydro-lyase activity" RELATED [EC:4.2.1.43]
synonym: "2-keto-3-deoxy-L-arabinonate dehydratase activity" RELATED [EC:4.2.1.43]
@@ -277427,53 +277449,42 @@ is_a: GO:0016836 ! hydro-lyase activity
[Term]
id: GO:0047450
-name: crotonoyl-[acyl-carrier-protein] hydratase activity
+name: (3R)-hydroxybutanoyl-[acyl-carrier-protein] hydratase activity
namespace: molecular_function
alt_id: GO:0080063
-def: "Catalysis of the reaction: (3R)-3-hydroxybutanoyl-[acyl-carrier protein] = H2O + but-2-enoyl-[acyl-carrier protein]." [EC:4.2.1.58, MetaCyc:4.2.1.58-RXN]
-synonym: "(3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydro-lyase activity" RELATED [EC:4.2.1.58]
-synonym: "(3R)-3-hydroxybutanoyl-acyl-carrier-protein hydro-lyase (but-2-enoyl-acyl-carrier protein-forming)" RELATED [EC:4.2.1.58]
-synonym: "(3R)-3-hydroxybutanoyl-acyl-carrier-protein hydro-lyase activity" RELATED [EC:4.2.1.58]
-synonym: "3-hydroxybutyryl acyl carrier protein dehydratase activity" RELATED [EC:4.2.1.58]
-synonym: "beta-hydroxybutyryl acyl carrier protein (ACP) dehydrase activity" RELATED [EC:4.2.1.58]
-synonym: "beta-hydroxybutyryl acyl carrier protein dehydrase activity" RELATED [EC:4.2.1.58]
+def: "Catalysis of the reaction: (3R)-hydroxybutanoyl-[acyl-carrier-protein] = (2E)-butenoyl-[acyl-carrier-protein] + H2O." [RHEA:41808]
+synonym: "(3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydro-lyase activity" EXACT []
+synonym: "3-hydroxybutyryl acyl carrier protein dehydratase activity" EXACT []
+synonym: "beta-hydroxybutyryl acyl carrier protein (ACP) dehydrase activity" EXACT []
synonym: "crotonoyl-[acyl-carrier protein] hydratase activity" EXACT []
+synonym: "crotonoyl-[acyl-carrier-protein] hydratase activity" BROAD []
synonym: "crotonoyl-ACP hydratase activity" EXACT []
-synonym: "crotonoyl-acyl-carrier-protein hydratase activity" RELATED [EC:4.2.1.58]
-synonym: "crotonyl acyl carrier protein hydratase activity" RELATED [EC:4.2.1.58]
-synonym: "enoyl acyl carrier protein hydrase activity" RELATED [EC:4.2.1.58]
-xref: EC:4.2.1.58
+synonym: "crotonoyl-acyl-carrier-protein hydratase activity" EXACT []
+synonym: "crotonyl acyl carrier protein hydratase activity" EXACT []
xref: KEGG_REACTION:R04428
xref: MetaCyc:4.2.1.58-RXN
-is_a: GO:0019171 ! 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity
+xref: RHEA:41808
+is_a: GO:0019171 ! (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity
[Term]
id: GO:0047451
-name: 3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
+name: (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (3R)-3-hydroxyoctanoyl-[acyl-carrier protein] = H2O + 2-octenoyl-[acyl-carrier protein]." [PMID:8910376, RHEA:41844]
-synonym: "(3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] hydro-lyase activity" RELATED [EC:4.2.1.59]
-synonym: "(3R)-3-hydroxyoctanoyl-acyl-carrier-protein hydro-lyase (oct-2-enoyl-acyl-carrier protein-forming)" RELATED [EC:4.2.1.59]
-synonym: "(3R)-3-hydroxyoctanoyl-acyl-carrier-protein hydro-lyase activity" RELATED [EC:4.2.1.59]
+def: "Catalysis of the reaction: (3R)-3-hydroxyoctanoyl-[acyl-carrier protein] = H2O + (2E)-octenoyl-[acyl-carrier protein]." [PMID:8910376, RHEA:41844]
+synonym: "(3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] hydro-lyase activity" RELATED []
synonym: "3-hydroxyoctanoyl-[acyl-carrier protein] dehydratase activity" EXACT []
+synonym: "3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity" BROAD []
synonym: "3-hydroxyoctanoyl-ACP dehydratase activity" EXACT []
-synonym: "3-hydroxyoctanoyl-acyl-carrier-protein dehydratase activity" RELATED [EC:4.2.1.59]
-synonym: "beta-hydroxyoctanoyl thioester dehydratase activity" RELATED [EC:4.2.1.59]
-synonym: "beta-hydroxyoctanoyl-ACP-dehydrase activity" RELATED [EC:4.2.1.59]
-synonym: "beta-hydroxyoctanoyl-acyl carrier protein dehydrase activity" RELATED [EC:4.2.1.59]
-synonym: "D-3-hydroxyoctanoyl-[acyl carrier protein] dehydratase activity" RELATED [EC:4.2.1.59]
-synonym: "D-3-hydroxyoctanoyl-acyl carrier protein dehydratase activity" RELATED [EC:4.2.1.59]
-xref: EC:4.2.1.59
xref: KEGG_REACTION:R04537
xref: MetaCyc:4.2.1.59-RXN
xref: RHEA:41844
-is_a: GO:0019171 ! 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity
+is_a: GO:0019171 ! (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity
[Term]
id: GO:0047452
name: protoaphin-aglucone dehydratase (cyclizing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: protoaphin aglucone = H(2)O + xanthoaphin." [EC:4.2.1.73, RHEA:23876]
+def: "Catalysis of the reaction: protoaphin aglucone = H2O + xanthoaphin." [EC:4.2.1.73, RHEA:23876]
synonym: "protoaphin dehydratase (cyclizing)" RELATED [EC:4.2.1.73]
synonym: "protoaphin dehydratase activity" RELATED [EC:4.2.1.73]
synonym: "protoaphin-aglucone hydro-lyase (cyclizing)" RELATED [EC:4.2.1.73]
@@ -277488,7 +277499,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047453
name: ATP-dependent NAD(P)H-hydrate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (6S)-6beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide + ATP = ADP + 3 H(+) + NADH + phosphate." [PMID:3061454, RHEA:19017]
+def: "Catalysis of the reaction: (6S)-6beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide + ATP = ADP + 3 H+ + NADH + phosphate." [PMID:3061454, RHEA:19017]
synonym: "(6S)-beta-6-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ATP-hydrolysing)" RELATED [EC:4.2.1.93]
synonym: "(6S)-beta-6-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase(ATP-hydrolysing; NADH-forming)" RELATED [EC:4.2.1.93]
synonym: "ATP-dependent H(4)NAD(P)OH dehydratase activity" EXACT []
@@ -277505,7 +277516,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047454
name: phaseollidin hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phaseollidin hydrate = H(2)O + phaseollidin." [EC:4.2.1.97, RHEA:19769]
+def: "Catalysis of the reaction: phaseollidin hydrate = H2O + phaseollidin." [EC:4.2.1.97, RHEA:19769]
synonym: "phaseollidin-hydrate hydro-lyase (phaseollidin-forming)" RELATED [EC:4.2.1.97]
synonym: "phaseollidin-hydrate hydro-lyase activity" RELATED [EC:4.2.1.97]
xref: EC:4.2.1.97
@@ -277538,7 +277549,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047456
name: 2-methylisocitrate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = cis-2-methylaconitate + H(2)O." [EC:4.2.1.99, RHEA:17941]
+def: "Catalysis of the reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = cis-2-methylaconitate + H2O." [EC:4.2.1.99, RHEA:17941]
synonym: "(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate hydro-lyase [(Z)-but-2-ene-1,2,3-tricarboxylate-forming]" RELATED [EC:4.2.1.99]
synonym: "(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate hydro-lyase activity" RELATED [EC:4.2.1.99]
xref: EC:4.2.1.99
@@ -277567,7 +277578,7 @@ is_a: GO:0016837 ! carbon-oxygen lyase activity, acting on polysaccharides
id: GO:0047458
name: beta-pyrazolylalanine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O-acetyl-L-serine + pyrazole = 3-(pyrazol-1-yl)-L-alanine + acetate + H(+)." [EC:2.5.1.51, RHEA:13117]
+def: "Catalysis of the reaction: O-acetyl-L-serine + pyrazole = 3-(pyrazol-1-yl)-L-alanine + acetate + H+." [EC:2.5.1.51, RHEA:13117]
synonym: "3-O-acetyl-L-serine:pyrazole 1-(2-amino-2-carboxyethyl)transferase activity" RELATED [EC:2.5.1.51]
synonym: "beta-(1-pyrazolyl)alanine synthase activity" RELATED [EC:2.5.1.51]
synonym: "beta-pyrazolealanine synthase activity" RELATED [EC:2.5.1.51]
@@ -277588,7 +277599,7 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0047459
name: 3-aminobutyryl-CoA ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-3-aminobutanoyl-CoA = crotonoyl-CoA + NH(4)(+)." [EC:4.3.1.14, RHEA:10056]
+def: "Catalysis of the reaction: (S)-3-aminobutanoyl-CoA = crotonoyl-CoA + NH4." [EC:4.3.1.14, RHEA:10056]
synonym: "L-3-aminobutyryl-CoA ammonia-lyase (crotonoyl-CoA-forming)" RELATED [EC:4.3.1.14]
synonym: "L-3-aminobutyryl-CoA ammonia-lyase activity" RELATED [EC:4.3.1.14]
synonym: "L-3-aminobutyryl-CoA deaminase activity" RELATED [EC:4.3.1.14]
@@ -277602,7 +277613,7 @@ is_a: GO:0016841 ! ammonia-lyase activity
id: GO:0047460
name: L-2-amino-4-chloropent-4-enoate dehydrochlorinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-2-amino-4-chloropent-4-enoate + H(2)O = 2-oxopent-4-enoate + chloride + H(+) + NH(4)(+)." [EC:4.5.1.4, RHEA:11620]
+def: "Catalysis of the reaction: L-2-amino-4-chloropent-4-enoate + H2O = 2-oxopent-4-enoate + chloride + H+ + NH4." [EC:4.5.1.4, RHEA:11620]
synonym: "L-2-amino-4-chloro-4-pentenoate dehalogenase activity" RELATED [EC:4.5.1.4]
synonym: "L-2-amino-4-chloropent-4-enoate chloride-lyase (adding H2O; deaminating; 2-oxopent-4-enoate-forming)" RELATED [EC:4.5.1.4]
synonym: "L-2-amino-4-chloropent-4-enoate chloride-lyase (deaminating)" RELATED [EC:4.5.1.4]
@@ -277628,7 +277639,7 @@ is_a: GO:0010334 ! sesquiterpene synthase activity
id: GO:0047462
name: phenylalanine racemase (ATP-hydrolyzing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-phenylalanine + ATP + H(2)O = D-phenylalanine + AMP + diphosphate + 2 H(+)." [EC:5.1.1.11, RHEA:20201]
+def: "Catalysis of the reaction: L-phenylalanine + ATP + H2O = D-phenylalanine + AMP + diphosphate + 2 H+." [EC:5.1.1.11, RHEA:20201]
synonym: "gramicidin S synthetase I" RELATED [EC:5.1.1.11]
synonym: "phenylalanine racemase (adenosine triphosphate-hydrolysing)" RELATED [EC:5.1.1.11]
synonym: "phenylalanine racemase (ATP-hydrolysing)" BROAD [EC:5.1.1.11]
@@ -277666,6 +277677,8 @@ synonym: "poly[(1,4)-beta-D-glucuronosyl-(1,4)-N-sulfo-alpha-D-glucosaminyl] glu
synonym: "polyglucuronate epimerase activity" RELATED [EC:5.1.3.17]
xref: EC:5.1.3.17
xref: MetaCyc:5.1.3.17-RXN
+xref: Reactome:R-HSA-2024100 "GLCE epimerises GlcA to IdoA"
+xref: Reactome:R-HSA-2076371 "GLCE epimerises more GlcA to IdoA as sulfate content rises"
xref: RHEA:20197
is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and derivatives
@@ -277766,7 +277779,7 @@ id: GO:0047472
name: 3-carboxy-cis,cis-muconate cycloisomerase activity
namespace: molecular_function
alt_id: GO:0018842
-def: "Catalysis of the reaction: 2-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate = 3-carboxy-cis,cis-muconate + H(+)." [PMID:15301541, PMID:17054713, RHEA:23656]
+def: "Catalysis of the reaction: 2-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate = 3-carboxy-cis,cis-muconate + H+." [PMID:15301541, PMID:17054713, RHEA:23656]
synonym: "3-carboxymuconate cycloisomerase type II activity" RELATED []
synonym: "3-carboxymuconate lactonizing enzyme activity" RELATED [EC:5.5.1.2]
synonym: "3-carboxymuconolactone hydrolase activity" RELATED []
@@ -277796,7 +277809,7 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0047474
name: long-chain fatty acid luciferin component ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: protein + an acid + ATP = an acyl-protein thiolester + diphosphate + AMP. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [EC:6.2.1.19, MetaCyc:6.2.1.19-RXN]
+def: "Catalysis of the reaction: protein + an acid + ATP = an acyl-protein thiolester + diphosphate + AMP. A long-chain fatty acid is a fatty acid with an aliphatic tail of 13 to 21 carbons." [EC:6.2.1.19, MetaCyc:6.2.1.19-RXN]
synonym: "acyl-protein synthetase activity" RELATED [EC:6.2.1.19]
synonym: "long-chain-fatty-acid luciferin component ligase activity" EXACT [GOC:mah]
synonym: "long-chain-fatty-acid-luciferin-component ligase activity" EXACT []
@@ -277810,7 +277823,7 @@ is_a: GO:0015645 ! fatty acid ligase activity
id: GO:0047475
name: phenylacetate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + CoA + phenylacetate = AMP + diphosphate + H(+) + phenylacetyl-CoA." [EC:6.2.1.30, RHEA:20956]
+def: "Catalysis of the reaction: ATP + CoA + phenylacetate = AMP + diphosphate + H+ + phenylacetyl-CoA." [EC:6.2.1.30, RHEA:20956]
synonym: "PA-CoA ligase activity" RELATED [EC:6.2.1.30]
synonym: "phenacyl coenzyme A synthetase activity" RELATED [EC:6.2.1.30]
synonym: "phenylacetate:CoA ligase (AMP-forming)" RELATED [EC:6.2.1.30]
@@ -277842,7 +277855,7 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0047478
name: aspartate-ammonia ligase (ADP-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-aspartate + ATP + NH(4)(+) = L-asparagine + ADP + 2 H(+) + phosphate." [EC:6.3.1.4, RHEA:14197]
+def: "Catalysis of the reaction: L-aspartate + ATP + NH4 = L-asparagine + ADP + 2 H+ + phosphate." [EC:6.3.1.4, RHEA:14197]
synonym: "asparagine synthetase (adenosine diphosphate-forming)" RELATED [EC:6.3.1.4]
synonym: "asparagine synthetase (ADP-forming) activity" RELATED [EC:6.3.1.4]
synonym: "L-aspartate:ammonia ligase (ADP-forming)" RELATED [EC:6.3.1.4]
@@ -277907,7 +277920,7 @@ is_a: GO:0016881 ! acid-amino acid ligase activity
id: GO:0047482
name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-lysine + ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine." [EC:6.3.2.7, RHEA:17969]
+def: "Catalysis of the reaction: L-lysine + ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate = ADP + 2 H+ + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine." [EC:6.3.2.7, RHEA:17969]
synonym: "L-lysine-adding enzyme activity" RELATED [EC:6.3.2.7]
synonym: "MurE synthetase activity" RELATED [EC:6.3.2.7]
synonym: "UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:L-lysine gamma-ligase (ADP-forming)" RELATED [EC:6.3.2.7]
@@ -277924,7 +277937,7 @@ is_a: GO:0016881 ! acid-amino acid ligase activity
id: GO:0047483
name: imidazoleacetate-phosphoribosyldiphosphate ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-phospho-alpha-D-ribose 1-diphosphate + ATP + H(2)O + imidazol-4-ylacetate = 1-(5-phosphoribosyl)imidazol-4-ylacetate + ADP + diphosphate + 2 H(+) + phosphate." [EC:6.3.4.8, RHEA:16485]
+def: "Catalysis of the reaction: 5-phospho-alpha-D-ribose 1-diphosphate + ATP + H2O + imidazol-4-ylacetate = 1-(5-phosphoribosyl)imidazol-4-ylacetate + ADP + diphosphate + 2 H+ + phosphate." [EC:6.3.4.8, RHEA:16485]
synonym: "5-phosphoribosylimidazoleacetate synthetase activity" RELATED [EC:6.3.4.8]
synonym: "imidazoleacetate:5-phosphoribosyl-diphosphate ligase (ADP- and diphosphate-forming)" RELATED [EC:6.3.4.8]
xref: EC:6.3.4.8
@@ -277943,23 +277956,26 @@ relationship: regulates GO:0006970 ! response to osmotic stress
[Term]
id: GO:0047485
-name: protein N-terminus binding
+name: obsolete protein N-terminus binding
namespace: molecular_function
-def: "Binding to a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN:0198506732]
+def: "OBSOLETE. Binding to a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN:0198506732]
+comment: It is out of GO scope.
synonym: "amino-terminal binding" RELATED [GOC:jsg]
synonym: "amino-terminus binding" RELATED [GOC:jsg]
synonym: "N-terminal binding" EXACT []
synonym: "N-terminal end binding" EXACT [GOC:jsg]
synonym: "NH2-terminal binding" NARROW [GOC:jsg]
synonym: "NH2-terminus binding" NARROW [GOC:jsg]
-is_a: GO:0005515 ! protein binding
+is_obsolete: true
+replaced_by: GO:0005515
[Term]
id: GO:0047486
-name: chondroitin ABC lyase activity
+name: obsolete chondroitin ABC lyase activity
namespace: molecular_function
-def: "Catalysis of the eliminative degradation of polysaccharides containing 1,4-beta-D-hexosaminyl and 1,3-beta-D-glucuronosyl or 1,3-alpha-L-iduronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups." [GOC:hjd]
-is_a: GO:0016837 ! carbon-oxygen lyase activity, acting on polysaccharides
+def: "OBSOLETE. Catalysis of the eliminative degradation of polysaccharides containing 1,4-beta-D-hexosaminyl and 1,3-beta-D-glucuronosyl or 1,3-alpha-L-iduronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups." [GOC:hjd]
+comment: This term represents an unnecessary grouping class.
+is_obsolete: true
[Term]
id: GO:0047487
@@ -278054,7 +278070,7 @@ is_a: GO:0016837 ! carbon-oxygen lyase activity, acting on polysaccharides
id: GO:0047493
name: ceramide cholinephosphotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: CDP-choline + ceramide = CMP + H(+) + sphingomyelin." [EC:2.7.8.3, RHEA:16273]
+def: "Catalysis of the reaction: CDP-choline + ceramide = CMP + H+ + sphingomyelin." [EC:2.7.8.3, RHEA:16273]
synonym: "CDP-choline:N-acylsphingosine cholinephosphotransferase activity" RELATED [EC:2.7.8.3]
synonym: "phosphorylcholine-ceramide transferase activity" RELATED [EC:2.7.8.3]
xref: EC:2.7.8.3
@@ -278067,7 +278083,7 @@ is_a: GO:0016780 ! phosphotransferase activity, for other substituted phosphate
id: GO:0047494
name: serine-phosphoethanolamine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-serine + CDP-ethanolamine = L-serine-phosphoethanolamine + CMP + H(+)." [EC:2.7.8.4, RHEA:22656]
+def: "Catalysis of the reaction: L-serine + CDP-ethanolamine = L-serine-phosphoethanolamine + CMP + H+." [EC:2.7.8.4, RHEA:22656]
synonym: "CDP-ethanolamine:L-serine ethanolamine phosphotransferase activity" RELATED [EC:2.7.8.4]
synonym: "serine ethanolamine phosphate synthetase activity" RELATED [EC:2.7.8.4]
synonym: "serine ethanolamine phosphodiester synthase activity" RELATED [EC:2.7.8.4]
@@ -278135,7 +278151,7 @@ is_a: GO:0004623 ! phospholipase A2 activity
id: GO:0047500
name: (+)-borneol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (+)-borneol + NAD(+) = (1R, 4R)-camphor + H(+) + NADH." [EC:1.1.1.198, RHEA:17329]
+def: "Catalysis of the reaction: (+)-borneol + NAD+ = (1R, 4R)-camphor + H+ + NADH." [EC:1.1.1.198, RHEA:17329]
synonym: "(+)-borneol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.198]
synonym: "bicyclic monoterpenol dehydrogenase activity" RELATED [EC:1.1.1.198]
xref: EC:1.1.1.198
@@ -278148,7 +278164,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047501
name: (+)-neomenthol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (+)-neomenthol + NADP(+) = (2S,5R)-menthone + H(+) + NADPH." [EC:1.1.1.208, RHEA:23812]
+def: "Catalysis of the reaction: (+)-neomenthol + NADP+ = (2S,5R)-menthone + H+ + NADPH." [EC:1.1.1.208, RHEA:23812]
synonym: "(+)-neomenthol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.208]
synonym: "monoterpenoid dehydrogenase activity" BROAD [EC:1.1.1.208]
xref: EC:1.1.1.208
@@ -278161,7 +278177,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047502
name: (+)-sabinol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (+)-cis-sabinol + NAD(+) = (1S,5S)-sabinone + H(+) + NADH." [EC:1.1.1.228, RHEA:18329]
+def: "Catalysis of the reaction: (+)-cis-sabinol + NAD+ = (1S,5S)-sabinone + H+ + NADH." [EC:1.1.1.228, RHEA:18329]
synonym: "(+)-cis-sabinol dehydrogenase activity" RELATED [EC:1.1.1.228]
synonym: "(+)-cis-sabinol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.228]
xref: EC:1.1.1.228
@@ -278174,7 +278190,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047503
name: (-)-borneol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (-)-borneol + NAD(+) = (1S,4S)-camphor + H(+) + NADH." [EC:1.1.1.227, RHEA:22128]
+def: "Catalysis of the reaction: (-)-borneol + NAD+ = (1S,4S)-camphor + H+ + NADH." [EC:1.1.1.227, RHEA:22128]
synonym: "(-)-borneol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.227]
xref: EC:1.1.1.227
xref: KEGG_REACTION:R02945
@@ -278186,7 +278202,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047504
name: (-)-menthol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (-)-menthol + NADP(+) = (2S,5R)-menthone + H(+) + NADPH." [EC:1.1.1.207, RHEA:13917]
+def: "Catalysis of the reaction: (-)-menthol + NADP+ = (2S,5R)-menthone + H+ + NADPH." [EC:1.1.1.207, RHEA:13917]
synonym: "(-)-menthol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.207]
synonym: "monoterpenoid dehydrogenase activity" BROAD [EC:1.1.1.207]
xref: EC:1.1.1.207
@@ -278200,7 +278216,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047505
name: (-)-menthol monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (-)-menthol + H(+) + NADPH + O(2) = 1,4-menthane-3,8-diol + H(2)O + NADP(+)." [EC:1.14.13.46, RHEA:11648]
+def: "Catalysis of the reaction: (-)-menthol + H+ + NADPH + O2 = 1,4-menthane-3,8-diol + H2O + NADP+." [EC:1.14.13.46, RHEA:11648]
synonym: "(-)-menthol,NADPH:oxygen oxidoreductase (8-hydroxylating)" RELATED [EC:1.14.13.46]
synonym: "l-menthol monooxygenase activity" RELATED [EC:1.14.13.46]
xref: EC:1.14.13.46
@@ -278213,7 +278229,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047506
name: (deoxy)adenylate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + dAMP = ADP + dADP." [EC:2.7.4.11, MetaCyc:DEOXYADENYLATE-KINASE-RXN]
+def: "Catalysis of the reaction: ATP + dAMP = ADP + dADP." [EC:2.7.4.11]
synonym: "ATP:(d)AMP phosphotransferase activity" RELATED [EC:2.7.4.11]
xref: EC:2.7.4.11
xref: MetaCyc:DEOXYADENYLATE-KINASE-RXN
@@ -278225,7 +278241,7 @@ is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
id: GO:0047507
name: (deoxy)nucleoside-phosphate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + deoxynucleoside phosphate = ADP + deoxynucleoside diphosphate." [EC:2.7.4.13, MetaCyc:DEOXYNUCLEOSIDE-PHOSPHATE-KINASE-RXN]
+def: "Catalysis of the reaction: ATP + deoxynucleoside phosphate = ADP + deoxynucleoside diphosphate." [EC:2.7.4.13]
synonym: "ATP:deoxynucleoside-phosphate phosphotransferase activity" RELATED [EC:2.7.4.13]
synonym: "deoxynucleoside monophosphate kinase activity" RELATED [EC:2.7.4.13]
synonym: "deoxynucleoside-5'-monophosphate kinase activity" RELATED [EC:2.7.4.13]
@@ -278240,7 +278256,7 @@ is_a: GO:0019205 ! nucleobase-containing compound kinase activity
id: GO:0047508
name: (R)-2-methylmalate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-citramalate = 2-methylmaleate + H(2)O." [EC:4.2.1.35, RHEA:22332]
+def: "Catalysis of the reaction: (R)-citramalate = 2-methylmaleate + H2O." [EC:4.2.1.35, RHEA:22332]
synonym: "(-)-citramalate hydro-lyase activity" RELATED [EC:4.2.1.35]
synonym: "(R)-2-methylmalate hydro-lyase (2-methylmaleate-forming)" RELATED [EC:4.2.1.35]
synonym: "(R)-2-methylmalate hydro-lyase activity" RELATED [EC:4.2.1.35]
@@ -278257,7 +278273,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047509
name: (R)-dehydropantoate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-4-dehydropantoate + H(2)O + NAD(+) = (R)-3,3-dimethylmalate + 2 H(+) + NADH." [EC:1.2.1.33, RHEA:19349]
+def: "Catalysis of the reaction: (R)-4-dehydropantoate + H2O + NAD+ = (R)-3,3-dimethylmalate + 2 H+ + NADH." [EC:1.2.1.33, RHEA:19349]
synonym: "(R)-4-dehydropantoate:NAD+ 4-oxidoreductase activity" RELATED [EC:1.2.1.33]
synonym: "D-2-hydroxy-3,3-dimethyl-3-formylpropionate:diphosphopyridine nucleotide (DPN+) oxidoreductase activity" RELATED [EC:1.2.1.33]
synonym: "D-aldopantoate dehydrogenase activity" RELATED [EC:1.2.1.33]
@@ -278271,7 +278287,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0047510
name: (S)-2-methylmalate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-citramalate = H(2)O + mesaconate." [EC:4.2.1.34, RHEA:13529]
+def: "Catalysis of the reaction: S-citramalate = H2O + mesaconate." [EC:4.2.1.34, RHEA:13529]
synonym: "(+)-citramalate hydro-lyase activity" RELATED [EC:4.2.1.34]
synonym: "(+)-citramalic hydro-lyase activity" RELATED [EC:4.2.1.34]
synonym: "(S)-2-methylmalate hydro-lyase (2-methylfumarate-forming)" RELATED [EC:4.2.1.34]
@@ -278291,7 +278307,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047511
name: (S)-methylmalonyl-CoA hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-methylmalonyl-CoA + H(2)O = CoA + H(+) + methylmalonate." [EC:3.1.2.17, RHEA:17345]
+def: "Catalysis of the reaction: (S)-methylmalonyl-CoA + H2O = CoA + H+ + methylmalonate." [EC:3.1.2.17, RHEA:17345]
synonym: "D-methylmalonyl-coenzyme A hydrolase activity" RELATED [EC:3.1.2.17]
xref: EC:3.1.2.17
xref: KEGG_REACTION:R02764
@@ -278303,7 +278319,7 @@ is_a: GO:0016289 ! CoA hydrolase activity
id: GO:0047512
name: (S,S)-butanediol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S,S)-butane-2,3-diol + NAD(+) = acetoin + H(+) + NADH." [EC:1.1.1.76, RHEA:12184]
+def: "Catalysis of the reaction: (S,S)-butane-2,3-diol + NAD+ = acetoin + H+ + NADH." [EC:1.1.1.76, RHEA:12184]
synonym: "(S,S)-butane-2,3-diol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.76]
synonym: "L(+)-2,3-butanediol dehydrogenase (L-acetoin forming)" RELATED [EC:1.1.1.76]
synonym: "L-BDH" RELATED [EC:1.1.1.76]
@@ -278390,7 +278406,7 @@ is_a: GO:0016763 ! pentosyltransferase activity
id: GO:0047518
name: 1-methyladenosine nucleosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-methyladenosine + H(2)O = 1-methyladenine + ribofuranose." [EC:3.2.2.13, RHEA:12865]
+def: "Catalysis of the reaction: 1-methyladenosine + H2O = 1-methyladenine + ribofuranose." [EC:3.2.2.13, RHEA:12865]
synonym: "1-methyladenosine hydrolase activity" RELATED [EC:3.2.2.13]
synonym: "1-methyladenosine ribohydrolase activity" RELATED [EC:3.2.2.13]
xref: EC:3.2.2.13
@@ -278417,7 +278433,7 @@ is_a: GO:0016901 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047520
name: 11-cis-retinyl-palmitate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 11-cis-retinyl palmitate + H(2)O = 11-cis-retinol + H(+) + palmitate." [EC:3.1.1.63, RHEA:19697]
+def: "Catalysis of the reaction: 11-cis-retinyl palmitate + H2O = 11-cis-retinol + H+ + palmitate." [EC:3.1.1.63, RHEA:19697]
synonym: "11-cis-retinol palmitate esterase activity" RELATED [EC:3.1.1.63]
synonym: "11-cis-retinyl-palmitate acylhydrolase activity" RELATED [EC:3.1.1.63]
synonym: "RPH" RELATED [EC:3.1.1.63]
@@ -278432,7 +278448,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0047521
name: 3alpha,7alpha,12beta-trihydroxy-5beta-cholanate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3alpha,7alpha,12beta-trihydroxy-5beta-cholanate + NADP(+) = 3alpha,7alpha-dihydroxy-12-oxo-5beta-cholanate + H(+) + NADPH." [EC:1.1.1.238, RHEA:21424]
+def: "Catalysis of the reaction: 3alpha,7alpha,12beta-trihydroxy-5beta-cholanate + NADP+ = 3alpha,7alpha-dihydroxy-12-oxo-5beta-cholanate + H+ + NADPH." [EC:1.1.1.238, RHEA:21424]
synonym: "12-beta-hydroxysteroid dehydrogenase activity" BROAD [EC:1.1.1.238]
synonym: "12beta-hydroxy steroid (nicotinamide adenine dinucleotide phosphate) dehydrogenase activity" BROAD [EC:1.1.1.238]
synonym: "12beta-hydroxysteroid dehydrogenase activity" BROAD [EC:1.1.1.238]
@@ -278486,7 +278502,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047526
name: 2'-hydroxyisoflavone reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: vestitone + NADP+ = 2'-hydroxyformononetin + NADPH + H+." [EC:1.3.1.45, MetaCyc:2-HYDROXYISOFLAVONE-REDUCTASE-RXN]
+def: "Catalysis of the reaction: vestitone + NADP+ = 2'-hydroxyformononetin + NADPH + H+." [RHEA:22560]
synonym: "2',7-dihydroxy-4',5'-methylenedioxyisoflavone reductase activity" RELATED [EC:1.3.1.45]
synonym: "isoflavone reductase activity" RELATED [EC:1.3.1.45]
synonym: "NADPH:2'-hydroxyisoflavone oxidoreductase activity" RELATED [EC:1.3.1.45]
@@ -278513,7 +278529,7 @@ is_a: GO:0016881 ! acid-amino acid ligase activity
id: GO:0047528
name: 2,3-dihydroxyindole 2,3-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,3-dihydroxyindole + O(2) = anthranilate + CO(2) + H(+)." [EC:1.13.11.23, RHEA:19445]
+def: "Catalysis of the reaction: 2,3-dihydroxyindole + O2 = anthranilate + CO2 + H+." [EC:1.13.11.23, RHEA:19445]
synonym: "2,3-dihydroxyindole:oxygen 2,3-oxidoreductase (decyclizing) activity" RELATED [EC:1.13.11.23]
xref: EC:1.13.11.23
xref: KEGG_REACTION:R00983
@@ -278548,25 +278564,22 @@ is_a: GO:0016639 ! oxidoreductase activity, acting on the CH-NH2 group of donors
[Term]
id: GO:0047531
-name: 2,5-diaminovalerate transaminase activity
+name: obsolete 2,5-diaminovalerate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + ornithine = 5-amino-2-oxopentanoate + L-glutamate." [EC:2.6.1.8, RHEA:16017]
+def: "OBSOLETE. Catalysis of the reaction: 2-oxoglutarate + ornithine = 5-amino-2-oxopentanoate + L-glutamate." [EC:2.6.1.8, RHEA:16017]
+comment: This term was obsoleted because this reaction is not believed to exist.
synonym: "2,5-diaminopentanoate:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.8]
synonym: "2,5-diaminovalerate aminotransferase activity" EXACT []
synonym: "diamino acid aminotransferase activity" RELATED [EC:2.6.1.8]
synonym: "diamino-acid aminotransferase activity" RELATED [EC:2.6.1.8]
synonym: "diamino-acid transaminase activity" RELATED [EC:2.6.1.8]
-xref: EC:2.6.1.8
-xref: KEGG_REACTION:R03248
-xref: MetaCyc:25-DIAMINOVALERATE-AMINOTRANSFERASE-RXN
-xref: RHEA:16017
-is_a: GO:0008483 ! transaminase activity
+is_obsolete: true
[Term]
id: GO:0047532
name: 2,5-dioxopiperazine hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,5-dioxopiperazine + H(2)O = glycylglycine." [EC:3.5.2.13, RHEA:21808]
+def: "Catalysis of the reaction: 2,5-dioxopiperazine + H2O = glycylglycine." [EC:3.5.2.13, RHEA:21808]
synonym: "2,5-dioxopiperazine amidohydrolase activity" RELATED [EC:3.5.2.13]
synonym: "cyclo(Gly-Gly) hydrolase activity" RELATED [EC:3.5.2.13]
synonym: "cyclo(glycylglycine) hydrolase activity" RELATED [EC:3.5.2.13]
@@ -278606,7 +278619,7 @@ is_a: GO:0016866 ! intramolecular transferase activity
id: GO:0047535
name: 2-alkyn-1-ol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-butyne-1,4-diol + NAD(+) = 4-hydroxy-2-butynal + H(+) + NADH." [EC:1.1.1.165, RHEA:19101]
+def: "Catalysis of the reaction: 2-butyne-1,4-diol + NAD+ = 4-hydroxy-2-butynal + H+ + NADH." [EC:1.1.1.165, RHEA:19101]
synonym: "2-butyne-1,4-diol:NAD+ 1-oxidoreductase activity" RELATED [EC:1.1.1.165]
xref: EC:1.1.1.165
xref: KEGG_REACTION:R03963
@@ -278653,7 +278666,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0047538
name: 2-carboxy-D-arabinitol-1-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-carboxy-D-arabinitol 1-phosphate + H(2)O = 2-carboxy-D-arabinitol + phosphate." [EC:3.1.3.63, RHEA:17837]
+def: "Catalysis of the reaction: 2-carboxy-D-arabinitol 1-phosphate + H2O = 2-carboxy-D-arabinitol + phosphate." [EC:3.1.3.63, RHEA:17837]
synonym: "2-carboxy-D-arabinitol 1-phosphate phosphohydrolase activity" RELATED [EC:3.1.3.63]
synonym: "2-carboxy-D-arabinitol-1-phosphate 1-phosphohydrolase activity" RELATED [EC:3.1.3.63]
synonym: "2-carboxyarabinitol 1-phosphatase activity" RELATED [EC:3.1.3.63]
@@ -278692,7 +278705,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047541
name: 2-furoate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-furoate + ATP + CoA = 2-furoyl-CoA + AMP + diphosphate + H(+)." [EC:6.2.1.31, RHEA:19269]
+def: "Catalysis of the reaction: 2-furoate + ATP + CoA = 2-furoyl-CoA + AMP + diphosphate + H+." [EC:6.2.1.31, RHEA:19269]
synonym: "2-furoate:CoA ligase (AMP-forming)" RELATED [EC:6.2.1.31]
synonym: "2-furoyl coenzyme A synthetase activity" RELATED [EC:6.2.1.31]
xref: EC:6.2.1.31
@@ -278706,7 +278719,7 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0047542
name: 2-furoyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-furoyl-CoA + A + H(2)O = 5-hydroxy-2-furoyl-CoA + AH(2) + H(+)." [EC:1.3.99.8, RHEA:21480]
+def: "Catalysis of the reaction: 2-furoyl-CoA + A + H2O = 5-hydroxy-2-furoyl-CoA + AH(2) + H+." [EC:1.3.99.8, RHEA:21480]
synonym: "2-furoyl coenzyme A dehydrogenase activity" RELATED [EC:1.3.99.8]
synonym: "2-furoyl coenzyme A hydroxylase activity" RELATED [EC:1.3.99.8]
synonym: "2-furoyl-CoA:(acceptor) 5-oxidoreductase (hydroxylating)" RELATED [EC:1.3.99.8]
@@ -278722,7 +278735,7 @@ is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
id: GO:0047543
name: 2-hexadecenal reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + palmitaldehyde = trans-hexadec-2-enal + H(+) + NADPH." [EC:1.3.1.27, RHEA:12444]
+def: "Catalysis of the reaction: NADP+ + palmitaldehyde = trans-hexadec-2-enal + H+ + NADPH." [EC:1.3.1.27, RHEA:12444]
synonym: "hexadecanal: NADP+ oxidoreductase activity" RELATED [EC:1.3.1.27]
synonym: "hexadecanal:NADP+ delta2-oxidoreductase activity" RELATED [EC:1.3.1.27]
xref: EC:1.3.1.27
@@ -278735,7 +278748,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047544
name: 2-hydroxybiphenyl 3-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: biphenyl-2-ol + H(+) + NADH + O(2) = biphenyl-2,3-diol + H(2)O + NAD(+)." [RHEA:11996]
+def: "Catalysis of the reaction: biphenyl-2-ol + H+ + NADH + O2 = biphenyl-2,3-diol + H2O + NAD+." [RHEA:11996]
synonym: "2-hydroxybiphenyl,NADH:oxygen oxidoreductase (3-hydroxylating)" RELATED [EC:1.14.13.44]
xref: EC:1.14.13.44
xref: KEGG_REACTION:R03964
@@ -278767,7 +278780,7 @@ is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
id: GO:0047546
name: 2-hydroxypyridine 5-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-hydroxypyridine + AH(2) + O(2) = 2,5-dihydroxypyridine + A + H(2)O." [EC:1.14.99.26, RHEA:16973]
+def: "Catalysis of the reaction: 2-hydroxypyridine + AH(2) + O2 = 2,5-dihydroxypyridine + A + H2O." [EC:1.14.99.26, RHEA:16973]
synonym: "2-hydroxypyridine oxygenase activity" RELATED [EC:1.14.99.26]
synonym: "2-hydroxypyridine,hydrogen-donor:oxygen oxidoreductase (5-hydroxylating)" RELATED [EC:1.14.99.26]
xref: EC:1.14.99.26
@@ -278781,7 +278794,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047547
name: 2-methylcitrate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2S,3S)-2-methylcitrate = cis-2-methylaconitate + H(2)O." [EC:4.2.1.79, RHEA:17725]
+def: "Catalysis of the reaction: (2S,3S)-2-methylcitrate = cis-2-methylaconitate + H2O." [EC:4.2.1.79, RHEA:17725]
synonym: "(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase [(Z)-but-2-ene-1,2,3-tricarboxylate-forming]" RELATED [EC:4.2.1.79]
synonym: "2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase activity" RELATED [EC:4.2.1.79]
synonym: "2-methylcitrate hydro-lyase activity" RELATED [EC:4.2.1.79]
@@ -278809,7 +278822,7 @@ is_a: GO:0016866 ! intramolecular transferase activity
id: GO:0047549
name: 2-nitrophenol 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-nitrophenol + 2 H(+) + 2 NADPH + O(2) = catechol + H(2)O + 2 NADP(+) + nitrite." [EC:1.14.13.31, RHEA:19457]
+def: "Catalysis of the reaction: 2-nitrophenol + 2 H+ + 2 NADPH + O2 = catechol + H2O + 2 NADP+ + nitrite." [EC:1.14.13.31, RHEA:19457]
synonym: "2-nitrophenol oxygenase activity" RELATED [EC:1.14.13.31]
synonym: "2-nitrophenol,NADPH:oxygen 2-oxidoreductase (2-hydroxylating, nitrite-forming)" RELATED [EC:1.14.13.31]
synonym: "nitrophenol oxygenase activity" BROAD [EC:1.14.13.31]
@@ -278824,7 +278837,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047550
name: 2-oxoadipate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-hydroxyadipate + NAD(+) = 2-oxoadipate + H(+) + NADH." [EC:1.1.1.172, RHEA:14793]
+def: "Catalysis of the reaction: 2-hydroxyadipate + NAD+ = 2-oxoadipate + H+ + NADH." [EC:1.1.1.172, RHEA:14793]
synonym: "2-hydroxyadipate:NAD+ 2-oxidoreductase activity" RELATED [EC:1.1.1.172]
synonym: "2-ketoadipate reductase activity" RELATED [EC:1.1.1.172]
synonym: "alpha-ketoadipate reductase activity" RELATED [EC:1.1.1.172]
@@ -278890,7 +278903,7 @@ is_a: GO:0016625 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0047554
name: 2-pyrone-4,6-dicarboxylate lactonase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxo-2H-pyran-4,6-dicarboxylate + H(2)O = 4-carboxy-2-hydroxyhexa-2,4-dienedioate + H(+)." [EC:3.1.1.57, RHEA:10644]
+def: "Catalysis of the reaction: 2-oxo-2H-pyran-4,6-dicarboxylate + H2O = 4-carboxy-2-hydroxyhexa-2,4-dienedioate + H+." [EC:3.1.1.57, RHEA:10644]
synonym: "2-pyrone-4,6-dicarboxylate lactonohydrolase activity" RELATED [EC:3.1.1.57]
xref: EC:3.1.1.57
xref: KEGG_REACTION:R04277
@@ -278903,7 +278916,7 @@ id: GO:0047555
name: 3',5'-cyclic-GMP phosphodiesterase activity
namespace: molecular_function
alt_id: GO:0004116
-def: "Catalysis of the reaction: guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate." [EC:3.1.4.35, MetaCyc:35-CYCLIC-GMP-PHOSPHODIESTERASE-RXN]
+def: "Catalysis of the reaction: 3',5'-cyclic GMP + H2O = GMP + H+." [RHEA:16957]
synonym: "3',5' cyclic-GMP phosphodiesterase activity" EXACT []
synonym: "3',5'-cyclic-GMP 5'-nucleotidohydrolase activity" RELATED [EC:3.1.4.35]
synonym: "cGMP phosphodiesterase activity" EXACT []
@@ -278927,7 +278940,7 @@ id: GO:0047556
name: 3,4-dihydroxyphthalate decarboxylase activity
namespace: molecular_function
alt_id: GO:0034913
-def: "Catalysis of the reaction: 3,4-dihydroxyphthalate + H(+) = 3,4-dihydroxybenzoate + CO(2)." [EC:4.1.1.69, RHEA:18601]
+def: "Catalysis of the reaction: 3,4-dihydroxyphthalate + H+ = 3,4-dihydroxybenzoate + CO2." [EC:4.1.1.69, RHEA:18601]
synonym: "3,4-dihydroxyphthalate 2-decarboxylase activity" EXACT []
synonym: "3,4-dihydroxyphthalate carboxy-lyase (3,4-dihydroxybenzoate-forming)" RELATED [EC:4.1.1.69]
synonym: "3,4-dihydroxyphthalate carboxy-lyase activity" RELATED [EC:4.1.1.69]
@@ -278942,7 +278955,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0047557
name: 3-aci-nitropropanoate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-aci-nitropropanoate + H(2)O + O(2) = 3-oxopropanoate + H(2)O(2) + nitrite." [EC:1.7.3.5, RHEA:22372]
+def: "Catalysis of the reaction: 3-aci-nitropropanoate + H2O + O2 = 3-oxopropanoate + H2O2 + nitrite." [EC:1.7.3.5, RHEA:22372]
synonym: "3-aci-nitropropanoate:oxygen oxidoreductase activity" RELATED [EC:1.7.3.5]
synonym: "propionate-3-nitronate oxidase activity" RELATED [EC:1.7.3.5]
xref: EC:1.7.3.5
@@ -278955,7 +278968,7 @@ is_a: GO:0016663 ! oxidoreductase activity, acting on other nitrogenous compound
id: GO:0047558
name: 3-cyanoalanine hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-asparagine = 3-cyano-L-alanine + H(2)O + H(+)." [EC:4.2.1.65, RHEA:15385]
+def: "Catalysis of the reaction: L-asparagine = 3-cyano-L-alanine + H2O + H+." [EC:4.2.1.65, RHEA:15385]
synonym: "beta-CNA nitrilase activity" RELATED [EC:4.2.1.65]
synonym: "beta-CNAla hydrolase activity" RELATED [EC:4.2.1.65]
synonym: "beta-cyanoalanine hydratase activity" RELATED [EC:4.2.1.65]
@@ -278985,7 +278998,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047560
name: 3-dehydrosphinganine reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + sphinganine = 3-dehydrosphinganine + H(+) + NADPH." [EC:1.1.1.102, RHEA:22640]
+def: "Catalysis of the reaction: NADP+ + sphinganine = 3-dehydrosphinganine + H+ + NADPH." [EC:1.1.1.102, RHEA:22640]
synonym: "3-ketosphinganine reductase activity" RELATED [EC:1.1.1.102]
synonym: "3-oxosphinganine reductase activity" RELATED [EC:1.1.1.102]
synonym: "3-oxosphinganine:NADPH oxidoreductase activity" RELATED [EC:1.1.1.102]
@@ -279006,7 +279019,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047561
name: 3-hydroxyanthranilate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxyanthranilate + O(2) = 6-imino-5-oxocyclohexa-1,3-dienecarboxylate + H(2)O(2)." [EC:1.10.3.5, RHEA:17245]
+def: "Catalysis of the reaction: 3-hydroxyanthranilate + O2 = 6-imino-5-oxocyclohexa-1,3-dienecarboxylate + H2O2." [EC:1.10.3.5, RHEA:17245]
synonym: "3-hydroxyanthranilate:oxygen oxidoreductase activity" RELATED [EC:1.10.3.5]
synonym: "3-hydroxyanthranilic acid oxidase activity" RELATED [EC:1.10.3.5]
xref: EC:1.10.3.5
@@ -279035,7 +279048,7 @@ is_a: GO:0016833 ! oxo-acid-lyase activity
id: GO:0047563
name: 3-hydroxybenzoate 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxybenzoate + AH(2) + O(2) = 2,3-dihydroxybenzoate + A + H(2)O." [EC:1.14.99.23, RHEA:14193]
+def: "Catalysis of the reaction: 3-hydroxybenzoate + AH(2) + O2 = 2,3-dihydroxybenzoate + A + H2O." [EC:1.14.99.23, RHEA:14193]
synonym: "3-HBA-2-hydroxylase activity" RELATED [EC:1.14.99.23]
synonym: "3-hydroxybenzoate 2-hydroxylase activity" EXACT []
synonym: "3-hydroxybenzoate,hydrogen-donor:oxygen oxidoreductase (2-hydroxylating)" RELATED [EC:1.14.99.23]
@@ -279062,7 +279075,7 @@ is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
id: GO:0047565
name: 3-hydroxypropionate dehydrogenase (NAD+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxypropanoate + NAD(+) = 3-oxopropanoate + H(+) + NADH." [EC:1.1.1.59, RHEA:13357]
+def: "Catalysis of the reaction: 3-hydroxypropanoate + NAD+ = 3-oxopropanoate + H+ + NADH." [EC:1.1.1.59, RHEA:13357]
synonym: "3-hydroxypropanoate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.59]
xref: EC:1.1.1.59
xref: KEGG_REACTION:R01608
@@ -279074,7 +279087,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047566
name: 3-ketovalidoxylamine C-N-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-nitrophenyl-3-ketovalidamine = 4-nitroaniline + 5-D-(5/6)-5-C-(hydroxymethyl)-2,6-dihydroxycyclohex-2-en-1-one + H(+)." [EC:4.3.3.1, RHEA:22768]
+def: "Catalysis of the reaction: 4-nitrophenyl-3-ketovalidamine = 4-nitroaniline + 5-D-(5/6)-5-C-(hydroxymethyl)-2,6-dihydroxycyclohex-2-en-1-one + H+." [EC:4.3.3.1, RHEA:22768]
synonym: "3-ketovalidoxylamine A C-N-lyase activity" RELATED [EC:4.3.3.1]
synonym: "4-nitrophenyl-3-ketovalidamine 4-nitroaniline-lyase [5-D-(5/6)-5-C-(hydroxymethyl)-2,6-dihydroxycyclohex-2-en-1-one-forming]" RELATED [EC:4.3.3.1]
synonym: "4-nitrophenyl-3-ketovalidamine 4-nitroaniline-lyase activity" RELATED [EC:4.3.3.1]
@@ -279089,7 +279102,7 @@ is_a: GO:0016843 ! amine-lyase activity
id: GO:0047567
name: 3-methyleneoxindole reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-methyloxindole + NADP(+) = 3-methyleneoxindole + H(+) + NADPH." [EC:1.3.1.17, RHEA:20257]
+def: "Catalysis of the reaction: 3-methyloxindole + NADP+ = 3-methyleneoxindole + H+ + NADPH." [EC:1.3.1.17, RHEA:20257]
synonym: "3-methyl-1,3-dihydroindol-2-one:NADP+ oxidoreductase activity" RELATED [EC:1.3.1.17]
synonym: "3-methyloxindole:NADP+ oxidoreductase activity" RELATED [EC:1.3.1.17]
xref: EC:1.3.1.17
@@ -279168,7 +279181,7 @@ is_a: GO:0033765 ! steroid dehydrogenase activity, acting on the CH-CH group of
id: GO:0047572
name: 3-phosphoglycerate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-phospho-D-glycerate + H(2)O = D-glycerate + phosphate." [EC:3.1.3.38, RHEA:12412]
+def: "Catalysis of the reaction: 3-phospho-D-glycerate + H2O = D-glycerate + phosphate." [EC:3.1.3.38, RHEA:12412]
synonym: "3-PGA phosphatase activity" RELATED [EC:3.1.3.38]
synonym: "D-3-phosphoglycerate phosphatase activity" RELATED [EC:3.1.3.38]
synonym: "D-glycerate-3-phosphate phosphohydrolase activity" RELATED [EC:3.1.3.38]
@@ -279194,7 +279207,7 @@ is_a: GO:0019213 ! deacetylase activity
id: GO:0047574
name: 4-acetamidobutyryl-CoA deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-acetamidobutanoyl-CoA + H(2)O = 4-aminobutanoyl-CoA + acetate." [EC:3.5.1.51, RHEA:22928]
+def: "Catalysis of the reaction: 4-acetamidobutanoyl-CoA + H2O = 4-aminobutanoyl-CoA + acetate." [EC:3.5.1.51, RHEA:22928]
synonym: "4-acetamidobutanoyl-CoA amidohydrolase activity" RELATED [EC:3.5.1.51]
synonym: "aminobutyryl-CoA thiolesterase activity" RELATED [EC:3.5.1.51]
synonym: "deacetylase-thiolesterase activity" RELATED [EC:3.5.1.51]
@@ -279209,7 +279222,7 @@ is_a: GO:0019213 ! deacetylase activity
id: GO:0047575
name: 4-carboxymuconolactone decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-2-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate + H(+) = 5-oxo-4,5-dihydro-2-furylacetate + CO(2)." [EC:4.1.1.44, RHEA:23348]
+def: "Catalysis of the reaction: (R)-2-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate + H+ = 5-oxo-4,5-dihydro-2-furylacetate + CO2." [EC:4.1.1.44, RHEA:23348]
synonym: "4-carboxymonolactone carboxy-lyase activity" RELATED [EC:4.1.1.44]
synonym: "4-carboxymuconolactone carboxy-lyase (4,5-dihydro-5-oxofuran-2-acetate-forming)" RELATED [EC:4.1.1.44]
synonym: "4-carboxymuconolactone carboxy-lyase activity" RELATED [EC:4.1.1.44]
@@ -279224,7 +279237,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0047576
name: 4-chlorobenzoate dehalogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-chlorobenzoate + H(2)O = 4-hydroxybenzoate + chloride + H(+)." [EC:3.8.1.6, RHEA:23440]
+def: "Catalysis of the reaction: 4-chlorobenzoate + H2O = 4-hydroxybenzoate + chloride + H+." [EC:3.8.1.6, RHEA:23440]
synonym: "4-chlorobenzoate chlorohydrolase activity" RELATED [EC:3.8.1.6]
synonym: "halobenzoate dehalogenase activity" RELATED [EC:3.8.1.6]
xref: EC:3.8.1.6
@@ -279237,7 +279250,7 @@ is_a: GO:0019120 ! hydrolase activity, acting on acid halide bonds, in C-halide
id: GO:0047577
name: 4-hydroxybutyrate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-hydroxybutanoate + NAD(+) = H(+) + NADH + succinate semialdehyde." [EC:1.1.1.61, RHEA:23948]
+def: "Catalysis of the reaction: 4-hydroxybutanoate + NAD+ = H+ + NADH + succinate semialdehyde." [EC:1.1.1.61, RHEA:23948]
synonym: "4-hydroxybutanoate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.61]
synonym: "gamma-hydroxybutyrate dehydrogenase activity" RELATED [EC:1.1.1.61]
xref: EC:1.1.1.61
@@ -279263,7 +279276,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0047579
name: 4-hydroxymandelate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-4-hydroxymandelate + H(+) + O(2) = 4-hydroxybenzaldehyde + CO(2) + H(2)O(2)." [EC:1.1.3.19, RHEA:15833]
+def: "Catalysis of the reaction: (S)-4-hydroxymandelate + H+ + O2 = 4-hydroxybenzaldehyde + CO2 + H2O2." [EC:1.1.3.19, RHEA:15833]
synonym: "(S)-2-hydroxy-2-(4-hydroxyphenyl)acetate:oxygen 1-oxidoreductase activity" RELATED [EC:1.1.3.19]
synonym: "L-4-hydroxymandelate oxidase (decarboxylating)" RELATED [EC:1.1.3.19]
xref: EC:1.1.3.19
@@ -279291,7 +279304,7 @@ is_a: GO:0047661 ! amino-acid racemase activity
id: GO:0047581
name: 4-methyleneglutamate-ammonia ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-methylene-L-glutamate + ATP + NH(4)(+) = 4-methylene-L-glutamine + AMP + diphosphate + 2 H(+)." [EC:6.3.1.7, RHEA:13853]
+def: "Catalysis of the reaction: 4-methylene-L-glutamate + ATP + NH4 = 4-methylene-L-glutamine + AMP + diphosphate + 2 H+." [EC:6.3.1.7, RHEA:13853]
synonym: "4-methylene-L-glutamate:ammonia ligase (AMP-forming)" RELATED [EC:6.3.1.7]
synonym: "4-methyleneglutamine synthetase activity" RELATED [EC:6.3.1.7]
xref: EC:6.3.1.7
@@ -279304,7 +279317,7 @@ is_a: GO:0016880 ! acid-ammonia (or amide) ligase activity
id: GO:0047582
name: 4-methyleneglutaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-methylene-L-glutamine + H(2)O = 4-methylene-L-glutamate + NH(4)(+)." [EC:3.5.1.67, RHEA:14741]
+def: "Catalysis of the reaction: 4-methylene-L-glutamine + H2O = 4-methylene-L-glutamate + NH4." [EC:3.5.1.67, RHEA:14741]
synonym: "4-methylene-L-glutamine amidohydrolase activity" RELATED [EC:3.5.1.67]
synonym: "4-methyleneglutamine amidohydrolase activity" RELATED [EC:3.5.1.67]
synonym: "4-methyleneglutamine deamidase activity" RELATED [EC:3.5.1.67]
@@ -279318,7 +279331,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047583
name: 4-methyloxaloacetate esterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-methoxy-2,4-dioxobutanoate + H(2)O = H(+) + methanol + oxaloacetate." [EC:3.1.1.44, RHEA:10564]
+def: "Catalysis of the reaction: 4-methoxy-2,4-dioxobutanoate + H2O = H+ + methanol + oxaloacetate." [EC:3.1.1.44, RHEA:10564]
synonym: "oxaloacetate-4-methyl-ester oxaloacetohydrolase activity" RELATED [EC:3.1.1.44]
xref: EC:3.1.1.44
xref: KEGG_REACTION:R01144
@@ -279330,7 +279343,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0047584
name: 4-oxalmesaconate hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate = (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate + H(2)O." [EC:4.2.1.83, RHEA:17401]
+def: "Catalysis of the reaction: 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate = (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate + H2O." [EC:4.2.1.83, RHEA:17401]
synonym: "2-hydroxy-4-oxobutane-1,2,4-tricarboxylate 2,3-hydro-lyase [(E)-4-oxobut-1-ene-1,2,4-tricarboxylate-forming]" RELATED [EC:4.2.1.83]
synonym: "2-hydroxy-4-oxobutane-1,2,4-tricarboxylate 2,3-hydro-lyase activity" RELATED [EC:4.2.1.83]
synonym: "4-carboxy-2-oxobutane-1,2,4-tricarboxylate 2,3-hydro-lyase activity" RELATED [EC:4.2.1.83]
@@ -279347,7 +279360,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047585
name: 4-pyridoxolactonase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-pyridoxolactone + H(2)O = 4-pyridoxate + H(+)." [EC:3.1.1.27, RHEA:14301]
+def: "Catalysis of the reaction: 4-pyridoxolactone + H2O = 4-pyridoxate + H+." [EC:3.1.1.27, RHEA:14301]
synonym: "4-pyridoxolactone lactonohydrolase activity" RELATED [EC:3.1.1.27]
xref: EC:3.1.1.27
xref: KEGG_REACTION:R02992
@@ -279371,7 +279384,7 @@ is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-
id: GO:0047587
name: 5-alpha-hydroxysteroid dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5alpha-ergosta-7,22-diene-3beta,5-diol = ergosterol + H(2)O." [EC:4.2.1.62, RHEA:22064]
+def: "Catalysis of the reaction: 5alpha-ergosta-7,22-diene-3beta,5-diol = ergosterol + H2O." [EC:4.2.1.62, RHEA:22064]
synonym: "5alpha-ergosta-7,22-diene-3beta,5-diol 5,6-hydro-lyase (ergosterol-forming)" RELATED [EC:4.2.1.62]
synonym: "5alpha-ergosta-7,22-diene-3beta,5-diol 5,6-hydro-lyase activity" RELATED [EC:4.2.1.62]
synonym: "5alpha-hydroxysteroid dehydratase activity" RELATED [EC:4.2.1.62]
@@ -279442,7 +279455,7 @@ is_a: GO:0008410 ! CoA-transferase activity
id: GO:0047592
name: 5-pyridoxate dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-pyridoxate + NADPH + O(2) = 2-(acetamidomethylene)-3-(hydroxymethyl)succinate) + NADP(+)." [RHEA:11152]
+def: "Catalysis of the reaction: 5-pyridoxate + NADPH + O2 = 2-(acetamidomethylene)-3-(hydroxymethyl)succinate) + NADP+." [RHEA:11152]
comment: Formerly EC:1.14.12.5.
synonym: "5-pyridoxate oxidase activity" RELATED [EC:1.14.13.241]
xref: EC:1.14.13.241
@@ -279455,7 +279468,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047593
name: 6-acetylglucose deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-acetyl-D-glucose + H(2)O = D-glucose + acetate + H(+)." [EC:3.1.1.33, RHEA:18485]
+def: "Catalysis of the reaction: 6-acetyl-D-glucose + H2O = D-glucose + acetate + H+." [EC:3.1.1.33, RHEA:18485]
synonym: "6-acetyl-D-glucose acetylhydrolase activity" RELATED [EC:3.1.1.33]
synonym: "6-O-acetylglucose deacetylase activity" RELATED [EC:3.1.1.33]
xref: EC:3.1.1.33
@@ -279469,7 +279482,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0047594
name: 6-beta-hydroxyhyoscyamine epoxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (6S)-6-hydroxyhyoscyamine + 2-oxoglutarate + O(2) = CO(2) + H(2)O + H(+) + scopolamine + succinate." [EC:1.14.20.13, RHEA:12797]
+def: "Catalysis of the reaction: (6S)-6-hydroxyhyoscyamine + 2-oxoglutarate + O2 = CO2 + H2O + H+ + scopolamine + succinate." [EC:1.14.20.13, RHEA:12797]
synonym: "(6S)-6-hydroxyhyoscyamine,2-oxoglutarate oxidoreductase (epoxide-forming)" RELATED [EC:1.14.20.13]
synonym: "6beta-hydroxyhyoscyamine epoxidase activity" RELATED [EC:1.14.20.13]
synonym: "hydroxyhyoscyamine dioxygenase activity" RELATED [EC:1.14.20.13]
@@ -279499,7 +279512,7 @@ is_a: GO:0016636 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047596
name: 6-methylsalicylate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-methylsalicylate + H(+) = 3-cresol + CO(2)." [EC:4.1.1.52, RHEA:23112]
+def: "Catalysis of the reaction: 6-methylsalicylate + H+ = 3-cresol + CO2." [EC:4.1.1.52, RHEA:23112]
synonym: "6-methylsalicylate carboxy-lyase (3-cresol-forming)" RELATED [EC:4.1.1.52]
synonym: "6-methylsalicylate carboxy-lyase activity" RELATED [EC:4.1.1.52]
synonym: "6-methylsalicylic acid (2,6-cresotic acid) decarboxylase activity" RELATED [EC:4.1.1.52]
@@ -279514,7 +279527,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0047597
name: 6-oxocineole dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-oxocineole + H(+) + NADPH + O(2) = 1,6,6-trimethyl-2,7-dioxabicyclo[3.2.2]nonan-3-one + H(2)O + NADP(+)." [EC:1.14.13.51, RHEA:24324]
+def: "Catalysis of the reaction: 6-oxocineole + H+ + NADPH + O2 = 1,6,6-trimethyl-2,7-dioxabicyclo[3.2.2]nonan-3-one + H2O + NADP+." [EC:1.14.13.51, RHEA:24324]
synonym: "6-oxocineole oxygenase activity" RELATED [EC:1.14.13.51]
synonym: "6-oxocineole,NADPH:oxygen oxidoreductase activity" RELATED [EC:1.14.13.51]
xref: EC:1.14.13.51
@@ -279543,7 +279556,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047599
name: 8-oxocoformycin reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: coformycin + NADP(+) = 8-oxocoformycin + 2 H(+) + NADPH." [EC:1.1.1.235, RHEA:23168]
+def: "Catalysis of the reaction: coformycin + NADP+ = 8-oxocoformycin + 2 H+ + NADPH." [EC:1.1.1.235, RHEA:23168]
synonym: "8-ketodeoxycoformycin reductase activity" RELATED [EC:1.1.1.235]
synonym: "coformycin:NADP+ 8-oxidoreductase activity" RELATED [EC:1.1.1.235]
xref: EC:1.1.1.235
@@ -279583,7 +279596,7 @@ is_a: GO:0016774 ! phosphotransferase activity, carboxyl group as acceptor
id: GO:0047602
name: acetoacetate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetoacetate + H(+) = acetone + CO(2)." [EC:4.1.1.4, RHEA:19729]
+def: "Catalysis of the reaction: acetoacetate + H+ = acetone + CO2." [EC:4.1.1.4, RHEA:19729]
synonym: "acetoacetate carboxy-lyase (acetone-forming)" RELATED [EC:4.1.1.4]
synonym: "acetoacetate carboxy-lyase activity" RELATED [EC:4.1.1.4]
synonym: "acetoacetic acid decarboxylase activity" RELATED [EC:4.1.1.4]
@@ -279597,7 +279610,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0047603
name: acetoacetyl-CoA hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetoacetyl-CoA + H(2)O = acetoacetate + CoA + H(+)." [EC:3.1.2.11, RHEA:15673]
+def: "Catalysis of the reaction: acetoacetyl-CoA + H2O = acetoacetate + CoA + H+." [EC:3.1.2.11, RHEA:15673]
synonym: "acetoacetyl CoA deacylase activity" RELATED [EC:3.1.2.11]
synonym: "acetoacetyl coenzyme A deacylase activity" RELATED [EC:3.1.2.11]
synonym: "acetoacetyl coenzyme A hydrolase activity" RELATED [EC:3.1.2.11]
@@ -279638,17 +279651,11 @@ name: hydroxynitrilase activity
namespace: molecular_function
alt_id: GO:0046991
def: "Catalysis of the reaction: a hydroxynitrile = cyanide + an aldehyde or ketone." [GOC:mah, PMID:3377504]
-synonym: "(S)-acetone-cyanohydrin lyase activity" NARROW []
-synonym: "2-hydroxyisobutyronitrile acetone-lyase (cyanide-forming)" NARROW []
-synonym: "2-hydroxyisobutyronitrile acetone-lyase activity" NARROW []
-synonym: "acetone-cyanhydrin lyase activity" NARROW []
-synonym: "acetone-cyanohydrin acetone-lyase (cyanide-forming)" NARROW []
-synonym: "acetone-cyanohydrin acetone-lyase activity" NARROW []
-synonym: "acetone-cyanohydrin lyase activity" NARROW []
synonym: "alpha-hydroxynitrile lyase activity" NARROW []
synonym: "hydroxynitrile lyase activity" EXACT []
synonym: "oxynitrilase activity" RELATED []
xref: EC:4.1.2.47
+xref: https://github.com/geneontology/go-ontology/issues/16166
xref: MetaCyc:ACETONE-CYANHYDRIN-LYASE-RXN
is_a: GO:0016832 ! aldehyde-lyase activity
@@ -279667,7 +279674,7 @@ is_a: GO:0016663 ! oxidoreductase activity, acting on other nitrogenous compound
id: GO:0047609
name: acetylputrescine deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-acetylputrescine + H(2)O = acetate + putrescine." [EC:3.5.1.62, RHEA:23412]
+def: "Catalysis of the reaction: N-acetylputrescine + H2O = acetate + putrescine." [EC:3.5.1.62, RHEA:23412]
synonym: "N-acetylputrescine acetylhydrolase activity" RELATED [EC:3.5.1.62]
xref: EC:3.5.1.62
xref: KEGG_REACTION:R01156
@@ -279680,7 +279687,7 @@ is_a: GO:0019213 ! deacetylase activity
id: GO:0047610
name: acetylsalicylate deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetylsalicylate + H(2)O = acetate + H(+) + salicylate." [EC:3.1.1.55, RHEA:11752]
+def: "Catalysis of the reaction: acetylsalicylate + H2O = acetate + H+ + salicylate." [EC:3.1.1.55, RHEA:11752]
synonym: "acetylsalicylate O-acetylhydrolase activity" RELATED [EC:3.1.1.55]
synonym: "acetylsalicylic acid esterase activity" RELATED [EC:3.1.1.55]
synonym: "aspirin esterase activity" RELATED [EC:3.1.1.55]
@@ -279696,7 +279703,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0047611
name: acetylspermidine deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(8)-acetylspermidine + H(2)O = acetate + spermidine." [EC:3.5.1.48, RHEA:23928]
+def: "Catalysis of the reaction: N(8)-acetylspermidine + H2O = acetate + spermidine." [EC:3.5.1.48, RHEA:23928]
synonym: "8-N-acetylspermidine amidohydrolase activity" RELATED [EC:3.5.1.48]
synonym: "N(1)-acetylspermidine amidohydrolase activity" RELATED [EC:3.5.1.48]
synonym: "N(8)-acetylspermidine amidohydrolase activity" RELATED [EC:3.5.1.48]
@@ -279718,7 +279725,7 @@ is_a: GO:0019213 ! deacetylase activity
id: GO:0047612
name: acid-CoA ligase (GDP-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: a carboxylate + CoA + GTP = acyl-CoA + GDP + H(+) + phosphate." [RHEA:10968]
+def: "Catalysis of the reaction: a carboxylate + CoA + GTP = acyl-CoA + GDP + H+ + phosphate." [RHEA:10968]
synonym: "acid:CoA ligase (GDP-forming)" RELATED [EC:6.2.1.10]
synonym: "acyl coenzyme A synthetase (guanosine diphosphate forming)" RELATED [EC:6.2.1.10]
synonym: "acyl-CoA synthetase (GDP-forming) activity" RELATED [EC:6.2.1.10]
@@ -279732,7 +279739,7 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0047613
name: aconitate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cis-aconitate + H(+) = CO(2) + itaconate." [EC:4.1.1.6, RHEA:15253]
+def: "Catalysis of the reaction: cis-aconitate + H+ = CO2 + itaconate." [EC:4.1.1.6, RHEA:15253]
synonym: "CAD activity" BROAD [EC:4.1.1.6]
synonym: "cis-aconitate carboxy-lyase (itaconate-forming)" RELATED [EC:4.1.1.6]
synonym: "cis-aconitate carboxy-lyase activity" RELATED [EC:4.1.1.6]
@@ -279747,7 +279754,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0047614
name: aconitate delta-isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: trans-aconitate = cis-aconitate." [EC:5.3.3.7, RHEA:17265]
+def: "Catalysis of the reaction: trans-aconitate = cis-aconitate." [RHEA:17265]
synonym: "aconitate D-isomerase activity" EXACT []
synonym: "aconitate delta2-delta3-isomerase activity" RELATED [EC:5.3.3.7]
synonym: "aconitate isomerase activity" BROAD [EC:5.3.3.7]
@@ -279810,7 +279817,7 @@ is_a: GO:0016289 ! CoA hydrolase activity
id: GO:0047618
name: acylagmatine amidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(4)-benzoylagmatine + H(2)O = agmatine + benzoate." [EC:3.5.1.40, RHEA:15065]
+def: "Catalysis of the reaction: N(4)-benzoylagmatine + H2O = agmatine + benzoate." [EC:3.5.1.40, RHEA:15065]
synonym: "acylagmatine amidohydrolase activity" RELATED [EC:3.5.1.40]
synonym: "acylagmatine deacylase activity" RELATED [EC:3.5.1.40]
synonym: "benzoylagmatine amidohydrolase activity" RELATED [EC:3.5.1.40]
@@ -279927,7 +279934,7 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0047626
name: adenosylmethionine hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + H(2)O = S-methyl-5'-thioadenosine + L-homoserine + H(+)." [EC:3.3.1.2, RHEA:14645]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + H2O = S-methyl-5'-thioadenosine + L-homoserine + H+." [EC:3.3.1.2, RHEA:14645]
synonym: "adenosyl methionine hydrolase activity" EXACT []
synonym: "adenosylmethionine lyase activity" RELATED [EC:3.3.1.2]
synonym: "methylmethionine-sulfonium-salt hydrolase activity" RELATED [EC:3.3.1.2]
@@ -279943,7 +279950,7 @@ is_a: GO:0016802 ! trialkylsulfonium hydrolase activity
id: GO:0047627
name: adenylylsulfatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5'-adenylyl sulfate + H(2)O = AMP + 2 H(+) + sulfate." [EC:3.6.2.1, RHEA:17041]
+def: "Catalysis of the reaction: 5'-adenylyl sulfate + H2O = AMP + 2 H+ + sulfate." [EC:3.6.2.1, RHEA:17041]
synonym: "adenosine 5-phosphosulfate sulfohydrolase activity" RELATED [EC:3.6.2.1]
synonym: "adenylylsulfate sulfohydrolase activity" RELATED [EC:3.6.2.1]
synonym: "adenylylsulphatase activity" EXACT []
@@ -279984,7 +279991,7 @@ is_a: GO:0047623 ! adenosine-phosphate deaminase activity
id: GO:0047630
name: ADP-phosphoglycerate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-ADP-2-phosphoglycerate + H(2)O = 3-ADP-glycerate + phosphate." [EC:3.1.3.28, RHEA:15861]
+def: "Catalysis of the reaction: 3-ADP-2-phosphoglycerate + H2O = 3-ADP-glycerate + phosphate." [EC:3.1.3.28, RHEA:15861]
synonym: "3-(ADP)-2-phosphoglycerate phosphohydrolase activity" RELATED [EC:3.1.3.28]
synonym: "adenosine diphosphate phosphoglycerate phosphatase activity" RELATED [EC:3.1.3.28]
synonym: "ADPphosphoglycerate phosphatase activity" RELATED [EC:3.1.3.28]
@@ -280030,7 +280037,7 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047633
name: agmatine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: agmatine + ATP = N(4)-phosphoagmatine + ADP + 3 H(+)." [EC:2.7.3.10, RHEA:15953]
+def: "Catalysis of the reaction: agmatine + ATP = N(4)-phosphoagmatine + ADP + 3 H+." [EC:2.7.3.10, RHEA:15953]
synonym: "ATP:agmatine 4-N-phosphotransferase activity" RELATED [EC:2.7.3.10]
synonym: "ATP:agmatine N4-phosphotransferase activity" RELATED [EC:2.7.3.10]
synonym: "phosphagen phosphokinase activity" RELATED [EC:2.7.3.10]
@@ -280045,7 +280052,7 @@ is_a: GO:0016775 ! phosphotransferase activity, nitrogenous group as acceptor
id: GO:0047634
name: agmatine N4-coumaroyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-coumaroyl-CoA + agmatine = N-(4-guanidiniumylbutyl)-4-hydroxycinnamamide + CoA + H(+)." [EC:2.3.1.64, RHEA:13405]
+def: "Catalysis of the reaction: 4-coumaroyl-CoA + agmatine = N-(4-guanidiniumylbutyl)-4-hydroxycinnamamide + CoA + H+." [EC:2.3.1.64, RHEA:13405]
synonym: "4-coumaroyl-CoA:agmatine 4-N-coumaroyltransferase activity" RELATED [EC:2.3.1.64]
synonym: "4-coumaroyl-CoA:agmatine N4-coumaroyltransferase activity" RELATED [EC:2.3.1.64]
synonym: "agmatine coumaroyltransferase activity" RELATED [EC:2.3.1.64]
@@ -280077,7 +280084,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0047636
name: alanopine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,2'-iminodipropanoate + H(2)O + NAD(+) = L-alanine + H(+) + NADH + pyruvate." [EC:1.5.1.17, RHEA:17589]
+def: "Catalysis of the reaction: 2,2'-iminodipropanoate + H2O + NAD+ = L-alanine + H+ + NADH + pyruvate." [EC:1.5.1.17, RHEA:17589]
synonym: "2,2'-iminodipropanoate:NAD+ oxidoreductase (L-alanine-forming)" RELATED [EC:1.5.1.17]
synonym: "ADH" RELATED [EC:1.5.1.17]
synonym: "alanopine: NAD oxidoreductase activity" RELATED [EC:1.5.1.17]
@@ -280108,7 +280115,7 @@ is_a: GO:0016755 ! aminoacyltransferase activity
id: GO:0047638
name: albendazole monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: albendazole + H(+) + NADPH + O(2) = albendazole S-oxide + H(2)O + NADP(+)." [EC:1.14.13.32, RHEA:10796]
+def: "Catalysis of the reaction: albendazole + H+ + NADPH + O2 = albendazole S-oxide + H2O + NADP+." [EC:1.14.13.32, RHEA:10796]
synonym: "albendazole oxidase activity" RELATED [EC:1.14.13.32]
synonym: "albendazole sulfoxidase activity" RELATED [EC:1.14.13.32]
synonym: "albendazole,NADPH:oxygen oxidoreductase (sulfoxide-forming)" RELATED [EC:1.14.13.32]
@@ -280149,7 +280156,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047641
name: aldose-6-phosphate reductase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glucitol 6-phosphate + NADP(+) = D-glucose 6-phosphate + H(+) + NADPH." [EC:1.1.1.200, RHEA:20037]
+def: "Catalysis of the reaction: D-glucitol 6-phosphate + NADP+ = D-glucose 6-phosphate + H+ + NADPH." [EC:1.1.1.200, RHEA:20037]
synonym: "A6PR" RELATED [EC:1.1.1.200]
synonym: "alditol 6-phosphate:NADP 1-oxidoreductase activity" RELATED [EC:1.1.1.200]
synonym: "aldose 6-phosphate reductase activity" RELATED [EC:1.1.1.200]
@@ -280191,7 +280198,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0047644
name: alizarin 2-beta-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: alizarin + UDP-D-glucose = 1-hydroxy-2-(beta-D-glucosyloxy)-9,10-anthraquinone + H(+) + UDP." [EC:2.4.1.103, RHEA:20677]
+def: "Catalysis of the reaction: alizarin + UDP-D-glucose = 1-hydroxy-2-(beta-D-glucosyloxy)-9,10-anthraquinone + H+ + UDP." [EC:2.4.1.103, RHEA:20677]
synonym: "alizarin 2-b-glucosyltransferase activity" EXACT []
synonym: "UDP-glucose:1,2-dihydroxy-9,10-anthraquinone 2-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.103]
synonym: "UDPglucose:1,2-dihydroxy-9,10-anthraquinone 2-O-beta-D-glucosyl-transferase activity" RELATED [EC:2.4.1.103]
@@ -280233,7 +280240,7 @@ is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047647
name: alkylacetylglycerophosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-alkyl-2-acetyl-sn-glycerol 3-phosphate + H(2)O = 2-acetyl-1-alkyl-sn-glycerol + phosphate." [EC:3.1.3.59, RHEA:18221]
+def: "Catalysis of the reaction: 1-alkyl-2-acetyl-sn-glycerol 3-phosphate + H2O = 2-acetyl-1-alkyl-sn-glycerol + phosphate." [EC:3.1.3.59, RHEA:18221]
synonym: "1-alkyl-2-acetyl-sn-glycero-3-phosphate phosphohydrolase activity" RELATED [EC:3.1.3.59]
synonym: "1-alkyl-2-lyso-sn-glycero-3-P:acetyl-CoA acetyltransferase activity" RELATED [EC:3.1.3.59]
synonym: "alkylacetylglycerophosphate phosphatase activity" RELATED [EC:3.1.3.59]
@@ -280247,7 +280254,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0047648
name: alkylamidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-methylhexanamide + H(2)O = hexanoate + methylammonium." [EC:3.5.1.39, RHEA:20081]
+def: "Catalysis of the reaction: N-methylhexanamide + H2O = hexanoate + methylammonium." [EC:3.5.1.39, RHEA:20081]
synonym: "N-methylhexanamide amidohydrolase activity" RELATED [EC:3.5.1.39]
xref: EC:3.5.1.39
xref: KEGG_REACTION:R03620
@@ -280259,7 +280266,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047649
name: alkylglycerol kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-alkyl-sn-glycerol + ATP = 1-alkyl-sn-glycerol 3-phosphate + ADP + 2 H(+)." [EC:2.7.1.93, RHEA:16937]
+def: "Catalysis of the reaction: 1-alkyl-sn-glycerol + ATP = 1-alkyl-sn-glycerol 3-phosphate + ADP + 2 H+." [EC:2.7.1.93, RHEA:16937]
synonym: "1-alkylglycerol kinase (phosphorylating)" RELATED [EC:2.7.1.93]
synonym: "alkylglycerol phosphotransferase activity" RELATED [EC:2.7.1.93]
synonym: "ATP-alkylglycerol phosphotransferase activity" RELATED [EC:2.7.1.93]
@@ -280276,7 +280283,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0047650
name: alkylglycerone kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O-alkylglycerone + ATP = O-alkylglycerone phosphate + ADP + 2 H(+)." [EC:2.7.1.84, RHEA:23088]
+def: "Catalysis of the reaction: O-alkylglycerone + ATP = O-alkylglycerone phosphate + ADP + 2 H+." [EC:2.7.1.84, RHEA:23088]
synonym: "alkyldihydroxyacetone kinase (phosphorylating)" RELATED [EC:2.7.1.84]
synonym: "alkyldihydroxyacetone kinase activity" RELATED [EC:2.7.1.84]
synonym: "ATP:O-alkylglycerone phosphotransferase activity" RELATED [EC:2.7.1.84]
@@ -280291,7 +280298,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0047651
name: alkylhalidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: bromochloromethane + H(2)O = bromide + chloride + formaldehyde + 2 H(+)." [RHEA:13765]
+def: "Catalysis of the reaction: bromochloromethane + H2O = bromide + chloride + formaldehyde + 2 H+." [RHEA:13765]
synonym: "alkyl-halide halidohydrolase activity" RELATED []
synonym: "haloalkane halidohydrolase activity" RELATED []
synonym: "halogenase activity" RELATED []
@@ -280345,7 +280352,7 @@ is_a: GO:0016846 ! carbon-sulfur lyase activity
id: GO:0047655
name: allyl-alcohol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: allyl alcohol + NADP(+) = acrolein + H(+) + NADPH." [EC:1.1.1.54, RHEA:12168]
+def: "Catalysis of the reaction: allyl alcohol + NADP+ = acrolein + H+ + NADPH." [EC:1.1.1.54, RHEA:12168]
synonym: "allyl-alcohol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.54]
xref: EC:1.1.1.54
xref: KEGG_REACTION:R03572
@@ -280413,7 +280420,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047660
name: amidinoaspartase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-amidino-L-aspartate + H(2)O = L-aspartate + urea." [EC:3.5.3.14, RHEA:14849]
+def: "Catalysis of the reaction: N-amidino-L-aspartate + H2O = L-aspartate + urea." [EC:3.5.3.14, RHEA:14849]
synonym: "amidinoaspartic amidinohydrolase activity" RELATED [EC:3.5.3.14]
synonym: "N-amidino-L-aspartate amidinohydrolase activity" RELATED [EC:3.5.3.14]
xref: EC:3.5.3.14
@@ -280449,7 +280456,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0047663
name: aminoglycoside 6'-N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + kanamycin B = N(6')-acetylkanamycin B + CoA + H(+). This is acetylation of the 6'-amino group of the 6-deoxy-6-aminoglucose ring." [EC:2.3.1.82, RHEA:16449]
+def: "Catalysis of the reaction: acetyl-CoA + kanamycin B = N(6')-acetylkanamycin B + CoA + H+. This is acetylation of the 6'-amino group of the 6-deoxy-6-aminoglucose ring." [EC:2.3.1.82, RHEA:16449]
synonym: "6'-aminoglycoside-N-acetyltransferase activity" RELATED [EC:2.3.1.82]
synonym: "AAC(6') activity" RELATED [EC:2.3.1.82]
synonym: "acetyl-CoA:kanamycin-B N6'-acetyltransferase activity" NARROW [EC:2.3.1.82]
@@ -280467,7 +280474,7 @@ is_a: GO:0034069 ! aminoglycoside N-acetyltransferase activity
id: GO:0047664
name: aminoimidazolase activity
namespace: molecular_function
-def: "Catalysis of the reaction:4-aminoimidazole + H20 = imidazol-4-one + NH(3)." [RHEA:22348]
+def: "Catalysis of the reaction:4-aminoimidazole + H20 = imidazol-4-one + NH3." [RHEA:22348]
synonym: "4-aminoimidazole aminohydrolase activity" RELATED [EC:3.5.4.8]
synonym: "4-aminoimidazole hydrolase activity" RELATED [EC:3.5.4.8]
xref: EC:3.5.4.8
@@ -280508,7 +280515,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0047666
name: ammonia kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + NH(4)(+) = ADP + 3 H(+) + phosphoramidate." [EC:2.7.3.8, RHEA:11024]
+def: "Catalysis of the reaction: ATP + NH4 = ADP + 3 H+ + phosphoramidate." [EC:2.7.3.8, RHEA:11024]
synonym: "ATP:ammonia phosphotransferase activity" RELATED [EC:2.7.3.8]
synonym: "phosphoramidate-adenosine diphosphate phosphotransferase activity" RELATED [EC:2.7.3.8]
synonym: "phosphoramidate-ADP-phosphotransferase activity" RELATED [EC:2.7.3.8]
@@ -280542,7 +280549,7 @@ id: GO:0047668
name: amygdalin beta-glucosidase activity
namespace: molecular_function
alt_id: GO:0080080
-def: "Catalysis of the reaction: (R)-amygdalin + H(2)O = (R)-prunasin + D-glucose." [EC:3.2.1.117, RHEA:14177]
+def: "Catalysis of the reaction: (R)-amygdalin + H2O = (R)-prunasin + D-glucose." [EC:3.2.1.117, RHEA:14177]
synonym: "(R)-amygdalin beta-glucosidase activity" EXACT []
synonym: "amygdalin b-glucosidase activity" EXACT []
synonym: "amygdalin beta-D-glucohydrolase activity" RELATED [EC:3.2.1.117]
@@ -280572,7 +280579,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0047670
name: anhydrotetracycline monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: anhydrotetracycline + H(+) + NADPH + O(2) = 12-dehydrotetracycline + H(2)O + NADP(+)." [EC:1.14.13.38, RHEA:11976]
+def: "Catalysis of the reaction: anhydrotetracycline + H+ + NADPH + O2 = 12-dehydrotetracycline + H2O + NADP+." [EC:1.14.13.38, RHEA:11976]
synonym: "anhydrotetracycline oxygenase activity" RELATED [EC:1.14.13.38]
synonym: "anhydrotetracycline,NADPH:oxygen oxidoreductase (6-hydroxylating)" RELATED [EC:1.14.13.38]
synonym: "ATC oxygenase activity" RELATED [EC:1.14.13.38]
@@ -280586,7 +280593,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047671
name: anthranilate adenylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: anthranilate + ATP = N-adenylylanthranilate + diphosphate + H(+)." [PMID:2995633, RHEA:35091]
+def: "Catalysis of the reaction: anthranilate + ATP = N-adenylylanthranilate + diphosphate + H+." [PMID:2995633, RHEA:35091]
synonym: "anthranilic acid adenylyltransferase activity" RELATED [EC:2.7.7.55]
synonym: "ATP:anthranilate adenylyltransferase activity" EXACT []
synonym: "ATP:anthranilate N-adenylyltransferase activity" RELATED [EC:2.7.7.55]
@@ -280624,7 +280631,7 @@ is_a: GO:0050735 ! N-malonyltransferase activity
id: GO:0047674
name: apiose 1-reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-apiitol + NAD(+) = D-apiose + H(+) + NADH." [EC:1.1.1.114, RHEA:15301]
+def: "Catalysis of the reaction: D-apiitol + NAD+ = D-apiose + H+ + NADH." [EC:1.1.1.114, RHEA:15301]
synonym: "D-apiitol reductase activity" RELATED [EC:1.1.1.114]
synonym: "D-apiitol:NAD+ 1-oxidoreductase activity" RELATED [EC:1.1.1.114]
synonym: "D-apiose reductase activity" RELATED [EC:1.1.1.114]
@@ -280638,7 +280645,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047675
name: arabinonate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-arabinonate = 2-dehydro-3-deoxy-D-arabinonate + H(2)O." [EC:4.2.1.5, RHEA:21836]
+def: "Catalysis of the reaction: D-arabinonate = 2-dehydro-3-deoxy-D-arabinonate + H2O." [EC:4.2.1.5, RHEA:21836]
synonym: "D-arabinonate hydro-lyase (2-dehydro-3-deoxy-D-arabinonate-forming)" RELATED [EC:4.2.1.5]
synonym: "D-arabinonate hydro-lyase activity" RELATED [EC:4.2.1.5]
xref: EC:4.2.1.5
@@ -280651,7 +280658,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047676
name: arachidonate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: arachidonate + ATP + CoA = AMP + arachidonoyl-CoA + diphosphate + H(+)." [RHEA:19713]
+def: "Catalysis of the reaction: arachidonate + ATP + CoA = AMP + arachidonoyl-CoA + diphosphate + H+." [RHEA:19713]
synonym: "arachidonate:CoA ligase (AMP-forming)" RELATED [EC:6.2.1.15]
synonym: "arachidonoyl-CoA synthetase activity" RELATED [EC:6.2.1.15]
xref: EC:6.2.1.15
@@ -280664,7 +280671,7 @@ is_a: GO:0004467 ! long-chain fatty acid-CoA ligase activity
id: GO:0047677
name: arachidonate 8(R)-lipoxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: arachidonate + O(2) = (5Z,8R,9E,11Z,14Z)-8-hydroperoxyicosa-5,9,11,14-tetraenoate." [EC:1.13.11.40, RHEA:14985]
+def: "Catalysis of the reaction: arachidonate + O2 = (5Z,8R,9E,11Z,14Z)-8-hydroperoxyicosa-5,9,11,14-tetraenoate." [EC:1.13.11.40, RHEA:14985]
comment: This activity produces the R-enantiomer of HPETE, 8(R)-HPETE. For the reaction producing the S-enantiomer, see GO:0036403.
synonym: "8(R)-lipoxygenase activity" RELATED [EC:1.13.11.40]
synonym: "8-lipoxygenase activity" NARROW [EC:1.13.11.40]
@@ -280680,7 +280687,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0047678
name: arginine 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arginine + O(2) = 4-guanidinobutanamide + CO(2) + H(2)O." [EC:1.13.12.1, RHEA:10548]
+def: "Catalysis of the reaction: L-arginine + O2 = 4-guanidinobutanamide + CO2 + H2O." [EC:1.13.12.1, RHEA:10548]
synonym: "arginine decarboxy-oxidase activity" RELATED [EC:1.13.12.1]
synonym: "arginine monooxygenase activity" RELATED [EC:1.13.12.1]
synonym: "arginine oxygenase (decarboxylating) activity" RELATED [EC:1.13.12.1]
@@ -280705,7 +280712,7 @@ is_a: GO:0047661 ! amino-acid racemase activity
id: GO:0047680
name: aryl-acylamidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: anilide + H(2)O = a carboxylate + aniline + H(+)." [EC:3.5.1.13, RHEA:20297]
+def: "Catalysis of the reaction: anilide + H2O = a carboxylate + aniline + H+." [EC:3.5.1.13, RHEA:20297]
synonym: "AAA-1" RELATED [EC:3.5.1.13]
synonym: "AAA-2" RELATED [EC:3.5.1.13]
synonym: "aryl-acylamide amidohydrolase activity" RELATED [EC:3.5.1.13]
@@ -280802,14 +280809,13 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0047687
name: obsolete ascorbate 2,3-dioxygenase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: L-ascorbate + H(2)O + O(2) = L-threonate + 2 H(+) + oxalate." [EC:1.13.11.13, RHEA:21784]
+def: "OBSOLETE. Catalysis of the reaction: L-ascorbate + H2O + O2 = L-threonate + 2 H+ + oxalate." [EC:1.13.11.13]
comment: This term was made obsolete because EC:1.13.11.13 was deleted; the activity is the sum of several enzymatic and spontaneous reactions.
synonym: "AAoxygenase activity" EXACT []
synonym: "ascorbate 2,3-dioxygenase activity" EXACT []
synonym: "ascorbate:oxygen 2,3-oxidoreductase (bond-cleaving)" EXACT []
xref: KEGG_REACTION:R00646
xref: MetaCyc:ASCORBATE-23-DIOXYGENASE-RXN
-xref: RHEA:21784
is_obsolete: true
[Term]
@@ -280849,7 +280855,7 @@ is_a: GO:0047661 ! amino-acid racemase activity
id: GO:0047690
name: aspartyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-asparagine + H(+) + hydroxylamine = beta-L-aspartylhydroxamate + NH(4)(+)." [EC:2.3.2.7, RHEA:11252]
+def: "Catalysis of the reaction: L-asparagine + H+ + hydroxylamine = beta-L-aspartylhydroxamate + NH4." [EC:2.3.2.7, RHEA:11252]
synonym: "aspartotransferase activity" RELATED [EC:2.3.2.7]
synonym: "beta-aspartyl transferase activity" RELATED [EC:2.3.2.7]
synonym: "L-asparagine:hydroxylamine gamma-aspartyltransferase activity" RELATED [EC:2.3.2.7]
@@ -280888,15 +280894,15 @@ is_a: GO:0047623 ! adenosine-phosphate deaminase activity
id: GO:0047693
name: ATP diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = AMP + diphosphate." [RHEA:14245]
-synonym: "adenosine triphosphate pyrophosphatase activity" RELATED [EC:3.6.1.8]
+def: "Catalysis of the reaction: ATP + H2O = AMP + H+ + diphosphate." [RHEA:14245]
+synonym: "adenosine triphosphate pyrophosphatase activity" EXACT [EC:3.6.1.8]
synonym: "ATP diphosphohydrolase" BROAD [EC:3.6.1.8]
-synonym: "ATP diphosphohydrolase (diphosphate-forming)" RELATED [EC:3.6.1.8]
+synonym: "ATP diphosphohydrolase (diphosphate-forming)" EXACT [EC:3.6.1.8]
synonym: "ATP pyrophosphatase activity" EXACT []
xref: EC:3.6.1.8
xref: MetaCyc:ATP-PYROPHOSPHATASE-RXN
xref: RHEA:14245
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0047694
@@ -280961,7 +280967,7 @@ is_a: GO:0004672 ! protein kinase activity
id: GO:0047697
name: beta-alanopine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-beta-alanopine + H(2)O + NAD(+) = beta-alanine + H(+) + NADH + pyruvate." [EC:1.5.1.26, RHEA:21684]
+def: "Catalysis of the reaction: (R)-beta-alanopine + H2O + NAD+ = beta-alanine + H+ + NADH + pyruvate." [EC:1.5.1.26, RHEA:21684]
synonym: "b-alanopine dehydrogenase activity" EXACT []
synonym: "N-(D-1-carboxyethyl)-beta-alanine:NAD+ oxidoreductase (beta-alanine-forming)" RELATED [EC:1.5.1.26]
xref: EC:1.5.1.26
@@ -280987,7 +280993,7 @@ is_a: GO:0016841 ! ammonia-lyase activity
id: GO:0047699
name: beta-diketone hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + nonane-4,6-dione = butanoate + H(+) + pentan-2-one." [EC:3.7.1.7, RHEA:11908]
+def: "Catalysis of the reaction: H2O + nonane-4,6-dione = butanoate + H+ + pentan-2-one." [EC:3.7.1.7, RHEA:11908]
synonym: "b-diketone hydrolase activity" EXACT []
synonym: "nonane-4,6-dione acylhydrolase activity" RELATED [EC:3.7.1.7]
synonym: "oxidized PVA hydrolase activity" RELATED [EC:3.7.1.7]
@@ -281042,7 +281048,7 @@ is_a: GO:0016869 ! intramolecular transferase activity, transferring amino group
id: GO:0047703
name: beta-nitroacrylate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-nitropropanoate + NADP(+) = 3-nitroacrylate + H(+) + NADPH." [EC:1.3.1.16, RHEA:23892]
+def: "Catalysis of the reaction: 3-nitropropanoate + NADP+ = 3-nitroacrylate + H+ + NADPH." [EC:1.3.1.16, RHEA:23892]
synonym: "3-nitropropanoate:NADP+ oxidoreductase activity" RELATED [EC:1.3.1.16]
synonym: "b-nitroacrylate reductase activity" EXACT []
xref: EC:1.3.1.16
@@ -281073,7 +281079,7 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0047705
name: bilirubin oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O." [EC:1.3.3.5, RHEA:20980]
+def: "Catalysis of the reaction: 2 bilirubin + O2 = 2 biliverdin + 2 H2O." [EC:1.3.3.5, RHEA:20980]
synonym: "bilirubin oxidase M-1" RELATED [EC:1.3.3.5]
synonym: "bilirubin:oxygen oxidoreductase activity" RELATED [EC:1.3.3.5]
xref: EC:1.3.3.5
@@ -281086,7 +281092,7 @@ is_a: GO:0016634 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047706
name: biochanin-A reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dihydrobiochanin A + NADP(+) = biochanin A + H(+) + NADPH." [EC:1.3.1.46, RHEA:12817]
+def: "Catalysis of the reaction: dihydrobiochanin A + NADP+ = biochanin A + H+ + NADPH." [EC:1.3.1.46, RHEA:12817]
synonym: "dihydrobiochanin-A:NADP+ delta2-oxidoreductase activity" RELATED [EC:1.3.1.46]
xref: EC:1.3.1.46
xref: KEGG_REACTION:R02954
@@ -281129,7 +281135,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047709
name: bis(2-ethylhexyl)phthalate esterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: bis(2-ethylhexyl)phthalate + H(2)O = 2-ethylhexan-1-ol + 2-ethylhexyl phthalate + H(+)." [EC:3.1.1.60, RHEA:15529]
+def: "Catalysis of the reaction: bis(2-ethylhexyl)phthalate + H2O = 2-ethylhexan-1-ol + 2-ethylhexyl phthalate + H+." [EC:3.1.1.60, RHEA:15529]
synonym: "bis(2-ethylhexyl)phthalate acylhydrolase activity" RELATED [EC:3.1.1.60]
synonym: "DEHP esterase activity" RELATED [EC:3.1.1.60]
xref: EC:3.1.1.60
@@ -281142,7 +281148,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0047710
name: bis(5'-adenosyl)-triphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: P(1),P(3)-bis(5'-adenosyl) triphosphate + H(2)O = ADP + AMP + 2 H(+)." [EC:3.6.1.29, RHEA:13893]
+def: "Catalysis of the reaction: P(1),P(3)-bis(5'-adenosyl) triphosphate + H2O = ADP + AMP + 2 H+." [EC:3.6.1.29, RHEA:13893]
synonym: "1-P,3-P-bis(5'-adenosyl)-triphosphate adenylohydrolase activity" RELATED [EC:3.6.1.29]
synonym: "AP(3)A hydrolase activity" RELATED [EC:3.6.1.29]
synonym: "AP(3)Aase activity" RELATED [EC:3.6.1.29]
@@ -281157,7 +281163,7 @@ xref: EC:3.6.1.29
xref: KEGG_REACTION:R00187
xref: MetaCyc:BIS5-ADENOSYL-TRIPHOSPHATASE-RXN
xref: RHEA:13893
-is_a: GO:0004551 ! nucleotide diphosphatase activity
+is_a: GO:0016462 ! pyrophosphatase activity
[Term]
id: GO:0047711
@@ -281191,7 +281197,7 @@ is_a: GO:0045289 ! luciferin monooxygenase activity
id: GO:0047713
name: galactitol 2-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: galactitol + NAD(+) = D-tagatose + H(+) + NADH." [EC:1.1.1.16, RHEA:20685]
+def: "Catalysis of the reaction: galactitol + NAD+ = D-tagatose + H+ + NADH." [EC:1.1.1.16, RHEA:20685]
xref: EC:1.1.1.16
xref: KEGG_REACTION:R02928
xref: MetaCyc:GALACTITOL-2-DEHYDROGENASE-RXN
@@ -281218,7 +281224,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0047715
name: hypotaurocyamine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + hypotaurocyamine = N(omega)-phosphohypotaurocyamine + ADP + 2 H(+)." [EC:2.7.3.6, RHEA:24008]
+def: "Catalysis of the reaction: ATP + hypotaurocyamine = N(omega)-phosphohypotaurocyamine + ADP + 2 H+." [EC:2.7.3.6, RHEA:24008]
synonym: "ATP:hypotaurocyamine N-phosphotransferase activity" RELATED [EC:2.7.3.6]
xref: EC:2.7.3.6
xref: KEGG_REACTION:R03939
@@ -281245,7 +281251,7 @@ is_a: GO:0008080 ! N-acetyltransferase activity
id: GO:0047717
name: imidazoleacetate 4-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + imidazol-4-ylacetate + NADH + O(2) = 5-hydroxyimidazole-4-acetate + H(2)O + NAD(+)." [EC:1.14.13.5, RHEA:19425]
+def: "Catalysis of the reaction: H+ + imidazol-4-ylacetate + NADH + O2 = 5-hydroxyimidazole-4-acetate + H2O + NAD+." [EC:1.14.13.5, RHEA:19425]
synonym: "4-imidazoleacetate,NADH:oxygen oxidoreductase (5-hydroxylating)" RELATED [EC:1.14.13.5]
synonym: "imidazoleacetate hydroxylase activity" RELATED [EC:1.14.13.5]
synonym: "imidazoleacetic hydroxylase activity" EXACT []
@@ -281270,7 +281276,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047719
name: indole 2,3-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: indole + O(2) = 2-formamidobenzaldehyde." [EC:1.13.11.17, RHEA:11212]
+def: "Catalysis of the reaction: indole + O2 = 2-formamidobenzaldehyde." [EC:1.13.11.17, RHEA:11212]
synonym: "IDO" RELATED [EC:1.13.11.17]
synonym: "indole oxidase activity" RELATED [EC:1.13.11.17]
synonym: "indole-oxygen 2,3-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.17]
@@ -281286,7 +281292,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0047720
name: indoleacetaldoxime dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (indol-3-yl)acetaldehyde oxime = (indol-3-yl)acetonitrile + H(2)O." [EC:4.99.1.6, RHEA:23156]
+def: "Catalysis of the reaction: (indol-3-yl)acetaldehyde oxime = (indol-3-yl)acetonitrile + H2O." [RHEA:23156]
synonym: "(indol-3-yl)acetaldehyde-oxime hydro-lyase [(indol-3-yl)acetonitrile-forming]" RELATED [EC:4.99.1.6]
synonym: "(indol-3-yl)acetaldehyde-oxime hydro-lyase activity" RELATED [EC:4.99.1.6]
synonym: "3-indoleacetaldoxime hydro-lyase activity" RELATED [EC:4.99.1.6]
@@ -281303,7 +281309,7 @@ is_a: GO:0016829 ! lyase activity
id: GO:0047721
name: indoleacetate-lysine synthetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (indol-3-yl)acetate + L-lysine + ATP = N(6)-[(indole-3-yl)acetyl]-L-lysine + ADP + 2 H(+) + phosphate." [EC:6.3.2.20, RHEA:14857]
+def: "Catalysis of the reaction: (indol-3-yl)acetate + L-lysine + ATP = N(6)-[(indole-3-yl)acetyl]-L-lysine + ADP + 2 H+ + phosphate." [EC:6.3.2.20, RHEA:14857]
synonym: "(indol-3-yl)acetate:L-lysine ligase (ADP-forming)" RELATED [EC:6.3.2.20]
synonym: "IAA-lysine synthetase activity" RELATED [EC:6.3.2.20]
synonym: "indoleacetate-lysine ligase activity" EXACT []
@@ -281319,7 +281325,7 @@ is_a: GO:0010279 ! indole-3-acetic acid amido synthetase activity
id: GO:0047722
name: indolelactate dehydrogenase (NADH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-(indol-3-yl)lactate + NAD(+) = 3-(indol-3-yl)pyruvate + H(+) + NADH." [RHEA:20133]
+def: "Catalysis of the reaction: 3-(indol-3-yl)lactate + NAD+ = 3-(indol-3-yl)pyruvate + H+ + NADH." [RHEA:20133]
synonym: "(indol-3-yl)lactate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.110]
synonym: "indole-3-lactate dehydrogenase activity" EXACT []
synonym: "indolelactate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.110]
@@ -281333,7 +281339,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047723
name: inosinate nucleosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + IMP = D-ribose 5-phosphate + hypoxanthine." [EC:3.2.2.12, RHEA:20469]
+def: "Catalysis of the reaction: H2O + IMP = D-ribose 5-phosphate + hypoxanthine." [EC:3.2.2.12, RHEA:20469]
synonym: "5'-inosinate phosphoribohydrolase activity" RELATED [EC:3.2.2.12]
xref: EC:3.2.2.12
xref: KEGG_REACTION:R01128
@@ -281397,7 +281403,7 @@ is_a: GO:0016866 ! intramolecular transferase activity
id: GO:0047728
name: carnitine 3-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: carnitine + NAD(+) = 3-dehydrocarnitine + H(+) + NADH." [EC:1.1.1.108, RHEA:19265]
+def: "Catalysis of the reaction: carnitine + NAD+ = 3-dehydrocarnitine + H+ + NADH." [EC:1.1.1.108, RHEA:19265]
synonym: "carnitine:NAD+ 3-oxidoreductase activity" RELATED [EC:1.1.1.108]
xref: EC:1.1.1.108
xref: KEGG_REACTION:R02395
@@ -281409,7 +281415,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047729
name: carnitine decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: carnitine + H(+) = 2-methylcholine + CO(2)." [EC:4.1.1.42, RHEA:21576]
+def: "Catalysis of the reaction: carnitine + H+ = 2-methylcholine + CO2." [EC:4.1.1.42, RHEA:21576]
synonym: "carnitine carboxy-lyase (2-methylcholine-forming)" RELATED [EC:4.1.1.42]
synonym: "carnitine carboxy-lyase activity" RELATED [EC:4.1.1.42]
xref: EC:4.1.1.42
@@ -281469,7 +281475,7 @@ is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and
id: GO:0047733
name: CDP-glucose 4,6-dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: CDP-D-glucose = CDP-4-dehydro-6-deoxy-D-glucose + H(2)O." [EC:4.2.1.45, RHEA:17153]
+def: "Catalysis of the reaction: CDP-D-glucose = CDP-4-dehydro-6-deoxy-D-glucose + H2O." [EC:4.2.1.45, RHEA:17153]
synonym: "CDP-glucose 4,6-hydro-lyase (CDP-4-dehydro-6-deoxy-D-glucose-forming)" RELATED [EC:4.2.1.45]
synonym: "CDP-glucose 4,6-hydro-lyase activity" RELATED [EC:4.2.1.45]
synonym: "CDPglucose 4,6-dehydratase activity" RELATED [EC:4.2.1.45]
@@ -281485,7 +281491,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047734
name: CDP-glycerol diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: CDP-glycerol + H(2)O = sn-glycerol 3-phosphate + CMP + 2 H(+)." [EC:3.6.1.16, RHEA:21692]
+def: "Catalysis of the reaction: CDP-glycerol + H2O = sn-glycerol 3-phosphate + CMP + 2 H+." [EC:3.6.1.16, RHEA:21692]
synonym: "CDP-glycerol phosphoglycerohydrolase activity" RELATED [EC:3.6.1.16]
synonym: "CDP-glycerol pyrophosphatase activity" EXACT []
synonym: "CDPglycerol diphosphatase activity" RELATED [EC:3.6.1.16]
@@ -281546,7 +281552,7 @@ is_a: GO:0004645 ! 1,4-alpha-oligoglucan phosphorylase activity
id: GO:0047739
name: cephalosporin-C deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cephalosporin C + H(2)O = acetate + deacetylcephalosporin C + H(+)." [EC:3.1.1.41, RHEA:22596]
+def: "Catalysis of the reaction: cephalosporin C + H2O = acetate + deacetylcephalosporin C + H+." [EC:3.1.1.41, RHEA:22596]
synonym: "cephalosporin acetylesterase activity" RELATED [EC:3.1.1.41]
synonym: "cephalosporin C acetyl-esterase activity" RELATED [EC:3.1.1.41]
synonym: "cephalosporin C acetyl-hydrolase activity" RELATED [EC:3.1.1.41]
@@ -281579,7 +281585,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0047741
name: cetraxate benzylesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: benzyl cetraxate + H(2)O = benzyl alcohol + cetraxate + H(+)." [EC:3.1.1.70, RHEA:23460]
+def: "Catalysis of the reaction: benzyl cetraxate + H2O = benzyl alcohol + cetraxate + H+." [EC:3.1.1.70, RHEA:23460]
synonym: "cetraxate-benzyl-ester benzylhydrolase activity" RELATED [EC:3.1.1.70]
xref: EC:3.1.1.70
xref: KEGG_REACTION:R03612
@@ -281602,7 +281608,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047743
name: chlordecone reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: chlordecone alcohol + NADP(+) = chlordecone + H(+) + NADPH." [EC:1.1.1.225, RHEA:14401]
+def: "Catalysis of the reaction: chlordecone alcohol + NADP+ = chlordecone + H+ + NADPH." [EC:1.1.1.225, RHEA:14401]
synonym: "CDR activity" RELATED [EC:1.1.1.225]
synonym: "chlordecone-alcohol:NADP+ 2-oxidoreductase activity" RELATED [EC:1.1.1.225]
xref: EC:1.1.1.225
@@ -281615,7 +281621,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047744
name: chloridazon-catechol dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-amino-4-chloro-2-(2,3-dihydroxyphenyl)pyridazin-3(2H)-one + O(2) = 5-amino-4-chloro-2-(2-hydroxymuconoyl)pyridazin-3(2H)-one + 2 H(+)." [EC:1.13.11.36, RHEA:20449]
+def: "Catalysis of the reaction: 5-amino-4-chloro-2-(2,3-dihydroxyphenyl)pyridazin-3(2H)-one + O2 = 5-amino-4-chloro-2-(2-hydroxymuconoyl)pyridazin-3(2H)-one + 2 H+." [EC:1.13.11.36, RHEA:20449]
synonym: "5-amino-4-chloro-2-(2,3-dihydroxyphenyl)-3(2H)-pyridazinone 1,2-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.36]
xref: EC:1.13.11.36
xref: KEGG_REACTION:R04602
@@ -281627,7 +281633,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0047745
name: chlorogenate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: chlorogenate + H(2)O = (-)-quinate + cis-caffeate + H(+)." [EC:3.1.1.42, RHEA:20689]
+def: "Catalysis of the reaction: chlorogenate + H2O = (-)-quinate + cis-caffeate + H+." [EC:3.1.1.42, RHEA:20689]
synonym: "chlorogenase activity" RELATED [EC:3.1.1.42]
synonym: "chlorogenic acid esterase activity" RELATED [EC:3.1.1.42]
xref: EC:3.1.1.42
@@ -281719,7 +281725,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047750
name: cholestenol delta-isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-alpha-cholest-7-en-3-beta-ol = 5-alpha-cholest-8-en-3-beta-ol." [EC:5.3.3.5, MetaCyc:CHOLESTENOL-DELTA-ISOMERASE-RXN]
+def: "Catalysis of the reaction: 5-alpha-cholest-7-en-3-beta-ol = 5-alpha-cholest-8-en-3-beta-ol." [RHEA:15281]
synonym: "cholestenol D-isomerase activity" EXACT []
synonym: "delta7-cholestenol delta7-delta8-isomerase activity" RELATED [EC:5.3.3.5]
xref: EC:5.3.3.5
@@ -281731,7 +281737,7 @@ is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds
id: GO:0047751
name: cholestenone 5-alpha-reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5alpha-cholestan-3-one + NADP(+) = cholest-4-en-3-one + H(+) + NADPH." [EC:1.3.1.22, RHEA:24552]
+def: "Catalysis of the reaction: 5alpha-cholestan-3-one + NADP+ = cholest-4-en-3-one + H+ + NADPH." [EC:1.3.1.22, RHEA:24552]
synonym: "3-oxo-5alpha-steroid:NADP+ delta4-oxidoreductase activity" RELATED [EC:1.3.1.22]
synonym: "3-oxosteroid 5alpha-reductase activity" RELATED [EC:1.3.1.22]
synonym: "3-oxosteroid delta4-dehydrogenase" BROAD [EC:1.3.1.22]
@@ -281758,7 +281764,7 @@ is_a: GO:0035671 ! enone reductase activity
id: GO:0047753
name: choline-sulfatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: choline sulfate + H(2)O = choline + H(+) + sulfate." [EC:3.1.6.6, RHEA:20820]
+def: "Catalysis of the reaction: choline sulfate + H2O = choline + H+ + sulfate." [EC:3.1.6.6, RHEA:20820]
synonym: "choline-sulfate sulfohydrolase activity" RELATED [EC:3.1.6.6]
synonym: "choline-sulphatase activity" EXACT []
xref: EC:3.1.6.6
@@ -281771,7 +281777,7 @@ is_a: GO:0008484 ! sulfuric ester hydrolase activity
id: GO:0047754
name: choline sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + choline = adenosine 3',5'-diphosphate + choline sulfate + H(+)." [EC:2.8.2.6, RHEA:21984]
+def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + choline = adenosine 3',5'-diphosphate + choline sulfate + H+." [EC:2.8.2.6, RHEA:21984]
synonym: "3'-phosphoadenylyl-sulfate:choline sulfotransferase activity" RELATED [EC:2.8.2.6]
synonym: "choline sulphokinase activity" RELATED [EC:2.8.2.6]
synonym: "choline sulphotransferase activity" EXACT []
@@ -281826,7 +281832,7 @@ is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and
id: GO:0047758
name: ATP:2-methylpropanoate phosphotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-methylpropanoate + ATP = 2-methylpropanoyl phosphate + ADP + H(+)." [EC:2.7.2.14, RHEA:24156]
+def: "Catalysis of the reaction: 2-methylpropanoate + ATP = 2-methylpropanoyl phosphate + ADP + H+." [EC:2.7.2.14, RHEA:24156]
synonym: "ATP:2-methylpropanoate 1-phosphotransferase activity" EXACT []
synonym: "ATP:2-methylpropanoate kinase activity" EXACT []
synonym: "ATP:branched-chain-fatty-acid 1-phosphotransferase activity" BROAD [EC:2.7.2.14, KEGG_REACTION:R04002]
@@ -281877,7 +281883,7 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0047761
name: butyrate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + butanoate = ADP + butanoyl phosphate + H(+)." [EC:2.7.2.7, RHEA:13585]
+def: "Catalysis of the reaction: ATP + butanoate = ADP + butanoyl phosphate + H+." [EC:2.7.2.7, RHEA:13585]
synonym: "ATP:butanoate 1-phosphotransferase activity" RELATED [EC:2.7.2.7]
xref: EC:2.7.2.7
xref: KEGG_REACTION:R01688
@@ -281890,7 +281896,7 @@ is_a: GO:0016774 ! phosphotransferase activity, carboxyl group as acceptor
id: GO:0047762
name: caffeate 3,4-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: trans-caffeate + O(2) = 3-(2-carboxyethenyl)-cis,cis-muconate + 2 H(+)." [EC:1.13.11.22, RHEA:22216]
+def: "Catalysis of the reaction: trans-caffeate + O2 = 3-(2-carboxyethenyl)-cis,cis-muconate + 2 H+." [EC:1.13.11.22, RHEA:22216]
synonym: "3,4-dihydroxy-trans-cinnamate:oxygen 3,4-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.22]
xref: EC:1.13.11.22
xref: KEGG_REACTION:R03365
@@ -281937,7 +281943,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0047766
name: carbamoyl-serine ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O-carbamoyl-L-serine + H(2)O + H(+) = CO(2) + 2 NH(4)(+) + pyruvate." [EC:4.3.1.13, RHEA:15445]
+def: "Catalysis of the reaction: O-carbamoyl-L-serine + H2O + H+ = CO2 + 2 NH4 + pyruvate." [EC:4.3.1.13, RHEA:15445]
synonym: "carbamoylserine deaminase activity" RELATED [EC:4.3.1.13]
synonym: "O-carbamoyl-L-serine ammonia-lyase (decarboxylating; pyruvate-forming)" RELATED [EC:4.3.1.13]
synonym: "O-carbamoyl-L-serine ammonia-lyase (pyruvate-forming)" RELATED [EC:4.3.1.13]
@@ -281992,7 +281998,7 @@ is_a: GO:0016903 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0047771
name: carboxymethylhydantoinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-5-carboxymethylhydantoin + H(2)O = N-carbamoyl-L-aspartate + H(+)." [EC:3.5.2.4, RHEA:12028]
+def: "Catalysis of the reaction: L-5-carboxymethylhydantoin + H2O = N-carbamoyl-L-aspartate + H+." [EC:3.5.2.4, RHEA:12028]
synonym: "hydantoin hydrolase activity" RELATED [EC:3.5.2.4]
synonym: "L-5-carboxymethylhydantoin amidohydrolase activity" RELATED [EC:3.5.2.4]
xref: EC:3.5.2.4
@@ -282018,7 +282024,7 @@ is_a: GO:0016835 ! carbon-oxygen lyase activity
id: GO:0047773
name: carnitinamidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-carnitinamide + H(2)O = (R)-carnitine + NH(4)(+)." [EC:3.5.1.73, RHEA:17537]
+def: "Catalysis of the reaction: (R)-carnitinamide + H2O = (R)-carnitine + NH4." [EC:3.5.1.73, RHEA:17537]
synonym: "carnitine amidase activity" RELATED [EC:3.5.1.73]
synonym: "L-carnitinamidase activity" RELATED [EC:3.5.1.73]
synonym: "L-carnitinamide amidohydrolase activity" RELATED [EC:3.5.1.73]
@@ -282110,7 +282116,7 @@ is_a: GO:0016790 ! thiolester hydrolase activity
id: GO:0047779
name: citrate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + citrate + CoA = (3S)-citryl-CoA + ADP + H(+) + phosphate." [EC:6.2.1.18, RHEA:21472]
+def: "Catalysis of the reaction: ATP + citrate + CoA = (3S)-citryl-CoA + ADP + H+ + phosphate." [EC:6.2.1.18, RHEA:21472]
synonym: "citrate thiokinase activity" RELATED [EC:6.2.1.18]
synonym: "citrate:CoA ligase (ADP-forming)" RELATED [EC:6.2.1.18]
synonym: "citrate:CoA ligase activity" RELATED [EC:6.2.1.18]
@@ -282198,7 +282204,7 @@ is_a: GO:0016413 ! O-acetyltransferase activity
id: GO:0047785
name: cortisol sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + cortisol = adenosine 3',5'-diphosphate + cortisol 21-sulfate + H(+)." [EC:2.8.2.18, RHEA:11884]
+def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + cortisol = adenosine 3',5'-diphosphate + cortisol 21-sulfate + H+." [EC:2.8.2.18, RHEA:11884]
synonym: "3'-phosphoadenylyl-sulfate:cortisol 21-sulfotransferase activity" RELATED [EC:2.8.2.18]
synonym: "cortisol sulphotransferase activity" EXACT []
synonym: "glucocorticoid sulfotransferase activity" RELATED [EC:2.8.2.18]
@@ -282211,21 +282217,21 @@ is_a: GO:0008146 ! sulfotransferase activity
[Term]
id: GO:0047786
-name: cortisone alpha-reductase activity
+name: obsolete cortisone alpha-reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4,5alpha-dihydrocortisone + NADP(+) = cortisone + H(+) + NADPH." [RHEA:17981]
+def: "OBSOLETE. Catalysis of the reaction: 4,5alpha-dihydrocortisone + NADP+ = cortisone + H+ + NADPH." [GOC:curators]
+comment: RHEA: not enough evidence that the activity exists
synonym: "4,5alpha-dihydrocortisone:NADP+ delta4-oxidoreductase activity" RELATED []
synonym: "cortisone a-reductase activity" EXACT []
synonym: "cortisone delta4-5alpha-reductase activity" RELATED []
-synonym: "delta4-3-ketosteroid reductase (5alpha)" RELATED [EC:1.3.1.4]
+synonym: "delta4-3-ketosteroid reductase (5alpha)" RELATED []
synonym: "delta4-3-oxosteroid-5alpha-reductase" RELATED []
synonym: "delta4-5alpha-reductase activity" RELATED []
-synonym: "microsomal steroid reductase (5alpha)" RELATED [EC:1.3.1.4]
+synonym: "microsomal steroid reductase (5alpha)" RELATED []
synonym: "NADPH:Delta4-3-oxosteroid-5alpha-oxidoreductase activity" RELATED []
xref: KEGG_REACTION:R02892
xref: MetaCyc:CORTISONE-ALPHA-REDUCTASE-RXN
-xref: RHEA:17981
-is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
+is_obsolete: true
[Term]
id: GO:0047787
@@ -282271,7 +282277,7 @@ is_a: GO:0035671 ! enone reductase activity
id: GO:0047788
name: 2-coumarate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-(2-hydroxyphenyl)propanoate + NAD(+) = trans-2-coumarate + H(+) + NADH." [EC:1.3.1.11, RHEA:21444]
+def: "Catalysis of the reaction: 3-(2-hydroxyphenyl)propanoate + NAD+ = trans-2-coumarate + H+ + NADH." [EC:1.3.1.11, RHEA:21444]
synonym: "3-(2-hydroxyphenyl)propanoate:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.11]
synonym: "coumarate reductase activity" EXACT []
synonym: "melilotate dehydrogenase activity" RELATED [EC:1.3.1.11]
@@ -282285,7 +282291,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047789
name: creatininase activity
namespace: molecular_function
-def: "Catalysis of the reaction: creatinine + H(2)O = creatine." [EC:3.5.2.10, RHEA:14533]
+def: "Catalysis of the reaction: creatinine + H2O = creatine." [EC:3.5.2.10, RHEA:14533]
synonym: "creatinine amidohydrolase activity" RELATED [EC:3.5.2.10]
synonym: "creatinine hydrolase" BROAD [EC:3.5.2.10]
xref: EC:3.5.2.10
@@ -282384,7 +282390,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047796
name: cyclohexane-1,3-dione hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cyclohexane-1,3-dione + H(2)O = 5-oxohexanoate + H(+)." [EC:3.7.1.10, RHEA:16473]
+def: "Catalysis of the reaction: cyclohexane-1,3-dione + H2O = 5-oxohexanoate + H+." [EC:3.7.1.10, RHEA:16473]
synonym: "1,3-cyclohexanedione hydrolase activity" RELATED [EC:3.7.1.10]
synonym: "cyclohexane-1,3-dione acylhydrolase (decyclizing)" RELATED [EC:3.7.1.10]
xref: EC:3.7.1.10
@@ -282424,7 +282430,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0047799
name: cyclopentanone monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cyclopentanone + H(+) + NADPH + O(2) = 5-valerolactone + H(2)O + NADP(+)." [EC:1.14.13.16, RHEA:15737]
+def: "Catalysis of the reaction: cyclopentanone + H+ + NADPH + O2 = 5-valerolactone + H2O + NADP+." [EC:1.14.13.16, RHEA:15737]
synonym: "cyclopentanone 1,2-monooxygenase activity" RELATED [EC:1.14.13.16]
synonym: "cyclopentanone oxygenase activity" RELATED [EC:1.14.13.16]
synonym: "cyclopentanone,NADPH:oxygen oxidoreductase (5-hydroxylating, lactonizing)" RELATED [EC:1.14.13.16]
@@ -282438,7 +282444,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047800
name: cysteamine dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cysteamine + O(2) = H(+) + hypotaurine." [EC:1.13.11.19, RHEA:14409]
+def: "Catalysis of the reaction: cysteamine + O2 = H+ + hypotaurine." [EC:1.13.11.19, RHEA:14409]
synonym: "2-aminoethanethiol:oxygen oxidoreductase activity" RELATED [EC:1.13.11.19]
synonym: "cysteamine oxygenase activity" RELATED [EC:1.13.11.19]
synonym: "cysteamine:oxygen oxidoreductase activity" RELATED [EC:1.13.11.19]
@@ -282510,7 +282516,7 @@ is_a: GO:0016846 ! carbon-sulfur lyase activity
id: GO:0047805
name: cytidylate cyclase activity
namespace: molecular_function
-def: "Catalysis of the reaction: CTP = 3',5'-cyclic CMP + diphosphate + H(+)." [EC:4.6.1.6, RHEA:14737]
+def: "Catalysis of the reaction: CTP = 3',5'-cyclic CMP + diphosphate + H+." [EC:4.6.1.6, RHEA:14737]
synonym: "3',5'-cyclic-CMP synthase activity" RELATED [EC:4.6.1.6]
synonym: "3'5'-cyclic-CMP synthase activity" RELATED [EC:4.6.1.6]
synonym: "CTP diphosphate-lyase (cyclizing)" RELATED [EC:4.6.1.6]
@@ -282561,7 +282567,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0047808
name: D(-)-tartrate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-tartrate = H(2)O + oxaloacetate." [EC:4.2.1.81, RHEA:18289]
+def: "Catalysis of the reaction: D-tartrate = H2O + oxaloacetate." [EC:4.2.1.81, RHEA:18289]
synonym: "(S,S)-tartrate hydro-lyase (oxaloacetate-forming)" RELATED [EC:4.2.1.81]
synonym: "(S,S)-tartrate hydro-lyase activity" RELATED [EC:4.2.1.81]
synonym: "D-tartrate dehydratase activity" RELATED [EC:4.2.1.81]
@@ -282607,7 +282613,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0047811
name: D-alanine gamma-glutamyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-alanine + L-glutamine = gamma-L-glutamyl-D-alanine + NH(4)(+)." [EC:2.3.2.14, RHEA:23556]
+def: "Catalysis of the reaction: D-alanine + L-glutamine = gamma-L-glutamyl-D-alanine + NH4." [EC:2.3.2.14, RHEA:23556]
synonym: "D-alanine g-glutamyltransferase activity" EXACT []
synonym: "L-glutamine:D-alanine gamma-glutamyltransferase activity" RELATED [EC:2.3.2.14]
xref: EC:2.3.2.14
@@ -282657,7 +282663,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0047815
name: D-arabinonolactonase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-arabinono-1,4-lactone + H(2)O = D-arabinonate + H(+)." [EC:3.1.1.30, RHEA:23108]
+def: "Catalysis of the reaction: D-arabinono-1,4-lactone + H2O = D-arabinonate + H+." [EC:3.1.1.30, RHEA:23108]
synonym: "D-arabinono-1,4-lactone lactonohydrolase activity" RELATED [EC:3.1.1.30]
xref: EC:3.1.1.30
xref: KEGG_REACTION:R02714
@@ -282682,7 +282688,7 @@ is_a: GO:0045290 ! D-arabinose 1-dehydrogenase [NAD(P)+] activity
id: GO:0047817
name: D-arginase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-arginine + H(2)O = D-ornithine + urea." [EC:3.5.3.10, RHEA:12901]
+def: "Catalysis of the reaction: D-arginine + H2O = D-ornithine + urea." [EC:3.5.3.10, RHEA:12901]
synonym: "D-arginine amidinohydrolase activity" RELATED [EC:3.5.3.10]
xref: EC:3.5.3.10
xref: KEGG_REACTION:R02458
@@ -282694,7 +282700,7 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047818
name: D-fuconate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-fuconate = 2-dehydro-3-deoxy-D-fuconate + H(2)O." [EC:4.2.1.67, RHEA:12949]
+def: "Catalysis of the reaction: D-fuconate = 2-dehydro-3-deoxy-D-fuconate + H2O." [EC:4.2.1.67, RHEA:12949]
synonym: "D-fuconate hydratase activity" EXACT []
synonym: "D-fuconate hydro-lyase (2-dehydro-3-deoxy-D-fuconate-forming)" RELATED [EC:4.2.1.67]
synonym: "D-fuconate hydro-lyase activity" RELATED [EC:4.2.1.67]
@@ -282708,7 +282714,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047819
name: D-glutamate(D-aspartate) oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glutamate + H2O + O2 = 2-oxoglutarate + NH3 + H2O2, and D-aspartate + H2O + O2 = oxaloacetate + NH3 + H2O2." [EC:1.4.3.15, MetaCyc:D-GLUTAMATED-ASPARTATE-OXIDASE-RXN]
+def: "Catalysis of the reaction: D-glutamate + H2O + O2 = 2-oxoglutarate + NH3 + H2O2, and D-aspartate + H2O + O2 = oxaloacetate + NH3 + H2O2." [EC:1.4.3.15]
comment: For the individual reactions, see instead 'D-glutamate oxidase activity ;GO:0047821' and 'D-aspartate oxidase activity ; GO:0008445'.
synonym: "D-glutamate(D-aspartate):oxygen oxidoreductase (deaminating)" RELATED [EC:1.4.3.15]
synonym: "D-glutamic-aspartic oxidase activity" RELATED [EC:1.4.3.15]
@@ -282721,7 +282727,7 @@ is_a: GO:0003884 ! D-amino-acid oxidase activity
id: GO:0047820
name: D-glutamate cyclase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glutamate = 5-oxo-D-proline + H(2)O." [EC:4.2.1.48, RHEA:22360]
+def: "Catalysis of the reaction: D-glutamate = 5-oxo-D-proline + H2O." [EC:4.2.1.48, RHEA:22360]
synonym: "D-glutamate hydro-lyase (cyclizing)" RELATED [EC:4.2.1.48]
synonym: "D-glutamate hydro-lyase (cyclizing; 5-oxo-D-proline-forming)" RELATED [EC:4.2.1.48]
xref: EC:4.2.1.48
@@ -282735,7 +282741,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047821
name: D-glutamate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glutamate + H2O + O2 = 2-oxoglutarate + NH3 + H2O2." [EC:1.4.3.7, MetaCyc:D-GLUTAMATE-OXIDASE-RXN]
+def: "Catalysis of the reaction: D-glutamate + H2O + O2 = 2-oxoglutarate + NH3 + H2O2." [EC:1.4.3.7]
synonym: "D-glutamate:oxygen oxidoreductase (deaminating)" RELATED [EC:1.4.3.7]
synonym: "D-glutamic acid oxidase activity" RELATED [EC:1.4.3.7]
synonym: "D-glutamic oxidase activity" RELATED [EC:1.4.3.7]
@@ -282749,14 +282755,12 @@ is_a: GO:0003884 ! D-amino-acid oxidase activity
id: GO:0047822
name: hypotaurine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + hypotaurine + NAD(+) = H(+) + NADH + taurine." [RHEA:17385]
-synonym: "hypotaurine:NAD+ oxidoreductase activity" RELATED [EC:1.8.1.3]
-xref: EC:1.8.1.3
-xref: KEGG_REACTION:R01681
+def: "Catalysis of the reaction: H+ + hypotaurine + NADPH + O2 = H2O + NADP+ + taurine." [RHEA:69819]
+xref: EC:1.14.13.8
xref: MetaCyc:HYPOTAURINE-DEHYDROGENASE-RXN
-xref: Reactome:R-HSA-1655453 "HTAUDH oxidises HTAU to TAU"
-xref: RHEA:17385
-is_a: GO:0016668 ! oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
+xref: Reactome:R-HSA-1655453 "FMO1:FAD oxidizes HTAU to TAU"
+xref: RHEA:69819
+is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0047823
@@ -282786,7 +282790,7 @@ is_a: GO:0031320 ! hexitol dehydrogenase activity
id: GO:0047825
name: D-lactate-2-sulfatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-2-O-sulfolactate + H(2)O = (R)-lactate + H(+) + sulfate." [EC:3.1.6.17, RHEA:20337]
+def: "Catalysis of the reaction: (R)-2-O-sulfolactate + H2O = (R)-lactate + H+ + sulfate." [EC:3.1.6.17, RHEA:20337]
synonym: "(S)-2-O-sulfolactate 2-sulfohydrolase activity" RELATED [EC:3.1.6.17]
synonym: "D-lactate-2-sulphatase activity" EXACT []
xref: EC:3.1.6.17
@@ -282813,7 +282817,7 @@ is_a: GO:0016869 ! intramolecular transferase activity, transferring amino group
id: GO:0047827
name: D-lysopine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-lysopine + H(2)O + NADP(+) = L-lysine + H(+) + NADPH + pyruvate." [EC:1.5.1.16, RHEA:17625]
+def: "Catalysis of the reaction: D-lysopine + H2O + NADP+ = L-lysine + H+ + NADPH + pyruvate." [EC:1.5.1.16, RHEA:17625]
synonym: "2-N-(D-1-carboxyethyl)-L-lysine:NADP+ oxidoreductase (L-lysine-forming)" RELATED [EC:1.5.1.16]
synonym: "D(+)-lysopine dehydrogenase activity" RELATED [EC:1.5.1.16]
synonym: "D-lysopine synthase activity" RELATED [EC:1.5.1.16]
@@ -282887,7 +282891,7 @@ is_a: GO:0016869 ! intramolecular transferase activity, transferring amino group
id: GO:0047832
name: D-pinitol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5D-5-O-methyl-chiro-inositol + NADP(+) = 2D-5-O-methyl-2,3,5/4,6-pentahydroxycyclohexanone + H(+) + NADPH." [EC:1.1.1.142, RHEA:20437]
+def: "Catalysis of the reaction: 5D-5-O-methyl-chiro-inositol + NADP+ = 2D-5-O-methyl-2,3,5/4,6-pentahydroxycyclohexanone + H+ + NADPH." [EC:1.1.1.142, RHEA:20437]
synonym: "1D-3-O-methyl-chiro-inositol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.142]
synonym: "5D-5-O-methyl-chiro-inositol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.142]
xref: EC:1.1.1.142
@@ -282928,7 +282932,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047835
name: D-tryptophan N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-tryptophan + acetyl-CoA = N-acetyl-D-tryptophan + CoA + H(+)." [EC:2.3.1.34, RHEA:10060]
+def: "Catalysis of the reaction: D-tryptophan + acetyl-CoA = N-acetyl-D-tryptophan + CoA + H+." [EC:2.3.1.34, RHEA:10060]
synonym: "acetyl-CoA-D-tryptophan-alpha-N-acetyltransferase activity" RELATED [EC:2.3.1.34]
synonym: "acetyl-CoA:D-tryptophan N-acetyltransferase activity" RELATED [EC:2.3.1.34]
synonym: "D-tryptophan acetyltransferase activity" RELATED [EC:2.3.1.34]
@@ -282942,7 +282946,7 @@ is_a: GO:0008080 ! N-acetyltransferase activity
id: GO:0047836
name: D-tryptophan N-malonyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-tryptophan + malonyl-CoA = N(2)-malonyl-D-tryptophan + CoA + H(+)." [EC:2.3.1.112, RHEA:23320]
+def: "Catalysis of the reaction: D-tryptophan + malonyl-CoA = N(2)-malonyl-D-tryptophan + CoA + H+." [EC:2.3.1.112, RHEA:23320]
synonym: "malonyl-CoA:D-tryptophan N-malonyltransferase activity" RELATED [EC:2.3.1.112]
xref: EC:2.3.1.112
xref: KEGG_REACTION:R02482
@@ -282954,7 +282958,7 @@ is_a: GO:0050735 ! N-malonyltransferase activity
id: GO:0047837
name: D-xylose 1-dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-xylose + NADP(+) = D-xylono-1,5-lactone + H(+) + NADPH." [EC:1.1.1.179, RHEA:22000]
+def: "Catalysis of the reaction: D-xylose + NADP+ = D-xylono-1,5-lactone + H+ + NADPH." [EC:1.1.1.179, RHEA:22000]
synonym: "D-xylose (nicotinamide adenine dinucleotide phosphate) dehydrogenase activity" RELATED [EC:1.1.1.179]
synonym: "D-xylose-NADP dehydrogenase activity" RELATED [EC:1.1.1.179]
synonym: "D-xylose:NADP+ 1-oxidoreductase activity" RELATED [EC:1.1.1.179]
@@ -282997,7 +283001,7 @@ is_a: GO:0140097 ! catalytic activity, acting on DNA
id: GO:0047840
name: dCTP diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dCTP + H2O = dCMP + diphosphate." [RHEA:22636]
+def: "Catalysis of the reaction: dCTP + H2O = dCMP + H+ + diphosphate." [RHEA:22636]
synonym: "dCTP nucleotidohydrolase activity" RELATED [EC:3.6.1.12]
synonym: "dCTP pyrophosphatase activity" EXACT []
synonym: "dCTPase activity" RELATED [EC:3.6.1.12]
@@ -283008,13 +283012,13 @@ xref: EC:3.6.1.12
xref: MetaCyc:DCTP-PYROPHOSPHATASE-RXN
xref: Reactome:R-HSA-6786257 "DCTPP1 hydrolyses 5idCTP"
xref: RHEA:22636
-is_a: GO:0047429 ! nucleoside-triphosphate diphosphatase activity
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0047841
name: dehydrogluconokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-dehydro-D-gluconate + ATP = 6-phospho-2-dehydro-D-gluconate + ADP + 2 H(+)." [EC:2.7.1.13, RHEA:10788]
+def: "Catalysis of the reaction: 2-dehydro-D-gluconate + ATP = 6-phospho-2-dehydro-D-gluconate + ADP + 2 H+." [EC:2.7.1.13, RHEA:10788]
synonym: "2-ketogluconate kinase activity" RELATED [EC:2.7.1.13]
synonym: "2-ketogluconokinase activity" RELATED [EC:2.7.1.13]
synonym: "ATP:2-dehydro-D-gluconate 6-phosphotransferase activity" RELATED [EC:2.7.1.13]
@@ -283032,7 +283036,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0047842
name: dehydro-L-gulonate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-dehydro-L-gulonate + H(+) = L-xylulose + CO(2)." [EC:4.1.1.34, RHEA:11084]
+def: "Catalysis of the reaction: 3-dehydro-L-gulonate + H+ = L-xylulose + CO2." [EC:4.1.1.34, RHEA:11084]
synonym: "3-dehydro-L-gulonate carboxy-lyase (L-xylulose-forming)" RELATED [EC:4.1.1.34]
synonym: "3-dehydro-L-gulonate carboxy-lyase activity" RELATED [EC:4.1.1.34]
synonym: "3-keto-L-gulonate decarboxylase activity" RELATED [EC:4.1.1.34]
@@ -283076,7 +283080,7 @@ is_a: GO:0019239 ! deaminase activity
id: GO:0047845
name: deoxylimonate A-ring-lactonase activity
namespace: molecular_function
-def: "Catalysis of the reaction: deoxylimonoate + H(2)O = deoxylimononate D-ring-lactone + H(+)." [EC:3.1.1.46, RHEA:14997]
+def: "Catalysis of the reaction: deoxylimonoate + H2O = deoxylimononate D-ring-lactone + H+." [EC:3.1.1.46, RHEA:14997]
synonym: "deoxylimonate A-ring-lactonohydrolase activity" RELATED [EC:3.1.1.46]
xref: EC:3.1.1.46
xref: KEGG_REACTION:R03803
@@ -283146,7 +283150,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0047850
name: diaminopimelate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: meso-2,6-diaminopimelate + H(2)O + NADP(+) = L-2-amino-6-oxopimelate + H(+) + NADPH + NH(4)(+)." [EC:1.4.1.16, RHEA:13561]
+def: "Catalysis of the reaction: meso-2,6-diaminopimelate + H2O + NADP+ = L-2-amino-6-oxopimelate + H+ + NADPH + NH4." [EC:1.4.1.16, RHEA:13561]
synonym: "meso-2,6-diaminoheptanedioate:NADP+ oxidoreductase (deaminating)" RELATED [EC:1.4.1.16]
synonym: "meso-alpha,epsilon-diaminopimelate dehydrogenase activity" RELATED [EC:1.4.1.16]
synonym: "meso-diaminopimelate D-dehydrogenase activity" RELATED [EC:1.4.1.16]
@@ -283187,10 +283191,10 @@ is_a: GO:0016723 ! oxidoreductase activity, acting on metal ions, NAD or NADP as
id: GO:0047853
name: difructose-anhydride synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + bis-D-fructose 2',1:2,1'-dianhydride = inulobiose." [EC:3.2.1.134, MetaCyc:DIFRUCTOSE-ANHYDRIDE-SYNTHASE-RXN]
-synonym: "bis-D-fructose 2',1:2,1'-dianhydride fructohydrolase activity" RELATED [EC:3.2.1.134]
-synonym: "inulobiose hydrolase activity" RELATED [EC:3.2.1.134]
-xref: EC:3.2.1.134
+def: "Catalysis of the reaction: H2O + bis-D-fructose 2',1:2,1'-dianhydride = inulobiose." [MetaCyc:DIFRUCTOSE-ANHYDRIDE-SYNTHASE-RXN, RHEA:15041]
+synonym: "bis-D-fructose 2',1:2,1'-dianhydride fructohydrolase activity" RELATED [EC:4.2.1.179]
+synonym: "inulobiose hydrolase activity" RELATED [EC:4.2.1.179]
+xref: EC:4.2.1.179
xref: MetaCyc:DIFRUCTOSE-ANHYDRIDE-SYNTHASE-RXN
xref: RHEA:15041
is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
@@ -283199,7 +283203,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0047854
name: diguanidinobutanase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,4-diguanidinobutane + H(2)O = agmatine + urea." [EC:3.5.3.20, RHEA:13597]
+def: "Catalysis of the reaction: 1,4-diguanidinobutane + H2O = agmatine + urea." [EC:3.5.3.20, RHEA:13597]
synonym: "1,4-diguanidinobutane amidinohydrolase activity" RELATED [EC:3.5.3.20]
xref: EC:3.5.3.20
xref: KEGG_REACTION:R01418
@@ -283211,7 +283215,7 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047855
name: dihydrobunolol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dihydrobunolol + NADP(+) = bunolol + H(+) + NADPH." [EC:1.1.1.160, RHEA:15925]
+def: "Catalysis of the reaction: dihydrobunolol + NADP+ = bunolol + H+ + NADPH." [EC:1.1.1.160, RHEA:15925]
synonym: "(+-)-5-[(tert-butylamino)-2'-hydroxypropoxy]-1,2,3,4-tetrahydro-1-naphthol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.160]
synonym: "bunolol reductase activity" RELATED [EC:1.1.1.160]
xref: EC:1.1.1.160
@@ -283224,7 +283228,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047856
name: dihydrocoumarin hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3,4-dihydrocoumarin + H(2)O = 3-(2-hydroxyphenyl)propanoate + H(+)." [EC:3.1.1.35, RHEA:10360]
+def: "Catalysis of the reaction: 3,4-dihydrocoumarin + H2O = 3-(2-hydroxyphenyl)propanoate + H+." [EC:3.1.1.35, RHEA:10360]
synonym: "dihydrocoumarin lactonohydrolase activity" RELATED [EC:3.1.1.35]
synonym: "dihydrocoumarin lipase activity" EXACT []
xref: EC:3.1.1.35
@@ -283237,7 +283241,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0047857
name: dihydrouracil oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5,6-dihydrouracil + O(2) = H(2)O(2) + uracil." [EC:1.3.3.7, RHEA:12384]
+def: "Catalysis of the reaction: 5,6-dihydrouracil + O2 = H2O2 + uracil." [EC:1.3.3.7, RHEA:12384]
synonym: "5,6-dihydrouracil:oxygen oxidoreductase activity" RELATED [EC:1.3.3.7]
xref: EC:1.3.3.7
xref: KEGG_REACTION:R00975
@@ -283249,7 +283253,7 @@ is_a: GO:0016634 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047858
name: dihydroxyfumarate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dihydroxyfumarate + H(+) = 2-hydroxy-3-oxopropanoate + CO(2)." [EC:4.1.1.54, RHEA:13845]
+def: "Catalysis of the reaction: dihydroxyfumarate + H+ = 2-hydroxy-3-oxopropanoate + CO2." [EC:4.1.1.54, RHEA:13845]
synonym: "dihydroxyfumarate carboxy-lyase (tartronate-semialdehyde-forming)" RELATED [EC:4.1.1.54]
synonym: "dihydroxyfumarate carboxy-lyase activity" RELATED [EC:4.1.1.54]
xref: EC:4.1.1.54
@@ -283275,7 +283279,7 @@ is_obsolete: true
id: GO:0047860
name: diiodophenylpyruvate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-(3,5-diiodo-4-hydroxyphenyl)lactate + NAD(+) = 3-(3,5-diiodo-4-hydroxyphenyl)pyruvate + H(+) + NADH." [EC:1.1.1.96, RHEA:20293]
+def: "Catalysis of the reaction: 3-(3,5-diiodo-4-hydroxyphenyl)lactate + NAD+ = 3-(3,5-diiodo-4-hydroxyphenyl)pyruvate + H+ + NADH." [EC:1.1.1.96, RHEA:20293]
synonym: "2-oxo acid reductase activity" RELATED [EC:1.1.1.96]
synonym: "3-(3,5-diiodo-4-hydroxyphenyl)lactate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.96]
synonym: "aromatic alpha-keto acid" RELATED [EC:1.1.1.96]
@@ -283305,7 +283309,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0047862
name: diisopropyl-fluorophosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: diisopropyl fluorophosphate + H(2)O = diisopropyl phosphate + 2 H(+) + hydrogen fluoride." [EC:3.1.8.2, RHEA:24100]
+def: "Catalysis of the reaction: diisopropyl fluorophosphate + H2O = diisopropyl phosphate + 2 H+ + hydrogen fluoride." [EC:3.1.8.2, RHEA:24100]
synonym: "DFPase activity" RELATED [EC:3.1.8.2]
synonym: "dialkylfluorophosphatase activity" RELATED [EC:3.1.8.2]
synonym: "diisopropyl phosphorofluoridate hydrolase activity" RELATED [EC:3.1.8.2]
@@ -283373,7 +283377,7 @@ is_a: GO:0046997 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0047866
name: dimethylglycine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N,N-dimethylglycine + H(2)O + O(2) = formaldehyde + H(2)O(2) + sarcosine." [EC:1.5.3.10, RHEA:17077]
+def: "Catalysis of the reaction: N,N-dimethylglycine + H2O + O2 = formaldehyde + H2O2 + sarcosine." [EC:1.5.3.10, RHEA:17077]
synonym: "N,N-dimethylglycine:oxygen oxidoreductase (demethylating)" RELATED [EC:1.5.3.10]
xref: EC:1.5.3.10
xref: KEGG_REACTION:R01564
@@ -283385,7 +283389,7 @@ is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0047867
name: dimethylmalate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-3,3-dimethylmalate + NAD(+) = 3-methyl-2-oxobutanoate + CO(2) + NADH." [EC:1.1.1.84, RHEA:13321]
+def: "Catalysis of the reaction: (R)-3,3-dimethylmalate + NAD+ = 3-methyl-2-oxobutanoate + CO2 + NADH." [EC:1.1.1.84, RHEA:13321]
synonym: "(R)-3,3-dimethylmalate:NAD+ oxidoreductase (decarboxylating)" RELATED [EC:1.1.1.84]
synonym: "beta,beta-dimethylmalate dehydrogenase activity" RELATED [EC:1.1.1.84]
xref: EC:1.1.1.84
@@ -283398,7 +283402,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047868
name: dimethylmaleate hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2R,3S)-2,3-dimethylmalate = dimethylmaleate + H(2)O." [EC:4.2.1.85, RHEA:20253]
+def: "Catalysis of the reaction: (2R,3S)-2,3-dimethylmalate = dimethylmaleate + H2O." [EC:4.2.1.85, RHEA:20253]
synonym: "(2R,3S)-2,3-dimethylmalate hydro-lyase (dimethylmaleate-forming)" RELATED [EC:4.2.1.85]
synonym: "(2R,3S)-2,3-dimethylmalate hydro-lyase activity" RELATED [EC:4.2.1.85]
xref: EC:4.2.1.85
@@ -283411,7 +283415,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047869
name: dimethylpropiothetin dethiomethylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S,S-dimethyl-beta-propiothetin = acrylate + dimethyl sulfide + H(+)." [EC:4.4.1.3, RHEA:19965]
+def: "Catalysis of the reaction: S,S-dimethyl-beta-propiothetin = acrylate + dimethyl sulfide + H+." [EC:4.4.1.3, RHEA:19965]
synonym: "desulfhydrase activity" RELATED [EC:4.4.1.3]
synonym: "S,S-dimethyl-beta-propiothetin dimethyl-sulfide-lyase (acrylate-forming)" RELATED [EC:4.4.1.3]
synonym: "S,S-dimethyl-beta-propiothetin dimethyl-sulfide-lyase activity" RELATED [EC:4.4.1.3]
@@ -283425,7 +283429,7 @@ is_a: GO:0016846 ! carbon-sulfur lyase activity
id: GO:0047870
name: discadenine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(6)-dimethylallyladenine + S-adenosyl-L-methionine(1+) = S-methyl-5'-thioadenosine + discadenine + H(+)." [EC:2.5.1.24, RHEA:19581]
+def: "Catalysis of the reaction: N(6)-dimethylallyladenine + S-adenosyl-L-methionine(1+) = S-methyl-5'-thioadenosine + discadenine + H+." [EC:2.5.1.24, RHEA:19581]
synonym: "discadenine synthetase activity" RELATED [EC:2.5.1.24]
synonym: "S-adenosyl-L-methionine:6-N-(Delta2-isopentenyl)-adenine 3-(3-amino-3-carboxypropyl)-transferase activity" RELATED [EC:2.5.1.24]
synonym: "S-adenosyl-L-methionine:N6-(Delta2-isopentenyl)-adenine 3-(3-amino-3-carboxypropyl)-transferas" RELATED [EC:2.5.1.24]
@@ -283439,7 +283443,7 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0047871
name: disulfoglucosamine-6-sulfatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(2),6-disulfo-D-glucosamine + H(2)O = N-sulfo-D-glucosamine + H(+) + sulfate." [EC:3.1.6.11, RHEA:15517]
+def: "Catalysis of the reaction: N(2),6-disulfo-D-glucosamine + H2O = N-sulfo-D-glucosamine + H+ + sulfate." [EC:3.1.6.11, RHEA:15517]
synonym: "6,N-disulfoglucosamine 6-O-sulfohydrolase activity" RELATED [EC:3.1.6.11]
synonym: "disulphoglucosamine-6-sulphatase activity" EXACT []
synonym: "N,6-O-disulfo-D-glucosamine 6-sulfohydrolase activity" RELATED [EC:3.1.6.11]
@@ -283502,7 +283506,7 @@ is_a: GO:0016462 ! pyrophosphatase activity
id: GO:0047875
name: ecdysone oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: Ecdysone + O(2) = 3-dehydroecdysone + H(2)O(2)." [EC:1.1.3.16, RHEA:11796]
+def: "Catalysis of the reaction: Ecdysone + O2 = 3-dehydroecdysone + H2O2." [EC:1.1.3.16, RHEA:11796]
synonym: "beta-ecdysone oxidase activity" RELATED [EC:1.1.3.16]
synonym: "ecdysone:oxygen 3-oxidoreductase activity" RELATED [EC:1.1.3.16]
xref: EC:1.1.3.16
@@ -283530,7 +283534,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0047877
name: ephedrine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (1R,2S)-ephedrine + NAD(+) = (R)-2-methylimino-1-phenylpropan-1-ol + 2 H(+) + NADH." [EC:1.5.1.18, RHEA:16289]
+def: "Catalysis of the reaction: (1R,2S)-ephedrine + NAD+ = (R)-2-methylimino-1-phenylpropan-1-ol + 2 H+ + NADH." [EC:1.5.1.18, RHEA:16289]
synonym: "(-)-ephedrine:NAD+ 2-oxidoreductase activity" RELATED [EC:1.5.1.18]
xref: EC:1.5.1.18
xref: KEGG_REACTION:R03614
@@ -283542,7 +283546,7 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0047878
name: erythritol kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + erythritol = D-erythritol 4-phosphate + ADP + 2 H(+)." [EC:2.7.1.27, RHEA:20708]
+def: "Catalysis of the reaction: ATP + erythritol = D-erythritol 4-phosphate + ADP + 2 H+." [EC:2.7.1.27, RHEA:20708]
synonym: "ATP:erythritol 4-phosphotransferase activity" RELATED [EC:2.7.1.27]
synonym: "erythritol kinase (phosphorylating)" RELATED [EC:2.7.1.27]
xref: EC:2.7.1.27
@@ -283568,7 +283572,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0047880
name: erythrulose reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-threitol + NADP(+) = D-erythrulose + H(+) + NADPH." [EC:1.1.1.162, RHEA:18005]
+def: "Catalysis of the reaction: D-threitol + NADP+ = D-erythrulose + H+ + NADPH." [EC:1.1.1.162, RHEA:18005]
synonym: "D-erythrulose reductase activity" RELATED [EC:1.1.1.162]
synonym: "erythritol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.162]
xref: EC:1.1.1.162
@@ -283598,7 +283602,7 @@ is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of
id: GO:0047882
name: estradiol 6-beta-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + estradiol-17beta + O(2) = 6beta-hydroxyestradiol-17beta + A + H(2)O." [EC:1.14.99.11, RHEA:19137]
+def: "Catalysis of the reaction: AH(2) + estradiol-17beta + O2 = 6beta-hydroxyestradiol-17beta + A + H2O." [EC:1.14.99.11, RHEA:19137]
synonym: "estradiol 6-beta-hydroxylase activity" RELATED [EC:1.14.99.11]
synonym: "estradiol 6b-hydroxylase activity" EXACT []
synonym: "estradiol 6b-monooxygenase activity" EXACT []
@@ -283616,18 +283620,18 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047883
name: ethanolamine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ethanolamine + H2O + O2 = glycolaldehyde + NH3 + H2O2." [EC:1.4.3.8, MetaCyc:ETHANOLAMINE-OXIDASE-RXN]
+def: "Catalysis of the reaction: ethanolamine + H2O + O2 = glycolaldehyde + NH3 + H2O2." [RHEA:18581]
synonym: "ethanolamine:oxygen oxidoreductase (deaminating)" RELATED [EC:1.4.3.8]
xref: EC:1.4.3.8
xref: MetaCyc:ETHANOLAMINE-OXIDASE-RXN
xref: RHEA:18581
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+is_a: GO:0052595 ! aliphatic amine oxidase activity
[Term]
id: GO:0047884
name: FAD diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: FAD + H2O = AMP + FMN." [EC:3.6.1.18, MetaCyc:FAD-PYROPHOSPHATASE-RXN]
+def: "Catalysis of the reaction: FAD + H2O = AMP + FMN." [RHEA:13889]
synonym: "FAD nucleotidohydrolase activity" RELATED [EC:3.6.1.18]
synonym: "FAD pyrophosphatase activity" EXACT []
synonym: "FAD pyrophosphohydrolase activity" EXACT [GOC:tb]
@@ -283638,7 +283642,7 @@ synonym: "riboflavine adenine dinucleotide pyrophosphatase activity" RELATED [EC
xref: EC:3.6.1.18
xref: MetaCyc:FAD-PYROPHOSPHATASE-RXN
xref: RHEA:13889
-is_a: GO:0004551 ! nucleotide diphosphatase activity
+is_a: GO:0004551 ! dinucleotide phosphatase activity
[Term]
id: GO:0047885
@@ -283657,7 +283661,7 @@ is_a: GO:0016859 ! cis-trans isomerase activity
id: GO:0047886
name: farnesol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-trans,6-trans-farnesol + NADP(+) = 2-trans,6-trans-farnesal + H(+) + NADPH." [EC:1.1.1.216, RHEA:14697]
+def: "Catalysis of the reaction: 2-trans,6-trans-farnesol + NADP+ = 2-trans,6-trans-farnesal + H+ + NADPH." [EC:1.1.1.216, RHEA:14697]
synonym: "2-trans,6-trans-farnesol:NADP+ 1-oxidoreductase activity" RELATED [EC:1.1.1.216]
synonym: "farnesol (nicotinamide adenine dinucleotide phosphate) dehydrogenase activity" RELATED [EC:1.1.1.216]
synonym: "NADP-farnesol dehydrogenase activity" RELATED [EC:1.1.1.216]
@@ -283686,7 +283690,7 @@ is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
id: GO:0047888
name: fatty acid peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 H(2)O(2) + H(+) + palmitate = CO(2) + 3 H(2)O + pentadecanal." [EC:1.11.1.3, RHEA:23960]
+def: "Catalysis of the reaction: 2 H2O2 + H+ + palmitate = CO2 + 3 H2O + pentadecanal." [EC:1.11.1.3, RHEA:23960]
synonym: "fatty-acid peroxidase activity" EXACT []
synonym: "hexadecanoate:hydrogen-peroxide oxidoreductase activity" RELATED [EC:1.11.1.3]
synonym: "long chain fatty acid peroxidase activity" RELATED [EC:1.11.1.3]
@@ -283776,7 +283780,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0047894
name: flavonol 3-sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + quercetin = adenosine 3',5'-diphosphate + H(+) + quercetin 3-sulfate." [EC:2.8.2.25, RHEA:13453]
+def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + quercetin = adenosine 3',5'-diphosphate + H+ + quercetin 3-sulfate." [EC:2.8.2.25, RHEA:13453]
subset: goslim_chembl
synonym: "3'-phosphoadenylyl-sulfate:quercetin 3-sulfotransferase activity" EXACT systematic_synonym [EC:2.8.2.25]
synonym: "flavonol 3-sulphotransferase activity" EXACT []
@@ -283818,7 +283822,7 @@ is_a: GO:0016744 ! transketolase or transaldolase activity
id: GO:0047897
name: formate-dihydrofolate ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7,8-dihydrofolate + ATP + formate = 10-formyldihydrofolate + ADP + H(+) + phosphate." [EC:6.3.4.17, RHEA:24328]
+def: "Catalysis of the reaction: 7,8-dihydrofolate + ATP + formate = 10-formyldihydrofolate + ADP + H+ + phosphate." [EC:6.3.4.17, RHEA:24328]
synonym: "dihydrofolate formyltransferase activity" RELATED [EC:6.3.4.17]
synonym: "formate:dihydrofolate ligase (ADP-forming)" RELATED [EC:6.3.4.17]
synonym: "formyl dihydrofolate synthase activity" RELATED [EC:6.3.4.17]
@@ -283844,7 +283848,7 @@ is_a: GO:0016622 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0047899
name: formate dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: formate + NADP(+) = CO(2) + NADPH." [EC:1.17.1.10, RHEA:12000]
+def: "Catalysis of the reaction: formate + NADP+ = CO2 + NADPH." [EC:1.17.1.10, RHEA:12000]
synonym: "formate:NADP+ oxidoreductase activity" RELATED [EC:1.17.1.10]
synonym: "NADP-dependent formate dehydrogenase activity" RELATED [EC:1.17.1.10]
xref: EC:1.17.1.10
@@ -283857,7 +283861,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0047900
name: formate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + formate = ADP + formyl phosphate + H(+)." [EC:2.7.2.6, RHEA:16009]
+def: "Catalysis of the reaction: ATP + formate = ADP + formyl phosphate + H+." [EC:2.7.2.6, RHEA:16009]
synonym: "ATP:formate phosphotransferase activity" RELATED [EC:2.7.2.6]
xref: EC:2.7.2.6
xref: KEGG_REACTION:R00518
@@ -283870,7 +283874,7 @@ is_a: GO:0016774 ! phosphotransferase activity, carboxyl group as acceptor
id: GO:0047901
name: formyl-CoA hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: formyl-CoA + H(2)O = CoA + formate + H(+)." [EC:3.1.2.10, RHEA:19741]
+def: "Catalysis of the reaction: formyl-CoA + H2O = CoA + formate + H+." [EC:3.1.2.10, RHEA:19741]
synonym: "formyl coenzyme A hydrolase activity" RELATED [EC:3.1.2.10]
xref: EC:3.1.2.10
xref: KEGG_REACTION:R00521
@@ -284017,7 +284021,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0047912
name: galacturonokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: alpha-D-galacturonate + ATP = 1-phospho-alpha-D-galacturonate + ADP + 2 H(+)." [EC:2.7.1.44, RHEA:12965]
+def: "Catalysis of the reaction: alpha-D-galacturonate + ATP = 1-phospho-alpha-D-galacturonate + ADP + 2 H+." [EC:2.7.1.44, RHEA:12965]
synonym: "ATP:D-galacturonate 1-phosphotransferase activity" RELATED [EC:2.7.1.44]
synonym: "galacturonokinase (phosphorylating) D-galacturonic acid kinase activity" RELATED [EC:2.7.1.44]
xref: EC:2.7.1.44
@@ -284095,7 +284099,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047917
name: GDP-glucosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GDP-D-glucose + H(2)O = D-glucose + GDP + H(+)." [EC:3.2.1.42, RHEA:15049]
+def: "Catalysis of the reaction: GDP-D-glucose + H2O = D-glucose + GDP + H+." [EC:3.2.1.42, RHEA:15049]
synonym: "GDP-glucose glucohydrolase activity" RELATED [EC:3.2.1.42]
synonym: "GDPglucose glucohydrolase activity" RELATED [EC:3.2.1.42]
synonym: "GDPglucosidase activity" RELATED [EC:3.2.1.42]
@@ -284111,20 +284115,19 @@ is_a: GO:0015926 ! glucosidase activity
id: GO:0047918
name: GDP-mannose 3,5-epimerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GDP-mannose = GDP-L-galactose." [EC:5.1.3.18]
+def: "Catalysis of the reaction: GDP-mannose = GDP-L-galactose." [PMID:16366586, PMID:8910301]
synonym: "GDP-D-mannose:GDP-L-galactose epimerase activity" RELATED [EC:5.1.3.18]
synonym: "GDPmannose 3,5-epimerase activity" RELATED [EC:5.1.3.18]
synonym: "guanosine 5'-diphosphate D-mannose:guanosine 5'-diphosphate L-galactose epimerase activity" RELATED [EC:5.1.3.18]
xref: EC:5.1.3.18
xref: MetaCyc:RXN-1882
-xref: RHEA:11144
is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and derivatives
[Term]
id: GO:0047919
name: GDP-mannose 6-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GDP-alpha-D-mannose + H(2)O + 2 NAD(+) = GDP-D-mannuronate + 3 H(+) + 2 NADH." [EC:1.1.1.132, RHEA:21728]
+def: "Catalysis of the reaction: GDP-alpha-D-mannose + H2O + 2 NAD+ = GDP-D-mannuronate + 3 H+ + 2 NADH." [EC:1.1.1.132, RHEA:21728]
synonym: "GDP mannose dehydrogenase activity" RELATED [EC:1.1.1.132]
synonym: "GDP-D-mannose:NAD+ 6-oxidoreductase activity" RELATED [EC:1.1.1.132]
synonym: "GDPmannose 6-dehydrogenase activity" RELATED [EC:1.1.1.132]
@@ -284140,7 +284143,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047920
name: geissoschizine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: geissoschizine + NADP(+) = 4,21-dehydrogeissoschizine + H(+) + NADPH." [EC:1.3.1.36, RHEA:11376]
+def: "Catalysis of the reaction: geissoschizine + NADP+ = 4,21-dehydrogeissoschizine + H+ + NADPH." [EC:1.3.1.36, RHEA:11376]
synonym: "geissoschizine:NADP+ 4,21-oxidoreductase activity" RELATED [EC:1.3.1.36]
xref: EC:1.3.1.36
xref: KEGG_REACTION:R03860
@@ -284152,7 +284155,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047921
name: aminoglycoside 2'-N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + gentamicin C(1a) = N(2')-acetylgentamicin C(1a) + CoA + H(+). This is acetylation of the 2'-amino group of the 6-deoxy-6-aminoglucose ring." [EC:2.3.1.59, RHEA:24516]
+def: "Catalysis of the reaction: acetyl-CoA + gentamicin C(1a) = N(2')-acetylgentamicin C(1a) + CoA + H+. This is acetylation of the 2'-amino group of the 6-deoxy-6-aminoglucose ring." [EC:2.3.1.59, RHEA:24516]
synonym: "acetyl-CoA:gentamicin-C1a N2'-acetyltransferase activity" NARROW [EC:2.3.1.59]
synonym: "acetyl-CoA:gentamycin-C1a N2'-acetyltransferase activity" NARROW [EC:2.3.1.59]
synonym: "gentamicin 2'-N-acetyltransferase activity" NARROW []
@@ -284169,7 +284172,7 @@ is_a: GO:0034069 ! aminoglycoside N-acetyltransferase activity
id: GO:0047922
name: gentisate 1,2-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,5-dihydroxybenzoate + O(2) = 3-maleylpyruvate + H(+)." [EC:1.13.11.4, RHEA:18237]
+def: "Catalysis of the reaction: 2,5-dihydroxybenzoate + O2 = 3-maleylpyruvate + H+." [EC:1.13.11.4, RHEA:18237]
synonym: "2,5-dihydroxybenzoate dioxygenase activity" RELATED [EC:1.13.11.4]
synonym: "gentisate dioxygenase activity" RELATED [EC:1.13.11.4]
synonym: "gentisate oxygenase activity" RELATED [EC:1.13.11.4]
@@ -284185,7 +284188,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0047923
name: gentisate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,5-dihydroxybenzoate + H(+) = CO(2) + hydroquinone." [EC:4.1.1.62, RHEA:21312]
+def: "Catalysis of the reaction: 2,5-dihydroxybenzoate + H+ = CO2 + hydroquinone." [EC:4.1.1.62, RHEA:21312]
synonym: "2,5-dihydroxybenzoate carboxy-lyase (hydroquinone-forming)" RELATED [EC:4.1.1.62]
synonym: "2,5-dihydroxybenzoate decarboxylase activity" RELATED [EC:4.1.1.62]
synonym: "gentisate carboxy-lyase activity" RELATED [EC:4.1.1.62]
@@ -284211,7 +284214,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047925
name: geranoyl-CoA carboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + bicarbonate + geranoyl-CoA = 3-(4-methylpent-3-en-1-yl)pent-2-enedioyl-CoA + ADP + 2 H(+) + phosphate." [EC:6.4.1.5, RHEA:17701]
+def: "Catalysis of the reaction: ATP + bicarbonate + geranoyl-CoA = 3-(4-methylpent-3-en-1-yl)pent-2-enedioyl-CoA + ADP + 2 H+ + phosphate." [EC:6.4.1.5, RHEA:17701]
synonym: "geranoyl coenzyme A carboxylase activity" RELATED [EC:6.4.1.5]
synonym: "geranoyl-CoA:carbon-dioxide ligase (ADP-forming)" RELATED [EC:6.4.1.5]
synonym: "geranyl-CoA carboxylase activity" RELATED [EC:6.4.1.5]
@@ -284272,7 +284275,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0047929
name: gluconate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H(2)O." [EC:4.2.1.39, RHEA:21612]
+def: "Catalysis of the reaction: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O." [EC:4.2.1.39, RHEA:21612]
synonym: "D-gluconate dehydratase activity" RELATED [EC:4.2.1.39]
synonym: "D-gluconate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)" RELATED [EC:4.2.1.39]
synonym: "D-gluconate hydro-lyase activity" RELATED [EC:4.2.1.39]
@@ -284323,7 +284326,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0047932
name: glucosamine N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glucosamine + acetyl-CoA = N-acetyl-D-glucosamine + CoA + H(+)." [EC:2.3.1.3, RHEA:21332]
+def: "Catalysis of the reaction: D-glucosamine + acetyl-CoA = N-acetyl-D-glucosamine + CoA + H+." [EC:2.3.1.3, RHEA:21332]
synonym: "acetyl-CoA:D-glucosamine N-acetyltransferase activity" RELATED [EC:2.3.1.3]
synonym: "glucosamine acetylase activity" RELATED [EC:2.3.1.3]
synonym: "glucosamine acetyltransferase activity" RELATED [EC:2.3.1.3]
@@ -284337,7 +284340,7 @@ is_a: GO:0008080 ! N-acetyltransferase activity
id: GO:0047933
name: glucose-1,6-bisphosphate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-phospho-D-glyceroyl phosphate + alpha-D-glucose 1-phosphate = 3-phospho-D-glycerate + alpha-D-glucose 1,6-bisphosphate + H(+)." [EC:2.7.1.106, RHEA:16769]
+def: "Catalysis of the reaction: 3-phospho-D-glyceroyl phosphate + alpha-D-glucose 1-phosphate = 3-phospho-D-glycerate + alpha-D-glucose 1,6-bisphosphate + H+." [EC:2.7.1.106, RHEA:16769]
synonym: "3-phospho-D-glyceroyl-phosphate:alpha-D-glucose-1-phosphate 6-phosphotransferase activity" RELATED [EC:2.7.1.106]
synonym: "3-phospho-D-glyceroyl-phosphate:D-glucose-1-phosphate 6-phosphotransferase activity" RELATED [EC:2.7.1.106]
synonym: "glucose 1,6-diphosphate synthase activity" RELATED [EC:2.7.1.106]
@@ -284361,7 +284364,8 @@ synonym: "D-glucose:NAD+ 1-oxidoreductase activity" RELATED [EC:1.1.1.118]
xref: EC:1.1.1.118
xref: MetaCyc:GLUCOSE-1-DEHYDROGENASE-NAD+-RXN
xref: RHEA:14293
-is_a: GO:0047936 ! glucose 1-dehydrogenase [NAD(P)] activity
+is_a: GO:0004344 ! glucose dehydrogenase activity
+is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0047935
@@ -284375,13 +284379,15 @@ synonym: "nicotinamide adenine dinucleotide phosphate-linked aldohexose dehydrog
xref: EC:1.1.1.119
xref: MetaCyc:GLUCOSE-1-DEHYDROGENASE-NADP+-RXN
xref: RHEA:14405
-is_a: GO:0047936 ! glucose 1-dehydrogenase [NAD(P)] activity
+is_a: GO:0004344 ! glucose dehydrogenase activity
+is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0047936
name: glucose 1-dehydrogenase [NAD(P)] activity
namespace: molecular_function
def: "Catalysis of the reaction: beta-D-glucose + NAD(P)+ = D-glucono-1,5-lactone + NAD(P)H." [EC:1.1.1.47]
+comment: This enzyme has similar activity with either NAD+ or NADP+.
synonym: "beta-D-glucose:NAD(P)+ 1-oxidoreductase activity" RELATED [EC:1.1.1.47]
synonym: "D-glucose dehydrogenase (NAD(P))" RELATED [EC:1.1.1.47]
synonym: "hexose phosphate dehydrogenase activity" RELATED [EC:1.1.1.47]
@@ -284420,7 +284426,7 @@ is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and
id: GO:0047939
name: L-glucuronate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-gulonate + NADP(+) = D-glucuronate + H(+) + NADPH." [EC:1.1.1.19, RHEA:14909]
+def: "Catalysis of the reaction: L-gulonate + NADP+ = D-glucuronate + H+ + NADPH." [EC:1.1.1.19, RHEA:14909]
synonym: "aldehyde reductase II activity" RELATED [EC:1.1.1.19]
synonym: "D-glucuronate dehydrogenase activity" RELATED [EC:1.1.1.19]
synonym: "D-glucuronate reductase activity" NARROW [EC:1.1.1.19]
@@ -284439,7 +284445,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047940
name: glucuronokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glucuronate + ATP = 1-phospho-alpha-D-glucuronate + ADP + 2 H(+)." [EC:2.7.1.43, RHEA:17005]
+def: "Catalysis of the reaction: D-glucuronate + ATP = 1-phospho-alpha-D-glucuronate + ADP + 2 H+." [EC:2.7.1.43, RHEA:17005]
synonym: "ATP:D-glucuronate 1-phosphotransferase activity" RELATED [EC:2.7.1.43]
synonym: "glucurono-glucuronokinase activity" RELATED [EC:2.7.1.43]
synonym: "glucuronokinase (phosphorylating)" RELATED [EC:2.7.1.43]
@@ -284454,7 +284460,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0047941
name: glucuronolactone reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-gulono-1,4-lactone + NADP(+) = D-glucurono-3,6-lactone + H(+) + NADPH." [EC:1.1.1.20, RHEA:18925]
+def: "Catalysis of the reaction: L-gulono-1,4-lactone + NADP+ = D-glucurono-3,6-lactone + H+ + NADPH." [EC:1.1.1.20, RHEA:18925]
xref: EC:1.1.1.20
xref: KEGG_REACTION:R03183
xref: MetaCyc:GLUCURONOLACTONE-REDUCTASE-RXN
@@ -284465,7 +284471,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047942
name: glutamate-ethylamine ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-glutamate + ATP + ethylamine = N(5)-ethyl-L-glutamine + ADP + 2 H(+) + phosphate." [EC:6.3.1.6, RHEA:20525]
+def: "Catalysis of the reaction: L-glutamate + ATP + ethylamine = N(5)-ethyl-L-glutamine + ADP + 2 H+ + phosphate." [EC:6.3.1.6, RHEA:20525]
synonym: "L-glutamate:ethylamine ligase (ADP-forming)" RELATED [EC:6.3.1.6]
synonym: "N(5)-ethyl-L-glutamine synthetase activity" RELATED [EC:6.3.1.6]
synonym: "N5-ethyl-L-glutamine synthetase activity" RELATED [EC:6.3.1.6]
@@ -284481,7 +284487,7 @@ is_a: GO:0016880 ! acid-ammonia (or amide) ligase activity
id: GO:0047943
name: glutamate-methylamine ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-glutamate + ATP + methylammonium = N(5)-methyl-L-glutamine + ADP + 2 H(+) + phosphate." [EC:6.3.4.12, RHEA:17117]
+def: "Catalysis of the reaction: L-glutamate + ATP + methylammonium = N(5)-methyl-L-glutamine + ADP + 2 H+ + phosphate." [EC:6.3.4.12, RHEA:17117]
synonym: "gamma-glutamylmethylamide synthetase activity" RELATED [EC:6.3.4.12]
synonym: "L-glutamate:methylamine ligase (ADP-forming)" RELATED [EC:6.3.4.12]
xref: EC:6.3.4.12
@@ -284494,7 +284500,7 @@ is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
id: GO:0047944
name: obsolete glutamate 1-kinase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: L-glutamate + ATP = alpha-L-glutamyl phosphate + ADP + H(+)." [GOC:curators]
+def: "OBSOLETE. Catalysis of the reaction: L-glutamate + ATP = alpha-L-glutamyl phosphate + ADP + H+." [GOC:curators]
comment: This term is slated for obsoletion. RHEA indicates the activity has been shown not to exist.
synonym: "ATP:L-glutamate 1-phosphotransferase activity" RELATED []
is_obsolete: true
@@ -284551,7 +284557,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0047948
name: glutarate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + CoA + glutarate = ADP + glutaryl-CoA + H(+) + phosphate." [EC:6.2.1.6, RHEA:14169]
+def: "Catalysis of the reaction: ATP + CoA + glutarate = ADP + glutaryl-CoA + H+ + phosphate." [EC:6.2.1.6, RHEA:14169]
synonym: "glutarate:CoA ligase (ADP-forming)" RELATED [EC:6.2.1.6]
synonym: "glutaryl coenzyme A synthetase activity" RELATED [EC:6.2.1.6]
synonym: "glutaryl-CoA synthetase activity" RELATED [EC:6.2.1.6]
@@ -284577,7 +284583,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0047950
name: glutathione oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 glutathione + O(2) = glutathione disulfide + H(2)O(2)." [EC:1.8.3.3, RHEA:24112]
+def: "Catalysis of the reaction: 2 glutathione + O2 = glutathione disulfide + H2O2." [EC:1.8.3.3, RHEA:24112]
synonym: "glutathione:oxygen oxidoreductase activity" RELATED [EC:1.8.3.3]
xref: EC:1.8.3.3
xref: KEGG_REACTION:R00120
@@ -284589,7 +284595,7 @@ is_a: GO:0016670 ! oxidoreductase activity, acting on a sulfur group of donors,
id: GO:0047951
name: glutathione thiolesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-acylglutathione + H(2)O = a carboxylate + glutathione + H(+)." [EC:3.1.2.7, RHEA:22708]
+def: "Catalysis of the reaction: S-acylglutathione + H2O = a carboxylate + glutathione + H+." [EC:3.1.2.7, RHEA:22708]
synonym: "citryl-glutathione thioesterhydrolase activity" RELATED [EC:3.1.2.7]
synonym: "glutathione thioesterase activity" EXACT []
synonym: "S-acylglutathione hydrolase activity" RELATED [EC:3.1.2.7]
@@ -284603,22 +284609,47 @@ is_a: GO:0016790 ! thiolester hydrolase activity
id: GO:0047952
name: glycerol-3-phosphate dehydrogenase [NAD(P)+] activity
namespace: molecular_function
+alt_id: GO:0004367
alt_id: GO:0036439
-def: "Catalysis of the reaction: sn-glycerol 3-phosphate + NAD(P)+ = glycerone phosphate + NAD(P)H + H+." [RHEA:11096]
+alt_id: GO:0106257
+def: "Catalysis of the reaction: sn-glycerol 3-phosphate + NAD(P)+ = glycerone phosphate + NAD(P)H + H+." [EC:1.1.1.94]
+synonym: "alpha-glycerol phosphate dehydrogenase (NAD) activity" RELATED [EC:1.1.1.8]
+synonym: "alpha-glycerophosphate dehydrogenase (NAD) activity" RELATED [EC:1.1.1.8]
+synonym: "glycerol 1-phosphate dehydrogenase activity" RELATED [EC:1.1.1.8]
+synonym: "glycerol phosphate dehydrogenase (NAD) activity" RELATED [EC:1.1.1.8]
synonym: "glycerol phosphate dehydrogenase (nicotinamide adenine dinucleotide (phosphate)) activity" RELATED [EC:1.1.1.94]
synonym: "glycerol-3-phosphate dehydrogenase (NAD(P)+) activity" EXACT []
+synonym: "glycerol-3-phosphate dehydrogenase (NAD) activity" RELATED [EC:1.1.1.8]
+synonym: "glycerol-3-phosphate dehydrogenase [NAD+] activity" NARROW []
+synonym: "glycerol-3-phosphate dehydrogenase [NADP+] activity" NARROW []
+synonym: "glycerophosphate dehydrogenase (NAD) activity" RELATED [EC:1.1.1.8]
+synonym: "hydroglycerophosphate dehydrogenase activity" BROAD [EC:1.1.1.8]
+synonym: "L-alpha-glycerol phosphate dehydrogenase activity" BROAD [EC:1.1.1.8]
+synonym: "L-alpha-glycerophosphate dehydrogenase activity" BROAD [EC:1.1.1.8]
+synonym: "L-glycerol phosphate dehydrogenase activity" BROAD [EC:1.1.1.8]
synonym: "L-glycerol-3-phosphate:NAD(P) oxidoreductase activity" RELATED [EC:1.1.1.94]
+synonym: "L-glycerophosphate dehydrogenase activity" BROAD [EC:1.1.1.8]
+synonym: "NAD-alpha-glycerophosphate dehydrogenase activity" RELATED [EC:1.1.1.8]
+synonym: "NAD-dependent glycerol phosphate dehydrogenase activity" RELATED [EC:1.1.1.8]
+synonym: "NAD-dependent glycerol-3-phosphate dehydrogenase activity" RELATED [EC:1.1.1.8]
+synonym: "NAD-L-glycerol-3-phosphate dehydrogenase activity" RELATED [EC:1.1.1.8]
+synonym: "NAD-linked glycerol 3-phosphate dehydrogenase activity" RELATED [EC:1.1.1.8]
+synonym: "NADH-dihydroxyacetone phosphate reductase activity" RELATED [EC:1.1.1.8]
synonym: "sn-glycerol-3-phosphate:NAD(P)+ 2-oxidoreductase activity" RELATED [EC:1.1.1.94]
+xref: EC:1.1.1.8
xref: EC:1.1.1.94
+xref: KEGG_REACTION:R00842
xref: KEGG_REACTION:R00844
+xref: MetaCyc:1.1.1.8-RXN
xref: MetaCyc:GLYC3PDEHYDROGBIOSYN-RXN
+xref: Reactome:R-HSA-75889 "DHAP is converted to G3P by GPD1/GPD1L"
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0047953
name: glycerol 2-dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycerol + NADP(+) = glycerone + H(+) + NADPH." [EC:1.1.1.156, RHEA:12753]
+def: "Catalysis of the reaction: glycerol + NADP+ = glycerone + H+ + NADPH." [EC:1.1.1.156, RHEA:12753]
synonym: "DHA oxidoreductase activity" RELATED [EC:1.1.1.156]
synonym: "dihydroxyacetone (reduced nicotinamide adenine dinucleotide phosphate) reductase activity" RELATED [EC:1.1.1.156]
synonym: "dihydroxyacetone reductase (NADPH)" RELATED [EC:1.1.1.156]
@@ -284634,7 +284665,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047954
name: glycerol-2-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycerol 2-phosphate + H(2)O = glycerol + phosphate." [EC:3.1.3.19, RHEA:13105]
+def: "Catalysis of the reaction: glycerol 2-phosphate + H2O = glycerol + phosphate." [EC:3.1.3.19, RHEA:13105]
synonym: "2-glycerophosphatase activity" RELATED [EC:3.1.3.19]
synonym: "beta-glycerophosphatase activity" RELATED [EC:3.1.3.19]
synonym: "beta-glycerophosphate phosphatase activity" RELATED [EC:3.1.3.19]
@@ -284741,7 +284772,7 @@ is_a: GO:0016410 ! N-acyltransferase activity
id: GO:0047962
name: glycine N-benzoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: benzoyl-CoA + glycine = N-benzoylglycine + CoA + H(+)." [EC:2.3.1.71, RHEA:18493]
+def: "Catalysis of the reaction: benzoyl-CoA + glycine = N-benzoylglycine + CoA + H+." [EC:2.3.1.71, RHEA:18493]
synonym: "benzoyl CoA-amino acid N-acyltransferase activity" RELATED [EC:2.3.1.71]
synonym: "benzoyl-CoA:glycine N-acyltransferase activity" RELATED [EC:2.3.1.71]
synonym: "benzoyl-CoA:glycine N-benzoyltransferase activity" RELATED [EC:2.3.1.71]
@@ -284749,7 +284780,8 @@ xref: EC:2.3.1.71
xref: KEGG_REACTION:R02452
xref: MetaCyc:GLYCINE-N-BENZOYLTRANSFERASE-RXN
xref: Reactome:R-HSA-159566 "benzoyl-CoA + glycine => benzoyl glycine (hippuric acid) + Coenzyme A"
-xref: Reactome:R-HSA-159574 "salicylate-CoA + glycine => salicyluric acid + Coenzyme A"
+xref: Reactome:R-HSA-159574 "GLYAT-like proteins transfer glycine to ST-CoA to form SUA"
+xref: Reactome:R-HSA-9750001 "GLYAT-like proteins transfer glycine to 2,5-DHB-CoA to form gentisuric acid"
xref: RHEA:18493
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
@@ -284800,7 +284832,7 @@ is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
id: GO:0047966
name: glycosulfatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glucose 6-sulfate + H(2)O = D-glucose + H(+) + sulfate." [EC:3.1.6.3, RHEA:19145]
+def: "Catalysis of the reaction: D-glucose 6-sulfate + H2O = D-glucose + H+ + sulfate." [EC:3.1.6.3, RHEA:19145]
synonym: "glucosulfatase activity" RELATED [EC:3.1.6.3]
synonym: "glycosulphatase activity" EXACT []
synonym: "sugar-sulfate sulfohydrolase activity" RELATED [EC:3.1.6.3]
@@ -284814,7 +284846,7 @@ is_a: GO:0008484 ! sulfuric ester hydrolase activity
id: GO:0047967
name: glycyrrhizinate beta-glucuronidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycyrrhizate + H(2)O = 2-(beta-D-glucuronosyl)-D-glucuronate + glycyrrhetinate." [EC:3.2.1.128, RHEA:17369]
+def: "Catalysis of the reaction: glycyrrhizate + H2O = 2-(beta-D-glucuronosyl)-D-glucuronate + glycyrrhetinate." [EC:3.2.1.128, RHEA:17369]
synonym: "glycyrrhizin beta-hydrolase activity" RELATED [EC:3.2.1.128]
synonym: "glycyrrhizin hydrolase activity" RELATED [EC:3.2.1.128]
synonym: "glycyrrhizinate b-glucuronidase activity" EXACT []
@@ -284830,7 +284862,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0047968
name: glyoxylate dehydrogenase (acylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: CoA + glyoxylate + NADP(+) = H(+) + NADPH + oxalyl-CoA." [EC:1.2.1.17, RHEA:21024]
+def: "Catalysis of the reaction: CoA + glyoxylate + NADP+ = H+ + NADPH + oxalyl-CoA." [EC:1.2.1.17, RHEA:21024]
synonym: "glyoxylate:NADP+ oxidoreductase (CoA-oxalylating)" RELATED [EC:1.2.1.17]
xref: EC:1.2.1.17
xref: KEGG_REACTION:R00468
@@ -284842,7 +284874,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0047969
name: glyoxylate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glyoxylate + H(2)O + O(2) = H(2)O(2) + H(+) + oxalate." [EC:1.2.3.5, RHEA:14837]
+def: "Catalysis of the reaction: glyoxylate + H2O + O2 = H2O2 + H+ + oxalate." [EC:1.2.3.5, RHEA:14837]
synonym: "glyoxylate:oxygen oxidoreductase activity" RELATED [EC:1.2.3.5]
xref: EC:1.2.3.5
xref: KEGG_REACTION:R00466
@@ -284855,7 +284887,7 @@ is_a: GO:0016623 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0047970
name: guanidinoacetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: guanidinoacetate + H(2)O = glycine + urea." [EC:3.5.3.2, RHEA:23268]
+def: "Catalysis of the reaction: guanidinoacetate + H2O = glycine + urea." [EC:3.5.3.2, RHEA:23268]
synonym: "glycocyaminase activity" RELATED [EC:3.5.3.2]
synonym: "guanidinoacetate amidinohydrolase activity" RELATED [EC:3.5.3.2]
xref: EC:3.5.3.2
@@ -284868,7 +284900,7 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047971
name: guanidinobutyrase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-guanidinobutanoate + H(2)O = 4-aminobutanoate + urea." [EC:3.5.3.7, RHEA:19501]
+def: "Catalysis of the reaction: 4-guanidinobutanoate + H2O = 4-aminobutanoate + urea." [EC:3.5.3.7, RHEA:19501]
synonym: "4-guanidinobutanoate amidinohydrolase activity" RELATED [EC:3.5.3.7]
synonym: "4-guanidinobutyrate amidinobutyrase activity" RELATED [EC:3.5.3.7]
synonym: "G-base activity" RELATED [EC:3.5.3.7]
@@ -284886,7 +284918,7 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047972
name: guanidinopropionase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-guanidinopropanoate + H(2)O = beta-alanine + urea." [EC:3.5.3.17, RHEA:16029]
+def: "Catalysis of the reaction: 3-guanidinopropanoate + H2O = beta-alanine + urea." [EC:3.5.3.17, RHEA:16029]
synonym: "3-guanidinopropanoate amidinopropionase activity" RELATED [EC:3.5.3.17]
synonym: "GPase activity" RELATED [EC:3.5.3.17]
synonym: "GPH" RELATED [EC:3.5.3.17]
@@ -284900,7 +284932,7 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047973
name: guanidinoacetate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + guanidinoacetate = ADP + 2 H(+) + phosphoguanidinoacetate." [EC:2.7.3.1, RHEA:14145]
+def: "Catalysis of the reaction: ATP + guanidinoacetate = ADP + 2 H+ + phosphoguanidinoacetate." [EC:2.7.3.1, RHEA:14145]
synonym: "ATP:guanidinoacetate N-phosphotransferase activity" RELATED [EC:2.7.3.1]
synonym: "glycocyamine kinase activity" RELATED [EC:2.7.3.1]
synonym: "guanidoacetate kinase activity" EXACT []
@@ -284940,7 +284972,7 @@ is_a: GO:0016763 ! pentosyltransferase activity
id: GO:0047976
name: hamamelose kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-hamamelose + ATP = D-hamamelose 2'-phosphate + ADP + 2 H(+)." [EC:2.7.1.102, RHEA:22796]
+def: "Catalysis of the reaction: D-hamamelose + ATP = D-hamamelose 2'-phosphate + ADP + 2 H+." [EC:2.7.1.102, RHEA:22796]
synonym: "ATP/hamamelose 2'-phosphotransferase activity" RELATED [EC:2.7.1.102]
synonym: "ATP:D-hamamelose 2'-phosphotransferase activity" RELATED [EC:2.7.1.102]
synonym: "hamamelose kinase (phosphorylating)" RELATED [EC:2.7.1.102]
@@ -284993,7 +285025,7 @@ is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047980
name: hippurate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-benzoylglycine + H(2)O = benzoate + glycine." [EC:3.5.1.32, RHEA:10424]
+def: "Catalysis of the reaction: N-benzoylglycine + H2O = benzoate + glycine." [EC:3.5.1.32, RHEA:10424]
synonym: "benzoylglycine amidohydrolase activity" RELATED [EC:3.5.1.32]
synonym: "hippuricase activity" RELATED [EC:3.5.1.32]
synonym: "N-benzoylamino-acid amidohydrolase activity" RELATED [EC:3.5.1.32]
@@ -285007,7 +285039,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0047981
name: histidine N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-histidine + acetyl-CoA = N(alpha)-acetyl-L-histidine + CoA + H(+)." [EC:2.3.1.33, RHEA:24596]
+def: "Catalysis of the reaction: L-histidine + acetyl-CoA = N(alpha)-acetyl-L-histidine + CoA + H+." [EC:2.3.1.33, RHEA:24596]
synonym: "acetyl-CoA:L-histidine N-acetyltransferase activity" RELATED [EC:2.3.1.33]
synonym: "acetylhistidine synthetase activity" RELATED [EC:2.3.1.33]
synonym: "histidine acetyltransferase activity" RELATED [EC:2.3.1.33]
@@ -285035,7 +285067,7 @@ is_a: GO:0016846 ! carbon-sulfur lyase activity
id: GO:0047983
name: homoglutathione synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: beta-alanine + L-gamma-glutamyl-L-cysteine + ATP = gamma-L-glutamyl-L-cysteinyl-beta-alanine + ADP + 2 H(+) + phosphate." [EC:6.3.2.23, RHEA:17993]
+def: "Catalysis of the reaction: beta-alanine + L-gamma-glutamyl-L-cysteine + ATP = gamma-L-glutamyl-L-cysteinyl-beta-alanine + ADP + 2 H+ + phosphate." [EC:6.3.2.23, RHEA:17993]
synonym: "beta-alanine specific hGSH synthetase activity" RELATED [EC:6.3.2.23]
synonym: "gamma-L-glutamyl-L-cysteine:beta-alanine ligase (ADP-forming)" RELATED [EC:6.3.2.23]
synonym: "homoglutathione synthetase activity" RELATED [EC:6.3.2.23]
@@ -285092,7 +285124,7 @@ is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
id: GO:0047989
name: hydroxybutyrate-dimer hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-3-[(R)-3-hydroxybutanoyloxy]butanoate + H(2)O = 2 (R)-3-hydroxybutanoate + H(+)." [EC:3.1.1.22, RHEA:10172]
+def: "Catalysis of the reaction: (R)-3-[(R)-3-hydroxybutanoyloxy]butanoate + H2O = 2 (R)-3-hydroxybutanoate + H+." [EC:3.1.1.22, RHEA:10172]
synonym: "(R)-3-((R)-3-hydroxybutanoyloxy)butanoate hydroxybutanoylhydrolase activity" RELATED [EC:3.1.1.22]
synonym: "D-(-)-3-hydroxybutyrate-dimer hydrolase activity" RELATED [EC:3.1.1.22]
xref: EC:3.1.1.22
@@ -285105,7 +285137,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0047990
name: hydroxyglutamate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxy-L-glutamate + H(+) = 4-amino-3-hydroxybutanoate + CO(2)." [EC:4.1.1.16, RHEA:14073]
+def: "Catalysis of the reaction: 3-hydroxy-L-glutamate + H+ = 4-amino-3-hydroxybutanoate + CO2." [EC:4.1.1.16, RHEA:14073]
synonym: "3-hydroxy-L-glutamate 1-carboxy-lyase (4-amino-3-hydroxybutanoate-forming)" RELATED [EC:4.1.1.16]
synonym: "3-hydroxy-L-glutamate 1-carboxy-lyase activity" RELATED [EC:4.1.1.16]
xref: EC:4.1.1.16
@@ -285118,7 +285150,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0047991
name: hydroxylamine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: hydroxylamine + O(2) = H(2)O + H(+) + nitrite." [RHEA:19969]
+def: "Catalysis of the reaction: hydroxylamine + O2 = H2O + H+ + nitrite." [RHEA:19969]
synonym: "HAO" RELATED [EC:1.7.3.6]
synonym: "hydroxylamine oxidoreductase" BROAD [EC:1.7.3.6]
synonym: "hydroxylamine:oxygen oxidoreductase activity" RELATED [EC:1.7.3.6]
@@ -285132,7 +285164,7 @@ is_a: GO:0016663 ! oxidoreductase activity, acting on other nitrogenous compound
id: GO:0047992
name: hydroxylysine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: erythro-5-hydroxy-L-lysine + GTP = 5-phosphonooxy-L-lysine + GDP + 2 H(+)." [EC:2.7.1.81, RHEA:19049]
+def: "Catalysis of the reaction: erythro-5-hydroxy-L-lysine + GTP = 5-phosphonooxy-L-lysine + GDP + 2 H+." [EC:2.7.1.81, RHEA:19049]
synonym: "GTP:5-hydroxy-L-lysine O-phosphotransferase activity" RELATED [EC:2.7.1.81]
synonym: "guanosine triphosphate:5-hydroxy-L-lysine O-phosphotransferase activity" RELATED [EC:2.7.1.81]
synonym: "hydroxylysine kinase (phosphorylating)" RELATED [EC:2.7.1.81]
@@ -285148,7 +285180,7 @@ is_a: GO:0019202 ! amino acid kinase activity
id: GO:0047993
name: hydroxymalonate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: hydroxymalonate + NAD(+) = H(+) + NADH + oxomalonate." [EC:1.1.1.167, RHEA:11284]
+def: "Catalysis of the reaction: hydroxymalonate + NAD+ = H+ + NADH + oxomalonate." [EC:1.1.1.167, RHEA:11284]
synonym: "hydroxymalonate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.167]
xref: EC:1.1.1.167
xref: KEGG_REACTION:R02969
@@ -285160,7 +285192,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047994
name: hydroxymethylglutaryl-CoA hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-3-hydroxy-3-methylglutaryl-CoA + H(2)O = 3-hydroxy-3-methylglutarate + CoA + H(+)." [EC:3.1.2.5, RHEA:16305]
+def: "Catalysis of the reaction: (S)-3-hydroxy-3-methylglutaryl-CoA + H2O = 3-hydroxy-3-methylglutarate + CoA + H+." [EC:3.1.2.5, RHEA:16305]
synonym: "(S)-3-hydroxy-3-methylglutaryl-CoA hydrolase activity" RELATED [EC:3.1.2.5]
synonym: "3-hydroxy-3-methylglutaryl-CoA hydrolase activity" RELATED [EC:3.1.2.5]
synonym: "beta-hydroxy-beta-methylglutaryl coenzyme A deacylase activity" RELATED [EC:3.1.2.5]
@@ -285189,7 +285221,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047996
name: hydroxyphytanate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2S)-2-hydroxyphytanate + O(2) = 2-oxophytanate + H(2)O(2)." [EC:1.1.3.27, RHEA:21680]
+def: "Catalysis of the reaction: (2S)-2-hydroxyphytanate + O2 = 2-oxophytanate + H2O2." [EC:1.1.3.27, RHEA:21680]
synonym: "L-2-hydroxyphytanate:oxygen 2-oxidoreductase" BROAD [EC:1.1.3.27]
xref: EC:1.1.3.27
xref: KEGG_REACTION:R07151
@@ -285201,7 +285233,7 @@ is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047997
name: hydroxypyruvate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxypyruvate + H(+) = CO(2) + glycolaldehyde." [EC:4.1.1.40, RHEA:20561]
+def: "Catalysis of the reaction: 3-hydroxypyruvate + H+ = CO2 + glycolaldehyde." [EC:4.1.1.40, RHEA:20561]
synonym: "hydroxypyruvate carboxy-lyase (glycolaldehyde-forming)" RELATED [EC:4.1.1.40]
synonym: "hydroxypyruvate carboxy-lyase activity" RELATED [EC:4.1.1.40]
xref: EC:4.1.1.40
@@ -285214,7 +285246,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0047998
name: hyoscyamine (6S)-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + L-hyoscyamine + O(2) = (6S)-6-hydroxyhyoscyamine + CO(2) + succinate." [EC:1.14.11.11, RHEA:12629]
+def: "Catalysis of the reaction: 2-oxoglutarate + L-hyoscyamine + O2 = (6S)-6-hydroxyhyoscyamine + CO2 + succinate." [EC:1.14.11.11, RHEA:12629]
synonym: "hyoscyamine (6S)-hydroxylase activity" RELATED [EC:1.14.11.11]
synonym: "hyoscyamine 6-beta-hydroxylase activity" RELATED [EC:1.14.11.11]
synonym: "hyoscyamine 6-hydroxylase activity" RELATED [EC:1.14.11.11]
@@ -285231,7 +285263,7 @@ is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
id: GO:0047999
name: hyponitrite reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 hydroxylamine + 2 NAD(+) = 2 H(+) + hyponitrous acid + 2 NADH." [EC:1.7.1.5, RHEA:19337]
+def: "Catalysis of the reaction: 2 hydroxylamine + 2 NAD+ = 2 H+ + hyponitrous acid + 2 NADH." [EC:1.7.1.5, RHEA:19337]
synonym: "hydroxylamine:NAD+ oxidoreductase activity" RELATED [EC:1.7.1.5]
synonym: "NADH2:hyponitrite oxidoreductase activity" RELATED [EC:1.7.1.5]
synonym: "NADH:hyponitrite oxidoreductase activity" RELATED [EC:1.7.1.5]
@@ -285258,7 +285290,7 @@ id: GO:0048001
name: erythrose-4-phosphate dehydrogenase activity
namespace: molecular_function
alt_id: GO:0033724
-def: "Catalysis of the reaction: D-erythrose 4-phosphate + H(2)O + NAD(+) = 4-phospho-D-erythronate + 2 H(+) + NADH." [EC:1.2.1.72, RHEA:12056]
+def: "Catalysis of the reaction: D-erythrose 4-phosphate + H2O + NAD+ = 4-phospho-D-erythronate + 2 H+ + NADH." [EC:1.2.1.72, RHEA:12056]
synonym: "D-erythrose 4-phosphate:NAD+ oxidoreductase activity" RELATED [EC:1.2.1.72]
synonym: "E4P dehydrogenase activity" RELATED [EC:1.2.1.72]
synonym: "E4PDH" RELATED [EC:1.2.1.72]
@@ -285313,7 +285345,7 @@ is_a: GO:0048003 ! antigen processing and presentation of lipid antigen via MHC
id: GO:0048008
name: platelet-derived growth factor receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a platelet-derived growth factor receptor binding to one of its physiological ligands." [GOC:ceb]
+def: "The series of molecular signals initiated by a ligand binding to a platelet-derived growth factor receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:ceb]
synonym: "PDGF receptor signaling pathway" EXACT []
synonym: "PDGF receptor signalling pathway" EXACT []
synonym: "PDGFR signaling pathway" EXACT []
@@ -285323,7 +285355,7 @@ is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling path
id: GO:0048009
name: insulin-like growth factor receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of the insulin-like growth factor receptor binding to one of its physiological ligands." [GOC:ceb]
+def: "The series of molecular signals initiated by a ligand binding to an insulin-like growth factor receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:ceb]
synonym: "IGF receptor signaling pathway" EXACT []
synonym: "IGF receptor signalling pathway" EXACT []
is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway
@@ -285332,7 +285364,7 @@ is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling path
id: GO:0048010
name: vascular endothelial growth factor receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:ceb, GOC:signaling]
+def: "The series of molecular signals initiated by a ligand binding to a vascular endothelial growth factor receptor (VEGFR) on the surface of the target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:ceb, GOC:signaling]
comment: In GO, a gene product with 'vascular endothelial growth factor-activated receptor activity ; GO:0005021' necessarily binds VEGF to transduce a signal. In contrast, the VEGFR refers to PR:000001971. To represent cross-talk between ligands and receptors, signaling pathways in GO are starting to be named after the receptor and/or the signal. GO:0048010 is for annotation of any pathway in which a ligand (VEGF or an alternative growth factor) binds and activates a VEGFR (PR:000001971). For annotation of signaling pathways where a VEGF binds to a cell surface receptor (VEGFR, PDGFR etc.), consider 'vascular endothelial growth factor signaling pathway ; GO:0038084'.
synonym: "VEGF receptor signaling pathway" EXACT []
synonym: "VEGF receptor signalling pathway" EXACT []
@@ -285343,7 +285375,7 @@ is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling path
id: GO:0048011
name: neurotrophin TRK receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a neurotrophin to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:ceb, GOC:jc, GOC:signaling, PMID:12065629, Wikipedia:Trk_receptor]
+def: "The series of molecular signals initiated by neurotrophin binding to its receptor on the surface of a target cell where the receptor possesses tyrosine kinase activity, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:ceb, GOC:jc, GOC:signaling, PMID:12065629, Wikipedia:Trk_receptor]
synonym: "TrkA signaling pathway" NARROW [Wikipedia:TrkA]
synonym: "TrkB signaling pathway" NARROW [Wikipedia:TrkB]
synonym: "TrkC signaling pathway" NARROW [Wikipedia:TrkC]
@@ -285355,7 +285387,7 @@ is_a: GO:0038179 ! neurotrophin signaling pathway
id: GO:0048012
name: hepatocyte growth factor receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of the hepatocyte growth factor receptor binding to one of its physiological ligands." [GOC:ceb]
+def: "The series of molecular signals initiated by a ligand binding to a hepatocyte growth factor receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:ceb]
synonym: "HGF receptor signaling pathway" EXACT []
synonym: "HGF receptor signalling pathway" EXACT []
synonym: "Met signaling pathway" NARROW []
@@ -285365,7 +285397,7 @@ is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling path
id: GO:0048013
name: ephrin receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin." [GOC:ceb]
+def: "The series of molecular signals initiated by ephrin binding to its receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:ceb]
synonym: "Eph receptor signaling pathway" EXACT []
synonym: "Eph receptor signalling pathway" EXACT []
is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway
@@ -285374,7 +285406,7 @@ is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling path
id: GO:0048014
name: Tie signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a Tie protein (a receptor) binding to one of its physiological ligands (an angiopoietin)." [GOC:ceb, GOC:signaling, PMID:11283723, PMID:11566266]
+def: "The series of molecular signals initiated by an angiopoietin binding to the Tie receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:ceb, GOC:signaling, PMID:11283723, PMID:11566266]
synonym: "angiopoietin-Tie signaling pathway" NARROW [PMID:22951441]
synonym: "angiopoietin/Tie signaling pathway" NARROW [PMID:11566266]
synonym: "Tek receptor signaling" EXACT []
@@ -285386,7 +285418,7 @@ is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling path
id: GO:0048015
name: phosphatidylinositol-mediated signaling
namespace: biological_process
-def: "A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives." [GOC:bf, GOC:ceb, ISBN:0198506732]
+def: "The series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives." [GOC:bf, GOC:ceb, ISBN:0198506732]
synonym: "inositol phospholipid-mediated signaling" BROAD []
synonym: "phosphatidylinositol-mediated signal transduction" EXACT [GOC:signaling]
synonym: "phosphatidylinositol-mediated signalling" EXACT []
@@ -285398,7 +285430,7 @@ is_a: GO:0048017 ! inositol lipid-mediated signaling
id: GO:0048016
name: inositol phosphate-mediated signaling
namespace: biological_process
-def: "Any intracellular signal transduction in which the signal is passed on within the cell via an inositol phosphate. Includes production of the inositol phosphate, and downstream effectors that further transmit the signal within the cell. Inositol phosphates are a group of mono- to poly-phosphorylated inositols, and include inositol monophosphate (IP), inositol trisphosphate (IP3), inositol pentakisphosphate (IP5) and inositol hexaphosphate (IP6)." [GOC:bf, GOC:ceb, GOC:signaling, ISBN:0198506732, PMID:11331907]
+def: "A intracellular signal transduction in which the signal is transmitted within the cell via an inositol phosphate. Includes production of the inositol phosphate, and downstream effectors that further transmit the signal within the cell. Inositol phosphates are a group of mono- to poly-phosphorylated inositols, and include inositol monophosphate (IP), inositol trisphosphate (IP3), inositol pentakisphosphate (IP5) and inositol hexaphosphate (IP6)." [GOC:bf, GOC:ceb, GOC:signaling, ISBN:0198506732, PMID:11331907]
synonym: "inositol phosphate-mediated signalling" EXACT []
is_a: GO:0019932 ! second-messenger-mediated signaling
@@ -285406,7 +285438,7 @@ is_a: GO:0019932 ! second-messenger-mediated signaling
id: GO:0048017
name: inositol lipid-mediated signaling
namespace: biological_process
-def: "A series of molecular signals in which a cell uses an inositol-containing lipid to convert a signal into a response. Inositol lipids include the phosphoinositides (phosphatidylinositol and its phosphorylated derivatives), ceramides containing inositol, and inositol glycolipids." [GOC:bf, GOC:ceb, PMID:16088939]
+def: "The series of molecular signals in which a cell uses an inositol-containing lipid to convert a signal into a response. Inositol lipids include the phosphoinositides (phosphatidylinositol and its phosphorylated derivatives), ceramides containing inositol, and inositol glycolipids." [GOC:bf, GOC:ceb, PMID:16088939]
synonym: "inositol lipid-mediated signal transduction" EXACT [GOC:signaling]
synonym: "inositol lipid-mediated signalling" EXACT []
synonym: "inositol phospholipid-mediated signaling" NARROW []
@@ -285420,6 +285452,7 @@ alt_id: GO:0071884
def: "The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands)." [GOC:kv, GOC:molecular_function_refactoring, GOC:pdt]
subset: goslim_chembl
subset: goslim_drosophila
+subset: goslim_generic
synonym: "receptor agonist activity" BROAD [GOC:molecular_function_refactoring]
synonym: "signaling molecule" EXACT []
synonym: "signaling receptor ligand activity" EXACT []
@@ -285675,7 +285708,7 @@ is_a: GO:0048038 ! quinone binding
id: GO:0048040
name: UDP-glucuronate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + UDP-alpha-D-glucuronate = CO(2) + UDP-alpha-D-xylose." [EC:4.1.1.35, RHEA:23916]
+def: "Catalysis of the reaction: H+ + UDP-alpha-D-glucuronate = CO2 + UDP-alpha-D-xylose." [EC:4.1.1.35, RHEA:23916]
synonym: "UDP-D-glucuronate carboxy-lyase (UDP-D-xylose-forming)" RELATED [EC:4.1.1.35]
synonym: "UDP-D-glucuronate carboxy-lyase activity" RELATED [EC:4.1.1.35]
synonym: "UDP-glucuronic acid decarboxylase activity" EXACT []
@@ -285699,16 +285732,16 @@ relationship: part_of GO:0007160 ! cell-matrix adhesion
[Term]
id: GO:0048045
-name: trans-pentaprenyltranstransferase activity
+name: obsolete trans-pentaprenyltranstransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: all-trans-pentaprenyl diphosphate + isopentenyl diphosphate = all-trans-hexaprenyl diphosphate + diphosphate." [RHEA:22632]
+def: "OBSOLETE. Catalysis of the reaction: all-trans-pentaprenyl diphosphate + isopentenyl diphosphate = all-trans-hexaprenyl diphosphate + diphosphate." [GOC:curators]
+comment: RHEA has obsoleted the xref to this term and replaced it with a term specifiying FAD, not NAD
synonym: "all-trans-hexaprenyl-diphosphate synthase activity" RELATED []
synonym: "all-trans-pentaprenyl-diphosphate:isopentenyl-diphosphate pentaprenyltranstransferase activity" RELATED []
synonym: "hexaprenyl diphosphate synthase activity" RELATED []
synonym: "hexaprenyl pyrophosphate synthetase activity" EXACT []
xref: KEGG_REACTION:R05613
-xref: RHEA:22632
-is_a: GO:0004659 ! prenyltransferase activity
+is_obsolete: true
[Term]
id: GO:0048046
@@ -286205,9 +286238,10 @@ is_a: GO:0035222 ! wing disc pattern formation
[Term]
id: GO:0048101
-name: calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity
+name: calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate. The reaction is calmodulin and calcium-sensitive." [GOC:jid]
+def: "Catalysis of the reactions: nucleoside 3',5'-cyclic GMP + H2O = GMP + H+; this activity is activated by binding to calcium-bound calmodulin." [GOC:jid]
+synonym: "calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity" BROAD []
synonym: "calcium- and calmodulin-regulated cGMP phosphodiesterase activity" RELATED []
synonym: "calcium- and calmodulin-regulated cGMP-specific phosphodiesterase activity" EXACT []
synonym: "calcium- and calmodulin-regulated cyclic-GMP phosphodiesterase activity" EXACT []
@@ -286387,7 +286421,7 @@ id: GO:0048143
name: astrocyte activation
namespace: biological_process
def: "A change in morphology and behavior of an astrocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, PMID:10526094, PMID:10695728, PMID:12529254, PMID:12580336, PMID:9585813]
-is_a: GO:0001775 ! cell activation
+is_a: GO:0061900 ! glial cell activation
relationship: part_of GO:0014002 ! astrocyte development
[Term]
@@ -286666,7 +286700,6 @@ namespace: cellular_component
def: "A protein complex that acts as an activin receptor. Heterodimeric activin receptors, comprising one Type I activin receptor and one Type II receptor polypeptide, and heterotrimeric receptors have been observed." [PMID:8307945, PMID:8622651]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
is_a: GO:1902554 ! serine/threonine protein kinase complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0048180
@@ -287201,7 +287234,7 @@ is_a: GO:0050432 ! catecholamine secretion
id: GO:0048244
name: phytanoyl-CoA dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + O(2) + phytanoyl-CoA = 2-hydroxyphytanoyl-CoA + CO(2) + succinate." [EC:1.14.11.18, RHEA:16065]
+def: "Catalysis of the reaction: 2-oxoglutarate + O2 + phytanoyl-CoA = 2-hydroxyphytanoyl-CoA + CO2 + succinate." [EC:1.14.11.18, RHEA:16065]
synonym: "phytanoyl-CoA 2 oxoglutarate dioxygenase activity" RELATED [EC:1.14.11.18]
synonym: "phytanoyl-CoA 2-hydroxylase activity" RELATED [EC:1.14.11.18]
synonym: "phytanoyl-CoA alpha-hydroxylase activity" RELATED [EC:1.14.11.18]
@@ -287264,7 +287297,6 @@ synonym: "mitochondrial iron ion transmembrane transport" RELATED []
synonym: "mitochondrial iron ion transport" RELATED []
synonym: "mitochondrial iron transport" EXACT []
is_a: GO:0034755 ! iron ion transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0048251
@@ -287311,7 +287343,7 @@ id: GO:0048256
name: flap endonuclease activity
namespace: molecular_function
def: "Catalysis of the cleavage of a flap structure in DNA, but not other DNA structures; processes the ends of Okazaki fragments in lagging strand DNA synthesis." [GOC:jid]
-is_a: GO:0004520 ! endodeoxyribonuclease activity
+is_a: GO:0004520 ! DNA endonuclease activity
[Term]
id: GO:0048257
@@ -287319,7 +287351,7 @@ name: 3'-flap endonuclease activity
namespace: molecular_function
def: "Catalysis of the cleavage of a 3' flap structure in DNA, but not other DNA structures; processes the 3' ends of Okazaki fragments in lagging strand DNA synthesis." [GOC:jid, PMID:10635319]
synonym: "3' flap endonuclease activity" EXACT []
-is_a: GO:0016889 ! endodeoxyribonuclease activity, producing 3'-phosphomonoesters
+is_a: GO:0016889 ! DNA endonuclease activity, producing 3'-phosphomonoesters
is_a: GO:0048256 ! flap endonuclease activity
[Term]
@@ -287427,7 +287459,7 @@ is_a: GO:0065003 ! protein-containing complex assembly
id: GO:0048269
name: methionine adenosyltransferase complex
namespace: cellular_component
-def: "A multimeric enzyme complex composed of variable numbers of catalytic alpha subunits, and noncatalytic beta subunits. The beta subunits are believed to have a regulatory function. The enzyme complex catalyzes the synthesis of S-adenosylmethionine (AdoMet), which is the major methyl group donor, participating in the methylation of proteins, DNA, RNA, phospholipids, and other small molecules." [EC:2.5.1.6, GOC:jid, PMID:10644686]
+def: "A multimeric enzyme complex composed of variable numbers of catalytic alpha subunits, and noncatalytic beta subunits. The beta subunits are believed to have a regulatory function. The enzyme complex catalyzes the synthesis of S-adenosylmethionine (AdoMet), which is the major methyl group donor, participating in the methylation of proteins, DNA, RNA, phospholipids, and other small molecules." [GOC:jid, PMID:10644686, PMID:25075345]
synonym: "MAT complex" EXACT []
is_a: GO:0140535 ! intracellular protein-containing complex
is_a: GO:1990234 ! transferase complex
@@ -289088,7 +289120,7 @@ is_a: GO:0048438 ! floral whorl development
id: GO:0048468
name: cell development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:go_curators]
+def: "The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place." [GOC:go_curators]
subset: goslim_candida
synonym: "terminal differentiation" RELATED [GOC:dph, GOC:tb]
is_a: GO:0048856 ! anatomical structure development
@@ -289099,7 +289131,7 @@ relationship: part_of GO:0030154 ! cell differentiation
id: GO:0048469
name: cell maturation
namespace: biological_process
-def: "A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state." [GOC:go_curators]
+def: "The cellular developmental process, independent of morphogenetic (shape) change, that is required for a specific cell to attain its fully functional state." [GOC:go_curators]
subset: goslim_pir
synonym: "functional differentiation" RELATED [GOC:dph]
is_a: GO:0048869 ! cellular developmental process
@@ -289119,7 +289151,7 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0048472
name: threonine-phosphate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O-phospho-L-threonine + H(+) = (R)-1-aminopropan-2-yl phosphate + CO(2)." [EC:4.1.1.81, RHEA:11492]
+def: "Catalysis of the reaction: O-phospho-L-threonine + H+ = (R)-1-aminopropan-2-yl phosphate + CO2." [EC:4.1.1.81, RHEA:11492]
synonym: "CobD" RELATED [EC:4.1.1.81]
synonym: "L-threonine O-3-phosphate carboxy-lyase [(R)-1-aminopropan-2-yl-phosphate-forming]" RELATED [EC:4.1.1.81]
synonym: "L-threonine O-3-phosphate carboxy-lyase activity" RELATED [EC:4.1.1.81]
@@ -289172,13 +289204,14 @@ is_a: GO:0007292 ! female gamete generation
[Term]
id: GO:0048478
-name: replication fork protection
+name: obsolete replication fork protection
namespace: biological_process
-def: "Any process that prevents the collapse of stalled replication forks." [GOC:vw, PMID:14560029]
+def: "OBSOLETE. Any process that prevents the collapse of stalled replication forks." [GOC:vw, PMID:14560029]
+comment: This term is obsoleted because it represents a phenotype and was unclearly defined.
synonym: "replication fork maintenance" BROAD []
synonym: "replication fork stabilization" BROAD []
-is_a: GO:0045005 ! DNA-dependent DNA replication maintenance of fidelity
-is_a: GO:2000104 ! negative regulation of DNA-dependent DNA replication
+is_obsolete: true
+consider: GO:0031297
[Term]
id: GO:0048479
@@ -289230,7 +289263,7 @@ relationship: part_of GO:0007399 ! nervous system development
id: GO:0048484
name: enteric nervous system development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the enteric nervous system over time, from its formation to the mature structure. The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gall bladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation." [FMA:66070, GOC:jid, GOC:sr]
+def: "The process whose specific outcome is the progression of the enteric nervous system over time, from its formation to the mature structure. The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gallbladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation." [FMA:66070, GOC:jid, GOC:sr]
is_a: GO:0048731 ! system development
relationship: part_of GO:0048483 ! autonomic nervous system development
@@ -289401,7 +289434,7 @@ id: GO:0048502
name: ABC-type thiamine transporter activity
namespace: molecular_function
alt_id: GO:0015619
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + thiamine(out) = ADP + H(+) + phosphate + thiamine(in)." [PMID:12175925, PMID:9535878, RHEA:29811]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + thiamine(out) = ADP + H+ + phosphate + thiamine(in)." [PMID:12175925, PMID:9535878, RHEA:29811]
synonym: "ATP-dependent thiamine transmembrane transporter activity" RELATED []
synonym: "ATPase-coupled thiamine transmembrane transporter activity" RELATED []
synonym: "thiamin pyrophosphate ABC transporter" EXACT []
@@ -289416,7 +289449,6 @@ xref: EC:7.6.2.15
xref: RHEA:29811
xref: TC:3.A.1.19.1
is_a: GO:0015234 ! thiamine transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0140394 ! ABC-type azole transporter activity
[Term]
@@ -289514,7 +289546,6 @@ synonym: "development of an organ" EXACT []
synonym: "organogenesis" EXACT []
xref: Wikipedia:Organogenesis
is_a: GO:0048856 ! anatomical structure development
-relationship: part_of GO:0048731 ! system development
[Term]
id: GO:0048514
@@ -289596,8 +289627,8 @@ synonym: "stimulation of behavior" NARROW []
synonym: "up regulation of behavior" EXACT []
synonym: "up-regulation of behavior" EXACT []
synonym: "upregulation of behavior" EXACT []
-is_a: GO:0048518 ! positive regulation of biological process
is_a: GO:0050795 ! regulation of behavior
+is_a: GO:0051240 ! positive regulation of multicellular organismal process
relationship: positively_regulates GO:0007610 ! behavior
[Term]
@@ -289609,8 +289640,8 @@ synonym: "down regulation of behavior" EXACT []
synonym: "down-regulation of behavior" EXACT []
synonym: "downregulation of behavior" EXACT []
synonym: "inhibition of behavior" NARROW []
-is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:0050795 ! regulation of behavior
+is_a: GO:0051241 ! negative regulation of multicellular organismal process
relationship: negatively_regulates GO:0007610 ! behavior
[Term]
@@ -289847,6 +289878,7 @@ synonym: "phytochrome chromophore anabolism" EXACT []
synonym: "phytochrome chromophore biosynthesis" EXACT []
synonym: "phytochrome chromophore formation" EXACT []
synonym: "phytochrome chromophore synthesis" EXACT []
+is_a: GO:0009058 ! biosynthetic process
is_a: GO:0046148 ! pigment biosynthetic process
[Term]
@@ -289854,13 +289886,11 @@ id: GO:0048544
name: recognition of pollen
namespace: biological_process
alt_id: GO:0009857
-def: "The process, involving the sharing and interaction of the single locus incompatibility haplotypes, involved in the recognition or rejection of the self pollen by cells in the stigma. This process ensures out-breeding in certain plant species." [GOC:dph, GOC:pj, GOC:tb]
+def: "A cell recognition process in which pollen is recognized and either accepted or rejected by cells in the stigma." [GOC:dph, GOC:pj, GOC:tb]
synonym: "pollen recognition" EXACT []
synonym: "recognition or rejection of self pollen" RELATED [GOC:dph, GOC:tb]
synonym: "self incompatibility" RELATED []
is_a: GO:0008037 ! cell recognition
-is_a: GO:0022414 ! reproductive process
-relationship: part_of GO:0009875 ! pollen-pistil interaction
[Term]
id: GO:0048545
@@ -290291,8 +290321,8 @@ id: GO:0048589
name: developmental growth
namespace: biological_process
def: "The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another." [GOC:go_curators]
-is_a: GO:0032502 ! developmental process
is_a: GO:0040007 ! growth
+relationship: part_of GO:0032502 ! developmental process
[Term]
id: GO:0048592
@@ -290703,7 +290733,7 @@ id: GO:0048641
name: regulation of skeletal muscle tissue development
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of skeletal muscle tissue development." [GOC:go_curators]
-is_a: GO:0016202 ! regulation of striated muscle tissue development
+is_a: GO:1901861 ! regulation of muscle tissue development
relationship: regulates GO:0007519 ! skeletal muscle tissue development
[Term]
@@ -290715,8 +290745,8 @@ synonym: "down regulation of skeletal muscle development" EXACT []
synonym: "down-regulation of skeletal muscle development" EXACT []
synonym: "downregulation of skeletal muscle development" EXACT []
synonym: "inhibition of skeletal muscle development" NARROW []
-is_a: GO:0045843 ! negative regulation of striated muscle tissue development
is_a: GO:0048641 ! regulation of skeletal muscle tissue development
+is_a: GO:1901862 ! negative regulation of muscle tissue development
relationship: negatively_regulates GO:0007519 ! skeletal muscle tissue development
[Term]
@@ -290729,8 +290759,8 @@ synonym: "stimulation of skeletal muscle development" NARROW []
synonym: "up regulation of skeletal muscle development" EXACT []
synonym: "up-regulation of skeletal muscle development" EXACT []
synonym: "upregulation of skeletal muscle development" EXACT []
-is_a: GO:0045844 ! positive regulation of striated muscle tissue development
is_a: GO:0048641 ! regulation of skeletal muscle tissue development
+is_a: GO:1901863 ! positive regulation of muscle tissue development
relationship: positively_regulates GO:0007519 ! skeletal muscle tissue development
[Term]
@@ -292388,12 +292418,12 @@ relationship: regulates GO:0048813 ! dendrite morphogenesis
[Term]
id: GO:0048815
-name: hermaphrodite genitalia morphogenesis
+name: obsolete hermaphrodite genitalia morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of hermaphrodite genitalia are generated and organized." [GOC:ems, ISBN:0140512888]
-is_a: GO:0035112 ! genitalia morphogenesis
-is_a: GO:0035262 ! gonad morphogenesis
-relationship: part_of GO:0040035 ! hermaphrodite genitalia development
+def: "OBSOLETE. The process in which the anatomical structures of hermaphrodite genitalia are generated and organized." [GOC:ems, ISBN:0140512888]
+comment: The reason for obsoletion is that this term maybe redundant with female genitalia morphogenesis.
+is_obsolete: true
+consider: GO:0048807
[Term]
id: GO:0048816
@@ -292582,7 +292612,7 @@ is_a: GO:0048834 ! specification of petal number
id: GO:0048837
name: sorocarp sorus development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the sorocarp sorus over time, from its formation to the mature structure. A sorocarp sorus is the spore containing structure of a sorocarp." [GOC:devbiol, GOC:mtg_sensu, PMID:4332228]
+def: "The process whose specific outcome is the progression of the sorocarp sorus over time, from its formation to the mature structure. A sorocarp sorus is the spore containing structure of a sorocarp." [GOC:devbiol, GOC:mtg_sensu, PMID:4332228]
synonym: "sorocarp sorus formation" EXACT []
synonym: "sorocarp spore head formation" EXACT []
synonym: "sorocarp spore head morphogenesis" RELATED []
@@ -292824,9 +292854,9 @@ is_a: GO:0051301 ! cell division
id: GO:0048861
name: leukemia inhibitory factor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals initiated by the binding of leukemia inhibitory factor to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:devbiol, GOC:signaling]
+def: "The series of molecular signals initiated by the binding of a leukemia inhibitory factor to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:devbiol, GOC:signaling]
synonym: "leukemia inhibitory factor signalling pathway" EXACT []
-is_a: GO:0007167 ! enzyme linked receptor protein signaling pathway
+is_a: GO:0007167 ! enzyme-linked receptor protein signaling pathway
[Term]
id: GO:0048863
@@ -292893,16 +292923,15 @@ def: "Any process involved in the controlled self-propelled movement of a cell t
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
+subset: prokaryote_subset
synonym: "cell locomotion" EXACT []
synonym: "cell movement" RELATED []
synonym: "movement of a cell" EXACT []
-is_a: GO:0006928 ! movement of cell or subcellular component
-is_a: GO:0040011 ! locomotion
-relationship: part_of GO:0051674 ! localization of cell
+is_a: GO:0009987 ! cellular process
[Term]
id: GO:0048871
-name: multicellular organismal homeostasis
+name: multicellular organismal-level homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state at the level of the multicellular organism." [GOC:isa_complete]
is_a: GO:0032501 ! multicellular organismal process
@@ -292915,7 +292944,7 @@ namespace: biological_process
def: "Any biological process involved in the maintenance of the steady-state number of cells within a population of cells." [GOC:isa_complete]
synonym: "cell population homeostasis" EXACT []
synonym: "homeostasis of cell number" EXACT [GOC:dph]
-is_a: GO:0042592 ! homeostatic process
+is_a: GO:0048871 ! multicellular organismal-level homeostasis
[Term]
id: GO:0048873
@@ -292937,19 +292966,19 @@ is_a: GO:0051851 ! modulation by host of symbiont process
[Term]
id: GO:0048875
-name: chemical homeostasis within a tissue
+name: obsolete chemical homeostasis within a tissue
namespace: biological_process
-def: "Any process involved in the maintenance of the internal steady state of the amount of a chemical at the level of the tissue." [GOC:isa_complete]
-is_a: GO:0001894 ! tissue homeostasis
-is_a: GO:0048878 ! chemical homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of the internal steady state of the amount of a chemical at the level of the tissue." [GOC:isa_complete]
+comment: The definition of this term is vague.
+is_obsolete: true
[Term]
id: GO:0048876
-name: chemical homeostasis within retina
+name: obsolete chemical homeostasis within retina
namespace: biological_process
-def: "Any process involved in the maintenance of the internal steady state of the amount of a chemical at the level of the retina." [GOC:isa_complete]
-is_a: GO:0001895 ! retina homeostasis
-is_a: GO:0048875 ! chemical homeostasis within a tissue
+def: "OBSOLETE. Any process involved in the maintenance of the internal steady state of the amount of a chemical at the level of the retina." [GOC:isa_complete]
+comment: The definition of this term is vague.
+is_obsolete: true
[Term]
id: GO:0048877
@@ -293557,7 +293586,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0050005
name: isohexenylglutaconyl-CoA hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA = 3-(4-methylpent-3-en-1-yl)pent-2-enedioyl-CoA + H(2)O." [EC:4.2.1.57, RHEA:24144]
+def: "Catalysis of the reaction: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA = 3-(4-methylpent-3-en-1-yl)pent-2-enedioyl-CoA + H2O." [EC:4.2.1.57, RHEA:24144]
synonym: "3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA hydro-lyase [3-(4-methylpent-3-en-1-yl)pent-2-enedioyl-CoA-forming]" RELATED [EC:4.2.1.57]
synonym: "3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA hydro-lyase activity" RELATED [EC:4.2.1.57]
synonym: "3-hydroxy-3-isohexenylglutaryl-CoA-hydrolase activity" RELATED [EC:4.2.1.57]
@@ -293588,7 +293617,7 @@ is_a: GO:0016866 ! intramolecular transferase activity
id: GO:0050007
name: isonocardicin synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + nocardicin E = S-methyl-5'-thioadenosine + H(+) + isonocardicin A." [EC:2.5.1.38, RHEA:19845]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + nocardicin E = S-methyl-5'-thioadenosine + H+ + isonocardicin A." [EC:2.5.1.38, RHEA:19845]
synonym: "nocardicin aminocarboxypropyltransferase activity" RELATED [EC:2.5.1.38]
synonym: "S-adenosyl-L-methionine:nocardicin-E 3-amino-3-carboxypropyltransferase activity" RELATED [EC:2.5.1.38]
xref: EC:2.5.1.38
@@ -293601,7 +293630,7 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0050008
name: isopiperitenone delta-isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: isopiperitenone = piperitenone." [EC:5.3.3.11, RHEA:21516]
+def: "Catalysis of the reaction: isopiperitenone = piperitenone." [RHEA:21516]
synonym: "isopiperitenone D-isomerase activity" EXACT []
synonym: "isopiperitenone delta8-delta4-isomerase activity" RELATED [EC:5.3.3.11]
xref: EC:5.3.3.11
@@ -293614,7 +293643,7 @@ is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds
id: GO:0050009
name: isopropanol dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + propan-2-ol = acetone + H(+) + NADPH." [EC:1.1.1.80, RHEA:21792]
+def: "Catalysis of the reaction: NADP+ + propan-2-ol = acetone + H+ + NADPH." [EC:1.1.1.80, RHEA:21792]
synonym: "propan-2-ol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.80]
xref: EC:1.1.1.80
xref: KEGG_REACTION:R01550
@@ -293626,7 +293655,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050010
name: isovitexin beta-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: isovitexin + UDP-D-glucose = H(+) + isovitexin 2''-O-beta-D-glucoside + UDP." [EC:2.4.1.106, RHEA:19529]
+def: "Catalysis of the reaction: isovitexin + UDP-D-glucose = H+ + isovitexin 2''-O-beta-D-glucoside + UDP." [EC:2.4.1.106, RHEA:19529]
synonym: "isovitexin b-glucosyltransferase activity" EXACT []
synonym: "UDP-glucose:isovitexin 2''-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.106]
synonym: "UDPglucose:isovitexin 2''-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.106]
@@ -293699,7 +293728,7 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0050015
name: kievitone hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: kievitone hydrate = H(2)O + H(+) + kievitone." [EC:4.2.1.95, RHEA:23604]
+def: "Catalysis of the reaction: kievitone hydrate = H2O + H+ + kievitone." [EC:4.2.1.95, RHEA:23604]
synonym: "KHase activity" RELATED [EC:4.2.1.95]
synonym: "kievitone-hydrate hydro-lyase (kievitone-forming)" RELATED [EC:4.2.1.95]
synonym: "kievitone-hydrate hydro-lyase activity" RELATED [EC:4.2.1.95]
@@ -293753,7 +293782,7 @@ is_a: GO:0016639 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0050019
name: L-arabinitol 4-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arabinitol + NAD(+) = L-xylulose + H(+) + NADH." [EC:1.1.1.12, RHEA:16381]
+def: "Catalysis of the reaction: L-arabinitol + NAD+ = L-xylulose + H+ + NADH." [EC:1.1.1.12, RHEA:16381]
xref: EC:1.1.1.12
xref: KEGG_REACTION:R01903
xref: MetaCyc:L-ARABINITOL-4-DEHYDROGENASE-RXN
@@ -293764,7 +293793,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050020
name: L-arabinonate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arabinonate = 2-dehydro-3-deoxy-L-arabinonate + H(2)O." [EC:4.2.1.25, RHEA:20968]
+def: "Catalysis of the reaction: L-arabinonate = 2-dehydro-3-deoxy-L-arabinonate + H2O." [EC:4.2.1.25, RHEA:20968]
synonym: "L-arabinonate hydro-lyase (2-dehydro-3-deoxy-L-arabinonate-forming)" RELATED [EC:4.2.1.25]
synonym: "L-arabinonate hydro-lyase activity" RELATED [EC:4.2.1.25]
synonym: "L-arabonate dehydrase activity" RELATED [EC:4.2.1.25]
@@ -293779,7 +293808,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0050021
name: L-arabinonolactonase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arabinono-1,4-lactone + H(2)O = L-arabinonate + H(+)." [EC:3.1.1.15, RHEA:16217]
+def: "Catalysis of the reaction: L-arabinono-1,4-lactone + H2O = L-arabinonate + H+." [EC:3.1.1.15, RHEA:16217]
synonym: "L-arabinono-1,4-lactone lactonohydrolase activity" RELATED [EC:3.1.1.15]
xref: EC:3.1.1.15
xref: KEGG_REACTION:R02526
@@ -293803,7 +293832,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050023
name: L-fuconate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-fuconate = 2-dehydro-3-deoxy-L-fuconate + H(2)O." [EC:4.2.1.68, RHEA:22772]
+def: "Catalysis of the reaction: L-fuconate = 2-dehydro-3-deoxy-L-fuconate + H2O." [EC:4.2.1.68, RHEA:22772]
synonym: "L-fuconate hydratase activity" EXACT []
synonym: "L-fuconate hydro-lyase (2-dehydro-3-deoxy-L-fuconate-forming)" RELATED [EC:4.2.1.68]
synonym: "L-fuconate hydro-lyase activity" RELATED [EC:4.2.1.68]
@@ -293818,7 +293847,7 @@ id: GO:0050024
name: L-galactonolactone oxidase activity
namespace: molecular_function
alt_id: GO:0033733
-def: "Catalysis of the reaction: L-galactono-1,4-lactone + O(2) = L-ascorbate + H(2)O(2) + H(+)." [EC:1.3.3.12, RHEA:20617]
+def: "Catalysis of the reaction: L-galactono-1,4-lactone + O2 = L-ascorbate + H2O2 + H+." [EC:1.3.3.12, RHEA:20617]
synonym: "L-galactono-1,4-lactone oxidase activity" RELATED [EC:1.3.3.12]
synonym: "L-galactono-1,4-lactone:oxygen 3-oxidoreductase activity" RELATED [EC:1.3.3.12]
synonym: "L-xylono-1,4-lactone oxidase activity" RELATED [EC:1.3.3.12]
@@ -293882,7 +293911,7 @@ consider: GO:0050572
id: GO:0050028
name: L-lysine-lactamase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-2-aminohexano-6-lactam + H(2)O = L-lysine." [EC:3.5.2.11, RHEA:21388]
+def: "Catalysis of the reaction: L-2-aminohexano-6-lactam + H2O = L-lysine." [EC:3.5.2.11, RHEA:21388]
synonym: "L-alpha-aminocaprolactam hydrolase activity" RELATED [EC:3.5.2.11]
synonym: "L-lysinamidase activity" RELATED [EC:3.5.2.11]
synonym: "L-lysine-1,6-lactam lactamhydrolase activity" RELATED [EC:3.5.2.11]
@@ -293896,7 +293925,7 @@ is_a: GO:0016812 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050029
name: L-lysine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-lysine + H(2)O + O(2) = 6-amino-2-oxohexanoate + H(2)O(2) + NH(4)(+)." [EC:1.4.3.14, RHEA:14437]
+def: "Catalysis of the reaction: L-lysine + H2O + O2 = 6-amino-2-oxohexanoate + H2O2 + NH4." [EC:1.4.3.14, RHEA:14437]
comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "L-lysine alpha-oxidase activity" RELATED [EC:1.4.3.14]
synonym: "L-lysine:oxygen 2-oxidoreductase (deaminating)" RELATED [EC:1.4.3.14]
@@ -293924,7 +293953,7 @@ is_a: GO:0016645 ! oxidoreductase activity, acting on the CH-NH group of donors
id: GO:0050031
name: L-pipecolate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-pipecolate + O(2) = 2,3,4,5-tetrahydropyridine-2-carboxylate + H(2)O(2) + H(+). Delta1-piperideine-6-carboxylate is also known as 2,3,4,5-tetrahydropyridine-2-carboxylate." [EC:1.5.3.7, RHEA:11992]
+def: "Catalysis of the reaction: L-pipecolate + O2 = 2,3,4,5-tetrahydropyridine-2-carboxylate + H2O2 + H+. Delta1-piperideine-6-carboxylate is also known as 2,3,4,5-tetrahydropyridine-2-carboxylate." [EC:1.5.3.7, RHEA:11992]
synonym: "L-pipecolate:oxygen 1,6-oxidoreductase activity" RELATED [EC:1.5.3.7]
synonym: "L-pipecolic acid oxidase activity" RELATED [EC:1.5.3.7]
xref: EC:1.5.3.7
@@ -293938,7 +293967,7 @@ is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0050032
name: L-rhamnonate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H(2)O." [EC:4.2.1.90, RHEA:23080]
+def: "Catalysis of the reaction: L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O." [EC:4.2.1.90, RHEA:23080]
synonym: "L-rhamnonate hydro-lyase (2-dehydro-3-deoxy-L-rhamnonate-forming)" RELATED [EC:4.2.1.90]
synonym: "L-rhamnonate hydro-lyase activity" RELATED [EC:4.2.1.90]
xref: EC:4.2.1.90
@@ -293951,7 +293980,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0050033
name: L-rhamnono-1,4-lactonase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-rhamnono-1,4-lactone + H(2)O = L-rhamnonate + H(+)." [EC:3.1.1.65, RHEA:10288]
+def: "Catalysis of the reaction: L-rhamnono-1,4-lactone + H2O = L-rhamnonate + H+." [EC:3.1.1.65, RHEA:10288]
synonym: "L-rhamno-gamma-lactonase activity" RELATED [EC:3.1.1.65]
synonym: "L-rhamnono-1,4-lactone lactonohydrolase activity" RELATED [EC:3.1.1.65]
synonym: "L-rhamnono-gamma-lactonase activity" RELATED [EC:3.1.1.65]
@@ -293965,7 +293994,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050034
name: L-rhamnose 1-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-rhamnofuranose + NAD(+) = L-rhamnono-1,4-lactone + H(+) + NADH." [EC:1.1.1.173, RHEA:12649]
+def: "Catalysis of the reaction: L-rhamnofuranose + NAD+ = L-rhamnono-1,4-lactone + H+ + NADH." [EC:1.1.1.173, RHEA:12649]
synonym: "L-rhamnofuranose:NAD+ 1-oxidoreductase activity" RELATED [EC:1.1.1.173]
xref: EC:1.1.1.173
xref: KEGG_REACTION:R03942
@@ -293977,7 +294006,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050035
name: L-sorbose oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-sorbose + O(2) = 5-dehydro-D-fructose + H(2)O(2)." [EC:1.1.3.11, RHEA:17853]
+def: "Catalysis of the reaction: L-sorbose + O2 = 5-dehydro-D-fructose + H2O2." [EC:1.1.3.11, RHEA:17853]
synonym: "L-sorbose:oxygen 5-oxidoreductase activity" RELATED [EC:1.1.3.11]
xref: EC:1.1.3.11
xref: KEGG_REACTION:R01695
@@ -293989,7 +294018,7 @@ is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050036
name: L-threonate 3-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-threonate + NAD(+) = 3-dehydro-L-threonate + H(+) + NADH." [EC:1.1.1.129, RHEA:23376]
+def: "Catalysis of the reaction: L-threonate + NAD+ = 3-dehydro-L-threonate + H+ + NADH." [EC:1.1.1.129, RHEA:23376]
synonym: "L-threonate:NAD+ 3-oxidoreductase activity" RELATED [EC:1.1.1.129]
synonym: "L-threonic acid dehydrogenase activity" RELATED [EC:1.1.1.129]
synonym: "threonate dehydrogenase activity" RELATED [EC:1.1.1.129]
@@ -294003,7 +294032,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050037
name: L-xylose 1-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: aldehydo-L-xylose + NADP(+) = L-xylono-1,4-lactone + H(+) + NADPH." [EC:1.1.1.113, RHEA:15789]
+def: "Catalysis of the reaction: aldehydo-L-xylose + NADP+ = L-xylono-1,4-lactone + H+ + NADPH." [EC:1.1.1.113, RHEA:15789]
synonym: "L-xylose dehydrogenase activity" RELATED [EC:1.1.1.113]
synonym: "L-xylose:NADP+ 1-oxidoreductase activity" RELATED [EC:1.1.1.113]
synonym: "NADPH-xylose reductase activity" RELATED [EC:1.1.1.113]
@@ -294017,7 +294046,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050038
name: L-xylulose reductase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + xylitol = L-xylulose + H(+) + NADPH." [EC:1.1.1.10, RHEA:17025]
+def: "Catalysis of the reaction: NADP+ + xylitol = L-xylulose + H+ + NADPH." [EC:1.1.1.10, RHEA:17025]
synonym: "L-xylulose reductase activity" BROAD []
xref: EC:1.1.1.10
xref: KEGG_REACTION:R01904
@@ -294031,7 +294060,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050039
name: lactaldehyde reductase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + propane-1,2-diol = (S)-lactaldehyde + H(+) + NADPH." [EC:1.1.1.55, RHEA:15885]
+def: "Catalysis of the reaction: NADP+ + propane-1,2-diol = (S)-lactaldehyde + H+ + NADPH." [EC:1.1.1.55, RHEA:15885]
synonym: "1,2-propanediol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.55]
synonym: "lactaldehyde (reduced nicotinamide adenine dinucleotide phosphate) reductase activity" RELATED [EC:1.1.1.55]
synonym: "NADP-1,2-propanediol dehydrogenase activity" RELATED [EC:1.1.1.55]
@@ -294047,7 +294076,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050040
name: lactate 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-lactate + O(2) = acetate + CO(2) + H(2)O." [EC:1.13.12.4, RHEA:16513]
+def: "Catalysis of the reaction: (S)-lactate + O2 = acetate + CO2 + H2O." [EC:1.13.12.4, RHEA:16513]
synonym: "(S)-lactate:oxygen 2-oxidoreductase (decarboxylating)" RELATED [EC:1.13.12.4]
synonym: "L-lactate monooxygenase activity" RELATED [EC:1.13.12.4]
synonym: "L-lactate-2-monooxygenase activity" RELATED [EC:1.13.12.4]
@@ -294190,7 +294219,7 @@ is_a: GO:0016639 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0050050
name: leucine N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-leucine + acetyl-CoA = N-acetyl-L-leucine + CoA + H(+)." [EC:2.3.1.66, RHEA:20089]
+def: "Catalysis of the reaction: L-leucine + acetyl-CoA = N-acetyl-L-leucine + CoA + H+." [EC:2.3.1.66, RHEA:20089]
synonym: "acetyl-CoA:L-leucine N-acetyltransferase activity" RELATED [EC:2.3.1.66]
synonym: "leucine acetyltransferase activity" RELATED [EC:2.3.1.66]
xref: EC:2.3.1.66
@@ -294220,7 +294249,7 @@ is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050052
name: leukotriene-E4 20-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + leukotriene E(4) + NADPH + O(2) = 20-hydroxy-leukotriene E(4) + H(2)O + NADP(+)." [EC:1.14.13.34, RHEA:24120]
+def: "Catalysis of the reaction: H+ + leukotriene E(4) + NADPH + O2 = 20-hydroxy-leukotriene E(4) + H2O + NADP+." [EC:1.14.13.34, RHEA:24120]
synonym: "(7E,9E,11Z,14Z)-(5S,6R)-6-(cystein-S-yl)-5-hydroxyicosa-7,9,11,14-tetraenoate,NADPH:oxygen oxidoreductase (20-hydroxylating)" RELATED [EC:1.14.13.34]
synonym: "leukotriene-E(4) omega-hydroxylase activity" RELATED [EC:1.14.13.34]
synonym: "leukotriene-E4 omega-hydroxylase activity" RELATED [EC:1.14.13.34]
@@ -294250,7 +294279,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0050054
name: lignostilbene alpha beta-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,2-bis(4-hydroxy-3-methoxyphenyl)ethylene + O(2) = 2 vanillin." [EC:1.13.11.43, RHEA:21340]
+def: "Catalysis of the reaction: 1,2-bis(4-hydroxy-3-methoxyphenyl)ethylene + O2 = 2 vanillin." [EC:1.13.11.43, RHEA:21340]
synonym: "1,2-bis(4-hydroxy-3-methoxyphenyl)ethylene:oxygen oxidoreductase (alphabeta-bond-cleaving)" RELATED [EC:1.13.11.43]
synonym: "lignostilbene ab-dioxygenase activity" EXACT []
synonym: "lignostilbene alphabeta-dioxygenase activity" RELATED [EC:1.13.11.43]
@@ -294277,7 +294306,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050056
name: linalool 8-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + linalool + O(2) = (2E)-2,6-dimethylocta-2,7-diene-1,6-diol + A + H(2)O." [EC:1.14.14.84, RHEA:32635]
+def: "Catalysis of the reaction: AH(2) + linalool + O2 = (2E)-2,6-dimethylocta-2,7-diene-1,6-diol + A + H2O." [EC:1.14.14.84, RHEA:32635]
synonym: "3,7-dimethylocta-1,6-dien-3-ol,hydrogen-donor:oxygen oxidoreductase (8-hydroxylating)" RELATED [EC:1.14.99.28]
xref: EC:1.14.14.84
xref: KEGG_REACTION:R04366
@@ -294439,7 +294468,7 @@ is_a: GO:0016869 ! intramolecular transferase activity, transferring amino group
id: GO:0050067
name: lysine 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-lysine + O(2) = 5-aminopentanamide + CO(2) + H(2)O." [EC:1.13.12.2, RHEA:14601]
+def: "Catalysis of the reaction: L-lysine + O2 = 5-aminopentanamide + CO2 + H2O." [EC:1.13.12.2, RHEA:14601]
synonym: "L-lysine-2-monooxygenase activity" RELATED [EC:1.13.12.2]
synonym: "L-lysine:oxygen 2-oxidoreductase (decarboxylating)" RELATED [EC:1.13.12.2]
synonym: "lysine monooxygenase activity" RELATED [EC:1.13.12.2]
@@ -294454,7 +294483,7 @@ is_a: GO:0016703 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0050068
name: lysine carbamoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-lysine + carbamoyl phosphate = L-homocitrulline + H(+) + phosphate." [EC:2.1.3.8, RHEA:17121]
+def: "Catalysis of the reaction: L-lysine + carbamoyl phosphate = L-homocitrulline + H+ + phosphate." [EC:2.1.3.8, RHEA:17121]
synonym: "carbamoyl-phosphate:L-lysine carbamoyltransferase activity" RELATED [EC:2.1.3.8]
synonym: "lysine transcarbamylase activity" RELATED [EC:2.1.3.8]
xref: EC:2.1.3.8
@@ -294502,22 +294531,25 @@ is_a: GO:0140101 ! catalytic activity, acting on a tRNA
[Term]
id: GO:0050072
-name: m7G(5')pppN diphosphatase activity
+name: obsolete m7G(5')pppN diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7-methylguanosine 5'-triphospho-5'-polynucleotide + H2O = 7-methylguanosine 5'-phosphate + polynucleotide." [EC:3.6.1.30, MetaCyc:M7G5PPPN-PYROPHOSPHATASE-RXN]
+def: "OBSOLETE. Catalysis of the reaction: 7-methylguanosine 5'-triphospho-5'-polynucleotide + H2O = 7-methylguanosine 5'-phosphate + polynucleotide." [EC:3.6.1.30, MetaCyc:M7G5PPPN-PYROPHOSPHATASE-RXN]
+comment: This term was obsoleted because the obsoleted EC was obsoleted.
synonym: "7-methylguanosine-5'-triphospho-5'-polynucleotide 7-methylguanosine-5'-phosphohydrolase activity" RELATED [EC:3.6.1.30]
synonym: "decapase activity" RELATED [EC:3.6.1.30]
synonym: "M(7)G(5')pppN pyrophosphatase activity" EXACT []
synonym: "m7G(5')pppN pyrophosphatase activity" RELATED [EC:3.6.1.30]
xref: EC:3.6.1.30
xref: MetaCyc:M7G5PPPN-PYROPHOSPHATASE-RXN
-is_a: GO:0016462 ! pyrophosphatase activity
+is_obsolete: true
+consider: GO:0140932
+consider: GO:0140933
[Term]
id: GO:0050073
name: macrolide 2'-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + oleandomycin = ADP + 2 H(+) + oleandomycin 2'-O-phosphate." [EC:2.7.1.136, RHEA:18333]
+def: "Catalysis of the reaction: ATP + oleandomycin = ADP + 2 H+ + oleandomycin 2'-O-phosphate." [EC:2.7.1.136, RHEA:18333]
synonym: "ATP:macrolide 2'-O-phosphotransferase activity" RELATED [EC:2.7.1.136]
xref: EC:2.7.1.136
xref: KEGG_REACTION:R03780
@@ -294544,7 +294576,7 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0050075
name: maleate hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-malate = H(2)O + maleate." [EC:4.2.1.31, RHEA:23692]
+def: "Catalysis of the reaction: (R)-malate = H2O + maleate." [EC:4.2.1.31, RHEA:23692]
synonym: "(R)-malate hydro-lyase (maleate-forming)" RELATED [EC:4.2.1.31]
synonym: "(R)-malate hydro-lyase activity" RELATED [EC:4.2.1.31]
synonym: "D-malate hydro-lyase activity" RELATED [EC:4.2.1.31]
@@ -294666,7 +294698,7 @@ is_a: GO:0016833 ! oxo-acid-lyase activity
id: GO:0050084
name: mannitol-1-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-mannitol 1-phosphate + H(2)O = D-mannitol + 2 H(+) + phosphate." [EC:3.1.3.22, RHEA:19537]
+def: "Catalysis of the reaction: D-mannitol 1-phosphate + H2O = D-mannitol + 2 H+ + phosphate." [EC:3.1.3.22, RHEA:19537]
synonym: "D-mannitol-1-phosphate phosphohydrolase activity" RELATED [EC:3.1.3.22]
synonym: "mannitol-1-phosphate phosphatase activity" RELATED [EC:3.1.3.22]
xref: EC:3.1.3.22
@@ -294679,7 +294711,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0050085
name: mannitol 2-dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-mannitol + NADP(+) = D-fructose + H(+) + NADPH." [EC:1.1.1.138, RHEA:16765]
+def: "Catalysis of the reaction: D-mannitol + NADP+ = D-fructose + H+ + NADPH." [EC:1.1.1.138, RHEA:16765]
synonym: "D-mannitol:NADP+ 2-oxidoreductase activity" RELATED [EC:1.1.1.138]
synonym: "NADP-dependent mannitol dehydrogenase activity" RELATED [EC:1.1.1.138]
xref: EC:1.1.1.138
@@ -294716,7 +294748,7 @@ is_a: GO:0016898 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050088
name: mannose-6-phosphate 6-reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-mannitol 1-phosphate + NADP(+) = D-mannose 6-phosphate + 3 H(+) + NADPH." [EC:1.1.1.224, RHEA:14925]
+def: "Catalysis of the reaction: D-mannitol 1-phosphate + NADP+ = D-mannose 6-phosphate + 3 H+ + NADPH." [EC:1.1.1.224, RHEA:14925]
synonym: "6-phosphomannose reductase activity" RELATED [EC:1.1.1.224]
synonym: "D-mannitol-1-phosphate:NADP+ 6-oxidoreductase activity" RELATED [EC:1.1.1.224]
synonym: "mannose-6-phosphate reductase activity" RELATED [EC:1.1.1.224]
@@ -294762,7 +294794,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050091
name: melilotate 3-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-(2-hydroxyphenyl)propanoate + H(+) + NADH + O(2) = 3-(2,3-dihydroxyphenyl)propanoate + H(2)O + NAD(+)." [EC:1.14.13.4, RHEA:17669]
+def: "Catalysis of the reaction: 3-(2-hydroxyphenyl)propanoate + H+ + NADH + O2 = 3-(2,3-dihydroxyphenyl)propanoate + H2O + NAD+." [EC:1.14.13.4, RHEA:17669]
synonym: "2-hydroxyphenylpropionate hydroxylase activity" RELATED [EC:1.14.13.4]
synonym: "2-hydroxyphenylpropionic hydroxylase activity" RELATED [EC:1.14.13.4]
synonym: "3-(2-hydroxyphenyl)propanoate,NADH:oxygen oxidoreductase (3-hydroxylating)" RELATED [EC:1.14.13.4]
@@ -294778,7 +294810,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050092
name: meso-tartrate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2R,3S)-tartrate + NAD(+) = dihydroxyfumarate + H(+) + NADH." [EC:1.3.1.7, RHEA:18553]
+def: "Catalysis of the reaction: (2R,3S)-tartrate + NAD+ = dihydroxyfumarate + H+ + NADH." [EC:1.3.1.7, RHEA:18553]
synonym: "meso-tartrate:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.7]
xref: EC:1.3.1.7
xref: KEGG_REACTION:R02544
@@ -294790,7 +294822,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0050093
name: methanol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: methanol + NAD(+) = formaldehyde + H(+) + NADH." [EC:1.1.1.244, RHEA:19401]
+def: "Catalysis of the reaction: methanol + NAD+ = formaldehyde + H+ + NADH." [EC:1.1.1.244, RHEA:19401]
synonym: "methanol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.244]
xref: EC:1.1.1.244
xref: KEGG_REACTION:R00605
@@ -294816,7 +294848,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0050095
name: methionine decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-methionine + H(+) = 3-methylthiopropanamine + CO(2)." [EC:4.1.1.57, RHEA:17757]
+def: "Catalysis of the reaction: L-methionine + H+ = 3-methylthiopropanamine + CO2." [EC:4.1.1.57, RHEA:17757]
synonym: "L-methionine carboxy-lyase (3-methylthiopropanamine-forming)" RELATED [EC:4.1.1.57]
synonym: "L-methionine carboxy-lyase activity" RELATED [EC:4.1.1.57]
synonym: "L-methionine decarboxylase activity" RELATED [EC:4.1.1.57]
@@ -294830,7 +294862,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0050096
name: methylaspartate ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: threo-3-methyl-L-aspartate = mesaconate + NH(4)(+)." [EC:4.3.1.2, RHEA:12829]
+def: "Catalysis of the reaction: threo-3-methyl-L-aspartate = mesaconate + NH4." [EC:4.3.1.2, RHEA:12829]
synonym: "3-methylaspartase activity" RELATED [EC:4.3.1.2]
synonym: "beta-methylaspartase activity" RELATED [EC:4.3.1.2]
synonym: "L-threo-3-methylaspartate ammonia-lyase (mesaconate-forming)" RELATED [EC:4.3.1.2]
@@ -294866,7 +294898,7 @@ is_a: GO:0016866 ! intramolecular transferase activity
id: GO:0050098
name: methylguanidinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + methylguanidine = methylammonium + urea." [EC:3.5.3.16, RHEA:11764]
+def: "Catalysis of the reaction: H2O + methylguanidine = methylammonium + urea." [EC:3.5.3.16, RHEA:11764]
synonym: "methylguanidine amidinohydrolase activity" RELATED [EC:3.5.3.16]
synonym: "methylguanidine hydrolase activity" RELATED [EC:3.5.3.16]
xref: EC:3.5.3.16
@@ -294879,7 +294911,7 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050099
name: methylglutamate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-methyl-L-glutamate + A + H(2)O = L-glutamate + AH(2) + formaldehyde." [EC:1.5.99.5, RHEA:22572]
+def: "Catalysis of the reaction: N-methyl-L-glutamate + A + H2O = L-glutamate + AH(2) + formaldehyde." [EC:1.5.99.5, RHEA:22572]
synonym: "N-methyl-L-glutamate:(acceptor) oxidoreductase (demethylating)" RELATED [EC:1.5.99.5]
synonym: "N-methyl-L-glutamate:acceptor oxidoreductase (demethylating)" RELATED [EC:1.5.99.5]
synonym: "N-methylglutamate dehydrogenase activity" RELATED [EC:1.5.99.5]
@@ -294893,7 +294925,7 @@ is_a: GO:0016645 ! oxidoreductase activity, acting on the CH-NH group of donors
id: GO:0050100
name: methylitaconate delta-isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-methylene-3-methylsuccinate = dimethylmaleate." [EC:5.3.3.6, RHEA:23480]
+def: "Catalysis of the reaction: 2-methylene-3-methylsuccinate = dimethylmaleate." [RHEA:23480]
synonym: "methylitaconate D-isomerase activity" EXACT []
synonym: "methylitaconate delta2-delta3-isomerase activity" RELATED [EC:5.3.3.6]
synonym: "methylitaconate isomerase activity" RELATED [EC:5.3.3.6]
@@ -294907,13 +294939,12 @@ is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds
id: GO:0050101
name: mimosinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-mimosine + H(2)O = 3-hydroxy-4H-pyrid-4-one + L-serine." [EC:3.5.1.61, RHEA:13373]
-synonym: "mimosine amidohydrolase activity" RELATED [EC:3.5.1.61]
-xref: EC:3.5.1.61
+def: "Catalysis of the reaction: L-mimosine + H2O = 3-hydroxy-4H-pyrid-4-one + L-serine." [GOC:curators]
+synonym: "mimosine amidohydrolase activity" RELATED []
+xref: EC:4.3.3.8
xref: KEGG_REACTION:R04350
xref: MetaCyc:MIMOSINASE-RXN
-xref: RHEA:13373
-is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
+is_a: GO:0016843 ! amine-lyase activity
[Term]
id: GO:0050102
@@ -294944,7 +294975,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0050104
name: L-gulonate 3-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-gulonate + NAD(+) = 3-dehydro-L-gulonate + H(+) + NADH." [EC:1.1.1.45, RHEA:12889]
+def: "Catalysis of the reaction: L-gulonate + NAD+ = 3-dehydro-L-gulonate + H+ + NADH." [EC:1.1.1.45, RHEA:12889]
synonym: "L-3-aldonate dehydrogenase activity" RELATED [EC:1.1.1.45]
synonym: "L-3-aldonic dehydrogenase activity" RELATED [EC:1.1.1.45]
synonym: "L-3-hydroxyacid dehydrogenase activity" RELATED [EC:1.1.1.45]
@@ -294978,7 +295009,7 @@ is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050106
name: monomethyl-sulfatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + monomethyl sulfate = H(+) + methanol + sulfate." [EC:3.1.6.16, RHEA:14221]
+def: "Catalysis of the reaction: H2O + monomethyl sulfate = H+ + methanol + sulfate." [EC:3.1.6.16, RHEA:14221]
synonym: "monomethyl-sulfate sulfohydrolase activity" RELATED [EC:3.1.6.16]
synonym: "monomethyl-sulphatase activity" EXACT []
xref: EC:3.1.6.16
@@ -295040,7 +295071,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0050111
name: mycocerosate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + 7n H(+) + n methylmalonyl-CoA + 2n NADPH = n CO(2) + n CoA + n H(2)O + multi-methyl-branched acyl-CoA + 2n NADP(+)." [EC:2.3.1.111, RHEA:10588]
+def: "Catalysis of the reaction: acyl-CoA + 7n H+ + n methylmalonyl-CoA + 2n NADPH = n CO2 + n CoA + n H2O + multi-methyl-branched acyl-CoA + 2n NADP+." [EC:2.3.1.111, RHEA:10588]
synonym: "acyl-CoA:methylmalonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing)" RELATED [EC:2.3.1.111]
synonym: "mycocerosic acid synthase activity" RELATED [EC:2.3.1.111]
xref: EC:2.3.1.111
@@ -295053,7 +295084,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0050112
name: inositol 2-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: myo-inositol + NAD(+) = 2,4,6/3,5-pentahydroxycyclohexanone + H(+) + NADH." [EC:1.1.1.18, RHEA:16949]
+def: "Catalysis of the reaction: myo-inositol + NAD+ = 2,4,6/3,5-pentahydroxycyclohexanone + H+ + NADH." [EC:1.1.1.18, RHEA:16949]
synonym: "inositol:NAD 2-dehydrogenase activity" EXACT []
synonym: "myo-inositol 2-dehydrogenase activity" EXACT []
xref: EC:1.1.1.18
@@ -295066,7 +295097,7 @@ is_a: GO:0004022 ! alcohol dehydrogenase (NAD+) activity
id: GO:0050113
name: inositol oxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: myo-inositol + O(2) = D-glucuronate + H(2)O + H(+)." [RHEA:23696]
+def: "Catalysis of the reaction: myo-inositol + O2 = D-glucuronate + H2O + H+." [RHEA:23696]
synonym: "meso-inositol oxygenase activity" RELATED [EC:1.13.99.1]
synonym: "MOO activity" RELATED [EC:1.13.99.1]
synonym: "myo-inositol oxygenase activity" EXACT []
@@ -295083,7 +295114,7 @@ is_a: GO:0016701 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0050114
name: myo-inosose-2 dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,4,6/3,5-pentahydroxycyclohexanone = 3D-3,5/4-trihydroxycyclohexane-1,2-dione + H(2)O." [EC:4.2.1.44, RHEA:14065]
+def: "Catalysis of the reaction: 2,4,6/3,5-pentahydroxycyclohexanone = 3D-3,5/4-trihydroxycyclohexane-1,2-dione + H2O." [EC:4.2.1.44, RHEA:14065]
synonym: "2,4,6/3,5-pentahydroxycyclohexanone hydro-lyase (3,5/4-trihydroxycyclohexa-1,2-dione-forming)" RELATED [EC:4.2.1.44]
synonym: "2,4,6/3,5-pentahydroxycyclohexanone hydro-lyase activity" RELATED [EC:4.2.1.44]
synonym: "inosose 2,3-dehydratase activity" RELATED [EC:4.2.1.44]
@@ -295114,7 +295145,7 @@ is_a: GO:0004721 ! phosphoprotein phosphatase activity
id: GO:0050116
name: N,N-dimethylformamidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N,N-dimethylformamide + H(2)O = dimethylamine + formate." [EC:3.5.1.56, RHEA:19517]
+def: "Catalysis of the reaction: N,N-dimethylformamide + H2O = dimethylamine + formate." [EC:3.5.1.56, RHEA:19517]
synonym: "dimethylformamidase activity" RELATED [EC:3.5.1.56]
synonym: "DMFase activity" RELATED [EC:3.5.1.56]
synonym: "N,N-dimethylformamide amidohydrolase activity" RELATED [EC:3.5.1.56]
@@ -295128,7 +295159,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050117
name: N-acetyl-beta-alanine deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-acetyl-beta-alanine + H(2)O = beta-alanine + acetate." [EC:3.5.1.21, RHEA:23212]
+def: "Catalysis of the reaction: N-acetyl-beta-alanine + H2O = beta-alanine + acetate." [EC:3.5.1.21, RHEA:23212]
synonym: "N-acetyl-beta-alanine amidohydrolase activity" RELATED [EC:3.5.1.21]
xref: EC:3.5.1.21
xref: KEGG_REACTION:R00909
@@ -295141,7 +295172,7 @@ is_a: GO:0019213 ! deacetylase activity
id: GO:0050118
name: N-acetyldiaminopimelate deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-acetyl-LL-2,6-diaminopimelate + H(2)O = LL-2,6-diaminopimelate + acetate." [EC:3.5.1.47, RHEA:20405]
+def: "Catalysis of the reaction: N-acetyl-LL-2,6-diaminopimelate + H2O = LL-2,6-diaminopimelate + acetate." [EC:3.5.1.47, RHEA:20405]
synonym: "6-N-acetyl-LL-2,6-diaminoheptanedioate amidohydrolase activity" RELATED [EC:3.5.1.47]
synonym: "N-acetyl-L-diaminopimelic acid deacylase activity" RELATED [EC:3.5.1.47]
synonym: "N-acetyl-LL-diaminopimelate deacylase activity" RELATED [EC:3.5.1.47]
@@ -295157,7 +295188,7 @@ is_a: GO:0019213 ! deacetylase activity
id: GO:0050119
name: N-acetylglucosamine deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-acetyl-D-glucosamine + H(2)O = D-glucosamine + acetate." [EC:3.5.1.33, RHEA:20593]
+def: "Catalysis of the reaction: N-acetyl-D-glucosamine + H2O = D-glucosamine + acetate." [EC:3.5.1.33, RHEA:20593]
synonym: "acetylaminodeoxyglucose acetylhydrolase activity" RELATED [EC:3.5.1.33]
synonym: "N-acetyl-D-glucosamine amidohydrolase activity" RELATED [EC:3.5.1.33]
synonym: "N-acetyl-D-glucosaminyl N-deacetylase activity" RELATED [EC:3.5.1.33]
@@ -295173,7 +295204,7 @@ is_a: GO:0019213 ! deacetylase activity
id: GO:0050120
name: N-acetylhexosamine 1-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-acetyl-D-glucosamine + H(2)O + NAD(+) = N-acetyl-D-glucosaminate + 2 H(+) + NADH." [EC:1.1.1.240, RHEA:23144]
+def: "Catalysis of the reaction: N-acetyl-D-glucosamine + H2O + NAD+ = N-acetyl-D-glucosaminate + 2 H+ + NADH." [EC:1.1.1.240, RHEA:23144]
synonym: "N-acetyl-D-hexosamine dehydrogenase activity" RELATED [EC:1.1.1.240]
synonym: "N-acetyl-D-hexosamine:NAD+ 1-oxidoreductase activity" RELATED [EC:1.1.1.240]
synonym: "N-acetylhexosamine dehydrogenase activity" RELATED [EC:1.1.1.240]
@@ -295203,7 +295234,7 @@ is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and
id: GO:0050122
name: N-acylhexosamine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-acetyl-D-glucosamine + H(2)O + O(2) = N-acetyl-D-glucosaminate + H(2)O(2) + H(+)." [EC:1.1.3.29, RHEA:13029]
+def: "Catalysis of the reaction: N-acetyl-D-glucosamine + H2O + O2 = N-acetyl-D-glucosaminate + H2O2 + H+." [EC:1.1.3.29, RHEA:13029]
synonym: "N-acyl-beta-D-hexosamine:oxygen 1-oxidoreductase activity" RELATED [EC:1.1.3.29]
synonym: "N-acyl-D-hexosamine oxidase activity" RELATED [EC:1.1.3.29]
synonym: "N-acyl-D-hexosamine:oxygen 1-oxidoreductase activity" RELATED [EC:1.1.3.29]
@@ -295217,7 +295248,7 @@ is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050123
name: N-acylmannosamine 1-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-acyl-D-mannosamine + NAD(+) = N-acyl-D-mannosaminolactone + H(+) + NADH." [EC:1.1.1.233, RHEA:11540]
+def: "Catalysis of the reaction: N-acyl-D-mannosamine + NAD+ = N-acyl-D-mannosaminolactone + H+ + NADH." [EC:1.1.1.233, RHEA:11540]
synonym: "N-acetyl-D-mannosamine dehydrogenase activity" RELATED [EC:1.1.1.233]
synonym: "N-acyl-D-mannosamine dehydrogenase activity" RELATED [EC:1.1.1.233]
synonym: "N-acyl-D-mannosamine:NAD+ 1-oxidoreductase activity" RELATED [EC:1.1.1.233]
@@ -295247,7 +295278,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0050125
name: N-benzyloxycarbonylglycine hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-benzyloxycarbonylglycine + H(2)O + H(+) = benzyl alcohol + CO(2) + glycine." [EC:3.5.1.58, RHEA:20900]
+def: "Catalysis of the reaction: N-benzyloxycarbonylglycine + H2O + H+ = benzyl alcohol + CO2 + glycine." [EC:3.5.1.58, RHEA:20900]
synonym: "benzyloxycarbonylglycine hydrolase activity" RELATED [EC:3.5.1.58]
synonym: "N-benzyloxycarbonylglycine urethanehydrolase activity" RELATED [EC:3.5.1.58]
synonym: "nalpha-benzyloxycarbonyl amino acid urethane hydrolase activity" RELATED [EC:3.5.1.58]
@@ -295263,7 +295294,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050126
name: N-carbamoylputrescine amidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-carbamoylputrescine + H(2)O + 2 H(+) = CO(2) + NH(4)(+) + putrescine." [EC:3.5.1.53, RHEA:22284]
+def: "Catalysis of the reaction: N-carbamoylputrescine + H2O + 2 H+ = CO2 + NH4 + putrescine." [EC:3.5.1.53, RHEA:22284]
synonym: "carbamoylputrescine hydrolase activity" RELATED [EC:3.5.1.53]
synonym: "N-carbamoylputrescine amidohydrolase activity" RELATED [EC:3.5.1.53]
synonym: "NCP" RELATED [EC:3.5.1.53]
@@ -295277,7 +295308,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050127
name: N-carbamoylsarcosine amidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-carbamoylsarcosine + H(2)O + 2 H(+) = CO(2) + NH(4)(+) + sarcosine." [EC:3.5.1.59, RHEA:20057]
+def: "Catalysis of the reaction: N-carbamoylsarcosine + H2O + 2 H+ = CO2 + NH4 + sarcosine." [EC:3.5.1.59, RHEA:20057]
synonym: "carbamoylsarcosine amidase activity" RELATED [EC:3.5.1.59]
synonym: "CSHase activity" RELATED [EC:3.5.1.59]
synonym: "N-carbamoylsarcosine amidohydrolase activity" RELATED [EC:3.5.1.59]
@@ -295291,7 +295322,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050128
name: N-feruloylglycine deacylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-feruloylglycine + H(2)O = ferulate + glycine." [EC:3.5.1.71, RHEA:10484]
+def: "Catalysis of the reaction: N-feruloylglycine + H2O = ferulate + glycine." [EC:3.5.1.71, RHEA:10484]
synonym: "N-feruloylglycine amidohydrolase activity" RELATED [EC:3.5.1.71]
synonym: "N-feruloylglycine hydrolase activity" RELATED [EC:3.5.1.71]
xref: EC:3.5.1.71
@@ -295304,7 +295335,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050129
name: N-formylglutamate deformylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-formyl-L-glutamate + H(2)O = L-glutamate + formate." [EC:3.5.1.68, RHEA:12476]
+def: "Catalysis of the reaction: N-formyl-L-glutamate + H2O = L-glutamate + formate." [EC:3.5.1.68, RHEA:12476]
synonym: "beta-citryl-L-glutamate amidase activity" RELATED [EC:3.5.1.68]
synonym: "beta-citryl-L-glutamate amidohydrolase activity" RELATED [EC:3.5.1.68]
synonym: "beta-citryl-L-glutamate hydrolase activity" RELATED [EC:3.5.1.68]
@@ -295323,7 +295354,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050130
name: N-methyl-2-oxoglutaramate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-methyl-2-oxoglutaramate + H(2)O = 2-oxoglutarate + methylammonium." [EC:3.5.1.36, RHEA:24108]
+def: "Catalysis of the reaction: N-methyl-2-oxoglutaramate + H2O = 2-oxoglutarate + methylammonium." [EC:3.5.1.36, RHEA:24108]
synonym: "5-hydroxy-N-methylpyroglutamate synthase activity" RELATED [EC:3.5.1.36]
synonym: "N-methyl-2-oxoglutaramate methylamidohydrolase activity" RELATED [EC:3.5.1.36]
xref: EC:3.5.1.36
@@ -295348,7 +295379,7 @@ is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0050132
name: N-methylalanine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-methyl-L-alanine + H(2)O + NADP(+) = H(+) + methylammonium + NADPH + pyruvate." [EC:1.4.1.17, RHEA:21768]
+def: "Catalysis of the reaction: N-methyl-L-alanine + H2O + NADP+ = H+ + methylammonium + NADPH + pyruvate." [EC:1.4.1.17, RHEA:21768]
synonym: "N-methyl-L-alanine:NADP+ oxidoreductase (demethylating, deaminating)" RELATED [EC:1.4.1.17]
xref: EC:1.4.1.17
xref: KEGG_REACTION:R01584
@@ -295376,7 +295407,7 @@ is_a: GO:0016413 ! O-acetyltransferase activity
id: GO:0050134
name: N6-methyl-lysine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(6)-methyl-L-lysine + H(2)O + O(2) = L-lysine + formaldehyde + H(2)O(2)." [EC:1.5.3.4, RHEA:23200]
+def: "Catalysis of the reaction: N(6)-methyl-L-lysine + H2O + O2 = L-lysine + formaldehyde + H2O2." [EC:1.5.3.4, RHEA:23200]
synonym: "6-N-methyl-L-lysine:oxygen oxidoreductase (demethylating)" RELATED [EC:1.5.3.4]
synonym: "epsilon-alkyl-L-lysine:oxygen oxidoreductase activity" RELATED [EC:1.5.3.4]
synonym: "epsilon-alkyllysinase activity" RELATED [EC:1.5.3.4]
@@ -295426,7 +295457,7 @@ is_a: GO:0003955 ! NAD(P)H dehydrogenase (quinone) activity
id: GO:0050137
name: NADPH peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O(2) + H(+) + NADPH = 2 H(2)O + NADP(+)." [EC:1.11.1.2, RHEA:15173]
+def: "Catalysis of the reaction: H2O2 + H+ + NADPH = 2 H2O + NADP+." [EC:1.11.1.2, RHEA:15173]
synonym: "NADP peroxidase activity" RELATED [EC:1.11.1.2]
synonym: "NADPH:hydrogen-peroxide oxidoreductase activity" RELATED [EC:1.11.1.2]
synonym: "nicotinamide adenine dinucleotide phosphate peroxidase activity" RELATED [EC:1.11.1.2]
@@ -295443,7 +295474,7 @@ is_a: GO:0004601 ! peroxidase activity
id: GO:0050138
name: nicotinate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + NADP(+) + nicotinate = 6-hydroxynicotinate + H(+) + NADPH." [EC:1.17.1.5, RHEA:12236]
+def: "Catalysis of the reaction: H2O + NADP+ + nicotinate = 6-hydroxynicotinate + H+ + NADPH." [EC:1.17.1.5, RHEA:12236]
synonym: "nicotinate hydroxylase activity" RELATED [EC:1.17.1.5]
synonym: "nicotinate:NADP+ 6-oxidoreductase (hydroxylating)" RELATED [EC:1.17.1.5]
synonym: "nicotinic acid hydroxylase activity" RELATED [EC:1.17.1.5]
@@ -295553,6 +295584,7 @@ xref: Reactome:R-HSA-73548 "(d)CMP or UMP + ATP <=> (d)CDP or UDP + ADP (CMPK1)"
xref: Reactome:R-HSA-73635 "dUMP or TMP + ATP <=> dUDP or TDP + ADP [DTYMK]"
xref: Reactome:R-HSA-75125 "(d)CDP or UDP + ADP <=> (d)CMP or UMP + ATP (CMPK1)"
xref: Reactome:R-HSA-75126 "dUDP or TDP + ADP <=> dUMP or TMP + ATP [DTYMK]"
+xref: Reactome:R-HSA-9754978 "Unknown kinase phosphorylates RBV-MP"
xref: RHEA:24036
is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
is_a: GO:0019205 ! nucleobase-containing compound kinase activity
@@ -295569,6 +295601,7 @@ synonym: "nucleotide:nucleoside 5'-phosphotransferase activity" RELATED [EC:2.7.
xref: EC:2.7.1.77
xref: MetaCyc:NUCLEOSIDE-PHOSPHOTRANSFERASE-RXN
xref: Reactome:R-HSA-2162066 "carbovir + IMP => carbovir monophosphate + inosine"
+xref: Reactome:R-HSA-9754916 "NT5C2 tetramer phosphorylates RBV"
xref: RHEA:19961
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
is_a: GO:0019205 ! nucleobase-containing compound kinase activity
@@ -295619,7 +295652,7 @@ id: GO:0050150
name: o-pyrocatechuate decarboxylase activity
namespace: molecular_function
alt_id: GO:0018790
-def: "Catalysis of the reaction: 2,3-dihydroxybenzoate + H(+) = catechol + CO(2)." [EC:4.1.1.46, RHEA:21492]
+def: "Catalysis of the reaction: 2,3-dihydroxybenzoate + H+ = catechol + CO2." [EC:4.1.1.46, RHEA:21492]
synonym: "2,3-DHBA decarboxylase activity" RELATED [EC:4.1.1.46]
synonym: "2,3-dihydroxybenzoate carboxy-lyase (catechol-forming)" RELATED [EC:4.1.1.46]
synonym: "2,3-dihydroxybenzoate carboxy-lyase activity" RELATED [EC:4.1.1.46]
@@ -295636,7 +295669,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0050151
name: oleate hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-10-hydroxystearate = H(2)O + oleate." [EC:4.2.1.53, RHEA:21852]
+def: "Catalysis of the reaction: (R)-10-hydroxystearate = H2O + oleate." [EC:4.2.1.53, RHEA:21852]
synonym: "(R)-10-hydroxystearate 10-hydro-lyase (oleate-forming)" RELATED [EC:4.2.1.53]
synonym: "(R)-10-hydroxystearate 10-hydro-lyase activity" RELATED [EC:4.2.1.53]
xref: EC:4.2.1.53
@@ -295662,7 +295695,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050153
name: omega-hydroxydecanoate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 10-hydroxydecanoate + NAD(+) = 10-oxodecanoate + H(+) + NADH." [EC:1.1.1.66, RHEA:20880]
+def: "Catalysis of the reaction: 10-hydroxydecanoate + NAD+ = 10-oxodecanoate + H+ + NADH." [EC:1.1.1.66, RHEA:20880]
synonym: "10-hydroxydecanoate:NAD+ 10-oxidoreductase activity" RELATED [EC:1.1.1.66]
synonym: "w-hydroxydecanoate dehydrogenase activity" EXACT []
xref: EC:1.1.1.66
@@ -295675,7 +295708,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050154
name: opheline kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + guanidinoethyl methyl phosphate = N'-phosphoguanidinoethyl methylphosphate + ADP + 2 H(+)." [EC:2.7.3.7, RHEA:17553]
+def: "Catalysis of the reaction: ATP + guanidinoethyl methyl phosphate = N'-phosphoguanidinoethyl methylphosphate + ADP + 2 H+." [EC:2.7.3.7, RHEA:17553]
synonym: "ATP:guanidinoethyl-methyl-phosphate phosphotransferase activity" RELATED [EC:2.7.3.7]
xref: EC:2.7.3.7
xref: KEGG_REACTION:R04388
@@ -295701,7 +295734,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0050156
name: ornithine N-benzoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-ornithine + 2 benzoyl-CoA = N(2),N(5)-dibenzoyl-L-ornithine + 2 CoA + 2 H(+)." [EC:2.3.1.127, RHEA:16929]
+def: "Catalysis of the reaction: L-ornithine + 2 benzoyl-CoA = N(2),N(5)-dibenzoyl-L-ornithine + 2 CoA + 2 H+." [EC:2.3.1.127, RHEA:16929]
synonym: "benzoyl-CoA:L-ornithine N-benzoyltransferase activity" RELATED [EC:2.3.1.127]
synonym: "ornithine N-acyltransferase activity" RELATED [EC:2.3.1.127]
xref: EC:2.3.1.127
@@ -295722,24 +295755,26 @@ is_a: GO:0047661 ! amino-acid racemase activity
[Term]
id: GO:0050158
-name: orotate reductase (NADPH) activity
+name: dihydroorotate dehydrogenase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-dihydroorotate + NADP(+) = H(+) + NADPH + orotate." [EC:1.3.1.15, RHEA:14861]
+def: "Catalysis of the reaction: (S)-dihydroorotate + NADP+ = H+ + NADPH + orotate." [RHEA:14861]
synonym: "(S)-dihydroorotate:NADP+ oxidoreductase activity" RELATED [EC:1.3.1.15]
synonym: "dihydro-orotic dehydrogenase activity" RELATED [EC:1.3.1.15]
synonym: "L-5,6-dihydro-orotate:NAD oxidoreductase activity" RELATED [EC:1.3.1.15]
+synonym: "orotate reductase (NADPH) activity" EXACT []
synonym: "orotate reductase activity" RELATED [EC:1.3.1.15]
xref: EC:1.3.1.15
xref: KEGG_REACTION:R01866
xref: MetaCyc:OROTATE-REDUCTASE-NADPH-RXN
xref: RHEA:14861
+is_a: GO:0004152 ! dihydroorotate dehydrogenase activity
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0050159
name: orsellinate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: o-orsellinate + H(+) = CO(2) + orcinol." [EC:4.1.1.58, RHEA:16733]
+def: "Catalysis of the reaction: o-orsellinate + H+ = CO2 + orcinol." [EC:4.1.1.58, RHEA:16733]
synonym: "orsellinate carboxy-lyase (orcinol-forming)" RELATED [EC:4.1.1.58]
synonym: "orsellinate carboxy-lyase activity" RELATED [EC:4.1.1.58]
xref: EC:4.1.1.58
@@ -295752,7 +295787,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0050160
name: orsellinate-depside hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + orsellinate depside = 2 o-orsellinate + H(+)." [EC:3.1.1.40, RHEA:19549]
+def: "Catalysis of the reaction: H2O + orsellinate depside = 2 o-orsellinate + H+." [EC:3.1.1.40, RHEA:19549]
synonym: "lecanorate hydrolase activity" RELATED [EC:3.1.1.40]
xref: EC:3.1.1.40
xref: KEGG_REACTION:R00054
@@ -295779,7 +295814,7 @@ is_a: GO:0008410 ! CoA-transferase activity
id: GO:0050162
name: oxalate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 H(+) + O(2) + oxalate = 2 CO(2) + H(2)O(2)." [RHEA:21880]
+def: "Catalysis of the reaction: 2 H+ + O2 + oxalate = 2 CO2 + H2O2." [RHEA:21880]
synonym: "aero-oxalo dehydrogenase activity" RELATED [EC:1.2.3.4]
synonym: "oxalate:oxygen oxidoreductase activity" RELATED [EC:1.2.3.4]
synonym: "oxalic acid oxidase activity" RELATED [EC:1.2.3.4]
@@ -295807,7 +295842,7 @@ is_a: GO:0016862 ! intramolecular oxidoreductase activity, interconverting keto-
id: GO:0050164
name: oxoglutarate dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + CoA + NADP(+) = CO(2) + NADPH + succinyl-CoA." [EC:1.2.1.52, RHEA:21400]
+def: "Catalysis of the reaction: 2-oxoglutarate + CoA + NADP+ = CO2 + NADPH + succinyl-CoA." [EC:1.2.1.52, RHEA:21400]
synonym: "2-oxoglutarate:NADP+ 2-oxidoreductase (CoA-succinylating)" RELATED [EC:1.2.1.52]
xref: EC:1.2.1.52
xref: KEGG_REACTION:R00265
@@ -295832,7 +295867,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0050166
name: pantoate 4-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-pantoate + NAD(+) = (R)-4-dehydropantoate + H(+) + NADH." [EC:1.1.1.106, RHEA:23000]
+def: "Catalysis of the reaction: (R)-pantoate + NAD+ = (R)-4-dehydropantoate + H+ + NADH." [EC:1.1.1.106, RHEA:23000]
synonym: "(R)-pantoate:NAD+ 4-oxidoreductase activity" RELATED [EC:1.1.1.106]
synonym: "D-pantoate:NAD+ 4-oxidoreductase activity" RELATED [EC:1.1.1.106]
synonym: "panthothenase activity" RELATED [EC:1.1.1.106]
@@ -295847,7 +295882,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050167
name: pantothenoylcysteine decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-[(R)-pantothenoyl]-L-cysteine + H(+) = (R)-pantetheine + CO(2)." [EC:4.1.1.30, RHEA:15077]
+def: "Catalysis of the reaction: N-[(R)-pantothenoyl]-L-cysteine + H+ = (R)-pantetheine + CO2." [EC:4.1.1.30, RHEA:15077]
synonym: "N-((R)-pantothenoyl)-L-cysteine carboxy-lyase activity" RELATED [EC:4.1.1.30]
synonym: "N-[(R)-pantothenoyl]-L-cysteine carboxy-lyase (pantetheine-forming)" RELATED [EC:4.1.1.30]
synonym: "N-[(R)-pantothenoyl]-L-cysteine carboxy-lyase activity" RELATED [EC:4.1.1.30]
@@ -295862,7 +295897,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0050168
name: pentanamidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + pentanamide = NH(4)(+) + valerate." [EC:3.5.1.50, RHEA:10000]
+def: "Catalysis of the reaction: H2O + pentanamide = NH4 + valerate." [EC:3.5.1.50, RHEA:10000]
synonym: "pentanamide amidohydrolase activity" RELATED [EC:3.5.1.50]
synonym: "valeramidase activity" RELATED [EC:3.5.1.50]
xref: EC:3.5.1.50
@@ -295873,17 +295908,17 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
[Term]
id: GO:0050169
-name: peptide-tryptophan 2,3-dioxygenase activity
+name: obsolete peptide-tryptophan 2,3-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: peptide tryptophan + O2 = peptide formylkynurenine." [EC:1.13.11.26, MetaCyc:PEPTIDE-TRYPTOPHAN-23-DIOXYGENASE-RXN, PMID:4403729]
+def: "OBSOLETE. Catalysis of the reaction: peptide tryptophan + O2 = peptide formylkynurenine." [EC:1.13.11.26, MetaCyc:PEPTIDE-TRYPTOPHAN-23-DIOXYGENASE-RXN, PMID:4403729]
+comment: This term was obsoleted because there is no enzyme known to catalyze this reaction.
synonym: "peptide-tryptophan:oxygen 2,3-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.26]
synonym: "peptidyltryptophan 2,3-dioxygenase activity" RELATED [EC:1.13.11.26]
synonym: "pyrrolooxygenase activity" RELATED [EC:1.13.11.26]
synonym: "tryptophan pyrrolooxygenase activity" RELATED [EC:1.13.11.26]
xref: EC:1.13.11.26
xref: MetaCyc:PEPTIDE-TRYPTOPHAN-23-DIOXYGENASE-RXN
-is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
-is_a: GO:0140096 ! catalytic activity, acting on a protein
+is_obsolete: true
[Term]
id: GO:0050170
@@ -295920,7 +295955,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0050172
name: phenylalanine 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-phenylalanine + O(2) = 2-phenylacetamide + CO(2) + H(2)O." [EC:1.13.12.9, RHEA:10712]
+def: "Catalysis of the reaction: L-phenylalanine + O2 = 2-phenylacetamide + CO2 + H2O." [EC:1.13.12.9, RHEA:10712]
synonym: "L-phenylalanine oxidase (deaminating and decarboxylating)" RELATED [EC:1.13.12.9]
synonym: "l-phenylalanine oxidase (deaminating and decarboxylating) activity" RELATED [EC:1.13.12.9]
synonym: "L-phenylalanine:oxygen 2-oxidoreductase (decarboxylating)" RELATED [EC:1.13.12.9]
@@ -295934,17 +295969,17 @@ is_a: GO:0016703 ! oxidoreductase activity, acting on single donors with incorpo
[Term]
id: GO:0050173
-name: phenylalanine adenylyltransferase activity
+name: obsolete phenylalanine adenylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-phenylalanine + ATP = N-adenylyl-L-phenylalanine + diphosphate + 2 H(+)." [EC:2.7.7.54, RHEA:17189]
+def: "OBSOLETE. Catalysis of the reaction: L-phenylalanine + ATP = N-adenylyl-L-phenylalanine + diphosphate + 2 H+." [EC:2.7.7.54]
+comment: This term was obsoleted because this reaction is not believed to exist anymore.
synonym: "ATP:L-phenylalanine adenylyltransferase activity" RELATED [EC:2.7.7.54]
synonym: "ATP:phenylalanine adenylyltransferase activity" EXACT []
synonym: "L-phenylalanine adenylyltransferase activity" RELATED [EC:2.7.7.54]
xref: EC:2.7.7.54
xref: KEGG_REACTION:R00687
xref: MetaCyc:PHENYLALANINE-ADENYLYLTRANSFERASE-RXN
-xref: RHEA:17189
-is_a: GO:0070566 ! adenylyltransferase activity
+is_obsolete: true
[Term]
id: GO:0050174
@@ -295978,7 +296013,7 @@ is_a: GO:0016639 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0050176
name: phenylalanine N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-phenylalanine + acetyl-CoA = N-acetyl-L-phenylalanine + CoA + H(+)." [EC:2.3.1.53, RHEA:17801]
+def: "Catalysis of the reaction: L-phenylalanine + acetyl-CoA = N-acetyl-L-phenylalanine + CoA + H+." [EC:2.3.1.53, RHEA:17801]
synonym: "acetyl-CoA-L-phenylalanine alpha-N-acetyltransferase activity" RELATED [EC:2.3.1.53]
synonym: "acetyl-CoA:L-phenylalanine N-acetyltransferase activity" RELATED [EC:2.3.1.53]
xref: EC:2.3.1.53
@@ -296003,10 +296038,10 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0050178
name: phenylpyruvate tautomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: keto-phenylpyruvate = enol-phenylpyruvate." [EC:5.3.2.1, MetaCyc:PHENYLPYRUVATE-TAUTOMERASE-RXN]
-synonym: "phenylpyruvate keto--enol tautomerase activity" RELATED [EC:5.3.2.1]
-synonym: "phenylpyruvate keto-enol-isomerase activity" RELATED [EC:5.3.2.1]
-synonym: "phenylpyruvic keto--enol isomerase activity" RELATED [EC:5.3.2.1]
+def: "Catalysis of the reaction: keto-phenylpyruvate = enol-phenylpyruvate." [RHEA:17097]
+synonym: "phenylpyruvate keto--enol tautomerase activity" EXACT [EC:5.3.2.1]
+synonym: "phenylpyruvate keto-enol-isomerase activity" EXACT [EC:5.3.2.1]
+synonym: "phenylpyruvic keto--enol isomerase activity" EXACT [EC:5.3.2.1]
xref: EC:5.3.2.1
xref: MetaCyc:PHENYLPYRUVATE-TAUTOMERASE-RXN
xref: RHEA:17097
@@ -296029,7 +296064,7 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0050180
name: phloretin hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + phloretin = H(+) + phloretate + phloroglucinol." [EC:3.7.1.4, RHEA:23396]
+def: "Catalysis of the reaction: H2O + phloretin = H+ + phloretate + phloroglucinol." [EC:3.7.1.4, RHEA:23396]
synonym: "2',4,4',6'-tetrahydroxydehydrochalcone 1,3,5-trihydroxybenzenehydrolase activity" RELATED [EC:3.7.1.4]
synonym: "lactase-phlorizin hydrolase" BROAD [EC:3.7.1.4]
xref: EC:3.7.1.4
@@ -296042,7 +296077,7 @@ is_a: GO:0016823 ! hydrolase activity, acting on acid carbon-carbon bonds, in ke
id: GO:0050181
name: phorbol-diester hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + phorbol 12,13-dibutanoate = butanoate + H(+) + phorbol 13-butanoate." [EC:3.1.1.51, RHEA:21316]
+def: "Catalysis of the reaction: H2O + phorbol 12,13-dibutanoate = butanoate + H+ + phorbol 13-butanoate." [EC:3.1.1.51, RHEA:21316]
synonym: "12,13-diacylphorbate 12-acylhydrolase activity" RELATED [EC:3.1.1.51]
synonym: "diacylphorbate 12-hydrolase activity" RELATED [EC:3.1.1.51]
synonym: "PDEH" RELATED [EC:3.1.1.51]
@@ -296070,7 +296105,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0050183
name: phosphatidylcholine 12-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine + H(+) + NADH + O(2) = 1-acyl-2-[(S)-12-hydroxyoleoyl]-sn-glycero-3-phosphocholine + H(2)O + NAD(+)." [RHEA:46360]
+def: "Catalysis of the reaction: 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine + H+ + NADH + O2 = 1-acyl-2-[(S)-12-hydroxyoleoyl]-sn-glycero-3-phosphocholine + H2O + NAD+." [RHEA:46360]
synonym: "1-acyl-2-oleoyl-sn-glycero-3-phosphocholine,NADH:oxygen oxidoreductase (12-hydroxylating)" RELATED [EC:1.14.18.4]
synonym: "oleate D12-hydroxylase activity" EXACT []
synonym: "oleate Delta(12)-hydroxylase activity" RELATED [EC:1.14.18.4]
@@ -296087,7 +296122,17 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050184
name: phosphatidylcholine desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine + NAD(+) = 1-acyl-2-linoleoyl-sn-glycero-3-phosphocholine + H(+) + NADH." [RHEA:12564]
+alt_id: GO:0102855
+alt_id: GO:0102857
+alt_id: GO:0102860
+alt_id: GO:0102861
+alt_id: GO:0102871
+def: "Catalysis of the reaction: An oleoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a linoleoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O." [GOC:curators]
+synonym: "1-16:0-2-18:1-phosphatidylcholine desaturase activity" NARROW []
+synonym: "1-18:1-2-18:2-phosphatidylcholine desaturase activity" NARROW []
+synonym: "1-18:1-2-18:2-phosphatidylcholine synthase activity" NARROW []
+synonym: "1-18:1-2-18:3-phosphatidylcholinedesaturase activity" NARROW []
+synonym: "1-18:2-2-18:1-phosphatidylcholine desaturase activity (SN2-18:2 forming)" NARROW []
synonym: "1-acyl-2-oleoyl-sn-glycero-3-phosphocholine:NAD+ delta12-oxidoreductase activity" RELATED []
synonym: "acyl-lipid omega-6 desaturase (cytochrome b5)" RELATED [EC:1.14.19.22]
synonym: "linoleate synthase activity" RELATED [EC:1.14.19.22]
@@ -296097,14 +296142,14 @@ synonym: "oleoylphosphatidylcholine desaturase activity" RELATED []
xref: EC:1.14.19.22
xref: KEGG_REACTION:R03475
xref: MetaCyc:PHOSPHATIDYLCHOLINE-DESATURASE-RXN
-xref: RHEA:12564
-is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
+xref: RHEA:46332
+is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
[Term]
id: GO:0050185
name: phosphatidylinositol deacylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + H(2)O = 1-acyl-sn-glycero-3-phospho-D-myo-inositol + a carboxylate + H(+)." [EC:3.1.1.52, RHEA:18001]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + H2O = 1-acyl-sn-glycero-3-phospho-D-myo-inositol + a carboxylate + H+." [EC:3.1.1.52, RHEA:18001]
synonym: "1-phosphatidyl-D-myo-inositol 2-acylhydrolase activity" RELATED [EC:3.1.1.52]
synonym: "phosphatidylinositol phospholipase A2 activity" RELATED [EC:3.1.1.52]
xref: EC:3.1.1.52
@@ -296132,7 +296177,7 @@ is_a: GO:0016819 ! hydrolase activity, acting on acid anhydrides, in sulfonyl-co
id: GO:0050187
name: phosphoamidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-phosphocreatine + H(2)O = creatine + phosphate." [EC:3.9.1.1, RHEA:12977]
+def: "Catalysis of the reaction: N-phosphocreatine + H2O = creatine + phosphate." [EC:3.9.1.1, RHEA:12977]
synonym: "creatine phosphatase activity" RELATED [EC:3.9.1.1]
synonym: "phosphamide hydrolase activity" RELATED [EC:3.9.1.1]
xref: EC:3.9.1.1
@@ -296162,7 +296207,7 @@ is_a: GO:0016868 ! intramolecular transferase activity, phosphotransferases
id: GO:0050189
name: phosphoenolpyruvate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + phosphoenolpyruvate = phosphate + pyruvate." [EC:3.1.3.60, RHEA:19997]
+def: "Catalysis of the reaction: H2O + phosphoenolpyruvate = phosphate + pyruvate." [EC:3.1.3.60, RHEA:19997]
synonym: "PEP phosphatase activity" RELATED [EC:3.1.3.60]
synonym: "phosphoenolpyruvate phosphohydrolase activity" RELATED [EC:3.1.3.60]
xref: EC:3.1.3.60
@@ -296175,7 +296220,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0050190
name: phosphoglucokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: alpha-D-glucose 1-phosphate + ATP = alpha-D-glucose 1,6-bisphosphate + ADP + 2 H(+)." [EC:2.7.1.10, RHEA:13377]
+def: "Catalysis of the reaction: alpha-D-glucose 1-phosphate + ATP = alpha-D-glucose 1,6-bisphosphate + ADP + 2 H+." [EC:2.7.1.10, RHEA:13377]
synonym: "ATP:alpha-D-glucose-1-phosphate 6-phosphotransferase activity" RELATED [EC:2.7.1.10]
synonym: "ATP:D-glucose-1-phosphate 6-phosphotransferase activity" RELATED [EC:2.7.1.10]
synonym: "glucose-phosphate kinase activity" RELATED [EC:2.7.1.10]
@@ -296191,7 +296236,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0050191
name: phosphoglycerate kinase (GTP) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-phospho-D-glycerate + GTP = 3-phospho-D-glyceroyl phosphate + GDP + H(+)." [EC:2.7.2.10, RHEA:23332]
+def: "Catalysis of the reaction: 3-phospho-D-glycerate + GTP = 3-phospho-D-glyceroyl phosphate + GDP + H+." [EC:2.7.2.10, RHEA:23332]
synonym: "GTP:3-phospho-D-glycerate 1-phosphotransferase activity" RELATED [EC:2.7.2.10]
xref: EC:2.7.2.10
xref: KEGG_REACTION:R01517
@@ -296204,7 +296249,7 @@ is_a: GO:0016774 ! phosphotransferase activity, carboxyl group as acceptor
id: GO:0050192
name: phosphoglycerate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-phospho-D-glycerate + H(2)O = D-glycerate + phosphate." [EC:3.1.3.20, RHEA:21156]
+def: "Catalysis of the reaction: 2-phospho-D-glycerate + H2O = D-glycerate + phosphate." [EC:3.1.3.20, RHEA:21156]
synonym: "D-2-phosphoglycerate phosphatase activity" RELATED [EC:3.1.3.20]
synonym: "D-glycerate-2-phosphate phosphohydrolase activity" RELATED [EC:3.1.3.20]
synonym: "glycerophosphate phosphatase activity" RELATED [EC:3.1.3.20]
@@ -296231,7 +296276,7 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0050194
name: phosphonoacetaldehyde hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + phosphonoacetaldehyde = acetaldehyde + H(+) + phosphate." [EC:3.11.1.1, RHEA:18905]
+def: "Catalysis of the reaction: H2O + phosphonoacetaldehyde = acetaldehyde + H+ + phosphate." [EC:3.11.1.1, RHEA:18905]
synonym: "2-oxoethylphosphonate phosphonohydrolase activity" RELATED [EC:3.11.1.1]
synonym: "2-phosphonoacetylaldehyde phosphonohydrolase activity" RELATED [EC:3.11.1.1]
synonym: "phosphonatase activity" RELATED [EC:3.11.1.1]
@@ -296246,7 +296291,7 @@ is_a: GO:0016827 ! hydrolase activity, acting on acid carbon-phosphorus bonds
id: GO:0050195
name: phosphoribokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-ribose 5-phosphate + ATP = D-ribose 1,5-diphosphate + ADP + 2 H(+)." [EC:2.7.1.18, RHEA:21216]
+def: "Catalysis of the reaction: D-ribose 5-phosphate + ATP = D-ribose 1,5-diphosphate + ADP + 2 H+." [EC:2.7.1.18, RHEA:21216]
synonym: "ATP:D-ribose-5-phosphate 1-phosphotransferase activity" RELATED [EC:2.7.1.18]
synonym: "phosphoribokinase (phosphorylating)" RELATED [EC:2.7.1.18]
xref: EC:2.7.1.18
@@ -296276,7 +296321,7 @@ is_a: GO:0004721 ! phosphoprotein phosphatase activity
id: GO:0050197
name: phytanate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + CoA + phytanate = AMP + diphosphate + H(+) + phytanoyl-CoA." [EC:6.2.1.24, RHEA:21380]
+def: "Catalysis of the reaction: ATP + CoA + phytanate = AMP + diphosphate + H+ + phytanoyl-CoA." [EC:6.2.1.24, RHEA:21380]
synonym: "phytanate:CoA ligase (AMP-forming)" RELATED [EC:6.2.1.24]
synonym: "phytanoyl-CoA ligase activity" RELATED [EC:6.2.1.24]
xref: EC:6.2.1.24
@@ -296291,7 +296336,7 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0050198
name: pinosylvin synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: trans-cinnamoyl-CoA + 3 H(+) + 3 malonyl-CoA = 4 CO(2) + 4 CoA + pinosylvin." [EC:2.3.1.146, RHEA:12552]
+def: "Catalysis of the reaction: trans-cinnamoyl-CoA + 3 H+ + 3 malonyl-CoA = 4 CO2 + 4 CoA + pinosylvin." [EC:2.3.1.146, RHEA:12552]
synonym: "malonyl-CoA:cinnamoyl-CoA malonyltransferase (cyclizing)" RELATED [EC:2.3.1.146]
synonym: "pine stilbene synthase activity" RELATED [EC:2.3.1.146]
synonym: "stilbene synthase activity" BROAD [EC:2.3.1.146]
@@ -296305,7 +296350,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0050199
name: piperidine N-piperoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (E,E)-piperoyl-CoA + piperidine = N-[(E,E)-piperoyl]piperidine + CoA + H(+)." [EC:2.3.1.145, RHEA:14561]
+def: "Catalysis of the reaction: (E,E)-piperoyl-CoA + piperidine = N-[(E,E)-piperoyl]piperidine + CoA + H+." [EC:2.3.1.145, RHEA:14561]
synonym: "(E,E)-piperoyl-CoA:piperidine N-piperoyltransferase activity" RELATED [EC:2.3.1.145]
synonym: "piperidine piperoyltransferase activity" RELATED [EC:2.3.1.145]
synonym: "piperoyl-CoA:piperidine N-piperoyltransferase activity" RELATED [EC:2.3.1.145]
@@ -296332,7 +296377,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0050201
name: fucokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-fucose + ATP = beta-L-fucose 1-phosphate + ADP + 2 H(+)." [EC:2.7.1.52, RHEA:13241]
+def: "Catalysis of the reaction: L-fucose + ATP = beta-L-fucose 1-phosphate + ADP + 2 H+." [EC:2.7.1.52, RHEA:13241]
synonym: "ATP:6-deoxy-L-galactose 1-phosphotransferase activity" RELATED [EC:2.7.1.52]
synonym: "ATP:beta-L-fucose 1-phosphotransferase activity" RELATED [EC:2.7.1.52]
synonym: "fucokinase (phosphorylating) activity" RELATED [EC:2.7.1.52]
@@ -296351,7 +296396,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0050202
name: octopamine dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-(4-hydroxyphenyl)-2-aminoethanol = (4-hydroxyphenyl)acetaldehyde + NH(4)(+)." [EC:4.2.1.87, RHEA:18173]
+def: "Catalysis of the reaction: 1-(4-hydroxyphenyl)-2-aminoethanol = (4-hydroxyphenyl)acetaldehyde + NH4." [EC:4.2.1.87, RHEA:18173]
synonym: "octopamine hydro-lyase (deaminating)" RELATED [EC:4.2.1.87]
synonym: "octopamine hydro-lyase [deaminating; (4-hydroxyphenyl)acetaldehyde-forming]" RELATED [EC:4.2.1.87]
synonym: "octopamine hydrolyase activity" RELATED [EC:4.2.1.87]
@@ -296365,7 +296410,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0050203
name: oxalate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + CoA + oxalate = AMP + diphosphate + H(+) + oxalyl-CoA." [RHEA:18293]
+def: "Catalysis of the reaction: ATP + CoA + oxalate = AMP + diphosphate + H+ + oxalyl-CoA." [RHEA:18293]
synonym: "oxalate:CoA ligase (AMP-forming)" RELATED [EC:6.2.1.8]
synonym: "oxalyl coenzyme A synthetase activity" RELATED [EC:6.2.1.8]
synonym: "oxalyl-CoA synthetase activity" RELATED [EC:6.2.1.8]
@@ -296423,18 +296468,16 @@ is_a: GO:0016769 ! transferase activity, transferring nitrogenous groups
id: GO:0050207
name: plasmanylethanolamine desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O-1-alkyl-2-acyl-sn-glycero-3-phosphoethanolamine + donor-H2 + O2 = O-1-alk-1-enyl-2-acyl-sn-glycero-3-phosphoethanolamine + acceptor + 2 H2O." [RHEA:22956]
-synonym: "1-O-alkyl 2-acyl-sn-glycero-3-phosphorylethanolamine desaturase activity" RELATED [EC:1.14.99.19]
-synonym: "1-O-alkyl-2-acyl-sn-glycero-3-phosphorylethanolamine desaturase activity" RELATED [EC:1.14.99.19]
-synonym: "alkylacylglycero-phosphorylethanolamine dehydrogenase activity" RELATED [EC:1.14.99.19]
-synonym: "alkylacylglycerophosphoethanolamine desaturase activity" RELATED [EC:1.14.99.19]
-synonym: "dehydrogenase, alkyl-acylglycerophosphorylethanolamine" RELATED [EC:1.14.99.19]
-synonym: "O-1-alkyl-2-acyl-sn-glycero-3-phosphoethanolamine,hydrogen-donor:oxygen oxidoreductase activity" RELATED [EC:1.14.99.19]
+def: "Catalysis of the reaction:1-(1,2-saturated alkyl)-2-acyl-sn-glycero-3-phosphoethanolamine + 2 Fe(II)-[cytochrome b5] + 2 H+ + O2 = 1-O-(1Z-alkenyl)-2-acyl-sn-glycero-3-phosphoethanolamine + 2 Fe(III)-[cytochrome b5] + 2 H2O." [RHEA:22956]
+synonym: "2-acyl-1-alkyl-sn-glycero-3-phosphoethanolamine desaturase activity" RELATED [EC:1.14.19.77]
+synonym: "alkylacylglycero-phosphorylethanolamine dehydrogenase activity" RELATED [EC:1.14.19.77]
+synonym: "alkylacylglycerophosphoethanolamine desaturase activity" RELATED [EC:1.14.19.77]
synonym: "plasmenylethanolamine desaturase activity" EXACT []
xref: EC:1.14.19.77
xref: MetaCyc:PLASMANYLETHANOLAMINE-DESATURASE-RXN
xref: RHEA:22956
-is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
+is_a: GO:0051213 ! dioxygenase activity
[Term]
id: GO:0050208
@@ -296499,7 +296542,7 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
id: GO:0050212
name: progesterone 11-alpha-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + O(2) + progesterone = 11alpha-hydroxyprogesterone + A + H(2)O." [EC:1.14.99.14, RHEA:18205]
+def: "Catalysis of the reaction: AH(2) + O2 + progesterone = 11alpha-hydroxyprogesterone + A + H2O." [EC:1.14.99.14, RHEA:18205]
synonym: "progesterone 11-alpha-hydroxylase activity" RELATED [EC:1.14.99.14]
synonym: "progesterone 11a-monooxygenase activity" EXACT []
synonym: "progesterone 11alpha-hydroxylase activity" RELATED [EC:1.14.99.14]
@@ -296531,7 +296574,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0050214
name: progesterone monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + O(2) + progesterone = A + H(2)O + testosterone acetate." [EC:1.14.99.4, RHEA:11984]
+def: "Catalysis of the reaction: AH(2) + O2 + progesterone = A + H2O + testosterone acetate." [EC:1.14.99.4, RHEA:11984]
synonym: "progesterone hydroxylase activity" RELATED [EC:1.14.99.4]
synonym: "progesterone,hydrogen-donor:oxygen oxidoreductase (hydroxylating)" RELATED [EC:1.14.99.4]
xref: EC:1.14.99.4
@@ -296545,7 +296588,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050215
name: propanediol dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: propane-1,2-diol = H(2)O + propanal." [EC:4.2.1.28, RHEA:14569]
+def: "Catalysis of the reaction: propane-1,2-diol = H2O + propanal." [EC:4.2.1.28, RHEA:14569]
synonym: "1,2-propanediol dehydratase activity" RELATED [EC:4.2.1.28]
synonym: "adenosylcobalamin-dependent diol dehydratase activity" RELATED [EC:4.2.1.28]
synonym: "coenzyme B12-dependent diol dehydrase activity" RELATED [EC:4.2.1.28]
@@ -296567,7 +296610,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0050216
name: propanediol-phosphate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD(+) + propane-1,2-diol 1-phosphate = H(+) + hydroxyacetone phosphate + NADH." [EC:1.1.1.7, RHEA:21584]
+def: "Catalysis of the reaction: NAD+ + propane-1,2-diol 1-phosphate = H+ + hydroxyacetone phosphate + NADH." [EC:1.1.1.7, RHEA:21584]
xref: EC:1.1.1.7
xref: KEGG_REACTION:R04236
xref: MetaCyc:PROPANEDIOL-PHOSPHATE-DEHYDROGENASE-RXN
@@ -296605,7 +296648,7 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0050219
name: prostaglandin-A1 delta-isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: prostaglandin A1 = prostaglandin C1." [EC:5.3.3.9, RHEA:10460]
+def: "Catalysis of the reaction: prostaglandin A1 = prostaglandin C1." [RHEA:10460]
synonym: "(13E)-(15S)-15-hydroxy-9-oxoprosta-10,13-dienoate delta10-delta11-isomerase activity" RELATED [EC:5.3.3.9]
synonym: "prostaglandin A isomerase activity" RELATED [EC:5.3.3.9]
synonym: "prostaglandin-A1 D-isomerase activity" EXACT []
@@ -296670,7 +296713,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050223
name: protocatechuate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3,4-dihydroxybenzoate + H(+) = catechol + CO(2)." [EC:4.1.1.63, RHEA:22416]
+def: "Catalysis of the reaction: 3,4-dihydroxybenzoate + H+ = catechol + CO2." [EC:4.1.1.63, RHEA:22416]
synonym: "3,4-dihydrobenzoate decarboxylase activity" RELATED [EC:4.1.1.63]
synonym: "3,4-dihydroxybenzoate carboxy-lyase (catechol-forming)" RELATED [EC:4.1.1.63]
synonym: "3,4-dihydroxybenzoate decarboxylase activity" RELATED [EC:4.1.1.63]
@@ -296685,7 +296728,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0050224
name: prunasin beta-glucosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-prunasin + H(2)O = D-glucose + mandelonitrile." [EC:3.2.1.118, RHEA:16489]
+def: "Catalysis of the reaction: (R)-prunasin + H2O = D-glucose + mandelonitrile." [EC:3.2.1.118, RHEA:16489]
synonym: "prunasin b-glucosidase activity" EXACT []
synonym: "prunasin beta-D-glucohydrolase activity" RELATED [EC:3.2.1.118]
synonym: "prunasin hydrolase activity" RELATED [EC:3.2.1.118]
@@ -296699,7 +296742,7 @@ is_a: GO:0008422 ! beta-glucosidase activity
id: GO:0050225
name: pseudouridine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + pseudouridine = ADP + 2 H(+) + pseudouridine 5'-phosphate." [EC:2.7.1.83, RHEA:22448]
+def: "Catalysis of the reaction: ATP + pseudouridine = ADP + 2 H+ + pseudouridine 5'-phosphate." [EC:2.7.1.83, RHEA:22448]
synonym: "ATP:pseudouridine 5'-phosphotransferase activity" RELATED [EC:2.7.1.83]
synonym: "pseudouridine kinase (phosphorylating)" RELATED [EC:2.7.1.83]
xref: EC:2.7.1.83
@@ -296749,15 +296792,17 @@ is_a: GO:0019239 ! deaminase activity
[Term]
id: GO:0050229
-name: pterocarpin synthase activity
+name: obsolete pterocarpin synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: medicarpin + NADP+ = vestitone + NADPH." [EC:1.1.1.246, MetaCyc:PTEROCARPIN-SYNTHASE-RXN]
+def: "OBSOLETE. Catalysis of the reaction: medicarpin + NADP+ = vestitone + NADPH." [EC:1.1.1.246, MetaCyc:PTEROCARPIN-SYNTHASE-RXN]
+comment: The reaction has been deleted as it is the result of the activity of two\n separate enzymes: vestitone reductase (EC 1.1.1.348 and medicarpin synthase\nEC 4.2.1.139.
synonym: "medicarpin:NADP+ 2'-oxidoreductase activity" RELATED [EC:1.1.1.246]
synonym: "pterocarpan synthase activity" RELATED [EC:1.1.1.246]
xref: EC:1.1.1.246
xref: MetaCyc:PTEROCARPIN-SYNTHASE-RXN
-xref: RHEA:13533
-is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+is_obsolete: true
+consider: GO:0140859
+consider: GO:0140860
[Term]
id: GO:0050230
@@ -296776,7 +296821,7 @@ is_a: GO:0016842 ! amidine-lyase activity
id: GO:0050231
name: putrescine carbamoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: carbamoyl phosphate + putrescine = N-carbamoylputrescine + H(+) + phosphate." [EC:2.1.3.6, RHEA:21936]
+def: "Catalysis of the reaction: carbamoyl phosphate + putrescine = N-carbamoylputrescine + H+ + phosphate." [EC:2.1.3.6, RHEA:21936]
synonym: "carbamoyl-phosphate:putrescine carbamoyltransferase activity" RELATED [EC:2.1.3.6]
synonym: "PTCase activity" RELATED [EC:2.1.3.6]
synonym: "putrescine synthase activity" RELATED [EC:2.1.3.6]
@@ -296796,13 +296841,13 @@ synonym: "putrescine:oxygen oxidoreductase (deaminating)" RELATED [EC:1.4.3.10]
xref: EC:1.4.3.10
xref: MetaCyc:PUTRESCINE-OXIDASE-RXN
xref: RHEA:18273
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+is_a: GO:0052597 ! diamine oxidase activity
[Term]
id: GO:0050233
name: pyranose oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glucose + O(2) = 2-dehydro-D-glucose + H(2)O(2)." [EC:1.1.3.10, RHEA:10552]
+def: "Catalysis of the reaction: D-glucose + O2 = 2-dehydro-D-glucose + H2O2." [EC:1.1.3.10, RHEA:10552]
synonym: "glucose 2-oxidase activity" RELATED [EC:1.1.3.10]
synonym: "pyranose-2-oxidase activity" RELATED [EC:1.1.3.10]
synonym: "pyranose:oxygen 2-oxidoreductase activity" RELATED [EC:1.1.3.10]
@@ -296816,7 +296861,7 @@ is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050234
name: pyrazolylalanine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-serine + pyrazole = 3-(pyrazol-1-yl)-L-alanine + H(2)O." [EC:4.2.1.50, RHEA:24512]
+def: "Catalysis of the reaction: L-serine + pyrazole = 3-(pyrazol-1-yl)-L-alanine + H2O." [EC:4.2.1.50, RHEA:24512]
synonym: "beta-pyrazolylalaninase activity" RELATED [EC:4.2.1.50]
synonym: "L-serine hydro-lyase (adding pyrazole)" RELATED [EC:4.2.1.50]
synonym: "L-serine hydro-lyase [adding pyrazole; 3-(pyrazol-1-yl)-L-alanine-forming]" RELATED [EC:4.2.1.50]
@@ -296830,7 +296875,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0050235
name: pyridoxal 4-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD(+) + pyridoxal = 4-pyridoxolactone + H(+) + NADH." [EC:1.1.1.107, RHEA:21336]
+def: "Catalysis of the reaction: NAD+ + pyridoxal = 4-pyridoxolactone + H+ + NADH." [EC:1.1.1.107, RHEA:21336]
synonym: "pyridoxal dehydrogenase activity" RELATED [EC:1.1.1.107]
synonym: "pyridoxal:NAD+ 4-oxidoreductase activity" RELATED [EC:1.1.1.107]
xref: EC:1.1.1.107
@@ -296843,7 +296888,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050236
name: pyridoxine:NADP 4-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + pyridoxine = H(+) + NADPH + pyridoxal." [EC:1.1.1.65, RHEA:16129]
+def: "Catalysis of the reaction: NADP+ + pyridoxine = H+ + NADPH + pyridoxal." [EC:1.1.1.65, RHEA:16129]
synonym: "PL reductase activity" RELATED [EC:1.1.1.65]
synonym: "pyridoxal reductase activity" RELATED [EC:1.1.1.65]
synonym: "pyridoxin dehydrogenase activity" RELATED [EC:1.1.1.65]
@@ -296901,7 +296946,7 @@ is_a: GO:0019239 ! deaminase activity
id: GO:0050240
name: pyrogallol 1,2-oxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O(2) + pyrogallol = (Z)-5-oxohex-2-enedioate + 2 H(+)." [EC:1.13.11.35, RHEA:19673]
+def: "Catalysis of the reaction: O2 + pyrogallol = (Z)-5-oxohex-2-enedioate + 2 H+." [EC:1.13.11.35, RHEA:19673]
synonym: "1,2,3-trihydroxybenzene:oxygen 1,2-oxidoreductase (decyclizing)" RELATED [EC:1.13.11.35]
synonym: "pyrogallol 1,2-dioxygenase activity" RELATED [EC:1.13.11.35]
xref: EC:1.13.11.35
@@ -296925,7 +296970,7 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0050242
name: pyruvate, phosphate dikinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + phosphate + pyruvate = AMP + diphosphate + 2 H(+) + phosphoenolpyruvate." [EC:2.7.9.1, RHEA:10756]
+def: "Catalysis of the reaction: ATP + phosphate + pyruvate = AMP + diphosphate + 2 H+ + phosphoenolpyruvate." [EC:2.7.9.1, RHEA:10756]
synonym: "ATP:pyruvate, phosphate phosphotransferase activity" RELATED [EC:2.7.9.1]
synonym: "orthophosphate dikinase pyruvate" RELATED [EC:2.7.9.1]
synonym: "PPDK" RELATED [EC:2.7.9.1]
@@ -296948,7 +296993,7 @@ is_a: GO:0016781 ! phosphotransferase activity, paired acceptors
id: GO:0050243
name: pyruvate dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: CoA + NADP(+) + pyruvate = acetyl-CoA + CO(2) + NADPH." [EC:1.2.1.51, RHEA:17425]
+def: "Catalysis of the reaction: CoA + NADP+ + pyruvate = acetyl-CoA + CO2 + NADPH." [EC:1.2.1.51, RHEA:17425]
synonym: "pyruvate:NADP(+) oxidoreductase activity" RELATED [EC:1.2.1.51]
synonym: "pyruvate:NADP+ 2-oxidoreductase (CoA-acetylating)" RELATED [EC:1.2.1.51]
synonym: "pyruvate:NADP+ oxidoreductase activity" RELATED [EC:1.2.1.51]
@@ -296962,7 +297007,7 @@ is_a: GO:0034603 ! pyruvate dehydrogenase [NAD(P)+] activity
id: GO:0050244
name: pyruvate oxidase (CoA-acetylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: CoA + H(+) + O(2) + pyruvate = acetyl-CoA + CO(2) + H(2)O(2)." [EC:1.2.3.6, RHEA:21912]
+def: "Catalysis of the reaction: CoA + H+ + O2 + pyruvate = acetyl-CoA + CO2 + H2O2." [EC:1.2.3.6, RHEA:21912]
synonym: "pyruvate:oxygen 2-oxidoreductase (CoA-acetylating)" RELATED [EC:1.2.3.6]
xref: EC:1.2.3.6
xref: KEGG_REACTION:R00211
@@ -296974,7 +297019,7 @@ is_a: GO:0016623 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0050245
name: quercitrinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + quercitrin = L-rhamnose + quercetin." [EC:3.2.1.66, RHEA:17465]
+def: "Catalysis of the reaction: H2O + quercitrin = L-rhamnose + quercetin." [EC:3.2.1.66, RHEA:17465]
synonym: "quercitrin 3-L-rhamnohydrolase activity" RELATED [EC:3.2.1.66]
xref: EC:3.2.1.66
xref: KEGG_REACTION:R02436
@@ -296986,7 +297031,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0050246
name: questin monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADPH + O(2) + questin = demethylsulochrin + NADP(+)." [EC:1.14.13.43, RHEA:10836]
+def: "Catalysis of the reaction: H+ + NADPH + O2 + questin = demethylsulochrin + NADP+." [EC:1.14.13.43, RHEA:10836]
synonym: "questin oxygenase activity" RELATED [EC:1.14.13.43]
synonym: "questin,NADPH:oxygen oxidoreductase (hydroxylating, anthraquinone-ring-opening)" RELATED [EC:1.14.13.43]
xref: EC:1.14.13.43
@@ -296999,7 +297044,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050247
name: raucaffricine beta-glucosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + raucaffricine = D-glucose + vomilenine." [EC:3.2.1.125, RHEA:14557]
+def: "Catalysis of the reaction: H2O + raucaffricine = D-glucose + vomilenine." [EC:3.2.1.125, RHEA:14557]
synonym: "raucaffricine b-glucosidase activity" EXACT []
synonym: "raucaffricine beta-D-glucohydrolase activity" RELATED [EC:3.2.1.125]
synonym: "raucaffricine beta-D-glucosidase activity" RELATED [EC:3.2.1.125]
@@ -297030,7 +297075,7 @@ is_a: GO:0045289 ! luciferin monooxygenase activity
id: GO:0050249
name: Renilla-luciferin sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + Renilla luciferin = adenosine 3',5'-diphosphate + H(+) + luciferyl sulfate." [EC:2.8.2.10, RHEA:20481]
+def: "Catalysis of the reaction: 3'-phospho-5'-adenylyl sulfate + Renilla luciferin = adenosine 3',5'-diphosphate + H+ + luciferyl sulfate." [EC:2.8.2.10, RHEA:20481]
synonym: "3'-phosphoadenylyl-sulfate:Renilla luciferin sulfotransferase activity" RELATED [EC:2.8.2.10]
synonym: "luciferin sulfokinase (3'-phosphoadenylyl sulfate:luciferin sulfotransferase)" RELATED [EC:2.8.2.10]
synonym: "luciferin sulfokinase activity" RELATED [EC:2.8.2.10]
@@ -297042,18 +297087,6 @@ xref: MetaCyc:RENILLA-LUCIFERIN-SULFOTRANSFERASE-RXN
xref: RHEA:20481
is_a: GO:0008146 ! sulfotransferase activity
-[Term]
-id: GO:0050250
-name: retinal oxidase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: retinal + O2 + H2O = retinoate + H2O2." [EC:1.2.3.11, MetaCyc:RETINAL-OXIDASE-RXN]
-synonym: "retinal:oxygen oxidoreductase activity" RELATED [EC:1.2.3.11]
-synonym: "retinene oxidase activity" RELATED [EC:1.2.3.11]
-xref: EC:1.2.3.11
-xref: MetaCyc:RETINAL-OXIDASE-RXN
-xref: RHEA:22520
-is_a: GO:0016623 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, oxygen as acceptor
-
[Term]
id: GO:0050251
name: retinol isomerase activity
@@ -297087,11 +297120,10 @@ id: GO:0050253
name: retinyl-palmitate esterase activity
namespace: molecular_function
def: "Catalysis of the reaction: retinyl palmitate + H2O = retinol + palmitate + H+." [RHEA:21508]
-synonym: "retinyl ester hydrolase activity" RELATED [EC:3.1.1.21]
-synonym: "retinyl palmitate hydrolase activity" RELATED [EC:3.1.1.21]
-synonym: "retinyl palmitate hydrolyase activity" RELATED [EC:3.1.1.21]
-synonym: "retinyl-palmitate palmitohydrolase activity" RELATED [EC:3.1.1.21]
-xref: EC:3.1.1.21
+synonym: "retinyl ester hydrolase activity" RELATED []
+synonym: "retinyl palmitate hydrolase activity" RELATED []
+synonym: "retinyl palmitate hydrolyase activity" RELATED []
+synonym: "retinyl-palmitate palmitohydrolase activity" RELATED []
xref: KEGG_REACTION:R02368
xref: MetaCyc:RETINYL-PALMITATE-ESTERASE-RXN
xref: Reactome:R-HSA-2404133 "A REH hydrolses atREs to atROL and FAs"
@@ -297105,29 +297137,23 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050254
name: rhodopsin kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + rhodopsin = ADP + phosphorhodopsin." [EC:2.7.11.14, MetaCyc:RHODOPSIN-KINASE-RXN]
-synonym: "ATP:rhodopsin phosphotransferase activity" RELATED [EC:2.7.11.14]
+def: "Catalysis of the reaction: ATP + rhodopsin = ADP + phosphorhodopsin." [PMID:14654303]
synonym: "cone opsin kinase activity" NARROW [EC:2.7.11.14]
-synonym: "G-protein-coupled receptor kinase 1 activity" NARROW [EC:2.7.11.14]
synonym: "GPCR kinase 1 activity" NARROW [EC:2.7.11.14]
-synonym: "GRK1" RELATED [EC:2.7.11.14]
-synonym: "GRK7" RELATED [EC:2.7.11.14]
synonym: "opsin kinase (phosphorylating) activity" RELATED [EC:2.7.11.14]
synonym: "opsin kinase activity" RELATED [EC:2.7.11.14]
-synonym: "rhodopsin kinase (phosphorylating) activity" RELATED [EC:2.7.11.14]
-synonym: "RK" RELATED [EC:2.7.11.14]
-synonym: "STK14" RELATED [EC:2.7.11.14]
+synonym: "rhodopsin kinase (phosphorylating) activity" EXACT [EC:2.7.11.14]
xref: EC:2.7.11.14
xref: MetaCyc:2.7.11.14-RXN
xref: Reactome:R-HSA-2581474 "GRK1,4,7 phosphorylate MII to p-MII"
xref: RHEA:23356
-is_a: GO:0004672 ! protein kinase activity
+is_a: GO:0004703 ! G protein-coupled receptor kinase activity
[Term]
id: GO:0050255
name: ribitol 2-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-ribitol + NAD(+) = D-ribulose + H(+) + NADH." [EC:1.1.1.56, RHEA:20053]
+def: "Catalysis of the reaction: D-ribitol + NAD+ = D-ribulose + H+ + NADH." [EC:1.1.1.56, RHEA:20053]
synonym: "adonitol dehydrogenase activity" RELATED [EC:1.1.1.56]
synonym: "ribitol dehydrogenase A (wild type)" RELATED [EC:1.1.1.56]
synonym: "ribitol dehydrogenase B (mutant enzyme with different properties)" RELATED [EC:1.1.1.56]
@@ -297170,7 +297196,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0050258
name: riboflavinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + H(+) + riboflavin = D-ribitol + lumichrome." [EC:3.5.99.1, RHEA:11408]
+def: "Catalysis of the reaction: H2O + H+ + riboflavin = D-ribitol + lumichrome." [EC:3.5.99.1, RHEA:11408]
synonym: "riboflavin hydrolase activity" RELATED [EC:3.5.99.1]
xref: EC:3.5.99.1
xref: KEGG_REACTION:R01732
@@ -297182,7 +297208,7 @@ is_a: GO:0016810 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050259
name: ribose 1-dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + NADP(+) + ribofuranose = D-ribonate + 2 H(+) + NADPH." [EC:1.1.1.115, RHEA:11676]
+def: "Catalysis of the reaction: H2O + NADP+ + ribofuranose = D-ribonate + 2 H+ + NADPH." [EC:1.1.1.115, RHEA:11676]
synonym: "D-ribose dehydrogenase (NADP+)" RELATED [EC:1.1.1.115]
synonym: "D-ribose:NADP+ 1-oxidoreductase activity" RELATED [EC:1.1.1.115]
synonym: "NADP-pentose-dehydrogenase activity" RELATED [EC:1.1.1.115]
@@ -297196,7 +297222,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050260
name: ribose-5-phosphate-ammonia ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-ribose 5-phosphate + ATP + NH(4)(+) = 5-phospho-D-ribosylamine + ADP + 2 H(+) + phosphate." [EC:6.3.4.7, RHEA:13777]
+def: "Catalysis of the reaction: D-ribose 5-phosphate + ATP + NH4 = 5-phospho-D-ribosylamine + ADP + 2 H+ + phosphate." [EC:6.3.4.7, RHEA:13777]
synonym: "5-phosphoribosylamine synthetase activity" RELATED [EC:6.3.4.7]
synonym: "ammonia-ribose 5-phosphate aminotransferase activity" RELATED [EC:6.3.4.7]
synonym: "ribose 5-phosphate aminotransferase activity" RELATED [EC:6.3.4.7]
@@ -297226,7 +297252,7 @@ id: GO:0050262
name: ribosylnicotinamide kinase activity
namespace: molecular_function
alt_id: GO:0000816
-def: "Catalysis of the reaction: N-ribosylnicotinamide + ATP = ADP + 2 H(+) + nicotinamide mononucleotide." [EC:2.7.1.22, PMID:17914902, RHEA:14017]
+def: "Catalysis of the reaction: N-ribosylnicotinamide + ATP = ADP + 2 H+ + nicotinamide mononucleotide." [EC:2.7.1.22, PMID:17914902, RHEA:14017]
synonym: "ATP:N-ribosylnicotinamide 5'-phosphotransferase activity" RELATED [EC:2.7.1.22]
synonym: "nicotinamide riboside kinase activity" EXACT [PMID:15137942]
synonym: "ribosylnicotinamide kinase (phosphorylating)" RELATED [EC:2.7.1.22]
@@ -297260,7 +297286,7 @@ is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
id: GO:0050264
name: rifamycin-B oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 H(+) + O(2) + rifamycin B = H(2)O(2) + rifamycin O." [EC:1.10.3.6, RHEA:11292]
+def: "Catalysis of the reaction: 2 H+ + O2 + rifamycin B = H2O2 + rifamycin O." [EC:1.10.3.6, RHEA:11292]
synonym: "rifamycin B oxidase activity" RELATED [EC:1.10.3.6]
synonym: "rifamycin-B-oxidase activity" EXACT []
synonym: "rifamycin-B:oxygen oxidoreductase activity" RELATED [EC:1.10.3.6]
@@ -297343,7 +297369,7 @@ is_a: GO:0004030 ! aldehyde dehydrogenase [NAD(P)+] activity
id: GO:0050270
name: S-adenosylhomocysteine deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-homocysteine + H(2)O + H(+) = S-inosyl-L-homocysteine + NH(4)(+)." [EC:3.5.4.28, RHEA:20716]
+def: "Catalysis of the reaction: S-adenosyl-L-homocysteine + H2O + H+ = S-inosyl-L-homocysteine + NH4." [EC:3.5.4.28, RHEA:20716]
synonym: "adenosylhomocysteine deaminase activity" RELATED [EC:3.5.4.28]
synonym: "S-adenosyl-L-homocysteine aminohydrolase activity" RELATED [EC:3.5.4.28]
xref: EC:3.5.4.28
@@ -297375,7 +297401,7 @@ is_a: GO:0016846 ! carbon-sulfur lyase activity
id: GO:0050272
name: S-carboxymethylcysteine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-chloro-L-alanine + thioglycolate = S-carboxymethyl-L-cysteine + chloride + H(+)." [EC:4.5.1.5, RHEA:22868]
+def: "Catalysis of the reaction: 3-chloro-L-alanine + thioglycolate = S-carboxymethyl-L-cysteine + chloride + H+." [EC:4.5.1.5, RHEA:22868]
synonym: "3-chloro-L-alanine chloride-lyase (adding thioglycolate)" RELATED [EC:4.5.1.5]
synonym: "3-chloro-L-alanine chloride-lyase (adding thioglycolate; S-carboxymethyl-L-cysteine-forming)" RELATED [EC:4.5.1.5]
synonym: "S-carboxymethyl-L-cysteine synthase activity" RELATED [EC:4.5.1.5]
@@ -297389,7 +297415,7 @@ is_a: GO:0016848 ! carbon-halide lyase activity
id: GO:0050273
name: S-succinylglutathione hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-succinylglutathione + H(2)O = glutathione + H(+) + succinate." [EC:3.1.2.13, RHEA:16713]
+def: "Catalysis of the reaction: S-succinylglutathione + H2O = glutathione + H+ + succinate." [EC:3.1.2.13, RHEA:16713]
xref: EC:3.1.2.13
xref: KEGG_REACTION:R00499
xref: MetaCyc:S-SUCCINYLGLUTATHIONE-HYDROLASE-RXN
@@ -297400,7 +297426,7 @@ is_a: GO:0016790 ! thiolester hydrolase activity
id: GO:0050274
name: salicyl-alcohol beta-D-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: salicyl alcohol + UDP-D-glucose = H(+) + salicin + UDP." [EC:2.4.1.172, RHEA:11512]
+def: "Catalysis of the reaction: salicyl alcohol + UDP-D-glucose = H+ + salicin + UDP." [EC:2.4.1.172, RHEA:11512]
synonym: "salicyl-alcohol b-D-glucosyltransferase activity" EXACT []
synonym: "salicyl-alcohol glucosyltransferase activity" EXACT []
synonym: "UDP-glucose:salicyl-alcohol beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.172]
@@ -297417,7 +297443,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0050275
name: scopoletin glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: scopoletin + UDP-D-glucose = H(+) + scopolin + UDP." [EC:2.4.1.128, RHEA:20453]
+def: "Catalysis of the reaction: scopoletin + UDP-D-glucose = H+ + scopolin + UDP." [EC:2.4.1.128, RHEA:20453]
synonym: "SGTase activity" RELATED [EC:2.4.1.128]
synonym: "UDP-glucose:scopoletin O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.128]
synonym: "UDPglucose:scopoletin glucosyltransferase activity" RELATED [EC:2.4.1.128]
@@ -297433,7 +297459,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0050276
name: scyllo-inosamine 4-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-amino-1-deoxy-scyllo-inositol + ATP = 1-amino-1-deoxy-scyllo-inositol 4-phosphate + ADP + 2 H(+)." [EC:2.7.1.65, RHEA:18605]
+def: "Catalysis of the reaction: 1-amino-1-deoxy-scyllo-inositol + ATP = 1-amino-1-deoxy-scyllo-inositol 4-phosphate + ADP + 2 H+." [EC:2.7.1.65, RHEA:18605]
synonym: "ATP:1-amino-1-deoxy-scyllo-inositol 4-phosphotransferase activity" RELATED [EC:2.7.1.65]
synonym: "ATP:inosamine phosphotransferase activity" RELATED [EC:2.7.1.65]
synonym: "scyllo-inosamine kinase (phosphorylating)" RELATED [EC:2.7.1.65]
@@ -297449,7 +297475,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0050277
name: sedoheptulokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + sedoheptulose = ADP + 2 H(+) + sedoheptulose 7-phosphate." [EC:2.7.1.14, RHEA:23844]
+def: "Catalysis of the reaction: ATP + sedoheptulose = ADP + 2 H+ + sedoheptulose 7-phosphate." [EC:2.7.1.14, RHEA:23844]
synonym: "ATP:sedoheptulose 7-phosphotransferase activity" RELATED [EC:2.7.1.14]
synonym: "heptulokinase activity" RELATED [EC:2.7.1.14]
synonym: "sedoheptulokinase (phosphorylating)" RELATED [EC:2.7.1.14]
@@ -297495,7 +297521,7 @@ is_a: GO:0019239 ! deaminase activity
id: GO:0050280
name: sequoyitol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1D-5-O-methyl-myo-inositol + NAD(+) = 2D-5-O-methyl-2,3,5/4,6-pentahydroxycyclohexanone + H(+) + NADH." [EC:1.1.1.143, RHEA:11300]
+def: "Catalysis of the reaction: 1D-5-O-methyl-myo-inositol + NAD+ = 2D-5-O-methyl-2,3,5/4,6-pentahydroxycyclohexanone + H+ + NADH." [EC:1.1.1.143, RHEA:11300]
synonym: "5-O-methyl-myo-inositol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.143]
xref: EC:1.1.1.143
xref: KEGG_REACTION:R03497
@@ -297561,7 +297587,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0050285
name: sinapine esterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O-sinapoylcholine + H(2)O = choline + H(+) + sinapate." [EC:3.1.1.49, RHEA:10016]
+def: "Catalysis of the reaction: O-sinapoylcholine + H2O = choline + H+ + sinapate." [EC:3.1.1.49, RHEA:10016]
synonym: "aromatic choline esterase activity" RELATED [EC:3.1.1.49]
synonym: "sinapoylcholine sinapohydrolase activity" RELATED [EC:3.1.1.49]
xref: EC:3.1.1.49
@@ -297574,7 +297600,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050286
name: sorbitol-6-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glucitol 6-phosphate + H(2)O = D-glucitol + phosphate." [EC:3.1.3.50, RHEA:24580]
+def: "Catalysis of the reaction: D-glucitol 6-phosphate + H2O = D-glucitol + phosphate." [EC:3.1.3.50, RHEA:24580]
synonym: "sorbitol-6-phosphate phosphatase activity" RELATED [EC:3.1.3.50]
synonym: "sorbitol-6-phosphate phosphohydrolase activity" RELATED [EC:3.1.3.50]
xref: EC:3.1.3.50
@@ -297587,7 +297613,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0050287
name: sorbose 5-dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-sorbose + NADP(+) = 5-dehydro-D-fructose + H(+) + NADPH." [EC:1.1.1.123, RHEA:15001]
+def: "Catalysis of the reaction: L-sorbose + NADP+ = 5-dehydro-D-fructose + H+ + NADPH." [EC:1.1.1.123, RHEA:15001]
synonym: "5-keto-D-fructose reductase activity" RELATED [EC:1.1.1.123]
synonym: "5-ketofructose reductase activity" RELATED [EC:1.1.1.123]
synonym: "L-sorbose:NADP+ 5-oxidoreductase activity" RELATED [EC:1.1.1.123]
@@ -297628,7 +297654,7 @@ is_a: GO:0016645 ! oxidoreductase activity, acting on the CH-NH group of donors
id: GO:0050290
name: sphingomyelin phosphodiesterase D activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + sphingomyelin = ceramide 1-phosphate + choline + H(+)." [EC:3.1.4.41, RHEA:20984]
+def: "Catalysis of the reaction: H2O + sphingomyelin = ceramide 1-phosphate + choline + H+." [EC:3.1.4.41, RHEA:20984]
synonym: "sphingomyelin ceramide-phosphohydrolase activity" RELATED [EC:3.1.4.41]
synonym: "sphingomyelinase D" RELATED [EC:3.1.4.41]
xref: EC:3.1.4.41
@@ -297658,7 +297684,7 @@ is_a: GO:0016410 ! N-acyltransferase activity
id: GO:0050292
name: steroid 9-alpha-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + O(2) + pregna-4,9(11)-diene-3,20-dione = 9,11alpha-epoxypregn-4-ene-3,20-dione + A + H(2)O." [EC:1.14.99.24, RHEA:19557]
+def: "Catalysis of the reaction: AH(2) + O2 + pregna-4,9(11)-diene-3,20-dione = 9,11alpha-epoxypregn-4-ene-3,20-dione + A + H2O." [EC:1.14.99.24, RHEA:19557]
synonym: "steroid 9-alpha-hydroxylase activity" RELATED [EC:1.14.99.24]
synonym: "steroid 9a-monooxygenase activity" EXACT []
synonym: "steroid 9alpha-hydroxylase activity" RELATED [EC:1.14.99.24]
@@ -297675,7 +297701,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050293
name: steroid-lactonase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + testololactone = H(+) + testolate." [EC:3.1.1.37, RHEA:13721]
+def: "Catalysis of the reaction: H2O + testololactone = H+ + testolate." [EC:3.1.1.37, RHEA:13721]
synonym: "testololactone lactonohydrolase activity" RELATED [EC:3.1.1.37]
xref: EC:3.1.1.37
xref: KEGG_REACTION:R03641
@@ -297687,7 +297713,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050294
name: steroid sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + a phenolic steroid = adenosine 3',5'-bisphosphate + steroid O-sulfate." [EC:2.8.2.15, MetaCyc:STEROID-SULFOTRANSFERASE-RXN]
+def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + a phenolic steroid = adenosine 3',5'-bisphosphate + steroid O-sulfate." [MetaCyc:STEROID-SULFOTRANSFERASE-RXN, RHEA:68460]
subset: goslim_chembl
synonym: "3'-phosphoadenylyl-sulfate:phenolic-steroid sulfotransferase activity" RELATED [EC:2.8.2.15]
synonym: "steroid alcohol sulfotransferase" BROAD [EC:2.8.2.15]
@@ -297697,13 +297723,14 @@ xref: MetaCyc:STEROID-SULFOTRANSFERASE-RXN
xref: Reactome:R-HSA-176517 "SULTs transfer (SO4)2- group to PREG"
xref: Reactome:R-HSA-176521 "beta-estradiol + PAPS => beta-estradiol 3-sulfate + PAP"
xref: Reactome:R-HSA-176631 "dehydroepiandrosterone (DHEA) + PAPS => DHEA sulfate + PAP"
+xref: RHEA:68460
is_a: GO:0008146 ! sulfotransferase activity
[Term]
id: GO:0050295
name: steryl-beta-glucosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cholesteryl-beta-D-glucoside + H(2)O = D-glucose + cholesterol." [EC:3.2.1.104, RHEA:11956]
+def: "Catalysis of the reaction: cholesteryl-beta-D-glucoside + H2O = D-glucose + cholesterol." [EC:3.2.1.104, RHEA:11956]
synonym: "cholesteryl-beta-D-glucoside glucohydrolase activity" RELATED [EC:3.2.1.104]
synonym: "steryl-b-glucosidase activity" EXACT []
xref: EC:3.2.1.104
@@ -297716,7 +297743,7 @@ is_a: GO:0008422 ! beta-glucosidase activity
id: GO:0050296
name: stipitatonate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + stipitatonate = CO(2) + H(+) + stipitatate." [EC:4.1.1.60, RHEA:13885]
+def: "Catalysis of the reaction: H2O + stipitatonate = CO2 + H+ + stipitatate." [EC:4.1.1.60, RHEA:13885]
synonym: "stipitatonate carboxy-lyase (decyclizing)" RELATED [EC:4.1.1.60]
synonym: "stipitatonate carboxy-lyase (decyclizing, stipitatate-forming)" RELATED [EC:4.1.1.60]
xref: EC:4.1.1.60
@@ -297751,7 +297778,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0050299
name: streptomycin 3''-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + streptomycin = ADP + 2 H(+) + streptomycin 3''-phosphate." [EC:2.7.1.87, RHEA:18377]
+def: "Catalysis of the reaction: ATP + streptomycin = ADP + 2 H+ + streptomycin 3''-phosphate." [EC:2.7.1.87, RHEA:18377]
synonym: "ATP:streptomycin 3''-phosphotransferase activity" RELATED [EC:2.7.1.87]
synonym: "streptomycin 3''-kinase (phosphorylating)" RELATED [EC:2.7.1.87]
synonym: "streptomycin 3''-phosphotransferase activity" RELATED [EC:2.7.1.87]
@@ -297765,7 +297792,7 @@ is_a: GO:0034071 ! aminoglycoside phosphotransferase activity
id: GO:0050300
name: aminoglycoside 6-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + streptomycin = ADP + 2 H(+) + streptomycin 6-phosphate." [EC:2.7.1.72, RHEA:22268]
+def: "Catalysis of the reaction: ATP + streptomycin = ADP + 2 H+ + streptomycin 6-phosphate." [EC:2.7.1.72, RHEA:22268]
synonym: "APH(6) activity" RELATED [EC:2.7.1.72]
synonym: "ATP:streptomycin 6-phosphotransferase activity" NARROW [EC:2.7.1.72]
synonym: "SM 6-kinase activity" NARROW [EC:2.7.1.72]
@@ -297785,7 +297812,7 @@ is_a: GO:0034071 ! aminoglycoside phosphotransferase activity
id: GO:0050301
name: streptomycin-6-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + streptomycin 6-phosphate = phosphate + streptomycin." [EC:3.1.3.39, RHEA:10688]
+def: "Catalysis of the reaction: H2O + streptomycin 6-phosphate = phosphate + streptomycin." [EC:3.1.3.39, RHEA:10688]
synonym: "streptomycin 6-phosphate phosphatase activity" RELATED [EC:3.1.3.39]
synonym: "streptomycin 6-phosphate phosphohydrolase activity" RELATED [EC:3.1.3.39]
synonym: "streptomycin-6-P phosphohydrolase activity" RELATED [EC:3.1.3.39]
@@ -297800,7 +297827,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0050302
name: indole-3-acetaldehyde oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (indol-3-yl)acetaldehyde + H(2)O + O(2) = (indol-3-yl)acetate + H(2)O(2) + H(+)." [EC:1.2.3.7, RHEA:16277]
+def: "Catalysis of the reaction: (indol-3-yl)acetaldehyde + H2O + O2 = (indol-3-yl)acetate + H2O2 + H+." [EC:1.2.3.7, RHEA:16277]
synonym: "(indol-3-yl)acetaldehyde:oxygen oxidoreductase activity" RELATED [EC:1.2.3.7]
synonym: "AO1" RELATED [EC:1.2.3.7]
synonym: "IAA oxidase activity" RELATED [EC:1.2.3.7]
@@ -297833,7 +297860,7 @@ is_a: GO:0016639 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0050304
name: nitrous-oxide reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + 2 cytochrome c + nitrogen = 2 reduced cytochrome c + nitrous oxide." [EC:1.7.2.4, MetaCyc:RXN-12130]
+def: "Catalysis of the reaction: H2O + 2 cytochrome c + nitrogen = 2 reduced cytochrome c + nitrous oxide." [EC:1.7.2.4, MetaCyc:RXN-12130]
synonym: "N2O reductase activity" RELATED [EC:1.7.2.4]
synonym: "nitrogen:(acceptor) oxidoreductase (N2O-forming)" RELATED [EC:1.7.2.4]
synonym: "nitrogen:acceptor oxidoreductase (N2O-forming)" RELATED [EC:1.7.2.4]
@@ -297848,7 +297875,7 @@ is_a: GO:0016662 ! oxidoreductase activity, acting on other nitrogenous compound
id: GO:0050305
name: strombine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-(carboxymethyl)-D-alanine + H(2)O + NAD(+) = glycine + H(+) + NADH + pyruvate." [EC:1.5.1.22, RHEA:14061]
+def: "Catalysis of the reaction: N-(carboxymethyl)-D-alanine + H2O + NAD+ = glycine + H+ + NADH + pyruvate." [EC:1.5.1.22, RHEA:14061]
synonym: "N-(carboxymethyl)-D-alanine: NAD+ oxidoreductase activity" RELATED [EC:1.5.1.22]
synonym: "N-(carboxymethyl)-D-alanine:NAD+ oxidoreductase (glycine-forming)" RELATED [EC:1.5.1.22]
synonym: "strombine[N-(carboxymethyl)-D-alanine]dehydrogenase activity" RELATED [EC:1.5.1.22]
@@ -297968,7 +297995,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0050314
name: sym-norspermidine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,3-diaminopropane + S-adenosylmethioninamine = S-methyl-5'-thioadenosine + bis(3-aminopropyl)amine + H(+)." [EC:2.5.1.23, RHEA:23244]
+def: "Catalysis of the reaction: 1,3-diaminopropane + S-adenosylmethioninamine = S-methyl-5'-thioadenosine + bis(3-aminopropyl)amine + H+." [EC:2.5.1.23, RHEA:23244]
synonym: "S-adenosylmethioninamine:propane-1,3-diamine 3-aminopropyltransferase activity" RELATED [EC:2.5.1.23]
xref: EC:2.5.1.23
xref: KEGG_REACTION:R03271
@@ -298004,7 +298031,7 @@ is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
id: GO:0050317
name: tagatose kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-tagatose + ATP = D-tagatose 6-phosphate + ADP + 2 H(+)." [EC:2.7.1.101, RHEA:15513]
+def: "Catalysis of the reaction: D-tagatose + ATP = D-tagatose 6-phosphate + ADP + 2 H+." [EC:2.7.1.101, RHEA:15513]
synonym: "ATP:D-tagatose 6-phosphotransferase activity" RELATED [EC:2.7.1.101]
synonym: "D-tagatose 6-phosphate kinase activity" RELATED [EC:2.7.1.101]
synonym: "tagatose 6-phosphate kinase (phosphorylating)" RELATED [EC:2.7.1.101]
@@ -298019,7 +298046,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0050318
name: tannase activity
namespace: molecular_function
-def: "Catalysis of the reaction: digallate + H(2)O = 2 gallate + H(+)." [EC:3.1.1.20, RHEA:16365]
+def: "Catalysis of the reaction: digallate + H2O = 2 gallate + H+." [EC:3.1.1.20, RHEA:16365]
synonym: "tannase S" RELATED [EC:3.1.1.20]
synonym: "tannin acetylhydrolase activity" RELATED [EC:3.1.1.20]
synonym: "tannin acylhydrolase activity" RELATED [EC:3.1.1.20]
@@ -298033,7 +298060,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050319
name: tartrate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tartrate + H(+) = D-glycerate + CO(2)." [EC:4.1.1.73, RHEA:13317]
+def: "Catalysis of the reaction: L-tartrate + H+ = D-glycerate + CO2." [EC:4.1.1.73, RHEA:13317]
synonym: "(R,R)-tartrate carboxy-lyase (D-glycerate-forming)" RELATED [EC:4.1.1.73]
synonym: "(R,R)-tartrate carboxy-lyase activity" RELATED [EC:4.1.1.73]
xref: EC:4.1.1.73
@@ -298100,7 +298127,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0050323
name: taurine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: A + H(2)O + taurine = AH(2) + NH(4)(+) + sulfoacetaldehyde." [EC:1.4.99.2, RHEA:18709]
+def: "Catalysis of the reaction: A + H2O + taurine = AH(2) + NH4 + sulfoacetaldehyde." [EC:1.4.99.2, RHEA:18709]
synonym: "taurine:(acceptor) oxidoreductase (deaminating)" RELATED [EC:1.4.99.2]
synonym: "taurine:acceptor oxidoreductase (deaminating)" RELATED [EC:1.4.99.2]
xref: EC:1.4.99.2
@@ -298113,7 +298140,7 @@ is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0050324
name: taurocyamine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + taurocyamine = N-phosphotaurocyamine + ADP + 2 H(+)." [EC:2.7.3.4, RHEA:22516]
+def: "Catalysis of the reaction: ATP + taurocyamine = N-phosphotaurocyamine + ADP + 2 H+." [EC:2.7.3.4, RHEA:22516]
synonym: "ATP:taurocyamine N-phosphotransferase activity" RELATED [EC:2.7.3.4]
synonym: "ATP:taurocyamine phosphotransferase activity" RELATED [EC:2.7.3.4]
synonym: "taurocyamine phosphotransferase activity" RELATED [EC:2.7.3.4]
@@ -298128,7 +298155,7 @@ is_a: GO:0016775 ! phosphotransferase activity, nitrogenous group as acceptor
id: GO:0050325
name: tauropine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + NAD(+) + tauropine = H(+) + NADH + pyruvate + taurine." [EC:1.5.1.23, RHEA:12580]
+def: "Catalysis of the reaction: H2O + NAD+ + tauropine = H+ + NADH + pyruvate + taurine." [EC:1.5.1.23, RHEA:12580]
synonym: "2-N-(D-1-carboxyethyl)taurine:NAD+ oxidoreductase (taurine-forming)" RELATED [EC:1.5.1.23]
synonym: "N2-(D-1-carboxyethyl)taurine:NAD+ oxidoreductase (taurine-forming)" RELATED [EC:1.5.1.23]
xref: EC:1.5.1.23
@@ -298165,7 +298192,7 @@ is_a: GO:0016634 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0050329
name: tetrahydroxypteridine cycloisomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: tetrahydroxypteridine = H(+) + xanthine-8-carboxylate." [EC:5.5.1.3, RHEA:18097]
+def: "Catalysis of the reaction: tetrahydroxypteridine = H+ + xanthine-8-carboxylate." [EC:5.5.1.3, RHEA:18097]
synonym: "tetrahydroxypteridine lyase (isomerizing)" RELATED [EC:5.5.1.3]
xref: EC:5.5.1.3
xref: KEGG_REACTION:R04154
@@ -298177,7 +298204,7 @@ is_a: GO:0016872 ! intramolecular lyase activity
id: GO:0050330
name: theanine hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(5)-ethyl-L-glutamine + H(2)O = L-glutamate + ethylamine." [EC:3.5.1.65, RHEA:18013]
+def: "Catalysis of the reaction: N(5)-ethyl-L-glutamine + H2O = L-glutamate + ethylamine." [EC:3.5.1.65, RHEA:18013]
synonym: "5-N-ethyl-L-glutamine amidohydrolase activity" RELATED [EC:3.5.1.65]
synonym: "L-theanine amidohydrolase activity" RELATED [EC:3.5.1.65]
synonym: "N5-ethyl-L-glutamine amidohydrolase activity" RELATED [EC:3.5.1.65]
@@ -298230,11 +298257,13 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
[Term]
id: GO:0050333
-name: thiamin-triphosphatase activity
+name: thiamine triphosphate phosphatase activity
namespace: molecular_function
alt_id: GO:0048253
-def: "Catalysis of the reaction: H(2)O + thiamine triphosphate = H(+) + phosphate + thiamine diphosphate." [EC:3.6.1.28, RHEA:11744]
-synonym: "thiamine-triphosphatase activity" EXACT []
+def: "Catalysis of the reaction: H2O + thiamine triphosphate = thiamine diphosphate + H+ + phosphate." [RHEA:11744]
+synonym: "thiamin-triphosphatase activity" RELATED []
+synonym: "thiamine triphosphatase activity" RELATED []
+synonym: "thiamine-triphosphatase activity" RELATED []
synonym: "thiamine-triphosphate phosphohydrolase activity" RELATED [EC:3.6.1.28]
synonym: "ThTPase activity" RELATED [EC:3.6.1.28]
xref: EC:3.6.1.28
@@ -298242,13 +298271,13 @@ xref: KEGG_REACTION:R00618
xref: MetaCyc:THIAMIN-TRIPHOSPHATASE-RXN
xref: Reactome:R-HSA-965067 "THTPA:Mg2+ hydrolyzes ThTP to TDP"
xref: RHEA:11744
-is_a: GO:0017111 ! nucleoside-triphosphatase activity
+is_a: GO:0016462 ! pyrophosphatase activity
[Term]
id: GO:0050334
name: thiaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + thiamine = 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-hydroxyethyl)-4-methylthiazole + H(+)." [EC:3.5.99.2, RHEA:17509]
+def: "Catalysis of the reaction: H2O + thiamine = 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-hydroxyethyl)-4-methylthiazole + H+." [EC:3.5.99.2, RHEA:17509]
synonym: "thiaminase II activity" NARROW [EC:3.5.99.2]
xref: EC:3.5.99.2
xref: KEGG_REACTION:R02133
@@ -298318,17 +298347,19 @@ is_a: GO:0016669 ! oxidoreductase activity, acting on a sulfur group of donors,
[Term]
id: GO:0050339
-name: thymidine-triphosphatase activity
+name: TTPase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dTTP + H2O = dTDP + phosphate." [EC:3.6.1.39, MetaCyc:THYMIDINE-TRIPHOSPHATASE-RXN]
+def: "Catalysis of the reaction: dTTP + H2O = dTDP + H+ + phosphate." [RHEA:19013]
synonym: "deoxythymidine-5'-triphosphatase activity" RELATED [EC:3.6.1.39]
synonym: "dTTP nucleotidohydrolase activity" RELATED [EC:3.6.1.39]
synonym: "dTTPase activity" RELATED [EC:3.6.1.39]
+synonym: "thymidine triphosphatase activity" EXACT []
synonym: "thymidine triphosphate nucleotidohydrolase activity" RELATED [EC:3.6.1.39]
+synonym: "thymidine-triphosphatase activity" EXACT []
xref: EC:3.6.1.39
xref: MetaCyc:THYMIDINE-TRIPHOSPHATASE-RXN
xref: RHEA:19013
-is_a: GO:0017111 ! nucleoside-triphosphatase activity
+is_a: GO:0017111 ! ribonucleoside triphosphate phosphatase activity
[Term]
id: GO:0050340
@@ -298346,7 +298377,7 @@ synonym: "thymidylate nucleotidase activity" RELATED [EC:3.1.3.35]
xref: EC:3.1.3.35
xref: MetaCyc:THYMIDYLATE-5-PHOSPHATASE-RXN
xref: RHEA:11080
-is_a: GO:0016791 ! phosphatase activity
+is_a: GO:0008253 ! 5'-nucleotidase activity
[Term]
id: GO:0050341
@@ -298390,7 +298421,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0050344
name: trans-cinnamate 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: trans-cinnamate + H(+) + NADPH + O(2) = 2-coumarate + H(2)O + NADP(+)." [EC:1.14.13.14, RHEA:10956]
+def: "Catalysis of the reaction: trans-cinnamate + H+ + NADPH + O2 = 2-coumarate + H2O + NADP+." [EC:1.14.13.14, RHEA:10956]
synonym: "cinnamate 2-hydroxylase activity" RELATED [EC:1.14.13.14]
synonym: "cinnamate 2-monooxygenase activity" RELATED [EC:1.14.13.14]
synonym: "cinnamic 2-hydroxylase activity" RELATED [EC:1.14.13.14]
@@ -298407,7 +298438,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050345
name: trans-epoxysuccinate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: trans-2,3-epoxysuccinate + H(2)O = (2R,3S)-tartrate." [EC:3.3.2.4, RHEA:20740]
+def: "Catalysis of the reaction: trans-2,3-epoxysuccinate + H2O = (2R,3S)-tartrate." [EC:3.3.2.4, RHEA:20740]
synonym: "tartrate epoxydase activity" RELATED [EC:3.3.2.4]
synonym: "trans-2,3-epoxysuccinate hydrolase activity" RELATED [EC:3.3.2.4]
synonym: "trans-epoxysuccinate hydratase activity" RELATED [EC:3.3.2.4]
@@ -298421,7 +298452,7 @@ is_a: GO:0016803 ! ether hydrolase activity
id: GO:0050346
name: trans-L-3-hydroxyproline dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: trans-L-3-hydroxyproline = 1-pyrroline-2-carboxylate + H(2)O + H(+)." [EC:4.2.1.77, RHEA:10320]
+def: "Catalysis of the reaction: trans-L-3-hydroxyproline = 1-pyrroline-2-carboxylate + H2O + H+." [EC:4.2.1.77, RHEA:10320]
synonym: "trans-L-3-hydroxyproline hydro-lyase (Delta1-pyrroline 2-carboxylate-forming)" RELATED [EC:4.2.1.77]
synonym: "trans-L-3-hydroxyproline hydro-lyase activity" RELATED [EC:4.2.1.77]
xref: EC:4.2.1.77
@@ -298430,25 +298461,6 @@ xref: MetaCyc:TRANS-L-3-HYDROXYPROLINE-DEHYDRATASE-RXN
xref: RHEA:10320
is_a: GO:0016836 ! hydro-lyase activity
-[Term]
-id: GO:0050347
-name: trans-octaprenyltranstransferase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: all-trans-octaprenyl diphosphate + isopentenyl diphosphate = all-trans-nonaprenyl diphosphate + diphosphate." [RHEA:11324]
-synonym: "(E)-octaprenyl-diphosphate:isopentenyl-diphosphate octaprenyltranstransferase activity" RELATED []
-synonym: "all-trans-nonaprenyl-diphosphate synthase activity" RELATED []
-synonym: "nonaprenyl pyrophosphate synthetase activity" RELATED []
-synonym: "polyprenylpyrophosphate synthetase activity" RELATED []
-synonym: "solanesyl pyrophosphate synthetase activity" RELATED []
-synonym: "solanesyl-diphosphate synthase activity" RELATED []
-synonym: "SPP synthase activity" RELATED []
-synonym: "terpenoidallyltransferase activity" RELATED []
-synonym: "terpenyl pyrophosphate synthetase activity" RELATED []
-synonym: "trans-prenyltransferase activity" RELATED []
-xref: KEGG_REACTION:R07267
-xref: RHEA:11324
-is_a: GO:0004659 ! prenyltransferase activity
-
[Term]
id: GO:0050348
name: trehalose O-mycolyltransferase activity
@@ -298466,7 +298478,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0050349
name: triacetate-lactonase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + triacetate lactone = triacetate." [EC:3.1.1.38, RHEA:22260]
+def: "Catalysis of the reaction: H2O + triacetate lactone = triacetate." [EC:3.1.1.38, RHEA:22260]
synonym: "TAL hydrolase activity" RELATED [EC:3.1.1.38]
synonym: "triacetate lactone hydrolase activity" RELATED [EC:3.1.1.38]
synonym: "triacetic acid lactone hydrolase activity" RELATED [EC:3.1.1.38]
@@ -298495,7 +298507,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0050351
name: trimetaphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + trimetaphosphate = 2 H(+) + triphosphate." [EC:3.6.1.2, RHEA:11088]
+def: "Catalysis of the reaction: H2O + trimetaphosphate = 2 H+ + triphosphate." [EC:3.6.1.2, RHEA:11088]
synonym: "inorganic trimetaphosphatase activity" RELATED [EC:3.6.1.2]
synonym: "trimetaphosphate hydrolase activity" RELATED [EC:3.6.1.2]
xref: EC:3.6.1.2
@@ -298508,7 +298520,7 @@ is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-
id: GO:0050352
name: trimethylamine-oxide aldolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + trimethylamine N-oxide = dimethylamine + formaldehyde." [EC:4.1.2.32, RHEA:20217]
+def: "Catalysis of the reaction: H+ + trimethylamine N-oxide = dimethylamine + formaldehyde." [EC:4.1.2.32, RHEA:20217]
synonym: "trimethylamine N-oxide aldolase activity" RELATED [EC:4.1.2.32]
synonym: "trimethylamine N-oxide demethylase activity" RELATED [EC:4.1.2.32]
synonym: "trimethylamine N-oxide formaldehyde-lyase activity" RELATED [EC:4.1.2.32]
@@ -298525,7 +298537,7 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0050353
name: trimethyllysine dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysine + O(2) = 3-hydroxy-N(6),N(6),N(6)-trimethyl-L-lysine + CO(2) + succinate." [EC:1.14.11.8, RHEA:14181]
+def: "Catalysis of the reaction: 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysine + O2 = 3-hydroxy-N(6),N(6),N(6)-trimethyl-L-lysine + CO2 + succinate." [EC:1.14.11.8, RHEA:14181]
synonym: "6-N,6-N,6-N-trimethyl-L-lysine,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)" RELATED [EC:1.14.11.8]
synonym: "epsilon-trimethyllysine 2-oxoglutarate dioxygenase activity" RELATED [EC:1.14.11.8]
synonym: "N6,N6,N6-trimethyl-L-lysine,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)" RELATED [EC:1.14.11.8]
@@ -298546,7 +298558,7 @@ is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
id: GO:0050354
name: triokinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glyceraldehyde + ATP = D-glyceraldehyde 3-phosphate + ADP + 2 H(+)." [EC:2.7.1.28, RHEA:13941]
+def: "Catalysis of the reaction: D-glyceraldehyde + ATP = D-glyceraldehyde 3-phosphate + ADP + 2 H+." [EC:2.7.1.28, RHEA:13941]
synonym: "ATP:D-glyceraldehyde 3-phosphotransferase activity" RELATED [EC:2.7.1.28]
synonym: "D-triokinase activity" RELATED [EC:2.7.1.28]
synonym: "trio triose kinase (phosphorylating)" RELATED [EC:2.7.1.28]
@@ -298561,10 +298573,11 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
[Term]
id: GO:0050355
-name: triphosphatase activity
+name: inorganic triphosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + triphosphate = diphosphate + phosphate." [EC:3.6.1.25, RHEA:14157]
+def: "Catalysis of the reaction: H2O + inorganic triphosphate = diphosphate + phosphate." [EC:3.6.1.25, RHEA:14157]
synonym: "inorganic triphosphatase activity" RELATED [EC:3.6.1.25]
+synonym: "triphosphatase activity" BROAD []
synonym: "triphosphate phosphohydrolase activity" RELATED [EC:3.6.1.25]
synonym: "tripolyphosphatase activity" EXACT [PMID:24004165]
xref: EC:3.6.1.25
@@ -298577,7 +298590,7 @@ is_a: GO:0016462 ! pyrophosphatase activity
id: GO:0050356
name: tropine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + tropine = H(+) + NADPH + tropinone." [EC:1.1.1.206, RHEA:18357]
+def: "Catalysis of the reaction: NADP+ + tropine = H+ + NADPH + tropinone." [EC:1.1.1.206, RHEA:18357]
synonym: "tropine:NADP+ 3alpha-oxidoreductase activity" RELATED [EC:1.1.1.206]
xref: EC:1.1.1.206
xref: KEGG_REACTION:R02832
@@ -298589,7 +298602,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050357
name: tropinesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: atropine + H(2)O = H(+) + tropate + tropine." [EC:3.1.1.10, RHEA:23304]
+def: "Catalysis of the reaction: atropine + H2O = H+ + tropate + tropine." [EC:3.1.1.10, RHEA:23304]
synonym: "atropinase activity" RELATED [EC:3.1.1.10]
synonym: "atropine acylhydrolase activity" RELATED [EC:3.1.1.10]
synonym: "atropine esterase activity" RELATED [EC:3.1.1.10]
@@ -298605,7 +298618,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050358
name: tropinone reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP(+) + pseudotropine = H(+) + NADPH + tropinone." [EC:1.1.1.236, RHEA:24244]
+def: "Catalysis of the reaction: NADP+ + pseudotropine = H+ + NADPH + tropinone." [EC:1.1.1.236, RHEA:24244]
synonym: "pseudotropine forming tropinone reductase activity" RELATED [EC:1.1.1.236]
synonym: "pseudotropine:NADP+ 3-oxidoreductase activity" RELATED [EC:1.1.1.236]
synonym: "tropinone (psi-tropine-forming) reductase activity" RELATED [EC:1.1.1.236]
@@ -298653,7 +298666,7 @@ is_a: GO:0016701 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0050361
name: tryptophan 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tryptophan + O(2) = CO(2) + H(2)O + indole-3-acetamide." [EC:1.13.12.3, RHEA:16165]
+def: "Catalysis of the reaction: L-tryptophan + O2 = CO2 + H2O + indole-3-acetamide." [EC:1.13.12.3, RHEA:16165]
synonym: "L-tryptophan:oxygen 2-oxidoreductase (decarboxylating)" RELATED [EC:1.13.12.3]
xref: EC:1.13.12.3
xref: KEGG_REACTION:R00679
@@ -298713,7 +298726,7 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0050365
name: tryptophanamidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tryptophanamide + H(2)O = L-tryptophan + NH(4)(+)." [EC:3.5.1.57, RHEA:11012]
+def: "Catalysis of the reaction: L-tryptophanamide + H2O = L-tryptophan + NH4." [EC:3.5.1.57, RHEA:11012]
synonym: "L-tryptophan aminopeptidase" BROAD [EC:3.5.1.57]
synonym: "L-tryptophanamide amidohydrolase activity" RELATED [EC:3.5.1.57]
synonym: "tryptophan aminopeptidase" BROAD [EC:3.5.1.57]
@@ -298742,7 +298755,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0050367
name: tyrosine-arginine ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arginine + L-tyrosine + ATP = L-tyrosyl-L-arginine + AMP + diphosphate + 2 H(+)." [EC:6.3.2.24, RHEA:15345]
+def: "Catalysis of the reaction: L-arginine + L-tyrosine + ATP = L-tyrosyl-L-arginine + AMP + diphosphate + 2 H+." [EC:6.3.2.24, RHEA:15345]
synonym: "kyotorphin synthase activity" RELATED [EC:6.3.2.24]
synonym: "kyotorphin synthetase activity" RELATED [EC:6.3.2.24]
synonym: "kyotorphin-synthesizing enzyme activity" RELATED [EC:6.3.2.24]
@@ -298798,7 +298811,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050371
name: tyrosine phenol-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tyrosine + H(2)O = NH(4)(+) + phenol + pyruvate." [EC:4.1.99.2, RHEA:21704]
+def: "Catalysis of the reaction: L-tyrosine + H2O = NH4 + phenol + pyruvate." [EC:4.1.99.2, RHEA:21704]
synonym: "beta-tyrosinase activity" RELATED [EC:4.1.99.2]
synonym: "L-tyrosine phenol-lyase (deaminating)" RELATED [EC:4.1.99.2]
synonym: "L-tyrosine phenol-lyase (deaminating; pyruvate-forming)" RELATED [EC:4.1.99.2]
@@ -298810,16 +298823,17 @@ is_a: GO:0016830 ! carbon-carbon lyase activity
[Term]
id: GO:0050372
-name: ubiquitin-calmodulin ligase activity
+name: obsolete ubiquitin-calmodulin ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: n ATP + calmodulin + n ubiquitin = n AMP + n diphosphate + ubiquitin(n)-calmodulin." [MetaCyc:UBIQUITIN--CALMODULIN-LIGASE-RXN]
+def: "OBSOLETE. Catalysis of the reaction: n ATP + calmodulin + n ubiquitin = n AMP + n diphosphate + ubiquitin(n)-calmodulin." [MetaCyc:UBIQUITIN--CALMODULIN-LIGASE-RXN]
+comment: This term was obsoleted because it represents a specific substrate.
synonym: "calmodulin:ubiquitin ligase (AMP-forming)" RELATED [EC:6.3.2.21]
synonym: "ubiquitin-calmodulin synthetase activity" RELATED [EC:6.3.2.21]
synonym: "ubiquityl-calmodulin synthase activity" RELATED [EC:6.3.2.21]
synonym: "ubiquityl-calmodulin synthetase activity" RELATED [EC:6.3.2.21]
synonym: "uCaM-synthetase activity" RELATED [EC:6.3.2.21]
xref: MetaCyc:UBIQUITIN--CALMODULIN-LIGASE-RXN
-is_a: GO:0004842 ! ubiquitin-protein transferase activity
+is_obsolete: true
[Term]
id: GO:0050373
@@ -298843,7 +298857,7 @@ is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and
id: GO:0050374
name: UDP-galacturonate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + UDP-alpha-D-galacturonate = CO(2) + UDP-L-arabinose." [EC:4.1.1.67, RHEA:19725]
+def: "Catalysis of the reaction: H+ + UDP-alpha-D-galacturonate = CO2 + UDP-L-arabinose." [EC:4.1.1.67, RHEA:19725]
synonym: "UDP-D-galacturonate carboxy-lyase (UDP-L-arabinose-forming)" RELATED [EC:4.1.1.67]
synonym: "UDP-D-galacturonate carboxy-lyase activity" RELATED [EC:4.1.1.67]
synonym: "UDP-galacturonic acid decarboxylase activity" RELATED [EC:4.1.1.67]
@@ -298871,7 +298885,7 @@ is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and
id: GO:0050377
name: UDP-glucose 4,6-dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: UDP-D-glucose = H(2)O + UDP-4-dehydro-6-deoxy-D-glucose." [EC:4.2.1.76, RHEA:21500]
+def: "Catalysis of the reaction: UDP-D-glucose = H2O + UDP-4-dehydro-6-deoxy-D-glucose." [EC:4.2.1.76, RHEA:21500]
synonym: "UDP-D-glucose oxidoreductase activity" RELATED [EC:4.2.1.76]
synonym: "UDP-D-glucose-4,6-hydrolyase activity" RELATED [EC:4.2.1.76]
synonym: "UDP-glucose 4,6-hydro-lyase (UDP-4-dehydro-6-deoxy-D-glucose-forming)" RELATED [EC:4.2.1.76]
@@ -298917,15 +298931,13 @@ synonym: "UDPglucuronate 5'-epimerase activity" RELATED []
synonym: "uridine diphosphoglucuronate 5'-epimerase activity" RELATED []
xref: KEGG_REACTION:R01387
xref: MetaCyc:UDP-GLUCURONATE-5-EPIMERASE-RXN
-xref: Reactome:R-HSA-2024100 "GLCE epimerises GlcA to IdoA"
-xref: Reactome:R-HSA-2076371 "GLCE epimerises more GlcA to IdoA as sulfate content rises"
is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and derivatives
[Term]
id: GO:0050380
name: undecaprenyl-diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H+ + phosphate." [PMID:18411271, RHEA:28094]
+def: "Catalysis of the reaction: di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H+ + phosphate." [PMID:18411271, RHEA:28094]
synonym: "C(55)-isoprenyl diphosphatase activity" RELATED [EC:3.6.1.27]
synonym: "C(55)-isoprenyl pyrophosphatase activity" RELATED [EC:3.6.1.27]
synonym: "C55-isoprenyl diphosphatase activity" RELATED [EC:3.6.1.27]
@@ -298942,7 +298954,7 @@ is_a: GO:0016462 ! pyrophosphatase activity
id: GO:0050382
name: uracil-5-carboxylate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + uracil 5-carboxylate = CO(2) + uracil." [EC:4.1.1.66, RHEA:17685]
+def: "Catalysis of the reaction: H+ + uracil 5-carboxylate = CO2 + uracil." [EC:4.1.1.66, RHEA:17685]
synonym: "uracil-5-carboxylate carboxy-lyase (uracil-forming)" RELATED [EC:4.1.1.66]
synonym: "uracil-5-carboxylate carboxy-lyase activity" RELATED [EC:4.1.1.66]
synonym: "uracil-5-carboxylic acid decarboxylase activity" RELATED [EC:4.1.1.66]
@@ -298966,7 +298978,7 @@ is_a: GO:0016725 ! oxidoreductase activity, acting on CH or CH2 groups
id: GO:0050384
name: urate-ribonucleotide phosphorylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-(beta-D-ribofuranosyl)uric acid + phosphate = alpha-D-ribose 1-phosphate + H(+) + urate." [EC:2.4.2.16, RHEA:13909]
+def: "Catalysis of the reaction: 3-(beta-D-ribofuranosyl)uric acid + phosphate = alpha-D-ribose 1-phosphate + H+ + urate." [EC:2.4.2.16, RHEA:13909]
synonym: "UAR phosphorylase activity" RELATED [EC:2.4.2.16]
synonym: "urate-ribonucleotide:phosphate alpha-D-ribosyltransferase activity" RELATED [EC:2.4.2.16]
synonym: "urate-ribonucleotide:phosphate D-ribosyltransferase activity" RELATED [EC:2.4.2.16]
@@ -298997,7 +299009,7 @@ is_a: GO:0016842 ! amidine-lyase activity
id: GO:0050386
name: ureidosuccinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-carbamoyl-L-aspartate + H(2)O + 2 H(+) = L-aspartate + CO(2) + NH(4)(+)." [EC:3.5.1.7, RHEA:14365]
+def: "Catalysis of the reaction: N-carbamoyl-L-aspartate + H2O + 2 H+ = L-aspartate + CO2 + NH4." [EC:3.5.1.7, RHEA:14365]
synonym: "N-carbamoyl-L-aspartate amidohydrolase activity" RELATED [EC:3.5.1.7]
xref: EC:3.5.1.7
xref: KEGG_REACTION:R00484
@@ -299009,7 +299021,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050387
name: urethanase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + H(+) + urethane = CO(2) + ethanol + NH(4)(+)." [EC:3.5.1.75, RHEA:21372]
+def: "Catalysis of the reaction: H2O + H+ + urethane = CO2 + ethanol + NH4." [EC:3.5.1.75, RHEA:21372]
synonym: "urethane amidohydrolase (decarboxylating)" RELATED [EC:3.5.1.75]
synonym: "urethane hydrolase activity" RELATED [EC:3.5.1.75]
xref: EC:3.5.1.75
@@ -299022,7 +299034,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050388
name: uronate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-galacturonate + H(2)O + NAD(+) = galactarate + 2 H(+) + NADH." [EC:1.1.1.203, RHEA:22404]
+def: "Catalysis of the reaction: D-galacturonate + H2O + NAD+ = galactarate + 2 H+ + NADH." [EC:1.1.1.203, RHEA:22404]
synonym: "uronate: NAD-oxidoreductase activity" RELATED [EC:1.1.1.203]
synonym: "uronate:NAD+ 1-oxidoreductase activity" RELATED [EC:1.1.1.203]
synonym: "uronic acid dehydrogenase activity" RELATED [EC:1.1.1.203]
@@ -299048,7 +299060,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050390
name: valine decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-valine + H(+) = 2-methylpropanamine + CO(2)." [EC:4.1.1.14, RHEA:18989]
+def: "Catalysis of the reaction: L-valine + H+ = 2-methylpropanamine + CO2." [EC:4.1.1.14, RHEA:18989]
synonym: "L-valine carboxy-lyase (2-methylpropanamine-forming)" RELATED [EC:4.1.1.14]
synonym: "L-valine carboxy-lyase activity" RELATED [EC:4.1.1.14]
synonym: "leucine decarboxylase activity" RELATED [EC:4.1.1.14]
@@ -299076,7 +299088,7 @@ is_a: GO:0016639 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0050392
name: vicianin beta-glucosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-vicianin + H(2)O = mandelonitrile + vicianose." [EC:3.2.1.119, RHEA:14041]
+def: "Catalysis of the reaction: (R)-vicianin + H2O = mandelonitrile + vicianose." [EC:3.2.1.119, RHEA:14041]
synonym: "(R)-vicianin beta-D-glucohydrolase activity" RELATED [EC:3.2.1.119]
synonym: "vicianin b-glucosidase activity" EXACT []
synonym: "vicianin hydrolase activity" RELATED [EC:3.2.1.119]
@@ -299090,7 +299102,7 @@ is_a: GO:0008422 ! beta-glucosidase activity
id: GO:0050393
name: vinylacetyl-CoA delta-isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: vinylacetyl-CoA = crotonoyl-CoA." [EC:5.3.3.3, RHEA:10572]
+def: "Catalysis of the reaction: vinylacetyl-CoA = (2E)-butenoyl-CoA." [RHEA:10572]
synonym: "delta3-cis-delta2-trans-enoyl-CoA isomerase" BROAD [EC:5.3.3.3]
synonym: "vinylacetyl coenzyme A delta-isomerase activity" RELATED [EC:5.3.3.3]
synonym: "vinylacetyl coenzyme A isomerase activity" RELATED [EC:5.3.3.3]
@@ -299120,7 +299132,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0050395
name: vitexin beta-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: UDP-D-glucose + vitexin = H(+) + UDP + vitexin 2''-O-beta-D-glucoside." [EC:2.4.1.105, RHEA:21956]
+def: "Catalysis of the reaction: UDP-D-glucose + vitexin = H+ + UDP + vitexin 2''-O-beta-D-glucoside." [EC:2.4.1.105, RHEA:21956]
synonym: "UDP-glucose:vitexin 2''-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.105]
synonym: "UDPglucose:vitexin 2''-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.105]
synonym: "uridine diphosphoglucose-vitexin 2''-glucosyltransferase activity" RELATED [EC:2.4.1.105]
@@ -299135,7 +299147,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0050396
name: vomifoliol 4'-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (6S,9R)-6-hydroxy-3-oxo-alpha-ionol + NAD(+) = (6S)-6-hydroxy-3-oxo-alpha-ionone + H(+) + NADH." [EC:1.1.1.221, RHEA:22804]
+def: "Catalysis of the reaction: (6S,9R)-6-hydroxy-3-oxo-alpha-ionol + NAD+ = (6S)-6-hydroxy-3-oxo-alpha-ionone + H+ + NADH." [EC:1.1.1.221, RHEA:22804]
synonym: "vomifoliol:NAD+ 4'-oxidoreductase activity" RELATED [EC:1.1.1.221]
xref: EC:1.1.1.221
xref: KEGG_REACTION:R04412
@@ -299174,7 +299186,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050399
name: xanthommatin reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5,12-dihydroxanthommatin + NAD(+) = H(+) + NADH + xanthommatin." [EC:1.3.1.41, RHEA:13417]
+def: "Catalysis of the reaction: 5,12-dihydroxanthommatin + NAD+ = H+ + NADH + xanthommatin." [EC:1.3.1.41, RHEA:13417]
synonym: "5,12-dihydroxanthommatin:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.41]
xref: EC:1.3.1.41
xref: KEGG_REACTION:R03787
@@ -299186,7 +299198,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0050400
name: xylitol kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + xylitol = ADP + 2 H(+) + xylitol 5-phosphate." [EC:2.7.1.122, RHEA:20209]
+def: "Catalysis of the reaction: ATP + xylitol = ADP + 2 H+ + xylitol 5-phosphate." [EC:2.7.1.122, RHEA:20209]
synonym: "ATP:xylitol 5-phosphotransferase activity" RELATED [EC:2.7.1.122]
synonym: "xylitol phosphotransferase activity" RELATED [EC:2.7.1.122]
xref: EC:2.7.1.122
@@ -299200,7 +299212,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0050401
name: xylonate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-xylonate = 2-dehydro-3-deoxy-D-arabinonate + H(2)O." [EC:4.2.1.82, RHEA:19157]
+def: "Catalysis of the reaction: D-xylonate = 2-dehydro-3-deoxy-D-arabinonate + H2O." [EC:4.2.1.82, RHEA:19157]
synonym: "D-xylo-aldonate dehydratase activity" RELATED [EC:4.2.1.82]
synonym: "D-xylonate dehydratase activity" RELATED [EC:4.2.1.82]
synonym: "D-xylonate hydro-lyase (2-dehydro-3-deoxy-D-xylonate-forming)" RELATED [EC:4.2.1.82]
@@ -299228,7 +299240,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050403
name: trans-zeatin O-beta-D-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: trans-zeatin + UDP-D-glucose = O-beta-D-glucosyl-trans-zeatin + H(+) + UDP." [EC:2.4.1.203, RHEA:23224]
+def: "Catalysis of the reaction: trans-zeatin + UDP-D-glucose = O-beta-D-glucosyl-trans-zeatin + H+ + UDP." [EC:2.4.1.203, RHEA:23224]
synonym: "UDP-glucose:trans-zeatin O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.203]
synonym: "UDPglucose:trans-zeatin O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.203]
synonym: "uridine diphosphoglucose-zeatin O-glucosyltransferase activity" RELATED [EC:2.4.1.203]
@@ -299245,7 +299257,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0050404
name: zeatin O-beta-D-xylosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: UDP-alpha-D-xylose + zeatin = O-beta-D-xylosylzeatin + H(+) + UDP." [EC:2.4.2.40, RHEA:14721]
+def: "Catalysis of the reaction: UDP-alpha-D-xylose + zeatin = O-beta-D-xylosylzeatin + H+ + UDP." [EC:2.4.2.40, RHEA:14721]
comment: Note that this function was formerly EC:2.4.1.204.
synonym: "UDP-D-xylose:zeatin O-beta-D-xylosyltransferase activity" RELATED [EC:2.4.2.40]
synonym: "uridine diphosphoxylose-zeatin xylosyltransferase activity" RELATED [EC:2.4.2.40]
@@ -299261,7 +299273,7 @@ is_a: GO:0035252 ! UDP-xylosyltransferase activity
id: GO:0050405
name: [acetyl-CoA carboxylase] kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + [acetyl-CoA carboxylase] = ADP + [acetyl-CoA carboxylase] phosphate." [EC:2.7.11.27, MetaCyc:[ACETYL-COA-CARBOXYLASE\]-KINASE-RXN]
+def: "Catalysis of the reaction: ATP + [acetyl-CoA carboxylase] = ADP + [acetyl-CoA carboxylase] phosphate." [EC:2.7.11.27, MetaCyc:\[ACETYL-COA-CARBOXYLASE\]-KINASE-RXN]
synonym: "acetyl coenzyme A carboxylase kinase (phosphorylating) activity" RELATED [EC:2.7.11.27]
synonym: "acetyl-CoA carboxylase bound kinase activity" NARROW [EC:2.7.11.27]
synonym: "acetyl-CoA carboxylase kinase (AMP-activated) activity" RELATED [EC:2.7.11.27]
@@ -299331,7 +299343,7 @@ is_a: GO:0004721 ! phosphoprotein phosphatase activity
id: GO:0050409
name: indolylacetylinositol arabinosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1L-1-O-(indol-3-yl)acetyl-myo-inositol + UDP-L-arabinose = (indol-3-yl)acetyl-myo-inositol 3-L-arabinoside + H(+) + UDP." [EC:2.4.2.34, RHEA:19505]
+def: "Catalysis of the reaction: 1L-1-O-(indol-3-yl)acetyl-myo-inositol + UDP-L-arabinose = (indol-3-yl)acetyl-myo-inositol 3-L-arabinoside + H+ + UDP." [EC:2.4.2.34, RHEA:19505]
synonym: "arabinosylindolylacetylinositol synthase activity" RELATED [EC:2.4.2.34]
synonym: "UDP-L-arabinose:(indol-3-yl)acetyl-myo-inositol L-arabinosyltransferase activity" RELATED [EC:2.4.2.34]
synonym: "UDP-L-arabinose:indol-3-ylacetyl-myo-inositol L-arabinosyltransferase activity" RELATED [EC:2.4.2.34]
@@ -299346,7 +299358,7 @@ is_a: GO:0052636 ! arabinosyltransferase activity
id: GO:0050410
name: 3-oxolaurate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-oxolaurate + H(+) = 2-undecanone + CO(2)." [EC:4.1.1.56, RHEA:13385]
+def: "Catalysis of the reaction: 3-oxolaurate + H+ = 2-undecanone + CO2." [EC:4.1.1.56, RHEA:13385]
synonym: "3-oxododecanoate carboxy-lyase (2-undecanone-forming)" RELATED [EC:4.1.1.56]
synonym: "3-oxododecanoate carboxy-lyase activity" RELATED [EC:4.1.1.56]
synonym: "beta-ketoacyl decarboxylase activity" RELATED [EC:4.1.1.56]
@@ -299390,7 +299402,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0050413
name: D-alanine 2-hydroxymethyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5,10-methylenetetrahydrofolate + D-alanine + H(2)O = (6S)-5,6,7,8-tetrahydrofolate + 2-methylserine." [EC:2.1.2.7, RHEA:10064]
+def: "Catalysis of the reaction: 5,10-methylenetetrahydrofolate + D-alanine + H2O = (6S)-5,6,7,8-tetrahydrofolate + 2-methylserine." [EC:2.1.2.7, RHEA:10064]
synonym: "2-methylserine hydroxymethyltransferase activity" RELATED [EC:2.1.2.7]
synonym: "5,10-methylenetetrahydrofolate:D-alanine 2-hydroxymethyltransferase activity" RELATED [EC:2.1.2.7]
synonym: "D-alanine hydroxymethyltransferase activity" EXACT []
@@ -299416,7 +299428,7 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050415
name: formimidoylglutamase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-formimidoyl-L-glutamate + H(2)O = L-glutamate + formamide." [EC:3.5.3.8, RHEA:22492]
+def: "Catalysis of the reaction: N-formimidoyl-L-glutamate + H2O = L-glutamate + formamide." [EC:3.5.3.8, RHEA:22492]
synonym: "formiminoglutamase activity" EXACT []
synonym: "formiminoglutamate hydrolase activity" RELATED [EC:3.5.3.8]
synonym: "N-formimidoyl-L-glutamate formimidoylhydrolase activity" RELATED [EC:3.5.3.8]
@@ -299472,7 +299484,7 @@ is_a: GO:0016661 ! oxidoreductase activity, acting on other nitrogenous compound
id: GO:0050419
name: hydroxymandelonitrile lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-hydroxymandelonitrile = 4-hydroxybenzaldehyde + hydrocyanate." [EC:4.1.2.11, MetaCyc:HYDROXYMANDELONITRILE-LYASE-RXN]
+def: "Catalysis of the reaction: 4-hydroxymandelonitrile = 4-hydroxybenzaldehyde + hydrocyanate." [RHEA:15977]
synonym: "(S)-4-hydroxymandelonitrile 4-hydroxybenzaldehyde-lyase (cyanide-forming)" RELATED [EC:4.1.2.11]
synonym: "(S)-4-hydroxymandelonitrile hydroxybenzaldehyde-lyase activity" RELATED [EC:4.1.2.11]
synonym: "hydroxynitrile lyase activity" BROAD [EC:4.1.2.11]
@@ -299502,7 +299514,7 @@ def: "Catalysis of the reaction: nitric oxide + H2O + ferricytochrome c = nitrit
comment: Note that EC:1.7.99.3 was merged into this term.
synonym: "[nitrite reductase (cytochrome)]" RELATED [EC:1.7.2.1]
synonym: "cd-cytochrome nitrite reductase activity" NARROW [EC:1.7.2.1]
-synonym: "cytochrome c-551:O(2), NO(2)(+) oxidoreductase activity" NARROW [EC:1.7.2.1]
+synonym: "cytochrome c-551:O2, NO2(+) oxidoreductase activity" RELATED [EC:1.7.2.1]
synonym: "cytochrome c-551:O2, NO2+ oxidoreductase activity" RELATED [EC:1.7.2.1]
synonym: "cytochrome cd activity" NARROW [EC:1.7.2.1]
synonym: "cytochrome cd1 activity" NARROW [EC:1.7.2.1]
@@ -299511,7 +299523,6 @@ synonym: "nitric-oxide:ferricytochrome-c oxidoreductase activity" RELATED [EC:1.
synonym: "nitrite reductase (cytochrome; NO-forming) activity" RELATED [EC:1.7.2.1]
synonym: "NO-forming nitrite reductase (cytochrome) activity" EXACT []
synonym: "NO-forming nitrite reductase activity" EXACT []
-synonym: "Pseudomonas cytochrome oxidase activity" NARROW [EC:1.7.2.1]
xref: EC:1.7.2.1
xref: MetaCyc:NITRITE-REDUCTASE-CYTOCHROME-RXN
xref: RHEA:15233
@@ -299522,7 +299533,7 @@ is_a: GO:0098809 ! nitrite reductase activity
id: GO:0050422
name: strictosidine beta-glucosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3alpha(S)-strictosidine + H(2)O = D-glucose + strictosidine aglycone." [EC:3.2.1.105, RHEA:12917]
+def: "Catalysis of the reaction: 3alpha(S)-strictosidine + H2O = D-glucose + strictosidine aglycone." [EC:3.2.1.105, RHEA:12917]
synonym: "strictosidine b-glucosidase activity" EXACT []
synonym: "strictosidine beta-D-glucohydrolase activity" RELATED [EC:3.2.1.105]
xref: EC:3.2.1.105
@@ -299636,7 +299647,7 @@ is_a: GO:0050427 ! 3'-phosphoadenosine 5'-phosphosulfate metabolic process
id: GO:0050429
name: calcium-dependent phospholipase C activity
namespace: molecular_function
-def: "Catalysis of the reaction: a phosphatidylcholine + H2O = 1,2-diacylglycerol + choline phosphate. This reaction requires Ca2+." [EC:3.1.4.3]
+def: "Catalysis of the reaction: a phosphatidylcholine + H2O = 1,2-diacylglycerol + choline phosphate. This reaction requires Ca2+." [PMID:25769297, PMID:9426125]
is_a: GO:0004629 ! phospholipase C activity
[Term]
@@ -299704,7 +299715,7 @@ is_a: GO:0005488 ! binding
id: GO:0050437
name: (-)-endo-fenchol synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: geranyl diphosphate + H(2)O = (-)-endo-fenchol + diphosphate." [EC:4.2.3.10, RHEA:20565]
+def: "Catalysis of the reaction: geranyl diphosphate + H2O = (-)-endo-fenchol + diphosphate." [EC:4.2.3.10, RHEA:20565]
synonym: "(-)-endo-fenchol cyclase activity" RELATED [EC:4.2.3.10]
synonym: "geranyl pyrophosphate:(-)-endo-fenchol cyclase activity" RELATED [EC:4.2.3.10]
synonym: "geranyl-diphosphate diphosphate-lyase [cyclizing, (-)-endo-fenchol-forming]" RELATED [EC:4.2.3.10]
@@ -299718,7 +299729,7 @@ is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
id: GO:0050438
name: 2-ethylmalate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxobutanate + acetyl-CoA + H(2)O = (R)-2-ethylmalate + CoA + H(+)." [EC:2.3.3.6, RHEA:23040]
+def: "Catalysis of the reaction: 2-oxobutanate + acetyl-CoA + H2O = (R)-2-ethylmalate + CoA + H+." [RHEA:23040]
synonym: "(R)-2-ethylmalate 2-oxobutanoyl-lyase (CoA-acetylating) activity" RELATED [EC:2.3.3.6]
synonym: "2-ethylmalate-3-hydroxybutanedioate synthase activity" RELATED [EC:2.3.3.6]
synonym: "acetyl-CoA:2-oxobutanoate C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming)" RELATED [EC:2.3.3.6]
@@ -299728,13 +299739,13 @@ xref: EC:2.3.3.6
xref: KEGG_REACTION:R00998
xref: MetaCyc:2-ETHYLMALATE-SYNTHASE-RXN
xref: RHEA:23040
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0050439
name: 2-hydroxy-3-oxoadipate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + glyoxylate + H(+) = 2-hydroxy-3-oxoadipate + CO(2)." [EC:2.2.1.5, RHEA:14341]
+def: "Catalysis of the reaction: 2-oxoglutarate + glyoxylate + H+ = 2-hydroxy-3-oxoadipate + CO2." [EC:2.2.1.5, RHEA:14341]
synonym: "2-hydroxy-3-oxoadipate glyoxylate-lyase (carboxylating) activity" RELATED [EC:2.2.1.5]
synonym: "2-hydroxy-3-oxoadipate synthetase activity" RELATED [EC:2.2.1.5]
synonym: "2-oxoglutarate:glyoxylate succinaldehydetransferase (decarboxylating)" RELATED [EC:2.2.1.5]
@@ -299751,7 +299762,7 @@ is_a: GO:0016744 ! transketolase or transaldolase activity
id: GO:0050440
name: 2-methylcitrate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + oxaloacetate + propanoyl-CoA = (2R,3S)-2-methylcitrate + CoA + H(+)." [EC:2.3.3.5, RHEA:23780]
+def: "Catalysis of the reaction: H2O + oxaloacetate + propanoyl-CoA = (2R,3S)-2-methylcitrate + CoA + H+." [RHEA:23780]
synonym: "2-methylcitrate oxaloacetate-lyase activity" RELATED [EC:2.3.3.5]
synonym: "MCS activity" RELATED [EC:2.3.3.5]
synonym: "methylcitrate synthase activity" RELATED [EC:2.3.3.5]
@@ -299761,13 +299772,13 @@ xref: EC:2.3.3.5
xref: KEGG_REACTION:R00931
xref: MetaCyc:2-METHYLCITRATE-SYNTHASE-RXN
xref: RHEA:23780
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0050441
name: 3-ethylmalate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: butanoyl-CoA + glyoxylate + H(2)O = 3-ethylmalate + CoA + H(+)." [EC:2.3.3.7, RHEA:10500]
+def: "Catalysis of the reaction: butanoyl-CoA + glyoxylate + H2O = 3-ethylmalate + CoA + H+." [RHEA:10500]
synonym: "2-ethyl-3-hydroxybutanedioate synthase activity" RELATED [EC:2.3.3.7]
synonym: "3-ethylmalate glyoxylate-lyase (CoA-butanoylating) activity" RELATED [EC:2.3.3.7]
synonym: "butanoyl-CoA:glyoxylate C-butanoyltransferase (thioester-hydrolysing, 1-carboxypropyl-forming)" RELATED [EC:2.3.3.7]
@@ -299775,13 +299786,13 @@ xref: EC:2.3.3.7
xref: KEGG_REACTION:R01180
xref: MetaCyc:3-ETHYLMALATE-SYNTHASE-RXN
xref: RHEA:10500
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0050442
name: 3-propylmalate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glyoxylate + H(2)O + pentanoyl-CoA = 3-propylmalate + CoA + H(+)." [EC:2.3.3.12, RHEA:14457]
+def: "Catalysis of the reaction: glyoxylate + H2O + pentanoyl-CoA = 3-propylmalate + CoA + H+." [RHEA:14457]
synonym: "3-(n-propyl)-malate synthase activity" RELATED [EC:2.3.3.12]
synonym: "3-propylmalate glyoxylate-lyase (CoA-pentanoylating) activity" RELATED [EC:2.3.3.12]
synonym: "beta-n-propylmalate synthase activity" RELATED [EC:2.3.3.12]
@@ -299791,7 +299802,7 @@ xref: EC:2.3.3.12
xref: KEGG_REACTION:R03040
xref: MetaCyc:3-PROPYLMALATE-SYNTHASE-RXN
xref: RHEA:14457
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0050444
@@ -299814,7 +299825,7 @@ is_obsolete: true
id: GO:0050445
name: asparagusate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-mercapto-2-mercaptomethylpropanoate + NAD(+) = asparagusate + H(+) + NADH." [RHEA:14881]
+def: "Catalysis of the reaction: 3-mercapto-2-mercaptomethylpropanoate + NAD+ = asparagusate + H+ + NADH." [RHEA:14881]
synonym: "3-mercapto-2-mercaptomethylpropanoate:NAD+ oxidoreductase activity" RELATED [EC:1.8.1.11]
synonym: "asparagusate dehydrogenase activity" RELATED [EC:1.8.1.11]
synonym: "asparagusate reductase (NADH) activity" EXACT []
@@ -299864,7 +299875,7 @@ is_a: GO:0046857 ! oxidoreductase activity, acting on other nitrogenous compound
id: GO:0050447
name: zeatin 9-aminocarboxyethyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O-acetyl-L-serine + zeatin = L-lupinate + acetate + H(+)." [EC:2.5.1.50, RHEA:17333]
+def: "Catalysis of the reaction: O-acetyl-L-serine + zeatin = L-lupinate + acetate + H+." [EC:2.5.1.50, RHEA:17333]
synonym: "3-O-acetyl-L-serine:zeatin 2-amino-2-carboxyethyltransferase activity" RELATED [EC:2.5.1.50]
synonym: "beta-(9-cytokinin)-alanine synthase activity" EXACT []
synonym: "beta-(9-cytokinin)alanine synthase activity" RELATED [EC:2.5.1.50]
@@ -299914,7 +299925,7 @@ is_a: GO:0010333 ! terpene synthase activity
id: GO:0050450
name: citrate (Re)-synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA, where the acetyl group is added to the re-face of oxaloacetate; acetyl-CoA provides the two carbon atoms of the pro-R carboxymethyl group." [EC:2.3.3.3, ISBN:0121227073, MetaCyc:CITRATE-RE-SYNTHASE-RXN]
+def: "Catalysis of the reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA, where the acetyl group is added to the re-face of oxaloacetate; acetyl-CoA provides the two carbon atoms of the pro-R carboxymethyl group." [PMID:17400742]
synonym: "(R)-citrate synthase activity" RELATED [EC:2.3.3.3]
synonym: "acetyl-CoA:oxaloacetate C-acetyltransferase [thioester-hydrolysing, (pro-R)-carboxymethyl-forming]" RELATED [EC:2.3.3.3]
synonym: "citrate oxaloacetate-lyase ((pro-3R)-CH(2)COO(-)->acetyl-CoA) activity" RELATED [EC:2.3.3.3]
@@ -299965,9 +299976,10 @@ is_a: GO:0016668 ! oxidoreductase activity, acting on a sulfur group of donors,
[Term]
id: GO:0050453
-name: cob(II)alamin reductase activity
+name: obsolete cob(II)alamin reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 cob(I)alamin + H(+) + NAD(+) = 2 cob(II)alamin + NADH." [RHEA:17481]
+def: "OBSOLETE. Catalysis of the reaction: 2 cob(I)alamin + H+ + NAD+ = 2 cob(II)alamin + NADH." [RHEA:17481]
+comment: The reason for obsoletion is that this term has been deleted from EC. RHEA:17481 with the note: "This reaction may occur spontaneously."
synonym: "B(12r) reductase activity" RELATED [EC:1.16.1.4]
synonym: "B12r reductase activity" RELATED [EC:1.16.1.4]
synonym: "cob(I)alamin:NAD+ oxidoreductase activity" RELATED [EC:1.16.1.4]
@@ -299980,15 +299992,14 @@ synonym: "vitamin B12r reductase activity" RELATED [EC:1.16.1.4]
xref: EC:1.16.1.4
xref: KEGG_REACTION:R00099
xref: MetaCyc:COBIIALAMIN-REDUCTASE-RXN
-xref: Reactome:R-HSA-3149560 "Unknown reductase reduces cob(II)alamin to cob(I)alamin"
xref: RHEA:17481
-is_a: GO:0016723 ! oxidoreductase activity, acting on metal ions, NAD or NADP as acceptor
+is_obsolete: true
[Term]
id: GO:0050454
name: coenzyme F420 hydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: coenzyme F420 + H(2) + H(+) = reduced coenzyme F420." [EC:1.12.98.1, RHEA:23760]
+def: "Catalysis of the reaction: coenzyme F420 + H(2) + H+ = reduced coenzyme F420." [EC:1.12.98.1, RHEA:23760]
synonym: "8-hydroxy-5-deazaflavin-reducing hydrogenase activity" RELATED [EC:1.12.98.1]
synonym: "coenzyme F420-dependent hydrogenase activity" RELATED [EC:1.12.98.1]
synonym: "F420-reducing hydrogenase activity" RELATED [EC:1.12.98.1]
@@ -300003,7 +300014,7 @@ is_a: GO:0046995 ! oxidoreductase activity, acting on hydrogen as donor, with ot
id: GO:0050455
name: columbamine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 columbamine + O(2) = 2 berberine + 2 H(2)O." [EC:1.21.3.2, RHEA:23564]
+def: "Catalysis of the reaction: 2 columbamine + O2 = 2 berberine + 2 H2O." [RHEA:23564]
synonym: "berberine synthase activity" RELATED [EC:1.21.3.2]
synonym: "columbamine:oxygen oxidoreductase (cyclizing)" RELATED [EC:1.21.3.2]
xref: EC:1.21.3.2
@@ -300016,7 +300027,7 @@ is_a: GO:0046993 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y
id: GO:0050456
name: cystine reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 L-cysteine + NAD(+) = L-cystine + H(+) + NADH." [EC:1.8.1.6, RHEA:20597]
+def: "Catalysis of the reaction: 2 L-cysteine + NAD+ = L-cystine + H+ + NADH." [EC:1.8.1.6, RHEA:20597]
synonym: "cystine reductase (NADH) activity" RELATED [EC:1.8.1.6]
synonym: "cystine reductase (NADH2)" RELATED [EC:1.8.1.6]
synonym: "L-cysteine:NAD+ oxidoreductase" RELATED [EC:1.8.1.6]
@@ -300033,7 +300044,7 @@ is_a: GO:0016668 ! oxidoreductase activity, acting on a sulfur group of donors,
id: GO:0050457
name: decylcitrate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + lauroyl-CoA + oxaloacetate = (2S,3S)-2-hydroxytridecane-1,2,3-tricarboxylate + CoA + H(+)." [EC:2.3.3.2, RHEA:16605]
+def: "Catalysis of the reaction: H2O + lauroyl-CoA + oxaloacetate = (2S,3S)-2-hydroxytridecane-1,2,3-tricarboxylate + CoA + H+." [RHEA:16605]
synonym: "(2S,3S)-2-hydroxytridecane-1,2,3-tricarboxylate oxaloacetate-lyase (CoA- acylating) activity" RELATED [EC:2.3.3.2]
synonym: "(2S,3S)-2-hydroxytridecane-1,2,3-tricarboxylate oxaloacetate-lyase (CoA-acylating)" RELATED [EC:2.3.3.2]
synonym: "2-decylcitrate synthase activity" RELATED [EC:2.3.3.2]
@@ -300042,13 +300053,13 @@ xref: EC:2.3.3.2
xref: KEGG_REACTION:R03735
xref: MetaCyc:DECYLCITRATE-SYNTHASE-RXN
xref: RHEA:16605
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0050458
name: decylhomocitrate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + H(2)O + lauroyl-CoA = (3S,4S)-3-hydroxytetradecane-1,3,4-tricarboxylate + CoA + H(+)." [EC:2.3.3.4, RHEA:10364]
+def: "Catalysis of the reaction: 2-oxoglutarate + H2O + lauroyl-CoA = (3S,4S)-3-hydroxytetradecane-1,3,4-tricarboxylate + CoA + H+." [RHEA:10364]
synonym: "2-decylhomocitrate synthase activity" RELATED [EC:2.3.3.4]
synonym: "3-hydroxytetradecane-1,3,4-tricarboxylate 2-oxoglutarate-lyase (CoA- acylating) activity" RELATED [EC:2.3.3.4]
synonym: "3-hydroxytetradecane-1,3,4-tricarboxylate 2-oxoglutarate-lyase (CoA-acylating)" RELATED [EC:2.3.3.4]
@@ -300057,13 +300068,13 @@ xref: EC:2.3.3.4
xref: KEGG_REACTION:R03859
xref: MetaCyc:DECYLHOMOCITRATE-SYNTHASE-RXN
xref: RHEA:10364
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0050459
name: ethanolamine-phosphate phospho-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + phosphoethanolamine = acetaldehyde + NH(4)(+) + phosphate." [EC:4.2.3.2, RHEA:17889]
+def: "Catalysis of the reaction: H2O + phosphoethanolamine = acetaldehyde + NH4 + phosphate." [EC:4.2.3.2, RHEA:17889]
synonym: "amino alcohol O-phosphate phospholyase activity" BROAD [EC:4.2.3.2]
synonym: "ethanolamine-phosphate phospho-lyase (deaminating)" RELATED [EC:4.2.3.2]
synonym: "ethanolamine-phosphate phospho-lyase (deaminating; acetaldehyde-forming)" RELATED [EC:4.2.3.2]
@@ -300204,7 +300215,7 @@ is_a: GO:0010334 ! sesquiterpene synthase activity
id: GO:0050468
name: reticuline oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-reticuline + O(2) = (S)-scoulerine + H(2)O(2) + H(+)." [EC:1.21.3.3, RHEA:19885]
+def: "Catalysis of the reaction: (S)-reticuline + O2 = (S)-scoulerine + H2O2 + H+." [RHEA:19885]
synonym: "(S)-reticuline:oxygen oxidoreductase (methylene-bridge-forming)" RELATED [EC:1.21.3.3]
synonym: "BBE" RELATED [EC:1.21.3.3]
synonym: "berberine bridge enzyme activity" RELATED [EC:1.21.3.3]
@@ -300220,7 +300231,7 @@ is_a: GO:0046993 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y
id: GO:0050469
name: sabinene-hydrate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: geranyl diphosphate + H(2)O = diphosphate + sabinene hydrate." [EC:4.2.3.11, RHEA:19565]
+def: "Catalysis of the reaction: geranyl diphosphate + H2O = diphosphate + sabinene hydrate." [EC:4.2.3.11, RHEA:19565]
synonym: "geranyl-diphosphate diphosphate-lyase (cyclizing, sabinene-hydrate-forming)" RELATED [EC:4.2.3.11]
synonym: "sabinene hydrate cyclase activity" RELATED [EC:4.2.3.11]
xref: EC:4.2.3.11
@@ -300262,7 +300273,7 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0050472
name: zeatin reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dihydrozeatin + NADP(+) = H(+) + NADPH + zeatin." [EC:1.3.1.69, RHEA:12757]
+def: "Catalysis of the reaction: dihydrozeatin + NADP+ = H+ + NADPH + zeatin." [EC:1.3.1.69, RHEA:12757]
synonym: "dihydrozeatin:NADP+ oxidoreductase activity" RELATED [EC:1.3.1.69]
xref: EC:1.3.1.69
xref: KEGG_REACTION:R05702
@@ -300346,8 +300357,8 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050478
name: obsolete anthranilate 3-monooxygenase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: 5,6,7,8-tetrahydrobiopterin + anthranilate + O(2) = 3-hydroxyanthranilate + 7,8-dihydrobiopterin + H(2)O." [GOC:curators]
-comment: This term is slated for obsoletion; According to RHEA the activity does not exist.
+def: "OBSOLETE. Catalysis of the reaction: 5,6,7,8-tetrahydrobiopterin + anthranilate + O2 = 3-hydroxyanthranilate + 7,8-dihydrobiopterin + H2O." [GOC:curators]
+comment: This term is slated for obsoletion; According to RHEA the activity does not exist.
synonym: "anthranilate 3-hydroxylase activity" EXACT []
synonym: "anthranilate,tetrahydrobiopterin:oxygen oxidoreductase (3-hydroxylating)" RELATED []
synonym: "anthranilic acid hydroxylase activity" BROAD []
@@ -300374,7 +300385,7 @@ is_a: GO:0016714 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050480
name: imidazolonepropionase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-3-(4-oxo-4,5-dihydro-1H-imidazol-5-yl)propanoic acid + H(2)O = N-formimidoyl-L-glutamate + H(+)." [EC:3.5.2.7, RHEA:23660]
+def: "Catalysis of the reaction: (S)-3-(4-oxo-4,5-dihydro-1H-imidazol-5-yl)propanoic acid + H2O = N-formimidoyl-L-glutamate + H+." [EC:3.5.2.7, RHEA:23660]
synonym: "3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate amidohydrolase activity" RELATED [EC:3.5.2.7]
synonym: "4(5)-imidazolone-5(4)-propionic acid hydrolase activity" RELATED [EC:3.5.2.7]
synonym: "imidazolone propionic acid hydrolase activity" RELATED [EC:3.5.2.7]
@@ -300389,7 +300400,7 @@ is_a: GO:0016812 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050481
name: mandelate 4-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-mandelate + 5,6,7,8-tetrahydrobiopterin + O(2) = (S)-4-hydroxymandelate + 7,8-dihydrobiopterin + H(2)O. (S)-2-hydroxy-2-phenylacetate is also known as S-mandelate." [EC:1.14.16.6, RHEA:21716]
+def: "Catalysis of the reaction: (S)-mandelate + 5,6,7,8-tetrahydrobiopterin + O2 = (S)-4-hydroxymandelate + 7,8-dihydrobiopterin + H2O. (S)-2-hydroxy-2-phenylacetate is also known as S-mandelate." [EC:1.14.16.6, RHEA:21716]
synonym: "(S)-2-hydroxy-2-phenylacetate,tetrahydrobiopterin:oxygen oxidoreductase (4-hydroxylating)" RELATED [EC:1.14.16.6]
synonym: "L-mandelate 4-hydroxylase activity" EXACT []
synonym: "mandelic acid 4-hydroxylase activity" RELATED [EC:1.14.16.6]
@@ -300451,7 +300462,7 @@ is_a: GO:0016866 ! intramolecular transferase activity
id: GO:0050487
name: sulfoacetaldehyde acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl phosphate + sulfite = phosphate + sulfoacetaldehyde." [EC:2.3.3.15, RHEA:24204]
+def: "Catalysis of the reaction: acetyl phosphate + sulfite = phosphate + sulfoacetaldehyde." [RHEA:24204]
comment: Note that the enzyme sulfoacetaldehyde acetyltransferase also has sulfoacetaldehyde lyase activity (GO:0050312).
synonym: "acetyl-phosphate:sulfite S-acetyltransferase (acyl-phosphate hydrolysing, 2-oxoethyl-forming)" RELATED [EC:2.3.3.15]
synonym: "sulphoacetaldehyde acetyltransferase activity" EXACT []
@@ -300459,7 +300470,7 @@ xref: EC:2.3.3.15
xref: KEGG_REACTION:R05651
xref: MetaCyc:RXN-2364
xref: RHEA:24204
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0050488
@@ -300486,7 +300497,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050491
name: sulcatone reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD(+) + sulcatol = H(+) + NADH + sulcatone." [EC:1.1.1.260, RHEA:24484]
+def: "Catalysis of the reaction: NAD+ + sulcatol = H+ + NADH + sulcatone." [EC:1.1.1.260, RHEA:24484]
synonym: "sulcatol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.260]
xref: EC:1.1.1.260
xref: KEGG_REACTION:R05678
@@ -300609,7 +300620,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0050502
name: cis-zeatin O-beta-D-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cis-zeatin + UDP-D-glucose = O-beta-D-glucosyl-cis-zeatin + H(+) + UDP." [EC:2.4.1.215, RHEA:20681]
+def: "Catalysis of the reaction: cis-zeatin + UDP-D-glucose = O-beta-D-glucosyl-cis-zeatin + H+ + UDP." [EC:2.4.1.215, RHEA:20681]
synonym: "cis-zeatin O-b-D-glucosyltransferase activity" EXACT []
synonym: "UDP-glucose:cis-zeatin O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.215]
synonym: "UDPglucose:cis-zeatin O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.215]
@@ -300634,7 +300645,7 @@ is_a: GO:0004645 ! 1,4-alpha-oligoglucan phosphorylase activity
id: GO:0050504
name: mannosyl-3-phosphoglycerate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-phospho-D-glycerate + GDP-alpha-D-mannose = 2-(alpha-D-mannosyl)-3-phosphoglycerate + GDP + H(+)." [EC:2.4.1.217, RHEA:13537]
+def: "Catalysis of the reaction: 3-phospho-D-glycerate + GDP-alpha-D-mannose = 2-(alpha-D-mannosyl)-3-phosphoglycerate + GDP + H+." [EC:2.4.1.217, RHEA:13537]
synonym: "GDP-mannose:3-phosphoglycerate 3-alpha-D-mannosyltransferase activity" RELATED [EC:2.4.1.217]
synonym: "MPG synthase activity" RELATED [EC:2.4.1.217]
xref: EC:2.4.1.217
@@ -300647,7 +300658,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0050505
name: hydroquinone glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: hydroquinone + UDP-D-glucose = H(+) + hydroquinone O-beta-D-glucopyranoside + UDP." [EC:2.4.1.218, RHEA:12560]
+def: "Catalysis of the reaction: hydroquinone + UDP-D-glucose = H+ + hydroquinone O-beta-D-glucopyranoside + UDP." [EC:2.4.1.218, RHEA:12560]
synonym: "arbutin synthase activity" RELATED [EC:2.4.1.218]
synonym: "hydroquinone:O-glucosyltransferase activity" RELATED [EC:2.4.1.218]
synonym: "UDP-glucose:hydroquinone-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.218]
@@ -300662,7 +300673,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0050506
name: vomilenine glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: UDP-D-glucose + vomilenine = H(+) + raucaffricine + UDP." [EC:2.4.1.219, RHEA:19385]
+def: "Catalysis of the reaction: UDP-D-glucose + vomilenine = H+ + raucaffricine + UDP." [EC:2.4.1.219, RHEA:19385]
synonym: "UDP-glucose:vomilenine 21-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.219]
synonym: "UDPG:vomilenine 21-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.219]
synonym: "UDPG:vomilenine 21beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.219]
@@ -300677,7 +300688,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0050507
name: indoxyl-UDPG glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: indoxyl + UDP-D-glucose = H(+) + indican + UDP." [EC:2.4.1.220, RHEA:12004]
+def: "Catalysis of the reaction: indoxyl + UDP-D-glucose = H+ + indican + UDP." [EC:2.4.1.220, RHEA:12004]
synonym: "indoxyl-UDPG-glucosyltransferase activity" RELATED [EC:2.4.1.220]
synonym: "UDP-glucose:indoxyl 3-O-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.220]
xref: EC:2.4.1.220
@@ -300778,7 +300789,7 @@ is_a: GO:0035250 ! UDP-galactosyltransferase activity
id: GO:0050513
name: glycoprotein 2-beta-D-xylosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl}-L-asparagine + UDP-alpha-D-xylose = N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-[beta-D-xylosyl-(1->2)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl}-L-asparagine + H(+) + UDP." [EC:2.4.2.38, RHEA:10612]
+def: "Catalysis of the reaction: N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl}-L-asparagine + UDP-alpha-D-xylose = N(4)-{N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6)]-[beta-D-xylosyl-(1->2)]-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl}-L-asparagine + H+ + UDP." [EC:2.4.2.38, RHEA:10612]
synonym: "1,2-beta-xylosyltransferase activity" RELATED [EC:2.4.2.38]
synonym: "beta-1,2-xylosyltransferase activity" RELATED [EC:2.4.2.38]
synonym: "glycoprotein 2-b-D-xylosyltransferase activity" EXACT []
@@ -300804,7 +300815,7 @@ id: GO:0050515
name: 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity
namespace: molecular_function
alt_id: GO:0008698
-def: "Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + 2 H(+)." [EC:2.7.1.148, RHEA:18437]
+def: "Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + 2 H+." [EC:2.7.1.148, RHEA:18437]
synonym: "4-diphosphocytidyl-2-C-methyl-D-erythritol kinase activity" RELATED [EC:2.7.1.148]
synonym: "4-diphosphocytidyl-2C-methyl-D-erythritol kinase activity" EXACT []
synonym: "ATP:4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol 2-phosphotransferase activity" RELATED [EC:2.7.1.148]
@@ -300850,8 +300861,6 @@ synonym: "ATP:1D-myo-inositol-hexakisphosphate 5-phosphotransferase activity" RE
synonym: "ATP:1D-myo-inositol-hexakisphosphate phosphotransferase activity" RELATED [EC:2.7.4.21]
synonym: "inositol hexakisphosphate kinase activity" EXACT []
synonym: "inositol-hexakisphosphate kinase activity" EXACT []
-xref: EC:2.7.4.21
-xref: MetaCyc:2.7.1.152-RXN
is_obsolete: true
[Term]
@@ -300890,7 +300899,7 @@ is_a: GO:0016779 ! nucleotidyltransferase activity
id: GO:0050520
name: phosphatidylcholine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: CDP-diacylglycerol + choline = 1,2-diacyl-sn-glycero-3-phosphocholine + CMP + H(+)." [EC:2.7.8.24, RHEA:14597]
+def: "Catalysis of the reaction: CDP-diacylglycerol + choline = 1,2-diacyl-sn-glycero-3-phosphocholine + CMP + H+." [EC:2.7.8.24, RHEA:14597]
synonym: "CDP-diacylglycerol:choline O-phosphatidyltransferase activity" RELATED [EC:2.7.8.24]
synonym: "CDP-diglyceride-choline O-phosphatidyltransferase activity" RELATED [EC:2.7.8.24]
synonym: "CDPdiglyceride-choline O-phosphatidyltransferase activity" RELATED [EC:2.7.8.24]
@@ -301015,7 +301024,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050529
name: polyneuridine-aldehyde esterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + polyneuridine aldehyde = 16-epivellosimine + CO(2) + methanol." [EC:3.1.1.78, RHEA:17501]
+def: "Catalysis of the reaction: H2O + polyneuridine aldehyde = 16-epivellosimine + CO2 + methanol." [EC:3.1.1.78, RHEA:17501]
synonym: "PNAE activity" RELATED [EC:3.1.1.78]
synonym: "polyneuridine aldehyde esterase activity" RELATED [EC:3.1.1.78]
synonym: "polyneuridine aldehyde hydrolase (decarboxylating)" RELATED [EC:3.1.1.78]
@@ -301029,7 +301038,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050530
name: glucosylglycerol 3-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-O-(beta-D-glucosyl)-sn-glycerol 3-phosphate + H(2)O = 2-O-(beta-D-glucosyl)-sn-glycerol + phosphate." [EC:3.1.3.69, RHEA:22652]
+def: "Catalysis of the reaction: 2-O-(beta-D-glucosyl)-sn-glycerol 3-phosphate + H2O = 2-O-(beta-D-glucosyl)-sn-glycerol + phosphate." [EC:3.1.3.69, RHEA:22652]
synonym: "2-(beta-D-glucosyl)-sn-glycerol-3-phosphate phosphohydrolase activity" RELATED [EC:3.1.3.69]
synonym: "salt tolerance protein A" RELATED [EC:3.1.3.69]
synonym: "StpA" RELATED [EC:3.1.3.69]
@@ -301043,7 +301052,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0050531
name: mannosyl-3-phosphoglycerate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-(alpha-D-mannosyl)-3-phosphoglycerate + H(2)O = 2-(alpha-D-mannosyl)-D-glycerate + phosphate." [EC:3.1.3.70, RHEA:19309]
+def: "Catalysis of the reaction: 2-(alpha-D-mannosyl)-3-phosphoglycerate + H2O = 2-(alpha-D-mannosyl)-D-glycerate + phosphate." [EC:3.1.3.70, RHEA:19309]
synonym: "alpha-D-mannosyl-3-phosphoglycerate phosphohydrolase activity" RELATED [EC:3.1.3.70]
xref: EC:3.1.3.70
xref: KEGG_REACTION:R05790
@@ -301055,7 +301064,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0050532
name: 2-phosphosulfolactate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2R)-O-phospho-3-sulfolactate + H(2)O = (R)-3-sulfolactate + phosphate." [EC:3.1.3.71, RHEA:23416]
+def: "Catalysis of the reaction: (2R)-O-phospho-3-sulfolactate + H2O = (R)-3-sulfolactate + phosphate." [EC:3.1.3.71, RHEA:23416]
synonym: "(2R)-phosphosulfolactate phosphohydrolase activity" RELATED [EC:3.1.3.71]
synonym: "(R)-2-phospho-3-sulfolactate phosphohydrolase activity" RELATED [EC:3.1.3.71]
synonym: "2-phosphosulpholactate phosphatase activity" EXACT []
@@ -301104,7 +301113,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0050536
name: (S)-N-acetyl-1-phenylethylamine hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-acetylphenylethylamine + H(2)O = acetate + phenylethylamine." [EC:3.5.1.85, RHEA:23952]
+def: "Catalysis of the reaction: N-acetylphenylethylamine + H2O = acetate + phenylethylamine." [EC:3.5.1.85, RHEA:23952]
synonym: "(S)-N-acetyl-1-phenylethylamine amidohydrolase activity" RELATED [EC:3.5.1.85]
synonym: "(S)-N-acetylphenylethylamine:H2O hydrolase activity" RELATED [EC:3.5.1.85]
xref: EC:3.5.1.85
@@ -301117,7 +301126,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050537
name: mandelamide amidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-mandelamide + H(2)O = (R)-mandelate + NH(4)(+)." [EC:3.5.1.86, RHEA:22876]
+def: "Catalysis of the reaction: (R)-mandelamide + H2O = (R)-mandelate + NH4." [EC:3.5.1.86, RHEA:22876]
synonym: "mandelamide hydrolase activity" RELATED [EC:3.5.1.86]
synonym: "Pseudomonas mandelamide hydrolase activity" RELATED [EC:3.5.1.86]
xref: EC:3.5.1.86
@@ -301142,7 +301151,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050539
name: maleimide hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + maleimide = H(+) + maleamate." [EC:3.5.2.16, RHEA:24476]
+def: "Catalysis of the reaction: H2O + maleimide = H+ + maleamate." [EC:3.5.2.16, RHEA:24476]
synonym: "cyclic imide hydrolase activity" RELATED [EC:3.5.2.16]
synonym: "cyclic-imide amidohydrolase (decyclicizing)" RELATED [EC:3.5.2.16]
synonym: "cyclic-imide amidohydrolase (decyclizing)" RELATED [EC:3.5.2.16]
@@ -301157,13 +301166,12 @@ is_a: GO:0016812 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0050540
name: 2-aminomuconate deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-aminomuconate + H(2)O + H(+) = (Z)-5-oxohex-2-enedioate + NH(4)(+)." [EC:3.5.99.5, RHEA:20996]
+def: "Catalysis of the reaction: 2-aminomuconate + H2O + H+ = (Z)-5-oxohex-2-enedioate + NH4." [EC:3.5.99.5, RHEA:20996]
synonym: "2-aminomuconate aminohydrolase activity" RELATED [EC:3.5.99.5]
xref: EC:3.5.99.5
xref: KEGG_REACTION:R03887
xref: MetaCyc:3.5.99.5-RXN
xref: RHEA:20996
-is_a: GO:0016810 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
is_a: GO:0019239 ! deaminase activity
[Term]
@@ -301196,7 +301204,6 @@ name: arachidonic acid binding
namespace: molecular_function
def: "Binding to arachidonic acid, a straight chain fatty acid with 20 carbon atoms and four double bonds per molecule. Arachidonic acid is the all-Z-(5,8,11,14)-isomer." [GOC:ai]
synonym: "arachidonate binding" EXACT []
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0050542 ! icosanoid binding
is_a: GO:0050543 ! icosatetraenoic acid binding
@@ -301204,7 +301211,7 @@ is_a: GO:0050543 ! icosatetraenoic acid binding
id: GO:0050545
name: sulfopyruvate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-sulfopyruvate + H(+) = CO(2) + sulfoacetaldehyde." [EC:4.1.1.79, RHEA:20948]
+def: "Catalysis of the reaction: 3-sulfopyruvate + H+ = CO2 + sulfoacetaldehyde." [EC:4.1.1.79, RHEA:20948]
synonym: "sulfopyruvate carboxy-lyase (2-sulfoacetaldehyde-forming)" RELATED [EC:4.1.1.79]
synonym: "sulfopyruvate carboxy-lyase activity" RELATED [EC:4.1.1.79]
synonym: "sulphopyruvate decarboxylase activity" EXACT []
@@ -301218,7 +301225,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0050546
name: 4-hydroxyphenylpyruvate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (4-hydroxyphenyl)pyruvate + H(+) = (4-hydroxyphenyl)acetaldehyde + CO(2)." [EC:4.1.1.80, RHEA:18697]
+def: "Catalysis of the reaction: (4-hydroxyphenyl)pyruvate + H+ = (4-hydroxyphenyl)acetaldehyde + CO2." [EC:4.1.1.80, RHEA:18697]
synonym: "4-hydroxyphenylpyruvate carboxy-lyase (4-hydroxyphenylacetaldehyde-forming)" RELATED [EC:4.1.1.80]
synonym: "4-hydroxyphenylpyruvate carboxy-lyase activity" RELATED [EC:4.1.1.80]
xref: EC:4.1.1.80
@@ -301256,7 +301263,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0050549
name: cyclohexyl-isocyanide hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-cyclohexylformamide + H(+) = cyclohexyl isocyanide + H(2)O." [EC:4.2.1.103, RHEA:18197]
+def: "Catalysis of the reaction: N-cyclohexylformamide + H+ = cyclohexyl isocyanide + H2O." [EC:4.2.1.103, RHEA:18197]
synonym: "isonitrile hydratase activity" RELATED [EC:4.2.1.103]
synonym: "N-cyclohexylformamide hydro-lyase (cyclohexyl-isocyanide-forming)" RELATED [EC:4.2.1.103]
synonym: "N-cyclohexylformamide hydro-lyase activity" RELATED [EC:4.2.1.103]
@@ -301361,7 +301368,7 @@ is_a: GO:0016846 ! carbon-sulfur lyase activity
id: GO:0050556
name: deacetylisoipecoside synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: deacetylisoipecoside + H(2)O = dopamine + secologanin." [EC:4.3.3.3, RHEA:21756]
+def: "Catalysis of the reaction: deacetylisoipecoside + H2O = dopamine + secologanin." [EC:4.3.3.3, RHEA:21756]
synonym: "deacetylisoipecoside dopamine-lyase (secologanin-forming)" RELATED [EC:4.3.3.3]
synonym: "deacetylisoipecoside dopamine-lyase activity" RELATED [EC:4.3.3.3]
xref: EC:4.3.3.3
@@ -301374,7 +301381,7 @@ is_a: GO:0016843 ! amine-lyase activity
id: GO:0050557
name: deacetylipecoside synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: deacetylipecoside + H(2)O = dopamine + secologanin." [EC:4.3.3.4, RHEA:12296]
+def: "Catalysis of the reaction: deacetylipecoside + H2O = dopamine + secologanin." [EC:4.3.3.4, RHEA:12296]
synonym: "deacetylipecoside dopamine-lyase (secologanin-forming)" RELATED [EC:4.3.3.4]
synonym: "deacetylipecoside dopamine-lyase activity" RELATED [EC:4.3.3.4]
xref: EC:4.3.3.4
@@ -301462,7 +301469,7 @@ is_a: GO:0016405 ! CoA-ligase activity
id: GO:0050564
name: N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-2-aminoadipate + L-cysteine + L-valine + 3 ATP + H(2)O = N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine + 3 AMP + 3 diphosphate + 6 H(+)." [EC:6.3.2.26, RHEA:23196]
+def: "Catalysis of the reaction: L-2-aminoadipate + L-cysteine + L-valine + 3 ATP + H2O = N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine + 3 AMP + 3 diphosphate + 6 H+." [EC:6.3.2.26, RHEA:23196]
synonym: "ACV synthetase activity" BROAD [EC:6.3.2.26]
synonym: "L-2-aminohexanedioate:L-cysteine:L-valine ligase (AMP-forming, valine-inverting)" RELATED [EC:6.3.2.26]
synonym: "L-alpha-aminoadipyl-cysteinyl-valine synthetase activity" RELATED [EC:6.3.2.26]
@@ -301477,12 +301484,10 @@ is_a: GO:0016881 ! acid-amino acid ligase activity
id: GO:0050565
name: aerobactin synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 N(6)-acetyl-N(6)-hydroxy-L-lysine + 4 ATP + citrate + 2 H(2)O = 4 ADP + aerobactin + 8 H(+) + 4 phosphate." [RHEA:11760]
+def: "Catalysis of the reaction: ATP + N2-citryl-N6-acetyl-N6-hydroxy-L-lysine + N6-acetyl-N6-hydroxy-L-lysine = aerobactin + AMP + diphosphate + H+." [RHEA:32167]
synonym: "citrate:6-N-acetyl-6-N-hydroxy-L-lysine ligase (ADP-forming)" EXACT []
synonym: "citrate:N6-acetyl-N6-hydroxy-L-lysine ligase (ADP-forming)" EXACT []
-xref: KEGG_REACTION:R04357
-xref: MetaCyc:6.3.2.27-RXN
-xref: RHEA:11760
+xref: RHEA:32167
is_a: GO:0016881 ! acid-amino acid ligase activity
[Term]
@@ -301542,12 +301547,13 @@ xref: EC:3.5.1.44
xref: MetaCyc:CHEBDEAMID-RXN
xref: RHEA:16441
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
+is_a: GO:0140096 ! catalytic activity, acting on a protein
[Term]
id: GO:0050569
name: glycolaldehyde dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycolaldehyde + H(2)O + NAD(+) = glycolate + 2 H(+) + NADH." [EC:1.2.1.21, RHEA:20001]
+def: "Catalysis of the reaction: glycolaldehyde + H2O + NAD(+) = glycolate + 2 H+ + NADH." [EC:1.2.1.21, RHEA:20001]
synonym: "glycol aldehyde dehydrogenase activity" RELATED [EC:1.2.1.21]
synonym: "glycolaldehyde:NAD+ oxidoreductase activity" RELATED [EC:1.2.1.21]
xref: EC:1.2.1.21
@@ -301576,7 +301582,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050571
name: 1,5-anhydro-D-fructose reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,5-anhydro-D-glucitol + NADP(+) = 1,5-anhydro-D-fructose + H(+) + NADPH." [EC:1.1.1.263, RHEA:20665]
+def: "Catalysis of the reaction: 1,5-anhydro-D-glucitol + NADP+ = 1,5-anhydro-D-fructose + H+ + NADPH." [EC:1.1.1.263, RHEA:20665]
synonym: "1,5-anhydro-D-glucitol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.263]
synonym: "AF reductase activity" RELATED [EC:1.1.1.263]
xref: EC:1.1.1.263
@@ -301599,7 +301605,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050573
name: dTDP-4-dehydro-6-deoxyglucose reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dTDP-D-fucose + NADP(+) = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H(+) + NADPH." [EC:1.1.1.266, RHEA:36583]
+def: "Catalysis of the reaction: dTDP-D-fucose + NADP+ = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H+ + NADPH." [EC:1.1.1.266, RHEA:36583]
synonym: "dTDP-4-keto-6-deoxyglucose reductase activity" RELATED [EC:1.1.1.266]
synonym: "dTDP-D-fucose:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.266]
xref: EC:1.1.1.266
@@ -301612,7 +301618,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050574
name: 2-(R)-hydroxypropyl-CoM dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-(R)-hydroxypropyl-coenzyme M + NAD(+) = 2-oxopropyl-coenzyme M + H(+) + NADH." [EC:1.1.1.268, RHEA:13249]
+def: "Catalysis of the reaction: 2-(R)-hydroxypropyl-coenzyme M + NAD+ = 2-oxopropyl-coenzyme M + H+ + NADH." [EC:1.1.1.268, RHEA:13249]
synonym: "2-(2-(R)-hydroxypropylthio)ethanesulfonate dehydrogenase activity" RELATED [EC:1.1.1.268]
synonym: "2-[2-(R)-hydroxypropylthio]ethanesulfonate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.268]
xref: EC:1.1.1.268
@@ -301626,7 +301632,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050575
name: 2-(S)-hydroxypropyl-CoM dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-(S)-hydroxypropyl-coenzyme M + NAD(+) = 2-oxopropyl-coenzyme M + H(+) + NADH." [EC:1.1.1.269, RHEA:21052]
+def: "Catalysis of the reaction: 2-(S)-hydroxypropyl-coenzyme M + NAD+ = 2-oxopropyl-coenzyme M + H+ + NADH." [EC:1.1.1.269, RHEA:21052]
synonym: "2-(2-(S)-hydroxypropylthio)ethanesulfonate dehydrogenase activity" RELATED [EC:1.1.1.269]
synonym: "2-[2-(S)-hydroxypropylthio]ethanesulfonate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.269]
xref: EC:1.1.1.269
@@ -301668,7 +301674,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050579
name: vellosimine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 10-deoxysarpagine + NADP(+) = H(+) + NADPH + vellosimine." [EC:1.1.1.273, RHEA:20029]
+def: "Catalysis of the reaction: 10-deoxysarpagine + NADP+ = H+ + NADPH + vellosimine." [EC:1.1.1.273, RHEA:20029]
synonym: "10-deoxysarpagine:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.273]
xref: EC:1.1.1.273
xref: KEGG_REACTION:R05827
@@ -301730,7 +301736,7 @@ is_a: GO:0016696 ! oxidoreductase activity, acting on hydrogen as donor, NAD or
id: GO:0050584
name: linoleate 11-lipoxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: linoleate + O(2) = (9Z,11S,12Z)-11-hydroperoxyoctadeca-9,12-dienoate." [EC:1.13.11.45, RHEA:18993]
+def: "Catalysis of the reaction: linoleate + O2 = (9Z,11S,12Z)-11-hydroperoxyoctadeca-9,12-dienoate." [EC:1.13.11.45, RHEA:18993]
synonym: "linoleate dioxygenase activity" RELATED [EC:1.13.11.45]
synonym: "linoleate:oxygen 11S-oxidoreductase activity" RELATED [EC:1.13.11.45]
synonym: "manganese lipoxygenase activity" RELATED [EC:1.13.11.45]
@@ -301756,7 +301762,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0050586
name: 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxy-2-methylquinolin-4(1H)-one + H(+) + O(2) = N-acetylanthranilate + CO." [EC:1.13.11.48, RHEA:21572]
+def: "Catalysis of the reaction: 3-hydroxy-2-methylquinolin-4(1H)-one + H+ + O2 = N-acetylanthranilate + CO." [EC:1.13.11.48, RHEA:21572]
synonym: "(1H)-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase activity" RELATED [EC:1.13.11.48]
synonym: "1H-3-hydroxy-4-oxo quinaldine 2,4-dioxygenase activity" EXACT []
synonym: "1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase activity" EXACT []
@@ -301773,7 +301779,7 @@ id: GO:0050587
name: chlorite O2-lyase activity
namespace: molecular_function
alt_id: GO:0030065
-def: "Catalysis of the reaction: chloride + O(2) = chlorite." [EC:1.13.11.49, RHEA:21404]
+def: "Catalysis of the reaction: chloride + O2 = chlorite." [EC:1.13.11.49, RHEA:21404]
synonym: "chloride:oxygen oxidoreductase activity" RELATED [EC:1.13.11.49]
synonym: "chlorite dismutase activity" RELATED [EC:1.13.11.49]
xref: EC:1.13.11.49
@@ -301787,7 +301793,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0050588
name: apo-beta-carotenoid-14',13'-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 8'-apo-beta-carotenol + O(2) = (E,E)-7-hydroxy-6-methylhepta-3,5-dienal + 14'-apo-beta-carotenal." [EC:1.13.11.67, RHEA:26023]
+def: "Catalysis of the reaction: 8'-apo-beta-carotenol + O2 = (E,E)-7-hydroxy-6-methylhepta-3,5-dienal + 14'-apo-beta-carotenal." [EC:1.13.11.67, RHEA:26023]
synonym: "8'-apo-beta-carotenol:O2 oxidoreductase activity" RELATED [EC:1.13.11.67]
synonym: "apo-b-carotenoid-14',13'-dioxygenase activity" EXACT []
xref: EC:1.13.11.67
@@ -301831,7 +301837,7 @@ is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
id: GO:0050591
name: quinine 3-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADPH + O(2) + quinine = 3-hydroxyquinine + H(2)O + NADP(+)." [EC:1.14.14.55, RHEA:20149]
+def: "Catalysis of the reaction: H+ + NADPH + O2 + quinine = 3-hydroxyquinine + H2O + NADP+." [EC:1.14.14.55, RHEA:20149]
synonym: "nifedipine oxidase activity" RELATED [EC:1.14.14.55]
synonym: "quinine 3-hydroxylase activity" EXACT []
synonym: "quinine,NADPH:oxygen oxidoreductase activity" RELATED [EC:1.14.14.55]
@@ -301845,7 +301851,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050592
name: 4-hydroxyphenylacetaldehyde oxime monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (Z)-(4-hydroxyphenyl)acetaldehyde oxime + H(+) + NADPH + O(2) = (S)-4-hydroxymandelonitrile + 2 H(2)O + NADP(+)." [EC:1.14.14.37, RHEA:18401]
+def: "Catalysis of the reaction: (Z)-(4-hydroxyphenyl)acetaldehyde oxime + H+ + NADPH + O2 = (S)-4-hydroxymandelonitrile + 2 H2O + NADP+." [EC:1.14.14.37, RHEA:18401]
synonym: "(Z)-4-hydroxyphenylacetaldehyde oxime,NADPH:oxygen oxidoreductase activity" RELATED [EC:1.14.14.37]
synonym: "4-hydroxybenzeneacetaldehyde oxime monooxygenase activity" RELATED [EC:1.14.14.37]
synonym: "4-hydroxyphenylacetaldehyde oxime,NADPH:oxygen oxidoreductase activity" RELATED [EC:1.14.14.37]
@@ -301863,7 +301869,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050593
name: N-methylcoclaurine 3'-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-N-methylcoclaurine + H(+) + NADPH + O(2) = (S)-3'-hydroxy-N-methylcoclaurine + H(2)O + NADP(+)." [EC:1.14.14.102, RHEA:16649]
+def: "Catalysis of the reaction: (S)-N-methylcoclaurine + H+ + NADPH + O2 = (S)-3'-hydroxy-N-methylcoclaurine + H2O + NADP+." [EC:1.14.14.102, RHEA:16649]
synonym: "(S)-N-methylcoclaurine 3'-hydroxylase activity" RELATED [EC:1.14.14.102]
synonym: "(S)-N-methylcoclaurine,NADPH:oxygen oxidoreductase (3'-hydroxylating)" RELATED [EC:1.14.14.102]
synonym: "cytochrome P450 80B1 activity" RELATED [EC:1.14.14.102]
@@ -301878,7 +301884,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050594
name: tabersonine 16-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADPH + O(2) + tabersonine = 16-hydroxytabersonine + H(2)O + NADP(+)." [EC:1.14.14.103, RHEA:14133]
+def: "Catalysis of the reaction: H+ + NADPH + O2 + tabersonine = 16-hydroxytabersonine + H2O + NADP+." [EC:1.14.14.103, RHEA:14133]
synonym: "tabersonine,NADPH:oxygen oxidoreductase (16-hydroxylating)" RELATED [EC:1.14.14.103]
xref: EC:1.14.14.103
xref: KEGG_REACTION:R05855
@@ -301890,18 +301896,17 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050595
name: 7-deoxyloganin 7-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7-deoxyloganin + NADPH + H+ + O2 = loganin + NADP+ + H2O." [EC:1.14.13.74, MetaCyc:1.14.13.74-RXN]
-synonym: "7-deoxyloganin,NADPH:oxygen oxidoreductase (7alpha-hydroxylating)" RELATED [EC:1.14.13.74]
-xref: EC:1.14.13.74
+def: "Catalysis of the reaction: 7-deoxyloganin + O2 + reduced [NADPH-hemoprotein reductase] = H+ + H2O + loganin + oxidized [NADPH-hemoprotein reductase]." [PMID:11524113, RHEA:11452]
+xref: EC:1.14.14.85
xref: MetaCyc:1.14.13.74-RXN
xref: RHEA:11452
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0050596
name: vinorine hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADPH + O(2) + vinorine = H(2)O + NADP(+) + vomilenine." [EC:1.14.14.104, RHEA:17257]
+def: "Catalysis of the reaction: H+ + NADPH + O2 + vinorine = H2O + NADP+ + vomilenine." [EC:1.14.14.104, RHEA:17257]
synonym: "vinorine,NADPH:oxygen oxidoreductase (21alpha-hydroxylating)" RELATED [EC:1.14.14.104]
xref: EC:1.14.14.104
xref: KEGG_REACTION:R05877
@@ -301913,7 +301918,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050597
name: taxane 10-beta-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADPH + O(2) + taxa-4(20),11-dien-5alpha-yl acetate = 10beta-hydroxytaxa-4(20),11-dien-5alpha-yl acetate + H(2)O + NADP(+)." [EC:1.14.14.105, RHEA:15241]
+def: "Catalysis of the reaction: H+ + NADPH + O2 + taxa-4(20),11-dien-5alpha-yl acetate = 10beta-hydroxytaxa-4(20),11-dien-5alpha-yl acetate + H2O + NADP+." [EC:1.14.14.105, RHEA:15241]
synonym: "5-alpha-taxadienol-10-beta-hydroxylase activity" RELATED [EC:1.14.14.105]
synonym: "taxa-4(20),11-dien-5alpha-yl acetate,NADPH:oxygen oxidoreductase (10beta-hydroxylating)" RELATED [EC:1.14.14.105]
synonym: "taxane 10b-hydroxylase activity" EXACT []
@@ -301928,7 +301933,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050598
name: taxane 13-alpha-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + NADPH + O(2) + taxa-4(20),11-dien-5alpha-ol = H(2)O + NADP(+) + taxa-4(20),11-dien-5alpha,13alpha-diol." [EC:1.14.14.106, RHEA:18949]
+def: "Catalysis of the reaction: H+ + NADPH + O2 + taxa-4(20),11-dien-5alpha-ol = H2O + NADP+ + taxa-4(20),11-dien-5alpha,13alpha-diol." [EC:1.14.14.106, RHEA:18949]
synonym: "taxa-4(20),11-dien-5alpha-ol,NADPH:oxygen oxidoreductase (13alpha-hydroxylating)" RELATED [EC:1.14.14.106]
synonym: "taxane 13a-hydroxylase activity" EXACT []
synonym: "taxane 13alpha-hydroxylase activity" RELATED [EC:1.14.14.106]
@@ -301943,7 +301948,7 @@ id: GO:0050599
name: deacetoxycephalosporin-C synthase activity
namespace: molecular_function
alt_id: GO:0045441
-def: "Catalysis of the reaction: 2-oxoglutarate + O(2) + penicillin N = CO(2) + deacetoxycephalosporin C + H(2)O + succinate." [EC:1.14.20.1, RHEA:20748]
+def: "Catalysis of the reaction: 2-oxoglutarate + O2 + penicillin N = CO2 + deacetoxycephalosporin C + H2O + succinate." [EC:1.14.20.1, RHEA:20748]
synonym: "DAOC synthase activity" RELATED [EC:1.14.20.1]
synonym: "DAOCS activity" RELATED [EC:1.14.20.1]
synonym: "deacetoxycephalosporin C synthetase activity" EXACT []
@@ -301958,48 +301963,34 @@ is_a: GO:0050498 ! oxidoreductase activity, acting on paired donors, with incorp
[Term]
id: GO:0050600
-name: myristoyl-CoA 11-(E) desaturase activity
+name: acyl-CoA 11-(E)-desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: myristoyl-CoA + NAD(P)H + H+ + O2 = (E)-11-tetradecenoyl-CoA + NAD(P)+ + 2 H2O." [RHEA:46396]
-synonym: "n-tetradecanoyl-CoA,NAD(P)H:O2 oxidoreductase [11-(E) desaturating]" RELATED [EC:1.14.19.24]
-synonym: "n-tetradecanoyl-CoA,NADPH:O2 oxidoreductase [11-(E) desaturating]" RELATED [EC:1.14.99.31]
+def: "Catalysis of the reaction: an 11,12-saturated fatty acyl-CoA + 2 Fe(II)-[cytochrome b5] + 2 H+ + O2 = an (11E)-delta11-fatty acyl-CoA + 2 Fe(III)-[cytochrome b5] + 2 H2O." [RHEA:46396]
+synonym: "acyl-CoA delta11-desaturase activity" BROAD []
+synonym: "myristoyl-CoA 11-(E) desaturase activity" NARROW []
xref: EC:1.14.19.24
xref: MetaCyc:1.14.99.31-RXN
xref: RHEA:46396
is_a: GO:0016215 ! acyl-CoA desaturase activity
-[Term]
-id: GO:0050601
-name: myristoyl-CoA 11-(Z) desaturase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: myristoyl-CoA + NAD(P)H + H+ + O2 = (Z)-11-tetradecenoyl-CoA + NAD(P)+ + 2 H2O." [RHEA:25852]
-synonym: "delta(11) desaturase" BROAD [EC:1.14.19.5]
-synonym: "delta(11)-fatty-acid desaturase" BROAD [EC:1.14.19.5]
-synonym: "delta(11)-palmitoyl-CoA desaturase" BROAD [EC:1.14.19.5]
-synonym: "fatty acid delta(11)-desaturase" BROAD [EC:1.14.19.5]
-synonym: "Z/E11-desaturase" BROAD [EC:1.14.19.5]
-xref: EC:1.14.19.5
-xref: MetaCyc:1.14.99.32-RXN
-xref: RHEA:25852
-is_a: GO:0016215 ! acyl-CoA desaturase activity
-
[Term]
id: GO:0050602
-name: monoprenyl isoflavone epoxidase activity
+name: obsolete monoprenyl isoflavone epoxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O2 + NADPH + H+ + 7-O-methylluteone = H2O + NADP+ + dihydrofurano derivatives." [EC:1.14.99.34, MetaCyc:1.14.99.34-RXN]
+def: "OBSOLETE. Catalysis of the reaction: O2 + NADPH + H+ + 7-O-methylluteone = H2O + NADP+ + dihydrofurano derivatives." [EC:1.14.99.34, MetaCyc:1.14.99.34-RXN]
+comment: This term was obsoleted because no enzyme has been shown to catalyze this reaction.
synonym: "7-O-methylluteone,NADPH:O2 oxidoreductase activity" RELATED [EC:1.14.99.34]
synonym: "7-O-methylluteone:O2 oxidoreductase activity" RELATED [EC:1.14.99.34]
synonym: "monoprenyl isoflavone monooxygenase activity" RELATED [EC:1.14.99.34]
xref: EC:1.14.99.34
xref: MetaCyc:1.14.99.34-RXN
-is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+is_obsolete: true
[Term]
id: GO:0050603
name: thiophene-2-carbonyl-CoA monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + O(2) + thiophene-2-carbonyl-CoA = 5-hydroxythiophene-2-carbonyl-CoA + A + H(2)O + H(+)." [EC:1.14.99.35, RHEA:18929]
+def: "Catalysis of the reaction: AH(2) + O2 + thiophene-2-carbonyl-CoA = 5-hydroxythiophene-2-carbonyl-CoA + A + H2O + H+." [EC:1.14.99.35, RHEA:18929]
synonym: "thiophene-2-carbonyl-CoA, hydrogen-donor:oxygen oxidoreductase activity" RELATED [EC:1.14.99.35]
synonym: "thiophene-2-carboxyl-CoA dehydrogenase activity" RELATED [EC:1.14.99.35]
synonym: "thiophene-2-carboxyl-CoA hydroxylase activity" RELATED [EC:1.14.99.35]
@@ -302016,7 +302007,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0050604
name: taxadiene 5-alpha-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + O(2) + taxa-4,11-diene = A + H(2)O + taxa-4(20),11-dien-5alpha-ol." [RHEA:14049]
+def: "Catalysis of the reaction: AH(2) + O2 + taxa-4,11-diene = A + H2O + taxa-4(20),11-dien-5alpha-ol." [RHEA:14049]
synonym: "taxa-4,11-diene,hydrogen-donor:oxygen oxidoreductase (5alpha-hydroxylating)" RELATED []
synonym: "taxadiene 5a-hydroxylase activity" EXACT []
synonym: "taxadiene 5alpha-hydroxylase activity" RELATED []
@@ -302044,7 +302035,7 @@ is_a: GO:0016721 ! oxidoreductase activity, acting on superoxide radicals as acc
id: GO:0050606
name: 4-carboxy-2-hydroxymuconate semialdehyde hemiacetal dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-carboxy-2-hydroxymuconate semialdehyde hemiacetal + NADP(+) = 2-oxo-2H-pyran-4,6-dicarboxylate + H(+) + NADPH." [RHEA:29587]
+def: "Catalysis of the reaction: 4-carboxy-2-hydroxymuconate semialdehyde hemiacetal + NADP+ = 2-oxo-2H-pyran-4,6-dicarboxylate + H+ + NADPH." [RHEA:29587]
synonym: "2-hydroxy-4-carboxymuconate 6-semialdehyde dehydrogenase activity" RELATED [EC:1.1.1.312]
synonym: "4-carboxy-2-hydroxy-cis,cis-muconate-6-semialdehyde:NADP(+) oxidoreductase activity" RELATED [EC:1.1.1.312]
synonym: "4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase activity" RELATED [EC:1.1.1.312]
@@ -302071,7 +302062,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0050608
name: vanillin dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + NAD(+) + vanillin = 2 H(+) + NADH + vanillate." [EC:1.2.1.67, RHEA:13309]
+def: "Catalysis of the reaction: H2O + NAD+ + vanillin = 2 H+ + NADH + vanillate." [EC:1.2.1.67, RHEA:13309]
synonym: "vanillin:NAD+ oxidoreductase activity" RELATED [EC:1.2.1.67]
xref: EC:1.2.1.67
xref: KEGG_REACTION:R05699
@@ -302083,7 +302074,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0050609
name: phosphonate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + NAD(+) + phosphonate = 2 H(+) + NADH + phosphate." [EC:1.20.1.1, RHEA:13173]
+def: "Catalysis of the reaction: H2O + NAD+ + phosphonate = 2 H+ + NADH + phosphate." [EC:1.20.1.1, RHEA:13173]
synonym: "NAD-dependent phosphite dehydrogenas activity" RELATED [EC:1.20.1.1]
synonym: "NAD:phosphite oxidoreductase activity" RELATED [EC:1.20.1.1]
synonym: "phosphite dehydrogenase activity" RELATED [EC:1.20.1.1]
@@ -302099,7 +302090,7 @@ is_a: GO:0050499 ! oxidoreductase activity, acting on phosphorus or arsenic in d
id: GO:0050610
name: methylarsonate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 glutathione + H(+) + methylarsonate = glutathione disulfide + H(2)O + methylarsonous acid." [EC:1.20.4.2, RHEA:15969]
+def: "Catalysis of the reaction: 2 glutathione + H+ + methylarsonate = glutathione disulfide + H2O + methylarsonous acid." [EC:1.20.4.2, RHEA:15969]
synonym: "glutathione:methylarsonate oxidoreductase activity" RELATED [EC:1.20.4.2]
synonym: "MMA(V) reductase activity" RELATED [EC:1.20.4.2]
xref: EC:1.20.4.2
@@ -302115,7 +302106,7 @@ id: GO:0050611
name: arsenate reductase (azurin) activity
namespace: molecular_function
alt_id: GO:0018691
-def: "Catalysis of the reaction: H(2)O + arsenite + 2 oxidized azurin = 2 H(+) + 2 reduced azurin + arsenate." [EC:1.20.9.1, MetaCyc:1.20.98.1-RXN]
+def: "Catalysis of the reaction: H2O + arsenite + 2 oxidized azurin = 2 H+ + 2 reduced azurin + arsenate." [EC:1.20.9.1, MetaCyc:1.20.98.1-RXN]
synonym: "arsenite oxidase activity" RELATED [EC:1.20.9.1]
synonym: "arsenite:azurin oxidoreductase activity" RELATED [EC:1.20.9.1]
xref: EC:1.20.9.1
@@ -302128,7 +302119,7 @@ is_a: GO:0052882 ! oxidoreductase activity, acting on phosphorus or arsenic in d
id: GO:0050612
name: arsenate reductase (donor) activity
namespace: molecular_function
-def: "Catalysis of the reaction: A + arsenite + H(2)O = AH(2) + arsenate + 2 H(+)." [EC:1.20.99.1, RHEA:18449]
+def: "Catalysis of the reaction: A + arsenite + H2O = AH(2) + arsenate + 2 H+." [EC:1.20.99.1, RHEA:18449]
synonym: "arsenate:(acceptor) oxidoreductase activity" RELATED [EC:1.20.99.1]
synonym: "arsenate:acceptor oxidoreductase activity" RELATED [EC:1.20.99.1]
xref: EC:1.20.99.1
@@ -302169,6 +302160,7 @@ xref: EC:1.3.1.72
xref: MetaCyc:1.3.1.72-RXN
xref: Reactome:R-HSA-196417 "Reduction of desmosterol to cholesterol"
xref: Reactome:R-HSA-6807064 "DHCR24 reduces ZYMOL to ZYMSTNL"
+xref: Reactome:R-HSA-9755937 "DHCR24 reduces LAN to 24,25-dhLAN"
xref: RHEA:13685
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
@@ -302176,7 +302168,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0050615
name: 1,2-dihydrovomilenine reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 17-O-acetylnorajmaline + NADP(+) = 1,2-dihydrovomilenine + H(+) + NADPH." [EC:1.3.1.73, RHEA:12320]
+def: "Catalysis of the reaction: 17-O-acetylnorajmaline + NADP+ = 1,2-dihydrovomilenine + H+ + NADPH." [EC:1.3.1.73, RHEA:12320]
synonym: "17-O-acetylnorajmaline:NADP+ oxidoreductase activity" RELATED [EC:1.3.1.73]
xref: EC:1.3.1.73
xref: KEGG_REACTION:R05879
@@ -302249,7 +302241,7 @@ is_a: GO:0016636 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0050621
name: tryptophan alpha,beta-oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tryptophan + O(2) = alpha,beta-didehydrotryptophan + H(2)O(2) + H(+)." [EC:1.3.3.10, RHEA:19901]
+def: "Catalysis of the reaction: L-tryptophan + O2 = alpha,beta-didehydrotryptophan + H2O2 + H+." [EC:1.3.3.10, RHEA:19901]
comment: Note that this was EC:1.4.3.17.
synonym: "L-tryptophan 2',3'-oxidase activity" RELATED [EC:1.3.3.10]
synonym: "L-tryptophan alpha,beta-dehydrogenase activity" RELATED [EC:1.3.3.10]
@@ -302278,7 +302270,7 @@ is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0050623
name: berberine reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-canadine + 2 NADP(+) = berberine + H(+) + 2 NADPH." [EC:1.5.1.31, RHEA:21268]
+def: "Catalysis of the reaction: (R)-canadine + 2 NADP+ = berberine + H+ + 2 NADPH." [EC:1.5.1.31, RHEA:21268]
synonym: "(R)-canadine synthase activity" RELATED [EC:1.5.1.31]
synonym: "(R)-tetrahydroberberine:NADP+ oxidoreductase activity" RELATED [EC:1.5.1.31]
xref: EC:1.5.1.31
@@ -302291,7 +302283,7 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0050624
name: vomilenine reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,2-dihydrovomilenine + NADP(+) = H(+) + NADPH + vomilenine." [EC:1.5.1.32, RHEA:16409]
+def: "Catalysis of the reaction: 1,2-dihydrovomilenine + NADP+ = H+ + NADPH + vomilenine." [EC:1.5.1.32, RHEA:16409]
synonym: "1,2-dihydrovomilenine:NADP+ oxidoreductase activity" RELATED [EC:1.5.1.32]
xref: EC:1.5.1.32
xref: KEGG_REACTION:R05878
@@ -302304,7 +302296,7 @@ id: GO:0050625
name: 2-hydroxy-1,4-benzoquinone reductase activity
namespace: molecular_function
alt_id: GO:0018540
-def: "Catalysis of the reaction: 2-hydroxy-1,4-benzoquinone + 2 H(+) + NADH = benzene-1,2,4-triol + NAD(+)." [EC:1.6.5.7, RHEA:12428]
+def: "Catalysis of the reaction: 2-hydroxy-1,4-benzoquinone + 2 H+ + NADH = benzene-1,2,4-triol + NAD+." [EC:1.6.5.7, RHEA:12428]
synonym: "1,2,4-trihydroxybenzene:NAD oxidoreductase activity" RELATED [EC:1.6.5.7]
synonym: "1,2,4-trihydroxybenzene:NAD+ oxidoreductase activity" RELATED [EC:1.6.5.7]
synonym: "2-hydroxy-1,4-benzoquinone:NADH oxidoreductase activity" RELATED [EC:1.6.5.7]
@@ -302346,7 +302338,7 @@ is_a: GO:0016668 ! oxidoreductase activity, acting on a sulfur group of donors,
id: GO:0050628
name: 2-oxopropyl-CoM reductase (carboxylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetoacetate + coenzyme M + NADP(+) = 2-oxopropyl-coenzyme M + CO(2) + NADPH." [EC:1.8.1.5, RHEA:16977]
+def: "Catalysis of the reaction: acetoacetate + coenzyme M + NADP+ = 2-oxopropyl-coenzyme M + CO2 + NADPH." [EC:1.8.1.5, RHEA:16977]
synonym: "2-KPCC activity" RELATED [EC:1.8.1.5]
synonym: "2-mercaptoethanesulfonate,acetoacetate:NADP+ oxidoreductase (decarboxylating)" RELATED [EC:1.8.1.5]
synonym: "NADPH:2-(2-ketopropylthio)ethanesulfonate oxidoreductase/carboxylase activity" RELATED [EC:1.8.1.5]
@@ -302386,7 +302378,7 @@ is_a: GO:0008171 ! O-methyltransferase activity
id: GO:0050631
name: corydaline synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + 2 NADPH + palmatine = S-adenosyl-L-homocysteine + corydaline + 2 NADP(+)." [EC:2.1.1.147, RHEA:14773]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + 2 NADPH + palmatine = S-adenosyl-L-homocysteine + corydaline + 2 NADP+." [EC:2.1.1.147, RHEA:14773]
synonym: "S-adenosyl-L-methionine:protoberberine 13-C-methyltransferase activity" RELATED [EC:2.1.1.147]
xref: EC:2.1.1.147
xref: KEGG_REACTION:R07241
@@ -302453,7 +302445,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0050635
name: acridone synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-methylanthranilyl-CoA + 3 H(+) + 3 malonyl-CoA = 1,3-dihydroxy-N-methylacridone + 3 CO(2) + 4 CoA + H(2)O." [EC:2.3.1.159, RHEA:22224]
+def: "Catalysis of the reaction: N-methylanthranilyl-CoA + 3 H+ + 3 malonyl-CoA = 1,3-dihydroxy-N-methylacridone + 3 CO2 + 4 CoA + H2O." [EC:2.3.1.159, RHEA:22224]
synonym: "malonyl-CoA:N-methylanthraniloyl-CoA malonyltransferase (cyclizing)" RELATED [EC:2.3.1.159]
xref: EC:2.3.1.159
xref: KEGG_REACTION:R07250
@@ -302477,7 +302469,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0050637
name: lovastatin nonaketide synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + acetyl-CoA + 18 H(+) + 8 malonyl-CoA + 11 NADPH = S-adenosyl-L-homocysteine + 8 CO(2) + 9 CoA + dihydromonacolin L + 6 H(2)O + 11 NADP(+)." [EC:2.3.1.161, RHEA:18565]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + acetyl-CoA + 18 H+ + 8 malonyl-CoA + 11 NADPH = S-adenosyl-L-homocysteine + 8 CO2 + 9 CoA + dihydromonacolin L + 6 H2O + 11 NADP+." [EC:2.3.1.161, RHEA:18565]
synonym: "acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing, thioester-hydrolysing)" RELATED [EC:2.3.1.161]
xref: EC:2.3.1.161
xref: KEGG_REACTION:R07251
@@ -302538,7 +302530,7 @@ is_a: GO:0016410 ! N-acyltransferase activity
id: GO:0050641
name: 6-methylsalicylic acid synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + 3 H(+) + 3 malonyl-CoA + NADPH = 6-methylsalicylate + 3 CO(2) + 4 CoA + H(2)O + NADP(+)." [EC:2.3.1.165, RHEA:12240]
+def: "Catalysis of the reaction: acetyl-CoA + 3 H+ + 3 malonyl-CoA + NADPH = 6-methylsalicylate + 3 CO2 + 4 CoA + H2O + NADP+." [EC:2.3.1.165, RHEA:12240]
synonym: "6-MSAS activity" RELATED [EC:2.3.1.165]
synonym: "acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl-reducing, thioester-hydrolysing and cyclizing)" RELATED [EC:2.3.1.165]
synonym: "MSAS activity" RELATED [EC:2.3.1.165]
@@ -302552,7 +302544,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0050642
name: 2-alpha-hydroxytaxane 2-O-benzoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 10-deacetyl-2-debenzoylbaccatin III + benzoyl-CoA = 10-deacetylbaccatin III + CoA." [EC:2.3.1.166, RHEA:18741]
+def: "Catalysis of the reaction: 10-deacetyl-2-debenzoylbaccatin III + benzoyl-CoA = 10-deacetylbaccatin III + CoA." [RHEA:18741]
synonym: "2-debenzoyl-7,13-diacetylbaccatin III-2-O-benzoyl transferase activity" RELATED [EC:2.3.1.166]
synonym: "2a-hydroxytaxane 2-O-benzoyltransferase activity" EXACT []
synonym: "2alpha-hydroxytaxane 2-O-benzoyltransferase activity" RELATED [EC:2.3.1.166]
@@ -302581,7 +302573,7 @@ is_a: GO:0016413 ! O-acetyltransferase activity
id: GO:0050644
name: cis-p-coumarate glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cis-4-coumarate + UDP-D-glucose = 4'-O-beta-D-glucosyl-cis-4-coumarate + H(+) + UDP." [EC:2.4.1.209, RHEA:13129]
+def: "Catalysis of the reaction: cis-4-coumarate + UDP-D-glucose = 4'-O-beta-D-glucosyl-cis-4-coumarate + H+ + UDP." [EC:2.4.1.209, RHEA:13129]
synonym: "UDP-glucose:cis-p-coumarate beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.209]
xref: EC:2.4.1.209
xref: KEGG_REACTION:R05324
@@ -302609,7 +302601,6 @@ namespace: molecular_function
def: "Binding to 5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid, a straight-chain fatty acid with twenty carbon atoms and four double bonds." [GOC:ai]
synonym: "5-oxo-6E,8Z,11Z,14Z-eicosatetraenoic acid binding" EXACT []
is_a: GO:0036041 ! long-chain fatty acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0050542 ! icosanoid binding
[Term]
@@ -302619,7 +302610,6 @@ namespace: molecular_function
def: "Binding to 5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid, a straight-chain fatty acid with twenty carbon atoms and four double bonds." [GOC:ai]
synonym: "5-hydroxy-6E,8Z,11Z,14Z-eicosatetraenoic acid binding" EXACT []
is_a: GO:0036041 ! long-chain fatty acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0050542 ! icosanoid binding
is_a: GO:1901567 ! fatty acid derivative binding
@@ -302630,7 +302620,6 @@ namespace: molecular_function
def: "Binding to 5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid, a straight-chain fatty acid with twenty carbon atoms and four double bonds." [GOC:ai]
synonym: "5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-eicosatetraenoic acid binding" EXACT []
is_a: GO:0036041 ! long-chain fatty acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0050542 ! icosanoid binding
is_a: GO:1901567 ! fatty acid derivative binding
@@ -302687,7 +302676,7 @@ synonym: "dermatan sulfate proteoglycan formation, polysaccharide chain formatio
synonym: "dermatan sulfate proteoglycan synthesis, polysaccharide chain synthesis" EXACT []
synonym: "dermatan sulphate proteoglycan biosynthesis, polysaccharide chain biosynthesis" EXACT []
synonym: "dermatan sulphate proteoglycan biosynthesis, polysaccharide chain biosynthetic process" EXACT []
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
+is_a: GO:0000271 ! polysaccharide biosynthetic process
relationship: part_of GO:0050651 ! dermatan sulfate proteoglycan biosynthetic process
[Term]
@@ -302702,7 +302691,7 @@ synonym: "chondroitin sulfate proteoglycan formation, polysaccharide chain forma
synonym: "chondroitin sulfate proteoglycan synthesis, polysaccharide chain synthesis" EXACT []
synonym: "chondroitin sulphate proteoglycan biosynthesis, polysaccharide chain biosynthesis" EXACT []
synonym: "chondroitin sulphate proteoglycan biosynthesis, polysaccharide chain biosynthetic process" EXACT []
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
+is_a: GO:0000271 ! polysaccharide biosynthetic process
relationship: part_of GO:0050650 ! chondroitin sulfate proteoglycan biosynthetic process
[Term]
@@ -302791,7 +302780,7 @@ def: "Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involve
synonym: "NADP or NADPH binding" RELATED [GOC:mah]
synonym: "NADP+ or NADPH binding" RELATED []
synonym: "nicotinamide adenine dinucleotide phosphate binding" EXACT []
-is_a: GO:0000166 ! nucleotide binding
+is_a: GO:0030554 ! adenyl nucleotide binding
[Term]
id: GO:0050662
@@ -302823,6 +302812,7 @@ synonym: "hydrogen peroxide generation" EXACT []
synonym: "hydrogen peroxide synthesis" EXACT []
is_a: GO:0042743 ! hydrogen peroxide metabolic process
is_a: GO:0044249 ! cellular biosynthetic process
+is_a: GO:1901576 ! organic substance biosynthetic process
is_a: GO:1903409 ! reactive oxygen species biosynthetic process
[Term]
@@ -302862,7 +302852,7 @@ synonym: "up regulation of homocysteine metabolic process" EXACT []
synonym: "up-regulation of homocysteine metabolic process" EXACT []
synonym: "upregulation of homocysteine metabolic process" EXACT []
is_a: GO:0031337 ! positive regulation of sulfur amino acid metabolic process
-is_a: GO:0045764 ! positive regulation of cellular amino acid metabolic process
+is_a: GO:0045764 ! positive regulation of amino acid metabolic process
is_a: GO:0050666 ! regulation of homocysteine metabolic process
relationship: positively_regulates GO:0050667 ! homocysteine metabolic process
@@ -303007,9 +302997,10 @@ relationship: negatively_regulates GO:0050673 ! epithelial cell proliferation
[Term]
id: GO:0050681
-name: androgen receptor binding
+name: nuclear androgen receptor binding
namespace: molecular_function
-def: "Binding to an androgen receptor." [GOC:ai]
+def: "Binding to a nuclear androgen receptor." [GOC:ai]
+synonym: "androgen receptor binding" BROAD []
synonym: "AR binding" EXACT []
is_a: GO:0016922 ! nuclear receptor binding
@@ -303103,16 +303094,6 @@ synonym: "negative regulation of antiviral response by host" EXACT [GOC:dph, GOC
is_a: GO:0050687 ! negative regulation of defense response to virus
is_a: GO:0050691 ! regulation of defense response to virus by host
-[Term]
-id: GO:0050690
-name: regulation of defense response to virus by virus
-namespace: biological_process
-def: "Any viral process that modulates the frequency, rate, or extent of the antiviral response of the host cell or organism." [GOC:ai, GOC:dph]
-synonym: "regulation by virus of antiviral response" EXACT []
-synonym: "regulation of antiviral response by virus" EXACT [GOC:dph]
-synonym: "viral regulation of antiviral response" EXACT []
-is_a: GO:0016032 ! viral process
-
[Term]
id: GO:0050691
name: regulation of defense response to virus by host
@@ -303380,43 +303361,48 @@ is_a: GO:0018212 ! peptidyl-tyrosine modification
[Term]
id: GO:0050740
-name: protein-FMN linkage via O3-riboflavin phosphoryl-L-threonine
+name: obsolete protein-FMN linkage via O3-riboflavin phosphoryl-L-threonine
namespace: biological_process
-def: "The formation of a protein-FMN linkage via O3-riboflavin phosphoryl-L-threonine." [RESID:AA0349]
+def: "OBSOLETE. The formation of a protein-FMN linkage via O3-riboflavin phosphoryl-L-threonine." [RESID:AA0349]
+comment: This is a molecular function.
xref: RESID:AA0349
-is_a: GO:0018309 ! protein-FMN linkage
+is_obsolete: true
[Term]
id: GO:0050741
-name: protein-FMN linkage via O3-riboflavin phosphoryl-L-serine
+name: obsolete protein-FMN linkage via O3-riboflavin phosphoryl-L-serine
namespace: biological_process
-def: "The formation of a protein-FMN linkage via O3-riboflavin phosphoryl-L-serine." [RESID:AA0350]
+def: "OBSOLETE. The formation of a protein-FMN linkage via O3-riboflavin phosphoryl-L-serine." [RESID:AA0350]
+comment: This is a molecular function.
xref: RESID:AA0350
-is_a: GO:0018309 ! protein-FMN linkage
+is_obsolete: true
[Term]
id: GO:0050742
-name: protein-FMN linkage via S-(4a-FMN)-L-cysteine
+name: obsolete protein-FMN linkage via S-(4a-FMN)-L-cysteine
namespace: biological_process
-def: "The formation of a protein-FMN linkage via S-(4a-FMN)-L-cysteine." [RESID:AA0351]
+def: "OBSOLETE. The formation of a protein-FMN linkage via S-(4a-FMN)-L-cysteine." [RESID:AA0351]
+comment: This is a molecular function.
xref: RESID:AA0351
-is_a: GO:0018309 ! protein-FMN linkage
+is_obsolete: true
[Term]
id: GO:0050743
-name: protein-FMN linkage via 1'-(8alpha-FMN)-L-histidine
+name: obsolete protein-FMN linkage via 1'-(8alpha-FMN)-L-histidine
namespace: biological_process
-def: "The formation of a protein-FMN linkage via 1'-(8alpha-FMN)-L-histidine." [PMID:8611516, RESID:AA0352]
+def: "OBSOLETE. The formation of a protein-FMN linkage via 1'-(8alpha-FMN)-L-histidine." [PMID:8611516, RESID:AA0352]
+comment: This is a molecular function.
xref: RESID:AA0352
-is_a: GO:0018309 ! protein-FMN linkage
+is_obsolete: true
[Term]
id: GO:0050744
-name: protein-FMN linkage via 3'-(8alpha-FMN)-L-histidine
+name: obsolete protein-FMN linkage via 3'-(8alpha-FMN)-L-histidine
namespace: biological_process
-def: "The formation of a protein-FMN linkage via 3'-(8alpha-FMN)-L-histidine." [RESID:AA0353]
+def: "OBSOLETE. The formation of a protein-FMN linkage via 3'-(8alpha-FMN)-L-histidine." [RESID:AA0353]
+comment: This is a molecular function.
xref: RESID:AA0353
-is_a: GO:0018309 ! protein-FMN linkage
+is_obsolete: true
[Term]
id: GO:0050745
@@ -303581,7 +303567,7 @@ id: GO:0050764
name: regulation of phagocytosis
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of phagocytosis, the process in which phagocytes engulf external particulate material." [GOC:ai]
-is_a: GO:0060627 ! regulation of vesicle-mediated transport
+is_a: GO:0030100 ! regulation of endocytosis
relationship: regulates GO:0006909 ! phagocytosis
[Term]
@@ -303593,8 +303579,8 @@ synonym: "down regulation of phagocytosis" EXACT []
synonym: "down-regulation of phagocytosis" EXACT []
synonym: "downregulation of phagocytosis" EXACT []
synonym: "inhibition of phagocytosis" NARROW []
+is_a: GO:0045806 ! negative regulation of endocytosis
is_a: GO:0050764 ! regulation of phagocytosis
-is_a: GO:0051051 ! negative regulation of transport
relationship: negatively_regulates GO:0006909 ! phagocytosis
[Term]
@@ -303607,8 +303593,8 @@ synonym: "stimulation of phagocytosis" NARROW []
synonym: "up regulation of phagocytosis" EXACT []
synonym: "up-regulation of phagocytosis" EXACT []
synonym: "upregulation of phagocytosis" EXACT []
+is_a: GO:0045807 ! positive regulation of endocytosis
is_a: GO:0050764 ! regulation of phagocytosis
-is_a: GO:0051050 ! positive regulation of transport
relationship: positively_regulates GO:0006909 ! phagocytosis
[Term]
@@ -303618,7 +303604,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of neurogenesis, the generation of cells in the nervous system." [GOC:ai]
is_a: GO:0051960 ! regulation of nervous system development
is_a: GO:0060284 ! regulation of cell development
-relationship: part_of GO:0048699 ! generation of neurons
relationship: regulates GO:0022008 ! neurogenesis
[Term]
@@ -303812,7 +303797,7 @@ is_a: GO:0046448 ! tropane alkaloid metabolic process
id: GO:0050784
name: cocaine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of cocaine, an alkaloid obtained from the dried leaves of the shrub Erythroxylon coca. It is a cerebral stimulant and narcotic." [ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of cocaine, an alkaloid obtained from the dried leaves of the shrub Erythroxylon coca. It is a cerebral stimulant and narcotic." [PMID:17132243]
synonym: "cocaine breakdown" EXACT []
synonym: "cocaine catabolism" EXACT []
synonym: "cocaine degradation" EXACT []
@@ -303874,7 +303859,6 @@ namespace: biological_process
alt_id: GO:0050791
def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators]
subset: gocheck_do_not_annotate
-subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
synonym: "regulation of physiological process" EXACT []
@@ -303926,7 +303910,7 @@ name: regulation of behavior
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." [GOC:go_curators, GOC:pr]
synonym: "regulation of behaviour" EXACT []
-is_a: GO:0050789 ! regulation of biological process
+is_a: GO:0051239 ! regulation of multicellular organismal process
relationship: regulates GO:0007610 ! behavior
[Term]
@@ -303992,11 +303976,12 @@ consider: GO:0006810
[Term]
id: GO:0050801
-name: ion homeostasis
+name: monoatomic ion homeostasis
namespace: biological_process
alt_id: GO:2000021
-def: "Any process involved in the maintenance of an internal steady state of ions within an organism or cell." [GOC:ai]
+def: "Any process involved in the maintenance of an internal steady state of monoatomic ions within an organism or cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." [GOC:ai]
synonym: "electrolyte homeostasis" RELATED []
+synonym: "ion homeostasis" BROAD []
synonym: "negative regulation of crystal formation" RELATED []
synonym: "regulation of ion homeostasis" RELATED []
is_a: GO:0048878 ! chemical homeostasis
@@ -304020,7 +304005,7 @@ is_a: GO:0065008 ! regulation of biological quality
id: GO:0050804
name: modulation of chemical synaptic transmission
namespace: biological_process
-def: "Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission." [GOC:ai]
+def: "Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission." [GOC:ai]
subset: goslim_synapse
synonym: "modulation of synaptic transmission" BROAD []
synonym: "regulation of chemical synaptic transmission" EXACT []
@@ -304128,7 +304113,7 @@ synonym: "regulation of acyl-CoA biosynthesis" EXACT []
synonym: "regulation of acyl-CoA formation" EXACT []
synonym: "regulation of acyl-CoA synthesis" EXACT []
is_a: GO:0019217 ! regulation of fatty acid metabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0042762 ! regulation of sulfur metabolic process
is_a: GO:1900371 ! regulation of purine nucleotide biosynthetic process
relationship: regulates GO:0071616 ! acyl-CoA biosynthetic process
@@ -304284,15 +304269,6 @@ synonym: "antifreeze activity" RELATED []
synonym: "ice nucleation inhibitor activity" RELATED []
is_a: GO:0009409 ! response to cold
-[Term]
-id: GO:0050828
-name: regulation of liquid surface tension
-namespace: biological_process
-def: "Any process that modulates the surface tension of a liquid. Surface tension is the property that makes a liquid behave as if it had an elastic skin on its surface at the interface with a gas or an immiscible liquid." [ISBN:0198506732]
-synonym: "regulation of surface tension of a liquid" EXACT []
-synonym: "surfactant activity" RELATED []
-is_a: GO:0042592 ! homeostatic process
-
[Term]
id: GO:0050829
name: defense response to Gram-negative bacterium
@@ -304353,7 +304329,7 @@ def: "Enables the transfer of pyruvate, 2-oxopropanoate, from one side of a memb
synonym: "monocarboxylate (lactate, pyruvate, mevalonate) uptake/efflux porter activity" RELATED []
xref: Reactome:R-HSA-372342 "MPC1:MPC2 cotransports PYR, H+ from cytosol to mitochondrial matrix"
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0050834
@@ -304491,7 +304467,7 @@ is_a: GO:0006082 ! organic acid metabolic process
id: GO:0050847
name: progesterone receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of a progesterone binding to its receptor." [GOC:ai, GOC:mah, PMID:14744870]
+def: "The series of molecular signals initiated by progesterone binding to its receptor in the cytoplasm." [GOC:ai, GOC:mah, PMID:14744870]
synonym: "progesterone receptor signalling pathway" EXACT []
is_a: GO:0030518 ! intracellular steroid hormone receptor signaling pathway
@@ -304537,7 +304513,7 @@ relationship: positively_regulates GO:0019722 ! calcium-mediated signaling
id: GO:0050851
name: antigen receptor-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the cross-linking of an antigen receptor on a B or T cell." [GOC:add]
+def: "The series of molecular signals initiated by the cross-linking of an antigen receptor on a B or T cell." [GOC:add]
synonym: "antigen receptor-mediated signalling pathway" EXACT []
is_a: GO:0002429 ! immune response-activating cell surface receptor signaling pathway
@@ -304545,7 +304521,7 @@ is_a: GO:0002429 ! immune response-activating cell surface receptor signaling pa
id: GO:0050852
name: T cell receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell." [GOC:add]
+def: "The series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell." [GOC:add]
synonym: "T lymphocyte receptor signaling pathway" EXACT []
synonym: "T lymphocyte receptor signalling pathway" EXACT []
synonym: "T-cell receptor signaling pathway" EXACT []
@@ -304559,7 +304535,7 @@ is_a: GO:0050851 ! antigen receptor-mediated signaling pathway
id: GO:0050853
name: B cell receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell." [GOC:add]
+def: "The series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell." [GOC:add]
synonym: "B cell receptor signalling pathway" EXACT []
synonym: "B lymphocyte receptor signaling pathway" EXACT []
synonym: "B lymphocyte receptor signalling pathway" EXACT []
@@ -304750,6 +304726,7 @@ name: regulation of cell activation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:ai]
is_a: GO:0050794 ! regulation of cellular process
+is_a: GO:0051239 ! regulation of multicellular organismal process
relationship: regulates GO:0001775 ! cell activation
[Term]
@@ -304763,6 +304740,7 @@ synonym: "downregulation of cell activation" EXACT []
synonym: "inhibition of cell activation" NARROW []
is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0050865 ! regulation of cell activation
+is_a: GO:0051241 ! negative regulation of multicellular organismal process
relationship: negatively_regulates GO:0001775 ! cell activation
[Term]
@@ -304777,6 +304755,7 @@ synonym: "up-regulation of cell activation" EXACT []
synonym: "upregulation of cell activation" EXACT []
is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:0050865 ! regulation of cell activation
+is_a: GO:0051240 ! positive regulation of multicellular organismal process
relationship: positively_regulates GO:0001775 ! cell activation
[Term]
@@ -304978,13 +304957,13 @@ is_a: GO:0050877 ! nervous system process
[Term]
id: GO:0050891
-name: multicellular organismal water homeostasis
+name: multicellular organismal-level water homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of water within a tissue, organ, or a multicellular organism." [GOC:dph, GOC:tb]
+def: "A chemical homeostatic process involved in the maintenance of a steady state level of water within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell." [GOC:dph, GOC:tb]
synonym: "body fluid osmoregulation" RELATED [GOC:dph, GOC:tb]
-is_a: GO:0030104 ! water homeostasis
-is_a: GO:0048871 ! multicellular organismal homeostasis
+synonym: "multicellular organismal water homeostasis" EXACT []
is_a: GO:0050878 ! regulation of body fluid levels
+is_a: GO:0140962 ! multicellular organismal-level chemical homeostasis
[Term]
id: GO:0050892
@@ -305021,6 +305000,7 @@ subset: goslim_agr
subset: goslim_flybase_ribbon
subset: goslim_mouse
subset: goslim_pir
+subset: prokaryote_subset
synonym: "physiological response to stimulus" EXACT []
is_a: GO:0008150 ! biological_process
@@ -306129,8 +306109,8 @@ synonym: "dimethylallyl pyrophosphate biosynthesis" EXACT []
synonym: "dimethylallyl pyrophosphate biosynthetic process" EXACT []
synonym: "DPP biosynthesis" EXACT []
synonym: "DPP biosynthetic process" EXACT []
-is_a: GO:0008654 ! phospholipid biosynthetic process
is_a: GO:0050993 ! dimethylallyl diphosphate metabolic process
+is_a: GO:1901576 ! organic substance biosynthetic process
[Term]
id: GO:0050993
@@ -306142,7 +306122,8 @@ synonym: "dimethylallyl pyrophosphate metabolic process" EXACT []
synonym: "dimethylallyl pyrophosphate metabolism" EXACT []
synonym: "DPP metabolic process" EXACT []
synonym: "DPP metabolism" EXACT []
-is_a: GO:0006644 ! phospholipid metabolic process
+is_a: GO:0006793 ! phosphorus metabolic process
+is_a: GO:0071704 ! organic substance metabolic process
[Term]
id: GO:0050994
@@ -306531,7 +306512,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of transcription as part of a meiotic cell cycle." [GOC:go_curators]
synonym: "meiotic regulation of transcription" EXACT []
synonym: "regulation of transcription, meiotic" EXACT [GOC:mah]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
is_a: GO:0022414 ! reproductive process
relationship: part_of GO:0051321 ! meiotic cell cycle
@@ -306547,7 +306528,7 @@ synonym: "inhibition of transcription during meiosis" NARROW [GOC:mah]
synonym: "meiotic repression of transcription" EXACT []
synonym: "negative regulation of meiotic transcription" EXACT []
synonym: "negative regulation of transcription, meiotic" EXACT [GOC:mah]
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
is_a: GO:0051037 ! regulation of transcription involved in meiotic cell cycle
[Term]
@@ -306562,7 +306543,7 @@ synonym: "stimulation of transcription during meiosis" NARROW [GOC:mah]
synonym: "up regulation of transcription during meiosis" EXACT [GOC:mah]
synonym: "up-regulation of transcription during meiosis" EXACT [GOC:mah]
synonym: "upregulation of transcription during meiosis" EXACT [GOC:mah]
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
is_a: GO:0051037 ! regulation of transcription involved in meiotic cell cycle
[Term]
@@ -306607,7 +306588,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain)." [GOC:ai]
is_a: GO:0030162 ! regulation of proteolysis
is_a: GO:0031329 ! regulation of cellular catabolic process
-is_a: GO:0032268 ! regulation of cellular protein metabolic process
is_a: GO:0042176 ! regulation of protein catabolic process
relationship: regulates GO:0006509 ! membrane protein ectodomain proteolysis
@@ -306915,7 +306895,7 @@ synonym: "dihydrolipoamide reduction" NARROW []
synonym: "dihydrothioctamide metabolic process" EXACT []
synonym: "dihydrothioctamide metabolism" EXACT []
is_a: GO:0006790 ! sulfur compound metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
@@ -306948,7 +306928,7 @@ synonym: "4-6-O-[(R)(1-carboxyethylidine)]-Gal-beta-1,3 metabolic process" EXACT
synonym: "4-6-O-[(R)(1-carboxyethylidine)]-Gal-beta-1,3 metabolism" EXACT []
synonym: "PvGal metabolic process" EXACT []
synonym: "PvGal metabolism" EXACT []
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
+is_a: GO:0005976 ! polysaccharide metabolic process
[Term]
id: GO:0051072
@@ -306963,7 +306943,7 @@ synonym: "4-6-O-[(R)(1-carboxyethylidine)]-Gal-beta-1,3 biosynthesis" EXACT []
synonym: "4-6-O-[(R)(1-carboxyethylidine)]-Gal-beta-1,3 biosynthetic process" EXACT []
synonym: "PvGal biosynthesis" EXACT []
synonym: "PvGal biosynthetic process" EXACT []
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
+is_a: GO:0000271 ! polysaccharide biosynthetic process
[Term]
id: GO:0051073
@@ -307050,7 +307030,7 @@ relationship: part_of GO:0007135 ! meiosis II
id: GO:0051081
name: nuclear membrane disassembly
namespace: biological_process
-def: "The controlled breakdown of the nuclear membranes, for example during cellular division." [GOC:ai]
+def: "The controlled breakdown of the nuclear membranes, for example during cellular division." [GOC:ai]
synonym: "nuclear envelope breakdown" RELATED []
synonym: "nuclear envelope catabolism" RELATED []
synonym: "nuclear envelope degradation" RELATED []
@@ -307084,10 +307064,10 @@ is_a: GO:0006458 ! 'de novo' protein folding
[Term]
id: GO:0051084
-name: 'de novo' posttranslational protein folding
+name: 'de novo' post-translational protein folding
namespace: biological_process
def: "The process of assisting in the correct noncovalent folding of newly formed polypeptides or folding intermediates of polypeptides that have exited the ribosome and/or have been stabilized and transferred by other chaperone proteins. This process could involve several cycles of ATP hydrolysis." [GOC:rb]
-synonym: "'de novo' post-translational protein folding" EXACT []
+synonym: "'de novo' posttranslational protein folding" EXACT []
is_a: GO:0006458 ! 'de novo' protein folding
[Term]
@@ -307101,7 +307081,7 @@ synonym: "chaperone co-factor-dependent protein refolding" EXACT []
synonym: "chaperone cofactor-dependent 'de novo' protein folding" EXACT [GOC:mah]
synonym: "chaperone cofactor-dependent protein folding" EXACT [GOC:rb]
synonym: "chaperone mediated protein folding requiring cofactor" RELATED []
-is_a: GO:0051084 ! 'de novo' posttranslational protein folding
+is_a: GO:0051084 ! 'de novo' post-translational protein folding
is_a: GO:0061077 ! chaperone-mediated protein folding
[Term]
@@ -307110,14 +307090,15 @@ name: chaperone mediated protein folding independent of cofactor
namespace: biological_process
def: "The process of assisting in the correct noncovalent assembly of posttranslational proteins and does not depend on additional protein cofactors. This function occurs over one or more cycles of nucleotide-dependent binding and release." [GOC:rb]
synonym: "chaperone cofactor-independent protein folding" EXACT [GOC:rb]
-is_a: GO:0051084 ! 'de novo' posttranslational protein folding
+is_a: GO:0051084 ! 'de novo' post-translational protein folding
is_a: GO:0061077 ! chaperone-mediated protein folding
[Term]
id: GO:0051087
-name: chaperone binding
+name: protein-folding chaperone binding
namespace: molecular_function
def: "Binding to a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport." [PMID:10585443]
+synonym: "chaperone binding" BROAD []
synonym: "chaperone protein binding" EXACT []
synonym: "co-chaperone activity" RELATED []
synonym: "co-chaperonin activity" RELATED []
@@ -307150,7 +307131,7 @@ synonym: "regulation of DNA binding transcription factor activity" EXACT []
synonym: "regulation of sequence-specific DNA binding transcription factor activity" EXACT []
synonym: "regulation of thyroid hormone receptor activity" NARROW []
synonym: "regulation of transcription factor activity" BROAD [GOC:dph, GOC:tb]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
is_a: GO:0065009 ! regulation of molecular function
[Term]
@@ -307308,7 +307289,7 @@ def: "The re-formation of a broken phosphodiester bond in the DNA backbone, carr
synonym: "DNA ligation during DNA-dependent DNA replication" RELATED [GOC:dph, GOC:tb]
synonym: "DNA ligation involved in DNA-dependent DNA replication" EXACT []
is_a: GO:0006266 ! DNA ligation
-relationship: part_of GO:0006261 ! DNA-dependent DNA replication
+relationship: part_of GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:0051105
@@ -307425,7 +307406,7 @@ consider: GO:0017103
id: GO:0051116
name: cobaltochelatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + Co(2+) + H(2)O + hydrogenobyrinate a,c-diamide = ADP + cob(II)yrinate a,c diamide + 4 H(+) + phosphate." [EC:6.6.1.2, RHEA:15341]
+def: "Catalysis of the reaction: ATP + Co(2+) + H2O + hydrogenobyrinate a,c-diamide = ADP + cob(II)yrinate a,c diamide + 4 H+ + phosphate." [EC:6.6.1.2, RHEA:15341]
synonym: "CobN-CobST" RELATED [EC:6.6.1.2]
synonym: "CobNST" NARROW []
synonym: "hydrogenobyrinic acid a,c-diamide cobaltochelatase activity" EXACT []
@@ -307509,7 +307490,7 @@ synonym: "RNA polymerase II transcription PIC formation" EXACT []
synonym: "RNA polymerase II transcriptional preinitiation complex assembly" EXACT []
synonym: "RNA polymerase II transcriptional preinitiation complex formation" EXACT []
is_a: GO:0070897 ! transcription preinitiation complex assembly
-relationship: part_of GO:0006367 ! transcription initiation from RNA polymerase II promoter
+relationship: part_of GO:0006367 ! transcription initiation at RNA polymerase II promoter
[Term]
id: GO:0051124
@@ -307748,14 +307729,14 @@ relationship: positively_regulates GO:0001865 ! NK T cell differentiation
[Term]
id: GO:0051139
-name: metal ion:proton antiporter activity
+name: metal cation:proton antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: metal ion(in) + H+(out) = metal ion(out) + H+(in)." [GOC:mlg]
synonym: "metal ion:hydrogen antiporter activity" EXACT []
+synonym: "metal ion:proton antiporter activity" EXACT []
xref: Reactome:R-HSA-435171 "NRAMP1 transports divalent metal ions across phagosomal membranes of macrophages"
-is_a: GO:0015299 ! solute:proton antiporter activity
-is_a: GO:0015491 ! cation:cation antiporter activity
-is_a: GO:0046873 ! metal ion transmembrane transporter activity
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0140828 ! metal cation:monoatomic cation antiporter activity
[Term]
id: GO:0051140
@@ -308122,9 +308103,7 @@ namespace: biological_process
alt_id: GO:1902593
def: "The directed movement of substances into the nucleus." [GOC:ai]
synonym: "nuclear import" EXACT []
-synonym: "single organism nuclear import" EXACT [GOC:TermGenie]
-synonym: "single-organism nuclear import" RELATED []
-synonym: "substance nuclear import" EXACT []
+synonym: "nuclear translocation" EXACT []
is_a: GO:0006913 ! nucleocytoplasmic transport
[Term]
@@ -308216,17 +308195,14 @@ name: meiotic sister chromatid cohesion
namespace: biological_process
def: "The cell cycle process in which sister chromatids of a replicated chromosome are joined along the entire length of the chromosome during meiosis." [GOC:ai]
is_a: GO:0007062 ! sister chromatid cohesion
-is_a: GO:0070192 ! chromosome organization involved in meiotic cell cycle
-relationship: part_of GO:0045144 ! meiotic sister chromatid segregation
[Term]
id: GO:0051178
-name: meiotic chromosome decondensation
+name: obsolete meiotic chromosome decondensation
namespace: biological_process
-def: "The cell cycle process in which chromosome structure is altered from the condensed form held during meiosis to the relaxed dispersed form held in resting cells." [GOC:ai]
-is_a: GO:0051312 ! chromosome decondensation
-is_a: GO:0070192 ! chromosome organization involved in meiotic cell cycle
-relationship: part_of GO:0045132 ! meiotic chromosome segregation
+def: "OBSOLETE. The cell cycle process in which chromosome structure is altered from the condensed form held during meiosis to the relaxed dispersed form held in resting cells." [GOC:ai]
+comment: This term was obsoleted because it is a spontaneous process.
+is_obsolete: true
[Term]
id: GO:0051179
@@ -308332,7 +308308,7 @@ synonym: "coenzyme and prosthetic group metabolic process" BROAD []
synonym: "coenzyme and prosthetic group metabolism" BROAD []
synonym: "prosthetic group metabolism" EXACT []
is_a: GO:0008152 ! metabolic process
-relationship: part_of GO:0044267 ! cellular protein metabolic process
+relationship: part_of GO:0019538 ! protein metabolic process
[Term]
id: GO:0051190
@@ -308346,7 +308322,7 @@ synonym: "prosthetic group catabolism" EXACT []
synonym: "prosthetic group degradation" EXACT []
is_a: GO:0009056 ! catabolic process
is_a: GO:0051189 ! prosthetic group metabolic process
-relationship: part_of GO:0044257 ! cellular protein catabolic process
+relationship: part_of GO:0030163 ! protein catabolic process
[Term]
id: GO:0051191
@@ -308450,20 +308426,21 @@ is_obsolete: true
[Term]
id: GO:0051199
-name: regulation of prosthetic group metabolic process
+name: obsolete regulation of prosthetic group metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a prosthetic group." [GOC:ai]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a prosthetic group." [GOC:ai]
+comment: This term was obsoleted because it conflates the regulation of a metabolic process and the role of its product.
synonym: "regulation of coenzyme and prosthetic group metabolic process" BROAD []
synonym: "regulation of coenzyme and prosthetic group metabolism" BROAD []
synonym: "regulation of prosthetic group metabolism" EXACT []
-is_a: GO:0019222 ! regulation of metabolic process
-relationship: regulates GO:0051189 ! prosthetic group metabolic process
+is_obsolete: true
[Term]
id: GO:0051200
-name: positive regulation of prosthetic group metabolic process
+name: obsolete positive regulation of prosthetic group metabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a prosthetic group." [GOC:ai]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a prosthetic group." [GOC:ai]
+comment: This term was obsoleted because it conflates the regulation of a metabolic process and the role of its product.
synonym: "activation of prosthetic group metabolic process" NARROW []
synonym: "positive regulation of coenzyme and prosthetic group metabolic process" BROAD []
synonym: "positive regulation of coenzyme and prosthetic group metabolism" BROAD []
@@ -308472,15 +308449,14 @@ synonym: "stimulation of prosthetic group metabolic process" NARROW []
synonym: "up regulation of prosthetic group metabolic process" EXACT []
synonym: "up-regulation of prosthetic group metabolic process" EXACT []
synonym: "upregulation of prosthetic group metabolic process" EXACT []
-is_a: GO:0032270 ! positive regulation of cellular protein metabolic process
-is_a: GO:0051199 ! regulation of prosthetic group metabolic process
-relationship: positively_regulates GO:0051189 ! prosthetic group metabolic process
+is_obsolete: true
[Term]
id: GO:0051201
-name: negative regulation of prosthetic group metabolic process
+name: obsolete negative regulation of prosthetic group metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a prosthetic group." [GOC:ai]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a prosthetic group." [GOC:ai]
+comment: This term was obsoleted because it conflates the regulation of a metabolic process and the role of its product.
synonym: "down regulation of prosthetic group metabolic process" EXACT []
synonym: "down-regulation of prosthetic group metabolic process" EXACT []
synonym: "downregulation of prosthetic group metabolic process" EXACT []
@@ -308488,9 +308464,7 @@ synonym: "inhibition of prosthetic group metabolic process" NARROW []
synonym: "negative regulation of coenzyme and prosthetic group metabolic process" BROAD []
synonym: "negative regulation of coenzyme and prosthetic group metabolism" BROAD []
synonym: "negative regulation of prosthetic group metabolism" EXACT []
-is_a: GO:0009892 ! negative regulation of metabolic process
-is_a: GO:0051199 ! regulation of prosthetic group metabolic process
-relationship: negatively_regulates GO:0051189 ! prosthetic group metabolic process
+is_obsolete: true
[Term]
id: GO:0051202
@@ -308499,6 +308473,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving phytochromobilin, the linear tetrapyrrole chromophore required for plant phytochrome photoactivity." [PMID:11500553]
synonym: "phytochromobilin metabolism" EXACT []
is_a: GO:0033013 ! tetrapyrrole metabolic process
+is_a: GO:0043648 ! dicarboxylic acid metabolic process
[Term]
id: GO:0051203
@@ -308533,14 +308508,14 @@ relationship: part_of GO:0070585 ! protein localization to mitochondrion
id: GO:0051205
name: protein insertion into membrane
namespace: biological_process
-def: "The process that results in the incorporation of a protein into a biological membrane. Incorporation in this context means having some part or covalently attached group that is inserted into the the hydrophobic region of one or both bilayers." [GOC:ai]
+def: "The process that results in the incorporation of a protein into a biological membrane. Incorporation in this context means having some part or covalently attached group that is inserted into the the hydrophobic region of one or both bilayers." [GOC:ai]
synonym: "integral membrane protein localization" EXACT []
synonym: "integral membrane protein positioning" EXACT []
synonym: "membrane protein localization" EXACT []
synonym: "membrane protein positioning" EXACT []
synonym: "protein-membrane insertion" EXACT []
is_a: GO:0090150 ! establishment of protein localization to membrane
-relationship: part_of GO:0034613 ! cellular protein localization
+relationship: part_of GO:0008104 ! protein localization
relationship: part_of GO:0061024 ! membrane organization
[Term]
@@ -308567,7 +308542,7 @@ synonym: "sequestering of calcium ion (Ca2+)" EXACT []
synonym: "sequestration of calcium ion (Ca2+)" EXACT []
synonym: "storage of calcium ion (Ca2+)" EXACT []
is_a: GO:0051651 ! maintenance of location in cell
-relationship: part_of GO:0006874 ! cellular calcium ion homeostasis
+relationship: part_of GO:0006874 ! intracellular calcium ion homeostasis
[Term]
id: GO:0051209
@@ -308628,20 +308603,22 @@ is_a: GO:0016491 ! oxidoreductase activity
id: GO:0051214
name: RNAi-mediated antiviral immunity against RNA virus
namespace: biological_process
-def: "Gene silencing induced by RNA viruses leading to a sequence-specific degradation of target mRNAs or post-transcriptional gene silencing. In plants, DCL4 is the primary Dicer to detect RNA viruses." [PMID:15165191, PMID:17693253]
+def: "An RNAi-mediated post-transcriptional gene silencing pathway induced by RNA viruses leading to a sequence-specific degradation of target mRNAs or inhibition of translation. In plants, DCL4 is the primary Dicer to detect RNA viruses." [PMID:15165191, PMID:17693253]
synonym: "RNA VIGS" EXACT []
synonym: "RNA virus induced gene silencing" EXACT []
synonym: "RNA virus-induced gene silencing" EXACT []
+synonym: "RNA virus-induced PTGS" EXACT []
is_a: GO:0009616 ! RNAi-mediated antiviral immune response
[Term]
id: GO:0051215
name: RNAi-mediated antiviral immunity against DNA virus
namespace: biological_process
-def: "Gene silencing induced by DNA viruses leading to a sequence-specific degradation of target mRNAs or post-transcriptional gene silencing. In plants, DCL3 is the primary Dicer to detect DNA viruses." [PMID:15165191, PMID:17693253, PMID:23151511]
+def: "An RNAi-mediated post-transcriptional gene silencing pathway induced by DNA viruses leading to a sequence-specific degradation of target mRNAs or inhibition of translation. In plants, DCL3 is the primary Dicer to detect DNA viruses." [PMID:15165191, PMID:17693253, PMID:23151511]
synonym: "DNA VIGS" EXACT []
synonym: "DNA virus induced gene silencing" EXACT []
synonym: "DNA virus-induced gene silencing" EXACT []
+synonym: "DNA virus-induced PTGS" EXACT []
is_a: GO:0009616 ! RNAi-mediated antiviral immune response
[Term]
@@ -308674,7 +308651,7 @@ id: GO:0051218
name: tungsten incorporation via L-selenocysteinyl tungsten bis(molybdopterin guanine dinucleotide)
namespace: biological_process
def: "The incorporation of tungsten into a protein via L-selenocysteinyl tungsten bis(molybdopterin guanine dinucleotide)." [PDB:1HOH, PMID:12220497, RESID:AA0376]
-xref: RESID:AA02376
+xref: RESID:AA0376
is_a: GO:0042042 ! tungsten incorporation into tungsten-molybdopterin complex
is_a: GO:0050844 ! peptidyl-selenocysteine modification
@@ -308761,6 +308738,7 @@ synonym: "spindle biosynthesis" EXACT []
synonym: "spindle formation" EXACT []
is_a: GO:0007051 ! spindle organization
is_a: GO:0140694 ! non-membrane-bounded organelle assembly
+relationship: part_of GO:0007059 ! chromosome segregation
[Term]
id: GO:0051228
@@ -308943,7 +308921,10 @@ relationship: negatively_regulates GO:0006968 ! cellular defense response
id: GO:0051246
name: regulation of protein metabolic process
namespace: biological_process
+alt_id: GO:0032268
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein." [GOC:ai]
+synonym: "regulation of cellular protein metabolic process" RELATED []
+synonym: "regulation of cellular protein metabolism" RELATED []
synonym: "regulation of protein metabolism" EXACT []
is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
is_a: GO:0060255 ! regulation of macromolecule metabolic process
@@ -308954,12 +308935,20 @@ relationship: regulates GO:0019538 ! protein metabolic process
id: GO:0051247
name: positive regulation of protein metabolic process
namespace: biological_process
+alt_id: GO:0032270
def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein." [GOC:ai]
+synonym: "activation of cellular protein metabolic process" NARROW []
synonym: "activation of protein metabolic process" NARROW []
+synonym: "positive regulation of cellular protein metabolic process" EXACT []
+synonym: "positive regulation of cellular protein metabolism" EXACT []
synonym: "positive regulation of protein metabolism" EXACT []
+synonym: "stimulation of cellular protein metabolic process" NARROW []
synonym: "stimulation of protein metabolic process" NARROW []
+synonym: "up regulation of cellular protein metabolic process" EXACT []
synonym: "up regulation of protein metabolic process" EXACT []
+synonym: "up-regulation of cellular protein metabolic process" EXACT []
synonym: "up-regulation of protein metabolic process" EXACT []
+synonym: "upregulation of cellular protein metabolic process" EXACT []
synonym: "upregulation of protein metabolic process" EXACT []
is_a: GO:0010604 ! positive regulation of macromolecule metabolic process
is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
@@ -308970,11 +308959,18 @@ relationship: positively_regulates GO:0019538 ! protein metabolic process
id: GO:0051248
name: negative regulation of protein metabolic process
namespace: biological_process
+alt_id: GO:0032269
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein." [GOC:ai]
+synonym: "down regulation of cellular protein metabolic process" EXACT []
synonym: "down regulation of protein metabolic process" EXACT []
+synonym: "down-regulation of cellular protein metabolic process" EXACT []
synonym: "down-regulation of protein metabolic process" EXACT []
+synonym: "downregulation of cellular protein metabolic process" EXACT []
synonym: "downregulation of protein metabolic process" EXACT []
+synonym: "inhibition of cellular protein metabolic process" NARROW []
synonym: "inhibition of protein metabolic process" NARROW []
+synonym: "negative regulation of cellular protein metabolic process" EXACT []
+synonym: "negative regulation of cellular protein metabolism" EXACT []
synonym: "negative regulation of protein metabolism" EXACT []
is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
@@ -309164,15 +309160,14 @@ is_a: GO:0051259 ! protein complex oligomerization
[Term]
id: GO:0051263
-name: microcin E492 biosynthetic process by siderophore ester modification of peptidyl-serine
+name: obsolete microcin E492 biosynthetic process by siderophore ester modification of peptidyl-serine
namespace: biological_process
-def: "The modification of serine to N-[5-(6-O-seryl-beta-glucosyl)-2,3-dihydroxybenzoyl]-O-[N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)seryl]seryl]serine as found in microcin E492 produced from the mceA gene in plasmid pJAM229 of the E. coli VCS257 strain and the K. pneumoniae RYC492 strain." [RESID:AA0374]
+def: "OBSOLETE. The modification of serine to N-[5-(6-O-seryl-beta-glucosyl)-2,3-dihydroxybenzoyl]-O-[N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)seryl]seryl]serine as found in microcin E492 produced from the mceA gene in plasmid pJAM229 of the E. coli VCS257 strain and the K. pneumoniae RYC492 strain." [RESID:AA0374]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "microcin E492 anabolism by siderophore ester modification of peptidyl-serine" EXACT []
synonym: "microcin E492 formation by siderophore ester modification of peptidyl-serine" EXACT []
synonym: "microcin E492 synthesis by siderophore ester modification of peptidyl-serine" EXACT []
-xref: RESID:AA0374
-is_a: GO:0018209 ! peptidyl-serine modification
-is_a: GO:0018350 ! protein esterification
+is_obsolete: true
[Term]
id: GO:0051264
@@ -309203,11 +309198,8 @@ is_a: GO:0016411 ! acylglycerol O-acyltransferase activity
id: GO:0051266
name: sirohydrochlorin ferrochelatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: siroheme + 2 H+ = Fe(2+) + sirohydrochlorin." [EC:4.99.1.4, RHEA:24360]
-synonym: "CysG" RELATED [EC:4.99.1.4]
-synonym: "Met8P" RELATED [EC:4.99.1.4]
-synonym: "SirB" RELATED [EC:4.99.1.4]
-synonym: "siroheme ferro-lyase (sirohydrochlorin-forming)" RELATED [EC:4.99.1.4]
+def: "Catalysis of the reaction: siroheme + 2 H+ = Fe(2+) + sirohydrochlorin." [RHEA:24360]
+synonym: "siroheme ferro-lyase (sirohydrochlorin-forming)" RELATED []
synonym: "siroheme synthase activity" BROAD []
synonym: "sirohydrochlorin ferro-lyase activity" EXACT []
xref: EC:4.99.1.4
@@ -309245,34 +309237,31 @@ is_a: GO:0016903 ! oxidoreductase activity, acting on the aldehyde or oxo group
[Term]
id: GO:0051270
-name: regulation of cellular component movement
+name: obsolete regulation of cellular component movement
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl]
+comment: This term was obsoleted because it was not a useful grouping class since it mixed both cell and cellular component terms.
synonym: "regulation of cell movement" RELATED []
synonym: "regulation of cellular component motion" EXACT [GOC:mah]
-is_a: GO:0032879 ! regulation of localization
-is_a: GO:0050794 ! regulation of cellular process
-relationship: regulates GO:0006928 ! movement of cell or subcellular component
+is_obsolete: true
[Term]
id: GO:0051271
-name: negative regulation of cellular component movement
+name: obsolete negative regulation of cellular component movement
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl]
+comment: This term was obsoleted because it was not a useful grouping class since it mixed both cell and cellular component terms.
synonym: "negative regulation of cellular component motion" EXACT [GOC:mah]
-is_a: GO:0048523 ! negative regulation of cellular process
-is_a: GO:0051270 ! regulation of cellular component movement
-relationship: negatively_regulates GO:0006928 ! movement of cell or subcellular component
+is_obsolete: true
[Term]
id: GO:0051272
-name: positive regulation of cellular component movement
+name: obsolete positive regulation of cellular component movement
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl]
+comment: This term was obsoleted because it was not a useful grouping class since it mixed both cell and cellular component terms.
synonym: "positive regulation of cellular component motion" EXACT [GOC:mah]
-is_a: GO:0048522 ! positive regulation of cellular process
-is_a: GO:0051270 ! regulation of cellular component movement
-relationship: positively_regulates GO:0006928 ! movement of cell or subcellular component
+is_obsolete: true
[Term]
id: GO:0051273
@@ -309280,7 +309269,7 @@ name: beta-glucan metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving beta-glucans, compounds composed of glucose residues linked by beta-D-glucosidic bonds." [GOC:ai]
synonym: "beta-glucan metabolism" EXACT []
-is_a: GO:0006073 ! cellular glucan metabolic process
+is_a: GO:0044042 ! glucan metabolic process
[Term]
id: GO:0051274
@@ -309303,13 +309292,13 @@ synonym: "beta-glucan breakdown" EXACT []
synonym: "beta-glucan catabolism" EXACT []
synonym: "beta-glucan degradation" EXACT []
is_a: GO:0009251 ! glucan catabolic process
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
is_a: GO:0051273 ! beta-glucan metabolic process
[Term]
id: GO:0051276
name: chromosome organization
namespace: biological_process
+alt_id: GO:0006323
alt_id: GO:0007001
alt_id: GO:0051277
def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah]
@@ -309318,6 +309307,8 @@ subset: goslim_drosophila
subset: goslim_pir
synonym: "chromosome organisation" EXACT []
synonym: "chromosome organization and biogenesis" RELATED [GOC:mah]
+synonym: "DNA condensation" EXACT []
+synonym: "DNA packaging" NARROW []
synonym: "maintenance of genome integrity" RELATED []
synonym: "nuclear genome maintenance" RELATED []
is_a: GO:0006996 ! organelle organization
@@ -309348,7 +309339,6 @@ synonym: "regulation of release of sequestered calcium ion (Ca2+)" BROAD []
synonym: "regulation of release of stored calcium ion (Ca2+)" BROAD []
synonym: "regulation of release of stored calcium ion (Ca2+) into cytoplasm" EXACT []
synonym: "regulation of release of stored calcium ion (Ca2+) into cytosol" EXACT []
-is_a: GO:0010522 ! regulation of calcium ion transport into cytosol
is_a: GO:0051282 ! regulation of sequestering of calcium ion
is_a: GO:1903169 ! regulation of calcium ion transmembrane transport
relationship: regulates GO:0051209 ! release of sequestered calcium ion into cytosol
@@ -309373,7 +309363,6 @@ synonym: "negative regulation of release of sequestered calcium ion into cytopla
synonym: "negative regulation of release of stored calcium ion (Ca2+)" BROAD []
synonym: "negative regulation of release of stored calcium ion (Ca2+) into cytoplasm" BROAD []
synonym: "negative regulation of release of stored calcium ion (Ca2+) into cytosol" EXACT []
-is_a: GO:0010523 ! negative regulation of calcium ion transport into cytosol
is_a: GO:0051279 ! regulation of release of sequestered calcium ion into cytosol
is_a: GO:0051284 ! positive regulation of sequestering of calcium ion
is_a: GO:1903170 ! negative regulation of calcium ion transmembrane transport
@@ -309400,7 +309389,6 @@ synonym: "stimulation of release of sequestered calcium ion into cytosol" NARROW
synonym: "up regulation of release of sequestered calcium ion into cytosol" EXACT []
synonym: "up-regulation of release of sequestered calcium ion into cytosol" EXACT []
synonym: "upregulation of release of sequestered calcium ion into cytosol" EXACT []
-is_a: GO:0010524 ! positive regulation of calcium ion transport into cytosol
is_a: GO:0051279 ! regulation of release of sequestered calcium ion into cytosol
is_a: GO:1904427 ! positive regulation of calcium ion transmembrane transport
relationship: positively_regulates GO:0051209 ! release of sequestered calcium ion into cytosol
@@ -309493,7 +309481,7 @@ subset: goslim_chembl
synonym: "NAD or NADH binding" RELATED [GOC:mah]
synonym: "NAD+ or NADH binding" RELATED []
synonym: "nicotinamide adenine dinucleotide binding" EXACT []
-is_a: GO:0000166 ! nucleotide binding
+is_a: GO:0030554 ! adenyl nucleotide binding
[Term]
id: GO:0051289
@@ -309675,7 +309663,7 @@ synonym: "chromosome movement" BROAD []
synonym: "chromosome movement to spindle pole" EXACT []
is_a: GO:0007018 ! microtubule-based movement
is_a: GO:0022402 ! cell cycle process
-is_a: GO:0051303 ! establishment of chromosome localization
+is_a: GO:0050000 ! chromosome localization
relationship: part_of GO:0098813 ! nuclear chromosome segregation
[Term]
@@ -309728,7 +309716,6 @@ name: metaphase plate congression
namespace: biological_process
def: "The alignment of chromosomes at the metaphase plate (spindle equator), a plane halfway between the poles of the spindle." [GOC:ai]
synonym: "chromosome congression" EXACT [GOC:ascb_2009, GOC:dph, GOC:tb]
-is_a: GO:0022402 ! cell cycle process
is_a: GO:0051303 ! establishment of chromosome localization
relationship: part_of GO:0098813 ! nuclear chromosome segregation
@@ -309744,10 +309731,11 @@ relationship: part_of GO:0045132 ! meiotic chromosome segregation
[Term]
id: GO:0051312
-name: chromosome decondensation
+name: obsolete chromosome decondensation
namespace: biological_process
-def: "The alteration of chromosome structure from the condensed form to a relaxed disperse form." [GOC:ai]
-is_a: GO:0051276 ! chromosome organization
+def: "OBSOLETE. The alteration of chromosome structure from the condensed form to a relaxed disperse form." [GOC:ai]
+comment: This term was obsoleted because it is a spontaneous process.
+is_obsolete: true
[Term]
id: GO:0051315
@@ -309825,6 +309813,7 @@ synonym: "meiosis" RELATED []
xref: Wikipedia:Meiosis
is_a: GO:0007049 ! cell cycle
is_a: GO:0022414 ! reproductive process
+relationship: part_of GO:0019953 ! sexual reproduction
[Term]
id: GO:0051322
@@ -310252,84 +310241,69 @@ relationship: part_of GO:0050957 ! equilibrioception
[Term]
id: GO:0051357
-name: peptide cross-linking via 3-(2-methylthio)ethyl-6-(4-hydroxybenzylidene)-5-iminopiperazin-2-one
+name: obsolete peptide cross-linking via 3-(2-methylthio)ethyl-6-(4-hydroxybenzylidene)-5-iminopiperazin-2-one
namespace: biological_process
-def: "The formation of a 2-keto-5-iminopiperazine protein chromophore cross-link from the alpha-amino nitrogen of residue n, a methionine, to the alpha-carboxyl carbon of residue n+1, a tyrosine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+2. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons." [PMID:10852900, PMID:11259412, PMID:15491166, RESID:AA0377]
-comment: Note that this predicted modification is now thought not to exist. See the biological process term 'peptide cross-linking via 2-imino-methionine 5-imidazolinone glycine ; GO:0051359'.
+def: "OBSOLETE. The formation of a 2-keto-5-iminopiperazine protein chromophore cross-link from the alpha-amino nitrogen of residue n, a methionine, to the alpha-carboxyl carbon of residue n+1, a tyrosine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+2. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons." [PMID:10852900, PMID:11259412, PMID:15491166, RESID:AA0377]
+comment: Note that this predicted modification is now thought not to exist. See the biological process term 'peptide cross-linking via 2-imino-methionine 5-imidazolinone glycine ; GO:0051359'. Term describes modified products or self-catalyzed processes.
synonym: "biosynthesis of protein-protein cross-link via L-methionyl-L-tyrosyl-2-keto-5-iminopiperazine" EXACT []
synonym: "biosynthetic process of protein-protein cross-link via L-methionyl-L-tyrosyl-2-keto-5-iminopiperazine" EXACT []
xref: RESID:AA0377
-is_a: GO:0018149 ! peptide cross-linking
-is_a: GO:0018206 ! peptidyl-methionine modification
-is_a: GO:0018212 ! peptidyl-tyrosine modification
-is_a: GO:0018298 ! protein-chromophore linkage
+is_obsolete: true
[Term]
id: GO:0051358
-name: peptide cross-linking via 2-imino-glutamic acid 5-imidazolinone glycine
+name: obsolete peptide cross-linking via 2-imino-glutamic acid 5-imidazolinone glycine
namespace: biological_process
-def: "The formation of the non-fluorescent protein chromophore cross-link from the alpha-carboxyl carbon of residue n, a glutamic acid, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons. This modification is found in the GFP-like non-fluorescent red chromoprotein from the sea anemone Radianthus macrodactylus." [PMID:11682051, RESID:AA0378]
-comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'.
+def: "OBSOLETE. The formation of the non-fluorescent protein chromophore cross-link from the alpha-carboxyl carbon of residue n, a glutamic acid, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons. This modification is found in the GFP-like non-fluorescent red chromoprotein from the sea anemone Radianthus macrodactylus." [PMID:11682051, RESID:AA0378]
+comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'. Term describes modified products or self-catalyzed processes.
synonym: "biosynthesis of protein-protein cross-link via 2-imino-glutamic acid 5-imidazolinone glycine" EXACT []
synonym: "biosynthetic process of protein-protein cross-link via 2-imino-glutamic acid 5-imidazolinone glycine" EXACT []
xref: RESID:AA0378
-is_a: GO:0018149 ! peptide cross-linking
-is_a: GO:0018200 ! peptidyl-glutamic acid modification
-is_a: GO:0018201 ! peptidyl-glycine modification
-is_a: GO:0018298 ! protein-chromophore linkage
+is_obsolete: true
[Term]
id: GO:0051359
-name: peptide cross-linking via 2-imino-methionine 5-imidazolinone glycine
+name: obsolete peptide cross-linking via 2-imino-methionine 5-imidazolinone glycine
namespace: biological_process
-def: "The formation of the fluorescent protein FP611 chromophore cross-link from the alpha-carboxyl carbon of residue n, a methionine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons. This modification is found in the GFP-like fluorescent chromoprotein from the sea anemone Entacmaea quadricolor." [PDB:1UIS, PDB:1XQM, PMID:10852900, PMID:12185250, PMID:12909624, PMID:15542608, RESID:AA0379]
-comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'.
+def: "OBSOLETE. The formation of the fluorescent protein FP611 chromophore cross-link from the alpha-carboxyl carbon of residue n, a methionine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons. This modification is found in the GFP-like fluorescent chromoprotein from the sea anemone Entacmaea quadricolor." [PDB:1UIS, PDB:1XQM, PMID:10852900, PMID:12185250, PMID:12909624, PMID:15542608, RESID:AA0379]
+comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'. Term describes modified products or self-catalyzed processes.
synonym: "biosynthesis of protein-protein cross-link via 2-imino-methionine 5-imidazolinone glycine" EXACT []
synonym: "biosynthetic process of protein-protein cross-link via 2-imino-methionine 5-imidazolinone glycine" EXACT []
xref: RESID:AA0379
-is_a: GO:0018149 ! peptide cross-linking
-is_a: GO:0018201 ! peptidyl-glycine modification
-is_a: GO:0018206 ! peptidyl-methionine modification
-is_a: GO:0018298 ! protein-chromophore linkage
+is_obsolete: true
[Term]
id: GO:0051360
-name: peptide cross-linking via L-asparagine 5-imidazolinone glycine
+name: obsolete peptide cross-linking via L-asparagine 5-imidazolinone glycine
namespace: biological_process
-def: "The formation of the fluorescent protein FP506 chromophore cross-link from the alpha-carboxyl carbon of residue n, an asparagine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons." [PMID:10504696, RESID:AA0380]
-comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'.
+def: "OBSOLETE. The formation of the fluorescent protein FP506 chromophore cross-link from the alpha-carboxyl carbon of residue n, an asparagine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons." [PMID:10504696, RESID:AA0380]
+comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'. Term describes modified products or self-catalyzed processes.
synonym: "biosynthesis of protein-protein cross-link via L-asparagine 5-imidazolinone glycine" EXACT []
synonym: "biosynthetic process of protein-protein cross-link via L-asparagine 5-imidazolinone glycine" EXACT []
xref: RESID:AA0380
-is_a: GO:0018196 ! peptidyl-asparagine modification
-is_a: GO:0018253 ! peptide cross-linking via 5-imidazolinone glycine
-is_a: GO:0018298 ! protein-chromophore linkage
+is_obsolete: true
[Term]
id: GO:0051361
-name: peptide cross-linking via L-lysine 5-imidazolinone glycine
+name: obsolete peptide cross-linking via L-lysine 5-imidazolinone glycine
namespace: biological_process
-def: "The formation of a fluorescent protein chromophore cross-link from the alpha-carboxyl carbon of residue n, a lysine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons." [PMID:10504696, RESID:AA0381]
-comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'.
+def: "OBSOLETE. The formation of a fluorescent protein chromophore cross-link from the alpha-carboxyl carbon of residue n, a lysine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons." [PMID:10504696, RESID:AA0381]
+comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'. Term describes modified products or self-catalyzed processes.
synonym: "biosynthesis of protein-protein cross-link via L-lysine 5-imidazolinone glycine" EXACT []
synonym: "biosynthetic process of protein-protein cross-link via L-lysine 5-imidazolinone glycine" EXACT []
xref: RESID:AA0381
-is_a: GO:0018205 ! peptidyl-lysine modification
-is_a: GO:0018253 ! peptide cross-linking via 5-imidazolinone glycine
-is_a: GO:0018298 ! protein-chromophore linkage
+is_obsolete: true
[Term]
id: GO:0051362
-name: peptide cross-linking via 2-tetrahydropyridinyl-5-imidazolinone glycine
+name: obsolete peptide cross-linking via 2-tetrahydropyridinyl-5-imidazolinone glycine
namespace: biological_process
-def: "The formation of a 2-tetrahydropyridinyl-5-imidazolinone protein chromophore cross-link from the alpha-carboxyl carbon of residue n, a lysine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons. In addition, the residue N lysine undergoes cyclization. The alpha-amino nitrogen is replaced by the epsilon-amino nitrogen, the peptide chain is broken, residue N-1 is released as an amide, and a double bond is formed between the alpha-carbon and the nitrogen so that a tetrahydropyridine ring results. This modification is found in the GFP-like fluorescent chromoprotein FP538 from the sea anemone Zoanthus species." [PDB:1XAE, PMID:10504696, PMID:15628861, RESID:AA0382]
-comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'.
+def: "OBSOLETE. The formation of a 2-tetrahydropyridinyl-5-imidazolinone protein chromophore cross-link from the alpha-carboxyl carbon of residue n, a lysine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons. In addition, the residue N lysine undergoes cyclization. The alpha-amino nitrogen is replaced by the epsilon-amino nitrogen, the peptide chain is broken, residue N-1 is released as an amide, and a double bond is formed between the alpha-carbon and the nitrogen so that a tetrahydropyridine ring results. This modification is found in the GFP-like fluorescent chromoprotein FP538 from the sea anemone Zoanthus species." [PDB:1XAE, PMID:10504696, PMID:15628861, RESID:AA0382]
+comment: See also the biological process term 'peptidyl-tyrosine dehydrogenation ; GO:0018251'. Term describes modified products or self-catalyzed processes.
synonym: "biosynthesis of protein-protein cross-link via 2-tetrahydropyridinyl-5-imidazolinone glycine" EXACT []
synonym: "biosynthetic process of protein-protein cross-link via 2-tetrahydropyridinyl-5-imidazolinone glycine" EXACT []
xref: RESID:AA0382
-is_a: GO:0018205 ! peptidyl-lysine modification
-is_a: GO:0018253 ! peptide cross-linking via 5-imidazolinone glycine
-is_a: GO:0018298 ! protein-chromophore linkage
+is_obsolete: true
[Term]
id: GO:0051363
@@ -310472,6 +310446,7 @@ name: norepinephrine binding
namespace: molecular_function
def: "Binding to norepinephrine, (3,4-dihydroxyphenyl-2-aminoethanol), a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine." [GOC:ai]
synonym: "noradrenaline binding" EXACT []
+is_a: GO:0043169 ! cation binding
is_a: GO:1901338 ! catecholamine binding
[Term]
@@ -310488,11 +310463,13 @@ id: GO:0051382
name: kinetochore assembly
namespace: biological_process
alt_id: GO:0000069
+alt_id: GO:0044768
def: "The aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules." [GOC:ai]
synonym: "centromere and kinetochore complex maturation" NARROW []
synonym: "centromere/kinetochore complex maturation" NARROW []
synonym: "chromosome-kinetochore attachment" NARROW [GOC:ascb_2009, GOC:dph, GOC:tb]
synonym: "kinetochore formation" RELATED []
+synonym: "NMS complex assembly" NARROW []
is_a: GO:0051383 ! kinetochore organization
is_a: GO:0065003 ! protein-containing complex assembly
is_a: GO:0140694 ! non-membrane-bounded organelle assembly
@@ -310718,7 +310695,7 @@ is_a: GO:0019904 ! protein domain specific binding
id: GO:0051402
name: neuron apoptotic process
namespace: biological_process
-def: "Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [CL:0000540, GOC:mtg_apoptosis, MeSH:A.08.663]
+def: "Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [CL:0000540, GOC:mtg_apoptosis]
synonym: "apoptosis of neuronal cells" EXACT []
synonym: "apoptosis of neurons" EXACT []
synonym: "neuron apoptosis" NARROW []
@@ -310736,7 +310713,7 @@ is_a: GO:0070997 ! neuron death
id: GO:0051403
name: stress-activated MAPK cascade
namespace: biological_process
-def: "A series of molecular signals in which a stress-activated MAP kinase cascade relays one or more of the signals; MAP kinase cascades involve at least three protein kinase activities and culminate in the phosphorylation and activation of a MAP kinase." [GOC:ai, PMID:15936270]
+def: "The series of molecular signals in which a stress-activated MAP kinase cascade relays a signal; MAP kinase cascades involve at least three protein kinase activities and culminate in the phosphorylation and activation of a MAP kinase." [GOC:ai, PMID:15936270]
synonym: "MAPK11 cascade" NARROW [GOC:add]
synonym: "MAPK12 cascade" NARROW [GOC:add]
synonym: "MAPK13 cascade" NARROW [GOC:add]
@@ -310805,7 +310782,6 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: glycerone phosphate(out) + phosphate(in) = glycerone phosphate(in) + phosphate(out)." [GOC:ai]
synonym: "dihydroxyacetone-phosphate:inorganic phosphate antiporter activity" EXACT []
is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
is_a: GO:0015315 ! organophosphate:inorganic phosphate antiporter activity
is_a: GO:0015605 ! organophosphate ester transmembrane transporter activity
is_a: GO:0015665 ! alcohol transmembrane transporter activity
@@ -310818,7 +310794,6 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: glyceraldehyde 3-phosphate(out) + phosphate(in) = glyceraldehyde 3-phosphate(in) + phosphate(out)." [GOC:ai]
is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0009670 ! triose-phosphate:phosphate antiporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
[Term]
id: GO:0051409
@@ -310998,7 +310973,7 @@ is_a: GO:0017046 ! peptide hormone binding
id: GO:0051425
name: PTB domain binding
namespace: molecular_function
-def: "Binding to a phosphotyrosine-binding (PTB) Binding to a phosphotyrosine-bindin domain." [Pfam:PF02174.5, PMID:15924411]
+def: "Binding to a phosphotyrosine-binding (PTB) Binding to a phosphotyrosine-bindin domain." [Pfam:PF02174, PMID:15924411]
synonym: "phosphotyrosine-interacting domain binding" EXACT []
synonym: "PID binding" BROAD []
is_a: GO:0019904 ! protein domain specific binding
@@ -311360,7 +311335,6 @@ synonym: "cellular acidification" EXACT []
synonym: "intracellular acidification" RELATED []
synonym: "reduction of cellular pH" EXACT []
synonym: "reduction of pH in cell" EXACT []
-is_a: GO:0045851 ! pH reduction
is_a: GO:0051453 ! regulation of intracellular pH
[Term]
@@ -311373,6 +311347,7 @@ synonym: "cellular pH regulation" EXACT []
synonym: "pH regulation in cell" EXACT []
synonym: "regulation of cell pH" EXACT []
is_a: GO:0030641 ! regulation of cellular pH
+is_a: GO:0065008 ! regulation of biological quality
[Term]
id: GO:0051454
@@ -311384,7 +311359,6 @@ synonym: "cellular alkalinization" EXACT []
synonym: "elevation of cellular pH" EXACT []
synonym: "intracellular alkalinization" EXACT []
synonym: "pH elevation in cell" EXACT []
-is_a: GO:0045852 ! pH elevation
is_a: GO:0051453 ! regulation of intracellular pH
[Term]
@@ -311601,9 +311575,9 @@ is_a: GO:0097576 ! vacuole fusion
id: GO:0051470
name: ectoine transport
namespace: biological_process
-def: "The directed movement of ectoine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) is a tetrahydropyrimidine commonly synthesized by halophilic bacteria." [GOC:ai]
+def: "The directed movement of ectoine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) is a tetrahydropyrimidine commonly synthesized by halophilic bacteria." [GOC:ai, RHEA:32791]
+xref: RHEA:32791
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0071705 ! nitrogen compound transport
[Term]
@@ -311612,9 +311586,9 @@ name: glucosylglycerol metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving glucosylglycerol, alpha-D-glucopyranosyl-alpha-(1,2)-glycerol." [GOC:ai]
synonym: "glucosylglycerol metabolism" EXACT []
-is_a: GO:0006073 ! cellular glucan metabolic process
is_a: GO:0016137 ! glycoside metabolic process
is_a: GO:0019400 ! alditol metabolic process
+is_a: GO:0044042 ! glucan metabolic process
[Term]
id: GO:0051473
@@ -311640,21 +311614,23 @@ is_a: GO:1901505 ! carbohydrate derivative transmembrane transporter activity
[Term]
id: GO:0051475
-name: glucosylglycerol transport
+name: glucosylglycerol transmembrane transport
namespace: biological_process
-def: "The directed movement of glucosylglycerol, alpha-D-glucopyranosyl-alpha-(1,2)-glycerol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
-is_a: GO:0008643 ! carbohydrate transport
-is_a: GO:0015791 ! polyol transport
+def: "The directed movement of glucosylglycerol, alpha-D-glucopyranosyl-alpha-(1,2)-glycerol, across a membrane." [GOC:ai]
+synonym: "glucosylglycerol transport" BROAD []
+is_a: GO:0015791 ! polyol transmembrane transport
+is_a: GO:0034219 ! carbohydrate transmembrane transport
is_a: GO:1901656 ! glycoside transport
[Term]
id: GO:0051476
-name: mannosylglycerate transport
+name: phosphoenolpyruvate-dependent mannosylglycerate phosphotransferase system
namespace: biological_process
-def: "The directed movement of mannosylglycerate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
-is_a: GO:0008643 ! carbohydrate transport
-is_a: GO:0015849 ! organic acid transport
+def: "A phosphoenolpyruvate-dependent sugar phosphotransferase transport specific for mammosylglycerate." [PMID:368051]
+synonym: "mannosylglycerate transport" BROAD []
+is_a: GO:0009401 ! phosphoenolpyruvate-dependent sugar phosphotransferase system
is_a: GO:1901656 ! glycoside transport
+is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:0051477
@@ -311671,9 +311647,9 @@ name: mannosylglycerate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving mannosylglycerate, a very common compatible solute in thermophilic and hyperthermophilic organisms." [GOC:ai, PMID:11562374]
synonym: "mannosylglycerate metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
+is_a: GO:0005975 ! carbohydrate metabolic process
is_a: GO:0016137 ! glycoside metabolic process
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
[Term]
id: GO:0051479
@@ -311684,9 +311660,9 @@ synonym: "mannosylglycerate anabolism" EXACT []
synonym: "mannosylglycerate biosynthesis" EXACT []
synonym: "mannosylglycerate formation" EXACT []
synonym: "mannosylglycerate synthesis" EXACT []
-is_a: GO:0016053 ! organic acid biosynthetic process
+is_a: GO:0016051 ! carbohydrate biosynthetic process
is_a: GO:0016138 ! glycoside biosynthetic process
-is_a: GO:0034637 ! cellular carbohydrate biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:0051478 ! mannosylglycerate metabolic process
[Term]
@@ -311702,7 +311678,7 @@ synonym: "cytosolic calcium ion concentration regulation" EXACT []
synonym: "regulation of calcium ion concentration in cytoplasm" BROAD []
synonym: "regulation of calcium ion concentration in cytosol" EXACT []
synonym: "regulation of cytoplasmic calcium ion concentration" BROAD []
-is_a: GO:0006874 ! cellular calcium ion homeostasis
+is_a: GO:0006874 ! intracellular calcium ion homeostasis
[Term]
id: GO:0051481
@@ -311715,7 +311691,7 @@ synonym: "reduction of calcium ion concentration in cytoplasm" BROAD []
synonym: "reduction of calcium ion concentration in cytosol" EXACT []
synonym: "reduction of cytoplasmic calcium ion concentration" BROAD []
synonym: "reduction of cytosolic calcium ion concentration" EXACT []
-is_a: GO:0051480 ! regulation of cytosolic calcium ion concentration
+is_a: GO:0065008 ! regulation of biological quality
[Term]
id: GO:0051482
@@ -312481,7 +312457,7 @@ synonym: "mitochondrial calcium ion concentration regulation" EXACT []
synonym: "regulation of calcium ion concentration in mitochondria" EXACT []
synonym: "regulation of calcium ion concentration in mitochondrion" EXACT []
synonym: "regulation of mitochondrial calcium ion concentration" EXACT []
-is_a: GO:0006874 ! cellular calcium ion homeostasis
+is_a: GO:0006874 ! intracellular calcium ion homeostasis
[Term]
id: GO:0051561
@@ -312715,7 +312691,6 @@ name: regulation of dopamine uptake involved in synaptic transmission
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the directed movement of the catecholamine neurotransmitter dopamine into a cell." [GOC:ai]
synonym: "regulation of dopamine import involved in synaptic transmission" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0043269 ! regulation of ion transport
is_a: GO:0051940 ! regulation of catecholamine uptake involved in synaptic transmission
relationship: regulates GO:0051583 ! dopamine uptake involved in synaptic transmission
@@ -312728,7 +312703,6 @@ synonym: "down regulation of dopamine uptake involved in synaptic transmission"
synonym: "down-regulation of dopamine uptake involved in synaptic transmission" EXACT []
synonym: "downregulation of dopamine uptake involved in synaptic transmission" EXACT []
synonym: "negative regulation of dopamine import involved in synaptic transmission" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0043271 ! negative regulation of ion transport
is_a: GO:0051584 ! regulation of dopamine uptake involved in synaptic transmission
is_a: GO:0051945 ! negative regulation of catecholamine uptake involved in synaptic transmission
relationship: negatively_regulates GO:0051583 ! dopamine uptake involved in synaptic transmission
@@ -312744,7 +312718,6 @@ synonym: "stimulation of dopamine uptake involved in synaptic transmission" NARR
synonym: "up regulation of dopamine uptake involved in synaptic transmission" EXACT []
synonym: "up-regulation of dopamine uptake involved in synaptic transmission" EXACT []
synonym: "upregulation of dopamine uptake involved in synaptic transmission" EXACT []
-is_a: GO:0043270 ! positive regulation of ion transport
is_a: GO:0051584 ! regulation of dopamine uptake involved in synaptic transmission
is_a: GO:0051944 ! positive regulation of catecholamine uptake involved in synaptic transmission
relationship: positively_regulates GO:0051583 ! dopamine uptake involved in synaptic transmission
@@ -312812,7 +312785,10 @@ name: response to calcium ion
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus." [GOC:ai]
synonym: "response to Ca2+ ion" EXACT []
+is_a: GO:0010033 ! response to organic substance
is_a: GO:0010038 ! response to metal ion
+is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0051593
@@ -312921,7 +312897,7 @@ is_a: GO:0009628 ! response to abiotic stimulus
[Term]
id: GO:0051603
-name: proteolysis involved in cellular protein catabolic process
+name: proteolysis involved in protein catabolic process
namespace: biological_process
def: "The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells." [GOC:ai, GOC:dph, GOC:tb]
subset: goslim_yeast
@@ -312931,8 +312907,9 @@ synonym: "peptidolysis involved in cellular protein catabolic process" EXACT []
synonym: "peptidolysis involved in cellular protein catabolism" EXACT []
synonym: "proteolysis during cellular protein catabolic process" RELATED []
synonym: "proteolysis during cellular protein catabolism" RELATED []
+synonym: "proteolysis involved in cellular protein catabolic process" EXACT []
is_a: GO:0006508 ! proteolysis
-relationship: part_of GO:0044257 ! cellular protein catabolic process
+relationship: part_of GO:0030163 ! protein catabolic process
[Term]
id: GO:0051604
@@ -312945,6 +312922,7 @@ subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
+subset: prokaryote_subset
is_a: GO:0019538 ! protein metabolic process
relationship: part_of GO:0010467 ! gene expression
@@ -312975,7 +312953,6 @@ id: GO:0051608
name: histamine transport
namespace: biological_process
def: "The directed movement of histamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Histamine is a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." [GOC:ai]
-is_a: GO:0006812 ! cation transport
is_a: GO:0071702 ! organic substance transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -313008,7 +312985,6 @@ synonym: "regulation of 5-HT uptake" EXACT []
synonym: "regulation of 5-hydroxytryptamine uptake" EXACT []
synonym: "regulation of 5HT uptake" EXACT []
synonym: "regulation of serotonin import" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0043269 ! regulation of ion transport
is_a: GO:0051580 ! regulation of neurotransmitter uptake
relationship: regulates GO:0051610 ! serotonin uptake
@@ -313024,7 +313000,6 @@ synonym: "negative regulation of 5-HT uptake" EXACT []
synonym: "negative regulation of 5-hydroxytryptamine uptake" EXACT []
synonym: "negative regulation of 5HT uptake" EXACT []
synonym: "negative regulation of serotonin import" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0043271 ! negative regulation of ion transport
is_a: GO:0051581 ! negative regulation of neurotransmitter uptake
is_a: GO:0051611 ! regulation of serotonin uptake
relationship: negatively_regulates GO:0051610 ! serotonin uptake
@@ -313043,7 +313018,6 @@ synonym: "stimulation of serotonin uptake" NARROW []
synonym: "up regulation of serotonin uptake" EXACT []
synonym: "up-regulation of serotonin uptake" EXACT []
synonym: "upregulation of serotonin uptake" EXACT []
-is_a: GO:0043270 ! positive regulation of ion transport
is_a: GO:0051582 ! positive regulation of neurotransmitter uptake
is_a: GO:0051611 ! regulation of serotonin uptake
relationship: positively_regulates GO:0051610 ! serotonin uptake
@@ -313075,7 +313049,6 @@ name: regulation of histamine uptake
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter histamine into a cell." [GOC:ai]
synonym: "regulation of histamine import" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0043269 ! regulation of ion transport
is_a: GO:0051580 ! regulation of neurotransmitter uptake
relationship: regulates GO:0051615 ! histamine uptake
@@ -313088,7 +313061,6 @@ synonym: "down regulation of histamine uptake" EXACT []
synonym: "down-regulation of histamine uptake" EXACT []
synonym: "downregulation of histamine uptake" EXACT []
synonym: "negative regulation of histamine import" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0043271 ! negative regulation of ion transport
is_a: GO:0051581 ! negative regulation of neurotransmitter uptake
is_a: GO:0051616 ! regulation of histamine uptake
relationship: negatively_regulates GO:0051615 ! histamine uptake
@@ -313104,7 +313076,6 @@ synonym: "stimulation of histamine uptake" NARROW []
synonym: "up regulation of histamine uptake" EXACT []
synonym: "up-regulation of histamine uptake" EXACT []
synonym: "upregulation of histamine uptake" EXACT []
-is_a: GO:0043270 ! positive regulation of ion transport
is_a: GO:0051582 ! positive regulation of neurotransmitter uptake
is_a: GO:0051616 ! regulation of histamine uptake
relationship: positively_regulates GO:0051615 ! histamine uptake
@@ -313263,7 +313234,6 @@ name: regulation of acetylcholine uptake
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter acetylcholine into a cell." [GOC:ai]
synonym: "regulation of acetylcholine import" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0043269 ! regulation of ion transport
is_a: GO:0051952 ! regulation of amine transport
relationship: regulates GO:0051630 ! acetylcholine uptake
@@ -313276,7 +313246,6 @@ synonym: "down regulation of acetylcholine uptake" EXACT []
synonym: "down-regulation of acetylcholine uptake" EXACT []
synonym: "downregulation of acetylcholine uptake" EXACT []
synonym: "negative regulation of acetylcholine import" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0043271 ! negative regulation of ion transport
is_a: GO:0051631 ! regulation of acetylcholine uptake
is_a: GO:0051953 ! negative regulation of amine transport
relationship: negatively_regulates GO:0051630 ! acetylcholine uptake
@@ -313292,7 +313261,6 @@ synonym: "stimulation of acetylcholine uptake" NARROW []
synonym: "up regulation of acetylcholine uptake" EXACT []
synonym: "up-regulation of acetylcholine uptake" EXACT []
synonym: "upregulation of acetylcholine uptake" EXACT []
-is_a: GO:0043270 ! positive regulation of ion transport
is_a: GO:0051631 ! regulation of acetylcholine uptake
is_a: GO:0051954 ! positive regulation of amine transport
relationship: positively_regulates GO:0051630 ! acetylcholine uptake
@@ -313386,7 +313354,7 @@ def: "Any process in which an organelle is transported to, and/or maintained in,
subset: goslim_pir
synonym: "establishment and maintenance of organelle localization" EXACT []
synonym: "organelle localisation" EXACT [GOC:mah]
-is_a: GO:0051641 ! cellular localization
+is_a: GO:0051179 ! localization
[Term]
id: GO:0051641
@@ -313498,7 +313466,6 @@ id: GO:0051650
name: establishment of vesicle localization
namespace: biological_process
def: "The directed movement of a vesicle to a specific location." [GOC:ai]
-subset: goslim_aspergillus
synonym: "establishment of vesicle localisation" EXACT [GOC:mah]
is_a: GO:0051648 ! vesicle localization
is_a: GO:0051649 ! establishment of localization in cell
@@ -313638,7 +313605,7 @@ synonym: "oocyte nucleus localization during oocyte axis determination" RELATED
synonym: "oocyte nucleus localization involved in oocyte dorsal-ventral axis specification" EXACT [GOC:mah]
synonym: "oocyte nucleus localization involved in oocyte dorsal/ventral axis determination" EXACT [GOC:dph, GOC:tb]
synonym: "oocyte nucleus localization involved in oocyte dorsoventral axis specification" EXACT [GOC:mah]
-is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
+is_a: GO:0022414 ! reproductive process
is_a: GO:0051647 ! nucleus localization
relationship: part_of GO:0007310 ! oocyte dorsal/ventral axis specification
@@ -313757,12 +313724,16 @@ is_obsolete: true
[Term]
id: GO:0051673
-name: membrane disruption in another organism
+name: disruption of membrane integrity in another organism
namespace: biological_process
-def: "The disruption of the membranes of another organism, leading to damage to its cells and possibly death of that organism." [GOC:ai]
+alt_id: GO:0044662
+def: "The disruption of a membrane of another organism, leading to damage or temporary subversion of the membrane." [GOC:ai, PMID:32299851]
synonym: "cytolysis, by membrane disruption, in other organism" NARROW []
+synonym: "disruption by organism of host cell membrane" EXACT []
+synonym: "disruption by virus of host cell membrane" NARROW []
+synonym: "membrane disruption in another organism" RELATED []
synonym: "membrane disruption in other organism" EXACT []
-is_a: GO:0035821 ! modulation of process of another organism
+is_a: GO:0140975 ! disruption of cellular component of another organism
[Term]
id: GO:0051674
@@ -313792,7 +313763,7 @@ name: pullulan metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving pullulan, a neutral linear polysaccharide composed of repeating units of maltotriose joined by alpha-(1,6)-linkages." [PMID:15013381]
synonym: "pullulan metabolism" EXACT []
-is_a: GO:0006073 ! cellular glucan metabolic process
+is_a: GO:0044042 ! glucan metabolic process
[Term]
id: GO:0051677
@@ -313808,7 +313779,6 @@ name: pullulan catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of pullulan, a neutral linear polysaccharide composed of repeating units of maltotriose joined by alpha-(1,6)-linkages." [GOC:ai]
is_a: GO:0009251 ! glucan catabolic process
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
is_a: GO:0051676 ! pullulan metabolic process
[Term]
@@ -313820,7 +313790,6 @@ synonym: "6-alpha-maltosylglucose metabolism" EXACT []
synonym: "isopanose metabolic process" EXACT []
synonym: "isopanose metabolism" EXACT []
is_a: GO:0009311 ! oligosaccharide metabolic process
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
[Term]
id: GO:0051680
@@ -313830,7 +313799,6 @@ def: "The chemical reactions and pathways resulting in the formation of 6-alpha-
synonym: "isopanose biosynthesis" EXACT []
synonym: "isopanose biosynthetic process" EXACT []
is_a: GO:0009312 ! oligosaccharide biosynthetic process
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
is_a: GO:0051679 ! 6-alpha-maltosylglucose metabolic process
[Term]
@@ -313841,7 +313809,6 @@ def: "The chemical reactions and pathways resulting in the breakdown of 6-alpha-
synonym: "isopanose catabolic process" EXACT []
synonym: "isopanose catabolism" EXACT []
is_a: GO:0009313 ! oligosaccharide catabolic process
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
is_a: GO:0051679 ! 6-alpha-maltosylglucose metabolic process
[Term]
@@ -313916,24 +313883,25 @@ is_a: GO:0051657 ! maintenance of organelle location
[Term]
id: GO:0051691
-name: cellular oligosaccharide metabolic process
+name: obsolete cellular oligosaccharide metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages, as carried out by individual cells." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways involving oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages, as carried out by individual cells." [GOC:ai]
+comment: This term was obsoleted because it is not different from its parent, oligosaccharide metabolic process ; GO:0009311.
synonym: "cellular oligosaccharide metabolism" EXACT []
-is_a: GO:0009311 ! oligosaccharide metabolic process
-is_a: GO:0044262 ! cellular carbohydrate metabolic process
+is_obsolete: true
+replaced_by: GO:0009311
[Term]
id: GO:0051692
-name: cellular oligosaccharide catabolic process
+name: obsolete cellular oligosaccharide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages, as carried out by individual cells." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages, as carried out by individual cells." [GOC:ai]
+comment: This term was obsoleted because it is not different from its parent, oligosaccharide catabolic process ; GO:0009313.
synonym: "cellular oligosaccharide breakdown" EXACT []
synonym: "cellular oligosaccharide catabolism" EXACT []
synonym: "cellular oligosaccharide degradation" EXACT []
-is_a: GO:0009313 ! oligosaccharide catabolic process
-is_a: GO:0044275 ! cellular carbohydrate catabolic process
-is_a: GO:0051691 ! cellular oligosaccharide metabolic process
+is_obsolete: true
+replaced_by: GO:0009313
[Term]
id: GO:0051693
@@ -313983,7 +313951,7 @@ id: GO:0051697
name: protein delipidation
namespace: biological_process
def: "The breakage of covalent bonds to detach lipid groups from a protein." [GOC:ai]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0051698
@@ -314106,15 +314074,15 @@ relationship: regulates GO:0031640 ! killing of cells of another organism
[Term]
id: GO:0051710
-name: regulation of cytolysis in another organism
+name: obsolete regulation of cytolysis in another organism
namespace: biological_process
alt_id: GO:0001902
-def: "Any process that modulates the frequency, rate or extent of the cytolysis by an organism of cells in another organism." [GOC:ai]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the cytolysis by an organism of cells in another organism." [GOC:ai]
+comment: This term was obsoleted because it has been used inconsistently.
synonym: "regulation of cytolysis in other organism" EXACT []
synonym: "regulation of cytolysis of cells of another organism" EXACT [GOC:bf]
-is_a: GO:0042268 ! regulation of cytolysis
-is_a: GO:0051709 ! regulation of killing of cells of another organism
-relationship: regulates GO:0051715 ! cytolysis in another organism
+is_obsolete: true
+consider: GO:0031640
[Term]
id: GO:0051711
@@ -314156,27 +314124,26 @@ relationship: positively_regulates GO:0031640 ! killing of cells of another orga
[Term]
id: GO:0051713
-name: negative regulation of cytolysis in another organism
+name: obsolete negative regulation of cytolysis in another organism
namespace: biological_process
alt_id: GO:0001903
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the cytolysis of cells in another organism." [GOC:ai]
+def: "OBSOLETE. Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the cytolysis of cells in another organism." [GOC:ai]
+comment: This term was obsoleted because it has been used inconsistently.
synonym: "down regulation of cytolysis of cells of another organism" EXACT []
synonym: "down-regulation of cytolysis of cells of another organism" EXACT []
synonym: "downregulation of cytolysis of cells of another organism" EXACT []
synonym: "inhibition of cytolysis of cells of another organism" NARROW []
synonym: "negative regulation of cytolysis in other organism" EXACT []
synonym: "negative regulation of cytolysis of cells of another organism" EXACT [GOC:bf]
-is_a: GO:0045918 ! negative regulation of cytolysis
-is_a: GO:0051710 ! regulation of cytolysis in another organism
-is_a: GO:0051711 ! negative regulation of killing of cells of another organism
-relationship: negatively_regulates GO:0051715 ! cytolysis in another organism
+is_obsolete: true
[Term]
id: GO:0051714
-name: positive regulation of cytolysis in another organism
+name: obsolete positive regulation of cytolysis in another organism
namespace: biological_process
alt_id: GO:0001904
-def: "Any process that activates or increases the frequency, rate or extent of the cytolysis by an organism of cells in another organism." [GOC:ai]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the cytolysis by an organism of cells in another organism." [GOC:ai]
+comment: This term was obsoleted because it has been used inconsistently.
synonym: "activation of cytolysis of cells of another organism" NARROW []
synonym: "positive regulation of cytolysis in other organism" EXACT []
synonym: "positive regulation of cytolysis of cells of another organism" EXACT [GOC:bf]
@@ -314184,19 +314151,20 @@ synonym: "stimulation of cytolysis of cells of another organism" NARROW []
synonym: "up regulation of cytolysis of cells of another organism" EXACT []
synonym: "up-regulation of cytolysis of cells of another organism" EXACT []
synonym: "upregulation of cytolysis of cells of another organism" EXACT []
-is_a: GO:0045919 ! positive regulation of cytolysis
-is_a: GO:0051710 ! regulation of cytolysis in another organism
-is_a: GO:0051712 ! positive regulation of killing of cells of another organism
-relationship: positively_regulates GO:0051715 ! cytolysis in another organism
+is_obsolete: true
+consider: GO:0031640
[Term]
id: GO:0051715
name: cytolysis in another organism
namespace: biological_process
alt_id: GO:0001901
-def: "The killing by an organism of a cell in another organism by means of the rupture of cell membranes and the loss of cytoplasm." [GOC:ai]
+alt_id: GO:0044649
+def: "The killing by an organism of a cell in another organism by means of the rupture of cell membranes and the loss of cytoplasm." [GOC:ai, PMID:22484288]
synonym: "cytolysis in other organism" EXACT []
synonym: "cytolysis of cells of another organism" EXACT [GOC:bf]
+synonym: "envenomation resulting in cytolysis in another organism" NARROW []
+synonym: "envenomation resulting in cytolysis in other organism" NARROW []
is_a: GO:0019835 ! cytolysis
is_a: GO:0031640 ! killing of cells of another organism
@@ -314298,7 +314266,7 @@ synonym: "oxidized NAD transporter activity" EXACT []
synonym: "oxidized nicotinamide adenine dinucleotide transmembrane transporter activity" EXACT []
synonym: "reduced NAD transporter activity" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide transmembrane transporter activity" EXACT []
-is_a: GO:0015215 ! nucleotide transmembrane transporter activity
+is_a: GO:0000295 ! adenine nucleotide transmembrane transporter activity
[Term]
id: GO:0051725
@@ -314312,7 +314280,7 @@ synonym: "protein poly(ADP-ribose) catabolism" EXACT []
synonym: "protein poly(ADP-ribose) degradation" EXACT []
synonym: "protein poly(ADP-ribose) hydrolysis" EXACT []
synonym: "removal of ADP-ribose from protein" EXACT []
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0051726
@@ -314397,14 +314365,11 @@ is_a: GO:0051728 ! cell cycle switching, mitotic to meiotic cell cycle
id: GO:0051730
name: GTP-dependent polyribonucleotide 5'-hydroxyl-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GTP + 5'-dephospho-RNA = GDP + 5'-phospho-RNA." [EC:2.7.1.78, PMID:8428918]
-synonym: "GTP-dependent polynucleotide 5'-hydroxyl-kinase activity" BROAD []
+def: "Catalysis of the reaction: GTP + 5'-dephospho-RNA = GDP + 5'-phospho-RNA." [PMID:8428918]
synonym: "GTP-dependent polyribonucleotide kinase activity" EXACT []
synonym: "GTP-dependent RNA 5'-hydroxyl-kinase activity" EXACT []
synonym: "GTP-dependent RNA kinase activity" EXACT []
-synonym: "GTP:5'-dephosphopolyribonucleotide 5'-phosphotransferase activity" EXACT []
-is_a: GO:0051732 ! polyribonucleotide kinase activity
-is_a: GO:0051735 ! GTP-dependent polynucleotide kinase activity
+is_a: GO:0051735 ! GTP-dependent polynucleotide 5'-hydroxyl-kinase activity
[Term]
id: GO:0051731
@@ -314422,72 +314387,67 @@ is_a: GO:0019205 ! nucleobase-containing compound kinase activity
[Term]
id: GO:0051732
-name: polyribonucleotide kinase activity
+name: obsolete polyribonucleotide kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NTP + 5'-dephospho-RNA = NDP + 5'-phospho-RNA." [GOC:curators]
+def: "OBSOLETE. Catalysis of the reaction: NTP + 5'-dephospho-RNA = NDP + 5'-phospho-RNA." [GOC:curators]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "5'-hydroxyl polyribonucleotide kinase activity" EXACT []
synonym: "5'-hydroxyl RNA kinase activity" EXACT []
synonym: "RNA 5'-hydroxyl kinase activity" EXACT []
synonym: "RNA kinase activity" EXACT []
-is_a: GO:0051731 ! polynucleotide 5'-hydroxyl-kinase activity
+is_obsolete: true
+consider: GO:0051736
[Term]
id: GO:0051733
-name: polydeoxyribonucleotide kinase activity
+name: obsolete polydeoxyribonucleotide kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NTP + 5'-dephospho-DNA = NDP + 5'-phospho-DNA." [GOC:curators]
+def: "OBSOLETE. Catalysis of the reaction: NTP + 5'-dephospho-DNA = NDP + 5'-phospho-DNA." [GOC:curators]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "DNA 5'-hydroxyl kinase activity" EXACT []
synonym: "DNA kinase activity" EXACT []
-is_a: GO:0051731 ! polynucleotide 5'-hydroxyl-kinase activity
+is_obsolete: true
+consider: GO:0046404
+consider: GO:0051737
[Term]
id: GO:0051734
-name: polynucleotide kinase activity
+name: ATP-dependent polynucleotide 5'-hydroxyl-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + 5'-dephosphopolynucleotide = ADP + 5'-phosphopolynucleotide. The polynucleotide may be DNA or RNA." [RHEA:54580]
-synonym: "ATP-dependent polynucleotide 5'-hydroxyl-kinase activity" EXACT []
+def: "Catalysis of the reaction: ATP + 5'-dephosphopolynucleotide = ADP + 5'-phosphopolynucleotide. The polynucleotide may be DNA or RNA." [EC:2.7.1.78]
synonym: "ATP-dependent polynucleotide kinase activity" RELATED []
-synonym: "ATP:5'-dephosphopolynucleotide 5'-phosphatase activity" RELATED [EC:2.7.1.78]
-synonym: "ATP:5'-dephosphopolynucleotide 5'-phosphotransferase activity" EXACT []
+synonym: "polynucleotide kinase activity" BROAD []
xref: EC:2.7.1.78
-xref: RHEA:54580
is_a: GO:0051731 ! polynucleotide 5'-hydroxyl-kinase activity
[Term]
id: GO:0051735
-name: GTP-dependent polynucleotide kinase activity
+name: GTP-dependent polynucleotide 5'-hydroxyl-kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: GTP + 5'-dephosphopolynucleotide = GDP + 5'-phosphopolynucleotide. The polynucleotide may be DNA or RNA." [GOC:curators]
-synonym: "GTP-dependent polynucleotide 5'-hydroxyl-kinase activity" EXACT []
-synonym: "GTP:5'-dephosphopolynucleotide 5'-phosphotransferase activity" EXACT []
+synonym: "GTP-dependent polynucleotide kinase activity" BROAD []
is_a: GO:0051731 ! polynucleotide 5'-hydroxyl-kinase activity
[Term]
id: GO:0051736
-name: polyribonucleotide 5'-hydroxyl-kinase activity
+name: ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + 5'-dephospho-RNA = ADP + 5'-phospho-RNA." [EC:2.7.1.78]
-synonym: "ATP-dependent polynucleotide 5'-hydroxyl-kinase activity" BROAD []
-synonym: "ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity" RELATED []
+def: "Catalysis of the reaction: ATP + 5'-dephospho-RNA = ADP + 5'-phospho-RNA." [RHEA:54580]
synonym: "ATP-dependent polyribonucleotide kinase activity" EXACT []
-synonym: "ATP-dependent RNA 5'-hydroxyl-kinase activity" EXACT []
synonym: "ATP-dependent RNA kinase activity" EXACT []
-synonym: "ATP:5'-dephosphopolyribonucleotide 5'-phosphotransferase activity" EXACT []
-is_a: GO:0051732 ! polyribonucleotide kinase activity
-is_a: GO:0051734 ! polynucleotide kinase activity
+synonym: "polyribonucleotide 5'-hydroxyl-kinase activity" BROAD []
+xref: RHEA:54580
+is_a: GO:0051734 ! ATP-dependent polynucleotide 5'-hydroxyl-kinase activity
[Term]
id: GO:0051737
name: GTP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GTP + 5'-dephospho-DNA = GDP + 5'-phospho-DNA." [EC:2.7.1.78, PMID:8428918]
+def: "Catalysis of the reaction: GTP + 5'-dephospho-DNA = GDP + 5'-phospho-DNA." [PMID:8428918]
synonym: "GTP-dependent DNA 5'-hydroxyl-kinase activity" EXACT []
synonym: "GTP-dependent DNA kinase activity" EXACT []
synonym: "GTP-dependent polydeoxyribonucleotide kinase activity" EXACT []
-synonym: "GTP-dependent polynucleotide 5'-hydroxyl-kinase activity" BROAD []
-synonym: "GTP:5'-dephosphopolydeoxyribonucleotide 5'-phosphotransferase activity" EXACT []
-is_a: GO:0051733 ! polydeoxyribonucleotide kinase activity
-is_a: GO:0051735 ! GTP-dependent polynucleotide kinase activity
+is_a: GO:0051735 ! GTP-dependent polynucleotide 5'-hydroxyl-kinase activity
[Term]
id: GO:0051738
@@ -314600,12 +314560,15 @@ is_a: GO:0008168 ! methyltransferase activity
[Term]
id: GO:0051750
-name: delta3,5-delta2,4-dienoyl-CoA isomerase activity
+name: delta(3,5)-delta(2,4)-dienoyl-CoA isomerase activity
namespace: molecular_function
alt_id: GO:0008416
-def: "Catalysis of the isomerization of 3,5-dienoyl-CoA to 2,4-dienoyl-CoA." [PMID:11278886, PMID:16040662]
+def: "Catalysis of the reaction: a (3E,5Z)-dienoyl-CoA = a (2E,4E)-(5,6-saturated)-dienoyl-CoA." [PMID:11278886, PMID:16040662, RHEA:45240]
synonym: "delta(3,5),delta(2,4)-dienoyl-coenzyme A isomerase activity" EXACT []
+synonym: "delta3,5-delta2,4-dienoyl-CoA isomerase activity" EXACT []
synonym: "delta5-delta2,4-dienoyl-CoA isomerase activity" RELATED []
+xref: EC:5.3.3.21
+xref: RHEA:45240
is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds
[Term]
@@ -314753,6 +314716,7 @@ id: GO:0051766
name: inositol trisphosphate kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: inositol trisphosphate + ATP = inositol tetrakisphosphate + ADP." [GOC:ai]
+synonym: "IP3K" BROAD []
is_a: GO:0016301 ! kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
@@ -315037,7 +315001,7 @@ consider: GO:0070848
id: GO:0051790
name: short-chain fatty acid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of fatty acids with a chain length of less than C6." [Wikipedia:Fatty_acid_metabolism]
+def: "The chemical reactions and pathways resulting in the formation of a fatty acid with an aliphatic tail of less than 6 carbons." [Wikipedia:Fatty_acid_metabolism]
synonym: "short chain fatty acid biosynthesis" EXACT []
synonym: "short chain fatty acid biosynthetic process" EXACT []
synonym: "short-chain fatty acid anabolism" EXACT []
@@ -315051,7 +315015,7 @@ is_a: GO:0046459 ! short-chain fatty acid metabolic process
id: GO:0051791
name: medium-chain fatty acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving medium-chain fatty acids, any fatty acid with a chain length of between C6 and C12." [Wikipedia:Fatty_acid_metabolisms]
+def: "The chemical reactions and pathways involving a medium-chain fatty acid, a fatty acid with an aliphatic tail of 6 to 12 carbons." [Wikipedia:Fatty_acid_metabolisms]
synonym: "medium chain fatty acid metabolic process" EXACT []
synonym: "medium chain fatty acid metabolism" EXACT []
synonym: "medium-chain fatty acid metabolism" EXACT []
@@ -315061,7 +315025,7 @@ is_a: GO:0006631 ! fatty acid metabolic process
id: GO:0051792
name: medium-chain fatty acid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of any fatty acid with a chain length of between C6 and C12." [Wikipedia:Fatty_acid_metabolism]
+def: "The chemical reactions and pathways resulting in the formation of a fatty acid with an aliphatic tail of 6 to 12 carbons." [Wikipedia:Fatty_acid_metabolism]
synonym: "medium chain fatty acid biosynthesis" EXACT []
synonym: "medium chain fatty acid biosynthetic process" EXACT []
synonym: "medium-chain fatty acid anabolism" EXACT []
@@ -315075,7 +315039,7 @@ is_a: GO:0051791 ! medium-chain fatty acid metabolic process
id: GO:0051793
name: medium-chain fatty acid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of any fatty acid with a chain length of between C6 and C12." [Wikipedia:Fatty_acid_metabolism]
+def: "The chemical reactions and pathways resulting in the breakdown of a fatty acid with an aliphatic tail of 6 to 12 carbons." [Wikipedia:Fatty_acid_metabolism]
synonym: "medium chain fatty acid catabolic process" EXACT []
synonym: "medium chain fatty acid catabolism" EXACT []
synonym: "medium-chain fatty acid breakdown" EXACT []
@@ -315164,7 +315128,7 @@ relationship: negatively_regulates GO:0001942 ! hair follicle development
id: GO:0051800
name: phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phosphatidylinositol-3,4-bisphosphate + H2O = phosphatidylinositol-4-phosphate + phosphate." [GOC:bf, PMID:9811831]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate." [GOC:bf, PMID:9811831]
synonym: "PTEN activity" BROAD []
xref: Reactome:R-HSA-1676149 "PI(3,4)P2 is dephosphorylated to PI4P by PTEN at the plasma membrane"
xref: Reactome:R-HSA-1676204 "PI(3,4)P2 is dephosphorylated to PI4P by TPTE2 at the Golgi membrane"
@@ -315287,7 +315251,7 @@ synonym: "induction of tumor, nodule, or growth containing transformed cells in
synonym: "induction of tumor, nodule, or growth containing transformed cells in other organism involved in symbiotic interaction" RELATED []
synonym: "induction of tumor, nodule, or growth in other organism during symbiotic interaction" RELATED [GOC:tb]
synonym: "induction of tumor, nodule, or growth in other organism involved in symbiotic interaction" RELATED []
-is_a: GO:0044003 ! modulation by symbiont of host process
+is_a: GO:0044068 ! modulation by symbiont of host cellular process
[Term]
id: GO:0051821
@@ -315370,38 +315334,38 @@ is_a: GO:0051873 ! killing by host of symbiont cells
[Term]
id: GO:0051839
-name: regulation by host of cytolysis of symbiont cells
+name: obsolete regulation by host of cytolysis of symbiont cells
namespace: biological_process
-def: "Any process in which an organism modulates the frequency, rate or extent of the cytolysis by that organism of cells in its symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:add]
-is_a: GO:0002831 ! regulation of response to biotic stimulus
-is_a: GO:0031347 ! regulation of defense response
-is_a: GO:0032101 ! regulation of response to external stimulus
-is_a: GO:0043903 ! regulation of biological process involved in symbiotic interaction
-is_a: GO:0051709 ! regulation of killing of cells of another organism
-relationship: regulates GO:0051838 ! cytolysis by host of symbiont cells
+def: "OBSOLETE. Any process in which an organism modulates the frequency, rate or extent of the cytolysis by that organism of cells in its symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:add]
+comment: This term was obsoleted because it has been used inconsistently.
+is_obsolete: true
+consider: GO:0051873
[Term]
id: GO:0051840
-name: negative regulation by host of cytolysis of symbiont cells
+name: obsolete negative regulation by host of cytolysis of symbiont cells
namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of cytolysis by that organism of cells in its symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:add]
+def: "OBSOLETE. Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of cytolysis by that organism of cells in its symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:add]
+comment: This term was obsoleted because it has been used inconsistently.
synonym: "down regulation by host of cytolysis of symbiont cells" EXACT []
synonym: "down-regulation by host of cytolysis of symbiont cells" EXACT []
synonym: "downregulation by host of cytolysis of symbiont cells" EXACT []
synonym: "inhibition by host of cytolysis of symbiont cells" NARROW []
-is_a: GO:0051839 ! regulation by host of cytolysis of symbiont cells
+is_obsolete: true
[Term]
id: GO:0051841
-name: positive regulation by host of cytolysis of symbiont cells
+name: obsolete positive regulation by host of cytolysis of symbiont cells
namespace: biological_process
-def: "Any process in which an organism activates or increases the frequency, rate or extent of cytolysis by that organism of cells in its symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:add]
+def: "OBSOLETE. Any process in which an organism activates or increases the frequency, rate or extent of cytolysis by that organism of cells in its symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:add]
+comment: This term was obsoleted because it has been used inconsistently.
synonym: "activation by host of cytolysis of symbiont cells" NARROW []
synonym: "stimulation by host of cytolysis of symbiont cells" NARROW []
synonym: "up regulation by host of cytolysis of symbiont cells" EXACT []
synonym: "up-regulation by host of cytolysis of symbiont cells" EXACT []
synonym: "upregulation by host of cytolysis of symbiont cells" EXACT []
-is_a: GO:0051839 ! regulation by host of cytolysis of symbiont cells
+is_obsolete: true
+consider: GO:0051873
[Term]
id: GO:0051842
@@ -315580,14 +315544,15 @@ is_obsolete: true
[Term]
id: GO:0051864
-name: histone H3-methyl-lysine-36 demethylase activity
+name: histone H3K36 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a modified lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:16362057]
synonym: "[histone-H3]-lysine-36 demethylase activity" EXACT []
synonym: "histone demethylase activity (H3-K36 specific)" EXACT []
-synonym: "histone H3-lysine-36 demethylase activity" RELATED []
-synonym: "histone H3K36 demethylase activity" RELATED []
-synonym: "histone-lysine (H3-K36) demethylase activity" RELATED []
+synonym: "histone H3-K36 demethylase activity" EXACT []
+synonym: "histone H3-lysine-36 demethylase activity" EXACT []
+synonym: "histone H3-methyl-lysine-36 demethylase activity" EXACT []
+synonym: "histone-lysine (H3-K36) demethylase activity" EXACT []
synonym: "histone-lysine demethylase activity (H3-K36 specific)" EXACT []
synonym: "histone-lysine(H3-K36) demethylase activity" EXACT []
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
@@ -315639,7 +315604,7 @@ namespace: molecular_function
def: "Binding to methotrexate, an antineoplastic antimetabolite with immunosuppressant properties. It is an inhibitor of tetrahydrofolate reductase and prevents the formation of tetrahydrofolate, necessary for synthesis of thymidylate, an essential component of DNA." [GOC:nln]
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0033218 ! amide binding
-is_a: GO:0043177 ! organic acid binding
+is_a: GO:0072341 ! modified amino acid binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -316100,7 +316065,7 @@ namespace: molecular_function
def: "Catalysis of the sequential cleavage of mononucleotides from a free 5' terminus of a double-stranded DNA molecule." [GOC:ai]
synonym: "double-stranded DNA specific 5'-3' exodeoxyribonuclease activity" RELATED []
is_a: GO:0008309 ! double-stranded DNA exodeoxyribonuclease activity
-is_a: GO:0035312 ! 5'-3' exodeoxyribonuclease activity
+is_a: GO:0035312 ! 5'-3' DNA exonuclease activity
[Term]
id: GO:0051909
@@ -316228,27 +316193,21 @@ relationship: positively_regulates GO:0042730 ! fibrinolysis
id: GO:0051920
name: peroxiredoxin activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH." [EC:1.11.1.15, RHEA:10008]
+def: "Catalysis of the reaction: [protein]-dithol + ROOH = [protein]-disulfide + H2O + ROH." [RHEA:10008]
comment: Includes redox chemistry as part of the catalytic reaction (2 R'-SH = R'-S-S-R'), where R' refers to peroxiredoxin itself). Not to be confused with GO:0004601 (peroxidase activity, EC:1.11.1.7), which has a different reaction mechanism.
-synonym: "AhpC activity" NARROW []
-synonym: "alkyl hydroperoxide reductase C22 activity" NARROW []
synonym: "PRDX activity" EXACT []
synonym: "Prx activity" EXACT []
-synonym: "thiol-containing-reductant:hydroperoxide oxidoreductase activity" RELATED [EC:1.11.1.15]
-xref: EC:1.11.1.24
-xref: MetaCyc:1.11.1.15-RXN
xref: Reactome:R-HSA-1222431 "Peroxynitrite is reduced to nitrite by AhpC"
xref: Reactome:R-HSA-1222755 "Peroxynitrite is reduced to nitrite by Tpx"
xref: Reactome:R-HSA-1500804 "Peroxynitrite is reduced by AhpE"
xref: RHEA:10008
-is_a: GO:0016209 ! antioxidant activity
-is_a: GO:0016684 ! oxidoreductase activity, acting on peroxide as acceptor
+is_a: GO:0004601 ! peroxidase activity
[Term]
id: GO:0051921
name: adenosylcobyric acid synthase (glutamine-hydrolyzing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4 L-glutamine + adenosylcob(III)yrinate a,c-diamide + 4 ATP + 4 H(2)O = 4 L-glutamate + adenosylcobyrate + 4 ADP + 8 H(+) + 4 phosphate." [EC:6.3.5.10, RHEA:23256]
+def: "Catalysis of the reaction: 4 L-glutamine + adenosylcob(III)yrinate a,c-diamide + 4 ATP + 4 H2O = 4 L-glutamate + adenosylcobyrate + 4 ADP + 8 H+ + 4 phosphate." [EC:6.3.5.10, RHEA:23256]
synonym: "5'-deoxy-5'-adenosylcobyrinic-acid-a,c-diamide:L-glutamine amido-ligase activity" EXACT []
synonym: "adenosylcobyric acid synthase (glutamine-hydrolysing) activity" EXACT []
synonym: "adenosylcobyrinic-acid-a,c-diamide:L-glutamine amido-ligase (ADP-forming)" RELATED [EC:6.3.5.10]
@@ -316265,8 +316224,8 @@ is_a: GO:0016884 ! carbon-nitrogen ligase activity, with glutamine as amido-N-do
id: GO:0051922
name: cholesterol sulfotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + cholesterol = adenosine 3',5'-bisphosphate + cholesterol sulfate." [PMID:12730293]
-xref: EC:2.8.2.-
+def: "Catalysis of the reaction: 3'-phosphoadenylyl sulfate + cholesterol = adenosine 3',5'-bisphosphate + cholesterol sulfate + H+." [PMID:11416019, PMID:12145317, PMID:12730293, RHEA:52368]
+xref: RHEA:52368
is_a: GO:0004027 ! alcohol sulfotransferase activity
[Term]
@@ -316311,7 +316270,7 @@ synonym: "down-regulation of calcium ion transport" EXACT []
synonym: "downregulation of calcium ion transport" EXACT []
synonym: "inhibition of calcium ion transport" NARROW []
synonym: "negative regulation of calcium transport" EXACT []
-is_a: GO:0043271 ! negative regulation of ion transport
+is_a: GO:0043271 ! negative regulation of monoatomic ion transport
is_a: GO:0051924 ! regulation of calcium ion transport
relationship: negatively_regulates GO:0006816 ! calcium ion transport
@@ -316341,7 +316300,7 @@ synonym: "stimulation of calcium ion transport" NARROW []
synonym: "up regulation of calcium ion transport" EXACT []
synonym: "up-regulation of calcium ion transport" EXACT []
synonym: "upregulation of calcium ion transport" EXACT []
-is_a: GO:0043270 ! positive regulation of ion transport
+is_a: GO:0043270 ! positive regulation of monoatomic ion transport
is_a: GO:0051924 ! regulation of calcium ion transport
relationship: positively_regulates GO:0006816 ! calcium ion transport
@@ -316381,7 +316340,7 @@ relationship: regulates GO:0007600 ! sensory perception
id: GO:0051932
name: synaptic transmission, GABAergic
namespace: biological_process
-def: "The vesicular release of gamma-aminobutyric acid (GABA). from a presynapse, across a chemical synapse, the subsequent activation of GABA receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." [GOC:dos, ISBN:0126603030]
+def: "The vesicular release of gamma-aminobutyric acid (GABA). from a presynapse, across a chemical synapse, the subsequent activation of GABA receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." [GOC:dos, ISBN:0126603030]
synonym: "GABAergic synaptic transmission" EXACT []
synonym: "synaptic transmission, GABA mediated" EXACT []
synonym: "synaptic transmission, gamma-aminobutyric acid mediated" EXACT []
@@ -316397,7 +316356,7 @@ synonym: "amino acid neurotransmitter import into glial cell" NARROW []
synonym: "amino acid neurotransmitter import into neuron" NARROW []
synonym: "amino acid neurotransmitter recycling" BROAD []
synonym: "amino acid uptake during transmission of nerve impulse" RELATED [GOC:dph, GOC:tb]
-is_a: GO:0043090 ! amino acid import
+is_a: GO:0006865 ! amino acid transport
is_a: GO:0098810 ! neurotransmitter reuptake
[Term]
@@ -316463,7 +316422,7 @@ synonym: "L-glutamate uptake" EXACT [GOC:dph, GOC:tb]
is_a: GO:0006835 ! dicarboxylic acid transport
is_a: GO:0015800 ! acidic amino acid transport
is_a: GO:0015807 ! L-amino acid transport
-is_a: GO:0043090 ! amino acid import
+is_a: GO:0042886 ! amide transport
[Term]
id: GO:0051939
@@ -316476,7 +316435,6 @@ synonym: "gamma-aminobutyrate import" EXACT []
synonym: "gamma-aminobutyric acid uptake" EXACT [GOC:dph, GOC:tb]
is_a: GO:0015800 ! acidic amino acid transport
is_a: GO:0015812 ! gamma-aminobutyric acid transport
-is_a: GO:0043090 ! amino acid import
[Term]
id: GO:0051940
@@ -316597,7 +316555,6 @@ synonym: "regulation of GABA uptake during transmission of nerve impulse" EXACT
synonym: "regulation of gamma-aminobutyric acid reuptake" EXACT []
synonym: "regulation of gamma-aminobutyric acid uptake during transmission of nerve impulse" RELATED [GOC:dph, GOC:tb]
synonym: "regulation of gamma-aminobutyric acid uptake involved in conduction of nerve impulse" EXACT [GOC:dph]
-is_a: GO:0044070 ! regulation of anion transport
is_a: GO:0051941 ! regulation of amino acid uptake involved in synaptic transmission
relationship: regulates GO:0051936 ! gamma-aminobutyric acid reuptake
@@ -316636,7 +316593,6 @@ synonym: "negative regulation of gamma-aminobutyric acid uptake during transmiss
synonym: "negative regulation of gamma-aminobutyric acid uptake involved in conduction of nerve impulse" EXACT [GOC:dph]
is_a: GO:0051942 ! negative regulation of amino acid uptake involved in synaptic transmission
is_a: GO:0051947 ! regulation of gamma-aminobutyric acid uptake involved in transmission of nerve impulse
-is_a: GO:1903792 ! negative regulation of anion transport
relationship: negatively_regulates GO:0051936 ! gamma-aminobutyric acid reuptake
[Term]
@@ -316658,7 +316614,6 @@ synonym: "up-regulation of gamma-aminobutyric acid uptake during transmission of
synonym: "upregulation of gamma-aminobutyric acid uptake during transmission of nerve impulse" EXACT []
is_a: GO:0051943 ! positive regulation of amino acid uptake involved in synaptic transmission
is_a: GO:0051947 ! regulation of gamma-aminobutyric acid uptake involved in transmission of nerve impulse
-is_a: GO:1903793 ! positive regulation of anion transport
relationship: positively_regulates GO:0051936 ! gamma-aminobutyric acid reuptake
[Term]
@@ -316760,8 +316715,8 @@ name: methotrexate transport
namespace: biological_process
def: "The directed movement of methotrexate, 4-amino-10-methylformic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Methotrexate is a folic acid analogue and a potent competitive inhibitor of dihydrofolate reductase." [GOC:ai]
is_a: GO:0006835 ! dicarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0042886 ! amide transport
+is_a: GO:0072337 ! modified amino acid transport
[Term]
id: GO:0051959
@@ -316895,7 +316850,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation." [GOC:ai]
synonym: "regulation of conduction of nerve impulse" EXACT [GOC:dph]
is_a: GO:0010646 ! regulation of cell communication
-is_a: GO:0023051 ! regulation of signaling
is_a: GO:0031644 ! regulation of nervous system process
relationship: regulates GO:0019226 ! transmission of nerve impulse
@@ -316910,7 +316864,6 @@ synonym: "downregulation of transmission of nerve impulse" EXACT []
synonym: "inhibition of transmission of nerve impulse" NARROW []
synonym: "negative regulation of conduction of nerve impulse" EXACT [GOC:dph]
is_a: GO:0010648 ! negative regulation of cell communication
-is_a: GO:0023057 ! negative regulation of signaling
is_a: GO:0031645 ! negative regulation of nervous system process
is_a: GO:0051969 ! regulation of transmission of nerve impulse
relationship: negatively_regulates GO:0019226 ! transmission of nerve impulse
@@ -316927,7 +316880,6 @@ synonym: "up regulation of transmission of nerve impulse" EXACT []
synonym: "up-regulation of transmission of nerve impulse" EXACT []
synonym: "upregulation of transmission of nerve impulse" EXACT []
is_a: GO:0010647 ! positive regulation of cell communication
-is_a: GO:0023056 ! positive regulation of signaling
is_a: GO:0031646 ! positive regulation of nervous system process
is_a: GO:0051969 ! regulation of transmission of nerve impulse
relationship: positively_regulates GO:0019226 ! transmission of nerve impulse
@@ -317045,7 +316997,7 @@ id: GO:0051983
name: regulation of chromosome segregation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets." [GOC:ai]
-is_a: GO:0050794 ! regulation of cellular process
+is_a: GO:0010564 ! regulation of cell cycle process
relationship: regulates GO:0007059 ! chromosome segregation
[Term]
@@ -317058,8 +317010,8 @@ synonym: "stimulation of chromosome segregation" NARROW []
synonym: "up regulation of chromosome segregation" EXACT []
synonym: "up-regulation of chromosome segregation" EXACT []
synonym: "upregulation of chromosome segregation" EXACT []
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:0051983 ! regulation of chromosome segregation
+is_a: GO:0090068 ! positive regulation of cell cycle process
relationship: positively_regulates GO:0007059 ! chromosome segregation
[Term]
@@ -317071,7 +317023,7 @@ synonym: "down regulation of chromosome segregation" EXACT []
synonym: "down-regulation of chromosome segregation" EXACT []
synonym: "downregulation of chromosome segregation" EXACT []
synonym: "inhibition of chromosome segregation" NARROW []
-is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:0010948 ! negative regulation of cell cycle process
is_a: GO:0051983 ! regulation of chromosome segregation
relationship: negatively_regulates GO:0007059 ! chromosome segregation
@@ -317084,7 +317036,6 @@ synonym: "down regulation of attachment of spindle microtubules to kinetochore"
synonym: "down-regulation of attachment of spindle microtubules to kinetochore" EXACT []
synonym: "downregulation of attachment of spindle microtubules to kinetochore" EXACT []
synonym: "inhibition of attachment of spindle microtubules to kinetochore" NARROW []
-is_a: GO:0010948 ! negative regulation of cell cycle process
is_a: GO:0051985 ! negative regulation of chromosome segregation
is_a: GO:0051988 ! regulation of attachment of spindle microtubules to kinetochore
relationship: negatively_regulates GO:0008608 ! attachment of spindle microtubules to kinetochore
@@ -317101,7 +317052,6 @@ synonym: "up-regulation of attachment of spindle microtubules to kinetochore" EX
synonym: "upregulation of attachment of spindle microtubules to kinetochore" EXACT []
is_a: GO:0051984 ! positive regulation of chromosome segregation
is_a: GO:0051988 ! regulation of attachment of spindle microtubules to kinetochore
-is_a: GO:0090068 ! positive regulation of cell cycle process
relationship: positively_regulates GO:0008608 ! attachment of spindle microtubules to kinetochore
[Term]
@@ -317418,11 +317368,13 @@ is_obsolete: true
[Term]
id: GO:0052018
-name: modulation by symbiont of RNA levels in host
+name: obsolete modulation by symbiont of RNA levels in host
namespace: biological_process
-def: "The alteration by an organism of the levels of RNA in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The alteration by an organism of the levels of RNA in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a readout.
synonym: "modulation by symbiont of host RNA levels" EXACT []
-is_a: GO:0044003 ! modulation by symbiont of host process
+is_obsolete: true
+consider: GO:0052167
[Term]
id: GO:0052019
@@ -317654,7 +317606,7 @@ alt_id: GO:0044054
def: "The process in which an organism effects a change that impairs the structure or function of the host cytoskeleton. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "modification by symbiont of host cytoskeleton" RELATED []
synonym: "rounding by symbiont of host cells" NARROW []
-is_a: GO:0052043 ! modification by symbiont of host cellular component
+is_a: GO:0052008 ! disruption by symbiont of host cellular component
[Term]
id: GO:0052040
@@ -317669,7 +317621,7 @@ relationship: regulates GO:0012501 ! programmed cell death
[Term]
id: GO:0052041
-name: negative regulation by symbiont of host programmed cell death
+name: suppression by symbiont of host programmed cell death
namespace: biological_process
def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "down regulation by symbiont of host programmed cell death" EXACT []
@@ -317677,14 +317629,14 @@ synonym: "down-regulation by symbiont of host programmed cell death" EXACT []
synonym: "downregulation by symbiont of host programmed cell death" EXACT []
synonym: "inhibition by symbiont of host programmed cell death" NARROW []
synonym: "inhibition of host programmed cell death" EXACT []
+synonym: "negative regulation by symbiont of host programmed cell death" EXACT []
synonym: "suppression by symbiont of host PCD" EXACT []
-synonym: "suppression by symbiont of host programmed cell death" EXACT []
is_a: GO:0052040 ! modulation by symbiont of host programmed cell death
relationship: negatively_regulates GO:0012501 ! programmed cell death
[Term]
id: GO:0052042
-name: positive regulation by symbiont of host programmed cell death
+name: induction by symbiont of host programmed cell death
namespace: biological_process
alt_id: GO:0012504
alt_id: GO:0052044
@@ -317702,10 +317654,10 @@ synonym: "enhancement of host programmed cell death by organism" EXACT []
synonym: "induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction" NARROW []
synonym: "induction by organism of programmed cell death in other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "induction by organism of programmed cell death in other organism involved in symbiotic interaction" EXACT []
-synonym: "induction by symbiont of host programmed cell death" EXACT []
synonym: "induction of non-apoptotic programmed cell death by other organism" RELATED []
synonym: "pathogenesis" RELATED []
synonym: "positive regulation by symbiont of host non-apoptotic programmed cell death" NARROW []
+synonym: "positive regulation by symbiont of host programmed cell death" EXACT []
synonym: "stimulation by symbiont of host programmed cell death" NARROW []
synonym: "upregulation by symbiont of host programmed cell death" EXACT []
is_a: GO:0051712 ! positive regulation of killing of cells of another organism
@@ -318551,14 +318503,6 @@ def: "OBSOLETE. The directed movement of a motile cell or organism on or near it
comment: This term was obsoleted because it represents both a process and a location.
is_obsolete: true
-[Term]
-id: GO:0052126
-name: movement in host environment
-namespace: biological_process
-def: "The directed movement of an organism or motile cell on, within or near its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-synonym: "movement in response to host" EXACT []
-is_a: GO:0051701 ! biological process involved in interaction with host
-
[Term]
id: GO:0052127
name: obsolete movement on or near host
@@ -318791,7 +318735,7 @@ synonym: "up-regulation by symbiont of host apoptosis" EXACT []
synonym: "upregulation by organism of host apoptotic programmed cell death" EXACT []
synonym: "upregulation by symbiont of host apoptosis" EXACT []
is_a: GO:0043065 ! positive regulation of apoptotic process
-is_a: GO:0052042 ! positive regulation by symbiont of host programmed cell death
+is_a: GO:0052042 ! induction by symbiont of host programmed cell death
is_a: GO:0052150 ! modulation by symbiont of host apoptotic process
[Term]
@@ -319137,10 +319081,17 @@ is_obsolete: true
[Term]
id: GO:0052183
-name: modification by host of symbiont structure
+name: disruption by host of symbiont structure
namespace: biological_process
-def: "The process in which an organism effects a change in an anatomical part or cellular component of the host organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0051851 ! modulation by host of symbiont process
+alt_id: GO:0052187
+alt_id: GO:0052367
+def: "The process in which a host organism destabilizes an anatomical part or a cellular component of the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+synonym: "degradation of symbiont cellular component by organism" RELATED []
+synonym: "disassembly by host of symbiont cellular component" RELATED []
+synonym: "disruption by host of symbiont cellular component" RELATED []
+synonym: "modification by host of symbiont cellular component" RELATED []
+synonym: "modification by host of symbiont structure" RELATED []
+is_a: GO:0051702 ! biological process involved in interaction with symbiont
[Term]
id: GO:0052184
@@ -319160,13 +319111,6 @@ comment: This term was obsoleted because it represents an unnecessary grouping c
synonym: "modification of structure of other organism during symbiotic interaction" RELATED [GOC:dph]
is_obsolete: true
-[Term]
-id: GO:0052187
-name: modification by host of symbiont cellular component
-namespace: biological_process
-def: "The process in which an organism effects a change in the structure or function of a symbiont cellular component. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052183 ! modification by host of symbiont structure
-
[Term]
id: GO:0052188
name: obsolete modification of cellular component in other organism involved in symbiotic interaction
@@ -320041,26 +319985,30 @@ is_obsolete: true
[Term]
id: GO:0052335
-name: modification by host of symbiont cytoskeleton
+name: obsolete modification by host of symbiont cytoskeleton
namespace: biological_process
-def: "The process in which an organism effects a change in the structure or function of the symbiont cytoskeleton. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052187 ! modification by host of symbiont cellular component
+def: "OBSOLETE. The process in which an organism effects a change in the structure or function of the symbiont cytoskeleton. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it was too vague.
+is_obsolete: true
[Term]
id: GO:0052336
-name: modification by host of symbiont cell wall
+name: obsolete modification by host of symbiont cell wall
namespace: biological_process
-def: "The process in which an organism effects a change in the structure or function of the symbiont cell wall. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The process in which an organism effects a change in the structure or function of the symbiont cell wall. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted bacause it was too vague.
synonym: "metabolism of symbiont cell wall by organism" EXACT []
-is_a: GO:0052187 ! modification by host of symbiont cellular component
+is_obsolete: true
+consider: GO:0052338
[Term]
id: GO:0052337
-name: modification by host of symbiont membrane
+name: disruption by host of symbiont membrane
namespace: biological_process
-def: "The process in which an organism effects a change in the structure or function of a symbiont cellular membrane. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "The process in which a host organism destabilizes a symbiont membrane. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "modification by host of symbiont cell membrane" NARROW [GOC:bf, GOC:jl]
-is_a: GO:0052187 ! modification by host of symbiont cellular component
+synonym: "modification by host of symbiont membrane" RELATED []
+is_a: GO:0052183 ! disruption by host of symbiont structure
[Term]
id: GO:0052338
@@ -320070,7 +320018,7 @@ def: "The chemical reactions and pathways performed by an organism resulting in
synonym: "catabolism of symbiont cell wall by organism" EXACT []
synonym: "degradation of symbiont cell wall by organism" EXACT []
synonym: "disassembly by host of symbiont cell wall" EXACT []
-is_a: GO:0052336 ! modification by host of symbiont cell wall
+is_a: GO:0052183 ! disruption by host of symbiont structure
[Term]
id: GO:0052339
@@ -320308,17 +320256,6 @@ comment: This term was obsoleted because it represents an unnecessary grouping c
synonym: "catabolism by organism of xylan in other organism during symbiotic interaction" RELATED [GOC:dph]
is_obsolete: true
-[Term]
-id: GO:0052367
-name: disruption by host of symbiont cellular component
-namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of cellular components of the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
-synonym: "catabolism of symbiont cellular component by organism" EXACT []
-synonym: "catabolism of symbiont structural constituent by organism" EXACT []
-synonym: "degradation of symbiont cellular component by organism" EXACT []
-synonym: "disassembly by host of symbiont cellular component" RELATED []
-is_a: GO:0052187 ! modification by host of symbiont cellular component
-
[Term]
id: GO:0052368
name: obsolete disruption by organism of cellular component in other organism involved in symbiotic interaction
@@ -320859,10 +320796,11 @@ is_obsolete: true
[Term]
id: GO:0052430
-name: modulation by host of symbiont RNA levels
+name: obsolete modulation by host of symbiont RNA levels
namespace: biological_process
-def: "The alteration by an organism of the levels of RNA in a symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0051851 ! modulation by host of symbiont process
+def: "OBSOLETE. The alteration by an organism of the levels of RNA in a symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a readout.
+is_obsolete: true
[Term]
id: GO:0052431
@@ -321389,10 +321327,11 @@ is_obsolete: true
[Term]
id: GO:0052494
-name: occlusion by host of symbiont vascular system
+name: obsolete occlusion by host of symbiont vascular system
namespace: biological_process
-def: "The process in which an organism reduces the flow of fluid within its symbiont's vascular system, the vessels and tissue that carry or circulate fluids, such as blood, lymph or sap, through the body of an animal or plant. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, http://www.thefreedictionary.com]
-is_a: GO:0052183 ! modification by host of symbiont structure
+def: "OBSOLETE. The process in which an organism reduces the flow of fluid within its symbiont's vascular system, the vessels and tissue that carry or circulate fluids, such as blood, lymph or sap, through the body of an animal or plant. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, http://www.thefreedictionary.com]
+comment: This term was obsoleted because this process is not known to exist.
+is_obsolete: true
[Term]
id: GO:0052495
@@ -321405,10 +321344,11 @@ is_obsolete: true
[Term]
id: GO:0052496
-name: occlusion by host of symbiont xylem
+name: obsolete occlusion by host of symbiont xylem
namespace: biological_process
-def: "The process in which an organism reduces the flow of fluid within the symbiont xylem, the tissue in plants that carries water and nutrients up from the roots to the shoot and leaves. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052494 ! occlusion by host of symbiont vascular system
+def: "OBSOLETE. The process in which an organism reduces the flow of fluid within the symbiont xylem, the tissue in plants that carries water and nutrients up from the roots to the shoot and leaves. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because this process is not known to exist.
+is_obsolete: true
[Term]
id: GO:0052497
@@ -321780,6 +321720,7 @@ def: "Any process in which callose is transported to, and/or maintained in, a sp
synonym: "callose deposition during defense response" RELATED [GOC:dph]
synonym: "callose localization during defense response" RELATED []
is_a: GO:0006952 ! defense response
+is_a: GO:0009743 ! response to carbohydrate
is_a: GO:0052545 ! callose localization
[Term]
@@ -322058,7 +321999,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0052581
name: (-)-isopiperitenone reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (6R)-isoperitenone + H(+) + NADPH = (2R,5R)-isopulegone + NADP(+)." [EC:1.3.1.82, RHEA:25649]
+def: "Catalysis of the reaction: (6R)-isoperitenone + H+ + NADPH = (2R,5R)-isopulegone + NADP+." [EC:1.3.1.82, RHEA:25649]
synonym: "(+)-cis-isopulegone:NADP+ oxidoreductase activity" RELATED [EC:1.3.1.82]
xref: EC:1.3.1.82
xref: KEGG_REACTION:R06417
@@ -322070,7 +322011,7 @@ is_a: GO:0035671 ! enone reductase activity
id: GO:0052582
name: (+)-menthofuran synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-pulegone + H(+) + NADPH + O(2) = (R)-menthofuran + 2 H(2)O + NADP(+)." [EC:1.14.14.143, RHEA:25658]
+def: "Catalysis of the reaction: (R)-pulegone + H+ + NADPH + O2 = (R)-menthofuran + 2 H2O + NADP+." [EC:1.14.14.143, RHEA:25658]
synonym: "(+)-MFS activity" BROAD [EC:1.14.13.104]
synonym: "(+)-pulegone 9-hydroxylase activity" RELATED [EC:1.14.14.143]
synonym: "(+)-pulegone,NADPH:oxygen oxidoreductase (9-hydroxylating) activity" RELATED [EC:1.14.14.143]
@@ -322120,7 +322061,7 @@ is_a: GO:0016661 ! oxidoreductase activity, acting on other nitrogenous compound
id: GO:0052587
name: diacetyl reductase ((R)-acetoin forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-acetoin + NAD(+) = diacetyl + H(+) + NADH." [EC:1.1.1.303, RHEA:22900]
+def: "Catalysis of the reaction: (R)-acetoin + NAD+ = diacetyl + H+ + NADH." [EC:1.1.1.303, RHEA:22900]
synonym: "(R)-acetoin dehydrogenase activity" RELATED [EC:1.1.1.303]
xref: EC:1.1.1.303
xref: KEGG_REACTION:R02855
@@ -322132,7 +322073,7 @@ is_a: GO:0019152 ! acetoin dehydrogenase activity
id: GO:0052588
name: diacetyl reductase ((S)-acetoin forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-acetoin + NAD(+) = diacetyl + H(+) + NADH." [EC:1.1.1.304, RHEA:27286]
+def: "Catalysis of the reaction: (S)-acetoin + NAD+ = diacetyl + H+ + NADH." [EC:1.1.1.304, RHEA:27286]
synonym: "(S)-acetoin dehydrogenase activity" RELATED [EC:1.1.1.304]
xref: EC:1.1.1.304
xref: KEGG_REACTION:R09078
@@ -322186,28 +322127,31 @@ is_a: GO:0016725 ! oxidoreductase activity, acting on CH or CH2 groups
id: GO:0052593
name: tryptamine:oxygen oxidoreductase (deaminating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: tryptamine + H2O + O2 = NH3 + indole acetaldehyde + hydrogen peroxide + H+." [MetaCyc:RXN-1401]
+def: "Catalysis of the reaction: tryptamine + H2O + O2 = NH3 + indole acetaldehyde + hydrogen peroxide + H+." [RHEA:59419]
xref: EC:1.4.3.21
xref: KEGG_REACTION:R02173
xref: MetaCyc:RXN-1401
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+xref: RHEA:59419
+is_a: GO:0052595 ! aliphatic amine oxidase activity
[Term]
id: GO:0052594
name: aminoacetone:oxygen oxidoreductase(deaminating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: aminoacetone + H2O + O2 = methylglyoxal + NH3 + hydrogen peroxide + H+." [MetaCyc:AMACETOXID-RXN]
+def: "Catalysis of the reaction: aminoacetone + H2O + O2 = methylglyoxal + NH3 + hydrogen peroxide + H+." [RHEA:28186]
xref: EC:1.4.3.21
xref: KEGG_REACTION:R02529
xref: MetaCyc:AMACETOXID-RXN
xref: RHEA:28186
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+is_a: GO:0008131 ! primary amine oxidase activity
+is_a: GO:0052595 ! aliphatic amine oxidase activity
[Term]
id: GO:0052595
-name: aliphatic-amine oxidase activity
+name: aliphatic amine oxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: an aliphatic amine + H2O + O2 = an aldehyde + NH3 + hydrogen peroxide + H+." [MetaCyc:AMINEOXID-RXN]
+synonym: "aliphatic-amine oxidase activity" EXACT []
synonym: "aliphatic-amine:oxygen oxidoreductase(deaminating) activity" EXACT []
xref: EC:1.4.3.21
xref: MetaCyc:AMINEOXID-RXN
@@ -322218,12 +322162,12 @@ is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0052596
name: phenethylamine:oxygen oxidoreductase (deaminating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: phenylethylamine + O2 + H2O = phenylacetaldehyde + NH3 + hydrogen peroxide + H+." [MetaCyc:AMINEPHEN-RXN]
+def: "Catalysis of the reaction: phenylethylamine + O2 + H2O = phenylacetaldehyde + NH3 + hydrogen peroxide + H+." [RHEA:25265]
xref: EC:1.4.3.21
xref: KEGG_REACTION:R02613
xref: MetaCyc:AMINEPHEN-RXN
xref: RHEA:25265
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+is_a: GO:0008131 ! primary amine oxidase activity
[Term]
id: GO:0052597
@@ -322248,18 +322192,18 @@ xref: KEGG_REACTION:R02150
xref: MetaCyc:RXN-9600
xref: Reactome:R-HSA-5696131 "AOC1 deaminates Hist"
xref: RHEA:25625
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+is_a: GO:0052597 ! diamine oxidase activity
[Term]
id: GO:0052599
name: methylputrescine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-methylputrescine + H2O + O2 = N-methylaminobutanal + NH3 + hydrogen peroxide + H+." [MetaCyc:RXN-8244]
+def: "Catalysis of the reaction: N-methylputrescine + H2O + O2 = N-methylaminobutanal + NH3 + hydrogen peroxide + H+." [MetaCyc:RXN-8244, PMID:17283012, PMID:24287136]
synonym: "N-methylputrescine:oxygen oxidoreductase (deaminating) activity" EXACT systematic_synonym [EC:1.4.3.22]
xref: EC:1.4.3.22
xref: KEGG_REACTION:R05334
xref: MetaCyc:RXN-8244
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+is_a: GO:0052597 ! diamine oxidase activity
[Term]
id: GO:0052600
@@ -322267,13 +322211,12 @@ name: propane-1,3-diamine oxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: propane-1,3-diamine + H2O + O2 = 3-aminopropanal + NH3 + hydrogen peroxide + H+." [MetaCyc:RXN-6381]
synonym: "1,3-diaminopropane oxidase activity" EXACT [KEGG:C00986]
-synonym: "propane-1,3-diamine:oxygen oxidoreductase (deaminating) activity" EXACT systematic_synonym [EC:1.4.3.22]
synonym: "trimethylenediamine oxidase activity" EXACT [CHEBI:15725]
xref: EC:1.4.3.22
xref: KEGG_REACTION:R03139
xref: MetaCyc:RXN-6381
xref: RHEA:30895
-is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
+is_a: GO:0052597 ! diamine oxidase activity
[Term]
id: GO:0052601
@@ -322500,7 +322443,7 @@ id: GO:0052621
name: diguanylate cyclase activity
namespace: molecular_function
alt_id: GO:0043789
-def: "Catalysis of the reaction: 2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate + 2 H(+)." [EC:2.7.7.65, RHEA:24898]
+def: "Catalysis of the reaction: 2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate + 2 H+." [EC:2.7.7.65, RHEA:24898]
synonym: "GTP:GTP guanylyltransferase activity" BROAD [EC:2.7.7.65]
xref: EC:2.7.7.65
xref: KEGG_REACTION:R08057
@@ -322595,7 +322538,7 @@ is_a: GO:0016881 ! acid-amino acid ligase activity
id: GO:0052629
name: phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + H2O = a 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate + 2 H+." [PMID:19901554, RHEA:39019]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate + 2 H+." [PMID:19901554, RHEA:39019]
xref: EC:3.1.3.95
xref: MetaCyc:RXN-10958
xref: Reactome:R-HSA-1676065 "PI(3,5)P2 is dephosphorylated to PI5P by MTM proteins at the late endosome membrane"
@@ -322778,7 +322721,7 @@ name: chlorophyllide a metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving chlorophyllide a, a chlorophyll lacking the terpenoid side chain, which is the functional parent of chlorophyll a." [PMID:7724548]
synonym: "chlorophyllide a metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
+is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:0052643 ! chlorophyllide metabolic process
[Term]
@@ -322882,8 +322825,8 @@ name: cyclic purine nucleotide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue and the base is a purine." [PMID:23911318]
synonym: "cyclic purine nucleotide metabolism" EXACT []
-is_a: GO:0006164 ! purine nucleotide biosynthetic process
-is_a: GO:0009190 ! cyclic nucleotide biosynthetic process
+is_a: GO:0006163 ! purine nucleotide metabolic process
+is_a: GO:0009187 ! cyclic nucleotide metabolic process
[Term]
id: GO:0052653
@@ -322896,6 +322839,7 @@ synonym: "cdiGMP metabolism" EXACT []
synonym: "cyclic diguanylate metabolic process" EXACT []
synonym: "cyclic diguanylate metabolism" EXACT []
is_a: GO:0009152 ! purine ribonucleotide biosynthetic process
+is_a: GO:0009190 ! cyclic nucleotide biosynthetic process
is_a: GO:0052652 ! cyclic purine nucleotide metabolic process
[Term]
@@ -323040,7 +322984,7 @@ name: zeaxanthin epoxidase activity
namespace: molecular_function
alt_id: GO:0009540
alt_id: GO:0052663
-def: "Catalysis of the reaction: all-trans-zeaxanthin + 4 H+ + 2 O2 + 4 reduced [2Fe-2S]-[ferredoxin] = all-trans-violaxanthin + 2 H2O + 4 oxidized [2Fe-2S]-[ferredoxin]." [RHEA:32443]
+def: "Catalysis of the reaction: all-trans-zeaxanthin + 4 H+ + 2 O2 + 4 reduced [2Fe-2S]-[ferredoxin] = all-trans-violaxanthin + 2 H2O + 4 oxidized [2Fe-2S]-[ferredoxin]." [RHEA:32443]
comment: Multi-step reaction: RHEA:14937 and RHEA:24084. Formerly EC:1.14.13.90.
synonym: "antheraxanthin epoxidase activity" NARROW []
synonym: "zea-epoxidase activity" RELATED [EC:1.14.15.21]
@@ -323107,7 +323051,7 @@ is_a: GO:0016427 ! tRNA (cytosine) methyltransferase activity
id: GO:0052667
name: phosphomethylethanolamine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+)." [RHEA:25321]
+def: "Catalysis of the reaction: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H+." [RHEA:25321]
synonym: "N-methylethanolamine phosphate N-methyltransferase activity" EXACT []
synonym: "S-adenosyl-L-methionine:methylethanolamine phosphate N-methyltransferase activity" EXACT systematic_synonym [KEGG_REACTION:R06868]
xref: EC:2.1.1.103
@@ -323358,32 +323302,16 @@ alt_id: GO:0004091
alt_id: GO:0004302
alt_id: GO:0004759
alt_id: GO:0016789
-def: "Catalysis of the hydrolysis of a carboxylic ester bond." [EC:3.1.1.-, EC:3.1.1.1, GOC:curators]
+def: "Catalysis of the hydrolysis of a carboxylic ester bond." [GOC:curators]
subset: goslim_drosophila
-synonym: "ali-esterase activity" NARROW [EC:3.1.1.1]
-synonym: "alpha-carboxylesterase activity" NARROW [EC:3.1.1.1]
-synonym: "B-esterase activity" RELATED [EC:3.1.1.1]
-synonym: "carboxyesterase activity" RELATED [EC:3.1.1.1]
-synonym: "carboxyl ester hydrolase activity" RELATED [EC:3.1.1.1]
-synonym: "carboxylate esterase activity" RELATED [EC:3.1.1.1]
-synonym: "carboxylesterase activity" EXACT []
-synonym: "carboxylic acid esterase activity" EXACT []
-synonym: "carboxylic esterase activity" RELATED [EC:3.1.1.1]
-synonym: "cocaine esterase activity" NARROW [EC:3.1.1.1]
-synonym: "esterase A" NARROW [EC:3.1.1.1]
-synonym: "esterase B" NARROW [EC:3.1.1.1]
-synonym: "nonspecific carboxylesterase activity" RELATED [EC:3.1.1.1]
-synonym: "procaine esterase activity" NARROW [EC:3.1.1.1]
-synonym: "serine esterase activity" NARROW []
-synonym: "triacetin esterase" NARROW [EC:3.1.1.1]
-synonym: "vitamin A esterase" NARROW [EC:3.1.1.1]
-xref: EC:3.1.1.1
+synonym: "carboxylate esterase activity" RELATED []
+synonym: "carboxylic esterase activity" RELATED []
+synonym: "hydrolase activity acting on ester bonds" RELATED [EC:3.1.1.-]
+xref: EC:3.1.1.-
xref: KEGG_REACTION:R00630
-xref: MetaCyc:CARBOXYLESTERASE-RXN
xref: Reactome:R-HSA-5693691 "CES1 trimer.CES2 hydrolyse COCN to BEG"
xref: Reactome:R-HSA-8937442 "CES3 hydrolyses CHEST to CHOL and LCFA(-)"
-xref: Reactome:R-HSA-9619024 "CES1trimer hydrolyses ACEI pro-drugs to ACEIs"
-xref: RHEA:21164
+xref: Reactome:R-HSA-9749792 "CES1,CES2 hydrolyze ASA- to ST"
xref: UM-BBD_reactionID:r1025
is_a: GO:0016788 ! hydrolase activity, acting on ester bonds
@@ -323677,6 +323605,7 @@ synonym: "N-alpha,N-alpha,N-alpha-trimethyl-L-histidine breakdown" EXACT []
synonym: "N-alpha,N-alpha,N-alpha-trimethyl-L-histidine catabolism" EXACT []
synonym: "N-alpha,N-alpha,N-alpha-trimethyl-L-histidine degradation" EXACT []
is_a: GO:0006579 ! amino-acid betaine catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0052708 ! N-alpha,N-alpha,N-alpha-trimethyl-L-histidine metabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
@@ -323740,8 +323669,10 @@ is_a: GO:0016682 ! oxidoreductase activity, acting on diphenols and related subs
id: GO:0052717
name: tRNA-specific adenosine-34 deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: adenosine-34 + H2O = inosine-34 + NH3, in a tRNA-Ala molecule." [PMID:17875641]
+def: "Catalysis of the reaction: adenosine-34 + H2O = inosine-34 + NH3, in a tRNA-Ala molecule." [PMID:17875641, RHEA:43168]
synonym: "tRNA(Ala)-A34 deaminase activity" EXACT []
+xref: EC:3.5.4.33
+xref: RHEA:43168
is_a: GO:0008251 ! tRNA-specific adenosine deaminase activity
[Term]
@@ -323762,7 +323693,7 @@ synonym: "abasic endoribonuclease activity" EXACT []
synonym: "AP endoribonuclease activity" EXACT []
synonym: "apurinic endoribonuclease activity" NARROW []
synonym: "apyrimidinic endoribonuclease activity" NARROW []
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0052720
@@ -323819,7 +323750,7 @@ is_a: GO:0000828 ! inositol hexakisphosphate kinase activity
id: GO:0052725
name: inositol-1,3,4-trisphosphate 6-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4-trisphosphate + ATP = 1D-myo-inositol 1,3,4,6-tetrakisphosphate + ADP + 2 H(+)." [EC:2.7.1.134]
+def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4-trisphosphate + ATP = 1D-myo-inositol 1,3,4,6-tetrakisphosphate + ADP + 2 H+." [EC:2.7.1.134]
synonym: "1D-myo-inositol-trisphosphate 6-kinase activity" BROAD []
synonym: "ATP:1D-myo-inositol-1,3,4-trisphosphate 6-phosphotransferase activity" RELATED [EC:2.7.1.127]
synonym: "inositol 1,3,4-trisphosphate 6-kinase activity" EXACT []
@@ -323838,7 +323769,7 @@ is_a: GO:0051766 ! inositol trisphosphate kinase activity
id: GO:0052726
name: inositol-1,3,4-trisphosphate 5-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4-trisphosphate + ATP = 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ADP + 2 H(+)." [EC:2.7.1.134]
+def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4-trisphosphate + ATP = 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ADP + 2 H+." [EC:2.7.1.134]
synonym: "1D-myo-inositol-trisphosphate 5-kinase activity" BROAD []
synonym: "ATP:1D-myo-inositol-1,3,4-trisphosphate 5-phosphotransferase activity" RELATED [EC:2.7.1.127]
synonym: "inositol 1,3,4-trisphosphate 5-kinase activity" EXACT []
@@ -324061,7 +323992,7 @@ id: GO:0052742
name: phosphatidylinositol kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + a phosphatidylinositol = ADP + a phosphatidylinositol phosphate." [GOC:ai]
-is_a: GO:0016301 ! kinase activity
+is_a: GO:0001727 ! lipid kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
[Term]
@@ -324075,7 +324006,7 @@ is_a: GO:0052745 ! inositol phosphate phosphatase activity
id: GO:0052744
name: phosphatidylinositol monophosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phosphatidylinositol monophosphate + H2O = phosphatidylinositol + phosphate." [GOC:ai]
+def: "Catalysis of the reaction: phosphatidyl-1D-myo-inositol monophosphate + H2O = phosphatidylinositol + phosphate." [GOC:ai]
is_a: GO:0052866 ! phosphatidylinositol phosphate phosphatase activity
[Term]
@@ -324087,14 +324018,14 @@ is_a: GO:0016791 ! phosphatase activity
[Term]
id: GO:0052746
-name: inositol phosphorylation
+name: obsolete inositol phosphorylation
namespace: biological_process
-def: "The process of introducing one or more phosphate groups into inositol. Inositol is the cyclic alcohol 1,2,3,4,5,6-cyclohexanehexol, which is widely distributed in nature and acts as a growth factor in animals and microorganisms." [ISBN:0198506732]
+def: "OBSOLETE. The process of introducing one or more phosphate groups into inositol. Inositol is the cyclic alcohol 1,2,3,4,5,6-cyclohexanehexol, which is widely distributed in nature and acts as a growth factor in animals and microorganisms." [ISBN:0198506732]
+comment: The reason for obsoletion is this is a single-step process.
synonym: "inositol and derivative phosphorylation" RELATED []
synonym: "myo-inositol and derivative phosphorylation" RELATED []
synonym: "myo-inositol phosphorylation" NARROW []
-is_a: GO:0006020 ! inositol metabolic process
-is_a: GO:0046835 ! carbohydrate phosphorylation
+is_obsolete: true
[Term]
id: GO:0052747
@@ -324310,7 +324241,6 @@ synonym: "1,6-alpha-mannosidase activity" BROAD []
synonym: "1,6-alpha-mannosyl-oligosaccharide alpha-D-mannohydrolase activity" EXACT []
synonym: "alpha-1,6-mannosidase activity" BROAD []
synonym: "alpha-1,6-mannosyl-oligosaccharide alpha-D-mannohydrolase activity" EXACT []
-xref: EC:3.1.1.-
is_a: GO:0015924 ! mannosyl-oligosaccharide mannosidase activity
[Term]
@@ -324322,7 +324252,6 @@ synonym: "1,3-alpha-mannosidase activity" BROAD []
synonym: "1,3-alpha-mannosyl-oligosaccharide alpha-D-mannohydrolase activity" EXACT []
synonym: "alpha-1,3-mannosidase activity" BROAD []
synonym: "alpha-1,3-mannosyl-oligosaccharide alpha-D-mannohydrolase activity" EXACT []
-xref: EC:3.1.1.-
is_a: GO:0015924 ! mannosyl-oligosaccharide mannosidase activity
[Term]
@@ -324704,7 +324633,7 @@ is_a: GO:0016837 ! carbon-oxygen lyase activity, acting on polysaccharides
id: GO:0052810
name: 1-phosphatidylinositol-5-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = a 1-phosphatidyl-1D-myo-inositol 5-phosphate + ADP + 2 H(+)." [PMID:12270933, PMID:9660759, RHEA:44680]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = a 1-phosphatidyl-1D-myo-inositol 5-phosphate + ADP + 2 H+." [PMID:12270933, PMID:9660759, RHEA:44680]
synonym: "1-phosphatidylinositol 5-kinase activity" EXACT []
synonym: "ATP:1-phosphatidyl-1D-myo-inositol 5-phosphotransferase activity" EXACT []
xref: Reactome:R-HSA-1675810 "PI is phosphorylated to PI5P by PIP5K1A/B at the plasma membrane"
@@ -324716,7 +324645,7 @@ is_a: GO:0052742 ! phosphatidylinositol kinase activity
id: GO:0052811
name: 1-phosphatidylinositol-3-phosphate 4-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + ADP + 2 H(+)." [PMID:9211928, PMID:9367159, PMID:9660759, RHEA:63688]
+def: "Catalysis of the reaction: a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + ADP + 2 H+." [PMID:9211928, PMID:9367159, PMID:9660759, RHEA:63688]
synonym: "ATP:1-phosphatidyl-1D-myo-inositol-3-phosphate 4-phosphotransferase activity" EXACT []
synonym: "phosphatidylinositol 3-phosphate 4-kinase activity" EXACT []
xref: Reactome:R-HSA-1676145 "PI3P is phosphorylated to PI(3,4)P2 by PIP4K2/5K1 at the plasma membrane"
@@ -324727,7 +324656,7 @@ is_a: GO:0016307 ! phosphatidylinositol phosphate kinase activity
id: GO:0052812
name: phosphatidylinositol-3,4-bisphosphate 5-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+)." [EC:2.7.1.153]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H+." [EC:2.7.1.153]
synonym: "ATP:1-phosphatidyl-1D-myo-inositol-3,4-bisphosphate 5-phosphotransferase activity" RELATED [EC:2.7.1.153]
xref: EC:2.7.1.153
xref: Reactome:R-HSA-1675773 "PI(3,4)P2 is phosphorylated to PI(3,4,5)P3 by PIP5K1A-C at the plasma membrane"
@@ -324738,7 +324667,7 @@ id: GO:0052813
name: phosphatidylinositol bisphosphate kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + a phosphatidylinositol bisphosphate = ADP + a phosphatidylinositol trisphosphate." [GOC:ai]
-is_a: GO:0016301 ! kinase activity
+is_a: GO:0001727 ! lipid kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
[Term]
@@ -324783,7 +324712,7 @@ synonym: "very long-chain acyl coenzyme A hydrolase activity" RELATED [EC:3.1.2.
synonym: "very long-chain acyl-thioester hydrolase activity" RELATED [EC:3.1.2.19]
synonym: "very long-chain hydrolase activity" RELATED [EC:3.1.2.19]
synonym: "very long-chain-acyl-CoA hydrolase activity" RELATED [EC:3.1.2.19]
-is_a: GO:0052816 ! long-chain acyl-CoA hydrolase activity
+is_a: GO:0047617 ! acyl-CoA hydrolase activity
[Term]
id: GO:0052818
@@ -324963,7 +324892,7 @@ is_a: GO:0052745 ! inositol phosphate phosphatase activity
id: GO:0052835
name: inositol-3,4,6-trisphosphate 1-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1D-myo-inositol 3,4,6-trisphosphate + ATP = 1D-myo-inositol 1,3,4,6-tetrakisphosphate + ADP + 2 H(+)." [GOC:curators]
+def: "Catalysis of the reaction: 1D-myo-inositol 3,4,6-trisphosphate + ATP = 1D-myo-inositol 1,3,4,6-tetrakisphosphate + ADP + 2 H+." [GOC:curators]
synonym: "1D-myo-inositol-trisphosphate 1-kinase activity" BROAD []
synonym: "ATP:1D-myo-inositol-3,4,6-trisphosphate 1-phosphotransferase activity" RELATED []
synonym: "inositol 3,4,6-trisphosphate 1-kinase activity" EXACT []
@@ -325026,38 +324955,38 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0052840
name: inositol diphosphate tetrakisphosphate diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: inositol diphosphate tetrakisphosphate + H2O = inositol 1,3,4,5,6-pentakisphosphate + phosphate." [MetaCyc:RXN-10963, PMID:10827188, PMID:11502751]
-xref: EC:3.6.1.52
+def: "Catalysis of the reaction: diphospho-1D-myo-inositol tetrakisphosphate + H2O = 1D-myo-inositol pentakisphosphate + phosphate." [PMID:10827188, PMID:11502751]
xref: MetaCyc:RXN-10963
xref: Reactome:R-HSA-1855166 "PP-IP4 is dephosphorylated to I(1,3,4,5,6)P5 by NUDT4 in the cytosol"
-is_a: GO:0016462 ! pyrophosphatase activity
+is_a: GO:0008486 ! diphosphoinositol-polyphosphate diphosphatase activity
[Term]
id: GO:0052841
name: inositol bisdiphosphate tetrakisphosphate diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: inositol bisdiphosphate tetrakisphosphate + H2O = inositol diphosphate pentakisphosphate + phosphate." [MetaCyc:RXN-10965, MetaCyc:RXN-10975, MetaCyc:RXN-10976, PMID:10827188, PMID:11502751]
+def: "Catalysis of the reaction: bisdiphospho-1D-myo-inositol tetrakisphosphate + H2O = diphospho-1D-myo-inositol pentakisphosphate + phosphate." [PMID:10827188, PMID:11502751]
xref: Reactome:R-HSA-1855165 "(PP)2-IP4 is dephosphorylated to 5-PP-IP5 by NUDT(1) in the cytosol"
xref: Reactome:R-HSA-2023973 "(PP)2-IP4 is dephosphorylated to 1/3-PP-IP5 by NUDT(1) in the cytosol"
-is_a: GO:0016462 ! pyrophosphatase activity
+is_a: GO:0008486 ! diphosphoinositol-polyphosphate diphosphatase activity
[Term]
id: GO:0052842
name: inositol diphosphate pentakisphosphate diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: inositol diphosphate pentakisphosphate + H2O = inositol hexakisphosphate + phosphate." [MetaCyc:RXN-10964, MetaCyc:RXN-10977, MetaCyc:RXN-10978, PMID:10827188, PMID:11502751]
-xref: EC:3.6.1.52
+def: "Catalysis of the reaction: diphospho-1D-myo-inositol pentakisphosphate + H2O = 1D-myo-inositol hexakisphosphate + phosphate." [PMID:10827188, PMID:11502751]
xref: KEGG_REACTION:R05779
xref: Reactome:R-HSA-1855198 "5-PP-IP5 is dephosphorylated to IP6 by NUDT(1) in the cytosol"
xref: Reactome:R-HSA-2023971 "1/3 PP-IP5 is dephosphorylated to IP6 by NUDT(1) in the cytosol"
-xref: RHEA:22384
-is_a: GO:0016462 ! pyrophosphatase activity
+is_a: GO:0008486 ! diphosphoinositol-polyphosphate diphosphatase activity
[Term]
id: GO:0052843
name: inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: inositol 1-diphosphate 2,3,4,5,6-pentakisphosphate + H2O = inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + 2 H+." [MetaCyc:RXN-10977, PMID:10827188, PMID:11502751]
+alt_id: GO:0101011
+def: "Catalysis of the reaction: 1-diphospho-1D-myo-inositol 2,3,4,5,6-pentakisphosphate + H2O = 1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + 2 H+." [PMID:10827188, PMID:11502751, PMID:26422458]
+synonym: "inositol 1-diphosphate 2,3,4,5,6-pentakisphosphate 1-diphosphatase activity" EXACT []
+synonym: "inositol 1-pyrophosphate 2,3,4,5,6-pentakisphosphate 1-pyrophosphatase activity" EXACT []
xref: MetaCyc:RXN-10977
is_a: GO:0052842 ! inositol diphosphate pentakisphosphate diphosphatase activity
@@ -325065,7 +324994,7 @@ is_a: GO:0052842 ! inositol diphosphate pentakisphosphate diphosphatase activity
id: GO:0052844
name: inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: inositol 3-diphosphate 1,2,4,5,6-pentakisphosphate + H2O = inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + 2 H+." [MetaCyc:RXN-10978, PMID:10827188, PMID:11502751]
+def: "Catalysis of the reaction: 3-diphospho-1D-myo-inositol 1,2,4,5,6-pentakisphosphate + H2O = 1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + 2 H+." [PMID:10827188, PMID:11502751]
xref: MetaCyc:RXN-10978
is_a: GO:0052842 ! inositol diphosphate pentakisphosphate diphosphatase activity
@@ -325073,15 +325002,20 @@ is_a: GO:0052842 ! inositol diphosphate pentakisphosphate diphosphatase activity
id: GO:0052845
name: inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate + H2O = inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + 2 H+." [MetaCyc:RXN-10964, PMID:10827188, PMID:11502751]
+def: "Catalysis of the reaction: 5-diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate + H2O = 1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + H+." [PMID:10827188, PMID:11502751, RHEA:22384]
+xref: KEGG_REACTION:R05779
xref: MetaCyc:RXN-10964
+xref: RHEA:22384
is_a: GO:0052842 ! inositol diphosphate pentakisphosphate diphosphatase activity
[Term]
id: GO:0052846
name: inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,5-bisdiphosphoinositol-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 1-diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate + phosphate + H+." [MetaCyc:RXN-10965, PMID:10827188, PMID:11502751]
+alt_id: GO:0101012
+def: "Catalysis of the reaction: 1,5-bisdiphospho-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 5-diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate + phosphate + H+." [PMID:10827188, PMID:11502751, PMID:26422458]
+synonym: "inositol 1,5-bisdiphosphate 2,3,4,6-tetrakisphosphate 1-diphosphatase activity" EXACT []
+synonym: "inositol 1,5-bispyrophosphate 2,3,4,6-tetrakisphosphate 1-pyrophosphatase activity" EXACT []
xref: MetaCyc:RXN-10965
is_a: GO:0052841 ! inositol bisdiphosphate tetrakisphosphate diphosphatase activity
@@ -325089,7 +325023,7 @@ is_a: GO:0052841 ! inositol bisdiphosphate tetrakisphosphate diphosphatase activ
id: GO:0052847
name: inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,5-bisdiphosphoinositol-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 1-diphospho-1D-myo-inositol 2,3,4,5,6-pentakisphosphate + phosphate + H+." [MetaCyc:RXN-10975, PMID:10827188, PMID:11502751]
+def: "Catalysis of the reaction: 1,5-bisdiphospho-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 1-diphospho-1D-myo-inositol 2,3,4,5,6-pentakisphosphate + phosphate + H+." [MetaCyc:RXN-10975, PMID:10827188, PMID:11502751]
xref: MetaCyc:RXN-10975
is_a: GO:0052841 ! inositol bisdiphosphate tetrakisphosphate diphosphatase activity
@@ -325097,8 +325031,9 @@ is_a: GO:0052841 ! inositol bisdiphosphate tetrakisphosphate diphosphatase activ
id: GO:0052848
name: inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3,5-bisdiphosphoinositol-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 3-diphospho-1D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate + H+." [MetaCyc:RXN-10976, PMID:10827188, PMID:11502751]
+def: "Catalysis of the reaction: 3,5-bisdiphospho-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 3-diphospho-1D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate + 2 H+." [PMID:10827188, PMID:11502751, RHEA:56312]
xref: MetaCyc:RXN-10976
+xref: RHEA:56312
is_a: GO:0052841 ! inositol bisdiphosphate tetrakisphosphate diphosphatase activity
[Term]
@@ -325123,7 +325058,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0052851
name: ferric-chelate reductase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 Fe3+-siderophore + NADP(+) + H(+) -> 2 Fe2+-siderophore + NADPH." [RHEA:28795]
+def: "Catalysis of the reaction: 2 Fe3+-siderophore + NADP+ + H+ -> 2 Fe2+-siderophore + NADPH." [RHEA:28795]
synonym: "ferric chelate reductase activity" BROAD []
synonym: "ferric reductase, NADPH-dependent activity" EXACT []
synonym: "iron chelate reductase activity" BROAD []
@@ -325138,7 +325073,7 @@ is_a: GO:0016723 ! oxidoreductase activity, acting on metal ions, NAD or NADP as
id: GO:0052855
name: ADP-dependent NAD(P)H-hydrate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (6S)-6beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide + ADP = AMP + 3 H(+) + NADH + phosphate." [EC:4.2.1.93, PMID:21994945]
+def: "Catalysis of the reaction: (6S)-6beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide + ADP = AMP + 3 H+ + NADH + phosphate." [EC:4.2.1.93, PMID:21994945]
synonym: "(6S)-beta-6-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ADP-hydrolysing)" RELATED [EC:4.2.1.136]
synonym: "(6S)-beta-6-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase(ADP-hydrolysing; NADH-forming)" RELATED [EC:4.2.1.136]
synonym: "ADP-dependent H(4)NAD(P)OH dehydratase activity" EXACT []
@@ -325193,7 +325128,7 @@ synonym: "endo-(1->4)-beta-D-glucanase activity" EXACT []
synonym: "endo-1,4-beta-D-glucanase activity" EXACT []
synonym: "endo-1,4-beta-glucanase activity" EXACT []
synonym: "endo-beta-1,4-glucanase activity" EXACT []
-xref: EC:3.2.1.-
+xref: EC:3.2.1.75
is_a: GO:0008422 ! beta-glucosidase activity
[Term]
@@ -325274,7 +325209,6 @@ synonym: "1-deoxy-D-xylulose 5-phosphate anabolism" EXACT []
synonym: "1-deoxy-D-xylulose 5-phosphate biosynthesis" EXACT []
synonym: "1-deoxy-D-xylulose 5-phosphate formation" EXACT []
synonym: "1-deoxy-D-xylulose 5-phosphate synthesis" EXACT []
-xref: UniPathway:UPA00064
is_a: GO:0052863 ! 1-deoxy-D-xylulose 5-phosphate metabolic process
is_a: GO:0090407 ! organophosphate biosynthetic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
@@ -325291,7 +325225,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0052867
name: phosphatidylinositol-1,4,5-trisphosphate 5-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phosphatidyl-1D-myo-inositol 1,4,5-trisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 1,4-bisphosphate + phosphate." [GOC:curators]
+def: "Catalysis of the reaction: phosphatidyl-1D-myo-inositol 1,4,5-trisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 1,4-bisphosphate + phosphate." [GOC:curators]
synonym: "phosphatidyl-myo-inositol-1,4,5-trisphosphate phosphatase activity" BROAD []
synonym: "phosphatidylinositol 1,4,5-trisphosphate phosphatase activity" BROAD []
synonym: "phosphatidylinositol-trisphosphatase activity" BROAD []
@@ -325351,21 +325285,8 @@ id: GO:0052873
name: FMN reductase (NADPH) activity
namespace: molecular_function
def: "Catalysis of the reaction: FMNH2 + NADP+ = FMN + NADPH + 2 H+." [RHEA:21624]
-synonym: "flavin mononucleotide reductase activity" BROAD [EC:1.5.1.29]
-synonym: "flavine mononucleotide reductase activity" BROAD [EC:1.5.1.29]
-synonym: "FMNH2:NADP+ oxidoreductase activity" RELATED [EC:1.5.1.29]
synonym: "NADPH dehydrogenase (FMN) activity" EXACT []
-synonym: "NADPH(2) dehydrogenase (FMN) activity" RELATED [EC:1.5.1.29]
-synonym: "NADPH(2):FMN oxidoreductase activity" RELATED [EC:1.5.1.29]
-synonym: "NADPH-dependent FMN reductase activity" RELATED [EC:1.5.1.29]
-synonym: "NADPH-FMN reductase activity" RELATED [EC:1.5.1.29]
-synonym: "NADPH2 dehydrogenase (FMN)" RELATED [EC:1.5.1.3]
-synonym: "NADPH2:FMN oxidoreductase activity" RELATED [EC:1.5.1.29]
-synonym: "NADPH:flavin oxidoreductase activity" RELATED [EC:1.5.1.29]
-synonym: "NADPH:FMN oxidoreductase activity" RELATED [EC:1.5.1.29]
-synonym: "SsuE" RELATED [EC:1.5.1.29]
xref: EC:1.5.1.38
-xref: EC:1.5.1.39
xref: KEGG_REACTION:R05706
xref: Reactome:R-HSA-1222399 "Iron is reduced and separates from mycobactin"
xref: RHEA:21624
@@ -325376,29 +325297,19 @@ id: GO:0052874
name: FMN reductase (NADH) activity
namespace: molecular_function
def: "Catalysis of the reaction: FMNH2 + NAD+ = FMN + NADH + 2 H+." [RHEA:21620]
-synonym: "flavin mononucleotide reductase activity" BROAD [EC:1.5.1.29]
-synonym: "flavine mononucleotide reductase activity" BROAD [EC:1.5.1.29]
-synonym: "FMNH2:NAD+ oxidoreductase activity" RELATED [EC:1.5.1.29]
synonym: "NADH dehydrogenase (FMN) activity" EXACT []
-synonym: "NADH(2) dehydrogenase (FMN) activity" RELATED [EC:1.5.1.29]
-synonym: "NADH(2):FMN oxidoreductase activity" RELATED [EC:1.5.1.29]
-synonym: "NADH-dependent FMN reductase activity" RELATED [EC:1.5.1.29]
-synonym: "NADH-FMN reductase activity" RELATED [EC:1.5.1.29]
-synonym: "NADH2 dehydrogenase (FMN)" RELATED [EC:1.5.1.3]
-synonym: "NADH2:FMN oxidoreductase activity" RELATED [EC:1.5.1.29]
-synonym: "NADH:flavin oxidoreductase activity" RELATED [EC:1.5.1.29]
-synonym: "NADH:FMN oxidoreductase activity" RELATED [EC:1.5.1.29]
-synonym: "SsuE" RELATED [EC:1.5.1.29]
-xref: EC:1.5.1.39
+synonym: "NADH-dependent FMN reductase activity" RELATED []
+synonym: "NADH-FMN reductase activity" RELATED []
+xref: EC:1.5.1.42
xref: KEGG_REACTION:R05705
xref: RHEA:21620
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0052875
-name: riboflavin reductase (NADH) activity
+name: riboflavin reductase (NAD(P)H) activity
namespace: molecular_function
-def: "Catalysis of the reaction: reduced riboflavin + NAD+ = riboflavin + NADH + 2 H+." [RHEA:31455]
+def: "Catalysis of the reaction: reduced riboflavin + NAD(P)+ = riboflavin + NAD(P)H + 2 H+. This reaction can utilize NADH and NADPH." [EC:1.5.1.41]
synonym: "flavin mononucleotide reductase activity" RELATED [EC:1.5.1.41]
synonym: "flavine mononucleotide reductase activity" RELATED [EC:1.5.1.41]
synonym: "NAD(P)H-dependent FMN reductase activity" RELATED [EC:1.5.1.41]
@@ -325409,6 +325320,8 @@ synonym: "NAD(P)H:FMN oxidoreductase activity" RELATED [EC:1.5.1.41]
synonym: "NAD(P)H:riboflavin oxidoreductase activity" RELATED [EC:1.5.1.41]
synonym: "riboflavin mononucleotide (reduced nicotinamide adenine dinucleotide) reductase activity" RELATED [EC:1.5.1.41]
synonym: "riboflavin mononucleotide reductase activity" RELATED [EC:1.5.1.41]
+synonym: "riboflavin reductase (NADH) activity" NARROW []
+synonym: "riboflavin reductase (NADPH) activity" NARROW []
synonym: "riboflavine mononucleotide reductase activity" RELATED [EC:1.5.1.41]
xref: EC:1.5.1.41
xref: KEGG_REACTION:R09750
@@ -325444,7 +325357,7 @@ is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0052878
name: linoleate 8R-lipoxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O(2) + linoleate = (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate." [RHEA:25395]
+def: "Catalysis of the reaction: O2 + linoleate = (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate." [RHEA:25395]
synonym: "5,8-LDS (bifunctional enzyme) activity" RELATED [EC:1.13.11.60]
synonym: "5,8-linoleate diol synthase (bifunctional enzyme) activity" RELATED [EC:1.13.11.60]
synonym: "7,8-LDS (bifunctional enzyme) activity" RELATED [EC:1.13.11.60]
@@ -325482,7 +325395,7 @@ is_a: GO:0016679 ! oxidoreductase activity, acting on diphenols and related subs
id: GO:0052881
name: 4-hydroxyphenylacetate 3-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (4-hydroxyphenyl)acetate + FADH(2) + O(2) = 3,4-dihydroxyphenylacetate + FAD + H(+) + H(2)O." [RHEA:30595]
+def: "Catalysis of the reaction: (4-hydroxyphenyl)acetate + FADH(2) + O2 = 3,4-dihydroxyphenylacetate + FAD + H+ + H2O." [RHEA:30595]
synonym: "4 HPA 3-hydroxylase activity" BROAD [EC:1.14.14.9]
synonym: "4-hydroxyphenylacetate,FADH:oxygen oxidoreductase (3-hydroxylating) activity" EXACT systematic_synonym []
synonym: "4-hydroxyphenylacetic acid-3-hydroxylase activity" BROAD [EC:1.14.14.9]
@@ -325508,7 +325421,7 @@ is_a: GO:0030613 ! oxidoreductase activity, acting on phosphorus or arsenic in d
id: GO:0052883
name: tyrosine ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tyrosine = NH(4)(+) + trans-4-coumarate." [RHEA:24906]
+def: "Catalysis of the reaction: L-tyrosine = NH4 + trans-4-coumarate." [RHEA:24906]
synonym: "L-tyrosine ammonia-lyase activity" RELATED [EC:4.3.1.23]
synonym: "TAL activity" BROAD [EC:4.3.1.23]
synonym: "tyrase activity" BROAD [EC:4.3.1.23]
@@ -325521,7 +325434,7 @@ is_a: GO:0016841 ! ammonia-lyase activity
id: GO:0052884
name: all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + all-trans-retinyl palmitate = 11-cis-retinol + H(+) + palmitate." [RHEA:31775]
+def: "Catalysis of the reaction: H2O + all-trans-retinyl palmitate = 11-cis-retinol + H+ + palmitate." [RHEA:31775]
synonym: "all-trans-retinol isomerase:hydrolase activity" BROAD [EC:3.1.1.64]
synonym: "all-trans-retinyl-palmitate hydrolase activity" BROAD [EC:3.1.1.64]
synonym: "retinoid isomerohydrolase activity" BROAD [EC:3.1.1.64]
@@ -325529,13 +325442,13 @@ synonym: "retinol isomerase activity" BROAD [EC:3.1.1.64]
xref: EC:3.1.1.64
xref: Reactome:R-HSA-2453833 "RPE65 isomero-hydrolyses atREs to 11cROL"
xref: RHEA:31775
-is_a: GO:0052689 ! carboxylic ester hydrolase activity
+is_a: GO:0050253 ! retinyl-palmitate esterase activity
[Term]
id: GO:0052885
name: all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + all-trans-retinyl ester = 11-cis-retinol + fatty acid." [RHEA:31771]
+def: "Catalysis of the reaction: H2O + all-trans-retinyl ester = 11-cis-retinol + fatty acid." [RHEA:31771]
synonym: "all-trans-retinol isomerase:hydrolase activity" BROAD [EC:3.1.1.64]
synonym: "all-trans-retinyl ester acylhydrolase, 11-cis retinol forming activity" RELATED [EC:3.1.1.64]
synonym: "all-trans-retinylester 11-cis isomerohydrolase activity" RELATED [EC:3.1.1.64]
@@ -325579,7 +325492,7 @@ id: GO:0052888
name: obsolete dihydroorotate oxidase (fumarate) activity
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate + succinate." [GOC:curators]
-comment: EC has determined that this reaction in fact does not exist and have withdrawn EC:1.3.3.1. Note: If fumarate is not shown to be involved, you may want to consider GO:0004152, dihydroorotate dehydrogenase activity (parent term); if the reaction involves fumarate, then use GO:0052888 dihydroorotate oxidase (fumarate) activity. Details at http://sourceforge.net/p/geneontology/ontology-requests/10770/, RHEA:30059 and EC:1.3.98 removed so as not to conflict with remapping
+comment: EC has determined that this reaction in fact does not exist and have withdrawn EC:1.3.3.1. Note: If fumarate is not shown to be involved, you may want to consider GO:0004152, dihydroorotate dehydrogenase activity (parent term); if the reaction involves fumarate, then use GO:0052888 dihydroorotate oxidase (fumarate) activity.
synonym: "DHOD activity" BROAD []
synonym: "DHOdase activity" BROAD []
synonym: "DHodehase activity" BROAD []
@@ -325615,35 +325528,26 @@ is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
id: GO:0052891
name: aliphatic (S)-hydroxynitrile lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an aliphatic (S)-hydroxynitrile = an aliphatic aldehyde or ketone + cyanide." [EC:4.1.2.47]
+def: "Catalysis of the reaction: an aliphatic (S)-hydroxynitrile = an aliphatic aldehyde or ketone + cyanide." [PMID:15299689]
synonym: "(S)-cyanohydrin carbonyl-lyase (cyanide forming) activity" BROAD [EC:4.1.2.47]
synonym: "(S)-cyanohydrin producing hydroxynitrile lyase activity" BROAD [EC:4.1.2.47]
synonym: "(S)-hydroxynitrile lyase activity" BROAD [EC:4.1.2.47]
synonym: "(S)-oxynitrilase activity" BROAD [EC:4.1.2.47]
synonym: "(S)-selective hydroxynitrile lyase activity" BROAD [EC:4.1.2.47]
-synonym: "hydroxynitrile lyase activity" BROAD [EC:4.1.2.47]
-synonym: "oxynitrilase activity" BROAD [EC:4.1.2.47]
-xref: EC:4.1.2.47
+xref: https://github.com/geneontology/go-ontology/issues/16166
xref: MetaCyc:RXN-11731
-is_a: GO:0016832 ! aldehyde-lyase activity
+is_a: GO:0047606 ! hydroxynitrilase activity
[Term]
id: GO:0052892
name: aromatic (S)-hydroxynitrile lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an aromatic (S)-hydroxynitrile = an aromatic aldehyde + cyanide." [EC:4.1.2.47, KEGG_REACTION:R09359]
-synonym: "(S)-cyanohydrin carbonyl-lyase (cyanide forming) activity" BROAD [EC:4.1.2.47]
-synonym: "(S)-cyanohydrin producing hydroxynitrile lyase activity" BROAD [EC:4.1.2.47]
-synonym: "(S)-hydroxynitrile lyase activity" BROAD [EC:4.1.2.47]
-synonym: "(S)-oxynitrilase activity" BROAD [EC:4.1.2.47]
-synonym: "(S)-selective hydroxynitrile lyase activity" BROAD [EC:4.1.2.47]
-synonym: "hydroxynitrile lyase activity" BROAD [EC:4.1.2.47]
-synonym: "oxynitrilase activity" BROAD [EC:4.1.2.47]
-xref: EC:4.1.2.47
+def: "Catalysis of the reaction: an aromatic (S)-hydroxynitrile = an aromatic aldehyde + cyanide." [RHEA:54660]
+xref: https://github.com/geneontology/go-ontology/issues/16166
xref: KEGG_REACTION:R09359
xref: MetaCyc:RXN-11732
xref: RHEA:54660
-is_a: GO:0016832 ! aldehyde-lyase activity
+is_a: GO:0047606 ! hydroxynitrilase activity
[Term]
id: GO:0052893
@@ -325654,7 +325558,7 @@ synonym: "polyamine oxidase (propane-1,3-diamine-forming) activity" BROAD [EC:1.
xref: EC:1.5.3.14
xref: MetaCyc:RXN-10465
xref: RHEA:25996
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+is_a: GO:0046592 ! polyamine oxidase activity
[Term]
id: GO:0052894
@@ -325664,7 +325568,7 @@ def: "Catalysis of the reaction: norspermine + oxygen + H2O = norspermidine + 3-
synonym: "norspermine oxidase activity" BROAD [EC:1.5.3.16]
xref: EC:1.5.3.16
xref: MetaCyc:RXN-10464
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+is_a: GO:0046592 ! polyamine oxidase activity
[Term]
id: GO:0052895
@@ -325674,70 +325578,69 @@ def: "Catalysis of the reaction: N1-acetylspermine + oxygen + H2O = N1-acetylspe
synonym: "N1-acetylspermine oxidase activity" BROAD [EC:1.5.3.16]
xref: EC:1.5.3.16
xref: MetaCyc:POLYAMINE-OXIDASE-RXN
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+is_a: GO:0046592 ! polyamine oxidase activity
[Term]
id: GO:0052896
name: spermidine oxidase (propane-1,3-diamine-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + O(2) + spermidine = 1,3-diaminopropane + 4-aminobutanal + H(2)O(2)." [RHEA:25820]
+def: "Catalysis of the reaction: H2O + O2 + spermidine = 1,3-diaminopropane + 4-aminobutanal + H2O2." [RHEA:25820]
synonym: "polyamine oxidase (propane-1,3-diamine-forming) activity" BROAD [EC:1.5.3.14]
synonym: "spermidine:(acceptor) oxidoreductase activity" BROAD [EC:1.5.3.14]
xref: EC:1.5.3.14
xref: KEGG_REACTION:R01914
xref: MetaCyc:RXN-10747
xref: RHEA:25820
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+is_a: GO:0046592 ! polyamine oxidase activity
[Term]
id: GO:0052897
name: N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + N(8)-acetylspermidine + O(2) = 1,3-diaminopropane + 4-acetamidobutanal + H(2)O(2)." [RHEA:25972]
+def: "Catalysis of the reaction: H2O + N(8)-acetylspermidine + O2 = 1,3-diaminopropane + 4-acetamidobutanal + H2O2." [RHEA:25972]
synonym: "N(8)-acetylspermidine oxidase (propane-1,3-diamine-forming) activity" BROAD [EC:1.5.3.15]
xref: EC:1.5.3.15
xref: KEGG_REACTION:R09075
xref: MetaCyc:RXN-10463
xref: RHEA:25972
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+is_a: GO:0046592 ! polyamine oxidase activity
[Term]
id: GO:0052898
-name: N1-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity
+name: obsolete N1-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + N(1)-acetylspermidine + O(2) = 1,3-diaminopropane + 4-acetamidobutanal + H(2)O(2)." [RHEA:25864]
-xref: EC:1.5.3.15
-xref: RHEA:25864
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+def: "OBSOLETE. Catalysis of the reaction: H2O + N(1)-acetylspermidine + O2 = 1,3-diaminopropane + 4-acetamidobutanal + H2O2." [GOC:curators]
+comment: The reason for the obsoletion is because there is no evidence for the reaction. RHEA:25864 used as the definition has been determined to not exit.
+is_obsolete: true
[Term]
id: GO:0052899
name: N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + N(1),N(12)-diacetylspermine + O(2) = 3-acetamidopropanal + H(2)O(2) + N(1)-acetylspermidine." [RHEA:25868]
+def: "Catalysis of the reaction: H2O + N(1),N(12)-diacetylspermine + O2 = 3-acetamidopropanal + H2O2 + N(1)-acetylspermidine." [RHEA:25868]
synonym: "N(1)-acetylpolyamine oxidase activity" BROAD [EC:1.5.3.13]
synonym: "polyamine oxidase activity" BROAD [EC:1.5.3.13, EC:1.5.3.17]
xref: EC:1.5.3.13
xref: MetaCyc:RXN-10460
xref: RHEA:25868
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+is_a: GO:0046592 ! polyamine oxidase activity
[Term]
id: GO:0052900
name: spermine oxidase (propane-1,3-diamine-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + O(2) + spermine = 1,3-diaminopropane + H(2)O(2) + N-(3-aminopropyl)-4-aminobutanal." [RHEA:25824]
+def: "Catalysis of the reaction: H2O + O2 + spermine = 1,3-diaminopropane + H2O2 + N-(3-aminopropyl)-4-aminobutanal." [RHEA:25824]
synonym: "polyamine oxidase (propane-1,3-diamine-forming) activity" BROAD [EC:1.5.3.14]
xref: EC:1.5.3.14
xref: MetaCyc:RXN-6421
xref: RHEA:25824
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+is_a: GO:0046592 ! polyamine oxidase activity
[Term]
id: GO:0052901
name: spermine:oxygen oxidoreductase (spermidine-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + O(2) + spermine = 3-aminopropanal + H(2)O(2) + spermidine." [RHEA:25804]
+def: "Catalysis of the reaction: H2O + O2 + spermine = 3-aminopropanal + H2O2 + spermidine." [RHEA:25804]
synonym: "N(1)-acetylpolyamine oxidase activity" BROAD [EC:1.5.3.13]
synonym: "non-specific polyamine oxidase activity" BROAD [EC:1.5.3.17]
synonym: "polyamine oxidase activity" BROAD [EC:1.5.3.13, EC:1.5.3.17]
@@ -325750,13 +325653,13 @@ xref: MetaCyc:1.5.3.17-RXN
xref: MetaCyc:RXN-9015
xref: Reactome:R-HSA-141341 "SMOX-3 oxidises SPN to SPM"
xref: RHEA:25804
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+is_a: GO:0046592 ! polyamine oxidase activity
[Term]
id: GO:0052902
name: spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + O(2) + spermidine = 3-aminopropanal + H(2)O(2) + putrescine." [RHEA:25808]
+def: "Catalysis of the reaction: H2O + O2 + spermidine = 3-aminopropanal + H2O2 + putrescine." [RHEA:25808]
synonym: "N(1)-acetylpolyamine oxidase activity" BROAD [EC:1.5.3.13]
synonym: "non-specific polyamine oxidase activity" BROAD [EC:1.5.3.17]
synonym: "polyamine oxidase activity" BROAD [EC:1.5.3.13, EC:1.5.3.17]
@@ -325766,13 +325669,13 @@ xref: KEGG_REACTION:R09077
xref: MetaCyc:RXN-10461
xref: MetaCyc:RXN-12089
xref: RHEA:25808
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+is_a: GO:0046592 ! polyamine oxidase activity
[Term]
id: GO:0052903
name: N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + N(1)-acetylspermine + O(2) = 3-acetamidopropanal + H(2)O(2) + spermidine." [RHEA:25800]
+def: "Catalysis of the reaction: H2O + N(1)-acetylspermine + O2 = 3-acetamidopropanal + H2O2 + spermidine." [RHEA:25800]
synonym: "N(1)-acetylpolyamine oxidase activity" BROAD [EC:1.5.3.13]
synonym: "non-specific polyamine oxidase activity" BROAD [EC:1.5.3.17]
synonym: "polyamine oxidase activity" BROAD [EC:1.5.3.13, EC:1.5.3.17]
@@ -325782,13 +325685,13 @@ xref: KEGG_REACTION:R03899
xref: MetaCyc:RXN-12090
xref: MetaCyc:RXN-9940
xref: RHEA:25800
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+is_a: GO:0046592 ! polyamine oxidase activity
[Term]
id: GO:0052904
name: N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + N(1)-acetylspermidine + O(2) = 3-acetamidopropanal + H(2)O(2) + putrescine." [RHEA:25812]
+def: "Catalysis of the reaction: H2O + N(1)-acetylspermidine + O2 = 3-acetamidopropanal + H2O2 + putrescine." [RHEA:25812]
synonym: "N(1)-acetylpolyamine oxidase activity" BROAD [EC:1.5.3.13]
synonym: "non-specific polyamine oxidase activity" BROAD [EC:1.5.3.17]
synonym: "polyamine oxidase activity" BROAD [EC:1.5.3.13, EC:1.5.3.17]
@@ -325800,7 +325703,7 @@ xref: MetaCyc:RXN-9942
xref: Reactome:R-HSA-141348 "PAO:FAD oxidises NASPM to PTCN"
xref: Reactome:R-HSA-141351 "PAOX:FAD oxidises NASPN to SPM"
xref: RHEA:25812
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+is_a: GO:0046592 ! polyamine oxidase activity
[Term]
id: GO:0052905
@@ -325971,7 +325874,7 @@ is_a: GO:0000009 ! alpha-1,6-mannosyltransferase activity
id: GO:0052918
name: dol-P-Man:Man(8)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: alpha-D-man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->6))-alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl D-mannosyl phosphate = H(+) + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->2)-alpha-D-Man-(1->6))-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate." [EC:2.4.1.261, RHEA:29539]
+def: "Catalysis of the reaction: alpha-D-man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->6))-alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl D-mannosyl phosphate = H+ + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->2)-alpha-D-Man-(1->6))-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate." [EC:2.4.1.261, RHEA:29539]
xref: EC:2.4.1.261
xref: KEGG_REACTION:R06261
xref: MetaCyc:RXN-5469
@@ -325987,29 +325890,25 @@ synonym: "(R)-HNL activity" BROAD [EC:4.1.2.46]
synonym: "(R)-hydroxynitrile lyase activity" BROAD [EC:4.1.2.46]
synonym: "(R)-oxynitrilase activity" BROAD [EC:4.1.2.46]
xref: EC:4.1.2.46
-is_a: GO:0016832 ! aldehyde-lyase activity
+is_a: GO:0047606 ! hydroxynitrilase activity
[Term]
id: GO:0052920
-name: (2R)-2-hydroxy-2-methylbutanenitrile lyase activity
+name: obsolete (2R)-2-hydroxy-2-methylbutanenitrile lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2R)-2-hydroxy-2-methylbutanenitrile = butan-2-one + hydrogen cyanide." [EC:4.1.2.46]
-xref: EC:4.1.2.46
-xref: KEGG_REACTION:R09358
-xref: MetaCyc:RXN-11733
-xref: RHEA:28170
-is_a: GO:0052919 ! aliphatic (R)-hydroxynitrile lyase activity
+def: "OBSOLETE. Catalysis of the reaction: (2R)-2-hydroxy-2-methylbutanenitrile = butan-2-one + hydrogen cyanide." [EC:4.1.2.46]
+comment: This term was obsoleted because it represents a specific substrate of aliphatic (R)-hydroxynitrile lyase activity ; GO:0052919.
+is_obsolete: true
+replaced_by: GO:0052919
[Term]
id: GO:0052921
-name: acetone-cyanohydrin acetone-lyase (cyanide-forming) activity
+name: obsolete acetone-cyanohydrin acetone-lyase (cyanide-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetone cyanohydrin = hydrogen cyanide + acetone." [KEGG_REACTION:R01553, MetaCyc:ACETONE-CYANHYDRIN-LYASE-RXN]
-xref: EC:4.1.2.46
-xref: KEGG_REACTION:R01553
-xref: MetaCyc:ACETONE-CYANHYDRIN-LYASE-RXN
-xref: RHEA:11932
-is_a: GO:0052919 ! aliphatic (R)-hydroxynitrile lyase activity
+def: "OBSOLETE. Catalysis of the reaction: acetone cyanohydrin = hydrogen cyanide + acetone." [KEGG_REACTION:R01553, MetaCyc:ACETONE-CYANHYDRIN-LYASE-RXN]
+comment: This term was obsoleted because it represents a specific substrate of aliphatic (R)-hydroxynitrile lyase activity ; GO:0052919.
+is_obsolete: true
+replaced_by: GO:0052919
[Term]
id: GO:0052922
@@ -326030,14 +325929,25 @@ is_a: GO:0004659 ! prenyltransferase activity
id: GO:0052923
name: all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity
namespace: molecular_function
+alt_id: GO:0050347
def: "Catalysis of the reaction: geranyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + all-trans-nonaprenyl diphosphate." [RHEA:27563]
+synonym: "(E)-octaprenyl-diphosphate:isopentenyl-diphosphate octaprenyltranstransferase activity" RELATED []
+synonym: "all-trans-nonaprenyl-diphosphate synthase activity" RELATED []
synonym: "nonaprenyl diphosphate synthase activity" BROAD [EC:2.5.1.84]
+synonym: "nonaprenyl pyrophosphate synthetase activity" RELATED []
+synonym: "polyprenylpyrophosphate synthetase activity" RELATED []
synonym: "solanesyl diphosphate synthetase activity" BROAD [EC:2.5.1.84]
-synonym: "solanesyl-diphosphate synthase activity" BROAD [EC:2.5.1.84]
+synonym: "solanesyl pyrophosphate synthetase activity" RELATED []
+synonym: "solanesyl-diphosphate synthase activity" RELATED []
synonym: "solPP synthase activity" BROAD [EC:2.5.1.84]
synonym: "SPP synthase activity" BROAD [EC:2.5.1.84]
synonym: "SPP-synthase activity" BROAD [EC:2.5.1.84]
+synonym: "terpenoidallyltransferase activity" RELATED []
+synonym: "terpenyl pyrophosphate synthetase activity" RELATED []
+synonym: "trans-octaprenyltranstransferase activity" RELATED []
+synonym: "trans-prenyltransferase activity" RELATED []
xref: EC:2.5.1.84
+xref: KEGG_REACTION:R07267
xref: KEGG_REACTION:R09250
xref: MetaCyc:TRANS-OCTAPRENYLTRANSTRANSFERASE-RXN
xref: RHEA:27563
@@ -326061,7 +325971,7 @@ is_a: GO:0004659 ! prenyltransferase activity
id: GO:0052925
name: dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an alpha-D-man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl D-mannosyl phosphate = H(+) + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->3)-alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate." [RHEA:29527]
+def: "Catalysis of the reaction: an alpha-D-man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl D-mannosyl phosphate = H+ + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->3)-alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate." [RHEA:29527]
synonym: "dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase activity" RELATED [EC:2.4.1.258]
synonym: "man(5)GlcNAc(2)-PP-Dol mannosyltransferase activity" RELATED [EC:2.4.1.258]
xref: EC:2.4.1.258
@@ -326074,7 +325984,7 @@ is_a: GO:0000033 ! alpha-1,3-mannosyltransferase activity
id: GO:0052926
name: dol-P-Man:Man(6)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: alpha-D-man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->3)-alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl D-mannosyl phosphate = H(+) + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate." [EC:2.4.1.259, RHEA:29531]
+def: "Catalysis of the reaction: alpha-D-man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->3)-alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl D-mannosyl phosphate = H+ + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate." [EC:2.4.1.259, RHEA:29531]
synonym: "dolichylphosphomannose-dependent ALG9 mannosyltransferase activity" RELATED [EC:2.4.1.259]
xref: EC:2.4.1.259
xref: KEGG_REACTION:R06259
@@ -326086,33 +325996,24 @@ is_a: GO:0000026 ! alpha-1,2-mannosyltransferase activity
id: GO:0052927
name: CTP:tRNA cytidylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a tRNA precursor + CTP = a tRNA with a 3' cytidine end + diphosphate." [KEGG_REACTION:R09383]
-xref: EC:2.7.7.72
-xref: KEGG_REACTION:R09383
-is_a: GO:0016779 ! nucleotidyltransferase activity
-is_a: GO:0140101 ! catalytic activity, acting on a tRNA
-
-[Term]
-id: GO:0052928
-name: CTP:3'-cytidine-tRNA cytidylyltransferase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: a tRNA with a 3' cytidine + CTP = a tRNA with a 3' CC end + diphosphate." [KEGG_REACTION:R09384]
-xref: EC:2.7.7.72
-xref: KEGG_REACTION:R09384
-is_a: GO:0016779 ! nucleotidyltransferase activity
+alt_id: GO:0052928
+def: "Catalysis of the reaction: a tRNA precursor + CTP = a tRNA with a 3' CC end + 2 diphosphate." [PMID:31936900, PMID:33095240, RHEA:60008]
+synonym: "CTP:3'-cytidine-tRNA cytidylyltransferase activity" RELATED []
+xref: RHEA:60008
+is_a: GO:0070567 ! cytidylyltransferase activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
[Term]
id: GO:0052929
name: ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a tRNA with a 3' CC end + ATP = a tRNA with a 3' CCA end + diphosphate." [RHEA:60012]
+def: "Catalysis of the reaction: a tRNA with a 3' CC end + ATP = a tRNA with a 3' CCA end + diphosphate." [PMID:31936900, PMID:33095240, RHEA:60012]
synonym: "ATP:3'-CC-tRNA adenylyltransferase activity" EXACT []
synonym: "ATP:tRNA adenylyltransferase activity" BROAD []
-xref: EC:2.7.7.72
xref: KEGG_REACTION:R09386
xref: RHEA:60012
-is_a: GO:0004810 ! tRNA adenylyltransferase activity
+is_a: GO:0070566 ! adenylyltransferase activity
+is_a: GO:0140101 ! catalytic activity, acting on a tRNA
[Term]
id: GO:0052933
@@ -326536,7 +326437,7 @@ relationship: part_of GO:0042597 ! periplasmic space
id: GO:0055041
name: cyclopentanol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cyclopentanol + NAD(+) = cyclopentanone + H(+) + NADH." [EC:1.1.1.163, RHEA:11728]
+def: "Catalysis of the reaction: cyclopentanol + NAD+ = cyclopentanone + H+ + NADH." [EC:1.1.1.163, RHEA:11728]
synonym: "cyclopentanol:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.163]
synonym: "cyclopentanol:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.163]
xref: EC:1.1.1.163
@@ -326604,18 +326505,21 @@ is_a: GO:0051225 ! spindle assembly
[Term]
id: GO:0055049
-name: astral spindle assembly
+name: obsolete astral spindle assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart, in the presence of centrosomes." [GOC:tb]
-is_a: GO:0051225 ! spindle assembly
+def: "OBSOLETE. The aggregation, arrangement and bonding together of a set of components to form the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart, in the presence of centrosomes." [GOC:tb]
+comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
+is_obsolete: true
+consider: GO:0051225
[Term]
id: GO:0055050
-name: astral spindle assembly involved in male meiosis
+name: obsolete astral spindle assembly involved in male meiosis
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form the astral spindle in male meiotic cells." [GOC:tb]
-is_a: GO:0007053 ! spindle assembly involved in male meiosis
-is_a: GO:0055049 ! astral spindle assembly
+def: "OBSOLETE. The aggregation, arrangement and bonding together of a set of components to form the astral spindle in male meiotic cells." [GOC:tb]
+comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
+is_obsolete: true
+consider: GO:0090306
[Term]
id: GO:0055051
@@ -326715,15 +326619,14 @@ def: "OBSOLETE. Any process involved in the maintenance of an internal steady st
comment: This term was made obsolete because it has been split.
synonym: "di-, tri-valent inorganic anion homeostasis" EXACT []
is_obsolete: true
-consider: GO:0072505
-consider: GO:0072506
+consider: GO:0055081
[Term]
id: GO:0055062
name: phosphate ion homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of phosphate ions within an organism or cell." [GOC:jid, GOC:mah]
-is_a: GO:0072506 ! trivalent inorganic anion homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0055063
@@ -326733,24 +326636,24 @@ alt_id: GO:0080174
def: "Any process involved in the maintenance of an internal steady state of sulfate ions within an organism or cell." [GOC:jid, GOC:mah]
synonym: "sulfate homeostasis" EXACT []
synonym: "sulphate ion homeostasis" EXACT []
-is_a: GO:0072505 ! divalent inorganic anion homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0055064
name: chloride ion homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of chloride ions within an organism or cell." [GOC:jid, GOC:mah]
-is_a: GO:0055083 ! monovalent inorganic anion homeostasis
+is_a: GO:0055081 ! monoatomic anion homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0055065
-name: metal ion homeostasis
+name: obsolete metal ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of metal ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
-subset: goslim_generic
-subset: goslim_pombe
-is_a: GO:0055080 ! cation homeostasis
-is_a: GO:0098771 ! inorganic ion homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of metal ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+consider: GO:0030003
[Term]
id: GO:0055066
@@ -326760,16 +326663,16 @@ def: "OBSOLETE. Any process involved in the maintenance of an internal steady st
comment: This term was made obsolete because it has been split.
synonym: "di-, tri-valent inorganic cation homeostasis" EXACT []
is_obsolete: true
-consider: GO:0072507
-consider: GO:0072508
+consider: GO:0055080
[Term]
id: GO:0055067
-name: monovalent inorganic cation homeostasis
+name: obsolete monovalent inorganic cation homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of monovalent inorganic cations within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
-is_a: GO:0055080 ! cation homeostasis
-is_a: GO:0098771 ! inorganic ion homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of monovalent inorganic cations within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0055080
[Term]
id: GO:0055068
@@ -326777,16 +326680,19 @@ name: cobalt ion homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of cobalt ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
synonym: "cobalt homeostasis" BROAD []
-is_a: GO:0055076 ! transition metal ion homeostasis
+is_a: GO:0055080 ! monoatomic cation homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0055069
-name: zinc ion homeostasis
+name: obsolete zinc ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of zinc ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of zinc ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
+comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent. For homeostasis terms, we would like to specify whether the homeostasis takes place intracellularly or at the level of the organism.
synonym: "zinc homeostasis" BROAD []
-is_a: GO:0055076 ! transition metal ion homeostasis
-is_a: GO:0072507 ! divalent inorganic cation homeostasis
+is_obsolete: true
+consider: GO:0006882
+consider: GO:0180002
[Term]
id: GO:0055070
@@ -326794,7 +326700,8 @@ name: copper ion homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of copper ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
synonym: "copper homeostasis" BROAD []
-is_a: GO:0055076 ! transition metal ion homeostasis
+is_a: GO:0055080 ! monoatomic cation homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0055071
@@ -326802,24 +326709,29 @@ name: manganese ion homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of manganese ions within an organism or cell." [GOC:jid, GOC:mah]
synonym: "manganese homeostasis" BROAD []
-is_a: GO:0055076 ! transition metal ion homeostasis
+is_a: GO:0055080 ! monoatomic cation homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0055072
-name: iron ion homeostasis
+name: obsolete iron ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "iron homeostasis" BROAD []
-is_a: GO:0055076 ! transition metal ion homeostasis
+is_obsolete: true
+consider: GO:0006879
+consider: GO:0060586
[Term]
id: GO:0055073
-name: cadmium ion homeostasis
+name: obsolete cadmium ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of cadmium ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of cadmium ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
+comment: This term was obsoleted because it is not a normal process.
synonym: "cadmium homeostasis" EXACT []
-is_a: GO:0055076 ! transition metal ion homeostasis
-is_a: GO:0072507 ! divalent inorganic cation homeostasis
+is_obsolete: true
+consider: GO:0071585
[Term]
id: GO:0055074
@@ -326827,23 +326739,25 @@ name: calcium ion homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell." [GOC:ceb, GOC:jid, GOC:mah]
synonym: "regulation of calcium ion concentration" EXACT []
-is_a: GO:0055065 ! metal ion homeostasis
-is_a: GO:0072507 ! divalent inorganic cation homeostasis
+is_a: GO:0055080 ! monoatomic cation homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0055075
name: potassium ion homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of potassium ions within an organism or cell." [GOC:jid, GOC:mah]
-is_a: GO:0055065 ! metal ion homeostasis
-is_a: GO:0055067 ! monovalent inorganic cation homeostasis
+is_a: GO:0055080 ! monoatomic cation homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0055076
-name: transition metal ion homeostasis
+name: obsolete transition metal ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of transition metal ions within an organism or cell. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver." [GOC:jid, GOC:mah, ISBN:0198506732]
-is_a: GO:0055065 ! metal ion homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of transition metal ions within an organism or cell. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver." [GOC:jid, GOC:mah, ISBN:0198506732]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+consider: GO:0030003
[Term]
id: GO:0055077
@@ -326859,46 +326773,52 @@ id: GO:0055078
name: sodium ion homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of sodium ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
-is_a: GO:0055065 ! metal ion homeostasis
-is_a: GO:0055067 ! monovalent inorganic cation homeostasis
+is_a: GO:0055080 ! monoatomic cation homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0055079
-name: aluminum ion homeostasis
+name: obsolete aluminum ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of aluminum ions within an organism or cell." [GOC:jid, GOC:lr, GOC:mah]
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of aluminum ions within an organism or cell." [GOC:jid, GOC:lr, GOC:mah]
+comment: This term was obsoleted because this process is not believed to exist.
synonym: "aluminium ion homeostasis" EXACT [GOC:mah]
-is_a: GO:0055065 ! metal ion homeostasis
+is_obsolete: true
+replaced_by: GO:0140982
[Term]
id: GO:0055080
-name: cation homeostasis
+name: monoatomic cation homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of cations within an organism or cell." [GOC:ceb, GOC:jid, GOC:mah]
-is_a: GO:0050801 ! ion homeostasis
+def: "Any process involved in the maintenance of an internal steady state of monoatomic cations within an organism or cell. Monatomic cations (also called simple cations) are cations consisting of exactly one atom." [GOC:ceb, GOC:jid, GOC:mah]
+synonym: "cation homeostasis" BROAD []
+is_a: GO:0050801 ! monoatomic ion homeostasis
[Term]
id: GO:0055081
-name: anion homeostasis
+name: monoatomic anion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of anions within an organism or cell." [GOC:ceb, GOC:jid, GOC:mah]
-is_a: GO:0050801 ! ion homeostasis
+def: "Any process involved in the maintenance of an internal steady state of monoatomic anions within an organism or cell. Monatomic anions (also called simple anions) are anions consisting of exactly one atom." [GOC:ceb, GOC:jid, GOC:mah]
+synonym: "anion homeostasis" BROAD []
+is_a: GO:0050801 ! monoatomic ion homeostasis
[Term]
id: GO:0055082
-name: cellular chemical homeostasis
+name: intracellular chemical homeostasis
namespace: biological_process
-def: "Any biological process involved in the maintenance of an internal steady state of a chemical at the level of the cell." [GOC:isa_complete, GOC:jid]
+def: "A homeostatic process involved in the maintenance of a steady state level of a chemical within a cell." [GOC:isa_complete, GOC:jid]
+synonym: "cellular chemical homeostasis" EXACT []
is_a: GO:0019725 ! cellular homeostasis
is_a: GO:0048878 ! chemical homeostasis
[Term]
id: GO:0055083
-name: monovalent inorganic anion homeostasis
+name: obsolete monovalent inorganic anion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of monovalent inorganic anions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
-is_a: GO:0055081 ! anion homeostasis
-is_a: GO:0098771 ! inorganic ion homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of monovalent inorganic anions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0055081
[Term]
id: GO:0055085
@@ -326926,6 +326846,7 @@ subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED []
synonym: "nucleobase, nucleoside and nucleotide metabolism" EXACT []
is_a: GO:0006139 ! nucleobase-containing compound metabolic process
@@ -326999,7 +326920,7 @@ is_a: GO:0010243 ! response to organonitrogen compound
id: GO:0055095
name: lipoprotein particle mediated signaling
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of a lipoprotein particle." [GOC:BHF, GOC:rl]
+def: "The series of molecular signals mediated by the detection of a lipoprotein particle." [GOC:BHF, GOC:rl]
synonym: "lipoprotein mediated signalling" EXACT []
synonym: "lipoprotein particle mediated signal transduction" EXACT [GOC:signaling]
synonym: "lipoprotein particle-mediated signaling" EXACT []
@@ -327010,7 +326931,7 @@ relationship: part_of GO:0071402 ! cellular response to lipoprotein particle sti
id: GO:0055096
name: low-density lipoprotein particle mediated signaling
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of low-density lipoprotein particle." [GOC:BHF, GOC:rl, PMID:16013438]
+def: "The series of molecular signals mediated by the detection of low-density lipoprotein particle." [GOC:BHF, GOC:rl, PMID:16013438]
synonym: "low-density lipoprotein mediated signalling" EXACT []
synonym: "low-density lipoprotein particle mediated signal transduction" EXACT [GOC:signaling]
synonym: "low-density lipoprotein particle-mediated signaling" EXACT []
@@ -327021,7 +326942,7 @@ relationship: part_of GO:0071404 ! cellular response to low-density lipoprotein
id: GO:0055097
name: high density lipoprotein particle mediated signaling
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of high density lipoprotein particle." [GOC:BHF, GOC:rl]
+def: "The series of molecular signals mediated by the detection of high density lipoprotein particle." [GOC:BHF, GOC:rl]
synonym: "high density lipoprotein mediated signalling" EXACT []
synonym: "high density lipoprotein particle mediated signal transduction" EXACT [GOC:signaling]
synonym: "high density lipoprotein particle-mediated signaling" EXACT []
@@ -327311,7 +327232,6 @@ namespace: biological_process
def: "The directed movement of copper ions out of a cell or organelle." [GOC:dph]
synonym: "copper export" EXACT [GOC:dph]
is_a: GO:0035434 ! copper ion transmembrane transport
-is_a: GO:0070839 ! metal ion export
[Term]
id: GO:0060004
@@ -327890,8 +327810,8 @@ synonym: "Wnt receptor signaling pathway, regulating spindle positioning" EXACT
synonym: "Wnt receptor signalling pathway, regulating spindle positioning" EXACT []
synonym: "Wnt-activated signaling pathway, regulating spindle positioning" EXACT [GOC:signaling]
is_a: GO:0010564 ! regulation of cell cycle process
+is_a: GO:0032879 ! regulation of localization
is_a: GO:0035567 ! non-canonical Wnt signaling pathway
-is_a: GO:0060341 ! regulation of cellular localization
is_a: GO:0070507 ! regulation of microtubule cytoskeleton organization
relationship: regulates GO:0040001 ! establishment of mitotic spindle localization
@@ -328100,6 +328020,7 @@ def: "A compound molecular function in which an effector function is controlled
subset: gocheck_do_not_manually_annotate
subset: goslim_generic
subset: goslim_pir
+subset: prokaryote_subset
is_a: GO:0003674 ! molecular_function
[Term]
@@ -328111,6 +328032,7 @@ def: "The binding activity of a molecule that brings together two or more molecu
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
+subset: prokaryote_subset
synonym: "binding, bridging" EXACT []
synonym: "protein complex scaffold activity" RELATED []
synonym: "protein-containing complex scaffold activity" RELATED []
@@ -328194,7 +328116,6 @@ id: GO:0060099
name: regulation of phagocytosis, engulfment
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis." [GOC:dph]
-is_a: GO:0030100 ! regulation of endocytosis
is_a: GO:0050764 ! regulation of phagocytosis
is_a: GO:1905153 ! regulation of membrane invagination
relationship: regulates GO:0006911 ! phagocytosis, engulfment
@@ -328204,7 +328125,6 @@ id: GO:0060100
name: positive regulation of phagocytosis, engulfment
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis." [GOC:dph]
-is_a: GO:0045807 ! positive regulation of endocytosis
is_a: GO:0050766 ! positive regulation of phagocytosis
is_a: GO:0060099 ! regulation of phagocytosis, engulfment
is_a: GO:1905155 ! positive regulation of membrane invagination
@@ -328215,7 +328135,6 @@ id: GO:0060101
name: negative regulation of phagocytosis, engulfment
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis." [GOC:dph]
-is_a: GO:0045806 ! negative regulation of endocytosis
is_a: GO:0050765 ! negative regulation of phagocytosis
is_a: GO:0060099 ! regulation of phagocytosis, engulfment
is_a: GO:1905154 ! negative regulation of membrane invagination
@@ -328513,6 +328432,7 @@ synonym: "thyrotrope development" EXACT []
synonym: "thyrotroph development" EXACT []
synonym: "TSH-secreting cell development" EXACT []
is_a: GO:0002068 ! glandular epithelial cell development
+is_a: GO:0048666 ! neuron development
relationship: part_of GO:0060129 ! thyroid-stimulating hormone-secreting cell differentiation
[Term]
@@ -328603,15 +328523,6 @@ is_a: GO:0048609 ! multicellular organismal reproductive process
relationship: part_of GO:0007567 ! parturition
relationship: part_of GO:0009792 ! embryo development ending in birth or egg hatching
-[Term]
-id: GO:0060139
-name: positive regulation of apoptotic process by virus
-namespace: biological_process
-def: "Any viral process that activates or increases the frequency, rate or extent of cell death by apoptotic process." [GOC:dph, GOC:mtg_apoptosis]
-synonym: "positive regulation of apoptosis by virus" NARROW []
-is_a: GO:0039526 ! modulation by virus of host apoptotic process
-is_a: GO:0052151 ! positive regulation by symbiont of host apoptotic process
-
[Term]
id: GO:0060140
name: modulation by virus of syncytium formation via plasma membrane fusion
@@ -328667,30 +328578,33 @@ is_obsolete: true
[Term]
id: GO:0060147
-name: regulation of posttranscriptional gene silencing
+name: regulation of post-transcriptional gene silencing
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism." [GOC:dph]
+synonym: "regulation of posttranscriptional gene silencing" EXACT []
is_a: GO:0010468 ! regulation of gene expression
-relationship: regulates GO:0016441 ! posttranscriptional gene silencing
+relationship: regulates GO:0016441 ! post-transcriptional gene silencing
[Term]
id: GO:0060148
-name: positive regulation of posttranscriptional gene silencing
+name: positive regulation of post-transcriptional gene silencing
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism." [GOC:dph]
+synonym: "positive regulation of posttranscriptional gene silencing" EXACT []
is_a: GO:0048518 ! positive regulation of biological process
-is_a: GO:0060147 ! regulation of posttranscriptional gene silencing
-relationship: positively_regulates GO:0016441 ! posttranscriptional gene silencing
+is_a: GO:0060147 ! regulation of post-transcriptional gene silencing
+relationship: positively_regulates GO:0016441 ! post-transcriptional gene silencing
[Term]
id: GO:0060149
-name: negative regulation of posttranscriptional gene silencing
+name: negative regulation of post-transcriptional gene silencing
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism." [GOC:dph]
+synonym: "negative regulation of posttranscriptional gene silencing" EXACT []
is_a: GO:0010628 ! positive regulation of gene expression
is_a: GO:0048519 ! negative regulation of biological process
-is_a: GO:0060147 ! regulation of posttranscriptional gene silencing
-relationship: negatively_regulates GO:0016441 ! posttranscriptional gene silencing
+is_a: GO:0060147 ! regulation of post-transcriptional gene silencing
+relationship: negatively_regulates GO:0016441 ! post-transcriptional gene silencing
[Term]
id: GO:0060151
@@ -328763,7 +328677,7 @@ relationship: part_of GO:0072001 ! renal system development
id: GO:0060158
name: phospholipase C-activating dopamine receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a dopamine receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent release of inositol trisphosphate (IP3) and diacylglycerol (DAG)." [GOC:dph, GOC:signaling, GOC:tb, PMID:12675914]
+def: "A phospholipase C-activating receptor G protein-coupled receptor signaling pathway initiated by dopamine binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:dph, GOC:signaling, GOC:tb, PMID:12675914]
synonym: "activation of phospholipase C activity by dopamine receptor signaling pathway" RELATED [GOC:signaling]
synonym: "activation of phospholipase C activity by dopamine receptor signalling pathway" RELATED [GOC:mah]
synonym: "dopamine receptor, phospholipase C activating pathway" RELATED [GOC:dph, GOC:tb]
@@ -328926,13 +328840,13 @@ relationship: part_of GO:0035108 ! limb morphogenesis
[Term]
id: GO:0060175
-name: brain-derived neurotrophic factor-activated receptor activity
+name: brain-derived neurotrophic factor receptor activity
namespace: molecular_function
def: "Combining with a brain-derived neurotrophic factor and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:bf, GOC:dph]
comment: Note that this term represents an activity and not a gene product, and should only be used when the receptor binds the ligand BDNF. For receptors that bind other growth factors, consider annotating to other terms under 'transmembrane signaling receptor activity ; GO:0004888.
synonym: "BDNF receptor activity" RELATED [GOC:dph]
synonym: "BDNF-activated receptor activity" EXACT [GOC:bf, GOC:signaling]
-synonym: "brain-derived neurotrophic factor receptor activity" EXACT [GOC:bf, GOC:signaling]
+synonym: "brain-derived neurotrophic factor-activated receptor activity" EXACT []
is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity
is_a: GO:0005030 ! neurotrophin receptor activity
@@ -328989,7 +328903,7 @@ is_a: GO:0008528 ! G protein-coupled peptide receptor activity
id: GO:0060183
name: apelin receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of an apelin receptor binding to one of its physiological ligands." [GOC:dph]
+def: "A G protein-coupled receptor signaling pathway initiated by apelin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:dph]
synonym: "apelin receptor signalling pathway" EXACT [GOC:mah]
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -329084,7 +328998,7 @@ id: GO:0060194
name: regulation of antisense RNA transcription
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA." [GOC:dph, GOC:jp, GOC:tb, PMID:18075583]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0140747 ! regulation of ncRNA transcription
relationship: regulates GO:0009300 ! antisense RNA transcription
[Term]
@@ -329092,7 +329006,7 @@ id: GO:0060195
name: negative regulation of antisense RNA transcription
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA." [GOC:dph, GOC:tb, PMID:18075583]
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
is_a: GO:0060194 ! regulation of antisense RNA transcription
relationship: negatively_regulates GO:0009300 ! antisense RNA transcription
@@ -329101,7 +329015,7 @@ id: GO:0060196
name: positive regulation of antisense RNA transcription
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA." [GOC:dph, GOC:tb, PMID:18075583]
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
is_a: GO:0060194 ! regulation of antisense RNA transcription
relationship: positively_regulates GO:0009300 ! antisense RNA transcription
@@ -329405,7 +329319,7 @@ relationship: part_of GO:0060220 ! camera-type eye photoreceptor cell fate commi
id: GO:0060228
name: phosphatidylcholine-sterol O-acyltransferase activator activity
namespace: molecular_function
-def: "Increases the activity of phosphatidylcholine-sterol O-acyltransferase, an enzyme that converts cholesterol and phosphatidylcholine (lecithins) to cholesteryl esters and lyso-phosphatidylcholines." [GOC:BHF, GOC:dph, GOC:tb, PMID:4335615]
+def: "Binds to and increases the activity of phosphatidylcholine-sterol O-acyltransferase." [GOC:BHF, GOC:dph, GOC:tb, PMID:4335615]
synonym: "LCAT activator activity" NARROW [GOC:tb]
is_a: GO:0008047 ! enzyme activator activity
@@ -329486,26 +329400,28 @@ relationship: regulates GO:0031505 ! fungal-type cell wall organization
id: GO:0060238
name: regulation of signal transduction involved in conjugation with cellular fusion
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of pheromone-dependent signal transduction during conjugation with cellular fusion, the series of molecular signals that bring about the relay, amplification or dampening of a signal generated in response to a cue, such as starvation or pheromone exposure, in organisms that undergo conjugation with cellular fusion." [GOC:dph, GOC:tb]
+def: "Any process that modulates the rate, frequency or extent of pheromone-dependent signal transduction during conjugation with cellular fusion." [GOC:dph, GOC:tb]
is_a: GO:0009966 ! regulation of signal transduction
is_a: GO:0031137 ! regulation of conjugation with cellular fusion
+is_a: GO:2000241 ! regulation of reproductive process
relationship: regulates GO:0032005 ! signal transduction involved in positive regulation of conjugation with cellular fusion
[Term]
id: GO:0060239
name: positive regulation of signal transduction involved in conjugation with cellular fusion
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of the series of molecular signals that bring about the relay, amplification or dampening of a signal generated in response to a cue, such as starvation or pheromone exposure, in organisms that undergo conjugation with cellular fusion." [GOC:dph, GOC:tb]
+def: "Any process that increases the rate, frequency or extent of signal transduction involved in conjugation with cellular fusion." [GOC:dph, GOC:tb]
is_a: GO:0009967 ! positive regulation of signal transduction
is_a: GO:0031139 ! positive regulation of conjugation with cellular fusion
is_a: GO:0060238 ! regulation of signal transduction involved in conjugation with cellular fusion
+is_a: GO:2000243 ! positive regulation of reproductive process
relationship: positively_regulates GO:0032005 ! signal transduction involved in positive regulation of conjugation with cellular fusion
[Term]
id: GO:0060240
name: negative regulation of signal transduction involved in conjugation with cellular fusion
namespace: biological_process
-def: "Any process that decreases the rate, frequency or extent of the series of molecular signals that bring about the relay, amplification or dampening of a signal generated in response to a cue, such as starvation or pheromone exposure, in organisms that undergo conjugation with cellular fusion." [GOC:dph, GOC:tb]
+def: "Any process that decreases the rate, frequency or extent of the series signal transduction involved in conjugation with cellular fusion." [GOC:dph, GOC:tb]
is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:0060238 ! regulation of signal transduction involved in conjugation with cellular fusion
is_a: GO:2000242 ! negative regulation of reproductive process
@@ -329559,7 +329475,7 @@ name: anatomical structure homeostasis
namespace: biological_process
def: "A homeostatic process involved in the maintenance of an internal steady state within a defined anatomical structure of an organism, including control of cellular proliferation and death and control of metabolic function. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph]
synonym: "anatomical structure maintenance" EXACT [GOC:dph]
-is_a: GO:0042592 ! homeostatic process
+is_a: GO:0048871 ! multicellular organismal-level homeostasis
[Term]
id: GO:0060250
@@ -329658,22 +329574,24 @@ relationship: regulates GO:0007631 ! feeding behavior
[Term]
id: GO:0060260
-name: regulation of transcription initiation from RNA polymerase II promoter
+name: regulation of transcription initiation by RNA polymerase II
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter." [GOC:dph, GOC:tb, GOC:txnOH]
+synonym: "regulation of transcription initiation from RNA polymerase II promoter" EXACT []
is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-is_a: GO:2000142 ! regulation of DNA-templated transcription, initiation
-relationship: regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter
+is_a: GO:2000142 ! regulation of DNA-templated transcription initiation
+relationship: regulates GO:0006367 ! transcription initiation at RNA polymerase II promoter
[Term]
id: GO:0060261
-name: positive regulation of transcription initiation from RNA polymerase II promoter
+name: positive regulation of transcription initiation by RNA polymerase II
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter." [GOC:dph, GOC:tb, GOC:txnOH]
+synonym: "positive regulation of transcription initiation from RNA polymerase II promoter" EXACT []
is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
-is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter
-is_a: GO:2000144 ! positive regulation of DNA-templated transcription, initiation
-relationship: positively_regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter
+is_a: GO:0060260 ! regulation of transcription initiation by RNA polymerase II
+is_a: GO:2000144 ! positive regulation of DNA-templated transcription initiation
+relationship: positively_regulates GO:0006367 ! transcription initiation at RNA polymerase II promoter
[Term]
id: GO:0060262
@@ -329757,14 +329675,14 @@ id: GO:0060269
name: centripetally migrating follicle cell migration
namespace: biological_process
def: "The cell migration process in which a follicle cell migrates as part of an epithelial sheet between the nurse cells and the oocyte. At the end of migration, they cover the anterior of the oocyte." [GOC:dph]
-is_a: GO:0007297 ! ovarian follicle cell migration
+is_a: GO:0007297 ! follicle cell of egg chamber migration
[Term]
id: GO:0060270
name: main body follicle cell migration
namespace: biological_process
def: "The ovarian follicle cell migration process in which follicle cells migrate posteriorly to form a columnar epithelium over the oocyte." [GOC:dph]
-is_a: GO:0007297 ! ovarian follicle cell migration
+is_a: GO:0007297 ! follicle cell of egg chamber migration
[Term]
id: GO:0060271
@@ -329804,7 +329722,7 @@ id: GO:0060274
name: maintenance of stationary phase
namespace: biological_process
def: "The homeostatic process in which a population of cells changes its metabolic activity resulting in the rate of death in the population equaling the rate of reproduction. Stationary phase can be in response to limited nutrients or a build-up of toxic substances in the environment." [GOC:dph]
-is_a: GO:0044764 ! multi-organism cellular process
+is_a: GO:0019725 ! cellular homeostasis
[Term]
id: GO:0060275
@@ -330077,11 +329995,12 @@ is_a: GO:1900121 ! negative regulation of receptor binding
[Term]
id: GO:0060303
-name: regulation of nucleosome density
+name: obsolete regulation of nucleosome density
namespace: biological_process
-def: "Any process that modulates the number of nucleosomes in a given region of a chromosome." [GOC:dph, GOC:tb]
-is_a: GO:0034728 ! nucleosome organization
-is_a: GO:0065008 ! regulation of biological quality
+def: "OBSOLETE. Any process that modulates the number of nucleosomes in a given region of a chromosome." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it represents a readout and in some cases a phenotype, and the term can be misconstrued for chromatin compaction.
+is_obsolete: true
+consider: GO:0140750
[Term]
id: GO:0060304
@@ -330107,8 +330026,8 @@ id: GO:0060306
name: regulation of membrane repolarization
namespace: biological_process
def: "Any process that modulates the establishment or extent of a membrane potential in the polarizing direction towards the resting potential, usually from positive to negative." [GOC:BHF, GOC:dph, GOC:mtg_cardiac_conduct_nov11, GOC:tb]
-is_a: GO:0034765 ! regulation of ion transmembrane transport
is_a: GO:0042391 ! regulation of membrane potential
+is_a: GO:0050789 ! regulation of biological process
relationship: regulates GO:0086009 ! membrane repolarization
[Term]
@@ -330150,7 +330069,6 @@ def: "Any process that modulates the rate, frequency or extent of elastin catabo
synonym: "regulation of elastin breakdown" RELATED [GOC:dph, GOC:tb]
synonym: "regulation of elastin catabolism" EXACT [GOC:dph, GOC:tb]
synonym: "regulation of elastin degradation" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0031329 ! regulation of cellular catabolic process
is_a: GO:0042176 ! regulation of protein catabolic process
is_a: GO:1903018 ! regulation of glycoprotein metabolic process
relationship: regulates GO:0060309 ! elastin catabolic process
@@ -330164,7 +330082,6 @@ synonym: "down-regulation of elastin catabolic process" EXACT []
synonym: "negative regulation of elastin breakdown" EXACT []
synonym: "negative regulation of elastin catabolism" EXACT []
synonym: "negative regulation of elastin degradation" EXACT []
-is_a: GO:0031330 ! negative regulation of cellular catabolic process
is_a: GO:0042177 ! negative regulation of protein catabolic process
is_a: GO:0060310 ! regulation of elastin catabolic process
is_a: GO:1903019 ! negative regulation of glycoprotein metabolic process
@@ -330255,17 +330172,21 @@ relationship: part_of GO:0060215 ! primitive hemopoiesis
id: GO:0060320
name: rejection of self pollen
namespace: biological_process
-def: "The process, involving the sharing and interaction of the single locus incompatibility haplotypes, involved in the rejection of the self pollen by cells in the stigma." [GOC:dph, GOC:tb]
+def: "The recognition and rejection of self pollen by cells in the stigma, mediated by the sharing and interaction of the single locus incompatibility haplotypes." [GOC:dph, GOC:tb, PMID:34848142]
+synonym: "self-incompatibility" RELATED []
is_a: GO:0048544 ! recognition of pollen
[Term]
id: GO:0060321
name: acceptance of pollen
namespace: biological_process
-def: "The process, involving the sharing and interaction of the single locus incompatibility haplotypes, involved in the acceptance of pollen by cells in the stigma." [GOC:dph, GOC:tb]
+def: "The recognition and acceptance of pollen by cells in the stigma, mediated by the sharing and interaction of the single locus incompatibility haplotypes." [GOC:dph, GOC:tb]
synonym: "acceptance of non-self pollen" RELATED [GOC:dph, GOC:tb]
synonym: "acceptance of self pollen" NARROW [GOC:dph, GOC:tb]
+synonym: "self-compatibility" RELATED []
+is_a: GO:0022414 ! reproductive process
is_a: GO:0048544 ! recognition of pollen
+relationship: part_of GO:0009875 ! pollen-pistil interaction
[Term]
id: GO:0060322
@@ -330335,144 +330256,143 @@ is_a: GO:0060327 ! cytoplasmic actin-based contraction involved in cell motility
[Term]
id: GO:0060330
-name: regulation of response to interferon-gamma
+name: regulation of response to type II interferon
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of a response to interferon-gamma. Response to interferon gamma is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus." [GOC:dph]
+def: "Any process that modulates the rate, frequency or extent of a response to type II interferon (interferon-gamma). Response to interferon gamma is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus." [GOC:dph]
synonym: "regulation of response to gamma-interferon" RELATED []
synonym: "regulation of response to immune interferon" EXACT []
-synonym: "regulation of response to type II IFN" BROAD []
-synonym: "regulation of response to type II interferon" BROAD []
+synonym: "regulation of response to interferon-gamma" BROAD []
+synonym: "regulation of response to type II IFN" EXACT []
is_a: GO:0045088 ! regulation of innate immune response
is_a: GO:0060759 ! regulation of response to cytokine stimulus
-relationship: regulates GO:0034341 ! response to interferon-gamma
+relationship: regulates GO:0034341 ! response to type II interferon
[Term]
id: GO:0060331
-name: negative regulation of response to interferon-gamma
+name: negative regulation of response to type II interferon
namespace: biological_process
-def: "Any process that decreases the rate, frequency or extent of a response to interferon-gamma. Response to interferon gamma is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus." [GOC:dph]
+def: "Any process that decreases the rate, frequency or extent of a response to type II interferon (interferon-gamma). Response to interferon gamma is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus." [GOC:dph]
synonym: "negative regulation of response to gamma-interferon" RELATED []
synonym: "negative regulation of response to immune interferon" EXACT []
+synonym: "negative regulation of response to interferon-gamma" EXACT []
synonym: "negative regulation of response to type II IFN" BROAD []
-synonym: "negative regulation of response to type II interferon" BROAD []
is_a: GO:0045824 ! negative regulation of innate immune response
-is_a: GO:0060330 ! regulation of response to interferon-gamma
+is_a: GO:0060330 ! regulation of response to type II interferon
is_a: GO:0060761 ! negative regulation of response to cytokine stimulus
-relationship: negatively_regulates GO:0034341 ! response to interferon-gamma
+relationship: negatively_regulates GO:0034341 ! response to type II interferon
[Term]
id: GO:0060332
-name: positive regulation of response to interferon-gamma
+name: positive regulation of response to type II interferon
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of a response to interferon-gamma. Response to interferon gamma is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus." [GOC:dph]
+def: "Any process that increases the rate, frequency or extent of a response to type II interferon (interferon-gamma). Response to interferon gamma is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus." [GOC:dph]
synonym: "positive regulation of response to gamma-interferon" RELATED []
synonym: "positive regulation of response to immune interferon" EXACT []
+synonym: "positive regulation of response to interferon-gamma" EXACT []
synonym: "positive regulation of response to type II IFN" BROAD []
-synonym: "positive regulation of response to type II interferon" BROAD []
is_a: GO:0045089 ! positive regulation of innate immune response
-is_a: GO:0060330 ! regulation of response to interferon-gamma
+is_a: GO:0060330 ! regulation of response to type II interferon
is_a: GO:0060760 ! positive regulation of response to cytokine stimulus
-relationship: positively_regulates GO:0034341 ! response to interferon-gamma
+relationship: positively_regulates GO:0034341 ! response to type II interferon
[Term]
id: GO:0060333
-name: interferon-gamma-mediated signaling pathway
+name: type II interferon-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far." [GOC:add, GOC:dph, GOC:signaling]
+def: "The series of molecular signals initiated by interferon-gamma binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far." [GOC:add, GOC:dph, GOC:signaling, PMID:28901902]
synonym: "gamma-interferon-mediated signaling pathway" EXACT [GOC:dph]
synonym: "immune interferon signaling pathway" EXACT [GOC:dph]
+synonym: "interferon-gamma-mediated signaling pathway" EXACT []
synonym: "interferon-gamma-mediated signalling pathway" EXACT [GOC:mah]
-synonym: "type II IFN-mediated signaling pathway" BROAD []
-synonym: "type II interferon-mediated signaling pathway" BROAD [GOC:dph]
-is_a: GO:0019221 ! cytokine-mediated signaling pathway
-relationship: part_of GO:0071346 ! cellular response to interferon-gamma
+synonym: "type II IFN-mediated signaling pathway" EXACT []
+is_a: GO:0140888 ! interferon-mediated signaling pathway
+relationship: part_of GO:0071346 ! cellular response to type II interferon
[Term]
id: GO:0060334
-name: regulation of interferon-gamma-mediated signaling pathway
+name: regulation of type II interferon-mediated signaling pathway
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor." [GOC:dph]
+def: "Any process that modulates the rate, frequency or extent of an interferon-gamma-mediated signaling pathway." [GOC:dph]
synonym: "regulation of gamma-interferon-mediated signaling pathway" RELATED [GOC:dph]
synonym: "regulation of immune interferon signaling pathway" EXACT [GOC:dph]
+synonym: "regulation of interferon-gamma-mediated signaling pathway" EXACT []
synonym: "regulation of interferon-gamma-mediated signalling pathway" EXACT [GOC:mah]
synonym: "regulation of type II IFN-mediated signaling pathway" BROAD [GOC:dph]
-synonym: "regulation of type II interferon-mediated signaling pathway" BROAD [GOC:dph]
is_a: GO:0001959 ! regulation of cytokine-mediated signaling pathway
-is_a: GO:0060330 ! regulation of response to interferon-gamma
-relationship: regulates GO:0060333 ! interferon-gamma-mediated signaling pathway
+is_a: GO:0060330 ! regulation of response to type II interferon
+relationship: regulates GO:0060333 ! type II interferon-mediated signaling pathway
[Term]
id: GO:0060335
-name: positive regulation of interferon-gamma-mediated signaling pathway
+name: positive regulation of type II interferon-mediated signaling pathway
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor." [GOC:dph]
+def: "Any process that increases the rate, frequency or extent of an interferon-gamma-mediated signaling pathway." [GOC:dph]
synonym: "positive regulation of gamma-interferon-mediated signaling pathway" RELATED [GOC:dph]
synonym: "positive regulation of immune interferon-mediated signaling pathway" EXACT [GOC:dph]
+synonym: "positive regulation of interferon-gamma-mediated signaling pathway" BROAD [GOC:dph]
synonym: "positive regulation of interferon-gamma-mediated signalling pathway" EXACT [GOC:mah]
synonym: "positive regulation of type II IFN-mediated pathway" BROAD [GOC:dph]
-synonym: "positive regulation of type II interferon-mediated signaling pathway" BROAD [GOC:dph]
is_a: GO:0001961 ! positive regulation of cytokine-mediated signaling pathway
-is_a: GO:0060332 ! positive regulation of response to interferon-gamma
-is_a: GO:0060334 ! regulation of interferon-gamma-mediated signaling pathway
-relationship: positively_regulates GO:0060333 ! interferon-gamma-mediated signaling pathway
+is_a: GO:0060332 ! positive regulation of response to type II interferon
+is_a: GO:0060334 ! regulation of type II interferon-mediated signaling pathway
+relationship: positively_regulates GO:0060333 ! type II interferon-mediated signaling pathway
[Term]
id: GO:0060336
-name: negative regulation of interferon-gamma-mediated signaling pathway
+name: negative regulation of type II interferon-mediated signaling pathway
namespace: biological_process
-def: "Any process that decreases the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor." [GOC:dph]
+def: "Any process that decreases the rate, frequency or extent of an interferon-gamma-mediated signaling pathway." [GOC:dph]
synonym: "negative regulation of gamma-interferon-mediated signaling pathway" RELATED [GOC:dph]
synonym: "negative regulation of immune interferon-mediated signaling pathway" EXACT [GOC:dph]
+synonym: "negative regulation of interferon-gamma-mediated signaling pathway" BROAD [GOC:dph]
synonym: "negative regulation of interferon-gamma-mediated signalling pathway" EXACT [GOC:mah]
synonym: "negative regulation of type II IFN-mediated signaling pathway" BROAD [GOC:dph]
-synonym: "negative regulation of type II interferon-mediated signaling pathway" BROAD [GOC:dph]
is_a: GO:0001960 ! negative regulation of cytokine-mediated signaling pathway
-is_a: GO:0060331 ! negative regulation of response to interferon-gamma
-is_a: GO:0060334 ! regulation of interferon-gamma-mediated signaling pathway
-relationship: negatively_regulates GO:0060333 ! interferon-gamma-mediated signaling pathway
+is_a: GO:0060331 ! negative regulation of response to type II interferon
+is_a: GO:0060334 ! regulation of type II interferon-mediated signaling pathway
+relationship: negatively_regulates GO:0060333 ! type II interferon-mediated signaling pathway
[Term]
id: GO:0060337
-name: type I interferon signaling pathway
+name: type I interferon-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." [GOC:add, GOC:dph, GOC:signaling]
+def: "The series of molecular signals initiated by type I interferon binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." [GOC:add, GOC:dph, GOC:signaling, PMID:32464097]
+synonym: "type I interferon signaling pathway" EXACT []
synonym: "type I interferon-activated signaling pathway" EXACT [GOC:signaling]
-synonym: "type I interferon-mediated signaling pathway" RELATED [GOC:signaling]
-synonym: "type I interferon-mediated signalling pathway" EXACT [GOC:mah]
-is_a: GO:0019221 ! cytokine-mediated signaling pathway
+is_a: GO:0140888 ! interferon-mediated signaling pathway
relationship: part_of GO:0071357 ! cellular response to type I interferon
[Term]
id: GO:0060338
name: regulation of type I interferon-mediated signaling pathway
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor." [GOC:dph]
+def: "Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway." [GOC:dph]
synonym: "regulation of type I interferon-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0001959 ! regulation of cytokine-mediated signaling pathway
is_a: GO:0045088 ! regulation of innate immune response
-relationship: regulates GO:0060337 ! type I interferon signaling pathway
+relationship: regulates GO:0060337 ! type I interferon-mediated signaling pathway
[Term]
id: GO:0060339
name: negative regulation of type I interferon-mediated signaling pathway
namespace: biological_process
-def: "Any process that decreases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor." [GOC:dph]
+def: "Any process that decreases the rate, frequency or extent of a type I interferon-mediated signaling pathway." [GOC:dph]
synonym: "negative regulation of type I interferon-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0001960 ! negative regulation of cytokine-mediated signaling pathway
is_a: GO:0045824 ! negative regulation of innate immune response
is_a: GO:0060338 ! regulation of type I interferon-mediated signaling pathway
-relationship: negatively_regulates GO:0060337 ! type I interferon signaling pathway
+relationship: negatively_regulates GO:0060337 ! type I interferon-mediated signaling pathway
[Term]
id: GO:0060340
name: positive regulation of type I interferon-mediated signaling pathway
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor." [GOC:dph]
+def: "Any process that increases the rate, frequency or extent of a type I interferon-mediated signaling pathway." [GOC:dph]
synonym: "positive regulation of type I interferon-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0001961 ! positive regulation of cytokine-mediated signaling pathway
is_a: GO:0045089 ! positive regulation of innate immune response
is_a: GO:0060338 ! regulation of type I interferon-mediated signaling pathway
-relationship: positively_regulates GO:0060337 ! type I interferon signaling pathway
+relationship: positively_regulates GO:0060337 ! type I interferon-mediated signaling pathway
[Term]
id: GO:0060341
@@ -330623,8 +330543,6 @@ def: "Any process that modulates the rate, frequency or extent of leucine import
synonym: "regulation of L-leucine import" NARROW [GOC:dph, GOC:tb]
synonym: "regulation of L-leucine uptake" NARROW [GOC:dph, GOC:tb]
synonym: "regulation of leucine uptake" EXACT [GOC:dph, GOC:tb]
-is_a: GO:1903959 ! regulation of anion transmembrane transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
is_a: GO:1905532 ! regulation of leucine import across plasma membrane
relationship: regulates GO:1903801 ! L-leucine import across plasma membrane
@@ -330634,8 +330552,6 @@ name: negative regulation of leucine import
namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of leucine import. Leucine import is the directed movement of leucine into a cell or organelle." [GOC:dph, GOC:tb]
is_a: GO:0060357 ! regulation of leucine import
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
-is_a: GO:1904063 ! negative regulation of cation transmembrane transport
is_a: GO:1905533 ! negative regulation of leucine import across plasma membrane
relationship: negatively_regulates GO:1903801 ! L-leucine import across plasma membrane
@@ -330714,7 +330630,7 @@ is_a: GO:0060363 ! cranial suture morphogenesis
id: GO:0060368
name: regulation of Fc receptor mediated stimulatory signaling pathway
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of the Fc receptor mediated stimulatory signaling pathway. The Fc receptor mediated stimulatory signaling pathway is a series of molecular signals generated as a consequence of a the binding of the Fc portion of an immunoglobulin by an Fc receptor capable of activating or perpetuating an immune response. The Fc portion of an immunoglobulin is its C-terminal constant region." [GOC:dph, GOC:tb]
+def: "Any process that modulates the rate, frequency or extent of the Fc receptor mediated stimulatory signaling pathway.." [GOC:dph, GOC:tb]
synonym: "regulation of Fc receptor mediated stimulatory signalling pathway" EXACT [GOC:mah]
is_a: GO:0009966 ! regulation of signal transduction
is_a: GO:0050776 ! regulation of immune response
@@ -330724,7 +330640,7 @@ relationship: regulates GO:0002431 ! Fc receptor mediated stimulatory signaling
id: GO:0060369
name: positive regulation of Fc receptor mediated stimulatory signaling pathway
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of the Fc receptor mediated stimulatory signaling pathway. The Fc receptor mediated stimulatory signaling pathway is a series of molecular signals generated as a consequence of a the binding of the Fc portion of an immunoglobulin by an Fc receptor capable of activating or perpetuating an immune response. The Fc portion of an immunoglobulin is its C-terminal constant region." [GOC:BHF, GOC:dph, GOC:tb]
+def: "Any process that increases the rate, frequency or extent of the Fc receptor mediated stimulatory signaling pathway." [GOC:BHF, GOC:dph, GOC:tb]
synonym: "positive regulation of Fc receptor mediated stimulatory signalling pathway" EXACT [GOC:mah]
is_a: GO:0009967 ! positive regulation of signal transduction
is_a: GO:0050778 ! positive regulation of immune response
@@ -330811,7 +330727,7 @@ namespace: biological_process
def: "Any process that modulates brood size. Brood size is the number of progeny that survive embryogenesis and are cared for at one time." [GOC:dph, GOC:tb]
is_a: GO:0044706 ! multi-multicellular organism process
is_a: GO:0048609 ! multicellular organismal reproductive process
-is_a: GO:0065008 ! regulation of biological quality
+is_a: GO:0065007 ! biological regulation
[Term]
id: GO:0060379
@@ -330919,7 +330835,7 @@ alt_id: GO:0007184
def: "Any process that modulates the rate, frequency or extent of SMAD protein signal transduction. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways." [GOC:BHF, GOC:dph, GOC:tb]
synonym: "regulation of SMAD protein nuclear translocation" NARROW [GOC:mah]
synonym: "SMAD protein import into nucleus" NARROW []
-is_a: GO:0009966 ! regulation of signal transduction
+is_a: GO:1902531 ! regulation of intracellular signal transduction
relationship: regulates GO:0060395 ! SMAD protein signal transduction
[Term]
@@ -330931,6 +330847,7 @@ synonym: "positive regulation of SMAD protein import into nucleus" NARROW []
synonym: "positive regulation of SMAD protein nuclear translocation" NARROW [GOC:mah]
is_a: GO:0060390 ! regulation of SMAD protein signal transduction
is_a: GO:0090100 ! positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
+is_a: GO:1902533 ! positive regulation of intracellular signal transduction
relationship: positively_regulates GO:0060395 ! SMAD protein signal transduction
[Term]
@@ -330942,6 +330859,7 @@ synonym: "negative regulation of SMAD protein import into nucleus" NARROW []
synonym: "negative regulation of SMAD protein nuclear translocation" NARROW [GOC:mah]
is_a: GO:0060390 ! regulation of SMAD protein signal transduction
is_a: GO:0090101 ! negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
+is_a: GO:1902532 ! negative regulation of intracellular signal transduction
relationship: negatively_regulates GO:0060395 ! SMAD protein signal transduction
[Term]
@@ -330966,8 +330884,8 @@ relationship: negatively_regulates GO:0060389 ! pathway-restricted SMAD protein
id: GO:0060395
name: SMAD protein signal transduction
namespace: biological_process
-def: "The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell." [GOC:BHF, GOC:dph, GOC:tb]
-is_a: GO:0007165 ! signal transduction
+def: "An intracellular signal transduction process that starts with the activation of a SMAD protein, and ultimately effecting a change in the functioning of the cell, for e. g. transcription. SMAD proteins are activated by protein serine/threonine kinase cell surface receptors." [GOC:BHF]
+is_a: GO:0035556 ! intracellular signal transduction
relationship: part_of GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway
[Term]
@@ -331018,21 +330936,13 @@ is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:0060398 ! regulation of growth hormone receptor signaling pathway
relationship: negatively_regulates GO:0060396 ! growth hormone receptor signaling pathway
-[Term]
-id: GO:0060401
-name: cytosolic calcium ion transport
-namespace: biological_process
-def: "The directed movement of calcium ions (Ca2+) into, out of or within the cytosol." [GOC:dph, GOC:tb]
-is_a: GO:0006816 ! calcium ion transport
-
[Term]
id: GO:0060402
name: calcium ion transport into cytosol
namespace: biological_process
def: "The directed movement of calcium ions (Ca2+) into the cytosol." [GOC:dph, GOC:tb]
is_a: GO:0007204 ! positive regulation of cytosolic calcium ion concentration
-is_a: GO:0051649 ! establishment of localization in cell
-is_a: GO:0060401 ! cytosolic calcium ion transport
+is_a: GO:0097553 ! calcium ion transmembrane import into cytosol
[Term]
id: GO:0060404
@@ -331077,7 +330987,8 @@ name: regulation of acetylcholine metabolic process
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues." [GOC:dph, GOC:tb]
is_a: GO:0001505 ! regulation of neurotransmitter levels
-is_a: GO:0033238 ! regulation of cellular amine metabolic process
+is_a: GO:0031323 ! regulation of cellular metabolic process
+is_a: GO:0033238 ! regulation of amine metabolic process
is_a: GO:0080090 ! regulation of primary metabolic process
relationship: regulates GO:0008291 ! acetylcholine metabolic process
@@ -331086,7 +330997,8 @@ id: GO:0060409
name: positive regulation of acetylcholine metabolic process
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues." [GOC:dph, GOC:tb]
-is_a: GO:0033240 ! positive regulation of cellular amine metabolic process
+is_a: GO:0031325 ! positive regulation of cellular metabolic process
+is_a: GO:0033240 ! positive regulation of amine metabolic process
is_a: GO:0060408 ! regulation of acetylcholine metabolic process
relationship: positively_regulates GO:0008291 ! acetylcholine metabolic process
@@ -331095,7 +331007,8 @@ id: GO:0060410
name: negative regulation of acetylcholine metabolic process
namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues." [GOC:dph, GOC:tb]
-is_a: GO:0033239 ! negative regulation of cellular amine metabolic process
+is_a: GO:0031324 ! negative regulation of cellular metabolic process
+is_a: GO:0033239 ! negative regulation of amine metabolic process
is_a: GO:0060408 ! regulation of acetylcholine metabolic process
relationship: negatively_regulates GO:0008291 ! acetylcholine metabolic process
@@ -331611,14 +331524,13 @@ relationship: part_of GO:0007343 ! egg activation
[Term]
id: GO:0060469
-name: positive regulation of transcription involved in egg activation
+name: obsolete positive regulation of transcription involved in egg activation
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of transcription as a part of the process of egg activation." [GOC:dph]
+def: "OBSOLETE. Any process that increases the rate, frequency or extent of transcription as a part of the process of egg activation." [GOC:dph]
+comment: This term was obsoleted because it represents GO-CAM model.
synonym: "activation of the egg genome" RELATED [GOC:dph]
synonym: "activation of the maternal genome" RELATED [GOC:dph]
-is_a: GO:0022414 ! reproductive process
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
-relationship: part_of GO:0007343 ! egg activation
+is_obsolete: true
[Term]
id: GO:0060470
@@ -331673,13 +331585,12 @@ relationship: part_of GO:0048240 ! sperm capacitation
[Term]
id: GO:0060475
-name: positive regulation of actin filament polymerization involved in acrosome reaction
+name: obsolete positive regulation of actin filament polymerization involved in acrosome reaction
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of actin polymerization as part of the acrosome reaction." [GOC:dph]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of actin polymerization as part of the acrosome reaction." [GOC:dph]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
synonym: "positive regulation of actin polymerization involved in acrosome reaction" RELATED [GOC:dph]
-is_a: GO:0022414 ! reproductive process
-is_a: GO:0030838 ! positive regulation of actin filament polymerization
-relationship: part_of GO:0007340 ! acrosome reaction
+is_obsolete: true
[Term]
id: GO:0060476
@@ -331687,9 +331598,9 @@ name: protein localization involved in acrosome reaction
namespace: biological_process
def: "The actin-based process in which a protein is transported to, or maintained in, a specific location in the sperm as part of the acrosome reaction." [GOC:dph]
synonym: "protein localisation involved in acrosome reaction" EXACT [GOC:mah]
+is_a: GO:0008104 ! protein localization
is_a: GO:0022414 ! reproductive process
is_a: GO:0030029 ! actin filament-based process
-is_a: GO:0034613 ! cellular protein localization
relationship: part_of GO:0007340 ! acrosome reaction
[Term]
@@ -332006,11 +331917,11 @@ is_a: GO:0061140 ! lung secretory cell differentiation
[Term]
id: GO:0060511
-name: creation of an inductive signal by a mesenchymal cell involved in lung induction
+name: obsolete creation of an inductive signal by a mesenchymal cell involved in lung induction
namespace: biological_process
-def: "The process in which splanchnic mesenchymal cells send a signal over a short range to endodermal cells inducing them to form the primary lung bud." [GOC:dph, GOC:mtg_lung]
-is_a: GO:0031130 ! creation of an inductive signal
-relationship: part_of GO:0060493 ! mesenchymal-endodermal cell signaling involved in lung induction
+def: "OBSOLETE. The process in which splanchnic mesenchymal cells send a signal over a short range to endodermal cells inducing them to form the primary lung bud." [GOC:dph, GOC:mtg_lung]
+comment: The reason for obsoletion is that the term is not clearly defined and there is no annotations.
+is_obsolete: true
[Term]
id: GO:0060512
@@ -332096,7 +332007,7 @@ relationship: part_of GO:0060516 ! primary prostatic bud elongation
id: GO:0060520
name: activation of prostate induction by androgen receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of an androgen binding to its receptor in the urogenital sinus mesenchyme that initiates prostate induction. Prostate induction is the close range interaction of the urogenital sinus mesenchyme and the urogenital sinus epithelium that causes the cells of the urogenital sinus epithelium to change their fates and specify the development of the prostate gland." [GOC:dph, GOC:tb, PMID:18977204]
+def: "The series of molecular signals initiated by androgen binding to its receptor in the urogenital sinus mesenchyme that initiates prostate induction. Prostate induction is the close range interaction of the urogenital sinus mesenchyme and the urogenital sinus epithelium that causes the cells of the urogenital sinus epithelium to change their fates and specify the development of the prostate gland." [GOC:dph, GOC:tb, PMID:18977204]
synonym: "activation of prostate induction by androgen receptor signalling pathway" EXACT [GOC:mah]
is_a: GO:0010647 ! positive regulation of cell communication
is_a: GO:0023056 ! positive regulation of signaling
@@ -332152,7 +332063,8 @@ id: GO:0060525
name: prostate glandular acinus development
namespace: biological_process
def: "The progression of a glandular acinus of the prostate gland over time, from its initial formation to the mature structure. The glandular acini are the saclike structures of the gland." [GOC:dph, PMID:18977204]
-is_a: GO:0048608 ! reproductive structure development
+is_a: GO:0003006 ! developmental process involved in reproduction
+is_a: GO:0048856 ! anatomical structure development
relationship: part_of GO:0030850 ! prostate gland development
[Term]
@@ -332476,29 +332388,31 @@ consider: GO:1990948
[Term]
id: GO:0060566
-name: positive regulation of DNA-templated transcription, termination
+name: positive regulation of termination of DNA-templated transcription
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of DNA-templated transcription termination, the process in which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA." [GOC:dph, GOC:tb, GOC:txnOH]
synonym: "positive regulation of DNA-dependent transcription, termination" EXACT [GOC:txnOH]
+synonym: "positive regulation of DNA-templated transcription, termination" EXACT []
synonym: "positive regulation of termination of DNA-dependent transcription" EXACT [GOC:jh2]
synonym: "positive regulation of transcription termination, DNA-dependent" EXACT [GOC:jh2]
-is_a: GO:0031554 ! regulation of DNA-templated transcription, termination
+is_a: GO:0031554 ! regulation of termination of DNA-templated transcription
is_a: GO:0043243 ! positive regulation of protein-containing complex disassembly
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
-relationship: positively_regulates GO:0006353 ! DNA-templated transcription, termination
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
+relationship: positively_regulates GO:0006353 ! DNA-templated transcription termination
[Term]
id: GO:0060567
-name: negative regulation of DNA-templated transcription, termination
+name: negative regulation of termination of DNA-templated transcription
namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of DNA-dependent transcription termination, the process in which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA." [GOC:dph, GOC:tb, GOC:txnOH]
synonym: "negative regulation of DNA-dependent transcription, termination" EXACT [GOC:txnOH]
+synonym: "negative regulation of DNA-templated transcription, termination" EXACT []
synonym: "negative regulation of termination of DNA-dependent transcription" EXACT [GOC:jh2]
synonym: "negative regulation of transcription termination, DNA-dependent" EXACT [GOC:jh2]
-is_a: GO:0031554 ! regulation of DNA-templated transcription, termination
+is_a: GO:0031554 ! regulation of termination of DNA-templated transcription
is_a: GO:0043242 ! negative regulation of protein-containing complex disassembly
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
-relationship: negatively_regulates GO:0006353 ! DNA-templated transcription, termination
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
+relationship: negatively_regulates GO:0006353 ! DNA-templated transcription termination
[Term]
id: GO:0060568
@@ -332506,7 +332420,7 @@ name: regulation of peptide hormone processing
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of peptide hormone processing. Peptide hormone processing is the generation of a mature peptide hormone by posttranslational processing of a prohormone." [GOC:dph, GOC:tb]
is_a: GO:0032350 ! regulation of hormone metabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0070613 ! regulation of protein processing
relationship: regulates GO:0016486 ! peptide hormone processing
@@ -332517,7 +332431,7 @@ namespace: biological_process
def: "Any process that increases the rate, frequency or extent of peptide hormone processing. Peptide hormone processing is the generation of a mature peptide hormone by posttranslational processing of a prohormone." [GOC:dph, GOC:tb]
is_a: GO:0010954 ! positive regulation of protein processing
is_a: GO:0032352 ! positive regulation of hormone metabolic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0060568 ! regulation of peptide hormone processing
relationship: positively_regulates GO:0016486 ! peptide hormone processing
@@ -332528,7 +332442,7 @@ namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of peptide hormone processing. Peptide hormone processing is the generation of a mature peptide hormone by posttranslational processing of a prohormone." [GOC:dph, GOC:tb]
is_a: GO:0010955 ! negative regulation of protein processing
is_a: GO:0032351 ! negative regulation of hormone metabolic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0060568 ! regulation of peptide hormone processing
relationship: negatively_regulates GO:0016486 ! peptide hormone processing
@@ -332664,11 +332578,13 @@ is_a: GO:0060584 ! regulation of prostaglandin-endoperoxide synthase activity
[Term]
id: GO:0060586
-name: multicellular organismal iron ion homeostasis
+name: multicellular organismal-level iron ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of the distribution of iron stores within tissues and organs of a multicellular organism." [GOC:dph, GOC:hjd, GOC:tb]
-is_a: GO:0048871 ! multicellular organismal homeostasis
-is_a: GO:0055072 ! iron ion homeostasis
+def: "A chemical homeostatic process involved in the maintenance of a steady state level of iron within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell." [PMID:31431773]
+synonym: "multicellular organismal iron ion homeostasis" EXACT []
+is_a: GO:0055080 ! monoatomic cation homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
+is_a: GO:0140962 ! multicellular organismal-level chemical homeostasis
[Term]
id: GO:0060587
@@ -332703,7 +332619,7 @@ name: ATPase regulator activity
namespace: molecular_function
def: "Binds to and modulates the activity of an ATP hydrolysis activity." [GOC:dph, GOC:tb]
synonym: "ATP hydrolysis regulator activity" EXACT []
-is_a: GO:0098772 ! molecular function regulator
+is_a: GO:0098772 ! molecular function regulator activity
[Term]
id: GO:0060591
@@ -332974,7 +332890,6 @@ name: regulation of cholesterol import
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of cholesterol import. Cholesterol import is the directed movement of cholesterol into a cell or organelle." [GOC:BHF, GOC:dph, GOC:tb]
is_a: GO:0032374 ! regulation of cholesterol transport
-is_a: GO:2000909 ! regulation of sterol import
relationship: regulates GO:0070508 ! cholesterol import
[Term]
@@ -332984,7 +332899,6 @@ namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of cholesterol import. Cholesterol import is the directed movement of cholesterol into a cell or organelle." [GOC:BHF, GOC:dph, GOC:tb]
is_a: GO:0032375 ! negative regulation of cholesterol transport
is_a: GO:0060620 ! regulation of cholesterol import
-is_a: GO:2000910 ! negative regulation of sterol import
relationship: negatively_regulates GO:0070508 ! cholesterol import
[Term]
@@ -332992,7 +332906,6 @@ id: GO:0060622
name: regulation of ascospore wall beta-glucan biosynthetic process
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of ascospore wall beta-glucan biosynthetic process, the chemical reactions and pathways resulting in the formation of beta-glucans, compounds composed of glucose residues linked by beta-D-glucosidic bonds, found in the walls of ascospores." [GOC:dph, GOC:tb]
-is_a: GO:0010564 ! regulation of cell cycle process
is_a: GO:0090093 ! regulation of fungal-type cell wall beta-glucan biosynthetic process
is_a: GO:2000241 ! regulation of reproductive process
relationship: regulates GO:0034412 ! ascospore wall beta-glucan biosynthetic process
@@ -333050,7 +332963,6 @@ id: GO:0060629
name: regulation of homologous chromosome segregation
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of homologous chromosome segregation, the cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the first division of the meiotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner; this pairing off, referred to as synapsis, permits genetic recombination. One homolog (both sister chromatids) of each morphologic type goes into each of the resulting chromosome sets." [GOC:dph, GOC:tb]
-is_a: GO:0010564 ! regulation of cell cycle process
is_a: GO:0051983 ! regulation of chromosome segregation
is_a: GO:2000241 ! regulation of reproductive process
relationship: regulates GO:0045143 ! homologous chromosome segregation
@@ -333078,27 +332990,25 @@ name: regulation of microtubule-based movement
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins." [GOC:dph, GOC:tb]
is_a: GO:0032886 ! regulation of microtubule-based process
-is_a: GO:0051270 ! regulation of cellular component movement
relationship: regulates GO:0007018 ! microtubule-based movement
[Term]
id: GO:0060633
-name: negative regulation of transcription initiation from RNA polymerase II promoter
+name: negative regulation of transcription initiation by RNA polymerase II
namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter." [GOC:dph, GOC:tb, GOC:txnOH]
+synonym: "negative regulation of transcription initiation from RNA polymerase II promoter" EXACT []
is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter
-is_a: GO:2000143 ! negative regulation of DNA-templated transcription, initiation
-relationship: negatively_regulates GO:0006367 ! transcription initiation from RNA polymerase II promoter
+is_a: GO:0060260 ! regulation of transcription initiation by RNA polymerase II
+is_a: GO:2000143 ! negative regulation of DNA-templated transcription initiation
+relationship: negatively_regulates GO:0006367 ! transcription initiation at RNA polymerase II promoter
[Term]
id: GO:0060634
name: regulation of 4,6-pyruvylated galactose residue biosynthetic process
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of 4,6-pyruvylated galactose residue biosynthetic process, the chemical reactions and pathways resulting in the formation of the pyruvylated galactose residue 4-6-O-[(R)(1-carboxyethylidine)]-Gal-beta-(1->3)-. The galactose residue is part of a larger polysaccharide chain." [GOC:dph, GOC:tb]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:0032885 ! regulation of polysaccharide biosynthetic process
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
relationship: regulates GO:0051072 ! 4,6-pyruvylated galactose residue biosynthetic process
[Term]
@@ -333108,9 +333018,8 @@ namespace: biological_process
def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of (1->3)-beta-D-glucans." [GOC:dph, GOC:tb]
synonym: "positive regulation of 1,3-beta-D-glucan biosynthetic process" EXACT []
is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:0032953 ! regulation of (1->3)-beta-D-glucan biosynthetic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
relationship: positively_regulates GO:0006075 ! (1->3)-beta-D-glucan biosynthetic process
[Term]
@@ -333119,9 +333028,9 @@ name: negative regulation of (1->3)-beta-D-glucan biosynthetic process
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of (1->3)-beta-D-glucans." [GOC:dph, GOC:tb]
synonym: "negative regulation of 1,3-beta-D-glucan biosynthetic process" EXACT []
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
+is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process
is_a: GO:0032953 ! regulation of (1->3)-beta-D-glucan biosynthetic process
-is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
relationship: negatively_regulates GO:0006075 ! (1->3)-beta-D-glucan biosynthetic process
[Term]
@@ -333300,6 +333209,7 @@ namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of mammary gland cord elongation as a result of a signal being created by a mesenchymal cell that is a precursor to the mammary fat and its subsequent reception and interpretation by an mammary cord epithelial cell." [GOC:dph, PMID:12558599]
synonym: "regulation of mammary gland cord elongation by mammary fat precursor cell-epithelial cell signalling" EXACT [GOC:mah]
is_a: GO:0007267 ! cell-cell signaling
+is_a: GO:0048638 ! regulation of developmental growth
relationship: regulates GO:0060654 ! mammary gland cord elongation
[Term]
@@ -333308,6 +333218,7 @@ name: nipple morphogenesis
namespace: biological_process
def: "The process in which the nipple is generated and organized." [GOC:dph]
is_a: GO:0009653 ! anatomical structure morphogenesis
+relationship: part_of GO:0060443 ! mammary gland morphogenesis
relationship: part_of GO:0060618 ! nipple development
[Term]
@@ -333399,7 +333310,6 @@ id: GO:0060669
name: embryonic placenta morphogenesis
namespace: biological_process
def: "The process in which the embryonic placenta is generated and organized." [GOC:dph]
-is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048598 ! embryonic morphogenesis
relationship: part_of GO:0001892 ! embryonic placenta development
@@ -333408,7 +333318,6 @@ id: GO:0060670
name: branching involved in labyrinthine layer morphogenesis
namespace: biological_process
def: "The process in which the branches of the fetal placental villi are generated and organized. The villous part of the placenta is called the labyrinth layer." [GOC:dph, PMID:16916377]
-is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048598 ! embryonic morphogenesis
is_a: GO:0061138 ! morphogenesis of a branching epithelium
relationship: part_of GO:0060713 ! labyrinthine layer morphogenesis
@@ -333440,7 +333349,6 @@ namespace: biological_process
def: "Any process that mediates the transfer of information from one cell to another." [GOC:dph, PMID:16916377]
synonym: "cell-cell signalling involved in placenta development" EXACT [GOC:mah]
is_a: GO:0007267 ! cell-cell signaling
-is_a: GO:0022414 ! reproductive process
relationship: part_of GO:0001892 ! embryonic placenta development
[Term]
@@ -333449,7 +333357,6 @@ name: placenta blood vessel development
namespace: biological_process
def: "The process whose specific outcome is the progression of a blood vessel of the placenta over time, from its formation to the mature structure." [GOC:dph, PMID:16916377]
is_a: GO:0001568 ! blood vessel development
-is_a: GO:0003006 ! developmental process involved in reproduction
relationship: part_of GO:0001890 ! placenta development
[Term]
@@ -333754,7 +333661,6 @@ id: GO:0060710
name: chorio-allantoic fusion
namespace: biological_process
def: "The cell-cell adhesion process in which the cells of the chorion fuse to the cells of the allantois." [GOC:dph]
-is_a: GO:0022414 ! reproductive process
is_a: GO:0098609 ! cell-cell adhesion
relationship: part_of GO:0060713 ! labyrinthine layer morphogenesis
@@ -333763,7 +333669,7 @@ id: GO:0060711
name: labyrinthine layer development
namespace: biological_process
def: "The process in which the labyrinthine layer of the placenta progresses, from its formation to its mature state." [GOC:dph]
-is_a: GO:0048608 ! reproductive structure development
+is_a: GO:0048856 ! anatomical structure development
relationship: part_of GO:0001892 ! embryonic placenta development
[Term]
@@ -333772,7 +333678,6 @@ name: spongiotrophoblast layer development
namespace: biological_process
def: "The process in which the spongiotrophoblast layer of the placenta progresses from its formation to its mature state." [GOC:dph]
is_a: GO:0009888 ! tissue development
-is_a: GO:0048608 ! reproductive structure development
relationship: part_of GO:0001892 ! embryonic placenta development
[Term]
@@ -333780,7 +333685,6 @@ id: GO:0060713
name: labyrinthine layer morphogenesis
namespace: biological_process
def: "The process in which the labyrinthine layer of the placenta is generated and organized." [GOC:dph]
-is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048598 ! embryonic morphogenesis
relationship: part_of GO:0060669 ! embryonic placenta morphogenesis
relationship: part_of GO:0060711 ! labyrinthine layer development
@@ -333790,7 +333694,6 @@ id: GO:0060714
name: labyrinthine layer formation
namespace: biological_process
def: "The developmental process pertaining to the initial formation of the labyrinthine layer of the placenta." [GOC:dph]
-is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
relationship: part_of GO:0060713 ! labyrinthine layer morphogenesis
@@ -333808,7 +333711,6 @@ name: labyrinthine layer blood vessel development
namespace: biological_process
def: "The process whose specific outcome is the progression of a blood vessel of the labyrinthine layer of the placenta over time, from its formation to the mature structure. The embryonic vessels grow through the layer to come in close contact with the maternal blood supply." [GOC:dph]
is_a: GO:0048568 ! embryonic organ development
-is_a: GO:0048608 ! reproductive structure development
is_a: GO:0060674 ! placenta blood vessel development
relationship: part_of GO:0060711 ! labyrinthine layer development
@@ -333857,7 +333759,6 @@ name: cell proliferation involved in embryonic placenta development
namespace: biological_process
def: "The multiplication or reproduction of cells, resulting in the expansion of the population in the embryonic placenta." [GOC:dph]
is_a: GO:0008283 ! cell population proliferation
-is_a: GO:0022414 ! reproductive process
relationship: part_of GO:0001892 ! embryonic placenta development
[Term]
@@ -333866,7 +333767,6 @@ name: regulation of cell proliferation involved in embryonic placenta developmen
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of cell proliferation involved in embryonic placenta development." [GOC:dph]
is_a: GO:0042127 ! regulation of cell population proliferation
-is_a: GO:2000241 ! regulation of reproductive process
relationship: regulates GO:0060722 ! cell proliferation involved in embryonic placenta development
[Term]
@@ -333929,7 +333829,6 @@ name: regulation of intestinal epithelial structure maintenance
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of intestinal epithelial structure maintenance, a tissue homeostatic process required for the maintenance of the structure of the intestinal epithelium." [GOC:BHF, GOC:dph, GOC:tb]
is_a: GO:0044058 ! regulation of digestive system process
-is_a: GO:0065008 ! regulation of biological quality
relationship: regulates GO:0060729 ! intestinal epithelial structure maintenance
[Term]
@@ -333946,9 +333845,9 @@ id: GO:0060732
name: positive regulation of inositol phosphate biosynthetic process
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of inositol phosphate biosynthesis. Inositol phosphate biosynthetic processes are the chemical reactions and pathways resulting in the formation of an inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached." [GOC:dph, GOC:tb]
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
is_a: GO:0010919 ! regulation of inositol phosphate biosynthetic process
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:0045937 ! positive regulation of phosphate metabolic process
is_a: GO:1902932 ! positive regulation of alcohol biosynthetic process
relationship: positively_regulates GO:0032958 ! inositol phosphate biosynthetic process
@@ -334508,7 +334407,7 @@ consider: GO:0060795
id: GO:0060797
name: transforming growth factor beta receptor signaling pathway involved in primary germ layer cell fate commitment
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, which contributes to an unspecified cell adopting a mesoderm fate." [GOC:dph, GOC:sdb_2009, GOC:tb]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a transforming growth factor beta receptor on the surface of a target cell, which contributes to an unspecified cell adopting a mesoderm fate." [GOC:dph, GOC:sdb_2009, GOC:tb]
synonym: "transforming growth factor beta receptor signalling pathway involved in primary germ layer cell fate commitment" EXACT [GOC:mah]
is_a: GO:0007179 ! transforming growth factor beta receptor signaling pathway
relationship: part_of GO:0060795 ! cell fate commitment involved in formation of primary germ layer
@@ -334542,11 +334441,12 @@ relationship: regulates GO:0060706 ! cell differentiation involved in embryonic
[Term]
id: GO:0060801
-name: negative regulation of trophoblast cell differentiation by transforming growth factor beta signaling pathway
+name: obsolete negative regulation of trophoblast cell differentiation by transforming growth factor beta signaling pathway
namespace: biological_process
-def: "The transforming growth factor signaling process that decreases the rate, frequency, or extent of trophoblast stem cells differentiating into the more mature cells of the trophoblast." [GOC:dph, GOC:sdb_2009, GOC:tb]
+def: "OBSOLETE. The transforming growth factor signaling process that decreases the rate, frequency, or extent of trophoblast stem cells differentiating into the more mature cells of the trophoblast." [GOC:dph, GOC:sdb_2009, GOC:tb]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "negative regulation of trophoblast cell differentiation by transforming growth factor beta signalling pathway" EXACT [GOC:mah]
-is_a: GO:0060806 ! negative regulation of cell differentiation involved in embryonic placenta development
+is_obsolete: true
[Term]
id: GO:0060802
@@ -334561,7 +334461,7 @@ relationship: part_of GO:0009948 ! anterior/posterior axis specification
id: GO:0060803
name: BMP signaling pathway involved in mesodermal cell fate specification
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to a cell becoming specified to adopt a mesodermal fate." [GOC:dph, GOC:sdb_2009, GOC:tb]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to its receptor on the surface of a target cell, which contributes to a cell becoming specified to adopt a mesodermal fate." [GOC:dph, GOC:sdb_2009, GOC:tb]
synonym: "BMP signalling pathway involved in mesodermal cell fate specification" EXACT [GOC:mah]
is_a: GO:0030509 ! BMP signaling pathway
relationship: part_of GO:0007501 ! mesodermal cell fate specification
@@ -334570,7 +334470,7 @@ relationship: part_of GO:0007501 ! mesodermal cell fate specification
id: GO:0060804
name: positive regulation of Wnt signaling pathway by BMP signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that results in an increase in the rate, frequency or extent of a Wnt signaling pathway." [GOC:dph, GOC:sdb_2009, GOC:tb]
+def: "The series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that results in an increase in the rate, frequency or extent of a Wnt signaling pathway." [GOC:dph, GOC:sdb_2009, GOC:tb]
synonym: "positive regulation of WNT receptor signaling pathway by BMP signaling pathway" EXACT [GOC:bf]
synonym: "positive regulation of WNT receptor signalling pathway by BMP signalling pathway" EXACT [GOC:mah]
synonym: "positive regulation of Wnt-activated signaling pathway by BMP signaling pathway" EXACT [GOC:signaling]
@@ -334579,10 +334479,11 @@ is_a: GO:0030509 ! BMP signaling pathway
[Term]
id: GO:0060805
-name: negative regulation of trophoblast cell differentiation by transcription regulation from RNA polymerase II promoter
+name: obsolete negative regulation of trophoblast cell differentiation by transcription regulation from RNA polymerase II promoter
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of transcription from an RNA polymerase II promoter ultimately resulting in a decrease in trophoblast stem cells differentiating into the more mature cells of the trophoblast." [GOC:dph, GOC:sdb_2009, GOC:tb]
-is_a: GO:0060806 ! negative regulation of cell differentiation involved in embryonic placenta development
+def: "OBSOLETE. Any process that modulates the rate, frequency or extent of transcription from an RNA polymerase II promoter ultimately resulting in a decrease in trophoblast stem cells differentiating into the more mature cells of the trophoblast." [GOC:dph, GOC:sdb_2009, GOC:tb]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0060806
@@ -334676,7 +334577,7 @@ relationship: part_of GO:0009948 ! anterior/posterior axis specification
id: GO:0060816
name: random inactivation of X chromosome
namespace: biological_process
-def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on either the paternal or maternal X-chromosome in the XX sex." [GOC:dph, GOC:sdb_2009, GOC:tb]
+def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on either the paternal or maternal X-chromosome in the XX sex." [GOC:dph, GOC:sdb_2009, GOC:tb, PMID:32189388]
is_a: GO:0009048 ! dosage compensation by inactivation of X chromosome
[Term]
@@ -334706,12 +334607,12 @@ is_a: GO:0009048 ! dosage compensation by inactivation of X chromosome
[Term]
id: GO:0060820
-name: inactivation of X chromosome by heterochromatin assembly
+name: inactivation of X chromosome by heterochromatin formation
namespace: biological_process
-def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex by the mechanism of heterochromatin formation." [GOC:dph, GOC:sdb_2009, GOC:tb]
-synonym: "inactivation of X chromosome by heterochromatin formation" EXACT []
+def: "Compensating for the two-fold variation in X-chromosome: autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex by the mechanism of heterochromatin formation." [GOC:dph, GOC:sdb_2009, GOC:tb]
+synonym: "inactivation of X chromosome by heterochromatin assembly" EXACT []
is_a: GO:0009048 ! dosage compensation by inactivation of X chromosome
-is_a: GO:0140719 ! constitutive heterochromatin assembly
+is_a: GO:0140719 ! constitutive heterochromatin formation
[Term]
id: GO:0060821
@@ -334766,7 +334667,7 @@ relationship: part_of GO:0021999 ! neural plate anterior/posterior regionalizati
id: GO:0060826
name: transforming growth factor beta receptor signaling pathway involved in neural plate anterior/posterior pattern formation
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, which contributes to the formation of the neural plate anterior/posterior pattern." [GOC:dph, GOC:sdb_2009, GOC:tb]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a transforming growth factor beta receptor on the surface of a target cell, which contributes to the formation of the neural plate anterior/posterior pattern." [GOC:dph, GOC:sdb_2009, GOC:tb]
synonym: "transforming growth factor beta receptor signalling pathway involved in neural plate anterior/posterior pattern formation" EXACT [GOC:mah]
is_a: GO:0007179 ! transforming growth factor beta receptor signaling pathway
relationship: part_of GO:0021999 ! neural plate anterior/posterior regionalization
@@ -334869,7 +334770,7 @@ is_a: GO:0000578 ! embryonic axis specification
id: GO:0060835
name: transforming growth factor receptor beta signaling pathway involved in oral/aboral axis specification
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, which contributes to the specification of the oral/aboral axis." [GOC:dph, GOC:sdb_2009, GOC:tb]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a transforming growth factor beta receptor on the surface of a target cell, which contributes to the specification of the oral/aboral axis." [GOC:dph, GOC:sdb_2009, GOC:tb]
synonym: "transforming growth factor receptor beta signalling pathway involved in oral/aboral axis specification" EXACT [GOC:mah]
is_a: GO:0007179 ! transforming growth factor beta receptor signaling pathway
relationship: part_of GO:0060834 ! oral/aboral axis specification
@@ -335158,7 +335059,7 @@ is_obsolete: true
id: GO:0060869
name: transmembrane receptor protein serine/threonine kinase signaling pathway involved in floral organ abscission
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses serine/threonine kinase activity, which contributes to the process of floral organ abscission." [GOC:dph, GOC:sdb_2009, GOC:signaling, GOC:tb]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of the target cell where the receptor possesses serine/threonine kinase activity, which contributes to the process of floral organ abscission." [GOC:dph, GOC:sdb_2009, GOC:signaling, GOC:tb]
synonym: "transmembrane receptor protein serine/threonine kinase signalling pathway involved in floral organ abscission" EXACT [GOC:mah]
is_a: GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway
is_a: GO:0022414 ! reproductive process
@@ -335255,16 +335156,12 @@ relationship: part_of GO:0060879 ! semicircular canal fusion
[Term]
id: GO:0060883
-name: regulation of basement membrane disassembly involved in semicircular canal fusion by cell communication
+name: obsolete regulation of basement membrane disassembly involved in semicircular canal fusion by cell communication
namespace: biological_process
-def: "Any process that mediates interactions between a cell and its surroundings that modulates of the rate, frequency or extent of basement membrane disassembly involved in semicircular canal fusion." [GOC:dph, GOC:sdb_2009, GOC:tb]
+def: "OBSOLETE. Any process that mediates interactions between a cell and its surroundings that modulates of the rate, frequency or extent of basement membrane disassembly involved in semicircular canal fusion." [GOC:dph, GOC:sdb_2009, GOC:tb]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "regulation of basal lamina disassembly involved in semicircular canal fusion by cell communication" RELATED []
-is_a: GO:0007154 ! cell communication
-is_a: GO:0010715 ! regulation of extracellular matrix disassembly
-is_a: GO:0045995 ! regulation of embryonic development
-is_a: GO:0110011 ! regulation of basement membrane organization
-is_a: GO:2000027 ! regulation of animal organ morphogenesis
-relationship: regulates GO:0060882 ! basement membrane disassembly involved in semicircular canal fusion
+is_obsolete: true
[Term]
id: GO:0060884
@@ -335430,7 +335327,7 @@ is_a: GO:0060070 ! canonical Wnt signaling pathway
id: GO:0060902
name: regulation of hair cycle by BMP signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that modulates the rate, frequency or extent of the hair cycle." [GOC:dph, GOC:sdb_2009, GOC:tb]
+def: "The series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that modulates the rate, frequency or extent of the hair cycle." [GOC:dph, GOC:sdb_2009, GOC:tb]
synonym: "regulation of hair cycle by BMP signalling pathway" EXACT [GOC:mah]
is_a: GO:0030509 ! BMP signaling pathway
is_a: GO:0042634 ! regulation of hair cycle
@@ -335465,14 +335362,16 @@ relationship: regulates GO:0031142 ! induction of conjugation upon nitrogen star
[Term]
id: GO:0060906
-name: negative regulation of heterochromatin assembly by small RNA
+name: negative regulation of small non-coding RNA-mediated heterochromatin formation
namespace: biological_process
-def: "Any process that decreases the frequency, rate or extent of heterochromatin assembly by small RNA." [GOC:dph, GOC:tb]
+def: "Any process that decreases the frequency, rate or extent of small non-coding RNA-mediated heterochromatin formation." [GOC:dph, GOC:tb]
synonym: "negative regulation of chromatin silencing by small RNA" RELATED []
+synonym: "negative regulation of heterochromatin assembly by small RNA" EXACT []
synonym: "negative regulation of RNAi-mediated heterochromatin assembly" EXACT []
-is_a: GO:0010964 ! regulation of heterochromatin assembly by small RNA
-is_a: GO:0031452 ! negative regulation of heterochromatin assembly
-relationship: negatively_regulates GO:0031048 ! heterochromatin assembly by small RNA
+is_a: GO:0010964 ! regulation of small non-coding RNA-mediated heterochromatin formation
+is_a: GO:0031452 ! negative regulation of heterochromatin formation
+is_a: GO:0060967 ! negative regulation of gene silencing by RNA
+relationship: negatively_regulates GO:0031048 ! small ncRNA-mediated heterochromatin formation
[Term]
id: GO:0060907
@@ -335495,7 +335394,7 @@ id: GO:0060909
name: regulation of DNA replication initiation involved in plasmid copy number maintenance
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of initiation of plasmid DNA replication that contributes to copy number maintenance." [GOC:dph, GOC:tb]
-is_a: GO:0030174 ! regulation of DNA-dependent DNA replication initiation
+is_a: GO:0030174 ! regulation of DNA-templated DNA replication initiation
relationship: part_of GO:0060908 ! plasmid copy number maintenance
[Term]
@@ -335503,7 +335402,7 @@ id: GO:0060910
name: negative regulation of DNA replication initiation involved in plasmid copy number maintenance
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of initiation of plasmid DNA replication that contributes to copy number maintenance." [GOC:dph, GOC:tb]
-is_a: GO:0032297 ! negative regulation of DNA-dependent DNA replication initiation
+is_a: GO:0032297 ! negative regulation of DNA-templated DNA replication initiation
is_a: GO:0060909 ! regulation of DNA replication initiation involved in plasmid copy number maintenance
[Term]
@@ -335571,15 +335470,18 @@ relationship: regulates GO:0006078 ! (1->6)-beta-D-glucan biosynthetic process
id: GO:0060918
name: auxin transport
namespace: biological_process
-def: "The directed movement of auxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:tb]
+def: "The directed movement of auxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Auxins are a group of plant hormones that regulates aspects of plant growth." [GOC:dph, GOC:tb]
is_a: GO:0009914 ! hormone transport
[Term]
id: GO:0060919
-name: auxin influx
+name: auxin import into cell
namespace: biological_process
-def: "The process involved in the transport of auxin into the cell." [GOC:dph, GOC:tb]
+def: "The directed movement of auxins from outside of a cell into a cell." [PMID:22773749]
+synonym: "auxin influx" BROAD []
is_a: GO:0060918 ! auxin transport
+is_a: GO:0098657 ! import into cell
+is_a: GO:0098739 ! import across plasma membrane
[Term]
id: GO:0060920
@@ -335969,24 +335871,24 @@ is_a: GO:0060962 ! regulation of ribosomal protein gene transcription by RNA pol
[Term]
id: GO:0060964
-name: regulation of gene silencing by miRNA
+name: regulation of miRNA-mediated gene silencing
namespace: biological_process
-def: "Any process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: RNA (often mRNA) cleavage or mRNA translational repression." [GOC:aruk, GOC:bc, GOC:dph, GOC:rl, GOC:tb, PMID:23985560, PMID:28379604]
+def: "A process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs)." [GOC:aruk, GOC:bc, GOC:dph, GOC:rl, GOC:tb, PMID:23985560, PMID:28379604]
synonym: "regulation of gene silencing by microRNA" EXACT [GOC:pr]
-is_a: GO:0060147 ! regulation of posttranscriptional gene silencing
-is_a: GO:0060966 ! regulation of gene silencing by RNA
-relationship: regulates GO:0035195 ! gene silencing by miRNA
+synonym: "regulation of gene silencing by miRNA" EXACT []
+is_a: GO:1900368 ! regulation of post-transcriptional gene silencing by RNA
+relationship: regulates GO:0035195 ! miRNA-mediated gene silencing
[Term]
id: GO:0060965
-name: negative regulation of gene silencing by miRNA
+name: negative regulation of miRNA-mediated gene silencing
namespace: biological_process
-def: "Any process that decreases the rate, frequency, or extent of gene silencing by miRNA." [GOC:aruk, GOC:bc, GOC:dph, GOC:rl, GOC:tb, PMID:23985560, PMID:28379604]
+def: "A process that decreases the rate, frequency, or extent of gene silencing by a microRNA (miRNA)." [GOC:aruk, GOC:bc, GOC:dph, GOC:rl, GOC:tb, PMID:23985560, PMID:28379604]
synonym: "negative regulation of gene silencing by microRNA" EXACT [GOC:bf, GOC:pr]
-is_a: GO:0060149 ! negative regulation of posttranscriptional gene silencing
-is_a: GO:0060964 ! regulation of gene silencing by miRNA
-is_a: GO:0060967 ! negative regulation of gene silencing by RNA
-relationship: negatively_regulates GO:0035195 ! gene silencing by miRNA
+synonym: "negative regulation of gene silencing by miRNA" EXACT []
+is_a: GO:0060964 ! regulation of miRNA-mediated gene silencing
+is_a: GO:1900369 ! negative regulation of post-transcriptional gene silencing by RNA
+relationship: negatively_regulates GO:0035195 ! miRNA-mediated gene silencing
[Term]
id: GO:0060966
@@ -335994,7 +335896,7 @@ name: regulation of gene silencing by RNA
namespace: biological_process
def: "Any process that regulates the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes." [GOC:dph, GOC:tb]
is_a: GO:0010468 ! regulation of gene expression
-relationship: regulates GO:0031047 ! gene silencing by RNA
+relationship: regulates GO:0031047 ! RNA-mediated gene silencing
[Term]
id: GO:0060967
@@ -336004,7 +335906,7 @@ def: "Any process that decreases the rate, frequency, or extent of gene silencin
is_a: GO:0010628 ! positive regulation of gene expression
is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:0060966 ! regulation of gene silencing by RNA
-relationship: negatively_regulates GO:0031047 ! gene silencing by RNA
+relationship: negatively_regulates GO:0031047 ! RNA-mediated gene silencing
[Term]
id: GO:0060968
@@ -336241,11 +336143,11 @@ relationship: part_of GO:0001822 ! kidney development
[Term]
id: GO:0060994
-name: regulation of transcription from RNA polymerase II promoter involved in kidney development
+name: obsolete regulation of transcription from RNA polymerase II promoter involved in kidney development
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the branching morphogenesis by which the kidney progresses from its initial formation to the mature state." [GOC:dph, GOC:mtg_kidney_jan10]
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-relationship: part_of GO:0001822 ! kidney development
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the branching morphogenesis by which the kidney progresses from its initial formation to the mature state." [GOC:dph, GOC:mtg_kidney_jan10]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0060995
@@ -336381,7 +336283,7 @@ is_a: GO:0048731 ! system development
id: GO:0061009
name: common bile duct development
namespace: biological_process
-def: "The progression of the common bile duct over time, from its formation to the mature structure. The common bile duct is formed from the joining of the common hepatic duct running from the liver, and the cystic duct running from the gall bladder. The common bile duct transports bile from the liver and gall bladder to the intestine." [PMID:20614624]
+def: "The progression of the common bile duct over time, from its formation to the mature structure. The common bile duct is formed from the joining of the common hepatic duct running from the liver, and the cystic duct running from the gallbladder. The common bile duct transports bile from the liver and gallbladder to the intestine." [PMID:20614624]
synonym: "bile duct development" EXACT [GOC:dph]
synonym: "CBD development" EXACT [PMID:20614624]
synonym: "EHBD development" BROAD [PMID:20614624]
@@ -336391,9 +336293,9 @@ relationship: part_of GO:0061008 ! hepaticobiliary system development
[Term]
id: GO:0061010
-name: gall bladder development
+name: gallbladder development
namespace: biological_process
-def: "The progression of the gall bladder over time, from its initial formation to the mature structure. The gall bladder is a cavitated organ that stores bile." [GOC:dph]
+def: "The progression of the gallbladder over time, from its initial formation to the mature structure. The gallbladder is a cavitated organ that stores bile." [GOC:dph]
is_a: GO:0048513 ! animal organ development
relationship: part_of GO:0061008 ! hepaticobiliary system development
@@ -336462,6 +336364,7 @@ subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
+subset: prokaryote_subset
synonym: "cellular membrane organisation" EXACT []
synonym: "cellular membrane organization" EXACT []
synonym: "membrane organisation" EXACT [GOC:mah]
@@ -336752,13 +336655,13 @@ relationship: part_of GO:0061053 ! somite development
id: GO:0061057
name: peptidoglycan recognition protein signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by binding of peptidoglycan to a receptor and ending with regulation of a downstream cellular process. The main outcome of the Imd signaling is the production of antimicrobial peptides." [GOC:dph, PMID:18688280]
+def: "The series of molecular signals initiated by binding of peptidoglycan to a receptor and ending with regulation of a downstream cellular process. The main outcome of the Imd signaling is the production of antimicrobial peptides." [GOC:dph, PMID:18688280, PMID:24706930]
synonym: "Imd signaling pathway" EXACT [GOC:dph]
synonym: "Imd signalling pathway" EXACT [GOC:dph]
synonym: "immune deficiency pathway" RELATED [GOC:dph]
synonym: "immune deficiency signaling pathway" RELATED [GOC:dph]
synonym: "PGRP signaling pathway" RELATED [GOC:dph]
-is_a: GO:0002764 ! immune response-regulating signaling pathway
+is_a: GO:0002221 ! pattern recognition receptor signaling pathway
relationship: part_of GO:0042742 ! defense response to bacterium
[Term]
@@ -336767,8 +336670,7 @@ name: regulation of peptidoglycan recognition protein signaling pathway
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of the peptidoglycan recognition protein signaling pathway." [GOC:dph]
synonym: "regulation of peptidoglycan recognition protein signalling pathway" EXACT [GOC:mah]
-is_a: GO:0009966 ! regulation of signal transduction
-is_a: GO:0050776 ! regulation of immune response
+is_a: GO:0062207 ! regulation of pattern recognition receptor signaling pathway
relationship: regulates GO:0061057 ! peptidoglycan recognition protein signaling pathway
[Term]
@@ -336777,8 +336679,8 @@ name: positive regulation of peptidoglycan recognition protein signaling pathway
namespace: biological_process
def: "Any process that increases the rate, frequency, or extent of the peptidoglycan recognition protein signaling pathway." [GOC:dph]
synonym: "positive regulation of peptidoglycan recognition protein signalling pathway" EXACT [GOC:mah]
-is_a: GO:0009967 ! positive regulation of signal transduction
is_a: GO:0061058 ! regulation of peptidoglycan recognition protein signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
is_a: GO:1900426 ! positive regulation of defense response to bacterium
relationship: positively_regulates GO:0061057 ! peptidoglycan recognition protein signaling pathway
@@ -336788,6 +336690,7 @@ name: negative regulation of peptidoglycan recognition protein signaling pathway
namespace: biological_process
def: "Any process that decreases the rate, frequency, or extent of the peptidoglycan recognition protein signaling pathway." [GOC:dph]
synonym: "negative regulation of peptidoglycan recognition protein signalling pathway" EXACT [GOC:mah]
+is_a: GO:0002683 ! negative regulation of immune system process
is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:0061058 ! regulation of peptidoglycan recognition protein signaling pathway
is_a: GO:1900425 ! negative regulation of defense response to bacterium
@@ -336939,7 +336842,6 @@ name: positive regulation of prostaglandin secretion involved in immune response
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the regulated release of a prostaglandin from a cell and contributes to the immune response." [GOC:BHF, GOC:dph]
synonym: "positive regulation of prostaglandin secretion during immune response" RELATED [GOC:dph]
-is_a: GO:0002702 ! positive regulation of production of molecular mediator of immune response
is_a: GO:0032308 ! positive regulation of prostaglandin secretion
relationship: positively_regulates GO:0090323 ! prostaglandin secretion involved in immune response
@@ -337027,7 +336929,6 @@ namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of sequestering of zinc ion. Sequestering of zinc ion is the process of binding or confining zinc ions such that they are separated from other components of a biological system." [GOC:BHF, GOC:dph, GOC:tb]
is_a: GO:0032879 ! regulation of localization
is_a: GO:0050794 ! regulation of cellular process
-is_a: GO:0050801 ! ion homeostasis
relationship: regulates GO:0032119 ! sequestering of zinc ion
[Term]
@@ -337143,6 +337044,7 @@ id: GO:0061101
name: neuroendocrine cell differentiation
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a neuroendocrine cell. A neuroendocrine cell is a cell that receives input form a neuron which controls the secretion of an endocrine substance." [GOC:dph]
+is_a: GO:0030182 ! neuron differentiation
is_a: GO:0060563 ! neuroepithelial cell differentiation
[Term]
@@ -337151,6 +337053,7 @@ name: stomach neuroendocrine cell differentiation
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the stomach epithelium." [GOC:dph, PMID:18173746]
synonym: "gastric neuroendocrine cell differentiation" RELATED [GOC:dph]
+is_a: GO:0035883 ! enteroendocrine cell differentiation
is_a: GO:0061101 ! neuroendocrine cell differentiation
relationship: part_of GO:0062094 ! stomach development
@@ -337177,6 +337080,7 @@ name: regulation of stomach neuroendocrine cell differentiation
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach." [GOC:dph]
is_a: GO:0030856 ! regulation of epithelial cell differentiation
+is_a: GO:0045664 ! regulation of neuron differentiation
relationship: regulates GO:0061102 ! stomach neuroendocrine cell differentiation
[Term]
@@ -337185,6 +337089,7 @@ name: negative regulation of stomach neuroendocrine cell differentiation
namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach." [GOC:dph]
is_a: GO:0002085 ! inhibition of neuroepithelial cell differentiation
+is_a: GO:0045665 ! negative regulation of neuron differentiation
is_a: GO:0061105 ! regulation of stomach neuroendocrine cell differentiation
relationship: negatively_regulates GO:0061102 ! stomach neuroendocrine cell differentiation
@@ -337201,8 +337106,8 @@ id: GO:0061108
name: seminal vesicle epithelium development
namespace: biological_process
def: "The progression of the seminal vesicle epithelium over time, from its formation to the mature structure." [GOC:dph]
+is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0035295 ! tube development
-is_a: GO:0048608 ! reproductive structure development
is_a: GO:0060429 ! epithelium development
relationship: part_of GO:0061107 ! seminal vesicle development
@@ -337405,7 +337310,7 @@ relationship: positively_regulates GO:0061131 ! pancreas field specification
id: GO:0061133
name: endopeptidase activator activity
namespace: molecular_function
-def: "Binds to and increases the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides." [GOC:dph, GOC:tb]
+def: "Binds to and increases the activity of an endopeptidase." [GOC:dph, GOC:tb]
is_a: GO:0016504 ! peptidase activator activity
is_a: GO:0061135 ! endopeptidase regulator activity
@@ -337428,7 +337333,8 @@ id: GO:0061136
name: regulation of proteasomal protein catabolic process
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome." [GOC:dph, GOC:tb]
-is_a: GO:1903050 ! regulation of proteolysis involved in cellular protein catabolic process
+is_a: GO:0042176 ! regulation of protein catabolic process
+is_a: GO:1903050 ! regulation of proteolysis involved in protein catabolic process
relationship: regulates GO:0010498 ! proteasomal protein catabolic process
[Term]
@@ -337530,7 +337436,7 @@ relationship: part_of GO:0003157 ! endocardium development
id: GO:0061149
name: BMP signaling pathway involved in ureter morphogenesis
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the shaping of the ureter. The ureter is a tube that extends from the kidney to the bladder." [GOC:dph, GOC:mtg_kidney_jan10]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to its receptor on the surface of a target cell, which contributes to the shaping of the ureter. The ureter is a tube that extends from the kidney to the bladder." [GOC:dph, GOC:mtg_kidney_jan10]
synonym: "BMP signalling pathway involved in ureter morphogenesis" EXACT [GOC:mah]
is_a: GO:0030509 ! BMP signaling pathway
relationship: part_of GO:0072197 ! ureter morphogenesis
@@ -337548,7 +337454,7 @@ is_a: GO:0072048 ! renal system pattern specification
id: GO:0061151
name: BMP signaling pathway involved in renal system segmentation
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the segmentation of the renal system." [GOC:dph, GOC:yaf]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to its receptor on the surface of a target cell, which contributes to the segmentation of the renal system." [GOC:dph, GOC:yaf]
synonym: "BMP signalling pathway involved in renal system segmentation" EXACT [GOC:mah]
is_a: GO:0030509 ! BMP signaling pathway
relationship: part_of GO:0061150 ! renal system segmentation
@@ -337750,7 +337656,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose." [GOC:BHF, GOC:dph]
synonym: "regulation of insulin secretion in response to glucose" EXACT [GOC:dph]
is_a: GO:0050796 ! regulation of insulin secretion
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0035773 ! insulin secretion involved in cellular response to glucose stimulus
[Term]
@@ -337821,32 +337726,36 @@ relationship: negatively_regulates GO:0061054 ! dermatome development
[Term]
id: GO:0061186
-name: negative regulation of silent mating-type cassette heterochromatin assembly
+name: negative regulation of silent mating-type cassette heterochromatin formation
namespace: biological_process
-def: "Any process that decreases the frequency, rate, or extent of chromatin silencing at silent mating-type cassette. Chromatin silencing at silent mating-type cassette is the repression of transcription at silent mating-type loci by altering the structure of chromatin." [GOC:dph, PMID:10388812]
+def: "Any process that decreases the frequency, rate, or extent of heterochromatin formation at silent mating-type cassette." [GOC:dph, PMID:10388812]
synonym: "negative regulation of chromatin silencing at silent mating-type cassette" EXACT []
-is_a: GO:0031452 ! negative regulation of heterochromatin assembly
-is_a: GO:0090054 ! regulation of silent mating-type cassette heterochromatin assembly
-relationship: negatively_regulates GO:0030466 ! silent mating-type cassette heterochromatin assembly
+synonym: "negative regulation of silent mating-type cassette heterochromatin assembly" EXACT []
+is_a: GO:0031452 ! negative regulation of heterochromatin formation
+is_a: GO:0090054 ! regulation of silent mating-type cassette heterochromatin formation
+relationship: negatively_regulates GO:0030466 ! silent mating-type cassette heterochromatin formation
[Term]
id: GO:0061187
-name: regulation of ribosomal DNA heterochromatin assembly
+name: regulation of rDNA heterochromatin formation
namespace: biological_process
-def: "Any process that modulates the rate, frequency, or extent of the repression of assembly of rDNA heterochromatin." [GOC:dph, PMID:10388812]
+def: "Any process that modulates the rate, frequency, or extent of rDNA heterochromatin formation." [PMID:10388812]
synonym: "regulation of chromatin silencing at rDNA" BROAD []
-is_a: GO:0031445 ! regulation of heterochromatin assembly
-relationship: regulates GO:0000183 ! rDNA heterochromatin assembly
+synonym: "regulation of ribosomal DNA heterochromatin assembly" EXACT []
+is_a: GO:0031445 ! regulation of heterochromatin formation
+relationship: regulates GO:0000183 ! rDNA heterochromatin formation
[Term]
id: GO:0061188
-name: negative regulation of ribosomal DNA heterochromatin assembly
+name: negative regulation of rDNA heterochromatin formation
namespace: biological_process
-def: "Any process that decreases the rate, frequency, or extent of the repression of assembly of rDNA heterochromatin." [GOC:dph, PMID:10388812]
+def: "Any process that decreases the rate, frequency, or extent of ribosomal DNA heterochromatin formation." [GOC:dph, PMID:10388812]
synonym: "negative regulation of chromatin silencing at rDNA" BROAD []
-is_a: GO:0031452 ! negative regulation of heterochromatin assembly
-is_a: GO:0061187 ! regulation of ribosomal DNA heterochromatin assembly
-relationship: negatively_regulates GO:0000183 ! rDNA heterochromatin assembly
+synonym: "negative regulation of ribosomal DNA heterochromatin assembly" EXACT []
+synonym: "negative regulation of ribosomal DNA heterochromatin formation" EXACT []
+is_a: GO:0031452 ! negative regulation of heterochromatin formation
+is_a: GO:0061187 ! regulation of rDNA heterochromatin formation
+relationship: negatively_regulates GO:0000183 ! rDNA heterochromatin formation
[Term]
id: GO:0061189
@@ -338080,11 +337989,11 @@ relationship: part_of GO:0001823 ! mesonephros development
[Term]
id: GO:0061216
-name: regulation of transcription from RNA polymerase II promoter involved in mesonephros development
+name: obsolete regulation of transcription from RNA polymerase II promoter involved in mesonephros development
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the mesonephros progressing from its initial formation to the mature state." [GOC:mtg_kidney_jan10]
-is_a: GO:0060994 ! regulation of transcription from RNA polymerase II promoter involved in kidney development
-relationship: part_of GO:0001823 ! mesonephros development
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the mesonephros progressing from its initial formation to the mature state." [GOC:mtg_kidney_jan10]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0061217
@@ -338421,29 +338330,32 @@ relationship: part_of GO:0061253 ! mesonephric glomerular parietal epithelial ce
[Term]
id: GO:0061256
-name: mesonephric glomerular visceral epithelial cell differentiation
+name: mesonephric podocyte differentiation
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires specialized features of a mesonephric glomerular visceral epithelial cell. A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros." [GOC:mtg_kidney_jan10]
+synonym: "mesonephric glomerular visceral epithelial cell differentiation" EXACT []
is_a: GO:0061250 ! mesonephric glomerular epithelial cell differentiation
-is_a: GO:0072112 ! glomerular visceral epithelial cell differentiation
+is_a: GO:0072112 ! podocyte differentiation
[Term]
id: GO:0061257
-name: mesonephric glomerular visceral epithelial cell development
+name: mesonephric podocyte development
namespace: biological_process
def: "The process whose specific outcome is the progression of a mesonephric glomerular visceral epithelial cell over time, from its formation to the mature structure. A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros." [GOC:mtg_kidney_jan10]
+synonym: "mesonephric glomerular visceral epithelial cell development" EXACT []
is_a: GO:0061251 ! mesonephric glomerular epithelial cell development
-is_a: GO:0072015 ! glomerular visceral epithelial cell development
-relationship: part_of GO:0061256 ! mesonephric glomerular visceral epithelial cell differentiation
+is_a: GO:0072015 ! podocyte development
+relationship: part_of GO:0061256 ! mesonephric podocyte differentiation
[Term]
id: GO:0061258
-name: mesonephric glomerular visceral epithelial cell fate commitment
+name: mesonephric podocyte cell fate commitment
namespace: biological_process
def: "The process in which the developmental fate of a cell becomes restricted such that it will develop into a mesonephric glomerular visceral epithelial cell. A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros." [GOC:mtg_kidney_jan10]
+synonym: "mesonephric glomerular visceral epithelial cell fate commitment" EXACT []
is_a: GO:0061251 ! mesonephric glomerular epithelial cell development
-is_a: GO:0072149 ! glomerular visceral epithelial cell fate commitment
-relationship: part_of GO:0061256 ! mesonephric glomerular visceral epithelial cell differentiation
+is_a: GO:0072149 ! podocyte cell fate commitment
+relationship: part_of GO:0061256 ! mesonephric podocyte differentiation
[Term]
id: GO:0061259
@@ -338925,7 +338837,7 @@ relationship: part_of GO:0061307 ! cardiac neural crest cell differentiation inv
id: GO:0061311
name: cell surface receptor signaling pathway involved in heart development
namespace: biological_process
-def: "Any series of molecular signals initiated by the binding of a receptor on the surface of a cell to a physiological ligand, which contributes to the progression of the heart over time." [GOC:dph, GOC:mtg_heart, GOC:signaling]
+def: "The series of molecular signals initiated by a ligand the binding to its receptor on the surface of a cell, which contributes to the progression of the heart over time." [GOC:dph, GOC:mtg_heart, GOC:signaling]
synonym: "cell surface receptor linked signaling pathway involved in heart development" EXACT [GOC:bf]
synonym: "cell surface receptor linked signalling pathway involved in heart development" EXACT [GOC:mah]
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -338935,7 +338847,7 @@ relationship: part_of GO:0007507 ! heart development
id: GO:0061312
name: BMP signaling pathway involved in heart development
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the progression of the heart over time." [GOC:dph, GOC:mtg_heart]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to its receptor on the surface of a target cell, which contributes to the progression of the heart over time." [GOC:dph, GOC:mtg_heart]
synonym: "BMP signalling pathway involved in heart development" EXACT [GOC:mah]
is_a: GO:0030509 ! BMP signaling pathway
is_a: GO:0061311 ! cell surface receptor signaling pathway involved in heart development
@@ -339158,7 +339070,6 @@ name: cardiac conduction
namespace: biological_process
def: "Transfer of an organized electrical impulse across the heart to coordinate the contraction of cardiac muscles. The process begins with generation of an action potential (in the sinoatrial node (SA) in humans) and ends with a change in the rate, frequency, or extent of the contraction of the heart muscles." [GOC:dph]
is_a: GO:0008016 ! regulation of heart contraction
-is_a: GO:0035637 ! multicellular organismal signaling
[Term]
id: GO:0061338
@@ -339289,7 +339200,7 @@ is_a: GO:0061334 ! cell rearrangement involved in Malpighian tubule morphogenesi
id: GO:0061353
name: BMP signaling pathway involved in Malpighian tubule cell chemotaxis
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to the directed movement of a Malpighian tubule cell toward a stimulus, thereby contributing to the shaping of the tubule." [GOC:dph, GOC:mtg_kidney_jan10, PMID:19783135]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to its receptor on the surface of a target cell, which contributes to the directed movement of a Malpighian tubule cell toward a stimulus, thereby contributing to the shaping of the tubule." [GOC:dph, GOC:mtg_kidney_jan10, PMID:19783135]
synonym: "bone morphogenic protein receptor signalling pathway involved in Malpighian tubule cell chemotaxis" EXACT [GOC:mah]
is_a: GO:0030509 ! BMP signaling pathway
relationship: part_of GO:0061352 ! cell chemotaxis involved in Malpighian tubule morphogenesis
@@ -339464,7 +339375,7 @@ relationship: part_of GO:0007507 ! heart development
id: GO:0061372
name: activin receptor signaling pathway involved in heart jogging
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the activin family to a receptor on the surface of a target cell, and contributing to the process of heart jogging." [GOC:dph, GOC:mtg_heart, GOC:signaling]
+def: "The series of molecular signals initiated by the binding of a member of the activin family to its receptor on the surface of a target cell, and contributing to the process of heart jogging." [GOC:dph, GOC:mtg_heart, GOC:signaling]
synonym: "activin receptor signalling pathway involved in heart jogging" EXACT [GOC:mah]
is_a: GO:0032924 ! activin receptor signaling pathway
is_a: GO:0061311 ! cell surface receptor signaling pathway involved in heart development
@@ -339642,20 +339553,23 @@ consider: GO:0071470
[Term]
id: GO:0061394
-name: regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance
+name: obsolete regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance
namespace: biological_process
-def: "Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides." [GOC:dph]
-is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress
-relationship: part_of GO:0071243 ! cellular response to arsenic-containing substance
+def: "OBSOLETE. Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides." [GOC:dph]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0006357
+consider: GO:0071722
[Term]
id: GO:0061395
-name: positive regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides." [GOC:dph]
-is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress
-is_a: GO:0061394 ! regulation of transcription from RNA polymerase II promoter in response to arsenic-containing substance
-is_a: GO:1901522 ! positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides." [GOC:dph]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0045944
+consider: GO:0071722
[Term]
id: GO:0061396
@@ -339689,19 +339603,21 @@ consider: GO:0071280
[Term]
id: GO:0061399
-name: positive regulation of transcription from RNA polymerase II promoter in response to cobalt ion
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to cobalt ion
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to a cobalt ion stimulus." [GOC:dph]
-is_a: GO:1901522 ! positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus
-relationship: part_of GO:0071279 ! cellular response to cobalt ion
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to a cobalt ion stimulus." [GOC:dph]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+replaced_by: GO:0045944
[Term]
id: GO:0061400
-name: positive regulation of transcription from RNA polymerase II promoter in response to calcium ion
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to calcium ion
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to a calcium ion stimulus." [GOC:dph]
-is_a: GO:1901522 ! positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus
-relationship: part_of GO:0071277 ! cellular response to calcium ion
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to a calcium ion stimulus." [GOC:dph]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0045944
[Term]
id: GO:0061401
@@ -339724,11 +339640,13 @@ is_a: GO:0071468 ! cellular response to acidic pH
[Term]
id: GO:0061403
-name: positive regulation of transcription from RNA polymerase II promoter in response to nitrosative stress
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to nitrosative stress
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions." [GOC:dph]
-is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress
-is_a: GO:0071500 ! cellular response to nitrosative stress
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions." [GOC:dph]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0045944
+consider: GO:0071500
[Term]
id: GO:0061404
@@ -339742,12 +339660,12 @@ consider: GO:0071472
[Term]
id: GO:0061405
-name: positive regulation of transcription from RNA polymerase II promoter in response to hydrostatic pressure
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to hydrostatic pressure
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hydrostatic pressure stimulus. Hydrostatic pressure is the force acting on an object in a system where the fluid is at rest (as opposed to moving). The weight of the fluid above the object creates pressure on it." [GOC:dph]
-is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress
-is_a: GO:1901522 ! positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus
-relationship: part_of GO:0071464 ! cellular response to hydrostatic pressure
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hydrostatic pressure stimulus. Hydrostatic pressure is the force acting on an object in a system where the fluid is at rest (as opposed to moving). The weight of the fluid above the object creates pressure on it." [GOC:dph]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+replaced_by: GO:0045944
[Term]
id: GO:0061406
@@ -339775,19 +339693,20 @@ is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II p
[Term]
id: GO:0061409
-name: positive regulation of transcription from RNA polymerase II promoter in response to freezing
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to freezing
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a freezing stimulus, temperatures below 0 degrees Celsius." [GOC:dph]
-is_a: GO:0061411 ! positive regulation of transcription from RNA polymerase II promoter in response to cold
-is_a: GO:0071497 ! cellular response to freezing
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a freezing stimulus, temperatures below 0 degrees Celsius." [GOC:dph]
+comment: This term was obsoleted because this is not a GO process.
+is_obsolete: true
[Term]
id: GO:0061410
-name: positive regulation of transcription from RNA polymerase II promoter in response to ethanol
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to ethanol
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an ethanol stimulus." [GOC:dph]
-is_a: GO:1901522 ! positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus
-relationship: part_of GO:0071361 ! cellular response to ethanol
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an ethanol stimulus." [GOC:dph]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+replaced_by: GO:0045944
[Term]
id: GO:0061411
@@ -339799,11 +339718,13 @@ is_a: GO:0070417 ! cellular response to cold
[Term]
id: GO:0061412
-name: positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of amino acids." [GOC:dph]
-is_a: GO:0034198 ! cellular response to amino acid starvation
-is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of amino acids." [GOC:dph]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0034198
+consider: GO:0045944
[Term]
id: GO:0061413
@@ -339865,35 +339786,41 @@ is_a: GO:1901522 ! positive regulation of transcription from RNA polymerase II p
[Term]
id: GO:0061420
-name: regulation of transcription from RNA polymerase II promoter in response to biotin starvation
+name: obsolete regulation of transcription from RNA polymerase II promoter in response to biotin starvation
namespace: biological_process
-def: "Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of biotin." [GOC:dph, PMID:16533810]
-is_a: GO:0009267 ! cellular response to starvation
-is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress
+def: "OBSOLETE. Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of deprivation of biotin." [GOC:dph, PMID:16533810]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0006357
[Term]
id: GO:0061421
-name: positive regulation of transcription by oleic acid
+name: obsolete positive regulation of transcription by oleic acid
namespace: biological_process
-def: "Any process involving oleic acid that activates or increases the rate of transcription." [GOC:dph, PMID:20395639]
-is_a: GO:0045991 ! carbon catabolite activation of transcription
+def: "OBSOLETE. Any process involving oleic acid that activates or increases the rate of transcription." [GOC:dph, PMID:20395639]
+comment: This term was obsoleted because it it not different from its child positive regulation of transcription from RNA polymerase II promoter by oleic acid ; GO:0061429.
+is_obsolete: true
[Term]
id: GO:0061422
-name: positive regulation of transcription from RNA polymerase II promoter in response to alkaline pH
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to alkaline pH
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a pH >7.0." [GOC:dph, PMID:11523797, PMID:15299026, PMID:21749328]
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a pH >7.0." [GOC:dph, PMID:11523797, PMID:15299026, PMID:21749328]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "positive regulation of transcription from RNA polymerase II promoter in response to alkalinity" BROAD []
-is_a: GO:0036003 ! positive regulation of transcription from RNA polymerase II promoter in response to stress
-is_a: GO:0071469 ! cellular response to alkaline pH
+is_obsolete: true
+consider: GO:0045944
+consider: GO:0071469
[Term]
id: GO:0061423
-name: positive regulation of sodium ion transport by positive regulation of transcription from RNA polymerase II promoter
+name: obsolete positive regulation of sodium ion transport by positive regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter resulting in the increased frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, PMID:11523797]
-is_a: GO:0010765 ! positive regulation of sodium ion transport
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter resulting in the increased frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, PMID:11523797]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0045944
+consider: GO:1902307
[Term]
id: GO:0061424
@@ -339914,11 +339841,13 @@ is_a: GO:1900066 ! positive regulation of ethanol catabolic process
[Term]
id: GO:0061426
-name: positive regulation of sulfite transport by positive regulation of transcription from RNA polymerase II promoter
+name: obsolete positive regulation of sulfite transport by positive regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter and activates or increases the frequency, rate or extent of sulfite transport." [GOC:dph, PMID:10234785, PMID:10870099]
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
-is_a: GO:1900072 ! positive regulation of sulfite transport
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter and activates or increases the frequency, rate or extent of sulfite transport." [GOC:dph, PMID:10234785, PMID:10870099]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0006357
+consider: GO:1900071
[Term]
id: GO:0061427
@@ -339942,7 +339871,6 @@ name: positive regulation of transcription from RNA polymerase II promoter by ol
namespace: biological_process
def: "Any process involving oleic acid that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dph, PMID:20395639]
is_a: GO:0000436 ! carbon catabolite activation of transcription from RNA polymerase II promoter
-is_a: GO:0061421 ! positive regulation of transcription by oleic acid
[Term]
id: GO:0061430
@@ -339992,7 +339920,7 @@ id: GO:0061435
name: positive regulation of transcription from a mobile element promoter
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of transcription from a mobile element promoter." [GOC:dph, PMID:12230120, PMID:9271107]
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
[Term]
id: GO:0061436
@@ -340002,8 +339930,7 @@ def: "Establishment of the epithelial barrier, the functional barrier in the ski
synonym: "epithelial barrier development" RELATED [GOC:dph]
synonym: "establishment of epithelial barrier" BROAD [GOC:dph]
synonym: "skin barrier development" RELATED [GOC:dph]
-is_a: GO:0033561 ! regulation of water loss via skin
-relationship: part_of GO:0043588 ! skin development
+is_a: GO:0098773 ! skin epidermis development
[Term]
id: GO:0061437
@@ -340155,12 +340082,13 @@ is_a: GO:0061856 ! Golgi calcium ion transmembrane transport
[Term]
id: GO:0061455
-name: integral component of muscle cell projection membrane
+name: obsolete integral component of muscle cell projection membrane
namespace: cellular_component
-def: "The component of the muscle cell projection membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:dph, GOC:tb]
+def: "OBSOLETE. The component of the muscle cell projection membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:dph, GOC:tb]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to muscle cell projection membrane" EXACT []
-is_a: GO:0005887 ! integral component of plasma membrane
-relationship: part_of GO:0036195 ! muscle cell projection membrane
+is_obsolete: true
+replaced_by: GO:0036195
[Term]
id: GO:0061456
@@ -340203,10 +340131,9 @@ synonym: "histidine/arginine/lysine/ornithine porter activity" NARROW []
synonym: "L-arginine transporter activity" EXACT []
synonym: "L-arginine-importing ATPase activity" NARROW []
xref: RHEA:32143
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015174 ! basic amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
+is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
[Term]
id: GO:0061462
@@ -340363,7 +340290,7 @@ is_a: GO:0042221 ! response to chemical
id: GO:0061483
name: sulfinylpropanyl adenylate synthase
namespace: molecular_function
-def: "Catalysis of the reaction: cysteine sulfanate + GTP + IMP = sulfinylpropanyl adenylate + GDP + 3 H(+) + phosphate." [GOC:dph, PMID:8346915]
+def: "Catalysis of the reaction: cysteine sulfanate + GTP + IMP = sulfinylpropanyl adenylate + GDP + 3 H+ + phosphate." [GOC:dph, PMID:8346915]
synonym: "SPA synthase" RELATED [PMID:8346915]
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
@@ -340504,17 +340431,18 @@ synonym: "2',3'-cyclic GAMP binding" EXACT []
synonym: "2',5-3',5'-cyclic GMP-AMP binding" EXACT []
synonym: "c[G(2',5')pA(3',5')p] binding" EXACT [PMID:23910378]
synonym: "cyclic-GMP-AMP binding" BROAD []
-is_a: GO:0030551 ! cyclic nucleotide binding
is_a: GO:0032559 ! adenyl ribonucleotide binding
is_a: GO:0032561 ! guanyl ribonucleotide binding
is_a: GO:0043168 ! anion binding
+is_a: GO:0140702 ! cyclic GMP-AMP binding
[Term]
id: GO:0061508
-name: CDP phosphorylation
+name: obsolete CDP phosphorylation
namespace: biological_process
-def: "The process of introducing a phosphate group into CDP to produce a CTP." [PMID:7499258]
-is_a: GO:0006165 ! nucleoside diphosphate phosphorylation
+def: "OBSOLETE. The process of introducing a phosphate group into CDP to produce a CTP." [PMID:7499258]
+comment: The reason for obsoletion is that this term represents a single step MF.
+is_obsolete: true
[Term]
id: GO:0061509
@@ -340554,16 +340482,17 @@ namespace: molecular_function
alt_id: GO:0008524
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: glucose 6-phosphate(out) + inorganic phosphate(in) = glucose 6-phosphate(in) + inorganic phosphate(out)." [GOC:dph, PMID:18337460]
synonym: "glucose 6-phosphate:phosphate antiporter activity" BROAD []
-xref: Reactome:R-HSA-198513 "Cytosolic glucose 6-phosphate is exchanged for orthophosphate from the endoplasmic reticulum lumen by SLC37A4"
+xref: Reactome:R-HSA-198513 "SLC7A4 exchanges G6P for Pi across the ER membrane"
xref: Reactome:R-HSA-3229118 "Defective SLC37A4 does not exchange G6P and Pi across the ER membrane"
-xref: Reactome:R-HSA-3257122 "SLC37A1, SLC37A2 exchange G6P for Pi across the endoplasmic reticulum membrane"
+xref: Reactome:R-HSA-3257122 "SLC37A1, SLC37A2 exchange G6P for Pi across the ER membrane"
+is_a: GO:0015152 ! glucose-6-phosphate transmembrane transporter activity
is_a: GO:0015526 ! hexose-phosphate:inorganic phosphate antiporter activity
[Term]
id: GO:0061514
name: interleukin-34-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-34 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:dph, PMID:18467591]
+def: "The series of molecular signals initiated by interleukin-34 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:dph, PMID:18467591]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
[Term]
@@ -340571,7 +340500,7 @@ id: GO:0061515
name: myeloid cell development
namespace: biological_process
def: "The process whose specific outcome is the progression of a myeloid cell over time, from its formation to the mature structure." [GOC:dph]
-is_a: GO:0048468 ! cell development
+is_a: GO:0030097 ! hemopoiesis
relationship: part_of GO:0030099 ! myeloid cell differentiation
[Term]
@@ -340663,8 +340592,8 @@ id: GO:0061527
name: dopamine secretion, neurotransmission
namespace: biological_process
def: "The regulated release of dopamine by a cell in which the dopamine acts as a neurotransmitter." [GOC:dph]
-is_a: GO:0007269 ! neurotransmitter secretion
is_a: GO:0099124 ! axonal dopamine secretion
+is_a: GO:0160043 ! catecholamine secretion, neurotransmission
relationship: part_of GO:0001963 ! synaptic transmission, dopaminergic
[Term]
@@ -340682,8 +340611,8 @@ name: epinephrine secretion, neurotransmission
namespace: biological_process
def: "The regulated release of epinephrine by a cell in which the epinephrine acts as a neurotransmitter." [GOC:dph]
synonym: "adrenaline secretion, neurotransmission" EXACT [GOC:dph]
-is_a: GO:0007269 ! neurotransmitter secretion
is_a: GO:0048242 ! epinephrine secretion
+is_a: GO:0160043 ! catecholamine secretion, neurotransmission
[Term]
id: GO:0061530
@@ -340706,7 +340635,8 @@ id: GO:0061532
name: primary amine secretion, neurotransmission
namespace: biological_process
def: "The regulated release of a primary amine by a cell, in which the primary amine acts as a neurotransmitter." [GOC:dph]
-is_a: GO:0061545 ! tyramine secretion
+is_a: GO:0007269 ! neurotransmitter secretion
+is_a: GO:0061531 ! primary amine secretion
[Term]
id: GO:0061533
@@ -340714,8 +340644,8 @@ name: norepinephrine secretion, neurotransmission
namespace: biological_process
def: "The regulated release of norepinephrine by a cell, in which the norepinephrine acts as a neurotransmitter." [GOC:dph]
synonym: "noradrenaline secretion, neurotransmission" EXACT [GOC:dph]
-is_a: GO:0007269 ! neurotransmitter secretion
is_a: GO:0048243 ! norepinephrine secretion
+is_a: GO:0160043 ! catecholamine secretion, neurotransmission
[Term]
id: GO:0061534
@@ -340733,6 +340663,7 @@ namespace: biological_process
def: "The controlled release of glutamate by a cell, in which the glutamate acts as a neurotransmitter." [GOC:dph]
is_a: GO:0007269 ! neurotransmitter secretion
is_a: GO:0014047 ! glutamate secretion
+is_a: GO:0051938 ! L-glutamate import
relationship: part_of GO:0035249 ! synaptic transmission, glutamatergic
[Term]
@@ -340759,6 +340690,8 @@ namespace: biological_process
def: "The controlled release of histamine by a cell, in which the histamine acts as a neurotransmitter." [GOC:dph]
is_a: GO:0001821 ! histamine secretion
is_a: GO:0007269 ! neurotransmitter secretion
+is_a: GO:0015801 ! aromatic amino acid transport
+is_a: GO:0015807 ! L-amino acid transport
[Term]
id: GO:0061539
@@ -340819,7 +340752,6 @@ id: GO:0061545
name: tyramine secretion
namespace: biological_process
def: "The regulated release of a tyramine by a cell." [GOC:dph]
-is_a: GO:0006812 ! cation transport
is_a: GO:0015844 ! monoamine transport
is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0061531 ! primary amine secretion
@@ -340830,6 +340762,7 @@ name: tyramine secretion, neurotransmission
namespace: biological_process
def: "The regulated release of a tyramine by a cell in which the tyramine acts as a neurotransmitter." [GOC:dph]
is_a: GO:0061532 ! primary amine secretion, neurotransmission
+is_a: GO:0061545 ! tyramine secretion
[Term]
id: GO:0061547
@@ -340848,7 +340781,6 @@ def: "The process whose specific outcome is the progression of a ganglion over t
synonym: "ganglia development" RELATED [GOC:dph]
synonym: "gangliogenesis" NARROW [GOC:BHF, GOC:rl]
is_a: GO:0009888 ! tissue development
-is_a: GO:0048513 ! animal organ development
relationship: part_of GO:0007399 ! nervous system development
[Term]
@@ -340883,7 +340815,6 @@ name: ganglion morphogenesis
namespace: biological_process
def: "The process in which the anatomical structures of ganglion are generated and organized." [GOC:dph]
synonym: "ganglia morphogenesis" RELATED [GOC:dph]
-is_a: GO:0009887 ! animal organ morphogenesis
is_a: GO:0048729 ! tissue morphogenesis
relationship: part_of GO:0061548 ! ganglion development
@@ -340893,7 +340824,7 @@ name: ganglion maturation
namespace: biological_process
def: "A developmental process, independent of morphogenetic (shape) change, that is required for ganglion to attain its fully functional state." [GOC:dph]
synonym: "ganglia maturation" RELATED [GOC:dph]
-is_a: GO:0048799 ! animal organ maturation
+is_a: GO:0071695 ! anatomical structure maturation
relationship: part_of GO:0061548 ! ganglion development
[Term]
@@ -341022,31 +340953,35 @@ is_a: GO:0046940 ! nucleoside monophosphate phosphorylation
[Term]
id: GO:0061568
-name: GDP phosphorylation
+name: obsolete GDP phosphorylation
namespace: biological_process
-def: "The process of introducing a phosphate group into GDP, guanosine diphosphate, to produce GTP." [GOC:dph, PMID:23416111]
-is_a: GO:0006165 ! nucleoside diphosphate phosphorylation
+def: "OBSOLETE. The process of introducing a phosphate group into GDP, guanosine diphosphate, to produce GTP." [GOC:dph, PMID:23416111]
+comment: The reason for obsoletion is that this term represents a single step MF.
+is_obsolete: true
[Term]
id: GO:0061569
-name: UDP phosphorylation
+name: obsolete UDP phosphorylation
namespace: biological_process
-def: "The process of introducing a phosphate group into UDP, uridine diphosphate, to produce UTP." [GOC:dph, PMID:23416111]
-is_a: GO:0006165 ! nucleoside diphosphate phosphorylation
+def: "OBSOLETE. The process of introducing a phosphate group into UDP, uridine diphosphate, to produce UTP." [GOC:dph, PMID:23416111]
+comment: The reason for obsoletion is that this term represents a single step MF.
+is_obsolete: true
[Term]
id: GO:0061570
-name: dCDP phosphorylation
+name: obsolete dCDP phosphorylation
namespace: biological_process
-def: "The process of introducing a phosphate group into dCDP to produce a dCTP." [GOC:dph, PMID:23416111]
-is_a: GO:0006165 ! nucleoside diphosphate phosphorylation
+def: "OBSOLETE. The process of introducing a phosphate group into dCDP to produce a dCTP." [GOC:dph, PMID:23416111]
+comment: The reason for obsoletion is that this term represents a single step MF.
+is_obsolete: true
[Term]
id: GO:0061571
-name: TDP phosphorylation
+name: obsolete TDP phosphorylation
namespace: biological_process
-def: "The process of introducing a phosphate group into TDP to produce a TTP." [GOC:dph, PMID:23416111]
-is_a: GO:0006165 ! nucleoside diphosphate phosphorylation
+def: "OBSOLETE. The process of introducing a phosphate group into TDP to produce a TTP." [GOC:dph, PMID:23416111]
+comment: The reason for obsoletion is that this term represents a single step MF.
+is_obsolete: true
[Term]
id: GO:0061572
@@ -341087,7 +341022,7 @@ id: GO:0061576
name: acyl-CoA ceramide synthase complex
namespace: cellular_component
def: "A protein complex that catalyzes the reaction acyl-CoA + sphingosine = CoA + N-acylsphingosine. In S. cerevisiae it contains three subunits: lag1, lac1 and lip1." [GOC:dph, PMID:15692566]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0061577
@@ -341099,10 +341034,12 @@ is_a: GO:0070588 ! calcium ion transmembrane transport
[Term]
id: GO:0061578
-name: Lys63-specific deubiquitinase activity
+name: K63-linked deubiquitinase activity
namespace: molecular_function
-def: "Hydrolysis of Lys63-Linked ubiquitin unit(s) from a ubiquitinated protein." [GOC:dph, GOC:pg, PMID:18313383]
-xref: Reactome:R-HSA-5357845 "RIPK1 is deubiquitinated"
+def: "Hydrolysis of a ubiquitin unit from a ubiquitinated protein linked via the Lys63 residue of ubiquitin." [GOC:dph, GOC:pg, PMID:18313383]
+synonym: "K63-specific deubiquitinase activity" EXACT []
+synonym: "Lys63-specific deubiquitinase activity" EXACT []
+xref: Reactome:R-HSA-5357845 "K63polyUb-RIPK1 is deubiquitinated"
xref: Reactome:R-HSA-5690856 "TNFAIP3 (A20) deubiquitinates K63polyUb-RIPK1"
xref: Reactome:R-HSA-5691411 "BRCA1-A complex deubiquitinates K63polyUb-histone H2A"
xref: Reactome:R-HSA-5691431 "PSMD14 cleaves K63-linked ubiquitin"
@@ -341113,6 +341050,10 @@ xref: Reactome:R-HSA-741411 "CYLD deubiquitinates NEMO"
xref: Reactome:R-HSA-8869506 "TNFAIP3 in OTUD7B:TNFAIP3:ZRANB1 deubiquitinates K63polyUb-TRAF6"
xref: Reactome:R-HSA-936381 "OTUD5 deubiquitinates TRAF3"
xref: Reactome:R-HSA-936390 "CYLD mediated deubiquitination of DDX58 (RIG-I)"
+xref: Reactome:R-HSA-9685219 "SARS-CoV-1 nsp3 deubiquinates K63-linked pUb oligo-TRAF6 (TLR7/8 signaling)"
+xref: Reactome:R-HSA-9711016 "SARS-CoV-1 nsp3 deubiquinates K63-linked pUb-STING"
+xref: Reactome:R-HSA-9750942 "USP14 deubiquitinates NLRC5"
+xref: Reactome:R-HSA-9817400 "CYLD hydrolyses K63polyUb on RIPK1 within the TNFR1 complex"
is_a: GO:0101005 ! deubiquitinase activity
[Term]
@@ -341136,7 +341077,7 @@ is_a: GO:0061582 ! intestinal epithelial cell migration
id: GO:0061581
name: corneal epithelial cell migration
namespace: biological_process
-def: "The orderly movement of a corneal epithelial cell from one site to another, often during the development of a multicellular organism." [GOC:dph]
+def: "The orderly movement of a corneal epithelial cell from one site to another, often during the development of a multicellular organism." [GOC:dph]
is_a: GO:0010631 ! epithelial cell migration
[Term]
@@ -341156,40 +341097,43 @@ is_a: GO:0061580 ! colon epithelial cell migration
[Term]
id: GO:0061584
-name: hypocretin secretion
+name: orexin secretion
namespace: biological_process
-def: "The controlled release of hypocretin from a cell or a tissue." [GOC:dph]
-synonym: "orexin secretion" EXACT [GOC:dph]
+def: "The controlled release of orexin from a cell or a tissue." [GOC:dph]
+synonym: "hypocretin secretion" EXACT []
is_a: GO:0002790 ! peptide secretion
[Term]
id: GO:0061585
-name: hypocretin secretion, neurotransmission
+name: orexin secretion, neurotransmission
namespace: biological_process
-def: "The controlled release of a peptide from a cell or a tissue in which the peptide acts as a neurotransmitter." [GOC:dph]
-synonym: "orexin secretion, neurotransmission" EXACT [GOC:dph]
+def: "The controlled release of orexin from a cell in which orexin acts as a neurotransmitter." [GOC:dph]
+synonym: "hypocretin secretion, neurotransmission" EXACT []
is_a: GO:0061544 ! peptide secretion, neurotransmission
-is_a: GO:0061584 ! hypocretin secretion
+is_a: GO:0061584 ! orexin secretion
[Term]
id: GO:0061586
name: positive regulation of transcription by transcription factor localization
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the localization of a transcription factor." [GOC:dph]
-is_a: GO:0034613 ! cellular protein localization
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0008104 ! protein localization
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
[Term]
id: GO:0061587
-name: transfer RNA gene-mediated silencing
+name: obsolete tRNA locus-associated negative regulation of gene expression
namespace: biological_process
-def: "The chromatin silencing that results in the inhibition of RNA polymerase II-transcribed genes located in the vicinity of tRNA genes." [GOC:dph, PMID:23707796]
+def: "OBSOLETE. The chromatin silencing process that results in the inhibition of RNA polymerase II-transcribed genes located in the vicinity of tRNA genes." [GOC:dph, PMID:23707796, PMID:30362930, PMID:30718362]
+comment: This term was obsoleted because there is no evidence that it is a separate process.
+synonym: "tDNA-mediated gene silencing" EXACT []
synonym: "tgm silencing" EXACT [PMID:23707796]
synonym: "transfer RNA gene-mediated chromatin silencing" EXACT [GOC:dph]
synonym: "transfer RNA gene-mediated gene silencing" EXACT [GOC:dph]
+synonym: "transfer RNA gene-mediated silencinga" EXACT []
synonym: "tRNA gene-mediated chromatin silencing" EXACT [GOC:dph]
synonym: "tRNA gene-mediated gene silencing" EXACT [GOC:dph]
-is_a: GO:0140458 ! pre-transcriptional gene silencing by RNA
+is_obsolete: true
[Term]
id: GO:0061588
@@ -341310,7 +341254,7 @@ is_a: GO:0070568 ! guanylyltransferase activity
id: GO:0061604
name: molybdopterin-synthase sulfurtransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: [Molybdopterin-synthase sulfur-carrier protein]-Gly-Gly-AMP + [cysteine desulfurase]-S-sulfanyl-L-cysteine <=> AMP [molybdopterin-synthase sulfur-carrier protein]-Gly-NH-CH(2)-C(O)SH + cysteine desulfurase." [EC:2.8.1.11, GOC:dph, PMID:18154309, PMID:22370186]
+def: "Catalysis of the reaction: [Molybdopterin-synthase sulfur-carrier protein]-Gly-Gly-AMP + [cysteine desulfurase]-S-sulfanyl-L-cysteine = AMP [molybdopterin-synthase sulfur-carrier protein]-Gly-NH-CH(2)-C(O)SH + cysteine desulfurase." [EC:2.8.1.11, GOC:dph, PMID:18154309, PMID:22370186]
xref: EC:2.8.1.11
xref: RHEA:48612
is_a: GO:0016783 ! sulfurtransferase activity
@@ -341403,7 +341347,8 @@ synonym: "miRNA gene transcription" EXACT []
synonym: "pri-miRNA transcription by RNA polymerase II" EXACT []
synonym: "pri-miRNA transcription from RNA polymerase II promoter" EXACT []
synonym: "primary miRNA gene transcription" EXACT []
-is_a: GO:0006351 ! transcription, DNA-templated
+is_a: GO:0006351 ! DNA-templated transcription
+is_a: GO:0010586 ! miRNA metabolic process
[Term]
id: GO:0061615
@@ -341434,7 +341379,6 @@ synonym: "MINOS complex" EXACT [GOC:dph]
synonym: "mitochondrial contact site and cristae organizing system" EXACT [GOC:dph]
synonym: "MitOS complex" EXACT [GOC:dph]
is_a: GO:0098800 ! inner mitochondrial membrane protein complex
-relationship: part_of GO:0031305 ! integral component of mitochondrial inner membrane
[Term]
id: GO:0061618
@@ -341464,7 +341408,7 @@ is_a: GO:0061615 ! glycolytic process through fructose-6-phosphate
id: GO:0061621
name: canonical glycolysis
namespace: biological_process
-def: "The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP." [GOC:dph, ISBN:0201090910, ISBN:0879010479]
+def: "The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP." [GOC:dph, ISBN:0201090910, ISBN:0879010479]
xref: MetaCyc:ANAGLYCOLYSIS-PWY
xref: MetaCyc:PWY66-400
xref: Reactome:R-HSA-70171 "Glycolysis, Homo sapiens"
@@ -341649,11 +341593,21 @@ xref: Reactome:R-HSA-934604 "Phosphorylated SPRY2 is ubiquitinated by CBL"
xref: Reactome:R-HSA-936462 "PIN1 mediated IRF3 degradation"
xref: Reactome:R-HSA-936475 "Negative regulation of DDX58/IFIH1 signaling by RNF216"
xref: Reactome:R-HSA-9604629 "FBXW7 promotes ubiquitination of p-NICD4"
+xref: Reactome:R-HSA-9685195 "SARS-CoV-1 9b recruits ITCH to MAVS"
xref: Reactome:R-HSA-9686920 "PELI1 ubiquitinates RIPK3 at K363"
xref: Reactome:R-HSA-9686969 "APC/C:Cdh1 polyubiquitinates SKP2"
+xref: Reactome:R-HSA-9705738 "SOCS1,3 ubiquitinates CSF3R in SOCS1,3:p-4Y-CSF3R:CSF3 dimer:LYN:p-Y-JAK1:p-JAK2:p-SYK:p-HCK:p-TYK2:CUL5:ELOB:ELOC:RNF7"
xref: Reactome:R-HSA-9706354 "Ubiquitination of FLT3"
xref: Reactome:R-HSA-9706356 "CBL mutants don't ubiquitinate FLT3"
-xref: Reactome:R-HSA-990526 "Recruitment of AIP4 and K48 ubiquitination of MAVS/IPS-1"
+xref: Reactome:R-HSA-9708517 "FBXL17 ubiquitinates BACH1 (in BACH1:FBXL17:SCF (SKP2))"
+xref: Reactome:R-HSA-9733316 "p-Y-CBL autoubiquitinates and multiubiquitinates p-Y561-CSF1R in CSF1 dimer:p-Y561-CSF1R dimer:p-Y-CBL"
+xref: Reactome:R-HSA-9755304 "MUL1 ubiquitinates UBXN7"
+xref: Reactome:R-HSA-9755505 "KEAP1:NEDD8-CUL3:RBX1 complex ubiquitinates NFE2L2"
+xref: Reactome:R-HSA-9759154 "TRIM21 ubiquitinates SQSTM1"
+xref: Reactome:R-HSA-9759172 "KEAP1:CUL3:RBX1 ubiquitinates p-S349 SQSTM1 oligomer"
+xref: Reactome:R-HSA-9762091 "NFE2L2 is ubiquitinated by BTRC:SKP1:CUL1:RBX1"
+xref: Reactome:R-HSA-9766645 "CUL3:RBX1 ubiquitinates KEAP1"
+xref: Reactome:R-HSA-990526 "Recruitment of ITCH and K48 ubiquitination of MAVS"
is_a: GO:0004842 ! ubiquitin-protein transferase activity
is_a: GO:0061659 ! ubiquitin-like protein ligase activity
@@ -341672,7 +341626,7 @@ is_a: GO:0061650 ! ubiquitin-like protein conjugating enzyme activity
id: GO:0061632
name: RNA lariat debranching enzyme activator activity
namespace: molecular_function
-def: "Increases the activity of an enzyme that catalyzes the hydrolysis of branched RNA structures that contain vicinal 2'-5'- and 3'-5'-phosphodiester bonds at a branch point nucleotide." [GOC:dph, PMID:24919400]
+def: "Binds to and increases the activity of an RNA lariat debranching enzyme." [GOC:dph, PMID:24919400]
is_a: GO:0008047 ! enzyme activator activity
[Term]
@@ -341726,14 +341680,6 @@ namespace: biological_process
def: "A cytokinesis that involves the function of a set of proteins that are part of the microfilament or microtubule cytoskeleton." [GOC:dph]
is_a: GO:0000910 ! cytokinesis
-[Term]
-id: GO:0061641
-name: CENP-A containing chromatin organization
-namespace: biological_process
-def: "Any process that results in the specification, formation or maintenance of the physical structure of CENP-A containing chromatin." [GOC:dph]
-synonym: "centromeric chromatin organization" RELATED [GOC:dph]
-is_a: GO:0006325 ! chromatin organization
-
[Term]
id: GO:0061642
name: chemoattraction of axon
@@ -341764,7 +341710,7 @@ is_a: GO:0071459 ! protein localization to chromosome, centromeric region
id: GO:0061645
name: endocytic patch
namespace: cellular_component
-def: "The part of the cell cortex consisting of an aggregation of proteins that will give rise to an endocytic vesicle." [GOC:dph, PMID:22949647]
+def: "The part of the cell cortex consisting of an aggregation of proteins that will give rise to an endocytic vesicle." [GOC:dph, PMID:22949647]
is_a: GO:0110165 ! cellular anatomical entity
relationship: part_of GO:0005938 ! cell cortex
@@ -341794,7 +341740,7 @@ is_a: GO:0042476 ! odontogenesis
id: GO:0061649
name: ubiquitin modification-dependent histone binding
namespace: molecular_function
-def: "Binding to a histone protein in which a residue has been modified by ubiquitination. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:dph, PMID:24526689]
+def: "Binding to a histone protein in which a residue has been modified by ubiquitination." [GOC:dph, PMID:24526689]
synonym: "ubiquitinated histone binding" RELATED []
is_a: GO:0042393 ! histone binding
is_a: GO:0140036 ! ubiquitin-dependent protein binding
@@ -341839,8 +341785,9 @@ is_a: GO:0061650 ! ubiquitin-like protein conjugating enzyme activity
id: GO:0061654
name: NEDD8 conjugating enzyme activity
namespace: molecular_function
-def: "Isoenergetic transfer of NEDD8 from one protein to another via the reaction X-NEDD8 + Y -> Y-NEDD8 + X, where both the X-NEDD8 and Y-NEDD8 linkages are thioester bonds between the C-terminal amino acid of NEDD8 and a sulfhydryl side group of a cysteine residue." [GOC:dph]
+def: "Isoenergetic transfer of NEDD8 from one protein to another via the reaction X-NEDD8 + Y = Y-NEDD8 + X, where both the X-NEDD8 and Y-NEDD8 linkages are thioester bonds between the C-terminal amino acid of NEDD8 and a sulfhydryl side group of a cysteine residue." [GOC:dph]
synonym: "E2" RELATED [GOC:dph]
+xref: EC:2.3.2.34
is_a: GO:0019788 ! NEDD8 transferase activity
is_a: GO:0061650 ! ubiquitin-like protein conjugating enzyme activity
@@ -341920,7 +341867,7 @@ is_a: GO:0061659 ! ubiquitin-like protein ligase activity
id: GO:0061663
name: NEDD8 ligase activity
namespace: molecular_function
-def: "Catalysis of the transfer of NEDD8 to a substrate protein via the reaction X-NEDD8 + S --> X + S-NEDD8, where X is either an E2 or E3 enzyme, the X-NEDD8 linkage is a thioester bond, and the S-NEDD8 linkage is an isopeptide bond between the C-terminal amino acid of NEDD8 and the epsilon-amino group of lysine residues in the substrate." [GOC:dph]
+def: "Catalysis of the transfer of NEDD8 to a substrate protein via the reaction X-NEDD8 + S = X + S-NEDD8, where X is either an E2 or E3 enzyme, the X-NEDD8 linkage is a thioester bond, and the S-NEDD8 linkage is an isopeptide bond between the C-terminal amino acid of NEDD8 and the epsilon-amino group of lysine residues in the substrate." [GOC:dph]
synonym: "E3" RELATED [GOC:dph]
is_a: GO:0019788 ! NEDD8 transferase activity
is_a: GO:0061659 ! ubiquitin-like protein ligase activity
@@ -342038,7 +341985,7 @@ id: GO:0061677
name: 2-dehydro-3-deoxy-D-gluconate aldolase activity
namespace: molecular_function
alt_id: GO:0043725
-def: "Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate <=> pyruvate + D-glyceraldehyde." [EC:4.1.2.51, GOC:dph, PMID:12824170, RHEA:35583]
+def: "Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate = pyruvate + D-glyceraldehyde." [GOC:dph, PMID:12824170, RHEA:35583]
synonym: "2-keto-3-deoxygluconate aldolase activity" EXACT []
synonym: "KDG aldolase activity" EXACT []
xref: EC:4.1.2.51
@@ -342053,7 +342000,7 @@ name: Entner-Doudoroff pathway
namespace: biological_process
def: "A cellular carbohydrate catabolic process that converts a carbohydrate to pyruvate and either glyceraldehyde or glyceraldehyde-3 phosphate by dehydration and aldol cleavage via a gluconate or 6-phosphogluconate intermediate." [GOC:dph, PMID:12921536]
xref: MetaCyc:Entner-Doudoroff-Pathways
-is_a: GO:0044275 ! cellular carbohydrate catabolic process
+is_a: GO:0016052 ! carbohydrate catabolic process
[Term]
id: GO:0061679
@@ -342118,7 +342065,7 @@ is_a: GO:0030163 ! protein catabolic process
id: GO:0061685
name: diphthine methylesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: diphthine methyl ester + H2O <=> diphthine + H+ + methanol." [GOC:dph, PMID:24739148, RHEA:42656]
+def: "Catalysis of the reaction: diphthine methyl ester + H2O = diphthine + H+ + methanol." [GOC:dph, PMID:24739148, RHEA:42656]
xref: EC:3.1.1.97
xref: RHEA:42656
is_a: GO:0052689 ! carboxylic ester hydrolase activity
@@ -342127,12 +342074,12 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0061686
name: hercynylcysteine sulfoxide synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-cysteine + N-alpha,N-alpha,N-alpha-trimethyl-L-histidine (hercynine) + O2 <=> hercynylcysteine sulfoxide + H2O." [GOC:dph, PMID:24828577, PMID:4276459, RHEA:42704]
+def: "Catalysis of the reaction: L-cysteine + N-alpha,N-alpha,N-alpha-trimethyl-L-histidine (hercynine) + O2 = hercynylcysteine sulfoxide + H2O." [GOC:dph, PMID:24828577, PMID:4276459, RHEA:42704]
synonym: "hercynylcysteine S-oxide synthase" EXACT [GOC:dph]
synonym: "hercynylcysteine sulfoxide synthase" EXACT []
-xref: EC:1.14.99.51
+xref: EC:1.21.3.10
xref: RHEA:42704
-is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+is_a: GO:0046993 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with oxygen as acceptor
[Term]
id: GO:0061687
@@ -342224,6 +342171,7 @@ def: "Catalysis of the reaction: H2O + N(6)-glutaryl-L-lysyl-[protein] + NAD(+)
comment: This reaction is the removal of a glutaryl group from a glutarylated lysine residue of a protein or peptide.
xref: RHEA:47664
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
+is_a: GO:0140096 ! catalytic activity, acting on a protein
[Term]
id: GO:0061698
@@ -342244,7 +342192,7 @@ id: GO:0061700
name: GATOR2 complex
namespace: cellular_component
def: "A multiprotein subcomplex of the GATOR complex that regulates TORC1 signaling by interacting with the Rag GTPase. In human, this complex consists of WDR24, WDR59, MIOS, SEH1L, and SEC13. In S. cerevisiae, this complex is referred to as SEACAT and contains the Sea2p, Sea3p, Sea4p, Seh1p, Sec13p proteins." [GOC:krc, GOC:rb, PMID:23723238, PMID:25934700]
-comment: The Rag GTPase complex corresponds to Gtr1-Gtr2 GTPase complex ; GO:1990131.
+comment: The Rag GTPase complex corresponds to Gtr1-Gtr2 GTPase complex ; GO:1990131.
synonym: "SEACAT complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0035859 ! Seh1-associated complex
@@ -342258,7 +342206,7 @@ is_a: GO:1903561 ! extracellular vesicle
[Term]
id: GO:0061702
-name: inflammasome complex
+name: canonical inflammasome complex
namespace: cellular_component
def: "A cytosolic protein complex that is capable of activating caspase-1." [GOC:dph, PMID:17599095]
is_a: GO:0032991 ! protein-containing complex
@@ -342309,7 +342257,8 @@ is_a: GO:0051650 ! establishment of vesicle localization
id: GO:0061708
name: tRNA-5-taurinomethyluridine 2-sulfurtransferase
namespace: molecular_function
-def: "Catalysis of 5-taurinomethyluridine in tRNA + a [protein]-S-sulfanylcysteine + ATP + a reduced electron acceptor = a 5-taurinomethyl-2-thiouridine in tRNA + a [protein]-L-cysteine + AMP + an oxidized electron acceptor + diphosphate + H+." [GOC:dph, PMID:15509579]
+def: "Catalysis of 5-taurinomethyluridine in tRNA + a [protein]-S-sulfanylcysteine + ATP + a reduced electron acceptor = a 5-taurinomethyl-2-thiouridine in tRNA + a [protein]-L-cysteine + AMP + an oxidized electron acceptor + diphosphate + H+." [GOC:dph, PMID:15509579, RHEA:47040]
+xref: EC:2.8.1.14
xref: MetaCyc:RXN-16821
xref: Reactome:R-HSA-6787447 "TRMU (MTO2, MTU1) transfers a sulfur atom to 5-taurinomethyluridine-34 in tRNA"
xref: RHEA:47040
@@ -342336,7 +342285,7 @@ is_a: GO:1903008 ! organelle disassembly
id: GO:0061710
name: L-threonylcarbamoyladenylate synthase
namespace: molecular_function
-def: "Catalysis of the reaction: L-threonine + ATP + bicarbonate = L-threonylcarbamoyladenylate + diphosphate + H(2)O." [EC:2.7.7.87]
+def: "Catalysis of the reaction: L-threonine + ATP + bicarbonate = L-threonylcarbamoyladenylate + diphosphate + H2O." [EC:2.7.7.87]
xref: EC:2.7.7.87
xref: MetaCyc:RXN-14569
xref: RHEA:36407
@@ -342382,11 +342331,12 @@ is_a: GO:0038024 ! cargo receptor activity
[Term]
id: GO:0061715
-name: miRNA 2'-O-methylation
+name: obsolete miRNA 2'-O-methylation
namespace: biological_process
-def: "The posttranscriptional addition of a methyl group to the 2' oxygen atom of a nucleotide residue in an miRNA molecule." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:20705645]
-is_a: GO:0001510 ! RNA methylation
-is_a: GO:0010586 ! miRNA metabolic process
+def: "OBSOLETE. The posttranscriptional addition of a methyl group to the 2' oxygen atom of a nucleotide residue in an miRNA molecule." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:20705645]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0090486
[Term]
id: GO:0061716
@@ -342445,9 +342395,6 @@ namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of 6-sulfoquinovose(1-) resulting in the formation of glycerone phosphate (DHAP) and pyruvate." [GOC:dph, PMID:24463506]
synonym: "sulfoglycolysis" EXACT [PMID:14602597]
is_a: GO:0006091 ! generation of precursor metabolites and energy
-is_a: GO:0006734 ! NADH metabolic process
-is_a: GO:0019674 ! NAD metabolic process
-is_a: GO:0046034 ! ATP metabolic process
is_a: GO:1902777 ! 6-sulfoquinovose(1-) catabolic process
[Term]
@@ -342536,23 +342483,29 @@ is_a: GO:0016728 ! oxidoreductase activity, acting on CH or CH2 groups, disulfid
[Term]
id: GO:0061732
-name: mitochondrial acetyl-CoA biosynthetic process from pyruvate
+name: obsolete mitochondrial acetyl-CoA biosynthetic process from pyruvate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate in the mitochondrion. The process begins with the transport of pyruvate from the cytosol to the mitochondrion where it is subsequently decarboxylated to form acetyl-CoA." [GOC:dph, ISBN:0201090910]
-xref: Reactome:R-HSA-372342.1
-xref: Reactome:R-HSA-71397.1
-is_a: GO:0006086 ! acetyl-CoA biosynthetic process from pyruvate
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate in the mitochondrion. The process begins with the transport of pyruvate from the cytosol to the mitochondrion where it is subsequently decarboxylated to form acetyl-CoA." [GOC:dph, ISBN:0201090910]
+comment: This term was obsoleted because it was representing the same process as its parent.
+is_obsolete: true
+replaced_by: GO:0006086
[Term]
id: GO:0061733
name: peptide-lysine-N-acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + lysine in peptide = CoA + N-acetyl-lysine-peptide." [GOC:dph]
+synonym: "peptide-lysine-N-acetylase activity" EXACT []
+synonym: "protein acetylase activity" BROAD []
+synonym: "protein acetyltransferase activity" BROAD []
+synonym: "protein-lysine-N-acetylase activity" EXACT []
xref: Reactome:R-HSA-6811508 "ING2-bound EP300 acetylates TP53"
xref: Reactome:R-HSA-8951966 "EP300 acetylates RUNX3"
xref: Reactome:R-HSA-9617758 "EP300,CREBBP acetylate FOXO4"
xref: Reactome:R-HSA-9620515 "KAT2B,EP300 acetylate FOXO3 under oxidative stress"
xref: Reactome:R-HSA-9626945 "CREBBP acetylates FOXO1"
+xref: Reactome:R-HSA-9701531 "p-Y705,S727 STAT3 is acetylated"
+xref: Reactome:R-HSA-9756494 "CREBBP acetylates SARS-CoV-2 N at K375"
is_a: GO:0034212 ! peptide N-acetyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -342585,7 +342538,7 @@ relationship: part_of GO:0000045 ! autophagosome assembly
id: GO:0061737
name: leukotriene signaling pathway
namespace: biological_process
-def: "A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-leukotriene interaction and ends with regulation of a downstream cellular process, e.g. transcription." [GOC:dph, PMID:21771892]
+def: "A G protein-coupled receptor signaling pathway initiated by leukotriene binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:dph, PMID:21771892]
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
[Term]
@@ -342664,7 +342617,7 @@ is_a: GO:0003678 ! DNA helicase activity
id: GO:0061750
name: acid sphingomyelin phosphodiesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + sphingomyelin = ceramide + choline phosphate + H(+) in an acidic environment." [GOC:dph, PMID:26493087]
+def: "Catalysis of the reaction: H2O + sphingomyelin = ceramide + choline phosphate + H+ in an acidic environment." [GOC:dph, PMID:26493087]
synonym: "acid SMase" RELATED [PMID:26493087]
synonym: "acid sphingomyelinase" EXACT [PMID:26493087]
is_a: GO:0004767 ! sphingomyelin phosphodiesterase activity
@@ -342673,7 +342626,7 @@ is_a: GO:0004767 ! sphingomyelin phosphodiesterase activity
id: GO:0061751
name: neutral sphingomyelin phosphodiesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + sphingomyelin = ceramide + choline phosphate + H(+) in a neutral environment." [GOC:dph, PMID:26493087]
+def: "Catalysis of the reaction: H2O + sphingomyelin = ceramide + choline phosphate + H+ in a neutral environment." [GOC:dph, PMID:26493087]
synonym: "neutral SMase" EXACT [PMID:26493087]
synonym: "neutral sphingomyelinase" EXACT [GOC:26493087]
is_a: GO:0004767 ! sphingomyelin phosphodiesterase activity
@@ -342766,7 +342719,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0061762
name: CAMKK-AMPK signaling cascade
namespace: biological_process
-def: "A series of molecular signals in which calmodulin-dependent protein kinase activity enabled by a CAMKK directly activates an AMPK. The cascade begins with calmodulin binding calcium which in turn binds CAMKK enabling its calmodulin-dependent protein kinase activity. The cascade ends with AMP-activated protein kinase activity." [GOC:dph, GOC:pad, GOC:PARL, PMID:23010169, PMID:24709372]
+def: "The series of molecular signals in which calmodulin-dependent protein kinase activity enabled by a CAMKK directly activates an AMPK. The cascade begins with calmodulin binding calcium which in turn binds CAMKK enabling its calmodulin-dependent protein kinase activity. The cascade ends with AMP-activated protein kinase activity." [GOC:dph, GOC:pad, GOC:PARL, PMID:23010169, PMID:24709372]
synonym: "stress-activated AMP-activated protein kinase signaling cascade" RELATED [GOC:dph]
is_a: GO:0019722 ! calcium-mediated signaling
is_a: GO:0099004 ! calmodulin dependent kinase signaling pathway
@@ -342822,13 +342775,13 @@ name: magnesium:sodium antiporter activity
namespace: molecular_function
def: "Catalysis of the reaction: Na+(in) + Mg2+(out) = Na+(out) + Mg2+(in)." [GOC:pad, GOC:PARL, PMID:22031603]
is_a: GO:0015081 ! sodium ion transmembrane transporter activity
-is_a: GO:0015491 ! cation:cation antiporter activity
+is_a: GO:0140828 ! metal cation:monoatomic cation antiporter activity
[Term]
id: GO:0061769
name: ribosylnicotinate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-ribosylnicotinate + ATP = ADP + 2 H(+) + nicotinate mononucleotide." [GOC:dph, PMID:17914902]
+def: "Catalysis of the reaction: N-ribosylnicotinate + ATP = ADP + 2 H+ + nicotinate mononucleotide." [GOC:dph, PMID:17914902]
xref: Reactome:R-HSA-8869606 "NMRK1 phosphorylates NAR to yield NAMN"
xref: Reactome:R-HSA-8869607 "NMRK2 phosphorylates NAR to yield NAMN"
is_a: GO:0016301 ! kinase activity
@@ -342877,11 +342830,12 @@ is_a: GO:0045875 ! negative regulation of sister chromatid cohesion
[Term]
id: GO:0061775
-name: cohesin loading activity
+name: cohesin loader activity
namespace: molecular_function
def: "Facilitating a conformational change to load a cohesin complex around sister chromatids, driven by ATP hydrolysis." [GOC:vw, PMID:26687354]
synonym: "ATP-dependent cohesin loading activity" EXACT []
synonym: "cohesin ATPase activity" EXACT []
+synonym: "cohesin loading activity" EXACT []
synonym: "cohesin loading ATPase" EXACT []
is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
@@ -343062,7 +343016,7 @@ name: pH-gated chloride channel activity
namespace: molecular_function
def: "A gated channel activity that enables the transmembrane transfer of a chloride ion by a channel that opens in response to a change in pH." [GOC:dph, PMID:27358471]
is_a: GO:0005254 ! chloride channel activity
-is_a: GO:0022836 ! gated channel activity
+is_a: GO:0022839 ! monoatomic ion gated channel activity
[Term]
id: GO:0061798
@@ -343078,7 +343032,7 @@ is_a: GO:0016830 ! carbon-carbon lyase activity
id: GO:0061799
name: cyclic pyranopterin monophosphate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate." [GOC:dph, GOC:ik, PMID:25896388]
+def: "Catalysis of the reaction: (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate." [GOC:dph, GOC:ik, PMID:25896388]
xref: EC:4.6.1.17
xref: MetaCyc:RXN-17809
xref: RHEA:49580
@@ -343204,13 +343158,16 @@ is_obsolete: true
[Term]
id: GO:0061815
-name: deubiquitinase, acting on linear ubiquitin
+name: Met1-linked polyubiquitin deubiquitinase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of ubiquitin units from linear ubiquitin chains." [GOC:dph, PMID:26503766, PMID:27702987]
+def: "Catalysis of the hydrolysis of ubiquitin units from Met1-linked (or linear) polyubiquitin chains." [GOC:dph, PMID:26503766, PMID:27702987]
+synonym: "cysteine-type deubiquitinase activity, acting on linear ubiquitin" EXACT []
+synonym: "deubiquitinase, acting on linear ubiquitin" BROAD []
synonym: "linear ubiquitin specific deubiquitinase activity" EXACT []
synonym: "Met1 linkage specific DUB" EXACT []
synonym: "ubiquitinyl hydrolase activity, acting on linear ubiquitin" EXACT []
-is_a: GO:0101005 ! deubiquitinase activity
+xref: Reactome:R-HSA-9818975 "CYLD hydrolyses M1polyUb on RIPK1 within the TNFR1 complex"
+is_a: GO:0004843 ! cysteine-type deubiquitinase activity
[Term]
id: GO:0061816
@@ -343390,7 +343347,7 @@ id: GO:0061838
name: CENP-T-W-S-X complex
namespace: cellular_component
def: "A histone-variant containing protein complex which forms a centromere specific nucleosomal structure, involved in centromeric chromatin organization." [PMID:22304909, PMID:22304917]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140513 ! nuclear protein-containing complex
relationship: part_of GO:0000775 ! chromosome, centromeric region
[Term]
@@ -343505,14 +343462,14 @@ relationship: part_of GO:0030027 ! lamellipodium
[Term]
id: GO:0061852
-name: retrograte transporter complex, Golgi to ER
+name: retrograde transporter complex, Golgi to ER
namespace: cellular_component
def: "Transporter complex that recognises, binds and returns endoplasmic reticulum (ER) resident proteins that have trafficked to Golgi compartments. Targets proteins lacking the HDEL motif recognised by COPI-coated vesicles." [GOC:bhm, PMID:16093310]
comment: An example of this is ERV41 in Saccharomyces cerevisiae (Q04651) in PMID:16093310 (inferred from direct assay).
synonym: "ERV41-ERV46 retrograde receptor complex" NARROW []
-synonym: "retrograte receptor complex, Golgi to endoplasmic reticulum" EXACT []
-synonym: "retrograte receptor complex, Golgi to ER" EXACT []
-synonym: "retrograte transporter complex, Golgi to endoplasmic reticulum" EXACT []
+synonym: "retrograde receptor complex, Golgi to endoplasmic reticulum" EXACT []
+synonym: "retrograde receptor complex, Golgi to ER" EXACT []
+synonym: "retrograde transporter complex, Golgi to endoplasmic reticulum" EXACT []
is_a: GO:1990351 ! transporter complex
[Term]
@@ -343563,6 +343520,7 @@ id: GO:0061860
name: DNA clamp unloader activity
namespace: molecular_function
def: "Facilitating the opening of the ring structure of the PCNA complex, or any of the related sliding clamp complexes, and their removal from the DNA duplex, driven by ATP hydrolysis." [GOC:vw, PMID:23499004]
+synonym: "DNA clamp unloading activity" EXACT []
is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
[Term]
@@ -343600,12 +343558,12 @@ is_a: GO:0061864 ! basement membrane constituent secretion
[Term]
id: GO:0061866
-name: negative regulation of histone H3-S10 phosphorylation
+name: obsolete negative regulation of histone H3-S10 phosphorylation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of one or more phosphate groups to histone H3 on a serine residue at position 10." [PMID:27521428]
-is_a: GO:0033128 ! negative regulation of histone phosphorylation
-is_a: GO:0033137 ! negative regulation of peptidyl-serine phosphorylation
-relationship: negatively_regulates GO:0043987 ! histone H3-S10 phosphorylation
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of one or more phosphate groups to histone H3 on a serine residue at position 10." [PMID:27521428]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0004860
[Term]
id: GO:0061867
@@ -343676,7 +343634,7 @@ id: GO:0061875
name: negative regulation of hepatic stellate cell contraction
namespace: biological_process
def: "Any process that modulates stops, prevents, or reduces the frequency, rate or extent of hepatic stellate cell contraction." [PMID:24204762]
-is_a: GO:0051271 ! negative regulation of cellular component movement
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0061873 ! regulation of hepatic stellate cell contraction
relationship: negatively_regulates GO:0061872 ! hepatic stellate cell contraction
@@ -343696,7 +343654,6 @@ namespace: biological_process
def: "Any process that activates or increasesthe frequency, rate or extent of the directed movement of mitochondria along microtubules in axons away from the cell body and towards the presynapse." [PMID:24302729]
synonym: "positive regulation of anterograde axon transport of mitochondria" EXACT []
is_a: GO:0032388 ! positive regulation of intracellular transport
-is_a: GO:0051272 ! positive regulation of cellular component movement
is_a: GO:0061880 ! regulation of anterograde axonal transport of mitochondrion
relationship: positively_regulates GO:0098957 ! anterograde axonal transport of mitochondrion
@@ -343707,7 +343664,6 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of mitochondria along microtubules in axons away from the cell body and towards the presynapse." [PMID:24302729]
synonym: "negative regulation of anterograde axon transport of mitochondria" EXACT []
is_a: GO:0032387 ! negative regulation of intracellular transport
-is_a: GO:0051271 ! negative regulation of cellular component movement
is_a: GO:0061880 ! regulation of anterograde axonal transport of mitochondrion
relationship: negatively_regulates GO:0098957 ! anterograde axonal transport of mitochondrion
@@ -343792,13 +343748,13 @@ name: calcium ion sensor activity
namespace: molecular_function
def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of calcium ions (Ca2+)." [PMID:16005298, PMID:17020874, PMID:28151650]
is_a: GO:0005509 ! calcium ion binding
-is_a: GO:0140299 ! small molecule sensor activity
+is_a: GO:0140784 ! metal ion sensor activity
[Term]
id: GO:0061896
name: all-trans retinol 3,4-desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: all-trans-retinol + 2 H(+) + O2 + 2 reduced [adrenodoxin] = all-trans-3,4-didehydro retinol + 2 H2O + 2 oxidized [adrenodoxin]." [PMID:27059013]
+def: "Catalysis of the reaction: all-trans-retinol + 2 H+ + O2 + 2 reduced [adrenodoxin] = all-trans-3,4-didehydro retinol + 2 H2O + 2 oxidized [adrenodoxin]." [PMID:27059013]
xref: RHEA:50292
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
@@ -343806,21 +343762,21 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0061897
name: all-trans retinal 3,4-desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: all-trans-retinal + 2 H(+) + O2 + 2 reduced [adrenodoxin] = all-trans-3,4-didehydro retinal + 2 H2O + 2 oxidized [adrenodoxin]." [PMID:27059013]
+def: "Catalysis of the reaction: all-trans-retinal + 2 H+ + O2 + 2 reduced [adrenodoxin] = all-trans-3,4-didehydro retinal + 2 H2O + 2 oxidized [adrenodoxin]." [PMID:27059013]
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
[Term]
id: GO:0061898
name: all-trans retinoic acid 3,4-desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: all-trans-retinoic acid + 2 H(+) + O2 + 2 reduced [adrenodoxin] = all-trans-3,4-didehydro retinoic acid + 2 H2O + 2 oxidized [adrenodoxin]." [PMID:27059013]
+def: "Catalysis of the reaction: all-trans-retinoic acid + 2 H+ + O2 + 2 reduced [adrenodoxin] = all-trans-3,4-didehydro retinoic acid + 2 H2O + 2 oxidized [adrenodoxin]." [PMID:27059013]
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
[Term]
id: GO:0061899
name: 11-cis-retinal 3,4-desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 11-cis-retinal + 2 H(+) + O2 + 2 reduced [adrenodoxin] = 11-cis-3,4-didehydro-retinal + 2 H2O + 2 oxidized [adrenodoxin]." [PMID:27059013]
+def: "Catalysis of the reaction: 11-cis-retinal + 2 H+ + O2 + 2 reduced [adrenodoxin] = 11-cis-3,4-didehydro-retinal + 2 H2O + 2 oxidized [adrenodoxin]." [PMID:27059013]
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
[Term]
@@ -343867,10 +343823,10 @@ id: GO:0061907
name: negative regulation of AMPA receptor activity
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of AMPA glutamate receptor activity." [GOC:aruk, GOC:bc, PMID:20739563]
+is_a: GO:0032413 ! negative regulation of ion transmembrane transporter activity
is_a: GO:1900450 ! negative regulation of glutamate receptor signaling pathway
is_a: GO:2000272 ! negative regulation of signaling receptor activity
is_a: GO:2000311 ! regulation of AMPA receptor activity
-is_a: GO:2001258 ! negative regulation of cation channel activity
[Term]
id: GO:0061908
@@ -343935,11 +343891,12 @@ relationship: negatively_regulates GO:0003419 ! growth plate cartilage chondrocy
[Term]
id: GO:0061915
-name: actin fusion focus localization
+name: obsolete actin fusion focus localization
namespace: biological_process
-def: "Any process in which an actin fusion focus are transported to, or maintained in, a specific location. The actin fusion focus is an aster-like, F-actin-containing structure at the mating projection tip where the cell wall is degraded during conjugation with cellular fusion." [PMID:28410370]
+def: "OBSOLETE. Any process in which an actin fusion focus are transported to, or maintained in, a specific location. The actin fusion focus is an aster-like, F-actin-containing structure at the mating projection tip where the cell wall is degraded during conjugation with cellular fusion." [PMID:28410370]
+comment: The reason for obsoletion is that this represents a phenotype.
synonym: "actin fusion focus localisation" EXACT []
-is_a: GO:0051641 ! cellular localization
+is_obsolete: true
[Term]
id: GO:0061916
@@ -343974,6 +343931,7 @@ id: GO:0061920
name: protein propionyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: propionyl-CoA + lysine in peptide = CoA + N-propionyl-lysine-peptide." [PMID:17267393]
+xref: RHEA:54020
is_a: GO:0016410 ! N-acyltransferase activity
[Term]
@@ -343989,6 +343947,7 @@ name: histone propionyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: propionyl-CoA + histone = CoA + propionyl-histone." [PMID:17267393]
is_a: GO:0061920 ! protein propionyltransferase activity
+is_a: GO:0140993 ! histone modifying activity
[Term]
id: GO:0061923
@@ -344233,21 +344192,19 @@ is_a: GO:0008174 ! mRNA methyltransferase activity
[Term]
id: GO:0061954
-name: positive regulation of actin filament polymerization involved in sperm capacitation
+name: obsolete positive regulation of actin filament polymerization involved in sperm capacitation
namespace: biological_process
-def: "Any process that icreases the rate or extent of actin polymerization as part of sperm capacitation. This process prevents a spontaneous acrosome reaction." [PMID:15749953, PMID:25966627, PMID:26514336, PMID:27178669]
-is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
-is_a: GO:0030838 ! positive regulation of actin filament polymerization
-relationship: part_of GO:0048240 ! sperm capacitation
+def: "OBSOLETE. Any process that icreases the rate or extent of actin polymerization as part of sperm capacitation. This process prevents a spontaneous acrosome reaction." [PMID:15749953, PMID:25966627, PMID:26514336, PMID:27178669]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0061955
-name: positive regulation of actin filament depolymerization involved in acrosome reaction
+name: obsolete positive regulation of actin filament depolymerization involved in acrosome reaction
namespace: biological_process
-def: "Any process that increases the rate or exent of actin depolymerization as part of the acrosome reaction. This allows the acrosomal membrane and plasma membrane to fuse." [PMID:20937821]
-is_a: GO:0022414 ! reproductive process
-is_a: GO:0030836 ! positive regulation of actin filament depolymerization
-relationship: part_of GO:0007340 ! acrosome reaction
+def: "OBSOLETE. Any process that increases the rate or exent of actin depolymerization as part of the acrosome reaction. This allows the acrosomal membrane and plasma membrane to fuse." [PMID:20937821]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0061956
@@ -344362,7 +344319,7 @@ is_a: GO:0061968 ! maintenance of left/right asymmetry
id: GO:0061971
name: replacement bone morphogenesis
namespace: biological_process
-def: "The process in which bones are generated and organized as a result of the conversion of another structural tissue into bone." [DOI:10.1002/(SICI)1097-4687(199608)229\:2<121\:\:AID-JMOR1>3.0.CO;2-4]
+def: "The process in which bones are generated and organized as a result of the conversion of another structural tissue into bone." [PMID:29852585]
is_a: GO:0060349 ! bone morphogenesis
[Term]
@@ -344384,7 +344341,6 @@ id: GO:0061974
name: perichondral bone morphogenesis
namespace: biological_process
def: "The process in which bones are generated and organized as a result of the conversion of initial connective tissue surrounding cartilage into bone." [PMID:21901110]
-is_a: GO:0060350 ! endochondral bone morphogenesis
is_a: GO:0061973 ! membrane bone morphogenesis
[Term]
@@ -344538,7 +344494,7 @@ namespace: molecular_function
alt_id: GO:0061994
def: "An activity that displaces proteins or protein complexes from DNA, sometimes in a 'wire stripping' fashion, driven by ATP hydrolysis." [PMID:18593879]
synonym: "ATP-dependent protein-nucleic acid complex displacement activity" NARROW []
-is_a: GO:0140083 ! ATP-dependent protein-DNA unloading activity
+is_a: GO:0140083 ! ATP-dependent protein-DNA unloader activity
[Term]
id: GO:0061999
@@ -344606,7 +344562,7 @@ def: "A protein complex that contributes to and regulates mitochondrial respirat
synonym: "COX pre-assemply complex" BROAD [GOC:lnp]
synonym: "COX1 preassemply complex" EXACT [GOC:lnp]
is_a: GO:0098800 ! inner mitochondrial membrane protein complex
-is_a: GO:0101031 ! chaperone complex
+is_a: GO:0101031 ! protein folding chaperone complex
[Term]
id: GO:0062012
@@ -344736,7 +344692,6 @@ namespace: biological_process
def: "Any process that starts or increases the frequency, rate or extent of sister chromatid segregation during mitosis." [PMID:12773390]
is_a: GO:0033047 ! regulation of mitotic sister chromatid segregation
is_a: GO:0051984 ! positive regulation of chromosome segregation
-is_a: GO:0090068 ! positive regulation of cell cycle process
is_a: GO:2001252 ! positive regulation of chromosome organization
relationship: positively_regulates GO:0000070 ! mitotic sister chromatid segregation
@@ -344892,7 +344847,7 @@ id: GO:0062054
name: fluoride channel activity
namespace: molecular_function
def: "Enables the facilitated diffusion of fluoride (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [PMID:23991286, PMID:25156118]
-is_a: GO:0005253 ! anion channel activity
+is_a: GO:0005253 ! monoatomic anion channel activity
is_a: GO:1903425 ! fluoride transmembrane transporter activity
[Term]
@@ -344917,7 +344872,7 @@ namespace: molecular_function
def: "Enables the transport of L-aspartate and fumarate across a membrane according to the reaction L-aspartate (out) + fumarate (in) = L-aspartate (in) + fumarate (out)." [PMID:29995997]
is_a: GO:0015138 ! fumarate transmembrane transporter activity
is_a: GO:0015183 ! L-aspartate transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
+is_a: GO:0015297 ! antiporter activity
[Term]
id: GO:0062058
@@ -345054,19 +345009,18 @@ relationship: part_of GO:0010208 ! pollen wall assembly
id: GO:0062076
name: acyl-CoA delta5-desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + reduced acceptor + O2 = delta5-acyl-CoA + acceptor + 2 H2O." [PMID:10601301, PMID:10769175, RHEA:46424]
+def: "Catalysis of the reaction: (8Z,11Z,14Z)-eicosatrienoyl-CoA + 2 Fe(II)-[cytochrome b5] + 2 H+ + O2 = (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA + 2 Fe(III)-[cytochrome b5] + 2 H2O. Can also use a substrate with 3 double bonds (a (8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA) and add a fourth double bond (a (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA)." [PMID:10601301, PMID:10769175, RHEA:46424]
synonym: "acyl-CoA (8-3)-desaturase" EXACT []
synonym: "acyl-CoA D5-desaturase activity" EXACT []
synonym: "acyl-CoA delta(5)-desaturase activity" EXACT []
xref: EC:1.14.19.44
-xref: RHEA:46424
is_a: GO:0016215 ! acyl-CoA desaturase activity
[Term]
id: GO:0062077
name: phenylacetyl-CoA 1,2-epoxidase complex
namespace: cellular_component
-def: "A protein complex capable of catalysing the reaction: phenylacetyl-CoA + H(+) + NADPH + O2 = 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + H2O + NADP(+)." [GOC:bhm, PMID:21247899]
+def: "A protein complex capable of catalysing the reaction: phenylacetyl-CoA + H+ + NADPH + O2 = 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + H2O + NADP+." [GOC:bhm, PMID:21247899]
synonym: "paaABCE complex" NARROW []
is_a: GO:1990204 ! oxidoreductase complex
@@ -345120,10 +345074,8 @@ id: GO:0062084
name: regulation of capsule polysaccharide biosynthetic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of polysaccharides that make up the capsule, a protective structure surrounding some species of bacteria and fungi." [PMID:21917918]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:0032885 ! regulation of polysaccharide biosynthetic process
is_a: GO:1901913 ! regulation of capsule organization
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
relationship: regulates GO:0045227 ! capsule polysaccharide biosynthetic process
[Term]
@@ -345132,8 +345084,7 @@ name: positive regulation of capsule polysaccharide biosynthetic process
namespace: biological_process
def: "Any process that activates, maintains or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of polysaccharides that make up the capsule, a protective structure surrounding some species of bacteria and fungi." [PMID:21917918]
is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:0062084 ! regulation of capsule polysaccharide biosynthetic process
is_a: GO:1901915 ! positive regulation of capsule organization
relationship: positively_regulates GO:0045227 ! capsule polysaccharide biosynthetic process
@@ -345284,6 +345235,7 @@ synonym: "peptide-aspartate beta-dioxygenase activity" EXACT []
synonym: "peptide-L-aspartate,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating) activity" RELATED [EC:1.14.11.16]
xref: EC:1.14.11.16
xref: MetaCyc:PEPTIDE-ASPARTATE-BETA-DIOXYGENASE-RXN
+xref: RESID:AA0026
xref: RHEA:11508
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -345295,16 +345247,6 @@ namespace: biological_process
def: "Division of a female germline stem cell to produce two germline stem cells of the same type as the parent." [GOC:ha, PMID:30248087]
is_a: GO:0098729 ! germline stem cell symmetric division
-[Term]
-id: GO:0062103
-name: double-stranded RNA biosynthetic process
-namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of double-stranded RNA." [PMID:19701182]
-synonym: "double-stranded RNA biosynthesis" EXACT []
-synonym: "dsRNA biosynthesis" EXACT []
-synonym: "dsRNA biosynthetic process" EXACT [GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:rl]
-is_a: GO:0032774 ! RNA biosynthetic process
-
[Term]
id: GO:0062104
name: pumilio-response element binding
@@ -345371,7 +345313,6 @@ def: "The chemical reactions and pathways resulting in the formation of a fatty
synonym: "FAPA biosynthesis" EXACT []
synonym: "FAPA biosynthetic process" EXACT []
synonym: "fatty acid amide biosynthesis" EXACT []
-is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:0043604 ! amide biosynthetic process
is_a: GO:0062126 ! fatty acid primary amide metabolic process
is_a: GO:1901566 ! organonitrogen compound biosynthetic process
@@ -345421,11 +345362,15 @@ relationship: part_of GO:0030999 ! linear element assembly
[Term]
id: GO:0062122
-name: histone methyltransferase activity (H3-K37 specific)
+name: histone H3K37 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 37) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 37). This reaction is the addition of a methyl group onto lysine at position 37 of the histone H3 protein." [PMID:30773398]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 37) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 37). This reaction is the addition of a methyl group to the lysine residue at position 37 of the histone H3 protein." [PMID:30773398]
+synonym: "histone H3K37 methylase activity" EXACT []
synonym: "histone lysine N-methyltransferase activity (H3-K37 specific)" EXACT []
-is_a: GO:0018024 ! histone-lysine N-methyltransferase activity
+synonym: "histone methyltransferase activity (H3-K37 specific)" EXACT []
+synonym: "histone-H3K37 methyltransferase activity" EXACT []
+is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
+is_a: GO:0140938 ! histone H3 methyltransferase activity
[Term]
id: GO:0062123
@@ -345458,8 +345403,7 @@ name: fatty acid primary amide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform primary fatty amides." [PMID:11128635]
synonym: "primary fatty amide metabolic process" EXACT []
-is_a: GO:0006629 ! lipid metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
is_a: GO:1901568 ! fatty acid derivative metabolic process
@@ -345469,7 +345413,6 @@ name: fatty acid primary amide catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of primary fatty amides." [PMID:11128635]
synonym: "primary fatty amide catabolic process" EXACT []
-is_a: GO:0016042 ! lipid catabolic process
is_a: GO:0062126 ! fatty acid primary amide metabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
is_a: GO:1901569 ! fatty acid derivative catabolic process
@@ -345524,7 +345467,7 @@ name: negative regulation of L-glutamine biosynthetic process
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of L-glutamine biosynthesis." [GOC:ha, PMID:19755423]
is_a: GO:0062132 ! regulation of L-glutamine biosynthetic process
-is_a: GO:2000283 ! negative regulation of cellular amino acid biosynthetic process
+is_a: GO:2000283 ! negative regulation of amino acid biosynthetic process
relationship: negatively_regulates GO:1901704 ! L-glutamine biosynthetic process
[Term]
@@ -345533,7 +345476,7 @@ name: positive regulation of L-glutamine biosynthetic process
namespace: biological_process
def: "Any process that starts, increases the frequency, rate or extent of L-glutamine biosynthesis." [GOC:ha, PMID:19755423]
is_a: GO:0062132 ! regulation of L-glutamine biosynthetic process
-is_a: GO:2000284 ! positive regulation of cellular amino acid biosynthetic process
+is_a: GO:2000284 ! positive regulation of amino acid biosynthetic process
relationship: positively_regulates GO:1901704 ! L-glutamine biosynthetic process
[Term]
@@ -345598,7 +345541,7 @@ is_a: GO:1901607 ! alpha-amino acid biosynthetic process
id: GO:0062144
name: L-propargylglycine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-2-amino-4-chloropent-4-enoate = chloride + H(+) + L-propargylglycine." [PMID:30867596, RHEA:59892]
+def: "Catalysis of the reaction: L-2-amino-4-chloropent-4-enoate = chloride + H+ + L-propargylglycine." [PMID:30867596, RHEA:59892]
xref: RHEA:59892
is_a: GO:0016848 ! carbon-halide lyase activity
@@ -345606,7 +345549,7 @@ is_a: GO:0016848 ! carbon-halide lyase activity
id: GO:0062145
name: L-propargylglycine--L-glutamate ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + L-glutamate + L-propargylglycine = ADP + H(+) + L-gamma-glutamyl-L-propargylglycine + phosphate." [PMID:30867596, RHEA:59896]
+def: "Catalysis of the reaction: ATP + L-glutamate + L-propargylglycine = ADP + H+ + L-gamma-glutamyl-L-propargylglycine + phosphate." [PMID:30867596, RHEA:59896]
xref: RHEA:59896
is_a: GO:0016881 ! acid-amino acid ligase activity
@@ -345622,7 +345565,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0062147
name: L-lysine 4-chlorinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + chloride + H(+) + L-lysine + O2 = 4-chloro-L-lysine + CO2 + H2O + succinate." [PMID:30867596, RHEA:59884]
+def: "Catalysis of the reaction: 2-oxoglutarate + chloride + H+ + L-lysine + O2 = 4-chloro-L-lysine + CO2 + H2O + succinate." [PMID:30867596, RHEA:59884]
xref: RHEA:59884
is_a: GO:0050498 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with 2-oxoglutarate as one donor, and the other dehydrogenated
@@ -345646,7 +345589,7 @@ relationship: part_of GO:0019233 ! sensory perception of pain
id: GO:0062150
name: amorpha-4,11-diene 12-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction:(+)-amorpha-4,11-diene + 3 O2 + 3 reduced [NADPH--hemoprotein reductase] = (+)-artemisinate + 4 H(+) + 4 H2O + 3 oxidized [NADPH--hemoprotein reductase]." [PMID:16458889, PMID:16612385, PMID:23246612, RHEA:32999]
+def: "Catalysis of the reaction:(+)-amorpha-4,11-diene + 3 O2 + 3 reduced [NADPH--hemoprotein reductase] = (+)-artemisinate + 4 H+ + 4 H2O + 3 oxidized [NADPH--hemoprotein reductase]." [PMID:16458889, PMID:16612385, PMID:23246612, RHEA:32999]
xref: EC:1.14.14.114
xref: RHEA:32999
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
@@ -345662,7 +345605,7 @@ is_a: GO:1990204 ! oxidoreductase complex
id: GO:0062152
name: mRNA (cytidine-5-)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a cytidine in mRNA + S-adenosyl-L-methionine = a 5-methylcytidine in mRNA + H(+) + S-adenosyl-L-homocysteine." [PMID:22395603, PMID:23871666, RHEA:61464]
+def: "Catalysis of the reaction: a cytidine in mRNA + S-adenosyl-L-methionine = a 5-methylcytidine in mRNA + H+ + S-adenosyl-L-homocysteine." [PMID:22395603, PMID:23871666, RHEA:61464]
synonym: "mRNA (cytosine-5-)-methyltransferase activity" EXACT []
xref: RHEA:61464
is_a: GO:0008174 ! mRNA methyltransferase activity
@@ -345677,10 +345620,15 @@ is_a: GO:0003723 ! RNA binding
[Term]
id: GO:0062154
-name: N6-mAMP deaminase activity
+name: N6-methyl-AMP deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(+) + H2O + N6-methyl-AMP = IMP + methylamine." [PMID:29884623, RHEA:16001]
+def: "Catalysis of the reaction: H+ + H2O + N6-methyl-AMP = IMP + methylamine. Can also use N6-methyl-dAMP as a substrate." [PMID:29884623, RHEA:16001]
synonym: "MAPDA" EXACT [PMID:29884623]
+synonym: "N6-mAMP deaminase activity" EXACT []
+synonym: "N6-methyl-AMP/dAMP aminohydrolase" EXACT [PMID:21755941]
+xref: Reactome:R-HSA-2161187 "ADAL1 hydrolyzes N6-methyl-AMP to IMP and methylamine"
+xref: Reactome:R-HSA-2161195 "abacavir monophosphate + H2O => carbovir monophosphate + cyclopropylamine"
+xref: Reactome:R-HSA-9731661 "ADAL1 hydrolyzes N6-methyl-dAMP to dIMP and methylamine"
xref: RHEA:16001
is_a: GO:0019239 ! deaminase activity
@@ -345701,7 +345649,7 @@ synonym: "mitochondrial potassium channel activity" EXACT []
synonym: "mitoK-ATP activity" EXACT []
is_a: GO:0005267 ! potassium channel activity
is_a: GO:0035381 ! ATP-gated ion channel activity
-is_a: GO:0099094 ! ligand-gated cation channel activity
+is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
[Term]
id: GO:0062157
@@ -345715,8 +345663,10 @@ id: GO:0062158
name: chloride:proton antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: chloride(out) + proton(in) = chloride(in) + proton(out)." [PMID:14985752]
-is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
-is_a: GO:0015299 ! solute:proton antiporter activity
+is_a: GO:0005452 ! solute:inorganic anion antiporter activity
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015108 ! chloride transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
[Term]
id: GO:0062159
@@ -345802,14 +345752,14 @@ def: "A protein-containing complex composed of six subunits of each of the three
synonym: "C1q" EXACT []
synonym: "Complement 1q" EXACT []
is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+relationship: part_of GO:0005576 ! extracellular region
[Term]
id: GO:0062168
name: negative regulation of plus-end directed microtubule sliding
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of plus-end directed microtubule sliding." [PMID:21892183]
-is_a: GO:0051271 ! negative regulation of cellular component movement
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0062169 ! regulation of plus-end directed microtubule sliding
relationship: negatively_regulates GO:0031535 ! plus-end directed microtubule sliding
@@ -345909,11 +345859,11 @@ is_a: GO:1901616 ! organic hydroxy compound catabolic process
[Term]
id: GO:0062176
-name: R-loop disassembly
+name: R-loop processing
namespace: biological_process
-def: "A DNA metabolic process that results in the disassembly of R-loops. R-loops are three-stranded nucleic acid structures consisitng of an RNA:DNA heteroduplex and a looped-out non-template strand. Aberrant formation and persistence of R-loops block transcription elongation and cause DNA damage. Mechanisms that resolve R-loops are essential for genome stability." [PMID:28790157]
-is_a: GO:0006259 ! DNA metabolic process
-relationship: part_of GO:0006261 ! DNA-dependent DNA replication
+def: "A DNA metabolic process that results in the disassembly of R-loops. R-loops are three-stranded nucleic acid structures consisitng of an RNA:DNA heteroduplex and a looped-out non-template strand. Aberrant formation and persistence of R-loops block transcription elongation and cause DNA damage. Mechanisms that resolve R-loops are essential for genome stability." [PMID:27252122, PMID:28790157, PMID:33986538]
+synonym: "R-loop disassembly" EXACT []
+is_a: GO:0006338 ! chromatin remodeling
[Term]
id: GO:0062177
@@ -345934,7 +345884,7 @@ is_a: GO:0004497 ! monooxygenase activity
id: GO:0062180
name: 25-hydroxycholecalciferol-23-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: calcidiol + 2 H(+) + O2 + 2 reduced [adrenodoxin] = (23S)-23,25-dihydroxycalciol + H2O + 2 oxidized [adrenodoxin]." [PMID:22100522, PMID:30205156, RHEA:46616]
+def: "Catalysis of the reaction: calcidiol + 2 H+ + O2 + 2 reduced [adrenodoxin] = (23S)-23,25-dihydroxycalciol + H2O + 2 oxidized [adrenodoxin]." [PMID:22100522, PMID:30205156, RHEA:46616]
xref: RHEA:46616
is_a: GO:0062179 ! vitamin D 23-hydroxylase activity
@@ -345942,7 +345892,7 @@ is_a: GO:0062179 ! vitamin D 23-hydroxylase activity
id: GO:0062181
name: 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity
namespace: molecular_function
-def: "Catatlysis of the reaction: calcitriol + 2 H(+) + O2 + 2 reduced [adrenodoxin] = 1alpha,23S,25-trihydroxycholecalciferol + H2O + 2 oxidized [adrenodoxin]." [PMID:22100522, PMID:30205156, RHEA:49192]
+def: "Catatlysis of the reaction: calcitriol + 2 H+ + O2 + 2 reduced [adrenodoxin] = 1alpha,23S,25-trihydroxycholecalciferol + H2O + 2 oxidized [adrenodoxin]." [PMID:22100522, PMID:30205156, RHEA:49192]
xref: RHEA:49192
is_a: GO:0062179 ! vitamin D 23-hydroxylase activity
@@ -345950,7 +345900,7 @@ is_a: GO:0062179 ! vitamin D 23-hydroxylase activity
id: GO:0062182
name: all-trans retinoic acid 4-hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: all-trans-retinoate + O2 + reduced [NADPH--hemoprotein reductase] = all-trans-(4S)-hydroxyretinoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase]." [PMID:9250660, PMID:9716180, RHEA:51492]
+def: "Catalysis of the reaction: all-trans-retinoate + O2 + reduced [NADPH--hemoprotein reductase] = all-trans-(4S)-hydroxyretinoate + H+ + H2O + oxidized [NADPH--hemoprotein reductase]." [PMID:9250660, PMID:9716180, RHEA:51492]
xref: RHEA:51492
is_a: GO:0008401 ! retinoic acid 4-hydroxylase activity
@@ -345958,7 +345908,7 @@ is_a: GO:0008401 ! retinoic acid 4-hydroxylase activity
id: GO:0062183
name: all-trans retinoic acid 18-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: all-trans-retinoate + O2 + reduced [NADPH--hemoprotein reductase] = all-trans-18-hydroxyretinoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase]." [PMID:22020119, RHEA:55856]
+def: "Catalysis of the reaction: all-trans-retinoate + O2 + reduced [NADPH--hemoprotein reductase] = all-trans-18-hydroxyretinoate + H+ + H2O + oxidized [NADPH--hemoprotein reductase]." [PMID:22020119, RHEA:55856]
xref: RHEA:55856
is_a: GO:0004497 ! monooxygenase activity
@@ -345966,7 +345916,7 @@ is_a: GO:0004497 ! monooxygenase activity
id: GO:0062184
name: testosterone 16-beta-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O2 + reduced [NADPH--hemoprotein reductase] + testosterone = 16beta,17beta-dihydroxyandrost-4-en-3-one + H(+) + H2O + oxidized [NADPH--hemoprotein reductase]." [PMID:21289075, RHEA:46304]
+def: "Catalysis of the reaction: O2 + reduced [NADPH--hemoprotein reductase] + testosterone = 16beta,17beta-dihydroxyandrost-4-en-3-one + H+ + H2O + oxidized [NADPH--hemoprotein reductase]." [PMID:21289075, RHEA:46304]
xref: RHEA:46304
is_a: GO:0004497 ! monooxygenase activity
@@ -345974,7 +345924,7 @@ is_a: GO:0004497 ! monooxygenase activity
id: GO:0062185
name: secalciferol 1-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction:2 H(+) + O2 + 2 reduced [adrenodoxin] + secalciferol = calcitetrol + H2O + 2 oxidized [adrenodoxin]." [PMID:10518789, RHEA:49064]
+def: "Catalysis of the reaction:2 H+ + O2 + 2 reduced [adrenodoxin] + secalciferol = calcitetrol + H2O + 2 oxidized [adrenodoxin]." [PMID:10518789, RHEA:49064]
xref: RHEA:49064
is_a: GO:0004497 ! monooxygenase activity
@@ -345990,7 +345940,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0062187
name: anandamide 8,9 epoxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + O2 + reduced [NADPH--hemoprotein reductase] = H(+) + H2O + N-(8,9-epoxy-5Z,11Z,14Z-eicosatrienoyl)-ethanolamine + oxidized [NADPH--hemoprotein reductase]." [PMID:21289075, RHEA:53140]
+def: "Catalysis of the reaction: N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + O2 + reduced [NADPH--hemoprotein reductase] = H+ + H2O + N-(8,9-epoxy-5Z,11Z,14Z-eicosatrienoyl)-ethanolamine + oxidized [NADPH--hemoprotein reductase]." [PMID:21289075, RHEA:53140]
xref: RHEA:53140
is_a: GO:0062186 ! anandamide epoxidase activity
@@ -345998,7 +345948,7 @@ is_a: GO:0062186 ! anandamide epoxidase activity
id: GO:0062188
name: anandamide 11,12 epoxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + O2 + reduced [NADPH--hemoprotein reductase] = H(+) + H2O + N-(11,12-epoxy-5Z,8Z,14Z-eicosatrienoyl)-ethanolamine + oxidized [NADPH--hemoprotein reductase]." [PMID:21289075, RHEA:53144]
+def: "Catalysis of the reaction: N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + O2 + reduced [NADPH--hemoprotein reductase] = H+ + H2O + N-(11,12-epoxy-5Z,8Z,14Z-eicosatrienoyl)-ethanolamine + oxidized [NADPH--hemoprotein reductase]." [PMID:21289075, RHEA:53144]
xref: RHEA:53144
is_a: GO:0062186 ! anandamide epoxidase activity
@@ -346006,7 +345956,7 @@ is_a: GO:0062186 ! anandamide epoxidase activity
id: GO:0062189
name: anandamide 14,15 epoxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + O2 + reduced [NADPH--hemoprotein reductase] = H(+) + H2O + N-(14,15-epoxy-5Z,8Z,11Z-eicosatrienoyl)-ethanolamine + oxidized [NADPH--hemoprotein reductase]." [PMID:21289075, RHEA:53148]
+def: "Catalysis of the reaction: N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + O2 + reduced [NADPH--hemoprotein reductase] = H+ + H2O + N-(14,15-epoxy-5Z,8Z,11Z-eicosatrienoyl)-ethanolamine + oxidized [NADPH--hemoprotein reductase]." [PMID:21289075, RHEA:53148]
xref: RHEA:53148
is_a: GO:0062186 ! anandamide epoxidase activity
@@ -346079,15 +346029,6 @@ def: "OBSOLETE. A region of heterochromatin associated with sites in rDNA repeat
comment: This term was obsoleted because it does not represent a specific cellular component.
is_obsolete: true
-[Term]
-id: GO:0062199
-name: chromosome, centromeric inner repeat region
-namespace: cellular_component
-def: "The portion of the centromeric region of a chromosome that contains the inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [PMID:21437270]
-synonym: "chromosome, centric outer repeat region" RELATED []
-is_a: GO:0098687 ! chromosomal region
-relationship: part_of GO:0000775 ! chromosome, centromeric region
-
[Term]
id: GO:0062200
name: RAM/MOR signaling pathway
@@ -346157,7 +346098,7 @@ name: regulation of pattern recognition receptor signaling pathway
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of a pattern recognition receptor signaling pathway." [PMID:30610168]
is_a: GO:0009966 ! regulation of signal transduction
-is_a: GO:0050776 ! regulation of immune response
+is_a: GO:0045088 ! regulation of innate immune response
relationship: regulates GO:0002221 ! pattern recognition receptor signaling pathway
[Term]
@@ -346166,6 +346107,7 @@ name: positive regulation of pattern recognition receptor signaling pathway
namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of a pattern recognition receptor signaling pathway." [PMID:30610168]
is_a: GO:0009967 ! positive regulation of signal transduction
+is_a: GO:0045089 ! positive regulation of innate immune response
is_a: GO:0062207 ! regulation of pattern recognition receptor signaling pathway
relationship: positively_regulates GO:0002221 ! pattern recognition receptor signaling pathway
@@ -346473,6 +346415,7 @@ subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
+subset: prokaryote_subset
synonym: "cellular macromolecule complex assembly" RELATED []
synonym: "cellular protein complex assembly" EXACT []
synonym: "cellular protein-containing complex assembly" RELATED []
@@ -346491,7 +346434,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex." [GOC:jl]
synonym: "DNA-protein complex assembly" EXACT [GOC:mah]
is_a: GO:0065003 ! protein-containing complex assembly
-is_a: GO:0071824 ! protein-DNA complex subunit organization
+is_a: GO:0071824 ! protein-DNA complex organization
[Term]
id: GO:0065005
@@ -346499,7 +346442,7 @@ name: protein-lipid complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins and lipids to form a protein-lipid complex." [GOC:jl]
is_a: GO:0065003 ! protein-containing complex assembly
-is_a: GO:0071825 ! protein-lipid complex subunit organization
+is_a: GO:0071825 ! protein-lipid complex organization
[Term]
id: GO:0065007
@@ -346575,7 +346518,6 @@ id: GO:0070005
name: cysteine-type aminopeptidase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of a single N-terminal amino acid residue from a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile." [GOC:mah, https://www.ebi.ac.uk/merops/about/glossary.shtml#AMINOPEPTIDASE, https://www.ebi.ac.uk/merops/about/glossary.shtml#CATTYPE]
-xref: EC:3.4.18.-
is_a: GO:0004177 ! aminopeptidase activity
is_a: GO:0070004 ! cysteine-type exopeptidase activity
@@ -346600,7 +346542,6 @@ id: GO:0070008
name: serine-type exopeptidase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine)." [GOC:mah, https://www.ebi.ac.uk/merops/about/glossary.shtml#CATTYPE, https://www.ebi.ac.uk/merops/about/glossary.shtml#EXOPEPTIDASE]
-xref: EC:3.4.21.-
is_a: GO:0008236 ! serine-type peptidase activity
is_a: GO:0008238 ! exopeptidase activity
@@ -346617,14 +346558,13 @@ id: GO:0070012
name: oligopeptidase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of a peptide bond in an oligopeptide, i.e. a molecule containing a small number (2 to 20) of amino acid residues connected by peptide bonds." [GOC:mah, ISBN:0198506732]
-is_a: GO:0008233 ! peptidase activity
+is_a: GO:0004175 ! endopeptidase activity
[Term]
id: GO:0070013
name: intracellular organelle lumen
namespace: cellular_component
def: "An organelle lumen that is part of an intracellular organelle." [GOC:mah]
-subset: goslim_mouse
is_a: GO:0043233 ! organelle lumen
relationship: part_of GO:0043229 ! intracellular organelle
@@ -346637,7 +346577,6 @@ synonym: "oligo-1,6-glucosidase complex" RELATED []
xref: Wikipedia:Sucrase-isomaltase
is_a: GO:0098797 ! plasma membrane protein complex
is_a: GO:1902687 ! glucosidase complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0070016
@@ -346762,6 +346701,7 @@ id: GO:0070027
name: carbon monoxide sensor activity
namespace: molecular_function
def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of carbon monoxide (CO)." [GOC:ecd]
+synonym: "carbon monoxide sensing activity" EXACT []
is_a: GO:0070025 ! carbon monoxide binding
is_a: GO:0140299 ! small molecule sensor activity
@@ -346964,7 +346904,6 @@ namespace: biological_process
def: "The cellular homeostatic process that preserves a neuron in a stable, differentiated functional and structural state." [GOC:BHF, GOC:mah]
synonym: "neuron maintenance" EXACT []
is_a: GO:0019725 ! cellular homeostasis
-is_a: GO:0060249 ! anatomical structure homeostasis
[Term]
id: GO:0070051
@@ -347003,7 +346942,7 @@ id: GO:0070055
name: obsolete mRNA endonucleolytic cleavage involved in unfolded protein response
namespace: biological_process
def: "OBSOLETE. The endonucleolytic cleavage of a mRNA containing an HAC1-type intron at the 5' and 3' splice sites. The cleavage step is part of unconventional mRNA splicing, and contributes to the endoplasmic reticulum unfolded protein response." [GOC:bf, GOC:krc, GOC:mah, PMID:10357823]
-comment: The reason for obsoletion is that this process represents a single step (molecular function) of the IRE1-mediated unfolded protein response (GO:0036498).
+comment: The reason for obsoletion is that this process represents a single step (molecular function) of the IRE1-mediated unfolded protein response (GO:0036498).
synonym: "ERN1-mediated XBP-1 mRNA cleavage" RELATED [HGNC:3449]
synonym: "HAC1 mRNA cleavage" NARROW [GOC:bf]
synonym: "HAC1-type intron splice site recognition and cleavage" NARROW []
@@ -347043,7 +346982,7 @@ is_a: GO:0051276 ! chromosome organization
id: GO:0070059
name: intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to a stimulus indicating endoplasmic reticulum (ER) stress, and ends when the execution phase of apoptosis is triggered. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen." [GOC:mah, GOC:mtg_apoptosis, PMID:18701708]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to a stimulus indicating endoplasmic reticulum (ER) stress, and ends when the execution phase of apoptosis is triggered. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen." [GOC:mah, GOC:mtg_apoptosis, PMID:18701708]
synonym: "apoptosis in response to endoplasmic reticulum stress" BROAD []
synonym: "apoptosis in response to ER stress" EXACT []
synonym: "apoptosis triggered by ER stress" EXACT []
@@ -347132,7 +347071,7 @@ id: GO:0070069
name: cytochrome complex
namespace: cellular_component
def: "A protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions." [GOC:mah]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0070070
@@ -347194,24 +347133,26 @@ is_a: GO:0016577 ! histone demethylation
[Term]
id: GO:0070077
-name: histone arginine demethylation
+name: obsolete histone arginine demethylation
namespace: biological_process
-def: "The modification of a histone by the removal of a methyl group from an arginine residue." [GOC:mah]
-is_a: GO:0016577 ! histone demethylation
+def: "OBSOLETE. The modification of a histone by the removal of a methyl group from an arginine residue." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0032452
[Term]
id: GO:0070078
name: histone H3-R2 demethylation
namespace: biological_process
def: "The modification of histone H3 by the removal of a methyl group from arginine at position 2 of the histone." [GOC:BHF, GOC:vk]
-is_a: GO:0070077 ! histone arginine demethylation
+is_a: GO:0016577 ! histone demethylation
[Term]
id: GO:0070079
name: histone H4-R3 demethylation
namespace: biological_process
def: "The modification of histone H4 by the removal of a methyl group from arginine at position 3 of the histone." [GOC:BHF, GOC:vk]
-is_a: GO:0070077 ! histone arginine demethylation
+is_a: GO:0016577 ! histone demethylation
[Term]
id: GO:0070080
@@ -347258,7 +347199,7 @@ name: protein initiator methionine removal
namespace: biological_process
def: "The protein modification process in which the translation-initiating methionine or formylmethionine residue is removed from a protein." [GOC:imk, GOC:mah]
synonym: "removal of initiator methionine from protein" EXACT []
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0070085
@@ -347289,11 +347230,12 @@ is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0070088
-name: PHA granule
+name: polyhydroxyalkanoate granule
namespace: cellular_component
-def: "An inclusion body located in the cytoplasm that consists of polyhydroxyalkanoate (PHA) molecules and associated proteins, surrounded by a phospholipid monolayer; the proteins include PHA synthase, PHA depolymerase and 3HB-oligomer hydroxylase, phasins (PhaPs), which are thought to be the major structural proteins of the membrane surrounding the inclusion, and the regulator of phasin expression PhaR." [GOC:mah, PMID:15762612]
+def: "An inclusion body located in the cytoplasm of prokaryotes that consists of polyhydroxyalkanoate (PHA) molecules and associated proteins, surrounded by a phospholipid monolayer; the proteins include PHA synthase, PHA depolymerase and 3HB-oligomer hydroxylase, phasins (PhaPs), which are thought to be the major structural proteins of the membrane surrounding the inclusion, and the regulator of phasin expression PhaR." [GOC:mah, PMID:15762612]
+synonym: "carbonosome" BROAD []
+synonym: "PHA granule" EXACT []
synonym: "PHB granule" NARROW []
-synonym: "polyhydroxyalkanoate granule" EXACT []
is_a: GO:0016234 ! inclusion body
is_a: GO:0043231 ! intracellular membrane-bounded organelle
relationship: part_of GO:0005737 ! cytoplasm
@@ -347303,8 +347245,8 @@ id: GO:0070089
name: chloride-activated potassium channel activity
namespace: molecular_function
def: "Enables the chloride concentration-regulatable energy-independent passage of potassium ions across a lipid bilayer down a concentration gradient." [GOC:kmv, GOC:mtg_transport]
-is_a: GO:0005267 ! potassium channel activity
-is_a: GO:0022839 ! ion gated channel activity
+is_a: GO:0005254 ! chloride channel activity
+is_a: GO:0022839 ! monoatomic ion gated channel activity
[Term]
id: GO:0070090
@@ -347386,7 +347328,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0070098
name: chemokine-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a chemokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling]
+def: "The series of molecular signals initiated by a chemokine binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling]
synonym: "chemokine-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
relationship: part_of GO:1990869 ! cellular response to chemokine
@@ -347395,7 +347337,7 @@ relationship: part_of GO:1990869 ! cellular response to chemokine
id: GO:0070099
name: regulation of chemokine-mediated signaling pathway
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of the series of molecular events generated as a consequence of a chemokine binding to a cell surface receptor." [GOC:mah]
+def: "Any process that modulates the rate, frequency or extent of a chemokine-mediated signaling pathway." [GOC:mah]
synonym: "regulation of chemokine-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0001959 ! regulation of cytokine-mediated signaling pathway
relationship: regulates GO:0070098 ! chemokine-mediated signaling pathway
@@ -347404,7 +347346,7 @@ relationship: regulates GO:0070098 ! chemokine-mediated signaling pathway
id: GO:0070100
name: negative regulation of chemokine-mediated signaling pathway
namespace: biological_process
-def: "Any process that decreases the rate, frequency or extent of the series of molecular events generated as a consequence of a chemokine binding to a cell surface receptor." [GOC:mah]
+def: "Any process that decreases the rate, frequency or extent of a chemokine-mediated signaling pathway." [GOC:mah]
synonym: "negative regulation of chemokine-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0001960 ! negative regulation of cytokine-mediated signaling pathway
is_a: GO:0070099 ! regulation of chemokine-mediated signaling pathway
@@ -347414,7 +347356,7 @@ relationship: negatively_regulates GO:0070098 ! chemokine-mediated signaling pat
id: GO:0070101
name: positive regulation of chemokine-mediated signaling pathway
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of the series of molecular events generated as a consequence of a chemokine binding to a cell surface receptor." [GOC:mah]
+def: "Any process that increases the rate, frequency or extent of a chemokine-mediated signaling pathway." [GOC:mah]
synonym: "positive regulation of chemokine-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0001961 ! positive regulation of cytokine-mediated signaling pathway
is_a: GO:0070099 ! regulation of chemokine-mediated signaling pathway
@@ -347424,7 +347366,7 @@ relationship: positively_regulates GO:0070098 ! chemokine-mediated signaling pat
id: GO:0070102
name: interleukin-6-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-6 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:add, GOC:BHF, GOC:mah, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-6 binding to a receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:add, GOC:BHF, GOC:mah, GOC:signaling]
synonym: "IL-6-mediated signaling pathway" RELATED []
synonym: "interleukin-6-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -347434,7 +347376,7 @@ relationship: part_of GO:0071354 ! cellular response to interleukin-6
id: GO:0070103
name: regulation of interleukin-6-mediated signaling pathway
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of the series of molecular events generated as a consequence of interleukin-6-mediated binding to a cell surface receptor." [GOC:BHF, GOC:mah]
+def: "Any process that modulates the rate, frequency or extent of an interleukin-6-mediated signaling pathway." [GOC:BHF, GOC:mah]
synonym: "regulation of IL-6-mediated signaling pathway" EXACT [GOC:mah]
synonym: "regulation of interleukin-6-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0001959 ! regulation of cytokine-mediated signaling pathway
@@ -347444,7 +347386,7 @@ relationship: regulates GO:0070102 ! interleukin-6-mediated signaling pathway
id: GO:0070104
name: negative regulation of interleukin-6-mediated signaling pathway
namespace: biological_process
-def: "Any process that decreases the rate, frequency or extent of the series of molecular events generated as a consequence of interleukin-6 binding to a cell surface receptor." [GOC:BHF, GOC:mah]
+def: "Any process that decreases the rate, frequency or extent of an interleukin-6-mediated signaling pathway." [GOC:BHF, GOC:mah]
synonym: "negative regulation of IL-6-mediated signaling pathway" EXACT [GOC:mah]
synonym: "negative regulation of interleukin-6-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0001960 ! negative regulation of cytokine-mediated signaling pathway
@@ -347455,7 +347397,7 @@ relationship: negatively_regulates GO:0070102 ! interleukin-6-mediated signaling
id: GO:0070105
name: positive regulation of interleukin-6-mediated signaling pathway
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of the series of molecular events generated as a consequence of interleukin-6 binding to a cell surface receptor." [GOC:BHF, GOC:mah]
+def: "Any process that increases the rate, frequency or extent of an interleukin-6-mediated signaling pathway." [GOC:BHF, GOC:mah]
synonym: "positive regulation of IL-6-mediated signaling pathway" EXACT [GOC:mah]
synonym: "positive regulation of interleukin-6-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0001961 ! positive regulation of cytokine-mediated signaling pathway
@@ -347466,7 +347408,7 @@ relationship: positively_regulates GO:0070102 ! interleukin-6-mediated signaling
id: GO:0070106
name: interleukin-27-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-27 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:add, GOC:BHF, GOC:mah, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-27 binding to a receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:add, GOC:BHF, GOC:mah, GOC:signaling]
synonym: "IL-27-mediated signaling pathway" EXACT [GOC:mah]
synonym: "IL27RA/IL6ST signaling pathway" EXACT [GOC:add]
synonym: "interleukin-27-mediated signalling pathway" EXACT [GOC:mah]
@@ -347476,7 +347418,7 @@ is_a: GO:0019221 ! cytokine-mediated signaling pathway
id: GO:0070107
name: regulation of interleukin-27-mediated signaling pathway
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of the series of molecular events generated as a consequence of interleukin-27-mediated binding to a cell surface receptor." [GOC:BHF, GOC:mah]
+def: "Any process that modulates the rate, frequency or extent of an interleukin-27-mediated signaling pathway." [GOC:BHF, GOC:mah]
synonym: "regulation of IL-27-mediated signaling pathway" EXACT [GOC:mah]
synonym: "regulation of IL27RA/IL6ST signaling pathway" EXACT [GOC:add]
synonym: "regulation of interleukin-27-mediated signalling pathway" EXACT [GOC:mah]
@@ -347487,7 +347429,7 @@ relationship: regulates GO:0070106 ! interleukin-27-mediated signaling pathway
id: GO:0070108
name: negative regulation of interleukin-27-mediated signaling pathway
namespace: biological_process
-def: "Any process that decreases the rate, frequency or extent of the series of molecular events generated as a consequence of interleukin-27 binding to a cell surface receptor." [GOC:BHF, GOC:mah]
+def: "Any process that decreases the rate, frequency or extent of an interleukin-27-mediated signaling pathway." [GOC:BHF, GOC:mah]
synonym: "negative regulation of IL-27-mediated signaling pathway" EXACT [GOC:mah]
synonym: "negative regulation of IL27RA/IL6ST signaling pathway" EXACT [GOC:add]
synonym: "negative regulation of interleukin-27-mediated signalling pathway" EXACT [GOC:mah]
@@ -347499,7 +347441,7 @@ relationship: negatively_regulates GO:0070106 ! interleukin-27-mediated signalin
id: GO:0070109
name: positive regulation of interleukin-27-mediated signaling pathway
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of the series of molecular events generated as a consequence of interleukin-27 binding to a cell surface receptor." [GOC:BHF, GOC:mah]
+def: "Any process that increases the rate, frequency or extent of an interleukin-27-mediated signaling pathway." [GOC:BHF, GOC:mah]
synonym: "positive regulation of IL-27-mediated signaling pathway" EXACT [GOC:mah]
synonym: "positive regulation of IL27RA/IL6ST signaling pathway" EXACT [GOC:add]
synonym: "positive regulation of interleukin-27-mediated signalling pathway" EXACT [GOC:mah]
@@ -347513,7 +347455,6 @@ name: ciliary neurotrophic factor receptor complex
namespace: cellular_component
def: "A protein complex that acts as a receptor for the cytokine ciliary neurotrophic factor (CNTF). In humans the receptor complex is a hexamer composed of two molecules each of CNTF and CNTFR and one molecule each of gp130 and LIFR." [GOC:BHF, GOC:mah, GOC:rl, PMID:12707266]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0070111
@@ -347598,7 +347539,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0070120
name: ciliary neurotrophic factor-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a ciliary neurotrophic factor (CNTF) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:mah]
+def: "The series of molecular signals initiated by the binding of a ciliary neurotrophic factor (CNTF) to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:mah]
synonym: "ciliary neurotrophic factor-mediated signalling pathway" EXACT [GOC:mah]
synonym: "CNTF-mediated signaling pathway" EXACT [GOC:rl]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -347613,10 +347554,12 @@ is_a: GO:0048856 ! anatomical structure development
[Term]
id: GO:0070122
-name: isopeptidase activity
+name: obsolete isopeptidase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of an isopeptide bond. An isopeptide bond is an amide linkage between a carboxyl group of one amino acid and an amino group of another amino acid in which at least one of these groups is not on the a-carbon of one of the amino acids (for example, the link between an epsilon-amino group of a lysine molecule to a carboxyl group on a second amino acid is an isopeptide bond)." [GOC:mah, Wikipedia:Isopeptidase]
-is_a: GO:0008233 ! peptidase activity
+def: "OBSOLETE. Catalysis of the hydrolysis of an isopeptide bond. An isopeptide bond is an amide linkage between a carboxyl group of one amino acid and an amino group of another amino acid in which at least one of these groups is not on the a-carbon of one of the amino acids (for example, the link between an epsilon-amino group of a lysine molecule to a carboxyl group on a second amino acid is an isopeptide bond)." [GOC:mah, Wikipedia:Isopeptidase]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0008233
[Term]
id: GO:0070123
@@ -347629,7 +347572,7 @@ synonym: "transforming growth factor beta ligand binding to type III receptor" R
synonym: "type III TGF-beta receptor activity" EXACT []
synonym: "type III TGFbeta receptor activity" EXACT []
synonym: "type III transforming growth factor beta receptor activity" EXACT []
-is_a: GO:0005024 ! transforming growth factor beta-activated receptor activity
+is_a: GO:0005024 ! transforming growth factor beta receptor activity
[Term]
id: GO:0070124
@@ -347765,16 +347708,7 @@ namespace: molecular_function
def: "Catalysis of the hydrolysis of peptide bonds between an alpha-carboxyl group and an alpha-amino group within a small protein such as ubiquitin or a ubiquitin-like protein (e.g. APG8, ISG15, NEDD8, SUMO)." [GOC:mah]
synonym: "small conjugating protein-specific endopeptidase activity" EXACT []
is_a: GO:0004197 ! cysteine-type endopeptidase activity
-is_a: GO:0019783 ! ubiquitin-like protein-specific protease activity
-
-[Term]
-id: GO:0070138
-name: ubiquitin-like protein-specific isopeptidase activity
-namespace: molecular_function
-def: "Catalysis of the hydrolysis of an isopeptide bond between a small protein such as ubiquitin or a ubiquitin-like protein (e.g. APG8, ISG15, NEDD8, SUMO) and a protein to which the small protein has been conjugated." [GOC:mah]
-synonym: "small conjugating protein-specific isopeptidase activity" EXACT [GOC:dph]
-is_a: GO:0019783 ! ubiquitin-like protein-specific protease activity
-is_a: GO:0070122 ! isopeptidase activity
+is_a: GO:0019783 ! ubiquitin-like protein peptidase activity
[Term]
id: GO:0070139
@@ -347784,17 +347718,8 @@ def: "Catalysis of the hydrolysis of peptide bonds between an alpha-carboxyl gro
xref: Reactome:R-HSA-2990840 "SENP1,2,5 proteolytically process SUMO1"
xref: Reactome:R-HSA-2990842 "SENP1,2,5 proteolytically process SUMO2"
xref: Reactome:R-HSA-2993763 "SENP1,2,5 proteolytically process SUMO3"
-is_a: GO:0016929 ! SUMO-specific protease activity
is_a: GO:0070137 ! ubiquitin-like protein-specific endopeptidase activity
-[Term]
-id: GO:0070140
-name: SUMO-specific isopeptidase activity
-namespace: molecular_function
-def: "Catalysis of the hydrolysis of an isopeptide bond between the small conjugating protein SUMO and a protein to which SUMO has been conjugated." [GOC:mah]
-is_a: GO:0016929 ! SUMO-specific protease activity
-is_a: GO:0070138 ! ubiquitin-like protein-specific isopeptidase activity
-
[Term]
id: GO:0070141
name: response to UV-A
@@ -348030,7 +347955,6 @@ id: GO:0070167
name: regulation of biomineral tissue development
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of biomineral tissue development, the formation of hard tissues that consist mainly of inorganic compounds." [GOC:mah]
-is_a: GO:0110149 ! regulation of biomineralization
is_a: GO:2000026 ! regulation of multicellular organismal development
relationship: regulates GO:0031214 ! biomineral tissue development
@@ -348040,9 +347964,7 @@ name: negative regulation of biomineral tissue development
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of biomineral tissue development, the formation of hard tissues that consist mainly of inorganic compounds." [GOC:mah]
is_a: GO:0051093 ! negative regulation of developmental process
-is_a: GO:0051241 ! negative regulation of multicellular organismal process
is_a: GO:0070167 ! regulation of biomineral tissue development
-is_a: GO:0110150 ! negative regulation of biomineralization
relationship: negatively_regulates GO:0031214 ! biomineral tissue development
[Term]
@@ -348051,9 +347973,7 @@ name: positive regulation of biomineral tissue development
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of biomineral tissue development, the formation of hard tissues that consist mainly of inorganic compounds." [GOC:mah]
is_a: GO:0051094 ! positive regulation of developmental process
-is_a: GO:0051240 ! positive regulation of multicellular organismal process
is_a: GO:0070167 ! regulation of biomineral tissue development
-is_a: GO:0110151 ! positive regulation of biomineralization
relationship: positively_regulates GO:0031214 ! biomineral tissue development
[Term]
@@ -348347,7 +348267,6 @@ name: regulation of establishment of protein localization to chromosome
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location on a chromosome." [GOC:BHF, GOC:mah]
synonym: "regulation of establishment of protein localisation to chromosome" EXACT [GOC:mah]
-is_a: GO:0060341 ! regulation of cellular localization
is_a: GO:0070201 ! regulation of establishment of protein localization
relationship: regulates GO:0070199 ! establishment of protein localization to chromosome
@@ -348365,7 +348284,7 @@ relationship: regulates GO:0070200 ! establishment of protein localization to te
id: GO:0070204
name: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + H(+) + isochorismate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO(2)." [RHEA:25593]
+def: "Catalysis of the reaction: 2-oxoglutarate + H+ + isochorismate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2." [RHEA:25593]
comment: Note that this function was formerly EC:4.1.3.18.
synonym: "MenD" RELATED [EC:2.2.1.9]
synonym: "SEPHCHC synthase activity" RELATED [EC:2.2.1.9]
@@ -348462,7 +348381,7 @@ synonym: "poly(ADP-ribose) addition to protein" EXACT [GOC:rl]
synonym: "protein amino acid poly-ADP-ribosylation" EXACT [GOC:bf]
synonym: "protein poly(ADP-ribose) metabolism" RELATED [GOC:rl]
synonym: "protein poly(ADP-ribose) synthesis" EXACT [GOC:rl]
-is_a: GO:0006471 ! protein ADP-ribosylation
+is_a: GO:0043687 ! post-translational protein modification
[Term]
id: GO:0070213
@@ -348470,7 +348389,7 @@ name: protein auto-ADP-ribosylation
namespace: biological_process
def: "The ADP-ribosylation by a protein of one or more of its own amino acid residues, or residues on an identical protein." [GOC:BHF, GOC:rl]
synonym: "protein amino acid auto-ADP-ribosylation" EXACT [GOC:bf]
-is_a: GO:0006471 ! protein ADP-ribosylation
+is_a: GO:0043687 ! post-translational protein modification
[Term]
id: GO:0070214
@@ -348478,8 +348397,8 @@ name: CSK-GAP-A.p62 complex
namespace: cellular_component
def: "A protein complex that contains the protein-tyrosine kinase CSK and the GTPase-activating protein (GAP)-associated p62 (GAP-A.p62); may mediate translocation of proteins, including GAP and CSK, to membrane or cytoskeletal regions upon c-Src activation." [PMID:7544435]
comment: Note that the gene/protein name 'APC' should not be confused with the abbreviation for 'anaphase promoting complex'.
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005737 ! cytoplasm
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0031252 ! cell leading edge
[Term]
@@ -348513,9 +348432,10 @@ is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0070218
-name: sulfide ion homeostasis
+name: obsolete sulfide ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of sulfide ions within an organism or cell." [GOC:mah]
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of sulfide ions within an organism or cell." [GOC:mah]
+comment: This term was obsoleted because it does not represent a GO process.
synonym: "sulfide generation" RELATED [GOC:mah]
synonym: "sulfide homeostasis" EXACT [GOC:mah]
synonym: "sulfide production" RELATED [GOC:mah]
@@ -348523,20 +348443,21 @@ synonym: "sulphide generation" RELATED [GOC:mah]
synonym: "sulphide homeostasis" EXACT [GOC:mah]
synonym: "sulphide ion homeostasis" EXACT [GOC:mah]
synonym: "sulphide production" RELATED [GOC:mah]
-is_a: GO:0055083 ! monovalent inorganic anion homeostasis
-is_a: GO:0072505 ! divalent inorganic anion homeostasis
+is_obsolete: true
+consider: GO:0140974
[Term]
id: GO:0070219
-name: cellular sulfide ion homeostasis
+name: obsolete intracellular sulfide ion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of sulfide ions at the level of a cell." [GOC:mah]
+def: "OBSOLETE. A homeostatic process involved in the maintenance of a steady state level of sulfide ions within a cell." [GOC:mah]
+comment: This term was obsoleted because it does not represent a GO process.
synonym: "cellular sulfide homeostasis" EXACT [GOC:mah]
+synonym: "cellular sulfide ion homeostasis" EXACT []
synonym: "cellular sulphide homeostasis" EXACT [GOC:mah]
synonym: "cellular sulphide ion homeostasis" EXACT [GOC:mah]
-is_a: GO:0030320 ! cellular monovalent inorganic anion homeostasis
-is_a: GO:0070218 ! sulfide ion homeostasis
-is_a: GO:0072501 ! cellular divalent inorganic anion homeostasis
+is_obsolete: true
+consider: GO:0140974
[Term]
id: GO:0070220
@@ -348579,7 +348500,8 @@ is_a: GO:0019418 ! sulfide oxidation
id: GO:0070224
name: sulfide:quinone oxidoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: hydrogen sulfide + a quinone = S0 + a hydroquinone." [MetaCyc:R17-RXN]
+def: "Catalysis of the reaction: H2S (hydrogen sulfide) + a quinone = S0 (sulfane sulfur) + a hydroquinone." [RHEA:30239]
+comment: Note that EC:1.8.5.4 describes this reaction as bacterial-specific, but it has also been observed in eukaryotes (PMID:22852582, PMID:10224084).
synonym: "sulfide-quinone reductase activity" EXACT [MetaCyc:MONOMER-12314]
synonym: "sulphide:quinone oxidoreductase activity" EXACT [GOC:mah]
xref: MetaCyc:R17-RXN
@@ -349327,7 +349249,7 @@ def: "The chemical reactions and pathways involving N-acylphosphatidylethanolami
synonym: "N-acylphosphatidylethanolamine metabolism" EXACT [GOC:elh, PMID:14634025, PMID:15878693]
synonym: "NAPE metabolic process" EXACT [GOC:elh, PMID:14634025, PMID:15878693]
synonym: "NAPE metabolism" EXACT [GOC:elh, PMID:14634025, PMID:15878693]
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0046337 ! phosphatidylethanolamine metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
@@ -349728,14 +349650,16 @@ id: GO:0070331
name: CD20-Lck-Fyn complex
namespace: cellular_component
def: "A protein complex that contains the cell-surface protein CD20 and the Src family tyrosine kinases Lck and Fyn." [GOC:mah, PMID:7545683]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0070332
name: CD20-Lck-Lyn-Fyn complex
namespace: cellular_component
def: "A protein complex that contains the cell-surface protein CD20 and the Src family tyrosine kinases Lck, Lyn and Fyn." [GOC:mah, PMID:7545683]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0070333
@@ -349761,7 +349685,6 @@ namespace: molecular_function
def: "Binding to aspartate, the alpha-amino-acid anion of 2-aminobutanedioic acid that has formula C4H5NO4." [CHEBI:29995, GOC:mah]
synonym: "aspartic acid binding" EXACT [GOC:mah]
is_a: GO:0016597 ! amino acid binding
-is_a: GO:0031406 ! carboxylic acid binding
[Term]
id: GO:0070336
@@ -349997,21 +349920,16 @@ def: "A process involved in the controlled movement of a bacterial cell powered
synonym: "cell motility by actin tail formation" EXACT [PMID:15773977]
is_a: GO:0048870 ! cell motility
-[Term]
-id: GO:0070359
-name: actin polymerization-dependent cell motility involved in migration of symbiont in host
-namespace: biological_process
-def: "A process involved in the controlled movement of a bacterial cell within a host cell, powered by the continuous polymerization of host actin at one pole of the cell." [GOC:jl, GOC:mah, PMID:15773977]
-synonym: "actin polymerization-dependent cell motility involved in migration of symbiont within host" EXACT []
-is_a: GO:0070358 ! actin polymerization-dependent cell motility
-relationship: part_of GO:0070360 ! migration of symbiont within host by polymerization of host actin
-
[Term]
id: GO:0070360
-name: migration of symbiont within host by polymerization of host actin
+name: actin polymerization-dependent cell migration in host
namespace: biological_process
-def: "The directional movement of an organism, usually a bacterial cell, from one place to another within its host organism, by a process involving continuous polymerization of host actin at one pole of the symbiont cell. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:jl, GOC:mah]
+alt_id: GO:0070359
+def: "The directional movement of an organism, usually a bacterial cell, from one place to another within its host organism, by a process involving continuous polymerization of actin at one pole of the symbiont cell. Some bacteria use host actin for migration. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:jl, GOC:mah, PMID:15773977]
+synonym: "actin polymerization-dependent cell motility involved in migration of symbiont in host" RELATED []
+synonym: "migration of symbiont within host by polymerization of host actin" RELATED []
is_a: GO:0044001 ! migration in host
+is_a: GO:0070358 ! actin polymerization-dependent cell motility
[Term]
id: GO:0070365
@@ -350245,7 +350163,7 @@ is_a: GO:0004896 ! cytokine receptor activity
id: GO:0070381
name: endosome to plasma membrane transport vesicle
namespace: cellular_component
-def: "A transport vesicle that mediates transport from the endosome to the plasma membrane, and fuses with the plasma membrane to deliver lipids and membrane proteins to the plasma membrane and to release various cargo molecules, such as proteins or hormones, by exocytosis." [GOC:kad, GOC:mah, PMID:10679016, PMID:12110576]
+def: "A transport vesicle that mediates transport from the endosome to the plasma membrane, and fuses with the plasma membrane to deliver lipids and membrane proteins to the plasma membrane and to release various cargo molecules, such as proteins or hormones, by exocytosis." [GOC:kad, GOC:mah, PMID:10679016, PMID:12110576]
synonym: "endosome to plasma membrane constitutive secretory pathway transport vesicle" EXACT []
synonym: "endosome-plasma membrane transport vesicle" EXACT [GOC:mah]
is_a: GO:0070382 ! exocytic vesicle
@@ -350627,6 +350545,7 @@ name: DNA ligase III-XRCC1 complex
namespace: cellular_component
def: "A protein complex that contains DNA ligase III and XRCC1, and is involved in base excision repair." [PMID:15141024, PMID:7760816]
is_a: GO:0140513 ! nuclear protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0070422
@@ -350642,10 +350561,10 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0070423
name: nucleotide-binding oligomerization domain containing signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to a nucleotide-binding oligomerization domain containing (NOD) protein." [GOC:add, PMID:17944960, PMID:18585455]
+def: "The series of molecular signals initiated by the binding of a ligand (such as a bacterial peptidoglycan) to a cytoplasmic nucleotide-binding oligomerization domain containing (NOD) protein receptor, and ending with regulation of a downstream cellular process." [GOC:add, PMID:17944960, PMID:18585455]
synonym: "NOD signaling pathway" EXACT [GOC:add]
synonym: "nucleotide-binding oligomerization domain containing signalling pathway" EXACT [GOC:mah]
-is_a: GO:0002753 ! cytoplasmic pattern recognition receptor signaling pathway
+is_a: GO:0002753 ! cytosolic pattern recognition receptor signaling pathway
is_a: GO:0035872 ! nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway
[Term]
@@ -350655,8 +350574,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate, or extent of a nucleotide-binding oligomerization domain containing (NOD) pathway." [GOC:add]
synonym: "regulation of NOD signaling pathway" EXACT [GOC:add]
synonym: "regulation of nucleotide-binding oligomerization domain containing signalling pathway" EXACT [GOC:mah]
-is_a: GO:0062207 ! regulation of pattern recognition receptor signaling pathway
-is_a: GO:1902531 ! regulation of intracellular signal transduction
+is_a: GO:0039531 ! regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
relationship: regulates GO:0070423 ! nucleotide-binding oligomerization domain containing signaling pathway
[Term]
@@ -350666,8 +350584,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of the nucleotide-binding oligomerization domain containing (NOD) pathway." [GOC:add]
synonym: "negative regulation of NOD signaling pathway" EXACT [GOC:add]
synonym: "negative regulation of nucleotide-binding oligomerization domain containing signalling pathway" EXACT [GOC:mah]
+is_a: GO:0039532 ! negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
is_a: GO:0070424 ! regulation of nucleotide-binding oligomerization domain containing signaling pathway
-is_a: GO:1902532 ! negative regulation of intracellular signal transduction
relationship: negatively_regulates GO:0070423 ! nucleotide-binding oligomerization domain containing signaling pathway
[Term]
@@ -350679,14 +350597,13 @@ synonym: "positive regulation of NOD signaling pathway" EXACT [GOC:add]
synonym: "positive regulation of nucleotide-binding oligomerization domain containing signalling pathway" EXACT [GOC:mah]
is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
is_a: GO:0070424 ! regulation of nucleotide-binding oligomerization domain containing signaling pathway
-is_a: GO:1902533 ! positive regulation of intracellular signal transduction
relationship: positively_regulates GO:0070423 ! nucleotide-binding oligomerization domain containing signaling pathway
[Term]
id: GO:0070427
name: nucleotide-binding oligomerization domain containing 1 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to nucleotide-binding oligomerization domain containing 1 (NOD1)." [GOC:add, PMID:17944960, PMID:18585455]
+def: "The series of molecular signals initiated by the binding of a ligand (such as a bacterial peptidoglycan) to a cytoplasmic nucleotide-binding oligomerization domain containing 1 (NOD1) protein receptor, and ending with regulation of a downstream cellular process." [GOC:add, PMID:17944960, PMID:18585455]
synonym: "NOD1 signaling pathway" EXACT [GOC:add]
synonym: "nucleotide-binding oligomerization domain containing 1 signalling pathway" EXACT [GOC:mah]
is_a: GO:0070423 ! nucleotide-binding oligomerization domain containing signaling pathway
@@ -350727,7 +350644,7 @@ relationship: positively_regulates GO:0070427 ! nucleotide-binding oligomerizati
id: GO:0070431
name: nucleotide-binding oligomerization domain containing 2 signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of binding to nucleotide-binding oligomerization domain containing 2 (NOD2)." [GOC:add, PMID:17944960, PMID:18585455]
+def: "The series of molecular signals initiated by the binding of a ligand (such as a bacterial peptidoglycan) to a cytoplasmic nucleotide-binding oligomerization domain containing 2 (NOD2) protein receptor, and ending with regulation of a downstream cellular process." [GOC:add, PMID:17944960, PMID:18585455]
synonym: "NOD2 signaling pathway" EXACT [GOC:add]
synonym: "nucleotide-binding oligomerization domain containing 2 signalling pathway" EXACT [GOC:mah]
is_a: GO:0070423 ! nucleotide-binding oligomerization domain containing signaling pathway
@@ -350939,7 +350856,7 @@ synonym: "stimulation of ergosterol biosynthetic process" NARROW []
synonym: "up regulation of ergosterol biosynthetic process" EXACT []
synonym: "up-regulation of ergosterol biosynthetic process" EXACT []
synonym: "upregulation of ergosterol biosynthetic process" EXACT []
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
+is_a: GO:0031325 ! positive regulation of cellular metabolic process
is_a: GO:0032443 ! regulation of ergosterol biosynthetic process
is_a: GO:0106120 ! positive regulation of sterol biosynthetic process
is_a: GO:1902932 ! positive regulation of alcohol biosynthetic process
@@ -351351,7 +351268,7 @@ is_a: GO:0030246 ! carbohydrate binding
id: GO:0070493
name: thrombin-activated receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of a thrombin-activated receptor binding to one of its physiological ligands." [GOC:mah, PMID:1672265]
+def: "A G protein-coupled receptor signaling pathway initiated by thrombin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:mah, PMID:1672265]
synonym: "thrombin receptor signaling pathway" EXACT []
synonym: "thrombin receptor signalling pathway" EXACT [GOC:mah]
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -351402,7 +351319,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0070498
name: interleukin-1-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-1 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:mah, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-1 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:mah, GOC:signaling]
synonym: "IL-1 alpha-mediated signaling pathway" NARROW [GOC:add]
synonym: "IL-1 beta-mediated signaling pathway" NARROW [GOC:add]
synonym: "IL-1-mediated signaling pathway" EXACT [GOC:mah]
@@ -351423,11 +351340,13 @@ is_a: GO:0045229 ! external encapsulating structure organization
[Term]
id: GO:0070500
-name: poly-gamma-glutamate metabolic process
+name: obsolete poly-gamma-glutamate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving poly-gamma-glutamate, a polymer of D- and/or L-glutamic acid residues linked by gamma-peptidyl bonds." [GOC:mah, PMID:16689787]
+def: "OBSOLETE. The chemical reactions and pathways involving poly-gamma-glutamate, a polymer of D- and/or L-glutamic acid residues linked by gamma-peptidyl bonds." [GOC:mah, PMID:16689787]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "poly-gamma-glutamate metabolism" EXACT [GOC:mah]
-is_a: GO:0044260 ! cellular macromolecule metabolic process
+is_obsolete: true
+consider: GO:0034722
[Term]
id: GO:0070501
@@ -351438,8 +351357,7 @@ synonym: "poly-gamma-glutamate anabolism" EXACT [GOC:mah]
synonym: "poly-gamma-glutamate biosynthesis" EXACT [GOC:mah]
synonym: "poly-gamma-glutamate formation" EXACT [GOC:mah]
synonym: "poly-gamma-glutamate synthesis" EXACT [GOC:mah]
-is_a: GO:0034645 ! cellular macromolecule biosynthetic process
-is_a: GO:0070500 ! poly-gamma-glutamate metabolic process
+is_a: GO:0009059 ! macromolecule biosynthetic process
[Term]
id: GO:0070502
@@ -351511,7 +351429,6 @@ namespace: biological_process
def: "The directed movement of cholesterol into a cell or organelle." [GOC:BHF, GOC:rl]
synonym: "cholesterol uptake" EXACT [GOC:rl]
is_a: GO:0030301 ! cholesterol transport
-is_a: GO:0035376 ! sterol import
[Term]
id: GO:0070509
@@ -351524,24 +351441,23 @@ is_a: GO:0006816 ! calcium ion transport
[Term]
id: GO:0070510
-name: regulation of histone H4-K20 methylation
+name: obsolete regulation of histone H4-K20 methylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 20 of histone H4." [GOC:mah]
-is_a: GO:0031060 ! regulation of histone methylation
-relationship: regulates GO:0034770 ! histone H4-K20 methylation
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 20 of histone H4." [GOC:mah]
+comment: This term was obsoleted because it represents regulation of a molecular function.
+is_obsolete: true
[Term]
id: GO:0070511
-name: negative regulation of histone H4-K20 methylation
+name: obsolete negative regulation of histone H4-K20 methylation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 20 of histone H4." [GOC:mah]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 20 of histone H4." [GOC:mah]
+comment: This term was obsoleted because it represents ergulation of a molecular function.
synonym: "down regulation of histone H4-K20 methylation" EXACT [GOC:mah]
synonym: "down-regulation of histone H4-K20 methylation" EXACT [GOC:mah]
synonym: "downregulation of histone H4-K20 methylation" EXACT [GOC:mah]
synonym: "inhibition of histone H4-K20 methylation" NARROW [GOC:mah]
-is_a: GO:0031061 ! negative regulation of histone methylation
-is_a: GO:0070510 ! regulation of histone H4-K20 methylation
-relationship: negatively_regulates GO:0034770 ! histone H4-K20 methylation
+is_obsolete: true
[Term]
id: GO:0070512
@@ -351554,8 +351470,6 @@ synonym: "up regulation of histone H4-K20 methylation" EXACT [GOC:mah]
synonym: "up-regulation of histone H4-K20 methylation" EXACT [GOC:mah]
synonym: "upregulation of histone H4-K20 methylation" EXACT [GOC:mah]
is_a: GO:0031062 ! positive regulation of histone methylation
-is_a: GO:0070510 ! regulation of histone H4-K20 methylation
-relationship: positively_regulates GO:0034770 ! histone H4-K20 methylation
[Term]
id: GO:0070513
@@ -351655,6 +351569,8 @@ def: "Catalysis of the reaction: an 11-beta-hydroxysteroid + NADP+ = an 11-oxost
synonym: "beta-hydroxysteroid dehydrogenase" BROAD []
synonym: "corticosteroid 11-beta-dehydrogenase activity" RELATED [EC:1.1.1.146]
xref: EC:1.1.1.146
+xref: Reactome:R-HSA-9757706 "HSD11B1 hydrogenates PREDN to PREDL in hepatic cell"
+xref: Reactome:R-HSA-9759259 "HSD11B2 dehydrogenates PREDL to PREDN"
xref: RHEA:11388
xref: Wikipedia:11beta-hydroxysteroid_dehydrogenase
is_a: GO:0003845 ! 11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity
@@ -351762,8 +351678,7 @@ id: GO:0070538
name: oleic acid binding
namespace: molecular_function
def: "Binding to oleic acid, the 18-carbon monounsaturated fatty acid (9Z)-octadec-9-enoic acid." [GOC:lp, GOC:mah]
-is_a: GO:0005504 ! fatty acid binding
-is_a: GO:0043177 ! organic acid binding
+is_a: GO:0036041 ! long-chain fatty acid binding
[Term]
id: GO:0070539
@@ -351771,7 +351686,6 @@ name: linoleic acid binding
namespace: molecular_function
def: "Binding to linoleic acid, the 18-carbon unsaturated fatty acid (9Z,12Z)-octadeca-9,12-dienoic acid." [GOC:lp, GOC:mah]
is_a: GO:0036041 ! long-chain fatty acid binding
-is_a: GO:0043177 ! organic acid binding
[Term]
id: GO:0070540
@@ -351779,7 +351693,6 @@ name: stearic acid binding
namespace: molecular_function
def: "Binding to stearic acid, the 18-carbon saturated fatty acid octadecanoic acid." [GOC:lp, GOC:mah]
is_a: GO:0036041 ! long-chain fatty acid binding
-is_a: GO:0043177 ! organic acid binding
[Term]
id: GO:0070541
@@ -351804,6 +351717,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a linoleic acid stimulus." [GOC:lp]
synonym: "response to linoleate" EXACT [GOC:mah]
is_a: GO:0070542 ! response to fatty acid
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0070544
@@ -351847,23 +351761,24 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0070549
name: siRNA-mediated gene silencing by inhibition of translation
namespace: biological_process
-def: "A process of negative regulation of translation that is mediated by the association of small interfering RNAs (siRNAs) with a cognate target mRNA." [GOC:mah, PMID:18771919]
-synonym: "down regulation of translation involved in RNA interference" EXACT [GOC:mah]
-synonym: "down-regulation of translation involved in RNA interference" EXACT [GOC:mah]
-synonym: "downregulation of translation involved in RNA interference" EXACT [GOC:mah]
-synonym: "inhibition of translation involved in RNA interference" NARROW [GOC:mah]
-synonym: "negative regulation of translation involved in RNA interference" EXACT []
+def: "An siRNA-mediated post-transcriptional gene silencing pathway that blocks the translation of target mRNAs into proteins. Once incorporated into a RNA-induced silencing complex (RISC), an siRNA will typically mediate repression of translation if the siRNA perfectly complements elements located in the 3' untranslated region of target mRNAs." [GOC:mah, PMID:18771919]
+synonym: "down regulation of translation involved in RNA interference" BROAD [GOC:mah]
+synonym: "down-regulation of translation involved in RNA interference" BROAD [GOC:mah]
+synonym: "downregulation of translation involved in RNA interference" BROAD [GOC:mah]
+synonym: "inhibition of translation involved in RNA interference" BROAD [GOC:mah]
+synonym: "negative regulation of translation involved in RNA interference" BROAD []
synonym: "RNA interference, negative regulation of translation" EXACT [GOC:mah]
-is_a: GO:0040033 ! RNA-mediated gene silencing by inhibition of translation
+is_a: GO:0017148 ! negative regulation of translation
+is_a: GO:0140766 ! siRNA-mediated gene silencing
[Term]
id: GO:0070550
-name: rDNA condensation
+name: rDNA chromatin condensation
namespace: biological_process
def: "The process in which the chromatin structure of the rDNA repeats is compacted. In S. cerevisiae, condensation and resolution of the rDNA occurs during anaphase." [GOC:dgf, PMID:10811823, PMID:15137940]
+synonym: "rDNA condensation" EXACT []
synonym: "rDNA packaging" EXACT []
-is_a: GO:0006323 ! DNA packaging
-relationship: part_of GO:0030261 ! chromosome condensation
+is_a: GO:0030261 ! chromosome condensation
relationship: part_of GO:1990700 ! nucleolar chromatin organization
[Term]
@@ -351872,7 +351787,7 @@ name: endoribonuclease activity, cleaving siRNA-paired mRNA
namespace: molecular_function
def: "Catalysis of the endonucleolytic cleavage of the mRNA in a double-stranded RNA molecule formed by the base pairing of an mRNA with an siRNA, yielding 5'-phosphomonoesters." [GOC:mah, PMID:15105377]
synonym: "argonaute endoribonuclease activity" RELATED [GOC:mah]
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0070552
@@ -351935,7 +351850,7 @@ name: lysosomal multienzyme complex
namespace: cellular_component
def: "A protein complex found in the lysosome that contains beta-galactosidase, cathepsin A, alpha-neuraminidase and N-acetylgalactosamine-6-sulfate sulfatase, and is involved in glycosaminoglycan catabolism." [GOC:mah, PMID:8910459]
synonym: "GALNS-lysosomal hydrolase 1.27 MDa complex" NARROW [CORUM:1379]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005764 ! lysosome
[Term]
@@ -352096,6 +352011,7 @@ comment: Note that this term is not intended for use in annotating lateral movem
synonym: "cadmium ion membrane transport" EXACT []
synonym: "transmembrane cadmium transport" EXACT [GOC:mah]
is_a: GO:0015691 ! cadmium ion transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -352143,7 +352059,8 @@ is_a: GO:1902555 ! endoribonuclease complex
id: GO:0070579
name: methylcytosine dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: methylcytosine + 2-oxoglutarate + O2 = 5-hydroxymethylcytosine + succinate + CO2." [PMID:19372391]
+def: "Catalysis of the reaction: methylcytosine + 2-oxoglutarate + O2 = 5-hydroxymethylcytosine + succinate + CO2." [PMID:19372391, PMID:21778364]
+xref: EC:1.14.11.80
xref: Reactome:R-HSA-5220952 "TET1,2,3 oxidizes 5-formylcytosine to 5-carboxylcytosine"
xref: Reactome:R-HSA-5220990 "TET1,2,3 oxidizes 5-hydroxymethylcytosine to 5-formylcytosine"
xref: Reactome:R-HSA-5221014 "TET1,2,3 oxidizes 5-methylcytosine to 5-hydroxymethylcytosine"
@@ -352165,7 +352082,7 @@ name: rolling circle DNA replication
namespace: biological_process
def: "A DNA-dependent DNA replication process in which a single-stranded DNA molecule is synthesized from a circular duplex template. Replication typically does not cease when one circumference has been replicated, but continues around the circumference several more times, producing a long single strand comprising multimers of the replicon." [GOC:cb, GOC:mah, ISBN:0198506732]
synonym: "rolling circle replication" EXACT [GOC:cb]
-is_a: GO:0006261 ! DNA-dependent DNA replication
+is_a: GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:0070582
@@ -352173,7 +352090,7 @@ name: theta DNA replication
namespace: biological_process
def: "A DNA-dependent DNA replication process in which a double-stranded DNA molecule is synthesized from a circular duplex template." [GOC:cb, GOC:mah, ISBN:0198506732]
synonym: "theta replication" EXACT [GOC:cb]
-is_a: GO:0006261 ! DNA-dependent DNA replication
+is_a: GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:0070583
@@ -352230,16 +352147,17 @@ comment: Note that this term is not intended for use in annotating lateral movem
synonym: "calcium ion membrane transport" EXACT []
synonym: "transmembrane calcium transport" EXACT [GOC:mah]
is_a: GO:0006816 ! calcium ion transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
id: GO:0070589
-name: cellular component macromolecule biosynthetic process
+name: obsolete cellular component macromolecule biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a macromolecule that is destined to form part of a specific cellular component." [GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of a macromolecule that is destined to form part of a specific cellular component." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "cellular component macromolecule biosynthesis" EXACT [GOC:mah]
-is_a: GO:0034645 ! cellular macromolecule biosynthetic process
-relationship: part_of GO:0044085 ! cellular component biogenesis
+is_obsolete: true
[Term]
id: GO:0070590
@@ -352267,9 +352185,8 @@ def: "The chemical reactions and pathways resulting in the formation of a polysa
synonym: "cell wall polysaccharide anabolism" EXACT [GOC:mah]
synonym: "cell wall polysaccharide biosynthesis" EXACT [GOC:mah]
synonym: "cell wall polysaccharide synthesis" EXACT [GOC:mah]
+is_a: GO:0000271 ! polysaccharide biosynthetic process
is_a: GO:0010383 ! cell wall polysaccharide metabolic process
-is_a: GO:0033692 ! cellular polysaccharide biosynthetic process
-is_a: GO:0044038 ! cell wall macromolecule biosynthetic process
[Term]
id: GO:0070593
@@ -352508,21 +352425,29 @@ relationship: regulates GO:0070600 ! fungal-type cell wall (1->3)-alpha-glucan b
[Term]
id: GO:0070611
-name: histone methyltransferase activity (H3-R2 specific)
+name: histone H3R2 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 2) = S-adenosyl-L-homocysteine + (histone H3)-N-methyl-arginine (position 2). This reaction is the addition of a methyl group to arginine at position 2 of histone H3." [GOC:mah, PMID:17898714]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 2) = S-adenosyl-L-homocysteine + (histone H3)-N-methyl-arginine (position 2). This reaction is the addition of a methyl group to the arginine residue at position 2 of histone H3." [GOC:mah, PMID:17898714]
+synonym: "histone H3R2 arginine methyltransferase activity" EXACT []
synonym: "histone methylase activity (H3-R2 specific)" EXACT [GOC:mah]
+synonym: "histone methyltransferase activity (H3-R2 specific)" EXACT []
synonym: "histone-arginine N-methyltransferase activity (H3-R2 specific)" EXACT [GOC:mah]
-is_a: GO:0008469 ! histone-arginine N-methyltransferase activity
+synonym: "histone-H3R2 methyltransferase activity" EXACT []
+is_a: GO:0016274 ! protein-arginine N-methyltransferase activity
+is_a: GO:0140938 ! histone H3 methyltransferase activity
[Term]
id: GO:0070612
-name: histone methyltransferase activity (H2A-R3 specific)
+name: histone H2AR3 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone H2A)-arginine (position 3) = S-adenosyl-L-homocysteine + (histone H2A)-N-methyl-arginine (position 3). This reaction is the addition of a methyl group to arginine at position 3 of histone H2A." [GOC:mah, PMID:17898714]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone H2A)-arginine (position 3) = S-adenosyl-L-homocysteine + (histone H2A)-N-methyl-arginine (position 3). This reaction is the addition of a methyl group to the arginine residue at position 3 of histone H2A." [GOC:mah, PMID:17898714, PMID:23451136]
+synonym: "histone H2AR3 arginine methyltransferase activity" EXACT [GOC:mah]
synonym: "histone methylase activity (H2A-R3 specific)" EXACT [GOC:mah]
+synonym: "histone methyltransferase activity (H2A-R3 specific)" EXACT []
synonym: "histone-arginine N-methyltransferase activity (H2A-R3 specific)" EXACT [GOC:mah]
-is_a: GO:0008469 ! histone-arginine N-methyltransferase activity
+synonym: "histone-H2AR3 methyltransferase activity" EXACT []
+is_a: GO:0016274 ! protein-arginine N-methyltransferase activity
+is_a: GO:0140940 ! histone H2A methyltransferase activity
[Term]
id: GO:0070613
@@ -352681,6 +352606,8 @@ synonym: "succino AMP-lyase activity" BROAD [EC:4.3.2.2, GOC:mah]
xref: EC:4.3.2.2
xref: KEGG_REACTION:R04559
xref: MetaCyc:AICARSYN-RXN
+xref: Reactome:R-HSA-73800 "SAICAR => AICAR + Fumarate"
+xref: Reactome:R-HSA-73828 "adenylosuccinate => adenosine 5'-monophosphate + fumarate"
xref: RHEA:23920
is_a: GO:0016842 ! amidine-lyase activity
@@ -352750,7 +352677,6 @@ id: GO:0070634
name: transepithelial ammonium transport
namespace: biological_process
def: "The directed movement of ammonium ions from one side of an epithelium to the other." [GOC:mah, GOC:yaf]
-is_a: GO:0006812 ! cation transport
is_a: GO:0070633 ! transepithelial transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -352878,7 +352804,7 @@ def: "A protein modification process in which one or more groups of a small prot
subset: goslim_drosophila
subset: goslim_pombe
subset: goslim_yeast
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0070648
@@ -353117,6 +353043,7 @@ synonym: "hypoxanthine/NAD(+) oxidoreductase activity" RELATED [EC:1.17.1.4]
synonym: "hypoxanthine/NAD+ oxidoreductase activity" RELATED [EC:1.17.1.4]
synonym: "hypoxanthine:NAD+ oxidoreductase activity" RELATED [EC:1.17.1.4]
synonym: "NAD-hypoxanthine dehydrogenase activity" RELATED [EC:1.17.1.4]
+xref: Reactome:R-HSA-9727347 "XDH dehydrogenates hypoxanthine to form xanthine"
is_a: GO:0016726 ! oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
[Term]
@@ -353125,12 +353052,12 @@ name: hypoxanthine oxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: hypoxanthine + H2O + O2 = xanthine + H2O2." [GOC:mah, GOC:pde]
synonym: "hypoxanthine-xanthine oxidase activity" BROAD [EC:1.17.3.2]
-synonym: "hypoxanthine:O(2) oxidoreductase activity" RELATED [EC:1.17.3.2]
synonym: "hypoxanthine:O2 oxidoreductase activity" RELATED [EC:1.17.3.2]
synonym: "hypoxanthine:oxygen oxidoreductase activity" RELATED [EC:1.17.3.2]
synonym: "schardinger enzyme" RELATED [EC:1.17.3.2]
synonym: "Schardinger enzyme activity" RELATED [EC:1.17.3.2]
synonym: "xanthine oxidoreductase activity" BROAD [EC:1.17.3.2]
+xref: Reactome:R-HSA-74247 "XDH oxidizes hypoxanthine to form xanthine"
is_a: GO:0016727 ! oxidoreductase activity, acting on CH or CH2 groups, oxygen as acceptor
[Term]
@@ -353261,6 +353188,7 @@ synonym: "threonine catabolic process to acetyl-CoA" BROAD [GOC:bf]
xref: MetaCyc:PWY-5436
is_a: GO:0006084 ! acetyl-CoA metabolic process
is_a: GO:0006567 ! threonine catabolic process
+is_a: GO:0043605 ! amide catabolic process
[Term]
id: GO:0070691
@@ -353474,7 +353402,7 @@ namespace: biological_process
def: "A mismatch repair process that corrects errors introduced that ensures the accuracy of DNA replication." [GOC:BHF, GOC:mah]
synonym: "mismatch repair involved in maintenance of fidelity during DNA-dependent DNA replication" RELATED [GOC:dph, GOC:tb]
is_a: GO:0006298 ! mismatch repair
-relationship: part_of GO:0045005 ! DNA-dependent DNA replication maintenance of fidelity
+relationship: part_of GO:0045005 ! DNA-templated DNA replication maintenance of fidelity
[Term]
id: GO:0070717
@@ -353538,7 +353466,6 @@ namespace: cellular_component
def: "A protein complex that acts as a receptor for bone morphogenetic proteins (BMPs); a homo- or heterodimer of type I and/or type II BMP receptor subunits." [GOC:mah, GOC:mh, PMID:19377468]
synonym: "bone morphogenetic protein receptor complex" EXACT [GOC:mah]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0070725
@@ -353614,10 +353541,10 @@ is_a: GO:0031967 ! organelle envelope
id: GO:0070733
name: protein adenylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + protein = diphosphate + adenylyl-protein; mediates the addition of an adenylyl (adenosine 5'-monophosphate; AMP group) to specific residues of target proteins." [GOC:mah, PMID:19039103, PMID:19362538]
+def: "Catalysis of the reaction: ATP + protein = diphosphate + adenylyl-protein; mediates the addition of an adenylyl (adenosine 5'-monophosphate; AMP group) to L-serine, L-threonine, and L-tyrosine residues in target proteins." [GOC:mah, PMID:19039103, PMID:19362538]
synonym: "adenosine monophosphate-protein transferase activity" EXACT [GOC:mah]
synonym: "AMPylator" RELATED [GOC:mah]
-xref: EC:2.7.7.n1
+xref: EC:2.7.7.108
is_a: GO:0070566 ! adenylyltransferase activity
[Term]
@@ -353681,6 +353608,7 @@ namespace: molecular_function
def: "Catalysis of the posttranslational transfer of one or more glutamate residues to the gamma-carboxyl group(s) of one or more specific glutamate residues on a tubulin molecule." [GOC:mah, PMID:19524510]
synonym: "tubulin glutamylase activity" EXACT [GOC:mah]
synonym: "tubulin-glutamate ligase activity" EXACT [GOC:mah]
+xref: EC:6.3.2.61
xref: Reactome:R-HSA-8865774 "TTLLs polyglutamylate tubulin"
xref: Reactome:R-HSA-8955869 "Polyglutamylase complex (TTLL1) polyglutamylates alpha subunits of tubulin"
is_a: GO:0070739 ! protein-glutamic acid ligase activity
@@ -353827,7 +353755,7 @@ relationship: positively_regulates GO:0070753 ! interleukin-35 production
id: GO:0070757
name: interleukin-35-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-35 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:add, GOC:mah, GOC:signaling]
+def: "The series of molecular signals initiated by interleukin-35 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:add, GOC:mah, GOC:signaling]
synonym: "IL-35-mediated signaling pathway" EXACT [GOC:add]
synonym: "interleukin-35-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -353836,7 +353764,7 @@ is_a: GO:0019221 ! cytokine-mediated signaling pathway
id: GO:0070758
name: regulation of interleukin-35-mediated signaling pathway
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of the series of molecular events generated as a consequence of interleukin-35-mediated binding to a cell surface receptor." [GOC:mah]
+def: "Any process that modulates the rate, frequency or extent of an interleukin-35-mediated signaling pathway." [GOC:mah]
synonym: "regulation of IL-35-mediated signaling pathway" EXACT [GOC:mah]
synonym: "regulation of interleukin-35-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0001959 ! regulation of cytokine-mediated signaling pathway
@@ -353846,7 +353774,7 @@ relationship: regulates GO:0070757 ! interleukin-35-mediated signaling pathway
id: GO:0070759
name: negative regulation of interleukin-35-mediated signaling pathway
namespace: biological_process
-def: "Any process that decreases the rate, frequency or extent of the series of molecular events generated as a consequence of interleukin-35 binding to a cell surface receptor." [GOC:mah]
+def: "Any process that decreases the rate, frequency or extent of an interleukin-35-mediated signaling pathway." [GOC:mah]
synonym: "negative regulation of IL-35-mediated signaling pathway" EXACT [GOC:add]
synonym: "negative regulation of interleukin-35-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0001960 ! negative regulation of cytokine-mediated signaling pathway
@@ -353857,7 +353785,7 @@ relationship: negatively_regulates GO:0070757 ! interleukin-35-mediated signalin
id: GO:0070760
name: positive regulation of interleukin-35-mediated signaling pathway
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of the series of molecular events generated as a consequence of interleukin-35 binding to a cell surface receptor." [GOC:mah]
+def: "Any process that increases the rate, frequency or extent of an interleukin-35-mediated signaling pathway." [GOC:mah]
synonym: "positive regulation of IL-35-mediated signaling pathway" EXACT [GOC:add]
synonym: "positive regulation of interleukin-35-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0001961 ! positive regulation of cytokine-mediated signaling pathway
@@ -353911,6 +353839,7 @@ synonym: "presenilin complex" EXACT []
synonym: "PS1 complex" NARROW []
synonym: "PS2 complex" NARROW []
is_a: GO:0098797 ! plasma membrane protein complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0070766
@@ -353974,9 +353903,12 @@ relationship: part_of GO:0005774 ! vacuolar membrane
id: GO:0070773
name: protein-N-terminal glutamine amidohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: protein-N-terminal-L-glutamine + H2O = protein-N-terminal-L-glutamate + NH3. This reaction is the deamidation of an N-terminal glutamine residue of a protein." [PMID:19560421]
+def: "Catalysis of the reaction: N-terminal L-glutaminyl-[protein] + H2O = N-terminal L-glutamyl-[protein] + NH3. This reaction is the deamidation of an N-terminal glutamine residue of a protein." [PMID:19560421, RHEA:50680]
synonym: "NtQ-amidase activity" EXACT [PMID:19560421]
+xref: EC:3.5.1.122
+xref: RHEA:50680
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
+is_a: GO:0140096 ! catalytic activity, acting on a protein
[Term]
id: GO:0070774
@@ -354019,9 +353951,7 @@ namespace: biological_process
alt_id: GO:0089712
def: "The directed movement of L-aspartate across a membrane." [PMID:21307582]
synonym: "L-aspartate transport" BROAD []
-is_a: GO:0015740 ! C4-dicarboxylate transport
-is_a: GO:0015807 ! L-amino acid transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0015810 ! aspartate transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -354033,9 +353963,9 @@ def: "The directed import of D-aspartate from the extracellular region across th
synonym: "D-aspartate import" BROAD []
synonym: "D-aspartate import into cell" EXACT []
synonym: "D-aspartate uptake" EXACT [GOC:mah]
+is_a: GO:0015810 ! aspartate transmembrane transport
is_a: GO:0070777 ! D-aspartate transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0070780
@@ -354336,7 +354266,7 @@ def: "The process in which glycerol-2-phosphate is transported across a membrane
synonym: "glycerol-2-phosphate transport" RELATED []
is_a: GO:0015711 ! organic anion transport
is_a: GO:0015748 ! organophosphate ester transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
is_a: GO:1901264 ! carbohydrate derivative transport
[Term]
@@ -354381,16 +354311,17 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
[Term]
id: GO:0070816
-name: phosphorylation of RNA polymerase II C-terminal domain
+name: obsolete phosphorylation of RNA polymerase II C-terminal domain
namespace: biological_process
alt_id: GO:0016245
-def: "The process of introducing a phosphate group on to an amino acid residue in the C-terminal domain of RNA polymerase II. Typically, this occurs during the transcription cycle and results in production of an RNA polymerase II enzyme where the carboxy-terminal domain (CTD) of the largest subunit is extensively phosphorylated, often referred to as hyperphosphorylated or the II(0) form. Specific types of phosphorylation within the CTD are usually associated with specific regions of genes, though there are exceptions. The phosphorylation state regulates the association of specific complexes such as the capping enzyme or 3'-RNA processing machinery to the elongating RNA polymerase complex." [GOC:krc, GOC:mah, PMID:17079683]
+def: "OBSOLETE. The process of introducing a phosphate group on to an amino acid residue in the C-terminal domain of RNA polymerase II. Typically, this occurs during the transcription cycle and results in production of an RNA polymerase II enzyme where the carboxy-terminal domain (CTD) of the largest subunit is extensively phosphorylated, often referred to as hyperphosphorylated or the II(0) form. Specific types of phosphorylation within the CTD are usually associated with specific regions of genes, though there are exceptions. The phosphorylation state regulates the association of specific complexes such as the capping enzyme or 3'-RNA processing machinery to the elongating RNA polymerase complex." [GOC:krc, GOC:mah, PMID:17079683]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:mah]
synonym: "generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:krc]
synonym: "generation of II(0) form of RNA polymerase II" EXACT [GOC:krc]
synonym: "hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:krc]
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-is_a: GO:0006468 ! protein phosphorylation
+is_obsolete: true
+consider: GO:0008353
[Term]
id: GO:0070817
@@ -354460,13 +354391,13 @@ namespace: cellular_component
def: "A histone deacetylase complex that contains a core of four proteins -- Clr1, Clr2, Clr3, and Mit1 in fission yeast -- and localizes to all heterochromatic regions in the genome as well as some euchromatic sites. The complex is involved in regulating nucleosome positioning to assemble higher-order chromatin structures." [GOC:mah, PMID:17289569]
synonym: "Snf2/HDAC containing repressor complex" EXACT [PMID:17289569, PMID:27105116]
synonym: "Snf2/Hdac repressive complex" EXACT [PMID:27105116]
-is_a: GO:0000118 ! histone deacetylase complex
+is_a: GO:0016581 ! NuRD complex
[Term]
id: GO:0070825
-name: micropyle
+name: chrorion micropyle
namespace: cellular_component
-def: "An external encapsulating structure part of the chorion. A single cone-shaped specialization that forms an opening in the egg chorion that allows sperm entry into the egg prior to fertilization." [GOC:cvs, GOC:mah, PMID:18649270]
+def: "A single cone-shaped specialization that forms an opening in the egg chorion that allows sperm entry into the egg prior to fertilization." [GOC:cvs, GOC:mah, PMID:18649270]
is_a: GO:0110165 ! cellular anatomical entity
relationship: part_of GO:0042600 ! egg chorion
@@ -354492,7 +354423,7 @@ name: heterochromatin organization
namespace: biological_process
def: "Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin, a compact and highly condensed form of chromatin." [GOC:mah]
synonym: "heterochromatin organisation" EXACT [GOC:mah]
-is_a: GO:0006325 ! chromatin organization
+is_a: GO:0006338 ! chromatin remodeling
[Term]
id: GO:0070829
@@ -354555,7 +354486,6 @@ id: GO:0070835
name: chromium ion transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of chromium (Cr) ions from one side of a membrane to the other." [GOC:mah, GOC:yaf]
-is_a: GO:0015075 ! ion transmembrane transporter activity
is_a: GO:0015318 ! inorganic molecular entity transmembrane transporter activity
[Term]
@@ -354576,14 +354506,6 @@ synonym: "dehydroascorbate transport" EXACT [GOC:sl]
is_a: GO:0015711 ! organic anion transport
is_a: GO:0051180 ! vitamin transport
-[Term]
-id: GO:0070839
-name: metal ion export
-namespace: biological_process
-def: "The directed movement of metal cations, out of a cell or organelle." [GOC:mah]
-synonym: "divalent metal ion export" NARROW []
-is_a: GO:0030001 ! metal ion transport
-
[Term]
id: GO:0070840
name: dynein complex binding
@@ -354654,7 +354576,7 @@ name: response to growth factor
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus." [GOC:BHF, GOC:mah]
synonym: "response to growth factor stimulus" EXACT [GOC:dos]
-is_a: GO:0010033 ! response to organic substance
+is_a: GO:0009719 ! response to endogenous stimulus
[Term]
id: GO:0070849
@@ -354663,7 +354585,6 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epidermal growth factor stimulus." [GOC:BHF, GOC:mah]
synonym: "response to EGF stimulus" EXACT [GOC:mah]
synonym: "response to epidermal growth factor stimulus" EXACT [GOC:dos]
-is_a: GO:0009719 ! response to endogenous stimulus
is_a: GO:0070848 ! response to growth factor
[Term]
@@ -354885,7 +354806,6 @@ name: regulation of glycogen metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glycogen." [GOC:mah]
synonym: "regulation of glycogen metabolism" EXACT [GOC:mah]
-is_a: GO:0010906 ! regulation of glucose metabolic process
is_a: GO:0032881 ! regulation of polysaccharide metabolic process
is_a: GO:0043467 ! regulation of generation of precursor metabolites and energy
relationship: regulates GO:0005977 ! glycogen metabolic process
@@ -354897,7 +354817,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glycogen." [GOC:mah]
synonym: "negative regulation of glycogen metabolism" EXACT [GOC:mah]
is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
+is_a: GO:0031324 ! negative regulation of cellular metabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:0070873 ! regulation of glycogen metabolic process
relationship: negatively_regulates GO:0005977 ! glycogen metabolic process
@@ -354909,6 +354830,7 @@ def: "Any process that activates or increases the frequency, rate or extent of t
synonym: "positive regulation of glycogen metabolism" EXACT [GOC:mah]
is_a: GO:0010604 ! positive regulation of macromolecule metabolic process
is_a: GO:0010907 ! positive regulation of glucose metabolic process
+is_a: GO:0031325 ! positive regulation of cellular metabolic process
is_a: GO:0070873 ! regulation of glycogen metabolic process
relationship: positively_regulates GO:0005977 ! glycogen metabolic process
@@ -354964,7 +354886,6 @@ id: GO:0070881
name: regulation of proline transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of proline transport." [GOC:mah]
-is_a: GO:0044070 ! regulation of anion transport
is_a: GO:0051955 ! regulation of amino acid transport
relationship: regulates GO:0015824 ! proline transport
@@ -355073,49 +354994,52 @@ is_a: GO:0038187 ! pattern recognition receptor activity
[Term]
id: GO:0070893
-name: transposon integration
+name: obsolete transposon integration
namespace: biological_process
-def: "Any process in which a transposable element is incorporated into another DNA molecule such as a chromosome." [GOC:jp, PMID:10882723]
-is_a: GO:0015074 ! DNA integration
-is_a: GO:0032196 ! transposition
+def: "OBSOLETE. Any process in which a transposable element is incorporated into another DNA molecule such as a chromosome." [GOC:jp, PMID:10882723]
+comment: This term was obsoleted because it represents a readout.
+is_obsolete: true
+consider: GO:0006313
+consider: GO:0032197
[Term]
id: GO:0070894
-name: regulation of transposon integration
+name: obsolete regulation of transposon integration
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of regulation of transposon integration, a process in which a transposable element is incorporated into another DNA molecule." [GOC:mah]
-is_a: GO:0010528 ! regulation of transposition
-is_a: GO:0051052 ! regulation of DNA metabolic process
-relationship: regulates GO:0070893 ! transposon integration
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of regulation of transposon integration, a process in which a transposable element is incorporated into another DNA molecule." [GOC:mah]
+comment: This term was obsoleted because it represents a readout.
+is_obsolete: true
+consider: GO:0006313
+consider: GO:0032197
[Term]
id: GO:0070895
-name: negative regulation of transposon integration
+name: obsolete negative regulation of transposon integration
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transposon integration, a process in which a transposable element is incorporated into another DNA molecule." [GOC:mah]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transposon integration, a process in which a transposable element is incorporated into another DNA molecule." [GOC:mah]
+comment: This term was obsoleted because it represents a readout.
synonym: "down regulation of transposon integration" EXACT [GOC:mah]
synonym: "down-regulation of transposon integration" EXACT [GOC:mah]
synonym: "downregulation of transposon integration" EXACT [GOC:mah]
synonym: "inhibition of transposon integration" NARROW [GOC:mah]
-is_a: GO:0010529 ! negative regulation of transposition
-is_a: GO:0051053 ! negative regulation of DNA metabolic process
-is_a: GO:0070894 ! regulation of transposon integration
-relationship: negatively_regulates GO:0070893 ! transposon integration
+is_obsolete: true
+consider: GO:0006313
+consider: GO:0032197
[Term]
id: GO:0070896
-name: positive regulation of transposon integration
+name: obsolete positive regulation of transposon integration
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of transposon integration, a process in which a transposable element is incorporated into another DNA molecule." [GOC:mah]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transposon integration, a process in which a transposable element is incorporated into another DNA molecule." [GOC:mah]
+comment: This term was obsoleted because it represents a readout.
synonym: "activation of transposon integration" NARROW [GOC:mah]
synonym: "stimulation of transposon integration" NARROW [GOC:mah]
synonym: "up regulation of transposon integration" EXACT [GOC:mah]
synonym: "up-regulation of transposon integration" EXACT [GOC:mah]
synonym: "upregulation of transposon integration" EXACT [GOC:mah]
-is_a: GO:0010530 ! positive regulation of transposition
-is_a: GO:0051054 ! positive regulation of DNA metabolic process
-is_a: GO:0070894 ! regulation of transposon integration
-relationship: positively_regulates GO:0070893 ! transposon integration
+is_obsolete: true
+consider: GO:0006313
+consider: GO:0032197
[Term]
id: GO:0070897
@@ -355132,7 +355056,7 @@ synonym: "transcription PIC biosynthesis" BROAD [GOC:mah]
synonym: "transcription PIC formation" BROAD [GOC:mah]
synonym: "transcriptional preinitiation complex formation" BROAD [GOC:mah]
is_a: GO:0065004 ! protein-DNA complex assembly
-relationship: part_of GO:0006352 ! DNA-templated transcription, initiation
+relationship: part_of GO:0006352 ! DNA-templated transcription initiation
[Term]
id: GO:0070898
@@ -355152,7 +355076,7 @@ synonym: "RNA polymerase III type 1 promoter transcriptional preinitiation compl
synonym: "RNA polymerase III type 2 promoter transcriptional preinitiation complex assembly" NARROW []
synonym: "RNA polymerase III type 3 promoter transcriptional preinitiation complex assembly" NARROW []
is_a: GO:0070897 ! transcription preinitiation complex assembly
-relationship: part_of GO:0006384 ! transcription initiation from RNA polymerase III promoter
+relationship: part_of GO:0006384 ! transcription initiation at RNA polymerase III promoter
[Term]
id: GO:0070899
@@ -355198,15 +355122,15 @@ is_a: GO:0070900 ! mitochondrial tRNA modification
[Term]
id: GO:0070904
-name: transepithelial L-ascorbic acid transport
+name: obsolete transepithelial L-ascorbic acid transport
namespace: biological_process
-def: "The directed movement of L-ascorbic acid from one side of an epithelium to the other." [GOC:mah, GOC:yaf]
+def: "OBSOLETE. The directed movement of L-ascorbic acid from one side of an epithelium to the other." [GOC:mah, GOC:yaf]
+comment: This term was obsoleted because it represents a combination of a process and an anatomical entity.
synonym: "transepithelial L-ascorbate transport" EXACT [GOC:mah]
synonym: "transepithelial vitamin C transport" EXACT [GOC:mah]
-is_a: GO:0008643 ! carbohydrate transport
-is_a: GO:0015849 ! organic acid transport
-is_a: GO:0046942 ! carboxylic acid transport
-is_a: GO:0070633 ! transepithelial transport
+is_obsolete: true
+consider: GO:0015882
+consider: GO:0070633
[Term]
id: GO:0070905
@@ -355215,7 +355139,6 @@ namespace: molecular_function
def: "Binding to 2-amino-3-hydroxypropanoic acid." [GOC:rph]
synonym: "Ser binding" EXACT [GOC:mah]
is_a: GO:0016597 ! amino acid binding
-is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0043169 ! cation binding
[Term]
@@ -355227,8 +355150,7 @@ synonym: "aspartate-alanine antiporter activity" EXACT [GOC:mah]
synonym: "aspartate/alanine antiporter activity" EXACT [GOC:mah]
xref: RHEA:33139
is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
-is_a: GO:0015298 ! solute:cation antiporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
+is_a: GO:0015297 ! antiporter activity
is_a: GO:0015556 ! C4-dicarboxylate transmembrane transporter activity
is_a: GO:0022858 ! alanine transmembrane transporter activity
@@ -355240,7 +355162,7 @@ def: "Catalysis of the reaction: histidine(out) + histamine(in) = histidine(in)
synonym: "histidine-histamine antiporter activity" EXACT [GOC:mah]
synonym: "histidine/histamine antiporter activity" EXACT [GOC:mah]
is_a: GO:0015173 ! aromatic amino acid transmembrane transporter activity
-is_a: GO:0015298 ! solute:cation antiporter activity
+is_a: GO:0015297 ! antiporter activity
is_a: GO:1901474 ! azole transmembrane transporter activity
[Term]
@@ -355252,7 +355174,7 @@ synonym: "tyrosine-tyramine antiporter activity" EXACT [GOC:mah]
synonym: "tyrosine/tyramine antiporter activity" EXACT [GOC:mah]
is_a: GO:0008504 ! monoamine transmembrane transporter activity
is_a: GO:0015173 ! aromatic amino acid transmembrane transporter activity
-is_a: GO:0015298 ! solute:cation antiporter activity
+is_a: GO:0015297 ! antiporter activity
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
[Term]
@@ -355264,8 +355186,10 @@ synonym: "glutamate-gamma-aminobutyric acid antiporter activity" EXACT [GOC:mah]
synonym: "glutamate/gamma-aminobutyric acid antiporter activity" EXACT [GOC:mah]
synonym: "glutamate: GABA antiporter activity" EXACT [GOC:dh]
is_a: GO:0015185 ! gamma-aminobutyric acid transmembrane transporter activity
-is_a: GO:0015301 ! anion:anion antiporter activity
+is_a: GO:0015297 ! antiporter activity
is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
+is_a: GO:0042887 ! amide transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0070910
@@ -355342,65 +355266,68 @@ is_a: GO:0030234 ! enzyme regulator activity
[Term]
id: GO:0070918
-name: production of small RNA involved in gene silencing by RNA
+name: regulatory ncRNA processing
namespace: biological_process
-def: "The process in which a double-stranded RNA precursor is processed into short (20-30 nt) fragments. RNA cleavage is catalyzed by a Dicer endonuclease." [GOC:mah, PMID:19239886]
-synonym: "gene silencing by RNA, production of guide RNA" EXACT [GOC:mah]
-synonym: "gene silencing by RNA, production of small RNA" EXACT [GOC:mah]
-is_a: GO:0031050 ! dsRNA processing
-relationship: part_of GO:0031047 ! gene silencing by RNA
-
-[Term]
-id: GO:0070919
-name: production of siRNA involved in gene silencing by small RNA
-namespace: biological_process
-def: "Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of gene silencing by small RNA." [GOC:mah, PMID:19239886]
-synonym: "chromatin silencing by small RNA, production of guide RNAs" EXACT []
-synonym: "chromatin silencing by small RNA, production of siRNA" EXACT [GOC:mah]
-synonym: "production of guide RNAs involved in chromatin silencing by small RNA" EXACT [GOC:mah]
-synonym: "production of siRNA involved in chromatin silencing by small RNA" EXACT []
-is_a: GO:0070918 ! production of small RNA involved in gene silencing by RNA
-relationship: part_of GO:0031048 ! heterochromatin assembly by small RNA
+alt_id: GO:0031051
+def: "A process leading to the generation of a functional regulatory non-coding RNA." [GOC:mah, PMID:15196465, PMID:19239886]
+subset: gocheck_do_not_annotate
+synonym: "gene silencing by RNA, production of guide RNA" NARROW [GOC:mah]
+synonym: "gene silencing by RNA, production of small RNA" NARROW [GOC:mah]
+synonym: "primary sncRNA processing" NARROW []
+synonym: "production of small RNA involved in gene silencing by RNA" NARROW []
+synonym: "small regulatory ncRNA maturation" NARROW []
+synonym: "small regulatory ncRNA processing" NARROW []
+synonym: "sncRNA processing" NARROW []
+synonym: "sncRNA production" NARROW []
+is_a: GO:0034470 ! ncRNA processing
+relationship: part_of GO:0031047 ! RNA-mediated gene silencing
[Term]
id: GO:0070920
-name: regulation of production of small RNA involved in gene silencing by RNA
+name: regulation of regulatory ncRNA processing
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the production of small RNA involved in gene silencing by RNA." [GOC:mah]
+def: "Any process that modulates the frequency, rate or extent of regulatory non-coding RNA processing." [GOC:mah]
synonym: "regulation of gene silencing by RNA, production of guide RNA" EXACT [GOC:mah]
synonym: "regulation of gene silencing by RNA, production of small RNA" EXACT [GOC:mah]
+synonym: "regulation of production of small RNA involved in gene silencing by RNA" NARROW []
is_a: GO:0051252 ! regulation of RNA metabolic process
is_a: GO:0060966 ! regulation of gene silencing by RNA
-relationship: regulates GO:0070918 ! production of small RNA involved in gene silencing by RNA
+relationship: regulates GO:0070918 ! regulatory ncRNA processing
[Term]
id: GO:0070921
-name: regulation of production of siRNA involved in gene silencing by small RNA
+name: regulation of siRNA processing
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the production of siRNA, the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of gene silencing by small RNA." [GOC:mah]
+alt_id: GO:0090065
+def: "Any process that modulates the frequency, rate or extent of siRNA processing." [GOC:mah]
synonym: "regulation of chromatin silencing by small RNA, production of siRNA" EXACT [GOC:mah]
synonym: "regulation of production of siRNA involved in chromatin silencing by small RNA" EXACT []
-is_a: GO:0070920 ! regulation of production of small RNA involved in gene silencing by RNA
+synonym: "regulation of production of siRNA involved in gene silencing by small RNA" RELATED []
+synonym: "regulation of production of siRNA involved in post-transcriptional gene silencing by RNA" RELATED []
+synonym: "regulation of production of siRNA involved in PTGS" RELATED []
+synonym: "regulation of production of siRNA involved in RNA interference" EXACT []
+synonym: "regulation of RNA interference, production of siRNA" EXACT [GOC:mah]
+synonym: "regulation of siRNA production" RELATED []
+is_a: GO:0070920 ! regulation of regulatory ncRNA processing
+relationship: regulates GO:0030422 ! siRNA processing
[Term]
id: GO:0070922
-name: small RNA loading onto RISC
+name: RISC complex assembly
namespace: biological_process
-def: "The process in which a single-stranded small RNA associates with the RNA-initiated silencing complex (RISC); occurs as part of a process of gene silencing by small RNA." [GOC:mah, PMID:19239886]
-synonym: "gene silencing by RNA, small RNA loading onto RISC" EXACT [GOC:mah]
+alt_id: GO:0035087
+alt_id: GO:0035280
+alt_id: GO:0070923
+def: "The process in which a single-stranded small RNA is incorporated within the RNA-initiated silencing complex (RISC). The assembly includes the maturation of the small RNA, the stabilization of the complex by accessory proteins of the RISC complex, duplex separation and the release of the second strand, forming a base-pairing completent complex that mediates gene silencing by small RNA." [PMID:14512631, PMID:14744438, PMID:19239886, PMID:22233755, PMID:27184117]
+synonym: "gene silencing by RNA, small RNA loading onto RISC" RELATED [GOC:mah]
+synonym: "miRISC assembly" BROAD []
+synonym: "miRNA loading onto RISC" NARROW []
synonym: "RISC assembly" RELATED [GOC:mah]
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
-relationship: part_of GO:0031047 ! gene silencing by RNA
-
-[Term]
-id: GO:0070923
-name: siRNA loading onto RISC involved in gene silencing by small RNA
-namespace: biological_process
-def: "The process in which a single-stranded small RNA associates with the RNA-initiated silencing complex (RISC); occurs as part of a process of chromatin gene by small RNA." [GOC:mah, PMID:19239886]
-synonym: "chromatin silencing by small RNA, siRNA loading onto RISC" EXACT [GOC:mah]
-synonym: "siRNA loading onto RISC involved in chromatin silencing by small RNA" EXACT []
-is_a: GO:0070922 ! small RNA loading onto RISC
-relationship: part_of GO:0031048 ! heterochromatin assembly by small RNA
+synonym: "siRNA loading onto RISC involved in gene silencing by small RNA" NARROW []
+synonym: "siRNA loading onto RISC involved in RNA interference" NARROW []
+synonym: "small RNA loading onto RISC" RELATED []
+is_a: GO:0022618 ! protein-RNA complex assembly
+relationship: part_of GO:0031047 ! RNA-mediated gene silencing
[Term]
id: GO:0070925
@@ -355416,9 +355343,9 @@ id: GO:0070926
name: regulation of ATP:ADP antiporter activity
namespace: biological_process
def: "Any process that modulates the activity of an ATP:ADP antiporter." [GOC:BHF, GOC:mah]
+is_a: GO:0022898 ! regulation of transmembrane transporter activity
is_a: GO:0032239 ! regulation of nucleobase-containing compound transport
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
-is_a: GO:1903959 ! regulation of anion transmembrane transport
+is_a: GO:1903959 ! regulation of monoatomic anion transmembrane transport
[Term]
id: GO:0070927
@@ -355430,7 +355357,7 @@ synonym: "down-regulation of ATP:ADP antiporter activity" EXACT [GOC:mah]
synonym: "downregulation of ATP:ADP antiporter activity" EXACT [GOC:mah]
synonym: "inhibition of ATP:ADP antiporter activity" NARROW [GOC:mah]
is_a: GO:0032240 ! negative regulation of nucleobase-containing compound transport
-is_a: GO:0032413 ! negative regulation of ion transmembrane transporter activity
+is_a: GO:0032410 ! negative regulation of transporter activity
is_a: GO:0070926 ! regulation of ATP:ADP antiporter activity
is_a: GO:1903960 ! negative regulation of anion transmembrane transport
@@ -355459,7 +355386,7 @@ comment: Note that this term is not a child of 'co-translational protein modific
synonym: "co-translational protein tagging" EXACT [GOC:jh2, GOC:jsg]
synonym: "cotranslational protein tagging" EXACT [GOC:mah]
synonym: "protein modification by trans-translation" EXACT [GOC:mah]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0070931
@@ -355516,8 +355443,7 @@ def: "A protein complex that binds to, and promotes stabilization of, mRNA molec
comment: See also the molecular function term 'alkyl hydroperoxide reductase activity ; GO:0008785'.
synonym: "coding-region determinant of instability-mediated mRNA stability complex" EXACT []
synonym: "coding-region instability determinant -mediated mRNA stability complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005737 ! cytoplasm
+is_a: GO:0140535 ! intracellular protein-containing complex
[Term]
id: GO:0070938
@@ -355542,14 +355468,15 @@ is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
[Term]
id: GO:0070940
-name: dephosphorylation of RNA polymerase II C-terminal domain
+name: obsolete dephosphorylation of RNA polymerase II C-terminal domain
namespace: biological_process
-def: "The process of removing a phosphate group from an amino acid residue in the C-terminal domain of RNA polymerase II. Some dephosphorylation occurs during transcription while some may occur after the enzyme is released from the template in order to prepare it for the beginning of the transcription cycle again. RNA polymerase II with little or no phosphorylation is referred to as the hypophosphorylated or II(A) form." [GOC:krc, GOC:mah, PMID:17079683]
+def: "OBSOLETE. The process of removing a phosphate group from an amino acid residue in the C-terminal domain of RNA polymerase II. Some dephosphorylation occurs during transcription while some may occur after the enzyme is released from the template in order to prepare it for the beginning of the transcription cycle again. RNA polymerase II with little or no phosphorylation is referred to as the hypophosphorylated or II(A) form." [GOC:krc, GOC:mah, PMID:17079683]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "CTD domain dephosphorylation of RNA polymerase II" EXACT [GOC:mah]
synonym: "generation of hypophosphorylated CTD of RNA polymerase II" EXACT [GOC:krc]
synonym: "generation of II(A) form of RNA polymerase II" EXACT [GOC:krc]
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-is_a: GO:0006470 ! protein dephosphorylation
+is_obsolete: true
+consider: GO:0008420
[Term]
id: GO:0070941
@@ -355869,7 +355796,6 @@ namespace: molecular_function
def: "Binding to pyrroloquinoline quinone, PQQ, the coenzyme or the prosthetic group of certain alcohol dehydrogenases and glucose dehydrogenases." [GOC:dh]
synonym: "PQQ binding" EXACT [GOC:dh]
is_a: GO:0031406 ! carboxylic acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0048038 ! quinone binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -355954,7 +355880,7 @@ is_a: GO:0000209 ! protein polyubiquitination
id: GO:0070980
name: biphenyl catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of biphenyl, a toxic aromatic hydrocarbon used as a heat transfer agent, as a fungistat in packaging citrus fruits and in plant disease control. Biphenyl can be chlorinated with 1-10 chlorine molecules to form polychlorinated biphenyls (PCBs)." [PMID:16310831, PMID:16339959, UniPathway:UPA00155]
+def: "The chemical reactions and pathways resulting in the breakdown of biphenyl, a toxic aromatic hydrocarbon used as a heat transfer agent, as a fungistat in packaging citrus fruits and in plant disease control. Biphenyl can be chlorinated with 1-10 chlorine molecules to form polychlorinated biphenyls (PCBs)." [PMID:16310831, PMID:16339959]
synonym: "biphenyl breakdown" EXACT [GOC:mah]
synonym: "biphenyl catabolism" EXACT [GOC:mah]
synonym: "biphenyl degradation" EXACT [GOC:mah]
@@ -355983,7 +355909,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving L-asparagine, (2S)-2-amino-3-carbamoylpropanoic acid." [GOC:mah]
synonym: "L-asparagine metabolism" EXACT [GOC:mah]
is_a: GO:0006528 ! asparagine metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
[Term]
id: GO:0070983
@@ -356057,9 +355983,10 @@ is_a: GO:0043021 ! ribonucleoprotein complex binding
id: GO:0070991
name: medium-chain-acyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor, where the acyl group is a medium-chain fatty acid residue. A medium chain fatty acid is any fatty acid with a chain length of between C6 and C12." [GOC:BHF, GOC:mah]
+def: "Catalysis of the reaction: a medium-chain 2,3-saturated fatty acyl-CoA + H+ + oxidized [electron-transfer flavoprotein] = a medium-chain trans-(2E)-enoyl-CoA + reduced [electron-transfer flavoprotein]. A medium chain fatty acid is any fatty acid with a chain length of between C6 and C12." [RHEA:14477]
synonym: "MCAD activity" EXACT [GOC:mah]
-xref: EC:1.3.99.-
+xref: EC:1.3.8.7
+xref: RHEA:14477
is_a: GO:0003995 ! acyl-CoA dehydrogenase activity
[Term]
@@ -356283,7 +356210,7 @@ is_a: GO:1902494 ! catalytic complex
id: GO:0071014
name: post-mRNA release spliceosomal complex
namespace: cellular_component
-def: "A spliceosomal complex that is formed following the release of the spliced product from the post-spliceosomal complex and contains the excised intron and three snRNPs, including U5." [GOC:ab, GOC:krc, GOC:mah, ISBN:0879695897, ISBN:0879697393, PMID:19239890]
+def: "A spliceosomal complex that is formed following the release of the spliced product from the post-spliceosomal complex and contains the excised intron and three snRNPs, either U2 or U12, U5, and either U6 or U6atac." [GOC:ab, GOC:krc, GOC:mah, ISBN:0879695897, PMID:19239890, PMID:20149226]
synonym: "mammalian spliceosomal complex I" NARROW [GOC:krc, GOC:mah, ISBN:0879695897, ISBN:0879697393]
is_a: GO:0005681 ! spliceosomal complex
@@ -356662,6 +356589,7 @@ namespace: cellular_component
def: "A protein complex that consists of an alphav-beta3 integrin complex bound to the transmembrane metallopeptidase ADAM15." [PMID:10944520, PMID:11882657]
synonym: "ITGAV-ITGB3-ADAM15 complex" NARROW [CORUM:2359]
is_a: GO:0098797 ! plasma membrane protein complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0071058
@@ -356752,6 +356680,7 @@ namespace: cellular_component
def: "A protein complex that consists of an alphav-beta3 integrin complex bound to the transmembrane metallopeptidase ADAM23." [PMID:10749942]
synonym: "ITGAV-ITGB3-ADAM23 complex" NARROW [CORUM:2364]
is_a: GO:0098797 ! plasma membrane protein complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0071068
@@ -356786,7 +356715,6 @@ synonym: "regulation of phospholipid anabolism" EXACT [GOC:mah]
synonym: "regulation of phospholipid biosynthesis" EXACT [GOC:mah]
synonym: "regulation of phospholipid formation" EXACT [GOC:mah]
synonym: "regulation of phospholipid synthesis" EXACT [GOC:mah]
-is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0046890 ! regulation of lipid biosynthetic process
is_a: GO:1903725 ! regulation of phospholipid metabolic process
relationship: regulates GO:0008654 ! phospholipid biosynthetic process
@@ -356804,7 +356732,6 @@ synonym: "negative regulation of phospholipid anabolism" EXACT [GOC:mah]
synonym: "negative regulation of phospholipid biosynthesis" EXACT [GOC:mah]
synonym: "negative regulation of phospholipid formation" EXACT [GOC:mah]
synonym: "negative regulation of phospholipid synthesis" EXACT [GOC:mah]
-is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
is_a: GO:0051055 ! negative regulation of lipid biosynthetic process
is_a: GO:0071071 ! regulation of phospholipid biosynthetic process
is_a: GO:1903726 ! negative regulation of phospholipid metabolic process
@@ -356824,7 +356751,6 @@ synonym: "stimulation of phospholipid biosynthetic process" NARROW [GOC:mah]
synonym: "up regulation of phospholipid biosynthetic process" EXACT [GOC:mah]
synonym: "up-regulation of phospholipid biosynthetic process" EXACT [GOC:mah]
synonym: "upregulation of phospholipid biosynthetic process" EXACT [GOC:mah]
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:0046889 ! positive regulation of lipid biosynthetic process
is_a: GO:0071071 ! regulation of phospholipid biosynthetic process
is_a: GO:1903727 ! positive regulation of phospholipid metabolic process
@@ -356869,6 +356795,7 @@ namespace: cellular_component
def: "A protein complex that consists of fibronectin bound to tissue transglutaminase, and is involved in cell adhesion." [PMID:10684262]
synonym: "FN-TGM2 complex" NARROW [CORUM:2375]
is_a: GO:0098797 ! plasma membrane protein complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0071079
@@ -356950,6 +356877,7 @@ namespace: cellular_component
def: "A protein complex that consists of an alpha5-beta1 integrin complex bound to tissue transglutaminase." [PMID:10684262]
synonym: "ITGA5-ITGB1-TGM2 complex" NARROW [CORUM:2433]
is_a: GO:0098797 ! plasma membrane protein complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0071089
@@ -356958,6 +356886,7 @@ namespace: cellular_component
def: "A protein complex that consists of an alphaV-beta3 integrin complex bound to tissue transglutaminase." [PMID:10684262]
synonym: "ITGAV-ITGB3-TGM2 complex" NARROW [CORUM:3095]
is_a: GO:0098797 ! plasma membrane protein complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0071090
@@ -356966,6 +356895,7 @@ namespace: cellular_component
def: "A protein complex that consists of an alphaIIb-beta3 integrin complex bound to fibronectin and tissue transglutaminase." [PMID:10684262]
synonym: "ITGA2b-ITGB3-FN1-TGM2 complex" NARROW [CORUM:2376]
is_a: GO:0098797 ! plasma membrane protein complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0071091
@@ -356974,6 +356904,7 @@ namespace: cellular_component
def: "A protein complex that consists of an alpha1-beta1 integrin complex bound to tissue transglutaminase." [PMID:10684262]
synonym: "ITGA1-ITGB1-TGM2 complex" NARROW [CORUM:2894]
is_a: GO:0098797 ! plasma membrane protein complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0071092
@@ -356982,6 +356913,7 @@ namespace: cellular_component
def: "A protein complex that consists of an alpha3-beta1 integrin complex bound to tissue transglutaminase." [PMID:10684262]
synonym: "ITGA3-ITGB1-TGM2 complex" NARROW [CORUM:2402]
is_a: GO:0098797 ! plasma membrane protein complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0071093
@@ -356990,6 +356922,7 @@ namespace: cellular_component
def: "A protein complex that consists of an alpha5-beta1 integrin complex bound to fibronectin and tissue transglutaminase." [PMID:10684262]
synonym: "ITGA5-ITGB1-FN1-TGM2 complex" NARROW [CORUM:2383]
is_a: GO:0098797 ! plasma membrane protein complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0071094
@@ -357127,17 +357060,17 @@ relationship: part_of GO:0021987 ! cerebral cortex development
[Term]
id: GO:0071110
-name: histone biotinylation
+name: obsolete histone biotinylation
namespace: biological_process
-def: "The modification of a histone by the addition of a biotinyl group." [GOC:rph, PMID:14613969, PMID:19019041]
-is_a: GO:0009305 ! protein biotinylation
-is_a: GO:0016570 ! histone modification
+def: "OBSOLETE. The modification of a histone by the addition of a biotinyl group." [GOC:rph, PMID:14613969, PMID:19019041]
+comment: This terms was obsoleted because it represents a molecular function as a biological process.
+is_obsolete: true
[Term]
id: GO:0071111
name: cyclic-guanylate-specific phosphodiesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cyclic di-3',5'-guanylate + H(2)O = 5'-phosphoguanylyl(3'->5')guanosine + H(+)." [EC:3.1.4.52, RHEA:24902]
+def: "Catalysis of the reaction: cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'->5')guanosine + H+." [EC:3.1.4.52, RHEA:24902]
synonym: "c-di-GMP phosphodiesterase activity" RELATED [EC:3.1.4.52]
synonym: "c-di-GMP-specific phosphodiesterase activity" RELATED [EC:3.1.4.52]
synonym: "cyclic bis(3->5')diguanylate phosphodiesterase activity" RELATED [EC:3.1.4.52]
@@ -357495,7 +357428,7 @@ name: DNA replication preinitiation complex assembly
namespace: biological_process
alt_id: GO:1902293
alt_id: GO:1902316
-def: "The aggregation, arrangement and bonding together of a set of components to form the DNA replication preinitiation complex, a protein-DNA complex that is assembled at DNA replication origins immediately prior to the initiation of DNA replication. The complex consists of proteins that initiate the DNA binding, melt the helix and enable helicase activity." [GOC:mah, PMID:28209641]
+def: "The aggregation, arrangement and bonding together of a set of components to form the DNA replication preinitiation complex, a protein-DNA complex that is assembled at DNA replication origins as part of initiation of DNA replication. The complex consists of proteins that initiate the DNA binding, melt the helix and enable helicase activity." [GOC:mah, PMID:28209641]
synonym: "DNA replication preinitiation complex formation" EXACT [GOC:mah]
synonym: "pre-IC complex assembly" EXACT []
is_a: GO:0022402 ! cell cycle process
@@ -357577,7 +357510,7 @@ namespace: biological_process
def: "A DNA replication termination process that takes place at the RTS1 termination site in the mating type locus, in a specific direction required for subsequent imprinting and mating-type switching." [GOC:vw, PMID:12009298, PMID:18723894]
is_a: GO:0022414 ! reproductive process
is_a: GO:0071170 ! site-specific DNA replication termination
-relationship: part_of GO:0071516 ! establishment of imprinting at mating-type locus
+relationship: part_of GO:0071515 ! mating-type locus imprinting
[Term]
id: GO:0071172
@@ -357867,7 +357800,6 @@ name: protein localization to juxtaparanode region of axon
namespace: biological_process
def: "Any process in which a protein is transported to, or maintained at, the juxtaparanode region of an axon." [GOC:BHF, GOC:mah]
synonym: "protein localisation to juxtaparanode region of axon" EXACT [GOC:mah]
-is_a: GO:0034613 ! cellular protein localization
is_a: GO:0099612 ! protein localization to axon
[Term]
@@ -358188,7 +358120,9 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a streptomycin stimulus. Streptomycin is a commonly used antibiotic in cell culture media which acts only on prokaryotes and blocks transition from initiation complex to chain elongating ribosome." [GOC:mah]
is_a: GO:0046679 ! response to streptomycin
is_a: GO:0071236 ! cellular response to antibiotic
+is_a: GO:1901699 ! cellular response to nitrogen compound
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071240
@@ -358251,6 +358185,7 @@ def: "Any process that results in a change in state or activity of a cell (in te
is_a: GO:0010157 ! response to chlorate
is_a: GO:0071241 ! cellular response to inorganic substance
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071247
@@ -358260,6 +358195,7 @@ def: "Any process that results in a change in state or activity of a cell (in te
is_a: GO:0046687 ! response to chromate
is_a: GO:0071241 ! cellular response to inorganic substance
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071248
@@ -358279,6 +358215,7 @@ def: "Any process that results in a change in state or activity of a cell (in te
is_a: GO:0010167 ! response to nitrate
is_a: GO:0071241 ! cellular response to inorganic substance
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
is_a: GO:1902170 ! cellular response to reactive nitrogen species
[Term]
@@ -358524,6 +358461,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving morphine, 17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-3,6alpha-diol. Morphine is a highly potent opiate analgesic psychoactive drug obtained form the opium poppy, Papaver somniferum." [GOC:mah]
synonym: "morphine metabolism" EXACT [GOC:mah]
xref: Wikipedia:Morphine
+is_a: GO:0006790 ! sulfur compound metabolic process
is_a: GO:0033076 ! isoquinoline alkaloid metabolic process
is_a: GO:1901376 ! organic heteropentacyclic compound metabolic process
@@ -358531,11 +358469,11 @@ is_a: GO:1901376 ! organic heteropentacyclic compound metabolic process
id: GO:0071273
name: morphine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of morphine, 17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-3,6alpha-diol. Morphine is a highly potent opiate analgesic psychoactive drug obtained form the opium poppy, Papaver somniferum." [GOC:ecd, GOC:mah]
+def: "The chemical reactions and pathways resulting in the breakdown of morphine, 17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-3,6alpha-diol. Morphine is a highly potent opiate analgesic psychoactive drug obtained form the opium poppy, Papaver somniferum." [GOC:ecd, GOC:mah, PMID:22193538]
synonym: "morphine breakdown" EXACT [GOC:mah]
synonym: "morphine catabolism" EXACT [GOC:mah]
synonym: "morphine degradation" EXACT [GOC:mah]
-xref: UniPathway:Q02198
+is_a: GO:0044273 ! sulfur compound catabolic process
is_a: GO:0071272 ! morphine metabolic process
is_a: GO:0071274 ! isoquinoline alkaloid catabolic process
is_a: GO:1901377 ! organic heteropentacyclic compound catabolic process
@@ -358550,10 +358488,7 @@ synonym: "isoquinoline alkaloid breakdown" EXACT [GOC:mah]
synonym: "isoquinoline alkaloid catabolism" EXACT [GOC:mah]
synonym: "isoquinoline alkaloid degradation" EXACT [GOC:mah]
is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:0019439 ! aromatic compound catabolic process
is_a: GO:0033076 ! isoquinoline alkaloid metabolic process
-is_a: GO:0046700 ! heterocycle catabolic process
-is_a: GO:1901361 ! organic cyclic compound catabolic process
[Term]
id: GO:0071275
@@ -358582,6 +358517,8 @@ def: "Any process that results in a change in state or activity of a cell (in te
synonym: "cellular response to Ca2+ ion" EXACT [GOC:mah]
is_a: GO:0051592 ! response to calcium ion
is_a: GO:0071248 ! cellular response to metal ion
+is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071278
@@ -358635,6 +358572,7 @@ def: "Any process that results in a change in state or activity of a cell (in te
synonym: "cellular response to iron(III)" EXACT [GOC:mah]
is_a: GO:0010041 ! response to iron(III) ion
is_a: GO:0071281 ! cellular response to iron ion
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071284
@@ -358651,6 +358589,8 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lithium (Li+) ion stimulus." [GOC:mah]
is_a: GO:0010226 ! response to lithium ion
is_a: GO:0071248 ! cellular response to metal ion
+is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071286
@@ -358778,6 +358718,7 @@ is_a: GO:0033591 ! response to L-ascorbic acid
is_a: GO:0071295 ! cellular response to vitamin
is_a: GO:0071326 ! cellular response to monosaccharide stimulus
is_a: GO:0071407 ! cellular response to organic cyclic compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071299
@@ -358811,6 +358752,7 @@ is_a: GO:0071295 ! cellular response to vitamin
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0071417 ! cellular response to organonitrogen compound
is_a: GO:0097306 ! cellular response to alcohol
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071302
@@ -358823,6 +358765,7 @@ is_a: GO:0071295 ! cellular response to vitamin
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0071417 ! cellular response to organonitrogen compound
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071303
@@ -358916,7 +358859,9 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetate stimulus." [GOC:mah]
is_a: GO:0010034 ! response to acetate
is_a: GO:0071310 ! cellular response to organic substance
+is_a: GO:1901699 ! cellular response to nitrogen compound
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071312
@@ -358944,6 +358889,7 @@ is_a: GO:0042220 ! response to cocaine
is_a: GO:0071312 ! cellular response to alkaloid
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071315
@@ -358952,6 +358898,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a morphine stimulus. Morphine is an opioid alkaloid, isolated from opium, with a complex ring structure." [GOC:mah]
is_a: GO:0043278 ! response to morphine
is_a: GO:0071317 ! cellular response to isoquinoline alkaloid
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071316
@@ -358981,6 +358928,7 @@ is_a: GO:0033198 ! response to ATP
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0071417 ! cellular response to organonitrogen compound
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071319
@@ -358990,6 +358938,7 @@ def: "Any process that results in a change in state or activity of a cell (in te
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0080021 ! response to benzoic acid
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071320
@@ -359114,7 +359063,7 @@ id: GO:0071333
name: cellular response to glucose stimulus
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus." [GOC:mah]
-is_a: GO:0001678 ! cellular glucose homeostasis
+is_a: GO:0001678 ! intracellular glucose homeostasis
is_a: GO:0009749 ! response to glucose
is_a: GO:0071331 ! cellular response to hexose stimulus
@@ -359240,14 +359189,14 @@ is_a: GO:0071310 ! cellular response to organic substance
[Term]
id: GO:0071346
-name: cellular response to interferon-gamma
+name: cellular response to type II interferon
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon gamma is the only member of the type II interferon found so far." [GOC:mah]
synonym: "cellular response to gamma-interferon" RELATED [GOC:mah]
synonym: "cellular response to immune interferon" EXACT [GOC:mah]
+synonym: "cellular response to interferon-gamma" BROAD [GOC:mah]
synonym: "cellular response to type II IFN" BROAD [GOC:mah]
-synonym: "cellular response to type II interferon" BROAD [GOC:mah]
-is_a: GO:0034341 ! response to interferon-gamma
+is_a: GO:0034341 ! response to type II interferon
is_a: GO:0071345 ! cellular response to cytokine stimulus
[Term]
@@ -359401,7 +359350,7 @@ name: cellular response to growth factor stimulus
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus." [GOC:mah]
is_a: GO:0070848 ! response to growth factor
-is_a: GO:0071310 ! cellular response to organic substance
+is_a: GO:0071495 ! cellular response to endogenous stimulus
[Term]
id: GO:0071364
@@ -359411,7 +359360,6 @@ def: "Any process that results in a change in state or activity of a cell (in te
synonym: "cellular response to EGF stimulus" EXACT [GOC:mah]
is_a: GO:0070849 ! response to epidermal growth factor
is_a: GO:0071363 ! cellular response to growth factor stimulus
-is_a: GO:0071495 ! cellular response to endogenous stimulus
[Term]
id: GO:0071365
@@ -359554,6 +359502,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a prostagladin stimulus." [GOC:mah]
is_a: GO:0032870 ! cellular response to hormone stimulus
is_a: GO:0034694 ! response to prostaglandin
+is_a: GO:0071396 ! cellular response to lipid
[Term]
id: GO:0071380
@@ -359664,6 +359613,7 @@ id: GO:0071391
name: cellular response to estrogen stimulus
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics." [GOC:mah]
+synonym: "cellular response to 17alpha-ethynylestradiol" RELATED []
synonym: "cellular response to oestrogen stimulus" EXACT [GOC:mah]
is_a: GO:0032870 ! cellular response to hormone stimulus
is_a: GO:0043627 ! response to estrogen
@@ -359741,6 +359691,7 @@ def: "Any process that results in a change in state or activity of a cell (in te
synonym: "cellular response to linoleate" EXACT [GOC:mah]
is_a: GO:0070543 ! response to linoleic acid
is_a: GO:0071398 ! cellular response to fatty acid
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071400
@@ -359883,6 +359834,7 @@ is_a: GO:0031427 ! response to methotrexate
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0071417 ! cellular response to organonitrogen compound
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071415
@@ -359949,6 +359901,7 @@ comment: Note that this term is not intended for use in annotating lateral movem
synonym: "manganese ion membrane transport" EXACT []
synonym: "transmembrane manganese transport" EXACT [GOC:mah]
is_a: GO:0006828 ! manganese ion transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -359960,7 +359913,6 @@ comment: Note that this term is not intended for use in annotating lateral movem
synonym: "succinate membrane transport" EXACT []
synonym: "transmembrane succinate transport" EXACT [GOC:mah]
is_a: GO:0015744 ! succinate transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -359972,14 +359924,14 @@ comment: Note that this term is not intended for use in annotating lateral movem
synonym: "malate membrane transport" EXACT []
synonym: "transmembrane malate transport" EXACT [GOC:mah]
is_a: GO:0015743 ! malate transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:0071424
name: rRNA (cytosine-N4-)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N4-methylcytosine." [GOC:imk, PMID:19965768]
+def: "Catalysis of the reaction: a cytidine in rRNA + S-adenosyl-L-methionine = an N(4)-methylcytidine in rRNA + H+ + S-adenosyl-L-homocysteine." [GOC:imk, PMID:19965768, RHEA:62520]
+xref: RHEA:62520
is_a: GO:0008170 ! N-methyltransferase activity
is_a: GO:0016434 ! rRNA (cytosine) methyltransferase activity
@@ -360123,34 +360075,36 @@ relationship: part_of GO:0030118 ! clathrin coat
[Term]
id: GO:0071440
-name: regulation of histone H3-K14 acetylation
+name: obsolete regulation of histone H3-K14 acetylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone." [GOC:mah]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "regulation of histone H3 acetylation at K14" EXACT [GOC:mah]
synonym: "regulation of histone H3K14 acetylation" EXACT [GOC:mah]
-is_a: GO:0035065 ! regulation of histone acetylation
-relationship: regulates GO:0044154 ! histone H3-K14 acetylation
+is_obsolete: true
+consider: GO:0006338
[Term]
id: GO:0071441
-name: negative regulation of histone H3-K14 acetylation
+name: obsolete negative regulation of histone H3-K14 acetylation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone." [GOC:mah]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of histone H3-K14 acetylation" EXACT [GOC:mah]
synonym: "down-regulation of histone H3-K14 acetylation" EXACT [GOC:mah]
synonym: "downregulation of histone H3-K14 acetylation" EXACT [GOC:mah]
synonym: "inhibition of histone H3-K14 acetylation" NARROW [GOC:mah]
synonym: "negative regulation of histone H3 acetylation at K14" EXACT [GOC:mah]
synonym: "negative regulation of histone H3K14 acetylation" EXACT [GOC:mah]
-is_a: GO:0035067 ! negative regulation of histone acetylation
-is_a: GO:0071440 ! regulation of histone H3-K14 acetylation
-relationship: negatively_regulates GO:0044154 ! histone H3-K14 acetylation
+is_obsolete: true
+consider: GO:0006338
[Term]
id: GO:0071442
-name: positive regulation of histone H3-K14 acetylation
+name: obsolete positive regulation of histone H3-K14 acetylation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone." [GOC:mah]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of histone H3-K14 acetylation" NARROW [GOC:mah]
synonym: "positive regulation of histone H3 acetylation at K14" EXACT [GOC:mah]
synonym: "positive regulation of histone H3K14 acetylation" EXACT [GOC:mah]
@@ -360158,9 +360112,8 @@ synonym: "stimulation of histone H3-K14 acetylation" NARROW [GOC:mah]
synonym: "up regulation of histone H3-K14 acetylation" EXACT [GOC:mah]
synonym: "up-regulation of histone H3-K14 acetylation" EXACT [GOC:mah]
synonym: "upregulation of histone H3-K14 acetylation" EXACT [GOC:mah]
-is_a: GO:0035066 ! positive regulation of histone acetylation
-is_a: GO:0071440 ! regulation of histone H3-K14 acetylation
-relationship: positively_regulates GO:0044154 ! histone H3-K14 acetylation
+is_obsolete: true
+consider: GO:0006338
[Term]
id: GO:0071443
@@ -360307,15 +360260,16 @@ is_a: GO:0034614 ! cellular response to reactive oxygen species
[Term]
id: GO:0071458
-name: integral component of cytoplasmic side of endoplasmic reticulum membrane
+name: obsolete integral component of cytoplasmic side of endoplasmic reticulum membrane
namespace: cellular_component
-def: "The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the cytoplasmic side of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the cytoplasmic side of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to cytosolic leaflet of endoplasmic reticulum membrane" EXACT [GOC:ab]
synonym: "integral to cytosolic side of endoplasmic reticulum membrane" EXACT []
synonym: "integral to cytosolic side of ER membrane" EXACT [GOC:mah]
synonym: "integral to ER membrane, cytosolic side" EXACT [GOC:vw]
-is_a: GO:0030176 ! integral component of endoplasmic reticulum membrane
-relationship: part_of GO:0098554 ! cytoplasmic side of endoplasmic reticulum membrane
+is_obsolete: true
+replaced_by: GO:0098554
[Term]
id: GO:0071459
@@ -360351,6 +360305,7 @@ is_a: GO:0009415 ! response to water
is_a: GO:0071214 ! cellular response to abiotic stimulus
is_a: GO:0071229 ! cellular response to acid chemical
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071463
@@ -360756,6 +360711,7 @@ def: "Any process that results in a change in state or activity of a cell or an
synonym: "response to mycophenolate" EXACT [GOC:mah]
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0071506
@@ -360766,6 +360722,7 @@ synonym: "cellular response to mycophenolate" EXACT [GOC:mah]
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0071505 ! response to mycophenolic acid
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0071507
@@ -360857,10 +360814,10 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0071514
name: genomic imprinting
namespace: biological_process
-def: "The establishment of epigenetic modifications (imprints) during gametogenesis, leading to an asymmetry in the heterochromatin between the maternal and paternal alleles, and differential expression of the corresponding alleles. This asymmetry results from the different epigenetic pathways acting in maternal and paternal gametes." [PMID:31896690]
+def: "The establishment of epigenetic modifications (imprints) during gametogenesis, leading to an asymmetry between the maternal and paternal alleles, leading to differential expression of the corresponding alleles. This can happen through heterochromatin formation or through differential chromatin loop formation." [PMID:24492710, PMID:31896690, PMID:31965998]
synonym: "DNA imprinting" EXACT [GOC:mah]
synonym: "genetic imprinting" EXACT []
-is_a: GO:0031507 ! heterochromatin assembly
+is_a: GO:0040029 ! epigenetic regulation of gene expression
[Term]
id: GO:0071515
@@ -360870,29 +360827,28 @@ def: "A genomic imprinting process in which a stable single-strand DNA lesion tr
synonym: "genetic imprinting at mating-type locus" EXACT []
synonym: "genomic imprinting at mating-type locus" EXACT []
synonym: "mating type determination, imprinting" EXACT [GOC:vw]
-is_a: GO:0022414 ! reproductive process
-is_a: GO:0031507 ! heterochromatin assembly
+is_a: GO:0022413 ! reproductive process in single-celled organism
relationship: part_of GO:0007533 ! mating type switching
[Term]
id: GO:0071516
-name: establishment of imprinting at mating-type locus
+name: obsolete establishment of imprinting at mating-type locus
namespace: biological_process
-def: "The initial formation of a stable single-strand DNA lesion that triggers programmed gene conversion at the mating-type locus, thereby restricting mating-type interconversion to one of the two sister chromatids during DNA replication." [GOC:mah, PMID:18723894]
+def: "OBSOLETE. The initial formation of a stable single-strand DNA lesion that triggers programmed gene conversion at the mating-type locus, thereby restricting mating-type interconversion to one of the two sister chromatids during DNA replication." [GOC:mah, PMID:18723894]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "mating type determination, establishment of imprinting" EXACT [GOC:vw]
-is_a: GO:0006259 ! DNA metabolic process
-is_a: GO:0022414 ! reproductive process
-relationship: part_of GO:0071515 ! mating-type locus imprinting
+is_obsolete: true
+replaced_by: GO:0071515
[Term]
id: GO:0071517
-name: maintenance of imprinting at mating-type locus
+name: obsolete maintenance of imprinting at mating-type locus
namespace: biological_process
-def: "Any process involved in preserving the structure of a stable single-strand DNA lesion that triggers programmed gene conversion at the mating-type locus, thereby restricting mating-type interconversion to one of the two sister chromatids during DNA replication." [GOC:mah, PMID:14765111, PMID:18723894]
+def: "OBSOLETE. Any process involved in preserving the structure of a stable single-strand DNA lesion that triggers programmed gene conversion at the mating-type locus, thereby restricting mating-type interconversion to one of the two sister chromatids during DNA replication." [GOC:mah, PMID:14765111, PMID:18723894]
+comment: Tis term was obsoleted because it represents a molecular function.
synonym: "mating type determination, maintenance of imprinting" EXACT [GOC:mah]
-is_a: GO:0006259 ! DNA metabolic process
-is_a: GO:0022414 ! reproductive process
-relationship: part_of GO:0071515 ! mating-type locus imprinting
+is_obsolete: true
+replaced_by: GO:0071515
[Term]
id: GO:0071518
@@ -360930,8 +360886,8 @@ name: Cdc42 GTPase complex
namespace: cellular_component
def: "A protein complex formed by the association of the small GTPase Cdc42 with additional proteins. In Schizosaccharomyces the complex contains the Cdc42, Ras1, Scd1, Scd2, andShk1 proteins, and functions in the Ras1-Scd GTPase signalling pathway." [GOC:mah, GOC:vw, PMID:10567532, PMID:7923372, PMID:8943016]
synonym: "Ras1-Scd1-Scd2-Cdc42-Shk1 complex" EXACT [GOC:vw]
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005737 ! cytoplasm
+is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1905360 ! GTPase complex
[Term]
id: GO:0071522
@@ -360961,10 +360917,10 @@ synonym: "pyrrolysine anabolism" EXACT [GOC:mah]
synonym: "pyrrolysine biosynthesis" EXACT [GOC:mah]
synonym: "pyrrolysine formation" EXACT [GOC:mah]
synonym: "pyrrolysine synthesis" EXACT [GOC:mah]
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
is_a: GO:0043604 ! amide biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:0071525 ! pyrrolysine metabolic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
@@ -360975,9 +360931,9 @@ namespace: biological_process
def: "The chemical reactions and pathways involving pyrrolysine, N6-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine." [GOC:mah, PMID:17204561]
synonym: "monomethylamine methyltransferase cofactor lysine adduct metabolic process" EXACT [CHEBI:21860]
synonym: "pyrrolysine metabolism" EXACT [GOC:mah]
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0006575 ! cellular modified amino acid metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
@@ -360985,7 +360941,7 @@ is_a: GO:1901360 ! organic cyclic compound metabolic process
id: GO:0071526
name: semaphorin-plexin signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand." [GOC:BHF, GOC:mah, GOC:vk, PMID:15239959]
+def: "The series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand." [GOC:BHF, GOC:mah, GOC:vk, PMID:15239959]
synonym: "semaphorin-plexin signalling pathway" EXACT [GOC:mah]
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -360993,7 +360949,7 @@ is_a: GO:0007166 ! cell surface receptor signaling pathway
id: GO:0071527
name: semaphorin-plexin signaling pathway involved in outflow tract morphogenesis
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand that contributes to outflow tract morphogenesis." [GOC:BHF, GOC:mah, GOC:vk, PMID:15239959]
+def: "The series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand that contributes to outflow tract morphogenesis." [GOC:BHF, GOC:mah, GOC:vk, PMID:15239959]
synonym: "semaphorin-plexin signalling pathway involved in outflow tract morphogenesis" EXACT [GOC:mah]
is_a: GO:0061311 ! cell surface receptor signaling pathway involved in heart development
is_a: GO:0071526 ! semaphorin-plexin signaling pathway
@@ -361020,7 +360976,7 @@ id: GO:0071530
name: obsolete FHA domain-mediated complex assembly
namespace: biological_process
def: "OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by an FHA (forkhead-associated) domain interaction." [GOC:amm, InterPro:IPR000253]
-comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
+comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
synonym: "forkhead-associated domain-mediated complex assembly" EXACT [GOC:mah]
is_obsolete: true
@@ -361029,7 +360985,7 @@ id: GO:0071531
name: obsolete Rel homology domain-mediated complex assembly
namespace: biological_process
def: "OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by a Rel homology domain (RHD) interaction." [GOC:amm, InterPro:IPR011539]
-comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
+comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
synonym: "RHD domain-mediated complex assembly" EXACT [GOC:mah]
is_obsolete: true
@@ -361046,7 +361002,7 @@ id: GO:0071533
name: obsolete ankyrin repeat-mediated complex assembly
namespace: biological_process
def: "OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by an ankyrin repeat interaction." [GOC:amm, InterPro:IPR002110]
-comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
+comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
synonym: "ANK repeat-mediated complex assembly" EXACT [GOC:amm]
is_obsolete: true
@@ -361055,7 +361011,7 @@ id: GO:0071534
name: obsolete zf-TRAF domain-mediated complex assembly
namespace: biological_process
def: "OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by a TRAF-type zinc finger (zf-TRAF) domain interaction." [GOC:amm, InterPro:IPR001293]
-comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
+comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
synonym: "TRAF-type zinc finger domain-mediated complex assembly" EXACT [GOC:mah]
synonym: "zinc finger TRAF-type domain-mediated complex assembly" EXACT [GOC:mah]
synonym: "zinc-finger-TRAF domain-mediated complex assembly" EXACT [GOC:mah]
@@ -361073,7 +361029,7 @@ id: GO:0071536
name: obsolete RING-like zinc finger domain-mediated complex assembly
namespace: biological_process
def: "OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by a RING-like zinc finger domain interaction." [GOC:amm, InterPro:IPR014857]
-comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
+comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
synonym: "RING-like domain-mediated complex assembly" EXACT [GOC:mah]
is_obsolete: true
@@ -361082,7 +361038,7 @@ id: GO:0071537
name: obsolete C3HC4-type RING finger domain-mediated complex assembly
namespace: biological_process
def: "OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by a C3HC4-type RING finger domain interaction." [GOC:amm, InterPro:IPR018957]
-comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
+comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
synonym: "zinc finger C3HC4 type domain-mediated complex assembly" EXACT [GOC:amm]
is_obsolete: true
@@ -361091,7 +361047,7 @@ id: GO:0071538
name: obsolete SH2 domain-mediated complex assembly
namespace: biological_process
def: "OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by an SH2 domain interaction." [GOC:amm]
-comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
+comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
is_obsolete: true
[Term]
@@ -361149,7 +361105,6 @@ id: GO:0071545
name: inositol phosphate catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of an inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached." [GOC:mah]
-comment: See also the biological process term 'inositol phosphate dephosphorylation ; GO:0046855'.
synonym: "inositol phosphate breakdown" EXACT [GOC:mah]
synonym: "inositol phosphate catabolism" EXACT [GOC:mah]
synonym: "inositol phosphate degradation" EXACT [GOC:mah]
@@ -361219,7 +361174,7 @@ id: GO:0071552
name: obsolete RIP homotypic interaction motif-mediated complex assembly
namespace: biological_process
def: "OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by a RIP homotypic interaction motif (RHIM) interaction." [GOC:amm, PMID:11734559]
-comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
+comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
synonym: "RHIM-mediated complex assembly" EXACT [GOC:mah]
is_obsolete: true
@@ -361245,6 +361200,7 @@ subset: goslim_chembl
subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "cell wall organisation or biogenesis" EXACT [GOC:mah]
synonym: "cell wall organization or biogenesis at cellular level" EXACT [GOC:mah]
synonym: "cellular cell wall organisation or biogenesis" EXACT [GOC:mah]
@@ -361272,15 +361228,16 @@ is_a: GO:0071554 ! cell wall organization or biogenesis
[Term]
id: GO:0071556
-name: integral component of lumenal side of endoplasmic reticulum membrane
+name: obsolete integral component of lumenal side of endoplasmic reticulum membrane
namespace: cellular_component
-def: "The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to ER membrane, lumenal side" EXACT [GOC:vw]
synonym: "integral to lumenal leaflet of endoplasmic reticulum membrane" EXACT [GOC:ab]
synonym: "integral to lumenal side of endoplasmic reticulum membrane" NARROW []
synonym: "integral to lumenal side of ER membrane" EXACT [GOC:mah]
-is_a: GO:0030176 ! integral component of endoplasmic reticulum membrane
-relationship: part_of GO:0098553 ! lumenal side of endoplasmic reticulum membrane
+is_obsolete: true
+replaced_by: GO:0098553
[Term]
id: GO:0071557
@@ -361292,10 +361249,11 @@ is_a: GO:0070076 ! histone lysine demethylation
[Term]
id: GO:0071558
-name: histone H3-tri/di-methyl-lysine-27 demethylase activity
+name: histone H3K27me2/H3K27me3 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a tri- or a dimethyl-lysine residue at position 27 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [GOC:sp, PMID:20622853]
synonym: "histone demethylase activity (H3-K27 specific)" BROAD []
+synonym: "histone H3-tri/di-methyl-lysine-27 demethylase activity" EXACT []
synonym: "histone H3K27me2 demethylase activity" RELATED []
synonym: "histone H3K27me3 demethylase activity" RELATED []
xref: EC:1.14.11.68
@@ -361314,7 +361272,6 @@ def: "Any process that results in a change in state or activity of a cell or an
synonym: "response to TGF-beta stimulus" EXACT [GOC:mah]
synonym: "response to TGFbeta stimulus" EXACT [GOC:mah]
synonym: "response to transforming growth factor beta stimulus" EXACT [GOC:dos]
-is_a: GO:0009719 ! response to endogenous stimulus
is_a: GO:0070848 ! response to growth factor
[Term]
@@ -361325,7 +361282,6 @@ def: "Any process that results in a change in state or activity of a cell (in te
synonym: "cellular response to TGF-beta stimulus" EXACT [GOC:mah]
synonym: "cellular response to TGFbeta stimulus" EXACT [GOC:mah]
is_a: GO:0071363 ! cellular response to growth factor stimulus
-is_a: GO:0071495 ! cellular response to endogenous stimulus
is_a: GO:0071559 ! response to transforming growth factor beta
[Term]
@@ -361342,7 +361298,7 @@ is_a: GO:0044232 ! organelle membrane contact site
id: GO:0071562
name: nucleus-vacuole junction assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form a nucleus-vacuole junction, which are membrane contact sites formed between the vacuole membrane and the outer nuclear membrane. In S. cerevisiae these contacts are mediated through direct physical interaction between Vac8p and Nvj1p." [GOC:jp, PMID:16709156]
+def: "The aggregation, arrangement and bonding together of a set of components to form a nucleus-vacuole junction (NVJ), membrane contact sites formed between the vacuole membrane and the outer nuclear membrane. In S. cerevisiae these contacts are mediated through direct physical interaction between Vac8p and Nvj1p. The NVJ plays roles in piecemeal microautophagy of the nucleus and in the cytoplasm-to-vacuole targeting pathway." [GOC:jp, PMID:16709156, PMID:28533415]
synonym: "nucleus-vacuole junction formation" EXACT [GOC:jp]
synonym: "NV junction assembly" EXACT [GOC:jp, PMID:16709156]
synonym: "NV junction formation" EXACT [GOC:jp, PMID:16709156]
@@ -361350,7 +361306,6 @@ synonym: "NVJ assembly" EXACT [GOC:mah, PMID:16806880]
synonym: "NVJ formation" EXACT [GOC:mah, PMID:16806880]
is_a: GO:0022607 ! cellular component assembly
is_a: GO:0140056 ! organelle localization by membrane tethering
-relationship: part_of GO:0034727 ! piecemeal microautophagy of the nucleus
[Term]
id: GO:0071563
@@ -361383,10 +361338,12 @@ is_a: GO:0008641 ! ubiquitin-like modifier activating enzyme activity
[Term]
id: GO:0071567
-name: UFM1 hydrolase activity
+name: deUFMylase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of UFM1, a small ubiquitin-related modifier, from previously modified substrates." [GOC:sp, PMID:20018847]
-is_a: GO:0019783 ! ubiquitin-like protein-specific protease activity
+def: "A thiol-dependent isopeptidase activity that cleaves UFM1 from a target protein to which it is conjugated." [GOC:sp, PMID:17182609, PMID:20018847]
+synonym: "UFM1 hydrolase activity" EXACT []
+is_a: GO:0008234 ! cysteine-type peptidase activity
+is_a: GO:0019783 ! ubiquitin-like protein peptidase activity
[Term]
id: GO:0071568
@@ -361414,7 +361371,7 @@ id: GO:0071571
name: obsolete LRR domain-mediated complex assembly
namespace: biological_process
def: "OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by an LRR (leucine-rich repeat) domain interaction." [GOC:amm, InterPro:IPR001611]
-comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
+comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
synonym: "leucine-rich repeat domain-mediated complex assembly" EXACT [GOC:mah]
is_obsolete: true
@@ -361448,13 +361405,14 @@ is_a: GO:0072741 ! protein localization to cell division site
[Term]
id: GO:0071575
-name: integral component of external side of plasma membrane
+name: obsolete integral component of external side of plasma membrane
namespace: cellular_component
-def: "The component of the plasma membrane consisting of the gene products that penetrate only the external side of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the plasma membrane consisting of the gene products that penetrate only the external side of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to external leaflet of plasma membrane" EXACT [GOC:ab]
synonym: "integral to external side of plasma membrane" NARROW []
-is_a: GO:0005887 ! integral component of plasma membrane
-is_a: GO:0031233 ! intrinsic component of external side of plasma membrane
+is_obsolete: true
+replaced_by: GO:0009897
[Term]
id: GO:0071576
@@ -361475,6 +361433,7 @@ synonym: "zinc II ion transmembrane transport" EXACT []
synonym: "zinc ion membrane transport" EXACT []
synonym: "zinc transmembrane transport" EXACT [GOC:mah]
is_a: GO:0006829 ! zinc ion transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -361492,6 +361451,7 @@ synonym: "low-affinity zinc II ion transport" NARROW []
synonym: "zinc II ion plasma membrane import" EXACT []
synonym: "zinc II ion transmembrane import" EXACT []
synonym: "zinc import" EXACT [GOC:mah]
+synonym: "zinc ion import into cell" EXACT []
synonym: "zinc ion transmembrane import" RELATED []
synonym: "zinc uptake" EXACT [GOC:mah]
is_a: GO:0071577 ! zinc ion transmembrane transport
@@ -361512,7 +361472,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the directed movement of zinc ions (Zn2+) from one side of a membrane to the other." [GOC:BHF, GOC:mah]
synonym: "regulation of zinc ion membrane transport" EXACT []
is_a: GO:0071579 ! regulation of zinc ion transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
+is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport
relationship: regulates GO:0071577 ! zinc ion transmembrane transport
[Term]
@@ -361528,7 +361488,7 @@ id: GO:0071582
name: negative regulation of zinc ion transport
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of zinc ions (Zn2+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:BHF, GOC:mah]
-is_a: GO:0043271 ! negative regulation of ion transport
+is_a: GO:0043271 ! negative regulation of monoatomic ion transport
is_a: GO:0071579 ! regulation of zinc ion transport
relationship: negatively_regulates GO:0006829 ! zinc ion transport
@@ -361580,7 +361540,7 @@ relationship: part_of GO:0080120 ! CAAX-box protein maturation
id: GO:0071588
name: hydrogen peroxide mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of hydrogen peroxide (H2O2)." [GOC:mah, PMID:17043891]
+def: "The series of molecular signals mediated by the detection of hydrogen peroxide (H2O2)." [GOC:mah, PMID:17043891]
synonym: "H2O2 mediated signaling pathway" EXACT [GOC:mah]
synonym: "hydrogen peroxide mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0007165 ! signal transduction
@@ -361900,17 +361860,23 @@ is_a: GO:0071617 ! lysophospholipid acyltransferase activity
[Term]
id: GO:0071619
-name: phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
+name: obsolete phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
namespace: biological_process
-def: "The process of introducing a phosphate group onto a serine residue at position 2 within the heptapeptide repeat (YSPTSPS) of the C-terminal domain of RNA polymerase II. Typically, phosphorylation of serine 2 (Ser2) occurs subsequent to phosphorylation of serine 5 and is thus seen in the middle and 3' ends of genes. In vivo, Ser2 phosphorylation is primarily performed by CTDK-I in S. cerevisiae or CDK9 in metazoans." [GOC:krc, PMID:17079683]
-is_a: GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain
+def: "OBSOLETE. The process of introducing a phosphate group onto a serine residue at position 2 within the heptapeptide repeat (YSPTSPS) of the C-terminal domain of RNA polymerase II. Typically, phosphorylation of serine 2 (Ser2) occurs subsequent to phosphorylation of serine 5 and is thus seen in the middle and 3' ends of genes. In vivo, Ser2 phosphorylation is primarily performed by CTDK-I in S. cerevisiae or CDK9 in metazoans." [GOC:krc, PMID:17079683]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0006366
+consider: GO:0140834
[Term]
id: GO:0071620
-name: phosphorylation of RNA polymerase II C-terminal domain serine 5 residues
+name: obsolete phosphorylation of RNA polymerase II C-terminal domain serine 5 residues
namespace: biological_process
-def: "The process of introducing a phosphate group onto a serine residue at position 5 within the heptapeptide repeat (YSPTSPS) of the C-terminal domain of RNA polymerase II. Typically, phosphorylation of serine 5 (Ser5) occurs near the 5' ends of genes. It is generally still observed in the middle of genes, overlapping with phosphorylation of serine 2, but is generally not present at the 3' ends of genes. In vivo, Ser5 phosphorylation occurs primarily through the action of TFIIH (KIN28 in S. cerevisiae, CKD7 in metazoans)." [GOC:krc, PMID:17079683]
-is_a: GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain
+def: "OBSOLETE. The process of introducing a phosphate group onto a serine residue at position 5 within the heptapeptide repeat (YSPTSPS) of the C-terminal domain of RNA polymerase II. Typically, phosphorylation of serine 5 (Ser5) occurs near the 5' ends of genes. It is generally still observed in the middle of genes, overlapping with phosphorylation of serine 2, but is generally not present at the 3' ends of genes. In vivo, Ser5 phosphorylation occurs primarily through the action of TFIIH (KIN28 in S. cerevisiae, CKD7 in metazoans)." [GOC:krc, PMID:17079683]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0006366
+consider: GO:0140836
[Term]
id: GO:0071621
@@ -361964,20 +361930,22 @@ is_a: GO:0022600 ! digestive system process
[Term]
id: GO:0071627
-name: integral component of fungal-type vacuolar membrane
+name: obsolete integral component of fungal-type vacuolar membrane
namespace: cellular_component
-def: "The component of the fungal-type vacuole membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the fungal-type vacuole membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to fungal-type vacuolar membrane" NARROW []
-is_a: GO:0031166 ! integral component of vacuolar membrane
-is_a: GO:0071628 ! intrinsic component of fungal-type vacuolar membrane
+is_obsolete: true
+replaced_by: GO:0000329
[Term]
id: GO:0071628
-name: intrinsic component of fungal-type vacuolar membrane
+name: obsolete intrinsic component of fungal-type vacuolar membrane
namespace: cellular_component
-def: "The component of a fungal-type vacuole membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-is_a: GO:0031310 ! intrinsic component of vacuolar membrane
-relationship: part_of GO:0000329 ! fungal-type vacuole membrane
+def: "OBSOLETE. The component of a fungal-type vacuole membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0000329
[Term]
id: GO:0071629
@@ -362011,8 +361979,10 @@ relationship: part_of GO:0071218 ! cellular response to misfolded protein
id: GO:0071631
name: mating pheromone secretion involved in positive regulation of conjugation with cellular fusion
namespace: biological_process
+alt_id: GO:0071833
def: "The regulated release of a mating pheromone, a peptide hormone that induces a behavioral or physiological response(s) from a responding organism or cell, that positively regulates a conjugation process that results in the union of cellular and genetic information from compatible mating types." [GOC:elh, GOC:jh, GOC:mah]
synonym: "mating-type pheromone secretion involved in conjugation with cellular fusion" EXACT [GOC:vw]
+synonym: "peptide pheromone export involved in positive regulation of conjugation with cellular fusion" RELATED []
is_a: GO:0031139 ! positive regulation of conjugation with cellular fusion
is_a: GO:0071834 ! mating pheromone secretion
@@ -362819,7 +362789,7 @@ synonym: "membrane macromolecule anabolism" EXACT [GOC:mah]
synonym: "membrane macromolecule biosynthesis" EXACT [GOC:mah]
synonym: "membrane macromolecule formation" EXACT [GOC:mah]
synonym: "membrane macromolecule synthesis" EXACT [GOC:mah]
-is_a: GO:0070589 ! cellular component macromolecule biosynthetic process
+is_a: GO:0009059 ! macromolecule biosynthetic process
relationship: part_of GO:0044091 ! membrane biogenesis
[Term]
@@ -362860,6 +362830,7 @@ name: icosanoid transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of icosanoids from one side of a membrane to the other." [GOC:sl]
synonym: "eicosanoid transmembrane transporter activity" EXACT [GOC:sl]
+is_a: GO:0005319 ! lipid transporter activity
is_a: GO:0022857 ! transmembrane transporter activity
[Term]
@@ -362882,8 +362853,7 @@ id: GO:0071717
name: thromboxane transport
namespace: biological_process
def: "The directed movement of thromboxanes into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A thromboxane is any of a class of oxygenated oxane derivatives, originally derived from prostaglandin precursors in platelets, that stimulate aggregation of platelets and constriction of blood vessels." [GOC:mah]
-is_a: GO:0006869 ! lipid transport
-is_a: GO:0015718 ! monocarboxylic acid transport
+is_a: GO:0015908 ! fatty acid transport
is_a: GO:0071715 ! icosanoid transport
[Term]
@@ -363447,7 +363417,6 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bone morphogenetic protein (BMP) stimulus." [GOC:mah, GOC:yaf]
synonym: "response to BMP stimulus" EXACT [GOC:dos]
synonym: "response to bone morphogenetic protein stimulus" EXACT [GOC:mah]
-is_a: GO:0009719 ! response to endogenous stimulus
is_a: GO:0070848 ! response to growth factor
[Term]
@@ -363457,7 +363426,6 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bone morphogenetic protein (BMP) stimulus." [GOC:mah, GOC:yaf]
synonym: "cellular response to bone morphogenetic protein stimulus" EXACT [GOC:mah]
is_a: GO:0071363 ! cellular response to growth factor stimulus
-is_a: GO:0071495 ! cellular response to endogenous stimulus
is_a: GO:0071772 ! response to BMP
[Term]
@@ -363467,7 +363435,6 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fibroblast growth factor stimulus." [GOC:mah]
synonym: "response to FGF stimulus" EXACT [GOC:mah]
synonym: "response to fibroblast growth factor stimulus" EXACT [GOC:dos]
-is_a: GO:0009719 ! response to endogenous stimulus
is_a: GO:0070848 ! response to growth factor
[Term]
@@ -363483,7 +363450,7 @@ is_obsolete: true
id: GO:0071781
name: endoplasmic reticulum cisternal network
namespace: cellular_component
-def: "A subcompartment of the endoplasmic reticulum consisting of flattened, disc-shaped domains known as cisternae. These are typically found close to the nucleus and are generally more prominent in secretory cells." [GOC:vw, PMID:16469703, PMID:20434336]
+def: "A subcompartment of the endoplasmic reticulum consisting of flattened, disc-shaped domains known as cisternae. These are typically found close to the nucleus and are generally more prominent in secretory cells." [GOC:vw, PMID:16469703, PMID:20434336]
synonym: "ER cisternal network" EXACT [GOC:mah]
is_a: GO:0098827 ! endoplasmic reticulum subcompartment
@@ -363697,6 +363664,7 @@ synonym: "high-affinity potassium ion import" NARROW []
synonym: "high-affinity potassium ion uptake" NARROW [GOC:dph, GOC:tb]
synonym: "potassium ion membrane transport" EXACT []
is_a: GO:0006813 ! potassium ion transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -363850,28 +363818,31 @@ is_a: GO:0043933 ! protein-containing complex organization
[Term]
id: GO:0071824
-name: protein-DNA complex subunit organization
+name: protein-DNA complex organization
namespace: biological_process
def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA complex." [GOC:mah]
synonym: "DNA-protein complex subunit organization" EXACT [GOC:mah]
synonym: "protein-DNA complex subunit organisation" EXACT [GOC:mah]
+synonym: "protein-DNA complex subunit organization" EXACT []
is_a: GO:0043933 ! protein-containing complex organization
[Term]
id: GO:0071825
-name: protein-lipid complex subunit organization
+name: protein-lipid complex organization
namespace: biological_process
def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-lipid complex." [GOC:mah]
synonym: "protein-lipid complex subunit organisation" EXACT [GOC:mah]
+synonym: "protein-lipid complex subunit organization" EXACT []
is_a: GO:0043933 ! protein-containing complex organization
[Term]
id: GO:0071826
-name: ribonucleoprotein complex subunit organization
+name: protein-RNA complex organization
namespace: biological_process
def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex." [GOC:mah]
synonym: "protein-RNA complex subunit organization" EXACT [GOC:mah]
synonym: "ribonucleoprotein complex subunit organisation" EXACT [GOC:mah]
+synonym: "ribonucleoprotein complex subunit organization" EXACT []
synonym: "RNA-protein complex subunit organization" EXACT [GOC:mah]
is_a: GO:0043933 ! protein-containing complex organization
@@ -363882,7 +363853,7 @@ namespace: biological_process
def: "A protein-lipid complex subunit organization process that results in the formation, disassembly, or alteration of a plasma lipoprotein particle. A plasma lipoprotein particle is a spherical particle with a hydrophobic core of triglycerides and/or cholesterol esters, surrounded by an amphipathic monolayer of phospholipids, cholesterol and apolipoproteins." [GOC:BHF, GOC:mah]
synonym: "plasma lipoprotein particle organisation" EXACT [GOC:mah]
is_a: GO:0032501 ! multicellular organismal process
-is_a: GO:0071825 ! protein-lipid complex subunit organization
+is_a: GO:0071825 ! protein-lipid complex organization
[Term]
id: GO:0071828
@@ -363918,22 +363889,6 @@ def: "The process in which a intermediate-density lipoprotein particle is remove
synonym: "IDL clearance" EXACT [GOC:BHF]
is_a: GO:0071830 ! triglyceride-rich lipoprotein particle clearance
-[Term]
-id: GO:0071832
-name: peptide pheromone export involved in regulation of conjugation
-namespace: biological_process
-def: "The directed movement of a peptide pheromone out of a cell by a secretion or export pathway used solely for the export of peptide pheromones that contributes to the union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms." [GOC:elh, GOC:jh, GOC:mah]
-is_a: GO:0000770 ! peptide pheromone export
-is_a: GO:0046999 ! regulation of conjugation
-
-[Term]
-id: GO:0071833
-name: peptide pheromone export involved in positive regulation of conjugation with cellular fusion
-namespace: biological_process
-def: "The directed movement of a peptide pheromone out of a cell by a secretion or export pathway used solely for the export of peptide pheromones that contributes to a conjugation process that results in the union of cellular and genetic information from compatible mating types." [GOC:elh, GOC:jh, GOC:mah]
-is_a: GO:0031139 ! positive regulation of conjugation with cellular fusion
-is_a: GO:0071832 ! peptide pheromone export involved in regulation of conjugation
-
[Term]
id: GO:0071834
name: mating pheromone secretion
@@ -363944,12 +363899,16 @@ is_a: GO:0030072 ! peptide hormone secretion
[Term]
id: GO:0071835
-name: mating pheromone secretion involved in regulation of conjugation
+name: mating pheromone secretion involved in regulation of conjugation with cellular fusion
namespace: biological_process
+alt_id: GO:0071832
def: "The regulated release of a mating pheromone, a peptide hormone that induces a behavioral or physiological response(s) from a responding organism or cell, that regulates the union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms." [GOC:elh, GOC:jh, GOC:mah]
+synonym: "mating pheromone secretion involved in regulation of conjugation" RELATED []
synonym: "mating-type pheromone secretion involved in conjugation" EXACT [GOC:mah, GOC:vw]
+synonym: "peptide pheromone export involved in regulation of conjugation" BROAD []
+is_a: GO:0022414 ! reproductive process
is_a: GO:0071834 ! mating pheromone secretion
-relationship: part_of GO:0000746 ! conjugation
+relationship: part_of GO:0000747 ! conjugation with cellular fusion
[Term]
id: GO:0071836
@@ -364011,7 +363970,7 @@ is_a: GO:0051014 ! actin filament severing
id: GO:0071847
name: TNFSF11-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of tumor necrosis factor ligand superfamily member 11 (TNFSF11) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling, PMID:18606301]
+def: "The series of molecular signals initiated by the binding of tumor necrosis factor ligand superfamily member 11 (TNFSF11) to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:signaling, PMID:18606301]
synonym: "RANKL-mediated signaling pathway" EXACT [GOC:BHF]
synonym: "receptor activator of nuclear factor kappa-B ligand signaling pathway" EXACT [Wikipedia:RANKL]
synonym: "TNF-related activation-induced cytokine-mediated signaling pathway" EXACT [Wikipedia:RANKL]
@@ -364247,7 +364206,7 @@ is_a: GO:0071873 ! response to norepinephrine
id: GO:0071875
name: adrenergic receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of an adrenergic receptor binding to one of its physiological ligands." [GOC:BHF]
+def: "A G protein-coupled receptor signaling pathway initiated by a ligand binding to an adrenergic receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:BHF]
synonym: "adrenergic receptor signalling pathway" EXACT [GOC:mah]
synonym: "adrenoceptor signaling pathway" EXACT [GOC:mah]
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -364300,7 +364259,7 @@ relationship: positively_regulates GO:0071875 ! adrenergic receptor signaling pa
id: GO:0071880
name: adenylate cyclase-activating adrenergic receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of an adrenergic receptor binding to its physiological ligand, where the pathway proceeds with activation of adenylyl cyclase and a subsequent increase in the concentration of cyclic AMP (cAMP)." [GOC:BHF, GOC:mah, GOC:signaling]
+def: "An adenylate cyclase-activating G protein-coupled receptor signaling pathway initiated by a ligand binding to an adrenergic receptor on the surface of the target cell, and ending with the regulation of a downstream cellular process." [GOC:BHF, GOC:mah, GOC:signaling]
synonym: "activation of adenylate cyclase activity by adrenergic receptor signaling pathway" RELATED [GOC:signaling]
synonym: "activation of adenylate cyclase activity by adrenergic receptor signalling pathway" EXACT [GOC:mah]
synonym: "adrenergic receptor, adenylate cyclase activating pathway" EXACT [GOC:mah]
@@ -364312,7 +364271,7 @@ is_a: GO:0071875 ! adrenergic receptor signaling pathway
id: GO:0071881
name: adenylate cyclase-inhibiting adrenergic receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of an adrenergic receptor binding to its physiological ligand, where the pathway proceeds with inhibition of adenylyl cyclase and a subsequent decrease in the concentration of cyclic AMP (cAMP)." [GOC:BHF, GOC:mah, GOC:signaling]
+def: "An adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway initiated by a ligand binding to an adrenergic receptor, and ending with the regulation of a downstream cellular process." [GOC:BHF, GOC:mah, GOC:signaling]
synonym: "adrenergic receptor, adenylate cyclase inhibiting pathway" EXACT [GOC:mah]
synonym: "adrenergic receptor, adenylyl cyclase inhibiting pathway" EXACT [GOC:mah]
synonym: "inhibition of adenylate cyclase activity by adrenergic receptor signaling pathway" RELATED [GOC:signaling]
@@ -364324,7 +364283,7 @@ is_a: GO:0071875 ! adrenergic receptor signaling pathway
id: GO:0071882
name: phospholipase C-activating adrenergic receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of an adrenergic receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent release of inositol trisphosphate (IP3) and diacylglycerol (DAG)." [GOC:BHF, GOC:mah, GOC:signaling]
+def: "A phospholipase C-activating receptor G protein-coupled receptor signaling pathway initiated by ligand binding to an adrenergic receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:BHF, GOC:mah, GOC:signaling]
synonym: "activation of phospholipase C activity by adrenergic receptor signaling pathway" RELATED [GOC:bf]
synonym: "activation of phospholipase C activity by adrenergic receptor signalling pathway" RELATED [GOC:mah]
synonym: "adrenergic receptor, phospholipase C activating pathway" RELATED [GOC:mah]
@@ -364348,7 +364307,9 @@ name: N-terminal protein N-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to the alpha-amino group of the N-terminal amino or imino acid residue of a protein substrate. For example, yeast Tae1p and mammalian family member METTL11A preferentially modify the N-terminal residue of substrates with the N-terminal sequence X-Pro-Lys, where X can be Pro, Ala, or Ser." [PMID:20481588]
synonym: "X-Pro-Lys N-terminal methyltransferase" NARROW [GOC:rn]
+xref: EC:2.1.1.244
is_a: GO:0008276 ! protein methyltransferase activity
+is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
[Term]
id: GO:0071886
@@ -364420,7 +364381,7 @@ relationship: part_of GO:0007596 ! blood coagulation
id: GO:0071893
name: BMP signaling pathway involved in nephric duct formation
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, which contributes to nephric duct formation." [GOC:mah, GOC:mtg_kidney_jan10]
+def: "The series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to its receptor on the surface of a target cell, which contributes to nephric duct formation." [GOC:mah, GOC:mtg_kidney_jan10]
synonym: "BMP signalling pathway involved in nephric duct formation" EXACT [GOC:mah]
is_a: GO:0030509 ! BMP signaling pathway
relationship: part_of GO:0072179 ! nephric duct formation
@@ -364429,7 +364390,7 @@ relationship: part_of GO:0072179 ! nephric duct formation
id: GO:0071894
name: histone H2B conserved C-terminal lysine ubiquitination
namespace: biological_process
-def: "A histone ubiquitination process in which a ubiquitin monomer is added to a conserved lysine residue in the C-terminus of histone H2B. The conserved lysine residue is K119 in fission yeast, K123 in budding yeast, or K120 in mammals." [GOC:mah, GOC:vw]
+def: "A histone ubiquitination process in which a ubiquitin monomer is added to a conserved lysine residue in the C-terminus of histone H2B. The conserved lysine residue is K119 in fission yeast, K123 in budding yeast, and K120 in mammals." [GOC:mah, GOC:vw]
synonym: "budding yeast H2B K123 ubiquitination" NARROW [GOC:vw]
synonym: "fission yeast H2B K119 ubiquitination" NARROW [GOC:vw]
synonym: "mammalian H2B K120 ubiquitination" NARROW [GOC:vw]
@@ -364461,13 +364422,13 @@ is_a: GO:0150105 ! protein localization to cell-cell junction
id: GO:0071897
name: DNA biosynthetic process
namespace: biological_process
-def: "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC:mah]
+def: "The biosynthetic process resulting in the formation of DNA." [GOC:mah]
synonym: "DNA anabolism" EXACT [GOC:mah]
synonym: "DNA biosynthesis" EXACT [GOC:mah]
synonym: "DNA formation" EXACT [GOC:mah]
synonym: "DNA synthesis" EXACT [GOC:mah]
is_a: GO:0006259 ! DNA metabolic process
-is_a: GO:0034645 ! cellular macromolecule biosynthetic process
+is_a: GO:0009059 ! macromolecule biosynthetic process
is_a: GO:0034654 ! nucleobase-containing compound biosynthetic process
[Term]
@@ -364517,7 +364478,6 @@ def: "A process of protein N-linked glycosylation via asparagine in which N-acet
synonym: "protein amino acid N-linked N-acetylglucosaminylation via asparagine" EXACT [GOC:bf]
xref: RESID:AA0151
is_a: GO:0018279 ! protein N-linked glycosylation via asparagine
-is_a: GO:1901135 ! carbohydrate derivative metabolic process
[Term]
id: GO:0071904
@@ -364527,7 +364487,6 @@ def: "A process of protein N-linked glycosylation via asparagine in which N-acet
synonym: "protein amino acid N-linked N-acetylgalactosaminylation via asparagine" EXACT [GOC:bf]
xref: RESID:AA0420
is_a: GO:0018279 ! protein N-linked glycosylation via asparagine
-is_a: GO:1901135 ! carbohydrate derivative metabolic process
[Term]
id: GO:0071905
@@ -364759,7 +364718,7 @@ def: "Any process that stop, prevents or decreases transcription as part of the
synonym: "negative regulation of transcription from RNA polymerase II promoter during G1/S phase of mitotic cell cycle" RELATED [GOC:mah]
synonym: "negative regulation of transcription from RNA polymerase II promoter involved in G1/S transition of mitotic cell cycle" EXACT [GOC:mah]
is_a: GO:0000083 ! regulation of transcription involved in G1/S transition of mitotic cell cycle
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
[Term]
id: GO:0071931
@@ -364769,7 +364728,7 @@ def: "Any process that activates or increases transcription as part of the G1/S
synonym: "positive regulation of transcription from RNA polymerase II promoter during G1/S phase of mitotic cell cycle" RELATED [GOC:mah]
synonym: "positive regulation of transcription from RNA polymerase II promoter involved in G1/S transition of mitotic cell cycle" EXACT [GOC:mah]
is_a: GO:0000083 ! regulation of transcription involved in G1/S transition of mitotic cell cycle
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
[Term]
id: GO:0071932
@@ -364798,7 +364757,6 @@ is_a: GO:0015888 ! thiamine transport
is_a: GO:0035461 ! vitamin transmembrane transport
is_a: GO:0045117 ! azole transmembrane transport
is_a: GO:0072531 ! pyrimidine-containing compound transmembrane transport
-is_a: GO:0098655 ! cation transmembrane transport
[Term]
id: GO:0071935
@@ -364831,12 +364789,14 @@ is_a: GO:0051180 ! vitamin transport
[Term]
id: GO:0071939
-name: vitamin A import
+name: vitamin A import into cell
namespace: biological_process
-def: "The directed movement of vitamin A into a cell or organelle. Vitamin A is any of several retinoid derivatives of beta-carotene, primarily retinol, retinal, or retinoic acid." [GOC:mah, PMID:16011460, PMID:1924551]
+def: "The directed movement of vitamin A from outside of a cell, across the plasma membrane and into the cytosol. Vitamin A is any of several retinoid derivatives of beta-carotene, primarily retinol, retinal, or retinoic acid." [GOC:mah, PMID:16011460, PMID:1924551]
+synonym: "vitamin A import" RELATED []
synonym: "vitamin A uptake" EXACT [GOC:mah, GOC:rs]
is_a: GO:0035461 ! vitamin transmembrane transport
is_a: GO:0071938 ! vitamin A transport
+is_a: GO:0140354 ! lipid import into cell
[Term]
id: GO:0071940
@@ -364856,6 +364816,7 @@ def: "A nitrogen compound metabolic process that contributes to the nitrogen cyc
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pombe
+subset: prokaryote_subset
xref: Wikipedia:Nitrogen_cycle
is_a: GO:0006807 ! nitrogen compound metabolic process
@@ -364877,7 +364838,7 @@ is_a: GO:0090575 ! RNA polymerase II transcription regulator complex
id: GO:0071944
name: cell periphery
namespace: cellular_component
-def: "The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures." [GOC:mah]
+def: "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." [GOC:pdt]
subset: goslim_flybase_ribbon
is_a: GO:0110165 ! cellular anatomical entity
@@ -364905,7 +364866,7 @@ name: protein deubiquitination involved in ubiquitin-dependent protein catabolic
namespace: biological_process
def: "The removal of one or more ubiquitin groups from a protein as part of a process of ubiquitin-dependent protein catabolism." [GOC:mah]
is_a: GO:0016579 ! protein deubiquitination
-is_a: GO:0051603 ! proteolysis involved in cellular protein catabolic process
+is_a: GO:0051603 ! proteolysis involved in protein catabolic process
relationship: part_of GO:0006511 ! ubiquitin-dependent protein catabolic process
[Term]
@@ -365256,8 +365217,6 @@ synonym: "Rag GEF" EXACT []
is_a: GO:0032045 ! guanyl-nucleotide exchange factor complex
is_a: GO:0098796 ! membrane protein complex
relationship: part_of GO:0005774 ! vacuolar membrane
-relationship: part_of GO:0031902 ! late endosome membrane
-relationship: part_of GO:0045121 ! membrane raft
[Term]
id: GO:0071987
@@ -365354,7 +365313,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of polysacc
synonym: "extracellular polysaccharide breakdown" EXACT [GOC:mah]
synonym: "extracellular polysaccharide catabolism" EXACT [GOC:mah]
synonym: "extracellular polysaccharide degradation" EXACT [GOC:mah]
-is_a: GO:0044247 ! cellular polysaccharide catabolic process
+is_a: GO:0000272 ! polysaccharide catabolic process
is_a: GO:0046379 ! extracellular polysaccharide metabolic process
[Term]
@@ -365367,8 +365326,8 @@ synonym: "ascus endolysis" RELATED [GOC:vw]
synonym: "extracellular polysaccharide breakdown involved in ascospore release from ascus" EXACT [GOC:mah]
synonym: "extracellular polysaccharide catabolism involved in ascospore release from ascus" EXACT [GOC:mah]
synonym: "extracellular polysaccharide degradation involved in ascospore release from ascus" EXACT [GOC:mah]
+is_a: GO:0022414 ! reproductive process
is_a: GO:0071999 ! extracellular polysaccharide catabolic process
-is_a: GO:1903046 ! meiotic cell cycle process
relationship: part_of GO:0071998 ! ascospore release from ascus
[Term]
@@ -365380,7 +365339,6 @@ subset: gocheck_do_not_annotate
synonym: "urinary system development" BROAD [GOC:yaf]
synonym: "urinary tract development" BROAD [GOC:yaf, PMID:17881463]
is_a: GO:0048731 ! system development
-relationship: part_of GO:0001655 ! urogenital system development
[Term]
id: GO:0072002
@@ -365497,12 +365455,12 @@ is_a: GO:0072080 ! nephron tubule development
[Term]
id: GO:0072015
-name: glomerular visceral epithelial cell development
+name: podocyte development
namespace: biological_process
def: "The process whose specific outcome is the progression of a glomerular visceral epithelial cell over time, from its formation to the mature structure. A glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells." [GOC:mtg_kidney_jan10]
-synonym: "podocyte development" RELATED [GOC:mtg_kidney_jan10]
+synonym: "glomerular visceral epithelial cell development" EXACT []
is_a: GO:0072310 ! glomerular epithelial cell development
-relationship: part_of GO:0072112 ! glomerular visceral epithelial cell differentiation
+relationship: part_of GO:0072112 ! podocyte differentiation
[Term]
id: GO:0072016
@@ -365788,6 +365746,7 @@ id: GO:0072048
name: renal system pattern specification
namespace: biological_process
def: "Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate into the anatomical structures of the renal system." [GOC:mtg_kidney_jan10]
+subset: gocheck_do_not_annotate
synonym: "renal system pattern formation" RELATED [GOC:mtg_kidney_jan10]
is_a: GO:0007389 ! pattern specification process
relationship: part_of GO:0072001 ! renal system development
@@ -366190,7 +366149,7 @@ relationship: negatively_regulates GO:0060681 ! branch elongation involved in ur
id: GO:0072097
name: negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor resulting in the reduction of the frequency, rate or extent of branch elongation involved in ureteric bud branching, the growth of a branch of the ureteric bud along its axis." [GOC:mtg_kidney_jan10]
+def: "The series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor resulting in the reduction of the frequency, rate or extent of branch elongation involved in ureteric bud branching, the growth of a branch of the ureteric bud along its axis." [GOC:mtg_kidney_jan10]
synonym: "negative regulation of branch elongation involved in ureteric bud branching by BMP signalling pathway" EXACT [GOC:mah]
is_a: GO:0030509 ! BMP signaling pathway
is_a: GO:0072096 ! negative regulation of branch elongation involved in ureteric bud branching
@@ -366229,7 +366188,7 @@ is_a: GO:0072099 ! anterior/posterior pattern specification involved in ureteric
id: GO:0072101
name: specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway
namespace: biological_process
-def: "A series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that results in the establishment of the ureteric bud such that there is a similar arrangement in form and relationship of parts along its anterior/posterior axis." [GOC:mtg_kidney_jan10]
+def: "The series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that results in the establishment of the ureteric bud such that there is a similar arrangement in form and relationship of parts along its anterior/posterior axis." [GOC:mtg_kidney_jan10]
synonym: "specification of ureteric bud anterior/posterior asymmetry by BMP signaling pathway" EXACT [GOC:dph]
synonym: "specification of ureteric bud anterior/posterior symmetry by BMP signalling pathway" EXACT [GOC:mah]
is_a: GO:0030509 ! BMP signaling pathway
@@ -366325,10 +366284,10 @@ relationship: part_of GO:0001822 ! kidney development
[Term]
id: GO:0072112
-name: glomerular visceral epithelial cell differentiation
+name: podocyte differentiation
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires specialized features of a glomerular visceral epithelial cell. A glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells." [GOC:mtg_kidney_jan10]
-synonym: "podocyte differentiation" RELATED [GOC:mtg_kidney_jan10]
+synonym: "glomerular visceral epithelial cell differentiation" EXACT []
is_a: GO:0061318 ! renal filtration cell differentiation
is_a: GO:0072311 ! glomerular epithelial cell differentiation
@@ -366643,13 +366602,13 @@ relationship: part_of GO:0030855 ! epithelial cell differentiation
[Term]
id: GO:0072149
-name: glomerular visceral epithelial cell fate commitment
+name: podocyte cell fate commitment
namespace: biological_process
def: "The process in which the developmental fate of a cell becomes restricted such that it will develop into a glomerular visceral epithelial cell. A glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells." [GOC:mtg_kidney_jan10]
-synonym: "podocyte cell fate commitment" RELATED [GOC:mtg_kidney_jan10]
+synonym: "glomerular visceral epithelial cell fate commitment" EXACT []
is_a: GO:0072148 ! epithelial cell fate commitment
is_a: GO:0072314 ! glomerular epithelial cell fate commitment
-relationship: part_of GO:0072112 ! glomerular visceral epithelial cell differentiation
+relationship: part_of GO:0072112 ! podocyte differentiation
[Term]
id: GO:0072150
@@ -366981,6 +366940,7 @@ id: GO:0072189
name: ureter development
namespace: biological_process
def: "The process whose specific outcome is the progression of the ureter over time, from its formation to the mature structure. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder or from the Malpighian tubule to the hindgut." [GOC:mtg_kidney_jan10]
+is_a: GO:0035295 ! tube development
is_a: GO:0048513 ! animal organ development
relationship: part_of GO:0072001 ! renal system development
@@ -367182,11 +367142,11 @@ relationship: part_of GO:0001656 ! metanephros development
[Term]
id: GO:0072212
-name: regulation of transcription from RNA polymerase II promoter involved in metanephros development
+name: obsolete regulation of transcription from RNA polymerase II promoter involved in metanephros development
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the branching morphogenesis by which the metanephros progresses from its initial formation to the mature state." [GOC:mtg_kidney_jan10]
-is_a: GO:0060994 ! regulation of transcription from RNA polymerase II promoter involved in kidney development
-relationship: part_of GO:0001656 ! metanephros development
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the branching morphogenesis by which the metanephros progresses from its initial formation to the mature state." [GOC:mtg_kidney_jan10]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0072213
@@ -367499,32 +367459,32 @@ relationship: part_of GO:0072245 ! metanephric glomerular parietal epithelial ce
[Term]
id: GO:0072248
-name: metanephric glomerular visceral epithelial cell differentiation
+name: metanephric podocyte differentiation
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires specialized features of a metanephric glomerular visceral epithelial cell. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros." [GOC:mtg_kidney_jan10]
-synonym: "metanephric podocyte differentiation" RELATED [GOC:mtg_kidney_jan10]
-is_a: GO:0072112 ! glomerular visceral epithelial cell differentiation
+synonym: "metanephric glomerular visceral epithelial cell differentiation" EXACT []
+is_a: GO:0072112 ! podocyte differentiation
is_a: GO:0072312 ! metanephric glomerular epithelial cell differentiation
[Term]
id: GO:0072249
-name: metanephric glomerular visceral epithelial cell development
+name: metanephric podocyte development
namespace: biological_process
def: "The process whose specific outcome is the progression of a metanephric glomerular visceral epithelial cell over time, from its formation to the mature structure. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros." [GOC:mtg_kidney_jan10]
-synonym: "metanephric podocyte development" RELATED [GOC:mtg_kidney_jan10]
-is_a: GO:0072015 ! glomerular visceral epithelial cell development
+synonym: "metanephric glomerular visceral epithelial cell development" EXACT []
+is_a: GO:0072015 ! podocyte development
is_a: GO:0072313 ! metanephric glomerular epithelial cell development
-relationship: part_of GO:0072248 ! metanephric glomerular visceral epithelial cell differentiation
+relationship: part_of GO:0072248 ! metanephric podocyte differentiation
[Term]
id: GO:0072250
-name: metanephric glomerular visceral epithelial cell fate commitment
+name: metanephric podocyte cell fate commitment
namespace: biological_process
def: "The process in which the developmental fate of a cell becomes restricted such that it will develop into a metanephric glomerular visceral epithelial cell. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros." [GOC:mtg_kidney_jan10]
-synonym: "metanephric podocyte cell fate commitment" RELATED [GOC:mtg_kidney_jan10]
-is_a: GO:0072149 ! glomerular visceral epithelial cell fate commitment
+synonym: "metanephric glomerular visceral epithelial cell fate commitment" EXACT []
+is_a: GO:0072149 ! podocyte cell fate commitment
is_a: GO:0072315 ! metanephric glomerular epithelial cell fate commitment
-relationship: part_of GO:0072248 ! metanephric glomerular visceral epithelial cell differentiation
+relationship: part_of GO:0072248 ! metanephric podocyte differentiation
[Term]
id: GO:0072251
@@ -368246,7 +368206,7 @@ is_a: GO:0035556 ! intracellular signal transduction
id: GO:0072332
name: intrinsic apoptotic signaling pathway by p53 class mediator
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, and ends when the execution phase of apoptosis is triggered." [GOC:mah, GOC:mtg_apoptosis]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, and ends when the execution phase of apoptosis is triggered." [GOC:mah, GOC:mtg_apoptosis]
synonym: "intrinsic apoptotic signaling pathway by signal transduction by p53 class mediator" EXACT []
synonym: "signal transduction by p53 class mediator resulting in induction of apoptosis" RELATED []
is_a: GO:0072331 ! signal transduction by p53 class mediator
@@ -368274,7 +368234,6 @@ synonym: "UDP-galactose membrane transport" EXACT []
synonym: "UDP-galactose transport" RELATED []
is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0072335
@@ -368312,38 +368271,44 @@ is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0072338
-name: cellular lactam metabolic process
+name: lactam metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving lactams, any cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring." [GOC:mah]
+synonym: "cellular lactam metabolic process" EXACT []
synonym: "cellular lactam metabolism" EXACT [GOC:mah]
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0044281 ! small molecule metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
+is_a: GO:1901360 ! organic cyclic compound metabolic process
+is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
id: GO:0072339
-name: cellular lactam biosynthetic process
+name: lactam biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of lactams, any cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring." [GOC:mah]
synonym: "cellular lactam anabolism" EXACT [GOC:mah]
synonym: "cellular lactam biosynthesis" EXACT [GOC:mah]
+synonym: "cellular lactam biosynthetic process" EXACT []
synonym: "cellular lactam formation" EXACT [GOC:mah]
synonym: "cellular lactam synthesis" EXACT [GOC:mah]
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0043604 ! amide biosynthetic process
-is_a: GO:0072338 ! cellular lactam metabolic process
+is_a: GO:0072338 ! lactam metabolic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+is_a: GO:1901566 ! organonitrogen compound biosynthetic process
[Term]
id: GO:0072340
-name: cellular lactam catabolic process
+name: lactam catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of lactams, any cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring." [GOC:mah]
synonym: "cellular lactam breakdown" EXACT [GOC:mah]
+synonym: "cellular lactam catabolic process" EXACT []
synonym: "cellular lactam catabolism" EXACT [GOC:mah]
synonym: "cellular lactam degradation" EXACT [GOC:mah]
-is_a: GO:0043605 ! cellular amide catabolic process
is_a: GO:0046700 ! heterocycle catabolic process
-is_a: GO:0072338 ! cellular lactam metabolic process
+is_a: GO:0072338 ! lactam metabolic process
[Term]
id: GO:0072341
@@ -368451,27 +368416,32 @@ is_a: GO:0072350 ! tricarboxylic acid metabolic process
[Term]
id: GO:0072353
-name: cellular age-dependent response to reactive oxygen species
+name: obsolete cellular age-dependent response to reactive oxygen species
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of reactive oxygen species, where the change varies according to the age of the cell or organism." [GOC:mah]
-is_a: GO:0001315 ! age-dependent response to reactive oxygen species
-is_a: GO:0034614 ! cellular response to reactive oxygen species
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of reactive oxygen species, where the change varies according to the age of the cell or organism." [GOC:mah]
+comment: This term was obsoleted because it represents a phenotype.
+is_obsolete: true
+consider: GO:0034599
[Term]
id: GO:0072354
-name: histone kinase activity (H3-T3 specific)
+name: histone H3T3 kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to the threonine-3 residue of the N-terminal tail of histone H3." [GOC:mah]
+def: "Catalysis of the reaction: histone H3-threonine (position 3) + ATP = histone H3-phosphothreonine (position 3) + ADP. This reaction is the addition of a phosphate group to the threonine residue at position 3 of histone H3." [GOC:mah]
+synonym: "histone H3-T3 kinase activity" EXACT []
+synonym: "histone kinase activity (H3-T3 specific)" EXACT []
synonym: "histone threonine kinase activity (H3-T3 specific)" EXACT [GOC:mah]
synonym: "histone-threonine kinase activity (H3-T3 specific)" EXACT [GOC:mah]
-is_a: GO:0035184 ! histone threonine kinase activity
+is_a: GO:0140996 ! histone H3 kinase activity
[Term]
id: GO:0072355
-name: histone H3-T3 phosphorylation
+name: obsolete histone H3-T3 phosphorylation
namespace: biological_process
-def: "The modification of histone H3 by the addition of an phosphate group to a threonine residue at position 3 of the histone." [GOC:mah]
-is_a: GO:0035405 ! histone-threonine phosphorylation
+def: "OBSOLETE. The modification of histone H3 by the addition of an phosphate group to a threonine residue at position 3 of the histone." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0035403
[Term]
id: GO:0072356
@@ -368490,7 +368460,7 @@ id: GO:0072357
name: PTW/PP1 phosphatase complex
namespace: cellular_component
def: "A protein serine/threonine phosphatase complex that contains a catalytic subunit (PPP1CA, PPP1CB or PPP1CC) and the regulatory subunits PPP1R10 (PNUTS), TOX4 and WDR82, and plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase." [GOC:mah, PMID:20516061]
-is_a: GO:0008287 ! protein serine/threonine phosphatase complex
+is_a: GO:0000164 ! protein phosphatase type 1 complex
[Term]
id: GO:0072359
@@ -368595,22 +368565,25 @@ is_obsolete: true
[Term]
id: GO:0072370
-name: histone H2A-S121 phosphorylation
+name: obsolete histone H2A-S121 phosphorylation
namespace: biological_process
-def: "The modification of histone H2A by the addition of an phosphate group to a serine residue at position 121 of the histone." [GOC:mah, PMID:19965387]
+def: "OBSOLETE. The modification of histone H2A by the addition of an phosphate group to a serine residue at position 121 of the histone." [GOC:mah, PMID:19965387]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H2A phosphorylation at S121" EXACT [GOC:mah]
synonym: "histone H2AS121 phosphorylation" EXACT [GOC:mah]
-is_a: GO:0035404 ! histone-serine phosphorylation
-is_a: GO:1990164 ! histone H2A phosphorylation
+is_obsolete: true
+consider: GO:0072371
[Term]
id: GO:0072371
-name: histone kinase activity (H2A-S121 specific)
+name: histone H2AS121 kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to the serine-121 residue of the N-terminal tail of histone H2A." [GOC:mah, PMID:19965387]
+def: "Catalysis of the reaction: histone H2A-serine (position 121) + ATP = histone H2A-phosphoserine (position 121) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 121 of histone H2A." [GOC:mah, PMID:19965387]
+synonym: "histone H2A-S121 kinase activity" EXACT []
+synonym: "histone kinase activity (H2A-S121 specific)" EXACT []
synonym: "histone serine kinase activity (H2A-S121 specific)" EXACT [GOC:mah]
synonym: "histone-serine kinase activity (H2A-S121 specific)" EXACT [GOC:mah]
-is_a: GO:0035174 ! histone serine kinase activity
+is_a: GO:0140995 ! histone H2A kinase activity
[Term]
id: GO:0072373
@@ -368640,11 +368613,10 @@ is_a: GO:0007613 ! memory
id: GO:0072376
name: protein activation cascade
namespace: biological_process
-def: "A response to a stimulus that consists of a sequential series of modifications to a set of proteins where the product of one reaction acts catalytically in the following reaction. The magnitude of the response is typically amplified at each successive step in the cascade. Modifications typically include proteolysis or covalent modification, and may also include binding events." [GOC:add, GOC:mah, GOC:pde]
+def: "A sequential series of modifications to a set of proteins where the product of one reaction catalyzes the following reaction, ultimately leading to the generation of a mature protein. Modifications typically include proteolysis or covalent modification, and may also include binding events." [GOC:add, GOC:mah, GOC:pde]
synonym: "protein activation pathway" EXACT [GOC:add]
synonym: "protein activitory cascade" EXACT [GOC:add]
-is_a: GO:0019538 ! protein metabolic process
-is_a: GO:0050896 ! response to stimulus
+is_a: GO:0051604 ! protein maturation
[Term]
id: GO:0072377
@@ -369424,7 +369396,7 @@ def: "The process in which methylammonium is transported across a membrane." [GO
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "methylammonium membrane transport" EXACT []
is_a: GO:0015843 ! methylammonium transport
-is_a: GO:0098655 ! cation transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0072490
@@ -369528,75 +369500,75 @@ consider: GO:0030522
[Term]
id: GO:0072501
-name: cellular divalent inorganic anion homeostasis
+name: obsolete cellular divalent inorganic anion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of divalent inorganic anions at the level of a cell." [GOC:mah]
-comment: Note that this term was split from 'cellular di-, tri-valent inorganic anion homeostasis ; GO:0030319' (sibling term 'cellular trivalent inorganic anion homeostasis' ; GO:0072502').
-is_a: GO:0030002 ! cellular anion homeostasis
-is_a: GO:0072505 ! divalent inorganic anion homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of divalent inorganic anions at the level of a cell." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0030002
[Term]
id: GO:0072502
-name: cellular trivalent inorganic anion homeostasis
+name: obsolete cellular trivalent inorganic anion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of trivalent inorganic anions at the level of a cell." [GOC:mah]
-comment: Note that this term was split from 'cellular di-, tri-valent inorganic anion homeostasis ; GO:0030319' (sibling term 'cellular divalent inorganic anion homeostasis' ; GO:0072501').
-is_a: GO:0030002 ! cellular anion homeostasis
-is_a: GO:0072506 ! trivalent inorganic anion homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of trivalent inorganic anions at the level of a cell." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0030002
[Term]
id: GO:0072503
-name: cellular divalent inorganic cation homeostasis
+name: obsolete cellular divalent inorganic cation homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of divalent cations at the level of a cell." [GOC:mah]
-comment: Note that this term was split from 'cellular di-, tri-valent inorganic cation homeostasis ; GO:0030005' (sibling term 'cellular trivalent inorganic cation homeostasis' ; GO:0072504').
-is_a: GO:0030003 ! cellular cation homeostasis
-is_a: GO:0072507 ! divalent inorganic cation homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of divalent cations at the level of a cell." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0030003
[Term]
id: GO:0072504
-name: cellular trivalent inorganic cation homeostasis
+name: obsolete cellular trivalent inorganic cation homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of trivalent cations at the level of a cell." [GOC:mah]
-comment: Note that this term was split from 'cellular di-, tri-valent inorganic cation homeostasis ; GO:0030005' (sibling term 'cellular divalent inorganic cation homeostasis' ; GO:0072503').
-is_a: GO:0030003 ! cellular cation homeostasis
-is_a: GO:0072508 ! trivalent inorganic cation homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of trivalent cations at the level of a cell." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0030003
[Term]
id: GO:0072505
-name: divalent inorganic anion homeostasis
+name: obsolete divalent inorganic anion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of divalent inorganic anions within an organism or cell." [GOC:mah]
-comment: Note that this term was split from 'di-, tri-valent inorganic anion homeostasis ; GO:0055061' (sibling term 'trivalent inorganic anion homeostasis' ; GO:0072506').
-is_a: GO:0055081 ! anion homeostasis
-is_a: GO:0098771 ! inorganic ion homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of divalent inorganic anions within an organism or cell." [GOC:mah]
+comment: This term was obsoleted beacuse it represents an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0055081
[Term]
id: GO:0072506
-name: trivalent inorganic anion homeostasis
+name: obsolete trivalent inorganic anion homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of trivalent inorganic anions within an organism or cell." [GOC:mah]
-comment: Note that this term was split from 'di-, tri-valent inorganic anion homeostasis ; GO:0055061' (sibling term 'divalent inorganic anion homeostasis' ; GO:0072505').
-is_a: GO:0055081 ! anion homeostasis
-is_a: GO:0098771 ! inorganic ion homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of trivalent inorganic anions within an organism or cell." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0055081
[Term]
id: GO:0072507
-name: divalent inorganic cation homeostasis
+name: obsolete divalent inorganic cation homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of divalent cations within an organism or cell." [GOC:mah]
-comment: Note that this term was split from 'di-, tri-valent inorganic cation homeostasis ; GO:0055066' (sibling term 'trivalent inorganic cation homeostasis' ; GO:0072508').
-is_a: GO:0055080 ! cation homeostasis
-is_a: GO:0098771 ! inorganic ion homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of divalent cations within an organism or cell." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0055080
[Term]
id: GO:0072508
-name: trivalent inorganic cation homeostasis
+name: obsolete trivalent inorganic cation homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of trivalent cations within an organism or cell." [GOC:mah]
-comment: Note that this term was split from 'di-, tri-valent inorganic cation homeostasis ; GO:0055066' (sibling term 'divalent inorganic cation homeostasis' ; GO:0072507').
-is_a: GO:0055080 ! cation homeostasis
-is_a: GO:0098771 ! inorganic ion homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of trivalent cations within an organism or cell." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0055080
[Term]
id: GO:0072513
@@ -369853,7 +369825,6 @@ namespace: cellular_component
def: "A protein complex that binds interleukin-23 and that consists of, at a minimum, a dimeric interleukin and its two receptor subunits as well as optional additional kinase subunits." [GOC:BHF, GOC:mah, PMID:12023369]
synonym: "IL-23 receptor complex" EXACT [GOC:mah]
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0072537
@@ -369895,10 +369866,10 @@ relationship: part_of GO:0072539 ! T-helper 17 cell differentiation
id: GO:0072541
name: peroxynitrite reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 R-SH + ONOO- = R-SS-R + NO2- + H2O." [GOC:rs, PMID:11001062]
+def: "Catalysis of the reaction: [protein]-dithiol + ONOO- = [protein]-disulfide + NO2- + H2O." [GOC:rs, PMID:11001062]
comment: Note that this activity is usually associated in vivo with an NADPH-dependent disulfide reductase activity, so that catalysis of the reduction of peroxynitrite to nitrite involves the possible creation of oxygen or water, using NADPH as reduction equivalent.
synonym: "peroxynitritase activity" EXACT [GOC:rs]
-is_a: GO:0051920 ! peroxiredoxin activity
+is_a: GO:0004601 ! peroxidase activity
[Term]
id: GO:0072542
@@ -369906,7 +369877,7 @@ name: protein phosphatase activator activity
namespace: molecular_function
alt_id: GO:0071862
alt_id: GO:0072543
-def: "Binds to and increases the activity of a protein phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a protein substrate molecule." [GOC:mah]
+def: "Binds to and increases the activity of a protein phosphatase." [GOC:mah]
synonym: "protein phosphatase 2 activator activity" NARROW [GOC:dph, GOC:rl]
synonym: "protein phosphatase type 1 activator activity" NARROW []
synonym: "protein phosphatase type 2A activator activity" NARROW []
@@ -369919,7 +369890,6 @@ name: L-DOPA binding
namespace: molecular_function
def: "Binding to L-DOPA, the modified amino acid (2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid." [GOC:mah, GOC:vw]
is_a: GO:0016597 ! amino acid binding
-is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0072341 ! modified amino acid binding
is_a: GO:0097159 ! organic cyclic compound binding
@@ -369942,7 +369912,7 @@ synonym: "endoplasmic reticulum membrane protein complex" BROAD []
synonym: "ER membrane protein complex" BROAD [GOC:mah]
is_a: GO:0098796 ! membrane protein complex
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
-relationship: part_of GO:0030176 ! integral component of endoplasmic reticulum membrane
+relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
[Term]
id: GO:0072547
@@ -370024,7 +369994,7 @@ id: GO:0072557
name: IPAF inflammasome complex
namespace: cellular_component
def: "An inflammasome complex that consists of three components, IPAF, NAIP and caspase-1, and includes among its functions the sensing of flagellin derived from Legionella pneumophila, Salmonella typhimurium, Pseudomonas aeruginosa and Shigella flexneri." [GOC:add, GOC:BHF, GOC:vp, PMID:20303873]
-is_a: GO:0061702 ! inflammasome complex
+is_a: GO:0061702 ! canonical inflammasome complex
[Term]
id: GO:0072558
@@ -370032,7 +370002,7 @@ name: NLRP1 inflammasome complex
namespace: cellular_component
def: "An inflammasome complex that consists of two components, NLRP1 (NALP1) and caspase-1 or caspase-5. The exact mechanisms of NLRP1 activation remain obscure, but potassium ion efflux appears to be essential." [GOC:add, GOC:BHF, GOC:vp, PMID:20303873]
synonym: "NALP1 inflammasome complex" EXACT []
-is_a: GO:0061702 ! inflammasome complex
+is_a: GO:0061702 ! canonical inflammasome complex
[Term]
id: GO:0072559
@@ -370040,7 +370010,7 @@ name: NLRP3 inflammasome complex
namespace: cellular_component
def: "An inflammasome complex that consists of three components, NLRP3 (NALP3), PYCARD and caspase-1. It is activated upon exposure to whole pathogens, as well as a number of structurally diverse pathogen- and danger-associated molecular patterns (PAMPs and DAMPs) and environmental irritants. Whole pathogens demonstrated to activate the NLRP3 inflammasome complex include the fungi Candida albicans and Saccharomyces cerevisiae, bacteria that produce pore-forming toxins, including Listeria monocytogenes and Staphylococcus aureus, and viruses such as Sendai virus, adenovirus, and influenza virus." [GOC:add, GOC:BHF, GOC:vp, PMID:20303873]
synonym: "NALP3 inflammasome complex" EXACT []
-is_a: GO:0061702 ! inflammasome complex
+is_a: GO:0061702 ! canonical inflammasome complex
[Term]
id: GO:0072560
@@ -370226,7 +370196,8 @@ id: GO:0072582
name: 17-beta-hydroxysteroid dehydrogenase (NADP+) activity
namespace: molecular_function
def: "Catalysis of the reaction: a 17-beta-hydroxysteroid + NADP+ = a 17-oxosteroid + NADPH + H+." [GOC:kad, PMID:17074428]
-is_a: GO:0004303 ! estradiol 17-beta-dehydrogenase activity
+xref: RHEA:69284
+is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0072583
@@ -370571,9 +370542,10 @@ id: GO:0072657
name: protein localization to membrane
namespace: biological_process
def: "A process in which a protein is transported to, or maintained in, a specific location in a membrane." [GOC:mah]
+subset: prokaryote_subset
synonym: "protein localisation in membrane" EXACT [GOC:mah]
synonym: "protein localization in membrane" EXACT []
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
is_a: GO:0051668 ! localization within membrane
[Term]
@@ -370677,6 +370649,7 @@ def: "A protein complex that catalyzes the ligation of cleaved pre-tRNAs by dire
synonym: "tRNA splicing ligase complex" EXACT [GOC:mah]
xref: MetaCyc:ENTMULTI-CPLX
is_a: GO:0140535 ! intracellular protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:0072670
@@ -370820,7 +370793,7 @@ def: "Endonucleolytic cleavage of the 3'-end of the pre-tRNA as part of the proc
synonym: "mitochondrial endonucleolytic tRNA 3'-end cleavage" EXACT [GOC:mah]
synonym: "mitochondrial endonucleolytic tRNA 3'-trailer cleavage" RELATED [GOC:mah]
synonym: "mitochondrial tRNA 3'-end cleavage, endonucleolytic" EXACT [GOC:mah]
-is_a: GO:0000963 ! mitochondrial RNA processing
+is_a: GO:0000965 ! mitochondrial RNA 3'-end processing
is_a: GO:0034414 ! tRNA 3'-trailer cleavage, endonucleolytic
[Term]
@@ -371003,6 +370976,8 @@ name: response to sodium dodecyl sulfate
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a sodium dodecyl sulfate (SDS) stimulus." [GOC:mah]
synonym: "response to SDS" EXACT [CHEBI:8984, GOC:mah]
+is_a: GO:0010033 ! response to organic substance
+is_a: GO:1901700 ! response to oxygen-containing compound
is_a: GO:1902074 ! response to salt
[Term]
@@ -371013,6 +370988,7 @@ def: "Any process that results in a change in state or activity of a cell (in te
synonym: "cellular response to SDS" EXACT [CHEBI:8984, GOC:mah]
is_a: GO:0071310 ! cellular response to organic substance
is_a: GO:0072706 ! response to sodium dodecyl sulfate
+is_a: GO:1901701 ! cellular response to oxygen-containing compound
is_a: GO:1902075 ! cellular response to salt
[Term]
@@ -371178,22 +371154,21 @@ is_a: GO:1901701 ! cellular response to oxygen-containing compound
[Term]
id: GO:0072726
-name: response to CCCP
+name: obsolete response to CCCP
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a CCCP stimulus." [GOC:mah]
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a CCCP stimulus." [GOC:mah]
+comment: This term is out of scope for GO.
synonym: "response to carbonyl cyanide m-chlorophenyl hydrazone" EXACT [CHEBI:3259, GOC:mah]
-is_a: GO:0010243 ! response to organonitrogen compound
-is_a: GO:0014070 ! response to organic cyclic compound
+is_obsolete: true
[Term]
id: GO:0072727
-name: cellular response to CCCP
+name: obsolete cellular response to CCCP
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a CCCP stimulus." [GOC:mah]
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a CCCP stimulus." [GOC:mah]
+comment: This term is out of scope for GO.
synonym: "cellular response to carbonyl cyanide m-chlorophenyl hydrazone" EXACT [CHEBI:3259, GOC:mah]
-is_a: GO:0071407 ! cellular response to organic cyclic compound
-is_a: GO:0071417 ! cellular response to organonitrogen compound
-is_a: GO:0072726 ! response to CCCP
+is_obsolete: true
[Term]
id: GO:0072728
@@ -371316,7 +371291,7 @@ name: protein localization to cell division site
namespace: biological_process
def: "A cellular protein localization process in which a protein is transported to, or maintained at, the site of cell division." [GOC:mah, PMID:19756689]
synonym: "protein localisation to cell division site" EXACT [GOC:mah]
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
[Term]
id: GO:0072742
@@ -371380,8 +371355,10 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tacrolimus (FK506) stimulus." [GOC:mah]
synonym: "cellular response to FK506" EXACT [CHEBI:61057]
synonym: "cellular response to tacrolimus hydrate" EXACT [CHEBI:61057]
-is_a: GO:0070887 ! cellular response to chemical stimulus
+is_a: GO:0071407 ! cellular response to organic cyclic compound
+is_a: GO:0071417 ! cellular response to organonitrogen compound
is_a: GO:1901327 ! response to tacrolimus
+is_a: GO:1901701 ! cellular response to oxygen-containing compound
[Term]
id: GO:0072749
@@ -371428,8 +371405,8 @@ id: GO:0072753
name: cellular response to glutathione
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glutathione stimulus." [GOC:mah]
+is_a: GO:0070887 ! cellular response to chemical stimulus
is_a: GO:1901370 ! response to glutathione
-is_a: GO:1901653 ! cellular response to peptide
[Term]
id: GO:0072754
@@ -371441,13 +371418,11 @@ is_a: GO:1901560 ! response to purvalanol A
[Term]
id: GO:0072755
-name: cellular response to benomyl
+name: obsolete cellular response to benomyl
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a benomyl stimulus." [GOC:mah]
-is_a: GO:0071407 ! cellular response to organic cyclic compound
-is_a: GO:0071417 ! cellular response to organonitrogen compound
-is_a: GO:1901561 ! response to benomyl
-is_a: GO:1901701 ! cellular response to oxygen-containing compound
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a benomyl stimulus." [GOC:mah]
+comment: This term is out of scope for GO.
+is_obsolete: true
[Term]
id: GO:0072756
@@ -371456,6 +371431,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a paraquat stimulus." [GOC:mah]
is_a: GO:0071310 ! cellular response to organic substance
is_a: GO:1901562 ! response to paraquat
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0072757
@@ -371604,7 +371580,7 @@ namespace: biological_process
def: "The attachment of a spore of the symbiont to its host via adhesion molecules, general stickiness etc. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
comment: Note that this term should not be used to annotate gene products of the host. It should only be used to annotate those gene products from the symbiont involved in this process.
synonym: "adhesion of symbiont spore to host during symbiotic interaction" EXACT []
-is_a: GO:0044406 ! adhesion of symbiont to host
+is_a: GO:0044650 ! adhesion of symbiont to host cell
[Term]
id: GO:0075009
@@ -371773,39 +371749,36 @@ relationship: part_of GO:0075016 ! appressorium formation
[Term]
id: GO:0075026
-name: regulation of appressorium initiation
+name: obsolete regulation of appressorium initiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of symbiont appressorium initiation." [GOC:pamgo_curators]
-comment: Note that this term should not be used to annotate gene products of the host. It should only be used to annotate those gene products from the symbiont involved in this process.
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of symbiont appressorium initiation." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a phenotype.
synonym: "regulation of appressorium initiation on or near host" RELATED []
synonym: "regulation of initiation of appressorium on or near host" EXACT []
-is_a: GO:0044145 ! modulation of formation of structure involved in a symbiotic process
-is_a: GO:0075017 ! regulation of appressorium formation
-relationship: regulates GO:0075025 ! initiation of appressorium formation
+is_obsolete: true
+consider: GO:0075017
[Term]
id: GO:0075027
-name: positive regulation of appressorium initiation
+name: obsolete positive regulation of appressorium initiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of symbiont appressorium initiation." [GOC:pamgo_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of symbiont appressorium initiation." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a phenotype.
synonym: "positive regulation of appressorium initiation on or near host" RELATED []
synonym: "positive regulation of initiation of appressorium on or near host" EXACT []
-is_a: GO:0044149 ! positive regulation of formation of structure involved in a symbiotic process
-is_a: GO:0075018 ! positive regulation of appressorium formation
-is_a: GO:0075026 ! regulation of appressorium initiation
-relationship: positively_regulates GO:0075025 ! initiation of appressorium formation
+is_obsolete: true
+consider: GO:0075018
[Term]
id: GO:0075028
-name: negative regulation of appressorium initiation
+name: obsolete negative regulation of appressorium initiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent symbiont appressorium initiation." [GOC:pamgo_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent symbiont appressorium initiation." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a phenotype.
synonym: "negative regulation of appressorium initiation on or near host" RELATED []
synonym: "negative regulation of initiation of appressorium on or near host" EXACT []
-is_a: GO:0044147 ! negative regulation of formation of structure involved in a symbiotic process
-is_a: GO:0075019 ! negative regulation of appressorium formation
-is_a: GO:0075026 ! regulation of appressorium initiation
-relationship: negatively_regulates GO:0075025 ! initiation of appressorium formation
+is_obsolete: true
+consider: GO:0075019
[Term]
id: GO:0075029
@@ -371827,7 +371800,7 @@ def: "Any process that modulates the frequency, rate or extent of symbiont germ
synonym: "modulation of germ tube tip of symbiont on or near the exterior of host" EXACT []
synonym: "modulation of symbiont germ tube hook structure formation on or near host" RELATED []
synonym: "regulation of formation of symbiont germ tube hook structure on or near host" EXACT []
-is_a: GO:0075026 ! regulation of appressorium initiation
+is_a: GO:0050793 ! regulation of developmental process
relationship: regulates GO:0075029 ! formation of appressorium germ tube hook structure
[Term]
@@ -371838,7 +371811,7 @@ def: "Any process that activates, maintains or increases the frequency, rate or
synonym: "positive regulation of formation of symbiont germ tube hook structure on or near host" EXACT []
synonym: "positive regulation of germ tube tip of symbiont on or near the exterior of host" EXACT []
synonym: "positive regulation of symbiont germ tube hook structure formation on or near host" RELATED []
-is_a: GO:0075027 ! positive regulation of appressorium initiation
+is_a: GO:0051094 ! positive regulation of developmental process
is_a: GO:0075030 ! modulation of formation of symbiont germ tube hook structure for appressorium development
relationship: positively_regulates GO:0075029 ! formation of appressorium germ tube hook structure
@@ -371850,7 +371823,7 @@ def: "Any process that stops, prevents, or reduces the frequency, rate or extent
synonym: "negative regulation of formation of symbiont germ tube hook structure on or near host" EXACT []
synonym: "negative regulation of germ tube tip of symbiont on or near the exterior of host" EXACT []
synonym: "negative regulation of symbiont germ tube hook structure formation on or near host" RELATED []
-is_a: GO:0075028 ! negative regulation of appressorium initiation
+is_a: GO:0051093 ! negative regulation of developmental process
is_a: GO:0075030 ! modulation of formation of symbiont germ tube hook structure for appressorium development
relationship: negatively_regulates GO:0075029 ! formation of appressorium germ tube hook structure
@@ -371888,37 +371861,36 @@ relationship: part_of GO:0075016 ! appressorium formation
[Term]
id: GO:0075036
-name: regulation of appressorium maturation
+name: obsolete regulation of appressorium maturation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of symbiont appressorium maturation." [GOC:pamgo_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of symbiont appressorium maturation." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a phenotype.
synonym: "regulation of appressorium maturation on or near host" RELATED []
synonym: "regulation of maturation of appressorium on or near host" EXACT []
-is_a: GO:0044145 ! modulation of formation of structure involved in a symbiotic process
-relationship: regulates GO:0075035 ! appressorium maturation
+is_obsolete: true
+consider: GO:0075017
[Term]
id: GO:0075037
-name: positive regulation of appressorium maturation
+name: obsolete positive regulation of appressorium maturation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of symbiont appressorium maturation." [GOC:pamgo_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of symbiont appressorium maturation." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a phenotype.
synonym: "positive regulation maturation of appressorium on or near host" EXACT []
synonym: "positive regulation of appressorium maturation on or near host" RELATED []
-is_a: GO:0044149 ! positive regulation of formation of structure involved in a symbiotic process
-is_a: GO:0075018 ! positive regulation of appressorium formation
-is_a: GO:0075036 ! regulation of appressorium maturation
-relationship: positively_regulates GO:0075035 ! appressorium maturation
+is_obsolete: true
+consider: GO:0075018
[Term]
id: GO:0075038
-name: negative regulation of appressorium maturation
+name: obsolete negative regulation of appressorium maturation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent symbiont appressorium maturation." [GOC:pamgo_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent symbiont appressorium maturation." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a phenotype.
synonym: "negative regulation of appressorium maturation on or near host" RELATED []
synonym: "negative regulation of maturation of appressorium on or near host" EXACT []
-is_a: GO:0044147 ! negative regulation of formation of structure involved in a symbiotic process
-is_a: GO:0075019 ! negative regulation of appressorium formation
-is_a: GO:0075036 ! regulation of appressorium maturation
-relationship: negatively_regulates GO:0075035 ! appressorium maturation
+is_obsolete: true
+consider: GO:0075019
[Term]
id: GO:0075039
@@ -371934,31 +371906,31 @@ relationship: part_of GO:0075035 ! appressorium maturation
[Term]
id: GO:0075040
-name: regulation of establishment of turgor in appressorium
+name: obsolete regulation of establishment of turgor in appressorium
namespace: biological_process
-def: "Any process modulates the frequency, rate or extent of turgor formation in the symbiont appressorium." [GOC:pamgo_curators]
+def: "OBSOLETE. Any process modulates the frequency, rate or extent of turgor formation in the symbiont appressorium." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a phenotype.
synonym: "regulation of turgor formation in appressorium" RELATED []
-is_a: GO:0044145 ! modulation of formation of structure involved in a symbiotic process
-relationship: regulates GO:0075039 ! establishment of turgor in appressorium
+is_obsolete: true
+consider: GO:0075017
[Term]
id: GO:0075041
-name: positive regulation of establishment of turgor in appressorium
+name: obsolete positive regulation of establishment of turgor in appressorium
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of turgor formation in the symbiont appressorium." [GOC:pamgo_curators]
-is_a: GO:0044149 ! positive regulation of formation of structure involved in a symbiotic process
-is_a: GO:0075018 ! positive regulation of appressorium formation
-is_a: GO:0075040 ! regulation of establishment of turgor in appressorium
-relationship: positively_regulates GO:0075039 ! establishment of turgor in appressorium
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of turgor formation in the symbiont appressorium." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a phenotype.
+is_obsolete: true
+consider: GO:0075018
[Term]
id: GO:0075042
-name: negative regulation of establishment of turgor in appressorium
+name: obsolete negative regulation of establishment of turgor in appressorium
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of turgor formation in the symbiont appressorium." [GOC:pamgo_curators]
-is_a: GO:0075038 ! negative regulation of appressorium maturation
-is_a: GO:0075040 ! regulation of establishment of turgor in appressorium
-relationship: negatively_regulates GO:0075039 ! establishment of turgor in appressorium
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of turgor formation in the symbiont appressorium." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a phenotype.
+is_obsolete: true
+consider: GO:0075019
[Term]
id: GO:0075043
@@ -371970,17 +371942,6 @@ synonym: "melanization of appressorium to maintain turgor pressure" EXACT []
is_a: GO:0043476 ! pigment accumulation
relationship: part_of GO:0075035 ! appressorium maturation
-[Term]
-id: GO:0075044
-name: positive regulation by symbiont of host autophagy
-namespace: biological_process
-def: "Any process in which a symbiont organism increases the frequency, rate or extent of autophagy in the host cell. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-synonym: "autophagy of host cells during interaction with symbiont" RELATED [GOC:dph]
-synonym: "autophagy of host cells involved in interaction with symbiont" RELATED []
-synonym: "positive regulation by symbiont of host autophagotic process" RELATED []
-is_a: GO:0075071 ! modulation by symbiont of host autophagy
-relationship: positively_regulates GO:0006914 ! autophagy
-
[Term]
id: GO:0075045
name: regulation of formation by symbiont of haustorium for nutrient acquisition from host
@@ -372633,7 +372594,7 @@ alt_id: GO:0075121
alt_id: GO:0075124
alt_id: GO:0075127
def: "Any process in which the symbiont modulates the frequency, rate or extent of the host G protein-coupled receptor signal transduction. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-comment: Note that this term is used to annotate gene products of the symbiont. To annotate host gene products, consider the biological process term "modulation by host of symbiont G protein-coupled receptor signal transduction ; GO:0075087".
+comment: Note that this term is used to annotate gene products of the symbiont. To annotate host gene products, consider the biological process term "modulation by host of symbiont G protein-coupled receptor signal transduction ; GO:0075087".
synonym: "modulation by symbiont of host G-protein coupled receptor protein signal transduction" EXACT []
synonym: "modulation by symbiont of host signal transduction mediated by G-protein alpha subunit" NARROW []
synonym: "modulation by symbiont of host signal transduction mediated by G-protein beta subunit" NARROW []
@@ -374148,6 +374109,7 @@ def: "Any process that activates, maintains or increases the frequency, rate or
is_a: GO:0010720 ! positive regulation of cell development
is_a: GO:0034307 ! regulation of ascospore formation
is_a: GO:0043941 ! positive regulation of sexual sporulation resulting in formation of a cellular spore
+is_a: GO:0090068 ! positive regulation of cell cycle process
relationship: positively_regulates GO:0030437 ! ascospore formation
[Term]
@@ -374156,6 +374118,7 @@ name: negative regulation of ascospore formation
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of ascospore formation, a process in which a sexual spore, named ascospore, from Ascomycete fungi was produced inside an ascus." [GOC:pamgo_curators]
is_a: GO:0010721 ! negative regulation of cell development
+is_a: GO:0010948 ! negative regulation of cell cycle process
is_a: GO:0034307 ! regulation of ascospore formation
is_a: GO:0043942 ! negative regulation of sexual sporulation resulting in formation of a cellular spore
relationship: negatively_regulates GO:0030437 ! ascospore formation
@@ -374821,7 +374784,7 @@ name: modulation by virus of host immune response
namespace: biological_process
def: "The process in which a virus effects a change in the host immune response." [GOC:bf, GOC:jl]
synonym: "regulation by virus of host immune system process" EXACT [GOC:jl]
-is_a: GO:0019054 ! modulation by virus of host cellular process
+is_a: GO:0019048 ! modulation by virus of host process
is_a: GO:0052553 ! modulation by symbiont of host immune response
relationship: regulates GO:0006955 ! immune response
@@ -375079,11 +375042,12 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
[Term]
id: GO:0080019
-name: fatty-acyl-CoA reductase (alcohol-forming) activity
+name: alcohol-forming very long-chain fatty acyl-CoA reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a very long chain fatty acyl-CoA + NADPH + H+ = a very long chain primary alcohol + NADP+ + CoA." [PMID:16980563]
+def: "Catalysis of the reaction: a very long chain fatty acyl-CoA + NADPH + H+ = a very long chain primary alcohol + NADP+ + CoA. A very long chain fatty acid (VLCFA) is a fatty acid with an aliphatic tail of 22 or more carbons." [PMID:16980563]
synonym: "fatty acyl CoA reductase (alcohol-forming) activity" EXACT []
synonym: "fatty acyl-CoA reductase (alcohol-forming) activity" EXACT [GOC:mah]
+synonym: "fatty-acyl-CoA reductase (alcohol-forming) activity" RELATED []
is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
[Term]
@@ -375102,6 +375066,7 @@ def: "Any process that results in a change in state or activity of a cell or an
synonym: "response to benzoic acid stimulus" EXACT [GOC:dos]
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0080022
@@ -375112,11 +375077,13 @@ is_a: GO:0048364 ! root development
[Term]
id: GO:0080023
-name: 3R-hydroxyacyl-CoA dehydratase activity
+name: obsolete (3R)-3-hydroxyacyl-CoA dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3R-hydroxyacyl-CoA = 2E-enoyl-CoA + H2O." [PMID:16982622]
-xref: Reactome:R-HSA-5676637 "PTPLs dehydrate VLC3HA-CoA to VLCTDA-CoA"
-is_a: GO:0016836 ! hydro-lyase activity
+def: "OBSOLETE. Catalysis of the reaction: a (3R)-3-hydroxyacyl-CoA = a (2E)-enoyl-CoA + H2O." [PMID:16982622, RHEA:26526]
+comment: This term was obsoleted because it represents a specific substrate of 3-hydroxyacyl-CoA dehydratase activity ; GO:0018812.
+synonym: "3R-hydroxyacyl-CoA dehydratase activity" EXACT []
+is_obsolete: true
+replaced_by: GO:0018812
[Term]
id: GO:0080024
@@ -375186,7 +375153,6 @@ def: "Catalysis of the reaction: methyl indole-3-acetate + H2O = indole-3-acetat
synonym: "indole-3-Acetic acid methyl ester esterase activity" EXACT []
synonym: "MeIAA esterase activity" EXACT []
synonym: "Methyl IAA esterase activity" EXACT []
-xref: EC:3.1.1.1
xref: MetaCyc:RXN-10711
is_a: GO:0052689 ! carboxylic ester hydrolase activity
@@ -375333,21 +375299,27 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0080047
name: GDP-L-galactose phosphorylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GDP-L-galactose + phosphate = L-galactose-1-P + GDP." [EC:2.7.7.69, PMID:18463094]
+alt_id: GO:0010475
+def: "Catalysis of the reaction: GDP-beta-L-galactose + phosphate = beta-L-galactose-1-phosphate + GDP." [PMID:17462988, PMID:18463094, RHEA:27698]
+synonym: "galactose-1-phosphate guanylyltransferase (GDP) activity" EXACT []
+synonym: "GDP:galactose-1-phosphate guanyltransferase activity" EXACT []
xref: EC:2.7.7.69
xref: MetaCyc:RXNQT-4141
xref: RHEA:27698
-is_a: GO:0004645 ! 1,4-alpha-oligoglucan phosphorylase activity
+is_a: GO:0070568 ! guanylyltransferase activity
[Term]
id: GO:0080048
name: GDP-D-glucose phosphorylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GDP-D-glucose + phosphate = D-glucose-1-P + GDP." [PMID:18463094]
+alt_id: GO:0010474
+def: "Catalysis of the reaction: GDP-alpha-D-glucose + phosphate = alpha-D-glucose-1-phosphate + GDP." [PMID:17462988, PMID:18463094]
+synonym: "GDP:glucose-1-phosphate guanyltransferase activity" EXACT []
+synonym: "glucose-1-phosphate guanylyltransferase (GDP) activity" EXACT []
xref: EC:2.7.7.78
xref: MetaCyc:RXN-12486
xref: RHEA:30387
-is_a: GO:0004645 ! 1,4-alpha-oligoglucan phosphorylase activity
+is_a: GO:0070568 ! guanylyltransferase activity
[Term]
id: GO:0080049
@@ -375417,7 +375389,7 @@ name: protein deglutathionylation
namespace: biological_process
def: "The protein modification process in which a glutathione molecule is removed from a protein amino acid by breaking a disulfide linkage." [GOC:tb]
synonym: "protein amino acid deglutathionylation" EXACT [GOC:bf]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0080059
@@ -375571,9 +375543,11 @@ is_a: GO:0008171 ! O-methyltransferase activity
id: GO:0080079
name: cellobiose glucosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cellobiose + H2O = 2 D-glucose." [PMID:15604686]
+def: "Catalysis of the reaction: D-cellobiose + H2O = 2 D-glucose." [PMID:15604686, RHEA:30679]
synonym: "cellobiose glucohydrolase activity" EXACT []
+synonym: "D-cellobiose glucosidase activity" EXACT []
xref: MetaCyc:RXN-10773
+xref: RHEA:30679
is_a: GO:0008422 ! beta-glucosidase activity
[Term]
@@ -375821,7 +375795,6 @@ name: DNA demethylation
namespace: biological_process
def: "The removal of a methyl group from one or more nucleotides within an DNA molecule." [PMID:17208187]
is_a: GO:0035510 ! DNA dealkylation
-is_a: GO:0044728 ! DNA methylation or demethylation
is_a: GO:0070988 ! demethylation
[Term]
@@ -375829,7 +375802,7 @@ id: GO:0080112
name: seed growth
namespace: biological_process
def: "The increase in size or mass of a seed. A seed is a propagating organ formed in the reproductive cycle of a spermatophyte, derived from the ovule and enclosing an embryo." [GOC:dhl, PO:0009010]
-is_a: GO:0003006 ! developmental process involved in reproduction
+is_a: GO:0022414 ! reproductive process
is_a: GO:0048589 ! developmental growth
relationship: part_of GO:0048316 ! seed development
@@ -375899,7 +375872,6 @@ namespace: biological_process
def: "A series of specific posttranslational modifications to the CAAX box region of CAAX box proteins. CAAX box proteins are eukaryotic proteins that contain a CAAX motif where the C is a cysteine, the two A residues are aliphatic amino acids and the X can be one of several amino acids. The CAAX-box proteins undergo three sequential, enzymatic, post-translational modifications essential to their targeting: First, the proteins are prenylated by one of two prenyltransferases called farnesyltransferase and geranylgeranyltransferase-I. Prenylation results in the covalent attachment of either farnesyl or geranylgeranyl isoprenoid groups to the cysteine in the CAAX box motif. Prenylation is followed by proteolytic removal of the last three amino acids of the protein (AAX). Finally, the newly exposed carboxylate group of the isoprenylcysteine is methylated by an ER-associated prenyl-dependent carboxylmethyltransferase." [PMID:12039957, PMID:17114793, PMID:18641086]
synonym: "CAAX-box protein processing" RELATED []
synonym: "farnesylated protein maturation" RELATED [GOC:vw]
-is_a: GO:0044267 ! cellular protein metabolic process
is_a: GO:0051604 ! protein maturation
[Term]
@@ -376110,19 +376082,21 @@ relationship: regulates GO:0032973 ! amino acid export across plasma membrane
[Term]
id: GO:0080144
-name: amino acid homeostasis
+name: intracellular amino acid homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of amino acid within an organism or cell." [PMID:19955263]
-is_a: GO:0048878 ! chemical homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of amino acids within a cell." [PMID:19955263]
+synonym: "amino acid homeostasis" BROAD []
+synonym: "cellular amino acid homeostasis" EXACT []
+is_a: GO:0055082 ! intracellular chemical homeostasis
[Term]
id: GO:0080145
-name: cysteine homeostasis
+name: intracellular cysteine homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of cysteine within an organism or cell." [PMID:19955263]
-is_a: GO:0055080 ! cation homeostasis
-is_a: GO:0055081 ! anion homeostasis
-is_a: GO:0080144 ! amino acid homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of cysteine within a cell." [PMID:19955263]
+synonym: "cellular cysteine homeostasis" EXACT []
+synonym: "cysteine homeostasis" EXACT []
+is_a: GO:0080144 ! intracellular amino acid homeostasis
[Term]
id: GO:0080146
@@ -376271,11 +376245,12 @@ is_a: GO:0022857 ! transmembrane transporter activity
[Term]
id: GO:0080162
-name: intracellular auxin transport
+name: endoplasmic reticulum to cytosol auxin transport
namespace: biological_process
-def: "The directed movement of auxins within a cell. Auxins are a group of plant hormones that regulates aspects of plant growth." [PMID:19506555]
-is_a: GO:0046907 ! intracellular transport
-is_a: GO:0060919 ! auxin influx
+def: "The directed movement of auxins from endoplasmic reticulum to cytosol." [PMID:19506555]
+synonym: "intracellular auxin transport" BROAD []
+is_a: GO:0055085 ! transmembrane transport
+is_a: GO:0060918 ! auxin transport
[Term]
id: GO:0080163
@@ -376323,7 +376298,6 @@ name: abscisic acid transport
namespace: biological_process
def: "The directed movement of abscisic acid into, out of, within or between cells by means of some external agent such as a transporter or pore." [PMID:20133881]
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0046865 ! terpenoid transport
@@ -376346,6 +376320,7 @@ def: "The process in which hydrogen peroxide is transported across a membrane."
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "hydrogen peroxide membrane transport" EXACT []
is_a: GO:0055085 ! transmembrane transport
+is_a: GO:0071702 ! organic substance transport
[Term]
id: GO:0080171
@@ -376405,7 +376380,7 @@ relationship: part_of GO:0009658 ! chloroplast organization
id: GO:0080178
name: 5-carbamoylmethyl uridine residue modification
namespace: biological_process
-def: "The chemical reactions and pathways involving the addition of a 5-carbamoylmethyl group to a uridine residue in RNA." [GOC:dph, GOC:tb]
+def: "The chemical reactions and pathways involving the addition of a 5-carbamoylmethyl group to a uridine residue in RNA." [GOC:dph, GOC:tb]
synonym: "5-carbamoylmethyluridine metabolic process" RELATED []
is_a: GO:0030488 ! tRNA methylation
@@ -376489,7 +376464,7 @@ synonym: "positive regulation by symbiont of plant HR" EXACT [GOC:pamgo_curators
synonym: "positive regulation by symbiont of plant hypersensitive response" EXACT [GOC:pamgo_curators]
xref: Wikipedia:Effector-triggered_immunity
is_a: GO:0034053 ! modulation by symbiont of host defense-related programmed cell death
-is_a: GO:0052042 ! positive regulation by symbiont of host programmed cell death
+is_a: GO:0052042 ! induction by symbiont of host programmed cell death
is_a: GO:0052158 ! modulation by symbiont of host resistance gene-dependent defense response
is_a: GO:0052390 ! induction by symbiont of host innate immune response
is_a: GO:0140404 ! effector-mediated modulation of host innate immune response by symbiont
@@ -376505,7 +376480,7 @@ is_a: GO:0048589 ! developmental growth
id: GO:0080187
name: floral organ senescence
namespace: biological_process
-def: "An organ senescence that has as a participant a floral organ." [PMID:21689171, PO:0025395]
+def: "The last stage of flower development during which programmed degradation of macromolecules and nutrient recycling take place." [PMID:19380421, PMID:21689171]
comment: Includes senescence of petals, sepals, anthers, and any other plant organ that is part of a flower. Floral organ senescence may follow pollination. In some flowers, the organs of the corolla abscise before they senesce.
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0090693 ! plant organ senescence
@@ -376515,12 +376490,12 @@ relationship: part_of GO:0048437 ! floral organ development
id: GO:0080188
name: gene silencing by RNA-directed DNA methylation
namespace: biological_process
-def: "A small RNA-based epigenetic gene silencing process in which small interfering RNAs (siRNAs) guide DNA methylation to the siRNA-generating genomic loci and other loci that are homologous to the siRNAs for de novo DNA methylation. This results in a heterochromatin assembly, a chromatin conformation that is refractory to transcription. In general this process consists of three phases: biogenesis of siRNAs, scaffold RNA production, and the formation of the guiding complex that recruits de novo DNA methyltransferases to the target loci. Transposable elements are silenced by this mechanism." [PMID:21420348]
+def: "A small RNA-based gene silencing process in which small interfering RNAs (siRNAs) guide DNA methylation to the siRNA-generating genomic loci and other loci that are homologous to the siRNAs for de novo DNA methylation. This results in a heterochromatin assembly, a chromatin conformation that is refractory to transcription. In general this process consists of three phases: biogenesis of siRNAs, scaffold RNA production, and the formation of the guiding complex that recruits de novo DNA methyltransferases to the target loci. Transposable elements are silenced by this mechanism." [PMID:21420348]
comment: This process has been shown in plants and in yeasts, but so far has not been detected in vertebrates, organisms that lack RNA-dependent RNA polymerase.
synonym: "RdDM" EXACT []
synonym: "RNA-directed DNA methylation" RELATED []
-is_a: GO:0006346 ! DNA methylation-dependent heterochromatin assembly
-is_a: GO:0140458 ! pre-transcriptional gene silencing by RNA
+is_a: GO:0006346 ! DNA methylation-dependent heterochromatin formation
+is_a: GO:0031048 ! small ncRNA-mediated heterochromatin formation
[Term]
id: GO:0080189
@@ -376980,7 +376955,6 @@ id: GO:0086009
name: membrane repolarization
namespace: biological_process
def: "The process in which ions are transported across a membrane such that the membrane potential changes in the repolarizing direction, toward the steady state potential. For example, the repolarization during an action potential is from a positive membrane potential towards a negative resting potential." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
-is_a: GO:0034220 ! ion transmembrane transport
is_a: GO:0042391 ! regulation of membrane potential
[Term]
@@ -377118,7 +377092,7 @@ relationship: part_of GO:0086070 ! SA node cell to atrial cardiac muscle cell co
id: GO:0086023
name: adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process
namespace: biological_process
-def: "A series of molecular signals beginning with a G protein-coupled adrenergic cell surface receptor combining with epinephrine or norepinephrine, to activate adenylate cyclase, which contributes to a circulatory system process carried out by the heart." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
+def: "The series of molecular signals beginning with a G protein-coupled adrenergic cell surface receptor combining with epinephrine or norepinephrine, to activate adenylate cyclase, which contributes to a circulatory system process carried out by the heart." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
synonym: "adrenergic receptor signaling pathway involved in heart process" EXACT []
synonym: "adrenergic receptor signalling pathway involved in heart process" EXACT [GOC:bf]
synonym: "beta-adrenergic receptor signalling pathway involved in heart process" NARROW [GOC:bf]
@@ -377735,7 +377709,7 @@ is_a: GO:1900129 ! positive regulation of G-protein activated inward rectifier p
id: GO:0086096
name: adenylate cyclase-inhibiting adrenergic receptor signaling pathway involved in heart process
namespace: biological_process
-def: "An adrenergic receptor signaling pathway which contributes to a circulatory system process carried out by the heart, where the activated adrenergic receptor transmits the signal by Gi-mediated inhibition of adenylate cyclase activity." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11, PMID:10571541]
+def: "An adenylate cyclase-inhibiting adrenergic receptor signaling pathway which contributes to a circulatory system process carried out by the heart." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11, PMID:10571541]
comment: Although Beta1-adrenergic receptors couple exclusively to the Gs protein, Beta2-adrenergic receptors couple to both Gs and Gi proteins. Coupling to Gi proteins may localize the Gs-mediated signaling.
synonym: "cardiac adrenergic receptor signaling pathway via inhibition of adenylate cyclase activity" EXACT [GOC:bf]
synonym: "G-inhibitory-coupled Beta2AR signaling pathway involved in heart process" EXACT [PMID:17376402]
@@ -377748,7 +377722,7 @@ is_a: GO:0086103 ! G protein-coupled receptor signaling pathway involved in hear
id: GO:0086097
name: phospholipase C-activating angiotensin-activated signaling pathway
namespace: biological_process
-def: "An angiotensin-mediated signaling pathway where the activated receptor transmits the signal via Gq-mediated activation of phospholipase C (PLC). PLC hydrolyses phosphatidylinositol 4,5-bisphosphate (PIP2) into the second messengers inositol-1,4,5,-triphosphate (IP3) and diacylglycerol (DAG). DAG activates protein kinase C (PKC), whilst IP3 binds intracellular receptors to induce the release of Ca2+ from intracellular stores." [GOC:bf, GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
+def: "A phospholipase C-activating G protein-coupled receptor signaling pathway initiated by angiotensin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
synonym: "angiotensin-mediated signaling pathway via activation of phospholipase C" EXACT [GOC:bf]
synonym: "Gq-coupled angiotensin receptor signaling pathway" EXACT [GOC:bf]
synonym: "phospholipase C-activating angiotensin receptor signaling pathway" EXACT [GOC:bf]
@@ -377785,7 +377759,7 @@ is_a: GO:0086098 ! angiotensin-activated signaling pathway involved in heart pro
id: GO:0086100
name: endothelin receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by an endothelin receptor binding to one of its physiological ligands, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, PMID:10977869]
+def: "A G protein-coupled receptor signaling pathway initiated by endothelin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:bf, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, PMID:10977869]
synonym: "endothelin signaling pathway" RELATED [GOC:bf]
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -377802,7 +377776,7 @@ is_a: GO:0086103 ! G protein-coupled receptor signaling pathway involved in hear
id: GO:0086102
name: adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway involved in negative regulation of heart rate
namespace: biological_process
-def: "A G protein-coupled acetylcholine receptor signaling pathway that contributes to an decrease in frequency or rate of heart contraction through inhibition of adenylate cyclase (AC) activity. Binding of acetylcholine to a G protein-coupled (muscarinic) receptor on the surface of the signal-receiving cell results in the activation of an intracellular Gi/o protein. Gi/o inhibits adenylate cyclase to decrease cyclic-AMP (cAMP) levels. Since cAMP binds directly to F-channels to allow an inward flow of sodium (funny current, If current), a reduction in cAMP reduces the funny current to bring about membrane hyperpolarization and a decrease in heart rate." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
+def: "An adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway that contributes to a decrease in frequency or rate of heart contraction through inhibition of adenylate cyclase (AC) activity. Binding of acetylcholine to a G protein-coupled (muscarinic) receptor on the surface of the signal-receiving cell results in the activation of an intracellular Gi/o protein. Gi/o inhibits adenylate cyclase to decrease cyclic-AMP (cAMP) levels. Since cAMP binds directly to F-channels to allow an inward flow of sodium (funny current, If current), a reduction in cAMP reduces the funny current to bring about membrane hyperpolarization and a decrease in heart rate." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
synonym: "AC-inhibiting muscarinic receptor signaling pathway involved in negative regulation of heart rate" RELATED [GOC:bf]
synonym: "adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway involved in negative regulation of heart rate" EXACT []
synonym: "G-protein coupled acetylcholine receptor signaling pathway involved in negative regulation of heart rate via inhibition of adenylate cyclase activity" EXACT [GOC:bf]
@@ -377866,11 +377840,8 @@ id: GO:0089704
name: L-glutamate transmembrane export from vacuole
namespace: biological_process
def: "The directed movement of L-glutamate out of the vacuole, across the vacuolar membrane." [PMID:21307582]
-is_a: GO:0006835 ! dicarboxylic acid transport
-is_a: GO:0015807 ! L-amino acid transport
+is_a: GO:0015813 ! L-glutamate transmembrane transport
is_a: GO:0032974 ! amino acid transmembrane export from vacuole
-is_a: GO:0098656 ! anion transmembrane transport
-is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
id: GO:0089705
@@ -377913,9 +377884,6 @@ namespace: biological_process
def: "The directed movement of L-histidine across a membrane." [PMID:21307582]
is_a: GO:0015801 ! aromatic amino acid transport
is_a: GO:0045117 ! azole transmembrane transport
-is_a: GO:0046942 ! carboxylic acid transport
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -377930,7 +377898,7 @@ id: GO:0089713
name: Cbf1-Met4-Met28 complex
namespace: cellular_component
def: "A heteromeric complex consisting of Cbf1 and basic leucine zipper (bZIP) containing transcriptional activators, Met4 and Met28, that forms over the sequence TCACGTG in the upstream activating sequence (UAS) of genes involved in sulfur amino acid metabolism, resulting in their transcriptional activation." [PMID:8665859, PMID:9171357]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0005667 ! transcription regulator complex
[Term]
id: GO:0089714
@@ -377959,10 +377927,12 @@ is_a: GO:0090575 ! RNA polymerase II transcription regulator complex
[Term]
id: GO:0089717
-name: spanning component of membrane
+name: obsolete spanning component of membrane
namespace: cellular_component
-def: "The component of a membrane consisting of gene products and protein complexes that have some part that spans both leaflets of the membrane." [GOC:dos]
-is_a: GO:0016021 ! integral component of membrane
+def: "OBSOLETE. The component of a membrane consisting of gene products and protein complexes that have some part that spans both leaflets of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0016020
[Term]
id: GO:0089718
@@ -377977,7 +377947,6 @@ synonym: "amino acid transmembrane import" BROAD []
synonym: "L-amino acid import" BROAD []
synonym: "L-amino acid uptake" NARROW []
is_a: GO:0003333 ! amino acid transmembrane transport
-is_a: GO:0043090 ! amino acid import
is_a: GO:0098657 ! import into cell
is_a: GO:0098739 ! import across plasma membrane
@@ -378005,7 +377974,6 @@ name: phosphoenolpyruvate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of a phosphoenolpyruvate from one side of a membrane to the other." [GOC:dos]
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015605 ! organophosphate ester transmembrane transporter activity
[Term]
@@ -378014,7 +377982,6 @@ name: phosphoenolpyruvate transmembrane transport
namespace: biological_process
def: "The directed movement of phosphoenolpytuvate across a membrane." [GOC:dos]
is_a: GO:0015714 ! phosphoenolpyruvate transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -378063,7 +378030,7 @@ relationship: part_of GO:0009948 ! anterior/posterior axis specification
id: GO:0090010
name: transforming growth factor beta receptor signaling pathway involved in primitive streak formation
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, which contributes to the formation of the primitive streak." [GOC:dph, GOC:sdb_2009, GOC:tb]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a transforming growth factor beta receptor on the surface of a target cell, which contributes to the formation of the primitive streak." [GOC:dph, GOC:sdb_2009, GOC:tb]
synonym: "TGFbeta signaling pathway involved in primitive streak formation" RELATED [GOC:dph, GOC:sdb_2009, GOC:tb]
synonym: "transforming growth factor beta receptor signalling pathway involved in primitive streak formation" EXACT [GOC:mah]
is_a: GO:0007179 ! transforming growth factor beta receptor signaling pathway
@@ -378423,41 +378390,45 @@ relationship: negatively_regulates GO:0002042 ! cell migration involved in sprou
[Term]
id: GO:0090052
-name: regulation of pericentric heterochromatin assembly
+name: regulation of pericentric heterochromatin formation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of chromatin silencing at the centromere. Chromatin silencing at the centromere is the repression of transcription of centromeric DNA by altering the structure of chromatin." [GOC:dph, GOC:tb]
+def: "Any process that modulates the frequency, rate or extent of heterochromatin formation at the centromere. Chromatin silencing at the centromere is the repression of transcription of centromeric DNA by altering the structure of chromatin." [GOC:dph, GOC:tb]
synonym: "regulation of chromatin silencing at centromere" EXACT []
-is_a: GO:0031445 ! regulation of heterochromatin assembly
-relationship: regulates GO:0031508 ! pericentric heterochromatin assembly
+synonym: "regulation of pericentric heterochromatin assembly" EXACT []
+is_a: GO:0031445 ! regulation of heterochromatin formation
+relationship: regulates GO:0031508 ! pericentric heterochromatin formation
[Term]
id: GO:0090053
-name: positive regulation of pericentric heterochromatin assembly
+name: positive regulation of pericentric heterochromatin formation
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of chromatin silencing at the centromere. Chromatin silencing at the centromere is the repression of transcription of centromeric DNA by altering the structure of chromatin." [GOC:dph, GOC:tb]
+def: "Any process that increases the frequency, rate or extent of pericentric heterochromatin formation." [GOC:dph, GOC:tb]
synonym: "positive regulation of chromatin silencing at centromere" EXACT []
-is_a: GO:0031453 ! positive regulation of heterochromatin assembly
-is_a: GO:0090052 ! regulation of pericentric heterochromatin assembly
-relationship: positively_regulates GO:0031508 ! pericentric heterochromatin assembly
+synonym: "positive regulation of pericentric heterochromatin assembly" EXACT []
+is_a: GO:0031453 ! positive regulation of heterochromatin formation
+is_a: GO:0090052 ! regulation of pericentric heterochromatin formation
+relationship: positively_regulates GO:0031508 ! pericentric heterochromatin formation
[Term]
id: GO:0090054
-name: regulation of silent mating-type cassette heterochromatin assembly
+name: regulation of silent mating-type cassette heterochromatin formation
namespace: biological_process
-def: "Any process that modulates the frequency, rate, or extent of chromatin silencing at silent mating-type cassette. Chromatin silencing at silent mating-type cassette is the repression of transcription at silent mating-type loci by altering the structure of chromatin." [GOC:dph, GOC:tb]
+def: "Any process that modulates the frequency, rate, or extent of heterochromatin formation at silent mating-type cassette." [GOC:dph, GOC:tb]
synonym: "regulation of chromatin silencing at silent mating-type cassette" EXACT []
-is_a: GO:0031445 ! regulation of heterochromatin assembly
-relationship: regulates GO:0030466 ! silent mating-type cassette heterochromatin assembly
+synonym: "regulation of silent mating-type cassette heterochromatin assembly" EXACT []
+is_a: GO:0031445 ! regulation of heterochromatin formation
+relationship: regulates GO:0030466 ! silent mating-type cassette heterochromatin formation
[Term]
id: GO:0090055
-name: positive regulation of silent mating-type cassette heterochromatin assembly
+name: positive regulation of silent mating-type cassette heterochromatin formation
namespace: biological_process
-def: "Any process that increases the frequency, rate, or extent of chromatin silencing at silent mating-type cassette. Chromatin silencing at silent mating-type cassette is the repression of transcription at silent mating-type loci by altering the structure of chromatin." [GOC:dph, GOC:tb]
+def: "Any process that increases the frequency, rate, or extent of heterochromatin formation at silent mating-type cassette." [GOC:dph, GOC:tb]
synonym: "positive regulation of chromatin silencing at silent mating-type cassette" EXACT []
-is_a: GO:0031453 ! positive regulation of heterochromatin assembly
-is_a: GO:0090054 ! regulation of silent mating-type cassette heterochromatin assembly
-relationship: positively_regulates GO:0030466 ! silent mating-type cassette heterochromatin assembly
+synonym: "positive regulation of silent mating-type cassette heterochromatin assembly" EXACT []
+is_a: GO:0031453 ! positive regulation of heterochromatin formation
+is_a: GO:0090054 ! regulation of silent mating-type cassette heterochromatin formation
+relationship: positively_regulates GO:0030466 ! silent mating-type cassette heterochromatin formation
[Term]
id: GO:0090056
@@ -378502,7 +378473,7 @@ id: GO:0090062
name: regulation of trehalose metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of trehalose metabolism, the chemical reactions and pathways involving trehalose, a disaccharide isomeric with sucrose and obtained from certain lichens and fungi." [GOC:dph, GOC:tb]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
+is_a: GO:0006109 ! regulation of carbohydrate metabolic process
relationship: regulates GO:0005991 ! trehalose metabolic process
[Term]
@@ -378521,15 +378492,6 @@ namespace: biological_process
def: "Any process that starts the inactive process of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell." [GOC:dph, GOC:tb]
is_a: GO:0090063 ! positive regulation of microtubule nucleation
-[Term]
-id: GO:0090065
-name: regulation of production of siRNA involved in RNA interference
-namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the production of siRNA, the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference." [GOC:dph, GOC:mah, GOC:tb]
-synonym: "regulation of RNA interference, production of siRNA" EXACT [GOC:mah]
-is_a: GO:0070920 ! regulation of production of small RNA involved in gene silencing by RNA
-relationship: regulates GO:0030422 ! production of siRNA involved in RNA interference
-
[Term]
id: GO:0090066
name: regulation of anatomical structure size
@@ -378854,7 +378816,7 @@ name: pancreatic epsilon cell differentiation
namespace: biological_process
def: "The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic epsilon cell. A pancreatic epsilon cell is a cell in the pancreas that secretes ghrelin." [GOC:dph, GOC:tb]
synonym: "pancreatic E cell differentiation" EXACT []
-is_a: GO:0030154 ! cell differentiation
+is_a: GO:0035883 ! enteroendocrine cell differentiation
relationship: part_of GO:0031018 ! endocrine pancreas development
[Term]
@@ -378862,7 +378824,7 @@ id: GO:0090105
name: pancreatic E cell development
namespace: biological_process
def: "The process whose specific outcome is the progression of a pancreatic E cell over time, from its formation to the mature structure." [GOC:dph, GOC:tb]
-is_a: GO:0048468 ! cell development
+is_a: GO:0002068 ! glandular epithelial cell development
relationship: part_of GO:0090104 ! pancreatic epsilon cell differentiation
[Term]
@@ -378932,10 +378894,11 @@ relationship: part_of GO:0006888 ! endoplasmic reticulum to Golgi vesicle-mediat
[Term]
id: GO:0090113
-name: regulation of ER to Golgi vesicle-mediated transport by GTP hydrolysis
+name: obsolete regulation of ER to Golgi vesicle-mediated transport by GTP hydrolysis
namespace: biological_process
-def: "The GTP hydrolysis process that modulates the rate, frequency, or extent of ER to Golgi vesicle-mediated transport, the directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles." [GOC:ascb_2009, GOC:dph, GOC:tb]
-is_a: GO:0060628 ! regulation of ER to Golgi vesicle-mediated transport
+def: "OBSOLETE. The GTP hydrolysis process that modulates the rate, frequency, or extent of ER to Golgi vesicle-mediated transport, the directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles." [GOC:ascb_2009, GOC:dph, GOC:tb]
+comment: This term was obsoleted because it represents a molecular function and a biological process.
+is_obsolete: true
[Term]
id: GO:0090114
@@ -379152,10 +379115,11 @@ is_a: GO:0098609 ! cell-cell adhesion
[Term]
id: GO:0090139
-name: mitochondrial DNA packaging
+name: mitochondrial chromosome packaging
namespace: biological_process
-def: "Any process in which mitochondrial DNA and associated proteins are formed into a compact, orderly structure." [GOC:ascb_2009, GOC:dph, GOC:tb]
-is_a: GO:0036385 ! nucleoid DNA packaging
+def: "A process in which mitochondrial chromosomal DNA and associated proteins organize into a compact, orderly structure." [GOC:ascb_2009, GOC:dph, GOC:tb]
+synonym: "mitochondrial DNA packaging" EXACT []
+is_a: GO:0051276 ! chromosome organization
[Term]
id: GO:0090140
@@ -379318,10 +379282,11 @@ relationship: negatively_regulates GO:0030148 ! sphingolipid biosynthetic proces
[Term]
id: GO:0090156
-name: cellular sphingolipid homeostasis
+name: intracellular sphingolipid homeostasis
namespace: biological_process
-def: "Any biological process involved in the maintenance of an internal steady state of sphingolipids at the level of the cell." [GOC:ascb_2009, GOC:dph, GOC:tb]
-is_a: GO:0055082 ! cellular chemical homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of sphingolipids within a cell." [GOC:ascb_2009, GOC:dph, GOC:tb]
+synonym: "cellular sphingolipid homeostasis" EXACT []
+is_a: GO:0055082 ! intracellular chemical homeostasis
is_a: GO:0055088 ! lipid homeostasis
[Term]
@@ -379812,7 +379777,6 @@ id: GO:0090214
name: spongiotrophoblast layer developmental growth
namespace: biological_process
def: "The increase in size or mass of the spongiotrophoblast layer of the placenta where the increase in size or mass contributes to the progression of that layer over time from its formation to its mature state." [GOC:dph, GOC:tb]
-is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048589 ! developmental growth
relationship: part_of GO:0060712 ! spongiotrophoblast layer development
@@ -379863,8 +379827,8 @@ name: chromosome localization to nuclear envelope involved in homologous chromos
namespace: biological_process
def: "The directed movement of a chromosome to the nuclear envelope that contributes to homologous chromosome segregation and precedes synapsis." [GOC:ascb_2009, GOC:dph, GOC:tb, PMID:19913287]
synonym: "chromosome localisation to nuclear envelope involved in homologous chromosome segregation" EXACT [GOC:mah]
+is_a: GO:0022414 ! reproductive process
is_a: GO:0051303 ! establishment of chromosome localization
-is_a: GO:1903046 ! meiotic cell cycle process
relationship: part_of GO:0045143 ! homologous chromosome segregation
[Term]
@@ -379900,17 +379864,17 @@ relationship: regulates GO:0007051 ! spindle organization
[Term]
id: GO:0090225
-name: regulation of spindle density
+name: obsolete regulation of spindle density
namespace: biological_process
-def: "Any process that modulates the number of microtubules in a given region of the spindle." [GOC:ascb_2009, GOC:dph, GOC:tb]
-is_a: GO:0065008 ! regulation of biological quality
-is_a: GO:0090224 ! regulation of spindle organization
+def: "OBSOLETE. Any process that modulates the number of microtubules in a given region of the spindle." [GOC:ascb_2009, GOC:dph, GOC:tb]
+comment: This term was obsoleted because it represents a phenotype.
+is_obsolete: true
[Term]
id: GO:0090226
name: regulation of microtubule nucleation by Ran protein signal transduction
namespace: biological_process
-def: "Any series of molecular signals in which a Ran GTPase relays one or more of the signals resulting in the modulation of the rate, frequency or extent of microtubule nucleation." [GOC:ascb_2009, GOC:dph, GOC:tb]
+def: "The series of molecular signals in which a Ran GTPase relays a signal resulting in the modulation of the rate, frequency or extent of microtubule nucleation." [GOC:ascb_2009, GOC:dph, GOC:tb]
is_a: GO:0010968 ! regulation of microtubule nucleation
is_a: GO:0031291 ! Ran protein signal transduction
@@ -379994,8 +379958,10 @@ relationship: negatively_regulates GO:0031577 ! spindle checkpoint signaling
id: GO:0090234
name: regulation of kinetochore assembly
namespace: biological_process
+alt_id: GO:1901719
def: "Any process that modulates the rate, frequency, or extent of kinetochore assembly, the aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules." [GOC:ascb_2009, GOC:dph, GOC:tb]
synonym: "regulation of chromosome-kinetochore attachment" NARROW [GOC:ascb_2009, GOC:dph, GOC:tb]
+synonym: "regulation of NMS complex assembly" NARROW []
is_a: GO:0090230 ! regulation of centromere complex assembly
is_a: GO:1902115 ! regulation of organelle assembly
relationship: regulates GO:0051382 ! kinetochore assembly
@@ -380006,8 +379972,7 @@ name: regulation of metaphase plate congression
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of metaphase plate congression, the alignment of chromosomes at the metaphase plate, a plane halfway between the poles of the spindle." [GOC:ascb_2009, GOC:dph, GOC:tb]
synonym: "regulation of chromosome congression" EXACT [GOC:ascb_2009, GOC:dph, GOC:tb]
-is_a: GO:0010564 ! regulation of cell cycle process
-is_a: GO:0060341 ! regulation of cellular localization
+is_a: GO:0032879 ! regulation of localization
relationship: regulates GO:0051310 ! metaphase plate congression
[Term]
@@ -380142,7 +380107,7 @@ name: protein localization involved in establishment of planar polarity
namespace: biological_process
def: "Any process in which a protein is transported to, and/or maintained in, a specific location in a cell that contributes to the establishment of planar polarity." [GOC:ascb_2009, GOC:dph, GOC:tb]
synonym: "protein localisation involved in establishment of planar polarity" EXACT [GOC:mah]
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
relationship: part_of GO:0001736 ! establishment of planar polarity
[Term]
@@ -380284,6 +380249,7 @@ name: regulation of mitotic cell cycle spindle assembly checkpoint
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of the mitotic cell cycle spindle assembly checkpoint, a cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle." [GOC:mtg_cell_cycle]
is_a: GO:0007088 ! regulation of mitotic nuclear division
+is_a: GO:0010965 ! regulation of mitotic sister chromatid separation
is_a: GO:0030071 ! regulation of mitotic metaphase/anaphase transition
is_a: GO:0033047 ! regulation of mitotic sister chromatid segregation
is_a: GO:1903504 ! regulation of mitotic spindle checkpoint
@@ -380442,32 +380408,33 @@ is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
[Term]
id: GO:0090283
-name: regulation of protein glycosylation in Golgi
+name: obsolete regulation of protein glycosylation in Golgi
namespace: biological_process
-def: "Any process that modulates the rate, frequency, or extent of the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in any compartment of the Golgi apparatus." [GOC:pr, GOC:tb]
+def: "OBSOLETE. Any process that modulates the rate, frequency, or extent of the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in any compartment of the Golgi apparatus." [GOC:pr, GOC:tb]
+comment: This term was obsoleted because it represented both a process and a cellular component.
synonym: "regulation of protein amino acid glycosylation in Golgi" EXACT [GOC:bf]
-is_a: GO:0060049 ! regulation of protein glycosylation
-relationship: regulates GO:0033578 ! protein glycosylation in Golgi
+is_obsolete: true
+replaced_by: GO:0060049
[Term]
id: GO:0090284
-name: positive regulation of protein glycosylation in Golgi
+name: obsolete positive regulation of protein glycosylation in Golgi
namespace: biological_process
-def: "Any process that increases the rate, frequency, or extent of the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in any compartment of the Golgi apparatus." [GOC:pr, GOC:tb]
+def: "OBSOLETE. Any process that increases the rate, frequency, or extent of the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in any compartment of the Golgi apparatus." [GOC:pr, GOC:tb]
+comment: This term was obsoleted because it represented both a process and a cellular component.
synonym: "positive regulation of protein amino acid glycosylation in Golgi" EXACT [GOC:bf]
-is_a: GO:0060050 ! positive regulation of protein glycosylation
-is_a: GO:0090283 ! regulation of protein glycosylation in Golgi
-relationship: positively_regulates GO:0033578 ! protein glycosylation in Golgi
+is_obsolete: true
+replaced_by: GO:0060050
[Term]
id: GO:0090285
-name: negative regulation of protein glycosylation in Golgi
+name: obsolete negative regulation of protein glycosylation in Golgi
namespace: biological_process
-def: "Any process that decreases the rate, frequency, or extent of the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in any compartment of the Golgi apparatus." [GOC:pr, GOC:tb]
+def: "OBSOLETE. Any process that decreases the rate, frequency, or extent of the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid in any compartment of the Golgi apparatus." [GOC:pr, GOC:tb]
+comment: This term was obsoleted because it represented both a process and a cellular component.
synonym: "negative regulation of protein amino acid glycosylation in Golgi" EXACT [GOC:bf]
-is_a: GO:0060051 ! negative regulation of protein glycosylation
-is_a: GO:0090283 ! regulation of protein glycosylation in Golgi
-relationship: negatively_regulates GO:0033578 ! protein glycosylation in Golgi
+is_obsolete: true
+replaced_by: GO:0060051
[Term]
id: GO:0090286
@@ -380484,7 +380451,6 @@ name: regulation of cellular response to growth factor stimulus
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus." [GOC:tb]
is_a: GO:0048583 ! regulation of response to stimulus
-is_a: GO:0050794 ! regulation of cellular process
relationship: regulates GO:0071363 ! cellular response to growth factor stimulus
[Term]
@@ -380492,7 +380458,6 @@ id: GO:0090288
name: negative regulation of cellular response to growth factor stimulus
namespace: biological_process
def: "Any process that decreases the rate, frequency, or extent of a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus." [GOC:BHF]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0048585 ! negative regulation of response to stimulus
is_a: GO:0090287 ! regulation of cellular response to growth factor stimulus
relationship: negatively_regulates GO:0071363 ! cellular response to growth factor stimulus
@@ -380538,7 +380503,7 @@ name: nitrogen catabolite regulation of transcription
namespace: biological_process
def: "A transcription regulation process in which the presence of one nitrogen source leads to the modulation of the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources." [GOC:mah, GOC:rb, PMID:19104072]
synonym: "regulation of transcription by nitrogen catabolites" EXACT [GOC:mah]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
is_a: GO:0006808 ! regulation of nitrogen utilization
is_a: GO:0031670 ! cellular response to nutrient
relationship: part_of GO:0071417 ! cellular response to organonitrogen compound
@@ -380549,7 +380514,7 @@ name: nitrogen catabolite activation of transcription
namespace: biological_process
def: "A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources." [GOC:mah, GOC:rb, PMID:19104072]
synonym: "positive regulation of transcription by nitrogen catabolites" EXACT [GOC:mah]
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
is_a: GO:0090293 ! nitrogen catabolite regulation of transcription
[Term]
@@ -380559,7 +380524,7 @@ namespace: biological_process
def: "A transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources." [GOC:mah, GOC:rb, PMID:19104072]
synonym: "negative regulation of transcription by nitrogen catabolites" EXACT [GOC:mah]
synonym: "nitrogen catabolite repression" EXACT [GOC:mah, GOC:rb]
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
is_a: GO:0061984 ! catabolite repression
is_a: GO:0090293 ! nitrogen catabolite regulation of transcription
@@ -380569,7 +380534,8 @@ name: regulation of mitochondrial DNA replication
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of the process in which new strands of DNA are synthesized in the mitochondrion." [GOC:tb]
synonym: "regulation of mitochondrial DNA synthesis" RELATED [GOC:tb]
-is_a: GO:0090329 ! regulation of DNA-dependent DNA replication
+is_a: GO:0090329 ! regulation of DNA-templated DNA replication
+is_a: GO:1901858 ! regulation of mitochondrial DNA metabolic process
relationship: regulates GO:0006264 ! mitochondrial DNA replication
[Term]
@@ -380579,7 +380545,8 @@ namespace: biological_process
def: "Any process that increases the rate, frequency or extent of the process in which new strands of DNA are synthesized in the mitochondrion." [GOC:tb]
synonym: "positive regulation of mitochondrial DNA synthesis" RELATED [GOC:tb]
is_a: GO:0090296 ! regulation of mitochondrial DNA replication
-is_a: GO:2000105 ! positive regulation of DNA-dependent DNA replication
+is_a: GO:1901860 ! positive regulation of mitochondrial DNA metabolic process
+is_a: GO:2000105 ! positive regulation of DNA-templated DNA replication
relationship: positively_regulates GO:0006264 ! mitochondrial DNA replication
[Term]
@@ -380589,7 +380556,8 @@ namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of the process in which new strands of DNA are synthesized in the mitochondrion." [GOC:tb]
synonym: "negative regulation of mitochondrial DNA synthesis" RELATED [GOC:tb]
is_a: GO:0090296 ! regulation of mitochondrial DNA replication
-is_a: GO:2000104 ! negative regulation of DNA-dependent DNA replication
+is_a: GO:1901859 ! negative regulation of mitochondrial DNA metabolic process
+is_a: GO:2000104 ! negative regulation of DNA-templated DNA replication
relationship: negatively_regulates GO:0006264 ! mitochondrial DNA replication
[Term]
@@ -380652,7 +380620,7 @@ def: "The aggregation, arrangement and bonding together of a set of components t
synonym: "spindle assembly involved in meiosis" EXACT []
is_a: GO:0000212 ! meiotic spindle organization
is_a: GO:0051225 ! spindle assembly
-relationship: part_of GO:0140013 ! meiotic nuclear division
+relationship: part_of GO:0045132 ! meiotic chromosome segregation
[Term]
id: GO:0090307
@@ -380662,36 +380630,39 @@ def: "Mitotic bipolar spindle assembly begins with spindle microtubule nucleatio
synonym: "spindle assembly involved in mitosis" EXACT []
is_a: GO:0007052 ! mitotic spindle organization
is_a: GO:0051225 ! spindle assembly
-relationship: part_of GO:0140014 ! mitotic nuclear division
+relationship: part_of GO:0000070 ! mitotic sister chromatid segregation
[Term]
id: GO:0090308
-name: regulation of DNA methylation-dependent heterochromatin assembly
+name: regulation of DNA methylation-dependent heterochromatin formation
namespace: biological_process
-def: "Any process that modulates the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:BHF]
+def: "Any process that modulates the rate, frequency, or extent of DNA methylation-dependent heterochromatin formation." [GOC:BHF]
+synonym: "regulation of DNA methylation-dependent heterochromatin assembly" EXACT []
synonym: "regulation of methylation-dependent chromatin silencing" BROAD []
-is_a: GO:0031445 ! regulation of heterochromatin assembly
-relationship: regulates GO:0006346 ! DNA methylation-dependent heterochromatin assembly
+is_a: GO:0031445 ! regulation of heterochromatin formation
+relationship: regulates GO:0006346 ! DNA methylation-dependent heterochromatin formation
[Term]
id: GO:0090309
-name: positive regulation of DNA methylation-dependent heterochromatin assembly
+name: positive regulation of DNA methylation-dependent heterochromatin formation
namespace: biological_process
-def: "Any process that increases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:BHF]
+def: "Any process that increases the rate, frequency, or extent of DNA methylation-dependent heterochromatin formation." [GOC:BHF]
+synonym: "positive regulation of DNA methylation-dependent heterochromatin assembly" EXACT []
synonym: "positive regulation of methylation-dependent chromatin silencing" BROAD []
-is_a: GO:0031453 ! positive regulation of heterochromatin assembly
-is_a: GO:0090308 ! regulation of DNA methylation-dependent heterochromatin assembly
-relationship: positively_regulates GO:0006346 ! DNA methylation-dependent heterochromatin assembly
+is_a: GO:0031453 ! positive regulation of heterochromatin formation
+is_a: GO:0090308 ! regulation of DNA methylation-dependent heterochromatin formation
+relationship: positively_regulates GO:0006346 ! DNA methylation-dependent heterochromatin formation
[Term]
id: GO:0090310
-name: negative regulation of DNA methylation-dependent heterochromatin assembly
+name: negative regulation of DNA methylation-dependent heterochromatin formation
namespace: biological_process
-def: "Any process that decreases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:BHF]
+def: "Any process that decreases the rate, frequency, or extent of DNA methylation-dependent heterochromatin formation." [GOC:BHF]
+synonym: "negative regulation of DNA methylation-dependent heterochromatin assembly" EXACT []
synonym: "negative regulation of methylation-dependent chromatin silencing" BROAD []
-is_a: GO:0031452 ! negative regulation of heterochromatin assembly
-is_a: GO:0090308 ! regulation of DNA methylation-dependent heterochromatin assembly
-relationship: negatively_regulates GO:0006346 ! DNA methylation-dependent heterochromatin assembly
+is_a: GO:0031452 ! negative regulation of heterochromatin formation
+is_a: GO:0090308 ! regulation of DNA methylation-dependent heterochromatin formation
+relationship: negatively_regulates GO:0006346 ! DNA methylation-dependent heterochromatin formation
[Term]
id: GO:0090311
@@ -380760,7 +380731,6 @@ is_a: GO:0032387 ! negative regulation of intracellular transport
is_a: GO:0033157 ! regulation of intracellular protein transport
is_a: GO:0051224 ! negative regulation of protein transport
relationship: negatively_regulates GO:0006886 ! intracellular protein transport
-relationship: negatively_regulates GO:0034613 ! cellular protein localization
[Term]
id: GO:0090318
@@ -380814,7 +380784,6 @@ namespace: biological_process
def: "The regulated release of a prostaglandin that contributes to the immune response. Prostaglandins are a group of biologically active metabolites which contain a cyclopentane ring." [GOC:dph, GOC:tb]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms.
subset: gocheck_do_not_annotate
-is_a: GO:0002440 ! production of molecular mediator of immune response
is_a: GO:0032310 ! prostaglandin secretion
relationship: part_of GO:0006955 ! immune response
@@ -380825,7 +380794,6 @@ namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis." [GOC:BHF]
is_a: GO:0002082 ! regulation of oxidative phosphorylation
is_a: GO:1901856 ! negative regulation of cellular respiration
-is_a: GO:1903579 ! negative regulation of ATP metabolic process
relationship: negatively_regulates GO:0006119 ! oxidative phosphorylation
[Term]
@@ -380869,11 +380837,12 @@ relationship: regulates GO:0008355 ! olfactory learning
[Term]
id: GO:0090329
-name: regulation of DNA-dependent DNA replication
+name: regulation of DNA-templated DNA replication
namespace: biological_process
-def: "Any process that modulates the rate, frequency, or extent of DNA-dependent DNA replication, the process in which new strands of DNA are synthesized, using parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands." [GOC:dph, GOC:tb]
+def: "Any process that modulates the rate, frequency, or extent of DNA-templated DNA replication, the process in which new strands of DNA are synthesized." [GOC:dph, GOC:tb]
+synonym: "regulation of DNA-dependent DNA replication" EXACT []
is_a: GO:0006275 ! regulation of DNA replication
-relationship: regulates GO:0006261 ! DNA-dependent DNA replication
+relationship: regulates GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:0090330
@@ -380985,32 +380954,28 @@ relationship: negatively_regulates GO:0033299 ! secretion of lysosomal enzymes
[Term]
id: GO:0090342
-name: regulation of cell aging
+name: obsolete regulation of cell aging
namespace: biological_process
-def: "Any process that modulates the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan." [GOC:BHF, GOC:dph, GOC:tb]
-is_a: GO:0050793 ! regulation of developmental process
-is_a: GO:0050794 ! regulation of cellular process
-relationship: regulates GO:0007569 ! cell aging
+def: "OBSOLETE. Any process that modulates the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan." [GOC:BHF, GOC:dph, GOC:tb]
+comment: This term was obsoleted because it represents a phenotype.
+is_obsolete: true
+consider: GO:2000772
[Term]
id: GO:0090343
-name: positive regulation of cell aging
+name: obsolete positive regulation of cell aging
namespace: biological_process
-def: "Any process that increases the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan." [GOC:BHF, GOC:dph, GOC:tb]
-is_a: GO:0048522 ! positive regulation of cellular process
-is_a: GO:0051094 ! positive regulation of developmental process
-is_a: GO:0090342 ! regulation of cell aging
-relationship: positively_regulates GO:0007569 ! cell aging
+def: "OBSOLETE. Any process that increases the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan." [GOC:BHF, GOC:dph, GOC:tb]
+comment: This term was obsoleted because it represents a phenotype.
+is_obsolete: true
[Term]
id: GO:0090344
-name: negative regulation of cell aging
+name: obsolete negative regulation of cell aging
namespace: biological_process
-def: "Any process that decreases the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan." [GOC:BHF, GOC:dph, GOC:tb]
-is_a: GO:0048523 ! negative regulation of cellular process
-is_a: GO:0051093 ! negative regulation of developmental process
-is_a: GO:0090342 ! regulation of cell aging
-relationship: negatively_regulates GO:0007569 ! cell aging
+def: "OBSOLETE. Any process that decreases the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan." [GOC:BHF, GOC:dph, GOC:tb]
+comment: This term was obsoleted because it represents a phenotype.
+is_obsolete: true
[Term]
id: GO:0090345
@@ -381132,7 +381097,7 @@ name: positive regulation of tryptophan metabolic process
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid." [GOC:tb]
synonym: "positive regulation of tryptophan metabolism" EXACT [GOC:tb]
-is_a: GO:0045764 ! positive regulation of cellular amino acid metabolic process
+is_a: GO:0045764 ! positive regulation of amino acid metabolic process
is_a: GO:0090357 ! regulation of tryptophan metabolic process
relationship: positively_regulates GO:0006568 ! tryptophan metabolic process
@@ -381247,26 +381212,26 @@ id: GO:0090371
name: regulation of glycerol transport
namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of the directed movement of glycerol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:jh, GOC:tb]
-is_a: GO:0051049 ! regulation of transport
-relationship: regulates GO:0015793 ! glycerol transport
+is_a: GO:0034762 ! regulation of transmembrane transport
+relationship: regulates GO:0015793 ! glycerol transmembrane transport
[Term]
id: GO:0090372
name: positive regulation of glycerol transport
namespace: biological_process
def: "Any process that increases the rate, frequency, or extent of the directed movement of glycerol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:jh, GOC:tb]
-is_a: GO:0051050 ! positive regulation of transport
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:0090371 ! regulation of glycerol transport
-relationship: positively_regulates GO:0015793 ! glycerol transport
+relationship: positively_regulates GO:0015793 ! glycerol transmembrane transport
[Term]
id: GO:0090373
name: negative regulation of glycerol transport
namespace: biological_process
def: "Any process that decreases the rate, frequency, or extent of the directed movement of glycerol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:jh, GOC:tb]
-is_a: GO:0051051 ! negative regulation of transport
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:0090371 ! regulation of glycerol transport
-relationship: negatively_regulates GO:0015793 ! glycerol transport
+relationship: negatively_regulates GO:0015793 ! glycerol transmembrane transport
[Term]
id: GO:0090374
@@ -381274,7 +381239,6 @@ name: oligopeptide export from mitochondrion
namespace: biological_process
def: "The process in which an oligopeptide is transported out of the mitochondrial matrix. Oligopeptides are molecules that contain a small number (2 to 20) of amino-acid residues connected by peptide linkages." [PMID:11251115]
is_a: GO:0035672 ! oligopeptide transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0090375
@@ -381461,8 +381425,7 @@ def: "Any process that prevents the establishment or decreases the extent of the
synonym: "negative regulation of EPSP" RELATED []
synonym: "negative regulation of excitatory post-synaptic membrane potential" EXACT []
synonym: "reduction of excitatory postsynaptic membrane potential" EXACT [GOC:bf]
-is_a: GO:0009968 ! negative regulation of signal transduction
-is_a: GO:0050805 ! negative regulation of synaptic transmission
+is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:0098815 ! modulation of excitatory postsynaptic potential
relationship: negatively_regulates GO:0060079 ! excitatory postsynaptic potential
@@ -381494,16 +381457,16 @@ is_a: GO:0090395 ! plant cell papilla
id: GO:0090398
name: cellular senescence
namespace: biological_process
-def: "A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest." [GOC:BHF]
-is_a: GO:0007569 ! cell aging
-is_a: GO:0033554 ! cellular response to stress
+def: "A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest." [GOC:BHF, PMID:28682291]
+is_a: GO:0044237 ! cellular metabolic process
+relationship: part_of GO:0033554 ! cellular response to stress
[Term]
id: GO:0090399
name: replicative senescence
namespace: biological_process
def: "A cell aging process associated with the dismantling of a cell as a response to telomere shortening and/or cellular aging." [GOC:BHF]
-is_a: GO:0007569 ! cell aging
+is_a: GO:0044237 ! cellular metabolic process
[Term]
id: GO:0090400
@@ -381575,15 +381538,15 @@ id: GO:0090408
name: phloem nitrate loading
namespace: biological_process
def: "The process of loading nitrate into the sieve tube or companion cell of the phloem for long distance transport from source to sink." [GOC:tb]
-is_a: GO:0015706 ! nitrate transport
+is_a: GO:0015706 ! nitrate transmembrane transport
is_a: GO:0110126 ! phloem loading
[Term]
id: GO:0090409
name: malonyl-CoA synthetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: malonate + ATP + coenzyme A = malonyl-CoA + AMP + diphosphate." [MetaCyc:RXN-12359]
-xref: EC:6.2.1.n3
+def: "Catalysis of the reaction: malonate + ATP + coenzyme A = malonyl-CoA + AMP + diphosphate." [RHEA:32139]
+xref: EC:6.2.1.76
xref: MetaCyc:RXN-12359
xref: RHEA:32139
is_a: GO:0015645 ! fatty acid ligase activity
@@ -381644,7 +381607,6 @@ namespace: molecular_function
def: "Enables the transfer of nicotinate from one side of a membrane to the other." [GOC:tb]
xref: Reactome:R-HSA-8869603 "SLC22A13 transports NCA from extracellular region to cytosol"
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
[Term]
id: GO:0090417
@@ -381681,7 +381643,7 @@ def: "Any process that inhibits or decreases the frequency, rate or extent of tr
synonym: "down-regulation of transcription from RNA polymerase II promoter during the G2/M transition of the mitotic cell cycle" RELATED []
synonym: "negative regulation of transcription from RNA polymerase II promoter during G2/M transition of the mitotic cell cycle" RELATED []
is_a: GO:0000117 ! regulation of transcription involved in G2/M transition of mitotic cell cycle
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
[Term]
id: GO:0090420
@@ -381710,6 +381672,7 @@ is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015234 ! thiamine transmembrane transporter activity
is_a: GO:0015605 ! organophosphate ester transmembrane transporter activity
is_a: GO:0015651 ! quaternary ammonium group transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0090423
@@ -381856,7 +381819,6 @@ def: "Enables the transfer of abscisic acid from one side of a membrane to the o
synonym: "abscisic acid transporter activity" EXACT []
is_a: GO:0005319 ! lipid transporter activity
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015665 ! alcohol transmembrane transporter activity
[Term]
@@ -381884,6 +381846,8 @@ name: FAR/SIN/STRIPAK complex
namespace: cellular_component
def: "A conserved protein phosphatase type 2A complex which contains a protein phosphatase type 2A, a protein phosphatase regulatory subunit, a striatin, an FHA domain protein and other subunits (at least six proteins). In fission yeast this complex negatively regulate the septation initiation network at the spindle pole body." [GOC:vw, PMID:21561862, PMID:22119525]
synonym: "FAR complex" RELATED [GOC:vw]
+synonym: "SIN inhibitory phosphatase (SIP) complex" EXACT []
+synonym: "SIN inhibitory phosphatase complex" EXACT []
synonym: "SIP complex" EXACT [PMID:22119525]
synonym: "striatin interacting phosphatase and kinase complex" EXACT [GOC:vw]
synonym: "STRIPAK signalling complex" RELATED [GOC:vw]
@@ -381928,7 +381892,6 @@ name: glucosinolate:proton symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: glucosinolate(out) + H+(out) = glucosinolate(in) + H+(in)." [PMID:22864417]
synonym: "glucosinolate:hydrogen symporter activity" EXACT []
-is_a: GO:0008509 ! anion transmembrane transporter activity
is_a: GO:0015295 ! solute:proton symporter activity
is_a: GO:1901505 ! carbohydrate derivative transmembrane transporter activity
is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
@@ -381956,6 +381919,7 @@ def: "The directed movement of lithium ions across a membrane." [GOC:tb]
synonym: "lithium ion import" NARROW []
synonym: "lithium ion uptake" EXACT [GOC:tb]
is_a: GO:0010351 ! lithium ion transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -381964,11 +381928,9 @@ name: aspartate transmembrane import into vacuole
namespace: biological_process
def: "The directed movement of aspartate into the vacuole across the vacuolar membrane." [GOC:tb]
synonym: "vacuolar aspartate import" EXACT [GOC:tb]
-is_a: GO:0015740 ! C4-dicarboxylate transport
+is_a: GO:0015810 ! aspartate transmembrane transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0034487 ! vacuolar amino acid transmembrane transport
-is_a: GO:0043090 ! amino acid import
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0090454
@@ -381979,7 +381941,7 @@ synonym: "vacuolar glutamate import" RELATED [GOC:tb]
is_a: GO:0006835 ! dicarboxylic acid transport
is_a: GO:0015800 ! acidic amino acid transport
is_a: GO:0032975 ! amino acid transmembrane import into vacuole
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0042886 ! amide transport
[Term]
id: GO:0090455
@@ -381990,66 +381952,69 @@ synonym: "vacuolar ornithine import" RELATED [GOC:tb]
is_a: GO:0003333 ! amino acid transmembrane transport
is_a: GO:0015822 ! ornithine transport
is_a: GO:0034486 ! vacuolar transmembrane transport
-is_a: GO:0043090 ! amino acid import
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0090459
-name: aspartate homeostasis
+name: intracellular aspartate homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of aspartate within an organism or cell." [GOC:tb]
-is_a: GO:0055081 ! anion homeostasis
-is_a: GO:0080144 ! amino acid homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of aspartate within a cell." [GOC:tb]
+synonym: "aspartate homeostasis" EXACT []
+synonym: "cellular aspartate homeostasis" EXACT []
+is_a: GO:0080144 ! intracellular amino acid homeostasis
[Term]
id: GO:0090460
-name: threonine homeostasis
+name: intracellular threonine homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of threonine within an organism or cell." [GOC:tb]
-is_a: GO:0080144 ! amino acid homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of threonine within a cell." [GOC:tb]
+synonym: "cellular threonine homeostasis" EXACT []
+synonym: "threonine homeostasis" EXACT []
+is_a: GO:0080144 ! intracellular amino acid homeostasis
[Term]
id: GO:0090461
-name: glutamate homeostasis
+name: intracellular glutamate homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of glutamate within an organism or cell." [GOC:tb]
-is_a: GO:0055081 ! anion homeostasis
-is_a: GO:0080144 ! amino acid homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of glutamate within a cell." [GOC:tb]
+synonym: "cellular glutamate homeostasis" EXACT []
+synonym: "glutamate homeostasis" EXACT []
+is_a: GO:0080144 ! intracellular amino acid homeostasis
[Term]
id: GO:0090462
-name: ornithine homeostasis
+name: intracellular ornithine homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of ornithine within an organism or cell." [GOC:tb]
-is_a: GO:0055080 ! cation homeostasis
-is_a: GO:0055081 ! anion homeostasis
-is_a: GO:0080144 ! amino acid homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of orthinine within a cell." [GOC:tb]
+synonym: "cellular ornithine homeostasis" EXACT []
+synonym: "ornithine homeostasis" EXACT []
+is_a: GO:0080144 ! intracellular amino acid homeostasis
[Term]
id: GO:0090463
-name: lysine homeostasis
+name: intracellular lysine homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of lysine within an organism or cell." [GOC:tb]
-is_a: GO:0055080 ! cation homeostasis
-is_a: GO:0055081 ! anion homeostasis
-is_a: GO:0080144 ! amino acid homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of lysine within a cell." [GOC:tb]
+synonym: "cellular lysine homeostasis" EXACT []
+synonym: "lysine homeostasis" EXACT []
+is_a: GO:0080144 ! intracellular amino acid homeostasis
[Term]
id: GO:0090464
-name: histidine homeostasis
+name: intracellular histidine homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of histidine within an organism or cell." [GOC:tb]
-is_a: GO:0080144 ! amino acid homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of histidine within a cell." [GOC:tb]
+synonym: "cellular histidine homeostasis" EXACT []
+synonym: "histidine homeostasis" EXACT []
+is_a: GO:0080144 ! intracellular amino acid homeostasis
[Term]
id: GO:0090465
-name: arginine homeostasis
+name: intracellular arginine homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of arginine within an organism or cell." [GOC:tb]
-is_a: GO:0055080 ! cation homeostasis
-is_a: GO:0055081 ! anion homeostasis
-is_a: GO:0080144 ! amino acid homeostasis
+def: "A homeostatic process involved in the maintenance of a steady state level of arginine within a cell." [GOC:tb]
+synonym: "arginine homeostasis" EXACT []
+synonym: "cellular arginine homeostasis" EXACT []
+is_a: GO:0080144 ! intracellular amino acid homeostasis
[Term]
id: GO:0090470
@@ -382148,9 +382113,12 @@ consider: GO:1903467
[Term]
id: GO:0090486
-name: small RNA 2'-O-methyltransferase
+name: small RNA 2'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the oxygen atom of a nucleoside residue in a small RNA molecule. Reaction: S-adenosyl-L-methionine + small RNA <=> S-adenosyl-L-homocysteine + small RNA containing a 3'-terminal 2'-O-methylnucleotide." [EC:2.1.1.n8, GOC:tb, GOC:vw]
+def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the oxygen atom of a nucleoside residue in a small RNA molecule. Reaction: S-adenosyl-L-methionine + small RNA = S-adenosyl-L-homocysteine + small RNA containing a 3'-terminal 2'-O-methylnucleotide." [GOC:tb, GOC:vw, RHEA:37887]
+synonym: "small RNA 2'-O-methyltransferase" EXACT []
+xref: EC:2.1.1.386
+xref: RHEA:37887
is_a: GO:0062105 ! RNA 2'-O-methyltransferase activity
[Term]
@@ -382366,11 +382334,8 @@ id: GO:0090514
name: L-tyrosine transmembrane import into vacuole
namespace: biological_process
def: "The directed movement of L-tyrosine into the vacuole across the vacuolar membrane." [GOC:al]
-is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0015828 ! tyrosine transport
is_a: GO:0032975 ! amino acid transmembrane import into vacuole
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -382379,7 +382344,6 @@ name: L-glutamate transmembrane import into vacuole
namespace: biological_process
def: "The directed movement of L-glutamate into the vacuole across the vacuolar membrane." [GOC:al]
is_a: GO:0015813 ! L-glutamate transmembrane transport
-is_a: GO:0051938 ! L-glutamate import
is_a: GO:0090454 ! glutamate transmembrane import into vacuole
[Term]
@@ -382389,8 +382353,6 @@ namespace: biological_process
def: "The directed movement of L-serine into the vacuole across the vacuolar membrane." [GOC:al]
is_a: GO:0015825 ! L-serine transport
is_a: GO:0034491 ! neutral amino acid transmembrane import into vacuole
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -382427,7 +382389,7 @@ is_a: GO:0034059 ! response to anoxia
id: GO:0090520
name: sphingolipid mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals mediated by a sphingolipid." [PMID:9525917]
+def: "The series of molecular signals mediated by a sphingolipid." [PMID:9525917]
synonym: "ceramide 1-phosphate signaling pathway" NARROW [PMID:20870412]
synonym: "ceramide signaling pathway" NARROW [PMID:20870412]
synonym: "sphingolipid mediated signal transduction" EXACT [GOC:signaling]
@@ -382438,17 +382400,17 @@ is_a: GO:0007165 ! signal transduction
[Term]
id: GO:0090521
-name: glomerular visceral epithelial cell migration
+name: podocyte cell migration
namespace: biological_process
def: "The orderly movement of a podocyte from one site to another, often during the development of a multicellular organism or multicellular structure. A podocyte is a specialized kidney epithelial cell." [GOC:pm, PMID:21402783]
-synonym: "podocyte cell migration" RELATED [GOC:pm]
+synonym: "glomerular visceral epithelial cell migration" EXACT []
is_a: GO:0010631 ! epithelial cell migration
[Term]
id: GO:0090522
name: vesicle tethering involved in exocytosis
namespace: biological_process
-def: "The initial, indirect interaction between a secretory vesicle membrane and a site of exocytosis in the plasma membrane. This interaction is mediated by tethering factors (or complexes), which interact with both membranes. Interaction can occur via direct binding to membrane phospholipids or membrane proteins, or via binding to vesicle coat proteins. This process is distinct from and prior to docking and fusion." [GOC:rn, PMID:10559876, PMID:17052174, PMID:17488620, PMID:22420621, PMID:27243008]
+def: "The initial, indirect interaction between a secretory vesicle membrane and a site of exocytosis in the plasma membrane. This interaction is mediated by tethering factors (or complexes), which interact with both membranes. Interaction can occur via direct binding to membrane phospholipids or membrane proteins, or via binding to vesicle coat proteins. This process is distinct from and prior to docking and fusion." [GOC:rn, PMID:10559876, PMID:17052174, PMID:17488620, PMID:22420621, PMID:27243008]
synonym: "vesicle tethering to plasma membrane" NARROW []
is_a: GO:0099022 ! vesicle tethering
is_a: GO:0140029 ! exocytic process
@@ -382509,7 +382471,7 @@ is_a: GO:0019853 ! L-ascorbic acid biosynthetic process
id: GO:0090532
name: L-ascorbic acid biosynthetic process via UDP-alpha-D-glucuronate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-ascorbic acid via the intermediate UDP-alpha-D-glucuronate." [BioCyc:PWY3DJ-35471, GOC:yaf, PMID:11153268, UniPathway:UPA00991]
+def: "The chemical reactions and pathways resulting in the formation of L-ascorbic acid via the intermediate UDP-alpha-D-glucuronate." [GOC:yaf, PMID:11153268]
comment: This pathway occurs in most vertebrates, although not in guinea pigs and primates, including humans.
synonym: "L-ascorbic acid biosynthesis via UDP-alpha-D-glucuronate" RELATED []
is_a: GO:0019853 ! L-ascorbic acid biosynthetic process
@@ -382570,7 +382532,7 @@ is_a: GO:0140115 ! export across plasma membrane
id: GO:0090540
name: bacterial cellulose biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation, as it occurs in certain types of bacteria, mainly Acetobacter, Sarcina ventriculi and Agrobacteria." [DOI:10.1016/S0268-005X(87)80024-3, DOI:10.1023/A\:1009272904582, GOC:tb, GOC:yaf, UniPathway:UPA00694]
+def: "The chemical reactions and pathways resulting in the formation of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation, as it occurs in certain types of bacteria, mainly Acetobacter, Sarcina ventriculi and Agrobacteria." [GOC:yaf, PMID:24097954]
synonym: "bacterial cellulose biosynthesis" EXACT [GOC:yaf]
is_a: GO:0030244 ! cellulose biosynthetic process
@@ -382982,7 +382944,7 @@ is_a: GO:0009611 ! response to wounding
id: GO:0090595
name: acetyl-CoA:L-lysine N6-acetyltransferase
namespace: molecular_function
-def: "Catalysis of the reaction: L-lysine + acetyl-CoA = N6-acetyl-L-lysine + CoA + H(+)." [MetaCyc:LYSACET-RXN]
+def: "Catalysis of the reaction: L-lysine + acetyl-CoA = N6-acetyl-L-lysine + CoA + H+." [MetaCyc:LYSACET-RXN]
is_a: GO:0008080 ! N-acetyltransferase activity
[Term]
@@ -383093,8 +383055,8 @@ is_a: GO:0001708 ! cell fate specification
id: GO:0090611
name: ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a protein or peptide, via the multivesicular body (MVB) sorting pathway; proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation. This process is independent of ubiquitination." [PMID:22547407]
-is_a: GO:0051603 ! proteolysis involved in cellular protein catabolic process
+def: "The chemical reactions and pathways resulting in the breakdown of a protein or peptide, via the multivesicular body (MVB) sorting pathway; proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation. This process is independent of ubiquitination." [PMID:22547407]
+is_a: GO:0051603 ! proteolysis involved in protein catabolic process
[Term]
id: GO:0090612
@@ -383104,6 +383066,7 @@ def: "Catalysis of the reaction: cyclic adenosine monophosphate + H2O = cyclic i
synonym: "cyclic adenosine monophosphate deaminase activity" EXACT []
xref: EC:3.5.4.46
xref: RHEA:22908
+is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
is_a: GO:0019239 ! deaminase activity
[Term]
@@ -383113,6 +383076,7 @@ namespace: molecular_function
def: "Catalysis of the reaction: 5'deoxyadenosine + H2O = 5'deoxyinosine + NH3." [PMID:23968233, RHEA:42892]
xref: EC:3.5.4.41
xref: RHEA:42892
+is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
is_a: GO:0019239 ! deaminase activity
[Term]
@@ -383122,6 +383086,7 @@ namespace: molecular_function
def: "Catalysis of the reaction: 5'methyl thioadenosine + H2O = 5'methyl thioinosine + NH3." [PMID:23968233, RHEA:25025]
xref: EC:3.5.4.31
xref: RHEA:25025
+is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
is_a: GO:0019239 ! deaminase activity
[Term]
@@ -383192,16 +383157,18 @@ id: GO:0090624
name: endoribonuclease activity, cleaving miRNA-paired mRNA
namespace: molecular_function
def: "Catalysis of the endonucleolytic cleavage of the mRNA in a double-stranded RNA molecule formed by the base pairing of an mRNA with an miRNA." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:15260970, PMID:19239888]
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0090625
-name: mRNA destabilization-mediated gene silencing by siRNA
+name: siRNA-mediated gene silencing by mRNA destabilization
namespace: biological_process
-def: "The process in which small interfering RNAs (siRNAs) direct the cleavage of target mRNAs. Once incorporated into a RNA-induced silencing complex (RISC), a siRNA will typically direct cleavage by base pairing with perfect or near-perfect complementarity to the target mRNA." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:15260970]
+def: "An siRNA-mediated post-transcriptional gene silencing pathway in which small interfering RNAs (siRNAs) direct the cleavage of target mRNAs. Once incorporated into a RNA-induced silencing complex (RISC), an siRNA will typically direct cleavage by base pairing with perfect or near-perfect complementarity to the target mRNA." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:15260970]
+synonym: "gene silencing by mRNA cleavage" BROAD []
synonym: "mRNA cleavage involved in gene silencing by siRNA" EXACT []
-is_a: GO:0035194 ! post-transcriptional gene silencing by RNA
-is_a: GO:0098795 ! mRNA destabilization-mediated gene silencing
+synonym: "mRNA destabilization-mediated gene silencing by siRNA" EXACT []
+is_a: GO:0061157 ! mRNA destabilization
+is_a: GO:0140766 ! siRNA-mediated gene silencing
[Term]
id: GO:0090626
@@ -383306,7 +383273,7 @@ relationship: part_of GO:0030057 ! desmosome
id: GO:0090636
name: outer dense plaque of desmosome
namespace: cellular_component
-def: "The desmosomal part containing plakoglobins, plakophilins, the N-termini of desmoplakins, as well as the cytoplasmic tails of the desmosomal cadherins, which together attach the plaque to the plasma membrane." [PMID:20066089]
+def: "The desmosomal part containing plakoglobins, plakophilins, the N-termini of desmoplakins, as well as the cytoplasmic tails of the desmosomal cadherins, which together attach the plaque to the plasma membrane." [PMID:20066089]
is_a: GO:0110165 ! cellular anatomical entity
relationship: part_of GO:0030057 ! desmosome
@@ -383382,17 +383349,17 @@ is_a: GO:0045087 ! innate immune response
id: GO:0090646
name: mitochondrial tRNA processing
namespace: biological_process
-def: "The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group, in the mitochondrion." [GOC:vw]
+def: "The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group, in the mitochondrion." [GOC:vw]
is_a: GO:0000963 ! mitochondrial RNA processing
is_a: GO:0008033 ! tRNA processing
[Term]
id: GO:0090647
-name: modulation of age-related behavioral decline
+name: obsolete modulation of age-related behavioral decline
namespace: biological_process
-def: "Any process that modulates the processes that arise as an organism progresses toward the end of its lifespan that results in a decline in behavioral activities such as locomotory behavior, and learning or memory." [GOC:cjm, GOC:kmv, PMID:20523893]
-is_a: GO:0065008 ! regulation of biological quality
-relationship: part_of GO:0007568 ! aging
+def: "OBSOLETE. Any process that modulates the processes that arise as an organism progresses toward the end of its lifespan that results in a decline in behavioral activities such as locomotory behavior, and learning or memory." [GOC:cjm, GOC:kmv, PMID:20523893]
+comment: This term was obsoleted because it represents a phenotype.
+is_obsolete: true
[Term]
id: GO:0090648
@@ -383613,8 +383580,8 @@ is_a: GO:0090673 ! endothelial cell-matrix adhesion
id: GO:0090675
name: intermicrovillar adhesion
namespace: biological_process
-def: "The biological adhesion process by which adjacent microvilli attach to each other through Ca(2+)-dependent adhesion links made of protocadherin-24 and mucin-like protocadherin." [GOC:lb, PMID:24725409]
-is_a: GO:0022610 ! biological adhesion
+def: "The cell-cell adhesion process by which adjacent microvilli attach to each other through Ca(2+)-dependent adhesion links made of protocadherin-24 and mucin-like protocadherin." [GOC:lb, PMID:24725409]
+is_a: GO:0034109 ! homotypic cell-cell adhesion
relationship: part_of GO:1904970 ! brush border assembly
[Term]
@@ -383650,10 +383617,11 @@ relationship: part_of GO:0090677 ! reversible differentiation
[Term]
id: GO:0090680
-name: disruption by virus of host outer membrane
+name: viral release via disruption of host outer membrane
namespace: biological_process
-def: "A process by which a virus has a negative effect on the functioning of a host outer membrane." [PMID:17900620]
-is_a: GO:0044662 ! disruption by virus of host cell membrane
+def: "The dissemination of mature viral particles from a host cell via the destabilization of the cell outer membrane." [PMID:17900620]
+synonym: "disruption by virus of host outer membrane" RELATED []
+is_a: GO:0044659 ! viral release from host cell by cytolysis
[Term]
id: GO:0090681
@@ -383702,10 +383670,12 @@ is_a: GO:0006403 ! RNA localization
[Term]
id: GO:0090686
-name: glycine betaine-activated nonselective monovalent cation channel activity
+name: glycine betaine-activated nonselective monoatomic cation channel activity
namespace: molecular_function
-def: "Enables the transmembrane transfer of a monovalent cation by a channel that opens when glycine betaine has been bound by the channel complex or one of its constituent parts." [GOC:kmv, PMID:24212673]
-is_a: GO:0099094 ! ligand-gated cation channel activity
+def: "Enables the transmembrane transfer of a monoatomic cation by a channel that opens when glycine betaine has been bound by the channel complex or one of its constituent parts." [GOC:kmv, PMID:24212673]
+synonym: "glycine betaine-activated nonselective monovalent cation channel activity" RELATED []
+is_a: GO:0015199 ! amino-acid betaine transmembrane transporter activity
+is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
[Term]
id: GO:0090687
@@ -383757,8 +383727,8 @@ relationship: part_of GO:0031966 ! mitochondrial membrane
id: GO:0090693
name: plant organ senescence
namespace: biological_process
-def: "The process that occurs in a plant organ near the end of its active life that is associated with the dismantling of cell components and membranes, and an overall decline in metabolism." [GOC:tb]
-is_a: GO:0007568 ! aging
+def: "A plant organ developmental process during which a plant dismantles cellular components to reclaim the cellular building blocks and nutrients that have been deposited in the plant organs during growth." [GOC:tb, PMID:17177638, PMID:34938309]
+is_a: GO:0032502 ! developmental process
relationship: part_of GO:0099402 ! plant organ development
[Term]
@@ -384023,6 +383993,7 @@ namespace: molecular_function
alt_id: GO:0050827
def: "Interacting selectively with one or more biological molecules in another (target) organism, initiating pathogenesis (leading to an abnormal, generally detrimental state) in the target organism. The activity should refer to an evolved function of the active gene product, i.e. one that was selected for. Examples include the activity of botulinum toxin, and snake venom." [GOC:pt]
subset: goslim_generic
+subset: prokaryote_subset
synonym: "toxin receptor binding" EXACT []
xref: Wikipedia:Toxin
is_a: GO:0003674 ! molecular_function
@@ -384100,11 +384071,12 @@ is_a: GO:0000723 ! telomere maintenance
[Term]
id: GO:0090740
-name: integral component of pigment granule membrane
+name: obsolete integral component of pigment granule membrane
namespace: cellular_component
-def: "The component of the pigment granule membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [PMID:11294610]
-is_a: GO:0031301 ! integral component of organelle membrane
-relationship: part_of GO:0090741 ! pigment granule membrane
+def: "OBSOLETE. The component of the pigment granule membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [PMID:11294610]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0090741
[Term]
id: GO:0090741
@@ -384223,7 +384195,7 @@ def: "Any process involved in the balance between food intake (energy input) and
synonym: "negative regulation of energy homeostasis" RELATED []
synonym: "positive regulation of energy homeostasis" RELATED []
synonym: "regulation of energy homeostasis" RELATED []
-is_a: GO:0048871 ! multicellular organismal homeostasis
+is_a: GO:0048871 ! multicellular organismal-level homeostasis
[Term]
id: GO:0097010
@@ -384370,7 +384342,7 @@ is_a: GO:0120031 ! plasma membrane bounded cell projection assembly
id: GO:0097027
name: ubiquitin-protein transferase activator activity
namespace: molecular_function
-def: "Binds to and increases the activity of a ubiquitin-protein transferase, an enzyme that catalyzes the covalent attachment of ubiquitin to lysine in a substrate protein." [GOC:rb, PMID:18321851]
+def: "Binds to and increases the activity of a ubiquitin-protein transferase." [GOC:rb, PMID:18321851]
is_a: GO:0008047 ! enzyme activator activity
is_a: GO:0055106 ! ubiquitin-protein transferase regulator activity
@@ -384503,12 +384475,13 @@ is_a: GO:0046189 ! phenol-containing compound biosynthetic process
[Term]
id: GO:0097042
-name: extrinsic component of fungal-type vacuolar membrane
+name: obsolete extrinsic component of fungal-type vacuolar membrane
namespace: cellular_component
-def: "The component of a fungal-type vacuolar membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:jh, PMID:21454883]
+def: "OBSOLETE. The component of a fungal-type vacuolar membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:jh, PMID:21454883]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "extrinsic to fungal-type vacuolar membrane" NARROW []
-is_a: GO:0000306 ! extrinsic component of vacuolar membrane
-relationship: part_of GO:0000329 ! fungal-type vacuole membrane
+is_obsolete: true
+consider: GO:0000329
[Term]
id: GO:0097043
@@ -384519,11 +384492,12 @@ is_a: GO:0043966 ! histone H3 acetylation
[Term]
id: GO:0097044
-name: histone H3-K56 acetylation in response to DNA damage
+name: obsolete histone H3-K56 acetylation in response to DNA damage
namespace: biological_process
-def: "The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 56 of the histone as a result of the detection of DNA damage within a cell." [GOC:pr, GOC:vw, PMID:18344406]
-is_a: GO:0097043 ! histone H3-K56 acetylation
-relationship: part_of GO:0006974 ! cellular response to DNA damage stimulus
+def: "OBSOLETE. The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 56 of the histone as a result of the detection of DNA damage within a cell." [GOC:pr, GOC:vw, PMID:18344406]
+comment: This term was obsoleted because it represents a molecular function and a GO-CAM model.
+is_obsolete: true
+consider: GO:0140861
[Term]
id: GO:0097045
@@ -384602,7 +384576,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of L-kynure
synonym: "L-kynurenine breakdown" EXACT []
synonym: "L-kynurenine catabolism" EXACT []
synonym: "L-kynurenine degradation" EXACT []
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0019439 ! aromatic compound catabolic process
is_a: GO:0042182 ! ketone catabolic process
is_a: GO:0097052 ! L-kynurenine metabolic process
@@ -384633,15 +384607,16 @@ is_a: GO:1901162 ! primary amino compound biosynthetic process
[Term]
id: GO:0097056
-name: selenocysteinyl-tRNA(Sec) biosynthetic process
+name: obsolete selenocysteinyl-tRNA(Sec) biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of selenocysteinyl-tRNA(Sec). This process occurs through the following steps: a unique serine-tRNA with a UGA recognizing anticodon is first aminoacylated with serine; this is then phosphorylated by phosphoseryl-tRNA[Ser]Sec kinase; lastly, selenium is swapped for the phosphate on the serine." [GOC:yaf, PMID:15317934, UniPathway:UPA00906]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of selenocysteinyl-tRNA(Sec). This process occurs through the following steps: a unique serine-tRNA with a UGA recognizing anticodon is first aminoacylated with serine; this is then phosphorylated by phosphoseryl-tRNA[Ser]Sec kinase; lastly, selenium is swapped for the phosphate on the serine." [GOC:yaf, PMID:15317934]
+comment: This term was obsoleted because it is the same process as GO:0001717 conversion of seryl-tRNAsec to selenocys-tRNAsec.
synonym: "selenocysteinyl-tRNA(Sec) anabolism" EXACT []
synonym: "selenocysteinyl-tRNA(Sec) biosynthesis" EXACT []
synonym: "selenocysteinyl-tRNA(Sec) formation" EXACT []
synonym: "selenocysteinyl-tRNA(Sec) synthesis" EXACT []
-is_a: GO:0006399 ! tRNA metabolic process
-is_a: GO:0032774 ! RNA biosynthetic process
+is_obsolete: true
+replaced_by: GO:0001717
[Term]
id: GO:0097057
@@ -384657,7 +384632,7 @@ namespace: cellular_component
def: "A heterodimeric protein complex that is composed of cardiotrophin-like cytokine factor 1 (product of the CLCF1 gene) and cytokine receptor-like factor 1 (product of the CRLF gene) and is secreted into the extracellular space. The CRLF-CLCF1 complex is a ligand for the ciliary neurotrophic factor (CNTF) receptor complex." [GOC:BHF, PMID:10966616]
synonym: "CLF-CLC complex" NARROW []
is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+relationship: part_of GO:0005576 ! extracellular region
[Term]
id: GO:0097059
@@ -384666,7 +384641,7 @@ namespace: cellular_component
def: "A protein complex that is composed of two soluble ciliary neurotrophic factor receptor alpha subunits (product of the CNTFR gene) and two molecules of cardiotrophin-like cytokine factor 1 (product of the CLCF1 gene). The complex is secreted into the extracellular space." [GOC:BHF, PMID:11285233]
synonym: "sCNTFR-CLC complex" NARROW []
is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+relationship: part_of GO:0005576 ! extracellular region
[Term]
id: GO:0097060
@@ -384700,7 +384675,7 @@ name: cadmium ion sensor activity
namespace: molecular_function
def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of cadmium (Cd++)." [GOC:rs, PMID:19456862]
is_a: GO:0046870 ! cadmium ion binding
-is_a: GO:0140299 ! small molecule sensor activity
+is_a: GO:0140784 ! metal ion sensor activity
[Term]
id: GO:0097064
@@ -384744,6 +384719,7 @@ synonym: "response to thyroxine stimulus" EXACT [GOC:dos]
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0043200 ! response to amino acid
is_a: GO:0097066 ! response to thyroid hormone
+is_a: GO:1902074 ! response to salt
is_a: GO:1904386 ! response to L-phenylalanine derivative
[Term]
@@ -384756,6 +384732,7 @@ is_a: GO:0071230 ! cellular response to amino acid stimulus
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0097067 ! cellular response to thyroid hormone stimulus
is_a: GO:0097068 ! response to thyroxine
+is_a: GO:1902075 ! cellular response to salt
is_a: GO:1904387 ! cellular response to L-phenylalanine derivative
[Term]
@@ -384811,7 +384788,7 @@ name: transforming growth factor beta activated kinase 1 complex
namespace: cellular_component
def: "A protein complex that possesses protein kinase activity and activates the I-kappa B kinase complex (IKK) and mitogen-activated protein (MAP) kinases in response to TRAF6 signaling. It comprises the catalytic subunit TAK1 complexed to the regulatory subunits, termed TABs (TAK1-binding subunits)." [GOC:cna, PMID:16410796, PMID:17496917, PMID:18021073]
synonym: "TAK1 kinase complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902911 ! protein kinase complex
[Term]
id: GO:0097077
@@ -384819,7 +384796,7 @@ name: copper ion sensor activity
namespace: molecular_function
def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+)." [GOC:rs, PMID:19928961]
is_a: GO:0005507 ! copper ion binding
-is_a: GO:0140299 ! small molecule sensor activity
+is_a: GO:0140784 ! metal ion sensor activity
[Term]
id: GO:0097078
@@ -384835,8 +384812,8 @@ namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: selenite(out) + H+(out) = selenite(in) + H+(in)." [GOC:mcc, PMID:20861301]
synonym: "selenite:H+ symporter activity" EXACT []
synonym: "selenite:hydrogen symporter activity" EXACT []
-is_a: GO:0008509 ! anion transmembrane transporter activity
is_a: GO:0015295 ! solute:proton symporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0097080
@@ -384844,7 +384821,7 @@ name: plasma membrane selenite transport
namespace: biological_process
def: "The directed movement of inorganic selenite (HSeO3-1 at physiological pH) across a plasma membrane." [GOC:mcc, PMID:20861301]
synonym: "plasma membrane hydrogenselenite transport" EXACT []
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0097081
@@ -384923,8 +384900,7 @@ name: methyl-branched fatty acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving methyl-branched fatty acids, aliphatic monocarboxylic acids with methyl branches on the main chain." [GOC:rs, PMID:19933331]
synonym: "methyl-branched fatty acid metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
-is_a: GO:0006629 ! lipid metabolic process
+is_a: GO:0006631 ! fatty acid metabolic process
[Term]
id: GO:0097090
@@ -385062,7 +385038,7 @@ relationship: part_of GO:0099068 ! postsynapse assembly
id: GO:0097105
name: presynaptic membrane assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form a presynaptic membrane, including any proteins associated with the membrane, but excluding other cellular components. A presynaptic membrane is a specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction." [GOC:BHF, GOC:pr, GOC:sjp, PMID:15797875, PMID:18550748]
+def: "The aggregation, arrangement and bonding together of a set of components to form a presynaptic membrane, including any proteins associated with the membrane, but excluding other cellular components. A presynaptic membrane is a specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction." [GOC:BHF, GOC:pr, GOC:sjp, PMID:15797875, PMID:18550748]
comment: Note that 'presynaptic membrane' in this term should not be mistaken with 'presynaptic active zone'. The latter encompasses more than the former, as it also includes the specialized cortical cytoskeletal matrix in the cell cortex of a presynaptic neuron.
subset: goslim_synapse
synonym: "pre-synaptic membrane assembly" EXACT []
@@ -385416,7 +385392,7 @@ id: GO:0097149
name: centralspindlin complex
namespace: cellular_component
def: "A heterotetrameric protein complex playing a key role in the formation of the central spindle in mitosis. Made up of two molecules each of a mitotic kinesin (ZEN-4 in Caenorhabditis elegans or MKLP1 in mammals) and of two molecules each of a GTPase activating protein (GAP) factor (CYK-4 in Caenorhabditis elegans or MgcRacGAP in mammals)." [GOC:ans, PMID:11782313, PMID:16236794]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140535 ! intracellular protein-containing complex
relationship: part_of GO:0072686 ! mitotic spindle
[Term]
@@ -385562,7 +385538,6 @@ def: "Any process that modulates the frequency, rate or extent of mRNA translati
synonym: "regulation of mRNA translation in response to circadian clock" EXACT []
is_a: GO:0006417 ! regulation of translation
is_a: GO:0007623 ! circadian rhythm
-is_a: GO:0032501 ! multicellular organismal process
[Term]
id: GO:0097168
@@ -385577,7 +385552,7 @@ id: GO:0097169
name: AIM2 inflammasome complex
namespace: cellular_component
def: "An inflammasome complex that consists of AIM2, ASC, and caspase-1. AIM2 is a member of the HN-200 protein family that appears to be the sensor of cytosolic double-stranded DNA." [GOC:vp, PMID:20303873]
-is_a: GO:0061702 ! inflammasome complex
+is_a: GO:0061702 ! canonical inflammasome complex
[Term]
id: GO:0097170
@@ -385592,7 +385567,7 @@ is_a: GO:0009225 ! nucleotide-sugar metabolic process
id: GO:0097171
name: ADP-L-glycero-beta-D-manno-heptose biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of ADP-L-glycero-beta-D-manno-heptose, an ADP-L-glycero-D-manno-heptose having beta-configuration at the anomeric centre of the heptose. ADP-L-glycero-beta-D-manno-heptose (also called ADP-L-beta-D-heptose or ADP-L-glycero-D-manno-heptose) is a nucleotide-sugar precursor of the inner core lipopolysaccharide (LPS) from D-glycero-beta-D-manno-heptose 7-phosphate." [GOC:yaf, UniPathway:UPA00356]
+def: "The chemical reactions and pathways resulting in the formation of ADP-L-glycero-beta-D-manno-heptose, an ADP-L-glycero-D-manno-heptose having beta-configuration at the anomeric centre of the heptose. ADP-L-glycero-beta-D-manno-heptose (also called ADP-L-beta-D-heptose or ADP-L-glycero-D-manno-heptose) is a nucleotide-sugar precursor of the inner core lipopolysaccharide (LPS) from D-glycero-beta-D-manno-heptose 7-phosphate." [GOC:yaf, PMID:11751812]
synonym: "ADP-L-glycero-beta-D-manno-heptose anabolism" EXACT []
synonym: "ADP-L-glycero-beta-D-manno-heptose biosynthesis" EXACT []
synonym: "ADP-L-glycero-beta-D-manno-heptose formation" EXACT []
@@ -385614,7 +385589,7 @@ is_a: GO:0019752 ! carboxylic acid metabolic process
id: GO:0097173
name: N-acetylmuramic acid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of N-acetylmuramic acid (MurNAc), a monosaccharide derivative of N-acetylglucosamine." [GOC:yaf, UniPathway:UPA00342]
+def: "The chemical reactions and pathways resulting in the breakdown of N-acetylmuramic acid (MurNAc), a monosaccharide derivative of N-acetylglucosamine." [GOC:yaf]
synonym: "N-acetylmuramate breakdown" EXACT [PubChem_Compound:5462244]
synonym: "N-acetylmuramate catabolic process" EXACT [PubChem_Compound:5462244]
synonym: "N-acetylmuramate catabolism" EXACT [PubChem_Compound:5462244]
@@ -385641,7 +385616,7 @@ is_a: GO:0032787 ! monocarboxylic acid metabolic process
id: GO:0097175
name: 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 1,6-anhydro-N-acetylmuramic acid, the 1,6-anhydro-derivative of N-acetyl-beta-muramic acid." [GOC:yaf, PMID:15901686, UniPathway:UPA00343]
+def: "The chemical reactions and pathways resulting in the breakdown of 1,6-anhydro-N-acetylmuramic acid, the 1,6-anhydro-derivative of N-acetyl-beta-muramic acid." [GOC:yaf, PMID:15901686]
synonym: "1,6-anhydro-N-acetyl-beta-muramate breakdown" EXACT []
synonym: "1,6-anhydro-N-acetyl-beta-muramate catabolic process" EXACT []
synonym: "1,6-anhydro-N-acetyl-beta-muramate catabolism" EXACT []
@@ -385746,6 +385721,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an azide stimulus." [GOC:yaf, PMID:16846222]
is_a: GO:0010035 ! response to inorganic substance
is_a: GO:1901698 ! response to nitrogen compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:0097185
@@ -385755,6 +385731,7 @@ def: "Any process that results in a change in state or activity of a cell (in te
is_a: GO:0071241 ! cellular response to inorganic substance
is_a: GO:0097184 ! response to azide
is_a: GO:1901699 ! cellular response to nitrogen compound
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:0097186
@@ -385798,7 +385775,7 @@ id: GO:0097190
name: apoptotic signaling pathway
namespace: biological_process
alt_id: GO:0008624
-def: "A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis]
+def: "The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis]
comment: This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways.
synonym: "apoptotic signalling pathway" EXACT [GOC:mah]
synonym: "induction of apoptosis by extracellular signals" EXACT []
@@ -385809,7 +385786,7 @@ relationship: part_of GO:0006915 ! apoptotic process
id: GO:0097191
name: extrinsic apoptotic signaling pathway
namespace: biological_process
-def: "A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis, GOC:yaf, PMID:17340152]
+def: "The series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with either a ligand binding to a cell surface receptor, or a ligand being withdrawn from a cell surface receptor (e.g. in the case of signaling by dependence receptors), and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis, GOC:yaf, PMID:17340152]
comment: Fas acts as a death receptor with a role in apoptosis, but can also act as a non-apoptotic signal transducer.
synonym: "death receptor-mediated apoptosis" NARROW []
synonym: "extrinsic apoptosis" NARROW []
@@ -385823,7 +385800,7 @@ is_a: GO:0097190 ! apoptotic signaling pathway
id: GO:0097192
name: extrinsic apoptotic signaling pathway in absence of ligand
namespace: biological_process
-def: "A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis, PMID:15044679, PMID:20816705]
+def: "The series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis, PMID:15044679, PMID:20816705]
comment: For dependence receptors, absence of a ligand or withdrawal of a ligand from a receptor acts as a signal. An example of 'extrinsic apoptotic signaling pathway in absence of ligand' is withdrawal of a growth factor such as NGF, even if traditionally apoptosis induced via growth factor withdrawal has been classified as an instance of intrinsic apoptosis. See an example in PMID:19767770. Ligands whose withdrawal or absence induce apoptosis should be annotated to GO:2001239 'regulation of extrinsic apoptotic signaling pathway in absence of ligand', rather than to the pathway term itself. Examples of gene products that may be annotated to GO:0097192 'extrinsic apoptotic signaling pathway in absence of ligand' include dependence receptors such as DCC or UNC5B, which relay lethal signals in the absence of their ligand (netrin-1). In the case of DCC and UNC5B, the signaling proceeds through the assembly of a DRAL- and TUCAN- (or NLRP1-) containing caspase-9-activating complex or by the dephosphorylation-mediated activation of death-associated protein kinase 1 (DAPK1) by UNC5B-bound protein phosphatase 2A (PP2A), respectively. DAPK1 can mediate the direct activation of executioner caspases or favor MOMP (reviewed in PMID:21760595). Also see PMID:21172653 (annotations to UNC5B and PR65beta, UniProt symbols O08722, PPP2R1B and P30154).
synonym: "dependence receptor signaling pathway" RELATED []
synonym: "extrinsic apoptosis in absence of ligand" NARROW []
@@ -385836,7 +385813,7 @@ id: GO:0097193
name: intrinsic apoptotic signaling pathway
namespace: biological_process
alt_id: GO:0008629
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP)." [GOC:mtg_apoptosis, GOC:yaf, PMID:11919192, PMID:17340152, PMID:18852119]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP)." [GOC:mtg_apoptosis, GOC:yaf, PMID:11919192, PMID:17340152, PMID:18852119]
comment: The signals that start intrinsic apoptosis may come from extracellular sources (e.g. oxidative stress, UV exposure), but the reception of the signal and thus the signaling pathway start inside the cell (as a result of DNA damage, redox imbalance, etc.). Examples are ZPR9 (ZNF622) and ASK1 (MAP3K5) (UniProt symbols Q969S3 and Q99683) in PMID:21771788. A diagram of the intrinsic apoptotic pathway including examples of molecular players can be found in Figure 2 in PMID:21760595.
synonym: "induction of apoptosis by intracellular signals" RELATED []
synonym: "intrinsic apoptosis" NARROW []
@@ -385871,7 +385848,7 @@ id: GO:0097196
name: Shu complex
namespace: cellular_component
def: "A protein complex involved in error-free DNA post-replication repair (PRR). In Saccharomyces cerevisiae the complex contains Csm2p, Psy3p, Shu1p, and Shu2p." [GOC:jh, PMID:15654096, PMID:19496932]
-is_a: GO:1990391 ! DNA repair complex
+is_a: GO:0032991 ! protein-containing complex
[Term]
id: GO:0097197
@@ -386111,7 +386088,6 @@ def: "OBSOLETE. Any constituent part of a sperm, a mature male germ cell that de
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_annotate
is_obsolete: true
-consider: CL:0000019
[Term]
id: GO:0097224
@@ -386133,9 +386109,9 @@ relationship: part_of GO:0036126 ! sperm flagellum
id: GO:0097226
name: sperm mitochondrial sheath
namespace: cellular_component
-def: "The tightly packed helical sheath of ATP-producing mitochondria restricted to the midpiece of the sperm flagellum." [GOC:cjm, MP:0009832]
+def: "The tightly packed helical sheath of ATP-producing mitochondria restricted to the midpiece of the sperm flagellum." [GOC:cjm, MP:0009832, PMID:32791035]
is_a: GO:0110165 ! cellular anatomical entity
-relationship: part_of GO:0036126 ! sperm flagellum
+relationship: part_of GO:0097225 ! sperm midpiece
[Term]
id: GO:0097227
@@ -386243,11 +386219,12 @@ is_a: GO:1901655 ! cellular response to ketone
[Term]
id: GO:0097239
-name: positive regulation of transcription from RNA polymerase II promoter in response to methylglyoxal
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to methylglyoxal
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to a methylglyoxal stimulus." [GOC:dgf, PMID:15773992]
-is_a: GO:1901522 ! positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus
-relationship: part_of GO:0097238 ! cellular response to methylglyoxal
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to a methylglyoxal stimulus." [GOC:dgf, PMID:15773992]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+replaced_by: GO:0045944
[Term]
id: GO:0097240
@@ -386340,7 +386317,7 @@ is_a: GO:0065003 ! protein-containing complex assembly
id: GO:0097251
name: leukotriene B4 biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of leukotriene B4, a leukotriene composed of (6Z,8E,10E,14Z)-eicosatetraenoic acid having (5S)- and (12R)-hydroxy substituents." [GOC:yaf, UniPathway:UPA00878]
+def: "The chemical reactions and pathways resulting in the formation of leukotriene B4, a leukotriene composed of (6Z,8E,10E,14Z)-eicosatetraenoic acid having (5S)- and (12R)-hydroxy substituents." [GOC:yaf]
synonym: "leukotriene B4 anabolism" EXACT []
synonym: "leukotriene B4 biosynthesis" EXACT []
synonym: "leukotriene B4 formation" EXACT []
@@ -386349,10 +386326,9 @@ synonym: "LTB4 anabolism" EXACT []
synonym: "LTB4 biosynthesis" EXACT []
synonym: "LTB4 formation" EXACT []
synonym: "LTB4 synthesis" EXACT []
-is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:0019370 ! leukotriene biosynthetic process
is_a: GO:0036102 ! leukotriene B4 metabolic process
-is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
+is_a: GO:0042759 ! long-chain fatty acid biosynthetic process
is_a: GO:1901570 ! fatty acid derivative biosynthetic process
is_a: GO:1901617 ! organic hydroxy compound biosynthetic process
@@ -386371,9 +386347,9 @@ namespace: molecular_function
def: "Enables the transfer of beta-hydroxybutyrate from one side of a membrane to the other. Beta-hydroxybutyrate is the conjugate base of (R)-3-hydroxybutyric acid." [GOC:dsf, PMID:22302940]
synonym: "(R)-3-hydroxybutyrate transmembrane transporter activity" EXACT []
synonym: "3-hydroxybutanoic acid transmembrane transporter activity" EXACT []
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015245 ! fatty acid transmembrane transporter activity
is_a: GO:0015665 ! alcohol transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0097254
@@ -386403,7 +386379,7 @@ is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
id: GO:0097257
name: leukotriene B4 12-hydroxy dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: leukotriene B4 + NADP(+) = 12-oxo-leukotriene B4 + NADPH + H(+)." [GOC:mw, KEGG_REACTION:R03864, PMID:8394361, PMID:9461497]
+def: "Catalysis of the reaction: leukotriene B4 + NADP+ = 12-oxo-leukotriene B4 + NADPH + H+." [GOC:mw, KEGG_REACTION:R03864, PMID:8394361, PMID:9461497]
synonym: "leukotriene B4 12-hydroxydehydrogenase activity" EXACT []
xref: Reactome:R-HSA-2161567 "LTB4 is oxidised to 12-oxoLTB4 by PTGR1"
xref: RHEA:50608
@@ -386413,7 +386389,7 @@ is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
id: GO:0097258
name: 20-hydroxy-leukotriene B4 omega oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 20-hydroxy-leukotriene B4 + O2 + reduced [NADPH-hemoprotein reductase] = 20-oxo-leukotriene B4 + H+ + 2 H2O + oxidized [NADPH-hemoprotein reductase]." [GOC:mw, PMID:2836406, PMID:9675028, RHEA:48668]
+def: "Catalysis of the reaction: 20-hydroxy-leukotriene B4 + O2 + reduced [NADPH-hemoprotein reductase] = 20-oxo-leukotriene B4 + H+ + 2 H2O + oxidized [NADPH-hemoprotein reductase]." [GOC:mw, PMID:2836406, PMID:9675028, RHEA:48668]
synonym: "20-hydroxy-leukotriene B4 omega-oxidase activity" EXACT []
synonym: "20-hydroxy-leukotriene B4 omega-oxidation" RELATED []
xref: Reactome:R-HSA-2161745 "20oh-LTB4 is oxidised to 20cho-LTB4 by CYP4F2/4F3"
@@ -386476,7 +386452,7 @@ is_a: GO:0006508 ! proteolysis
id: GO:0097265
name: 5(S)-hydroxyeicosatetraenoic acid dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-HETE + NADP(+) = 5-oxo-ETE + NADPH + H(+)." [GOC:mw, PMID:1326548]
+def: "Catalysis of the reaction: 5-HETE + NADP+ = 5-oxo-ETE + NADPH + H+." [GOC:mw, PMID:1326548]
synonym: "5(S)-HETE dehydrogenase activity" EXACT []
synonym: "5-HETE dehydrogenase activity" EXACT []
synonym: "5-hydroxy-eicosatetraenoic acid dehydrogenase activity" EXACT []
@@ -386487,7 +386463,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0097266
name: phenylacetyl-CoA 1,2-epoxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phenylacetyl-CoA + H(+) + NADPH + O2 = 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + H2O + NADP(+)." [EC:1.14.13.149, GOC:bf, GOC:gk, PMID:20660314, PMID:21247899]
+def: "Catalysis of the reaction: phenylacetyl-CoA + H+ + NADPH + O2 = 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + H2O + NADP+." [EC:1.14.13.149, GOC:bf, GOC:gk, PMID:20660314, PMID:21247899]
synonym: "phenylacetyl-CoA epoxidase activity" EXACT [GOC:bf]
synonym: "phenylacetyl-CoA monooxygenase activity" RELATED [EC:1.14.13.149]
synonym: "ring 1,2-phenylacetyl-CoA epoxidase activity" RELATED [EC:1.14.13.149]
@@ -386509,7 +386485,7 @@ id: GO:0097268
name: cytoophidium
namespace: cellular_component
def: "A subcellular filamentary structure where CTP synthase is compartmentalized in a range of organisms including bacteria, yeast, fruit fly, rat and human." [GOC:mag, PMID:20513629, PMID:21930098, Wikipedia:CTP_synthase#Cytoophidium]
-is_a: GO:0110165 ! cellular anatomical entity
+is_a: GO:0099512 ! supramolecular fiber
[Term]
id: GO:0097269
@@ -386537,7 +386513,7 @@ namespace: biological_process
def: "A process in which a protein is transported to, or maintained at, a location within a cellular bud neck." [GOC:rb, PMID:22344253]
synonym: "protein localisation to bud neck" EXACT [GOC:mah]
synonym: "protein localization to cellular bud neck" EXACT []
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
[Term]
id: GO:0097272
@@ -386545,46 +386521,53 @@ name: ammonium homeostasis
namespace: biological_process
def: "Any biological process involved in the maintenance of an internal steady state of ammonium." [GOC:yaf, PMID:12695560]
synonym: "ammonia homeostasis" EXACT []
-is_a: GO:0055067 ! monovalent inorganic cation homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
[Term]
id: GO:0097273
-name: creatinine homeostasis
+name: obsolete creatinine homeostasis
namespace: biological_process
-def: "Any biological process involved in the maintenance of an internal steady state of creatinine." [GOC:yaf, PMID:12695560]
-is_a: GO:0048878 ! chemical homeostasis
+def: "OBSOLETE. Any biological process involved in the maintenance of an internal steady state of creatinine." [GOC:yaf, PMID:12695560]
+comment: This term was obsoleted because this process does not exist: creatinine is a waste product, there are no biological processes to maintain its level, although some mutants accumulate excesses.
+is_obsolete: true
+consider: GO:0003014
[Term]
id: GO:0097274
-name: urea homeostasis
+name: obsolete urea homeostasis
namespace: biological_process
-def: "Any biological process involved in the maintenance of an internal steady state of urea." [GOC:yaf, PMID:12695560]
-is_a: GO:0048878 ! chemical homeostasis
+def: "OBSOLETE. Any biological process involved in the maintenance of an internal steady state of urea." [GOC:yaf, PMID:12695560]
+comment: This term was obsoleted because this process does not exist: urea is a waste product, there are no biological processes to maintain its level, although some mutants accumulate excesses.
+is_obsolete: true
+consider: GO:0003014
[Term]
id: GO:0097275
-name: cellular ammonium homeostasis
+name: intracellular ammonium homeostasis
namespace: biological_process
-def: "Any biological process involved in the maintenance of an internal steady state of ammonium at the level of the cell." [GOC:yaf, PMID:12695560]
+def: "A homeostatic process involved in the maintenance of a steady state level of ammonium within a cell." [GOC:yaf, PMID:12695560]
synonym: "cellular ammonia homeostasis" EXACT []
-is_a: GO:0030004 ! cellular monovalent inorganic cation homeostasis
+synonym: "cellular ammonium homeostasis" EXACT []
+is_a: GO:0055082 ! intracellular chemical homeostasis
is_a: GO:0097272 ! ammonium homeostasis
[Term]
id: GO:0097276
-name: cellular creatinine homeostasis
+name: obsolete cellular creatinine homeostasis
namespace: biological_process
-def: "Any biological process involved in the maintenance of an internal steady state of creatinine at the level of the cell." [GOC:yaf, PMID:12695560]
-is_a: GO:0055082 ! cellular chemical homeostasis
-is_a: GO:0097273 ! creatinine homeostasis
+def: "OBSOLETE. Any biological process involved in the maintenance of an internal steady state of creatinine at the level of the cell." [GOC:yaf, PMID:12695560]
+comment: This term was obsoleted because this process does not exist: creatinine is a waste product, there are no biological processes to maintain its level, although some mutants accumulate excesses.
+is_obsolete: true
+consider: GO:0003014
[Term]
id: GO:0097277
-name: cellular urea homeostasis
+name: obsolete cellular urea homeostasis
namespace: biological_process
-def: "Any biological process involved in the maintenance of an internal steady state of urea at the level of the cell." [GOC:yaf, PMID:12695560]
-is_a: GO:0055082 ! cellular chemical homeostasis
-is_a: GO:0097274 ! urea homeostasis
+def: "OBSOLETE. Any biological process involved in the maintenance of an internal steady state of urea at the level of the cell." [GOC:yaf, PMID:12695560]
+comment: This term was obsoleted because this process does not exist: urea is a waste product, there are no biological processes to maintain its level, although some mutants accumulate excesses.
+is_obsolete: true
+consider: GO:0003014
[Term]
id: GO:0097278
@@ -386609,6 +386592,7 @@ namespace: biological_process
def: "Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface." [GOC:add, GOC:rv, PMID:11490155, PMID:1719184]
is_a: GO:0002437 ! inflammatory response to antigenic stimulus
is_a: GO:0002441 ! histamine secretion involved in inflammatory response
+is_a: GO:0034776 ! response to histamine
[Term]
id: GO:0097281
@@ -386666,7 +386650,7 @@ is_a: GO:1901360 ! organic cyclic compound metabolic process
id: GO:0097288
name: 7-cyano-7-deazaguanine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of the Q nucleoside precursor 7-cyano-7-deazaguanine, also known as 2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile or preQo." [GOC:yaf, PMID:364423, UniPathway:UPA00391]
+def: "The chemical reactions and pathways resulting in the formation of the Q nucleoside precursor 7-cyano-7-deazaguanine, also known as 2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile or preQo." [GOC:yaf, PMID:364423]
synonym: "7-cyano-7-deazaguanine anabolism" EXACT []
synonym: "7-cyano-7-deazaguanine biosynthesis" EXACT []
synonym: "7-cyano-7-deazaguanine formation" EXACT []
@@ -386736,7 +386720,7 @@ is_a: GO:0097292 ! XMP metabolic process
id: GO:0097294
name: 'de novo' XMP biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of XMP, xanthosine monophosphate, from simpler precursors." [GOC:yaf, MetaCyc:IMP-DEHYDROG-RXN, UniPathway:UPA00601]
+def: "The chemical reactions and pathways resulting in the formation of XMP, xanthosine monophosphate, from simpler precursors." [GOC:yaf, MetaCyc:IMP-DEHYDROG-RXN, PMID:27590927]
synonym: "'de novo' XMP anabolism" EXACT []
synonym: "'de novo' XMP biosynthesis" EXACT []
synonym: "'de novo' XMP formation" EXACT []
@@ -386747,12 +386731,13 @@ is_a: GO:0097293 ! XMP biosynthetic process
id: GO:0097295
name: morphine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of morphine, 17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-3,6alpha-diol. Morphine is a highly potent opiate analgesic psychoactive drug obtained form the opium poppy, Papaver somniferum." [GOC:yaf, UniPathway:UPA00852]
+def: "The chemical reactions and pathways resulting in the formation of morphine, 17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-3,6alpha-diol. Morphine is a highly potent opiate analgesic psychoactive drug obtained form the opium poppy, Papaver somniferum." [GOC:yaf, PMID:19567876]
synonym: "morphine anabolism" EXACT []
synonym: "morphine biosynthesis" EXACT []
synonym: "morphine formation" EXACT []
synonym: "morphine synthesis" EXACT []
is_a: GO:0033075 ! isoquinoline alkaloid biosynthetic process
+is_a: GO:0044272 ! sulfur compound biosynthetic process
is_a: GO:0071272 ! morphine metabolic process
is_a: GO:1901378 ! organic heteropentacyclic compound biosynthetic process
@@ -386768,12 +386753,13 @@ is_a: GO:2001269 ! positive regulation of cysteine-type endopeptidase activity i
[Term]
id: GO:0097297
-name: activation of cysteine-type endopeptidase activity involved in execution phase of apoptosis
+name: obsolete activation of cysteine-type endopeptidase activity involved in execution phase of apoptosis
namespace: biological_process
-def: "Any process that initiates the activity of an inactive cysteine-type endopeptidase involved in the execution phase of apoptosis." [GOC:mtg_apoptosis]
-comment: Note that this term should only be used to annotate gene products directly involved in the initiation or start up of an inactive cysteine-type endopeptidase activity involved in the execution phase of apoptosis (also known as an effector caspase). If the evidence provided is not sufficient to account for direct activation of this enzymatic activity, consider using the more generic terms GO:2001272 positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis or GO:0043280 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process.
+def: "OBSOLETE. Any process that initiates the activity of an inactive cysteine-type endopeptidase involved in the execution phase of apoptosis." [GOC:mtg_apoptosis]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of effector caspase activity" NARROW []
-is_a: GO:2001272 ! positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis
+is_obsolete: true
+consider: GO:0016505
[Term]
id: GO:0097298
@@ -386806,13 +386792,14 @@ is_a: GO:0070265 ! necrotic cell death
[Term]
id: GO:0097301
-name: regulation of potassium ion concentration by positive regulation of transcription from RNA polymerase II promoter
+name: obsolete regulation of potassium ion concentration by positive regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "Any process that regulates the internal concentration of potassium ions at the level of a cell by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:20412803]
+def: "OBSOLETE. Any process that regulates the internal concentration of potassium ions at the level of a cell by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, PMID:20412803]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "cellular potassium ion homeostasis by positive regulation of transcription from RNA polymerase II promoter" EXACT []
synonym: "potassium ion homeostasis by positive regulation of transcription from RNA polymerase II promoter" BROAD []
-is_a: GO:0030007 ! cellular potassium ion homeostasis
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
+is_obsolete: true
+consider: GO:0045944
[Term]
id: GO:0097302
@@ -387113,7 +387100,6 @@ namespace: biological_process
def: "The process in which glycolate is transported across a membrane. Glycolate is the anion of hydroxyethanoic acid (glycolic acid)." [GOC:am, PMID:11283302, PMID:11785976]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "glycolate membrane transport" EXACT []
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1900866 ! glycolate transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
@@ -387209,7 +387195,8 @@ relationship: part_of GO:0001780 ! neutrophil homeostasis
id: GO:0097351
name: toxin sequestering activity
namespace: molecular_function
-def: "Binding to a toxic protein, disabling its function. There may be more than one antitoxin to a toxic protein. Instances of this activity are known only in prokaryotes, where the toxic protein may be a ribonuclease, a DNA gyrase, or other." [GOC:rs, PMID:19143615, PMID:19325885, PMID:21819231, PMID:22545240, PMID:24806488, Wikipedia:Toxin-antitoxin_system#Type_II]
+def: "Binding to a toxin to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active." [GOC:rs, PMID:19143615, PMID:19325885, PMID:21819231, PMID:22545240, PMID:24806488, Wikipedia:Toxin-antitoxin_system#Type_II]
+comment: There may be more than one antitoxin to a toxic protein. Instances of this activity are known only in prokaryotes, where the toxic protein may be a ribonuclease, a DNA gyrase, or other.
synonym: "toxin-antitoxin pair type I binding" NARROW []
synonym: "toxin-antitoxin pair type II binding" NARROW []
is_a: GO:0140313 ! molecular sequestering activity
@@ -387285,8 +387272,7 @@ name: CIA complex
namespace: cellular_component
def: "The cytosolic iron-sulfur protein assembly (CIA) complex mediates the incorporation of iron-sulfur clusters into apoproteins involved in DNA metabolism and genomic integrity." [GOC:sp, PMID:22678362]
synonym: "cytosolic iron-sulfur protein assembly complex" RELATED []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005829 ! cytosol
+is_a: GO:0140535 ! intracellular protein-containing complex
[Term]
id: GO:0097362
@@ -387297,31 +387283,34 @@ is_a: GO:0042555 ! MCM complex
[Term]
id: GO:0097363
-name: protein O-GlcNAc transferase activity
+name: protein O-acetylglucosaminyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: UDP-N-acetyl-D-glucosamine + [protein]-L-serine = UDP + [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine, or UDP-N-acetyl-D-glucosamine + [protein]-L-threonine = UDP + [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-threonine." [GOC:jsg, GOC:sart, PMID:22158438]
synonym: "O-GlcNAc transferase" EXACT []
synonym: "O-linked N-acetylglucosaminyltransferase" EXACT []
synonym: "OGTase" EXACT []
+synonym: "protein O-GlcNAc transferase activity" EXACT []
synonym: "UDP-N-acetyl-D-glucosamine:protein-O-beta-N-acetyl-D-glucosaminyl transferase" EXACT []
xref: EC:2.4.1.255
xref: Reactome:R-HSA-9687828 "O-GlcNAcylation of RIPK3 (TLR4 signaling)"
-is_a: GO:0016757 ! glycosyltransferase activity
+is_a: GO:0008375 ! acetylglucosaminyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
[Term]
id: GO:0097364
-name: stretch-activated, cation-selective, calcium channel activity involved in regulation of action potential
+name: stretch-activated, monoatomic cation-selective, calcium channel activity involved in regulation of action potential
namespace: molecular_function
def: "Enables the transmembrane transfer of a calcium ion by a channel that opens in response to a mechanical stress in the form of stretching, and contributing to the regulation of action potential." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11, PMID:21290758]
-is_a: GO:0015275 ! stretch-activated, cation-selective, calcium channel activity
+synonym: "stretch-activated, cation-selective, calcium channel activity involved in regulation of action potential" BROAD []
+is_a: GO:0015275 ! stretch-activated, monoatomic cation-selective, calcium channel activity
[Term]
id: GO:0097365
-name: stretch-activated, cation-selective, calcium channel activity involved in regulation of cardiac muscle cell action potential
+name: stretch-activated, monoatomic cation-selective, calcium channel activity involved in regulation of cardiac muscle cell action potential
namespace: molecular_function
def: "Enables the transmembrane transfer of a calcium ion by a channel that opens in response to a mechanical stress in the form of stretching, and contributing to the regulation of action potential in a cardiac muscle cell." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11, PMID:21290758]
-is_a: GO:0097364 ! stretch-activated, cation-selective, calcium channel activity involved in regulation of action potential
+synonym: "stretch-activated, cation-selective, calcium channel activity involved in regulation of cardiac muscle cell action potential" BROAD []
+is_a: GO:0097364 ! stretch-activated, monoatomic cation-selective, calcium channel activity involved in regulation of action potential
[Term]
id: GO:0097366
@@ -387359,7 +387348,6 @@ name: protein O-GlcNAcylation via threonine
namespace: biological_process
def: "The glycosylation of a protein by addition of N-acetylglucosamine via the O3 atom of peptidyl-threonine, forming O3-N-acetylglucosamine-L-threonine." [GOC:pr, GOC:sart, PMID:22158438]
is_a: GO:0018243 ! protein O-linked glycosylation via threonine
-is_a: GO:1901135 ! carbohydrate derivative metabolic process
[Term]
id: GO:0097371
@@ -387370,11 +387358,13 @@ is_a: GO:0005515 ! protein binding
[Term]
id: GO:0097372
-name: NAD-dependent histone deacetylase activity (H3-K18 specific)
+name: NAD-dependent histone H3K18 deacetylase activity
namespace: molecular_function
def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 18) + H2O = histone H3 L-lysine (position 18) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 18 of the histone H3 protein." [GOC:sp, PMID:22722849, PMID:28450737]
+synonym: "NAD-dependent histone deacetylase activity (H3-K18 specific)" EXACT []
+synonym: "NAD-dependent histone H3-K18 deacetylase activity" EXACT []
is_a: GO:0017136 ! NAD-dependent histone deacetylase activity
-is_a: GO:0034739 ! histone deacetylase activity (H4-K16 specific)
+is_a: GO:0034739 ! histone H4K16 deacetylase activity
[Term]
id: GO:0097373
@@ -387448,20 +387438,22 @@ relationship: part_of GO:0001750 ! photoreceptor outer segment
[Term]
id: GO:0097382
-name: deoxynucleoside-diphosphatase activity
+name: obsolete deoxynucleoside-diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a deoxynucleoside diphosphate + H2O = a deoxynucleotide + phosphate." [GOC:pde]
-is_a: GO:0016462 ! pyrophosphatase activity
+def: "OBSOLETE. Catalysis of the reaction: a deoxynucleoside diphosphate + H2O = a deoxynucleotide + phosphate." [GOC:pde]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
+is_obsolete: true
+consider: GO:0017110
[Term]
id: GO:0097383
-name: dIDP diphosphatase activity
+name: dIDP phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dIDP + H2O = dIMP + phosphate." [GOC:pde, PMID:20385596]
-synonym: "deoxyinosine-diphosphatase activity" EXACT []
+def: "Catalysis of the reaction: dIDP + H2O = dIMP + H+ + phosphate." [GOC:pde, PMID:20385596, RHEA:35211]
+synonym: "deoxyinosine-diphosphatase activity" RELATED []
xref: Reactome:R-HSA-2509793 "NUDT16 hydrolyses dIDP to dIMP"
xref: RHEA:35211
-is_a: GO:0097382 ! deoxynucleoside-diphosphatase activity
+is_a: GO:0017110 ! nucleoside diphosphate phosphatase activity
[Term]
id: GO:0097384
@@ -387607,7 +387599,7 @@ is_a: GO:0097396 ! response to interleukin-17
id: GO:0097399
name: interleukin-32-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-32 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:ic, PMID:21602493]
+def: "The series of molecular signals initiated by interleukin-32 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:ic, PMID:21602493]
synonym: "IL-32-mediated signaling pathway" EXACT []
synonym: "IL-32-mediated signalling pathway" EXACT []
synonym: "interleukin-32-mediated signalling pathway" EXACT []
@@ -387618,7 +387610,7 @@ relationship: part_of GO:0097397 ! cellular response to interleukin-32
id: GO:0097400
name: interleukin-17-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-17 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:ic, PMID:21602493]
+def: "The series of molecular signals initiated by interleukin-17 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:ic, PMID:21602493]
synonym: "IL-17-mediated signaling pathway" EXACT []
synonym: "IL-17-mediated signalling pathway" EXACT []
synonym: "interleukin-17-mediated signalling pathway" EXACT []
@@ -387692,7 +387684,7 @@ relationship: part_of GO:0021766 ! hippocampus development
id: GO:0097411
name: hypoxia-inducible factor-1alpha signaling pathway
namespace: biological_process
-def: "A series of molecular signals mediated by hypoxia-inducible factor (HIF1) in response to lowered oxygen levels (hypoxia). Under hypoxic conditions, the oxygen-sensitive alpha-subunit of hypoxia-inducible factor (HIF)-1 dimerizes with a HIF1-beta subunit (also called ARNT or aryl-hydrocarbon-receptor nuclear translocator), translocates to the nucleus and activates transcription of genes whose products participate in responding to hypoxia." [GOC:bf, GOC:jc, http://www.sabiosciences.com/pathway.php?sn=HIF1Alpha_Pathway]
+def: "The series of molecular signals mediated by hypoxia-inducible factor (HIF1) in response to lowered oxygen levels (hypoxia). Under hypoxic conditions, the oxygen-sensitive alpha-subunit of hypoxia-inducible factor (HIF)-1 dimerizes with a HIF1-beta subunit (also called ARNT or aryl-hydrocarbon-receptor nuclear translocator), translocates to the nucleus and activates transcription of genes whose products participate in responding to hypoxia." [GOC:bf, GOC:jc, http://www.sabiosciences.com/pathway.php?sn=HIF1Alpha_Pathway]
synonym: "HIF1alpha pathway" EXACT []
synonym: "hypoxia-inducible factor signaling" EXACT [GOC:bf]
synonym: "hypoxia-inducible factor-1alpha signalling pathway" EXACT []
@@ -387860,6 +387852,7 @@ name: amino acid ligation activity by nonribosomal peptide synthase
namespace: molecular_function
def: "Catalysis of the ligation of an amino acid to another amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate, carried out by a nonribosomal peptide synthase." [GOC:vw]
is_a: GO:0016881 ! acid-amino acid ligase activity
+is_a: GO:1904091 ! non-ribosomal peptide synthetase activity
[Term]
id: GO:0097430
@@ -387868,7 +387861,6 @@ namespace: biological_process
def: "The directed movement of copper ions from outside of a cell, across an ascospore-type prospore membrane and into the cytosol." [GOC:al, GOC:vw, PMID:21828039]
synonym: "copper ion import into ascospore-type prospore" RELATED []
synonym: "copper ion transport into forespores" RELATED []
-is_a: GO:0015677 ! copper ion import
is_a: GO:0035434 ! copper ion transmembrane transport
[Term]
@@ -387985,7 +387977,7 @@ is_a: GO:0005768 ! endosome
id: GO:0097444
name: spine apparatus
namespace: cellular_component
-def: "A specialization of the endomembrane system found in some classes of dendritic spines consisting of two or more closely apposed lamellae with interspersed electron dense material. The endomembrane component is continuous with the smooth endoplasmic reticulum." [NIF_Subcellular:sao725931194, PMID:20400711, PMID:8987748]
+def: "A specialization of the endomembrane system found in some classes of dendritic spines consisting of two or more closely apposed lamellae with interspersed electron dense material. The endomembrane component is continuous with the smooth endoplasmic reticulum." [NIF_Subcellular:sao725931194, PMID:20400711, PMID:8987748]
subset: goslim_synapse
synonym: "dense material" NARROW [NIF_Subcellular:sao1004601938]
xref: NIF_Subcellular:sao725931194
@@ -388119,7 +388111,6 @@ def: "OBSOLETE. Any constituent part of a neuron, the basic cellular unit of ner
subset: gocheck_do_not_annotate
subset: goslim_flybase_ribbon
is_obsolete: true
-consider: CL:0000540
[Term]
id: GO:0097462
@@ -388317,7 +388308,7 @@ synonym: "neurite guidance" NARROW []
synonym: "neuron process guidance" EXACT []
synonym: "neuron protrusion guidance" EXACT []
synonym: "neuronal cell projection guidance" EXACT []
-is_a: GO:0006928 ! movement of cell or subcellular component
+is_a: GO:0031175 ! neuron projection development
relationship: part_of GO:0006935 ! chemotaxis
relationship: part_of GO:0048812 ! neuron projection morphogenesis
@@ -388642,7 +388633,7 @@ is_a: GO:0097525 ! spliceosomal snRNP complex
id: GO:0097527
name: necroptotic signaling pathway
namespace: biological_process
-def: "A series of molecular signals which triggers the necroptotic death of a cell. The pathway starts with reception of a signal, is characterized by activation of receptor-interacting serine/threonine-protein kinase 1 and/or 3 (RIPK1/3, also called RIP1/3), and ends when the execution phase of necroptosis is triggered." [GOC:mtg_apoptosis, PMID:20823910]
+def: "The series of molecular signals which triggers the necroptotic death of a cell. The pathway starts with reception of a signal, is characterized by activation of receptor-interacting serine/threonine-protein kinase 1 and/or 3 (RIPK1/3, also called RIP1/3), and ends when the execution phase of necroptosis is triggered." [GOC:mtg_apoptosis, PMID:20823910]
comment: Gene products that may be annotated to this term include: 1) ligands such as TNF-alpha; 2) receptors such as TNFR (though care should be taken because TNF-alpha and TNFR may also be involved in non-necroptotic processes); 3) signaling molecules such as TNFR-associated death domain (TRADD), receptor-interacting protein kinase 1 (RIP1), cellular inhibitor of apoptosis 1 (cIAP1), cIAP2, TNFR-associated factor 2 (TRAF2) and TRAF5. Within the so-called complex I, RIP1 is polyubiquitinated by cIAPs, thereby providing a docking site for the recruitment of transforming growth factor beta (TGFbeta)-activated kinase 1 (TAK1), TAK1-binding protein 2 (TAB2) and TAB3 (which together deliver a pro-survival signal by activating the transcription factor NF-kB). In some pathophysiological and experimental settings, and in particular when caspase-8 is absent or when caspases are inhibited by pharmacological agents, cylindromatosis (CYLD)-deubiquitinated RIP1 engage in physical and functional interactions with its homolog RIP3, ultimately activating the execution of necrotic cell death. (The pathway downstream of RIPK3 remains largely unknown, although ROS generation, calcium overload, and the opening of the mitochondrial permeability transition pore have been implicated (PMID:22265414)). A necroptotic signaling pathway may also be induced by alkylating DNA damage (possibly by the overactivation of poly(ADP-ribose) polymerase 1, PARP1). This is sometimes referred to as PARP-dependent cell death or parthanatos; it is still being debated if it constitutes an independent cell death modality.
synonym: "necroptosis signaling" RELATED []
synonym: "necroptosis signaling pathway" EXACT []
@@ -388772,7 +388763,7 @@ synonym: "distal appendage of centriole" RELATED [GOC:krc]
synonym: "distal appendage of mother centriole" RELATED [GOC:krc]
synonym: "transition fiber" BROAD []
synonym: "transition fibre" BROAD []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140535 ! intracellular protein-containing complex
relationship: part_of GO:0005929 ! cilium
[Term]
@@ -388929,9 +388920,10 @@ is_a: GO:0097551 ! mitochondrial double-strand break repair
id: GO:0097553
name: calcium ion transmembrane import into cytosol
namespace: biological_process
+alt_id: GO:0060401
def: "A process in which a calcium ion is transported from one side of a membrane to the other into the cytosol by means of some agent such as a transporter or pore." [GOC:vw]
synonym: "calcium transmembrane import into cytosol" BROAD []
-is_a: GO:0060402 ! calcium ion transport into cytosol
+synonym: "cytosolic calcium ion transport" BROAD []
is_a: GO:0070588 ! calcium ion transmembrane transport
[Term]
@@ -389108,11 +389100,14 @@ is_a: GO:0005634 ! nucleus
[Term]
id: GO:0097573
-name: glutathione oxidoreductase activity
+name: obsolete glutathione oxidoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: protein-S-S-glutathione + glutathione-SH = protein-SH + glutathione-S-S-glutathione." [GOC:jd, PMID:18992757]
-comment: Note that this activity is different from GO:0015038 'glutathione disulfide oxidoreductase activity'. See PMID:18992757: "Grxs [glutaredoxins] can also reduce mixed disulfides between proteins or low molecular weight thiols and GSH in reactions that require only their N-terminal active- site cysteine. It is important to note that the reduction of glutathionylated substrates through the monothiol mechanism seems to be the major activity of Grxs; all dithiol Grxs described so far catalyze these reactions, but not all dithiol Grxs catalyze the reduction of protein disulfides by the dithiol mechanism".
-is_a: GO:0015035 ! protein-disulfide reductase activity
+def: "OBSOLETE. Catalysis of the reaction: protein-S-S-glutathione + glutathione-SH = protein-SH + glutathione-S-S-glutathione." [GOC:jd, PMID:18992757]
+comment: This term was obsoleted because it is redundant with other terms.
+is_obsolete: true
+consider: GO:0004362
+consider: GO:0015038
+consider: GO:0045174
[Term]
id: GO:0097574
@@ -389151,7 +389146,7 @@ synonym: "sequestration of iron ion" EXACT []
synonym: "storage of iron ion" EXACT []
is_a: GO:0051238 ! sequestering of metal ion
is_a: GO:0051651 ! maintenance of location in cell
-relationship: part_of GO:0006879 ! cellular iron ion homeostasis
+relationship: part_of GO:0006879 ! intracellular iron ion homeostasis
[Term]
id: GO:0097578
@@ -389165,7 +389160,7 @@ synonym: "copper ion storage" EXACT []
synonym: "retention of copper ion" EXACT []
synonym: "sequestration of copper ion" EXACT []
synonym: "storage of copper ion" EXACT []
-is_a: GO:0006878 ! cellular copper ion homeostasis
+is_a: GO:0006878 ! intracellular copper ion homeostasis
is_a: GO:0051238 ! sequestering of metal ion
is_a: GO:0051651 ! maintenance of location in cell
@@ -389182,7 +389177,7 @@ synonym: "extracellular retention of copper ion" EXACT []
synonym: "extracellular sequestration of copper ion" EXACT []
synonym: "extracellular storage of copper ion" EXACT []
is_a: GO:0097578 ! sequestering of copper ion
-relationship: part_of GO:0006878 ! cellular copper ion homeostasis
+relationship: part_of GO:0006878 ! intracellular copper ion homeostasis
[Term]
id: GO:0097580
@@ -389197,7 +389192,7 @@ synonym: "intracellular retention of copper ion" EXACT []
synonym: "intracellular sequestration of copper ion" EXACT []
synonym: "intracellular storage of copper ion" EXACT []
is_a: GO:0097578 ! sequestering of copper ion
-relationship: part_of GO:0006878 ! cellular copper ion homeostasis
+relationship: part_of GO:0006878 ! intracellular copper ion homeostasis
[Term]
id: GO:0097581
@@ -389412,8 +389407,7 @@ synonym: "heat-activated ion channel activity" NARROW []
synonym: "temperature gated ion channel activity" EXACT []
synonym: "temperature-activated ion channel activity" EXACT []
synonym: "temperature-dependent ion channel activity" EXACT []
-is_a: GO:0005216 ! ion channel activity
-is_a: GO:0022836 ! gated channel activity
+is_a: GO:0022839 ! monoatomic ion gated channel activity
[Term]
id: GO:0097604
@@ -389424,7 +389418,7 @@ synonym: "heat-activated cation channel activity" NARROW []
synonym: "temperature gated cation channel activity" EXACT []
synonym: "temperature-activated cation channel activity" EXACT []
synonym: "temperature-dependent cation channel activity" EXACT []
-is_a: GO:0005261 ! cation channel activity
+is_a: GO:0005261 ! monoatomic cation channel activity
is_a: GO:0097603 ! temperature-gated ion channel activity
[Term]
@@ -389576,11 +389570,10 @@ is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
id: GO:0097621
name: monoamine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: RCH2NHR' + H2O + O2 = RCHO + R'NH2 + H2O2." [GOC:pr, RHEA:26414]
-comment: Acts on primary amines, and also on some secondary and tertiary amines. It differs from EC:1.4.3.21, primary-amine oxidase as it can oxidize secondary and tertiary amines but not methylamine.
+def: "Catalysis of the reaction: RCH2NHR' + H2O + O2 = RCHO + R'NH2 + H2O2." [GOC:pr, PMID:15279562, PMID:16129825]
+comment: Acts on primary amines, and also on some secondary and tertiary amines. It differs from EC:1.4.3.21, primary amine oxidase as it can oxidize secondary and tertiary amines but not methylamine.
synonym: "amine:oxygen oxidoreductase (deaminating) activity" EXACT []
xref: EC:1.4.3.4
-xref: RHEA:26414
is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
[Term]
@@ -389601,7 +389594,6 @@ synonym: "potassium export" BROAD [GOC:mah]
synonym: "potassium export across plasma membrane" EXACT []
synonym: "potassium ion export" BROAD []
synonym: "potassium ion export from cell" EXACT []
-is_a: GO:0070839 ! metal ion export
is_a: GO:0071805 ! potassium ion transmembrane transport
is_a: GO:0140115 ! export across plasma membrane
@@ -389657,22 +389649,24 @@ relationship: part_of GO:1903349 ! omegasome membrane
[Term]
id: GO:0097630
-name: intrinsic component of omegasome membrane
+name: obsolete intrinsic component of omegasome membrane
namespace: cellular_component
-def: "The component of the omegasome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:mf, PMID:18725538, PMID:24591649]
+def: "OBSOLETE. The component of the omegasome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:mf, PMID:18725538, PMID:24591649]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to omegasome membrane" NARROW []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:1903349 ! omegasome membrane
+is_obsolete: true
+replaced_by: GO:1903349
[Term]
id: GO:0097631
-name: integral component of omegasome membrane
+name: obsolete integral component of omegasome membrane
namespace: cellular_component
-def: "The component of the omegasome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:mf, PMID:18725538, PMID:24591649]
+def: "OBSOLETE. The component of the omegasome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:mf, PMID:18725538, PMID:24591649]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to omegasome membrane" NARROW []
synonym: "omegasome integral membrane protein" RELATED []
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:0097630 ! intrinsic component of omegasome membrane
+is_obsolete: true
+replaced_by: GO:1903349
[Term]
id: GO:0097632
@@ -389687,54 +389681,59 @@ relationship: part_of GO:0034045 ! phagophore assembly site membrane
[Term]
id: GO:0097633
-name: intrinsic component of phagophore assembly site membrane
+name: obsolete intrinsic component of phagophore assembly site membrane
namespace: cellular_component
-def: "The component of the phagophore assembly site membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:mf]
+def: "OBSOLETE. The component of the phagophore assembly site membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:mf]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to phagophore assembly site membrane" NARROW []
-is_a: GO:0031224 ! intrinsic component of membrane
-relationship: part_of GO:0034045 ! phagophore assembly site membrane
+is_obsolete: true
+replaced_by: GO:0034045
[Term]
id: GO:0097634
-name: integral component of phagophore assembly site membrane
+name: obsolete integral component of phagophore assembly site membrane
namespace: cellular_component
-def: "The component of the phagophore assembly site membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:mf]
+def: "OBSOLETE. The component of the phagophore assembly site membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:mf]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to phagophore assembly site membrane" NARROW []
synonym: "phagophore assembly site integral membrane protein" RELATED []
-is_a: GO:0016021 ! integral component of membrane
-is_a: GO:0097633 ! intrinsic component of phagophore assembly site membrane
+is_obsolete: true
+replaced_by: GO:0034045
[Term]
id: GO:0097635
-name: extrinsic component of autophagosome membrane
+name: obsolete extrinsic component of autophagosome membrane
namespace: cellular_component
-def: "The component of the autophagosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:autophagy, GOC:mf]
+def: "OBSOLETE. The component of the autophagosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:autophagy, GOC:mf]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "autophagic vacuole peripheral membrane" RELATED []
synonym: "extrinsic component of autophagic vacuole membrane" EXACT [GOC:autophagy]
synonym: "extrinsic to autophagic vacuole membrane" EXACT []
-is_a: GO:0000306 ! extrinsic component of vacuolar membrane
-relationship: part_of GO:0000421 ! autophagosome membrane
+is_obsolete: true
+consider: GO:0000421
[Term]
id: GO:0097636
-name: intrinsic component of autophagosome membrane
+name: obsolete intrinsic component of autophagosome membrane
namespace: cellular_component
-def: "The component of the autophagosome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:autophagy, GOC:mf]
+def: "OBSOLETE. The component of the autophagosome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:autophagy, GOC:mf]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic component of autophagic vacuole membrane" EXACT [GOC:autophagy]
synonym: "intrinsic to autophagic vacuole membrane" NARROW []
-is_a: GO:0031310 ! intrinsic component of vacuolar membrane
-relationship: part_of GO:0000421 ! autophagosome membrane
+is_obsolete: true
+replaced_by: GO:0000421
[Term]
id: GO:0097637
-name: integral component of autophagosome membrane
+name: obsolete integral component of autophagosome membrane
namespace: cellular_component
-def: "The component of the autophagosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:autophagy, GOC:mf]
+def: "OBSOLETE. The component of the autophagosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:autophagy, GOC:mf]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "autophagic vacuole integral membrane protein" RELATED []
synonym: "integral component of autophagic vacuole membrane" EXACT [GOC:autophagy]
synonym: "integral to autophagic vacuole membrane" NARROW []
-is_a: GO:0031166 ! integral component of vacuolar membrane
-is_a: GO:0097636 ! intrinsic component of autophagosome membrane
+is_obsolete: true
+replaced_by: GO:0000421
[Term]
id: GO:0097638
@@ -389745,10 +389744,8 @@ alt_id: GO:1902765
def: "The directed movement of L-arginine from outside of a cell, across the plasma membrane and into the cytosol." [GOC:krc, PMID:8195186]
synonym: "arginine import" BROAD []
synonym: "L-arginine import into cell" EXACT []
-is_a: GO:0015807 ! L-amino acid transport
+is_a: GO:0072337 ! modified amino acid transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -389814,7 +389811,7 @@ is_a: GO:0097644 ! calcitonin family binding
id: GO:0097646
name: calcitonin family receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by an extracellular member of the calcitonin family (e.g. adrenomedullin, adrenomedullin 2 (intermedin), amylin, calcitonin and calcitonin gene-related peptides (CGRPs)) combining with a calcitonin family receptor on the surface of the target cell. Calcitonin family receptors may form dimers, trimers or tetramers; adrenomedullin and amylin receptors have only been observed as dimers so far." [GOC:bhm, PMID:10871296, PMID:12037140, PMID:18687416]
+def: "A G protein-coupled receptor signaling pathway initiated by an extracellular member of the calcitonin family (e.g. adrenomedullin, adrenomedullin 2 (intermedin), amylin, calcitonin and calcitonin gene-related peptides (CGRPs)) binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:bhm, PMID:10871296, PMID:12037140, PMID:18687416]
synonym: "calcitonin family receptor signalling pathway" EXACT []
is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
@@ -389822,7 +389819,7 @@ is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
id: GO:0097647
name: amylin receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by an extracellular amylin combining with a dimeric amylin receptor on the surface of the target cell." [GOC:bhm, PMID:10871296, PMID:12037140, PMID:18687416]
+def: "A G protein-coupled receptor signaling pathway initiated by amylin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:bhm, PMID:10871296, PMID:12037140, PMID:18687416]
synonym: "amilyn receptor signalling pathway" EXACT []
is_a: GO:0097646 ! calcitonin family receptor signaling pathway
@@ -389833,7 +389830,6 @@ namespace: cellular_component
def: "A protein complex that contains G protein-coupled receptors." [GOC:bhm]
synonym: "G-protein coupled receptor complex" EXACT []
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:0097649
@@ -389926,7 +389922,7 @@ relationship: part_of GO:0005637 ! nuclear inner membrane
id: GO:0097659
name: nucleic acid-templated transcription
namespace: biological_process
-def: "The cellular synthesis of RNA on a template of nucleic acid (DNA or RNA)." [GOC:pr, GOC:txnOH, GOC:vw]
+def: "The synthesis of an RNA transcript from a nucleic acid template (DNA or RNA)." [GOC:pr, GOC:txnOH, GOC:vw]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_manually_annotate
subset: goslim_mouse
@@ -390093,11 +390089,12 @@ is_a: GO:0006303 ! double-strand break repair via nonhomologous end joining
[Term]
id: GO:0097682
-name: intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity
+name: intracellular phosphatidylinositol-3,5-bisphosphate-sensitive monatomic cation channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of cations by a channel that opens when phosphatidylinositol-3,5-bisphosphate has been bound by the channel complex or one of its constituent parts." [GOC:ha, PMID:24375408]
-is_a: GO:0005217 ! intracellular ligand-gated ion channel activity
-is_a: GO:0099094 ! ligand-gated cation channel activity
+synonym: "intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity" BROAD []
+is_a: GO:0005217 ! intracellular ligand-gated monoatomic ion channel activity
+is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
[Term]
id: GO:0097683
@@ -390158,7 +390155,7 @@ namespace: molecular_function
def: "Binds to and stops, prevents, or reduces the activity of an iron ion transmembrane transporter." [GOC:BHF, GOC:kom, PMID:15514116]
comment: An example of this is human hepcidin (UniProt symbol P81172), which regulates iron transport out of cells (see PMID:15514116).
synonym: "iron channel inhibitor activity" EXACT []
-is_a: GO:0140678 ! molecular function inhibitor activity
+is_a: GO:0098772 ! molecular function regulator activity
[Term]
id: GO:0097691
@@ -390444,13 +390441,14 @@ is_a: GO:0097722 ! sperm motility
[Term]
id: GO:0097725
-name: histone H3-K79 dimethylation
+name: obsolete histone H3-K79 dimethylation
namespace: biological_process
-def: "The modification of histone H3 by addition of two methyl groups to lysine at position 79 of the histone." [GOC:hbye, PMID:27541139]
+def: "OBSOLETE. The modification of histone H3 by addition of two methyl groups to lysine at position 79 of the histone." [GOC:hbye, PMID:27541139]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H3 K79 dimethylation" EXACT []
synonym: "histone lysine H3 K79 dimethylation" EXACT []
-is_a: GO:0018027 ! peptidyl-lysine dimethylation
-is_a: GO:0034729 ! histone H3-K79 methylation
+is_obsolete: true
+consider: GO:0031151
[Term]
id: GO:0097726
@@ -390561,8 +390559,9 @@ namespace: biological_process
def: "The process by which hyphae grow in an upward or outward direction from the surface of the substrate; from there, propagative spores develop in or on characteristic structures that are distinctive of some fungal and bacterial species. The species that form an aerial mycelium develop conidiophores at the ends of the aerial hyphae." [GOC:di, PMID:12832397]
synonym: "aerial hyphal growth" RELATED []
synonym: "fertile mycelium formation" RELATED []
-is_a: GO:0019954 ! asexual reproduction
+is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048856 ! anatomical structure development
+relationship: part_of GO:0019954 ! asexual reproduction
[Term]
id: GO:0097737
@@ -390577,8 +390576,9 @@ id: GO:0097738
name: substrate mycelium formation
namespace: biological_process
def: "The process by which, in some fungal species, hyphae grow as a network of invasive thread-like filaments formed from chains of attached cells within a solid or semi-solid substrate." [GOC:di, PMID:10021365]
-is_a: GO:0019954 ! asexual reproduction
+is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048856 ! anatomical structure development
+relationship: part_of GO:0019954 ! asexual reproduction
[Term]
id: GO:0097739
@@ -390676,7 +390676,7 @@ is_a: GO:0140098 ! catalytic activity, acting on RNA
id: GO:0097748
name: 3'-5' RNA polymerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template, via extension of the 5'-end." [GOC:pf, PMID:22456265, PMID:27484477]
+def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template, via extension of the 5'-end." [GOC:pf, PMID:22456265, PMID:27484477, PMID:30917604]
xref: RHEA:57528
is_a: GO:0097747 ! RNA polymerase activity
@@ -390999,20 +390999,22 @@ is_a: GO:0098035 ! viral DNA genome packaging via site-specific sequence recogni
[Term]
id: GO:0098038
-name: non-replicative transposition, DNA-mediated
+name: non-replicative DNA transposition
namespace: biological_process
def: "Process by which a transposable element is excised from the donor site and integrated at the target site without replication of the element. Also referred to as cut-and-paste transposition." [GOC:bm, PMID:2553270]
synonym: "cut-and-paste transposition" EXACT [GOC:bm]
-is_a: GO:0006313 ! transposition, DNA-mediated
+synonym: "non-replicative transposition, DNA-mediated" EXACT []
+is_a: GO:0006313 ! DNA transposition
[Term]
id: GO:0098039
-name: replicative transposition, DNA-mediated
+name: replicative DNA transposition
namespace: biological_process
-def: "Process of transposition in which the existing element is replicated and one of the copies is excised and integrated at a new target site. Also referred to as copy-and-paste transposition." [GOC:bm, PMID:10540284]
+def: "Process of transposition in which the existing element is replicated and one of the copies is excised and integrated at a new target site. Also referred to as copy-and-paste transposition." [GOC:bm, PMID:10540284, PMID:1660177]
synonym: "copy-and-paste transposition" EXACT [GOC:bm]
+synonym: "replicative transposition, DNA-mediated" EXACT []
synonym: "transpositional DNA genome replication" EXACT []
-is_a: GO:0006313 ! transposition, DNA-mediated
+is_a: GO:0006313 ! DNA transposition
[Term]
id: GO:0098045
@@ -391042,19 +391044,19 @@ is_a: GO:0044423 ! virion component
[Term]
id: GO:0098501
-name: polynucleotide dephosphorylation
+name: obsolete polynucleotide dephosphorylation
namespace: biological_process
-def: "The process of removing one or more phosphate groups from a polynucleotide." [GOC:DOS]
-is_a: GO:0006139 ! nucleobase-containing compound metabolic process
-is_a: GO:0016311 ! dephosphorylation
-is_a: GO:0043170 ! macromolecule metabolic process
+def: "OBSOLETE. The process of removing one or more phosphate groups from a polynucleotide." [GOC:DOS]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0098502
-name: DNA dephosphorylation
+name: obsolete DNA dephosphorylation
namespace: biological_process
-def: "The process of removing one or more phosphate groups from a DNA molecule." [GOC:DOS]
-is_a: GO:0016311 ! dephosphorylation
+def: "OBSOLETE. The process of removing one or more phosphate groups from a DNA molecule." [GOC:DOS]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0098503
@@ -391175,19 +391177,22 @@ is_a: GO:0098513 ! detection of humidity
[Term]
id: GO:0098518
-name: polynucleotide phosphatase activity
+name: obsolete polynucleotide phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phosphopolynucleotide + H2O = polynucleotide + phosphate." [GOC:mah]
-is_a: GO:0016791 ! phosphatase activity
+def: "OBSOLETE. Catalysis of the reaction: phosphopolynucleotide + H2O = polynucleotide + phosphate." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+is_obsolete: true
+consider: GO:0046403
+consider: GO:0140818
[Term]
id: GO:0098519
-name: nucleotide phosphatase activity, acting on free nucleotides
+name: obsolete nucleotide phosphatase activity, acting on free nucleotides
namespace: molecular_function
-def: "Catalysis of the reaction: nucleotide + H2O = nucleotide + phosphate." [GOC:dos]
-comment: To be used for NTP->NDP or NDP -> NMP. For nucleotide -> nucleoside (all phosphates removed) use nucleotidase.
+def: "OBSOLETE. Catalysis of the reaction: nucleotide + H2O = nucleotide + phosphate." [GOC:dos]
+comment: This term was obsoleted because it represented an unnecessary grouping class.
synonym: "nucleotide phosphatase activity" EXACT []
-is_a: GO:0016791 ! phosphatase activity
+is_obsolete: true
[Term]
id: GO:0098520
@@ -391211,7 +391216,7 @@ id: GO:0098522
name: neuromuscular junction of skeletal muscle fiber
namespace: cellular_component
def: "A neuromuscular junction in which the target muscle cell is a skeletal muscle fiber." [GOC:dos]
-comment: In vertebrates, the term 'neuromuscular junction' is limited to synapses targeting skeletal muscle fibers - all of which are cholinergic and excitatory. Both inhibitory and excitatory neuromuscular junctions exist in invertebrates, utilizing a range of neurotransmitters including glutamate, GABA and 5-HT.
+comment: In vertebrates, the term 'neuromuscular junction' is limited to synapses targeting skeletal muscle fibers - all of which are cholinergic and excitatory. Both inhibitory and excitatory neuromuscular junctions exist in invertebrates, utilizing a range of neurotransmitters including glutamate, GABA and 5-HT.
is_a: GO:0098520 ! excitatory neuromuscular junction
is_a: GO:0098523 ! neuromuscular junction of myotube
is_a: GO:0098981 ! cholinergic synapse
@@ -391344,7 +391349,7 @@ is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
id: GO:0098537
name: obsolete lobed nucleus
namespace: cellular_component
-def: "OBSOLETE. Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin. Examples include the nuclei of mature basophils, eosinophils and neutrophils in mice and humans." [GOC:dos, GOC:tfm]
+def: "OBSOLETE. Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin. Examples include the nuclei of mature basophils, eosinophils and neutrophils in mice and humans." [GOC:dos, GOC:tfm]
comment: This term was obsoleted because it does not correspond to a specific type of nucleus, it is a morphologically different nucleus present in certain cell types.
is_obsolete: true
@@ -391391,6 +391396,7 @@ namespace: biological_process
alt_id: GO:0009814
def: "Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism." [GOC:dos]
subset: goslim_generic
+subset: prokaryote_subset
synonym: "defence response incompatible interaction" NARROW []
synonym: "defence response to pathogen, incompatible interaction" NARROW []
synonym: "defense response, incompatible interaction" NARROW []
@@ -391445,7 +391451,7 @@ relationship: part_of GO:0000139 ! Golgi membrane
id: GO:0098549
name: somatic ring canal
namespace: cellular_component
-def: "A stable intercellular bridge between somatic cells. Examples include the intercellular bridges between ovarian follicle cells in insects and between imaginal disc cells in insects." [GOC:dos, PMID:22135360, PMID:670316]
+def: "A stable intercellular bridge between somatic cells. Examples include the intercellular bridges between ovarian follicle cells in insects and between imaginal disc cells in insects." [GOC:dos, PMID:22135360, PMID:670316]
is_a: GO:0045171 ! intercellular bridge
[Term]
@@ -391563,12 +391569,12 @@ is_a: GO:0098552 ! side of membrane
[Term]
id: GO:0098563
-name: intrinsic component of synaptic vesicle membrane
+name: obsolete intrinsic component of synaptic vesicle membrane
namespace: cellular_component
-def: "The component of the synaptic vesicle membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0030672 ! synaptic vesicle membrane
+def: "OBSOLETE. The component of the synaptic vesicle membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0030672
[Term]
id: GO:0098564
@@ -391644,12 +391650,13 @@ relationship: part_of GO:0055035 ! plastid thylakoid membrane
[Term]
id: GO:0098573
-name: intrinsic component of mitochondrial membrane
+name: obsolete intrinsic component of mitochondrial membrane
namespace: cellular_component
-def: "The component of the mitochondrial membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos]
+def: "OBSOLETE. The component of the mitochondrial membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to mitochondrial membrane" NARROW []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0031966 ! mitochondrial membrane
+is_obsolete: true
+replaced_by: GO:0031966
[Term]
id: GO:0098574
@@ -391714,7 +391721,7 @@ is_obsolete: true
id: GO:0098581
name: detection of external biotic stimulus
namespace: biological_process
-def: "The series of events in which an external biotic stimulus is detected and converted into a molecular signal. An external biotic stimulus is defined as one caused or produced by a living organism other than the one being stimulated." [GOC:dos]
+def: "The series of events in which an external biotic stimulus is detected and converted into a molecular signal. An external biotic stimulus is defined as one caused or produced by a living organism other than the one being stimulated." [GOC:dos]
synonym: "detection of exogenous biotic stimulus" EXACT []
is_a: GO:0009595 ! detection of biotic stimulus
is_a: GO:0043207 ! response to external biotic stimulus
@@ -391797,7 +391804,7 @@ relationship: part_of GO:0016324 ! apical plasma membrane
id: GO:0098593
name: goblet cell theca
namespace: cellular_component
-def: "A cup shaped specialization of the cytoskeleton that forms a thin layer located just below the apical mass of mature mucin secretory granules in the cytoplasm of goblet cells of the intestinal epithelium. It consists of an orderly network of intermediate filaments and microtubules. Microtubules are arranged vertically, like barrel staves, along the inner aspect of the theta. Intermediate filaments form two networks: an inner, basketlike network and an outer series of circumferential bundles resembling the hoops of a barrel." [PMID:6541604]
+def: "A cup shaped specialization of the cytoskeleton that forms a thin layer located just below the apical mass of mature mucin secretory granules in the cytoplasm of goblet cells of the intestinal epithelium. It consists of an orderly network of intermediate filaments and microtubules. Microtubules are arranged vertically, like barrel staves, along the inner aspect of the theta. Intermediate filaments form two networks: an inner, basketlike network and an outer series of circumferential bundles resembling the hoops of a barrel." [PMID:6541604]
is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
relationship: part_of GO:0005737 ! cytoplasm
relationship: part_of GO:0005856 ! cytoskeleton
@@ -392092,8 +392099,9 @@ is_a: GO:0098743 ! cell aggregation
id: GO:0098631
name: cell adhesion mediator activity
namespace: molecular_function
-def: "The binding by a cell-adhesion protein on a cell surface to an adhesion molecule on another cell surface, to mediate adhesion of the cell to the external substrate or to another cell." [GOC:vw, Wikipedia:Cell_adhesion]
+def: "The binding by a cell-adhesion protein on a cell surface to an adhesion molecule on another cell surface or an external substrate, to mediate adhesion of the cell to the external substrate or to another cell." [GOC:vw, Wikipedia:Cell_adhesion]
subset: goslim_generic
+subset: prokaryote_subset
synonym: "cell adhesion molecule" EXACT []
synonym: "protein binding involved in cell adhesion" EXACT []
is_a: GO:0050839 ! cell adhesion molecule binding
@@ -392284,27 +392292,29 @@ name: CENP-A recruiting complex
namespace: cellular_component
def: "A protein complex that includes Mis16(Yippee family) and/or Mis18 (WD repeat) subunits that is involved in the deposition of centromere specific (CENP-A containing) nucleosomes at the centromere." [PMID:24774534]
synonym: "MIS18 complex" NARROW [GOC:bhm, GOC:vw]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140513 ! nuclear protein-containing complex
[Term]
id: GO:0098655
-name: cation transmembrane transport
+name: monoatomic cation transmembrane transport
namespace: biological_process
alt_id: GO:0099132
-def: "The process in which a cation is transported across a membrane." [GOC:dos, GOC:vw]
+def: "The process in which a monoatomic cation is transported across a membrane. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom." [GOC:dos, GOC:vw]
synonym: "ATP hydrolysis coupled cation transmembrane transport" NARROW []
-is_a: GO:0006812 ! cation transport
-is_a: GO:0034220 ! ion transmembrane transport
+synonym: "cation transmembrane transport" BROAD []
+is_a: GO:0006812 ! monoatomic cation transport
+is_a: GO:0034220 ! monoatomic ion transmembrane transport
[Term]
id: GO:0098656
-name: anion transmembrane transport
+name: monoatomic anion transmembrane transport
namespace: biological_process
alt_id: GO:0099133
-def: "The process in which an anion is transported across a membrane." [GOC:dos, GOC:vw]
+def: "The process in which a monoatomic anion is transported across a membrane. Monatomic anions (also called simple anions) are negatively charged ions consisting of exactly one atom." [GOC:dos, GOC:vw]
+synonym: "anion transmembrane transport" EXACT []
synonym: "ATP hydrolysis coupled anion transmembrane transport" NARROW []
-is_a: GO:0006820 ! anion transport
-is_a: GO:0034220 ! ion transmembrane transport
+is_a: GO:0006820 ! monoatomic anion transport
+is_a: GO:0034220 ! monoatomic ion transmembrane transport
[Term]
id: GO:0098657
@@ -392340,7 +392350,7 @@ def: "The process in which an inorganic ion is transported across a membrane." [
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "inorganic ion membrane transport" EXACT []
synonym: "transmembrane inorganic ion transport" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0034220 ! ion transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0098661
@@ -392351,7 +392361,6 @@ comment: Note that this term is not intended for use in annotating lateral movem
synonym: "inorganic anion membrane transport" EXACT []
synonym: "transmembrane inorganic anion transport" EXACT [GOC:dph, GOC:tb]
is_a: GO:0015698 ! inorganic anion transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:0098660 ! inorganic ion transmembrane transport
[Term]
@@ -392366,7 +392375,6 @@ synonym: "divalent inorganic cation transport" NARROW []
synonym: "inorganic cation membrane transport" EXACT []
synonym: "monovalent inorganic cation transport" NARROW []
synonym: "transmembrane inorganic cation transport" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0098655 ! cation transmembrane transport
is_a: GO:0098660 ! inorganic ion transmembrane transport
[Term]
@@ -392408,7 +392416,7 @@ is_a: GO:0098665 ! serotonin receptor complex
id: GO:0098669
name: superinfection exclusion
namespace: biological_process
-def: "The process by which a preexisting viral infection prevents a secondary infection with the same or a closely related virus. Typically some aspect of viral entry is inhibited, but post entry mechanisms have also been documented." [PMID:11985726, PMID:23692331, PMID:24089557, PMID:8012757, VZ:3971]
+def: "The process by which a preexisting viral infection prevents a secondary infection with the same or a closely related virus. Typically some aspect of viral entry is inhibited, but post entry mechanisms have also been documented." [PMID:11985726, PMID:23692331, PMID:24089557, PMID:8012757, VZ:3971]
xref: VZ:3971
is_a: GO:0016032 ! viral process
@@ -392434,18 +392442,19 @@ is_a: GO:0046813 ! receptor-mediated virion attachment to host cell
id: GO:0098672
name: inhibition of host CRISPR-cas system by virus
namespace: biological_process
-def: "A process by which a virus inhibits the CRISPR-cas system of its host." [PMID:23242138, PMID:23446421, PMID:26416740]
+def: "A process by which a virus inhibits the CRISPR-cas system of its host." [PMID:23242138, PMID:23446421, PMID:26416740, PMID:28749735]
synonym: "anti-CRISPR" BROAD []
synonym: "CRISPR-cas system evasion by virus" EXACT [VZ:3962]
synonym: "evasion by virus of CRISPR-cas system" RELATED []
xref: VZ:3962
-is_a: GO:0019049 ! mitigation of host defenses by virus
+is_a: GO:0019049 ! mitigation of host antiviral defense response
+relationship: negatively_regulates GO:0099048 ! CRISPR-cas system
[Term]
id: GO:0098673
name: inhibition of host DNA replication by virus
namespace: biological_process
-def: "Any process by which a virus inhibits DNA replication in its host cell. Some bacteriophages are known to do this, possibly as a way of increasing the pool of nucleotides available for virus replication." [PMID:17010157, PMID:21205014]
+def: "Any process by which a virus inhibits DNA replication in its host cell. Some bacteriophages are known to do this, possibly as a way of increasing the pool of nucleotides available for virus replication." [PMID:17010157, PMID:21205014]
is_a: GO:0019054 ! modulation by virus of host cellular process
[Term]
@@ -392459,27 +392468,26 @@ relationship: part_of GO:0099012 ! neuronal dense core vesicle membrane
[Term]
id: GO:0098675
-name: intrinsic component of neuronal dense core vesicle membrane
+name: obsolete intrinsic component of neuronal dense core vesicle membrane
namespace: cellular_component
-def: "The component of the neuronal dense core vesicle membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the neuronal dense core vesicle membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to neuronal dense core granule membrane" EXACT []
-is_a: GO:0098956 ! intrinsic component of dense core granule membrane
-relationship: part_of GO:0099012 ! neuronal dense core vesicle membrane
+is_obsolete: true
+replaced_by: GO:0099012
[Term]
id: GO:0098676
name: modulation of host virulence by virus
namespace: biological_process
-def: "Any process by which a virus modulates the ability of its host to infect and/or damage an organism for which it is a host. Typically this involves a phage modulating the virulence of a bacterium. Mechanisms include the expression of factors that modulate a bacterial adhesion to a host cell, spread through host tissues, production exotoxins or provide protection against host immune defenses." [PMID:10913072, PMID:11553559, PMID:23981100, VZ:3965]
-xref: VZ:3965
+def: "A process by which a virus improves the virulence of its host for that host's respective host. Common in but not limited to bacteriophages; also occurs in phage-bearing bacteria infecting plants or animals for example. Mechanisms include the expression of factors that modulate a bacterial adhesion to a host cell, spread through host tissues, production of exotoxins or provide protection against host immune defenses." [PMID:10913072, PMID:11553559, PMID:22919604, PMID:8658163, VZ:3965]
is_a: GO:0019048 ! modulation by virus of host process
[Term]
id: GO:0098677
name: virion maturation
namespace: biological_process
-def: "Maturation of a virion after separation from the host cell. Not all viruses mature after separation. In those that do, maturation typically involves rearangement and/or cleavage of viral proteins, resulting in the virion becoming competent for reinfection." [ISBN:0781718325, UniProtKB-KW:KW-0917, VZ:1946]
+def: "Maturation of a virion after separation from the host cell. Not all viruses mature after separation. In those that do, maturation typically involves rearangement and/or cleavage of viral proteins, resulting in the virion becoming competent for reinfection." [ISBN:0781718325, UniProtKB-KW:KW-0917, VZ:1946]
synonym: "viral particle maturation" EXACT []
synonym: "virus particle maturation" RELATED []
xref: UniProtKB-KW:KW-0917
@@ -392491,7 +392499,7 @@ relationship: part_of GO:0019075 ! virus maturation
id: GO:0098678
name: viral tropism switching
namespace: biological_process
-def: "A process by which the range of hosts which a virus can bind and infect is changed. Examples include phages that switch between types of fibers via the action of a virally encoded invertase." [PMID:6232613, VZ:4498]
+def: "A process by which the range of hosts which a virus can bind and infect is changed. Examples include phages that switch between types of fibers via the action of a virally encoded invertase." [PMID:6232613, VZ:4498]
xref: VZ:4498
is_a: GO:0016032 ! viral process
@@ -392516,7 +392524,7 @@ is_a: GO:0140098 ! catalytic activity, acting on RNA
id: GO:0098681
name: synaptic ribbon
namespace: cellular_component
-def: "A non-membrane bound, electron dense structure associated that extends perpendicular to the presynaptic membrane in ribbon synapses. The ribbon's surface is studded with small particles to which synaptic vesicles tether via fine filaments. The tethered vesicles function as a pool, several fold greater than the docked pool available for fast release, which supports sustained release of vesicles. Synaptic ribbons may be plate like or spherical." [PMID:15626493]
+def: "A non-membrane bound, electron dense structure associated that extends perpendicular to the presynaptic membrane in ribbon synapses. The ribbon's surface is studded with small particles to which synaptic vesicles tether via fine filaments. The tethered vesicles function as a pool, several fold greater than the docked pool available for fast release, which supports sustained release of vesicles. Synaptic ribbons may be plate like or spherical." [PMID:15626493]
is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
[Term]
@@ -392539,7 +392547,7 @@ is_a: GO:0097470 ! ribbon synapse
id: GO:0098684
name: photoreceptor ribbon synapse
namespace: cellular_component
-def: "A ribbon synapse between a retinal photoreceptor cell (rod or cone) and a retinal bipolar cell. These contain a plate-like synaptic ribbon." [PMID:15626493]
+def: "A ribbon synapse between a retinal photoreceptor cell (rod or cone) and a retinal bipolar cell. These contain a plate-like synaptic ribbon." [PMID:15626493]
subset: goslim_synapse
is_a: GO:0097470 ! ribbon synapse
@@ -392564,7 +392572,7 @@ id: GO:0098687
name: chromosomal region
namespace: cellular_component
def: "Any subdivision of a chromosome along its length." [GOC:dos]
-comment: Chromosomal regions include parts that are not part of the chromatin. Examples include the kinetochore.
+comment: Chromosomal regions include parts that are not part of the chromatin. Examples include the kinetochore.
synonym: "chromosome region" EXACT []
is_a: GO:0110165 ! cellular anatomical entity
relationship: part_of GO:0005694 ! chromosome
@@ -392581,7 +392589,7 @@ is_a: GO:0060076 ! excitatory synapse
id: GO:0098689
name: latency-replication decision
namespace: biological_process
-def: "The process by which a virus switches on its replication cycle in an infected cell. The process is typically controlled by a genetic swtich controlled by environmental factors such as cell type, cell shape, the availability of nutrients, superinfection or exposure of infected cells to UV or various chemical stimuli." [PMID:19416825, PMID:24339346, VZ:3964]
+def: "The process by which a virus switches on its replication cycle in an infected cell. The process is typically controlled by a genetic swtich controlled by environmental factors such as cell type, cell shape, the availability of nutrients, superinfection or exposure of infected cells to UV or various chemical stimuli." [PMID:19416825, PMID:24339346, VZ:3964]
synonym: "Latency-replication switch" EXACT []
synonym: "lytic switch" EXACT []
synonym: "prophage induction" NARROW []
@@ -392686,7 +392694,7 @@ is_a: GO:0099181 ! structural constituent of presynapse
id: GO:0098700
name: neurotransmitter loading into synaptic vesicle
namespace: biological_process
-def: "The active transport of neurotransmitters into a synaptic vesicle. This import is fuelled by an electrochemical gradient across the vesicle membrane, established by the action of proton pumps." [GOC:bf, GOC:pad, GOC:PARL, PMID:10099709, PMID:15217342]
+def: "The active transport of neurotransmitters into a synaptic vesicle. This import is fuelled by an electrochemical gradient across the vesicle membrane, established by the action of proton pumps." [GOC:bf, GOC:pad, GOC:PARL, PMID:10099709, PMID:15217342]
subset: goslim_synapse
synonym: "neurotransmitter import into synaptic vesicle" EXACT []
synonym: "neurotransmitter uptake into synaptic vesicle" EXACT [PMID:15217342]
@@ -392717,7 +392725,6 @@ synonym: "calcium ion import into cell" EXACT []
synonym: "calcium ion uptake into cell" EXACT [GOC:vw]
is_a: GO:0097553 ! calcium ion transmembrane import into cytosol
is_a: GO:0098659 ! inorganic cation import across plasma membrane
-is_a: GO:1902656 ! calcium ion import into cytosol
[Term]
id: GO:0098704
@@ -392742,7 +392749,6 @@ synonym: "copper ion import into cell" EXACT []
synonym: "high affinity copper ion transport" NARROW []
synonym: "high affinity copper transport" NARROW []
synonym: "high-affinity copper ion transport" NARROW []
-is_a: GO:0015677 ! copper ion import
is_a: GO:0015679 ! plasma membrane copper ion transport
is_a: GO:0098659 ! inorganic cation import across plasma membrane
@@ -392770,8 +392776,8 @@ alt_id: GO:1990821
def: "The directed movement of glucose from outside of a cell, across the plasma membrane and into the cytosol." [GOC:dos]
synonym: "glucose import into cell" EXACT []
synonym: "high affinity glucose import" NARROW []
-is_a: GO:0046323 ! glucose import
is_a: GO:0140271 ! hexose import across plasma membrane
+is_a: GO:1904659 ! glucose transmembrane transport
[Term]
id: GO:0098709
@@ -392782,7 +392788,8 @@ def: "The directed movement of glutathione from outside of a cell, across the pl
synonym: "glutathione import into cell" EXACT []
synonym: "glutathione uptake" EXACT [GOC:bf]
is_a: GO:0034775 ! glutathione transmembrane transport
-is_a: GO:0140207 ! tripeptide import across plasma membrane
+is_a: GO:0098657 ! import into cell
+is_a: GO:0098739 ! import across plasma membrane
[Term]
id: GO:0098710
@@ -392823,7 +392830,6 @@ synonym: "L-glutamate import into cell" EXACT []
synonym: "L-glutamate(1-) import across plasma membrane" BROAD []
synonym: "L-glutamate(1-) import into cell" EXACT []
is_a: GO:0015813 ! L-glutamate transmembrane transport
-is_a: GO:0051938 ! L-glutamate import
is_a: GO:0089718 ! amino acid import across plasma membrane
[Term]
@@ -392892,8 +392898,6 @@ def: "The directed movement of serine from outside of a cell, across the plasma
synonym: "serine import into cell" EXACT []
is_a: GO:0032329 ! serine transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0098719
@@ -392965,7 +392969,7 @@ is_a: GO:0051301 ! cell division
id: GO:0098726
name: symmetric division of skeletal muscle satellite stem cell
namespace: biological_process
-def: "The symmetric division of a skeletal muscle satellite stem cell, resulting in two skeletal muscle satellite stem cells. This process is involved in amplification of the pool of these cells." [PMID:23303905]
+def: "The symmetric division of a skeletal muscle satellite stem cell, resulting in two skeletal muscle satellite stem cells. This process is involved in amplification of the pool of these cells." [PMID:23303905]
is_a: GO:0048103 ! somatic stem cell division
is_a: GO:0098724 ! symmetric stem cell division
@@ -392996,7 +393000,7 @@ is_a: GO:0098724 ! symmetric stem cell division
id: GO:0098730
name: male germline stem cell symmetric division
namespace: biological_process
-def: "The symmetric division of a male germline stem cell to produce two male germline stem cells. An example of this is found in mammalian spermatogonial stem cells, some proportion of which divide symmetrically, so amplifying the population. The choice between asymmetric and symmetric division in this case appears to be internal and stochastic." [GOC:dos, PMID:19948499]
+def: "The symmetric division of a male germline stem cell to produce two male germline stem cells. An example of this is found in mammalian spermatogonial stem cells, some proportion of which divide symmetrically, so amplifying the population. The choice between asymmetric and symmetric division in this case appears to be internal and stochastic." [GOC:dos, PMID:19948499]
is_a: GO:0098729 ! germline stem cell symmetric division
[Term]
@@ -393046,7 +393050,7 @@ is_a: GO:0002026 ! regulation of the force of heart contraction
id: GO:0098737
name: protein insertion into plasma membrane
namespace: biological_process
-def: "The process that results in the incorporation of a protein into a plasma membrane. Incorporation in this context means having some part or covalently attached group that is inserted into the the hydrophobic region of one or both bilayers." [GOC:DOS]
+def: "The process that results in the incorporation of a protein into a plasma membrane. Incorporation in this context means having some part or covalently attached group that is inserted into the the hydrophobic region of one or both bilayers." [GOC:DOS]
is_a: GO:0051205 ! protein insertion into membrane
is_a: GO:1990778 ! protein localization to cell periphery
@@ -393077,7 +393081,7 @@ is_a: GO:0098609 ! cell-cell adhesion
id: GO:0098743
name: cell aggregation
namespace: biological_process
-def: "The clustering together and adhesion of initially separate cells to form an aggregate. Examples include the clustering of unicellular organisms or blood cells in suspension and the condensation of mesenchymal cells during cartilage formation." [GOC:dos]
+def: "The clustering together and adhesion of initially separate cells to form an aggregate. Examples include the clustering of unicellular organisms or blood cells in suspension and the condensation of mesenchymal cells during cartilage formation." [GOC:dos]
is_a: GO:0009987 ! cellular process
[Term]
@@ -393130,27 +393134,28 @@ id: GO:0098751
name: bone cell development
namespace: biological_process
def: "The process whose specific outcome is the progression of a bone cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." [GOC:dos]
-comment: Not to be used for manual annotation. Please choose a more specific cell development term or if not possible, bone or bone tissue development.
+comment: Not to be used for manual annotation. Please choose a more specific cell development term or if not possible, bone or bone tissue development.
subset: gocheck_do_not_annotate
is_a: GO:0048468 ! cell development
relationship: part_of GO:0060348 ! bone development
[Term]
id: GO:0098752
-name: integral component of the cytoplasmic side of the plasma membrane
+name: obsolete integral component of the cytoplasmic side of the plasma membrane
namespace: cellular_component
-def: "The component of the plasma membrane consisting of the gene products that penetrate only the cytoplasmic side of the membrane." [GOC:dos]
-is_a: GO:0005887 ! integral component of plasma membrane
-is_a: GO:0031235 ! intrinsic component of the cytoplasmic side of the plasma membrane
+def: "OBSOLETE. The component of the plasma membrane consisting of the gene products that penetrate only the cytoplasmic side of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0009898
[Term]
id: GO:0098753
-name: anchored component of the cytoplasmic side of the plasma membrane
+name: obsolete anchored component of the cytoplasmic side of the plasma membrane
namespace: cellular_component
-def: "The component of the plasma membrane consisting of gene products and protein complexes with covalently attached hydrophobic anchors products that penetrate only the cytoplasmic side of the membrane." [GOC:dos]
-comment: Examples include many myristoylated proteins.
-is_a: GO:0031235 ! intrinsic component of the cytoplasmic side of the plasma membrane
-is_a: GO:0046658 ! anchored component of plasma membrane
+def: "OBSOLETE. The component of the plasma membrane consisting of gene products and protein complexes with covalently attached hydrophobic anchors products that penetrate only the cytoplasmic side of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0009898
[Term]
id: GO:0098754
@@ -393159,6 +393164,7 @@ namespace: biological_process
def: "Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." [GOC:dos]
subset: goslim_generic
subset: goslim_pombe
+subset: prokaryote_subset
is_a: GO:0008150 ! biological_process
relationship: part_of GO:0009636 ! response to toxic substance
@@ -393281,6 +393287,7 @@ namespace: biological_process
def: "The meiotic cell cycle phase in eukaryotes between meiotic prophase I and meiotic metaphase I. During meiotic prometaphase I, the nuclear envelope breaks down and one kinetochore forms per chromosome. Chromosomes attach to spindle microtubules and begin to move towards the metaphase plate." [PMID:16012859]
comment: This term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation should be to 'regulation of x/y phase transition' or to a process which occurs during the reported phase (e.g. mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
subset: gocheck_do_not_annotate
+is_a: GO:0051327 ! meiotic M phase
is_a: GO:0098764 ! meiosis I cell cycle phase
[Term]
@@ -393302,16 +393309,19 @@ id: GO:0098771
name: inorganic ion homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of inorganic ions within an organism or cell." [GOC:dos]
-is_a: GO:0050801 ! ion homeostasis
+subset: goslim_pombe
+is_a: GO:0048878 ! chemical homeostasis
[Term]
id: GO:0098772
-name: molecular function regulator
+name: molecular function regulator activity
namespace: molecular_function
def: "A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition." [GOC:dos, GOC:pt]
subset: gocheck_do_not_annotate
subset: goslim_flybase_ribbon
subset: goslim_generic
+subset: prokaryote_subset
+synonym: "molecular function regulator" EXACT []
is_a: GO:0003674 ! molecular_function
[Term]
@@ -393337,7 +393347,7 @@ relationship: part_of GO:0097311 ! bacterial biofilm matrix
id: GO:0098775
name: curli assembly
namespace: biological_process
-def: "The process of assembly of curli, extracellular fibers produced by enteric bacteria. This process occurs outside the cell, where it is coupled to secretion across the cell outer membrane via nucleation by elements of the transporter complex." [PMID:16704339]
+def: "The process of assembly of curli, extracellular fibers produced by enteric bacteria. This process occurs outside the cell, where it is coupled to secretion across the cell outer membrane via nucleation by elements of the transporter complex." [PMID:16704339]
is_a: GO:0009297 ! pilus assembly
[Term]
@@ -393386,7 +393396,7 @@ id: GO:0098781
name: ncRNA transcription
namespace: biological_process
def: "The transcription of non (protein) coding RNA from a DNA template." [GOC:dos]
-is_a: GO:0006351 ! transcription, DNA-templated
+is_a: GO:0006351 ! DNA-templated transcription
[Term]
id: GO:0098782
@@ -393395,7 +393405,7 @@ namespace: molecular_function
def: "Enables the transmembrane transfer of a potassium ion by a channel that opens in response to a mechanical stress." [PMID:22282805, PMID:25471887, PMID:25500157]
synonym: "mechanically-gated potassium channel activity" EXACT []
is_a: GO:0005267 ! potassium channel activity
-is_a: GO:0140135 ! mechanosensitive cation channel activity
+is_a: GO:0140135 ! mechanosensitive monoatomic cation channel activity
[Term]
id: GO:0098784
@@ -393442,7 +393452,7 @@ is_a: GO:0044292 ! dendrite terminus
id: GO:0098789
name: pre-mRNA cleavage required for polyadenylation
namespace: biological_process
-def: "The targeted, endonucleolytic cleavage of a pre-mRNA, required for polyadenylation of the 3' end. This cleavage is directed by binding sites near the 3' end of the mRNA and leaves a 3' hydoxyl end which then becomes a target for adenylation." [http://www.ncbi.nlm.nih.gov/books/NBK21563/#_A2878_]
+def: "The targeted, endonucleolytic cleavage of a pre-mRNA, required for polyadenylation of the 3' end. This cleavage is directed by binding sites near the 3' end of the mRNA and leaves a 3' hydoxyl end which then becomes a target for adenylation." [http://www.ncbi.nlm.nih.gov/books/NBK21563/#_A2878_]
synonym: "cleavage and polyadenylylation specificity factor activity" RELATED []
synonym: "pre-mRNA cleavage factor activity" EXACT []
is_a: GO:0098787 ! mRNA cleavage involved in mRNA processing
@@ -393495,11 +393505,16 @@ relationship: part_of GO:0045202 ! synapse
[Term]
id: GO:0098795
-name: mRNA destabilization-mediated gene silencing
+name: global gene silencing by mRNA cleavage
namespace: biological_process
-def: "A gene silencing mechanism that involves the destabilization of an mRNA." [GOC:BHF, GOC:BHF_miRNA, GOC:dos]
-synonym: "mRNA cleavage involved in gene silencing" EXACT []
-is_a: GO:0016441 ! posttranscriptional gene silencing
+alt_id: GO:0030423
+def: "A posttranscriptional gene silencing pathway that involves the cleavage of mRNAs in a non-gene-specific manner." [PMID:15009896]
+synonym: "gene silencing by mRNA cleavage" BROAD []
+synonym: "mRNA cleavage involved in gene silencing" BROAD []
+synonym: "mRNA destabilization-mediated gene silencing" RELATED []
+synonym: "RNA interference, targeting of mRNA for destruction" RELATED [GOC:mah]
+synonym: "targeting of mRNA for destruction involved in RNA interference" RELATED []
+is_a: GO:0016441 ! post-transcriptional gene silencing
[Term]
id: GO:0098796
@@ -393584,11 +393599,14 @@ relationship: part_of GO:0097730 ! non-motile cilium
[Term]
id: GO:0098806
-name: mRNA deadenylation-mediated gene silencing by miRNA
+name: obsolete miRNA-mediated gene silencing by mRNA deadenylation
namespace: biological_process
-def: "Shortening of the poly(A) tail of a nuclear-transcribed mRNA following miRNA binding to mRNA, resulting in destabilization of the mRNA and a reduction in the efficiency of its translation." [GOC:BHF, GOC:dos, PMID:21118121, PMID:23209154]
+def: "OBSOLETE. An RNA interference pathway in which a miRNA binding to mRNA triggers shortening of the poly(A) tail of a nuclear-transcribed mRNA, resulting in destabilization of the mRNA and a reduction the amount of translated transcript." [GOC:BHF, GOC:dos, PMID:21118121, PMID:23209154]
+comment: This term was obsoleted because it represents the same process as miRNA-mediated gene silencing by mRNA destabilization ; GO:0035279.
synonym: "deadenylation involved in gene silencing by miRNA" EXACT []
-is_a: GO:0035279 ! miRNA-mediated gene silencing by mRNA destabilization
+synonym: "mRNA deadenylation-mediated gene silencing by miRNA" EXACT []
+is_obsolete: true
+replaced_by: GO:0035279
[Term]
id: GO:0098807
@@ -393651,7 +393669,6 @@ name: nuclear chromosome segregation
namespace: biological_process
def: "The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles." [GOC:dos]
is_a: GO:0007059 ! chromosome segregation
-is_a: GO:0022402 ! cell cycle process
[Term]
id: GO:0098814
@@ -393692,14 +393709,14 @@ is_a: GO:0060079 ! excitatory postsynaptic potential
id: GO:0098818
name: hyperpolarization of postsynaptic membrane
namespace: biological_process
-def: "A process that hyerpolarizes a postsynaptic membrane relative to its resting potential. This has an inhibitory effect on the post-synaptic cell, moving the membrane potential away from the firing threshold." [GOC:dos]
+def: "A process that hyerpolarizes a postsynaptic membrane relative to its resting potential. This has an inhibitory effect on the post-synaptic cell, moving the membrane potential away from the firing threshold." [GOC:dos]
is_a: GO:0060078 ! regulation of postsynaptic membrane potential
[Term]
id: GO:0098819
name: depolarization of postsynaptic membrane
namespace: biological_process
-def: "A process that depolarizes a postsynaptic membrane relative to its resting potential. This has an excitatory effect on the post-synaptic cell, moving the membrane potential towards the firing threshold." [GOC:dos]
+def: "A process that depolarizes a postsynaptic membrane relative to its resting potential. This has an excitatory effect on the post-synaptic cell, moving the membrane potential towards the firing threshold." [GOC:dos]
is_a: GO:0060078 ! regulation of postsynaptic membrane potential
[Term]
@@ -393789,8 +393806,8 @@ is_a: GO:0050892 ! intestinal absorption
id: GO:0098830
name: presynaptic endosome
namespace: cellular_component
-def: "An endosome present in the presynapse that fuses with endocytic vesicles arising in the presynaptic endocytic zone. This organelle is believed to be involved in regeneration of synaptic vesicles." [PMID:20200227, PMID:25939282]
-comment: As of 2015, there is still controversy over the nature of presynaptic endosomes and their relationship to regular endosomes. See Jahne et al., 2015 (PMID:25939282) for details.
+def: "An endosome present in the presynapse that fuses with endocytic vesicles arising in the presynaptic endocytic zone. This organelle is believed to be involved in regeneration of synaptic vesicles." [PMID:20200227, PMID:25939282]
+comment: As of 2015, there is still controversy over the nature of presynaptic endosomes and their relationship to regular endosomes. See Jahne et al., 2015 (PMID:25939282) for details.
subset: goslim_synapse
is_a: GO:0005768 ! endosome
relationship: part_of GO:0098793 ! presynapse
@@ -393817,7 +393834,7 @@ is_a: GO:0055037 ! recycling endosome
id: GO:0098833
name: presynaptic endocytic zone
namespace: cellular_component
-def: "A specialized region of the plasma membrane and underlying cytoplasm which surround the the active zone, into which synaptic vesicle membranes are recycled following exocytosis. It is especially enriched in endocytic proteins following intense activity." [PMID:17455288]
+def: "A specialized region of the plasma membrane and underlying cytoplasm which surround the the active zone, into which synaptic vesicle membranes are recycled following exocytosis. It is especially enriched in endocytic proteins following intense activity." [PMID:17455288]
comment: May be identical to periactive zone?
subset: goslim_synapse
is_a: GO:0110165 ! cellular anatomical entity
@@ -393847,7 +393864,7 @@ relationship: part_of GO:0098833 ! presynaptic endocytic zone
id: GO:0098836
name: cytoskeleton of dendritic spine
namespace: cellular_component
-def: "The portion of the cytoskeleton that lies within a dendritic spine. The actin component of this cytoskeleton is involved in spine head remodelling in response to postsynaptic signalling." [PMID:24854120]
+def: "The portion of the cytoskeleton that lies within a dendritic spine. The actin component of this cytoskeleton is involved in spine head remodelling in response to postsynaptic signalling." [PMID:24854120]
is_a: GO:0099571 ! postsynaptic cytoskeleton
relationship: part_of GO:0043197 ! dendritic spine
@@ -393855,7 +393872,7 @@ relationship: part_of GO:0043197 ! dendritic spine
id: GO:0098837
name: postsynaptic recycling endosome
namespace: cellular_component
-def: "A recycling endosome of the postsynapse. In postsynaptic terminals with dendritic spines, it is typically located at the base of a dendritic spine. It is involved in recycling of neurotransmitter receptors to the postsynaptic membrane. In some cases at least, this recycling is activated by postsynaptic signalling and so can play a role in long term potentiation." [PMID:20820847]
+def: "A recycling endosome of the postsynapse. In postsynaptic terminals with dendritic spines, it is typically located at the base of a dendritic spine. It is involved in recycling of neurotransmitter receptors to the postsynaptic membrane. In some cases at least, this recycling is activated by postsynaptic signalling and so can play a role in long term potentiation." [PMID:20820847]
subset: goslim_synapse
synonym: "postsynaptic endosomal recycling compartment" BROAD [PMID:20820847]
synonym: "postsynaptic recycling outpost" EXACT [PMID:20820847]
@@ -393871,7 +393888,6 @@ synonym: "folic acid transmembrane transport" RELATED []
synonym: "reduced folate transmembrane transport" NARROW []
is_a: GO:0015884 ! folic acid transport
is_a: GO:0035461 ! vitamin transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -393923,7 +393939,7 @@ relationship: part_of GO:0098794 ! postsynapse
id: GO:0098844
name: postsynaptic endocytic zone membrane
namespace: cellular_component
-def: "The region of the postsynaptic membrane that is part of the postsynaptic endocytic zone. This region of membrane is associated with stable clathrin puncta." [PMID:17880892]
+def: "The region of the postsynaptic membrane that is part of the postsynaptic endocytic zone. This region of membrane is associated with stable clathrin puncta." [PMID:17880892]
subset: goslim_synapse
is_a: GO:0097060 ! synaptic membrane
relationship: part_of GO:0045211 ! postsynaptic membrane
@@ -393973,7 +393989,7 @@ name: cellular detoxification of cadmium ion
namespace: biological_process
def: "Any process that reduces or removes the toxicity of cadmium cations in a cell. These include transport of cadmium cations away from sensitive areas and to compartments or complexes whose purpose is sequestration." [GOC:dos, GOC:vw]
is_a: GO:0071585 ! detoxification of cadmium ion
-is_a: GO:1990748 ! cellular detoxification
+is_a: GO:0140961 ! cellular detoxification of metal ion
relationship: part_of GO:0071276 ! cellular response to cadmium ion
[Term]
@@ -394078,7 +394094,7 @@ relationship: part_of GO:0098858 ! actin-based cell projection
id: GO:0098860
name: actin filament bundle of stereocilium
namespace: cellular_component
-def: "A bundle of hundreds of cross-linked actin filaments (an actin cable), that is the supporting structure of a stereocilium. Filaments are oriented such that the the plus (barbed) ends are at the tip of the protrusion and are capped by a tip complex which bridges to the plasma membrane." [PMID:15661519]
+def: "A bundle of hundreds of cross-linked actin filaments (an actin cable), that is the supporting structure of a stereocilium. Filaments are oriented such that the the plus (barbed) ends are at the tip of the protrusion and are capped by a tip complex which bridges to the plasma membrane." [PMID:15661519]
is_a: GO:0098859 ! actin filament bundle of actin-based cell projection
relationship: part_of GO:0032420 ! stereocilium
@@ -394111,13 +394127,14 @@ id: GO:0098864
name: modification by symbiont of host tight cell-cell junction
namespace: biological_process
def: "The process in which a symbiont organism effects a change in the structure or function of its host tight junction, a cell-cell junction that seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other." [PMID:24287273]
-is_a: GO:0044067 ! modification by symbiont of host intercellular junctions
+is_a: GO:0044067 ! modification by symbiont of host cell-cell junction
[Term]
id: GO:0098865
-name: modification by symbiont of host bicellular tight junctions
+name: disruption by symbiont of host tight cell-cell junction
namespace: biological_process
-def: "The process in which an organism effects a change in the structure or function of its host bicellular tight junctions, an occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet." [PMID:24287273]
+def: "The disruption of host host tight cell-cell junctions, a cell-cell junction that seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other." [PMID:24287273]
+synonym: "modification by symbiont of host bicellular tight junctions" RELATED []
is_a: GO:0098864 ! modification by symbiont of host tight cell-cell junction
[Term]
@@ -394141,6 +394158,7 @@ name: bone growth
namespace: biological_process
def: "The increase in size or mass of a bone that contributes to the shaping of that bone." [GOC:dos]
is_a: GO:0035265 ! organ growth
+relationship: part_of GO:0060348 ! bone development
[Term]
id: GO:0098869
@@ -394153,7 +394171,7 @@ is_a: GO:1990748 ! cellular detoxification
id: GO:0098870
name: action potential propagation
namespace: biological_process
-def: "The propagation of an action potential along the plane of an excitable membrane. Action potentials typically propagate once triggered because the depolarization of adjacent membrane regions due to an action potential crosses the firing threshold." [GOC:dos]
+def: "The propagation of an action potential along the plane of an excitable membrane. Action potentials typically propagate once triggered because the depolarization of adjacent membrane regions due to an action potential crosses the firing threshold." [GOC:dos]
is_a: GO:0001508 ! action potential
[Term]
@@ -394327,13 +394345,13 @@ relationship: part_of GO:0042734 ! presynaptic membrane
[Term]
id: GO:0098889
-name: intrinsic component of presynaptic membrane
+name: obsolete intrinsic component of presynaptic membrane
namespace: cellular_component
-def: "The component of the presynaptic membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the presynaptic membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to presynaptic membrane" NARROW []
-is_a: GO:0099240 ! intrinsic component of synaptic membrane
-relationship: part_of GO:0042734 ! presynaptic membrane
+is_obsolete: true
+replaced_by: GO:0042734
[Term]
id: GO:0098890
@@ -394535,7 +394553,7 @@ relationship: regulates GO:0086014 ! atrial cardiac muscle cell action potential
id: GO:0098911
name: regulation of ventricular cardiac muscle cell action potential
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a ventricular cardiac muscle cell contributing to the regulation of its contraction. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
+def: "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a ventricular cardiac muscle cell contributing to the regulation of its contraction. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
is_a: GO:0086004 ! regulation of cardiac muscle cell contraction
is_a: GO:0098901 ! regulation of cardiac muscle cell action potential
relationship: regulates GO:0086005 ! ventricular cardiac muscle cell action potential
@@ -394627,7 +394645,7 @@ is_a: GO:0099541 ! trans-synaptic signaling by lipid
id: GO:0098921
name: retrograde trans-synaptic signaling by endocannabinoid
namespace: biological_process
-def: "Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by an endocannabinoid ligand." [GOC:dos]
+def: "Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by an endocannabinoid ligand." [GOC:dos]
subset: goslim_synapse
is_a: GO:0098920 ! retrograde trans-synaptic signaling by lipid
is_a: GO:0099542 ! trans-synaptic signaling by endocannabinoid
@@ -394673,8 +394691,6 @@ id: GO:0098926
name: postsynaptic signal transduction
namespace: biological_process
def: "Signal transduction in which the initial step occurs in a postsynapse." [GOC:dos]
-comment: Do not directly annotate. This term is intended for automatically grouping annotations to signal transduction classes extended with has_start_location/occurs_in postsynapse or one of its parts.
-subset: gocheck_do_not_manually_annotate
subset: goslim_synapse
synonym: "postsynaptic signaling pathway" EXACT syngo_official_label []
is_a: GO:0007165 ! signal transduction
@@ -394692,20 +394708,19 @@ id: GO:0098928
name: presynaptic signal transduction
namespace: biological_process
def: "Signal transduction in which the initial step occurs in a presynapse." [GOC:dos]
-comment: Do not directly annotate. This term intended for grouping. Annotate to either a subclass or to some other subclass of signal transduction extended with has_start_location/occurs_in presynapse or one of its parts. Such extensions will result in automatic annotation to this term.
-subset: gocheck_do_not_manually_annotate
subset: goslim_synapse
synonym: "presynaptic signaling pathway" EXACT syngo_official_label []
is_a: GO:0007165 ! signal transduction
[Term]
id: GO:0098929
-name: extrinsic component of spine apparatus membrane
+name: obsolete extrinsic component of spine apparatus membrane
namespace: cellular_component
-def: "The component of the spine apparatus membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:dos]
+def: "OBSOLETE. The component of the spine apparatus membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
subset: goslim_synapse
-is_a: GO:0031312 ! extrinsic component of organelle membrane
-relationship: part_of GO:0098897 ! spine apparatus membrane
+is_obsolete: true
+consider: GO:0098897
[Term]
id: GO:0098930
@@ -394745,6 +394760,7 @@ id: GO:0098933
name: disruption by symbiont of host cell envelope
namespace: biological_process
def: "The process by which a symbiont breaks down the cell wall of its host. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+is_a: GO:0052008 ! disruption by symbiont of host cellular component
is_a: GO:0052020 ! modification by symbiont of host cell wall
[Term]
@@ -394766,13 +394782,13 @@ is_a: GO:0008088 ! axo-dendritic transport
[Term]
id: GO:0098936
-name: intrinsic component of postsynaptic membrane
+name: obsolete intrinsic component of postsynaptic membrane
namespace: cellular_component
-def: "The component of the postsynaptic membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the postsynaptic membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to postsynaptic membrane" NARROW []
-is_a: GO:0099240 ! intrinsic component of synaptic membrane
-relationship: part_of GO:0045211 ! postsynaptic membrane
+is_obsolete: true
+replaced_by: GO:0045211
[Term]
id: GO:0098937
@@ -394851,89 +394867,90 @@ relationship: part_of GO:0098837 ! postsynaptic recycling endosome
[Term]
id: GO:0098945
-name: intrinsic component of presynaptic active zone membrane
+name: obsolete intrinsic component of presynaptic active zone membrane
namespace: cellular_component
-def: "The component of the presynaptic active zone membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the presynaptic active zone membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to presynaptic acive zone membrane" NARROW []
-is_a: GO:0098889 ! intrinsic component of presynaptic membrane
-relationship: part_of GO:0048787 ! presynaptic active zone membrane
+is_obsolete: true
+replaced_by: GO:0048787
[Term]
id: GO:0098946
-name: intrinsic component of presynaptic endocytic zone membrane
+name: obsolete intrinsic component of presynaptic endocytic zone membrane
namespace: cellular_component
-def: "The component of the presynaptic endocytic zone membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the presynaptic endocytic zone membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to presynaptic acive zone membrane" NARROW []
-is_a: GO:0098889 ! intrinsic component of presynaptic membrane
-relationship: part_of GO:0098835 ! presynaptic endocytic zone membrane
+is_obsolete: true
+replaced_by: GO:0098835
[Term]
id: GO:0098947
-name: intrinsic component of postsynaptic endocytic zone membrane
+name: obsolete intrinsic component of postsynaptic endocytic zone membrane
namespace: cellular_component
-def: "The component of the postsynaptic endocytic zone membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the postsynaptic endocytic zone membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to postsynaptic acive zone membrane" NARROW []
-is_a: GO:0098936 ! intrinsic component of postsynaptic membrane
-relationship: part_of GO:0098844 ! postsynaptic endocytic zone membrane
+is_obsolete: true
+replaced_by: GO:0098844
[Term]
id: GO:0098948
-name: intrinsic component of postsynaptic specialization membrane
+name: obsolete intrinsic component of postsynaptic specialization membrane
namespace: cellular_component
-def: "The component of the postsynaptic specialization membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the postsynaptic specialization membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to postsynaptic specialization membrane" NARROW []
-is_a: GO:0098936 ! intrinsic component of postsynaptic membrane
-relationship: part_of GO:0099634 ! postsynaptic specialization membrane
+is_obsolete: true
+replaced_by: GO:0099634
[Term]
id: GO:0098949
-name: intrinsic component of postsynaptic endosome membrane
+name: obsolete intrinsic component of postsynaptic endosome membrane
namespace: cellular_component
-def: "The component of the postsynaptic endosome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the postsynaptic endosome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to postsynaptic endosome membrane" NARROW []
-is_a: GO:0031302 ! intrinsic component of endosome membrane
-relationship: part_of GO:0098895 ! postsynaptic endosome membrane
+is_obsolete: true
+replaced_by: GO:0098895
[Term]
id: GO:0098950
-name: intrinsic component of postsynaptic early endosome membrane
+name: obsolete intrinsic component of postsynaptic early endosome membrane
namespace: cellular_component
-def: "The component of the postsynaptic early endosome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the postsynaptic early endosome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to postsynaptic early endosome membrane" NARROW []
-is_a: GO:0098949 ! intrinsic component of postsynaptic endosome membrane
-relationship: part_of GO:0098896 ! postsynaptic early endosome membrane
+is_obsolete: true
+replaced_by: GO:0098896
[Term]
id: GO:0098951
-name: intrinsic component of postsynaptic recycling endosome membrane
+name: obsolete intrinsic component of postsynaptic recycling endosome membrane
namespace: cellular_component
-def: "The component of the postsynaptic recycling endosome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the postsynaptic recycling endosome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to postsynaptic recycling endosome membrane" EXACT []
-is_a: GO:0098949 ! intrinsic component of postsynaptic endosome membrane
-relationship: part_of GO:0098944 ! postsynaptic recycling endosome membrane
+is_obsolete: true
+replaced_by: GO:0098944
[Term]
id: GO:0098952
-name: intrinsic component of spine apparatus membrane
+name: obsolete intrinsic component of spine apparatus membrane
namespace: cellular_component
-def: "The component of the spine apparatus membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the spine apparatus membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
subset: goslim_synapse
synonym: "intrinsic to spine apparatus membrane" EXACT []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0098897 ! spine apparatus membrane
+is_obsolete: true
+replaced_by: GO:0098897
[Term]
id: GO:0098953
name: receptor diffusion trapping
namespace: biological_process
-def: "The process by which a membrane receptor, diffusing freely within the plasma membeane, becomes trapped in some plasma membrane region. This can happen when a receptor bind, directly or indirectly, to some component of the underlying matrix." [PMID:18832033]
+def: "The process by which a membrane receptor, diffusing freely within the plasma membeane, becomes trapped in some plasma membrane region. This can happen when a receptor bind, directly or indirectly, to some component of the underlying matrix." [PMID:18832033]
is_a: GO:0031503 ! protein-containing complex localization
is_a: GO:0051668 ! localization within membrane
@@ -394948,22 +394965,23 @@ relationship: part_of GO:0098830 ! presynaptic endosome
[Term]
id: GO:0098955
-name: intrinsic component of presynaptic endosome membrane
+name: obsolete intrinsic component of presynaptic endosome membrane
namespace: cellular_component
-def: "The component of the presynaptic endosome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the presynaptic endosome membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to presynaptic endosome membrane" EXACT []
-is_a: GO:0031302 ! intrinsic component of endosome membrane
-relationship: part_of GO:0098954 ! presynaptic endosome membrane
+is_obsolete: true
+replaced_by: GO:0098954
[Term]
id: GO:0098956
-name: intrinsic component of dense core granule membrane
+name: obsolete intrinsic component of dense core granule membrane
namespace: cellular_component
-def: "The component of the dense core granule membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+def: "OBSOLETE. The component of the dense core granule membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to dense core granule membrane" EXACT []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0032127 ! dense core granule membrane
+is_obsolete: true
+replaced_by: GO:0032127
[Term]
id: GO:0098957
@@ -395067,7 +395085,7 @@ relationship: part_of GO:0099535 ! synapse-associated extracellular matrix
id: GO:0098967
name: exocytic insertion of neurotransmitter receptor to postsynaptic membrane
namespace: biological_process
-def: "The exocytic fusion of neurotransmitter receptor containing vesicles with the postsynaptic membrane resulting in the integration of NT receptors, enabling them to participate in neurotransmitter reception. This process includes tethering and docking steps that prepare vesicles for fusion." [PMID:19503082]
+def: "The exocytic fusion of neurotransmitter receptor containing vesicles with the postsynaptic membrane resulting in the integration of NT receptors, enabling them to participate in neurotransmitter reception. This process includes tethering and docking steps that prepare vesicles for fusion." [PMID:19503082]
subset: goslim_synapse
is_a: GO:0006887 ! exocytosis
is_a: GO:0099072 ! regulation of postsynaptic membrane neurotransmitter receptor levels
@@ -395177,7 +395195,7 @@ is_a: GO:0045202 ! synapse
id: GO:0098979
name: polyadic synapse
namespace: cellular_component
-def: "A synapse consisting of a single presynapse and multiple postsynapses. These postsynapses may come from the same cell of from different cells. Polyadic synapses are common in arthropod and nematode central nervous systems." [PMID:26780543]
+def: "A synapse consisting of a single presynapse and multiple postsynapses. These postsynapses may come from the same cell of from different cells. Polyadic synapses are common in arthropod and nematode central nervous systems." [PMID:26780543]
is_a: GO:0045202 ! synapse
[Term]
@@ -395199,7 +395217,7 @@ is_a: GO:0045202 ! synapse
id: GO:0098982
name: GABA-ergic synapse
namespace: cellular_component
-def: "A synapse that uses GABA as a neurotransmitter. These synapses are typically inhibitory." [GOC:dos]
+def: "A synapse that uses GABA as a neurotransmitter. These synapses are typically inhibitory." [GOC:dos]
subset: goslim_synapse
is_a: GO:0045202 ! synapse
@@ -395232,7 +395250,7 @@ is_a: GO:0098978 ! glutamatergic synapse
id: GO:0098986
name: T-bar
namespace: cellular_component
-def: "A T-shaped presynpatic density. These are common in arhropod central nervous systems." [GOC:dos, PMID:26780543]
+def: "A T-shaped presynpatic density. These are common in arhropod central nervous systems." [GOC:dos, PMID:26780543]
is_a: GO:0098980 ! presynaptic density
[Term]
@@ -395258,14 +395276,14 @@ is_a: GO:0008066 ! glutamate receptor activity
id: GO:0098989
name: NMDA selective glutamate receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by glutamate binding to an NMDA-selective glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:dos, ISBN:9780071120005]
+def: "The series of molecular signals initiated by glutamate binding to an NMDA-selective glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:dos, ISBN:9780071120005]
is_a: GO:0035235 ! ionotropic glutamate receptor signaling pathway
[Term]
id: GO:0098990
name: AMPA selective glutamate receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by glutamate binding to an AMPA-selective glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:dos, ISBN:9780071120005]
+def: "The series of molecular signals initiated by glutamate binding to an AMPA-selective glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:dos, ISBN:9780071120005]
subset: goslim_synapse
is_a: GO:0035235 ! ionotropic glutamate receptor signaling pathway
@@ -395273,7 +395291,7 @@ is_a: GO:0035235 ! ionotropic glutamate receptor signaling pathway
id: GO:0098991
name: kainate selective glutamate receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by glutamate binding to an kainate-selective glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, ISBN:9780071120005]
+def: "The series of molecular signals initiated by glutamate binding to an kainate-selective glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex, ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, ISBN:9780071120005]
subset: goslim_synapse
is_a: GO:0035235 ! ionotropic glutamate receptor signaling pathway
@@ -395281,18 +395299,18 @@ is_a: GO:0035235 ! ionotropic glutamate receptor signaling pathway
id: GO:0098992
name: neuronal dense core vesicle
namespace: cellular_component
-def: "A dense core vesicle (granule) that is part of a neuron. These vesicles typically contain neuropeptides. They can be found in all parts of neurons, including the soma, dendrites, axonal swellings (varicosities) and synaptic terminals." [GOC:dos, ISBN:978-0-07-181001-2, Wikipedia:Neuropeptide&oldid=713905176]
+def: "A dense core vesicle (granule) that is part of a neuron. These vesicles typically contain neuropeptides. They can be found in all parts of neurons, including the soma, dendrites, axonal swellings (varicosities) and synaptic terminals." [GOC:dos, ISBN:978-0-07-181001-2, Wikipedia:Neuropeptide&oldid=713905176]
subset: goslim_synapse
is_a: GO:0031045 ! dense core granule
[Term]
id: GO:0098993
-name: anchored component of synaptic vesicle membrane
+name: obsolete anchored component of synaptic vesicle membrane
namespace: cellular_component
-def: "The component of the synaptic vesicle membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0031225 ! anchored component of membrane
-is_a: GO:0098563 ! intrinsic component of synaptic vesicle membrane
+def: "OBSOLETE. The component of the synaptic vesicle membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0030672
[Term]
id: GO:0098994
@@ -395307,7 +395325,7 @@ relationship: part_of GO:0046718 ! viral entry into host cell
id: GO:0098995
name: disruption by virus of host envelope lipopolysaccharide during virus entry
namespace: biological_process
-def: "The breakdown of lipopolysaccharides in a host cell envelope during virus entry into a host cell. For example a phage entering a gram-negative bacterium may actively break down outer membrane lipopolysaccharides." [GOC:dos, VZ:3940]
+def: "The breakdown of lipopolysaccharides in a host cell envelope during virus entry into a host cell. For example a phage entering a gram-negative bacterium may actively break down outer membrane lipopolysaccharides." [GOC:dos, VZ:3940]
synonym: "degradation of host cell envelope lipopolysaccharide during viral entry" EXACT []
synonym: "degradation of host lipopolysaccharide during virus entry" EXACT [VZ:3940]
synonym: "disassembly by virus of outer membrane lipopolysaccharide during viral entry" NARROW []
@@ -395363,7 +395381,7 @@ relationship: part_of GO:0098895 ! postsynaptic endosome membrane
id: GO:0099000
name: viral genome ejection through host cell envelope, contractile tail mechanism
namespace: biological_process
-def: "Ejection by a non-enveloped prokaryotic virus of its genome into the host cytoplasm via a contractile tail ejection system consisting of a baseplate, a central tube and an external contractile sheath. Upon binding to the host cell surface, the baseplate changes its conformation and triggers sheath contraction, driving the rigid internal tail tube through the cell envelope." [GOC:dos, PMID:26283379, VZ:3950]
+def: "Ejection by a non-enveloped prokaryotic virus of its genome into the host cytoplasm via a contractile tail ejection system consisting of a baseplate, a central tube and an external contractile sheath. Upon binding to the host cell surface, the baseplate changes its conformation and triggers sheath contraction, driving the rigid internal tail tube through the cell envelope." [GOC:dos, PMID:26283379, VZ:3950]
synonym: "viral contractile tail ejection system" EXACT [VZ:3950]
xref: VZ:3950
is_a: GO:0039678 ! viral genome ejection through host cell envelope
@@ -395372,7 +395390,7 @@ is_a: GO:0039678 ! viral genome ejection through host cell envelope
id: GO:0099001
name: viral genome ejection through host cell envelope, long flexible tail mechanism
namespace: biological_process
-def: "Ejection by a non-enveloped prokaryotic virus of its genome into the host cytoplasm via a long, flexible tail ejection system consisting a baseplate, a central tube and a terminator complex which attaches the tail to the phage capsid. Upon binding to the host cell surface, the baseplate changes its conformation and triggers genome ejection into the host cell cytoplasm." [GOC:dos, PMID:22297512, VZ:3952]
+def: "Ejection by a non-enveloped prokaryotic virus of its genome into the host cytoplasm via a long, flexible tail ejection system consisting a baseplate, a central tube and a terminator complex which attaches the tail to the phage capsid. Upon binding to the host cell surface, the baseplate changes its conformation and triggers genome ejection into the host cell cytoplasm." [GOC:dos, PMID:22297512, VZ:3952]
synonym: "viral long flexible tail ejection system" EXACT [VZ:3952]
xref: VZ:3952
is_a: GO:0039678 ! viral genome ejection through host cell envelope
@@ -395382,7 +395400,7 @@ is_a: GO:0046794 ! transport of virus
id: GO:0099002
name: viral genome ejection through host cell envelope, short tail mechanism
namespace: biological_process
-def: "Ejection by a non-enveloped prokaryotic virus of its genome into the host cytoplasm via a short tail ejection system consisting a central tube, the connector which attaches the tail to the phage capsid and releases inner core proteins. Upon binding to the host cell surface, the phage displays a tube-like extension of its short tail that penetrates both host membranes. This tail extension comes from the release of viral core proteins with channel forming properties." [GOC:dos, PMID:22297513, VZ:3954]
+def: "Ejection by a non-enveloped prokaryotic virus of its genome into the host cytoplasm via a short tail ejection system consisting a central tube, the connector which attaches the tail to the phage capsid and releases inner core proteins. Upon binding to the host cell surface, the phage displays a tube-like extension of its short tail that penetrates both host membranes. This tail extension comes from the release of viral core proteins with channel forming properties." [GOC:dos, PMID:22297513, VZ:3954]
synonym: "viral short tail ejection system" EXACT [VZ:3954]
xref: VZ:3954
is_a: GO:0039678 ! viral genome ejection through host cell envelope
@@ -395417,7 +395435,7 @@ relationship: part_of GO:0098944 ! postsynaptic recycling endosome membrane
id: GO:0099006
name: viral entry via permeabilization of endosomal membrane
namespace: biological_process
-def: "The entry of a non-enveloped virus into a host eukaryotic cell, following endocytosis, via permeabilization of the endosomal membrane by membrane penetration protein(s) associated with the viral capsid. In some cases, viral membrane-penetration protein require first to be activated to display its membrane penetrating activity. Activation can be due to receptor binding or the acidic pH of the endosomal lumen." [PMID:15329727, PMID:25055856, VZ:985]
+def: "The entry of a non-enveloped virus into a host eukaryotic cell, following endocytosis, via permeabilization of the endosomal membrane by membrane penetration protein(s) associated with the viral capsid. In some cases, viral membrane-penetration protein require first to be activated to display its membrane penetrating activity. Activation can be due to receptor binding or the acidic pH of the endosomal lumen." [PMID:15329727, PMID:25055856, VZ:985]
synonym: "viral penetration via permeabilization of host membrane" BROAD [vz:985]
xref: VZ:985
is_a: GO:0140267 ! viral entry via permeabilization of host membrane
@@ -395435,7 +395453,7 @@ relationship: part_of GO:0098954 ! presynaptic endosome membrane
id: GO:0099008
name: viral entry via permeabilization of inner membrane
namespace: biological_process
-def: "The entry of a non-enveloped virus into the cytoplasm of a host prokaryotic cell, following fusion with the outer membrane, via permeabilization of the plasma (inner) membrane. In the case of some double stranded RNA viruses of prokaryotes this occurs via interaction of a membrane-interacting component of the capsid, leading to depolarization an permeabilization of the plasma membrane." [PMID:15795287, PMID:20427561, VZ:985]
+def: "The entry of a non-enveloped virus into the cytoplasm of a host prokaryotic cell, following fusion with the outer membrane, via permeabilization of the plasma (inner) membrane. In the case of some double stranded RNA viruses of prokaryotes this occurs via interaction of a membrane-interacting component of the capsid, leading to depolarization an permeabilization of the plasma membrane." [PMID:15795287, PMID:20427561, VZ:985]
synonym: "viral penetration via permeabilization of host membrane" BROAD [vz:985]
xref: VZ:985
is_a: GO:0140267 ! viral entry via permeabilization of host membrane
@@ -395494,17 +395512,18 @@ is_a: GO:0061109 ! dense core granule organization
id: GO:0099015
name: degradation of host chromosome by virus
namespace: biological_process
-def: "The catabolic breakdown of the DNA of a host chromosome by a virus. This occurs during infection of bacteria by some phages. It frees up a large pool of nucleoside 5'-triphophates for use in viral DNA synthesis." [PMID:163355, PMID:335083, PMID:3972821, PMID:5263754, VZ:3947]
+def: "The catabolic breakdown of the DNA of a host chromosome by a virus. This occurs during infection of bacteria by some phages. It frees up a large pool of nucleoside 5'-triphophates for use in viral DNA synthesis." [PMID:163355, PMID:335083, PMID:3972821, PMID:5263754, VZ:3947]
xref: VZ:3947
is_a: GO:0039637 ! catabolism by virus of host DNA
[Term]
id: GO:0099016
-name: DNA end degradation evasion by virus
+name: evasion by virus of DNA end degradation
namespace: biological_process
def: "A process by which a virus evades and ends degradation of its DNA when free viral-DNA ends are exposed as part of its life-cycle. For example, some bacteriophages encode proteins that bind to free viral DNA ends, protecting them from degradation by host exonucleases." [GOC:dos]
+synonym: "DNA end degradation evasion by virus" EXACT []
xref: VZ:3963
-is_a: GO:0019049 ! mitigation of host defenses by virus
+is_a: GO:0019049 ! mitigation of host antiviral defense response
[Term]
id: GO:0099017
@@ -395516,11 +395535,12 @@ is_a: GO:0032507 ! maintenance of protein location in cell
[Term]
id: GO:0099018
-name: restriction-modification system evasion by virus
+name: evasion by virus of host restriction-modification system
namespace: biological_process
def: "Any process, either active or passive, by which a virus evades the DNA restriction modification system of its host. Some viruses encode their own methyltransferase in order to protect their genome from host restriction enzymes. Others directly inhibit restruction enzymes while some use unusual bases in their genome to avoid restriction." [PMID:20348932, PMID:23979432, PMID:24123737, VZ:3966]
+synonym: "restriction-modification system evasion by virus" EXACT []
xref: VZ:3966
-is_a: GO:0019049 ! mitigation of host defenses by virus
+is_a: GO:0019049 ! mitigation of host antiviral defense response
[Term]
id: GO:0099019
@@ -395550,7 +395570,7 @@ relationship: part_of GO:0032541 ! cortical endoplasmic reticulum
id: GO:0099022
name: vesicle tethering
namespace: biological_process
-def: "The initial, indirect interaction between a vesicle membrane and a membrane to which it is targeted for fusion. This interaction is mediated by tethering factors (or complexes), which interact with both membranes. Interaction can occur via direct binding to membrane phospholipids or membrane proteins, or via binding to vesicle coat proteins. This process is distinct from and prior to interaction between factors involved in fusion." [PMID:27243008]
+def: "The initial, indirect interaction between a vesicle membrane and a membrane to which it is targeted for fusion. This interaction is mediated by tethering factors (or complexes), which interact with both membranes. Interaction can occur via direct binding to membrane phospholipids or membrane proteins, or via binding to vesicle coat proteins. This process is distinct from and prior to interaction between factors involved in fusion." [PMID:27243008]
is_a: GO:0016043 ! cellular component organization
relationship: part_of GO:0006903 ! vesicle targeting
@@ -395570,121 +395590,123 @@ is_a: GO:0010324 ! membrane invagination
[Term]
id: GO:0099025
-name: anchored component of postsynaptic membrane
+name: obsolete anchored component of postsynaptic membrane
namespace: cellular_component
-def: "The component of the postsynaptic membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098936 ! intrinsic component of postsynaptic membrane
-is_a: GO:0099144 ! anchored component of synaptic membrane
+def: "OBSOLETE. The component of the postsynaptic membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0045211
[Term]
id: GO:0099026
-name: anchored component of presynaptic membrane
+name: obsolete anchored component of presynaptic membrane
namespace: cellular_component
-def: "The component of the presynaptic membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the presynaptic membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "anchored component of presynaptic plasma membrane" EXACT []
-is_a: GO:0098889 ! intrinsic component of presynaptic membrane
-is_a: GO:0099144 ! anchored component of synaptic membrane
+is_obsolete: true
+replaced_by: GO:0042734
[Term]
id: GO:0099027
-name: anchored component of presynaptic endocytic zone membrane
+name: obsolete anchored component of presynaptic endocytic zone membrane
namespace: cellular_component
-def: "The component of the presynaptic endocytic zone membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098946 ! intrinsic component of presynaptic endocytic zone membrane
-is_a: GO:0099026 ! anchored component of presynaptic membrane
+def: "OBSOLETE. The component of the presynaptic endocytic zone membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098835
[Term]
id: GO:0099028
-name: anchored component of postynaptic endocytic zone membrane
+name: obsolete anchored component of postynaptic endocytic zone membrane
namespace: cellular_component
-def: "The component of the postynaptic endocytic zone membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098947 ! intrinsic component of postsynaptic endocytic zone membrane
-is_a: GO:0099025 ! anchored component of postsynaptic membrane
+def: "OBSOLETE. The component of the postynaptic endocytic zone membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098844
[Term]
id: GO:0099029
-name: anchored component of presynaptic active zone membrane
+name: obsolete anchored component of presynaptic active zone membrane
namespace: cellular_component
-def: "The component of the presynaptic active zone membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098945 ! intrinsic component of presynaptic active zone membrane
-is_a: GO:0099026 ! anchored component of presynaptic membrane
+def: "OBSOLETE. The component of the presynaptic active zone membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0048787
[Term]
id: GO:0099030
-name: anchored component of postsynaptic specialization membrane
+name: obsolete anchored component of postsynaptic specialization membrane
namespace: cellular_component
-def: "The component of the postsynaptic specialization membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098948 ! intrinsic component of postsynaptic specialization membrane
-is_a: GO:0099025 ! anchored component of postsynaptic membrane
+def: "OBSOLETE. The component of the postsynaptic specialization membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0099634
[Term]
id: GO:0099031
-name: anchored component of postsynaptic density membrane
+name: obsolete anchored component of postsynaptic density membrane
namespace: cellular_component
-def: "The component of the postsynaptic density membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0099030 ! anchored component of postsynaptic specialization membrane
-is_a: GO:0099146 ! intrinsic component of postsynaptic density membrane
+def: "OBSOLETE. The component of the postsynaptic density membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098839
[Term]
id: GO:0099032
-name: anchored component of postsynaptic early endosome membrane
+name: obsolete anchored component of postsynaptic early endosome membrane
namespace: cellular_component
-def: "The component of the postsynaptic early endosome membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+def: "OBSOLETE. The component of the postsynaptic early endosome membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
subset: goslim_synapse
-is_a: GO:0098950 ! intrinsic component of postsynaptic early endosome membrane
-is_a: GO:0099034 ! anchored component of postsynaptic endosome membrane
+is_obsolete: true
+replaced_by: GO:0098896
[Term]
id: GO:0099033
-name: anchored component of postsynaptic recycling endosome membrane
+name: obsolete anchored component of postsynaptic recycling endosome membrane
namespace: cellular_component
-def: "The component of the postsynaptic recycling endosome membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098951 ! intrinsic component of postsynaptic recycling endosome membrane
-is_a: GO:0099034 ! anchored component of postsynaptic endosome membrane
+def: "OBSOLETE. The component of the postsynaptic recycling endosome membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098944
[Term]
id: GO:0099034
-name: anchored component of postsynaptic endosome membrane
+name: obsolete anchored component of postsynaptic endosome membrane
namespace: cellular_component
-def: "The component of the postsynaptic endosome membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0031225 ! anchored component of membrane
-is_a: GO:0098949 ! intrinsic component of postsynaptic endosome membrane
+def: "OBSOLETE. The component of the postsynaptic endosome membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098895
[Term]
id: GO:0099035
-name: anchored component of spine apparatus membrane
+name: obsolete anchored component of spine apparatus membrane
namespace: cellular_component
-def: "The component of the spine apparatus membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+def: "OBSOLETE. The component of the spine apparatus membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
subset: goslim_synapse
-is_a: GO:0031225 ! anchored component of membrane
-is_a: GO:0098952 ! intrinsic component of spine apparatus membrane
+is_obsolete: true
+replaced_by: GO:0098897
[Term]
id: GO:0099036
-name: anchored component of neuronal dense core vesicle membrane
+name: obsolete anchored component of neuronal dense core vesicle membrane
namespace: cellular_component
-def: "The component of the neuronal dense core vesicle membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0031225 ! anchored component of membrane
-is_a: GO:0098675 ! intrinsic component of neuronal dense core vesicle membrane
+def: "OBSOLETE. The component of the neuronal dense core vesicle membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0099012
[Term]
id: GO:0099037
-name: anchored component of presynaptic endosome membrane
+name: obsolete anchored component of presynaptic endosome membrane
namespace: cellular_component
-def: "The component of the presynaptic endosome membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0031225 ! anchored component of membrane
-is_a: GO:0098955 ! intrinsic component of presynaptic endosome membrane
+def: "OBSOLETE. The component of the presynaptic endosome membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098954
[Term]
id: GO:0099038
@@ -395717,16 +395739,17 @@ is_a: GO:0099039 ! sphingolipid translocation
id: GO:0099041
name: vesicle tethering to Golgi
namespace: biological_process
-def: "The initial, indirect interaction between a transport vesicle membrane and the membrane of the Golgi. This interaction is mediated by tethering factors (or complexes), which interact with both membranes. Interaction can occur via direct binding to membrane phospholipids or membrane proteins, or via binding to vesicle coat proteins. This process is distinct from and prior fusion." [PMID:27243008]
+def: "The initial, indirect interaction between a transport vesicle membrane and the membrane of the Golgi. This interaction is mediated by tethering factors (or complexes), which interact with both membranes. Interaction can occur via direct binding to membrane phospholipids or membrane proteins, or via binding to vesicle coat proteins. This process is distinct from and prior fusion." [PMID:27243008]
is_a: GO:0099022 ! vesicle tethering
[Term]
id: GO:0099042
-name: nucleation of clathrin-coated pit
+name: obsolete nucleation of clathrin-coated pit
namespace: biological_process
-def: "The first step in clathrin-dependent endocytosis: invagination of the plasma membrane to form a pit." [GOC:dos, GOC:vw, PMID:21779028]
-is_a: GO:0099024 ! plasma membrane invagination
-relationship: part_of GO:0072583 ! clathrin-dependent endocytosis
+def: "OBSOLETE. The first step in clathrin-dependent endocytosis: invagination of the plasma membrane to form a pit." [GOC:dos, GOC:vw, PMID:21779028]
+comment: The reason for obsoletion is this term is describing a process similar to that of clathrin coat assembly.
+is_obsolete: true
+replaced_by: GO:0048268
[Term]
id: GO:0099043
@@ -395740,14 +395763,14 @@ relationship: part_of GO:0072583 ! clathrin-dependent endocytosis
id: GO:0099044
name: vesicle tethering to endoplasmic reticulum
namespace: biological_process
-def: "The initial, indirect interaction between a transport vesicle membrane and the membrane of the endoplasmic reticulum. This interaction is mediated by tethering factors (or complexes), which interact with both membranes. Interaction can occur via direct binding to membrane phospholipids or membrane proteins, or via binding to vesicle coat proteins. This process is distinct from and prior fusion." [PMID:27243008]
+def: "The initial, indirect interaction between a transport vesicle membrane and the membrane of the endoplasmic reticulum. This interaction is mediated by tethering factors (or complexes), which interact with both membranes. Interaction can occur via direct binding to membrane phospholipids or membrane proteins, or via binding to vesicle coat proteins. This process is distinct from and prior fusion." [PMID:27243008]
is_a: GO:0099022 ! vesicle tethering
[Term]
id: GO:0099045
name: viral extrusion
namespace: biological_process
-def: "The process whereby a filamentous phage particle is released from a bacterial host cell via a concerted mechanism of assembly and secretion. Neosynthesized virions are coordinately exported as they are assembled at the cell surface in a secretory process that leaves the host cell fully viable. Non-capsid proteins form structures that facilitate translocation through the inner membrane and outer membranes. A viral single-stranded DNA binding protein coats progeny viral DNA molecules to generate the intracellular precursor for assembly of phage particles as they are extruded through the membranes of the bacterial host. The structural proteins of the virus are anchored in the inner membrane before their incorporation into the phage particle. As assembly proceeds, the phage genome traverses the inner and outer membranes until the entire DNA molecule has been coated and extruded." [PMID:15567492, VZ:3951]
+def: "The process whereby a filamentous phage particle is released from a bacterial host cell via a concerted mechanism of assembly and secretion. Neosynthesized virions are coordinately exported as they are assembled at the cell surface in a secretory process that leaves the host cell fully viable. Non-capsid proteins form structures that facilitate translocation through the inner membrane and outer membranes. A viral single-stranded DNA binding protein coats progeny viral DNA molecules to generate the intracellular precursor for assembly of phage particles as they are extruded through the membranes of the bacterial host. The structural proteins of the virus are anchored in the inner membrane before their incorporation into the phage particle. As assembly proceeds, the phage genome traverses the inner and outer membranes until the entire DNA molecule has been coated and extruded." [PMID:15567492, VZ:3951]
xref: VZ:3951
is_a: GO:0046753 ! non-lytic viral release
@@ -395769,7 +395792,7 @@ is_a: GO:0099046 ! clearance of foreign intracellular nucleic acids
id: GO:0099048
name: CRISPR-cas system
namespace: biological_process
-def: "An adaptive immune response of bacteria that serves to clear host cells of foreign DNA and RNA. It has three distinct stage: acquisition of foreign DNA by integration into CRISPR loci in the host chromosome, CRISPR RNA (crRNA) biogenesis, and target interference. CISPR stands for Clustered Regularly Interspaced Short Palindromic Repeat, which describes the nature of the loci." [PMID:23495939]
+def: "A defense response of that serves to clear host cells of foreign DNA and RNA. It has three distinct stage: acquisition of foreign DNA by integration into CRISPR loci in the host chromosome, CRISPR RNA (crRNA) biogenesis, and target interference. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeat, which describes the nature of the loci." [PMID:23495939, PMID:27302758, PMID:29440578]
is_a: GO:0099046 ! clearance of foreign intracellular nucleic acids
[Term]
@@ -395808,7 +395831,7 @@ relationship: part_of GO:0072583 ! clathrin-dependent endocytosis
id: GO:0099053
name: activating signal cointegrator 1 complex
namespace: cellular_component
-def: "A protein complex that contains TRIP4 (ASC1) and acts a transcriptional coactivator by interacting with transcription factors such as NF-kappa B. In humans this complex has 4 subunits: TRIP4 + ASCC1-3." [PMID:12077347]
+def: "A protein complex that contains TRIP4 (ASC1) and acts a transcriptional coactivator by interacting with transcription factors such as NF-kappa B. In humans this complex has 4 subunits: TRIP4 + ASCC1-3." [PMID:12077347]
synonym: "ASC-1 complex" EXACT [PMID:12077347]
is_a: GO:0090575 ! RNA polymerase II transcription regulator complex
@@ -395826,121 +395849,122 @@ relationship: part_of GO:0007416 ! synapse assembly
[Term]
id: GO:0099055
-name: integral component of postsynaptic membrane
+name: obsolete integral component of postsynaptic membrane
namespace: cellular_component
-def: "The component of the postsynaptic membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098936 ! intrinsic component of postsynaptic membrane
-is_a: GO:0099699 ! integral component of synaptic membrane
+def: "OBSOLETE. The component of the postsynaptic membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0045211
[Term]
id: GO:0099056
-name: integral component of presynaptic membrane
+name: obsolete integral component of presynaptic membrane
namespace: cellular_component
-def: "The component of the presynaptic membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the presynaptic membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral component of presynaptic plasma membrane" EXACT []
-is_a: GO:0098889 ! intrinsic component of presynaptic membrane
-is_a: GO:0099699 ! integral component of synaptic membrane
+is_obsolete: true
+replaced_by: GO:0042734
[Term]
id: GO:0099057
-name: integral component of presynaptic endocytic zone membrane
+name: obsolete integral component of presynaptic endocytic zone membrane
namespace: cellular_component
-def: "The component of the presynaptic endocytic zone membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098946 ! intrinsic component of presynaptic endocytic zone membrane
-is_a: GO:0099056 ! integral component of presynaptic membrane
+def: "OBSOLETE. The component of the presynaptic endocytic zone membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098835
[Term]
id: GO:0099058
-name: integral component of postsynaptic endocytic zone membrane
+name: obsolete integral component of postsynaptic endocytic zone membrane
namespace: cellular_component
-def: "The component of the postsynaptic endocytic zone membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098947 ! intrinsic component of postsynaptic endocytic zone membrane
-is_a: GO:0099055 ! integral component of postsynaptic membrane
+def: "OBSOLETE. The component of the postsynaptic endocytic zone membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098844
[Term]
id: GO:0099059
-name: integral component of presynaptic active zone membrane
+name: obsolete integral component of presynaptic active zone membrane
namespace: cellular_component
-def: "The component of the presynaptic active zone membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098945 ! intrinsic component of presynaptic active zone membrane
-is_a: GO:0099056 ! integral component of presynaptic membrane
+def: "OBSOLETE. The component of the presynaptic active zone membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0048787
[Term]
id: GO:0099060
-name: integral component of postsynaptic specialization membrane
+name: obsolete integral component of postsynaptic specialization membrane
namespace: cellular_component
-def: "The component of the postsynaptic specialization membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098948 ! intrinsic component of postsynaptic specialization membrane
-is_a: GO:0099055 ! integral component of postsynaptic membrane
+def: "OBSOLETE. The component of the postsynaptic specialization membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0099634
[Term]
id: GO:0099061
-name: integral component of postsynaptic density membrane
+name: obsolete integral component of postsynaptic density membrane
namespace: cellular_component
-def: "The component of the postsynaptic density membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0099060 ! integral component of postsynaptic specialization membrane
-is_a: GO:0099146 ! intrinsic component of postsynaptic density membrane
+def: "OBSOLETE. The component of the postsynaptic density membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098839
[Term]
id: GO:0099062
-name: integral component of postsynaptic early endosome membrane
+name: obsolete integral component of postsynaptic early endosome membrane
namespace: cellular_component
-def: "The component of the postsynaptic early endosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098950 ! intrinsic component of postsynaptic early endosome membrane
-is_a: GO:0099064 ! integral component of postsynaptic endosome membrane
+def: "OBSOLETE. The component of the postsynaptic early endosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098896
[Term]
id: GO:0099063
-name: integral component of postsynaptic recycling endosome membrane
+name: obsolete integral component of postsynaptic recycling endosome membrane
namespace: cellular_component
-def: "The component of the postsynaptic recycling endosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098951 ! intrinsic component of postsynaptic recycling endosome membrane
-is_a: GO:0099064 ! integral component of postsynaptic endosome membrane
+def: "OBSOLETE. The component of the postsynaptic recycling endosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098944
[Term]
id: GO:0099064
-name: integral component of postsynaptic endosome membrane
+name: obsolete integral component of postsynaptic endosome membrane
namespace: cellular_component
-def: "The component of the postsynaptic endosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0031303 ! integral component of endosome membrane
-is_a: GO:0098949 ! intrinsic component of postsynaptic endosome membrane
+def: "OBSOLETE. The component of the postsynaptic endosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098895
[Term]
id: GO:0099065
-name: integral component of spine apparatus membrane
+name: obsolete integral component of spine apparatus membrane
namespace: cellular_component
-def: "The component of the spine apparatus membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+def: "OBSOLETE. The component of the spine apparatus membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
subset: goslim_synapse
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:0098952 ! intrinsic component of spine apparatus membrane
+is_obsolete: true
+replaced_by: GO:0098897
[Term]
id: GO:0099066
-name: integral component of neuronal dense core vesicle membrane
+name: obsolete integral component of neuronal dense core vesicle membrane
namespace: cellular_component
-def: "The component of the neuronal dense core vesicle membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:0098675 ! intrinsic component of neuronal dense core vesicle membrane
+def: "OBSOLETE. The component of the neuronal dense core vesicle membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0099012
[Term]
id: GO:0099067
-name: integral component of presynaptic endosome membrane
+name: obsolete integral component of presynaptic endosome membrane
namespace: cellular_component
-def: "The component of the presynaptic endosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0031303 ! integral component of endosome membrane
-is_a: GO:0098955 ! intrinsic component of presynaptic endosome membrane
+def: "OBSOLETE. The component of the presynaptic endosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098954
[Term]
id: GO:0099068
@@ -395990,7 +396014,7 @@ is_a: GO:0065008 ! regulation of biological quality
id: GO:0099073
name: mitochondrion-derived vesicle
namespace: cellular_component
-def: "A vesicle derived via budding from a mitochondrion. These vesicles often contain inner membrane and, much more rarely, cristae." [GOC:bc, GOC:pad, GOC:PARL-UCL, PMID:18207745, PMID:20619655, PMID:22226745, PMID:23300790]
+def: "A vesicle derived via budding from a mitochondrion. These vesicles often contain inner membrane and, much more rarely, cristae." [GOC:bc, GOC:pad, GOC:PARL-UCL, PMID:18207745, PMID:20619655, PMID:22226745, PMID:23300790]
synonym: "MDV" EXACT [PMID:26618722]
is_a: GO:0031410 ! cytoplasmic vesicle
@@ -396029,14 +396053,13 @@ id: GO:0099078
name: BORC complex
namespace: cellular_component
def: "A protein complex that is involved in positioning of the lysosome within the cytoplasm and which is composed of BLOC1S1, BLOC1S2, BORCS5, BORCS6, BORCS7, BORCS8, KXD1 and SNAPIN. The BORC complex recruits ARL8 at the cytosolic face of lysosomes and couples them to microtubule plus-end-directed kinesin motors." [GOC:dos, GOC:li, PMID:25898167]
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005829 ! cytosol
+is_a: GO:0140535 ! intracellular protein-containing complex
[Term]
id: GO:0099079
name: actin body
namespace: cellular_component
-def: "An amorphous cytoskeletal structure consisting of aggregated actin filaments and associated proteins (including fibrin and capping protein) in which there is little or no actin filament turnover. In yeast (S. pombe and S. cerevisiae) these are found only in quiescent cells and are thought to serve as a reserve store of actin." [PMID:16914523]
+def: "An amorphous cytoskeletal structure consisting of aggregated actin filaments and associated proteins (including fibrin and capping protein) in which there is little or no actin filament turnover. In yeast (S. pombe and S. cerevisiae) these are found only in quiescent cells and are thought to serve as a reserve store of actin." [PMID:16914523]
is_a: GO:0110165 ! cellular anatomical entity
relationship: part_of GO:0015629 ! actin cytoskeleton
@@ -396163,23 +396186,24 @@ synonym: "mitochondrial calcium ion export" BROAD [GOC:vw]
synonym: "mitochondrial calcium release" EXACT []
is_a: GO:0006851 ! mitochondrial calcium ion transmembrane transport
is_a: GO:0051209 ! release of sequestered calcium ion into cytosol
-is_a: GO:1901660 ! calcium ion export
[Term]
id: GO:0099094
-name: ligand-gated cation channel activity
+name: ligand-gated monoatomic cation channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an inorganic cation by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729]
-is_a: GO:0005261 ! cation channel activity
-is_a: GO:0015276 ! ligand-gated ion channel activity
+synonym: "ligand-gated cation channel activity" BROAD []
+is_a: GO:0005261 ! monoatomic cation channel activity
+is_a: GO:0015276 ! ligand-gated monoatomic ion channel activity
[Term]
id: GO:0099095
-name: ligand-gated anion channel activity
+name: ligand-gated monoatomic anion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an inorganic anion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." [GOC:mtg_transport, ISBN:0815340729]
-is_a: GO:0005253 ! anion channel activity
-is_a: GO:0015276 ! ligand-gated ion channel activity
+synonym: "ligand-gated anion channel activity" BROAD []
+is_a: GO:0005253 ! monoatomic anion channel activity
+is_a: GO:0015276 ! ligand-gated monoatomic ion channel activity
[Term]
id: GO:0099096
@@ -396197,19 +396221,21 @@ is_a: GO:0007018 ! microtubule-based movement
[Term]
id: GO:0099099
-name: G-protein gated ion channel activity
+name: G-protein gated monoatomic ion channel activity
namespace: molecular_function
def: "An ion channel activity that is gated by binding of a G-protein beta-gamma dimer." [GOC:dos]
-is_a: GO:0015075 ! ion transmembrane transporter activity
-is_a: GO:0022836 ! gated channel activity
+synonym: "G-protein gated ion channel activity" BROAD []
+synonym: "https://github.com/geneontology/go-ontology/issues/24479" BROAD []
+is_a: GO:0022839 ! monoatomic ion gated channel activity
[Term]
id: GO:0099100
-name: G-protein gated cation channel activity
+name: G-protein gated monoatomic cation channel activity
namespace: molecular_function
def: "A cation channel activity that is gated by binding of a G-protein beta-gamma dimer." [GOC:dos]
-is_a: GO:0005261 ! cation channel activity
-is_a: GO:0099099 ! G-protein gated ion channel activity
+synonym: "G-protein gated cation channel activity" BROAD []
+is_a: GO:0005261 ! monoatomic cation channel activity
+is_a: GO:0099099 ! G-protein gated monoatomic ion channel activity
[Term]
id: GO:0099101
@@ -396217,7 +396243,7 @@ name: G-protein gated potassium channel activity
namespace: molecular_function
def: "A potassium channel activity that is gated by binding of a G-protein beta-gamma dimer." [GOC:dos, PMID:9429760]
is_a: GO:0005267 ! potassium channel activity
-is_a: GO:0099100 ! G-protein gated cation channel activity
+is_a: GO:0099100 ! G-protein gated monoatomic cation channel activity
[Term]
id: GO:0099102
@@ -396234,7 +396260,6 @@ namespace: molecular_function
def: "Direct interaction with a channel (binding or modification), resulting in its opening. A channel catalyzes energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel." [GOC:dos]
synonym: "channel gating activity" EXACT []
is_a: GO:0016247 ! channel regulator activity
-is_a: GO:0140677 ! molecular function activator activity
[Term]
id: GO:0099104
@@ -396298,9 +396323,8 @@ is_a: GO:1990896 ! protein localization to cell cortex of cell tip
id: GO:0099111
name: microtubule-based transport
namespace: biological_process
-def: "A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules." [GOC:cjm, ISBN:0815316194]
+def: "A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules." [GOC:cjm, ISBN:0815316194]
is_a: GO:0006810 ! transport
-is_a: GO:0007018 ! microtubule-based movement
[Term]
id: GO:0099112
@@ -396308,7 +396332,6 @@ name: microtubule polymerization based protein transport
namespace: biological_process
def: "The transport of a protein driven by polymerization of a microtubule to which it is attached." [GOC:dos, GOC:vw, PMID:11018050]
is_a: GO:0006886 ! intracellular protein transport
-is_a: GO:0099098 ! microtubule polymerization based movement
is_a: GO:0099118 ! microtubule-based protein transport
[Term]
@@ -396318,7 +396341,6 @@ namespace: biological_process
def: "Any process that decreases the concentration of calcium ions in the presynaptic cytosol." [GOC:dos]
subset: goslim_synapse
is_a: GO:0051481 ! negative regulation of cytosolic calcium ion concentration
-is_a: GO:0099509 ! regulation of presynaptic cytosolic calcium ion concentration
[Term]
id: GO:0099115
@@ -396340,8 +396362,8 @@ name: tRNA 5'-end processing
namespace: biological_process
def: "The process in which the 5' end of a pre-tRNA molecule is converted to that of a mature tRNA." [GOC:dos, GOC:pf, PMID:27484477]
synonym: "tRNA 5' processing" EXACT []
+is_a: GO:0000966 ! RNA 5'-end processing
is_a: GO:0008033 ! tRNA processing
-is_a: GO:0034471 ! ncRNA 5'-end processing
[Term]
id: GO:0099117
@@ -396356,6 +396378,7 @@ id: GO:0099118
name: microtubule-based protein transport
namespace: biological_process
def: "A microtubule-based process that results in the transport of proteins." [GOC:vw]
+is_a: GO:0007017 ! microtubule-based process
is_a: GO:0015031 ! protein transport
is_a: GO:0099111 ! microtubule-based transport
@@ -396371,7 +396394,7 @@ id: GO:0099120
name: socially cooperative development
namespace: biological_process
alt_id: GO:0090702
-def: "The process whose specific outcome is the progression of a non-reproductive fruiting body over time, from its formation to the mature structure. A non-reproductive fruiting body is a colonial multicellular structure consisting of co-operating unicellular organisms, some of which are spores. An example of such a process is found in Dictyostelium discoideum and Myxococcus xanthus colonies." [GOC:pf, PMID:12448714]
+def: "The process whose specific outcome is the progression of a non-reproductive fruiting body over time, from its formation to the mature structure. A non-reproductive fruiting body is a colonial multicellular structure consisting of co-operating unicellular organisms, some of which are spores. An example of such a process is found in Dictyostelium discoideum and Myxococcus xanthus colonies." [GOC:pf, PMID:12448714]
synonym: "colonial development" EXACT []
synonym: "non-reproductive fruiting body development" RELATED []
synonym: "socially co-operative development" EXACT []
@@ -396437,11 +396460,12 @@ relationship: part_of GO:0062023 ! collagen-containing extracellular matrix
[Term]
id: GO:0099127
-name: envenomation resulting in positive regulation of argininosuccinate synthase activity in another organism
+name: obsolete envenomation resulting in positive regulation of argininosuccinate synthase activity in another organism
namespace: biological_process
-def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the activation of the cytosolic argininosuccinate synthase in the bitten organism." [PMID:19491403]
+def: "OBSOLETE. A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the activation of the cytosolic argininosuccinate synthase in the bitten organism." [PMID:19491403]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in positive regulation of argininosuccinate synthase activity in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
+is_obsolete: true
[Term]
id: GO:0099128
@@ -396454,8 +396478,8 @@ is_a: GO:0098798 ! mitochondrial protein-containing complex
id: GO:0099129
name: cochlear outer hair cell electromotile response
namespace: biological_process
-def: "A rapid, force generating length change of an outer hair cell in response to electical stimulation. This occurs naturally as during hearing where it serves a source of mechanical amplification." [PMID:12239568, PMID:2187727]
-is_a: GO:0006928 ! movement of cell or subcellular component
+def: "A rapid, force generating length change of an outer hair cell in response to electical stimulation. This occurs naturally as during hearing where it serves a source of mechanical amplification." [PMID:12239568, PMID:16887876, PMID:2187727]
+is_a: GO:0070252 ! actin-mediated cell contraction
[Term]
id: GO:0099130
@@ -396527,7 +396551,7 @@ is_a: GO:0099187 ! presynaptic cytoskeleton organization
id: GO:0099141
name: cellular response to protozoan
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a protozoan." [GOC:dos]
+def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a protozoan." [GOC:dos]
is_a: GO:0001562 ! response to protozoan
[Term]
@@ -396535,7 +396559,7 @@ id: GO:0099142
name: intracellularly ATP-gated ion channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of an ion by a channel that opens when ATP has been bound by the channel complex or one of its constituent parts on the intracellular side of the plasma membrane." [PMID:9755289]
-is_a: GO:0005217 ! intracellular ligand-gated ion channel activity
+is_a: GO:0005217 ! intracellular ligand-gated monoatomic ion channel activity
is_a: GO:0035381 ! ATP-gated ion channel activity
[Term]
@@ -396549,12 +396573,12 @@ is_a: GO:0099569 ! presynaptic cytoskeleton
[Term]
id: GO:0099144
-name: anchored component of synaptic membrane
+name: obsolete anchored component of synaptic membrane
namespace: cellular_component
-def: "The component of the synaptic membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0046658 ! anchored component of plasma membrane
-is_a: GO:0099240 ! intrinsic component of synaptic membrane
+def: "OBSOLETE. The component of the synaptic membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0097060
[Term]
id: GO:0099145
@@ -396572,13 +396596,13 @@ relationship: regulates GO:0098967 ! exocytic insertion of neurotransmitter rece
[Term]
id: GO:0099146
-name: intrinsic component of postsynaptic density membrane
+name: obsolete intrinsic component of postsynaptic density membrane
namespace: cellular_component
-def: "The component of the postsynaptic density membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the postsynaptic density membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to postsynaptic specialization membrane" NARROW []
-is_a: GO:0098948 ! intrinsic component of postsynaptic specialization membrane
-relationship: part_of GO:0098839 ! postsynaptic density membrane
+is_obsolete: true
+replaced_by: GO:0098839
[Term]
id: GO:0099147
@@ -396645,7 +396669,7 @@ relationship: regulates GO:0098887 ! neurotransmitter receptor transport, endoso
id: GO:0099153
name: synaptic transmission, serotonergic
namespace: biological_process
-def: "The vesicular release of serotonin from a presynapse, across a chemical synapse, the subsequent activation of serotonin receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." [GOC:dos, GOC:dph]
+def: "The vesicular release of serotonin from a presynapse, across a chemical synapse, the subsequent activation of serotonin receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." [GOC:dos, GOC:dph]
synonym: "serotonergic synaptic transmission" EXACT []
is_a: GO:0007268 ! chemical synaptic transmission
@@ -396757,47 +396781,47 @@ relationship: part_of GO:0099629 ! postsynaptic specialization of symmetric syna
id: GO:0099165
name: postsynaptic specialization of symmetric synapse, intracellular component
namespace: cellular_component
-def: "A network of proteins adjacent to the postsynaptic membrane of a symmetric synapse. Its major components include that spatially and functionally organize neurotransmitter receptors in the adjacent membrane, such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components. This structure is not as thick or electron dense as the postsynaptic density found in asymmetric synapses." [GOC:dos]
+def: "A network of proteins adjacent to the postsynaptic membrane of a symmetric synapse. Its major components include that spatially and functionally organize neurotransmitter receptors in the adjacent membrane, such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components. This structure is not as thick or electron dense as the postsynaptic density found in asymmetric synapses." [GOC:dos]
subset: goslim_synapse
is_a: GO:0099091 ! postsynaptic specialization, intracellular component
relationship: part_of GO:0099629 ! postsynaptic specialization of symmetric synapse
[Term]
id: GO:0099166
-name: intrinsic component of postsynaptic specialization membrane of symmetric synapse
+name: obsolete intrinsic component of postsynaptic specialization membrane of symmetric synapse
namespace: cellular_component
-def: "The component of the postsynaptic specialization membrane of a symmetric synapse consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the postsynaptic specialization membrane of a symmetric synapse consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to postsynaptic specialization membrane of symmetric synapse" NARROW []
-is_a: GO:0098948 ! intrinsic component of postsynaptic specialization membrane
-relationship: part_of GO:0099164 ! postsynaptic specialization membrane of symmetric synapse
+is_obsolete: true
+replaced_by: GO:0099164
[Term]
id: GO:0099167
-name: integral component of postsynaptic specialization membrane of symmetric synapse
+name: obsolete integral component of postsynaptic specialization membrane of symmetric synapse
namespace: cellular_component
-def: "The component of the postsynaptic specialization membrane of a symmetric synapse consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0099060 ! integral component of postsynaptic specialization membrane
-is_a: GO:0099166 ! intrinsic component of postsynaptic specialization membrane of symmetric synapse
+def: "OBSOLETE. The component of the postsynaptic specialization membrane of a symmetric synapse consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0099164
[Term]
id: GO:0099168
-name: extrinsic component of postsynaptic specialization membrane of symmetric synapse
+name: obsolete extrinsic component of postsynaptic specialization membrane of symmetric synapse
namespace: cellular_component
-def: "The component of the postsynaptic specialization membrane of a symmetric synapse consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0098892 ! extrinsic component of postsynaptic specialization membrane
-relationship: part_of GO:0099164 ! postsynaptic specialization membrane of symmetric synapse
+def: "OBSOLETE. The component of the postsynaptic specialization membrane of a symmetric synapse consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+consider: GO:0099164
[Term]
id: GO:0099169
-name: anchored component of postsynaptic specialization membrane of symmetric synapse
+name: obsolete anchored component of postsynaptic specialization membrane of symmetric synapse
namespace: cellular_component
-def: "The component of the postsynaptic specialization membrane of a symmetric synapse consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
-subset: goslim_synapse
-is_a: GO:0099030 ! anchored component of postsynaptic specialization membrane
-is_a: GO:0099166 ! intrinsic component of postsynaptic specialization membrane of symmetric synapse
+def: "OBSOLETE. The component of the postsynaptic specialization membrane of a symmetric synapse consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0099164
[Term]
id: GO:0099170
@@ -396954,7 +396978,7 @@ is_a: GO:0099186 ! structural constituent of postsynapse
id: GO:0099185
name: postsynaptic intermediate filament cytoskeleton organization
namespace: biological_process
-def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprised of intermediate filament and their associated proteins in the postsynaptic cytoskeleton." [GOC:dos]
+def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprised of intermediate filament and their associated proteins in the postsynaptic cytoskeleton." [GOC:dos]
subset: goslim_synapse
is_a: GO:0045104 ! intermediate filament cytoskeleton organization
is_a: GO:0099188 ! postsynaptic cytoskeleton organization
@@ -397020,13 +397044,13 @@ is_a: GO:0045202 ! synapse
[Term]
id: GO:0099240
-name: intrinsic component of synaptic membrane
+name: obsolete intrinsic component of synaptic membrane
namespace: cellular_component
-def: "The component of the synaptic membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
-subset: goslim_synapse
+def: "OBSOLETE. The component of the synaptic membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:dos, GOC:mah]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic to synaptic membrane" NARROW []
-is_a: GO:0031226 ! intrinsic component of plasma membrane
-relationship: part_of GO:0097060 ! synaptic membrane
+is_obsolete: true
+replaced_by: GO:0097060
[Term]
id: GO:0099243
@@ -397041,7 +397065,7 @@ relationship: part_of GO:0097060 ! synaptic membrane
id: GO:0099400
name: caveola neck
namespace: cellular_component
-def: "A membrane microdomain that forms a necklace around the bulb (crater) of a caveola. Intramembrane particles are concentrated in this region and cytoskeletal components, including actin, are highly enriched in the area underlying it." [GOC:pad, GOC:PARL, PMID:17227843]
+def: "A membrane microdomain that forms a necklace around the bulb (crater) of a caveola. Intramembrane particles are concentrated in this region and cytoskeletal components, including actin, are highly enriched in the area underlying it." [GOC:pad, GOC:PARL, PMID:17227843]
is_a: GO:0098590 ! plasma membrane region
is_a: GO:0098857 ! membrane microdomain
relationship: part_of GO:0005901 ! caveola
@@ -397050,7 +397074,7 @@ relationship: part_of GO:0005901 ! caveola
id: GO:0099401
name: caveola bulb
namespace: cellular_component
-def: "The region of a caveola that extends into the cytoplasm, excluding the neck (rim). This region is associated with intracellular caveola proteins." [GOC:PARL, GOC:POD, PMID:17227843]
+def: "The region of a caveola that extends into the cytoplasm, excluding the neck (rim). This region is associated with intracellular caveola proteins." [GOC:PARL, GOC:POD, PMID:17227843]
synonym: "caveola crater" EXACT []
is_a: GO:0098857 ! membrane microdomain
@@ -397147,7 +397171,7 @@ is_a: GO:0099514 ! synaptic vesicle cytoskeletal transport
[Term]
id: GO:0099507
-name: ligand-gated ion channel activity involved in regulation of presynaptic membrane potential
+name: ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential
namespace: molecular_function
def: "Any ligand-gated ion channel activity, occurring in the presynaptic membrane, that is involved in regulation of presynaptic membrane potential." [GOC:dos, PMID:15145529, PMID:19558451]
subset: goslim_synapse
@@ -397155,11 +397179,12 @@ synonym: "ligand gated ion channel activity involved in regulation of presynapti
synonym: "ligand-dependent ion channel activity involved in regulation of pre-synaptic membrane potential" EXACT []
synonym: "ligand-dependent ion channel activity involved in regulation of presynaptic membrane potential" EXACT []
synonym: "ligand-gated ion channel activity involved in regulation of pre-synaptic membrane potential" EXACT []
-is_a: GO:0015276 ! ligand-gated ion channel activity
+synonym: "ligand-gated ion channel activity involved in regulation of presynaptic membrane potential" BROAD []
+is_a: GO:0015276 ! ligand-gated monoatomic ion channel activity
[Term]
id: GO:0099508
-name: voltage-gated ion channel activity involved in regulation of presynaptic membrane potential
+name: voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential
namespace: molecular_function
def: "Voltage-gated ion channel activity, occurring in the presynaptic membrane, involved in regulation of presynaptic membrane potential. This is a key step in synaptic transmission, following the arrival of an action potential at the synapse." [GOC:dos]
subset: goslim_synapse
@@ -397167,7 +397192,8 @@ synonym: "voltage gated ion channel activity involved in regulation of presynapt
synonym: "voltage-dependent ion channel activity involved in regulation of pre-synaptic membrane potential" EXACT []
synonym: "voltage-dependent ion channel activity involved in regulation of presynaptic membrane potential" EXACT []
synonym: "voltage-gated ion channel activity involved in regulation of pre-synaptic membrane potential" EXACT []
-is_a: GO:0005244 ! voltage-gated ion channel activity
+synonym: "voltage-gated ion channel activity involved in regulation of presynaptic membrane potential" BROAD []
+is_a: GO:0005244 ! voltage-gated monoatomic ion channel activity
[Term]
id: GO:0099509
@@ -397258,11 +397284,12 @@ is_a: GO:1901950 ! dense core granule transport
[Term]
id: GO:0099520
-name: ion antiporter activity involved in regulation of presynaptic membrane potential
+name: monoatomic ion antiporter activity involved in regulation of presynaptic membrane potential
namespace: molecular_function
def: "Any ion antiporter activity, occurring in the presynaptic membrane, that is involved in regulation of presynaptic membrane potential." [GOC:dos]
subset: goslim_synapse
synonym: "ion antiporter activity involved in regulation of pre-synaptic membrane potential" EXACT []
+synonym: "ion antiporter activity involved in regulation of presynaptic membrane potential" EXACT []
is_a: GO:0015297 ! antiporter activity
[Term]
@@ -397315,7 +397342,7 @@ is_a: GO:0099011 ! neuronal dense core vesicle exocytosis
id: GO:0099526
name: presynapse to nucleus signaling pathway
namespace: biological_process
-def: "A series of molecular signals that conveys information from the presynapse to the nucleus via cytoskeletal transport of a protein from a presynapse to the component to the nucleus where it affects biochemical processes that occur in the nucleus (e.g DNA transcription, mRNA splicing, or DNA/histone modifications)." [GOC:dos, PMID:24317321, PMID:25652077]
+def: "The series of molecular signals that conveys information from the presynapse to the nucleus via cytoskeletal transport of a protein from a presynapse to the component to the nucleus where it affects biochemical processes that occur in the nucleus (e.g DNA transcription, mRNA splicing, or DNA/histone modifications)." [GOC:dos, PMID:24317321, PMID:25652077]
comment: This class does not cover the cellular machinery (motor proteins, cargo-recognition proteins) that transports the signaling protein along the cytoskeleton towards the nucleus. For these cases, annotate to the appropriate transport/trafficking term.
subset: goslim_synapse
synonym: "presynaptic signaling to nucleus" EXACT []
@@ -397325,7 +397352,7 @@ is_a: GO:0098928 ! presynaptic signal transduction
id: GO:0099527
name: postsynapse to nucleus signaling pathway
namespace: biological_process
-def: "A series of molecular signals that conveys information from the postsynapse to the nucleus via cytoskeletal transport of a protein from a postsynapse to the component to the nucleus where it affects biochemical processes that occur in the nucleus (e.g DNA transcription, mRNA splicing, or DNA/histone modifications)." [GOC:dos, PMID:24317321, PMID:25652077]
+def: "The series of molecular signals that conveys information from the postsynapse to the nucleus via cytoskeletal transport of a protein from a postsynapse to the component to the nucleus where it affects biochemical processes that occur in the nucleus (e.g DNA transcription, mRNA splicing, or DNA/histone modifications)." [GOC:dos, PMID:24317321, PMID:25652077]
subset: goslim_synapse
synonym: "postsynaptic signaling to nucleus" EXACT []
is_a: GO:0098926 ! postsynaptic signal transduction
@@ -397371,7 +397398,7 @@ id: GO:0099532
name: synaptic vesicle endosomal processing
namespace: biological_process
def: "The process in which synaptic vesicles fuse to the presynaptic endosome followed by sorting of synaptic vesicle components and budding of new synaptic vesicles." [GOC:aruk, GOC:bc, GOC:dos]
-comment: This covers processing of synaptic vesicles trafficked to synapse as well as of endocytosed vesicles as part of recycling. It is there for not part of the synaptic vesicle cycle.
+comment: This covers processing of synaptic vesicles trafficked to synapse as well as of endocytosed vesicles as part of recycling. It is there for not part of the synaptic vesicle cycle.
subset: goslim_synapse
synonym: "synaptic vesicle processing via endosome" EXACT []
is_a: GO:0016197 ! endosomal transport
@@ -397383,7 +397410,6 @@ namespace: biological_process
def: "Any process that increases the concentration of calcium ions in the presynaptic cytosol." [GOC:dos]
subset: goslim_synapse
is_a: GO:0007204 ! positive regulation of cytosolic calcium ion concentration
-is_a: GO:0099509 ! regulation of presynaptic cytosolic calcium ion concentration
[Term]
id: GO:0099534
@@ -397535,8 +397561,8 @@ namespace: biological_process
def: "Cell-cell signaling between presynapse and postsynapse, across the synaptic cleft, that modulates the synaptic transmission properties of the synapse." [GOC:dos]
comment: Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua.
subset: goslim_synapse
+is_a: GO:0050804 ! modulation of chemical synaptic transmission
is_a: GO:0099537 ! trans-synaptic signaling
-relationship: regulates GO:0007268 ! chemical synaptic transmission
[Term]
id: GO:0099551
@@ -397678,7 +397704,6 @@ id: GO:0099565
name: chemical synaptic transmission, postsynaptic
namespace: biological_process
def: "The part of synaptic transmission occurring in the post-synapse: a signal transduction pathway consisting of neurotransmitter receptor activation and its effects on postsynaptic membrane potential and the ionic composition of the postsynaptic cytosol." [GOC:dos]
-subset: gocheck_do_not_annotate
subset: goslim_synapse
synonym: "postsynaptic process involved in chemical synaptic transmission" RELATED syngo_official_label []
is_a: GO:0050877 ! nervous system process
@@ -397814,11 +397839,12 @@ is_a: GO:0099530 ! G protein-coupled receptor activity involved in regulation of
[Term]
id: GO:0099580
-name: ion antiporter activity involved in regulation of postsynaptic membrane potential
+name: monoatomic ion antiporter activity involved in regulation of postsynaptic membrane potential
namespace: molecular_function
def: "Any ion antiporter activity, occurring in the postsynaptic membrane, that is involved in regulation of postsynaptic membrane potential." [GOC:dos]
subset: goslim_synapse
synonym: "ion antiporter activity involved in regulation of post-synaptic membrane potential" EXACT []
+synonym: "ion antiporter activity involved in regulation of postsynaptic membrane potential" EXACT []
is_a: GO:0015297 ! antiporter activity
[Term]
@@ -397856,7 +397882,7 @@ namespace: biological_process
def: "The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the presynaptic cytosol." [GOC:dos]
subset: goslim_synapse
is_a: GO:0051209 ! release of sequestered calcium ion into cytosol
-is_a: GO:0099533 ! positive regulation of presynaptic cytosolic calcium concentration
+is_a: GO:0051649 ! establishment of localization in cell
[Term]
id: GO:0099586
@@ -397865,7 +397891,7 @@ namespace: biological_process
def: "The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the postsynaptic cytosol." [GOC:dos]
subset: goslim_synapse
is_a: GO:0051209 ! release of sequestered calcium ion into cytosol
-is_a: GO:0099588 ! positive regulation of postsynaptic cytosolic calcium concentration
+is_a: GO:0051649 ! establishment of localization in cell
[Term]
id: GO:0099587
@@ -397884,7 +397910,6 @@ namespace: biological_process
def: "Any process that increases the concentration of calcium ions in the postsynaptic cytosol." [GOC:dos]
subset: goslim_synapse
is_a: GO:0007204 ! positive regulation of cytosolic calcium ion concentration
-is_a: GO:0099566 ! regulation of postsynaptic cytosolic calcium ion concentration
[Term]
id: GO:0099589
@@ -397940,7 +397965,7 @@ name: ligand-gated calcium channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of a calcium ions by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." [GOC:dos]
is_a: GO:0005262 ! calcium channel activity
-is_a: GO:0099094 ! ligand-gated cation channel activity
+is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
[Term]
id: GO:0099605
@@ -398101,7 +398126,6 @@ id: GO:0099622
name: cardiac muscle cell membrane repolarization
namespace: biological_process
def: "The process in which ions are transported across the plasma membrane of a cardiac muscle cell such that the membrane potential changes in the repolarizing direction, toward the steady state potential. For example, the repolarization during an action potential is from a positive membrane potential towards a negative resting potential." [GOC:BHF]
-is_a: GO:0051649 ! establishment of localization in cell
is_a: GO:0086009 ! membrane repolarization
[Term]
@@ -398142,7 +398166,7 @@ is_a: GO:0099511 ! voltage-gated calcium channel activity involved in regulation
id: GO:0099627
name: neurotransmitter receptor cycle
namespace: biological_process
-def: "The process during which neurotransmitter receptors, anchored in some region of the synaptic membrane, are recycled via the endosome. This cycle includes release from anchoring, diffusion in the synaptic membrane to an endocytic region, endocytosis, transport to the endosome, recycling in the endosome, transport back the synaptic membrane and subsequent anchoring (trapping)." [GOC:dos]
+def: "The process during which neurotransmitter receptors, anchored in some region of the synaptic membrane, are recycled via the endosome. This cycle includes release from anchoring, diffusion in the synaptic membrane to an endocytic region, endocytosis, transport to the endosome, recycling in the endosome, transport back the synaptic membrane and subsequent anchoring (trapping)." [GOC:dos]
is_a: GO:0099637 ! neurotransmitter receptor transport
[Term]
@@ -398167,7 +398191,7 @@ relationship: part_of GO:0032280 ! symmetric synapse
id: GO:0099630
name: postsynaptic neurotransmitter receptor cycle
namespace: biological_process
-def: "The process during which neurotransmitter receptors in the postsynaptic specialization membrane are recycled via the endosome. This cycle includes release from anchoring (trapping), diffusion in the synaptic membrane to the postsynaptic endocytic region, endocytosis, transport to the endosome, recycling in the endosome, transport back the synaptic membrane and subsequent trapping in the postsynaptic specialization membrane." [PMID:18832033]
+def: "The process during which neurotransmitter receptors in the postsynaptic specialization membrane are recycled via the endosome. This cycle includes release from anchoring (trapping), diffusion in the synaptic membrane to the postsynaptic endocytic region, endocytosis, transport to the endosome, recycling in the endosome, transport back the synaptic membrane and subsequent trapping in the postsynaptic specialization membrane." [PMID:18832033]
is_a: GO:0051649 ! establishment of localization in cell
is_a: GO:0099627 ! neurotransmitter receptor cycle
@@ -398210,9 +398234,10 @@ relationship: part_of GO:0099572 ! postsynaptic specialization
id: GO:0099635
name: voltage-gated calcium channel activity involved in positive regulation of presynaptic cytosolic calcium levels
namespace: molecular_function
-def: "Positive regulation of presynaptic cytosolic calcium ion concentrations via the directed movement of calcium ions across the plasma-membrane into the cytosol via the action of voltage-gated calcium ion channels. This is the first step in synaptic transmission." [GOC:dos]
+def: "Positive regulation of presynaptic cytosolic calcium ion concentrations via the directed movement of calcium ions across the plasma-membrane into the cytosol via the action of voltage-gated calcium ion channels. This is the first step in synaptic transmission." [GOC:dos]
subset: goslim_synapse
-is_a: GO:0099626 ! voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels
+xref: Reactome:R-HSA-9659515 "CACNA1D:CACNA2D2:CACNB2 (Cav1.3 channel) transports Ca2+ into the cytosol of an inner hair cell"
+is_a: GO:0005245 ! voltage-gated calcium channel activity
[Term]
id: GO:0099636
@@ -398325,18 +398350,19 @@ is_a: GO:0099637 ! neurotransmitter receptor transport
[Term]
id: GO:0099699
-name: integral component of synaptic membrane
+name: obsolete integral component of synaptic membrane
namespace: cellular_component
-def: "The component of the synaptic membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+def: "OBSOLETE. The component of the synaptic membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
subset: goslim_synapse
-is_a: GO:0005887 ! integral component of plasma membrane
-is_a: GO:0099240 ! intrinsic component of synaptic membrane
+is_obsolete: true
+replaced_by: GO:0097060
[Term]
id: GO:0099703
name: induction of synaptic vesicle exocytosis by positive regulation of presynaptic cytosolic calcium ion concentration
namespace: biological_process
-def: "The induction of synaptic vesicle release by any process that leads to a rise in intracellular calcium ion concentration at the presynapse. This is the first step in synaptic transmission." [GOC:dos, ISBN:9780071120005]
+def: "The induction of synaptic vesicle release by any process that leads to a rise in intracellular calcium ion concentration at the presynapse. This is the first step in synaptic transmission." [GOC:dos, ISBN:9780071120005]
subset: goslim_synapse
is_a: GO:0099171 ! presynaptic modulation of chemical synaptic transmission
is_a: GO:0099533 ! positive regulation of presynaptic cytosolic calcium concentration
@@ -398363,10 +398389,12 @@ is_a: GO:0014819 ! regulation of skeletal muscle contraction
[Term]
id: GO:0100002
-name: negative regulation of protein kinase activity by protein phosphorylation
+name: obsolete negative regulation of protein kinase activity by protein phosphorylation
namespace: biological_process
-def: "Any protein phosphorylation process that negatively regulates protein kinase activity." [GOC:cjm, GOC:obol]
-is_a: GO:0006468 ! protein phosphorylation
+def: "OBSOLETE. Any protein phosphorylation process that negatively regulates protein kinase activity." [GOC:cjm, GOC:obol]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0004860
[Term]
id: GO:0100003
@@ -398548,11 +398576,12 @@ is_obsolete: true
[Term]
id: GO:0100026
-name: positive regulation of DNA repair by transcription from RNA polymerase II promoter
+name: obsolete positive regulation of DNA repair by transcription from RNA polymerase II promoter
namespace: biological_process
-def: "Any transcription from RNA polymerase II promoter process that positively regulates DNA repair." [GOC:cjm, GOC:obol]
-is_a: GO:0006366 ! transcription by RNA polymerase II
-relationship: positively_regulates GO:0006281 ! DNA repair
+def: "OBSOLETE. Any transcription from RNA polymerase II promoter process that positively regulates DNA repair." [GOC:cjm, GOC:obol]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+replaced_by: GO:0006281
[Term]
id: GO:0100027
@@ -398699,11 +398728,12 @@ is_obsolete: true
[Term]
id: GO:0100045
-name: negative regulation of arginine catabolic process by transcription from RNA polymerase II promoter
+name: obsolete negative regulation of arginine catabolic process by transcription from RNA polymerase II promoter
namespace: biological_process
-def: "Any transcription from RNA polymerase II promoter process that negatively regulates arginine catabolic process." [GOC:cjm, GOC:obol]
-is_a: GO:0006366 ! transcription by RNA polymerase II
-relationship: negatively_regulates GO:0006527 ! arginine catabolic process
+def: "OBSOLETE. Any transcription from RNA polymerase II promoter process that negatively regulates arginine catabolic process." [GOC:cjm, GOC:obol]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:1900082
[Term]
id: GO:0100046
@@ -398909,7 +398939,7 @@ is_obsolete: true
id: GO:0101002
name: ficolin-1-rich granule
namespace: cellular_component
-def: "Highly exocytosable gelatinase-poor granules found in neutrophils and rich in ficolin-1. Ficolin-1 is released from neutrophil granules by stimulation with fMLP or PMA, and the majority becomes associated with the surface membrane of the cells and can be detected by flow cytometry." [GOC:mec, PMID:19741154]
+def: "Highly exocytosable gelatinase-poor granules found in neutrophils and rich in ficolin-1. Ficolin-1 is released from neutrophil granules by stimulation with fMLP or PMA, and the majority becomes associated with the surface membrane of the cells and can be detected by flow cytometry." [GOC:mec, PMID:19741154]
synonym: "ficolin granule" RELATED []
synonym: "ficolin-1 rich granule" EXACT []
is_a: GO:0030141 ! secretory granule
@@ -398936,11 +398966,11 @@ id: GO:0101005
name: deubiquitinase activity
namespace: molecular_function
alt_id: GO:1904265
-def: "Catalysis of the hydrolysis of ubiquitin from proteins." [GOC:mec]
+def: "An isopeptidase activity that cleaves ubiquitin from a target protein to which it is conjugated." [GOC:mec, PMID:30783221]
comment: There are two main classes of deubiquitinating enzymes: cysteine proteases (i.e., thiol dependent) and metalloproteases.
synonym: "ubiquitinyl hydrolase activity" EXACT []
xref: Reactome:R-HSA-9674127 "USP30 deubiquitinates ATM dimer:Ub-p-PEX5"
-is_a: GO:0019783 ! ubiquitin-like protein-specific protease activity
+is_a: GO:0019783 ! ubiquitin-like protein peptidase activity
[Term]
id: GO:0101006
@@ -398982,30 +399012,14 @@ namespace: biological_process
def: "The reorganization or renovation of existing pulmonary blood vessels." [GOC:mec]
is_a: GO:0001974 ! blood vessel remodeling
-[Term]
-id: GO:0101011
-name: inositol 1-diphosphate 2,3,4,5,6-pentakisphosphate 1-diphosphatase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: myo-inositol 1-diphosphate 2,3,4,5,6-pentakisphosphate + H2O = myo-inositol hexakisphosphate + phosphate." [GOC:mah, PMID:26422458]
-synonym: "inositol 1-pyrophosphate 2,3,4,5,6-pentakisphosphate 1-pyrophosphatase activity" EXACT []
-is_a: GO:0052745 ! inositol phosphate phosphatase activity
-
-[Term]
-id: GO:0101012
-name: inositol 1,5-bisdiphosphate 2,3,4,6-tetrakisphosphate 1-diphosphatase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: myo-inositol 1,5-bisdiphosphate 2,3,4,6-tetrakisphosphate + H2O = myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate + phosphate." [GOC:mah, PMID:26422458]
-synonym: "inositol 1,5-bispyrophosphate 2,3,4,6-tetrakisphosphate 1-pyrophosphatase activity" EXACT []
-is_a: GO:0052745 ! inositol phosphate phosphatase activity
-
[Term]
id: GO:0101013
name: mechanosensitive voltage-gated sodium channel activity
namespace: molecular_function
-def: "Enables the transmembrane transfer of a sodium ion by a voltage-gated channel whose activity is modulated in response to mechanical stress. Response to mechanical stress and voltage gating together is different than the sum of individual responses. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded." [PMID:21041530, PMID:26838316]
+def: "Enables the transmembrane transfer of a sodium ion by a voltage-gated channel whose activity is modulated in response to mechanical stress. Response to mechanical stress and voltage gating together is different than the sum of individual responses. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded." [PMID:21041530, PMID:26838316]
synonym: "mechanically-modulated voltage-gated sodium channel activity" EXACT []
is_a: GO:0005248 ! voltage-gated sodium channel activity
-is_a: GO:0140135 ! mechanosensitive cation channel activity
+is_a: GO:0140135 ! mechanosensitive monoatomic cation channel activity
[Term]
id: GO:0101014
@@ -399112,19 +399126,21 @@ is_a: GO:0031103 ! axon regeneration
[Term]
id: GO:0101028
-name: positive regulation of liquid surface tension
+name: obsolete positive regulation of liquid surface tension
namespace: biological_process
-def: "Any process that activates or increases the surface tension of a liquid." [GOC:sl, PMID:20949060]
+def: "OBSOLETE. Any process that activates or increases the surface tension of a liquid." [GOC:sl, PMID:20949060]
+comment: Never been used.
synonym: "positive regulation of surface tension of a liquid" EXACT []
-is_a: GO:0050828 ! regulation of liquid surface tension
+is_obsolete: true
[Term]
id: GO:0101029
-name: negative regulation of liquid surface tension
+name: obsolete negative regulation of liquid surface tension
namespace: biological_process
-def: "Any process that prevents or reduces the surface tension of a liquid." [GOC:sl, PMID:20949060]
+def: "OBSOLETE. Any process that prevents or reduces the surface tension of a liquid." [GOC:sl, PMID:20949060]
+comment: Never been used.
synonym: "negative regulation of surface tension of a liquid" EXACT []
-is_a: GO:0050828 ! regulation of liquid surface tension
+is_obsolete: true
[Term]
id: GO:0101030
@@ -399135,11 +399151,12 @@ is_a: GO:0006400 ! tRNA modification
[Term]
id: GO:0101031
-name: chaperone complex
+name: protein folding chaperone complex
namespace: cellular_component
def: "A protein complex required for the non-covalent folding or unfolding, maturation, stabilization or assembly or disassembly of macromolecular structures. Usually active during or immediately after completion of translation. Many chaperone complexes contain heat shock proteins." [GOC:bhm, PMID:21855797]
comment: An example of this is HSP90AB1 in human (P08238) in PMID:21855797 (inferred from direct assay).
-is_a: GO:0032991 ! protein-containing complex
+synonym: "chaperone complex" BROAD []
+is_a: GO:0140535 ! intracellular protein-containing complex
[Term]
id: GO:0102001
@@ -399196,6 +399213,9 @@ def: "Catalysis of the reaction: H2O + an N-acyl-L-homoserine lactone <=> H+ + a
xref: EC:3.1.1.81
xref: MetaCyc:3.1.1.81-RXN
xref: Reactome:R-HSA-8932633 "PON1,2,3:Ca2+ dimers hydrolyse 5-HETEL to 5-HETE"
+xref: Reactome:R-HSA-9756136 "PON1,3 hydrolyse 2-OH-ATVL to 2-OH-ATV"
+xref: Reactome:R-HSA-9756150 "PON1,3 hydrolyse 4-OH-ATVL to 4-OH-ATV"
+xref: Reactome:R-HSA-9756177 "PON1,3 hydrolyse ATVL to ATV"
xref: RHEA:22576
is_a: GO:0046573 ! lactonohydrolase activity
@@ -399241,6 +399261,7 @@ xref: RHEA:29871
is_a: GO:0043225 ! ATPase-coupled inorganic anion transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0102027
@@ -399293,7 +399314,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0102033
name: long-chain fatty acid omega-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an omega-methyl-long-chain fatty acid + O2 + reduced [NADPH--hemoprotein reductase] = an omega-hydroxy-long-chain fatty acid + H(+) + H2O + oxidized [NADPH--hemoprotein reductase]." [GOC:krc, PMID:18544608, RHEA:56748]
+def: "Catalysis of the reaction: an omega-methyl-long-chain fatty acid + O2 + reduced [NADPH--hemoprotein reductase] = an omega-hydroxy-long-chain fatty acid + H+ + H2O + oxidized [NADPH--hemoprotein reductase]." [GOC:krc, PMID:18544608, RHEA:56748]
synonym: "cytochrome P450 fatty acid omega-hydroxylase activity" RELATED []
xref: EC:1.14.14.80
xref: MetaCyc:RXN-16394
@@ -399307,7 +399328,7 @@ namespace: molecular_function
def: "Catalysis of the reaction: H+ + isobutyryl-CoA + FAD <=> methacrylyl-CoA + FADH2." [GOC:pz, PMID:3988734]
xref: EC:1.3.8.5
xref: MetaCyc:MEPROPCOA-FAD-RXN
-is_a: GO:0052890 ! oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor
+is_a: GO:0003995 ! acyl-CoA dehydrogenase activity
[Term]
id: GO:0102036
@@ -399337,19 +399358,21 @@ is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors,
[Term]
id: GO:0102039
-name: alkylhydroperoxide reductase activity
+name: NADH-dependent peroxiredoxin activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + NAD + an alcohol <=> NADH + H+ + an organic hydroperoxide." [GOC:pz, PMID:12517450]
+def: "Catalysis of the reaction: a hydroperoxide + H+ + NADH = an alcohol + H2O + NAD+." [GOC:pz, PMID:12517450, RHEA:62628]
+synonym: "alkylhydroperoxide reductase activity" EXACT []
xref: EC:1.11.1.26
xref: MetaCyc:R4-RXN
-is_a: GO:0016668 ! oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
+xref: RHEA:62628
+is_a: GO:0051920 ! peroxiredoxin activity
[Term]
id: GO:0102040
name: fumarate reductase (menaquinone)
namespace: molecular_function
def: "Catalysis of the reaction: fumarate + a menaquinol = succinate + a menaquinone." [GOC:pz, PMID:11850430, RHEA:27834]
-xref: EC:1.3.5.4
+xref: EC:1.3.5.1
xref: MetaCyc:R601-RXN
xref: RHEA:27834
is_a: GO:0016635 ! oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor
@@ -399460,7 +399483,7 @@ is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
id: GO:0102053
name: (-)-jasmonoyl-isoleucine synthetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (-)-jasmonate + L-isoleucine + ATP(4-) <=> H+ + (-)-jasmonoyl-L-isoleucine + AMP(2-) + diphosphoric acid." [GOC:pz]
+def: "Catalysis of the reaction: (-)-jasmonate + L-isoleucine + ATP(4-) <=> H+ + (-)-jasmonoyl-L-isoleucine + AMP(2-) + diphosphoric acid." [GOC:pz]
xref: MetaCyc:RXN-10435
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
@@ -399498,7 +399521,7 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0102057
name: jasmonoyl-valine synthetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-valine + ATP(4-) + a jasmonic acid <=> AMP(2-) + diphosphoric acid + a jasmonoyl-valine." [GOC:pz, PMID:17291501]
+def: "Catalysis of the reaction: L-valine + ATP(4-) + a jasmonic acid <=> AMP(2-) + diphosphoric acid + a jasmonoyl-valine." [GOC:pz, PMID:17291501]
xref: EC:6.3.2.52
xref: MetaCyc:RXN-10457
xref: RHEA:55772
@@ -399508,7 +399531,7 @@ is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
id: GO:0102058
name: jasmonoyl-leucine synthetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-leucine + ATP(4-) + a jasmonic acid <=> AMP(2-) + diphosphoric acid + a jasmonoyl-leucine." [GOC:pz, PMID:17291501]
+def: "Catalysis of the reaction: L-leucine + ATP(4-) + a jasmonic acid <=> AMP(2-) + diphosphoric acid + a jasmonoyl-leucine." [GOC:pz, PMID:17291501]
xref: EC:6.3.2.52
xref: MetaCyc:RXN-10459
xref: RHEA:55772
@@ -399653,27 +399676,30 @@ consider: GO:0004316
[Term]
id: GO:0102073
-name: OPC8-trans-2-enoyl-CoA hydratase activity
+name: obsolete OPC8-trans-2-enoyl-CoA hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: OPC8-3-hydroxyacyl-CoA <=> OPC8-trans-2-enoyl-CoA + H2O." [EC:4.2.1.17, GOC:pz]
-xref: MetaCyc:RXN-10697
-is_a: GO:0016836 ! hydro-lyase activity
+def: "OBSOLETE. Catalysis of the reaction: OPC8-3-hydroxyacyl-CoA <=> OPC8-trans-2-enoyl-CoA + H2O." [EC:4.2.1.17, GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate of enoyl-CoA hydratase activity ; GO:0004300.
+is_obsolete: true
+replaced_by: GO:0004300
[Term]
id: GO:0102074
-name: OPC6-trans-2-enoyl-CoA hydratase activity
+name: obsolete OPC6-trans-2-enoyl-CoA hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: OPC6-3-hydroxyacyl-CoA <=> OPC6-trans-2-enoyl-CoA + H2O." [EC:4.2.1.17, GOC:pz]
-xref: MetaCyc:RXN-10704
-is_a: GO:0016836 ! hydro-lyase activity
+def: "OBSOLETE. Catalysis of the reaction: OPC6-3-hydroxyacyl-CoA <=> OPC6-trans-2-enoyl-CoA + H2O." [EC:4.2.1.17, GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate of enoyl-CoA hydratase activity ; GO:0004300.
+is_obsolete: true
+replaced_by: GO:0004300
[Term]
id: GO:0102075
-name: OPC4-trans-2-enoyl-CoA hydratase activity
+name: obsolete OPC4-trans-2-enoyl-CoA hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: OPC4-3-hydroxyacyl-CoA <=> OPC4-trans-2-enoyl-CoA + H2O." [EC:4.2.1.17, GOC:pz]
-xref: MetaCyc:RXN-10705
-is_a: GO:0016836 ! hydro-lyase activity
+def: "OBSOLETE. Catalysis of the reaction: OPC4-3-hydroxyacyl-CoA <=> OPC4-trans-2-enoyl-CoA + H2O." [EC:4.2.1.17, GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate of enoyl-CoA hydratase activity ; GO:0004300.
+is_obsolete: true
+replaced_by: GO:0004300
[Term]
id: GO:0102076
@@ -399685,16 +399711,6 @@ xref: MetaCyc:RXN-10741
xref: RHEA:26389
is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
-[Term]
-id: GO:0102077
-name: oleamide hydrolase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: oleamide + H2O <=> oleate + ammonium." [EC:3.5.1.99, GOC:pz]
-xref: EC:3.5.1.99
-xref: MetaCyc:RXN-10756
-xref: RHEA:26506
-is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
-
[Term]
id: GO:0102080
name: phenylacetyl-coenzyme A:glycine N-acyltransferase activity
@@ -399717,7 +399733,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0102082
name: demethylrebeccamycin--D-glucose O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4'-demethylrebeccamycin + S-adenosyl-L-methionine <=> H+ + rebeccamycin + S-adenosyl-L-homocysteine." [EC:2.1.1.164, GOC:pz]
+def: "Catalysis of the reaction: 4'-demethylrebeccamycin + S-adenosyl-L-methionine <=> H+ + rebeccamycin + S-adenosyl-L-homocysteine." [EC:2.1.1.164, GOC:pz]
xref: EC:2.1.1.164
xref: MetaCyc:RXN-10847
xref: RHEA:27353
@@ -399735,7 +399751,7 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0102084
name: L-dopa O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-dopa + S-adenosyl-L-methionine <=> 3-O-methyldopa + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.6, GOC:pz]
+def: "Catalysis of the reaction: L-dopa + S-adenosyl-L-methionine <=> 3-O-methyldopa + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.6, GOC:pz]
xref: EC:2.1.1.6
xref: MetaCyc:RXN-10870
is_a: GO:0008168 ! methyltransferase activity
@@ -399784,26 +399800,18 @@ is_a: GO:0046993 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y
id: GO:0102090
name: adrenaline O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-adrenaline(1+) + S-adenosyl-L-methionine <=> metanephrine + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.6, GOC:pz]
+def: "Catalysis of the reaction: (R)-adrenaline(1+) + S-adenosyl-L-methionine <=> metanephrine + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.6, GOC:pz]
xref: MetaCyc:RXN-10909
is_a: GO:0008168 ! methyltransferase activity
[Term]
id: GO:0102091
-name: phosphatidylinositol-5-phosphate 5-phosphatase activity
+name: phosphatidylinositol-5-phosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + a 1-phosphatidyl-1D-myo-inositol 5-phosphate = hydrogenphosphate + an L-1-phosphatidyl-inositol." [EC:3.1.3.-, GOC:pz]
+def: "Catalysis of the reaction: H2O + a 1-phosphatidyl-1D-myo-inositol 5-phosphate = an 1-phosphatidyl-1D-myo-inositol + phosphate." [GOC:pz, PMID:12878591]
+synonym: "phosphatidylinositol-5-phosphate 5-phosphatase activity" EXACT []
xref: MetaCyc:RXN-10962
-is_a: GO:0016791 ! phosphatase activity
-
-[Term]
-id: GO:0102092
-name: 5-diphosphoinositol pentakisphosphate 3-kinase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 5-diphospho-1D-myo-inositol pentakisphosphate + ATP = 3,5-bisdiphosphoinositol-1D-myo-inositol 2,3,4,6-tetrakisphosphate + ADP." [EC:2.7.4.24, GOC:pz]
-xref: EC:2.7.4.24
-xref: MetaCyc:RXN-10979
-is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
+is_a: GO:0052744 ! phosphatidylinositol monophosphate phosphatase activity
[Term]
id: GO:0102093
@@ -399817,7 +399825,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0102094
name: S-adenosylmethionine:2-demethylmenaquinol methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + a demethylmenaquinol <=> S-adenosyl-L-homocysteine + H+ + a menaquinol." [GOC:pz, PMID:1444716, PMID:9045837, RHEA:26466]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + a demethylmenaquinol <=> S-adenosyl-L-homocysteine + H+ + a menaquinol." [GOC:pz, PMID:1444716, PMID:9045837, RHEA:26466]
xref: EC:2.1.1.163
xref: MetaCyc:RXN-11046
xref: RHEA:26466
@@ -399877,7 +399885,7 @@ is_a: GO:0050497 ! alkylthioltransferase activity
id: GO:0102102
name: homocarnosine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: gamma-aminobutyric acid + L-histidine + ATP = H+ + homocarnosine + ADP + hydrogenphosphate." [EC:6.3.2.11, GOC:pz]
+def: "Catalysis of the reaction: gamma-aminobutyric acid + L-histidine + ATP = H+ + homocarnosine + ADP + hydrogenphosphate." [EC:6.3.2.11, GOC:pz]
xref: EC:6.3.2.11
xref: MetaCyc:RXN-11222
xref: RHEA:59568
@@ -399925,7 +399933,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0102109
name: tricaffeoyl spermidine O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: tricaffeoyl spermidine + 3 S-adenosyl-L-methionine <=> 3 H+ + triferuloyl spermidine + 3 S-adenosyl-L-homocysteine." [GOC:pz, PMID:19077165]
+def: "Catalysis of the reaction: tricaffeoyl spermidine + 3 S-adenosyl-L-methionine <=> 3 H+ + triferuloyl spermidine + 3 S-adenosyl-L-homocysteine." [GOC:pz, PMID:19077165]
xref: MetaCyc:RXN-11261
is_a: GO:0008168 ! methyltransferase activity
@@ -399937,23 +399945,14 @@ def: "Catalysis of the reaction: gibberellin A20 + 2-oxoglutarate + O2 <=> gibbe
xref: MetaCyc:RXN-113
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
-[Term]
-id: GO:0102113
-name: hypoxia-inducible factor-asparagine oxygenase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + O2 + a hypoxia inducible factor (HIF) alpha subunit = succinate + carbon dioxide + a (3S)-3-hydroxy-L-asparagine-HIF alpha subunit." [GOC:pz, RHEA:54268]
-xref: EC:1.14.11.30
-xref: MetaCyc:RXN-11321
-xref: RHEA:54268
-is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
-
[Term]
id: GO:0102114
-name: caprate dehydroxylase activity
+name: obsolete caprate dehydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: decanoate + NADPH + O2 + H+ <=> 10-hydroxycaprate + NADP + H2O." [EC:1.14.13.-, GOC:pz]
-xref: MetaCyc:RXN-11325
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+def: "OBSOLETE. Catalysis of the reaction: decanoate + NADPH + O2 + H+ <=> 10-hydroxycaprate + NADP + H2O." [EC:1.14.13.-, GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate and is beyond the scope of GO MF.
+is_obsolete: true
+replaced_by: GO:0140981
[Term]
id: GO:0102115
@@ -399965,17 +399964,18 @@ is_a: GO:0016880 ! acid-ammonia (or amide) ligase activity
[Term]
id: GO:0102116
-name: laurate hydroxylase activity
+name: obsolete laurate hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dodecanoate + NADPH + O2 + H+ <=> 11-hydroxylaurate + NADP + H2O." [EC:1.14.13.-, GOC:pz]
-xref: MetaCyc:RXN-11340
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+def: "OBSOLETE. Catalysis of the reaction: dodecanoate + NADPH + O2 + H+ <=> 11-hydroxylaurate + NADP + H2O." [EC:1.14.13.-, GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate and is beyond the scope of GO MF.
+is_obsolete: true
+replaced_by: GO:0140981
[Term]
id: GO:0102117
name: gibberellin A9 carboxyl methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: gibberellin A9 + S-adenosyl-L-methionine <=> gibberellin A9 methyl ester + S-adenosyl-L-homocysteine." [EC:2.1.1.275, GOC:pz]
+def: "Catalysis of the reaction: gibberellin A9 + S-adenosyl-L-methionine <=> gibberellin A9 methyl ester + S-adenosyl-L-homocysteine." [EC:2.1.1.275, GOC:pz]
xref: EC:2.1.1.275
xref: MetaCyc:RXN-11358
xref: RHEA:36119
@@ -399985,7 +399985,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102118
name: gibberellin A4 carboxyl methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: gibberellin A4 + S-adenosyl-L-methionine <=> gibberellin A4 methyl ester + S-adenosyl-L-homocysteine." [EC:2.1.1.276, GOC:pz]
+def: "Catalysis of the reaction: gibberellin A4 + S-adenosyl-L-methionine <=> gibberellin A4 methyl ester + S-adenosyl-L-homocysteine." [EC:2.1.1.276, GOC:pz]
xref: EC:2.1.1.276
xref: MetaCyc:RXN-11359
xref: RHEA:36107
@@ -399995,7 +399995,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102119
name: gibberellin A20 carboxyl methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: gibberellin A20 + S-adenosyl-L-methionine <=> gibberellin A20 methyl ester + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: gibberellin A20 + S-adenosyl-L-methionine <=> gibberellin A20 methyl ester + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-11360
is_a: GO:0008168 ! methyltransferase activity
@@ -400012,7 +400012,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0102122
name: gibberellin A34 carboxyl methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: gibberellin A34 + S-adenosyl-L-methionine = gibberellin A34 methyl ester + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz, RHEA:36127]
+def: "Catalysis of the reaction: gibberellin A34 + S-adenosyl-L-methionine = gibberellin A34 methyl ester + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz, RHEA:36127]
xref: MetaCyc:RXN-11384
xref: RHEA:36127
is_a: GO:0008168 ! methyltransferase activity
@@ -400072,7 +400072,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0102130
name: malonyl-CoA methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + a malonyl-[acp] = S-adenosyl-L-homocysteine + a malonyl-[acp] methyl ester." [GOC:pz, RHEA:17105]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + a malonyl-[acp] = S-adenosyl-L-homocysteine + a malonyl-[acp] methyl ester." [GOC:pz, RHEA:17105]
xref: EC:2.1.1.197
xref: MetaCyc:RXN-11475
xref: RHEA:17105
@@ -400213,7 +400213,7 @@ is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
id: GO:0102146
name: tricetin O-methytransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: tricetin + S-adenosyl-L-methionine = H+ + 3'-O-methyltricetin + S-adenosyl-L-homocysteine." [GOC:pz, RHEA:27493]
+def: "Catalysis of the reaction: tricetin + S-adenosyl-L-methionine = H+ + 3'-O-methyltricetin + S-adenosyl-L-homocysteine." [GOC:pz, RHEA:27493]
xref: MetaCyc:RXN-11582
xref: RHEA:27493
is_a: GO:0008168 ! methyltransferase activity
@@ -400222,7 +400222,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102147
name: 3'-O-methyltricetin O methyl transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + 3'-O-methyltricetin = H+ + S-adenosyl-L-homocysteine + 3',5'-di-O-methyltricetin." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + 3'-O-methyltricetin = H+ + S-adenosyl-L-homocysteine + 3',5'-di-O-methyltricetin." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-11583
xref: RHEA:27497
is_a: GO:0008168 ! methyltransferase activity
@@ -400240,7 +400240,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0102149
name: farnesylcysteine lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-[(2E,6E)-farnesyl]-L-cysteine + O2 + H2O <=> (2-trans,6-trans)-farnesal + L-cysteine + hydrogen peroxide." [EC:1.8.3.6, GOC:pz]
+def: "Catalysis of the reaction: S-[(2E,6E)-farnesyl]-L-cysteine + O2 + H2O <=> (2-trans,6-trans)-farnesal + L-cysteine + hydrogen peroxide." [EC:1.8.3.6, GOC:pz]
xref: EC:1.8.3.6
xref: MetaCyc:RXN-11623
xref: RHEA:30231
@@ -400307,13 +400307,13 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
[Term]
id: GO:0102158
-name: very-long-chain 3-hydroxyacyl-CoA dehydratase activity
+name: obsolete very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a very-long-chain (3R)-3-hydroxyacyl-CoA = H2O + a very-long-chain trans-2,3-dehydroacyl-CoA." [GOC:pz, RHEA:45812]
-xref: EC:4.2.1.134
-xref: MetaCyc:RXN-11750
-xref: RHEA:45812
-is_a: GO:0016836 ! hydro-lyase activity
+def: "OBSOLETE. Catalysis of the reaction: a very-long-chain (3R)-3-hydroxyacyl-CoA = H2O + a very-long-chain (2E)-enoyl-CoA." [GOC:pz, RHEA:45812]
+comment: This term was obsoleted because it represents a specific substrate of 3-hydroxyacyl-CoA dehydratase activity ; GO:0018812.
+synonym: "very-long-chain 3-hydroxyacyl-CoA dehydratase activity" EXACT []
+is_obsolete: true
+replaced_by: GO:0018812
[Term]
id: GO:0102159
@@ -400347,7 +400347,7 @@ is_a: GO:0016836 ! hydro-lyase activity
[Term]
id: GO:0102162
-name: all-trans-8'-apo-beta-carotenal 15,15'-oxygenase
+name: all-trans-8'-apo-beta-carotenal 15,15'-oxygenase activity
namespace: molecular_function
def: "Catalysis of the reaction: 8'-apo-beta,psi-caroten-8'-al + O2 <=> all-trans-retinal + 2,6-dimethylocta-2,4,6-trienedial." [EC:1.13.11.75, GOC:pz]
xref: EC:1.13.11.75
@@ -400407,7 +400407,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0102168
name: 5-methyl-phenazine-1-carboxylate N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phenazine-1-carboxylate + S-adenosyl-L-methionine <=> 5-methylphenazine-1-carboxylate + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: phenazine-1-carboxylate + S-adenosyl-L-methionine <=> 5-methylphenazine-1-carboxylate + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-11897
xref: RHEA:49112
is_a: GO:0008168 ! methyltransferase activity
@@ -400472,7 +400472,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102175
name: 3-beta-hydroxysteroid dehydrogenase/C4-decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 3beta-hydroxysteroid-4alpha-carboxylate + NAD(+) = a 3-oxosteroid + CO2 + NADH." [GOC:pz, RHEA:34775]
+def: "Catalysis of the reaction: a 3beta-hydroxysteroid-4alpha-carboxylate + NAD+ = a 3-oxosteroid + CO2 + NADH." [GOC:pz, RHEA:34775]
xref: MetaCyc:RXN-11928
xref: RHEA:34775
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -400652,9 +400652,10 @@ is_a: GO:0016881 ! acid-amino acid ligase activity
id: GO:0102196
name: cortisol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cortisol + NADP <=> cortisone + NADPH + H+." [GOC:pz, PMID:16216911]
+def: "Catalysis of the reaction: cortisol + NADP <=> cortisone + NADPH + H+." [GOC:pz, PMID:16216911, RHEA:68616]
xref: EC:1.1.1.146
xref: MetaCyc:RXN-12085
+xref: RHEA:68616
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
@@ -400737,19 +400738,19 @@ is_a: GO:0016758 ! hexosyltransferase activity
[Term]
id: GO:0102207
-name: docosanoate omega-hydroxylase activity
+name: obsolete docosanoate omega-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: docosanoate + O2 + reduced [NADPH--hemoprotein reductase] = 22-hydroxydocosanoate + H(+) + H2O + oxidized [NADPH--hemoprotein reductase]." [GOC:krc, GOC:pz, RHEA:40079]
+def: "OBSOLETE. Catalysis of the reaction: docosanoate + O2 + reduced [NADPH--hemoprotein reductase] = 22-hydroxydocosanoate + H+ + H2O + oxidized [NADPH--hemoprotein reductase]." [GOC:krc, GOC:pz, RHEA:40079]
+comment: This term was obsoleted because it represents a specific substrate and is beyond the scope of GO MF.
synonym: "behenate omega-hydroxylase activity" EXACT []
-xref: MetaCyc:RXN-12155
-xref: RHEA:40079
-is_a: GO:0120250 ! fatty acid omega-hydroxylase activity
+is_obsolete: true
+replaced_by: GO:0140692
[Term]
id: GO:0102208
name: 2-polyprenyl-6-hydroxyphenol methylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + a 3-(all-trans-polyrenyl)benzene-1,2-diol <=> S-adenosyl-L-homocysteine + H+ + a 2-methoxy-6-(all-trans-polyprenyl)phenol." [EC:2.1.1.222, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + a 3-(all-trans-polyrenyl)benzene-1,2-diol <=> S-adenosyl-L-homocysteine + H+ + a 2-methoxy-6-(all-trans-polyprenyl)phenol." [EC:2.1.1.222, GOC:pz]
xref: MetaCyc:RXN-12160
xref: RHEA:31411
is_a: GO:0008168 ! methyltransferase activity
@@ -400815,7 +400816,7 @@ is_a: GO:0016405 ! CoA-ligase activity
id: GO:0102215
name: thiocyanate methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: thiocyanate + S-adenosyl-L-methionine <=> methyl thiocyanate + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: thiocyanate + S-adenosyl-L-methionine <=> methyl thiocyanate + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-12189
xref: RHEA:28014
is_a: GO:0008168 ! methyltransferase activity
@@ -400878,12 +400879,21 @@ is_obsolete: true
[Term]
id: GO:0102223
-name: 4,4'-diapophytoene desaturase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 4 H+ + 15-cis-4,4'-diapophytoene + 4 FAD <=> 4,4'-diapolycopene + 4 FADH2." [EC:1.3.8.2, GOC:pz]
+name: 4,4'-diapophytoene desaturase (4,4'-diaponeurosporene-forming)
+namespace: molecular_function
+alt_id: GO:0102225
+alt_id: GO:0102961
+alt_id: GO:0102962
+def: "Catalysis of the reaction: 4 H+ + 15-cis-4,4'-diapophytoene + 4 FAD = 4,4'-diapolycopene + 4 FADH2. This reaction consists of three successive dehydrogenations that lead to the introduction of three double bonds into 4,4'-diapophytoene (dehydrosqualene), with 4,4'-diapophytofluene, 4,4'-diapo-zeta-carotene and 4,4'-diapolycopene as intermediates, and 4,4'-diapolycopene as the end product." [GOC:pz, PMID:8002598, RHEA:31391]
+synonym: "4,4'-diapo-zeta-carotene desaturase activity" NARROW []
+synonym: "4,4'-diaponeurosporene desaturase activity" NARROW []
+synonym: "4,4'-diapophytoene desaturase activity" BROAD []
+synonym: "4,4'-diapophytofluene desaturase activity" NARROW []
xref: EC:1.3.8.2
xref: MetaCyc:RXN-12224
+xref: MetaCyc:RXN-12258
xref: RHEA:31391
+xref: RHEA:42800
is_a: GO:0052890 ! oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor
[Term]
@@ -400895,15 +400905,6 @@ xref: MetaCyc:RXN-12236
xref: RHEA:46316
is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
-[Term]
-id: GO:0102225
-name: 4,4'-diaponeurosporene desaturase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 4,4'-diaponeurosporene + FAD + H+ <=> 4,4'-diapolycopene + FADH2." [EC:1.3.8.-, GOC:pz]
-xref: MetaCyc:RXN-12258
-xref: RHEA:31407
-is_a: GO:0052890 ! oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor
-
[Term]
id: GO:0102229
name: amylopectin maltohydrolase activity
@@ -401005,7 +401006,7 @@ is_a: GO:0052671 ! geranylgeraniol kinase activity
id: GO:0102244
name: 3-aminopropanal dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-ammoniopropanal + NAD + H2O <=> 2 H+ + beta-alanine + NADH." [EC:1.2.1.-, GOC:pz]
+def: "Catalysis of the reaction: 3-ammoniopropanal + NAD + H2O <=> 2 H+ + beta-alanine + NADH." [EC:1.2.1.-, GOC:pz]
xref: MetaCyc:RXN-12332
is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
@@ -401155,7 +401156,8 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0102262
name: tRNA-dihydrouridine16 synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 5,6-dihydrouracil16 in tRNA + NAD(P) <=> H+ + a uracil16 in tRNA + NAD(P)H." [EC:1.3.1.88, GOC:pz]
+def: "Catalysis of the reaction: a 5,6-dihydrouracil16 in tRNA + NAD(P) = H+ + a uracil16 in tRNA + NAD(P)H." [GOC:pz]
+xref: EC:1.3.1.88
xref: MetaCyc:RXN-12454
is_a: GO:0017150 ! tRNA dihydrouridine synthase activity
@@ -401163,7 +401165,7 @@ is_a: GO:0017150 ! tRNA dihydrouridine synthase activity
id: GO:0102263
name: tRNA-dihydrouridine17 synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 5,6-dihydrouracil17 in tRNA + NAD(P) <=> H+ + a uracil17 in tRNA + NAD(P)H." [EC:1.3.1.88, GOC:pz]
+def: "Catalysis of the reaction: a 5,6-dihydrouracil17 in tRNA + NAD(P) = H+ + a uracil17 in tRNA + NAD(P)H." [GOC:pz]
xref: EC:1.3.1.88
xref: MetaCyc:RXN-12455
is_a: GO:0017150 ! tRNA dihydrouridine synthase activity
@@ -401172,7 +401174,7 @@ is_a: GO:0017150 ! tRNA dihydrouridine synthase activity
id: GO:0102264
name: tRNA-dihydrouridine20 synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 5,6-dihydrouracil20 in tRNA + NAD(P) <=> H+ + a uracil20 in tRNA + NAD(P)H." [EC:1.3.1.91, GOC:pz]
+def: "Catalysis of the reaction: a 5,6-dihydrouracil20 in tRNA + NAD(P) = H+ + a uracil20 in tRNA + NAD(P)H." [EC:1.3.1.91, GOC:pz]
xref: EC:1.3.1.91
xref: MetaCyc:RXN-12456
is_a: GO:0017150 ! tRNA dihydrouridine synthase activity
@@ -401181,7 +401183,7 @@ is_a: GO:0017150 ! tRNA dihydrouridine synthase activity
id: GO:0102265
name: tRNA-dihydrouridine47 synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 5,6-dihydrouracil47 in tRNA + NAD(P) <=> H+ + a uracil47 in tRNA + NAD(P)H." [EC:1.3.1.89, GOC:pz]
+def: "Catalysis of the reaction: a 5,6-dihydrouracil47 in tRNA + NAD(P) = H+ + a uracil47 in tRNA + NAD(P)H." [EC:1.3.1.89, GOC:pz]
xref: EC:1.3.1.89
xref: MetaCyc:RXN-12457
is_a: GO:0017150 ! tRNA dihydrouridine synthase activity
@@ -401190,7 +401192,7 @@ is_a: GO:0017150 ! tRNA dihydrouridine synthase activity
id: GO:0102266
name: tRNA-dihydrouridine20a synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 5,6-dihydrouracil20a in tRNA + NAD(P) <=> H+ + a uracil20a in tRNA + NAD(P)H." [EC:1.3.1.90, GOC:pz]
+def: "Catalysis of the reaction: a 5,6-dihydrouracil20a in tRNA + NAD(P) = H+ + a uracil20a in tRNA + NAD(P)H." [GOC:pz]
xref: EC:1.3.1.90
xref: MetaCyc:RXN-12475
is_a: GO:0017150 ! tRNA dihydrouridine synthase activity
@@ -401199,7 +401201,8 @@ is_a: GO:0017150 ! tRNA dihydrouridine synthase activity
id: GO:0102267
name: tRNA-dihydrouridine20b synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 5,6-dihydrouracil20b in tRNA + NAD(P) <=> H+ + a uracil20b in tRNA + NAD(P)H." [EC:1.3.1.90, GOC:pz]
+def: "Catalysis of the reaction: a 5,6-dihydrouracil20b in tRNA + NAD(P) = H+ + a uracil20b in tRNA + NAD(P)H." [GOC:pz]
+xref: EC:1.3.1.90
xref: MetaCyc:RXN-12476
is_a: GO:0017150 ! tRNA dihydrouridine synthase activity
@@ -401423,7 +401426,7 @@ is_a: GO:0016779 ! nucleotidyltransferase activity
id: GO:0102298
name: selenocystathione synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-selenocysteine + O-phosphonato-L-homoserine = hydrogenphosphate + L-selenocystathionine." [EC:2.5.1.-, GOC:pz]
+def: "Catalysis of the reaction: L-selenocysteine + O-phosphonato-L-homoserine = hydrogenphosphate + L-selenocystathionine." [EC:2.5.1.-, GOC:pz]
xref: MetaCyc:RXN-12728
is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups
@@ -401459,7 +401462,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0102302
name: mycinamicin VI 2''-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + mycinamicin VI <=> S-adenosyl-L-homocysteine + mycinamicin III(1+) + H+." [EC:2.1.1.238, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + mycinamicin VI <=> S-adenosyl-L-homocysteine + mycinamicin III(1+) + H+." [EC:2.1.1.238, GOC:pz]
xref: EC:2.1.1.238
xref: MetaCyc:RXN-12801
xref: RHEA:31643
@@ -401469,7 +401472,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102303
name: resveratrol 3,5-O-dimethyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + trans-resveratrol <=> 2 S-adenosyl-L-homocysteine + pterostilbene + 2 H+." [EC:2.1.1.240, GOC:pz]
+def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + trans-resveratrol <=> 2 S-adenosyl-L-homocysteine + pterostilbene + 2 H+." [EC:2.1.1.240, GOC:pz]
xref: EC:2.1.1.240
xref: MetaCyc:RXN-12805
xref: RHEA:32103
@@ -401509,7 +401512,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0102307
name: erythromycin C 3''-o-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + erythromycin C <=> S-adenosyl-L-homocysteine + erythromycin A + H+." [EC:2.1.1.254, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + erythromycin C <=> S-adenosyl-L-homocysteine + erythromycin A + H+." [EC:2.1.1.254, GOC:pz]
xref: EC:2.1.1.254
xref: MetaCyc:RXN-12923
xref: RHEA:32647
@@ -401519,7 +401522,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102308
name: erythromycin D 3''-o-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + erythromycin D <=> S-adenosyl-L-homocysteine + erythromycin B + H+." [EC:2.1.1.254, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + erythromycin D <=> S-adenosyl-L-homocysteine + erythromycin B + H+." [EC:2.1.1.254, GOC:pz]
xref: EC:2.1.1.254
xref: MetaCyc:RXN-12924
xref: RHEA:32651
@@ -401575,7 +401578,7 @@ is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
id: GO:0102317
name: 4-methylaminobutyrate oxidase (demethylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-(methylamino)butyric acid + O2 + H2O <=> gamma-aminobutyric acid + formaldehyde + hydrogen peroxide." [EC:1.5.3.19, GOC:pz]
+def: "Catalysis of the reaction: 4-(methylamino)butyric acid + O2 + H2O <=> gamma-aminobutyric acid + formaldehyde + hydrogen peroxide." [EC:1.5.3.19, GOC:pz]
xref: EC:1.5.3.19
xref: MetaCyc:RXN-13067
xref: RHEA:33907
@@ -401633,8 +401636,9 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102323
name: 2-isopropylphenol monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-isopropylphenol + O2 + NADH + H+ = 3-isopropylcatechol + H2O + NAD." [GOC:pz]
+def: "Catalysis of the reaction: 2-isopropylphenol + O2 + NADH + H+ = 3-isopropylcatechol + H2O + NAD." [GOC:pz, RHEA:63520]
xref: MetaCyc:RXN-13152
+xref: RHEA:63520
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
[Term]
@@ -401803,38 +401807,39 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
[Term]
id: GO:0102343
-name: 3-hydroxy-arachidoyl-CoA dehydratase activity
+name: obsolete 3-hydroxy-arachidoyl-CoA dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-3-hydroxyicosanoyl-CoA <=> trans-2-icosenoyl-CoA + H2O." [EC:4.2.1.134, GOC:pz]
-xref: EC:4.2.1.134
-xref: MetaCyc:RXN-13302
-is_a: GO:0016836 ! hydro-lyase activity
+def: "OBSOLETE. Catalysis of the reaction: (R)-3-hydroxyicosanoyl-CoA <=> trans-2-icosenoyl-CoA + H2O." [EC:4.2.1.134, GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate of 3-hydroxyacyl-CoA dehydratase activity ; GO:0018812.
+is_obsolete: true
+replaced_by: GO:0018812
[Term]
id: GO:0102344
-name: 3-hydroxy-behenoyl-CoA dehydratase activity
+name: obsolete 3-hydroxy-behenoyl-CoA dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-3-hydroxybehenoyl-CoA <=> trans-2-docosenoyl-CoA + H2O." [EC:4.2.1.134, GOC:pz]
-xref: EC:4.2.1.134
-xref: MetaCyc:RXN-13303
-is_a: GO:0016836 ! hydro-lyase activity
+def: "OBSOLETE. Catalysis of the reaction: (R)-3-hydroxybehenoyl-CoA <=> trans-2-docosenoyl-CoA + H2O." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate of 3-hydroxyacyl-CoA dehydratase activity ; GO:0018812.
+is_obsolete: true
+replaced_by: GO:0018812
[Term]
id: GO:0102345
-name: 3-hydroxy-lignoceroyl-CoA dehydratase activity
+name: obsolete 3-hydroxy-lignoceroyl-CoA dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-3-hydroxylignoceroyl-CoA(4-) <=> trans-2-tetracosenoyl-CoA + H2O." [EC:4.2.1.134, GOC:pz]
-xref: EC:4.2.1.134
-xref: MetaCyc:RXN-13304
-is_a: GO:0016836 ! hydro-lyase activity
+def: "OBSOLETE. Catalysis of the reaction: (R)-3-hydroxylignoceroyl-CoA(4-) <=> trans-2-tetracosenoyl-CoA + H2O." [EC:4.2.1.134, GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate of 3-hydroxyacyl-CoA dehydratase activity ; GO:0018812.
+is_obsolete: true
+replaced_by: GO:0018812
[Term]
id: GO:0102346
-name: 3-hydroxy-cerotoyl-CoA dehydratase activity
+name: obsolete 3-hydroxy-cerotoyl-CoA dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-3-hydroxycerotoyl-CoA(4-) <=> trans-2-hexacosenoyl-CoA(4-) + H2O." [EC:4.2.1.134, GOC:pz]
-xref: MetaCyc:RXN-13305
-is_a: GO:0016836 ! hydro-lyase activity
+def: "OBSOLETE. Catalysis of the reaction: (R)-3-hydroxycerotoyl-CoA(4-) <=> trans-2-hexacosenoyl-CoA(4-) + H2O." [EC:4.2.1.134, GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate of 3-hydroxyacyl-CoA dehydratase activity ; GO:0018812.
+is_obsolete: true
+replaced_by: GO:0018812
[Term]
id: GO:0102347
@@ -401872,7 +401877,7 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0102351
name: gamma-aminobutyrate transaminase (glyoxylate dependent) activity
namespace: molecular_function
-def: "Catalysis of the reaction: gamma-aminobutyric acid + 2-oxo monocarboxylic acid anion = 4-oxobutanoate + glycine." [EC:2.6.1.96, GOC:pz]
+def: "Catalysis of the reaction: gamma-aminobutyric acid + 2-oxo monocarboxylic acid anion = 4-oxobutanoate + glycine." [EC:2.6.1.96, GOC:pz]
xref: EC:2.6.1.96
xref: MetaCyc:RXN-13328
xref: RHEA:32267
@@ -401925,7 +401930,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0102358
name: daphnetin-8-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + 7,8-dihydroxycoumarin <=> S-adenosyl-L-homocysteine + 7-hydroxy-8-methoxycoumarin + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + 7,8-dihydroxycoumarin <=> S-adenosyl-L-homocysteine + 7-hydroxy-8-methoxycoumarin + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13448
is_a: GO:0008168 ! methyltransferase activity
@@ -401968,7 +401973,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0102363
name: isoscopoletin-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: isoscopoletin + S-adenosyl-L-methionine <=> scoparone + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: isoscopoletin + S-adenosyl-L-methionine <=> scoparone + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13475
is_a: GO:0008168 ! methyltransferase activity
@@ -402043,7 +402048,7 @@ namespace: molecular_function
def: "Catalysis of the reaction: uvaol + NADPH + O2 + H+ <=> ursolic aldehyde + NADP + 2 H2O." [GOC:pz, PMID:22039103]
xref: EC:1.14.14.126
xref: MetaCyc:RXN-13501
-is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0102374
@@ -402195,7 +402200,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0102391
name: decanoate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + decanoate + CoA = AMP + diphosphate + decanoyl-CoA." [GOC:pz, RHEA:33627]
+def: "Catalysis of the reaction: ATP + decanoate + CoA = AMP + diphosphate + decanoyl-CoA." [GOC:pz, RHEA:33627]
xref: MetaCyc:RXN-13614
xref: RHEA:33627
is_a: GO:0031956 ! medium-chain fatty acid-CoA ligase activity
@@ -402212,7 +402217,7 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0102393
name: decanoyl-[acp] 2-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: FAD + H+ + a decanoyl-HmqF protein <=> FADH2(2-) + a 2,3-dehydro-decanoyl-HmqF." [EC:1.3.8.-, GOC:pz]
+def: "Catalysis of the reaction: FAD + H+ + a decanoyl-HmqF protein = FADH2(2-) + a 2,3-dehydro-decanoyl-HmqF." [EC:1.3.8.-, GOC:pz]
xref: MetaCyc:RXN-13624
is_a: GO:0052890 ! oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor
@@ -402248,7 +402253,7 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0102398
name: dTDP-3-amino-4-oxo-2,3,6-trideoxy-alpha-D-glucose N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + dTDP-3-amino-4-dehydro-2,3,6-trideoxy-alpha-D-glucose <=> S-adenosyl-L-homocysteine + dTDP-3-N-methylamino-4-oxo-2,3,6-trideoxy-alpha-D-glucose + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + dTDP-3-amino-4-dehydro-2,3,6-trideoxy-alpha-D-glucose <=> S-adenosyl-L-homocysteine + dTDP-3-N-methylamino-4-oxo-2,3,6-trideoxy-alpha-D-glucose + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13657
is_a: GO:0008168 ! methyltransferase activity
@@ -402256,7 +402261,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102399
name: dTDP-3-N-methylamino-4-oxo-2,3,6-trideoxy-alpha-D-glucose N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + dTDP-3-N-methylamino-4-oxo-2,3,6-trideoxy-alpha-D-glucose <=> S-adenosyl-L-homocysteine + dTDP-3-N,N-dimethylamino-4-oxo-2,3,6-trideoxy-alpha-D-glucose + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + dTDP-3-N-methylamino-4-oxo-2,3,6-trideoxy-alpha-D-glucose <=> S-adenosyl-L-homocysteine + dTDP-3-N,N-dimethylamino-4-oxo-2,3,6-trideoxy-alpha-D-glucose + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13658
is_a: GO:0008168 ! methyltransferase activity
@@ -402264,7 +402269,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102400
name: dTDP-3-amino-4-oxo-2,3,6-trideoxy-alpha-D-glucose N,N-dimethyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + dTDP-3-amino-4-dehydro-2,3,6-trideoxy-alpha-D-glucose <=> 2 S-adenosyl-L-homocysteine + dTDP-3-N,N-dimethylamino-4-oxo-2,3,6-trideoxy-alpha-D-glucose + 2 H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + dTDP-3-amino-4-dehydro-2,3,6-trideoxy-alpha-D-glucose <=> 2 S-adenosyl-L-homocysteine + dTDP-3-N,N-dimethylamino-4-oxo-2,3,6-trideoxy-alpha-D-glucose + 2 H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13667
is_a: GO:0008168 ! methyltransferase activity
@@ -402495,24 +402500,18 @@ def: "Catalysis of the reaction: genistin + UDP-alpha-D-glucose <=> genistin 7-g
xref: MetaCyc:RXN-13831
is_a: GO:0016758 ! hexosyltransferase activity
-[Term]
-id: GO:0102430
-name: alpha-linolenate delta5 desaturase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: alpha-linolenate + O2 + a reduced electron acceptor = coniferonate + 2 H2O + an oxidized electron acceptor." [EC:1.14.19.-, GOC:pz]
-xref: MetaCyc:RXN-13857
-xref: RHEA:38039
-is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
-
[Term]
id: GO:0102431
-name: acyl-lipid omega-(9-4) desaturase
+name: acyl-lipid omega-(9-4) desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: linoleoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H(+) <=> pinolenoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O." [GOC:pz, RHEA:46236]
+alt_id: GO:0102430
+def: "Catalysis of the reaction: a (9Z,12Z)-octadecadienoyl-containing glycerolipid + 2 Fe(II)-[cytochrome b5] + 2 H(+) + O2 = a (5Z,9Z,12Z)-octadecatrienoyl-containing glycerolipid + 2 Fe(III)-[cytochrome b5] + 2 H2O. Can also use a substrate with 3 double bonds (a (9Z,12Z,15Z)-octadecatrienoyl-containing glycerolipid) and add a fourth double bond (a (5Z,9Z,12Z,15Z)-octadecatetraenoyl-containing glycerolipid)." [GOC:pz, RHEA:38039, RHEA:46236]
+synonym: "acyl-lipid omega-(9-4) desaturase" EXACT []
+synonym: "alpha-linolenate delta5 desaturase activity" NARROW []
synonym: "linoleate delta5 desaturase activity" RELATED []
xref: EC:1.14.19.12
+xref: MetaCyc:RXN-13857
xref: MetaCyc:RXN-13858
-xref: RHEA:46236
is_a: GO:0004497 ! monooxygenase activity
is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
@@ -402520,7 +402519,7 @@ is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidat
id: GO:0102432
name: quercetin 7-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: quercetin-7-olate + S-adenosyl-L-methionine <=> rhamnetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: quercetin-7-olate + S-adenosyl-L-methionine <=> rhamnetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13906
is_a: GO:0008168 ! methyltransferase activity
@@ -402528,7 +402527,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102433
name: phenylalanine 4-hydroxylase (N10-formyl-tetrahydrofolate dependent) activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-phenylalanine + O2 + an N10-formyl-tetrahydrofolate <=> L-tyrosine + a 10-formyltetrahydrofolate-4a-carbinolamine." [EC:1.14.16.1, GOC:pz]
+def: "Catalysis of the reaction: L-phenylalanine + O2 + an N10-formyl-tetrahydrofolate <=> L-tyrosine + a 10-formyltetrahydrofolate-4a-carbinolamine." [EC:1.14.16.1, GOC:pz]
xref: MetaCyc:RXN-13907
is_a: GO:0016714 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen
@@ -402544,7 +402543,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0102435
name: myricetin 7-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: myricetin(1-) + S-adenosyl-L-methionine <=> 7-O-methylmyricetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: myricetin(1-) + S-adenosyl-L-methionine <=> 7-O-methylmyricetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13910
is_a: GO:0008168 ! methyltransferase activity
@@ -402552,7 +402551,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102436
name: 7-methylmyricetin 4'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7-O-methylmyricetin + S-adenosyl-L-methionine <=> 7,4'-dimethylmyricetin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 7-O-methylmyricetin + S-adenosyl-L-methionine <=> 7,4'-dimethylmyricetin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13911
is_a: GO:0008168 ! methyltransferase activity
@@ -402560,7 +402559,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102438
name: laricitrin 4'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: laricitrin(1-) + S-adenosyl-L-methionine <=> H+ + 3',4'-dimethylmyricetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: laricitrin(1-) + S-adenosyl-L-methionine <=> H+ + 3',4'-dimethylmyricetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13914
is_a: GO:0008168 ! methyltransferase activity
@@ -402568,7 +402567,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102439
name: 3',4',5'-trimethylmyricetin 7-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3',4',5'-trimethylmyricetin + S-adenosyl-L-methionine <=> 7,3',4',5'-tetramethylmyricetin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 3',4',5'-trimethylmyricetin + S-adenosyl-L-methionine <=> 7,3',4',5'-tetramethylmyricetin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13916
is_a: GO:0008168 ! methyltransferase activity
@@ -402576,7 +402575,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102440
name: 3',4',5'-trimethylmyricetin 3-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3',4',5'-trimethylmyricetin + S-adenosyl-L-methionine <=> 3,3',4',5'-tetramethylmyricetin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 3',4',5'-trimethylmyricetin + S-adenosyl-L-methionine <=> 3,3',4',5'-tetramethylmyricetin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13918
is_a: GO:0008168 ! methyltransferase activity
@@ -402584,7 +402583,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102441
name: syringetin 7-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: syringetin(1-) + S-adenosyl-L-methionine <=> 7,3',5'-trimethylmyricetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: syringetin(1-) + S-adenosyl-L-methionine <=> 7,3',5'-trimethylmyricetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13919
is_a: GO:0008168 ! methyltransferase activity
@@ -402592,7 +402591,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102442
name: syringetin 3-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: syringetin(1-) + S-adenosyl-L-methionine <=> 3,3',5'-trimethylmyricetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: syringetin(1-) + S-adenosyl-L-methionine <=> 3,3',5'-trimethylmyricetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13920
is_a: GO:0008168 ! methyltransferase activity
@@ -402610,7 +402609,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0102444
name: isorhamnetin 3-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: isorhamnetin + S-adenosyl-L-methionine <=> 3,3'-dimethylquercetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: isorhamnetin + S-adenosyl-L-methionine <=> 3,3'-dimethylquercetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13929
is_a: GO:0008168 ! methyltransferase activity
@@ -402618,7 +402617,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102445
name: 3-methylquercetin 3'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3',4',5-trihydroxy-3-methoxyflavon-7-olate + S-adenosyl-L-methionine <=> 3,3'-dimethylquercetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 3',4',5-trihydroxy-3-methoxyflavon-7-olate + S-adenosyl-L-methionine <=> 3,3'-dimethylquercetin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13930
is_a: GO:0008168 ! methyltransferase activity
@@ -402626,7 +402625,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102446
name: rhamnetin 3-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: rhamnetin + S-adenosyl-L-methionine <=> 3',4',5-trihydroxy-3,7-dimethoxyflavone + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: rhamnetin + S-adenosyl-L-methionine <=> 3',4',5-trihydroxy-3,7-dimethoxyflavone + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13932
is_a: GO:0008168 ! methyltransferase activity
@@ -402634,7 +402633,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102447
name: rhamnetin 3'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: rhamnetin + S-adenosyl-L-methionine <=> 7,3'-dimethylquercetin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: rhamnetin + S-adenosyl-L-methionine <=> 7,3'-dimethylquercetin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13933
is_a: GO:0008168 ! methyltransferase activity
@@ -402642,7 +402641,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102448
name: rhamnetin 4'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: rhamnetin + S-adenosyl-L-methionine <=> ombuin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: rhamnetin + S-adenosyl-L-methionine <=> ombuin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13934
is_a: GO:0008168 ! methyltransferase activity
@@ -402650,7 +402649,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102449
name: kaempferol 3-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: kaempferol oxoanion + S-adenosyl-L-methionine <=> 3-O-methylkaempferol + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: kaempferol oxoanion + S-adenosyl-L-methionine <=> 3-O-methylkaempferol + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13935
is_a: GO:0008168 ! methyltransferase activity
@@ -402658,7 +402657,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102450
name: kaempferide 7-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: kaempferide + S-adenosyl-L-methionine <=> 7,4'-dimethylkaempferol + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: kaempferide + S-adenosyl-L-methionine <=> 7,4'-dimethylkaempferol + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13936
is_a: GO:0008168 ! methyltransferase activity
@@ -402666,7 +402665,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102451
name: kaempferide 3-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: kaempferide + S-adenosyl-L-methionine <=> 3,4'-dimethylkaempferol + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: kaempferide + S-adenosyl-L-methionine <=> 3,4'-dimethylkaempferol + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-13937
is_a: GO:0008168 ! methyltransferase activity
@@ -402739,11 +402738,12 @@ is_a: GO:0016758 ! hexosyltransferase activity
[Term]
id: GO:0102459
-name: 8-oxo-deoxyadenine diphosphate phosphatase activity
+name: 8-oxo-dADP diphosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 8-oxo-dADP + H2O = 8-oxo-dAMP + hydrogenphosphate + H+." [EC:3.6.1.-, GOC:pz]
+def: "Catalysis of the reaction: 8-oxo-dADP + H2O = 8-oxo-dAMP + hydrogenphosphate + H+." [GOC:pz]
+synonym: "8-oxo-deoxyadenine diphosphate phosphatase activity" EXACT []
xref: MetaCyc:RXN-14005
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+is_a: GO:0017110 ! nucleoside diphosphate phosphatase activity
[Term]
id: GO:0102460
@@ -402963,66 +402963,94 @@ is_a: GO:0016758 ! hexosyltransferase activity
[Term]
id: GO:0102485
-name: dATP phosphohydrolase activity
+name: obsolete dATP phosphohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dATP + 2 H2O = dAMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+def: "OBSOLETE. Catalysis of the reaction: dATP + 2 H2O = dAMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+comment: This term has been obsoleted because it represents two molecular functions, 'nucleoside diphosphate phosphatase activity' and 'nucleoside triphosphate phosphatase activity'.
xref: EC:3.6.1.5
+xref: https://github.com/geneontology/go-ontology/issues/23454
xref: MetaCyc:RXN-14195
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+is_obsolete: true
+consider: GO:0017110
+consider: GO:0017111
[Term]
id: GO:0102486
-name: dCTP phosphohydrolase activity
+name: obsolete dCTP phosphohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dCTP + 2 H2O = dCMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+def: "OBSOLETE. Catalysis of the reaction: dCTP + 2 H2O = dCMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+comment: This term has been obsoleted because it represents two molecular functions, 'nucleoside diphosphate phosphatase activity' and 'nucleoside triphosphate phosphatase activity'.
xref: EC:3.6.1.5
+xref: https://github.com/geneontology/go-ontology/issues/23454
xref: MetaCyc:RXN-14198
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+is_obsolete: true
+consider: GO:0017110
+consider: GO:0017111
[Term]
id: GO:0102487
-name: dUTP phosphohydrolase activity
+name: obsolete dUTP phosphohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dUTP + 2 H2O = dUMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+def: "OBSOLETE. Catalysis of the reaction: dUTP + 2 H2O = dUMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+comment: This term has been obsoleted because it represents two molecular functions, 'nucleoside diphosphate phosphatase activity' and 'nucleoside triphosphate phosphatase activity'.
xref: EC:3.6.1.5
+xref: https://github.com/geneontology/go-ontology/issues/23454
xref: MetaCyc:RXN-14199
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+is_obsolete: true
+consider: GO:0017110
+consider: GO:0017111
[Term]
id: GO:0102488
-name: dTTP phosphohydrolase activity
+name: obsolete dTTP phosphohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dTTP + 2 H2O = dTMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+def: "OBSOLETE. Catalysis of the reaction: dTTP + 2 H2O = dTMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+comment: This term has been obsoleted because it represents two molecular functions, 'nucleoside diphosphate phosphatase activity' and 'nucleoside triphosphate phosphatase activity'.
xref: EC:3.6.1.5
+xref: https://github.com/geneontology/go-ontology/issues/23454
xref: MetaCyc:RXN-14200
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+is_obsolete: true
+consider: GO:0017110
+consider: GO:0017111
[Term]
id: GO:0102489
-name: GTP phosphohydrolase activity
+name: obsolete GTP phosphohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GTP + 2 H2O = GMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+def: "OBSOLETE. Catalysis of the reaction: GTP + 2 H2O = GMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+comment: This term has been obsoleted because it represents two molecular functions, 'nucleoside diphosphate phosphatase activity' and 'nucleoside triphosphate phosphatase activity'.
xref: EC:3.6.1.5
+xref: https://github.com/geneontology/go-ontology/issues/23454
xref: MetaCyc:RXN-14201
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+is_obsolete: true
+consider: GO:0017110
+consider: GO:0017111
[Term]
id: GO:0102490
-name: 8-oxo-dGTP phosphohydrolase activity
+name: obsolete 8-oxo-dGTP phosphohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 8-oxo-dGTP + 2 H2O <=> 8-oxo-dGMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+def: "OBSOLETE. Catalysis of the reaction: 8-oxo-dGTP + 2 H2O <=> 8-oxo-dGMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+comment: This term has been obsoleted because it represents two molecular functions, 'nucleoside diphosphate phosphatase activity' and 'ribonucleoside triphosphate phosphatase activity'.
xref: EC:3.6.1.5
+xref: https://github.com/geneontology/go-ontology/issues/23454
xref: MetaCyc:RXN-14205
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+is_obsolete: true
+consider: GO:0017110
+consider: GO:0017111
[Term]
id: GO:0102491
-name: dGTP phosphohydrolase activity
+name: obsolete dGTP phosphohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dGTP + 2 H2O = dGMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+def: "OBSOLETE. Catalysis of the reaction: dGTP + 2 H2O = dGMP + 2 hydrogenphosphate + 2 H+." [EC:3.6.1.5, GOC:pz]
+comment: This term has been obsoleted because it represents two molecular functions, 'nucleoside diphosphate phosphatase activity' and 'nucleoside triphosphate phosphatase activity'.
xref: EC:3.6.1.5
+xref: https://github.com/geneontology/go-ontology/issues/23454
xref: MetaCyc:RXN-14208
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+is_obsolete: true
+consider: GO:0017110
+consider: GO:0017111
[Term]
id: GO:0102493
@@ -403241,7 +403269,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102520
name: L-threonine O-3-phosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O-phospho-L-threonine + H2O = L-threonine + hydrogenphosphate." [EC:3.1.3.-, GOC:pz]
+def: "Catalysis of the reaction: O-phospho-L-threonine + H2O = L-threonine + hydrogenphosphate." [EC:3.1.3.-, GOC:pz]
xref: MetaCyc:RXN-14505
is_a: GO:0016791 ! phosphatase activity
@@ -403249,7 +403277,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0102521
name: tRNA-4-demethylwyosine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: pyruvate + S-adenosyl-L-methionine + N1-methylguanine37 in tRNAPhe = L-methionine + 5'-deoxyadenosine + carbon dioxide + H2O + 4-demethylwyosine37 in tRNAPhe." [GOC:pz, PMID:34184886, RHEA:36347]
+def: "Catalysis of the reaction: pyruvate + S-adenosyl-L-methionine + N1-methylguanine37 in tRNAPhe = L-methionine + 5'-deoxyadenosine + carbon dioxide + H2O + 4-demethylwyosine37 in tRNAPhe." [GOC:pz, PMID:34184886, RHEA:36347]
xref: EC:4.1.3.44
xref: MetaCyc:RXN-14516
xref: RHEA:36347
@@ -403260,7 +403288,7 @@ is_a: GO:0140101 ! catalytic activity, acting on a tRNA
id: GO:0102522
name: tRNA 4-demethylwyosine alpha-amino-alpha-carboxypropyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + 4-demethylwyosine37 in tRNAPhe <=> 5'-S-methyl-5'-thioadenosine + H+ + 7-[(3S)-3-amino-3-carboxypropyl]-4-demethylwyosine37 in tRNAPhe." [EC:2.5.1.114, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + 4-demethylwyosine37 in tRNAPhe <=> 5'-S-methyl-5'-thioadenosine + H+ + 7-[(3S)-3-amino-3-carboxypropyl]-4-demethylwyosine37 in tRNAPhe." [EC:2.5.1.114, GOC:pz]
xref: EC:2.5.1.114
xref: MetaCyc:RXN-14518
xref: RHEA:36355
@@ -403302,7 +403330,7 @@ is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
id: GO:0102526
name: 8-demethylnovobiocic acid C8-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + 8-desmethylnovobiocic acid <=> S-adenosyl-L-homocysteine + novobiocic acid + H+." [EC:2.1.1.284, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + 8-desmethylnovobiocic acid <=> S-adenosyl-L-homocysteine + novobiocic acid + H+." [EC:2.1.1.284, GOC:pz]
xref: EC:2.1.1.284
xref: MetaCyc:RXN-14543
xref: RHEA:36651
@@ -403322,7 +403350,7 @@ is_a: GO:0016880 ! acid-ammonia (or amide) ligase activity
id: GO:0102528
name: 7,8,4'-trihydroxyflavone methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + 7,8,4'-trihydroxyflavone <=> H+ + S-adenosyl-L-homocysteine + 7,4'-dihydroxy, 8-methoxyflavone." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + 7,8,4'-trihydroxyflavone <=> H+ + S-adenosyl-L-homocysteine + 7,4'-dihydroxy, 8-methoxyflavone." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-14658
is_a: GO:0008168 ! methyltransferase activity
@@ -403330,7 +403358,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102529
name: apigenin 7-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + apigenin-7-olate <=> S-adenosyl-L-homocysteine + genkwanin." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + apigenin-7-olate <=> S-adenosyl-L-homocysteine + genkwanin." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-14661
is_a: GO:0008168 ! methyltransferase activity
@@ -403338,7 +403366,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102530
name: aclacinomycin T methylesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: aclacinomycin T(1+) + H2O <=> 15-demethylaclacinomycin T + methanol + H+." [EC:3.1.1.95, GOC:pz]
+def: "Catalysis of the reaction: aclacinomycin T(1+) + H2O <=> 15-demethylaclacinomycin T + methanol + H+." [EC:3.1.1.95, GOC:pz]
xref: EC:3.1.1.95
xref: MetaCyc:RXN-14703
xref: RHEA:37891
@@ -403365,7 +403393,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102533
name: genkwanin 4'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: genkwanin + S-adenosyl-L-methionine <=> H+ + apigenin-7,4'-dimethyl ether + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: genkwanin + S-adenosyl-L-methionine <=> H+ + apigenin-7,4'-dimethyl ether + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-14750
is_a: GO:0008168 ! methyltransferase activity
@@ -403381,7 +403409,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102535
name: ladanein 6-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ladanein + S-adenosyl-L-methionine <=> H+ + salvigenin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: ladanein + S-adenosyl-L-methionine <=> H+ + salvigenin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-14752
is_a: GO:0008168 ! methyltransferase activity
@@ -403499,7 +403527,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0102550
name: 2-methyl-6-geranylgeranyl-1,4-benzoquinol methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + 2-methyl-6-geranylgeranyl-1,4-benzoquinol <=> S-adenosyl-L-homocysteine + 2,3-dimethyl-6-geranylgeranyl-1,4-benzoquinol + H+." [EC:2.1.1.295, GOC:pz]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + 2-methyl-6-geranylgeranyl-1,4-benzoquinol <=> S-adenosyl-L-homocysteine + 2,3-dimethyl-6-geranylgeranyl-1,4-benzoquinol + H+." [EC:2.1.1.295, GOC:pz]
xref: EC:2.1.1.295
xref: MetaCyc:RXN-14917
xref: RHEA:38007
@@ -403517,39 +403545,30 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
[Term]
id: GO:0102552
-name: lipoyl synthase activity (acting on glycine-cleavage complex H protein
+name: obsolete lipoyl synthase activity (acting on glycine-cleavage complex H protein
namespace: molecular_function
-def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + a [glycine-cleavage complex H protein] N6-octanoyl-L-lysine + 2 a sulfurated [sulfur carrier] = 2 L-methionine + 2 5'-deoxyadenosine + a [glycine-cleavage complex H protein] N6-lipoyl-L-lysine + 2 an unsulfurated [sulfur carrier]." [EC:2.8.1.8, GOC:pz]
-xref: EC:2.8.1.8
-xref: MetaCyc:RXN-14950
-is_a: GO:0016783 ! sulfurtransferase activity
+def: "OBSOLETE. Catalysis of the reaction: 2 S-adenosyl-L-methionine + a [glycine-cleavage complex H protein] N6-octanoyl-L-lysine + 2 a sulfurated [sulfur carrier] = 2 L-methionine + 2 5'-deoxyadenosine + a [glycine-cleavage complex H protein] N6-lipoyl-L-lysine + 2 an unsulfurated [sulfur carrier]." [EC:2.8.1.8, GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+is_obsolete: true
+replaced_by: GO:0016992
[Term]
id: GO:0102553
-name: lipoyl synthase activity (acting on pyruvate dehydrogenase E2 protein)
+name: obsolete lipoyl synthase activity (acting on pyruvate dehydrogenase E2 protein)
namespace: molecular_function
-def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + a [pyruvate dehydrogenase E2 protein] N6-octanoyl-L-lysine + 2 a sulfurated [sulfur carrier] = 2 L-methionine + 2 5'-deoxyadenosine + 2 H+ + a [pyruvate dehydrogenase E2 protein] N6-lipoyl-L-lysine + 2 an unsulfurated [sulfur carrier]." [EC:2.8.1.8, GOC:pz]
-xref: EC:2.8.1.8
-xref: MetaCyc:RXN-14957
-is_a: GO:0016783 ! sulfurtransferase activity
+def: "OBSOLETE. Catalysis of the reaction: 2 S-adenosyl-L-methionine + a [pyruvate dehydrogenase E2 protein] N6-octanoyl-L-lysine + 2 a sulfurated [sulfur carrier] = 2 L-methionine + 2 5'-deoxyadenosine + 2 H+ + a [pyruvate dehydrogenase E2 protein] N6-lipoyl-L-lysine + 2 an unsulfurated [sulfur carrier]." [EC:2.8.1.8, GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+is_obsolete: true
+replaced_by: GO:0016992
[Term]
id: GO:0102554
-name: lipoyl synthase activity (acting on 2-oxoglutarate-dehydrogenase E2 protein
-namespace: molecular_function
-def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + a [2-oxoglutarate-dehydrogenase E2 protein] N6-octanoyl-L-lysine + 2 a sulfurated [sulfur carrier] = 2 L-methionine + 2 5'-deoxyadenosine + 2 H+ + a [2-oxoglutarate dehydrogenase E2 protein] N6-lipoyl-L-lysine + 2 an unsulfurated [sulfur carrier]." [EC:2.8.1.8, GOC:pz]
-xref: MetaCyc:RXN-14959
-is_a: GO:0016783 ! sulfurtransferase activity
-
-[Term]
-id: GO:0102555
-name: octanoyl transferase activity (acting on glycine-cleavage complex H protein)
+name: obsolete lipoyl synthase activity (acting on 2-oxoglutarate-dehydrogenase E2 protein
namespace: molecular_function
-def: "Catalysis of the reaction: [glycine cleavage system lipoyl-carrier protein]-L-lysine + octanoyl-ACP = H+ + a [glycine-cleavage complex H protein] N6-octanoyl-L-lysine + a holo-[acyl-carrier protein]." [GOC:pz, RHEA:17665]
-xref: EC:2.3.1.181
-xref: MetaCyc:RXN-14966
-xref: RHEA:17665
-is_a: GO:0016415 ! octanoyltransferase activity
+def: "OBSOLETE. Catalysis of the reaction: 2 S-adenosyl-L-methionine + a [2-oxoglutarate-dehydrogenase E2 protein] N6-octanoyl-L-lysine + 2 a sulfurated [sulfur carrier] = 2 L-methionine + 2 5'-deoxyadenosine + 2 H+ + a [2-oxoglutarate dehydrogenase E2 protein] N6-lipoyl-L-lysine + 2 an unsulfurated [sulfur carrier]." [EC:2.8.1.8, GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+is_obsolete: true
+replaced_by: GO:0016992
[Term]
id: GO:0102556
@@ -403575,7 +403594,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102559
name: protein-(glutamine-N5) methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + a [release factor]-L-glutamine = S-adenosyl-L-homocysteine + H+ + a [release factor]-N5-methyl-L-glutamine." [GOC:pz, RHEA:42896]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + a [release factor]-L-glutamine = S-adenosyl-L-homocysteine + H+ + a [release factor]-N5-methyl-L-glutamine." [GOC:pz, RHEA:42896]
xref: EC:2.1.1.297
xref: MetaCyc:RXN-14992
xref: RHEA:42896
@@ -403649,7 +403668,7 @@ is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
id: GO:0102570
name: tyrosine:phenylpyruvate aminotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: keto-phenylpyruvate + L-tyrosine = L-phenylalanine + 3-(4-hydroxyphenyl)pyruvate." [EC:2.6.1.-, GOC:pz]
+def: "Catalysis of the reaction: keto-phenylpyruvate + L-tyrosine = L-phenylalanine + 3-(4-hydroxyphenyl)pyruvate." [EC:2.6.1.-, GOC:pz]
xref: MetaCyc:RXN-15200
is_a: GO:0008483 ! transaminase activity
@@ -403675,7 +403694,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0102573
name: aminodeoxyfutalosine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-[(1-carboxylatovinyl)oxy]benzoate(2-) + S-adenosyl-L-methionine + H2O <=> aminodeoxyfutalosinate + L-methionine + hydrogencarbonate + H+." [EC:2.5.1.120, GOC:pz]
+def: "Catalysis of the reaction: 3-[(1-carboxylatovinyl)oxy]benzoate(2-) + S-adenosyl-L-methionine + H2O <=> aminodeoxyfutalosinate + L-methionine + hydrogencarbonate + H+." [EC:2.5.1.120, GOC:pz]
xref: EC:2.5.1.120
xref: MetaCyc:RXN-15264
xref: RHEA:33075
@@ -403913,20 +403932,10 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102603
name: 12-demethyl-elloramycin C12a O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 12-demethyl-elloramycin + S-adenosyl-L-methionine <=> elloramycin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 12-demethyl-elloramycin + S-adenosyl-L-methionine <=> elloramycin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-15402
is_a: GO:0008168 ! methyltransferase activity
-[Term]
-id: GO:0102604
-name: naringenin,NADPH:oxygen oxidoreductase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: (S)-naringenin(1-) + O2 + NADPH + H+ <=> 2-hydroxy-2,3-dihydrogenistein-7-olate + NADP + H2O." [EC:1.14.14.87, GOC:pz]
-xref: EC:1.14.14.87
-xref: MetaCyc:RXN-1541
-xref: RHEA:35487
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
-
[Term]
id: GO:0102605
name: cyclooctat-9-en-5,7-diol C18-monooxygenase activity
@@ -403957,7 +403966,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102608
name: tetracenomycin B3 8-O-methyl transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: tetracenomycin B3 + S-adenosyl-L-methionine <=> tetracenomycin E + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: tetracenomycin B3 + S-adenosyl-L-methionine <=> tetracenomycin E + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-15435
is_a: GO:0008168 ! methyltransferase activity
@@ -404071,7 +404080,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0102623
name: scutellarein 7-methyl ether 6-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: scutellarein 7-methyl ether + S-adenosyl-L-methionine <=> cirsimaritin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: scutellarein 7-methyl ether + S-adenosyl-L-methionine <=> cirsimaritin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-15528
is_a: GO:0008168 ! methyltransferase activity
@@ -404079,7 +404088,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102624
name: scutellarein 7-methyl ether 4'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: scutellarein 7-methyl ether + S-adenosyl-L-methionine <=> ladanein + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: scutellarein 7-methyl ether + S-adenosyl-L-methionine <=> ladanein + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-15529
is_a: GO:0008168 ! methyltransferase activity
@@ -404087,7 +404096,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102625
name: cirsimaritin 4'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cirsimaritin + S-adenosyl-L-methionine <=> salvigenin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: cirsimaritin + S-adenosyl-L-methionine <=> salvigenin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-15530
is_a: GO:0008168 ! methyltransferase activity
@@ -404119,7 +404128,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102629
name: patuletin 3'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: patuletin + S-adenosyl-L-methionine <=> quercetagetin 3',6-dimethyl ether + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: patuletin + S-adenosyl-L-methionine <=> quercetagetin 3',6-dimethyl ether + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-15534
is_a: GO:0008168 ! methyltransferase activity
@@ -404127,7 +404136,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102630
name: gossypetin 8-methyl ester 3'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3',4',5,7-pentahydroxy-8-methoxyflavon-3-olate + S-adenosyl-L-methionine <=> gossypetin 3',8-dimethyl ether + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 3',4',5,7-pentahydroxy-8-methoxyflavon-3-olate + S-adenosyl-L-methionine <=> gossypetin 3',8-dimethyl ether + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-15536
is_a: GO:0008168 ! methyltransferase activity
@@ -404135,7 +404144,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102631
name: caffeoylglucose 3-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-O-caffeoyl-beta-D-glucose + S-adenosyl-L-methionine <=> 1-O-feruloyl-beta-D-glucose + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 1-O-caffeoyl-beta-D-glucose + S-adenosyl-L-methionine <=> 1-O-feruloyl-beta-D-glucose + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-15537
is_a: GO:0008168 ! methyltransferase activity
@@ -404284,7 +404293,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0102650
name: cyclo-acetoacetyl-L-tryptophan synthetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetoacetyl-ACP + L-tryptophan + ATP <=> cyclo-acetoacetyl-L-tryptophan + AMP + diphosphoric acid + 2 H+ + a holo-[acyl-carrier protein]." [EC:6.3.2.-, GOC:pz]
+def: "Catalysis of the reaction: acetoacetyl-ACP + L-tryptophan + ATP <=> cyclo-acetoacetyl-L-tryptophan + AMP + diphosphoric acid + 2 H+ + a holo-[acyl-carrier protein]." [EC:6.3.2.-, GOC:pz]
xref: MetaCyc:RXN-15811
is_a: GO:0016881 ! acid-amino acid ligase activity
@@ -404396,7 +404405,7 @@ is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
id: GO:0102664
name: indole-3-acetyl-leucine synthetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: indole-3-acetate + L-leucine + ATP <=> H+ + indole-3-acetyl-leucine + diphosphoric acid + AMP." [EC:6.3.-.-, GOC:pz]
+def: "Catalysis of the reaction: indole-3-acetate + L-leucine + ATP <=> H+ + indole-3-acetyl-leucine + diphosphoric acid + AMP." [EC:6.3.-.-, GOC:pz]
xref: MetaCyc:RXN-2945
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
@@ -404424,16 +404433,6 @@ def: "Catalysis of the reaction: 1-O-(indol-3-ylacetyl)-beta-D-glucose + H2O <=>
xref: MetaCyc:RXN-3165
is_a: GO:0016788 ! hydrolase activity, acting on ester bonds
-[Term]
-id: GO:0102668
-name: liquiritigenin,NADPH:oxygen oxidoreductase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: liquiritigenin + NADPH + O2 + H+ <=> 2,4',7-trihydroxyisoflavanone + NADP(3-) + H2O." [EC:1.14.14.87, GOC:pz]
-xref: EC:1.14.14.87
-xref: MetaCyc:RXN-3283
-xref: RHEA:31723
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
-
[Term]
id: GO:0102669
name: isoflavone-7-O-glucoside beta-glucosidase activity
@@ -404446,7 +404445,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0102670
name: 2,7,4'-trihydroxyisoflavanone-4'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,4',7-trihydroxyisoflavanone + S-adenosyl-L-methionine <=> H+ + 2,7-dihydroxy-4'-methoxyisoflavanone + S-adenosyl-L-homocysteine." [EC:2.1.1.212, GOC:pz]
+def: "Catalysis of the reaction: 2,4',7-trihydroxyisoflavanone + S-adenosyl-L-methionine <=> H+ + 2,7-dihydroxy-4'-methoxyisoflavanone + S-adenosyl-L-homocysteine." [EC:2.1.1.212, GOC:pz]
xref: EC:2.1.1.212
xref: MetaCyc:RXN-3624
xref: RHEA:31371
@@ -404456,7 +404455,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102671
name: 6a-hydroxymaackiain-3-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (+)-6a-hydroxymaackiain + S-adenosyl-L-methionine <=> H+ + (+)-pisatin + S-adenosyl-L-homocysteine." [EC:2.1.1.270, GOC:pz]
+def: "Catalysis of the reaction: (+)-6a-hydroxymaackiain + S-adenosyl-L-methionine <=> H+ + (+)-pisatin + S-adenosyl-L-homocysteine." [EC:2.1.1.270, GOC:pz]
xref: EC:2.1.1.270
xref: MetaCyc:RXN-4002
xref: RHEA:35471
@@ -404480,19 +404479,21 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
[Term]
id: GO:0102674
-name: C4-demethylase activity
+name: obsolete C4-demethylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 24-methylenelophenol + a demethylated methyl acceptor <=> 9xi-episterol + a methylated methyl acceptor." [EC:2.1.1.-, GOC:pz]
+def: "OBSOLETE. Catalysis of the reaction: 24-methylenelophenol + a demethylated methyl acceptor <=> 9xi-episterol + a methylated methyl acceptor." [EC:2.1.1.-, GOC:pz]
+comment: This term was obsoleted because there is no evidence that this actvity exists.
xref: MetaCyc:RXN-4181
-is_a: GO:0008168 ! methyltransferase activity
+is_obsolete: true
[Term]
id: GO:0102675
-name: C4-methyltransferase activity
+name: obsolete C4-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 24-ethylidenelophenol + a demethylated methyl acceptor <=> avenasterol + a methylated methyl acceptor." [EC:2.1.1.-, GOC:pz]
+def: "OBSOLETE. Catalysis of the reaction: 24-ethylidenelophenol + a demethylated methyl acceptor <=> avenasterol + a methylated methyl acceptor." [EC:2.1.1.-, GOC:pz]
+comment: This term was obsoleted because there is no evidence that this actvity exists.
xref: MetaCyc:RXN-4208
-is_a: GO:0008168 ! methyltransferase activity
+is_obsolete: true
[Term]
id: GO:0102676
@@ -404555,7 +404556,7 @@ is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
id: GO:0102684
name: L-phenylalanine N-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-phenylalanine + 2 NADPH + 2 O2 + 2 H+ <=> (E)-phenylacetaldehyde oxime + 2 NADP + 3 H2O + carbon dioxide." [EC:1.14.14.40, GOC:pz]
+def: "Catalysis of the reaction: L-phenylalanine + 2 NADPH + 2 O2 + 2 H+ <=> (E)-phenylacetaldehyde oxime + 2 NADP + 3 H2O + carbon dioxide." [EC:1.14.14.40, GOC:pz]
xref: EC:1.14.14.40
xref: MetaCyc:RXN-4602
xref: RHEA:33263
@@ -404734,7 +404735,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0102705
name: serine decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H+ + L-serine <=> ethanolaminium(1+) + carbon dioxide." [GOC:pz, PMID:11461929, RHEA:45824]
+def: "Catalysis of the reaction: H+ + L-serine <=> ethanolaminium(1+) + carbon dioxide." [GOC:pz, PMID:11461929, RHEA:45824]
xref: MetaCyc:RXN-5641
xref: RHEA:45824
is_a: GO:0016831 ! carboxy-lyase activity
@@ -404753,7 +404754,7 @@ is_a: GO:0046993 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y
id: GO:0102707
name: S-adenosyl-L-methionine:beta-alanine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: beta-alanine + S-adenosyl-L-methionine = H+ + N-methyl-beta-alanine + S-adenosyl-L-homocysteine." [EC:2.1.1.49, GOC:pz]
+def: "Catalysis of the reaction: beta-alanine + S-adenosyl-L-methionine = H+ + N-methyl-beta-alanine + S-adenosyl-L-homocysteine." [EC:2.1.1.49, GOC:pz]
xref: EC:2.1.1.49
xref: MetaCyc:RXN-6461
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
@@ -404762,7 +404763,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0102708
name: S-adenosyl-L-methionine:N-methyl-beta-alanine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-methyl-beta-alanine + S-adenosyl-L-methionine = H+ + N,N-dimethyl-beta-alanine + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: N-methyl-beta-alanine + S-adenosyl-L-methionine = H+ + N,N-dimethyl-beta-alanine + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-6462
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
@@ -404770,7 +404771,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0102709
name: S-adenosyl-L-methionine:N,N-dimethyl-beta-alanine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N,N-dimethyl-beta-alanine + S-adenosyl-L-methionine = H+ + beta-alanine betaine + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: N,N-dimethyl-beta-alanine + S-adenosyl-L-methionine = H+ + beta-alanine betaine + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-6464
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
@@ -404846,7 +404847,7 @@ is_a: GO:0050498 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102718
name: TRIBOA-glucoside methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: TRIBOA-beta-D-glucoside + S-adenosyl-L-methionine <=> (2R)-DIMBOA glucoside + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.241, GOC:pz]
+def: "Catalysis of the reaction: TRIBOA-beta-D-glucoside + S-adenosyl-L-methionine <=> (2R)-DIMBOA glucoside + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.241, GOC:pz]
xref: EC:2.1.1.241
xref: MetaCyc:RXN-6687
xref: RHEA:32099
@@ -404856,7 +404857,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102719
name: S-adenosyl-L-methionine:eugenol-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: eugenol + S-adenosyl-L-methionine = H+ + O-methyleugenol + S-adenosyl-L-homocysteine." [EC:2.1.1.146, GOC:pz]
+def: "Catalysis of the reaction: eugenol + S-adenosyl-L-methionine = H+ + O-methyleugenol + S-adenosyl-L-homocysteine." [EC:2.1.1.146, GOC:pz]
xref: EC:2.1.1.146
xref: MetaCyc:RXN-6741
is_a: GO:0008168 ! methyltransferase activity
@@ -405027,7 +405028,7 @@ is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
id: GO:0102740
name: theobromine:S-adenosyl-L-methionine 1-N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: theobromine + S-adenosyl-L-methionine <=> H+ + caffeine + S-adenosyl-L-homocysteine." [EC:2.1.1.160, GOC:pz]
+def: "Catalysis of the reaction: theobromine + S-adenosyl-L-methionine <=> H+ + caffeine + S-adenosyl-L-homocysteine." [EC:2.1.1.160, GOC:pz]
xref: EC:2.1.1.160
xref: MetaCyc:RXN-7599
xref: RHEA:20944
@@ -405037,7 +405038,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102741
name: paraxanthine:S-adenosyl-L-methionine 3-N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,7-dimethylxanthine + S-adenosyl-L-methionine <=> H+ + caffeine + S-adenosyl-L-homocysteine." [EC:2.1.1.160, GOC:pz]
+def: "Catalysis of the reaction: 1,7-dimethylxanthine + S-adenosyl-L-methionine <=> H+ + caffeine + S-adenosyl-L-homocysteine." [EC:2.1.1.160, GOC:pz]
xref: EC:2.1.1.160
xref: MetaCyc:RXN-7601
xref: RHEA:10280
@@ -405173,7 +405174,8 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0102757
name: NADPH phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADPH + H2O = NADH + hydrogenphosphate." [EC:3.1.3.-, GOC:pz]
+def: "Catalysis of the reaction: NADPH + H2O = NADH + hydrogenphosphate." [GOC:pz, RHEA:60664]
+xref: EC:3.1.3.108
xref: MetaCyc:RXN-7703
xref: RHEA:60664
is_a: GO:0016791 ! phosphatase activity
@@ -405208,7 +405210,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102761
name: eriodictyol 3'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: eriodictyol + S-adenosyl-L-methionine <=> H+ + homoeriodictyol + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: eriodictyol + S-adenosyl-L-methionine <=> H+ + homoeriodictyol + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-7753
xref: RHEA:60948
is_a: GO:0008168 ! methyltransferase activity
@@ -405217,7 +405219,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102762
name: eriodictyol 4'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: eriodictyol + S-adenosyl-L-methionine <=> H+ + hesperetin(1-) + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: eriodictyol + S-adenosyl-L-methionine <=> H+ + hesperetin(1-) + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-7754
is_a: GO:0008168 ! methyltransferase activity
@@ -405250,7 +405252,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0102766
name: naringenin 7-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-naringenin(1-) + S-adenosyl-L-methionine <=> sakuranetin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.232, GOC:pz]
+def: "Catalysis of the reaction: (S)-naringenin(1-) + S-adenosyl-L-methionine <=> sakuranetin + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.232, GOC:pz]
xref: EC:2.1.1.232
xref: MetaCyc:RXN-7773
xref: RHEA:31539
@@ -405260,7 +405262,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102767
name: flavanone 4'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-naringenin + S-adenosyl-L-methionine = 2 H+ + ponciretin + S-adenosyl-L-homocysteine." [EC:2.1.1.231, GOC:pz]
+def: "Catalysis of the reaction: (S)-naringenin + S-adenosyl-L-methionine = 2 H+ + ponciretin + S-adenosyl-L-homocysteine." [EC:2.1.1.231, GOC:pz]
xref: EC:2.1.1.231
xref: MetaCyc:RXN-7777
xref: RHEA:31743
@@ -405352,9 +405354,9 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
[Term]
id: GO:0102778
-name: Delta9-tetrahydrocannabinolate synthase activity
+name: delta9-tetrahydrocannabinolate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cannabigerolate + O2 <=> Delta(9)-tetrahydrocannabinolic acid + hydrogen peroxide." [GOC:pz, RHEA:34135]
+def: "Catalysis of the reaction: cannabigerolate + O2 <=> delta(9)-tetrahydrocannabinolic acid + hydrogen peroxide." [GOC:pz, RHEA:34135]
xref: EC:1.21.3.7
xref: MetaCyc:RXN-7854
xref: RHEA:34135
@@ -405364,7 +405366,7 @@ is_a: GO:0046993 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y
id: GO:0102779
name: cannabidiolate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cannabigerolate + O2 <=> cannabidiolate + hydrogen peroxide." [EC:1.21.3.8, GOC:pz]
+def: "Catalysis of the reaction: cannabigerolate + O2 <=> cannabidiolate + hydrogen peroxide." [GOC:pz, RHEA:34411]
xref: EC:1.21.3.8
xref: MetaCyc:RXN-7855
xref: RHEA:34411
@@ -405516,27 +405518,27 @@ is_a: GO:0016623 ! oxidoreductase activity, acting on the aldehyde or oxo group
[Term]
id: GO:0102797
-name: geranial:oxygen oxidoreductase activity
+name: obsolete geranial:oxygen oxidoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: geranial + O2 + H2O = H+ + geranate + hydrogen peroxide." [EC:1.2.3.1, GOC:pz]
-xref: EC:1.2.3.1
-xref: MetaCyc:RXN-8093
-is_a: GO:0016623 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, oxygen as acceptor
+def: "OBSOLETE. Catalysis of the reaction: geranial + O2 + H2O = H+ + geranate + hydrogen peroxide." [GOC:pz]
+comment: This term has been obsoleted because it is beyond the scope of GO.
+is_obsolete: true
+replaced_by: GO:0004031
[Term]
id: GO:0102798
-name: heptaldehyde:oxygen oxidoreductase activity
+name: obsolete heptaldehyde:oxygen oxidoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: heptanal + O2 + H2O = H+ + heptanoate + hydrogen peroxide." [EC:1.2.3.1, GOC:pz]
-xref: EC:1.2.3.1
-xref: MetaCyc:RXN-8094
-is_a: GO:0016623 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, oxygen as acceptor
+def: "OBSOLETE. Catalysis of the reaction: heptanal + O2 + H2O = H+ + heptanoate + hydrogen peroxide." [GOC:pz]
+comment: This term has been obsoleted because it is beyond the scope of GO.
+is_obsolete: true
+replaced_by: GO:0004031
[Term]
id: GO:0102799
name: glucosinolate glucohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + a glucosinolate = alpha-D-glucose + a thiohydroximate-O-sulfate. Glucosinolates are a subclass of thioglucosides." [EC:3.2.1.147, GOC:pz]
+def: "Catalysis of the reaction: H2O + a glucosinolate = alpha-D-glucose + a thiohydroximate-O-sulfate. Glucosinolates are a subclass of thioglucosides." [EC:3.2.1.147, GOC:pz]
xref: EC:3.2.1.147
xref: MetaCyc:RXN-8134
is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
@@ -405719,7 +405721,7 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0102820
name: norbixin methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: norbixin + S-adenosyl-L-methionine <=> bixin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: norbixin + S-adenosyl-L-methionine <=> bixin + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-8238
is_a: GO:0008168 ! methyltransferase activity
@@ -405727,7 +405729,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102821
name: bixin methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: bixin + S-adenosyl-L-methionine <=> bixin dimethyl ester + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: bixin + S-adenosyl-L-methionine <=> bixin dimethyl ester + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-8239
is_a: GO:0008168 ! methyltransferase activity
@@ -405735,7 +405737,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102822
name: quercetin 3'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: quercetin-7-olate + S-adenosyl-L-methionine = H+ + isorhamnetin + S-adenosyl-L-homocysteine." [EC:2.1.1.42, GOC:pz]
+def: "Catalysis of the reaction: quercetin-7-olate + S-adenosyl-L-methionine = H+ + isorhamnetin + S-adenosyl-L-homocysteine." [EC:2.1.1.42, GOC:pz]
xref: EC:2.1.1.42
xref: MetaCyc:RXN-8262
xref: RHEA:55332
@@ -406016,16 +406018,6 @@ def: "Catalysis of the reaction: 1-18:2-2-18:1-phosphatidylcholine + O2 + a redu
xref: MetaCyc:RXN-8321
is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
-[Term]
-id: GO:0102855
-name: 1-18:1-2-18:2-phosphatidylcholine desaturase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 1-18:1-2-18:2-phosphatidylcholine + O2 + a reduced electron acceptor <=> 1-18:2-2-18:2-sn-glycerol-3-phosphocholine + 2 H2O + an oxidized electron acceptor." [GOC:pz, RHEA:46332]
-xref: EC:1.14.19.22
-xref: MetaCyc:RXN-8322
-xref: RHEA:46332
-is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
-
[Term]
id: GO:0102856
name: 1-18:2-2-18:2-sn-glycerol-3-phosphocholine desaturase activity
@@ -406035,15 +406027,6 @@ xref: EC:1.14.19.25
xref: MetaCyc:RXN-8323
is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
-[Term]
-id: GO:0102857
-name: 1-18:1-2-18:3-phosphatidylcholinedesaturase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 1-18:1-2-18:3-phosphatidylcholine + O2 + a reduced electron acceptor <=> 1-18:2-2-18:3-phosphatidylcholine + 2 H2O + an oxidized electron acceptor." [GOC:pz]
-xref: EC:1.14.19.22
-xref: MetaCyc:RXN-8324
-is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
-
[Term]
id: GO:0102858
name: 1-18:2-2-18:3-phosphatidylcholine desaturase activity
@@ -406062,24 +406045,6 @@ xref: MetaCyc:RXN-8326
xref: RHEA:46404
is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
-[Term]
-id: GO:0102860
-name: 1-18:1-2-18:2-phosphatidylcholine synthase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 1-18:1-2-18:1-sn-glycerol-3-phosphocholine + O2 + a reduced electron acceptor <=> 1-18:1-2-18:2-phosphatidylcholine + 2 H2O + an oxidized electron acceptor." [GOC:pz]
-xref: EC:1.14.19.22
-xref: MetaCyc:RXN-8327
-is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
-
-[Term]
-id: GO:0102861
-name: 1-18:2-2-18:1-phosphatidylcholine desaturase activity (SN2-18:2 forming)
-namespace: molecular_function
-def: "Catalysis of the reaction: 1-18:2-2-18:1-phosphatidylcholine + O2 + a reduced electron acceptor = 1-18:2-2-18:2-sn-glycerol-3-phosphocholine + 2 H2O + an oxidized electron acceptor." [GOC:pz]
-xref: EC:1.14.19.22
-xref: MetaCyc:RXN-8328
-is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
-
[Term]
id: GO:0102862
name: 1-18:2-2-18:2-sn-glycerol-3-phosphocholine desaturase activity (SN2-18:3 forming)
@@ -406109,7 +406074,7 @@ is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidat
id: GO:0102865
name: delta6-acyl-lipid desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a gamma-linolenoyl-[glycerolipid] + 2 ferrocytochrome b5 + O(2) + 2 H(+) <=> a (9Z,12Z)-octadeca-9,12-dien-6-ynoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H(2)O." [GOC:pz, PMID:10848999, RHEA:46536]
+def: "Catalysis of the reaction: a gamma-linolenoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ <=> a (9Z,12Z)-octadeca-9,12-dien-6-ynoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O." [GOC:pz, PMID:10848999, RHEA:46536]
xref: EC:1.14.19.38
xref: MetaCyc:RXN-8343
xref: RHEA:46536
@@ -406128,7 +406093,7 @@ is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidat
id: GO:0102867
name: molybdenum cofactor sulfurtransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 H+ + MoO2-molybdopterin cofactor(2-) + L-cysteine <=> thio-molybdenum cofactor + L-alanine + H2O." [EC:2.8.1.9, GOC:pz]
+def: "Catalysis of the reaction: 2 H+ + MoO2-molybdopterin cofactor(2-) + L-cysteine <=> thio-molybdenum cofactor + L-alanine + H2O." [EC:2.8.1.9, GOC:pz]
xref: EC:2.8.1.9
xref: MetaCyc:RXN-8351
xref: RHEA:42636
@@ -406158,15 +406123,6 @@ def: "Catalysis of the reaction: UDP-alpha-D-glucose + 7-hydroxyflavone <=> 7-O-
xref: MetaCyc:RXN-8355
is_a: GO:0016758 ! hexosyltransferase activity
-[Term]
-id: GO:0102871
-name: 1-16:0-2-18:1-phosphatidylcholine desaturase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 1-16:0-2-18:1-phosphatidylcholine + O2 + a reduced electron acceptor <=> 1-palmitoyl-2-linoleoyl-phosphatidylcholine + 2 H2O + an oxidized electron acceptor." [GOC:pz, PMID:475773]
-xref: EC:1.14.19.22
-xref: MetaCyc:RXN-8360
-is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
-
[Term]
id: GO:0102872
name: 1-16:0-2-18:2-phosphatidylcholine desaturase activity
@@ -406527,7 +406483,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0102913
name: 3-aminomethylindole N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: indol-3-ylmethylamine + S-adenosyl-L-methionine = H+ + N-methyl-3-aminomethylindole + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: indol-3-ylmethylamine + S-adenosyl-L-methionine = H+ + N-methyl-3-aminomethylindole + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-8686
xref: RHEA:52268
is_a: GO:0008168 ! methyltransferase activity
@@ -406536,7 +406492,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102914
name: N-methyl-3-aminomethylindole N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-methyl-3-aminomethylindole + S-adenosyl-L-methionine = H+ + gramine + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: N-methyl-3-aminomethylindole + S-adenosyl-L-methionine = H+ + gramine + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-8687
xref: RHEA:52272
is_a: GO:0008168 ! methyltransferase activity
@@ -406564,7 +406520,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102917
name: (S)-reticuline 7-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-reticulinium(1+) + S-adenosyl-L-methionine <=> H+ + laudanine(1+) + S-adenosyl-L-homocysteine." [GOC:pz, RHEA:10444]
+def: "Catalysis of the reaction: (S)-reticulinium(1+) + S-adenosyl-L-methionine <=> H+ + laudanine(1+) + S-adenosyl-L-homocysteine." [GOC:pz, RHEA:10444]
xref: EC:2.1.1.291
xref: MetaCyc:RXN-8700
xref: RHEA:10444
@@ -406574,7 +406530,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102918
name: (R)-reticuline 7-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-reticulinium(1+) + S-adenosyl-L-methionine <=> (R)-laudanine(1+) + S-adenosyl-L-homocysteine + H+." [GOC:pz, RHEA:38907]
+def: "Catalysis of the reaction: (R)-reticulinium(1+) + S-adenosyl-L-methionine <=> (R)-laudanine(1+) + S-adenosyl-L-homocysteine + H+." [GOC:pz, RHEA:38907]
xref: EC:2.1.1.291
xref: MetaCyc:RXN-8701
xref: RHEA:38907
@@ -406749,7 +406705,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0102938
name: orcinol O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: orcinol + S-adenosyl-L-methionine = H+ + 3-methoxy-5-hydroxytoluene + S-adenosyl-L-homocysteine." [EC:2.1.1.6, GOC:pz]
+def: "Catalysis of the reaction: orcinol + S-adenosyl-L-methionine = H+ + 3-methoxy-5-hydroxytoluene + S-adenosyl-L-homocysteine." [EC:2.1.1.6, GOC:pz]
xref: EC:2.1.1.6
xref: MetaCyc:RXN-9017
is_a: GO:0008168 ! methyltransferase activity
@@ -406758,7 +406714,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102939
name: 3-methoxy-5-hydroxytoluene O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-methoxy-5-hydroxytoluene + S-adenosyl-L-methionine = H+ + 3,5-dimethoxytoluene + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 3-methoxy-5-hydroxytoluene + S-adenosyl-L-methionine = H+ + 3,5-dimethoxytoluene + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-9018
is_a: GO:0008168 ! methyltransferase activity
@@ -406766,7 +406722,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102940
name: phloroglucinol O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phloroglucinol + S-adenosyl-L-methionine = H+ + 3,5-dihydroxyanisole + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: phloroglucinol + S-adenosyl-L-methionine = H+ + 3,5-dihydroxyanisole + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-9020
is_a: GO:0008168 ! methyltransferase activity
@@ -406774,7 +406730,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102941
name: 3,5-dihydroxyanisole O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3,5-dihydroxyanisole + S-adenosyl-L-methionine = H+ + 3,5-dimethoxyphenol + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 3,5-dihydroxyanisole + S-adenosyl-L-methionine = H+ + 3,5-dimethoxyphenol + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-9021
is_a: GO:0008168 ! methyltransferase activity
@@ -406782,7 +406738,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102942
name: 3,5-dimethoxyphenol O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3,5-dimethoxyphenol + S-adenosyl-L-methionine = H+ + 1,3,5-trimethoxybenzene + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 3,5-dimethoxyphenol + S-adenosyl-L-methionine = H+ + 1,3,5-trimethoxybenzene + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-9022
is_a: GO:0008168 ! methyltransferase activity
@@ -406790,7 +406746,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102943
name: trans-2,3-dihydro-3-hydroxy-anthranilate isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2S,3S)-2,3-dihydro-3-hydroxyanthranilic acid = (1R,6S)-6-ammonio-5-oxocyclohex-2-ene-1-carboxylate." [GOC:pz, RHEA:28182]
+def: "Catalysis of the reaction: (2S,3S)-2,3-dihydro-3-hydroxyanthranilic acid = (1R,6S)-6-ammonio-5-oxocyclohex-2-ene-1-carboxylate." [GOC:pz, RHEA:28182]
xref: EC:5.3.3.17
xref: MetaCyc:RXN-9031
xref: RHEA:28182
@@ -406848,7 +406804,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0102950
name: indole-3-acetyl-valine synthetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: indole-3-acetate + L-valine + ATP = H+ + indole-3-acetyl-valine + AMP + diphosphoric acid." [EC:6.3.-.-, GOC:pz]
+def: "Catalysis of the reaction: indole-3-acetate + L-valine + ATP = H+ + indole-3-acetyl-valine + AMP + diphosphoric acid." [EC:6.3.-.-, GOC:pz]
xref: MetaCyc:RXN-9083
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
@@ -406856,7 +406812,7 @@ is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
id: GO:0102951
name: indole-3-acetyl-phenylalanine synthetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: indole-3-acetate + L-phenylalanine + ATP = H+ + indole-3-acetyl-phenylalanine + AMP + diphosphoric acid." [EC:6.3.-.-, GOC:pz]
+def: "Catalysis of the reaction: indole-3-acetate + L-phenylalanine + ATP = H+ + indole-3-acetyl-phenylalanine + AMP + diphosphoric acid." [EC:6.3.-.-, GOC:pz]
xref: MetaCyc:RXN-9084
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
@@ -406890,7 +406846,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0102955
name: S-adenosylmethionine:2-demethylmenaquinol-7 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-demethylmenaquinol-7 + S-adenosyl-L-methionine = menaquinol-7 + S-adenosyl-L-homocysteine + H+." [GOC:pz, PMID:1444716, PMID:9045837, RHEA:33255]
+def: "Catalysis of the reaction: 2-demethylmenaquinol-7 + S-adenosyl-L-methionine = menaquinol-7 + S-adenosyl-L-homocysteine + H+." [GOC:pz, PMID:1444716, PMID:9045837, RHEA:33255]
xref: EC:2.1.1.163
xref: MetaCyc:RXN-9191
xref: RHEA:33255
@@ -406915,24 +406871,6 @@ xref: MetaCyc:RXN-9290
xref: RHEA:25367
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
-[Term]
-id: GO:0102961
-name: 4,4'-diapophytofluene desaturase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: all-trans-4,4'-diapophytofluene + FAD + H+ = all-trans-4,4'-diapo-zeta-carotene + FADH2." [EC:1.3.8.-, GOC:pz]
-xref: MetaCyc:RXN-9304
-xref: RHEA:31399
-is_a: GO:0052890 ! oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor
-
-[Term]
-id: GO:0102962
-name: 4,4'-diapo-zeta-carotene desaturase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: all-trans-4,4'-diapo-zeta-carotene + FAD + H+ = 4,4'-diaponeurosporene + FADH2." [EC:1.3.8.-, GOC:pz]
-xref: MetaCyc:RXN-9305
-xref: RHEA:31403
-is_a: GO:0052890 ! oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor
-
[Term]
id: GO:0102963
name: (S)-corytuberine synthase activity
@@ -406947,16 +406885,17 @@ is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidat
id: GO:0102964
name: S-adenosyl-L-methionine:(S)-corytuberine-N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-corytuberine + S-adenosyl-L-methionine <=> H+ + magnoflorine + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: (S)-corytuberine + S-adenosyl-L-methionine <=> H+ + magnoflorine + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-9315
xref: RHEA:51524
is_a: GO:0008168 ! methyltransferase activity
[Term]
id: GO:0102965
-name: alcohol-forming fatty acyl-CoA reductase activity
+name: alcohol-forming long-chain fatty acyl-CoA reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 NADPH + 2 H+ + a long-chain acyl-CoA = coenzyme A + 2 NADP + a long-chain alcohol." [EC:1.2.1.84, GOC:pz]
+def: "Catalysis of the reaction: a long-chain fatty acyl-CoA + 2 H+ + 2 NADPH = a long-chain primary fatty alcohol + CoA + 2 NADP+. A long-chain fatty acid (LCFA) is a fatty acid with an aliphatic tail of 13 to 21 carbons." [GOC:pz, RHEA:52716]
+synonym: "alcohol-forming fatty acyl-CoA reductase activity" BROAD []
xref: EC:1.2.1.84
xref: MetaCyc:RXN-9344
xref: RHEA:52716
@@ -407190,7 +407129,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0102990
name: 5-n-alk(en)ylresorcinol O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-(pentadeca-8,11,14-trien-1-yl)resorcinol + S-adenosyl-L-methionine <=> H+ + 5-(pentadeca-8,11,14-trien-1-yl)resorcinol monomethyl ether + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 5-(pentadeca-8,11,14-trien-1-yl)resorcinol + S-adenosyl-L-methionine <=> H+ + 5-(pentadeca-8,11,14-trien-1-yl)resorcinol monomethyl ether + S-adenosyl-L-homocysteine." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN-9619
xref: RHEA:26325
is_a: GO:0008168 ! methyltransferase activity
@@ -407329,7 +407268,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0103007
name: indole-3-acetate carboxyl methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: indole-3-acetate + S-adenosyl-L-methionine <=> methyl (indol-3-yl)acetate + S-adenosyl-L-homocysteine." [EC:2.1.1.278, GOC:pz]
+def: "Catalysis of the reaction: indole-3-acetate + S-adenosyl-L-methionine <=> methyl (indol-3-yl)acetate + S-adenosyl-L-homocysteine." [EC:2.1.1.278, GOC:pz]
xref: EC:2.1.1.278
xref: MetaCyc:RXN-9825
xref: RHEA:36131
@@ -407393,7 +407332,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0103015
name: 4-amino-4-deoxy-L-arabinose transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (Kdo)2-lipid A + 2 4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,poly-cis-undecaprenyl phosphate = (beta-L-Ara4N)2-(KDO)2-lipid A + 2 ditrans,polycis-undecaprenyl phosphate." [EC:2.4.2.43, GOC:pz]
+def: "Catalysis of the reaction: (Kdo)2-lipid A + 2 4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,poly-cis-undecaprenyl phosphate = (beta-L-Ara4N)2-(KDO)2-lipid A + 2 ditrans,polycis-undecaprenyl phosphate." [EC:2.4.2.43, GOC:pz]
xref: EC:2.4.2.43
xref: MetaCyc:RXN0-2001
xref: RHEA:35371
@@ -407420,20 +407359,11 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0103023
name: ITPase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ITP + H2O <=> H+ + IDP + hydrogenphosphate." [GOC:pz, PMID:16216582, RHEA:28330]
+def: "Catalysis of the reaction: ITP + H2O = IDP + H+ + phosphate." [GOC:pz, PMID:16216582, RHEA:28330]
xref: EC:3.6.1.73
xref: MetaCyc:RXN0-5073
xref: RHEA:28330
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
-
-[Term]
-id: GO:0103025
-name: alpha-amylase activity (releasing maltohexaose)
-namespace: molecular_function
-def: "Catalysis of the reaction: n H2O + a 1,4-alpha-D-glucan = alpha-maltohexaose + a 1,4-alpha-D-glucan." [EC:3.2.1.1, GOC:pz]
-xref: EC:3.2.1.1
-xref: MetaCyc:RXN0-5181
-is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
+is_a: GO:0017111 ! ribonucleoside triphosphate phosphatase activity
[Term]
id: GO:0103026
@@ -407523,7 +407453,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0103039
name: protein methylthiotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + a [ribosomal protein S12] L-aspartate89 + a sulfurated [sulfur carrier] + a reduced electron acceptor = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2 H+ + a [ribosomal protein S12] 3-methylthio-L-aspartate89 + an unsulfurated [sulfur carrier] + an oxidized electron acceptor." [EC:2.8.4.4, GOC:pz]
+def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + a [ribosomal protein S12] L-aspartate89 + a sulfurated [sulfur carrier] + a reduced electron acceptor = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2 H+ + a [ribosomal protein S12] 3-methylthio-L-aspartate89 + an unsulfurated [sulfur carrier] + an oxidized electron acceptor." [EC:2.8.4.4, GOC:pz]
xref: EC:2.8.4.4
xref: MetaCyc:RXN0-6366
xref: RHEA:37087
@@ -407577,7 +407507,7 @@ is_a: GO:0018169 ! ribosomal S6-glutamic acid ligase activity
id: GO:0103045
name: methione N-acyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-methionine + acetyl-CoA = N-acetyl-L-methionine + coenzyme A + H+." [EC:2.3.1.1, GOC:pz]
+def: "Catalysis of the reaction: L-methionine + acetyl-CoA = N-acetyl-L-methionine + coenzyme A + H+." [EC:2.3.1.1, GOC:pz]
xref: EC:2.3.1.1
xref: MetaCyc:RXN0-6948
xref: RHEA:44144
@@ -407605,7 +407535,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0103048
name: tRNA m2A37 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + an adenine37 in tRNA <=> S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + a 2-methyladenine37 in tRNA." [EC:2.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + an adenine37 in tRNA <=> S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + a 2-methyladenine37 in tRNA." [EC:2.1.1.-, GOC:pz]
xref: MetaCyc:RXN0-7007
is_a: GO:0016426 ! tRNA (adenine) methyltransferase activity
@@ -407710,7 +407640,7 @@ xref: EC:2.4.1.370
xref: https://github.com/geneontology/go-ontology/issues/21803
xref: MetaCyc:RXN3O-663
xref: RHEA:64596
-is_a: GO:0016758 ! hexosyltransferase activity
+is_a: GO:0000030 ! mannosyltransferase activity
[Term]
id: GO:0103066
@@ -407744,7 +407674,7 @@ is_a: GO:0016755 ! aminoacyltransferase activity
id: GO:0103069
name: 17-hydroxyprogesterone 21-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 17alpha-hydroxyprogesterone + O2 + reduced [NADPH--hemoprotein reductase] = 11-deoxycortisol + H(+) + H2O + oxidized [NADPH--hemoprotein reductase]." [GOC:pz, RHEA:50308]
+def: "Catalysis of the reaction: 17alpha-hydroxyprogesterone + O2 + reduced [NADPH--hemoprotein reductase] = 11-deoxycortisol + H+ + H2O + oxidized [NADPH--hemoprotein reductase]." [GOC:pz, RHEA:50308]
xref: MetaCyc:RXN66-356
xref: RHEA:50308
is_a: GO:0004509 ! steroid 21-monooxygenase activity
@@ -407765,16 +407695,6 @@ def: "Catalysis of the reaction: a (R)-2-hydroxy even numbered straight chain 2,
xref: MetaCyc:RXN66-475
is_a: GO:0016830 ! carbon-carbon lyase activity
-[Term]
-id: GO:0103073
-name: anandamide amidohydrolase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: anandamide + H2O <=> arachidonate + ethanolaminium(1+)." [EC:3.5.1.99, GOC:pz]
-xref: EC:3.5.1.99
-xref: MetaCyc:RXN6666-2
-xref: RHEA:26136
-is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
-
[Term]
id: GO:0103074
name: glucose-6-phosphate 3-dehydrogenase activity
@@ -407820,7 +407740,7 @@ namespace: molecular_function
def: "Catalysis of the reaction: 5-methylthio-2-oxopentanoate + acetyl-CoA + H2O <=> H+ + 2-(3-methylthiopropyl)malate + coenzyme A." [EC:2.3.3.-, GOC:pz]
xref: MetaCyc:RXNQT-4163
xref: RHEA:25605
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0103080
@@ -407845,7 +407765,7 @@ name: 2-(4'-methylthio)butylmalate synthase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-oxo-6-methylthiohexanoate + acetyl-CoA + H2O <=> H+ + 2-(4'-methylthio)butylmalate + coenzyme A." [EC:2.3.3.-, GOC:pz]
xref: MetaCyc:RXNQT-4166
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0103083
@@ -407869,7 +407789,7 @@ name: 2-(5'-methylthio)pentylmalate synthase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-oxo-7-methylthioheptanoate + acetyl-CoA + H2O <=> H+ + 2-(5'-methylthio)pentylmalate + coenzyme A." [EC:2.3.3.-, GOC:pz]
xref: MetaCyc:RXNQT-4169
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0103086
@@ -407893,7 +407813,7 @@ name: 2-(6'-methylthio)hexylmalate synthase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-oxo-8-methylthiooctanoate + acetyl-CoA + H2O <=> H+ + 2-(6'-methylthio)hexylmalate + coenzyme A." [EC:2.3.3.-, GOC:pz]
xref: MetaCyc:RXNQT-4172
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0103089
@@ -407917,7 +407837,7 @@ name: 2-(7'-methylthio)heptylmalate synthase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-oxo-9-methylthiononanoate + acetyl-CoA + H2O <=> H+ + 2-(7'-methylthio)heptylmalate + coenzyme A." [EC:2.3.3.-, GOC:pz]
xref: MetaCyc:RXNQT-4175
-is_a: GO:0046912 ! acyltransferase, acyl groups converted into alkyl on transfer
+is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
[Term]
id: GO:0103092
@@ -408105,7 +408025,7 @@ id: GO:0104005
name: obsolete hijacked molecular function
namespace: molecular_function
def: "OBSOLETE. A function that was not selected for in the evolution of an organism, but arises from co-option by another organism, e.g. a human protein used as a virus receptor." [GOC:pdt]
-comment: This term was obsoleted because it was an unnecessary grouping class.
+comment: This term was obsoleted because it is an unnecessary grouping class.
is_obsolete: true
[Term]
@@ -408189,6 +408109,7 @@ synonym: "BAR domain adaptor" NARROW []
synonym: "cytoskeletal protein membrane adaptor" BROAD []
synonym: "cytoskeletal protein membrane anchor activity" BROAD []
synonym: "cytoskeletal protein membrane tether activity" BROAD []
+synonym: "cytoskeletal protein to membrane recruiting activity" EXACT []
synonym: "cytoskeletal protein-membrane adaptor activity" BROAD []
synonym: "F-BAR domain adaptor" NARROW []
synonym: "membrane-cytoskeletal protein anchor activity" BROAD []
@@ -408208,7 +408129,7 @@ is_a: GO:0034453 ! microtubule anchoring
id: GO:0106008
name: 2-oxoglutaramate amidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutaramate + H(2)O = 2-oxoglutarate + NH(3)." [EC:3.5.1.111, PMID:21288482]
+def: "Catalysis of the reaction: 2-oxoglutaramate + H2O = 2-oxoglutarate + NH3." [EC:3.5.1.111, PMID:21288482]
xref: EC:3.5.1.111
xref: RHEA:32963
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
@@ -408280,21 +408201,21 @@ relationship: positively_regulates GO:0090594 ! inflammatory response to woundin
id: GO:0106017
name: phosphatidylinositol-3,4-bisphosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-phosphatidyl-myo-inositol 3,4-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol phosphate + phosphate." [GOC:hjd]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol phosphate + phosphate." [GOC:hjd]
is_a: GO:0034593 ! phosphatidylinositol bisphosphate phosphatase activity
[Term]
id: GO:0106018
name: phosphatidylinositol-3,5-bisphosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-phosphatidyl-myo-inositol 3,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol phosphate + phosphate." [GOC:hjd]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol phosphate + phosphate." [GOC:hjd]
is_a: GO:0034593 ! phosphatidylinositol bisphosphate phosphatase activity
[Term]
id: GO:0106019
name: phosphatidylinositol-4,5-bisphosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol phosphate + phosphate." [GOC:hjd]
+def: "Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol phosphate + phosphate." [GOC:hjd]
is_a: GO:0034593 ! phosphatidylinositol bisphosphate phosphatase activity
[Term]
@@ -408303,7 +408224,8 @@ name: regulation of vesicle docking
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of vesicle docking." [PMID:22810233]
synonym: "regulation of vesicle to membrane docking" EXACT []
-is_a: GO:0060341 ! regulation of cellular localization
+is_a: GO:0032879 ! regulation of localization
+is_a: GO:0050794 ! regulation of cellular process
relationship: regulates GO:0048278 ! vesicle docking
[Term]
@@ -408371,7 +408293,7 @@ is_a: GO:0120036 ! plasma membrane bounded cell projection organization
id: GO:0106028
name: neuron projection retraction
namespace: biological_process
-def: "The organization process which results in the disassembly (either partial or complete) of constituent parts of a neuron projection. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:aruk, GOC:bc, PMID:11585923.]
+def: "The organization process which results in the disassembly (either partial or complete) of constituent parts of a neuron projection. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:aruk, GOC:bc, PMID:11585923]
synonym: "neuron projection disassembly" EXACT []
is_a: GO:0106027 ! neuron projection organization
@@ -408514,6 +408436,7 @@ id: GO:0106045
name: guanine deglycation, methylglyoxal removal
namespace: biological_process
def: "The removal of methylglyoxal from a glycated guanine, to form lactate and a deglycated guanine." [PMID:28596309]
+is_a: GO:0009438 ! methylglyoxal metabolic process
is_a: GO:0106044 ! guanine deglycation
is_a: GO:0140041 ! cellular detoxification of methylglyoxal
@@ -408607,9 +408530,11 @@ relationship: positively_regulates GO:0097720 ! calcineurin-mediated signaling
[Term]
id: GO:0106059
-name: tRNA (cytidine 56-2'-O)-methyltransferase
+name: tRNA (cytidine 56-2'-O)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + cytidine56 in tRNA= S-adenosyl-L-homocysteine + 2'-O-methylcytidine56 in tRNA." [EC:2.1.1.206]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + cytidine56 in tRNA= S-adenosyl-L-homocysteine + 2'-O-methylcytidine56 in tRNA." [RHEA:42968]
+xref: EC:2.1.1.206
+xref: RHEA:42968
is_a: GO:0052666 ! tRNA (cytosine-2'-O-)-methyltransferase activity
[Term]
@@ -408751,6 +408676,7 @@ name: histone succinyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: succinyl-CoA + histone = CoA + succinyl-histone." [PMID:29211711]
is_a: GO:0106075 ! peptide N-succinyltransferase activity
+is_a: GO:0140993 ! histone modifying activity
[Term]
id: GO:0106080
@@ -408783,7 +408709,6 @@ def: "Any protein complex that is part of the nuclear membrane." [GOC:lnp, PMID:
is_a: GO:0098796 ! membrane protein complex
is_a: GO:0140513 ! nuclear protein-containing complex
relationship: part_of GO:0005635 ! nuclear envelope
-relationship: part_of GO:0031224 ! intrinsic component of membrane
[Term]
id: GO:0106084
@@ -408866,7 +408791,6 @@ synonym: "DCS1 decapping scavenger complex" EXACT []
synonym: "M(7)G(5')pppN pyrophosphatase enzyme" EXACT []
synonym: "m7G(5')pppN diphosphatase enzyme" EXACT []
synonym: "m7G(5')pppN pyrophosphatase enzyme" EXACT []
-is_a: GO:0034518 ! RNA cap binding complex
is_a: GO:1903293 ! phosphatase complex
[Term]
@@ -409170,6 +409094,9 @@ id: GO:0106130
name: purine phosphoribosyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: RMP + diphosphate = R + 5-phospho-alpha-D-ribose 1-diphosphate." [PMID:5123876]
+xref: Reactome:R-HSA-74215 "HPRT1 catalyzes the conversion of guanine or hypoxanthine to GMP or IMP"
+xref: Reactome:R-HSA-9734274 "Defective HPRT1 does not convert guanine or hypoxanthine to GMP or IMP"
+xref: Reactome:R-HSA-9748951 "HPRT1 tetramer transfers phosphoribosyl group to 6MP to form 6TIMP"
is_a: GO:0016763 ! pentosyltransferase activity
[Term]
@@ -409186,7 +409113,7 @@ id: GO:0106135
name: negative regulation of cardiac muscle cell contraction
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle cell contraction." [PMID:19525381]
-is_a: GO:0051271 ! negative regulation of cellular component movement
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0055118 ! negative regulation of cardiac muscle contraction
is_a: GO:0086004 ! regulation of cardiac muscle cell contraction
relationship: negatively_regulates GO:0086003 ! cardiac muscle cell contraction
@@ -409241,7 +409168,7 @@ is_a: GO:0004659 ! prenyltransferase activity
id: GO:0106142
name: rRNA (adenine-N1-)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + adenine(645) in 25S rRNA = S-adenosyl-L-homocysteine + N(1)-methyladenine(645) in 25S rRNA." [EC:2.1.1.287, PMID:23180764]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + adenine(645) in 25S rRNA = S-adenosyl-L-homocysteine + N(1)-methyladenine(645) in 25S rRNA." [EC:2.1.1.287, PMID:23180764]
comment: The m(1)A modification at position 645 in the large rRNA is highly conserved in eukaryotes.
synonym: "25S rRNA (adenine(645)-N(1))-methyltransferase" RELATED [EC:2.1.1.287]
synonym: "25S rRNA m(1)A(645) methyltransferase" RELATED [EC:2.1.1.287]
@@ -409302,7 +409229,7 @@ is_a: GO:0019756 ! cyanogenic glycoside biosynthetic process
id: GO:0106149
name: indole-3-carbonyl nitrile 4-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: indole-3-carbonyl nitrile + NADPH +O2=4-hydroxyindole-3- carbonyl nitrile + NADP(+) + H20." [GOC:lr, PMID:26352477, RHEA:57864]
+def: "Catalysis of the reaction: indole-3-carbonyl nitrile + NADPH +O2=4-hydroxyindole-3- carbonyl nitrile + NADP+ + H20." [GOC:lr, PMID:26352477, RHEA:57864]
xref: EC:1.14.14.165
xref: RHEA:57864
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
@@ -409314,6 +409241,7 @@ namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of zearalenone, a mycotoxin produced by several Fusarium species, is most commonly found as a contaminant in stored grain and has chronic estrogenic effects on mammals." [GOC:ach, PMID:16517624, PMID:20578001]
is_a: GO:0033068 ! macrolide biosynthetic process
is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:0046189 ! phenol-containing compound biosynthetic process
[Term]
id: GO:0106151
@@ -409327,7 +409255,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0106153
name: phosphorylated histone binding
namespace: molecular_function
-def: "Binding to a histone in which a residue has been modified by phosphorylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:mah, PMID:20679485]
+def: "Binding to a histone in which a residue has been modified by phosphorylation." [GOC:mah, PMID:20679485]
is_a: GO:0042393 ! histone binding
is_a: GO:0140031 ! phosphorylation-dependent protein binding
@@ -409364,6 +409292,7 @@ namespace: molecular_function
alt_id: GO:0140554
def: "Catalyzes the reaction: 2-oxoglutarate + [protein]-L-arginine + O2 = [protein]-(3R)-3-hydroxy-L-arginine + CO2 + succinate." [PMID:29563586]
synonym: "L-arginine 3-hydroxylase activity" EXACT []
+xref: EC:1.14.11.73
xref: RHEA:56744
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -409380,36 +409309,33 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
[Term]
id: GO:0106159
-name: regulation of small RNA loading onto RISC
+name: obsolete regulation of small RNA loading onto RISC
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent small RNA loading onto RISC." [GOC:ha, PMID:29775584]
-is_a: GO:0043254 ! regulation of protein-containing complex assembly
-relationship: regulates GO:0070922 ! small RNA loading onto RISC
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent small RNA loading onto RISC." [GOC:ha, PMID:29775584]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0106160
-name: negative regulation of small RNA loading onto RISC
+name: obsolete negative regulation of small RNA loading onto RISC
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of small RNA loading onto RISC." [GOC:ha, PMID:29775584]
-is_a: GO:0031333 ! negative regulation of protein-containing complex assembly
-is_a: GO:0060967 ! negative regulation of gene silencing by RNA
-is_a: GO:0106159 ! regulation of small RNA loading onto RISC
-relationship: negatively_regulates GO:0070922 ! small RNA loading onto RISC
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of small RNA loading onto RISC." [GOC:ha, PMID:29775584]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0106161
-name: positive regulation of small RNA loading onto RISC
+name: obsolete positive regulation of small RNA loading onto RISC
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of small RNA loading onto RISC." [GOC:ha, PMID:29775584]
-is_a: GO:0031334 ! positive regulation of protein-containing complex assembly
-is_a: GO:0106159 ! regulation of small RNA loading onto RISC
-relationship: positively_regulates GO:0070922 ! small RNA loading onto RISC
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of small RNA loading onto RISC." [GOC:ha, PMID:29775584]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0106162
name: mRNA N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a cytidine in mRNA + acetyl-CoA + ATP + H2O = ADP + an N(4)-acetylcytidine in mRNA + CoA + H(+) + phosphate." [GOC:sp, PMID:30449621]
+def: "Catalysis of the reaction: a cytidine in mRNA + acetyl-CoA + ATP + H2O = ADP + an N(4)-acetylcytidine in mRNA + CoA + H+ + phosphate." [GOC:sp, PMID:30449621]
xref: RHEA:58480
is_a: GO:0008080 ! N-acetyltransferase activity
@@ -409453,7 +409379,7 @@ is_a: GO:0140475 ! spindle pole body anchor activity
id: GO:0106167
name: extracellular ATP signaling
namespace: biological_process
-def: "A series of molecular signals mediated by the detection of extracellular ATP." [GOC:tb, PMID:12948585, PMID:20817461, PMID:29274390]
+def: "The series of molecular signals mediated by the detection of extracellular ATP." [GOC:tb, PMID:12948585, PMID:20817461, PMID:29274390]
is_a: GO:0007165 ! signal transduction
is_a: GO:0071318 ! cellular response to ATP
@@ -409571,13 +409497,15 @@ is_obsolete: true
[Term]
id: GO:0106185
-name: histone H3-K37 methylation
+name: obsolete histone H3-K37 methylation
namespace: biological_process
-def: "The modification of histone H3 by addition of one or more methyl groups to lysine at position 37 of the histone." [GOC:mah, PMID:30773398]
+def: "OBSOLETE. The modification of histone H3 by addition of one or more methyl groups to lysine at position 37 of the histone." [GOC:mah, PMID:30773398]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H3 K37 methylation" EXACT []
synonym: "histone H3K37me" EXACT []
synonym: "histone lysine H3 K37 methylation" EXACT []
-is_a: GO:0034968 ! histone lysine methylation
+is_obsolete: true
+consider: GO:0062122
[Term]
id: GO:0106186
@@ -409750,7 +409678,7 @@ is_a: GO:1902653 ! secondary alcohol biosynthetic process
id: GO:0106211
name: inositol-5-diphosphate-1,3,4,6-tetrakisphosphate diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-diphospho-1D-myo-inositol 1,3,4,6-tetrakisphosphate + H2O = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + H(+) + phosphate." [GOC:rn, PMID:29540476]
+def: "Catalysis of the reaction: 5-diphospho-1D-myo-inositol 1,3,4,6-tetrakisphosphate + H2O = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + H+ + phosphate." [GOC:rn, PMID:29540476]
synonym: "5-diphospho-myo-inositol 1,3,4,6-tetrakisphosphate diphosphatase activity" EXACT []
synonym: "5-diphosphoinositol 1,3,4,6-tetrakisphosphate diphosphatase activity" EXACT []
synonym: "5-PP-InsP4 activity" EXACT []
@@ -409826,7 +409754,7 @@ name: zinc ion sensor activity
namespace: molecular_function
def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of zinc." [GOC:vw, PMID:31239353]
is_a: GO:0008270 ! zinc ion binding
-is_a: GO:0140299 ! small molecule sensor activity
+is_a: GO:0140784 ! metal ion sensor activity
[Term]
id: GO:0106220
@@ -409842,7 +409770,7 @@ is_a: GO:1901566 ! organonitrogen compound biosynthetic process
id: GO:0106222
name: lncRNA binding
namespace: molecular_function
-def: "Binding to a long noncoding RNA (lncRNA)." [PMID:25578728]
+def: "Binding to a long noncoding RNA (lncRNA)." [PMID:25578728]
synonym: "long noncoding RNA binding" EXACT []
is_a: GO:0003723 ! RNA binding
@@ -409851,7 +409779,7 @@ id: GO:0106223
name: germacrene A hydroxylase activity
namespace: molecular_function
alt_id: GO:0102260
-def: "Catalysis of the reaction:(+)-(R)-germacrene A + 3 O2 + 3 reduced [NADPH--hemoprotein reductase] = germacra-1(10),4,11(13)-trien-12-oate + 4 H(+) + 4 H2O + 3 oxidized [NADPH--hemoprotein reductase]." [PMID:11299372, PMID:20351109, RHEA:30303]
+def: "Catalysis of the reaction:(+)-(R)-germacrene A + 3 O2 + 3 reduced [NADPH--hemoprotein reductase] = germacra-1(10),4,11(13)-trien-12-oate + 4 H+ + 4 H2O + 3 oxidized [NADPH--hemoprotein reductase]." [PMID:11299372, PMID:20351109, RHEA:30303]
comment: Formerly EC:1.1.1.314.
synonym: "germacrene A alcohol dehydrogenase activity" RELATED []
xref: EC:1.14.14.95
@@ -409895,6 +409823,7 @@ name: histone glutaryltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: glutaryl-CoA + histone = CoA + H+ + N6-glutaryl-histone." [GOC:sp, PMID:31542297]
is_a: GO:0106228 ! peptide glutaryltransferase activity
+is_a: GO:0140993 ! histone modifying activity
[Term]
id: GO:0106230
@@ -409907,7 +409836,7 @@ is_a: GO:0035601 ! protein deacylation
id: GO:0106231
name: protein-propionyllysine depropionylase activity
namespace: molecular_function
-def: "Catalysis of the reaction:H2O + N(6)-propanoyl-L-lysyl-[protein] + NAD(+) = 3''-O-propanoyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide." [GOC:sp, PMID:30026585, RHEA:23500]
+def: "Catalysis of the reaction:H2O + N(6)-propanoyl-L-lysyl-[protein] + NAD+ = 3''-O-propanoyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide." [GOC:sp, PMID:30026585, RHEA:23500]
comment: This reaction is the removal of a propionyl group from a propionylated lysine residue of a protein or peptide.
xref: RHEA:23500
is_a: GO:0016410 ! N-acyltransferase activity
@@ -409960,7 +409889,7 @@ is_a: GO:0009247 ! glycolipid biosynthetic process
id: GO:0106237
name: arachidonate 12(R)-lipoxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: arachidonate + O(2)=(5Z,8Z,10E,12R,14Z)-12-hydroperoxyicosa-5,8,10,14-tetraenoate." [GOC:gap, PMID:10100631, PMID:11256953, RHEA:41336]
+def: "Catalysis of the reaction: arachidonate + O2 = (5Z,8Z,10E,12R,14Z)-12-hydroperoxyicosa-5,8,10,14-tetraenoate." [GOC:gap, PMID:10100631, PMID:11256953, RHEA:41336]
xref: RHEA:41336
is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
@@ -409986,7 +409915,7 @@ is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
id: GO:0106240
name: labd-13Z-ene-9,15,16-triol synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction:O2 + peregrinol + reduced [NADPH--hemoprotein reductase] = H(+) + H2O + labd-13Z-ene-9,15,16-triol + oxidized [NADPH--hemoprotein reductase]." [GOC:eab, PMID:29315936, RHEA:62192]
+def: "Catalysis of the reaction:O2 + peregrinol + reduced [NADPH--hemoprotein reductase] = H+ + H2O + labd-13Z-ene-9,15,16-triol + oxidized [NADPH--hemoprotein reductase]." [GOC:eab, PMID:29315936, RHEA:62192]
xref: RHEA:62192
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
@@ -410086,6 +410015,7 @@ id: GO:0106254
name: lipid sensor activity
namespace: molecular_function
def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of a lipid." [GOC:vw, PMID:30075144]
+synonym: "lipid sensing activity" EXACT []
is_a: GO:0140299 ! small molecule sensor activity
[Term]
@@ -410101,24 +410031,16 @@ is_a: GO:0050486 ! intramolecular transferase activity, transferring hydroxy gro
id: GO:0106256
name: hydroperoxy icosatetraenoate dehydratase activity
namespace: molecular_function
-def: "A hydroperoxy icosatetraenoate <=> an oxoicosatetraenoate + H(2)O." [PMID:12881489, RHEA:55556]
+def: "A hydroperoxy icosatetraenoate <=> an oxoicosatetraenoate + H2O." [PMID:12881489, RHEA:55556]
xref: EC:4.2.1.152
xref: RHEA:55556
is_a: GO:0016836 ! hydro-lyase activity
-[Term]
-id: GO:0106257
-name: glycerol-3-phosphate dehydrogenase [NADP+] activity
-namespace: molecular_function
-def: "Catalysis of the reaction: sn-glycerol 3-phosphate + NADP+ = glycerone phosphate + NADH + H+." [RHEA:11096]
-xref: RHEA:11096
-is_a: GO:0047952 ! glycerol-3-phosphate dehydrogenase [NAD(P)+] activity
-
[Term]
id: GO:0106258
name: L-serine-phosphatidylcholine phosphatidyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 1,2-diacyl-sn-glycero-3-phosphocholine + L-serine = 1,2-diacyl-sn-glycero-3-phospho-L-serine + choline." [PMID:19014349., RHEA:45088]
+def: "Catalysis of the reaction: a 1,2-diacyl-sn-glycero-3-phosphocholine + L-serine = 1,2-diacyl-sn-glycero-3-phospho-L-serine + choline." [PMID:19014349, RHEA:45088]
xref: RHEA:45088
is_a: GO:0016780 ! phosphotransferase activity, for other substituted phosphate groups
@@ -410144,7 +410066,8 @@ is_a: GO:0060090 ! molecular adaptor activity
id: GO:0106261
name: tRNA uridine(34) acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + H2O + S-adenosyl-L-methionine + uridine(34) in tRNA = 5'-deoxyadenosine + carboxymethyluridine(34) in tRNA + CoA + 2 H(+) + L-methionine." [PMID:25151136, PMID:30733442, RHEA:61020]
+def: "Catalysis of the reaction: acetyl-CoA + H2O + S-adenosyl-L-methionine + uridine(34) in tRNA = 5'-deoxyadenosine + carboxymethyluridine(34) in tRNA + CoA + 2 H+ + L-methionine." [PMID:25151136, PMID:30733442, RHEA:61020]
+xref: EC:2.3.1.311
xref: RHEA:61020
is_a: GO:0016407 ! acetyltransferase activity
@@ -410168,9 +410091,9 @@ is_a: GO:0008374 ! O-acyltransferase activity
id: GO:0106264
name: protein serine kinase activity (using GTP as donor)
namespace: molecular_function
-def: "Catalysis of the reactions: GTP + L-seryl-[protein] = GDP + H(+) + O-phospho-L-seryl-[protein]." [GOC:sp, PMID:32322062, RHEA:64020]
+def: "Catalysis of the reactions: GTP + L-seryl-[protein] = GDP + H+ + O-phospho-L-seryl-[protein]." [GOC:sp, PMID:32322062, RHEA:64020]
xref: RHEA:64020
-is_a: GO:0106310 ! protein serine kinase activity
+is_a: GO:0004672 ! protein kinase activity
[Term]
id: GO:0106265
@@ -410233,19 +410156,24 @@ is_a: GO:0015031 ! protein transport
id: GO:0106274
name: NAD+-protein-arginine ADP-ribosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD+ + L-arginine = nicotinamide + N2-(ADP-D-ribosyl)-L-arginine." [RHEA:19149]
+alt_id: GO:0003956
+alt_id: GO:0106275
+def: "Catalysis of the reaction: L-arginyl-[protein] + NAD+ = H+ + (ADP-D-ribosyl)-L-arginyl-[protein] + nicotinamide." [RHEA:19149]
+synonym: "ADP-ribosyltransferase activity" BROAD [EC:2.4.2.31]
+synonym: "mono(ADP-ribosyl)transferase activity" BROAD [EC:2.4.2.31]
+synonym: "NAD(+):L-arginine ADP-D-ribosyltransferase activity" EXACT [EC:2.4.2.31]
+synonym: "NAD(P)(+)--arginine ADP-ribosyltransferase activity" EXACT [EC:2.4.2.31]
+synonym: "NAD(P)+-protein-arginine ADP-ribosyltransferase activity" BROAD []
+synonym: "NAD(P)+:L-arginine ADP-D-ribosyltransferase activity" EXACT [EC:2.4.2.31]
+synonym: "NAD(P)+:protein-L-arginine ADP-D-ribosyltransferase activity" RELATED [EC:2.4.2.31]
+synonym: "NADP+-protein-arginine ADP-ribosyltransferase activity" BROAD []
+synonym: "peptidyl-arginine ADP-ribosylation activity" EXACT []
+synonym: "protein-arginine ADP-ribosyltransferase activity" EXACT []
xref: EC:2.4.2.31
+xref: MetaCyc:2.4.2.31-RXN
+xref: Reactome:R-HSA-1972385 "ADP-Ribosylation of HNP-1"
xref: RHEA:19149
-is_a: GO:0003956 ! NAD(P)+-protein-arginine ADP-ribosyltransferase activity
-
-[Term]
-id: GO:0106275
-name: NADP+-protein-arginine ADP-ribosyltransferase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: NADP+ + L-arginine = nicotinamide + N2-(ADP-D-ribosyl)-L-arginine." [RHEA:54884]
-xref: EC:2.4.2.31
-xref: RHEA:54884
-is_a: GO:0003956 ! NAD(P)+-protein-arginine ADP-ribosyltransferase activity
+is_a: GO:1990404 ! NAD+-protein ADP-ribosyltransferase activity
[Term]
id: GO:0106276
@@ -410269,7 +410197,7 @@ is_a: GO:0004074 ! biliverdin reductase (NAD(P)+) activity
id: GO:0106278
name: regulation of UDP-N-acetylglucosamine biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the UDP-N_acetylglucosamine biosynthetic process." [PMID:32579556]
+def: "Any process that modulates the frequency, rate or extent of the UDP-N_acetylglucosamine biosynthetic process." [PMID:32579556]
synonym: "regulation of UDP-GlcNAc biosynthetic process" RELATED []
synonym: "regulation of UDP-N-acetylglucosamine anabolism" RELATED []
synonym: "regulation of UDP-N-acetylglucosamine biosynthesis" RELATED []
@@ -410320,7 +410248,7 @@ relationship: positively_regulates GO:0006048 ! UDP-N-acetylglucosamine biosynth
id: GO:0106281
name: chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: chenodeoxycholate + NAD(+) = 7-oxolithocholate + H(+) + NADH." [PMID:12917011, RHEA:42036]
+def: "Catalysis of the reaction: chenodeoxycholate + NAD+ = 7-oxolithocholate + H+ + NADH." [PMID:12917011, RHEA:42036]
xref: RHEA:42036
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -410328,7 +410256,7 @@ is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of
id: GO:0106282
name: isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3beta,7beta-dihydroxy-5beta-cholan-24-oate + NAD(+) = 3beta-hydroxy-7-oxo-5beta-cholan-24-oate + H(+) + NADH." [PMID:12917011, RHEA:42024]
+def: "Catalysis of the reaction: 3beta,7beta-dihydroxy-5beta-cholan-24-oate + NAD+ = 3beta-hydroxy-7-oxo-5beta-cholan-24-oate + H+ + NADH." [PMID:12917011, RHEA:42024]
xref: RHEA:42024
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -410336,7 +410264,7 @@ is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of
id: GO:0106283
name: ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD(+) + ursodeoxycholate = 7-oxolithocholate + H(+) + NADH." [PMID:12917011, RHEA:42028]
+def: "Catalysis of the reaction: NAD+ + ursodeoxycholate = 7-oxolithocholate + H+ + NADH." [PMID:12917011, RHEA:42028]
xref: RHEA:42028
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -410375,9 +410303,9 @@ is_a: GO:0016405 ! CoA-ligase activity
[Term]
id: GO:0106291
-name: superoxide-generating NADH oxidase activity.
+name: superoxide-generating NADH oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADH + 2 O2 = H(+) + NAD(+) + 2 superoxide." [RHEA:63184]
+def: "Catalysis of the reaction: NADH + 2 O2 = H+ + NAD+ + 2 superoxide." [RHEA:63184]
xref: RHEA:63184
is_a: GO:0016175 ! superoxide-generating NAD(P)H oxidase activity
@@ -410385,7 +410313,7 @@ is_a: GO:0016175 ! superoxide-generating NAD(P)H oxidase activity
id: GO:0106292
name: superoxide-generating NADPH oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADPH + 2 O2 = H(+) + NADP(+) + 2 superoxide." [RHEA:63180]
+def: "Catalysis of the reaction: NADPH + 2 O2 = H+ + NADP+ + 2 superoxide." [RHEA:63180]
xref: RHEA:63180
is_a: GO:0016175 ! superoxide-generating NAD(P)H oxidase activity
@@ -410411,7 +410339,8 @@ name: resolvin biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of resolvins, di- or trihydroxy fatty acids derived from omega-3 polyunsaturated fatty acids, specifically icosapentaenoic acid, docosahexaenoic acid and docosapentaenoic acid." [PMID:24899309]
comment: Resolvin biosynthesis is a combination of oxidation, reduction and hydrolysis reactions involving lipoxygenases and cyclooxygenases.
-is_a: GO:0006633 ! fatty acid biosynthetic process
+is_a: GO:0042759 ! long-chain fatty acid biosynthetic process
+is_a: GO:0046173 ! polyol biosynthetic process
[Term]
id: GO:0106296
@@ -410473,7 +410402,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving mannogen, a mannose-containing polysaccharide that is a major energy reserve in Leishmania." [PMID:12902334, PMID:16766650, PMID:31513773, PMID:31662278]
synonym: "beta-1,2-mannan metabolic process" RELATED []
synonym: "mannogen metabolism" RELATED []
-is_a: GO:0044264 ! cellular polysaccharide metabolic process
+is_a: GO:0005976 ! polysaccharide metabolic process
[Term]
id: GO:0106304
@@ -410485,6 +410414,7 @@ synonym: "mannogen anabolism" RELATED []
synonym: "mannogen biosynthesis" RELATED []
synonym: "mannogen formation" RELATED []
synonym: "mannogen synthesis" RELATED []
+is_a: GO:0000271 ! polysaccharide biosynthetic process
is_a: GO:0106303 ! mannogen metabolic process
[Term]
@@ -410497,13 +410427,14 @@ synonym: "beta-1,2-mannan catabolism" RELATED []
synonym: "mannogen breakdown" RELATED []
synonym: "mannogen catabolism" RELATED []
synonym: "mannogen degradation" RELATED []
+is_a: GO:0000272 ! polysaccharide catabolic process
is_a: GO:0106303 ! mannogen metabolic process
[Term]
id: GO:0106309
name: progesterone 21-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O2 + progesterone + reduced [NADPH--hemoprotein reductase] = 21-hydroxyprogesterone + H(+) + H2O + oxidized [NADPH--hemoprotein reductase]." [PMID:25855791, RHEA:50304]
+def: "Catalysis of the reaction: O2 + progesterone + reduced [NADPH--hemoprotein reductase] = 21-hydroxyprogesterone + H+ + H2O + oxidized [NADPH--hemoprotein reductase]." [PMID:25855791, RHEA:50304]
xref: RHEA:50304
is_a: GO:0004509 ! steroid 21-monooxygenase activity
@@ -410513,6 +410444,8 @@ name: protein serine kinase activity
namespace: molecular_function
def: "Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate." [RHEA:17989]
comment: Note that this term is to annotate proteins the specifically phosphorylate a serine residue on a protein. An example is human PIKFYVE (UniProt:Q9Y2I7). For dual specificity protein kinases, use 'protein serine/threonine kinase activity' ; GO:0004712.
+synonym: "protein-serine kinase activity" EXACT []
+xref: Reactome:R-HSA-9729330 "SRPK1/2 phosphorylates nucleoprotein"
xref: RHEA:17989
is_a: GO:0004672 ! protein kinase activity
@@ -410622,7 +410555,7 @@ is_a: GO:0052601 ! (S)-limonene 1,2-monooxygenase activity
id: GO:0106325
name: acetylgalactosaminyl-O-glycosyl-seryl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + H(+) + UDP." [RHEA:56188]
+def: "Catalysis of the reaction: 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + H+ + UDP." [RHEA:56188]
xref: EC:2.4.1.148
xref: RHEA:56188
is_a: GO:0047225 ! acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity
@@ -410631,7 +410564,7 @@ is_a: GO:0047225 ! acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acety
id: GO:0106326
name: acetylgalactosaminyl-O-glycosyl-threonyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + H(+) + UDP." [RHEA:56192]
+def: "Catalysis of the reaction: 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + H+ + UDP." [RHEA:56192]
xref: EC:2.4.1.148
xref: RHEA:56192
is_a: GO:0047225 ! acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity
@@ -410640,7 +410573,7 @@ is_a: GO:0047225 ! acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acety
id: GO:0106327
name: acetylgalactosaminyl-O-glycosyl-threonyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + H(+) + UDP." [RHEA:46880]
+def: "Catalysis of the reaction: 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + H+ + UDP." [RHEA:46880]
xref: EC:2.4.1.147
xref: RHEA:46880
is_a: GO:0047224 ! acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity
@@ -410649,7 +410582,7 @@ is_a: GO:0047224 ! acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,3-N-acety
id: GO:0106328
name: acetylgalactosaminyl-O-glycosyl-seryl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + H(+) + UDP." [RHEA:46884]
+def: "Catalysis of the reaction: 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + H+ + UDP." [RHEA:46884]
xref: EC:2.4.1.147
xref: RHEA:46884
is_a: GO:0047224 ! acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity
@@ -410666,7 +410599,7 @@ is_a: GO:0001716 ! L-amino-acid oxidase activity
id: GO:0106330
name: sialate 9-O-acetylesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + N-acetyl-9-O-acetylneuraminate = acetate + H(+) + N-acetylneuraminate." [RHEA:22600]
+def: "Catalysis of the reaction: H2O + N-acetyl-9-O-acetylneuraminate = acetate + H+ + N-acetylneuraminate." [RHEA:22600]
xref: EC:3.1.1.53
xref: RHEA:22600
is_a: GO:0001681 ! sialate O-acetylesterase activity
@@ -410675,7 +410608,7 @@ is_a: GO:0001681 ! sialate O-acetylesterase activity
id: GO:0106331
name: sialate 4-O-acetylesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + N-acetyl-4-O-acetylneuraminate = acetate + H(+) + N-acetylneuraminate." [RHEA:25564]
+def: "Catalysis of the reaction: H2O + N-acetyl-4-O-acetylneuraminate = acetate + H+ + N-acetylneuraminate." [RHEA:25564]
xref: EC:3.1.1.53
xref: RHEA:25564
is_a: GO:0001681 ! sialate O-acetylesterase activity
@@ -410685,7 +410618,7 @@ id: GO:0106332
name: ds/ssDNA junction-specific dsDNA endonuclease activity
namespace: molecular_function
def: "Catalysis of the endonucleolytic cleavage of double-stranded DNA near a double-strand/single-strand DNA junction." [PMID:14528010]
-is_a: GO:1990238 ! double-stranded DNA endodeoxyribonuclease activity
+is_a: GO:1990238 ! double-stranded DNA endonuclease activity
[Term]
id: GO:0106333
@@ -410699,9 +410632,10 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:0106334
name: 3'-deoxyribose phosphate lyase activity
namespace: molecular_function
-def: "Catalysis of the conversion of a 3'-deoxyribose phosphate in DNA to a 3'-phosphate." [GOC:mah, PMID:21276450, PMID:22084197, PMID:22375014]
+def: "Catalysis of the conversion of a 3'-deoxyribose phosphate in DNA to a 3'-phosphate." [GOC:mah, PMID:21276450, PMID:22084197, PMID:22375014, RHEA:65764]
synonym: "3'-dRP lyase" RELATED []
synonym: "3'-dRP lyase activity" RELATED []
+xref: RHEA:65764
is_a: GO:0016829 ! lyase activity
is_a: GO:0140097 ! catalytic activity, acting on DNA
@@ -410712,8 +410646,7 @@ namespace: molecular_function
def: "Catalysis of the reaction: carboxymethyluridine34 in tRNA + S-adenosyl-L-methionine = 5-(2-methoxy-2-oxoethyl)uridine34 in tRNA + S-adenosyl-L-homocysteine." [PMID:20123966, RHEA:43208]
xref: EC:2.1.1.229
xref: RHEA:43208
-is_a: GO:0008168 ! methyltransferase activity
-is_a: GO:0140101 ! catalytic activity, acting on a tRNA
+is_a: GO:0008175 ! tRNA methyltransferase activity
[Term]
id: GO:0106336
@@ -410729,6 +410662,8 @@ id: GO:0106339
name: tRNA (cytidine 32-2'-O)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + cytosine32 in tRNA= S-adenosyl-L-homocysteine + 2'-O-methylcytidine32 in tRNA." [PMID:25404562]
+xref: EC:2.1.1.205
+xref: RHEA:42396
is_a: GO:0052666 ! tRNA (cytosine-2'-O-)-methyltransferase activity
[Term]
@@ -410766,7 +410701,7 @@ is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
id: GO:0106344
name: 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity from histidine and PLP
namespace: molecular_function
-def: "Catalysis of the reaction: 2 Fe(3+) + 4 H2O + L-histidyl-[4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase] + N(6)-(pyridoxal phosphate)-L-lysyl-[4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase] = (2S)-2-amino-5-hydroxy-4-oxopentanoyl-[4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase] + 3-oxopropanoate + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 2 Fe(2+) + 2 H(+) + L-lysyl-[4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase]." [PMID:22568620, RHEA:65756]
+def: "Catalysis of the reaction: 2 Fe(3+) + 4 H2O + L-histidyl-[4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase] + N(6)-(pyridoxal phosphate)-L-lysyl-[4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase] = (2S)-2-amino-5-hydroxy-4-oxopentanoyl-[4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase] + 3-oxopropanoate + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 2 Fe(2+) + 2 H+ + L-lysyl-[4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase]." [PMID:22568620, RHEA:65756]
xref: RHEA:65756
is_a: GO:0016740 ! transferase activity
@@ -410816,22 +410751,6 @@ xref: EC:2.5.1.90
xref: RHEA:27798
is_a: GO:0004659 ! prenyltransferase activity
-[Term]
-id: GO:0106351
-name: aspartate dehydrogenase NAD activity
-namespace: molecular_function
-def: "Catalysis of the reaction: L-aspartate + H2O + NAD+ = oxaloacetate + NH3 + NADH+ H+." [RHEA:11788]
-xref: RHEA:11788
-is_a: GO:0033735 ! aspartate dehydrogenase activity
-
-[Term]
-id: GO:0106352
-name: aspartate dehydrogenase NADP activity
-namespace: molecular_function
-def: "Catalysis of the reaction: L-aspartate + H2O + NADP+ = oxaloacetate + NH3 + NADPH+ H+." [RHEA:11784]
-xref: RHEA:11784
-is_a: GO:0033735 ! aspartate dehydrogenase activity
-
[Term]
id: GO:0106354
name: tRNA surveillance
@@ -410876,7 +410795,8 @@ is_a: GO:0050492 ! glycerol-1-phosphate dehydrogenase [NAD(P)+] activity
id: GO:0106359
name: 2-hydroxyacyl-CoA lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: A 2-hydroxyacyl-CoA = formyl-CoA + a propanol." [PMID:21708296, PMID:28289220]
+def: "Catalysis of the reaction: a 2-hydroxyacyl-CoA = a fatty aldehyde + formyl-CoA. The reaction acts on 3-methyl-branched fatty acids and 2-hydroxy long-chain fatty acids." [PMID:21708296, PMID:28289220]
+xref: EC:4.1.2.63
is_a: GO:0016832 ! aldehyde-lyase activity
[Term]
@@ -410891,7 +410811,7 @@ is_a: GO:0106359 ! 2-hydroxyacyl-CoA lyase activity
id: GO:0106361
name: protein-arginine rhamnosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dTDP-beta-L-rhamnose + L-arginyl-[protein] = dTDP + H(+) + N(omega)-(L-rhamnosyl)-L-arginyl-[protein]." [GOC:sp, PMID:25686373, PMID:26060278, RHEA:66692]
+def: "Catalysis of the reaction: dTDP-beta-L-rhamnose + L-arginyl-[protein] = dTDP + H+ + N(omega)-(L-rhamnosyl)-L-arginyl-[protein]." [GOC:sp, PMID:25686373, PMID:26060278, RHEA:66692]
xref: RHEA:66692
is_a: GO:0046527 ! glucosyltransferase activity
@@ -410899,7 +410819,7 @@ is_a: GO:0046527 ! glucosyltransferase activity
id: GO:0106362
name: protein-arginine N-acetylglucosaminyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = H(+) + N(omega)-(N-acetyl-beta-D-glucosaminyl)-L-arginyl-[protein] + UDP." [GOC:sp, PMID:23955153, PMID:30619781, RHEA:66632]
+def: "Catalysis of the reaction: L-arginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = H+ + N(omega)-(N-acetyl-beta-D-glucosaminyl)-L-arginyl-[protein] + UDP." [GOC:sp, PMID:23955153, PMID:30619781, RHEA:66632]
xref: RHEA:66632
is_a: GO:0016262 ! protein N-acetylglucosaminyltransferase activity
@@ -410907,7 +410827,9 @@ is_a: GO:0016262 ! protein N-acetylglucosaminyltransferase activity
id: GO:0106363
name: protein-cysteine methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-cysteinyl-[protein] + S-adenosyl-L-methionine = H(+) + S-adenosyl-L-homocysteine + S-methyl-L-cysteinyl-[protein]." [GOC:sp, PMID:21481189, PMID:22158122, PMID:24235145, PMID:25412445, RHEA:66544]
+def: "Catalysis of the reaction: L-cysteinyl-[protein] + S-adenosyl-L-methionine = H+ + S-adenosyl-L-homocysteine + S-methyl-L-cysteinyl-[protein]." [GOC:sp, PMID:21481189, PMID:22158122, PMID:24235145, PMID:25412445, RHEA:66544]
+synonym: "protein cysteine methylase activity" EXACT []
+synonym: "protein cysteine methyltransferase activity" EXACT []
xref: RHEA:66544
is_a: GO:0008172 ! S-methyltransferase activity
is_a: GO:0008276 ! protein methyltransferase activity
@@ -410997,7 +410919,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0106373
name: 3-deoxyglucosone dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-deoxyglucosone + H2O + NAD(+) = 2-dehydro-3-deoxy-D-gluconate + 2 H(+) + NADH." [PMID:17175089, RHEA:67244]
+def: "Catalysis of the reaction: 3-deoxyglucosone + H2O + NAD+ = 2-dehydro-3-deoxy-D-gluconate + 2 H+ + NADH." [PMID:17175089, RHEA:67244]
xref: RHEA:67244
is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
@@ -411005,7 +410927,7 @@ is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
id: GO:0106375
name: deoxynucleoside triphosphate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dNTP + H2O = 2'-deoxynucleoside + H+ + triphosphate." [RHEA:46148]
+def: "Catalysis of the reaction: dNTP + H2O = 2'-deoxynucleoside + H+ + triphosphate." [RHEA:46148]
xref: RHEA:46148
is_a: GO:0016793 ! triphosphoric monoester hydrolase activity
@@ -411021,24 +410943,27 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0106377
name: 2-hydroxy-ATP hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-hydroxy-ATP + H2O = 2-hydroxy-AMP + diphosphate." [PMID:11139615, RHEA:67392]
+def: "Catalysis of the reaction: 2-hydroxy-ATP + H2O = 2-hydroxy-AMP + H+ + diphosphate." [PMID:11139615, RHEA:67392]
+xref: Reactome:R-HSA-2395872 "NUDT1 hydrolyses 2-oxo-ATP to 2-oxo-AMP"
xref: RHEA:67392
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0106378
name: 2-hydroxy-dATP hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-hydroxy-dATP + H2O = 2-hydroxy-dAMP + diphosphate." [PMID:11139615, RHEA:31583]
+def: "Catalysis of the reaction: 2-hydroxy-dATP + H2O = 2-hydroxy-dAMP + H+ + diphosphate." [PMID:11139615, RHEA:31583]
+xref: Reactome:R-HSA-2395818 "NUDT1 hydrolyses 2-oxo-dATP to 2-oxo-dAMP"
xref: RHEA:31583
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0106379
name: 8-oxo-(d)RTP hydrolase activity
namespace: molecular_function
def: "Catalysis of the reaction: 8-oxo-(d)RTP + H20 = 8-oxo-(d)RMP + diphosphate + H+." [PMID:11139615]
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+xref: Reactome:R-HSA-9731228 "NUDT1 hydrolyses 8-oxo-dATP to 8-oxo-dAMP"
+is_a: GO:0047429 ! nucleoside triphosphate diphosphatase activity
[Term]
id: GO:0106380
@@ -411084,7 +411009,7 @@ is_a: GO:0106381 ! purine deoxyribonucleotide salvage
id: GO:0106386
name: (3R)-hydroxyacyl-CoA dehydrogenase (NAD) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3R-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH." [PMID:19571038, PMID:25203508]
+def: "Catalysis of the reaction: 3R-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH." [PMID:19571038, PMID:25203508]
xref: EC:1.1.1.n12
xref: RHEA:32711
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -411110,9 +411035,11 @@ is_a: GO:0140102 ! catalytic activity, acting on a rRNA
id: GO:0106389
name: ecdysteroid 22-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an ecdysteroid + ATP = an ecdysteroid 22-phosphate + ADP + H+." [PMID:16899460]
+def: "Catalysis of the reaction: an ecdysteroid + ATP = an ecdysteroid 22-phosphate + ADP + H+." [PMID:16899460, RHEA:67972]
+synonym: "EcKinase" RELATED []
xref: MetaCyc:RXN-14755
-is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
+xref: RHEA:67972
+is_a: GO:0016301 ! kinase activity
[Term]
id: GO:0106391
@@ -411192,7 +411119,7 @@ relationship: negatively_regulates GO:0007465 ! R7 cell fate commitment
id: GO:0106399
name: acyl-coenzyme A diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an acyl-CoA + H2O = adenosine 3',5'-bisphosphate + an acyl-4'-phosphopantetheine + 2 H(+)." [PMID:32915949, RHEA:50044]
+def: "Catalysis of the reaction: an acyl-CoA + H2O = adenosine 3',5'-bisphosphate + an acyl-4'-phosphopantetheine + 2 H+." [PMID:32915949, RHEA:50044]
xref: RHEA:50044
is_a: GO:0016462 ! pyrophosphatase activity
@@ -411210,7 +411137,7 @@ namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of a Lewis x epitope, a trisaccharide (beta-D-galactosyl-(1,4)-[alpha-L-fucosyl-(1,3)]-N-acetyl-beta-D-glucosamine) expressed on several glycolipids, glycoproteins, and proteoglycans of the nervous system. The related Lewis x epitope is formed by alpha(1,3) fucosylation of the N-acetylglucosaminyl residue of a type 2 histo-blood group antigen precursor disaccharide." [PMID:16973732, PMID:23000574]
synonym: "sialyl-Lewis X biosynthetic process" RELATED []
synonym: "sLeX biosynthetic process" RELATED []
-is_a: GO:0005975 ! carbohydrate metabolic process
+is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
[Term]
id: GO:0106405
@@ -411223,7 +411150,7 @@ is_a: GO:0016462 ! pyrophosphatase activity
id: GO:0106407
name: Glc2Man9GlcNAc2 oligosaccharide glucosidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: Glc(2)Man(9)GlcNAc(2)-[protein] + H(2)O = GlcMan(9)GlcNAc(2)-[protein] + beta-D-glucopyranose." [PMID:30389790]
+def: "Catalysis of the reaction: Glc(2)Man(9)GlcNAc(2)-[protein] + H2O = GlcMan(9)GlcNAc(2)-[protein] + beta-D-glucopyranose." [PMID:30389790]
comment: Trims Glc alpha 1,3 Glc bond in Glc2Man9GlcNAc2 oligosaccharide in inmature glycoproteins.
synonym: "Glucosidase II" BROAD []
is_a: GO:0004573 ! Glc3Man9GlcNAc2 oligosaccharide glucosidase activity
@@ -411254,7 +411181,7 @@ id: GO:0106410
name: box C/D RNA 5'-end processing
namespace: biological_process
def: "Any process involved in forming the mature 5' end of a box C/D RNA molecule." [PMID:34352089]
-is_a: GO:0034471 ! ncRNA 5'-end processing
+is_a: GO:0000966 ! RNA 5'-end processing
is_a: GO:0034963 ! box C/D RNA processing
[Term]
@@ -411281,6 +411208,222 @@ namespace: molecular_function
def: "Catalysis of the reaction: mRNA-uracil + acceptor = mRNA-dihydrouridine + reduced acceptor." [PMID:34798057]
is_a: GO:0106413 ! dihydrouridine synthase activity
+[Term]
+id: GO:0106415
+name: muramoyltetrapeptide carboxypeptidase activity
+namespace: molecular_function
+def: "GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine + H2O = GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelate + D-alanine." [PMID:10428950, PMID:15361936]
+xref: EC:3.4.17.13
+xref: RHEA:48688
+is_a: GO:0004180 ! carboxypeptidase activity
+
+[Term]
+id: GO:0106417
+name: dopaminechrome tautomerase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: dopaminechrome = 5,6-dihydroxyindole." [PMID:34388859, RHEA:70199]
+xref: RHEA:70199
+is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds
+
+[Term]
+id: GO:0106418
+name: UDP-N-acetylmuramate-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate ligase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: ATP + UDP-N-acetyl-alpha-D-muramate + L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate." [PMID:17384195, PMID:8808921, RHEA:29563]
+synonym: "murein peptide ligase" RELATED [EC:6.3.2.45]
+xref: EC:6.3.2.45
+xref: RHEA:29563
+is_a: GO:0016881 ! acid-amino acid ligase activity
+
+[Term]
+id: GO:0106419
+name: NAD-dependent protein lipoamidase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: (R)-N6-lipoyl-L-lysyl-[protein] + H2O + NAD+ = 2''-O-lipoyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide." [PMID:25525879, RHEA:63640]
+xref: RHEA:63640
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+
+[Term]
+id: GO:0106420
+name: NAD-dependent protein biotinidase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + N6-biotinyl-L-lysyl-[protein] + NAD+ = 2''-O-biotinyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide." [PMID:25525879, RHEA:70479]
+xref: RHEA:70479
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+
+[Term]
+id: GO:0106421
+name: L-glutamate:proton antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: L-glutamate(out) + H+(in) = L-glutamate(in) + H+(out)." [PMID:29273736]
+is_a: GO:0005313 ! L-glutamate transmembrane transporter activity
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0140848 ! amino acid:monoatomic cation antiporter activity
+
+[Term]
+id: GO:0106422
+name: carotenoid isomerooxygenase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: Zeaxanthin + O2 <=> (3R)-11-cis-3-hydroxyretinal + (3R)-all-trans-3-hydroxyretinal." [PMID:19020100, PMID:19889630, RHEA:33931]
+xref: EC:1.13.11.65
+xref: RHEA:33931
+is_a: GO:0010436 ! carotenoid dioxygenase activity
+
+[Term]
+id: GO:0106423
+name: tubulin-tyrosine carboxypeptidase
+namespace: molecular_function
+def: "Catalysis of the reaction: C-terminal L-alpha-aminoacyl-L-glutamyl-L-glutamyl-L-tyrosyl-[tubulin] + H2O = C-terminal L-alpha-aminoacyl-L-glutamyl-L-glutamyl-[tubulin] + L-tyrosine." [PMID:29146869, PMID:35482892, RHEA:57444]
+synonym: "tubulinyl-Tyr carboxypeptidase" EXACT [EC:3.4.17.17]
+xref: EC:3.4.17.17
+xref: RHEA:57444
+is_a: GO:0004181 ! metallocarboxypeptidase activity
+
+[Term]
+id: GO:0106425
+name: 3,4-dihydroxyphenylacetaldehyde synthase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-dopa + O2 + H2O + H+ <=> 3,4-dihydroxyphenylacetaldehyde + CO2 + NH(4)+ + H2O2." [PMID:21283636, RHEA:55524]
+synonym: "DHPAA synthase" EXACT []
+xref: EC:4.1.1.107
+xref: RHEA:55524
+is_a: GO:0016831 ! carboxy-lyase activity
+
+[Term]
+id: GO:0106426
+name: regulation of kainate selective glutamate receptor signaling pathway
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of tge kainate selective glutamate receptor signaling pathway." [PMID:12597860]
+is_a: GO:1900449 ! regulation of glutamate receptor signaling pathway
+relationship: regulates GO:0098991 ! kainate selective glutamate receptor signaling pathway
+
+[Term]
+id: GO:0106427
+name: negative regulation of kainate selective glutamate receptor signaling pathway
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of the kainate selective glutamate receptor signaling pathway." [PMID:12597860]
+is_a: GO:0048519 ! negative regulation of biological process
+is_a: GO:0106426 ! regulation of kainate selective glutamate receptor signaling pathway
+
+[Term]
+id: GO:0106428
+name: positive regulation of kainate selective glutamate receptor signaling pathway
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of the kainate selective glutamate receptor signaling pathway." [PMID:12597860]
+is_a: GO:0048518 ! positive regulation of biological process
+is_a: GO:0106426 ! regulation of kainate selective glutamate receptor signaling pathway
+
+[Term]
+id: GO:0106429
+name: 11-cis-retinol dehydrogenase
+namespace: molecular_function
+def: "Catalysis of the reaction:11-cis-retinol-[retinal-binding-protein] + NAD+ <=> 11-cis-retinal-[retinol-binding-protein] + NADH." [RHEA:55668]
+xref: EC:1.1.1.315
+xref: RHEA:55668
+is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+
+[Term]
+id: GO:0106430
+name: dihydroorotate dehydrogenase (quinone) activity
+namespace: molecular_function
+def: "(S)-dihydroorotate + a quinone = orotate + a quinol." [RHEA:30187]
+xref: EC:1.3.5.2
+xref: RHEA:30187
+is_a: GO:0004152 ! dihydroorotate dehydrogenase activity
+is_a: GO:0016635 ! oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor
+
+[Term]
+id: GO:0106431
+name: N6-methyl-(d)ATP hydrolase activity
+namespace: molecular_function
+def: "Catalysis of the reaction N6-methyl-(d)ATP + H2O = N6-methyl-(d)AMP + diphosphate + H+." [PMID:32144205]
+is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+
+[Term]
+id: GO:0106432
+name: queuosine nucleosidase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: a N-D-queuosine + H2O = queuine + D-ribose." [PMID:35940128]
+synonym: "queuosine nucleoside glycosylase" EXACT []
+synonym: "tRNA queuosine nucleoside glycosylase" EXACT []
+is_a: GO:0008477 ! purine nucleosidase activity
+
+[Term]
+id: GO:0106433
+name: O6-methyl-dGTP hydrolase activity
+namespace: molecular_function
+def: "Catalysis of the reaction O6-methyl-dGTP + H2O = O6-methyl-dGMP + diphosphate + H+." [PMID:30304478, RHEA:67600]
+xref: RHEA:67600
+is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+
+[Term]
+id: GO:0106434
+name: retinal isomerization
+namespace: biological_process
+def: "The reactions involved in isomerization of all trans to all cis retnal." [PMID:21447403]
+comment: This process term replaces 'retinal isomerase' because the Enzyme Commission has determined that the reaction is known to be catalyzed by a pathway involving multiple steps, catalyzed by EC:1.1.1.300, EC:2.3.1.135, EC:3.1.1.64, and EC:1.1.1.315.
+is_a: GO:0042574 ! retinal metabolic process
+
+[Term]
+id: GO:0106435
+name: carboxylesterase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: a carboxylic ester + H2O = a carboxylate + an alcohol + H(+)." [RHEA:21164]
+comment: Note: This covers a broad range of specificity; also hydrolyzes vitamin A esters.
+synonym: "ali-esterase activity" RELATED [EC:3.1.1.1]
+synonym: "alpha-carboxylesterase activity" NARROW []
+synonym: "B-esterase activity" NARROW [EC:3.1.1.1]
+synonym: "cocaine esterase" NARROW [EC:3.1.1.1]
+synonym: "nonspecific carboxylesterase activity" RELATED []
+synonym: "procaine esterase" NARROW [] {comment="EC:3.1.1.1"}
+synonym: "serine esterase activity" NARROW []
+synonym: "triacetin esterase" NARROW []
+synonym: "vitamin A esterase" NARROW []
+xref: EC:3.1.1.1
+xref: MetaCyc:CARBOXYLESTERASE-RXN
+xref: Reactome:R-HSA-9619024 "CES1trimer hydrolyses ACEI pro-drugs to ACEIs"
+xref: Reactome:R-HSA-9727567 "CES1 hydrolyses sacubitril to sacubitrilat"
+xref: Reactome:R-HSA-9749647 "CES2 hydrolyzes ASA-"
+xref: RHEA:21164
+is_a: GO:0052689 ! carboxylic ester hydrolase activity
+
+[Term]
+id: GO:0106436
+name: glutathione-dependent sulfide quinone oxidoreductase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: a quinone + glutathione + H(+) + hydrogen sulfide <=> a quinol + S-sulfanylglutathione." [RHEA:55156]
+synonym: "eukaryotic sulfide quinone oxidoreductase" RELATED []
+xref: EC:1.8.5.8
+xref: RHEA:55156
+is_a: GO:0016672 ! oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor
+
+[Term]
+id: GO:0106437
+name: protein-glutamic acid ligase activity, initiating
+namespace: molecular_function
+def: "Catalytic reaction: ATP + L-glutamate + L-glutamyl-[protein] = ADP + H(+) + L-gamma-glutamyl-L-glutamyl-[protein] + phosphate." [PMID:32747782, Rhea:60144]
+xref: Rhea:60144
+is_a: GO:0070739 ! protein-glutamic acid ligase activity
+
+[Term]
+id: GO:0106438
+name: protein-glutamic acid ligase activity, elongating
+namespace: molecular_function
+def: "Catalytic reaction :(L-glutamyl)n-L-gamma-glutamyl-L-glutamyl-[protein] + ATP + L-glutamate = (L-glutamyl)n+1-L-gamma-glutamyl-L-glutamyl-[protein] + ADP + H(+) + phosphate." [PMID:32747782, Rhea:60148]
+xref: Rhea:60148
+is_a: GO:0070739 ! protein-glutamic acid ligase activity
+
+[Term]
+id: GO:0106439
+name: L-lysine:L-arginine antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: L-lysine(out) + L-arginine(in) = L-lysine(in) + L-arginine(out)." [PMID:10903140, RHEA:70827]
+comment: L-arginine:L-lysine antiporter activity
+xref: RHEA:70827
+is_a: GO:0015189 ! L-lysine transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0061459 ! L-arginine transmembrane transporter activity
+
[Term]
id: GO:0110001
name: toxin-antitoxin complex
@@ -411389,7 +411532,6 @@ id: GO:0110015
name: positive regulation of elastin catabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of elastin catabolism, the chemical reactions and pathways resulting in the breakdown of elastin." [GOC:BHF, GOC:BHF_miRNA, GOC:rph]
-is_a: GO:0031331 ! positive regulation of cellular catabolic process
is_a: GO:0045732 ! positive regulation of protein catabolic process
is_a: GO:0060310 ! regulation of elastin catabolic process
is_a: GO:1903020 ! positive regulation of glycoprotein metabolic process
@@ -411439,7 +411581,7 @@ relationship: regulates GO:0031032 ! actomyosin structure organization
id: GO:0110021
name: cardiac muscle myoblast proliferation
namespace: biological_process
-def: "The multiplication or reproduction of cardiac muscle myoblasts, resulting in the expansion of a cardiac muscle myoblast cell population. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:26512644]
+def: "The multiplication or reproduction of cardiac muscle myoblasts, resulting in the expansion of a cardiac muscle myoblast cell population. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:26512644]
is_a: GO:0051450 ! myoblast proliferation
[Term]
@@ -411489,9 +411631,8 @@ id: GO:0110027
name: negative regulation of DNA strand resection involved in replication fork processing
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA strand resection involved in replication fork processing." [GOC:mah, PMID:28475874]
-is_a: GO:0051053 ! negative regulation of DNA metabolic process
is_a: GO:0110026 ! regulation of DNA strand resection involved in replication fork processing
-is_a: GO:2000104 ! negative regulation of DNA-dependent DNA replication
+is_a: GO:2000104 ! negative regulation of DNA-templated DNA replication
relationship: negatively_regulates GO:0110025 ! DNA strand resection involved in replication fork processing
[Term]
@@ -411677,8 +411818,10 @@ relationship: part_of GO:0051728 ! cell cycle switching, mitotic to meiotic cell
id: GO:0110050
name: deaminated glutathione amidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-(4-oxoglutarate)-L-cysteinylglycine + H(2)O = 2-oxoglutarate + L-cysteinylglycine." [GOC:ka, PMID:28373563]
+def: "Catalysis of the reaction: N-(4-oxoglutarate)-L-cysteinylglycine + H2O = 2-oxoglutarate + L-cysteinylglycine." [GOC:ka, PMID:28373563, RHEA:54532]
comment: N-(4-oxoglutarate)-L-cysteinylglycine = deaminated glutathione
+xref: EC:3.5.1.128
+xref: RHEA:54532
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
[Term]
@@ -411794,7 +411937,7 @@ name: regulation of interphase mitotic telomere clustering
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of mitotic telomere clustering during interphase." [GOC:vw, PMID:25778919]
synonym: "regulation of mitotic telomere clustering during interphase" EXACT []
-is_a: GO:0060341 ! regulation of cellular localization
+is_a: GO:0032879 ! regulation of localization
relationship: regulates GO:0120110 ! interphase mitotic telomere clustering
[Term]
@@ -411804,7 +411947,7 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of mitotic telomere clustering during interphase." [GOC:vw, PMID:25778919]
synonym: "negative regulation of mitotic telomere clustering during interphase" EXACT []
synonym: "telomere dispersion during interphase" EXACT [GOC:vw, PMID:25778919]
-is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:0110065 ! regulation of interphase mitotic telomere clustering
relationship: negatively_regulates GO:0120110 ! interphase mitotic telomere clustering
@@ -411915,7 +412058,6 @@ name: regulation of placenta blood vessel development
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of placenta blood vessel development." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:27748453]
is_a: GO:1901342 ! regulation of vasculature development
-is_a: GO:2000241 ! regulation of reproductive process
relationship: regulates GO:0060674 ! placenta blood vessel development
[Term]
@@ -411925,7 +412067,6 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of placenta blood vessel development." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:27748453]
is_a: GO:0051094 ! positive regulation of developmental process
is_a: GO:0110079 ! regulation of placenta blood vessel development
-is_a: GO:2000243 ! positive regulation of reproductive process
relationship: positively_regulates GO:0060674 ! placenta blood vessel development
[Term]
@@ -411935,7 +412076,6 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of placenta blood vessel development." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:27748453]
is_a: GO:0051093 ! negative regulation of developmental process
is_a: GO:0110079 ! regulation of placenta blood vessel development
-is_a: GO:2000242 ! negative regulation of reproductive process
relationship: negatively_regulates GO:0060674 ! placenta blood vessel development
[Term]
@@ -412068,7 +412208,6 @@ id: GO:0110097
name: regulation of calcium import into the mitochondrion
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of calcium import into the mitochondrion." [GOC:sl, PMID:24085037]
-is_a: GO:0090279 ! regulation of calcium ion import
is_a: GO:1903169 ! regulation of calcium ion transmembrane transport
relationship: regulates GO:0036444 ! calcium import into the mitochondrion
@@ -412077,7 +412216,6 @@ id: GO:0110098
name: positive regulation of calcium import into the mitochondrion
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of calcium import into the mitochondrion." [GOC:sl, PMID:24085037]
-is_a: GO:0090280 ! positive regulation of calcium ion import
is_a: GO:0110097 ! regulation of calcium import into the mitochondrion
is_a: GO:1904427 ! positive regulation of calcium ion transmembrane transport
relationship: positively_regulates GO:0036444 ! calcium import into the mitochondrion
@@ -412087,7 +412225,6 @@ id: GO:0110099
name: negative regulation of calcium import into the mitochondrion
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion import into the mitochondrion." [GOC:sl, PMID:24085037]
-is_a: GO:0090281 ! negative regulation of calcium ion import
is_a: GO:0110097 ! regulation of calcium import into the mitochondrion
is_a: GO:1903170 ! negative regulation of calcium ion transmembrane transport
relationship: negatively_regulates GO:0036444 ! calcium import into the mitochondrion
@@ -412334,8 +412471,7 @@ id: GO:0110129
name: SHREC2 complex
namespace: cellular_component
def: "A histone deacetylase complex formed by the association of an HP1 protein with a SHREC complex. The SHREC2 complex is required for deacetylation of H3K14, and mediates transcriptional gene silencing by limiting RNA polymerase II access to heterochromatin. In fission yeast, the complex contains the SHREC subunits Clr1, Clr2, Clr3, and Mit1, and the HP1 protein Chp2." [GOC:mah, PMID:19111658]
-is_a: GO:0000118 ! histone deacetylase complex
-is_a: GO:0005667 ! transcription regulator complex
+is_a: GO:0016581 ! NuRD complex
[Term]
id: GO:0110130
@@ -412392,7 +412528,7 @@ name: protein-RNA complex remodeling
namespace: biological_process
def: "The acquisition, loss, or modification of macromolecules within a protein-RNA complex, resulting in the alteration of an existing complex." [GOC:rn, PMID:19737519, PMID:20542003, PMID:24240281]
is_a: GO:0034367 ! protein-containing complex remodeling
-is_a: GO:0071826 ! ribonucleoprotein complex subunit organization
+is_a: GO:0071826 ! protein-RNA complex organization
[Term]
id: GO:0110137
@@ -412435,8 +412571,6 @@ name: L-glutamate import into mitochondrion
namespace: biological_process
def: "The process in which L-glutamate is transported from the cytosol into the mitochondrial matrix." [GOC:vw, PMID:30297026]
is_a: GO:0015813 ! L-glutamate transmembrane transport
-is_a: GO:0051938 ! L-glutamate import
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0110142
@@ -412487,59 +412621,58 @@ is_a: GO:0051604 ! protein maturation
[Term]
id: GO:0110148
-name: biomineralization
+name: obsolete biomineralization
namespace: biological_process
-def: "The process where mineral crystals are formed and deposited in an organized fashion in a matrix (either cellular or extracellular) by living organisms. This gives rise to inorganic compound-based structures such as skeleton, teeth, ivory, shells, cuticle, and corals as well as bacterial biomineralization products." [GOC:aa, PMID:24395694, PMID:28229486]
+def: "OBSOLETE. The process where mineral crystals are formed and deposited in an organized fashion in a matrix (either cellular or extracellular) by living organisms. This gives rise to inorganic compound-based structures such as skeleton, teeth, ivory, shells, cuticle, and corals as well as bacterial biomineralization products." [GOC:aa, PMID:24395694, PMID:28229486]
+comment: This term was obsoleted because it grouped multicellular organism processes and cellular processes.
synonym: "biomineral formation" NARROW []
synonym: "biomineralisation" EXACT []
synonym: "mineralisation" EXACT []
synonym: "mineralization" EXACT []
xref: Wikipedia:Biomineralization
-is_a: GO:0008150 ! biological_process
+is_obsolete: true
[Term]
id: GO:0110149
-name: regulation of biomineralization
+name: obsolete regulation of biomineralization
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of biomineralization, the formation and deposition of mineral crystals by living organisms." [PMID:22992051]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of biomineralization, the formation and deposition of mineral crystals by living organisms." [PMID:22992051]
+comment: This term was obsoleted because it grouped multicellular organism processes and cellular processes.
synonym: "regulation of biomineral formation" NARROW []
synonym: "regulation of biomineralisation" EXACT []
synonym: "regulation of mineralisation" EXACT []
synonym: "regulation of mineralization" EXACT []
-is_a: GO:0050789 ! regulation of biological process
-relationship: regulates GO:0110148 ! biomineralization
+is_obsolete: true
[Term]
id: GO:0110150
-name: negative regulation of biomineralization
+name: obsolete negative regulation of biomineralization
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of biomineralization, the formation and deposition of mineral crystals by living organisms." [PMID:22992051]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of biomineralization, the formation and deposition of mineral crystals by living organisms." [PMID:22992051]
+comment: This term was obsoleted because it grouped multicellular organism processes and cellular processes.
synonym: "negative regulation of biomineral formation" NARROW []
synonym: "negative regulation of biomineralisation" EXACT []
synonym: "negative regulation of mineralisation" EXACT []
synonym: "negative regulation of mineralization" EXACT []
-is_a: GO:0048519 ! negative regulation of biological process
-is_a: GO:0110149 ! regulation of biomineralization
-relationship: negatively_regulates GO:0110148 ! biomineralization
+is_obsolete: true
[Term]
id: GO:0110151
-name: positive regulation of biomineralization
+name: obsolete positive regulation of biomineralization
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of biomineralization, the formation and deposition of mineral crystals by living organisms." [PMID:22992051]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of biomineralization, the formation and deposition of mineral crystals by living organisms." [PMID:22992051]
+comment: This term was obsoleted because it grouped multicellular organism processes and cellular processes.
synonym: "positive regulation of biomineral formation" NARROW []
synonym: "positive regulation of biomineralisation" EXACT []
synonym: "positive regulation of mineralisation" EXACT []
synonym: "positive regulation of mineralization" EXACT []
-is_a: GO:0048518 ! positive regulation of biological process
-is_a: GO:0110149 ! regulation of biomineralization
-relationship: positively_regulates GO:0110148 ! biomineralization
+is_obsolete: true
[Term]
id: GO:0110152
name: RNA NAD-cap (NAD-forming) hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 5'-end NAD(+)-phospho-ribonucleoside in mRNA + H2O = a 5'-end phospho-ribonucleoside in mRNA + H(+) + NAD(+)." [GOC:sp, PMID:28283058, RHEA:60880]
+def: "Catalysis of the reaction: a 5'-end NAD+-phospho-ribonucleoside in mRNA + H2O = a 5'-end phospho-ribonucleoside in mRNA + H+ + NAD+." [GOC:sp, PMID:28283058, RHEA:60880]
comment: This reaction specifically hydrolyzes the nicotinamide adenine dinucleotide (NAD) cap from a subset of RNAs by removing the entire NAD moiety from the 5'-end of an NAD-capped RNA.
xref: RHEA:60880
is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
@@ -412549,10 +412682,10 @@ is_a: GO:0140098 ! catalytic activity, acting on RNA
id: GO:0110153
name: RNA NAD-cap (NMN-forming) hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 5'-end NAD(+)-phospho-ribonucleoside in mRNA + H2O = a 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-nicotinamide D-ribonucleotide + 2 H(+)." [GOC:sp, PMID:25533955, PMID:31101919, RHEA:60876]
+def: "Catalysis of the reaction: a 5'-end NAD+-phospho-ribonucleoside in mRNA + H2O = a 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-nicotinamide D-ribonucleotide + 2 H+." [GOC:sp, PMID:25533955, PMID:31101919, RHEA:60876]
comment: This reaction specifically removes the nicotinamide adenine dinucleotide (NAD) cap from a subset of mRNAs by hydrolyzing the diphosphate linkage to produce nicotinamide mononucleotide (NMN) and 5' monophosphate mRNA.
xref: RHEA:60876
-is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+is_a: GO:0016462 ! pyrophosphatase activity
is_a: GO:0140098 ! catalytic activity, acting on RNA
[Term]
@@ -412626,7 +412759,7 @@ relationship: positively_regulates GO:0061804 ! mitotic spindle formation (spind
id: GO:0110162
name: regulation of mitotic spindle elongation (spindle phase three)
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the cell cycle process in which the distance is lengthened between poles of the mitotic spindle during mitotic prophase (spindle phase three)." [GOC:vw, PMID:27697865]
+def: "Any process that modulates the frequency, rate or extent of the cell cycle process in which the distance is lengthened between poles of the mitotic spindle during mitotic anaphase B (spindle phase three)." [GOC:vw, PMID:27697865]
is_a: GO:0032888 ! regulation of mitotic spindle elongation
is_a: GO:0060236 ! regulation of mitotic spindle organization
relationship: regulates GO:0061805 ! mitotic spindle elongation (spindle phase three)
@@ -412635,7 +412768,7 @@ relationship: regulates GO:0061805 ! mitotic spindle elongation (spindle phase t
id: GO:0110163
name: negative regulation of mitotic spindle elongation (spindle phase three)
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of the cell cycle process in which the distance is lengthened between poles of the mitotic spindle during mitotic prophase (spindle phase three)." [GOC:vw, PMID:27697865]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of the cell cycle process in which the distance is lengthened between poles of the mitotic spindle during mitotic anaphase B (spindle phase three)." [GOC:vw, PMID:27697865]
is_a: GO:0051494 ! negative regulation of cytoskeleton organization
is_a: GO:0110162 ! regulation of mitotic spindle elongation (spindle phase three)
is_a: GO:1902845 ! negative regulation of mitotic spindle elongation
@@ -412645,7 +412778,7 @@ relationship: negatively_regulates GO:0061805 ! mitotic spindle elongation (spin
id: GO:0110164
name: positive regulation of mitotic spindle elongation (spindle phase three)
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the cell cycle process in which the distance is lengthened between poles of the mitotic spindle during mitotic prophase (spindle phase three)." [GOC:vw, PMID:27697865]
+def: "Any process that activates or increases the frequency, rate or extent of the cell cycle process in which the distance is lengthened between poles of the mitotic spindle during mitotic anaphase B (spindle phase three)." [GOC:vw, PMID:27697865]
is_a: GO:0110028 ! positive regulation of mitotic spindle organization
is_a: GO:0110162 ! regulation of mitotic spindle elongation (spindle phase three)
is_a: GO:1902846 ! positive regulation of mitotic spindle elongation
@@ -412675,7 +412808,8 @@ namespace: cellular_component
def: "A scallop-shaped plaque, also referred to as an asymmetric unit membrane (AUM), found in the apical plasma membrane of urothelial superficial (umbrella) cells which form a a barrier to the passage of water and soluble toxic compounds found in urine. The plaques are thickened regions of membrane composed of uroplakin transmembrane proteins which form a crystalline array." [GOC:krc, PMID:21468280, PMID:21887288]
synonym: "asymmetric unit membrane" EXACT []
synonym: "AUM" RELATED []
-is_a: GO:0005887 ! integral component of plasma membrane
+is_a: GO:0005886 ! plasma membrane
+is_a: GO:0098590 ! plasma membrane region
relationship: part_of GO:0016324 ! apical plasma membrane
[Term]
@@ -413363,12 +413497,13 @@ is_a: GO:0046847 ! filopodium assembly
[Term]
id: GO:0120085
-name: transposon integration involved in RNA-mediated transposition
+name: obsolete transposon integration involved in RNA-mediated transposition
namespace: biological_process
-def: "Any transposon integration that contributes to a process of RNA-mediated transposition." [GOC:mah, PMID:26358720]
+def: "OBSOLETE. Any transposon integration that contributes to a process of RNA-mediated transposition." [GOC:mah, PMID:26358720]
+comment: This term was obsoleted because it represents a readout.
synonym: "retrotransposon integration" EXACT []
-is_a: GO:0070893 ! transposon integration
-relationship: part_of GO:0032197 ! transposition, RNA-mediated
+is_obsolete: true
+consider: GO:0032197
[Term]
id: GO:0120086
@@ -413427,8 +413562,8 @@ name: glycosylphosphatidylinositol-mannosyltransferase II complex
namespace: cellular_component
def: "A protein complex that is involved in the transfer of the second mannose to the glycosylphosphatidylinositol (GPI) during GPI precursor assembly. In yeast S. cerevisiae this complex consists of GPI18p and PGA1p." [GOC:bhm, PMID:17615295]
synonym: "GPI-MT-I complex" RELATED []
+is_a: GO:0031501 ! mannosyltransferase complex
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
-is_a: GO:1990234 ! transferase complex
[Term]
id: GO:0120098
@@ -413461,7 +413596,7 @@ namespace: cellular_component
def: "A hetero-hexameric complex of 2 membrane proteins, A and B, with stoichiometry A4B2. The A and B proteins form a channel through which flow the ions that power the bacterial-type flagellum. They form the stator, or nonrotating portion, of the flagellum motor with the B protein apparently attached to the peptidoglycan cell wall. Examples include the H+ driven MotA-MotB stator complex of Escherichia coli and Salmonella enterica, and the Na+ driven PomA-PomB stator complex of Vibrio and Shewanella species." [GOC:cilia, PMID:10572114, PMID:12624192, PMID:24697492, PMID:25251856]
synonym: "bacterial-type flagellum motor force generator complex" EXACT [PMID:24697492]
synonym: "bacterial-type flagellum torque generator complex" EXACT [DOI:10.1002/9780470015902.a0000744.pub4]
-is_a: GO:0005887 ! integral component of plasma membrane
+is_a: GO:0098797 ! plasma membrane protein complex
relationship: part_of GO:0120100 ! bacterial-type flagellum motor
[Term]
@@ -413481,7 +413616,7 @@ def: "A protein complex which assembles on the mother centriole during cilium fo
synonym: "subdistal appendage of basal body" EXACT [GOC:krc]
synonym: "subdistal appendage of centriole" EXACT [GOC:krc]
synonym: "subdistal appendage of mother centriole" EXACT [GOC:krc]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140535 ! intracellular protein-containing complex
relationship: part_of GO:0005929 ! cilium
[Term]
@@ -413523,11 +413658,11 @@ relationship: part_of GO:0120100 ! bacterial-type flagellum motor
id: GO:0120108
name: DNA-3'-diphospho-5'-guanosine diphosphatase
namespace: molecular_function
-def: "Catalysis of the reaction: (DNA)-3'-diphospho-5'-guanosine + H(2)O <=> (DNA)-3'-phosphate + GMP." [PMID:26007660, RHEA:52140]
+def: "Catalysis of the reaction: (DNA)-3'-diphospho-5'-guanosine + H2O = (DNA)-3'-phosphate + GMP." [PMID:26007660, RHEA:52140]
synonym: "DNA-3'pp5'G guanylate hydrolase" EXACT []
xref: EC:3.6.1.72
xref: RHEA:52140
-is_a: GO:0016788 ! hydrolase activity, acting on ester bonds
+is_a: GO:0016462 ! pyrophosphatase activity
[Term]
id: GO:0120109
@@ -413645,7 +413780,7 @@ name: prolactin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving prolactin, a protein hormone of the anterior pituitary gland that promotes lactation in response to the suckling stimulus of hungry young mammals." [PMID:11015620]
synonym: "prolactin metabolism" EXACT []
-is_a: GO:0034754 ! cellular hormone metabolic process
+is_a: GO:0042445 ! hormone metabolic process
[Term]
id: GO:0120123
@@ -413748,7 +413883,7 @@ synonym: "ATP:dUMP phosphotransferase activity" EXACT []
synonym: "deoxyuridine monophosphate kinase activity" EXACT []
synonym: "dUMP-kinase activity" EXACT []
xref: RHEA:30655
-is_a: GO:0009041 ! uridylate kinase activity
+is_a: GO:0009041 ! UMP/dUMP kinase activity
[Term]
id: GO:0120137
@@ -413832,9 +413967,9 @@ is_a: GO:0051861 ! glycolipid binding
[Term]
id: GO:0120147
-name: Formylglycine-generating oxidase activity
+name: formylglycine-generating oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: A [sulfatase]-L-cysteine + O(2) + 2 a thiol = a [sulfatase]-3-oxo-L-alanine + hydrogen sulfide + a disulfide + H(2)O." [EC:1.8.3.7, RHEA:51152]
+def: "Catalysis of the reaction: A [sulfatase]-L-cysteine + O2 + 2 a thiol = a [sulfatase]-3-oxo-L-alanine + hydrogen sulfide + a disulfide + H2O." [EC:1.8.3.7, RHEA:51152]
xref: EC:1.8.3.7
xref: MetaCyc:RXN-16226
xref: RHEA:51152
@@ -413991,7 +414126,6 @@ def: "Any process that modulates the frequency, rate or extent of cold-induced t
synonym: "regulation of CIT" RELATED []
is_a: GO:0019222 ! regulation of metabolic process
is_a: GO:0051239 ! regulation of multicellular organismal process
-is_a: GO:0065008 ! regulation of biological quality
relationship: regulates GO:0106106 ! cold-induced thermogenesis
[Term]
@@ -414089,20 +414223,19 @@ is_a: GO:0032991 ! protein-containing complex
[Term]
id: GO:0120172
-name: positive regulation of actin filament bundle convergence involved in mitotic contractile ring assembly
+name: obsolete positive regulation of actin filament bundle convergence involved in mitotic contractile ring assembly
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of actin filament bundle convergence involved in mitotic contractile ring assembly." [GOC:vw, PMID:24798735]
-is_a: GO:0120173 ! regulation of actin filament bundle convergence involved in mitotic contractile ring assembly
-is_a: GO:1903482 ! positive regulation of actin filament organization involved in mitotic actomyosin contractile ring assembly
-relationship: positively_regulates GO:1903478 ! actin filament bundle convergence involved in mitotic contractile ring assembly
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of actin filament bundle convergence involved in mitotic contractile ring assembly." [GOC:vw, PMID:24798735]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0120173
-name: regulation of actin filament bundle convergence involved in mitotic contractile ring assembly
+name: obsolete regulation of actin filament bundle convergence involved in mitotic contractile ring assembly
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of actin filament bundle convergence involved in mitotic contractile ring assembly." [GOC:vw, PMID:24798735]
-is_a: GO:1903480 ! regulation of actin filament organization involved in mitotic actomyosin contractile ring assembly
-relationship: regulates GO:1903478 ! actin filament bundle convergence involved in mitotic contractile ring assembly
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of actin filament bundle convergence involved in mitotic contractile ring assembly." [GOC:vw, PMID:24798735]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0120174
@@ -414147,7 +414280,6 @@ name: steroid hormone biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of any steroid hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." [GOC:krc, GOC:nln]
is_a: GO:0006694 ! steroid biosynthetic process
-is_a: GO:0042446 ! hormone biosynthetic process
[Term]
id: GO:0120179
@@ -414214,7 +414346,6 @@ name: negative regulation of protein localization to chromatin
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to chromatin." [PMID:20889714, PMID:29899453]
synonym: "negative regulation of protein localisation to chromatin" EXACT [GOC:krc]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905634 ! regulation of protein localization to chromatin
relationship: negatively_regulates GO:0071168 ! protein localization to chromatin
@@ -414225,7 +414356,6 @@ name: positive regulation of protein localization to chromatin
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of protein localization to chromatin." [PMID:20889714, PMID:29899453]
synonym: "positive regulation of protein localisation to chromatin" EXACT [GOC:krc]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905634 ! regulation of protein localization to chromatin
relationship: positively_regulates GO:0071168 ! protein localization to chromatin
@@ -414235,7 +414365,7 @@ id: GO:0120188
name: regulation of bile acid secretion
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:22767443]
-is_a: GO:0044070 ! regulation of anion transport
+is_a: GO:0032890 ! regulation of organic acid transport
is_a: GO:0051046 ! regulation of secretion
relationship: regulates GO:0032782 ! bile acid secretion
@@ -414244,9 +414374,9 @@ id: GO:0120189
name: positive regulation of bile acid secretion
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:22767443]
+is_a: GO:0032892 ! positive regulation of organic acid transport
is_a: GO:0051047 ! positive regulation of secretion
is_a: GO:0120188 ! regulation of bile acid secretion
-is_a: GO:1903793 ! positive regulation of anion transport
relationship: positively_regulates GO:0032782 ! bile acid secretion
[Term]
@@ -414254,9 +414384,9 @@ id: GO:0120190
name: negative regulation of bile acid secretion
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:22767443]
+is_a: GO:0032891 ! negative regulation of organic acid transport
is_a: GO:0051048 ! negative regulation of secretion
is_a: GO:0120188 ! regulation of bile acid secretion
-is_a: GO:1903792 ! negative regulation of anion transport
relationship: negatively_regulates GO:0032782 ! bile acid secretion
[Term]
@@ -414294,7 +414424,7 @@ synonym: "repression of termination of RNA polymerase II transcription" NARROW [
synonym: "repression of transcription termination from Pol II promoter" NARROW [GOC:krc]
synonym: "repression of transcription termination from RNA polymerase II promoter" NARROW [GOC:krc]
is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:0060567 ! negative regulation of DNA-templated transcription, termination
+is_a: GO:0060567 ! negative regulation of termination of DNA-templated transcription
is_a: GO:1904594 ! regulation of termination of RNA polymerase II transcription
relationship: negatively_regulates GO:0006369 ! termination of RNA polymerase II transcription
@@ -414471,6 +414601,7 @@ namespace: cellular_component
def: "A centrosome-based structure consisting of two cylindrical microtubule-based centrioles and associated components which anchors the flagellum to the sperm head." [GOC:krc, PMID:24415959, PMID:30032984]
synonym: "head-tail coupling apparatus" EXACT [PMID:24415959, PMID:30032984]
synonym: "HTCA" RELATED [PMID:24415959]
+synonym: "implantation fossa" RELATED []
is_a: GO:0110165 ! cellular anatomical entity
[Term]
@@ -414515,7 +414646,7 @@ synonym: "negative regulation of histidine biosynthesis" EXACT [GOC:krc]
synonym: "negative regulation of histidine formation" EXACT [GOC:krc]
synonym: "negative regulation of histidine synthesis" EXACT [GOC:krc]
is_a: GO:0120213 ! regulation of histidine biosynthetic process
-is_a: GO:2000283 ! negative regulation of cellular amino acid biosynthetic process
+is_a: GO:2000283 ! negative regulation of amino acid biosynthetic process
relationship: negatively_regulates GO:0000105 ! histidine biosynthetic process
[Term]
@@ -414548,7 +414679,7 @@ synonym: "upregulation of histidine biosynthetic process" EXACT [GOC:krc]
synonym: "upregulation of histidine formation" EXACT [GOC:krc]
synonym: "upregulation of histidine synthesis" EXACT [GOC:krc]
is_a: GO:0120213 ! regulation of histidine biosynthetic process
-is_a: GO:2000284 ! positive regulation of cellular amino acid biosynthetic process
+is_a: GO:2000284 ! positive regulation of amino acid biosynthetic process
relationship: positively_regulates GO:0000105 ! histidine biosynthetic process
[Term]
@@ -414644,7 +414775,6 @@ name: succinyl-CoA binding
namespace: molecular_function
def: "Binding to succinyl-CoA, an omega-carboxyacyl-CoA having succinoyl as the S-acyl component." [GOC:krc]
synonym: "succinyl-coenzyme A binding" EXACT []
-is_a: GO:0043168 ! anion binding
is_a: GO:0120227 ! acyl-CoA binding
[Term]
@@ -414656,6 +414786,7 @@ synonym: "acyl binding" BROAD []
synonym: "acyl-coenzyme A binding" EXACT []
is_a: GO:0032559 ! adenyl ribonucleotide binding
is_a: GO:0033218 ! amide binding
+is_a: GO:0043168 ! anion binding
is_a: GO:1901681 ! sulfur compound binding
[Term]
@@ -414731,28 +414862,30 @@ relationship: part_of GO:0032420 ! stereocilium
[Term]
id: GO:0120235
-name: regulation of posttranslational protein targeting to membrane, translocation
+name: regulation of post-translational protein targeting to membrane, translocation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of posttranslational protein translocation through the ER membrane." [GOC:krc, GOC:rn, PMID:32513868]
synonym: "regulation of N-terminal signal peptide-independent translocation into the ER" NARROW [GOC:rn]
synonym: "regulation of posttranslational endoplasmic reticulum membrane protein translocation" EXACT [GOC:rn]
+synonym: "regulation of posttranslational protein targeting to membrane, translocation" EXACT []
synonym: "regulation of SRP-independent endoplasmic reticulum protein-membrane targeting, translocation" NARROW [GOC:rn]
is_a: GO:0033157 ! regulation of intracellular protein transport
is_a: GO:0034762 ! regulation of transmembrane transport
-relationship: regulates GO:0031204 ! posttranslational protein targeting to membrane, translocation
+relationship: regulates GO:0031204 ! post-translational protein targeting to membrane, translocation
[Term]
id: GO:0120236
-name: negative regulation of posttranslational protein targeting to membrane, translocation
+name: negative regulation of post-translational protein targeting to membrane, translocation
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of posttranslational protein translocation through the ER membrane." [GOC:krc, GOC:rn, PMID:32513868]
synonym: "negative regulation of N-terminal signal peptide-independent translocation into the ER" NARROW [GOC:rn]
synonym: "negative regulation of posttranslational endoplasmic reticulum membrane protein translocation" EXACT [GOC:rn]
+synonym: "negative regulation of posttranslational protein targeting to membrane, translocation" EXACT []
synonym: "negative regulation of SRP-independent endoplasmic reticulum protein-membrane targeting, translocation" NARROW [GOC:rn]
is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:0090317 ! negative regulation of intracellular protein transport
-is_a: GO:0120235 ! regulation of posttranslational protein targeting to membrane, translocation
-relationship: negatively_regulates GO:0031204 ! posttranslational protein targeting to membrane, translocation
+is_a: GO:0120235 ! regulation of post-translational protein targeting to membrane, translocation
+relationship: negatively_regulates GO:0031204 ! post-translational protein targeting to membrane, translocation
[Term]
id: GO:0120237
@@ -414800,7 +414933,6 @@ synonym: "2-iminopropanoate deaminase" NARROW [EC:3.5.99.10]
synonym: "enamine/imine deaminase" BROAD [EC:3.5.99.10]
synonym: "imine intermediate deaminase activity" RELATED [] {comment="EC:3.5.99.10"}
xref: EC:3.5.99.10
-is_a: GO:0016810 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
is_a: GO:0019239 ! deaminase activity
[Term]
@@ -414865,8 +414997,8 @@ synonym: "alkyne substituted compound anabolism" EXACT [GOC:krc]
synonym: "alkyne substituted compound biosynthesis" EXACT [GOC:krc]
synonym: "alkyne substituted compound biosynthetic process" EXACT [GOC:krc]
synonym: "alkyne substituted compound synthesis" EXACT [GOC:krc]
-is_a: GO:0009058 ! biosynthetic process
is_a: GO:0120246 ! acetylenic compound metabolic process
+is_a: GO:1901576 ! organic substance biosynthetic process
[Term]
id: GO:0120248
@@ -414877,8 +415009,8 @@ synonym: "alkyne substituted compound breakdown" EXACT [GOC:krc]
synonym: "alkyne substituted compound catabolic process" EXACT [GOC:krc]
synonym: "alkyne substituted compound catabolism" EXACT [GOC:krc]
synonym: "alkyne substituted compound degradation" EXACT [GOC:krc]
-is_a: GO:0009056 ! catabolic process
is_a: GO:0120246 ! acetylenic compound metabolic process
+is_a: GO:1901575 ! organic substance catabolic process
[Term]
id: GO:0120249
@@ -414894,10 +415026,9 @@ is_a: GO:0097574 ! lateral part of cell
id: GO:0120250
name: fatty acid omega-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an omega-methyl fatty acid + O2 + reduced [NADPH--hemoprotein reductase] = an omega-hydroxy fatty acid + H(+) + H2O + oxidized [NADPH--hemoprotein reductase]." [GOC:krc, RHEA:39023]
+def: "Catalysis of the reaction: an omega-methyl fatty acid + O2 + reduced [NADPH--hemoprotein reductase] = an omega-hydroxy fatty acid + H+ + H2O + oxidized [NADPH--hemoprotein reductase]." [GOC:krc, RHEA:39023]
xref: RHEA:39023
-is_a: GO:0004497 ! monooxygenase activity
-is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0120251
@@ -414949,8 +415080,8 @@ synonym: "alkene substituted compound anabolism" EXACT [GOC:krc]
synonym: "alkene substituted compound biosynthesis" EXACT [GOC:krc]
synonym: "alkene substituted compound biosynthetic process" EXACT [GOC:krc]
synonym: "alkene substituted compound synthesis" EXACT [GOC:krc]
-is_a: GO:0009058 ! biosynthetic process
is_a: GO:0120254 ! olefinic compound metabolic process
+is_a: GO:1901576 ! organic substance biosynthetic process
[Term]
id: GO:0120256
@@ -414961,8 +415092,8 @@ synonym: "alkene substituted compound breakdown" EXACT [GOC:krc]
synonym: "alkene substituted compound catabolic process" EXACT [GOC:krc]
synonym: "alkene substituted compound catabolism" EXACT [GOC:krc]
synonym: "alkene substituted compound degradation" EXACT [GOC:krc]
-is_a: GO:0009056 ! catabolic process
is_a: GO:0120254 ! olefinic compound metabolic process
+is_a: GO:1901575 ! organic substance catabolic process
[Term]
id: GO:0120257
@@ -415040,7 +415171,7 @@ name: regulation of chromosome attachment to the nuclear envelope
namespace: biological_process
def: "Any process that modulates the frequency, rate, extent or location of chromosome attachment to the nuclear envelope." [GOC:krc]
is_a: GO:0010564 ! regulation of cell cycle process
-is_a: GO:0060341 ! regulation of cellular localization
+is_a: GO:0032879 ! regulation of localization
relationship: regulates GO:0097240 ! chromosome attachment to the nuclear envelope
[Term]
@@ -415097,7 +415228,7 @@ name: ciliary centrin arm
namespace: cellular_component
def: "A rod-shaped protein complex containing Centrin4 protein that flanks the flagellum attachment zone (FAZ) filament and the quartet microtubules." [GOC:ach, GOC:krc, PMID:26540076, PMID:31217284]
comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane.
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140535 ! intracellular protein-containing complex
relationship: part_of GO:0020016 ! ciliary pocket
[Term]
@@ -415140,6 +415271,7 @@ id: GO:0120274
name: virus coreceptor activity
namespace: molecular_function
def: "Combining with a virus component, and in cooperation with a nearby primary receptor, initiating a change in cell activity." [GOC:ha, GOC:krc, PMID:16051304]
+subset: goslim_generic
synonym: "viral coreceptor activity" EXACT []
is_a: GO:0140272 ! exogenous protein binding
@@ -415245,7 +415377,6 @@ namespace: molecular_function
def: "Binding to 2-amino-3-(1H-indol-3-yl)propanoic acid." [GOC:krc]
synonym: "Trp binding" EXACT [GOC:krc]
is_a: GO:0016597 ! amino acid binding
-is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0043169 ! cation binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -415255,16 +415386,18 @@ id: GO:0120285
name: tyrosine sensor activity
namespace: molecular_function
def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of tyrosine." [GOC:krc, PMID:31498992]
+synonym: "tyrosine sensing activity" EXACT []
is_a: GO:0072545 ! tyrosine binding
-is_a: GO:0140299 ! small molecule sensor activity
+is_a: GO:0140785 ! amino acid sensor activity
[Term]
id: GO:0120286
name: tryptophan sensor activity
namespace: molecular_function
def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of tryptophan." [GOC:krc, PMID:31498992]
+synonym: "tryptophan sensing activity" EXACT []
is_a: GO:0120284 ! tryptophan binding
-is_a: GO:0140299 ! small molecule sensor activity
+is_a: GO:0140785 ! amino acid sensor activity
[Term]
id: GO:0120287
@@ -415303,28 +415436,29 @@ relationship: part_of GO:0031297 ! replication fork processing
[Term]
id: GO:0120291
-name: negative regulation of mitotic recombination involved in replication fork processing
+name: negative regulation of mitotic recombination-dependent replication fork processing
namespace: biological_process
-def: "Any process that inhibits or decreases the rate of mitotic DNA recombination during replication fork processing. Suppression of recombination at replication forks is necessary to prevent template switching." [GOC:krc, GOC:mah, PMID:28586299, PMID:30667359, PMID:31149897]
+def: "Any process that inhibits or decreases the rate of mitotic recombination-dependent replication fork processing. Suppression of recombination at replication forks is necessary to prevent template switching." [GOC:krc, GOC:mah, PMID:28586299, PMID:30667359, PMID:31149897]
synonym: "maintenance of template fidelity during replication fork processing" EXACT []
+synonym: "negative regulation of mitotic recombination involved in replication fork processing" RELATED []
synonym: "negative regulation of template switch recombination involved in replication fork processing" EXACT []
synonym: "suppression of template switching during replication fork processing" EXACT []
is_a: GO:0010948 ! negative regulation of cell cycle process
-is_a: GO:0045950 ! negative regulation of mitotic recombination
-is_a: GO:1903221 ! regulation of mitotic recombination involved in replication fork processing
-relationship: negatively_regulates GO:1903211 ! mitotic recombination involved in replication fork processing
-relationship: part_of GO:0031297 ! replication fork processing
+is_a: GO:0051053 ! negative regulation of DNA metabolic process
+is_a: GO:1903221 ! regulation of mitotic recombination-dependent replication fork processing
+relationship: negatively_regulates GO:1990426 ! mitotic recombination-dependent replication fork processing
[Term]
id: GO:0120292
name: positive regulation of mitotic recombination-dependent replication fork processing
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of replication fork processing that includes recombination between DNA near the arrested fork and homologous sequences. Proteins involved in homologous recombination are required for replication restart." [GOC:krc, GOC:mah, PMID:23093942, PMID:28586299, PMID:31149897]
+def: "Any process that activates or increases the frequency, rate or extent of mitotic recombination-dependent replication fork processing. Regulation of mitotic recombination prevents recombination between inappropriate homologous sequences. Proteins involved in homologous recombination are required for replication restart." [GOC:krc, GOC:mah, PMID:23093942, PMID:28586299, PMID:31149897]
synonym: "positive regulation of homologous recombination dependent replication fork recovery" RELATED [PMID:23093942]
-synonym: "positive regulation of homologous recombination-dependent replication fork processing" EXACT []
+synonym: "positive regulation of mitotic recombination involved in replication fork processing" RELATED []
synonym: "positive regulation of recombination-dependent DNA replication" EXACT []
is_a: GO:0051054 ! positive regulation of DNA metabolic process
is_a: GO:0090068 ! positive regulation of cell cycle process
+is_a: GO:1903221 ! regulation of mitotic recombination-dependent replication fork processing
relationship: positively_regulates GO:1990426 ! mitotic recombination-dependent replication fork processing
[Term]
@@ -415350,6 +415484,7 @@ name: histone serotonyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-glutaminyl-[histone] + serotonin = 5-serotonyl-L-glutamyl-[histone] + NH4(+)." [GOC:sp, PMID:30867594]
is_a: GO:0120294 ! peptide serotonyltransferase activity
+is_a: GO:0140993 ! histone modifying activity
[Term]
id: GO:0120296
@@ -415365,6 +415500,7 @@ name: histone dopaminyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: dopamine + L-glutaminyl-[histone] = 5-dopaminyl-L-glutamyl-[histone] + NH4(+)." [GOC:sp, PMID:32273471]
is_a: GO:0120296 ! peptide dopaminyltransferase activity
+is_a: GO:0140993 ! histone modifying activity
[Term]
id: GO:0120298
@@ -415386,7 +415522,7 @@ is_a: GO:0016410 ! N-acyltransferase activity
id: GO:0120300
name: peptide lactyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (L-lysyl-[protein] + lactoyl-CoA = CoA + H(+) + N(6)-lactoyl-L-lysyl-[protein]." [GOC:sp, PMID:31645732, RHEA:61996]
+def: "Catalysis of the reaction: (L-lysyl-[protein] + lactoyl-CoA = CoA + H+ + N(6)-lactoyl-L-lysyl-[protein]." [GOC:sp, PMID:31645732, RHEA:61996]
xref: RHEA:61996
is_a: GO:0016410 ! N-acyltransferase activity
@@ -415394,8 +415530,9 @@ is_a: GO:0016410 ! N-acyltransferase activity
id: GO:0120301
name: histone lactyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (L-lysyl-[histone] + lactoyl-CoA = CoA + H(+) + N(6)-lactoyl-L-lysyl-[histone]." [GOC:sp, PMID:31645732]
+def: "Catalysis of the reaction: (L-lysyl-[histone] + lactoyl-CoA = CoA + H+ + N(6)-lactoyl-L-lysyl-[histone]." [GOC:sp, PMID:31645732]
is_a: GO:0120300 ! peptide lactyltransferase activity
+is_a: GO:0140993 ! histone modifying activity
[Term]
id: GO:0120302
@@ -415553,7 +415690,8 @@ id: GO:0120317
name: sperm mitochondrial sheath assembly
namespace: biological_process
def: "The assembly and organization of the sperm mitochondrial sheath, the tightly packed helical sheath of ATP-producing mitochondria restricted to the midpiece of the sperm flagellum." [GOC:krc, PMID:32791035]
-is_a: GO:0003006 ! developmental process involved in reproduction
+is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
+is_a: GO:0022607 ! cellular component assembly
relationship: part_of GO:0120316 ! sperm flagellum assembly
[Term]
@@ -415629,7 +415767,7 @@ def: "Penetration by a symbiont into a host organism via an appressorium. The ho
synonym: "appressorium-mediated host invasion" EXACT [GOC:ach]
synonym: "appressorium-mediated host penetration" EXACT [GOC:ach]
synonym: "appressorium-mediated invasion into host" EXACT [GOC:ach]
-synonym: "appressorium-mediated penetration into host" EXACT [] {EXACT="GOC:ach"}
+synonym: "appressorium-mediated penetration into host" EXACT [GOC:ach]
is_a: GO:0044409 ! entry into host
[Term]
@@ -415643,10 +415781,43 @@ is_a: GO:0120025 ! plasma membrane bounded cell projection
id: GO:0120328
name: ATP-dependent DNA (cytosine-5-)-methyltransferase activity
namespace: molecular_function
-def: "Catalytic activity that acts to transfer a methyl group to a DNA molecule, driven by ATP hydrolysis." [GOC:krc, PMID:31955845, PMID:32437639]
+def: "Catalytic activity that acts to transfer a methyl group to a DNA molecule, driven by ATP hydrolysis." [GOC:krc, PMID:31955845, PMID:32437639, RHEA:68984]
+xref: RHEA:68984
is_a: GO:0003886 ! DNA (cytosine-5-)-methyltransferase activity
is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
+[Term]
+id: GO:0120329
+name: protein localization to centriolar satellite
+namespace: biological_process
+def: "A process in which a protein is transported to, or maintained in, a location within a centriolar satellite." [PMID:34782749]
+synonym: "protein localisation to centriolar satellite" EXACT []
+is_a: GO:0071539 ! protein localization to centrosome
+
+[Term]
+id: GO:0120330
+name: rixosome complex
+namespace: cellular_component
+def: "A conserved RNA endonuclease complex required for spreading and epigenetic inheritance of heterochromatin. The rixosome contains six unique subunits: three structural subunits (Crb3, Rix1, and Ipi1) which form the core of the complex, and three catalytic subunits (the endonuclease Las1, the polynucleotide kinase Grc3, and the AAA-type ATPase Mdn1), which are involved in the processing of ribosomal RNA precursors. All subunits are essential for viability and are conserved from yeast to mammals, including humans." [GOC:vw, PMID:32491985, PMID:35355014]
+is_a: GO:1902555 ! endoribonuclease complex
+
+[Term]
+id: GO:0120331
+name: endothelial tube formation
+namespace: biological_process
+def: "The developmental process pertaining to the initial formation of an endothelial tube." [GOC:sl, PMID:23239824]
+is_a: GO:0072175 ! epithelial tube formation
+relationship: part_of GO:0061154 ! endothelial tube morphogenesis
+
+[Term]
+id: GO:0120332
+name: host-mediated regulation of oral microbiota composition
+namespace: biological_process
+def: "The biological process involved in maintaining the steady-state number of cells within a population of free-living cells, such as the bacteria, in the mouth." [PMID:31882545]
+synonym: "host-induced regulation of oral microbiota composition" RELATED []
+is_a: GO:0048872 ! homeostasis of number of cells
+is_a: GO:0051851 ! modulation by host of symbiont process
+
[Term]
id: GO:0140007
name: KICSTOR complex
@@ -415714,9 +415885,7 @@ namespace: biological_process
def: "The process in which ADP is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:2541251]
is_a: GO:0015866 ! ADP transport
is_a: GO:0072530 ! purine-containing compound transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1901679 ! nucleotide transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0140022
@@ -415870,8 +416039,7 @@ is_a: GO:0090615 ! mitochondrial mRNA processing
id: GO:0140041
name: cellular detoxification of methylglyoxal
namespace: biological_process
-def: "Any process carried out at the cellular level that reduces or removes the toxicity of methylglyoxal." [PMID:15042280]
-is_a: GO:0009438 ! methylglyoxal metabolic process
+def: "Any process carried out at the cellular level that reduces or removes the toxicity of methylglyoxal. These may include chemical modification or transport of methylglyoxal away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." [PMID:15042280]
is_a: GO:0110095 ! cellular detoxification of aldehyde
relationship: part_of GO:0097238 ! cellular response to methylglyoxal
@@ -415910,7 +416078,6 @@ name: manganese ion export across plasma membrane
namespace: biological_process
def: "The directed movement of manganese ions from inside of a cell, across the plasma membrane and into the extracellular region." [PMID:25319704]
synonym: "manganese ion export from cell" EXACT []
-is_a: GO:0070839 ! metal ion export
is_a: GO:0071421 ! manganese ion transmembrane transport
is_a: GO:0140115 ! export across plasma membrane
@@ -415950,8 +416117,7 @@ synonym: "cellular response to oxidised LDL particle stimulus" EXACT []
synonym: "cellular response to oxidized LDL particle stimulus" EXACT []
synonym: "cellular response to oxidized low-density lipoprotein particle stimulus" EXACT []
synonym: "cellular response to oxLDL particle stimulus" EXACT []
-is_a: GO:0055094 ! response to lipoprotein particle
-is_a: GO:0071402 ! cellular response to lipoprotein particle stimulus
+is_a: GO:0071404 ! cellular response to low-density lipoprotein particle stimulus
[Term]
id: GO:0140053
@@ -416060,6 +416226,7 @@ name: histone crotonyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: crotonyl-CoA + histone = CoA + crotonyl-histone." [PMID:25818647]
is_a: GO:0140064 ! peptide crotonyltransferase activity
+is_a: GO:0140993 ! histone modifying activity
[Term]
id: GO:0140069
@@ -416067,6 +416234,16 @@ name: histone butyryltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: butyryl-CoA + histone = CoA + butyryl-histone." [PMID:27105113]
is_a: GO:0140065 ! peptide butyryltransferase activity
+is_a: GO:0140993 ! histone modifying activity
+
+[Term]
+id: GO:0140070
+name: hydrogen peroxide channel activity
+namespace: molecular_function
+def: "Enables the transfer of hydrogen peroxide from one side of a membrane to the other." [PMID:23541115, PMID:27256569]
+synonym: "hydrogen peroxide transmembrane transporter activity" RELATED []
+is_a: GO:0015267 ! channel activity
+is_a: GO:0015318 ! inorganic molecular entity transmembrane transporter activity
[Term]
id: GO:0140074
@@ -416149,9 +416326,10 @@ is_a: GO:0061665 ! SUMO ligase activity
[Term]
id: GO:0140083
-name: ATP-dependent protein-DNA unloading activity
+name: ATP-dependent protein-DNA unloader activity
namespace: molecular_function
def: "Facilitating the removal of a protein or protein complex from a DNA molecule driven by ATP hydrolysis. This can be achieved for example by introducing non-canonical DNA structures or generating torque to directly inhibit a protein-DNA binding interaction." [PMID:28552615]
+synonym: "ATP-dependent protein-DNA unloading activity" EXACT []
synonym: "protein-DNA unloading ATPase activity" EXACT []
is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
@@ -416162,7 +416340,7 @@ namespace: biological_process
def: "The fusion of haploid amoebae cells with matching mating types to form a larger cell, which ingests additional amoebae and forms a cellulose wall. The resulting macrocyst undergoes recombination and meiosis followed by release of haploid amoebae. An example of this process can be found in Dictyostelium discoideum." [PMID:16592095, PMID:20089169]
synonym: "macrocyst formation" RELATED []
synonym: "sexual fusion" RELATED []
-is_a: GO:0019953 ! sexual reproduction
+is_a: GO:0022413 ! reproductive process in single-celled organism
[Term]
id: GO:0140090
@@ -416206,6 +416384,7 @@ name: catalytic activity, acting on a protein
namespace: molecular_function
def: "Catalytic activity that acts to modify a protein." [GOC:molecular_function_refactoring, GOC:pdt]
subset: goslim_generic
+subset: prokaryote_subset
is_a: GO:0003824 ! catalytic activity
[Term]
@@ -416214,6 +416393,7 @@ name: catalytic activity, acting on DNA
namespace: molecular_function
def: "Catalytic activity that acts to modify DNA." [GOC:molecular_function_refactoring, GOC:pdt]
subset: goslim_generic
+subset: prokaryote_subset
is_a: GO:0140640 ! catalytic activity, acting on a nucleic acid
[Term]
@@ -416222,6 +416402,7 @@ name: catalytic activity, acting on RNA
namespace: molecular_function
def: "Catalytic activity that acts to modify RNA, driven by ATP hydrolysis." [GOC:molecular_function_refactoring, GOC:pdt]
subset: goslim_generic
+subset: prokaryote_subset
is_a: GO:0140640 ! catalytic activity, acting on a nucleic acid
[Term]
@@ -416253,13 +416434,17 @@ def: "Directly binding to a specific ion or molecule and delivering it either to
comment: Note that a carrier moves with its substrate/cargo, while a transporter does not move with the cargo, but facilitates the change in localization.
subset: gocheck_do_not_annotate
subset: goslim_generic
+subset: prokaryote_subset
+xref: Reactome:R-HSA-3000074 "TCN2 binds RCbl in the circulation"
+xref: Reactome:R-HSA-3000120 "CBLIF binds RCbl"
+xref: Reactome:R-HSA-3132759 "TCN1 binds RCbl"
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0140105
name: interleukin-10-mediated signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of interleukin-10 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [PMID:11244051]
+def: "The series of molecular signals initiated by interleukin-10 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [PMID:11244051]
synonym: "IL-10-mediated signaling pathway" EXACT []
synonym: "interleukin-10-mediated signalling pathway" EXACT []
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -416285,6 +416470,7 @@ namespace: molecular_function
def: "A molecular function that controls the rate, timing and/or magnitude of gene transcription. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism. Genes are transcriptional units, and include bacterial operons." [GOC:pg, GOC:txnOH-2018, Wikipedia:Transcription_factor]
subset: gocheck_do_not_annotate
subset: goslim_flybase_ribbon
+subset: goslim_generic
subset: goslim_plant
is_a: GO:0003674 ! molecular_function
@@ -416316,7 +416502,8 @@ is_a: GO:0140112 ! extracellular vesicle biogenesis
id: GO:0140114
name: cellular detoxification of fluoride
namespace: biological_process
-def: "Any process carried out at the cellular level that reduces or removes the toxicity of a fluoride. These may include transport of fluoride away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." [GOC:vw]
+def: "Any process carried out at the cellular level that reduces or removes the toxicity of a fluoride. These may include chemical modification or transport of fluoride away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." [GOC:vw]
+is_a: GO:0061687 ! detoxification of inorganic compound
is_a: GO:1990748 ! cellular detoxification
relationship: part_of GO:1902618 ! cellular response to fluoride
@@ -416407,12 +416594,15 @@ is_a: GO:0052170 ! suppression by symbiont of host innate immune response
[Term]
id: GO:0140135
-name: mechanosensitive cation channel activity
+name: mechanosensitive monoatomic cation channel activity
namespace: molecular_function
-def: "Enables the transmembrane transfer of a cation by a channel that opens in response to a mechanical stress." [GOC:ha, PMID:22343900]
+def: "Enables the transmembrane transfer of a monoatomic cation by a channel that opens in response to a mechanical stress." [GOC:ha, PMID:22343900]
synonym: "mechanically-gated cation channel activity" EXACT []
-is_a: GO:0005261 ! cation channel activity
-is_a: GO:0008381 ! mechanosensitive ion channel activity
+synonym: "mechanosensitive cation channel activity" BROAD []
+xref: Reactome:R-HSA-9659380 "Mechanoelectrical transduction (MET) channel transports cations from the extracellular region into the cytosol of stereocilia of inner hair cell"
+xref: Reactome:R-HSA-9663363 "Mechanoelectrical transduction (MET) channel transports cations into the cytosol of stereocilia of cochlear outer hair cell"
+is_a: GO:0005261 ! monoatomic cation channel activity
+is_a: GO:0008381 ! mechanosensitive monoatomic ion channel activity
[Term]
id: GO:0140140
@@ -416420,7 +416610,6 @@ name: mitochondrial guanine nucleotide transmembrane transport
namespace: biological_process
def: "The process in which a guanine nucleotide is transported across a mitochondrial membrane, into or out of the mitochondrion." [GOC:vw, PMID:14998997]
is_a: GO:1903716 ! guanine transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0140141
@@ -416428,7 +416617,6 @@ name: mitochondrial potassium ion transmembrane transport
namespace: biological_process
def: "The process in which a potassium ion is transported across a mitochondrial membrane, into or out of the mitochondrion." [GOC:vw, PMID:20197279]
is_a: GO:0071805 ! potassium ion transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0140142
@@ -416449,7 +416637,7 @@ name: copper ion export from vacuole
namespace: biological_process
def: "The directed movement of copper ions out of the vacuole across the vacuolar membrane." [GOC:vw, PMID:12244050]
is_a: GO:0034486 ! vacuolar transmembrane transport
-is_a: GO:0060003 ! copper ion export
+is_a: GO:0035434 ! copper ion transmembrane transport
[Term]
id: GO:0140146
@@ -416457,9 +416645,7 @@ name: calcium ion import into vacuole
namespace: biological_process
def: "The directed movement of calcium cations into the vacuole across the vacuolar membrane." [GOC:vw, PMID:8628289]
is_a: GO:0034486 ! vacuolar transmembrane transport
-is_a: GO:0060401 ! cytosolic calcium ion transport
is_a: GO:0070588 ! calcium ion transmembrane transport
-is_a: GO:1901660 ! calcium ion export
[Term]
id: GO:0140147
@@ -416467,7 +416653,6 @@ name: zinc ion export from vacuole
namespace: biological_process
def: "The directed movement of zinc ions from inside the vacuole across the vacuolar membrane and into the cytosol." [GOC:vw, PMC:PMC203372]
is_a: GO:0034486 ! vacuolar transmembrane transport
-is_a: GO:0070839 ! metal ion export
is_a: GO:0071577 ! zinc ion transmembrane transport
[Term]
@@ -416476,8 +416661,7 @@ name: ammonium import across plasma membrane
namespace: biological_process
def: "The directed movement of an ammonium ion from outside of a cell, across the plasma membrane and into the cytosol." [GOC:vw, PMID:16999738]
is_a: GO:0072488 ! ammonium transmembrane transport
-is_a: GO:0098657 ! import into cell
-is_a: GO:0098739 ! import across plasma membrane
+is_a: GO:0098659 ! inorganic cation import across plasma membrane
[Term]
id: GO:0140159
@@ -416701,7 +416885,6 @@ name: regulation of D-aspartate import across plasma membrane
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the directed import of D-aspartate from the extracellular region across the plasma membrane and into the cytosol." [PMID:27663541]
is_a: GO:0010958 ! regulation of amino acid import across plasma membrane
-is_a: GO:1903959 ! regulation of anion transmembrane transport
relationship: regulates GO:0070779 ! D-aspartate import across plasma membrane
[Term]
@@ -416709,9 +416892,9 @@ id: GO:0140216
name: negative regulation of D-aspartate import across plasma membrane
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of the directed import of D-aspartate from the extracellular region across the plasma membrane and into the cytosol." [PMID:27663541]
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:0051956 ! negative regulation of amino acid transport
is_a: GO:0140215 ! regulation of D-aspartate import across plasma membrane
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
relationship: negatively_regulates GO:0070779 ! D-aspartate import across plasma membrane
[Term]
@@ -416719,9 +416902,9 @@ id: GO:0140217
name: positive regulation of D-aspartate import across plasma membrane
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the directed import of D-aspartate from the extracellular region across the plasma membrane and into the cytosol." [PMID:27663541]
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:0051957 ! positive regulation of amino acid transport
is_a: GO:0140215 ! regulation of D-aspartate import across plasma membrane
-is_a: GO:1903961 ! positive regulation of anion transmembrane transport
relationship: positively_regulates GO:0070779 ! D-aspartate import across plasma membrane
[Term]
@@ -416795,7 +416978,7 @@ is_a: GO:0140098 ! catalytic activity, acting on RNA
id: GO:0140227
name: serotonin-gated cation-selective signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by serotonin binding to a seratonin receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bhm, PMID:25392484, PMID:27764665]
+def: "The series of molecular signals initiated by serotonin binding to a seratonin receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bhm, PMID:25392484, PMID:27764665]
synonym: "5-HT-gated cation-selective signaling pathway" EXACT []
synonym: "5-HT-gated cation-selective signalling pathway" EXACT []
synonym: "5-hydroxytryptamine-gated cation-selective signaling pathway" EXACT []
@@ -417133,7 +417316,6 @@ def: "A mitochondrial intermembrane space bridging complex consisting of compone
synonym: "mitochondrial intermembrane space bridging complex" EXACT []
synonym: "mitofilin complex" EXACT []
is_a: GO:0098800 ! inner mitochondrial membrane protein complex
-relationship: part_of GO:0031305 ! integral component of mitochondrial inner membrane
[Term]
id: GO:0140276
@@ -417270,10 +417452,12 @@ is_a: GO:0070603 ! SWI/SNF superfamily-type complex
[Term]
id: GO:0140289
-name: protein mono-ADP-ribosylation
+name: obsolete protein mono-ADP-ribosylation
namespace: biological_process
-def: "The transfer, from NAD, of a single (mono) ADP-ribose molecule to protein amino acids." [PMID:25043379]
-is_a: GO:0006471 ! protein ADP-ribosylation
+def: "OBSOLETE. The transfer, from NAD, of a single (mono) ADP-ribose molecule to protein amino acids." [PMID:25043379]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0003950
[Term]
id: GO:0140290
@@ -417316,7 +417500,9 @@ name: pathogen-derived receptor ligand activity
namespace: molecular_function
def: "The activity of a pathogen-derived entity that interacts with a host receptor to activate effector-triggered immunity." [PMID:20601497]
comment: Note that this term is meant to annotate effectors for which the evolved activity is to act as a ligand to activate (for necrotrophs) or suppress (for biotrophs) the host immune system. It should not be used to annotate PAMPs (pathogen-associated molecular pattern molecules) or similar types of microbial proteins recognized by the host innate immune system (for example, PAMPs are recognized by toll-like receptors (TLRs) and other pattern recognition receptors (PRRs) in both plants and animals). PAMPs activate innate immune responses, protecting the host from infection, but this is not the molecular function of PAMPs; those usually form the structure of the bacterial cell wall.
+synonym: "host-selective toxin" RELATED []
synonym: "innate receptor ligand activity" RELATED []
+synonym: "necrotrophic effector" RELATED []
is_a: GO:0048018 ! receptor ligand activity
[Term]
@@ -417355,7 +417541,9 @@ namespace: molecular_function
def: "Binding to a small molecule and eliciting a change in the protein's activity in response to the intracellular level of that small molecule." [PMID:26328879]
subset: goslim_drosophila
subset: goslim_generic
+subset: prokaryote_subset
synonym: "small molecular sensor activity" EXACT []
+synonym: "small molecule sensing activity" EXACT []
is_a: GO:0003674 ! molecular_function
[Term]
@@ -417365,10 +417553,6 @@ namespace: biological_process
def: "The process in which serine is transported from the cytosol into the mitochondrial matrix." [PMID:30442778]
is_a: GO:0003333 ! amino acid transmembrane transport
is_a: GO:0032329 ! serine transport
-is_a: GO:0043090 ! amino acid import
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0140301
@@ -417404,7 +417588,7 @@ is_a: GO:0140318 ! protein transporter activity
id: GO:0140311
name: protein sequestering activity
namespace: molecular_function
-def: "The selective interaction of a protein with a specific protein, to prevent it from interacting with other partners or inhibiting its localization to other areas of the cell." [PMID:1493333]
+def: "Binding to a protein to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active." [PMID:1493333]
is_a: GO:0140313 ! molecular sequestering activity
[Term]
@@ -417420,23 +417604,25 @@ is_a: GO:0030674 ! protein-macromolecule adaptor activity
id: GO:0140313
name: molecular sequestering activity
namespace: molecular_function
-def: "The selective interaction of a protein with a specific molecule to prevent it from interacting with other partners or inhibiting its localization to other areas of the cell." [PMID:13130076]
+def: "Binding to a specific molecule to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active." [PMID:13130076]
subset: goslim_drosophila
subset: goslim_generic
+subset: prokaryote_subset
+xref: Reactome:R-HSA-3245898 "TCN1 binds correnoids in the circulation"
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0140314
name: calcium ion sequestering activity
namespace: molecular_function
-def: "The selective interaction of a protein with a calcium ion to prevent it from interacting with other partners or inhibiting its localization to other areas of the cell." [PMID:13130076]
+def: "Binding to a calcium ion to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active." [PMID:13130076]
is_a: GO:0140487 ! metal ion sequestering activity
[Term]
id: GO:0140315
name: iron ion sequestering activity
namespace: molecular_function
-def: "The selective interaction of a protein with an iron ion to prevent it from interacting with other partners or inhibiting its localization to other areas of the cell." [PMID:27780864]
+def: "Binding to an iron ion to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active." [PMID:27780864]
is_a: GO:0140487 ! metal ion sequestering activity
[Term]
@@ -417471,7 +417657,7 @@ id: GO:0140319
name: receptor decoy activity
namespace: molecular_function
alt_id: GO:0005040
-def: "Recognizing, binding and sequestering a specific receptor ligand to prevent it from binding to its regular receptor." [Wikipedia:Decoy_receptors]
+def: "Binding and sequestering a specific receptor ligand to prevent it from binding to its regular receptor." [Wikipedia:Decoy_receptors]
synonym: "decoy death receptor activity" NARROW []
synonym: "decoy receptor" EXACT []
is_a: GO:0140313 ! molecular sequestering activity
@@ -417480,27 +417666,28 @@ is_a: GO:0140313 ! molecular sequestering activity
id: GO:0140320
name: PAMP receptor decoy activity
namespace: molecular_function
-def: "A gene product which recognizes, binds and sequesters PAMP ligands in order to prevent them from binding and activating to the host PAMP receptor. Usually this activity is encoded by a symbiont or a pathogen to prevent activation of the host innate immune response." [PMID:20724636]
+def: "Binding and sequestering PAMP ligands in order to prevent them from binding and activating to the host PAMP receptor. Usually this activity is encoded by a symbiont or a pathogen to prevent activation of the host innate immune response." [PMID:20724636]
synonym: "pathogen-associated molecular pattern receptor decoy activity" EXACT []
synonym: "pattern recognition receptor decoy activity" EXACT []
is_a: GO:0140319 ! receptor decoy activity
[Term]
id: GO:0140321
-name: negative regulation by symbiont of host autophagy
+name: suppression of host autophagy
namespace: biological_process
def: "Any process in which a symbiont organism decreases the frequency, rate or extent of autophagy in the host cell. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pg]
+synonym: "negative regulation by symbiont of host autophagy" EXACT []
is_a: GO:0075071 ! modulation by symbiont of host autophagy
relationship: negatively_regulates GO:0006914 ! autophagy
[Term]
id: GO:0140323
-name: solute:anion antiporter activity
+name: obsolete solute:monoatomic anion antiporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: anion(in) + solute(out) = anion(out) + solute(in)." [GOC:pg]
-is_a: GO:0008509 ! anion transmembrane transporter activity
-is_a: GO:0015297 ! antiporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+def: "OBSOLETE. Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: anion(in) + solute(out) = anion(out) + solute(in)." [GOC:pg]
+comment: This term was obsoleted because it is an unnecessary grouping class.
+synonym: "solute:anion antiporter activity" EXACT []
+is_obsolete: true
[Term]
id: GO:0140325
@@ -417564,7 +417751,7 @@ id: GO:0140330
name: xenobiotic detoxification by transmembrane export across the cell outer membrane
namespace: biological_process
def: "A process that reduces or removes the toxicity of a xenobiotic by exporting it outside the cell through the outer membrane." [PMID:11948170]
-is_a: GO:0046618 ! xenobiotic export
+is_a: GO:0042908 ! xenobiotic transport
is_a: GO:0140317 ! export across cell outer membrane
relationship: part_of GO:0098754 ! detoxification
@@ -417755,7 +417942,6 @@ namespace: biological_process
def: "The directed movement of heme from inside the vacuole across the vacuolar membrane and into the cytosol." [PMID:28193844]
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0035351 ! heme transmembrane transport
-is_a: GO:0097037 ! heme export
[Term]
id: GO:0140358
@@ -417782,11 +417968,11 @@ synonym: "ATP binding cassette transporter" EXACT []
synonym: "ATP-binding cassette (ABC) transporter activity" EXACT []
synonym: "ATP-binding cassette transporter" EXACT []
xref: Reactome:R-HSA-266070 "LTC4 is exported from the cytosol by ABCC1"
-xref: Reactome:R-HSA-5223313 "ABCD4 may transport Cbl from lysosomal lumen to cytosol"
+xref: Reactome:R-HSA-429157 "ABCC4 accumulation of dense granule contents"
xref: Reactome:R-HSA-5362459 "VCP-catalyzed ATP hydrolysis promotes the translocation of Hh-C into the cytosol"
xref: Reactome:R-HSA-5387389 "Hh processing variants are translocated to the cytosol in a VCP-dependent manner"
-xref: Reactome:R-HSA-5683325 "Defective ABCD4 does not transport Cbl from lysosomal lumen to cytosol"
xref: Reactome:R-HSA-9661405 "ABCC1 transports BIL from cytosol to extracellular region (blood)"
+xref: Reactome:R-HSA-9750656 "ABCC2, ABCC3 transport salicylate metabolites from cytosol to extracellular region of hepatic cells"
xref: TC:3.A.1
xref: Wikipedia:ATP-binding_cassette_transporter
is_a: GO:0042626 ! ATPase-coupled transmembrane transporter activity
@@ -417810,7 +417996,6 @@ is_a: GO:0015711 ! organic anion transport
is_a: GO:0015868 ! purine ribonucleotide transport
is_a: GO:0051503 ! adenine nucleotide transport
is_a: GO:0070729 ! cyclic nucleotide transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:0098657 ! import into cell
is_a: GO:0098739 ! import across plasma membrane
is_a: GO:1903790 ! guanine nucleotide transmembrane transport
@@ -417864,21 +418049,24 @@ is_a: GO:0043235 ! receptor complex
[Term]
id: GO:0140372
-name: histone H3 ubiquitination
+name: obsolete histone H3 ubiquitination
namespace: biological_process
-def: "The modification of histone H3 by the addition of one or more ubiquitin groups." [GOC:mah, PMID:31468675]
+def: "OBSOLETE. The modification of histone H3 by the addition of one or more ubiquitin groups." [GOC:mah, PMID:31468675]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H3 ubiquitylation" EXACT []
-is_a: GO:0016574 ! histone ubiquitination
+is_obsolete: true
[Term]
id: GO:0140373
-name: histone H3-K14 ubiquitination
+name: obsolete histone H3-K14 ubiquitination
namespace: biological_process
-def: "The modification of histone H3 by the addition of one or more ubiquitin groups to a lysine residue at position 14 of the histone." [GOC:mah, PMID:31468675]
+def: "OBSOLETE. The modification of histone H3 by the addition of one or more ubiquitin groups to a lysine residue at position 14 of the histone." [GOC:mah, PMID:31468675]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H3 ubiquitination at K14" EXACT []
synonym: "histone H3-K14 ubiquitylation" EXACT []
synonym: "histone H3K14 ubiquitination" EXACT []
-is_a: GO:0140372 ! histone H3 ubiquitination
+is_obsolete: true
+consider: GO:0140851
[Term]
id: GO:0140374
@@ -417930,7 +418118,7 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0140382
name: tryptamine 4-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: tryptamine + reduced acceptor + O(2) <=> 4-hydroxytryptamine + acceptor + H(2)O." [PMID:28763571]
+def: "Catalysis of the reaction: tryptamine + reduced acceptor + O2 <=> 4-hydroxytryptamine + acceptor + H2O." [PMID:28763571]
xref: EC:1.14.99.59
xref: RHEA:15865
is_a: GO:0004497 ! monooxygenase activity
@@ -417939,7 +418127,7 @@ is_a: GO:0004497 ! monooxygenase activity
id: GO:0140383
name: 4-hydroxytryptamine kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-hydroxytryptamine + ATP = 4-hydoxytryptamine 4-phosphate + ADP + H(+)." [PMID:28763571]
+def: "Catalysis of the reaction: 4-hydroxytryptamine + ATP = 4-hydoxytryptamine 4-phosphate + ADP + H+." [PMID:28763571]
xref: EC:2.7.1.222
xref: RHEA:55564
is_a: GO:0016301 ! kinase activity
@@ -417955,7 +418143,7 @@ is_a: GO:0044114 ! development of symbiont in host
id: GO:0140393
name: norsolorinic acid ketoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (1'S)-averantin + NADP(+) <=> norsolorinic acid + NADPH." [PMID:10584035, PMID:8368836, RHEA:35447]
+def: "Catalysis of the reaction: (1'S)-averantin + NADP+ <=> norsolorinic acid + NADPH." [PMID:10584035, PMID:8368836, RHEA:35447]
xref: EC:1.1.1.349
xref: KEGG_REACTION:R10309
xref: MetaCyc:RXN-9480
@@ -417977,7 +418165,7 @@ is_a: GO:1901474 ! azole transmembrane transporter activity
id: GO:0140395
name: averantin hydroxylase activity
namespace: molecular_function
-def: "Catalyzes the reaction: (1'S)-averantin + [reduced NADPH--hemoprotein reductase] + O(2) <=> (1'S,5'S)-5'-hydroxyaverantin + [oxidized NADPH--hemoprotein reductase] + H(2)O. Involved in aflatoxin biosynthesis." [EC:1.14.14.116, PMID:8368836]
+def: "Catalyzes the reaction: (1'S)-averantin + [reduced NADPH--hemoprotein reductase] + O2 <=> (1'S,5'S)-5'-hydroxyaverantin + [oxidized NADPH--hemoprotein reductase] + H2O. Involved in aflatoxin biosynthesis." [EC:1.14.14.116, PMID:8368836]
xref: EC:1.14.14.116
xref: MetaCyc:RXN-9482
xref: RHEA:35575
@@ -417987,7 +418175,7 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0140396
name: 5'-hydroxyaverantin dehydrogenase activity
namespace: molecular_function
-def: "Catalyzes the reaction: (1'S,5'S)-hydroxyaverantin + NAD(+) <=> 5'-oxoaverantin + NADH." [EC:1.1.1.352, PMID:14602595]
+def: "Catalyzes the reaction: (1'S,5'S)-hydroxyaverantin + NAD+ <=> 5'-oxoaverantin + NADH." [EC:1.1.1.352, PMID:14602595]
xref: EC:1.1.1.352
xref: RHEA:35475
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -417996,7 +418184,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0140397
name: versiconal hemiacetal acetate esterase activity
namespace: molecular_function
-def: "Catalyzes the reactions: versiconal hemiacetal acetate + H(2)O <=> versiconal + acetate, as well as versiconol acetate + H(2)O <=> versiconol + acetate." [EC:3.1.1.94, PMID:15006741, PMID:15932995, PMID:8368837]
+def: "Catalyzes the reactions: versiconal hemiacetal acetate + H2O <=> versiconal + acetate, as well as versiconol acetate + H2O <=> versiconol + acetate." [EC:3.1.1.94, PMID:15006741, PMID:15932995, PMID:8368837]
xref: EC:3.1.1.94
xref: MetaCyc:RXN-9488
xref: MetaCyc:RXN-9493
@@ -418007,7 +418195,7 @@ is_a: GO:0016788 ! hydrolase activity, acting on ester bonds
id: GO:0140398
name: versicolorin B desaturase activity
namespace: molecular_function
-def: "Catalyzes the reaction: versicolorin B + NADPH + O(2) <=> versicolorin A + NADP(+) + 2 H(2)O. Uses heme-thiolate as a co-factor. Involved in the synthesis of aflatoxins in the fungus Aspergillus parasiticus." [PMID:15006741, PMID:8368837]
+def: "Catalyzes the reaction: versicolorin B + NADPH + O2 <=> versicolorin A + NADP+ + 2 H2O. Uses heme-thiolate as a co-factor. Involved in the synthesis of aflatoxins in the fungus Aspergillus parasiticus." [PMID:15006741, PMID:8368837]
xref: KEGG_REACTION:R10479
xref: MetaCyc:RXN-9495
xref: RHEA:35743
@@ -418017,7 +418205,7 @@ is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidat
id: GO:0140399
name: aflatoxin B synthase activity
namespace: molecular_function
-def: "Catalyzes the reaction: 8-O-methylsterigmatocystin + 2 [reduced NADPH--hemoprotein reductase] + 2 O(2) <=> aflatoxin B + 2 [oxidized NADPH--hemoprotein reductase] + H(2)O + methanol + CO(2). Produces both aflatoxin B(1) and aflatoxin B(2)." [EC:1.14.14.117]
+def: "Catalyzes the reaction: 8-O-methylsterigmatocystin + 2 [reduced NADPH--hemoprotein reductase] + 2 O2 <=> aflatoxin B + 2 [oxidized NADPH--hemoprotein reductase] + H2O + methanol + CO2. Produces both aflatoxin B(1) and aflatoxin B(2)." [EC:1.14.14.117]
xref: EC:1.14.14.117
xref: MetaCyc:RXN-9497
xref: MetaCyc:RXN-9502
@@ -418038,7 +418226,7 @@ synonym: "effector-mediated suppression of host innate immunity" EXACT []
synonym: "effector-triggered suppression of host immune innate response by symbiont" EXACT []
is_a: GO:0052170 ! suppression by symbiont of host innate immune response
is_a: GO:0140404 ! effector-mediated modulation of host innate immune response by symbiont
-is_a: GO:0140590 ! effector-mediated suppression of host defenses
+is_a: GO:0140590 ! effector-mediated suppression of host defense response
[Term]
id: GO:0140404
@@ -418074,9 +418262,9 @@ id: GO:0140407
name: L-alanine:proton antiporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(out) + L-alanine(in) = H+(in) + L-alanine(out)." [PMID:26073055, PMID:31591285]
+is_a: GO:0015078 ! proton transmembrane transporter activity
is_a: GO:0015180 ! L-alanine transmembrane transporter activity
-is_a: GO:0015299 ! solute:proton antiporter activity
-is_a: GO:0015491 ! cation:cation antiporter activity
+is_a: GO:0140848 ! amino acid:monoatomic cation antiporter activity
[Term]
id: GO:0140408
@@ -418097,28 +418285,27 @@ relationship: positively_regulates GO:0110104 ! mRNA alternative polyadenylation
[Term]
id: GO:0140410
-name: solute:bicarbonate symporter activity
+name: monoatomic cation:bicarbonate symporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + HCO3-(out) = solute(in) + HCO3-(in)." [PMID:27166256]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: monoatomic cation(out) + HCO3-(out) = monoatomic cation(in) + HCO3-(in)." [PMID:27166256]
+synonym: "solute:bicarbonate symporter activity" BROAD []
is_a: GO:0015106 ! bicarbonate transmembrane transporter activity
-is_a: GO:0015293 ! symporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
+is_a: GO:0015294 ! solute:monoatomic cation symporter activity
[Term]
id: GO:0140412
name: zinc:bicarbonate symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: zinc(out) + HCO3-(out) = zinc(in) + HCO3-(in)." [PMID:27166256]
-is_a: GO:0015294 ! solute:cation symporter activity
is_a: GO:0046915 ! transition metal ion transmembrane transporter activity
-is_a: GO:0140410 ! solute:bicarbonate symporter activity
+is_a: GO:0140410 ! monoatomic cation:bicarbonate symporter activity
[Term]
id: GO:0140413
name: zinc:bicarbonate:selenite symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: zinc(out) + HCO3-(out) + HO3Se-(out) = zinc(in) + HCO3-(in) + HO3Se-(out)." [PMID:27166256]
-is_a: GO:0015296 ! anion:cation symporter activity
+is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
is_a: GO:0140412 ! zinc:bicarbonate symporter activity
[Term]
@@ -418144,7 +418331,7 @@ namespace: molecular_function
def: "A molecular function regulator that inhibits the activity of a transcription regulator via direct binding and/or post-translational modification." [PMID:10652346]
comment: Usage guidance: transcription regulator inhibitors bind to a transcription regulator to prevent it from reaching the chromatin. This activity does not occur at the promoter. For activities that do occur at the promoter, consider GO:0001217 ; DNA-binding transcription repressor activity or GO:0003714 ; transcription corepressor activity. An example of a transcription regulator is TCF23 Q7RTU1 is an example of a protein that regulates transcription factors by heterodimerising or binding to DbTFs and prevent DNA binding and their specific genomic binding site where the dbTF would have activated or repressed transcription. Also an example is NFKBIA P25963 which has a different way of regulating transcription factor activity by sequestering the dbTF (complex) in the cytoplasm. Another example is the HSP90 and HSP23 proteins that sequester steroid receptors away from the DNA.
synonym: "DNA-binding transcription factor inhibitor activity" NARROW []
-is_a: GO:0140678 ! molecular function inhibitor activity
+is_a: GO:0098772 ! molecular function regulator activity
[Term]
id: GO:0140417
@@ -418178,7 +418365,7 @@ name: endocytic heme import into cell
namespace: biological_process
def: "The directed movement into cell of externally available heme by receptor-mediated endocytosis." [PMID:28193844]
synonym: "heme assimilation" BROAD []
-is_a: GO:0006898 ! receptor-mediated endocytosis
+is_a: GO:0140298 ! endocytic iron import into cell
is_a: GO:0140420 ! heme import into cell
[Term]
@@ -418199,19 +418386,19 @@ name: galactose import across plasma membrane
namespace: biological_process
def: "The directed movement of galactose from outside of a cell, across the plasma membrane and into the cytosol." [PMID:23254763]
is_a: GO:0015757 ! galactose transmembrane transport
-is_a: GO:0098657 ! import into cell
-is_a: GO:0098739 ! import across plasma membrane
+is_a: GO:0140271 ! hexose import across plasma membrane
[Term]
id: GO:0140426
-name: PAMP-triggered immunity signalling pathway
+name: pathogen-associated molecular pattern receptor signaling pathway
namespace: biological_process
-def: "Any series of molecular signals generated as a consequence of a pattern recognition receptor (PRR) binding to one of its physiological ligands to activate a plant innate immune response. PAMP-triggered immunity PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species." [PMID:25744358]
+def: "The series of molecular signals initiated by a ligand binding of a pattern recognition receptor (PRR) to activate a plant innate immune response. PAMP-triggered immunity PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species." [PMID:25744358]
synonym: "MAMP-triggered immunity signalling" EXACT []
+synonym: "PAMP receptor signaling pathway" EXACT []
+synonym: "PAMP-triggered immunity signalling pathway" EXACT []
synonym: "pathogen-associated molecular pattern signalling" EXACT []
synonym: "PTI signalling" EXACT []
is_a: GO:0002221 ! pattern recognition receptor signaling pathway
-is_a: GO:0002758 ! innate immune response-activating signal transduction
[Term]
id: GO:0140429
@@ -418256,7 +418443,7 @@ id: GO:0140432
name: 5'-hydroxyl dinucleotide hydrolase
namespace: molecular_function
def: "Catalysis of the hydrolysis of phosphodiester bonds in 5'OH-RNA according to the reaction 5'OH-RNA + H20 = 5'OH-NpN (dinucleotide) + 5'P-RNA." [PMID:31777937]
-is_a: GO:0004540 ! ribonuclease activity
+is_a: GO:0004540 ! RNA nuclease activity
[Term]
id: GO:0140433
@@ -418464,14 +418651,6 @@ def: "Catalysis of the removal of a methyl group from a protein." [PMID:24498420
is_a: GO:0032451 ! demethylase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
-[Term]
-id: GO:0140458
-name: pre-transcriptional gene silencing by RNA
-namespace: biological_process
-def: "Any gene inactivation (silencing) process mediated by small RNA molecules that occur before the trancription begins." [PMID:21420348]
-is_a: GO:0031047 ! gene silencing by RNA
-is_a: GO:0031507 ! heterochromatin assembly
-
[Term]
id: GO:0140459
name: response to Gram-positive bacterium
@@ -418499,26 +418678,29 @@ id: GO:0140462
name: pericentric heterochromatin organization
namespace: biological_process
def: "The organization of chromatin into heterochromatin at the pericentric region of a chromosome." [PMID:26744419]
-is_a: GO:0070828 ! heterochromatin organization
+is_a: GO:0031507 ! heterochromatin formation
[Term]
id: GO:0140463
-name: chromatin-protein adaptor
+name: chromatin-protein adaptor activity
namespace: molecular_function
def: "The binding activity of a molecule that brings together a protein or a protein complex with a nucleosome, to establish or maintain the chromatin localization of the protein, or protein complex." [PMID:32277274]
synonym: "chromatin adaptor" EXACT []
synonym: "chromatin adaptor activity" EXACT []
synonym: "chromatin receptor" EXACT []
synonym: "chromatin recruitment" RELATED []
+synonym: "chromatin-protein adaptor" EXACT []
synonym: "protein-chromatin adaptor activity" EXACT []
is_a: GO:0030674 ! protein-macromolecule adaptor activity
[Term]
id: GO:0140464
-name: silent mating-type cassette heterochromatin organization
+name: subnuclear spatial organization of silent mating-type cassette heterochromatin
namespace: biological_process
-def: "The organization of chromatin into heterochromatin at a silent mating-type cassette locus." [PMID:26744419]
-is_a: GO:0070828 ! heterochromatin organization
+def: "The localization of silent mating-type cassette heterochromatin at a specific location in the nucleus." [PMID:26744419]
+synonym: "silent mating-type cassette heterochromatin organization" RELATED []
+synonym: "silent mating-type cassette heterochromatin spatial organization in the nucleus" EXACT []
+is_a: GO:0097240 ! chromosome attachment to the nuclear envelope
[Term]
id: GO:0140466
@@ -418526,7 +418708,6 @@ name: iron-sulfur cluster export from the mitochondrion
namespace: biological_process
def: "The directed movement of iron sulfur clusters from inside the mitochondrion into the cytosol by crossing the inner mitochondrial membrane." [PMID:31040179]
is_a: GO:1902497 ! iron-sulfur cluster transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0140467
@@ -418635,7 +418816,7 @@ id: GO:0140482
name: iron sensor activity
namespace: molecular_function
def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of iron." [PMID:11956219, PMID:25806539]
-is_a: GO:0140299 ! small molecule sensor activity
+is_a: GO:0140784 ! metal ion sensor activity
[Term]
id: GO:0140483
@@ -418654,8 +418835,6 @@ def: "The directed movement of 5-aminolevulinic acid from outside of a cell, acr
is_a: GO:0015695 ! organic cation transport
is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0140485
@@ -418666,20 +418845,20 @@ xref: RHEA:64816
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0015101 ! organic cation transmembrane transporter activity
is_a: GO:0015171 ! amino acid transmembrane transporter activity
-is_a: GO:0140360 ! cyclic-GMP-AMP transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:0140486
name: zinc ion sequestering activity
namespace: molecular_function
-def: "The selective interaction of a protein with a zinc ion to prevent it from interacting with sensitive components of a biological system." [PMID:12050156]
+def: "Binding to a zinc ion to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active." [PMID:12050156]
is_a: GO:0140487 ! metal ion sequestering activity
[Term]
id: GO:0140487
name: metal ion sequestering activity
namespace: molecular_function
-def: "The selective interaction of a protein with a metal ion to prevent it from interacting with sensitive components of a biological system." [PMID:12050156]
+def: "Binding to a metal ion to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active." [PMID:12050156]
is_a: GO:0140313 ! molecular sequestering activity
[Term]
@@ -418704,19 +418883,11 @@ def: "The action of a molecule that provides a shape mimicking the end of a micr
synonym: "microtubule nucleation template activity" EXACT []
is_a: GO:0140489 ! molecular template activity
-[Term]
-id: GO:0140491
-name: ubiquitin-like hydrolase activity
-namespace: molecular_function
-def: "An activity that cleaves ubiquitin or ubiquitin-like proteins (ULP) from target proteins." [PMID:19489724]
-synonym: "ubiquitinyl-like hydrolase activity" EXACT []
-is_a: GO:0008233 ! peptidase activity
-
[Term]
id: GO:0140492
name: metal-dependent deubiquitinase activity
namespace: molecular_function
-def: "Catalysis of the metal-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin." [PMID:19489724]
+def: "An metal-dependent isopeptidase activity that cleaves ubiquitin from a target protein to which it is conjugated." [PMID:19489724]
synonym: "metal-dependent ubiquitin-like hydrolase activity" EXACT []
synonym: "metal-dependent ubiquitinyl-like hydrolase activity" EXACT []
is_a: GO:0008237 ! metallopeptidase activity
@@ -418726,7 +418897,7 @@ is_a: GO:0101005 ! deubiquitinase activity
id: GO:0140493
name: very long-chain fatty acid beta-oxidation
namespace: biological_process
-def: "A fatty acid beta-oxidation pathway acting on fatty acid which has a chain length greater than C22 in which the initial step, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA oxidase; the electrons removed by oxidation pass directly to oxygen and produce hydrogen peroxide, which is cleaved by peroxisomal catalases. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively)." [GOC:ha, PMID:17028011, PMID:32169171]
+def: "A fatty acid beta-oxidation pathway acting on a very long chain fatty acid, a fatty acid with an aliphatic tail of 22 or more carbons. The partway stars with the conversion of an acyl-CoA to a trans-2-enoyl-CoA, catalyzed by acyl-CoA oxidase; the electrons removed by oxidation pass directly to oxygen and produce hydrogen peroxide, which is cleaved by peroxisomal catalases. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively)." [GOC:ha, PMID:17028011, PMID:32169171]
is_a: GO:0033540 ! fatty acid beta-oxidation using acyl-CoA oxidase
is_a: GO:0042760 ! very long-chain fatty acid catabolic process
@@ -418742,7 +418913,7 @@ id: GO:0140495
name: migracytosis
namespace: biological_process
def: "A cell migration-dependent mechanism for releasing cellular contents." [PMID:25342562]
-is_a: GO:0016477 ! cell migration
+is_a: GO:0140352 ! export from cell
[Term]
id: GO:0140496
@@ -418848,7 +419019,7 @@ is_a: GO:0043495 ! protein-membrane adaptor activity
id: GO:0140507
name: granzyme-mediated programmed cell death signaling pathway
namespace: biological_process
-def: "A series of molecular signals induced by granzymes which triggers the cell death of a cell. The pathway starts with reception of a granzyme signal, and ends when the execution phase of cell death is triggered. Granzymes are serine proteases that are secreted by cytotoxic T cells and natural killer cells to induce cell death in target cells." [PMID:32299851]
+def: "The series of molecular signals induced by granzymes which triggers the cell death of a cell. The pathway starts with reception of a granzyme signal, and ends when the execution phase of cell death is triggered. Granzymes are serine proteases that are secreted by cytotoxic T cells and natural killer cells to induce cell death in target cells." [PMID:32299851]
synonym: "granzyme-mediated cell death signaling pathway" BROAD []
is_a: GO:0007165 ! signal transduction
relationship: part_of GO:0012501 ! programmed cell death
@@ -419044,7 +419215,7 @@ name: transcription regulator activator activity
namespace: molecular_function
def: "A molecular function regulator that increases the activity of a transcription regulator via direct binding and/or post-translational modification." [PMID:9597751]
comment: Usage guidance: transcription regulator activators bind to a transcription regulator to allow it to reach the chromatin or to contact other transcriptional regulators. This activity does not occur at the promoter. For activities that do occur at the promoter, consider GO:0001216 ; DNA-binding transcription activator activity or GO:0003713; transcription coactivator activity; those activities respectively bind DNA themselves or positively regulate a transcription regulator when it is located at the chromatin.
-is_a: GO:0140677 ! molecular function activator activity
+is_a: GO:0098772 ! molecular function regulator activity
[Term]
id: GO:0140538
@@ -419087,7 +419258,7 @@ id: GO:0140542
name: regulation of piRNA transcription
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the synthesis of a piRNA." [PMID:28847004]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0140747 ! regulation of ncRNA transcription
relationship: regulates GO:0140541 ! piRNA transcription
[Term]
@@ -419095,7 +419266,7 @@ id: GO:0140543
name: positive regulation of piRNA transcription
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of the synthesis of piRNA." [PMID:28847004]
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
is_a: GO:0140542 ! regulation of piRNA transcription
relationship: positively_regulates GO:0140541 ! piRNA transcription
@@ -419109,10 +419280,13 @@ is_a: GO:0032185 ! septin cytoskeleton organization
[Term]
id: GO:0140545
-name: protein disaggregase activity
+name: ATP-dependent protein disaggregase activity
namespace: molecular_function
def: "An ATP-dependent molecular chaperone activity that mediates the solubilization of ordered protein aggregates." [PMID:26312418]
+synonym: "protein disaggregase activity" BROAD []
+synonym: "protein unfoldase activity" BROAD []
is_a: GO:0140657 ! ATP-dependent activity
+is_a: GO:0140776 ! protein-containing complex destabilizing activity
[Term]
id: GO:0140546
@@ -419153,7 +419327,8 @@ id: GO:0140550
name: phosphatidylinositol-4,5-bisphosphate sensor activity
namespace: molecular_function
def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of phosphatidylinositol-4,5-bisphosphate." [PMID:33172987]
-is_a: GO:0140299 ! small molecule sensor activity
+synonym: "phosphatidylinositol-4,5-bisphosphate sensing activity" EXACT []
+is_a: GO:0106254 ! lipid sensor activity
[Term]
id: GO:0140552
@@ -419211,19 +419386,19 @@ is_a: GO:0035252 ! UDP-xylosyltransferase activity
[Term]
id: GO:0140566
-name: histone reader
+name: histone reader activity
namespace: molecular_function
def: "A chromatin adaptor that recognizes specific forms of histones, either modified by a post-translational modification, or the unmodified form. Histone readers have roles in many processes, including in centromere function or in modulating the accessibility of cis-regulatory regions to the transcription machinery." [PMID:11498575, PMID:25688442, PMID:31082667, PMID:32260176, PMID:34726351]
synonym: "epigenetic reader" BROAD []
-is_a: GO:0140463 ! chromatin-protein adaptor
+synonym: "histone reader" EXACT []
+is_a: GO:0140463 ! chromatin-protein adaptor activity
[Term]
id: GO:0140567
-name: transmembrane protein dislocase activity
+name: membrane protein dislocase activity
namespace: molecular_function
def: "The activity of removing a protein from a membrane, by binding to a transmembrane helical fragment of a tail-anchored protein and releasing it from the the hydrophobic region of one or both lipid bilayers. The reaction is driven by ATP hydrolysis." [PMID:24821790, PMID:28712723, PMID:32973005]
-synonym: "transmembrane helix dislocase" RELATED []
-xref: RHEA:66168
+synonym: "transmembrane helix dislocase\ntransmembrane protein dislocase activity" RELATED []
is_a: GO:0140318 ! protein transporter activity
is_a: GO:0140657 ! ATP-dependent activity
@@ -419292,7 +419467,7 @@ name: ascorbate homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of ascorbate at the level of a cell." [PMID:1623014, PMID:17068337, PMID:32547589]
synonym: "cellular ascorbate homeostasis" NARROW []
-is_a: GO:0055081 ! anion homeostasis
+is_a: GO:0048878 ! chemical homeostasis
[Term]
id: GO:0140579
@@ -419321,13 +419496,13 @@ xref: EC:7.2.2.8
xref: RHEA:25792
is_a: GO:0005375 ! copper ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
[Term]
id: GO:0140582
name: adenylate cyclase-activating G protein-coupled cAMP receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by cAMP binding to its receptor on the surface of the target cell, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex." [PMID:9578623]
+def: "An adenylate cyclase-activating G protein-coupled receptor signaling pathway initiated by extracellular cAMP binding to its receptor on the surface of the target cell, and ending with the regulation of a downstream cellular process." [PMID:9578623]
synonym: "extracellular cAMP signaling pathway" EXACT []
is_a: GO:0007189 ! adenylate cyclase-activating G protein-coupled receptor signaling pathway
@@ -419380,9 +419555,10 @@ is_a: GO:0006325 ! chromatin organization
[Term]
id: GO:0140590
-name: effector-mediated suppression of host defenses
+name: effector-mediated suppression of host defense response
namespace: biological_process
def: "A process mediated by a molecule secreted by a symbiont that results in the supression of a defense response. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:28082413]
+synonym: "effector-mediated suppression of host defenses" RELATED []
synonym: "effector-mediated suppression of host defenses by symbiont" EXACT []
is_a: GO:0044414 ! suppression of host defenses by symbiont
is_a: GO:0140415 ! effector-mediated modulation of host defenses by symbiont
@@ -419396,10 +419572,15 @@ is_a: GO:0051168 ! nuclear export
[Term]
id: GO:0140592
-name: histone methyltransferase activity (H3-R8 specific)
+name: histone H3R8 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 8) = S-adenosyl-L-homocysteine + (histone H3-N-methyl-arginine (position 8). This reaction is the addition of a methyl group to arginine at position 8 of histone H3." [PMID:20708585, PMID:31533925]
-is_a: GO:0008469 ! histone-arginine N-methyltransferase activity
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 8) = S-adenosyl-L-homocysteine + (histone H3-N-methyl-arginine (position 8). This reaction is the addition of a methyl group to the arginine residue at position 8 of histone H3." [PMID:20708585, PMID:31533925]
+synonym: "histone H3R8 arginine methylase activity" EXACT []
+synonym: "histone H3R8 arginine methyltransferase activity" EXACT []
+synonym: "histone methyltransferase activity (H3-R8 specific)" EXACT []
+synonym: "histone-H3R8 methyltransferase activity" EXACT []
+is_a: GO:0016274 ! protein-arginine N-methyltransferase activity
+is_a: GO:0140938 ! histone H3 methyltransferase activity
[Term]
id: GO:0140593
@@ -419509,7 +419690,7 @@ is_a: GO:0033014 ! tetrapyrrole biosynthetic process
id: GO:0140610
name: RNA sequestering activity
namespace: molecular_function
-def: "The selective interaction of a protein with a specific RNA molecule to prevent it from interacting with other partners or inhibiting its localization to other areas of the cell." [PMID:29084823]
+def: "Binding to a specific RNA molecule to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active." [PMID:29084823]
is_a: GO:0140313 ! molecular sequestering activity
[Term]
@@ -419517,6 +419698,7 @@ id: GO:0140612
name: DNA damage sensor activity
namespace: molecular_function
def: "A molecule that recognises toxic DNA structures, for example, double-strand breaks or collapsed replication forks, and initiates a signalling response." [PMID:31995034]
+synonym: "DNA damage sensing activity" EXACT []
is_a: GO:0140299 ! small molecule sensor activity
[Term]
@@ -419527,7 +419709,7 @@ def: "Enables the transfer of a solute or solutes from one side of a membrane to
xref: RHEA:66820
is_a: GO:0005384 ! manganese ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
[Term]
id: GO:0140614
@@ -419552,7 +419734,7 @@ is_a: GO:1990234 ! transferase complex
id: GO:0140616
name: iodotyrosine deiodinase activity
namespace: molecular_function
-def: "Catalyzes the reaction: 2 iodide + L-tyrosine + 2 NADP+ = 3,5-diiodo-L-tyrosine + H+ + 2 NADPH." [PMID:15289438, PMID:18434651, PMID:25395621, PMID:27643701, RHEA:32479]
+def: "Catalyzes the reaction: 2 iodide + L-tyrosine + 2 NADP+ = 3,5-diiodo-L-tyrosine + H+ + 2 NADPH. Note that this activity has only been demonstrated in the direction of 3-deiodination. 3-bromo-L-tyrosine and 3-chloro-L-tyrosine can also be used as substrates." [PMID:15289438, PMID:18434651, PMID:25395621, PMID:27643701, RHEA:32479]
synonym: "iodide peroxidase-tyrosine iodinase activity" RELATED []
synonym: "iodotyrosine deiodase activity" RELATED []
synonym: "monoiodotyrosine deiodinase activity" RELATED []
@@ -419563,16 +419745,18 @@ is_a: GO:0046992 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y
[Term]
id: GO:0140617
-name: transvection
+name: obsolete transvection
namespace: biological_process
-def: "An epigenetic regulation of transcription by physical interaction between a cis-acting element (enhancer, silencer) of one allele on one chromosome and the promoter of the corresponding allele on the homologous chromosome. Transvection can lead to either gene activation or repression." [PMID:24236213, PMID:33479152]
-is_a: GO:0040029 ! regulation of gene expression, epigenetic
+def: "OBSOLETE. An epigenetic regulation of transcription by physical interaction between a cis-acting element (enhancer, silencer) of one allele on one chromosome and the promoter of the corresponding allele on the homologous chromosome. Transvection can lead to either gene activation or repression." [PMID:24236213, PMID:33479152]
+comment: This term was obsoleted because it represents an observation, not a GO process.
+is_obsolete: true
+consider: GO:0040029
[Term]
id: GO:0140618
name: ferric-chelate reductase (NADH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 Fe3+-siderophore + NAD(+) + H(+) -> 2 Fe2+-siderophore + NADH." [RHEA:15061]
+def: "Catalysis of the reaction: 2 Fe3+-siderophore + NAD+ + H+ -> 2 Fe2+-siderophore + NADH." [RHEA:15061]
synonym: "ferric chelate reductase activity" BROAD []
synonym: "iron chelate reductase activity" BROAD []
synonym: "NADH:Fe(3+) oxidoreductase activity" EXACT [EC:1.16.1.7]
@@ -419698,7 +419882,7 @@ is_a: GO:0004857 ! enzyme inhibitor activity
[Term]
id: GO:0140632
-name: inflammasome complex assembly
+name: canonical inflammasome complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form an inflammasome complex." [PMID:33420028, PMID:33420033, PMID:33542150]
is_a: GO:0065003 ! protein-containing complex assembly
@@ -419708,14 +419892,14 @@ id: GO:0140633
name: CARD8 inflammasome complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a CARD8 inflammasome complex." [PMID:33420028, PMID:33420033, PMID:33542150]
-is_a: GO:0140632 ! inflammasome complex assembly
+is_a: GO:0140632 ! canonical inflammasome complex assembly
[Term]
id: GO:0140634
name: CARD8 inflammasome complex
namespace: cellular_component
def: "An inflammasome complex that consists of CARD8 and CASP1." [PMID:33420028, PMID:33420033, PMID:33542150]
-is_a: GO:0061702 ! inflammasome complex
+is_a: GO:0061702 ! canonical inflammasome complex
[Term]
id: GO:0140635
@@ -419729,9 +419913,7 @@ id: GO:0140636
name: copper import into the mitochondrion
namespace: biological_process
def: "The process in which copper is transported from the cytosol into the mitochondrial matrix." [PMID:32979421]
-is_a: GO:0015677 ! copper ion import
is_a: GO:0035434 ! copper ion transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0140638
@@ -419739,7 +419921,7 @@ name: small ribosomal subunit processing complex
namespace: cellular_component
def: "A small heterodimeric protein complex that is required during early maturation of nascent 40S ribosomal subunits. The complex has endonuclease activity, it interacts with the small ribosomal subunit pre-rRNA and cleave it it to produce the mature 18S (or small ribosomal subunit) rRNA. In S. cerevisiae it is composed of Rcl1p and Bms1p." [GOC:lnp, PMID:21849504, PMID:25064857]
synonym: "small ribosomal subunit maturation complex" RELATED []
-is_a: GO:1905348 ! endonuclease complex
+is_a: GO:1902555 ! endoribonuclease complex
[Term]
id: GO:0140639
@@ -419776,7 +419958,7 @@ is_a: GO:0090306 ! meiotic spindle assembly
id: GO:0140643
name: hydroxymethylglutaryl-CoA reductase (NADH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-mevalonate + CoA + 2 NAD(+) <=> 3-hydroxy-3-methylglutaryl-CoA + 2 NADH." [PMID:29224355, RHEA:14833]
+def: "Catalysis of the reaction: (R)-mevalonate + CoA + 2 NAD+ <=> 3-hydroxy-3-methylglutaryl-CoA + 2 NADH." [PMID:29224355, RHEA:14833]
comment: Note that this activity is not present in eukaryotes, see PMID:29224355.
synonym: "3-hydroxy-3-methylglutaryl coenzyme A reductase activity" BROAD [EC:1.1.1.88]
synonym: "beta-hydroxy-beta-methylglutaryl CoA-reductase activity" BROAD [EC:1.1.1.88]
@@ -419877,17 +420059,16 @@ is_a: GO:1901362 ! organic cyclic compound biosynthetic process
[Term]
id: GO:0140653
-name: fumitremorgin C biosynthetic process
+name: obsolete fumitremorgin C biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of fumitremorgin C." [GOC:ach, PMID:19226505]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of the indole alkaloid fumitremorgin C." [GOC:ach, PMID:19226505]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "fumitremorgin C anabolism" EXACT []
synonym: "fumitremorgin C biosynthesis" EXACT []
synonym: "fumitremorgin C formation" EXACT []
synonym: "fumitremorgin C synthesis" EXACT []
-is_a: GO:0019438 ! aromatic compound biosynthetic process
-is_a: GO:0035835 ! indole alkaloid biosynthetic process
-is_a: GO:1901378 ! organic heteropentacyclic compound biosynthetic process
-is_a: GO:1901503 ! ether biosynthetic process
+is_obsolete: true
+replaced_by: GO:1900772
[Term]
id: GO:0140654
@@ -419928,6 +420109,7 @@ subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_yeast
+subset: prokaryote_subset
synonym: "ATP hydrolysis-dependent activity" EXACT []
synonym: "ATPase activity" EXACT []
synonym: "ATPase activity, coupled" EXACT []
@@ -419952,7 +420134,7 @@ name: cytoskeletal motor regulator activity
namespace: molecular_function
def: "Binds to and modulates the activity of a motor protein." [PMID:23142046, PMID:33221250]
synonym: "motor activity regulator activity" BROAD []
-is_a: GO:0098772 ! molecular function regulator
+is_a: GO:0098772 ! molecular function regulator activity
[Term]
id: GO:0140660
@@ -419961,7 +420143,6 @@ namespace: molecular_function
def: "Binds to and increases the activity of a motor protein." [PMID:33221250]
synonym: "motor activity activator activity" BROAD []
is_a: GO:0140659 ! cytoskeletal motor regulator activity
-is_a: GO:0140677 ! molecular function activator activity
[Term]
id: GO:0140661
@@ -419970,7 +420151,6 @@ namespace: molecular_function
def: "Binds to and stops, prevents, or reduces the activity of a motor protein." [PMID:23142046]
synonym: "motor activity inhibitor activity" BROAD []
is_a: GO:0140659 ! cytoskeletal motor regulator activity
-is_a: GO:0140678 ! molecular function inhibitor activity
[Term]
id: GO:0140662
@@ -419993,20 +420173,23 @@ id: GO:0140664
name: ATP-dependent DNA damage sensor activity
namespace: molecular_function
def: "A molecule that recognises toxic DNA structures, and initiates a signalling response, driven by ATP hydrolysis." [PMID:33302090, PMID:33510387]
+synonym: "ATP-dependent DNA damage sensing activity" EXACT []
is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
is_a: GO:0140612 ! DNA damage sensor activity
[Term]
id: GO:0140665
-name: ATP-dependent H3-H4 histone complex loader activity
+name: ATP-dependent H3-H4 histone complex chaperone activity
namespace: molecular_function
-def: "Loading of a histone H3-H4 complex onto DNA, driven by ATP hydrolysis." [PMID:31848341, PMID:33658433]
+def: "A histone chaperone that carries a H3-H4 histone complex, driven by ATP hydrolysis." [PMID:31848341, PMID:33658433]
+synonym: "ATP-dependent H3-H4 histone complex loader activity" NARROW []
synonym: "H3-H4 dimer loading activity" EXACT []
synonym: "H3-H4 histone chaperone" BROAD []
synonym: "H3-H4 histone complex loader activity" BROAD []
synonym: "histone chaperone" RELATED []
synonym: "histone H3-H4 dimer loading activity" EXACT []
-is_a: GO:0140674 ! ATP-dependent histone loader activity
+is_a: GO:0000510 ! H3-H4 histone complex chaperone activity
+is_a: GO:0140674 ! ATP-dependent histone chaperone activity
[Term]
id: GO:0140666
@@ -420015,6 +420198,7 @@ namespace: molecular_function
alt_id: GO:0097617
def: "An activity that facilitates the formation of a complementary double-stranded polynucleotide molecule." [PMID:22888405]
synonym: "renaturation" RELATED []
+xref: Reactome:R-HSA-5686642 "RAD52 promotes single strand annealing at resected DNA DSBs"
is_a: GO:0003676 ! nucleic acid binding
[Term]
@@ -420045,10 +420229,12 @@ relationship: negatively_regulates GO:0036162 ! oxytocin production
[Term]
id: GO:0140670
-name: ATP-dependent cohesin unloading activity
+name: cohesin unloader activity
namespace: molecular_function
-def: "Facilitating a conformational change to unload a cohesin complex from sister chromatids, driven by ATP hydrolysis." [PMID:26687354]
-is_a: GO:0140083 ! ATP-dependent protein-DNA unloading activity
+def: "Facilitating a conformational change to unload a cohesin complex from sister chromatids." [PMID:26687354]
+synonym: "ATP-dependent cohesin unloader activity" RELATED []
+synonym: "ATP-dependent cohesin unloading activity" RELATED []
+is_a: GO:0140097 ! catalytic activity, acting on DNA
[Term]
id: GO:0140671
@@ -420077,34 +420263,38 @@ is_a: GO:0070461 ! SAGA-type complex
[Term]
id: GO:0140673
-name: co-transcriptional chromatin reassembly
+name: transcription elongation-coupled chromatin remodeling
namespace: biological_process
-def: "The reestablishment of chromatin structure that was disrupted upon passage of RNA polymerase II during transcription elongation. This process prevents cryptic intragenic transcription initiation." [PMID:22922743]
-comment: Note: Do not confuse with 'GO:0045815 epigenetic maintenance of chromatin in transcription-competent conformation', which describes the maintenance of chromatin in an open conformation (indeendent of transcription).
+def: "A chromatin remodeling process that reestablishes the chromatin structure following the passage of RNA polymerase II during transcription elongation, thus preventing cryptic transcription initiation." [PMID:22922743, PMID:28053344]
+comment: Note: Do not confuse with 'GO:0045815 transcriptional initiation-coupled chromatin remodeling', which describes the maintenance of chromatin in an open conformation, allowing the transcriptional machinery to access the DNA.
synonym: "chromatin maintenance during transcription elongation" RELATED []
+synonym: "co-transcriptional chromatin reassembly" EXACT []
+synonym: "DNA replication-independent chromatin organization" RELATED []
synonym: "euchromatin maintenance during transcription elongation" EXACT []
synonym: "maintainance of chromatin integrity during transcription elongation by RNAPII" EXACT []
synonym: "maintenance of transcriptionally active chromatin during transcription elongation" EXACT []
-is_a: GO:0031497 ! chromatin assembly
-relationship: part_of GO:0006368 ! transcription elongation from RNA polymerase II promoter
+synonym: "transciptional elongation-coupled chromatin remodeling" EXACT []
+synonym: "transcription elongation coupled chromatin remodeling" EXACT []
+synonym: "transcriptional elongation-coupled chromatin remodeling" EXACT []
+is_a: GO:0006338 ! chromatin remodeling
+relationship: part_of GO:0006368 ! transcription elongation by RNA polymerase II
[Term]
id: GO:0140674
-name: ATP-dependent histone loader activity
-namespace: molecular_function
-def: "Depositing a histone or a histone complex onto DNA." [PMID:26459557]
-synonym: "histone loader activity" BROAD []
-synonym: "histone loading activity" EXACT []
-is_a: GO:0140658 ! ATP-dependent chromatin remodeler activity
-
-[Term]
-id: GO:0140675
-name: ATP-dependent histone unloader activity
-namespace: molecular_function
-def: "Removing a histone or a histone complex from DNA." [PMID:26459557]
-synonym: "histone unloader activity" BROAD []
-synonym: "histone unloading activity" EXACT []
+name: ATP-dependent histone chaperone activity
+namespace: molecular_function
+alt_id: GO:0140675
+def: "Binding to and carrying a histone or a histone complex to unload or deposit it as a nucleosome, driven by ATP hydrolysis." [PMID:26459557]
+synonym: "ATP-dependent histone loader activity" NARROW []
+synonym: "ATP-dependent histone unloader activity" NARROW []
+synonym: "histone loader activity" NARROW []
+synonym: "histone loading activity" NARROW []
+synonym: "histone unloader activity" NARROW []
+synonym: "histone unloading activity" NARROW []
+synonym: "nucleosome remodeling activity" RELATED []
+is_a: GO:0140096 ! catalytic activity, acting on a protein
is_a: GO:0140658 ! ATP-dependent chromatin remodeler activity
+is_a: GO:0140713 ! histone chaperone activity
[Term]
id: GO:0140676
@@ -420119,14 +420309,14 @@ id: GO:0140677
name: molecular function activator activity
namespace: molecular_function
def: "A molecular function regulator that activates or increases the activity of its target via non-covalent binding that does not result in covalent modification to the target." [GOC:curators]
-is_a: GO:0098772 ! molecular function regulator
+is_a: GO:0098772 ! molecular function regulator activity
[Term]
id: GO:0140678
name: molecular function inhibitor activity
namespace: molecular_function
def: "A molecular function regulator that inhibits or decreases the activity of its target via non-covalent binding that does not result in covalent modification to the target." [GOC:curators]
-is_a: GO:0098772 ! molecular function regulator
+is_a: GO:0098772 ! molecular function regulator activity
[Term]
id: GO:0140679
@@ -420137,78 +420327,84 @@ xref: EC:7.2.2.4
xref: RHEA:14633
xref: TC:3.A.1.115.1
is_a: GO:0015081 ! sodium ion transmembrane transporter activity
-is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
[Term]
id: GO:0140680
-name: histone H3-di/monomethyl-lysine-36 demethylase activity
+name: histone H3K36me/H3K36me2 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:20531378]
+synonym: "histone H3-di/monomethyl-lysine-36 demethylase activity" EXACT []
synonym: "histone H3K36me demethylase activity" RELATED []
synonym: "histone H3K36me2 demethylase activity" BROAD []
xref: EC:1.14.11.27
xref: MetaCyc:RXN-8661
xref: RHEA:42032
-is_a: GO:0051864 ! histone H3-methyl-lysine-36 demethylase activity
+is_a: GO:0051864 ! histone H3K36 demethylase activity
[Term]
id: GO:0140681
-name: histone H3-tri/dimethyl-lysine-36 demethylase activity
+name: histone H3K36me2/H3K36me3 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a tri- or a dimethyl-lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:21914792]
+synonym: "histone H3-tri/dimethyl-lysine-36 demethylase activity" EXACT []
synonym: "histone H3K36me2 demethylase activity" BROAD []
synonym: "histone H3K36me3 demethylase activity" RELATED []
xref: EC:1.14.11.69
xref: MetaCyc:RXN-8660
xref: RHEA:60236
-is_a: GO:0051864 ! histone H3-methyl-lysine-36 demethylase activity
+is_a: GO:0051864 ! histone H3K36 demethylase activity
[Term]
id: GO:0140682
-name: histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity
+name: FAD-dependent H3K4me/H3K4me3 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 4 of the histone H3 protein. This is a flavin adenine dinucleotide (FAD)-dependent amine oxidation reaction." [PMID:22473470]
+synonym: "histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity" EXACT []
synonym: "histone H3K4me demethylase activity" RELATED []
synonym: "histone H3K4me2 demethylase activity" BROAD []
xref: EC:1.14.99.66
xref: RHEA:60244
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
-is_a: GO:0032453 ! histone H3-methyl-lysine-4 demethylase activity
+is_a: GO:0032453 ! histone H3K4 demethylase activity
[Term]
id: GO:0140683
-name: histone H3-di/monomethyl-lysine-9 demethylase activity
+name: histone H3K9me/H3K9me2 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a di or a monomethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:16603238]
+synonym: "histone H3-di/monomethyl-lysine-9 demethylase activity" EXACT []
synonym: "histone H3K9me demethylase activity" BROAD []
synonym: "histone H3K9me2 demethylase activity" BROAD []
xref: EC:1.14.11.65
xref: RHEA:60188
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
-is_a: GO:0032454 ! histone H3-methyl-lysine-9 demethylase activity
+is_a: GO:0032454 ! histone H3K9 demethylase activity
[Term]
id: GO:0140684
-name: histone H3-tri/dimethyl-lysine-9 demethylase activity
+name: histone H3K9me2/H3K9me3 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a tri or a dimethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:20208542, PMID:20531378]
+synonym: "histone H3-tri/dimethyl-lysine-9 demethylase activity" EXACT []
synonym: "histone H3K9me2 demethylase activity" BROAD []
synonym: "histone H3K9me3 demethylase activity" RELATED []
xref: EC:1.14.11.66
xref: RHEA:60200
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
-is_a: GO:0032454 ! histone H3-methyl-lysine-9 demethylase activity
+is_a: GO:0032454 ! histone H3K9 demethylase activity
[Term]
id: GO:0140685
-name: histone H3-di/monomethyl-lysine-9 FAD-dependent demethylase activity
+name: FAD-dependent histone H3K9me/H3K9me2 demethylase activity
namespace: molecular_function
def: "Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 9 of the histone H3 protein. This is a flavin adenine dinucleotide (FAD)-dependent amine oxidation reaction." [PMID:22473470]
+synonym: "histone H3-di/monomethyl-lysine-9 FAD-dependent demethylase activity" EXACT []
synonym: "histone H3K9me demethylase activity" BROAD []
synonym: "histone H3K9me2 demethylase activity" BROAD []
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
-is_a: GO:0032454 ! histone H3-methyl-lysine-9 demethylase activity
+is_a: GO:0032454 ! histone H3K9 demethylase activity
[Term]
id: GO:0140690
@@ -420223,14 +420419,14 @@ id: GO:0140691
name: RNA folding chaperone
namespace: molecular_function
def: "Binding to an RNA or an RNA-containing complex to assist the folding process." [PMID:31165735]
-subset: goslim_generic
is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0140692
name: very long-chain fatty acid omega-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an omega-methyl-very-long-chain fatty acid + O2 + reduced [NADPH-hemoprotein reductase] = an omega-hydroxy-very-long-chain fatty acid + H+ + H2O + oxidized [NADPH-hemoprotein reductase]." [PMID:16547005]
+def: "Catalysis of the reaction: an omega-methyl-very-long-chain fatty acid + O2 + reduced [NADPH-hemoprotein reductase] = an omega-hydroxy-very-long-chain fatty acid + H+ + H2O + oxidized [NADPH-hemoprotein reductase]. A very long chain fatty acid is a fatty acid with an aliphatic tail of 22 or more carbons." [PMID:16547005, RHEA:67952]
+xref: RHEA:67952
is_a: GO:0120250 ! fatty acid omega-hydroxylase activity
[Term]
@@ -420238,6 +420434,8 @@ id: GO:0140693
name: molecular condensate scaffold activity
namespace: molecular_function
def: "Binding and bringing together two or more macromolecules in contact, permitting those molecules to organize as a molecular condensate." [PMID:28225081]
+synonym: "phase separation nucleation activity" EXACT []
+synonym: "phase separation nucleator activity" EXACT []
is_a: GO:0030674 ! protein-macromolecule adaptor activity
[Term]
@@ -420307,9 +420505,6 @@ namespace: molecular_function
def: "Binding to cyclic GMP-AMP (cGAMP) nucleotide." [PMID:23258412]
subset: gocheck_do_not_annotate
is_a: GO:0030551 ! cyclic nucleotide binding
-is_a: GO:0032559 ! adenyl ribonucleotide binding
-is_a: GO:0032561 ! guanyl ribonucleotide binding
-is_a: GO:0043168 ! anion binding
[Term]
id: GO:0140703
@@ -420320,7 +420515,10 @@ synonym: "3',3' cyclic-GMP-AMP binding" EXACT []
synonym: "3',3'-cGAMP binding" EXACT []
synonym: "3',3'-cGMP-AMP binding" EXACT []
synonym: "3',3'-cyclic GAMP binding" EXACT []
-is_a: GO:0030551 ! cyclic nucleotide binding
+is_a: GO:0032559 ! adenyl ribonucleotide binding
+is_a: GO:0032561 ! guanyl ribonucleotide binding
+is_a: GO:0043168 ! anion binding
+is_a: GO:0140702 ! cyclic GMP-AMP binding
[Term]
id: GO:0140704
@@ -420330,7 +420528,7 @@ def: "Binding to 3',2' cyclic GMP-AMP (cGAMP) nucleotide, a cyclic purine dinucl
synonym: "3',2' cyclic-GMP-AMP binding" EXACT []
synonym: "3',2'-cGAMP binding" EXACT []
synonym: "3',2'-cyclic GAMP binding" EXACT []
-is_a: GO:0030551 ! cyclic nucleotide binding
+is_a: GO:0043168 ! anion binding
[Term]
id: GO:0140706
@@ -420343,7 +420541,7 @@ is_a: GO:0031503 ! protein-containing complex localization
id: GO:0140707
name: chromatin-nuclear membrane anchor activity
namespace: molecular_function
-def: "Binding to chromatin and the nuclear inner membrane, in order to establish and maintain the heterochromatin location and organization, or to enable equal segregation of the nuclear membrane during mitosis." [PMID:24184107]
+def: "Binding to chromatin and the nuclear inner membrane, in order to establish and maintain the heterochromatin location and organization, or to enable equal segregation of the nuclear membrane during mitosis." [PMID:24184107, PMID:31048766]
is_a: GO:0043495 ! protein-membrane adaptor activity
[Term]
@@ -420352,6 +420550,7 @@ name: CAT tailing
namespace: biological_process
def: "The C-terminal elongation of 60S-anchored stalled nascent polypeptide chains with untemplated alanine and threonine tails (CAT tails). CAT tails participate in the recognition of stalled nascent chains by the ribosome quality control sytem." [PMID:25554787, PMID:32934225]
is_a: GO:0002182 ! cytoplasmic translational elongation
+relationship: part_of GO:0072344 ! rescue of stalled ribosome
relationship: part_of GO:1990116 ! ribosome-associated ubiquitin-dependent protein catabolic process
[Term]
@@ -420399,8 +420598,9 @@ relationship: negatively_regulates GO:0140709 ! Frizzled Nuclear Import pathway
id: GO:0140713
name: histone chaperone activity
namespace: molecular_function
-def: "Binding to and carrying a histone or a histone complex until it is deposited on DNA, or degraded." [PMID:26459557]
+def: "Binding to and carrying a histone or a histone complex to unload or deposit it as a nucleosome. The histone can be newly synthesized or result from nucleosome disassembly (either spontaneously, or by a histone chaperone)." [PMID:26459557]
synonym: "histone carrier activity" EXACT []
+synonym: "nucleosome remodeling activity" RELATED []
is_a: GO:0140597 ! protein carrier chaperone
[Term]
@@ -420408,7 +420608,7 @@ id: GO:0140714
name: large ribosomal subunit pre-assembly complex
namespace: cellular_component
def: "A protein complex that assists early maturation of nascent 60S ribosomal subunits. The complex interacts with the large ribosomal subunit rRNA via one of the components (Urb2 in S. cerevisiae) and requires a RNA helicase (Dbp6 in S. cerevisiae)." [GOC:lnp, PMID:17145778, PMID:9528757]
-is_a: GO:0101031 ! chaperone complex
+is_a: GO:0101031 ! protein folding chaperone complex
[Term]
id: GO:0140715
@@ -420421,23 +420621,27 @@ is_a: GO:1902494 ! catalytic complex
id: GO:0140717
name: entry into host through the stromata
namespace: biological_process
-def: "Entry of a symbiont into host plant tissue via the stromata, microscopic pores in the epidermis of the aerial parts of terrestrial plants. These pores are essential for photosynthesis, as they allow CO(2) to diffuse into the plant. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:16959560, PMID:17419713, PMID:29307013]
+def: "Entry of a symbiont into host plant tissue via the stromata, microscopic pores in the epidermis of the aerial parts of terrestrial plants. These pores are essential for photosynthesis, as they allow CO2 to diffuse into the plant. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:16959560, PMID:17419713, PMID:29307013]
is_a: GO:0044409 ! entry into host
[Term]
id: GO:0140718
-name: facultative heterochromatin assembly
+name: facultative heterochromatin formation
namespace: biological_process
-def: "The assembly of facultative heterochromatin, heterochromatin that can be converted to euchromatin and allow transcription under specific contexts. These can be temporal (e.g., developmental states or specific cell-cycle stages), spatial (e.g., nuclear localization changes from the center to the periphery or vice versa due to exogenous factors/signals), or parental/heritable (e.g., monoallelic gene expression)." [PMID:17936700]
+def: "The compaction of chromatin into a conformation that is refactory to transcription but that be converted to euchromatin and allow transcription in specific contexts. These can be temporal (e.g., developmental states or specific cell-cycle stages), spatial (e.g., nuclear localization changes from the center to the periphery or vice versa due to exogenous factors/signals), or parental/heritable (e.g., monoallelic gene expression)." [PMID:17936700]
+comment: Note that facultative heterochromatin can be reprogrammed, as opposed to constitutive heterochromatin which usually cannot be reprogrammed to a transcriptionally-competent state.
+synonym: "facultative heterochromatin assembly" EXACT []
synonym: "fHC assembly" EXACT []
-is_a: GO:0031507 ! heterochromatin assembly
+is_a: GO:0031507 ! heterochromatin formation
[Term]
id: GO:0140719
-name: constitutive heterochromatin assembly
+name: constitutive heterochromatin formation
namespace: biological_process
-def: "The assembly of constitutive heterochromatin, heterochromatin that is always in a conformation refactory to transcription." [PMID:17936700]
-is_a: GO:0031507 ! heterochromatin assembly
+def: "The compaction of chromatin into a conformation that is refactory to transcription." [PMID:17936700]
+comment: Note that constitutive heterochromatin indicates that it usually cannot be reprogrammed to a transcriptionally-competent state, as opposed to facultative heterochromatin, which can be reprogrammed.
+synonym: "constitutive heterochromatin assembly" EXACT []
+is_a: GO:0031507 ! heterochromatin formation
[Term]
id: GO:0140720
@@ -420485,6 +420689,8 @@ synonym: "patulin formation" EXACT []
synonym: "patulin synthesis" EXACT []
is_a: GO:0030639 ! polyketide biosynthetic process
is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:0046165 ! alcohol biosynthetic process
+is_a: GO:1901336 ! lactone biosynthetic process
[Term]
id: GO:0140724
@@ -420495,6 +420701,7 @@ synonym: "positive regulation of patulin anabolism" EXACT []
synonym: "positive regulation of patulin formation" EXACT []
synonym: "positive regulation of patulin synthesis" EXACT []
is_a: GO:1900734 ! positive regulation of polyketide biosynthetic process
+is_a: GO:1902932 ! positive regulation of alcohol biosynthetic process
relationship: positively_regulates GO:0140723 ! patulin biosynthetic process
[Term]
@@ -420507,11 +420714,14 @@ is_a: GO:0098754 ! detoxification
[Term]
id: GO:0140727
-name: siRNA-dependent pericentric heterochromatin assembly
+name: siRNA-dependent pericentric heterochromatin formation
namespace: biological_process
-def: "The assembly of pericentric heterochromatin by a process mediated by a small interfering RNA." [PMID:15289661]
+def: "The formation of pericentric heterochromatin by a process mediated by a small interfering RNA." [PMID:15289661]
+synonym: "RNAi-mediated heterochromatin assembly at centromere" EXACT []
synonym: "siRNA dependent pericentric heterochromatin assembly" EXACT []
-is_a: GO:0031508 ! pericentric heterochromatin assembly
+synonym: "siRNA-dependent pericentric heterochromatin assembly" EXACT []
+is_a: GO:0031048 ! small ncRNA-mediated heterochromatin formation
+is_a: GO:0031508 ! pericentric heterochromatin formation
[Term]
id: GO:0140728
@@ -420568,7 +420778,7 @@ relationship: positively_regulates GO:0140730 ! amphiregulin production
id: GO:0140733
name: tRNA ligase activator activity
namespace: molecular_function
-def: "Binds to and increases the activity of a tRNA ligase, an enzyme that catalyzes the formation of aminoacyl-tRNA." [PMID:30943413]
+def: "Binds to and increases the activity of a tRNA ligase." [PMID:30943413]
is_a: GO:0008047 ! enzyme activator activity
is_a: GO:0055103 ! ligase regulator activity
@@ -420604,12 +420814,12 @@ synonym: "monacolin K biosynthesis" EXACT []
synonym: "monacolin K biosynthetic process" EXACT []
synonym: "monacolin K formation" EXACT []
synonym: "monacolin K synthesis" EXACT []
-xref: KEGG_PATHWAY:M00893
+xref: kegg.module:M00893
xref: MetaCyc:PWY-7535
-is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:0030639 ! polyketide biosynthetic process
is_a: GO:0043386 ! mycotoxin biosynthetic process
is_a: GO:1901336 ! lactone biosynthetic process
+is_a: GO:1901570 ! fatty acid derivative biosynthetic process
[Term]
id: GO:0140736
@@ -420636,22 +420846,23 @@ id: GO:0140738
name: NLRP6 inflammasome complex
namespace: cellular_component
def: "An inflammasome complex that consists of NLRP6, PYCARD/ASC and caspase-1 or caspase-4/caspase-11." [PMID:30674671, PMID:34678144]
-is_a: GO:0061702 ! inflammasome complex
+is_a: GO:0061702 ! canonical inflammasome complex
[Term]
id: GO:0140739
name: NLRP6 inflammasome complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a NLRP6 inflammasome complex." [PMID:30674671, PMID:34678144]
-is_a: GO:0140632 ! inflammasome complex assembly
+is_a: GO:0140632 ! canonical inflammasome complex assembly
[Term]
id: GO:0140740
name: ADP-riboxanase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arginyl-[protein] + NAD(+) = ADP-riboxanated L-argininyl-[protein] + H(+) + NH4(+) + nicotinamide." [PMID:34671164]
+def: "Catalysis of the reaction: L-arginyl-[protein] + NAD+ = ADP-riboxanated L-argininyl-[protein] + H+ + NH4(+) + nicotinamide." [PMID:34671164, RHEA:69500]
comment: Note that this activity has two steps: a transfer of an ADP-robose group, followed by the elimitation of an ammonia group.
xref: EC:4.3.99.-
+xref: RHEA:69500
is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups
is_a: GO:0016841 ! ammonia-lyase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -420682,7 +420893,7 @@ id: GO:0140743
name: regulation of lncRNA transcription
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the synthesis of a lncRNA." [PMID:33767452, PMID:33913806]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0140747 ! regulation of ncRNA transcription
relationship: regulates GO:0140742 ! lncRNA transcription
[Term]
@@ -420690,7 +420901,7 @@ id: GO:0140744
name: negative regulation of lncRNA transcription
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the synthesis of a lncRNA." [PMID:33767452, PMID:33913806]
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
is_a: GO:0140743 ! regulation of lncRNA transcription
relationship: negatively_regulates GO:0140742 ! lncRNA transcription
@@ -420699,7 +420910,7 @@ id: GO:0140745
name: siRNA transcription
namespace: biological_process
def: "The transcription of a small interfering RNA from an RNA template." [PMID:23001036]
-is_a: GO:0001172 ! transcription, RNA-templated
+is_a: GO:0001172 ! RNA-templated transcription
[Term]
id: GO:0140746
@@ -420708,6 +420919,2492 @@ namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of small interfering RNA transcripts (siRNAs)." [PMID:25928405]
is_a: GO:0034661 ! ncRNA catabolic process
+[Term]
+id: GO:0140747
+name: regulation of ncRNA transcription
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of transcription of a non-protein coding gene from a DNA-template." [GOC:pg]
+is_a: GO:0006355 ! regulation of DNA-templated transcription
+relationship: regulates GO:0098781 ! ncRNA transcription
+
+[Term]
+id: GO:0140748
+name: positive regulation of regulation of ascospore wall (1->3)-beta-D-glucan biosynthetic process
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of ascospore wall (1->3)-beta-D-glucan biosynthetic process." [PMID:19189958]
+is_a: GO:0060624 ! regulation of ascospore wall (1->3)-beta-D-glucan biosynthetic process
+is_a: GO:0060635 ! positive regulation of (1->3)-beta-D-glucan biosynthetic process
+is_a: GO:2000243 ! positive regulation of reproductive process
+relationship: positively_regulates GO:0034413 ! ascospore wall (1->3)-beta-D-glucan biosynthetic process
+
+[Term]
+id: GO:0140749
+name: phlorizin hydrolase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: phlorizin + H2O = beta-D-glucose + phloretin." [PMID:9762914, RHEA:69639]
+is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
+
+[Term]
+id: GO:0140750
+name: nucleosome array spacer activity
+namespace: molecular_function
+def: "A histone octamer slider activity that spaces nucleosomes along chromosomal DNA. This activity is involved in assembling chromatin in uniform nucleosome arrays to regulate transcription by RNA polymerases I, II, and III, as well as DNA replication, recombination and repair." [PMID:11683384, PMID:16468993]
+comment: In Drosphila, this is mediated by ISWI, in human, by SMARCA5 and in S. cerevisiae by ISW1 and and ISW2.
+synonym: "nucleosome array spacing activity" EXACT []
+is_a: GO:0140751 ! histone octamer slider activity
+
+[Term]
+id: GO:0140751
+name: histone octamer slider activity
+namespace: molecular_function
+def: "A chromatin remodeler activity that slides core histone octamers along chromosomal DNA." [PMID:10466730]
+comment: This activity is mediated by at least three subfamilies of the SNF2 remodellers, namely the bromodomain domain, the chromodomain containing and the imitation switch subfamilies.
+synonym: "histone octamer sliding activity" EXACT []
+is_a: GO:0140658 ! ATP-dependent chromatin remodeler activity
+
+[Term]
+id: GO:0140752
+name: branched 1,3-beta-D-glucan synthase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: UDP-glucose + [(1->3)-beta-D-glucosyl](n) = UDP + a branched [(1->3)-beta-D-glucosyl](n+1)." [PMID:34959732]
+is_a: GO:0003843 ! 1,3-beta-D-glucan synthase activity
+
+[Term]
+id: GO:0140753
+name: linear 1,3-beta-D-glucan synthase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: UDP-glucose + [(1->3)-beta-D-glucosyl](n) = UDP + a linear [(1->3)-beta-D-glucosyl](n+1)." [PMID:34959732]
+is_a: GO:0003843 ! 1,3-beta-D-glucan synthase activity
+
+[Term]
+id: GO:0140754
+name: reorganization of cellular membranes to establish viral sites of replication
+namespace: biological_process
+def: "A process in intracellular membranes are reorganized by viral proteins that perturb membrane integrity and can cause an extensive rearrangement of cellular membranes, forming membranous webs, which are thought to be the site of replication or certain viruses, for example the HPV virus." [PMID:19376974]
+is_a: GO:0051702 ! biological process involved in interaction with symbiont
+
+[Term]
+id: GO:0140755
+name: reorganization of host cellular membranes to establish sites of replication
+namespace: biological_process
+def: "A process in which a virus triggers host intracellular membranes to be reorganized, forming membranous webs, which are thought to be the site of replication or certain viruses, for example the HPV virus." [PMID:34699787, PMID:4372566]
+is_a: GO:0019054 ! modulation by virus of host cellular process
+
+[Term]
+id: GO:0140756
+name: structural constituent of proteasome
+namespace: molecular_function
+def: "The action of a molecule that contributes to the structural integrity of the proteasome." [PMID:10500111, PMID:28525752, PMID:28583440, PMID:29652515]
+is_a: GO:0005198 ! structural molecule activity
+
+[Term]
+id: GO:0140757
+name: cysteine-type deNEDDylase activity
+namespace: molecular_function
+def: "An thiol-dependent isopeptidase activity that cleaves NEDD8 from a target protein to which it is conjugated." [PMID:25628956]
+is_a: GO:0008234 ! cysteine-type peptidase activity
+is_a: GO:0019784 ! deNEDDylase activity
+
+[Term]
+id: GO:0140758
+name: metal-dependent deNEDDylase activity
+namespace: molecular_function
+def: "An metal-dependent isopeptidase activity that cleaves NEDD8 from a target protein to which it is conjugated." [PMID:25628956]
+is_a: GO:0008237 ! metallopeptidase activity
+is_a: GO:0019784 ! deNEDDylase activity
+
+[Term]
+id: GO:0140759
+name: histone H3K56 methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 56) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 56). This reaction is the addition of a methyl group to the lysine residue at position 56 of the histone H3 protein." [PMID:23451023, PMID:28743002]
+synonym: "histone H3K56 methylase activity" EXACT []
+synonym: "histone lysine N-methyltransferase activity (H3-K56 specific)" EXACT []
+synonym: "histone methyltransferase activity (H3-K56 specific)" EXACT []
+synonym: "histone-H3K56 methyltransferase activity" EXACT []
+is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
+is_a: GO:0140938 ! histone H3 methyltransferase activity
+
+[Term]
+id: GO:0140760
+name: histone H3K56me2/H3K56me3 demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a tri or a dimethyl-lysine residue at position 56 of the histone H3 protein." [PMID:23451023, PMID:28743002]
+synonym: "histone demethylase activity (H3-K56 specific)" RELATED []
+synonym: "histone H3-tri/dimethyl-lysine-56 demethylase activity" EXACT []
+synonym: "histone H3K56me2 demethylase activity" RELATED []
+synonym: "histone H3K56me3 demethylase activity" RELATED []
+is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
+is_a: GO:0032452 ! histone demethylase activity
+
+[Term]
+id: GO:0140761
+name: calmodulin-activated 3',5'-cyclic-AMP phosphodiesterase activity
+namespace: molecular_function
+def: "Catalysis of the reactions: nucleoside 3',5'-cyclic AMP + H2O = AMP + H+; this activity is activated by binding to calcium-bound calmodulin." [PMID:15901640]
+synonym: "calcium- and calmodulin-regulated 3',5'-cyclic-AMP phosphodiesterase activity" BROAD []
+synonym: "calcium- and calmodulin-regulated AMP-specific phosphodiesterase activity" EXACT []
+synonym: "calcium- and calmodulin-regulated cAMP phosphodiesterase activity" RELATED []
+synonym: "calcium- and calmodulin-regulated cyclic-AMP phosphodiesterase activity" EXACT []
+synonym: "calcium/calmodulin-regulated cAMP-specific phosphodiesterase activity" EXACT []
+is_a: GO:0004115 ! 3',5'-cyclic-AMP phosphodiesterase activity
+
+[Term]
+id: GO:0140762
+name: glucose dehydrogenase (FAD, quinone) activity
+namespace: molecular_function
+def: "Catalysis of the reaction: a quinone + D-glucose = a quinol + D-glucono-1,5-lactone." [RHEA:47372]
+xref: EC:1.1.5.9
+xref: RHEA:47372
+is_a: GO:0004344 ! glucose dehydrogenase activity
+
+[Term]
+id: GO:0140763
+name: programmed DNA elimination by elimination of internal DNA segments
+namespace: biological_process
+def: "A programmed DNA elimination mechanism in which specific sequences, namely, internal eliminated sequences (IES) and breakage eliminated sequences (BES) are removed from the genome. This process is known to occur in ciliates." [PMID:18708581]
+is_a: GO:0031049 ! programmed DNA elimination
+
+[Term]
+id: GO:0140764
+name: small RNA binding translational repressor activity
+namespace: molecular_function
+def: "A translational repressor activity that binds to a single-stranded small regulatory RNA (either a miRNA or a siRNA) to guide it to its target mRNA." [PMID:27184117, PMID:34117606]
+comment: This term is intended for activities such as that mediated by argonaute in the RISC complex, that bring a miRNA or an siRNA to their target mRNA.
+is_a: GO:0030371 ! translation repressor activity
+
+[Term]
+id: GO:0140765
+name: NAD-dependent histone H3K56 deacetylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 56) + H2O = histone H3 L-lysine (position 56) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 56 of the histone H3 protein." [PMID:23911928, PMID:30374165]
+synonym: "NAD-dependent histone deacetylase activity (H3-K56 specific)" EXACT []
+synonym: "NAD-dependent histone H3-K56 deacetylase activity" EXACT []
+is_a: GO:0017136 ! NAD-dependent histone deacetylase activity
+
+[Term]
+id: GO:0140766
+name: siRNA-mediated gene silencing
+namespace: biological_process
+def: "A post-transcriptional gene silencing pathway in which small interfering RNAs (siRNAs) elicit silencing of specific target genes. siRNAs are 21-23 nucleotide RNA duplexes that are fully complementary to their target mRNA. siRNAs can be exported and act in other cells, including in germline cells. Once incorporated into a RNA-induced silencing complex (RISC), siRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: endonucleolytic cleavage of the mRNA or mRNA translational repression. siRNAs are present in lower animals and plants, but not found in mammals; whereas miRNAs are present in all the animals and in plants." [PMID:26372022]
+synonym: "gene silencing by siRNA" EXACT []
+synonym: "post-transcriptional gene silencing by siRNA" EXACT []
+synonym: "posttranscriptional gene silencing by siRNA" EXACT []
+synonym: "siRNA-mediated PTGS" EXACT []
+is_a: GO:0035194 ! ncRNA-mediated post-transcriptional gene silencing
+
+[Term]
+id: GO:0140767
+name: enzyme-substrate adaptor activity
+namespace: molecular_function
+def: "An adaptor that brings together an enzyme and its substrate. Adaptors recruit the substrate to its enzyme, thus contributing to substrate selection and specificity." [PMID:16250895, PMID:34358446]
+synonym: "protein-substrate adaptor activity" BROAD []
+is_a: GO:0030674 ! protein-macromolecule adaptor activity
+
+[Term]
+id: GO:0140768
+name: protein ADP-ribosyltransferase-substrate adaptor activity
+namespace: molecular_function
+def: "An enzyme-substrate adaptor that bings together a protein ADP-ribosyl transferase and its substrate." [PMID:32028527]
+is_a: GO:0140767 ! enzyme-substrate adaptor activity
+
+[Term]
+id: GO:0140769
+name: ACP-dependent peptidyl-lysine N6-myristoyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl-[protein] + tetradecanoyl-[ACP] = H+ + holo-[ACP] + N(6)-tetradecanoyl-L-lysyl-[protein]." [PMID:32461253, RHEA:70611]
+xref: RHEA:70611
+is_a: GO:0018030 ! peptidyl-lysine N6-myristoyltransferase activity
+
+[Term]
+id: GO:0140770
+name: CoA-dependent peptidyl-lysine N6-myristoyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl-[protein] + tetradecanoyl-CoA = CoA + H+ + N(6)-tetradecanoyl-L-lysyl-[protein]." [PMID:1402651, RHEA:59752]
+xref: RHEA:59752
+is_a: GO:0018030 ! peptidyl-lysine N6-myristoyltransferase activity
+
+[Term]
+id: GO:0140771
+name: ACP-dependent peptidyl-lysine N6-palmitoyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: hexadecanoyl-[ACP] + L-lysyl-[protein] = H+ + holo-[ACP] + N(6)-hexadecanoyl-L-lysyl-[protein]." [PMID:32461253, RHEA:70615]
+xref: RHEA:70615
+is_a: GO:0018031 ! peptidyl-lysine N6-palmitoyltransferase activity
+
+[Term]
+id: GO:0140772
+name: CoA-dependent peptidyl-lysine N6-palmitoyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl-[protein] + hexadecanoyl-CoA = CoA + H+ + N(6)-hexadecanoyl-L-lysyl-[protein]." [PMID:30061757]
+is_a: GO:0018031 ! peptidyl-lysine N6-palmitoyltransferase activity
+
+[Term]
+id: GO:0140773
+name: NAD-dependent protein demyristoylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: N6-tetradecanoyl-L-lysyl-[protein] + NAD+ + H2O = tetradecanoyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide." [PMID:23552949, RHEA:70567]
+xref: RHEA:70567
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+
+[Term]
+id: GO:0140774
+name: NAD-dependent protein depalmitoylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: N6-octadecanoyl-L-lysyl-[protein] + NAD+ + H2O = octadecanoyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide." [PMID:23552949, RHEA:70563]
+xref: RHEA:70563
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+
+[Term]
+id: GO:0140775
+name: actin filament debranching activity
+namespace: molecular_function
+def: "Binding to an actin filament and promoting the dissociation of an actin filament branch." [PMID:20362448]
+synonym: "actin debranching activity" EXACT []
+is_a: GO:0140776 ! protein-containing complex destabilizing activity
+
+[Term]
+id: GO:0140776
+name: protein-containing complex destabilizing activity
+namespace: molecular_function
+def: "A molecular function that involves direct binding to one of the subunits of a protein-containing complex and promoting the dissociation of one or many subunits. This often happens by changing the conformation of the protein being bound, which decreases its affinity for the rest of the complex." [PMID:23727094, PMID:29779865, PMID:34836783]
+synonym: "protein unfoldase activity" BROAD []
+is_a: GO:0003674 ! molecular_function
+
+[Term]
+id: GO:0140777
+name: protein-containing complex stabilizing activity
+namespace: molecular_function
+def: "A molecular function that involves direct binding to one of the subunits of a protein-containing complex, thus preventing an interaction with a factor that would promote dissociation of the complex." [PMID:34040253]
+is_a: GO:0003674 ! molecular_function
+
+[Term]
+id: GO:0140778
+name: microtubule stabilizing activity
+namespace: molecular_function
+def: "A protein-containing complex stabilizing activity that prevents dissociation of microtubules." [PMID:34970964]
+is_a: GO:0140777 ! protein-containing complex stabilizing activity
+
+[Term]
+id: GO:0140779
+name: XCL1 production
+namespace: biological_process
+def: "The appearance of XCL1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [PMID:7973732]
+comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms.
+subset: gocheck_do_not_annotate
+synonym: "lymphotactin production" EXACT []
+xref: Wikipedia:XCL1
+is_a: GO:0001816 ! cytokine production
+
+[Term]
+id: GO:0140780
+name: obsolete modulation by symbiont of host system process
+namespace: biological_process
+def: "OBSOLETE. The process in which a symbiont organism effects a change in an anatomical system process of its host organism." [GOC:pg]
+comment: This term was obsoleted because it is not sufficiently precise.
+is_obsolete: true
+
+[Term]
+id: GO:0140781
+name: ilicicolin H biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of ilicicolin H, a 4-hydroxy-2-pyridone alkaloid that has potent and broad antifungal activities by inhibiting the mitochondrial respiration chain." [PMID:30905148, PMID:31216742, PMID:34947016]
+synonym: "ilicicolin H anabolism" EXACT []
+synonym: "ilicicolin H biosynthesis" EXACT []
+synonym: "ilicicolin H formation" EXACT []
+synonym: "ilicicolin H synthesis" EXACT []
+is_a: GO:0009821 ! alkaloid biosynthetic process
+is_a: GO:0030639 ! polyketide biosynthetic process
+is_a: GO:0042181 ! ketone biosynthetic process
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:0046189 ! phenol-containing compound biosynthetic process
+is_a: GO:0072525 ! pyridine-containing compound biosynthetic process
+
+[Term]
+id: GO:0140782
+name: novofumigatonin biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of novofumigatonin, a heavily oxygenated meroterpenoid containing a unique orthoester moiety." [PMID:29968715]
+synonym: "novofumigatonin anabolism" EXACT []
+synonym: "novofumigatonin biosynthesis" EXACT []
+synonym: "novofumigatonin formation" EXACT []
+synonym: "novofumigatonin synthesis" EXACT []
+is_a: GO:0016114 ! terpenoid biosynthetic process
+is_a: GO:0018130 ! heterocycle biosynthetic process
+is_a: GO:0042181 ! ketone biosynthetic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+
+[Term]
+id: GO:0140783
+name: (M)-viriditoxin biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of (M)-viriditoxin, a fungal secondary metabolite with antibacterial activity." [PMID:31045362, PMID:31304040]
+synonym: "(M)-viriditoxin anabolism" EXACT []
+synonym: "(M)-viriditoxin biosynthesis" EXACT []
+synonym: "(M)-viriditoxin formation" EXACT []
+synonym: "(M)-viriditoxin synthesis" EXACT []
+synonym: "viriditoxin anabolism" BROAD []
+synonym: "viriditoxin biosynthesis" BROAD []
+synonym: "viriditoxin formation" BROAD []
+synonym: "viriditoxin synthesis" BROAD []
+is_a: GO:0030639 ! polyketide biosynthetic process
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:0046189 ! phenol-containing compound biosynthetic process
+is_a: GO:1901503 ! ether biosynthetic process
+
+[Term]
+id: GO:0140784
+name: metal ion sensor activity
+namespace: molecular_function
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of a metal ion." [GOC:pg]
+is_a: GO:0140299 ! small molecule sensor activity
+
+[Term]
+id: GO:0140785
+name: amino acid sensor activity
+namespace: molecular_function
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of an amino acid." [GOC:pg]
+synonym: "amino acid sensing activity" EXACT []
+is_a: GO:0140299 ! small molecule sensor activity
+
+[Term]
+id: GO:0140786
+name: glutamine sensor activity
+namespace: molecular_function
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of glutamine." [PMID:34535752]
+synonym: "glutamine sensing activity" EXACT []
+is_a: GO:0140785 ! amino acid sensor activity
+
+[Term]
+id: GO:0140787
+name: phosphate ion uniporter activity
+namespace: molecular_function
+def: "Catalysis of the active transport of a phosphate ion across a membrane by a mechanism involving conformational change, where energy for active transport is derived from membrane potential if the solute is charged." [PMID:29642010]
+is_a: GO:0015114 ! phosphate ion transmembrane transporter activity
+is_a: GO:0022810 ! membrane potential driven uniporter activity
+
+[Term]
+id: GO:0140788
+name: L-glutamate uniporter activity
+namespace: molecular_function
+def: "Catalysis of the active transport of a L-glutamate across a membrane by a mechanism involving conformational change, where energy for active transport is derived from membrane potential if the solute is charged." [PMID:27133463, PMID:29642010]
+synonym: "glutamate uniporter activity" BROAD []
+xref: RHEA:66336
+is_a: GO:0005313 ! L-glutamate transmembrane transporter activity
+is_a: GO:0022810 ! membrane potential driven uniporter activity
+
+[Term]
+id: GO:0140789
+name: histone phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: a phosphorylated histone + H2O = a protein + phosphate." [PMID:19351884]
+is_a: GO:0004721 ! phosphoprotein phosphatase activity
+is_a: GO:0140993 ! histone modifying activity
+
+[Term]
+id: GO:0140790
+name: obsolete histone serine/threonine phosphatase activity
+namespace: molecular_function
+def: "OBSOLETE. Catalysis of the reaction: histone serine phosphate + H2O = histone serine + phosphate, and histone threonine phosphate + H2O = histone threonine + phosphate." [PMID:18614045]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0140789
+
+[Term]
+id: GO:0140791
+name: histone H2AXS140 phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: histone H2AX serine phosphate (position 140) + H2O = histone H2AX serine (position 140) + phosphate." [PMID:18614045]
+synonym: "histone H2-S140 serine phosphatase activity" EXACT []
+synonym: "histone H2S140 phosphatase activity" RELATED []
+synonym: "histone serine phosphatase activity (H2-S140 specific)" EXACT []
+is_a: GO:0140789 ! histone phosphatase activity
+
+[Term]
+id: GO:0140792
+name: obsolete histone tyrosine phosphatase activity
+namespace: molecular_function
+def: "OBSOLETE. Catalysis of the reaction: histone tyrosine phosphate + H2O = histone tyrosine + phosphate." [PMID:19234442, PMID:19351884]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
+is_obsolete: true
+replaced_by: GO:0140789
+
+[Term]
+id: GO:0140793
+name: histone H2AXY142 phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: histone H2AX tyrosine phosphate (position 142) + H2O = histone H2AX tyrosine (position 142) + phosphate." [PMID:19234442, PMID:19351884]
+synonym: "histone H2-Y142 phosphatase activity" EXACT []
+synonym: "histone H2Y142 phosphatase activity" RELATED []
+synonym: "histone tyrosine phosphatase activity (H2-Y142 specific)" EXACT []
+is_a: GO:0140789 ! histone phosphatase activity
+
+[Term]
+id: GO:0140794
+name: histone arginine deiminase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + histone 3 L-arginyl = histone 3 L-citrullyl + NH4+, resulting in histone citrullination." [PMID:15339660]
+comment: The substrate for histone deiminase may be methyl-arginine, rather than arginine (see PMID:35197210 and PMID:16567635).
+synonym: "histone citrullination" RELATED []
+synonym: "histone-arginine deiminase activity" EXACT []
+is_a: GO:0004668 ! protein-arginine deiminase activity
+is_a: GO:0140993 ! histone modifying activity
+
+[Term]
+id: GO:0140795
+name: histone H3R2 arginine deiminase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + histone 3 L-arginyl (position 2)= histone 3 L-citrullyl (position 2) + NH4+, resulting in histone H3 citrullination at position 2." [PMID:15339660]
+comment: The substrate for histone deiminase may be methyl-arginine, rather than arginine (see PMID:35197210 and PMID:16567635).
+synonym: "H3-R2 citrullination" EXACT []
+synonym: "histone H3-R2 arginine deiminase activity" EXACT []
+synonym: "histone-arginine deiminase activity (H3-R2 specific)" EXACT []
+is_a: GO:0140794 ! histone arginine deiminase activity
+
+[Term]
+id: GO:0140796
+name: histone H3R8 arginine deiminase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + histone 3 L-arginyl (position 8)= histone 3 L-citrullyl (position 8) + NH4+, resulting in histone H3 citrullination at position 8." [PMID:15339660]
+comment: The substrate for histone deiminase may be methyl-arginine, rather than arginine (see PMID:35197210 and PMID:16567635).
+synonym: "H3-R8 citrullination" EXACT []
+synonym: "histone H3-R8 arginine deiminase activity" EXACT []
+synonym: "histone-arginine deiminase activity (H3-R8 specific)" EXACT []
+is_a: GO:0140794 ! histone arginine deiminase activity
+
+[Term]
+id: GO:0140797
+name: histone H3R17 arginine deiminase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + histone 3 L-arginyl (position 17)= histone 3 L-citrullyl (position 17) + NH4+, resulting in histone H3 citrullination at position 17." [PMID:15339660]
+comment: The substrate for histone deiminase may be methyl-arginine, rather than arginine (see PMID:35197210 and PMID:16567635).
+synonym: "H3-R17 citrullination" EXACT []
+synonym: "histone H3-R17 arginine deiminase activity" EXACT []
+synonym: "histone-arginine deiminase activity (H3-R17 specific)" EXACT []
+is_a: GO:0140794 ! histone arginine deiminase activity
+
+[Term]
+id: GO:0140798
+name: histone H3R26 arginine deiminase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + histone 3 L-arginyl (position 26)= histone 3 L-citrullyl (position 26) + NH4+, resulting in histone H3 citrullination at position 26." [PMID:15339660]
+comment: The substrate for histone deiminase may be methyl-arginine, rather than arginine (see PMID:35197210 and PMID:16567635).
+synonym: "H3-R26 citrullination" EXACT []
+synonym: "histone H3-R26 arginine deiminase activity" EXACT []
+synonym: "histone-arginine deiminase activity (H3-R26 specific)" EXACT []
+is_a: GO:0140794 ! histone arginine deiminase activity
+
+[Term]
+id: GO:0140799
+name: glycine:proton antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: glycine(out) + H+(in) = glycine(in) + H+(out)." [PMID:16701208, PMID:26912364]
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015187 ! glycine transmembrane transporter activity
+is_a: GO:0140848 ! amino acid:monoatomic cation antiporter activity
+
+[Term]
+id: GO:0140800
+name: gamma-aminobutyric acid:proton antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: 4-aminobutanoate(out) + H+(in) = 4-aminobutanoate(in) + H+(out)." [PMID:16701208, PMID:26912364, PMID:27601664]
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015185 ! gamma-aminobutyric acid transmembrane transporter activity
+is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
+is_a: GO:0140848 ! amino acid:monoatomic cation antiporter activity
+
+[Term]
+id: GO:0140801
+name: histone H2AXY142 kinase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: histone H2AX-tyrosine (position 142) + ATP = (histone H2AX-phosphotyrosine (position 142) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 142 of histone variant H2AX." [PMID:19092802]
+synonym: "gamma-H2AX-S142 kinase activity" EXACT []
+synonym: "histone H2AX-Y142 kinase activity" EXACT []
+synonym: "histone H2AY142 kinase activity" RELATED []
+synonym: "histone kinase activity (H2AX-Y142 specific)" EXACT []
+is_a: GO:0141003 ! histone H2AX kinase activity
+
+[Term]
+id: GO:0140802
+name: NAD+-protein-C-terminal glycine ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: [protein]-C-terminal glycine + NAD+ = [protein]-C-terminal O-(ADP-D-ribosyl)-glycine + nicotinamide." [PMID:28525742, RHEA:58268]
+xref: RHEA:58268
+is_a: GO:1990404 ! NAD+-protein ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140803
+name: NAD+- protein-cysteine ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-cysteinyl-[protein] + NAD+ = H+ + nicotinamide + S-(ADP-D-ribosyl)-L-cysteinyl-[protein]." [PMID:25043379, RHEA:56612]
+xref: RHEA:56612
+is_a: GO:1990404 ! NAD+-protein ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140804
+name: NAD+- protein-lysine ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl-[protein] + NAD+ = H+ + N(6)-(ADP-D-ribosyl)-L-lysyl-[protein] + nicotinamide." [PMID:25043379, RHEA:58220]
+xref: RHEA:58220
+is_a: GO:1990404 ! NAD+-protein ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140805
+name: NAD+-protein-serine ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-seryl-[protein] + NAD+ = H+ + nicotinamide + O-(ADP-D-ribosyl)-L-seryl-[protein]." [PMID:32028527, PMID:33186521, RHEA:58232]
+xref: RHEA:58232
+is_a: GO:1990404 ! NAD+-protein ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140806
+name: NAD+- protein-aspartate ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-aspartyl-[protein] + NAD+ = 4-O-(ADP-D-ribosyl)-L-aspartyl-[protein] + nicotinamide." [PMID:19764761, PMID:25043379, RHEA:54424]
+is_a: GO:1990404 ! NAD+-protein ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140807
+name: NAD+-protein-glutamate ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-glutamyl-[protein] + NAD+ = 5-O-(ADP-D-ribosyl)-L-glutamyl-[protein] + nicotinamide." [PMID:19764761, PMID:25043379, RHEA:58224]
+is_a: GO:1990404 ! NAD+-protein ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140808
+name: NAD+-protein-tyrosine ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-tyrosyl-[protein] + NAD+ = H+ + nicotinamide + O-(ADP-D-ribosyl)-L-tyrosyl-[protein]." [PMID:29954836, PMID:30257210, RHEA:58236]
+xref: RHEA:58236
+is_a: GO:1990404 ! NAD+-protein ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140809
+name: histone H4R3 arginine deiminase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + histone 4 L-arginyl (position 3)= histone 4 L-citrullyl (position 3) + NH4+, resulting in histone H3 citrullination at position 3." [PMID:16567635]
+comment: The substrate for histone deiminase may be methyl-arginine, rather than arginine (see PMID:35197210 and PMID:16567635).
+synonym: "H4-R3 citrullination" EXACT []
+synonym: "histone H4-R3 arginine deiminase activity" EXACT []
+synonym: "histone-arginine deiminase activity (H4-R3 specific)" EXACT []
+is_a: GO:0140794 ! histone arginine deiminase activity
+
+[Term]
+id: GO:0140810
+name: histone H1R54 arginine deiminase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + histone 1 L-arginyl (position 54)= histone 1 L-citrullyl (position 54) + NH4+, resulting in histone H1 citrullination at position 54." [PMID:24463520]
+comment: The substrate for histone deiminase may be methyl-arginine, rather than arginine (see PMID:35197210 and PMID:16567635).
+synonym: "H1-R54 citrullination" EXACT []
+synonym: "histone H1-R54 deiminase activity" EXACT []
+synonym: "histone-arginine deiminase activity (H1-R54 specific)" EXACT []
+is_a: GO:0140794 ! histone arginine deiminase activity
+
+[Term]
+id: GO:0140811
+name: histone H2AR3 arginine deiminase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + histone 2A L-arginyl (position 3)= histone 2A L-citrullyl (position 3) + NH4+, resulting in histone H2A citrullination at position 3." [PMID:15823041]
+comment: The substrate for histone deiminase may be methyl-arginine, rather than arginine (see PMID:35197210 and PMID:16567635).
+synonym: "H2A-R3 citrullination" EXACT []
+synonym: "histone H2A-R3 arginine deiminase activity" EXACT []
+synonym: "histone-arginine deiminase activity (H2A-R3 specific)" EXACT []
+is_a: GO:0140794 ! histone arginine deiminase activity
+
+[Term]
+id: GO:0140812
+name: orotate:monoatomic anion antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: orotate(out) + anion (in) = orotate (in) + anion (out)." [PMID:21350910, PMID:35144162]
+synonym: "orotate:anion antiporter activity" BROAD []
+synonym: "orotate:organic anion antiporter activity" NARROW []
+is_a: GO:0008509 ! monoatomic anion transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
+
+[Term]
+id: GO:0140813
+name: urate:monoatomic anion antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: urate(out) + anion (in) = urate (in) + anion (out)." [PMID:12024214, PMID:18411268]
+synonym: "urate:anion antiporter activity" BROAD []
+synonym: "urate:organic anion antiporter activity" NARROW []
+is_a: GO:0008509 ! monoatomic anion transmembrane transporter activity
+is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
+
+[Term]
+id: GO:0140814
+name: glycine betaine:sodium:chloride symporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: glycine betaine(out) + Na+(out) + Cl-(out)= glycine betaine(in) + Na+(in) + Cl-(in)." [PMID:10358010]
+synonym: "sodium/chloride-dependent glycine betaine transporter activity" BROAD []
+xref: RHEA:71175
+is_a: GO:0015199 ! amino-acid betaine transmembrane transporter activity
+is_a: GO:0015378 ! sodium:chloride symporter activity
+
+[Term]
+id: GO:0140815
+name: NAD+-protein-histidine ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-histidyl-[protein] + NAD+ = H+ + Nt-(ADP-D-ribosyl)-L-histidyl-[protein] + nicotinamide." [PMID:35393539]
+xref: RHEA:72071
+is_a: GO:1990404 ! NAD+-protein ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140816
+name: NAD+-histone H2BS6 serine ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of ADP-ribose groups to the serine-6 or an equivalent residue of the N-terminal tail of histone H2B." [PMID:34874266]
+synonym: "NAD+-histone H2B-S6 serine ADP-ribosyltransferase activity" EXACT []
+synonym: "NAD+-histone-serine ADP-ribosyltransferase activity (H2B-S6 specific)" EXACT []
+is_a: GO:0140805 ! NAD+-protein-serine ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140817
+name: NAD+-histone H3S10 serine ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of ADP-ribose groups to the serine-10 or an equivalent residue of the N-terminal tail of histone H3." [PMID:34874266]
+synonym: "NAD+-histone H3-S10 serine ADP-ribosyltransferase activity" EXACT []
+synonym: "NAD+-histone-serine ADP-ribosyltransferase activity (H3-S10 specific)" EXACT []
+is_a: GO:0140805 ! NAD+-protein-serine ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140818
+name: mRNA 5'-phosphatase activity
+namespace: molecular_function
+def: "A 5'-end triphospho-[mRNA] + H2O = a 5'-end diphospho-[mRNA] + H+ + phosphate." [PMID:9473487]
+synonym: "mRNA 5'-triphosphate monophosphatase activity" EXACT []
+xref: EC:3.6.1.74
+xref: RHEA:67004
+is_a: GO:0016462 ! pyrophosphatase activity
+is_a: GO:0140098 ! catalytic activity, acting on RNA
+
+[Term]
+id: GO:0140819
+name: UDP-beta-L-arabinofuranose transporter activity
+namespace: molecular_function
+def: "Enables the transfer of UDP-beta-L-arabinofuranose from one side of a membrane to the other." [PMID:28373556]
+is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0015165 ! pyrimidine nucleotide-sugar transmembrane transporter activity
+
+[Term]
+id: GO:0140820
+name: cytosol to Golgi apparatus transport
+namespace: biological_process
+def: "The directed movement of substances from the cytosol into the Golgi apparatus of a cell." [PMID:28373556]
+is_a: GO:0055085 ! transmembrane transport
+
+[Term]
+id: GO:0140821
+name: UDP-beta-L-arabinofuranose import into Golgi lumen
+namespace: biological_process
+def: "The directed movement of UDP-beta-L-arabinofuranose from the cytosol to the Golgi apparatus of a cell." [PMID:28373556]
+synonym: "cytosol to Golgi apparatus UDP-beta-L-arabinofuranose transport" EXACT []
+is_a: GO:0015711 ! organic anion transport
+is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
+is_a: GO:0140820 ! cytosol to Golgi apparatus transport
+
+[Term]
+id: GO:0140822
+name: NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of ADP-ribose groups to the glutamate-35 residue of the N-terminal tail of histone H2B (or an equivalent residue)." [PMID:32822587]
+synonym: "NAD+-histone H2B-E35 glutamate ADP-ribosyltransferase activity" EXACT []
+synonym: "NAD+-histone-glutamate ADP-ribosyltransferase activity (H2B-E35 specific)" EXACT []
+is_a: GO:0140807 ! NAD+-protein-glutamate ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140823
+name: histone H2BS36 kinase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: histone H2B-serine (position 36) + ATP = histone H2B-phosphoserine (position 36) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 36 of histone H2B." [PMID:32822587]
+synonym: "histone H2B-S36 kinase activity" EXACT []
+synonym: "histone kinase activity (H2B-S36 specific)" EXACT []
+is_a: GO:0140998 ! histone H2B kinase activity
+
+[Term]
+id: GO:0140824
+name: thioredoxin-dependent peroxiredoxin activity
+namespace: molecular_function
+def: "Catalysis of the reaction: [thioredoxin]-dithiol + a hydroperoxide = [thioredoxin]-disulfide + an alcohol + H2O." [PMID:12707274, PMID:19820102, RHEA:62620]
+xref: EC:1.11.1.24
+xref: RHEA:62620
+is_a: GO:0051920 ! peroxiredoxin activity
+
+[Term]
+id: GO:0140825
+name: lactoperoxidase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O." [PMID:19339248, RHEA:56136]
+synonym: "peroxidase activity" BROAD []
+xref: EC:1.11.1.7
+xref: RHEA:56136
+is_a: GO:0004601 ! peroxidase activity
+
+[Term]
+id: GO:0140826
+name: zinc:proton antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of zinc from one side of a membrane to the other according to the reaction: H+(out) + Zn2+(in) = H+(in) + Zn2+(out)." [PMID:19366695, PMID:30893306]
+comment: Some transporters exchange 1 H+ for a Zn2+ while others are electroneutral and exchange 2 H+.
+is_a: GO:0046915 ! transition metal ion transmembrane transporter activity
+is_a: GO:0051139 ! metal cation:proton antiporter activity
+
+[Term]
+id: GO:0140827
+name: zinc chaperone activity
+namespace: molecular_function
+def: "Binding to and delivering zinc ions to a target protein." [PMID:35584675]
+is_a: GO:0016530 ! metallochaperone activity
+
+[Term]
+id: GO:0140828
+name: metal cation:monoatomic cation antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + Na+(in) = solute(in) + Na+(out)." [GOC:pg]
+synonym: "solute:metal cation antiporter activity" BROAD []
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
+is_a: GO:0046873 ! metal ion transmembrane transporter activity
+
+[Term]
+id: GO:0140829
+name: bicarbonate:monoatomic anion antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(in) + HCO3-(out) = solute(out) + HCO3-(in)." [PMID:12440690]
+synonym: "bicarbonate:anion antiporter activity" BROAD []
+xref: TC:2.A.31.1.1
+is_a: GO:0008509 ! monoatomic anion transmembrane transporter activity
+is_a: GO:0015106 ! bicarbonate transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
+
+[Term]
+id: GO:0140830
+name: L-glutamine, sodium:proton antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(in) + L-glutamine(out) + Na+(out) = H+(out) + L-glutamine(in) + Na+(in)." [PMID:10619430, PMID:11742981, PMID:11850497]
+xref: RHEA:71127
+is_a: GO:0015186 ! L-glutamine transmembrane transporter activity
+is_a: GO:0015385 ! sodium:proton antiporter activity
+is_a: GO:0140848 ! amino acid:monoatomic cation antiporter activity
+
+[Term]
+id: GO:0140831
+name: L-asparagine, sodium:proton antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(in) + L-asparagine(out) + Na+(out) = H+(out) + L-asparagine(in) + Na+(in)." [PMID:10619430, PMID:11742981]
+xref: RHEA:71131
+is_a: GO:0015182 ! L-asparagine transmembrane transporter activity
+is_a: GO:0015385 ! sodium:proton antiporter activity
+is_a: GO:0140848 ! amino acid:monoatomic cation antiporter activity
+
+[Term]
+id: GO:0140832
+name: L-histidine, sodium:proton antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(in) + L-histidine(out) + Na+(out) = H+(out) + L-histidine(in) + Na+(in)." [PMID:10619430, PMID:11742981]
+xref: RHEA:71135
+is_a: GO:0005290 ! L-histidine transmembrane transporter activity
+is_a: GO:0015385 ! sodium:proton antiporter activity
+is_a: GO:0045119 ! azole:proton antiporter activity
+is_a: GO:0140848 ! amino acid:monoatomic cation antiporter activity
+
+[Term]
+id: GO:0140833
+name: RNA polymerase II CTD heptapeptide repeat Y1 kinase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: ATP + RNA polymerase II large subunit CTD heptapeptide repeat (consensus YSPTSPS) = ADP + H+ + RNA polymerase II large subunit phosphotyrosine (position 1)." [PMID:28248323]
+synonym: "RNA polymerase II C-terminal domain Y1 kinase activity" EXACT []
+is_a: GO:0008353 ! RNA polymerase II CTD heptapeptide repeat kinase activity
+
+[Term]
+id: GO:0140834
+name: RNA polymerase II CTD heptapeptide repeat S2 kinase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: ATP + RNA polymerase II large subunit CTD heptapeptide repeat (consensus YSPTSPS) = ADP + H+ + RNA polymerase II large subunit phosphoserine (position 2)." [PMID:28248323]
+synonym: "RNA polymerase II C-terminal domain S2 kinase activity" EXACT []
+is_a: GO:0008353 ! RNA polymerase II CTD heptapeptide repeat kinase activity
+
+[Term]
+id: GO:0140835
+name: RNA polymerase II CTD heptapeptide repeat T4 kinase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: ATP + RNA polymerase II large subunit CTD heptapeptide repeat (consensus YSPTSPS) = ADP + H+ + RNA polymerase II large subunit phosphothreonine (position 4)." [PMID:28248323]
+synonym: "RNA polymerase II C-terminal domain T4 kinase activity" EXACT []
+is_a: GO:0008353 ! RNA polymerase II CTD heptapeptide repeat kinase activity
+
+[Term]
+id: GO:0140836
+name: RNA polymerase II CTD heptapeptide repeat S5 kinase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: ATP + RNA polymerase II large subunit CTD heptapeptide repeat (consensus YSPTSPS) = ADP + H+ + RNA polymerase II large subunit phosphoserine (position 5)." [PMID:28248323]
+synonym: "RNA polymerase II C-terminal domain S5 kinase activity" EXACT []
+is_a: GO:0008353 ! RNA polymerase II CTD heptapeptide repeat kinase activity
+
+[Term]
+id: GO:0140837
+name: RNA polymerase II CTD heptapeptide repeat S7 kinase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: ATP + RNA polymerase II large subunit CTD heptapeptide repeat (consensus YSPTSPS) = ADP + H+ + RNA polymerase II large subunit phosphoserine (position 7)." [PMID:28248323]
+synonym: "RNA polymerase II C-terminal domain S7 kinase activity" EXACT []
+is_a: GO:0008353 ! RNA polymerase II CTD heptapeptide repeat kinase activity
+
+[Term]
+id: GO:0140838
+name: RNA polymerase II CTD heptapeptide repeat peptidyl-prolyl isomerase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: RNA polymerase II large subunit CTD heptapeptide repeat (consensus YSPTSPS) cis-proline (omega=180) = RNA polymerase II large subunit trans-proline (omega=0)." [PMID:28248323]
+is_a: GO:0003755 ! peptidyl-prolyl cis-trans isomerase activity
+is_a: GO:0140994 ! RNA polymerase II CTD heptapeptide repeat modifying activity
+
+[Term]
+id: GO:0140839
+name: RNA polymerase II CTD heptapeptide repeat P3 isomerase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: RNA polymerase II large subunit CTD heptapeptide repeat (consensus YSPTSPS) cis-proline (omega=180) (position 3) = RNA polymerase II large subunit trans-proline (omega=0) (position 3)." [PMID:28248323]
+synonym: "RNA polymerase II C-terminal domain P3 isomerase activity" EXACT []
+is_a: GO:0140838 ! RNA polymerase II CTD heptapeptide repeat peptidyl-prolyl isomerase activity
+
+[Term]
+id: GO:0140840
+name: RNA polymerase II CTD heptapeptide repeat P6 isomerase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: RNA polymerase II large subunit CTD heptapeptide repeat (consensus YSPTSPS) cis-proline (omega=180) (position 6) = RNA polymerase II large subunit trans-proline (omega=0) (position 6)." [PMID:28248323]
+synonym: "RNA polymerase II C-terminal domain P6 isomerase activity" EXACT []
+is_a: GO:0140838 ! RNA polymerase II CTD heptapeptide repeat peptidyl-prolyl isomerase activity
+
+[Term]
+id: GO:0140841
+name: RNA polymerase II C-terminal domain O-GlcNAc transferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: UDP-N-acetyl-D-glucosamine + RNA polymerase II large subunit CTD heptapeptide repeat (YSPTSPS) = UDP + RNA polymerase II large subunit CTD heptapeptide repeat 3-O-(N-acetyl-D-glucosaminyl)-L-serine." [PMID:22605332]
+is_a: GO:0097363 ! protein O-acetylglucosaminyltransferase activity
+
+[Term]
+id: GO:0140842
+name: RNA polymerase II C-terminal domain S5 O-GlcNAc transferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: UDP-N-acetyl-D-glucosamine + RNA polymerase II large subunit CTD heptapeptide repeat (YSPTSPS) = UDP + RNA polymerase II large subunit CTD heptapeptide repeat 3-O-(N-acetyl-D-glucosaminyl)-L-serine (position 5)." [PMID:22605332]
+is_a: GO:0140841 ! RNA polymerase II C-terminal domain O-GlcNAc transferase activity
+
+[Term]
+id: GO:0140843
+name: RNA polymerase II C-terminal domain S7 O-GlcNAc transferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: UDP-N-acetyl-D-glucosamine + RNA polymerase II large subunit CTD heptapeptide repeat (YSPTSPS) = UDP + RNA polymerase II large subunit CTD heptapeptide repeat 3-O-(N-acetyl-D-glucosaminyl)-L-serine (position 7)." [PMID:22605332]
+is_a: GO:0140841 ! RNA polymerase II C-terminal domain O-GlcNAc transferase activity
+
+[Term]
+id: GO:0140844
+name: NAD+-histone H2BE2 glutamate ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of ADP-ribose groups to the glutamate-2 residue of the N-terminal tail of histone H2B (or an equivalent residue)." [PMID:27530147]
+synonym: "NAD+-histone H2B-E2 glutamate ADP-ribosyltransferase activity" EXACT []
+synonym: "NAD+-histone-glutamate ADP-ribosyltransferase activity (H2B-E2 specific)" EXACT []
+is_a: GO:0140807 ! NAD+-protein-glutamate ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140845
+name: regulation of promoter clearance from RNA polymerase II promoter
+namespace: biological_process
+def: "A process that modulates the frequency, rate or extent of the transition from the initiation to the elongation phases of transcription by RNA polymerase II." [PMID:28248323]
+is_a: GO:2001141 ! regulation of RNA biosynthetic process
+relationship: regulates GO:0001111 ! RNA polymerase II promoter clearance
+
+[Term]
+id: GO:0140846
+name: positive regulation of promoter clearance from RNA polymerase II promoter
+namespace: biological_process
+def: "A process that activates or increases the frequency, rate or extent of the transition from the initiation to the elongation phases of transcription by RNA polymerase II." [PMID:28248323]
+is_a: GO:0140845 ! regulation of promoter clearance from RNA polymerase II promoter
+is_a: GO:1902680 ! positive regulation of RNA biosynthetic process
+relationship: positively_regulates GO:0001111 ! RNA polymerase II promoter clearance
+
+[Term]
+id: GO:0140847
+name: negative regulation of promoter clearance from RNA polymerase II promoter
+namespace: biological_process
+def: "A process that stops, prevents or reduces the transition from the initiation to the elongation phases of transcription by RNA polymerase II." [PMID:28248323]
+is_a: GO:0140845 ! regulation of promoter clearance from RNA polymerase II promoter
+is_a: GO:1902679 ! negative regulation of RNA biosynthetic process
+relationship: negatively_regulates GO:0001111 ! RNA polymerase II promoter clearance
+
+[Term]
+id: GO:0140848
+name: amino acid:monoatomic cation antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + monoatomic cation(in) = solute(in) + monoatomic cation(out). Monoatomic cations include H+, Mg2+, Ca2+, etc." [GOC:curators]
+is_a: GO:0008324 ! monoatomic cation transmembrane transporter activity
+is_a: GO:0015171 ! amino acid transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
+
+[Term]
+id: GO:0140849
+name: ATP-dependent H2AZ histone chaperone activity
+namespace: molecular_function
+def: "A histone chaperone that mediates the exchange of histone H2A-H2B dimer and histone H2AZ-H2B dimers in a nucleosome, driven by ATP hydrolysis. Some chaperones insert H2AZ-H2B dimers and remove H2A-H2B, while others do the opposite." [PMID:21241891, PMID:23580526, PMID:30309918]
+comment: Drosophila H2AV corresponds to histone H2AZ.
+synonym: "ATP-dependent H2A.Z histone chaperone activity" EXACT []
+synonym: "H2AZ histone exchange activity" RELATED []
+is_a: GO:0140674 ! ATP-dependent histone chaperone activity
+
+[Term]
+id: GO:0140850
+name: histone H2B C-terminal K residue ubiquitin ligase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a ubiquitin molecule to a histone 2B at the conserved C-terminal lysine (K) residue. The last K residue is at position 119 in fission yeast, 123 in budding yeast, and 120 in mammals." [PMID:17363370, PMID:28624371]
+synonym: "histone H2B conserved C-terminal lysine ubiquitin ligase activity" EXACT []
+synonym: "histone H2B-K120 ubiquitin ligase activity" EXACT []
+synonym: "histone H2BK120 ubiquitin ligase activity" EXACT []
+synonym: "histone ubiquitin ligase activity (H2B-K120 specific)" EXACT []
+is_a: GO:0140852 ! histone ubiquitin ligase activity
+
+[Term]
+id: GO:0140851
+name: histone H3K14 ubiquitin ligase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a ubiquitin molecule to histone 3 at the lysine-14 residue." [PMID:28624371, PMID:31468675, PMID:34010645]
+synonym: "histone H3-K14 ubiquitin ligase activity" EXACT []
+synonym: "histone ubiquitin ligase activity (H3-K14 specific)" EXACT []
+is_a: GO:0140852 ! histone ubiquitin ligase activity
+
+[Term]
+id: GO:0140852
+name: histone ubiquitin ligase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of ubiquitin to a histone substrate." [GOC:curators]
+is_a: GO:0061630 ! ubiquitin protein ligase activity
+is_a: GO:0140993 ! histone modifying activity
+
+[Term]
+id: GO:0140853
+name: cholesterol-protein transferase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a cholesterol to an acceptor protein." [PMID:8824192]
+synonym: "cholesterol transferase activity" BROAD []
+is_a: GO:0016740 ! transferase activity
+is_a: GO:0140096 ! catalytic activity, acting on a protein
+
+[Term]
+id: GO:0140854
+name: interleukin-19-mediated signaling pathway
+namespace: biological_process
+def: "The series of molecular signals initiated by interleukin-19 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [PMID:34052656]
+synonym: "IL19-mediated signalling pathway" EXACT [GOC:bf]
+is_a: GO:0019221 ! cytokine-mediated signaling pathway
+
+[Term]
+id: GO:0140855
+name: histone H3S57 kinase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: histone H3-serine (position 57) + ATP = histone H3-phosphoserine (position 57) + ADP. This reaction is the addition of a phosphate group to the serine residue at position 57 of histone H3." [PMID:24820035]
+synonym: "histone kinase activity (H3-S57 specific)" EXACT []
+synonym: "histone serine kinase activity (H3-S57 specific)" EXACT []
+synonym: "histone-serine kinase activity (H3-S57 specific)" EXACT []
+is_a: GO:0140996 ! histone H3 kinase activity
+
+[Term]
+id: GO:0140856
+name: histone H2AK13 ubiquitin ligase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a ubiquitin molecule to histone 2A at the lysine-13 residue." [PMID:22980979, PMID:28624371]
+synonym: "histone ubiquitin ligase activity (H2A-K13 specific)" EXACT []
+is_a: GO:0140852 ! histone ubiquitin ligase activity
+
+[Term]
+id: GO:0140857
+name: histone H3T45 kinase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: histone H3-threonine (position 45) + ATP = histone H3-phosphothreonine (position 45) + ADP. This reaction is the addition of a phosphate group to the threonine residue at position 45 of histone H3." [PMID:24820035]
+synonym: "histone kinase activity (H3-T45 specific)" EXACT []
+synonym: "histone threonine kinase activity (H3-T45 specific)" EXACT []
+synonym: "histone-threonine kinase activity (H3-T45 specific)" EXACT []
+is_a: GO:0140996 ! histone H3 kinase activity
+
+[Term]
+id: GO:0140858
+name: histone H2AK15 ubiquitin ligase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a ubiquitin molecule to histone 2A at the lysine-15 residue." [PMID:22980979, PMID:28624371]
+synonym: "histone ubiquitin ligase activity (H2A-K15 specific)" EXACT []
+is_a: GO:0140852 ! histone ubiquitin ligase activity
+
+[Term]
+id: GO:0140859
+name: pterocarpan synthase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + medicarpin = 4'-methoxyisoflavan-2',4,7-triol." [PMID:7805842, RHEA:35811]
+synonym: "2',7-dihydroxy-4'-methoxyisoflavanol dehydratase activity" EXACT [EC:4.2.1.139]
+synonym: "2'-hydroxyisoflavanol 4,2'-dehydratase activity" EXACT [EC:4.2.1.139]
+synonym: "7,2'-dihydroxy-4'-methoxyisoflavanol dehydratase activity" EXACT [EC:4.2.1.139]
+synonym: "medicarpan synthase activity" EXACT [EC:4.2.1.139]
+synonym: "medicarpin synthase activity" EXACT [EC:4.2.1.139]
+xref: EC:4.2.1.139
+xref: RHEA:35407
+is_a: GO:0016836 ! hydro-lyase activity
+
+[Term]
+id: GO:0140860
+name: (3R)-2'-hydroxyisoflavanone reductase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: a (3R,4R)-4,2'-dihydroxyisoflavan + NADP+ = a (3R)-2'-hydroxyisoflavanone + H+ + NADPH." [PMID:7625843, RHEA:56284]
+synonym: "vestitone reductase activity" NARROW [EC:1.1.1.348]
+is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+
+[Term]
+id: GO:0140861
+name: DNA repair-dependent chromatin remodeling
+namespace: biological_process
+def: "A chromatin remodeling process that allows DNA repair enzyme to access genomic DNA and repair DNA lesions." [PMID:15528408, PMID:28053344, PMID:29095668, PMID:35689883]
+synonym: "DNA damage-dependent chromatin remodeling" EXACT []
+is_a: GO:0006338 ! chromatin remodeling
+relationship: part_of GO:0006974 ! DNA damage response
+
+[Term]
+id: GO:0140862
+name: histone H2AK119 ubiquitin ligase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a ubiquitin molecule to histone 2A at the lysine-119 residue." [PMID:22844243, PMID:25470042, PMID:28624371]
+synonym: "histone H2A-K119 ubiquitin ligase activity" EXACT []
+synonym: "histone ubiquitin ligase activity (H2A-K119 specific)" EXACT []
+is_a: GO:0140852 ! histone ubiquitin ligase activity
+
+[Term]
+id: GO:0140863
+name: histone H2AK127 ubiquitin ligase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a ubiquitin molecule to histone 2A at the lysine-127 residue." [PMID:28624371]
+synonym: "histone H2A-K127 ubiquitin ligase activity" EXACT []
+synonym: "histone ubiquitin ligase activity (H2A-K127 specific)" EXACT []
+is_a: GO:0140852 ! histone ubiquitin ligase activity
+
+[Term]
+id: GO:0140864
+name: histone H2AK129 ubiquitin ligase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a ubiquitin molecule to histone 2A at the lysine-129 residue." [PMID:28624371]
+synonym: "histone H2A-K129 ubiquitin ligase activity" EXACT []
+synonym: "histone ubiquitin ligase activity (H2A-K129 specific)" EXACT []
+is_a: GO:0140852 ! histone ubiquitin ligase activity
+
+[Term]
+id: GO:0140865
+name: interleukin-22-mediated signaling pathway
+namespace: biological_process
+def: "The series of molecular signals initiated by interleukin-22 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [PMID:34755534]
+synonym: "IL-22-mediated signaling pathway" EXACT []
+synonym: "interleukin-22-mediated signalling pathway" EXACT []
+is_a: GO:0019221 ! cytokine-mediated signaling pathway
+
+[Term]
+id: GO:0140866
+name: interleukin-20-mediated signaling pathway
+namespace: biological_process
+def: "The series of molecular signals initiated by interleukin-20 binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [PMID:34755534]
+synonym: "IL-20-mediated signaling pathway" EXACT []
+synonym: "interleukin-20-mediated signalling pathway" EXACT []
+is_a: GO:0019221 ! cytokine-mediated signaling pathway
+
+[Term]
+id: GO:0140867
+name: NAD+-histone H2BE18 glutamate ADP-ribosyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of ADP-ribose groups to the glutamate-18 residue of histone H2B (or an equivalent residue)." [PMID:28252050]
+synonym: "NAD+-histone H2B-E18 glutamate ADP-ribosyltransferase activity" EXACT []
+synonym: "NAD+-histone-glutamate ADP-ribosyltransferase activity (H2B-E18 specific)" EXACT []
+is_a: GO:0140807 ! NAD+-protein-glutamate ADP-ribosyltransferase activity
+
+[Term]
+id: GO:0140868
+name: 4,4'-diapophytoene desaturase (4,4'-diapolycopene-forming)
+namespace: molecular_function
+def: "Catalysis of the reaction: 3 H+ + 15-cis-4,4'-diapophytoene + 4 FAD = 4,4'-diapolycopene + 3 FADH2. This reaction consists of three successive dehydrogenations that lead to the introduction of three double bonds into 4,4'-diapophytoene (dehydrosqualene), with 4,4'-diapophytofluene and 4,4'-diapo-zeta-carotene as intermediates, and 4,4'-diaponeurosporene (the major deep-yellow pigment in staphylococci strains) as the end product." [PMID:15933032, RHEA:42800]
+synonym: "4,4'-diapophytoene desaturase activity" BROAD []
+xref: EC:1.3.8.2
+xref: RHEA:42800
+is_a: GO:0052890 ! oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor
+
+[Term]
+id: GO:0140869
+name: miRNA inhibitor activity via base-pairing
+namespace: molecular_function
+def: "Stops, prevents or reduces the activity of miRNA-mediated gene silencing activity by base-pairing with a target miRNA. An example of this activity is mediated by long non-coding RNAs (lncRNAs)." [PMID:34454184]
+comment: This term is intended for regulatory non-coding RNAs that act by base-pairing with a target microRNA.
+synonym: "base-pairing target-directed microRNA suppressor activity" RELATED []
+synonym: "base-pairing target-directed miRNA suppressor activity" RELATED []
+synonym: "miRNA base-pairing repressor activity" NARROW []
+synonym: "miRNA binding involved in posttranscriptional gene silencing" EXACT []
+synonym: "miRNA inhibitor activity" BROAD []
+synonym: "miRNA sponge" NARROW []
+is_a: GO:0035198 ! miRNA binding
+is_a: GO:0140678 ! molecular function inhibitor activity
+
+[Term]
+id: GO:0140870
+name: RNA polymerase inhibitor activity
+namespace: molecular_function
+def: "Binds to and stops, prevents or reduces the activity of RNA polymerase." [PMID:15300239, PMID:18313387, PMID:31048766]
+is_a: GO:0004857 ! enzyme inhibitor activity
+
+[Term]
+id: GO:0140871
+name: repressor of RNA polymerase inhibitor activity
+namespace: molecular_function
+def: "Binds to and stops, prevents or reduces the activity of an RNA polymerase inhibitor." [PMID:28475895, PMID:31048766]
+is_a: GO:0098772 ! molecular function regulator activity
+
+[Term]
+id: GO:0140872
+name: viridicatumtoxin biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of viridicatumtoxin, a tetracycline-like fungal meroterpenoid with a unique, fused spirobicyclic ring system." [PMID:20534346, PMID:24161266]
+synonym: "viridicatumtoxin anabolism" EXACT []
+synonym: "viridicatumtoxin biosynthesis" EXACT []
+synonym: "viridicatumtoxin formation" EXACT []
+synonym: "viridicatumtoxin synthesis" EXACT []
+xref: MetaCyc:PWY-7659
+is_a: GO:0030639 ! polyketide biosynthetic process
+is_a: GO:0042181 ! ketone biosynthetic process
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:0043604 ! amide biosynthetic process
+is_a: GO:0046189 ! phenol-containing compound biosynthetic process
+is_a: GO:0120255 ! olefinic compound biosynthetic process
+is_a: GO:1901503 ! ether biosynthetic process
+is_a: GO:1901566 ! organonitrogen compound biosynthetic process
+is_a: GO:1902645 ! tertiary alcohol biosynthetic process
+is_a: GO:1902653 ! secondary alcohol biosynthetic process
+
+[Term]
+id: GO:0140873
+name: paxilline biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of paxilline, a mycotoxin that acts as an inhibitor of mammalian maxi-K channels." [PMID:23949005]
+synonym: "paxilline anabolism" EXACT []
+synonym: "paxilline biosynthesis" EXACT []
+synonym: "paxilline formation" EXACT []
+synonym: "paxilline synthesis" EXACT []
+xref: MetaCyc:PWY-7493
+is_a: GO:0009709 ! terpenoid indole alkaloid biosynthetic process
+is_a: GO:0016102 ! diterpenoid biosynthetic process
+is_a: GO:0018130 ! heterocycle biosynthetic process
+is_a: GO:0042181 ! ketone biosynthetic process
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:0120255 ! olefinic compound biosynthetic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+is_a: GO:1902645 ! tertiary alcohol biosynthetic process
+
+[Term]
+id: GO:0140874
+name: paraherquonin biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of paraherquonin, a meroterpenoid with a unique, highly congested hexacyclic molecular architecture." [PMID:27602587]
+synonym: "paraherquonin anabolism" EXACT []
+synonym: "paraherquonin biosynthesis" EXACT []
+synonym: "paraherquonin formation" EXACT []
+synonym: "paraherquonin synthesis" EXACT []
+is_a: GO:0016114 ! terpenoid biosynthetic process
+is_a: GO:0042181 ! ketone biosynthetic process
+is_a: GO:1901336 ! lactone biosynthetic process
+is_a: GO:1902645 ! tertiary alcohol biosynthetic process
+
+[Term]
+id: GO:0140875
+name: PR-toxin biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of PR-toxin, a bicyclic sesquiterpene belonging to the eremophilane class and acting as a mycotoxin." [PMID:24239699, PMID:27921136]
+synonym: "PR-toxin anabolism" EXACT []
+synonym: "PR-toxin biosynthesis" EXACT []
+synonym: "PR-toxin formation" EXACT []
+synonym: "PR-toxin synthesis" EXACT []
+is_a: GO:0016106 ! sesquiterpenoid biosynthetic process
+is_a: GO:0018130 ! heterocycle biosynthetic process
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+
+[Term]
+id: GO:0140876
+name: andrastin A biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of andrastin A, a meroterpenoid that exhibits inhibitory activity against ras farnesyltransferase, suggesting that it could have promising antitumor activity." [DOI:10.1016/j.tet.2013.07.029]
+synonym: "andrastin A anabolism" EXACT []
+synonym: "andrastin A biosynthesis" EXACT []
+synonym: "andrastin A formation" EXACT []
+synonym: "andrastin A synthesis" EXACT []
+is_a: GO:0006694 ! steroid biosynthetic process
+is_a: GO:0042181 ! ketone biosynthetic process
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:0046184 ! aldehyde biosynthetic process
+is_a: GO:0120255 ! olefinic compound biosynthetic process
+is_a: GO:1900620 ! acetate ester biosynthetic process
+is_a: GO:1901617 ! organic hydroxy compound biosynthetic process
+
+[Term]
+id: GO:0140877
+name: mevastatin biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of mevastatin , also known as compactin or ML-236B, and which acts as a potent competitive inhibitor of HMG-CoA reductase." [PMID:12172803, PMID:12242508]
+synonym: "mevastatin anabolism" EXACT []
+synonym: "mevastatin biosynthesis" EXACT []
+synonym: "mevastatin formation" EXACT []
+synonym: "mevastatin synthesis" EXACT []
+is_a: GO:0030639 ! polyketide biosynthetic process
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:1901336 ! lactone biosynthetic process
+
+[Term]
+id: GO:0140878
+name: griseofulvin biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of griseofulvin, an important antifungal drug that has been in use for a long time for treating dermatophyte infections." [PMID:20534346, PMID:23978092]
+synonym: "griseofulvin anabolism" EXACT []
+synonym: "griseofulvin biosynthesis" EXACT []
+synonym: "griseofulvin formation" EXACT []
+synonym: "griseofulvin synthesis" EXACT []
+xref: MetaCyc:PWY-7653
+is_a: GO:0018130 ! heterocycle biosynthetic process
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+
+[Term]
+id: GO:0140879
+name: conidiogenone biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of conidiogenone , a diterpene known to induce the conidiation." [PMID:30343633]
+synonym: "conidiogenone anabolism" EXACT []
+synonym: "conidiogenone biosynthesis" EXACT []
+synonym: "conidiogenone formation" EXACT []
+synonym: "conidiogenone synthesis" EXACT []
+is_a: GO:0016102 ! diterpenoid biosynthetic process
+is_a: GO:0042181 ! ketone biosynthetic process
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+is_a: GO:1902653 ! secondary alcohol biosynthetic process
+
+[Term]
+id: GO:0140880
+name: terrein biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of terrein, a fungal metabolite with ecological, antimicrobial, antiproliferative, and antioxidative activities." [PMID:24816227]
+synonym: "terrein anabolism" EXACT []
+synonym: "terrein biosynthesis" EXACT []
+synonym: "terrein formation" EXACT []
+synonym: "terrein synthesis" EXACT []
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:0046173 ! polyol biosynthetic process
+
+[Term]
+id: GO:0140881
+name: positive regulation terrein biosynthetic process
+namespace: biological_process
+def: "Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of the fungal metabolite terrein." [PMID:24816227, PMID:25852654]
+is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
+is_a: GO:1900378 ! positive regulation of secondary metabolite biosynthetic process
+is_a: GO:1902932 ! positive regulation of alcohol biosynthetic process
+relationship: positively_regulates GO:0140880 ! terrein biosynthetic process
+
+[Term]
+id: GO:0140882
+name: zinc export across plasma membrane
+namespace: biological_process
+def: "The directed movement of zinc ions from a cell, into the extracellular region." [PMID:17355957]
+synonym: "zinc ion export from cell" EXACT []
+is_a: GO:0071577 ! zinc ion transmembrane transport
+is_a: GO:0140115 ! export across plasma membrane
+
+[Term]
+id: GO:0140883
+name: induction by virus of host reticulophagy
+namespace: biological_process
+def: "Any process in which a virus activates or increases the frequency, rate or extent of reticulophagy in the host." [PMID:35239449]
+synonym: "activation of host reticulophagy by virus" EXACT []
+synonym: "positive regulation by virus of host reticulophagy" BROAD []
+is_a: GO:0039520 ! induction by virus of host autophagy
+is_a: GO:0140501 ! positive regulation of reticulophagy
+
+[Term]
+id: GO:0140884
+name: suppression by virus of host type II interferon-mediated signaling pathway
+namespace: biological_process
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type II interferon-mediated signaling in the host organism. Type II interferon is also known as interferon-gamma." [PMID:28901902]
+synonym: "negative regulation by virus of host type II interferon-mediated signaling pathway" EXACT []
+synonym: "suppression by virus of host type II IFN-mediated signaling pathway" EXACT []
+synonym: "suppression by virus of host type II interferon-mediated signalling pathway" EXACT []
+is_a: GO:0060336 ! negative regulation of type II interferon-mediated signaling pathway
+is_a: GO:0140886 ! suppression by virus of host interferon-mediated signaling pathway
+
+[Term]
+id: GO:0140885
+name: suppression by virus of host type III interferon-mediated signaling pathway
+namespace: biological_process
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type III interferon-mediated signaling in the host organism. Type III interferon is also known as interferon-lambda." [PMID:32464097]
+synonym: "negative regulation by virus of host type III interferon-mediated signaling pathway" EXACT []
+synonym: "suppression by virus of host type III IFN-mediated signaling pathway" EXACT []
+synonym: "suppression by virus of host type III interferon-mediated signalling pathway" EXACT []
+is_a: GO:0140886 ! suppression by virus of host interferon-mediated signaling pathway
+relationship: negatively_regulates GO:0038196 ! type III interferon-mediated signaling pathway
+
+[Term]
+id: GO:0140886
+name: suppression by virus of host interferon-mediated signaling pathway
+namespace: biological_process
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of interferon-mediated signaling in the host organism." [PMID:33097660]
+synonym: "inhibition of host interferon signaling pathway by virus" RELATED []
+synonym: "negative regulation by virus of host interferon-mediated signaling pathway" EXACT []
+synonym: "suppression by virus of host IFN-mediated signaling pathway" EXACT []
+synonym: "suppression by virus of host interferon-mediated signalling pathway" EXACT []
+is_a: GO:0001960 ! negative regulation of cytokine-mediated signaling pathway
+is_a: GO:0039503 ! suppression by virus of host innate immune response
+relationship: negatively_regulates GO:0140888 ! interferon-mediated signaling pathway
+
+[Term]
+id: GO:0140887
+name: positive regulation of nucleosome disassembly
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of the controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA." [PMID:34471130, PMID:35308047]
+is_a: GO:0031334 ! positive regulation of protein-containing complex assembly
+is_a: GO:1905269 ! positive regulation of chromatin organization
+relationship: positively_regulates GO:0006334 ! nucleosome assembly
+
+[Term]
+id: GO:0140888
+name: interferon-mediated signaling pathway
+namespace: biological_process
+def: "The series of molecular signals initiated by type II interferon binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. Type II interferon is also known as interferon-gamma." [GOC:add, GOC:dph, GOC:signaling, PMID:32464097]
+synonym: "interferon signaling pathway" EXACT []
+synonym: "interferon-activated signaling pathway" EXACT [GOC:signaling]
+is_a: GO:0019221 ! cytokine-mediated signaling pathway
+
+[Term]
+id: GO:0140889
+name: DNA replication-dependent chromatin disassembly
+namespace: biological_process
+def: "The disruption of nucleosomes during DNA replication to allow the replication machinery to access the DNA." [PMID:34471130, PMID:35308047]
+is_a: GO:0006325 ! chromatin organization
+
+[Term]
+id: GO:0140890
+name: H1 histone chaperone activity
+namespace: molecular_function
+def: "A histone chaperone that carries a H1 histone." [PMID:12509435]
+synonym: "H1 histone carrier activity" EXACT []
+is_a: GO:0140713 ! histone chaperone activity
+
+[Term]
+id: GO:0140891
+name: tRNA-derived small RNA processing
+namespace: biological_process
+def: "A process leading to the generation of a functional small regulatory non-coding RNA derived from a tRNA." [PMID:29120263]
+is_a: GO:0070918 ! regulatory ncRNA processing
+
+[Term]
+id: GO:0140892
+name: sodium,bicarbonate:chloride antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction chloride(in) + 2 hydrogencarbonate(out) + Na+(out) = chloride(out) + 2 hydrogencarbonate(in) + Na+(in)." [PMID:18577713, PMID:20389022, PMID:8189393]
+synonym: "sodium-dependent chloride/bicarbonate exchanger activity" EXACT []
+xref: TC:2.A.31.2.4
+is_a: GO:0015081 ! sodium ion transmembrane transporter activity
+is_a: GO:0140828 ! metal cation:monoatomic cation antiporter activity
+is_a: GO:0140900 ! chloride:bicarbonate antiporter activity
+
+[Term]
+id: GO:0140893
+name: neutral amino acid, sodium:proton antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: H+(in) + amino acid(out) + Na+(out) = H+(out) + amino acid(in) + Na+(in)." [PMID:11698233, PMID:34704597]
+synonym: "amino acid-coupled Na+/H+ exchanger activity" EXACT []
+xref: TC:2.A.18.6.8
+is_a: GO:0015385 ! sodium:proton antiporter activity
+
+[Term]
+id: GO:0140894
+name: endolysosomal toll-like receptor signaling pathway
+namespace: biological_process
+def: "The series of molecular signals initiated by a ligand binding to an endolysosomal pattern recognition receptor (PRR) of the toll-like family. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species." [PMID:29679565]
+synonym: "endolysosomal pattern recognition receptor signaling pathway" EXACT []
+is_a: GO:0002753 ! cytosolic pattern recognition receptor signaling pathway
+
+[Term]
+id: GO:0140895
+name: cell surface toll-like receptor signaling pathway
+namespace: biological_process
+def: "The series of molecular signals initiated by a ligand binding to a cell surface pattern recognition receptor (PRR) of the toll-like family." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967]
+synonym: "cell surface TLR signaling pathway" EXACT []
+is_a: GO:0002752 ! cell surface pattern recognition receptor signaling pathway
+
+[Term]
+id: GO:0140896
+name: cGAS/STING signaling pathway
+namespace: biological_process
+def: "The series of molecular signals initiated by the binding of a double-stranded DNA or RNA from another organism to cytosolic cyclic GMP-AMP (cGAMP) synthase (cGAS) that activates innate immune responses through production of the second messenger cGAMP, which activates the adaptor STING." [PMID:27648547, PMID:34261127, PMID:34261128]
+is_a: GO:0002753 ! cytosolic pattern recognition receptor signaling pathway
+
+[Term]
+id: GO:0140897
+name: mechanoreceptor activity
+namespace: molecular_function
+def: "Combining with a mechanical force and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction." [PMID:23907979, PMID:34666001]
+is_a: GO:0004888 ! transmembrane signaling receptor activity
+
+[Term]
+id: GO:0140898
+name: CENP-A eviction from euchromatin
+namespace: biological_process
+def: "A chromatin remodeling process in which CENP-A is removed from euchromatin regions to prevent neocentromere formation." [PMID:27666591]
+is_a: GO:0006338 ! chromatin remodeling
+
+[Term]
+id: GO:0140899
+name: plastid gene expression
+namespace: biological_process
+def: "The process in which a plastid gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [PMID:28377785]
+is_a: GO:0010467 ! gene expression
+
+[Term]
+id: GO:0140900
+name: chloride:bicarbonate antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: chloride(in) + HCO3-(out) = chloride(out) + HCO3-(in)." [PMID:10428871, PMID:16606687, RHEA:72203]
+synonym: "bicarbonate:chloride antiporter activity" EXACT []
+xref: RHEA:72203
+xref: TC:2.A.53.2.18
+is_a: GO:0005452 ! solute:inorganic anion antiporter activity
+is_a: GO:0015108 ! chloride transmembrane transporter activity
+is_a: GO:0140829 ! bicarbonate:monoatomic anion antiporter activity
+
+[Term]
+id: GO:0140901
+name: L-asparagine:sodium symporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: L-asparagine(out) + Na+(out) = L-asparagine(in) + Na+(in)." [PMID:21511949, PMID:28416685]
+synonym: "asparagine:sodium symporter activity" EXACT []
+synonym: "sodium:asparagine symporter activity" EXACT []
+synonym: "sodium:L-asparagine symporter activity" EXACT []
+xref: RHEA:71383
+xref: TC:2.A.18.6.13
+is_a: GO:0005295 ! neutral L-amino acid:sodium symporter activity
+is_a: GO:0015182 ! L-asparagine transmembrane transporter activity
+is_a: GO:0015655 ! alanine:sodium symporter activity
+
+[Term]
+id: GO:0140902
+name: L-glutamine:sodium symporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: L-glutamine(out) + Na+(out) = L-glutamine(in) + Na+(in)." [PMID:28416685]
+synonym: "glutamine:sodium symporter activity" EXACT []
+synonym: "sodium:glutamine symporter activity" EXACT []
+synonym: "sodium:L-glutamine symporter activity" EXACT []
+xref: TC:2.A.18.6.13
+is_a: GO:0005295 ! neutral L-amino acid:sodium symporter activity
+is_a: GO:0015186 ! L-glutamine transmembrane transporter activity
+is_a: GO:0015655 ! alanine:sodium symporter activity
+
+[Term]
+id: GO:0140903
+name: histone H3R26 methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone H3)-arginine (position 26) = S-adenosyl-L-homocysteine + (histone H3)-N-methyl-arginine (position 26). This reaction is the addition of a methyl group to the arginine residue at position 26 of histone H3." [PMID:17882261]
+synonym: "histone H3R26 arginine methyltransferase activity" EXACT [GOC:mah]
+synonym: "histone methylase activity (H3-R26 specific)" EXACT []
+synonym: "histone methyltransferase activity (H3-R26 specific)" EXACT []
+synonym: "histone-arginine N-methyltransferase activity (H3-R26 specific)" EXACT []
+synonym: "histone-H3R26 methyltransferase activity" EXACT []
+is_a: GO:0016274 ! protein-arginine N-methyltransferase activity
+is_a: GO:0140938 ! histone H3 methyltransferase activity
+
+[Term]
+id: GO:0140904
+name: cytoophidium organization
+namespace: biological_process
+def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a cytoophidium. Cytoophidia are mesoscale, intracellular, filamentous structures that contain metabolic enzymes." [PMID:25223282, PMID:27362644]
+is_a: GO:0097435 ! supramolecular fiber organization
+
+[Term]
+id: GO:0140905
+name: haloperoxidase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: R-CH + a halogen + H2O2 = R-C-halogen + H2O." [PMID:28466644, PMID:34368824]
+is_a: GO:0004601 ! peroxidase activity
+is_a: GO:0140906 ! halogenase activity
+
+[Term]
+id: GO:0140906
+name: halogenase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: R-CH + a halogen + oxygen donor = R-C-halogen +H2O." [PMID:28466644, PMID:34368824]
+is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+
+[Term]
+id: GO:0140907
+name: flavin-dependent halogenase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: R-CH + a halogen + FADH2 + O2 = R-C-halogen + FAD + H2O." [PMID:28466644, PMID:34368824]
+is_a: GO:0140906 ! halogenase activity
+
+[Term]
+id: GO:0140908
+name: histone H3K122 acetyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: acetyl-CoA + histone H3 L-lysine (position 122) = CoA + histone H3 N6-acetyl-L-lysine (position 122)." [PMID:23415232]
+synonym: "histone acetylase activity (H3-K122 specific)" EXACT []
+synonym: "histone acetyltransferase activity (H3-K122 specific)" EXACT []
+synonym: "histone H3-K122 acetyltransferase activity" EXACT []
+synonym: "histone lysine N-acetyltransferase activity (H3-K122 specific)" EXACT []
+is_a: GO:0010484 ! histone H3 acetyltransferase activity
+
+[Term]
+id: GO:0140909
+name: kinetoplast DNA replication
+namespace: biological_process
+def: "The process of doubling of the number of maxicircles and minicircles and distribution of the progeny into two daughter networks, which are identical to the parent kinetoplast DNA network." [GOC:ach, PMID:12455998, PMID:15967722, PMID:17462016, PMID:8045928, PMID:8561456]
+synonym: "kDNA replication" EXACT []
+synonym: "kinetoplast DNA synthesis" EXACT []
+synonym: "replication of kinetoplast DNA" EXACT []
+is_a: GO:0006264 ! mitochondrial DNA replication
+
+[Term]
+id: GO:0140910
+name: iRhom2/ADAM17 sheddase complex
+namespace: cellular_component
+def: "A complex consisting of ADAM17 in complex with regulatory iRhoms and FERM domain containing proteins." [PMID:29897336]
+is_a: GO:0032991 ! protein-containing complex
+
+[Term]
+id: GO:0140911
+name: pore-forming activity
+namespace: molecular_function
+alt_id: GO:0034290
+alt_id: GO:0034291
+alt_id: GO:0034292
+def: "An activity in which a protein is inserted into the membrane of another cell where it forms transmembrane pores. Pores disrupts the integrity of the cell membrane, resulting in deregulated ion homeostasis, cellular dysfunction, and can result in cell death." [PMID:1406491, PMID:25157079, PMID:34387717]
+synonym: "canonical holin activity" NARROW []
+synonym: "holin activity" NARROW []
+synonym: "pinholin activity" NARROW []
+synonym: "pore forming activity" EXACT []
+xref: TC:1.C
+is_a: GO:0003674 ! molecular_function
+
+[Term]
+id: GO:0140912
+name: membrane destabilizing activity
+namespace: molecular_function
+def: "Binding to a membrane and increasing its permeability. This may lead to cell membrane lysis and cell content release." [PMID:34496967]
+synonym: "antimicrobial peptide" BROAD []
+is_a: GO:0003674 ! molecular_function
+
+[Term]
+id: GO:0140913
+name: viral release via disruption of host peptidoglycan cell wall
+namespace: biological_process
+def: "The dissemination of mature viral particles from a host cell, caused by a virus hydrolyzing the peptidoglycan cell wall of the host organism. Peptidoglycans are any of a class of glycoconjugates found in bacterial cell walls." [PMID:24585055, PMID:26085488, PMID:29495305]
+is_a: GO:0044659 ! viral release from host cell by cytolysis
+
+[Term]
+id: GO:0140914
+name: zinc ion import into secretory vesicle
+namespace: biological_process
+def: "The directed import of zinc(2+) from the cytosol, across an organelle membrane, into a secretory vesicle." [PMID:19496757]
+is_a: GO:0062111 ! zinc ion import into organelle
+
+[Term]
+id: GO:0140915
+name: zinc ion import into zymogen granule
+namespace: biological_process
+def: "The directed import of zinc(2+) from the cytosol, across an organelle membrane, into a zymogen granule." [PMID:20133611]
+is_a: GO:0140914 ! zinc ion import into secretory vesicle
+
+[Term]
+id: GO:0140916
+name: zinc ion import into lysosome
+namespace: biological_process
+def: "The directed import of zinc(2+) from the cytosol, across an organelle membrane, into a lysosome." [PMID:25808614]
+is_a: GO:0007041 ! lysosomal transport
+is_a: GO:0034486 ! vacuolar transmembrane transport
+is_a: GO:0062111 ! zinc ion import into organelle
+
+[Term]
+id: GO:0140917
+name: zinc ion import into mitochondrion
+namespace: biological_process
+def: "The directed import of zinc(2+) from the cytosol, across an organelle membrane, into a mitochondrion." [PMID:21289295]
+is_a: GO:0062111 ! zinc ion import into organelle
+
+[Term]
+id: GO:0140918
+name: centrosomal core
+namespace: cellular_component
+def: "The core region of the centrosome, a layered structure containing proteins, surrounded by the centrosomal corona. The core duplicates once per cell cycle at the G2/M transition when two outer layers form the mitotic spindle poles." [PMID:28104305, PMID:30413081]
+synonym: "centrosome core" EXACT []
+is_a: GO:0110165 ! cellular anatomical entity
+relationship: part_of GO:0005813 ! centrosome
+
+[Term]
+id: GO:0140919
+name: thermomorphogenesis
+namespace: biological_process
+def: "The suite of morphological and architectural changes in an organism induced by high ambient temperatures, below the heat-stress range." [PMID:27250752]
+is_a: GO:0009266 ! response to temperature stimulus
+is_a: GO:0009791 ! post-embryonic development
+
+[Term]
+id: GO:0140920
+name: regulation of thermomorphogenesis
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of thermomorphogenesis." [PMID:27250752]
+is_a: GO:0048580 ! regulation of post-embryonic development
+is_a: GO:0048583 ! regulation of response to stimulus
+relationship: regulates GO:0140919 ! thermomorphogenesis
+
+[Term]
+id: GO:0140921
+name: negative regulation of thermomorphogenesis
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of thermomorphogenesis." [PMID:27250752]
+is_a: GO:0048581 ! negative regulation of post-embryonic development
+is_a: GO:0048585 ! negative regulation of response to stimulus
+is_a: GO:0140920 ! regulation of thermomorphogenesis
+relationship: negatively_regulates GO:0140919 ! thermomorphogenesis
+
+[Term]
+id: GO:0140922
+name: positive regulation of thermomorphogenesis
+namespace: biological_process
+def: "Any process that increases the rate, frequency or extent of thermomorphogenesis." [PMID:27250752]
+is_a: GO:0048582 ! positive regulation of post-embryonic development
+is_a: GO:0048584 ! positive regulation of response to stimulus
+is_a: GO:0140920 ! regulation of thermomorphogenesis
+relationship: positively_regulates GO:0140919 ! thermomorphogenesis
+
+[Term]
+id: GO:0140923
+name: magnetosome assembly
+namespace: biological_process
+def: "The aggregation, arrangement and bonding together of a set of components to form a magnetosome. Magnetosomes are specialized organelles for magnetic navigation that comprise membrane-enveloped, nano-sized crystals of a magnetic iron mineral; they are formed by a diverse group of magnetotactic bacteria (MTB)." [PMID:19575557, PMID:34723168]
+synonym: "magnetosome formation" EXACT []
+is_a: GO:0070925 ! organelle assembly
+
+[Term]
+id: GO:0140924
+name: L-kynurenine transmembrane transport
+namespace: biological_process
+def: "The directed movement of L-kynurenine across a membrane." [PMID:35245456]
+is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
+
+[Term]
+id: GO:0140925
+name: L-phenylalanine import across plasma membrane
+namespace: biological_process
+def: "The directed movement of L-phenylalanine from outside of a cell, across the plasma membrane and into the cytosol." [PMID:11069779]
+is_a: GO:0015801 ! aromatic amino acid transport
+is_a: GO:0015823 ! phenylalanine transport
+is_a: GO:0089718 ! amino acid import across plasma membrane
+is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
+
+[Term]
+id: GO:0140926
+name: L-kynurenine transmembrane transporter activity
+namespace: molecular_function
+def: "Enables the transfer of L-kynurenine from one side of a membrane to the other." [PMID:35245456]
+is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
+
+[Term]
+id: GO:0140927
+name: cyclic-di-GMP transmembrane transporter activity
+namespace: molecular_function
+def: "Enables the transfer of cyclic-di-GMP from one side of a membrane to the other." [PMID:34965418]
+is_a: GO:0001409 ! guanine nucleotide transmembrane transporter activity
+is_a: GO:0005346 ! purine ribonucleotide transmembrane transporter activity
+is_a: GO:0008514 ! organic anion transmembrane transporter activity
+
+[Term]
+id: GO:0140928
+name: inhibition of non-skeletal tissue mineralization
+namespace: biological_process
+def: "A homeostatic process involved in the maintenance of non-mineral tissue, by preventing mineralization of non-skeletal tissue." [PMID:21490328, PMID:30030150]
+synonym: "inhibition of ectopic tissue mineralization" NARROW []
+is_a: GO:0001894 ! tissue homeostasis
+
+[Term]
+id: GO:0140929
+name: mannose:sodium symporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: D-mannose(out) + Na+(out) = D-mannose(in) + Na+(in)." [PMID:22212718, PMID:23451068, PMID:24573086]
+is_a: GO:0005402 ! carbohydrate:monoatomic cation symporter activity
+is_a: GO:0015370 ! solute:sodium symporter activity
+is_a: GO:0015578 ! mannose transmembrane transporter activity
+
+[Term]
+id: GO:0140930
+name: fructose:sodium symporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: D-fructose(out) + Na+(out) = D-fructose(in) + Na+(in)." [PMID:22212718, PMID:23451068]
+is_a: GO:0005353 ! fructose transmembrane transporter activity
+is_a: GO:0005402 ! carbohydrate:monoatomic cation symporter activity
+is_a: GO:0015370 ! solute:sodium symporter activity
+
+[Term]
+id: GO:0140931
+name: neutral L-amino acid:sodium:chloride symporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: neutral L-amino acid(out) + Na+(out) + Cl-(out) = neutral L-amino acid(in) + Na+(in)+ Cl-(in)." [PMID:19478081]
+synonym: "neutral amino acid:sodium:chloride symporter activity" EXACT []
+is_a: GO:0005283 ! amino acid:sodium symporter activity
+is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
+is_a: GO:0015378 ! sodium:chloride symporter activity
+
+[Term]
+id: GO:0140932
+name: 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: a 5'-end (N2,N2,N7-trimethyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O = a 5'-end diphospho-ribonucleoside in mRNA + 2 H+ + N7-methyl-GMP. Can also use (N7-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA as a substrate." [PMID:24742626, PMID:32723815]
+synonym: "m(7)GpppN m(7)GMP phosphohydrolase activity" EXACT [EC:3.6.1.59]
+synonym: "m(7)GpppX diphosphatase activity" EXACT [EC:3.6.1.59]
+synonym: "m(7)GpppX pyrophosphatase activity" EXACT [EC:3.6.1.59]
+xref: EC:3.6.1.59
+is_a: GO:0034353 ! mRNA 5'-diphosphatase activity
+
+[Term]
+id: GO:0140933
+name: 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: a 5'-end (N7-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O = a 5'-end phospho-ribonucleoside in mRNA + N7-methyl-GDP + H+." [PMID:18820299, PMID:29483298]
+synonym: "m(7)GpppN-mRNA hydrolase activity" EXACT []
+xref: EC:3.6.1.62
+xref: RHEA:67484
+is_a: GO:0140818 ! mRNA 5'-phosphatase activity
+
+[Term]
+id: GO:0140934
+name: histone deubiquitinase activity
+namespace: molecular_function
+def: "A deubiquitinase that cleaves ubiquitin from a histone protein to which it is conjugated." [PMID:18206972, PMID:18226187]
+synonym: "histone deubiquitination" RELATED []
+is_a: GO:0101005 ! deubiquitinase activity
+is_a: GO:0140993 ! histone modifying activity
+
+[Term]
+id: GO:0140935
+name: histone H2B conserved C-terminal lysine deubiquitinase activity
+namespace: molecular_function
+def: "A histone deubiquitinase that cleaves ubiquitin from the conserved C-terminal lysine residue of a histone H2B protein to which it is conjugated. The conserved lysine residue is K119 in fission yeast, K123 in budding yeast, and K120 in mammals." [PMID:15657442]
+synonym: "histone conserved C-terminal lysine deubiquitination" RELATED []
+is_a: GO:0140936 ! histone H2B deubiquitinase activity
+
+[Term]
+id: GO:0140936
+name: histone H2B deubiquitinase activity
+namespace: molecular_function
+def: "A histone deubiquitinase that cleaves ubiquitin from a histone H2B protein to which it is conjugated." [PMID:18206972, PMID:29352077]
+synonym: "histone H2B deubiquitination" RELATED []
+is_a: GO:0140934 ! histone deubiquitinase activity
+
+[Term]
+id: GO:0140937
+name: histone H4K12 deacetylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 12) + H2O = histone H4 L-lysine (position 12) + acetate. This reaction represents the removal of an acetyl group from lysine at position 12 of the histone H4 protein." [GOC:vw, PMID:15293224]
+synonym: "histone deacetylase activity (H4-K12 specific)" EXACT []
+synonym: "histone H4-K12 deacetylase activity" EXACT []
+synonym: "histone H4-K12 deacetylation" RELATED []
+synonym: "histone H4K12 deacetylation" RELATED []
+is_a: GO:0004407 ! histone deacetylase activity
+
+[Term]
+id: GO:0140938
+name: histone H3 methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + a histone H3 = S-adenosyl-L-homocysteine + a methylated histone H3. Histone methylation generally occurs on either an arginine or a lysine residue." [PMID:28450737]
+synonym: "histone H3 methylase activity" EXACT []
+synonym: "histone H3 methylation" RELATED []
+is_a: GO:0042054 ! histone methyltransferase activity
+
+[Term]
+id: GO:0140939
+name: histone H4 methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: Catalysis of the reaction: S-adenosyl-L-methionine + a histone H4 = S-adenosyl-L-homocysteine + a methylated histone H4. Histone methylation generally occurs on either an arginine or a lysine residue." [PMID:28450737]
+synonym: "histone H4 methylase activity" EXACT []
+synonym: "histone H4 methylation" EXACT []
+is_a: GO:0042054 ! histone methyltransferase activity
+
+[Term]
+id: GO:0140940
+name: histone H2A methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + a histone H2 = S-adenosyl-L-homocysteine + a methylated histone H2A. Histone methylation generally occurs on either an arginine or a lysine residue." [PMID:28450737]
+synonym: "histone H2A methylase activity" EXACT []
+synonym: "histone H2A methylation" RELATED []
+is_a: GO:0042054 ! histone methyltransferase activity
+
+[Term]
+id: GO:0140941
+name: histone H4K20me methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: N(6)-methyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-methionine = H+ + N(6),N(6)-dimethyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-homocysteine. This reaction is the addition of a methyl group to the monomethlyated lysine residue at position 20 of histone H4, producing H4K20me2." [RHEA:60348]
+synonym: "histone H4 methyl lysine(20) N-methyltransferase activity (H4-K20 specific)" EXACT []
+synonym: "histone H4-K20 dimethylation" BROAD []
+synonym: "histone H4K20 dimethylation" BROAD []
+synonym: "histone H4K20me methylase activity" EXACT []
+xref: EC:2.1.1.362
+xref: RHEA:60348
+is_a: GO:0042799 ! histone H4K20 methyltransferase activity
+
+[Term]
+id: GO:0140942
+name: histone H3K9 dimethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl9-[histone H3] + 2 S-adenosyl-L-methionine = 2 H+ + N6,N6-dimethyl-L-lysyl9-[histone H3] + 2 S-adenosyl-L-homocysteine. This reaction is the successive addition of two methyl groups to the unmethylated lysine residue at position 9 of histone H3, producing histone H3K9me2." [RHEA:64444]
+synonym: "histone H3-K9 dimethylation" BROAD []
+synonym: "histone H3K9 dimethylase activity" EXACT []
+synonym: "histone H3K9 dimethylation" BROAD []
+synonym: "histone H3K9 mono/dimethylase activity" EXACT []
+synonym: "histone lysine N-dimethyltransferase activity (H3-K9 specific)" EXACT []
+xref: EC:2.1.1.368
+xref: RHEA:64444
+is_a: GO:0046974 ! histone H3K9 methyltransferase activity
+
+[Term]
+id: GO:0140943
+name: histone H4K20 trimethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl(20)-[histone H4] + 3 S-adenosyl-L-methionine = 3 H+ + N(6),N(6),N(6)-trimethyl-L-lysyl(20)-[histone H4] + 3 S-adenosyl-L-homocysteine. This reaction is the addition of three methyl groups to the lysine residue at position 20 of the histone H4 protein, producing histone H4K20me3." [RHEA:64456]
+synonym: "histone H4K20 trimethylase activity" EXACT []
+synonym: "histone H4K20 trimethylation" EXACT []
+synonym: "histone lysine N-trimethyltransferase activity (H4-K20 specific)" EXACT []
+xref: EC:2.1.1.372
+xref: RHEA:64456
+is_a: GO:0042799 ! histone H4K20 methyltransferase activity
+
+[Term]
+id: GO:0140944
+name: histone H4K20 monomethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl20-[histone H4] + S-adenosyl-L-methionine = H+ + N6-methyl-L-lysyl20-[histone H4] + S-adenosyl-L-homocysteine. This reaction is the addition of a methyl group to the unmethylated lysine residue at position 20 of histone H4, producing histone H4K20me." [RHEA:60344]
+synonym: "histone H4-K20 methylation" BROAD []
+synonym: "histone H4K20 methylase activity" BROAD []
+synonym: "histone H4K20 methylation" BROAD []
+synonym: "histone H4K20 monomethylation" EXACT []
+synonym: "histone lysine N-monomethyltransferase activity (H4-K20 specific)" EXACT []
+xref: EC:2.1.1.361
+xref: RHEA:60344
+is_a: GO:0042799 ! histone H4K20 methyltransferase activity
+
+[Term]
+id: GO:0140945
+name: histone H3K4 monomethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl4-[histone H3] + S-adenosyl-L-methionine = H+ + N6-methyl-L-lysyl4-[histone H3] + S-adenosyl-L-homocysteine. This reaction is the addition of a single methyl group to the unmethylated lysine residue at position 4 of histone H3, producing histone H3K4me." [RHEA:60264]
+synonym: "histone H3K4 monomethylase activity" EXACT []
+synonym: "histone H4-K4 methylation" BROAD []
+synonym: "histone H4K4 methylation" BROAD []
+synonym: "histone lysine N-monomethyltransferase activity (H3-K4 specific)" EXACT []
+xref: EC:2.1.1.364
+xref: RHEA:60264
+is_a: GO:0042800 ! histone H3K4 methyltransferase activity
+
+[Term]
+id: GO:0140946
+name: histone H3K4 dimethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl4-[histone H3] + 2 S-adenosyl-L-methionine = 2 H+ + N6,N6-dimethyl-L-lysyl4-[histone H3] + 2 S-adenosyl-L-homocysteine. This reaction is the successive addition of two methyl groups to the unmethylated lysine residue at position 4 of histone H3, producing histone H3K4me2." [RHEA:64448]
+synonym: "histone H3-K4 dimethylation" BROAD []
+synonym: "histone H3K4 dimethylase activity" EXACT []
+synonym: "histone H3K4 dimethylation" BROAD []
+synonym: "histone lysine N-dimethyltransferase activity (H3-K4 specific)" EXACT []
+xref: EC:2.1.1.370
+xref: RHEA:64448
+is_a: GO:0042800 ! histone H3K4 methyltransferase activity
+
+[Term]
+id: GO:0140947
+name: histone H3K9me2 methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: N6,N6-dimethyl-L-lysyl9-[histone H3] + S-adenosyl-L-methionine = H+ + N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + S-adenosyl-L-homocysteine. This reaction is the addition of a single methyl group to the dimethylated lysine residue at position 9 of histone H3, producing histone H3K9me3." [RHEA:60280]
+synonym: "histone dimethyl-lysine(H3K9) N-methyltransferase activity (H3-K9 specific)" EXACT []
+synonym: "histone H3-K9 trimethylation" BROAD []
+synonym: "histone H3K9 trimethylation" BROAD []
+synonym: "histone H3K9me2 methylase activity" EXACT []
+xref: EC:2.1.1.366
+xref: RHEA:60280
+is_a: GO:0046974 ! histone H3K9 methyltransferase activity
+
+[Term]
+id: GO:0140948
+name: histone H3K9 monomethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl9-[histone H3] + S-adenosyl-L-methionine = H+ + N6-methyl-L-lysyl9-[histone H3] + S-adenosyl-L-homocysteine. This reaction is the addition of a methyl group to the unmethylated lysine residue at position 9 of histone H3, producing histone H3K9me." [RHEA:60288]
+synonym: "histone H3-K9 methylation" BROAD []
+synonym: "histone H3K9 methylation" BROAD []
+synonym: "histone H3K9 monomethylase activity" EXACT []
+synonym: "histone lysine N-monomethyltransferase activity (H3-K9 specific)" EXACT []
+xref: EC:2.1.1.367
+xref: RHEA:60288
+is_a: GO:0046974 ! histone H3K9 methyltransferase activity
+
+[Term]
+id: GO:0140949
+name: histone H3K9 trimethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl9-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the unmethylated lysine residue at position 9 of histone H3, producing histone H3K9me3." [RHEA:60276]
+synonym: "histone H3-K9 trimethylation" BROAD []
+synonym: "histone H3K9 mono/di/trimethylase activity" EXACT []
+synonym: "histone H3K9 trimethylase activity" EXACT []
+synonym: "histone H3K9 trimethylation" BROAD []
+synonym: "histone lysine N-trimethyltransferase activity (H3-K9 specific)" EXACT []
+xref: EC:2.1.1.355
+xref: RHEA:60276
+is_a: GO:0046974 ! histone H3K9 methyltransferase activity
+
+[Term]
+id: GO:0140950
+name: histone H2A deubiquitinase activity
+namespace: molecular_function
+def: "A histone deubiquitinase that cleaves ubiquitin from a histone H2A protein to which it is conjugated." [PMID:18226187, PMID:20436459]
+synonym: "histone H2A deubiquitination" RELATED []
+is_a: GO:0140934 ! histone deubiquitinase activity
+
+[Term]
+id: GO:0140951
+name: histone H3K27 trimethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl27-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl27-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the unmethylated lysine residue at position 27 of histone H3, producing histone H3K27me3." [RHEA:60292]
+synonym: "histone H3-K27 trimethylase activity" EXACT []
+synonym: "histone H3-K27 trimethylation" BROAD []
+synonym: "histone H3K27 mono/di/trimethylase activity" EXACT []
+synonym: "histone H3K27 trimethylase activity" EXACT []
+synonym: "histone H3K27 trimethylation" BROAD []
+synonym: "histone lysine N-trimethyltransferase activity (H3-K27 specific)" EXACT []
+xref: EC:2.1.1.356
+xref: RHEA:60292
+is_a: GO:0046976 ! histone H3K27 methyltransferase activity
+
+[Term]
+id: GO:0140952
+name: histone H3K27 dimethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl27-[histone H3] + 2 S-adenosyl-L-methionine = 2 H+ + N6,N6-dimethyl-L-lysyl27-[histone H3] + 2 S-adenosyl-L-homocysteine. This reaction is the successive addition of two methyl groups to the unmethylated lysine residue at position 27 of histone H3, producing histone H3K27me2." [RHEA:64452]
+synonym: "histone H3-K27 dimethylase activity" EXACT []
+synonym: "histone H3-K27 dimethylation" BROAD []
+synonym: "histone H3K27 dimethylase activity" EXACT []
+synonym: "histone H3K27 dimethylation" BROAD []
+synonym: "histone H3K27 mono/dimethylase activity" EXACT []
+synonym: "histone lysine N-dimethyltransferase activity (H3-K27 specific)" EXACT []
+xref: EC:2.1.1.371
+xref: RHEA:64452
+is_a: GO:0046976 ! histone H3K27 methyltransferase activity
+
+[Term]
+id: GO:0140953
+name: histone H3K27 monomethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl27-[histone H3] + S-adenosyl-L-methionine = H+ + N6-methyl-L-lysyl27-[histone H3] + S-adenosyl-L-homocysteine. This reaction is the addition of a single methyl group to the unmethylated lysine residue at position 27 of histone H3, producing histone H3K27me." [RHEA:60296]
+synonym: "histone H3-K27 methylation" BROAD []
+synonym: "histone H3-K27 monomethylase activity" EXACT []
+synonym: "histone H3K27 methylation" BROAD []
+synonym: "histone H3K27 monomethylase activity" EXACT []
+synonym: "histone lysine N-monomethyltransferase activity (H3-K27 specific)" EXACT []
+xref: EC:2.1.1.369
+xref: RHEA:60296
+is_a: GO:0046976 ! histone H3K27 methyltransferase activity
+
+[Term]
+id: GO:0140954
+name: histone H3K36 dimethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl36-[histone H3] + 2 S-adenosyl-L-methionine = 2 H+ + N6,N6-dimethyl-L-lysyl36-[histone H3] + 2 S-adenosyl-L-homocysteine. This reaction is the successive addition of two methyl groups to the lysine residue at position 36 of histone H3, producing histone H3K36me2." [RHEA:60308]
+synonym: "histone H3-K36 dimethylation" BROAD []
+synonym: "histone H3K36 dimethylase activity" EXACT []
+synonym: "histone H3K36 dimethylation" BROAD []
+synonym: "histone H3K36 mono/dimethylase activity" EXACT []
+synonym: "histone lysine N-dimethyltransferase activity (H3-K36 specific)" EXACT []
+xref: EC:2.1.1.357
+xref: RHEA:60308
+is_a: GO:0046975 ! histone H3K36 methyltransferase activity
+
+[Term]
+id: GO:0140955
+name: histone H3K36 trimethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl36-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl36-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the lysine residue at position 36 of histone H3, producing histone H3K36me3." [RHEA:60324]
+synonym: "histone H3-K36 trimethylation" BROAD []
+synonym: "histone H3K36 mono/di/trimethylase activity" EXACT []
+synonym: "histone H3K36 trimethylase activity" EXACT []
+synonym: "histone H3K36 trimethylation" BROAD []
+synonym: "histone lysine N-trimethyltransferase activity (H3-K36 specific)" EXACT []
+xref: EC:2.1.1.359
+xref: RHEA:60324
+is_a: GO:0046975 ! histone H3K36 methyltransferase activity
+
+[Term]
+id: GO:0140956
+name: histone H3K79 trimethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl79-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl79-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of up to three methyl group to the lysine residue at position 79 of the histone H3 protein, producing H3K79me3." [PMID:15371351, RHEA:60328]
+synonym: "histone H3-K79 trimethylation" BROAD []
+synonym: "histone H3K79 trimethylase activity" EXACT []
+synonym: "histone H3K79 trimethylation" BROAD []
+synonym: "histone lysine N-trimethyltransferase activity (H3-K79 specific)" EXACT []
+synonym: "histone trimethylase activity (H3-K79 specific)" EXACT [GOC:mah]
+synonym: "histone trimethyltransferase activity (H3-K79 specific)" EXACT []
+synonym: "histone-H3K79 trimethyltransferase activity" EXACT []
+xref: EC:2.1.1.360
+xref: RHEA:60328
+is_a: GO:0031151 ! histone H3K79 methyltransferase activity
+
+[Term]
+id: GO:0140958
+name: target-directed miRNA degradation
+namespace: biological_process
+def: "The process in which a miRNA is targeted for degradation by a non-coding RNA or mRNA. The binding of an RNA to a target miRNA within a RISC complex results in either ubiquitin-mediated degradation of AGO protein or the displacement of the 3' end of the miRNA, exposing it to nucleases." [PMID:33184237, PMID:36150386]
+synonym: "target-directed microRNA degradation" EXACT []
+synonym: "TDMD" EXACT []
+is_a: GO:0010587 ! miRNA catabolic process
+is_a: GO:0060965 ! negative regulation of miRNA-mediated gene silencing
+
+[Term]
+id: GO:0140959
+name: obsolete base-pairing target-directed miRNA suppressor activity
+namespace: molecular_function
+def: "OBSOLETE. An inhibitor activity that acts by base-pairing with a miRNA, exposing it to nuclease-mediated degradation." [PMID:33184237, PMID:36150386]
+comment: This term was obsoleted because it represents the same function as miRNA inhibitor activity, GO:0140869.
+synonym: "base-pairing target-directed microRNA suppressor activity" EXACT []
+is_obsolete: true
+replaced_by: GO:0140869
+
+[Term]
+id: GO:0140961
+name: cellular detoxification of metal ion
+namespace: biological_process
+def: "Any process carried out at the cellular level that reduces or removes the toxicity of a metal ion." [PMID:26729300, PMID:33046888, PMID:34442707]
+synonym: "cellular detoxification of metal cation" EXACT []
+is_a: GO:0061687 ! detoxification of inorganic compound
+is_a: GO:1990748 ! cellular detoxification
+
+[Term]
+id: GO:0140962
+name: multicellular organismal-level chemical homeostasis
+namespace: biological_process
+def: "A homeostatic process involved in the maintenance of a steady state level of a chemical within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell." [GOC:curators]
+synonym: "multicellular organism level chemical homeostasis" EXACT []
+synonym: "organismal level chemical homeostasis" EXACT []
+is_a: GO:0048871 ! multicellular organismal-level homeostasis
+is_a: GO:0048878 ! chemical homeostasis
+
+[Term]
+id: GO:0140963
+name: multicellular organismal-level auxin homeostasis
+namespace: biological_process
+def: "A chemical homeostatic process involved in the maintenance of a steady state level of auxin within extracellular body fluids, such as the xylem or phloem of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell." [GOC:curators]
+synonym: "auxin homeostasis" BROAD []
+synonym: "multicellular organismal auxin homeostasis" EXACT []
+is_a: GO:0140962 ! multicellular organismal-level chemical homeostasis
+
+[Term]
+id: GO:0140964
+name: intracellular auxin homeostasis
+namespace: biological_process
+def: "A homeostatic process involved in the maintenance of a steady state level of auxin within a cell." [PMID:19506555, PMID:22314799]
+synonym: "auxin homeostasis" BROAD []
+synonym: "cellular auxin homeostasis" EXACT []
+is_a: GO:0055082 ! intracellular chemical homeostasis
+
+[Term]
+id: GO:0140965
+name: secondary piRNA processing
+namespace: biological_process
+def: "A process leading to the generation of a functional secondary piRNA, involving a self-perpetuating piRNA loop, often called the ping-pong cycle, in which piRNAs are amplified by pairing with complementary transcripts (for example the transposable element mRNA target). In Drosophila, the processing involves the piwi proteins aubergine and Argonaute 3 and in mice, the piwi proteins Piwil2 and Piwil4." [PMID:29281264, PMID:32895365]
+synonym: "ping-pong amplification" RELATED []
+synonym: "ping-pong derived piRNA" EXACT []
+synonym: "secondary piRNA biogenesis" EXACT []
+synonym: "secondary PIWI-associated RNA processing" EXACT []
+is_a: GO:0034587 ! piRNA processing
+
+[Term]
+id: GO:0140966
+name: piRNA-directed heterochromatin formation
+namespace: biological_process
+def: "The formation of heterochromatin into a heterochromatin domain, enriched in histone H3 methylated on lysine 9 (H3K9me), by a process mediated by a small interfering piRNA." [PMID:23329111]
+synonym: "piwiRNA-directed heterochromatin formation" EXACT []
+is_a: GO:0031048 ! small ncRNA-mediated heterochromatin formation
+
+[Term]
+id: GO:0140967
+name: manganese import into cell
+namespace: biological_process
+def: "The directed movement of mangnanese ions from outside of a cell into a cell." [PMID:22773749]
+synonym: "manganese influx" BROAD []
+is_a: GO:0071421 ! manganese ion transmembrane transport
+is_a: GO:0098659 ! inorganic cation import across plasma membrane
+
+[Term]
+id: GO:0140968
+name: polyspecific organic cation:proton antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of various organic cations in exchange for a proton, according to the reaction: H+(out) + organic cation(in) = H+(in) + organic cation(out). The transported substrates are usually toxic molecules, drugs and xenobiotics." [PMID:17047166, PMID:17509534]
+synonym: "proton:polyspecific organic cation antiporter activity" RELATED []
+xref: TC:2.A.66.1.20
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
+
+[Term]
+id: GO:0140969
+name: determination of lung left/right asymmetry
+namespace: biological_process
+def: "Determination of the asymmetric location of the lungs with respect to the left and right halves of the organism." [GOC:BHFL, GOC:rl, PMID:19944405, PMID:20007846, PMID:21131974]
+is_a: GO:0007368 ! determination of left/right symmetry
+relationship: part_of GO:0007507 ! heart development
+
+[Term]
+id: GO:0140970
+name: AIM2 inflammasome complex assembly
+namespace: biological_process
+def: "The aggregation, arrangement and bonding together of a set of components to form the AIM2 inflammasome complex." [PMID:33467177]
+is_a: GO:0065003 ! protein-containing complex assembly
+
+[Term]
+id: GO:0140971
+name: regulation of AIM2 inflammasome complex assembly
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of AIM2 inflammasome complex assembly." [PMID:33467177]
+is_a: GO:0043254 ! regulation of protein-containing complex assembly
+relationship: regulates GO:0140970 ! AIM2 inflammasome complex assembly
+
+[Term]
+id: GO:0140972
+name: negative regulation of AIM2 inflammasome complex assembly
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of AIM2 inflammasome complex assembly." [PMID:33467177]
+is_a: GO:0031333 ! negative regulation of protein-containing complex assembly
+is_a: GO:0140971 ! regulation of AIM2 inflammasome complex assembly
+relationship: negatively_regulates GO:0140970 ! AIM2 inflammasome complex assembly
+
+[Term]
+id: GO:0140973
+name: positive regulation of AIM2 inflammasome complex assembly
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of AIM2 inflammasome complex assembly." [PMID:33467177]
+is_a: GO:0031334 ! positive regulation of protein-containing complex assembly
+is_a: GO:0140971 ! regulation of AIM2 inflammasome complex assembly
+relationship: positively_regulates GO:0140970 ! AIM2 inflammasome complex assembly
+
+[Term]
+id: GO:0140974
+name: cellular detoxification of sulfide
+namespace: biological_process
+def: "Any process carried out at the cellular level that reduces or removes the toxicity of a sulfide. These may include chemical modification or transport of sulfide away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." [PMID:20077566, PMID:25747485]
+is_a: GO:1990748 ! cellular detoxification
+
+[Term]
+id: GO:0140975
+name: disruption of cellular component of another organism
+namespace: biological_process
+def: "The disruption of a cellular component of another organism, leading to damage or temporary subversion of that structure. In some cases this can cause malfunctioning of the cells and death of the target organism." [GOC:pg]
+is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms
+
+[Term]
+id: GO:0140976
+name: defense response against disruption of plasma membrane integrity
+namespace: biological_process
+def: "The cellular processes and signaling pathways by which a cell responds to disruption of the integrity of its plasma membrane by another organism. Some toxins produced by other organisms can form pores in membranes, or affect the membrane permeability." [PMID:17234446, PMID:21518219]
+is_a: GO:0098542 ! defense response to other organism
+
+[Term]
+id: GO:0140977
+name: cellular detoxification of acetone
+namespace: biological_process
+def: "Any process carried out at the cellular level that reduces or removes the toxicity of acetone. These may include chemical modification, for example to methylglyoxal." [PMID:22314896, PMID:26958851]
+is_a: GO:1990748 ! cellular detoxification
+
+[Term]
+id: GO:0140978
+name: mitochondrial large ribosomal subunit binding
+namespace: molecular_function
+def: "Binding to a mitochondrial large ribosomal subunit." [PMID:28892042]
+synonym: "mitochondrial ribosomal large subunit binding" EXACT []
+is_a: GO:0043023 ! ribosomal large subunit binding
+is_a: GO:0097177 ! mitochondrial ribosome binding
+
+[Term]
+id: GO:0140979
+name: intracellular nucleotide homeostasis
+namespace: biological_process
+def: "A homeostatic process involved in the maintenance of a steady state level of nucleotides within a cell." [PMID:23416111, PMID:34880500]
+is_a: GO:0055082 ! intracellular chemical homeostasis
+
+[Term]
+id: GO:0140980
+name: intracellular nucleoside homeostasis
+namespace: biological_process
+def: "A homeostatic process involved in the maintenance of a steady state level of nucleosides within a cell." [PMID:23416111, PMID:34880500]
+is_a: GO:0055082 ! intracellular chemical homeostasis
+
+[Term]
+id: GO:0140981
+name: medium-chain fatty acid omega-hydroxylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: an omega-methyl-medium-chain fatty acid + O2 + reduced [NADPH--hemoprotein reductase] = an omega-hydroxy-medium-chain fatty acid + H+ + H2O + oxidized [NADPH--hemoprotein reductase]. A medium-chain fatty acid is a fatty acid with an aliphatic tail of 6 to 12 carbons." [PMID:35934685]
+xref: MetaCyc:RXN-19719
+is_a: GO:0120250 ! fatty acid omega-hydroxylase activity
+
+[Term]
+id: GO:0140982
+name: detoxification of aluminum ion
+namespace: biological_process
+def: "Any process that reduce or remove the toxicity of aluminum ions. These can include transport of the aluminum away from sensitive areas, sequesteration, or chemical modification to an inert form." [PMID:10845450, PMID:23888867, PMID:9576769]
+synonym: "aluminum ion homeostasis" RELATED []
+is_a: GO:0061687 ! detoxification of inorganic compound
+
+[Term]
+id: GO:0140983
+name: calcium:manganese antiporter activity
+namespace: molecular_function
+def: "Catalysis of the reaction: Ca2+(in) + Mn2+(out) = Ca2+(out) + Mn2+(in)." [PMID:30755481]
+synonym: "manganese:calcium antiporter activity" EXACT []
+xref: RHEA:73059
+is_a: GO:0005384 ! manganese ion transmembrane transporter activity
+is_a: GO:0015368 ! calcium:monoatomic cation antiporter activity
+
+[Term]
+id: GO:0140984
+name: histone H4K12 methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H4 L-lysine (position 12) = S-adenosyl-L-homocysteine + histone H4 N6-methyl-L-lysine (position 12). This reaction is the addition of a methyl group to the lysine residue at position 12 of the histone H4 protein." [PMID:12086618]
+comment: Note that in some species, the methyl group may be added to a lysine in a slightly different position of the histone H4 protein, but that this term still applies.
+synonym: "histone H4 lysine 12-specific methyltransferase activity" EXACT []
+synonym: "histone H4K12 methylase activity" BROAD []
+synonym: "histone H4K12 methylation" EXACT []
+synonym: "histone lysine N-methyltransferase activity (H4-K12 specific)" EXACT []
+synonym: "histone methylase activity (H4-K12 specific)" EXACT []
+synonym: "histone methyltransferase activity (H4-K12 specific)" EXACT []
+synonym: "histone-H4K12 methyltransferase activity" EXACT []
+is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
+is_a: GO:0140939 ! histone H4 methyltransferase activity
+
+[Term]
+id: GO:0140985
+name: G protein-coupled chemorepellent receptor activity
+namespace: molecular_function
+def: "Combining with a chemorepellent and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [PMID:30462573]
+synonym: "G protein chemorepellent receptor activity" EXACT []
+synonym: "G-protein chemorepellent receptor activity" EXACT []
+synonym: "G-protein coupled chemorepellent receptor activity" EXACT []
+is_a: GO:0004930 ! G protein-coupled receptor activity
+
+[Term]
+id: GO:0140986
+name: G protein-coupled chemorepellent receptor signaling pathway
+namespace: biological_process
+def: "A G protein-coupled receptor signaling pathway initiated by an opioid binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. cytoskeleton reorganization." [PMID:30462573]
+is_a: GO:0007186 ! G protein-coupled receptor signaling pathway
+
+[Term]
+id: GO:0140987
+name: ATP:inorganic phosphate antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of ATP from one side of a membrane to the other according to the reaction: ATP(out) + inorganic phosphate(in) = ATP(in) + inorganic phosphate(out)." [PMID:15123600]
+synonym: "inorganic phosphate:ATP antiporter activity" EXACT []
+xref: RHEA:65840
+is_a: GO:0005315 ! inorganic phosphate transmembrane transporter activity
+is_a: GO:0005347 ! ATP transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+
+[Term]
+id: GO:0140988
+name: ADP:inorganic phosphate antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of ADP from one side of a membrane to the other according to the reaction: ADP(out) + inorganic phosphate(in) = ADP(in) + inorganic phosphate(out)." [PMID:15123600]
+synonym: "inorganic phosphate:ADP antiporter activity" EXACT []
+xref: RHEA:65844
+is_a: GO:0005315 ! inorganic phosphate transmembrane transporter activity
+is_a: GO:0015217 ! ADP transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+
+[Term]
+id: GO:0140989
+name: 7-deoxyloganate 7-hydroxylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: 7-deoxyloganate + O2 + reduced [NADPH-hemoprotein reductase] = H+ + H2O + loganate + oxidized [NADPH-hemoprotein reductase]." [PMID:24710322, RHEA:57576]
+xref: EC:1.14.14.85
+xref: RHEA:57576
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
+
+[Term]
+id: GO:0140990
+name: primary piRNA processing
+namespace: biological_process
+def: "The process involved in converting precursor piRNAs into non-overlapping, contiguous primary piRNAs (approximately 24-30-nt piRNAs with a preference for a 5' uridine (U) via the endonucleolytic activity of cytosolic PIWI. This may include pre-piRNA maturation of 3' ends by trimming and 2'-O-methylation." [PMID:22907665, PMID:26166577, PMID:34469728]
+is_a: GO:0034587 ! piRNA processing
+
+[Term]
+id: GO:0140991
+name: piRNA-mediated gene silencing by mRNA destabilization
+namespace: biological_process
+def: "A cytoplasmic post-transcriptional gene silencing pathway in which piRNAs direct the cleavage of target mRNAs. The target mRNA, often transcribed from a transposable element, is destabilized by the activity of a PIWI class endonuclease within the piRNA-induced silencing complex. This may also be accompanied by mRNA deadenylation and decapping." [PMID:29281264, PMID:33419460]
+is_a: GO:0035194 ! ncRNA-mediated post-transcriptional gene silencing
+is_a: GO:0061157 ! mRNA destabilization
+
+[Term]
+id: GO:0140993
+name: histone modifying activity
+namespace: molecular_function
+def: "A catalytic activity that acts on a histone protein. Reversible histone modifications contribute to regulation of gene expression." [GOC:pg]
+is_a: GO:0140096 ! catalytic activity, acting on a protein
+
+[Term]
+id: GO:0140994
+name: RNA polymerase II CTD heptapeptide repeat modifying activity
+namespace: molecular_function
+def: "A catalytic activity that acts on the RNA polymerase II large subunit CTD heptapeptide repeat (consensus YSPTSPS). Reversible modifications cof the RNA polymerase II CTD repeats contribute to regulation of RNA polymerase activity." [GOC:pg]
+synonym: "RNA polymerase II CTD repeat modifying activity" EXACT []
+synonym: "RNA polymerase II large subunit CTD heptapeptide repeat modifying activity" EXACT []
+is_a: GO:0140096 ! catalytic activity, acting on a protein
+
+[Term]
+id: GO:0140995
+name: histone H2A kinase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a phosphate group to a histone H2A." [PMID:25303536]
+is_a: GO:0035173 ! histone kinase activity
+
+[Term]
+id: GO:0140996
+name: histone H3 kinase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a phosphate group to a histone H3." [PMID:25303536]
+is_a: GO:0035173 ! histone kinase activity
+
+[Term]
+id: GO:0140997
+name: histone H4 kinase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a phosphate group to a histone H4." [PMID:25303536]
+is_a: GO:0035173 ! histone kinase activity
+
+[Term]
+id: GO:0140998
+name: histone H2B kinase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a phosphate group to a histone H2B." [PMID:25303536]
+is_a: GO:0035173 ! histone kinase activity
+
+[Term]
+id: GO:0140999
+name: histone H3K4 trimethyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-lysyl4-[histone H3] + 3 S-adenosyl-L-methionine = 2 H+ + N6,N6-trimethyl-L-lysyl4-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the unmethylated lysine residue at position 4 of histone H3, producing histone H3K4me3." [PMID:18375658, RHEA:60260]
+synonym: "histone H3-K4 trimethylation" BROAD []
+synonym: "histone H3K4 trimethylase activity" EXACT []
+synonym: "histone H3K4 trimethylation" BROAD []
+synonym: "histone lysine N-trimethyltransferase activity (H3-K4 specific)" EXACT []
+xref: EC:2.1.1.354
+xref: RHEA:60260
+is_a: GO:0042800 ! histone H3K4 methyltransferase activity
+
+[Term]
+id: GO:0141000
+name: histone H4K91 ubiquitin ligase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a ubiquitin molecule to histone 4 at the lysine-91 residue." [PMID:19818714]
+synonym: "histone H4-K91 ubiquitin ligase activity" EXACT []
+synonym: "histone ubiquitin ligase activity (H4-K91 specific)" EXACT []
+is_a: GO:0140852 ! histone ubiquitin ligase activity
+
+[Term]
+id: GO:0141002
+name: histone H4K16 propionyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: histone H4 L-lysine (position 16) + propionyl-CoA = CoA + H+ + histone H3 N6-propionyl-L-lysyl (position 16)." [PMID:17267393, PMID:29321206, PMID:31794431]
+is_a: GO:0061922 ! histone propionyltransferase activity
+
+[Term]
+id: GO:0141003
+name: histone H2AX kinase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of a phosphate group to a histone variant H2AX." [GOC:bf]
+is_a: GO:0035173 ! histone kinase activity
+
+[Term]
+id: GO:0141005
+name: retrotransposon silencing by heterochromatin formation
+namespace: biological_process
+def: "A retrotransposon silencing mechanism involving heterochromatin assembly. Heterochromatin is a chromatin conformation that is refractory to transcription." [PMID:25247314, PMID:28951459, PMID:32823517]
+is_a: GO:0010526 ! retrotransposon silencing
+
+[Term]
+id: GO:0141006
+name: piRNA-mediated retrotransposon silencing by heterochromatin formation
+namespace: biological_process
+def: "A retrotransposon silencing mechanism in which a piRNA triggers heterochromatin assembly. Heterochromatin is a chromatin conformation that is refractory to transcription." [PMID:32381626, PMID:32674113]
+is_a: GO:0141005 ! retrotransposon silencing by heterochromatin formation
+
+[Term]
+id: GO:0141007
+name: siRNA-mediated retrotransposon silencing by heterochromatin formation
+namespace: biological_process
+def: "A retrotransposon silencing mechanism in which a siRNA triggers heterochromatin assembly. Heterochromatin is a chromatin conformation that is refractory to transcription." [PMID:36570931]
+is_a: GO:0141005 ! retrotransposon silencing by heterochromatin formation
+
+[Term]
+id: GO:0141008
+name: retrotransposon silencing by mRNA destabilization
+namespace: biological_process
+def: "A retrotransposon silencing mechanism in which mRNAs transcribed from transposons are targeted for degradation." [GOC:curators]
+is_a: GO:0010526 ! retrotransposon silencing
+
+[Term]
+id: GO:0141009
+name: piRNA-mediated retrotransposon silencing by mRNA destabilization
+namespace: biological_process
+def: "A retrotransposon silencing mechanism in which mRNAs transcribed from transposons are targeted for degradation by a piRNA." [PMID:22121019]
+is_a: GO:0141008 ! retrotransposon silencing by mRNA destabilization
+
+[Term]
+id: GO:0141010
+name: retrotransposon silencing by RNA-directed DNA methylation
+namespace: biological_process
+def: "A retrotransposon silencing mechanism mediated by RNA-directed DNA methylation. RNA-directed DNA methylation is a gene silencing process in which small interfering RNAs (siRNAs) guide DNA methylation to the siRNA-generating genomic loci and other loci that are homologous to the siRNAs for de novo DNA methylation. This results in a heterochromatin assembly, a chromatin conformation that is refractory to transcription." [PMID:28633017, PMID:32381626, PMID:32719317, PMID:36570931]
+synonym: "retrostransposon silencing by RdDM" EXACT []
+is_a: GO:0080188 ! gene silencing by RNA-directed DNA methylation
+is_a: GO:0141005 ! retrotransposon silencing by heterochromatin formation
+
+[Term]
+id: GO:0141011
+name: siRNA-mediated retrotransposon silencing by mRNA destabilization
+namespace: biological_process
+def: "A retrotransposon silencing mechanism in which mRNAs transcribed from transposons are targeted for degradation by a siRNA." [PMID:36570931]
+is_a: GO:0141008 ! retrotransposon silencing by mRNA destabilization
+
+[Term]
+id: GO:0141013
+name: purine nucleotide import into lysosome
+namespace: biological_process
+def: "The directed import of purine nucleotide from the cytosol, across the lysosomal membrane, into the lysosome." [PMID:18375752, PMID:23876310]
+is_a: GO:0007041 ! lysosomal transport
+is_a: GO:0034486 ! vacuolar transmembrane transport
+is_a: GO:0072530 ! purine-containing compound transmembrane transport
+
+[Term]
+id: GO:0141014
+name: ribosome hibernation
+namespace: biological_process
+def: "A cellular process that results in the silencing of ribosomes in quiescent cells. Quiescence takes place when cells encounter unfavorable conditions and cease to grow in bacteria and yeast. It also takes place in some specialized cells in higher eukaryotes, such as eggs. Ribosomes in a hibernation state are kept silent via association with proteins with inhibitory and protective functions." [PMID:28468753, PMID:30177741, PMID:36653451]
+is_a: GO:0090071 ! negative regulation of ribosome biogenesis
+
+[Term]
+id: GO:0141016
+name: G/T mismatch-specific thymine-DNA glycosylase activity
+namespace: molecular_function
+def: "Hydrolyzes mismatched double-stranded DNA and polynucleotides, releasing free thymine and leaving an apyrimidinic (AP) site." [EC:3.2.2.29, PMID:12711670]
+xref: EC:3.2.2.29
+is_a: GO:0008263 ! pyrimidine-specific mismatch base pair DNA N-glycosylase activity
+
[Term]
id: GO:0150001
name: primary dendrite
@@ -420925,7 +423622,6 @@ name: regulation of protein localization to lysosome
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to lysosome." [GOC:aruk, GOC:bc, PMID:24305806]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0061462 ! protein localization to lysosome
[Term]
@@ -420933,7 +423629,6 @@ id: GO:0150032
name: positive regulation of protein localization to lysosome
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of protein localization to lysosome." [GOC:aruk, GOC:bc]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:0150031 ! regulation of protein localization to lysosome
is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:0061462 ! protein localization to lysosome
@@ -420943,7 +423638,6 @@ id: GO:0150033
name: negative regulation of protein localization to lysosome
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to lysosome." [GOC:aruk, GOC:bc, PMID:24305806]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0150031 ! regulation of protein localization to lysosome
is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:0061462 ! protein localization to lysosome
@@ -421122,7 +423816,7 @@ is_a: GO:1903440 ! amylin receptor complex
id: GO:0150059
name: amylin receptor 1 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by an extracellular amylin, or another ligand, combining with an amylin receptor 1 (AMY1), a G protein-coupled receptor complex, on the surface of the target cell. Other ligands that have been shown to initiate the AMY1 signaling pathway include the calcitonin related peptide (CGRP) and adrenomedullin (AM/ADM)." [GOC:aruk, GOC:bc, PMID:22500019]
+def: "The series of molecular signals initiated by an extracellular amylin, or another ligand, combining with an amylin receptor 1 (AMY1), a G protein-coupled receptor complex, on the surface of the target cell. Other ligands that have been shown to initiate the AMY1 signaling pathway include the calcitonin related peptide (CGRP) and adrenomedullin (AM/ADM)." [GOC:aruk, GOC:bc, PMID:22500019]
synonym: "AMY1 signaling pathway" EXACT []
is_a: GO:0097647 ! amylin receptor signaling pathway
@@ -421130,7 +423824,7 @@ is_a: GO:0097647 ! amylin receptor signaling pathway
id: GO:0150060
name: amylin receptor 2 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by an extracellular amylin, or another ligand, combining with an amylin receptor 2 (AMY2), a G protein-coupled receptor complex, on the surface of the target cell. The AMY2 signaling pathway can also be initiated by adrenomedullin (AM/ADM)." [GOC:aruk, GOC:bc, PMID:22500019]
+def: "The series of molecular signals initiated by an extracellular amylin, or another ligand, combining with an amylin receptor 2 (AMY2), a G protein-coupled receptor complex, on the surface of the target cell. The AMY2 signaling pathway can also be initiated by adrenomedullin (AM/ADM)." [GOC:aruk, GOC:bc, PMID:22500019]
synonym: "AMY2 signaling pathway" EXACT []
is_a: GO:0097647 ! amylin receptor signaling pathway
@@ -421138,7 +423832,7 @@ is_a: GO:0097647 ! amylin receptor signaling pathway
id: GO:0150061
name: amylin receptor 3 signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by an extracellular amylin, or another ligand, combining with an amylin receptor 3 (AMY3), a G protein-coupled receptor complex, on the surface of the target cell. The AMY3 signaling pathway can also be initiated by the amyloid-beta complex. AMY3 signaling results in increased import of calcium ions into the cytosol across plasma membrane, increased phosphorylation of ERK1/2, Act, and a PKA regulatory subunit II, as well as increased expression of cFos." [GOC:aruk, GOC:bc, PMID:22500019]
+def: "The series of molecular signals initiated by an extracellular amylin, or another ligand, combining with an amylin receptor 3 (AMY3), a G protein-coupled receptor complex, on the surface of the target cell. The AMY3 signaling pathway can also be initiated by the amyloid-beta complex. AMY3 signaling results in increased import of calcium ions into the cytosol across plasma membrane, increased phosphorylation of ERK1/2, Act, and a PKA regulatory subunit II, as well as increased expression of cFos." [GOC:aruk, GOC:bc, PMID:22500019]
synonym: "AMY3 signaling pathway" EXACT []
is_a: GO:0097647 ! amylin receptor signaling pathway
@@ -421428,17 +424122,6 @@ synonym: "neurone-glial cell signaling" EXACT []
synonym: "neurone-glial cell signalling" EXACT []
is_a: GO:0007267 ! cell-cell signaling
-[Term]
-id: GO:0150100
-name: RNA binding involved in posttranscriptional gene silencing
-namespace: molecular_function
-def: "Any RNA binding that is involved in posttranscriptional gene silencing." [GOC:aruk, GOC:bc, GOC:rl, PMID:23985560, PMID:28379604]
-synonym: "RNA binding involved in cosuppression" RELATED []
-synonym: "RNA binding involved in post-transcriptional gene silencing" EXACT []
-synonym: "RNA binding involved in PTGS" EXACT []
-synonym: "RNA binding involved in quelling" EXACT []
-is_a: GO:0003723 ! RNA binding
-
[Term]
id: GO:0150101
name: regulation of microtubule anchoring at centrosome
@@ -421453,8 +424136,8 @@ name: negative regulation of monocyte activation
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of monocyte activation." [GOC:aruk, PMID:15597323]
synonym: "repression of monocyte activation" EXACT []
-is_a: GO:0002694 ! regulation of leukocyte activation
-relationship: regulates GO:0042117 ! monocyte activation
+is_a: GO:0002695 ! negative regulation of leukocyte activation
+relationship: negatively_regulates GO:0042117 ! monocyte activation
[Term]
id: GO:0150103
@@ -421499,13 +424182,12 @@ relationship: positively_regulates GO:0150105 ! protein localization to cell-cel
[Term]
id: GO:0150110
-name: negative regulation of cholesterol esterification
+name: obsolete negative regulation of cholesterol esterification
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of cholesterol esterification." [GOC:aruk, GOC:bc, PMID:21810484, PMID:24201375]
-is_a: GO:0010872 ! regulation of cholesterol esterification
-is_a: GO:0031324 ! negative regulation of cellular metabolic process
-is_a: GO:0045939 ! negative regulation of steroid metabolic process
-relationship: negatively_regulates GO:0034435 ! cholesterol esterification
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of cholesterol esterification." [GOC:aruk, GOC:bc, PMID:21810484, PMID:24201375]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0008203
[Term]
id: GO:0150111
@@ -421781,58 +424463,53 @@ relationship: negatively_regulates GO:0150155 ! interleukin-34 production
[Term]
id: GO:0150163
-name: miRNA-mediated activation of transcription by RNA polymerase II
+name: obsolete miRNA-mediated activation of transcription by RNA polymerase II
namespace: biological_process
-def: "Any process mediated by a microRNA (miRNA) that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:aruk, PMID:20737563, PMID:27145859]
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
-is_a: GO:0150164 ! miRNA-mediated regulation of transcription by RNA polymerase II
-is_a: GO:1903313 ! positive regulation of mRNA metabolic process
-relationship: positively_regulates GO:0042789 ! mRNA transcription by RNA polymerase II
+def: "OBSOLETE. Any process mediated by a microRNA (miRNA) that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:aruk, PMID:20737563, PMID:27145859]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0150164
-name: miRNA-mediated regulation of transcription by RNA polymerase II
+name: obsolete miRNA-mediated regulation of transcription by RNA polymerase II
namespace: biological_process
-def: "Any process mediated by a microRNA (miRNA) that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:aruk, PMID:20737563, PMID:27145859]
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-is_a: GO:1903311 ! regulation of mRNA metabolic process
-relationship: regulates GO:0042789 ! mRNA transcription by RNA polymerase II
+def: "OBSOLETE. Any process mediated by a microRNA (miRNA) that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:aruk, PMID:20737563, PMID:27145859]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0150165
-name: miRNA-mediated inhibition of transcription by RNA polymerase II
+name: obsolete miRNA-mediated inhibition of transcription by RNA polymerase II
namespace: biological_process
-def: "Any process mediated by a microRNA (miRNA) that stops, prevents or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:aruk]
-is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:0150164 ! miRNA-mediated regulation of transcription by RNA polymerase II
-is_a: GO:1903312 ! negative regulation of mRNA metabolic process
-relationship: negatively_regulates GO:0042789 ! mRNA transcription by RNA polymerase II
+def: "OBSOLETE. Any process mediated by a microRNA (miRNA) that stops, prevents or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:aruk]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0150166
-name: regulation of histone H3-K4 acetylation
+name: obsolete regulation of histone H3-K4 acetylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone H3-K4 acetylation." [GOC:aruk]
-is_a: GO:0035065 ! regulation of histone acetylation
-relationship: regulates GO:0043973 ! histone H3-K4 acetylation
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone H3-K4 acetylation." [GOC:aruk]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0044016
[Term]
id: GO:0150167
-name: positive regulation of histone H3-K4 acetylation
+name: obsolete positive regulation of histone H3-K4 acetylation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of histone H3-K4 acetylation." [GOC:aruk, PMID:20737563]
-is_a: GO:0035066 ! positive regulation of histone acetylation
-is_a: GO:0150166 ! regulation of histone H3-K4 acetylation
-relationship: positively_regulates GO:0043973 ! histone H3-K4 acetylation
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of histone H3-K4 acetylation." [GOC:aruk, PMID:20737563]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0044016
[Term]
id: GO:0150168
-name: negative regulation of histone H3-K4 acetylation
+name: obsolete negative regulation of histone H3-K4 acetylation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K4 acetylation." [GOC:aruk]
-is_a: GO:0035067 ! negative regulation of histone acetylation
-is_a: GO:0150166 ! regulation of histone H3-K4 acetylation
-relationship: negatively_regulates GO:0043973 ! histone H3-K4 acetylation
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K4 acetylation." [GOC:aruk]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0150172
@@ -422031,11 +424708,11 @@ is_a: GO:0160002 ! ADP-D-ribose modification-dependent protein binding
id: GO:0160005
name: PAT complex
namespace: cellular_component
-def: "A transmembrane protein complex located in the endoplasmic reticulum (ER) involved in the correct folding of multipass membrane proteins in the ER membrane after their release from the Sec61 translocon. In human, the substrate-binding Asterix (PAT10, WDR83OS) forms an obligate heterodimer with CCDC47." [PMID:32814900, PMID:33082068, PMID:33960686]
+def: "A transmembrane protein complex located in the endoplasmic reticulum (ER) involved in the correct folding of multipass membrane proteins in the ER membrane. In human, the substrate-binding Asterix (PAT10, WDR83OS) forms an obligate heterodimer with CCDC47." [PMID:32814900, PMID:33082068, PMID:33960686]
comment: PAT complex functions by shielding exposed hydrophilicity of transmembrane domains (TMDs) to prevent premature degradation and promote proper folding and bundling of TMDs.
is_a: GO:0098796 ! membrane protein complex
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
-relationship: part_of GO:0030176 ! integral component of endoplasmic reticulum membrane
+relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
[Term]
id: GO:0160006
@@ -422054,13 +424731,13 @@ name: glutathione import into mitochondrion
namespace: biological_process
def: "The process in which glutathione is transported from the cytosol into the mitochondrial matrix." [PMID:34707288]
is_a: GO:0034775 ! glutathione transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0160008
name: protein decrotonylase activity
namespace: molecular_function
def: "Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[protein] = (2E)-2-butenoate + L-lysyl-[protein]." [PMID:28497810, PMID:30279482, PMID:34608293]
+xref: RHEA:69172
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
[Term]
@@ -422068,6 +424745,7 @@ id: GO:0160009
name: histone decrotonylase activity
namespace: molecular_function
def: "Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[histone] = (2E)-2-butenoate + L-lysyl-[histone]." [PMID:28497810]
+is_a: GO:0140993 ! histone modifying activity
is_a: GO:0160008 ! protein decrotonylase activity
[Term]
@@ -422075,6 +424753,7 @@ id: GO:0160010
name: protein de-2-hydroxyisobutyrylase activity
namespace: molecular_function
def: "Catalysis of the reaction: H2O + N6-(2-hydroxyisobutanoyl)-L-lysyl-[protein] = 2-hydroxy-2-methylpropanoate + L-lysyl-[protein]." [PMID:29192674]
+xref: RHEA:69176
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
[Term]
@@ -422082,6 +424761,7 @@ id: GO:0160011
name: NAD-dependent protein decrotonylase activity
namespace: molecular_function
def: "Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[protein] + NAD+ = 2''-O-(2E)-but-2-enoyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide." [PMID:28497810]
+xref: RHEA:69332
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
@@ -422089,6 +424769,7 @@ id: GO:0160012
name: NAD-dependent histone decrotonylase activity
namespace: molecular_function
def: "Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[histone] + NAD+ = 2''-O-(2E)-but-2-enoyl-ADP-D-ribose + L-lysyl-[histone] + nicotinamide." [PMID:28497810]
+is_a: GO:0160009 ! histone decrotonylase activity
is_a: GO:0160011 ! NAD-dependent protein decrotonylase activity
[Term]
@@ -422106,6 +424787,718 @@ namespace: cellular_component
def: "An extracellular vesicle that is approximately four microns in diameter, released by budding out of cells into the extracellular space, and hypothesized to be a mechanism for disposal of unwanted cellular material including protein aggregates and damaged organelles." [PMID:28178240, PMID:33016946, PMID:33027673, PMID:33659873, PMID:34288362, PMID:34475208]
is_a: GO:1903561 ! extracellular vesicle
+[Term]
+id: GO:0160015
+name: platelet rolling
+namespace: biological_process
+def: "Transient adhesive interactions between platelets and endothelial cells lining blood vessels. Carbohydrates on circulating platelets bind selectins or other molecules on the vessel wall causing the platelets to slow down and roll along the inner surface of the vessel wall. During this rolling motion, transitory bonds are formed and broken between surface molecules of platelets and endothelium." [GOC:sl, PMID:29018081]
+is_a: GO:0034113 ! heterotypic cell-cell adhesion
+
+[Term]
+id: GO:0160016
+name: CCACCA tRNA nucleotidyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: an unstable tRNA + 2 ATP + 4 CTP = a tRNA with a 3' CCACCA end + 6 diphosphate." [PMID:22076379]
+is_a: GO:0004810 ! CCA tRNA nucleotidyltransferase activity
+
+[Term]
+id: GO:0160017
+name: regulation of platelet rolling
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of platelet rolling." [GO_REF:0000058, GOC:sl]
+is_a: GO:0034114 ! regulation of heterotypic cell-cell adhesion
+relationship: regulates GO:0160015 ! platelet rolling
+
+[Term]
+id: GO:0160018
+name: positive regulation of platelet rolling
+namespace: biological_process
+def: "Any process that increases the rate, frequency, or extent of platelet rolling." [GO_REF:0000058, GOC:sl]
+is_a: GO:0034116 ! positive regulation of heterotypic cell-cell adhesion
+is_a: GO:0160017 ! regulation of platelet rolling
+relationship: positively_regulates GO:0160015 ! platelet rolling
+
+[Term]
+id: GO:0160019
+name: negative regulation of platelet rolling
+namespace: biological_process
+def: "Any process that decreases the rate, frequency, or extent of platelet rolling." [GO_REF:0000058, GOC:sl, PMID:15738422]
+is_a: GO:0034115 ! negative regulation of heterotypic cell-cell adhesion
+is_a: GO:0160017 ! regulation of platelet rolling
+relationship: negatively_regulates GO:0160015 ! platelet rolling
+
+[Term]
+id: GO:0160020
+name: positive regulation of ferroptosis
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of ferroptosis." [PMID:32015325]
+is_a: GO:0043068 ! positive regulation of programmed cell death
+is_a: GO:0110075 ! regulation of ferroptosis
+relationship: positively_regulates GO:0097707 ! ferroptosis
+
+[Term]
+id: GO:0160021
+name: maternal-to-zygotic transition of gene expression
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of gene expression by which developmental control passes from the maternal genome to the zygotic genome." [PMID:19204068, PMID:32558204]
+synonym: "MZT" RELATED []
+is_a: GO:0010468 ! regulation of gene expression
+
+[Term]
+id: GO:0160022
+name: apocrine secretion
+namespace: biological_process
+def: "The controlled release of a substance by a cell or a tissue by discharging a portion of the secreting cell when intracellular components are freed into a lumen through the shedding of whole pieces of the cytoplasm." [PMID:25960390]
+synonym: "secretion by cell decapitation" RELATED [ORCID:0000-0002-2825-0621]
+synonym: "secretion by membrane budding" RELATED [ORCID:0000-0002-2825-0621]
+is_a: GO:0046903 ! secretion
+
+[Term]
+id: GO:0160023
+name: sneeze reflex
+namespace: biological_process
+def: "A reflex process that expels air forcibly from the mouth and nose in an explosive, spasmodic involuntary action resulting chiefly from irritation of the nasal mucous membrane." [https://www.thefreedictionary.com/sneeze, PMID:34133943]
+synonym: "sternutation" EXACT [https://en.wikipedia.org/wiki/Sneeze]
+is_a: GO:0060004 ! reflex
+
+[Term]
+id: GO:0160024
+name: Leydig cell proliferation
+namespace: biological_process
+def: "The multiplication or reproduction of Leydig cells, resulting in the expansion of a cell population. Leydig cells are interstitial cells located adjacent to the seminiferous tubules in the testis which produce testosterone." [PMID:29632025]
+is_a: GO:0008283 ! cell population proliferation
+
+[Term]
+id: GO:0160025
+name: sensory perception of itch
+namespace: biological_process
+def: "A sensory perception which causes the desire or reflex to scratch." [PMID:26015312, PMID:29723501, PMID:30734045, Wikipedia:Itch]
+synonym: "pruritus" EXACT []
+is_a: GO:0007600 ! sensory perception
+
+[Term]
+id: GO:0160027
+name: egg deposition
+namespace: biological_process
+def: "The multicellular organismal reproductive process that results in the movement of an egg from within an organism into the external environment." [PMID:18050396, PMID:31164023]
+is_a: GO:0048609 ! multicellular organismal reproductive process
+
+[Term]
+id: GO:0160028
+name: negative regulation of pyroptosis
+namespace: biological_process
+def: "Any process that decreases the frequency, rate or extent of pyroptosis." [PMID:34637033]
+is_a: GO:0043069 ! negative regulation of programmed cell death
+relationship: negatively_regulates GO:0070269 ! pyroptosis
+
+[Term]
+id: GO:0160029
+name: kidney cortex tubule cell dedifferentiation
+namespace: biological_process
+def: "The process in which a kidney cortex tubule cell (specialized epithelial cell of the kidney) loses the structural or functional features that characterize it in the mature organism, or some other relatively stable phase of the organism's life history. Under certain conditions, these cells can revert back to the features of the stem cells that were their ancestors." [PMID:18987110, PMID:31847447]
+comment: Following injury, renal cortex tubular epithelial cell appears to be undergoing epithelial-mesenchymal transition, detected by overexpression of vimentin. {xref="PMID:31847447"}
+is_a: GO:0043697 ! cell dedifferentiation
+
+[Term]
+id: GO:0160030
+name: pollen intine formation
+namespace: biological_process
+def: "Formation of pollen intine, the inner layer of the pollen wall. The reticulate pollen wall pattern consists of two layers, exine and intine." [PMID:35498668]
+is_a: GO:0010208 ! pollen wall assembly
+
+[Term]
+id: GO:0160031
+name: endoplasmic reticulum membrane biogenesis
+namespace: biological_process
+def: "The process in which an endoplasmic reticulum membrane is synthesized, aggregates, and bonds together." [PMID:19825355, PMID:24373967, PMID:34617598]
+synonym: "ER membrane biogenesis" EXACT []
+is_a: GO:0044091 ! membrane biogenesis
+relationship: part_of GO:0090158 ! endoplasmic reticulum membrane organization
+
+[Term]
+id: GO:0160032
+name: Toll receptor ligand protein activation cascade
+namespace: biological_process
+def: "A protein activation cascade that generates the active Toll receptor ligand and consists of the cascade of enzymatic reactions initiated by extracellular recognition factors, leading to the cleavage of the inactive form of spatzle family of ligands." [PMID:23632253]
+comment: This term specifically mentions the Toll receptor and its ligand spatzle because this is the only known example of such an activation cascade for a ligand.
+is_a: GO:0072376 ! protein activation cascade
+
+[Term]
+id: GO:0160033
+name: regulation of Toll receptor ligand protein activation cascade
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of the Toll receptor ligand protein activation cascade." [PMID:23632253]
+is_a: GO:2000257 ! regulation of protein activation cascade
+relationship: regulates GO:0160032 ! Toll receptor ligand protein activation cascade
+
+[Term]
+id: GO:0160034
+name: positive regulation of Toll receptor ligand protein activation cascade
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of Toll receptor ligand protein activation cascade." [PMID:23632253]
+is_a: GO:0160033 ! regulation of Toll receptor ligand protein activation cascade
+is_a: GO:2000259 ! positive regulation of protein activation cascade
+relationship: positively_regulates GO:0160032 ! Toll receptor ligand protein activation cascade
+
+[Term]
+id: GO:0160035
+name: negative regulation of Toll receptor ligand protein activation cascade
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of Toll receptor ligand protein activation cascade." [PMID:23632253]
+is_a: GO:0160033 ! regulation of Toll receptor ligand protein activation cascade
+is_a: GO:2000258 ! negative regulation of protein activation cascade
+relationship: negatively_regulates GO:0160032 ! Toll receptor ligand protein activation cascade
+
+[Term]
+id: GO:0160036
+name: positive regulation of postsynaptic density assembly
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of postsynaptic density assembly." [PMID:17626212]
+is_a: GO:0099151 ! regulation of postsynaptic density assembly
+is_a: GO:1902117 ! positive regulation of organelle assembly
+is_a: GO:1905876 ! positive regulation of postsynaptic density organization
+relationship: positively_regulates GO:0097107 ! postsynaptic density assembly
+
+[Term]
+id: GO:0160037
+name: negative regulation of postsynaptic density assembly
+namespace: biological_process
+def: "Any process that decreases the rate, frequency, or extent of postsynaptic density assembly." [PMID:17626212]
+is_a: GO:0099151 ! regulation of postsynaptic density assembly
+is_a: GO:1902116 ! negative regulation of organelle assembly
+is_a: GO:1905875 ! negative regulation of postsynaptic density organization
+relationship: negatively_regulates GO:0097107 ! postsynaptic density assembly
+
+[Term]
+id: GO:0160038
+name: somatic sensory system development
+namespace: biological_process
+def: "The process whose specific outcome is the progression of a somatic sensory system over time from its formation to the mature structure. Somatic sensory system is the sensory system for the sense of touch and pain." [PMID:25832476, PMID:31399790]
+synonym: "somatosensory system development" EXACT []
+is_a: GO:0048880 ! sensory system development
+
+[Term]
+id: GO:0160039
+name: serotonin-gated chloride channel activity
+namespace: molecular_function
+def: "Enables the transmembrane transfer of a chloride ion by a channel that opens when the biogenic amine serotonin has been bound by the channel complex or one of its constituent parts. Serotonin (5-hydroxytryptamine) is a neurotransmitter and hormone found in vertebrates and invertebrates." [PMID:11100728]
+xref: TC:1.A.9
+xref: Wikipedia:Ligand-gated_ion_channel
+is_a: GO:0005254 ! chloride channel activity
+is_a: GO:0022824 ! transmitter-gated monoatomic ion channel activity
+is_a: GO:0099095 ! ligand-gated monoatomic anion channel activity
+is_a: GO:0099589 ! serotonin receptor activity
+
+[Term]
+id: GO:0160040
+name: mitocytosis
+namespace: biological_process
+def: "A migrasome-mediated selective removal of damaged mitochondria process that maintains mitochondrion homeostasis in migrating cells." [PMID:34108688]
+is_a: GO:0048311 ! mitochondrion distribution
+is_a: GO:0051654 ! establishment of mitochondrion localization
+is_a: GO:0140495 ! migracytosis
+
+[Term]
+id: GO:0160041
+name: neuropeptide activity
+namespace: molecular_function
+def: "The receptor ligand activity of any polypeptide expressed in, and secreted from a neuron." [PMID:18806786, PMID:21922398]
+is_a: GO:0048018 ! receptor ligand activity
+
+[Term]
+id: GO:0160042
+name: purine nucleotide uniporter activity
+namespace: molecular_function
+def: "Catalysis of the active transport of purine nucleotides across a membrane by a mechanism involving conformational change, where energy for active transport is derived from membrane potential if the solute is charged." [PMID:18375752, PMID:27477609]
+is_a: GO:0015216 ! purine nucleotide transmembrane transporter activity
+is_a: GO:0022810 ! membrane potential driven uniporter activity
+
+[Term]
+id: GO:0160043
+name: catecholamine secretion, neurotransmission
+namespace: biological_process
+def: "The regulated release of catecholamine by a cell in which the catecholamine acts as a neurotransmitter." [PMID:10191060]
+is_a: GO:0007269 ! neurotransmitter secretion
+is_a: GO:0050432 ! catecholamine secretion
+
+[Term]
+id: GO:0160044
+name: sulfate:chloride antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: chloride(in) + sulfate(out) = chloride(out) + sulfate(in)." [PMID:17442754]
+is_a: GO:0005452 ! solute:inorganic anion antiporter activity
+is_a: GO:0008271 ! secondary active sulfate transmembrane transporter activity
+is_a: GO:0015108 ! chloride transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
+
+[Term]
+id: GO:0160045
+name: TMEM240-body
+namespace: cellular_component
+def: "A multilamellar subcellular structure formed in the cytoplasm of developing neuron, composed of Tmem240 and Emd proteins." [PMID:32535204]
+synonym: "T240-body" EXACT []
+is_a: GO:0043231 ! intracellular membrane-bounded organelle
+
+[Term]
+id: GO:0160046
+name: oxalate:chloride antiporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: chloride(out) + oxalate(in) = chloride(in) + oxalate(out)." [PMID:17442754]
+is_a: GO:0005452 ! solute:inorganic anion antiporter activity
+is_a: GO:0015108 ! chloride transmembrane transporter activity
+is_a: GO:0019531 ! oxalate transmembrane transporter activity
+is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
+
+[Term]
+id: GO:0160047
+name: muramyl dipeptide kinase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: ATP + muramyl dipeptide = ADP + H(+) + 6-O-phospho-muramyl dipeptide." [PMID:36002575]
+is_a: GO:0016301 ! kinase activity
+
+[Term]
+id: GO:0160048
+name: craniofacial suture closure
+namespace: biological_process
+def: "The process of fusing together the edges of a craniofacial suture." [PMID:33842480]
+is_a: GO:0060349 ! bone morphogenesis
+
+[Term]
+id: GO:0160049
+name: negative regulation of cGAS/STING signaling pathway
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of cGAS/STING signaling pathway." [PMID:29875158]
+is_a: GO:0039532 ! negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
+relationship: negatively_regulates GO:0140896 ! cGAS/STING signaling pathway
+
+[Term]
+id: GO:0160050
+name: xanthine binding
+namespace: molecular_function
+def: "Binding to xanthine, a purine base." [PMID:32345632, PMID:34125892]
+is_a: GO:0002060 ! purine nucleobase binding
+
+[Term]
+id: GO:0160051
+name: Cyc8(Ssn6)-Tup1 general repressor complex
+namespace: cellular_component
+def: "A corepressor complex containing the WD-repeat protein Tup1p (S. cerevisiae) and Tup11/Tup12 (fission yeast) and the TPR repeat protein Cyc8p (S. cerevisiae) ssn6 (fission yeast) that is recruited to target genes by DNA-bound repressor proteins preferentially at regions where histones are deacetylated by the Clr6 class I HDAC, and recruits the SWI/SNF and SAGA complexes to promoters." [GOC:vw, PMID:10871883, PMID:17101775, PMID:22156212]
+synonym: "Tup11/Tup12 repressor complex" EXACT []
+is_a: GO:0090571 ! RNA polymerase II transcription repressor complex
+
+[Term]
+id: GO:0160052
+name: mitotic nuclear envelope segregation
+namespace: biological_process
+def: "The mitotic cell cycle process in which the nuclear envelope, including nuclear pores, is equally distributed to the two daughter cells during the mitotic cell cycle." [GOC:vw, PMID:24184107]
+is_a: GO:1903047 ! mitotic cell cycle process
+relationship: part_of GO:0140014 ! mitotic nuclear division
+
+[Term]
+id: GO:0160053
+name: serine-based site-specific recombinase activity
+namespace: molecular_function
+def: "Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a phosphoseryl intermediate in which the target sequence is first cleaved by the nucleophilic attack by a serine in the active site." [PMID:16756503, PMID:29316791]
+is_a: GO:0009009 ! site-specific recombinase activity
+
+[Term]
+id: GO:0160054
+name: microfibril assembly
+namespace: biological_process
+def: "The aggregation, arrangement and bonding together of microfibril." [PMID:32855533]
+is_a: GO:0022607 ! cellular component assembly
+is_a: GO:0097435 ! supramolecular fiber organization
+
+[Term]
+id: GO:0160055
+name: glideosome
+namespace: cellular_component
+def: "A protein complex composed of at least GAP45 (gliding-associated protein), GAP50 and myosin heavy and light chains. Anchored via GAP50 to the inner membrane complex of motile and invasive forms of apicomplexan parasites and regulates parasite gliding motility and invasion of host cells." [PMID:12139608, PMID:15123738, PMID:19577950]
+is_a: GO:0032991 ! protein-containing complex
+
+[Term]
+id: GO:0160056
+name: macropinosome membrane
+namespace: cellular_component
+def: "The lipid bilayer surrounding a macropinosome." [PMID:19690049]
+is_a: GO:0010008 ! endosome membrane
+relationship: part_of GO:0044354 ! macropinosome
+
+[Term]
+id: GO:0160057
+name: plant endodermal cell fate specification
+namespace: biological_process
+def: "The process in which a cell becomes capable of differentiating autonomously into a plant endodermal cell in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed." [PMID:26415082]
+is_a: GO:0001708 ! cell fate specification
+
+[Term]
+id: GO:0160058
+name: plant endodermal cell differentiation
+namespace: biological_process
+def: "The process in which a relatively unspecialized cell acquires specialized features of a plant endodermal cell." [PMID:21735349]
+is_a: GO:0030154 ! cell differentiation
+
+[Term]
+id: GO:0160059
+name: programmed cell death in response to retinoic acid
+namespace: biological_process
+def: "Cell death resulting from activation of endogenous cellular processes and occurring as a result of a retinoic acid." [PMID:17869331, PMID:9187263]
+synonym: "retinoic acid-induced apoptosis" EXACT []
+is_a: GO:0012501 ! programmed cell death
+relationship: part_of GO:0071300 ! cellular response to retinoic acid
+
+[Term]
+id: GO:0160060
+name: sleep homeostasis
+namespace: biological_process
+def: "A homeostatic process in which the drive for sleep increases sleep propensity with prolonged wakefulness." [PMID:30509635]
+is_a: GO:0048871 ! multicellular organismal-level homeostasis
+
+[Term]
+id: GO:0160061
+name: respiratory chemosensitivity
+namespace: biological_process
+def: "A homeostatic process by which the sensing of CO2 and/or H+ by the brain leads to appropriate altering in breathing to regulate blood gas and tissue pH." [PMID:26068853]
+is_a: GO:0048871 ! multicellular organismal-level homeostasis
+
+[Term]
+id: GO:0160062
+name: cutin-based cuticle development
+namespace: biological_process
+def: "The process whose specific outcome is the progression of the cutin-based cuticle over time, from its formation to the mature structure. Cutin-based cuticle is an extracellular structure composed of a covalently linked macromolecular scaffold of cutin and a variety of organic solvent-soluble lipids that are collectively termed waxes. Such structures are found on the external face of polysaccharide cell walls in land plants." [PMID:23893170]
+is_a: GO:0048856 ! anatomical structure development
+
+[Term]
+id: GO:0160063
+name: multi-pass transmembrane protein insertion into ER membrane
+namespace: biological_process
+def: "A process of protein insertion of multi-pass membrane proteins into the endoplasmic reticulum (ER) membrane. Insertion of multi-pass membrane proteins is mediated by the multi-pass translocon complex and takes place following membrane insertion of the first few transmembrane segments of proteins by the SEC61 complex to promote insertion of subsequent transmembrane regions." [PMID:36261522, PMID:36261528]
+is_a: GO:0045048 ! protein insertion into ER membrane
+
+[Term]
+id: GO:0160064
+name: multi-pass translocon complex
+namespace: cellular_component
+def: "A protein complex that mediates the insertion of multi-pass transmembrane proteins into endoplasmic reticulum (ER) membrane. Substrates enter via the lateral gate of the Sec61 translocon. The complex comprises the GEL subcomplex (composed of RAB5IF/OPTI and TMCO1), the BOS subcomplex (composed of NCLN/Nicalin, NOMO and TMEM147) and the PAT subcomplex (composed of WDR83OS/Asterix and CCDC47)." [PMID:36261522, PMID:36261528]
+synonym: "MPT complex" EXACT []
+synonym: "TMCO1 translocon" RELATED []
+is_a: GO:0072379 ! ER membrane insertion complex
+
+[Term]
+id: GO:0160065
+name: SIN/MEN signalling complex
+namespace: cellular_component
+def: "A protein complex associated with the mitotic spindle pole body during interphase and mitosis and comprises of the proteins of the septation initiation signalling network (SIN) of fission yeast or mitotic exit network (MEN) of budding yeast, organized by two scaffold/adaptor proteins." [PMID:21131906, PMID:22525225, PMID:22684255]
+synonym: "Hippo singalling complex" NARROW []
+synonym: "MEN signalling complex" NARROW []
+synonym: "SIN singnalling complex" NARROW []
+is_a: GO:0032991 ! protein-containing complex
+relationship: part_of GO:0061499 ! outer plaque of mitotic spindle pole body
+
+[Term]
+id: GO:0160066
+name: interphase SIN signalling complex
+namespace: cellular_component
+def: "A SIN signalling complex associated with the old mitotic spindle pole body during interphase and early M-phase and characterised by the presence active ubiquitin ligase (Dma1 in fission yeast) and GTPase activator (Spg1 in fission yeast) to inactivate SIN signalling." [PMID:21131906]
+is_a: GO:0160065 ! SIN/MEN signalling complex
+
+[Term]
+id: GO:0160067
+name: new spindle pole body SIN signalling complex
+namespace: cellular_component
+def: "A SIN signalling complex associated with the new mitotic spindle pole body during anaphase and characterised by the presence activated (GTP bound) GTPase (Spg1 in fission yeast) to activate SIN signalling." [PMID:21131906]
+is_a: GO:0160065 ! SIN/MEN signalling complex
+
+[Term]
+id: GO:0160068
+name: negative regulation of pollen tube guidance
+namespace: biological_process
+def: "Any process that decreases the rate, frequency or extent of pollen tube guidance towards ovules. This is one mechanism to prevent polytuby, the simultaneous penetration of ovules by multiple pollen tubes." [PMID:33790463]
+synonym: "prevention of polytuby" BROAD []
+is_a: GO:0050928 ! negative regulation of positive chemotaxis
+is_a: GO:2000242 ! negative regulation of reproductive process
+relationship: negatively_regulates GO:0010183 ! pollen tube guidance
+
+[Term]
+id: GO:0160070
+name: intracellular borate homeostasis
+namespace: biological_process
+def: "A homeostatic process involved in the maintenance of a steady state level of tetrahydroxoborate within a cell." [PMID:15525507]
+synonym: "intracellular boron homeostasis" EXACT []
+synonym: "intracellular tetrahydroxoborate homeostasis" EXACT []
+is_a: GO:0055082 ! intracellular chemical homeostasis
+is_a: GO:0098771 ! inorganic ion homeostasis
+
+[Term]
+id: GO:0160071
+name: prevention of polyspermy during double fertilization
+namespace: biological_process
+def: "The regulation of double fertilization forming a zygote and endosperm process that ensures that only a single sperm cell fertilizes one egg cell and another single sperm cell fertilizes one central cell." [PMID:27951463]
+is_a: GO:0080155 ! regulation of double fertilization forming a zygote and endosperm
+
+[Term]
+id: GO:0160072
+name: ubiquitin ligase complex scaffold activity
+namespace: molecular_function
+def: "The binding activity of a molecule that brings together an ubiquitin ligase and an ubiquitin ligase-substrate adaptor, permitting those molecules to function in a coordinated way." [PMID:27664236]
+synonym: "core protein activity for the CUL-RING ubiquitin ligase complex" NARROW []
+is_a: GO:0030674 ! protein-macromolecule adaptor activity
+
+[Term]
+id: GO:0160073
+name: Casparian strip assembly
+namespace: biological_process
+def: "The aggregation, arrangement and bonding together of a set of components to form a Casparian strip, a region of plant cell wall specialised to act as a seal to prevent back leakage of secreted material." [PMID:28104889]
+synonym: "Casparian strip formation" EXACT []
+is_a: GO:0022607 ! cellular component assembly
+relationship: part_of GO:0071668 ! plant-type cell wall assembly
+
+[Term]
+id: GO:0160074
+name: non-canonical inflammasome complex
+namespace: cellular_component
+def: "An inflammasome complex containing CASP4, known as caspase-11 (Casp11) in mouse, which assembles upon cytosolic lipopolysaccharide-binding and directly activates Gasdermin-D (GSDMD)." [PMID:33187725]
+is_a: GO:0032991 ! protein-containing complex
+relationship: part_of GO:0005829 ! cytosol
+
+[Term]
+id: GO:0160075
+name: non-canonical inflammasome complex assembly
+namespace: biological_process
+def: "The aggregation, arrangement and bonding together of a set of components to form a non-canonical inflammasome complex." [PMID:27291964]
+is_a: GO:0065003 ! protein-containing complex assembly
+
+[Term]
+id: GO:0160076
+name: negative regulation of non-canonical inflammasome complex assembly
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of non-canonical inflammasome complex assembly." [PMID:22002608, PMID:26375259]
+is_a: GO:0031333 ! negative regulation of protein-containing complex assembly
+relationship: negatively_regulates GO:0160075 ! non-canonical inflammasome complex assembly
+
+[Term]
+id: GO:0160077
+name: lipid droplet fusion
+namespace: biological_process
+def: "The process by which a single lipid droplet is created from the fusion of two or more lipid droplets." [PMID:34508658, PMID:36477540]
+is_a: GO:0034389 ! lipid droplet organization
+is_a: GO:0048284 ! organelle fusion
+
+[Term]
+id: GO:0160078
+name: negative regulation of lipid droplet fusion
+namespace: biological_process
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of lipid droplet fusion." [PMID:36477540]
+is_a: GO:0010639 ! negative regulation of organelle organization
+relationship: negatively_regulates GO:0160077 ! lipid droplet fusion
+
+[Term]
+id: GO:0170002
+name: halotropism
+namespace: biological_process
+def: "A sodium-specific negative tropism that is crucial for surviving and thriving under high salinity." [PMID:36243013]
+synonym: "root halotropism" EXACT []
+is_a: GO:0009606 ! tropism
+
+[Term]
+id: GO:0170005
+name: cyclic nucleotide phosphodiesterase activator activity
+namespace: molecular_function
+def: "Binds to and increases the activity of cyclic nucleotide phosphodiesterase." [PMID:6087882, PMID:6259174, PMID:6667031]
+is_a: GO:0008047 ! enzyme activator activity
+
+[Term]
+id: GO:0170008
+name: mRNA phosphatase activator activity
+namespace: molecular_function
+def: "Binds to and increases the activity of mRNA phosphatase." [PMID:22323607]
+is_a: GO:0008047 ! enzyme activator activity
+
+[Term]
+id: GO:0170010
+name: nonsense-mediated decay complex
+namespace: cellular_component
+def: "A highly conserved protein complex that recognises and elicits the rapid degradation of mRNAs in which an amino-acid codon has changed to a nonsense codon; occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction." [GOC:lnp, PMID:1569946, PMID:29282598, PMID:9032286]
+synonym: "Upf complex" EXACT []
+xref: IntAct:EBI-16420380
+is_a: GO:1902494 ! catalytic complex
+
+[Term]
+id: GO:0170011
+name: stalled ribosome sensor activity
+namespace: molecular_function
+def: "A molecule that recognizes stalled ribosomes and initiates a signalling response." [PMID:32289254, PMID:32610081, PMID:36638793]
+is_a: GO:0043022 ! ribosome binding
+
+[Term]
+id: GO:0170012
+name: histone H3K18 decrotonylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[histone H3 position 18] + NAD+ = 2''-O-(2E)-but-2-enoyl-ADP-D-ribose + L-lysyl-[histone H3] + nicotinamide." [PMID:34927582]
+is_a: GO:0160012 ! NAD-dependent histone decrotonylase activity
+
+[Term]
+id: GO:0170013
+name: channel complex
+namespace: cellular_component
+def: "A protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient." [PMID:10839820]
+is_a: GO:0098796 ! membrane protein complex
+
+[Term]
+id: GO:0170014
+name: ankyrin-1 complex
+namespace: cellular_component
+def: "A complex composed of ANK1, RHCE, RHAG, SLC4A1, EPB42, GYPA, GYPB and AQP1, that functions in the stability and shape of the erythrocyte membrane in human." [PMID:35835865]
+synonym: "ankyrin complex" EXACT []
+synonym: "erythrocyte ankyrin-1 complex" EXACT []
+is_a: GO:0098796 ! membrane protein complex
+
+[Term]
+id: GO:0170015
+name: carbon dioxide receptor activity
+namespace: molecular_function
+def: "Combining with carbon dioxide to initiate a change in cell activity." [PMID:24240097]
+is_a: GO:0038023 ! signaling receptor activity
+
+[Term]
+id: GO:0180000
+name: histone methyltransferase inhibitor activity
+namespace: molecular_function
+def: "Binds to and stops, prevents or reduces the activity of a histone methyltransferase." [PMID:30923826]
+is_a: GO:0004857 ! enzyme inhibitor activity
+
+[Term]
+id: GO:0180001
+name: cyclic-di-AMP binding
+namespace: molecular_function
+def: "Binding to a cyclic di-AMP nucleotide." [PMID:32843560, PMID:36629470]
+synonym: "cyclic dimeric adenosine monophosphate binding" EXACT []
+is_a: GO:0030551 ! cyclic nucleotide binding
+is_a: GO:0032559 ! adenyl ribonucleotide binding
+
+[Term]
+id: GO:0180002
+name: renal zinc excretion
+namespace: biological_process
+def: "The elimination of zinc ions from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine." [PMID:28196538]
+synonym: "renal zinc ion excretion" EXACT []
+synonym: "renal zinc secretion" EXACT []
+is_a: GO:0097254 ! renal tubular secretion
+
+[Term]
+id: GO:0180003
+name: S-adenosyl-L-methionine:S-adenosyl-L-homocysteine antiporter activity
+namespace: molecular_function
+def: "Catalysis of the reaction: S-adenosyl-L-homocysteine(out) + S-adenosyl-L-methionine(in) = S-adenosyl-L-homocysteine(in) + S-adenosyl-L-methionine(out)." [PMID:14674884, PMID:34375635]
+is_a: GO:0000095 ! S-adenosyl-L-methionine transmembrane transporter activity
+is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
+is_a: GO:0015211 ! purine nucleoside transmembrane transporter activity
+is_a: GO:0015297 ! antiporter activity
+is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
+
+[Term]
+id: GO:0180004
+name: RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: RNA polymerase II large subunit CTD heptapeptide repeat--phospho-L-tyrosine (consensus YSPTSPS)(position 1) + H2O = RNA polymerase II large subunit + phosphate." [PMID:22622228]
+synonym: "RNA polymerase II C-terminal domain Y1 phosphatase activity" EXACT []
+is_a: GO:0008420 ! RNA polymerase II CTD heptapeptide repeat phosphatase activity
+
+[Term]
+id: GO:0180005
+name: RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: RNA polymerase II large subunit CTD heptapeptide repeat--phospho-L-threonine (consensus YSPTSPS)(position 4) + H2O = RNA polymerase II large subunit + phosphate." [PMID:22622228]
+synonym: "RNA polymerase II C-terminal domain T4 phosphatase activity" EXACT []
+is_a: GO:0008420 ! RNA polymerase II CTD heptapeptide repeat phosphatase activity
+
+[Term]
+id: GO:0180006
+name: RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: RNA polymerase II large subunit CTD heptapeptide repeat--phospho-L-serine (consensus YSPTSPS)(position 2) + H2O = RNA polymerase II large subunit + phosphate." [PMID:22622228]
+synonym: "RNA polymerase II C-terminal domain S2 phosphatase activity" EXACT []
+is_a: GO:0008420 ! RNA polymerase II CTD heptapeptide repeat phosphatase activity
+
+[Term]
+id: GO:0180007
+name: RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: RNA polymerase II large subunit CTD heptapeptide repeat--phospho-L-serine (consensus YSPTSPS)(position 5) + H2O = RNA polymerase II large subunit + phosphate." [PMID:22622228]
+synonym: "RNA polymerase II C-terminal domain S5 phosphatase activity" EXACT []
+is_a: GO:0008420 ! RNA polymerase II CTD heptapeptide repeat phosphatase activity
+
+[Term]
+id: GO:0180008
+name: RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: RNA polymerase II large subunit CTD heptapeptide repeat--phospho-L-serine (consensus YSPTSPS)(position 7) + H2O = RNA polymerase II large subunit + phosphate." [PMID:22622228]
+synonym: "RNA polymerase II C-terminal domain S7 phosphatase activity" EXACT []
+is_a: GO:0008420 ! RNA polymerase II CTD heptapeptide repeat phosphatase activity
+
+[Term]
+id: GO:0180010
+name: co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway
+namespace: biological_process
+def: "Any process involved in transcription termination-coupled 3' processing of RNA polymerase II mRNA transcripts by the 3' end cleavage and addition of a poly(A) tail. This pathway is required for the maturation of primary protein-encoding transcripts into functional mRNAs that can be exported from the nucleus and translated in the cytoplasm, but is also required for polyadenylation-dependent decay." [PMID:31499460]
+synonym: "cotranscriptional 3' processing of RNA polymerase II mRNA transcripts" EXACT []
+is_a: GO:0031124 ! mRNA 3'-end processing
+is_a: GO:0180012 ! co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway
+
+[Term]
+id: GO:0180011
+name: cytoplasmic polyadenylation
+namespace: biological_process
+def: "Any process by which dormant, translationally inactive mRNAs become activated via the elongation of their poly(A) tails in the cytosol." [PMID:21536428]
+is_a: GO:0031124 ! mRNA 3'-end processing
+
+[Term]
+id: GO:0180012
+name: co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway
+namespace: biological_process
+def: "Any process involved in transcription termination-coupled 3' processing of RNA polymerase II RNA transcripts by 3' end cleavage and addition of a poly(A) tail. This pathway is required for the maturation of primary protein-encoding transcripts into functional RNAs that can be exported from the nucleus and translated in the cytoplasm, but is also required for polyadenylation-dependent decay." [PMID:31499460]
+synonym: "cotranscriptional 3'-end processing of RNA polymerase II transcripts" EXACT []
+xref: PMID:31499460
+is_a: GO:0006396 ! RNA processing
+
+[Term]
+id: GO:0180013
+name: lysophosphatidylserine flippase activity
+namespace: molecular_function
+def: "Catalysis of the movement of a lysophosphatidylserine from the exoplasmic to the cytosolic leaftlet of a membrane, using energy from the hydrolysis of ATP." [PMID:34645814]
+is_a: GO:0140333 ! glycerophospholipid flippase activity
+
+[Term]
+id: GO:0180014
+name: protein-tRNA adaptor activity
+namespace: molecular_function
+def: "The binding activity of a protein that brings together another protein and a tRNA, permitting those molecules to function in a coordinated way." [PMID:31048492]
+synonym: "tRNA carrier" RELATED []
+is_a: GO:0140517 ! protein-RNA adaptor activity
+
+[Term]
+id: GO:0180015
+name: nucleoside import across plasma membrane
+namespace: biological_process
+def: "The directed movement of nucleoside from outside of a cell, across the plasma membrane and into the cytosol." [PMID:21998139, PMID:30658162]
+is_a: GO:0098657 ! import into cell
+is_a: GO:0098739 ! import across plasma membrane
+is_a: GO:1901642 ! nucleoside transmembrane transport
+
+[Term]
+id: GO:0180016
+name: SUMO ligase regulator activity
+namespace: molecular_function
+def: "Binds to and modulates the activity of a SUMO ligase." [PMID:19363481, PMID:33446573]
+is_a: GO:0055103 ! ligase regulator activity
+
+[Term]
+id: GO:0180017
+name: K11-linked deubiquitinase activity
+namespace: molecular_function
+def: "Hydrolysis of a ubiquitin unit from a ubiquitinated protein linked via the Lys11 residue of ubiquitin." [PMID:26412298]
+is_a: GO:0101005 ! deubiquitinase activity
+
[Term]
id: GO:0198738
name: cell-cell signaling by wnt
@@ -422367,11 +425760,13 @@ relationship: positively_regulates GO:0002534 ! cytokine production involved in
[Term]
id: GO:1900018
-name: phosphorylation of RNA polymerase II C-terminal domain serine 5 residues involved in recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex
+name: obsolete phosphorylation of RNA polymerase II C-terminal domain serine 5 residues involved in recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex
namespace: biological_process
-def: "Any phosphorylation of RNA polymerase II C-terminal domain serine 5 residues that is involved in recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex." [GOC:rb, GOC:TermGenie, PMID:10594013, PMID:19666497]
-is_a: GO:0071620 ! phosphorylation of RNA polymerase II C-terminal domain serine 5 residues
-relationship: part_of GO:0036031 ! recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex
+def: "OBSOLETE. Any phosphorylation of RNA polymerase II C-terminal domain serine 5 residues that is involved in recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex." [GOC:rb, GOC:TermGenie, PMID:10594013, PMID:19666497]
+comment: This term was obsoleted because it represents both a molecular function and a biological process.
+is_obsolete: true
+consider: GO:0006370
+consider: GO:0140836
[Term]
id: GO:1900019
@@ -422400,7 +425795,7 @@ name: regulation of D-erythro-sphingosine kinase activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of D-erythro-sphingosine kinase activity." [GOC:signaling, GOC:TermGenie]
synonym: "regulation of sphingosine kinase activity" EXACT [GOC:TermGenie]
-is_a: GO:0043549 ! regulation of kinase activity
+is_a: GO:0043550 ! regulation of lipid kinase activity
[Term]
id: GO:1900023
@@ -422410,7 +425805,7 @@ def: "Any process that activates or increases the frequency, rate or extent of D
synonym: "positive regulation of sphingosine kinase activity" EXACT [GOC:TermGenie]
synonym: "up regulation of D-erythro-sphingosine kinase activity" RELATED [GOC:TermGenie]
synonym: "up regulation of sphingosine kinase activity" EXACT [GOC:TermGenie]
-is_a: GO:0033674 ! positive regulation of kinase activity
+is_a: GO:0090218 ! positive regulation of lipid kinase activity
is_a: GO:1900022 ! regulation of D-erythro-sphingosine kinase activity
[Term]
@@ -422420,7 +425815,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of substrate adhesion-dependent cell spreading." [GOC:TermGenie, GOC:yaf]
synonym: "regulation of cell spreading during cell substrate adhesion" EXACT [GOC:TermGenie]
synonym: "regulation of substrate adhesion dependent cell spreading" EXACT [GOC:TermGenie]
-is_a: GO:0010769 ! regulation of cell morphogenesis involved in differentiation
is_a: GO:0010810 ! regulation of cell-substrate adhesion
relationship: regulates GO:0034446 ! substrate adhesion-dependent cell spreading
@@ -422434,7 +425828,6 @@ synonym: "down regulation of substrate adhesion dependent cell spreading" EXACT
synonym: "down regulation of substrate adhesion-dependent cell spreading" RELATED [GOC:TermGenie]
synonym: "negative regulation of cell spreading during cell substrate adhesion" EXACT [GOC:TermGenie]
synonym: "negative regulation of substrate adhesion dependent cell spreading" EXACT [GOC:TermGenie]
-is_a: GO:0010771 ! negative regulation of cell morphogenesis involved in differentiation
is_a: GO:0010812 ! negative regulation of cell-substrate adhesion
is_a: GO:1900024 ! regulation of substrate adhesion-dependent cell spreading
relationship: negatively_regulates GO:0034446 ! substrate adhesion-dependent cell spreading
@@ -422449,7 +425842,6 @@ synonym: "positive regulation of substrate adhesion dependent cell spreading" EX
synonym: "up regulation of cell spreading during cell substrate adhesion" EXACT [GOC:TermGenie]
synonym: "up regulation of substrate adhesion dependent cell spreading" EXACT [GOC:TermGenie]
synonym: "up regulation of substrate adhesion-dependent cell spreading" RELATED [GOC:TermGenie]
-is_a: GO:0010770 ! positive regulation of cell morphogenesis involved in differentiation
is_a: GO:0010811 ! positive regulation of cell-substrate adhesion
is_a: GO:1900024 ! regulation of substrate adhesion-dependent cell spreading
relationship: positively_regulates GO:0034446 ! substrate adhesion-dependent cell spreading
@@ -422501,9 +425893,7 @@ synonym: "regulation of pectin anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of pectin biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of pectin formation" EXACT [GOC:TermGenie]
synonym: "regulation of pectin synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:0032885 ! regulation of polysaccharide biosynthetic process
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
relationship: regulates GO:0045489 ! pectin biosynthetic process
[Term]
@@ -422801,20 +426191,23 @@ relationship: positively_regulates GO:0007599 ! hemostasis
[Term]
id: GO:1900049
-name: regulation of histone exchange
+name: obsolete regulation of histone exchange
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone exchange." [GOC:TermGenie, PMID:20332092]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone exchange." [GOC:TermGenie, PMID:20332092]
+comment: This term was obsoleted because it represents a molecular function (histone chaperone activity).
synonym: "regulation of histone chaperone" RELATED [GOC:TermGenie]
synonym: "regulation of histone displacement" EXACT [GOC:TermGenie]
synonym: "regulation of histone replacement" EXACT [GOC:TermGenie]
-is_a: GO:1902275 ! regulation of chromatin organization
-relationship: regulates GO:0043486 ! histone exchange
+is_obsolete: true
+consider: GO:0006338
+consider: GO:0140713
[Term]
id: GO:1900050
-name: negative regulation of histone exchange
+name: obsolete negative regulation of histone exchange
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone exchange." [GOC:TermGenie, PMID:20332092]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone exchange." [GOC:TermGenie, PMID:20332092]
+comment: This term was obsoleted because it represents a molecular function, histone chaperone activity.
synonym: "down regulation of histone chaperone" RELATED [GOC:TermGenie]
synonym: "down regulation of histone exchange" RELATED [GOC:TermGenie]
synonym: "down regulation of histone replacement" EXACT [GOC:TermGenie]
@@ -422829,15 +426222,16 @@ synonym: "inhibition of histone exchange" RELATED [GOC:TermGenie]
synonym: "inhibition of histone replacement" EXACT [GOC:TermGenie]
synonym: "negative regulation of histone chaperone" RELATED [GOC:TermGenie]
synonym: "negative regulation of histone replacement" EXACT [GOC:TermGenie]
-is_a: GO:1900049 ! regulation of histone exchange
-is_a: GO:1905268 ! negative regulation of chromatin organization
-relationship: negatively_regulates GO:0043486 ! histone exchange
+is_obsolete: true
+consider: GO:0006338
+consider: GO:0140713
[Term]
id: GO:1900051
-name: positive regulation of histone exchange
+name: obsolete positive regulation of histone exchange
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of histone exchange." [GOC:TermGenie, PMID:20332092]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of histone exchange." [GOC:TermGenie, PMID:20332092]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of histone chaperone" RELATED [GOC:TermGenie]
synonym: "activation of histone exchange" RELATED [GOC:TermGenie]
synonym: "activation of histone replacement" EXACT [GOC:TermGenie]
@@ -422852,9 +426246,9 @@ synonym: "up-regulation of histone replacement" EXACT [GOC:TermGenie]
synonym: "upregulation of histone chaperone" RELATED [GOC:TermGenie]
synonym: "upregulation of histone exchange" RELATED [GOC:TermGenie]
synonym: "upregulation of histone replacement" EXACT [GOC:TermGenie]
-is_a: GO:1900049 ! regulation of histone exchange
-is_a: GO:1905269 ! positive regulation of chromatin organization
-relationship: positively_regulates GO:0043486 ! histone exchange
+is_obsolete: true
+consider: GO:0006338
+consider: GO:0140713
[Term]
id: GO:1900052
@@ -423016,7 +426410,7 @@ synonym: "negative regulation of ceramide anabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of ceramide biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of ceramide formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of ceramide synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0090155 ! negative regulation of sphingolipid biosynthetic process
is_a: GO:2000303 ! regulation of ceramide biosynthetic process
relationship: negatively_regulates GO:0046513 ! ceramide biosynthetic process
@@ -423158,8 +426552,7 @@ def: "Any process that modulates the frequency, rate or extent of ethanol catabo
synonym: "regulation of ethanol breakdown" EXACT [GOC:TermGenie]
synonym: "regulation of ethanol catabolism" EXACT [GOC:TermGenie]
synonym: "regulation of ethanol degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009894 ! regulation of catabolic process
-is_a: GO:0062012 ! regulation of small molecule metabolic process
+is_a: GO:1900419 ! regulation of cellular alcohol catabolic process
relationship: regulates GO:0006068 ! ethanol catabolic process
[Term]
@@ -423186,9 +426579,8 @@ synonym: "upregulation of ethanol breakdown" EXACT [GOC:TermGenie]
synonym: "upregulation of ethanol catabolic process" RELATED [GOC:TermGenie]
synonym: "upregulation of ethanol catabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of ethanol degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009896 ! positive regulation of catabolic process
-is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1900065 ! regulation of ethanol catabolic process
+is_a: GO:1900421 ! positive regulation of cellular alcohol catabolic process
relationship: positively_regulates GO:0006068 ! ethanol catabolic process
[Term]
@@ -423261,7 +426653,7 @@ name: regulation of sulfite transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of sulfite transport." [GOC:TermGenie, PMID:10234785, PMID:10870099]
synonym: "regulation of sulphite transport" EXACT [GOC:TermGenie]
-is_a: GO:0044070 ! regulation of anion transport
+is_a: GO:0051049 ! regulation of transport
relationship: regulates GO:0000316 ! sulfite transport
[Term]
@@ -423278,8 +426670,8 @@ synonym: "up-regulation of sulfite transport" RELATED [GOC:TermGenie]
synonym: "up-regulation of sulphite transport" EXACT [GOC:TermGenie]
synonym: "upregulation of sulfite transport" RELATED [GOC:TermGenie]
synonym: "upregulation of sulphite transport" EXACT [GOC:TermGenie]
+is_a: GO:0051050 ! positive regulation of transport
is_a: GO:1900071 ! regulation of sulfite transport
-is_a: GO:1903793 ! positive regulation of anion transport
relationship: positively_regulates GO:0000316 ! sulfite transport
[Term]
@@ -423396,7 +426788,7 @@ synonym: "upregulation of arginine biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of arginine formation" EXACT [GOC:TermGenie]
synonym: "upregulation of arginine synthesis" EXACT [GOC:TermGenie]
is_a: GO:1900079 ! regulation of arginine biosynthetic process
-is_a: GO:2000284 ! positive regulation of cellular amino acid biosynthetic process
+is_a: GO:2000284 ! positive regulation of amino acid biosynthetic process
relationship: positively_regulates GO:0006526 ! arginine biosynthetic process
[Term]
@@ -423408,7 +426800,8 @@ synonym: "regulation of arginine breakdown" EXACT [GOC:TermGenie]
synonym: "regulation of arginine catabolism" EXACT [GOC:TermGenie]
synonym: "regulation of arginine degradation" EXACT [GOC:TermGenie]
is_a: GO:0000821 ! regulation of arginine metabolic process
-is_a: GO:0033241 ! regulation of cellular amine catabolic process
+is_a: GO:0031329 ! regulation of cellular catabolic process
+is_a: GO:0033241 ! regulation of amine catabolic process
relationship: regulates GO:0006527 ! arginine catabolic process
[Term]
@@ -423435,7 +426828,8 @@ synonym: "inhibition of arginine degradation" NARROW [GOC:TermGenie]
synonym: "negative regulation of arginine breakdown" EXACT [GOC:TermGenie]
synonym: "negative regulation of arginine catabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of arginine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0033242 ! negative regulation of cellular amine catabolic process
+is_a: GO:0031330 ! negative regulation of cellular catabolic process
+is_a: GO:0033242 ! negative regulation of amine catabolic process
is_a: GO:0045763 ! negative regulation of cellular amino acid metabolic process
is_a: GO:1900081 ! regulation of arginine catabolic process
relationship: negatively_regulates GO:0006527 ! arginine catabolic process
@@ -423535,9 +426929,6 @@ synonym: "regulation of myo-inositol biosynthesis" NARROW [GOC:TermGenie]
synonym: "regulation of myo-inositol biosynthetic process" NARROW [GOC:TermGenie]
synonym: "regulation of vitamin Bh biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of vitamin Bh biosynthetic process" EXACT [GOC:TermGenie]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
-is_a: GO:0031326 ! regulation of cellular biosynthetic process
-is_a: GO:0043255 ! regulation of carbohydrate biosynthetic process
is_a: GO:1902930 ! regulation of alcohol biosynthetic process
relationship: regulates GO:0006021 ! inositol biosynthetic process
@@ -423590,8 +426981,6 @@ synonym: "negative regulation of myo-inositol biosynthesis" NARROW [GOC:TermGeni
synonym: "negative regulation of myo-inositol biosynthetic process" NARROW [GOC:TermGenie]
synonym: "negative regulation of vitamin Bh biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of vitamin Bh biosynthetic process" EXACT [GOC:TermGenie]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
-is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
is_a: GO:1900088 ! regulation of inositol biosynthetic process
is_a: GO:1902931 ! negative regulation of alcohol biosynthetic process
relationship: negatively_regulates GO:0006021 ! inositol biosynthetic process
@@ -423645,8 +427034,6 @@ synonym: "upregulation of myo-inositol biosynthesis" NARROW [GOC:TermGenie]
synonym: "upregulation of myo-inositol biosynthetic process" NARROW [GOC:TermGenie]
synonym: "upregulation of vitamin Bh biosynthesis" EXACT [GOC:TermGenie]
synonym: "upregulation of vitamin Bh biosynthetic process" EXACT [GOC:TermGenie]
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:1900088 ! regulation of inositol biosynthetic process
is_a: GO:1902932 ! positive regulation of alcohol biosynthetic process
relationship: positively_regulates GO:0006021 ! inositol biosynthetic process
@@ -423734,9 +427121,10 @@ relationship: positively_regulates GO:0033529 ! raffinose biosynthetic process
[Term]
id: GO:1900094
-name: regulation of transcription from RNA polymerase II promoter involved in determination of left/right symmetry
+name: obsolete regulation of transcription from RNA polymerase II promoter involved in determination of left/right symmetry
namespace: biological_process
-def: "Any regulation of transcription from RNA polymerase II promoter that is involved in determination of left/right symmetry." [GOC:BHF, GOC:TermGenie]
+def: "OBSOLETE. Any regulation of transcription from RNA polymerase II promoter that is involved in determination of left/right symmetry." [GOC:BHF, GOC:TermGenie]
+comment: This term has been obsoleted because it represents a GO-CAM model.
synonym: "global transcription regulation from Pol II promoter of determination of left/right asymmetry" RELATED [GOC:TermGenie]
synonym: "global transcription regulation from Pol II promoter of determination of left/right symmetry" RELATED [GOC:TermGenie]
synonym: "regulation of gene-specific transcription from RNA polymerase II promoter of determination of left/right asymmetry" RELATED [GOC:TermGenie]
@@ -423749,8 +427137,7 @@ synonym: "regulation of transcription from RNA polymerase II promoter of determi
synonym: "regulation of transcription from RNA polymerase II promoter of determination of left/right symmetry" EXACT [GOC:TermGenie]
synonym: "regulation of transcription from RNA polymerase II promoter, global of determination of left/right asymmetry" RELATED [GOC:TermGenie]
synonym: "regulation of transcription from RNA polymerase II promoter, global of determination of left/right symmetry" RELATED [GOC:TermGenie]
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-relationship: part_of GO:0007368 ! determination of left/right symmetry
+is_obsolete: true
[Term]
id: GO:1900095
@@ -423761,6 +427148,7 @@ synonym: "regulation of Barr body formation" RELATED [GOC:TermGenie]
synonym: "regulation of chromosome inactivation" BROAD [GOC:TermGenie]
synonym: "regulation of X chromosome inactivation" EXACT [GOC:TermGenie]
is_a: GO:0010468 ! regulation of gene expression
+is_a: GO:1902275 ! regulation of chromatin organization
relationship: regulates GO:0009048 ! dosage compensation by inactivation of X chromosome
[Term]
@@ -423787,8 +427175,8 @@ synonym: "inhibition of X chromosome inactivation" EXACT [GOC:TermGenie]
synonym: "negative regulation of Barr body formation" RELATED [GOC:TermGenie]
synonym: "negative regulation of chromosome inactivation" BROAD [GOC:TermGenie]
synonym: "negative regulation of X chromosome inactivation" EXACT [GOC:TermGenie]
-is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:1900095 ! regulation of dosage compensation by inactivation of X chromosome
+is_a: GO:1905268 ! negative regulation of chromatin organization
relationship: negatively_regulates GO:0009048 ! dosage compensation by inactivation of X chromosome
[Term]
@@ -423815,8 +427203,8 @@ synonym: "upregulation of Barr body formation" RELATED [GOC:TermGenie]
synonym: "upregulation of chromosome inactivation" BROAD [GOC:TermGenie]
synonym: "upregulation of dosage compensation, by inactivation of X chromosome" EXACT [GOC:TermGenie]
synonym: "upregulation of X chromosome inactivation" EXACT [GOC:TermGenie]
-is_a: GO:0048518 ! positive regulation of biological process
is_a: GO:1900095 ! regulation of dosage compensation by inactivation of X chromosome
+is_a: GO:1905269 ! positive regulation of chromatin organization
relationship: positively_regulates GO:0009048 ! dosage compensation by inactivation of X chromosome
[Term]
@@ -424606,7 +427994,6 @@ name: regulation of nodal signaling pathway involved in determination of left/ri
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of a nodal signaling pathway, where the nodal signaling pathway is involved in determination of left/right asymmetry." [GOC:BHF, GOC:signaling, GOC:TermGenie, GOC:vk]
synonym: "regulation of nodal signalling pathway involved in determination of left/right asymmetry" EXACT [GOC:mah]
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
is_a: GO:1900107 ! regulation of nodal signaling pathway
relationship: regulates GO:0038107 ! nodal signaling pathway involved in determination of left/right asymmetry
@@ -424928,13 +428315,14 @@ relationship: positively_regulates GO:0035630 ! bone mineralization involved in
[Term]
id: GO:1900160
-name: plastid DNA packaging
+name: plastid chromosome packaging
namespace: biological_process
-def: "Any process in which plastidial DNA and associated proteins are formed into a compact, orderly structure." [GOC:emb, GOC:TermGenie, PMID:12081370]
+def: "A process in which plastidial DNA and associated proteins organize into a compact, orderly structure." [GOC:emb, GOC:TermGenie, PMID:12081370]
synonym: "DNA organisation in plastid" EXACT [GOC:TermGenie]
synonym: "DNA organization in plastid" EXACT [GOC:TermGenie]
+synonym: "plastid DNA packaging" EXACT []
synonym: "plastidial DNA packaging" EXACT [GOC:emb]
-is_a: GO:0036385 ! nucleoid DNA packaging
+is_a: GO:0051276 ! chromosome organization
[Term]
id: GO:1900161
@@ -424974,7 +428362,7 @@ is_a: GO:1900161 ! regulation of phospholipid scramblase activity
id: GO:1900164
name: nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of a nodal protein to an activin receptor on the surface of a target cell, which contributes to the establishment of lateral mesoderm with respect to the left and right halves." [GOC:BHF, GOC:TermGenie, GOC:vk]
+def: "The series of molecular signals initiated by a nodal protein binding to an activin receptor on the surface of a target cell, which contributes to the establishment of lateral mesoderm with respect to the left and right halves." [GOC:BHF, GOC:TermGenie, GOC:vk]
synonym: "nodal signaling of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie]
synonym: "nodal signaling pathway of determination of left/right asymmetry in lateral mesoderm" EXACT [GOC:TermGenie]
synonym: "nodal signalling pathway involved in determination of lateral mesoderm left/right asymmetry" EXACT [GOC:mah]
@@ -425096,6 +428484,7 @@ synonym: "regulation of aflatoxin biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of aflatoxin formation" EXACT [GOC:TermGenie]
synonym: "regulation of aflatoxin synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031326 ! regulation of cellular biosynthetic process
+is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
is_a: GO:1900376 ! regulation of secondary metabolite biosynthetic process
relationship: regulates GO:0045122 ! aflatoxin biosynthetic process
@@ -425130,6 +428519,7 @@ synonym: "negative regulation of aflatoxin biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of aflatoxin formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of aflatoxin synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
+is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1900177 ! regulation of aflatoxin biosynthetic process
is_a: GO:1900377 ! negative regulation of secondary metabolite biosynthetic process
@@ -425165,6 +428555,7 @@ synonym: "upregulation of aflatoxin biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of aflatoxin formation" EXACT [GOC:TermGenie]
synonym: "upregulation of aflatoxin synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
+is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1900177 ! regulation of aflatoxin biosynthetic process
is_a: GO:1900378 ! positive regulation of secondary metabolite biosynthetic process
@@ -425179,7 +428570,6 @@ synonym: "regulation of protein localisation to nucleus" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in cell nucleus" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in nucleus" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0034504 ! protein localization to nucleus
[Term]
@@ -425206,7 +428596,6 @@ synonym: "inhibition of protein localization to nucleus" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to nucleus" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in cell nucleus" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in nucleus" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1900180 ! regulation of protein localization to nucleus
is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:0034504 ! protein localization to nucleus
@@ -425235,7 +428624,6 @@ synonym: "upregulation of protein localisation to nucleus" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization in cell nucleus" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization in nucleus" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to nucleus" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1900180 ! regulation of protein localization to nucleus
is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:0034504 ! protein localization to nucleus
@@ -426453,11 +429841,8 @@ synonym: "upregulation of MDA-5 signaling pathway" EXACT [GOC:TermGenie]
synonym: "upregulation of MDA5 signaling pathway" NARROW [GOC:TermGenie]
synonym: "upregulation of melanoma differentiation-associated gene 5 signaling pathway" EXACT [GOC:TermGenie]
is_a: GO:0002699 ! positive regulation of immune effector process
-is_a: GO:0002833 ! positive regulation of response to biotic stimulus
-is_a: GO:0032103 ! positive regulation of response to external stimulus
is_a: GO:0039533 ! regulation of MDA-5 signaling pathway
is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
-is_a: GO:1902533 ! positive regulation of intracellular signal transduction
relationship: positively_regulates GO:0039530 ! MDA-5 signaling pathway
[Term]
@@ -426480,11 +429865,8 @@ synonym: "up-regulation of RIG-I signaling pathway" EXACT [GOC:TermGenie]
synonym: "upregulation of DDX58 signaling pathway" EXACT [GOC:TermGenie]
synonym: "upregulation of retinoic acid inducible gene I signaling pathway" EXACT [GOC:TermGenie]
synonym: "upregulation of RIG-I signaling pathway" EXACT [GOC:TermGenie]
-is_a: GO:0002833 ! positive regulation of response to biotic stimulus
-is_a: GO:0032103 ! positive regulation of response to external stimulus
is_a: GO:0039535 ! regulation of RIG-I signaling pathway
is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
-is_a: GO:1902533 ! positive regulation of intracellular signal transduction
relationship: positively_regulates GO:0039529 ! RIG-I signaling pathway
[Term]
@@ -426567,15 +429949,11 @@ is_a: GO:2000273 ! positive regulation of signaling receptor activity
[Term]
id: GO:1900259
-name: regulation of RNA-directed 5'-3' RNA polymerase activity
+name: regulation of RNA-dependent RNA polymerase activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of RNA-directed 5'-3' RNA polymerase activity." [GOC:pf, GOC:TermGenie]
synonym: "regulation of 3D polymerase activity" EXACT [GOC:TermGenie]
synonym: "regulation of nucleoside-triphosphate:RNA nucleotidyltransferase (RNA-directed)" EXACT [GOC:TermGenie]
-synonym: "regulation of PB1 proteins" RELATED [GOC:TermGenie]
-synonym: "regulation of PB2 proteins" RELATED [GOC:TermGenie]
-synonym: "regulation of phage f2 replicase" NARROW [GOC:TermGenie]
-synonym: "regulation of polymerase L" RELATED [GOC:TermGenie]
synonym: "regulation of Q-beta replicase activity" EXACT [GOC:TermGenie]
synonym: "regulation of RDRP" RELATED [GOC:TermGenie]
synonym: "regulation of ribonucleic acid replicase activity" EXACT [GOC:TermGenie]
@@ -426587,25 +429965,21 @@ synonym: "regulation of RNA nucleotidyltransferase (RNA-directed) activity" EXAC
synonym: "regulation of RNA replicase activity" EXACT [GOC:TermGenie]
synonym: "regulation of RNA synthetase activity" RELATED [GOC:TermGenie]
synonym: "regulation of RNA-dependent ribonucleate nucleotidyltransferase activity" EXACT [GOC:TermGenie]
-synonym: "regulation of RNA-dependent RNA polymerase activity" EXACT [GOC:TermGenie]
synonym: "regulation of RNA-dependent RNA replicase activity" EXACT [GOC:TermGenie]
-synonym: "regulation of RNA-directed RNA polymerase activity" BROAD []
+synonym: "regulation of RNA-directed 5'-3' RNA polymerase activity" EXACT []
synonym: "regulation of transcriptase" BROAD [GOC:TermGenie]
is_a: GO:0051338 ! regulation of transferase activity
is_a: GO:1903506 ! regulation of nucleic acid-templated transcription
[Term]
id: GO:1900260
-name: negative regulation of RNA-directed 5'-3' RNA polymerase activity
+name: negative regulation of RNA-dependent RNA polymerase activity
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of RNA-directed 5'-3' RNA polymerase activity." [GOC:pf, GOC:TermGenie]
-synonym: "down regulation of 3D polymerase activity" EXACT [GOC:TermGenie]
-synonym: "down regulation of nucleoside-triphosphate:RNA nucleotidyltransferase (RNA-directed)" EXACT [GOC:TermGenie]
synonym: "down regulation of PB1 proteins" RELATED [GOC:TermGenie]
synonym: "down regulation of PB2 proteins" RELATED [GOC:TermGenie]
synonym: "down regulation of phage f2 replicase" NARROW [GOC:TermGenie]
synonym: "down regulation of polymerase L" RELATED [GOC:TermGenie]
-synonym: "down regulation of Q-beta replicase activity" EXACT [GOC:TermGenie]
synonym: "down regulation of RDRP" RELATED [GOC:TermGenie]
synonym: "down regulation of ribonucleic acid replicase activity" EXACT [GOC:TermGenie]
synonym: "down regulation of ribonucleic acid-dependent ribonucleate nucleotidyltransferase activity" EXACT [GOC:TermGenie]
@@ -426620,18 +429994,12 @@ synonym: "down regulation of RNA-dependent RNA polymerase activity" EXACT [GOC:T
synonym: "down regulation of RNA-dependent RNA replicase activity" EXACT [GOC:TermGenie]
synonym: "down regulation of RNA-directed RNA polymerase activity" EXACT [GOC:TermGenie]
synonym: "down regulation of transcriptase" BROAD [GOC:TermGenie]
-synonym: "down-regulation of 3D polymerase activity" EXACT [GOC:TermGenie]
-synonym: "down-regulation of nucleoside-triphosphate:RNA nucleotidyltransferase (RNA-directed)" EXACT [GOC:TermGenie]
synonym: "down-regulation of PB1 proteins" RELATED [GOC:TermGenie]
synonym: "down-regulation of PB2 proteins" RELATED [GOC:TermGenie]
synonym: "down-regulation of phage f2 replicase" NARROW [GOC:TermGenie]
synonym: "down-regulation of polymerase L" RELATED [GOC:TermGenie]
-synonym: "down-regulation of Q-beta replicase activity" EXACT [GOC:TermGenie]
synonym: "down-regulation of RDRP" RELATED [GOC:TermGenie]
synonym: "down-regulation of ribonucleic acid replicase activity" EXACT [GOC:TermGenie]
-synonym: "down-regulation of ribonucleic acid-dependent ribonucleate nucleotidyltransferase activity" EXACT [GOC:TermGenie]
-synonym: "down-regulation of ribonucleic acid-dependent ribonucleic acid polymerase activity" EXACT [GOC:TermGenie]
-synonym: "down-regulation of ribonucleic replicase activity" EXACT [GOC:TermGenie]
synonym: "down-regulation of ribonucleic synthetase activity" RELATED [GOC:TermGenie]
synonym: "down-regulation of RNA nucleotidyltransferase (RNA-directed) activity" EXACT [GOC:TermGenie]
synonym: "down-regulation of RNA replicase activity" EXACT [GOC:TermGenie]
@@ -426641,13 +430009,11 @@ synonym: "down-regulation of RNA-dependent RNA polymerase activity" EXACT [GOC:T
synonym: "down-regulation of RNA-dependent RNA replicase activity" EXACT [GOC:TermGenie]
synonym: "down-regulation of RNA-directed RNA polymerase activity" EXACT [GOC:TermGenie]
synonym: "down-regulation of transcriptase" BROAD [GOC:TermGenie]
-synonym: "downregulation of 3D polymerase activity" EXACT [GOC:TermGenie]
synonym: "downregulation of nucleoside-triphosphate:RNA nucleotidyltransferase (RNA-directed)" EXACT [GOC:TermGenie]
synonym: "downregulation of PB1 proteins" RELATED [GOC:TermGenie]
synonym: "downregulation of PB2 proteins" RELATED [GOC:TermGenie]
synonym: "downregulation of phage f2 replicase" NARROW [GOC:TermGenie]
synonym: "downregulation of polymerase L" RELATED [GOC:TermGenie]
-synonym: "downregulation of Q-beta replicase activity" EXACT [GOC:TermGenie]
synonym: "downregulation of RDRP" RELATED [GOC:TermGenie]
synonym: "downregulation of ribonucleic acid replicase activity" EXACT [GOC:TermGenie]
synonym: "downregulation of ribonucleic acid-dependent ribonucleate nucleotidyltransferase activity" EXACT [GOC:TermGenie]
@@ -426662,13 +430028,11 @@ synonym: "downregulation of RNA-dependent RNA polymerase activity" EXACT [GOC:Te
synonym: "downregulation of RNA-dependent RNA replicase activity" EXACT [GOC:TermGenie]
synonym: "downregulation of RNA-directed RNA polymerase activity" EXACT [GOC:TermGenie]
synonym: "downregulation of transcriptase" BROAD [GOC:TermGenie]
-synonym: "inhibition of 3D polymerase activity" EXACT [GOC:TermGenie]
synonym: "inhibition of nucleoside-triphosphate:RNA nucleotidyltransferase (RNA-directed)" EXACT [GOC:TermGenie]
synonym: "inhibition of PB1 proteins" RELATED [GOC:TermGenie]
synonym: "inhibition of PB2 proteins" RELATED [GOC:TermGenie]
synonym: "inhibition of phage f2 replicase" NARROW [GOC:TermGenie]
synonym: "inhibition of polymerase L" RELATED [GOC:TermGenie]
-synonym: "inhibition of Q-beta replicase activity" EXACT [GOC:TermGenie]
synonym: "inhibition of RDRP" RELATED [GOC:TermGenie]
synonym: "inhibition of ribonucleic acid replicase activity" EXACT [GOC:TermGenie]
synonym: "inhibition of ribonucleic acid-dependent ribonucleate nucleotidyltransferase activity" EXACT [GOC:TermGenie]
@@ -426689,7 +430053,6 @@ synonym: "negative regulation of PB1 proteins" RELATED [GOC:TermGenie]
synonym: "negative regulation of PB2 proteins" RELATED [GOC:TermGenie]
synonym: "negative regulation of phage f2 replicase" NARROW [GOC:TermGenie]
synonym: "negative regulation of polymerase L" RELATED [GOC:TermGenie]
-synonym: "negative regulation of Q-beta replicase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of RDRP" RELATED [GOC:TermGenie]
synonym: "negative regulation of ribonucleic acid replicase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of ribonucleic acid-dependent ribonucleate nucleotidyltransferase activity" EXACT [GOC:TermGenie]
@@ -426700,17 +430063,17 @@ synonym: "negative regulation of RNA nucleotidyltransferase (RNA-directed) activ
synonym: "negative regulation of RNA replicase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of RNA synthetase activity" RELATED [GOC:TermGenie]
synonym: "negative regulation of RNA-dependent ribonucleate nucleotidyltransferase activity" EXACT [GOC:TermGenie]
-synonym: "negative regulation of RNA-dependent RNA polymerase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of RNA-dependent RNA replicase activity" EXACT [GOC:TermGenie]
+synonym: "negative regulation of RNA-directed 5'-3' RNA polymerase activity" EXACT []
synonym: "negative regulation of RNA-directed RNA polymerase activity" BROAD []
synonym: "negative regulation of transcriptase" BROAD [GOC:TermGenie]
is_a: GO:0051348 ! negative regulation of transferase activity
-is_a: GO:1900259 ! regulation of RNA-directed 5'-3' RNA polymerase activity
+is_a: GO:1900259 ! regulation of RNA-dependent RNA polymerase activity
is_a: GO:1903507 ! negative regulation of nucleic acid-templated transcription
[Term]
id: GO:1900261
-name: positive regulation of RNA-directed 5'-3' RNA polymerase activity
+name: positive regulation of RNA-dependent RNA polymerase activity
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of RNA-directed 5'-3' RNA polymerase activity." [GOC:pf, GOC:TermGenie]
synonym: "activation of 3D polymerase activity" EXACT [GOC:TermGenie]
@@ -426719,7 +430082,6 @@ synonym: "activation of PB1 proteins" RELATED [GOC:TermGenie]
synonym: "activation of PB2 proteins" RELATED [GOC:TermGenie]
synonym: "activation of phage f2 replicase" NARROW [GOC:TermGenie]
synonym: "activation of polymerase L" RELATED [GOC:TermGenie]
-synonym: "activation of Q-beta replicase activity" EXACT [GOC:TermGenie]
synonym: "activation of RDRP" RELATED [GOC:TermGenie]
synonym: "activation of ribonucleic acid replicase activity" EXACT [GOC:TermGenie]
synonym: "activation of ribonucleic acid-dependent ribonucleate nucleotidyltransferase activity" EXACT [GOC:TermGenie]
@@ -426740,7 +430102,6 @@ synonym: "positive regulation of PB1 proteins" RELATED [GOC:TermGenie]
synonym: "positive regulation of PB2 proteins" RELATED [GOC:TermGenie]
synonym: "positive regulation of phage f2 replicase" NARROW [GOC:TermGenie]
synonym: "positive regulation of polymerase L" RELATED [GOC:TermGenie]
-synonym: "positive regulation of Q-beta replicase activity" EXACT [GOC:TermGenie]
synonym: "positive regulation of RDRP" RELATED [GOC:TermGenie]
synonym: "positive regulation of ribonucleic acid replicase activity" EXACT [GOC:TermGenie]
synonym: "positive regulation of ribonucleic acid-dependent ribonucleate nucleotidyltransferase activity" EXACT [GOC:TermGenie]
@@ -426751,8 +430112,8 @@ synonym: "positive regulation of RNA nucleotidyltransferase (RNA-directed) activ
synonym: "positive regulation of RNA replicase activity" EXACT [GOC:TermGenie]
synonym: "positive regulation of RNA synthetase activity" RELATED [GOC:TermGenie]
synonym: "positive regulation of RNA-dependent ribonucleate nucleotidyltransferase activity" EXACT [GOC:TermGenie]
-synonym: "positive regulation of RNA-dependent RNA polymerase activity" EXACT [GOC:TermGenie]
synonym: "positive regulation of RNA-dependent RNA replicase activity" EXACT [GOC:TermGenie]
+synonym: "positive regulation of RNA-directed 5'-3' RNA polymerase activity" EXACT []
synonym: "positive regulation of RNA-directed RNA polymerase activity" BROAD []
synonym: "positive regulation of transcriptase" BROAD [GOC:TermGenie]
synonym: "up regulation of 3D polymerase activity" EXACT [GOC:TermGenie]
@@ -426819,7 +430180,7 @@ synonym: "upregulation of RNA-dependent RNA replicase activity" EXACT [GOC:TermG
synonym: "upregulation of RNA-directed RNA polymerase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of transcriptase" BROAD [GOC:TermGenie]
is_a: GO:0051347 ! positive regulation of transferase activity
-is_a: GO:1900259 ! regulation of RNA-directed 5'-3' RNA polymerase activity
+is_a: GO:1900259 ! regulation of RNA-dependent RNA polymerase activity
[Term]
id: GO:1900262
@@ -426862,7 +430223,7 @@ synonym: "regulation of Tca DNA polymerase" NARROW [GOC:TermGenie]
synonym: "regulation of theta DNA polymerase activity" NARROW [GOC:TermGenie]
synonym: "regulation of zeta DNA polymerase activity" NARROW [GOC:TermGenie]
is_a: GO:0051338 ! regulation of transferase activity
-is_a: GO:0090329 ! regulation of DNA-dependent DNA replication
+is_a: GO:0090329 ! regulation of DNA-templated DNA replication
is_a: GO:2000278 ! regulation of DNA biosynthetic process
[Term]
@@ -427498,7 +430859,7 @@ name: regulation of cellobiose catabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of cellobiose catabolic process." [GOC:mengo_curators, GOC:TermGenie]
synonym: "regulation of cellobiose catabolism" EXACT [GOC:TermGenie]
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
is_a: GO:2000930 ! regulation of cellobiose metabolic process
relationship: regulates GO:2000892 ! cellobiose catabolic process
@@ -427516,7 +430877,7 @@ synonym: "downregulation of cellobiose catabolism" EXACT [GOC:TermGenie]
synonym: "inhibition of cellobiose catabolic process" NARROW [GOC:TermGenie]
synonym: "inhibition of cellobiose catabolism" NARROW [GOC:TermGenie]
synonym: "negative regulation of cellobiose catabolism" EXACT [GOC:TermGenie]
-is_a: GO:0031330 ! negative regulation of cellular catabolic process
+is_a: GO:0009895 ! negative regulation of catabolic process
is_a: GO:1900282 ! regulation of cellobiose catabolic process
is_a: GO:2000931 ! negative regulation of cellobiose metabolic process
relationship: negatively_regulates GO:2000892 ! cellobiose catabolic process
@@ -427535,7 +430896,7 @@ synonym: "up-regulation of cellobiose catabolic process" EXACT [GOC:TermGenie]
synonym: "up-regulation of cellobiose catabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of cellobiose catabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of cellobiose catabolism" EXACT [GOC:TermGenie]
-is_a: GO:0031331 ! positive regulation of cellular catabolic process
+is_a: GO:0009896 ! positive regulation of catabolic process
is_a: GO:1900282 ! regulation of cellobiose catabolic process
is_a: GO:2000932 ! positive regulation of cellobiose metabolic process
relationship: positively_regulates GO:2000892 ! cellobiose catabolic process
@@ -427759,37 +431120,35 @@ relationship: positively_regulates GO:2001102 ! hexasaccharide transport
[Term]
id: GO:1900300
-name: regulation of laminarabiose transport
+name: obsolete regulation of laminarabiose transport
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of laminarabiose transport." [GOC:mengo_curators, GOC:TermGenie]
-is_a: GO:0051049 ! regulation of transport
-relationship: regulates GO:2001086 ! laminarabiose transport
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of laminarabiose transport." [GOC:mengo_curators, GOC:TermGenie]
+comment: This term has been obsoleted because it does not represent an evolved process.
+is_obsolete: true
[Term]
id: GO:1900301
-name: negative regulation of laminarabiose transport
+name: obsolete negative regulation of laminarabiose transport
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of laminarabiose transport." [GOC:mengo_curators, GOC:TermGenie]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of laminarabiose transport." [GOC:mengo_curators, GOC:TermGenie]
+comment: This term has been obsoleted because it does not represent an evolved process.
synonym: "down regulation of laminarabiose transport" EXACT [GOC:TermGenie]
synonym: "down-regulation of laminarabiose transport" EXACT [GOC:TermGenie]
synonym: "downregulation of laminarabiose transport" EXACT [GOC:TermGenie]
synonym: "inhibition of laminarabiose transport" NARROW [GOC:TermGenie]
-is_a: GO:0051051 ! negative regulation of transport
-is_a: GO:1900300 ! regulation of laminarabiose transport
-relationship: negatively_regulates GO:2001086 ! laminarabiose transport
+is_obsolete: true
[Term]
id: GO:1900302
-name: positive regulation of laminarabiose transport
+name: obsolete positive regulation of laminarabiose transport
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of laminarabiose transport." [GOC:mengo_curators, GOC:TermGenie]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of laminarabiose transport." [GOC:mengo_curators, GOC:TermGenie]
+comment: This term has been obsoleted because it does not represent an evolved process.
synonym: "activation of laminarabiose transport" NARROW [GOC:TermGenie]
synonym: "up regulation of laminarabiose transport" EXACT [GOC:TermGenie]
synonym: "up-regulation of laminarabiose transport" EXACT [GOC:TermGenie]
synonym: "upregulation of laminarabiose transport" EXACT [GOC:TermGenie]
-is_a: GO:0051050 ! positive regulation of transport
-is_a: GO:1900300 ! regulation of laminarabiose transport
-relationship: positively_regulates GO:2001086 ! laminarabiose transport
+is_obsolete: true
[Term]
id: GO:1900303
@@ -427977,8 +431336,8 @@ id: GO:1900318
name: regulation of methane biosynthetic process from dimethylamine
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of methane biosynthetic process from dimethylamine." [GOC:mengo_curators, GOC:TermGenie]
+is_a: GO:0033238 ! regulation of amine metabolic process
is_a: GO:0043457 ! regulation of cellular respiration
-is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
is_a: GO:1901577 ! regulation of alkane biosynthetic process
relationship: regulates GO:2001129 ! methane biosynthetic process from dimethylamine
@@ -427991,7 +431350,7 @@ synonym: "down regulation of methane biosynthetic process from dimethylamine" EX
synonym: "down-regulation of methane biosynthetic process from dimethylamine" EXACT [GOC:TermGenie]
synonym: "downregulation of methane biosynthetic process from dimethylamine" EXACT [GOC:TermGenie]
synonym: "inhibition of methane biosynthetic process from dimethylamine" NARROW [GOC:TermGenie]
-is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
+is_a: GO:0033239 ! negative regulation of amine metabolic process
is_a: GO:1900318 ! regulation of methane biosynthetic process from dimethylamine
is_a: GO:1901578 ! negative regulation of alkane biosynthetic process
is_a: GO:1901856 ! negative regulation of cellular respiration
@@ -428006,7 +431365,7 @@ synonym: "activation of methane biosynthetic process from dimethylamine" NARROW
synonym: "up regulation of methane biosynthetic process from dimethylamine" EXACT [GOC:TermGenie]
synonym: "up-regulation of methane biosynthetic process from dimethylamine" EXACT [GOC:TermGenie]
synonym: "upregulation of methane biosynthetic process from dimethylamine" EXACT [GOC:TermGenie]
-is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
+is_a: GO:0033240 ! positive regulation of amine metabolic process
is_a: GO:1900318 ! regulation of methane biosynthetic process from dimethylamine
is_a: GO:1901579 ! positive regulation of alkane biosynthetic process
is_a: GO:1901857 ! positive regulation of cellular respiration
@@ -428119,8 +431478,8 @@ id: GO:1900330
name: regulation of methane biosynthetic process from trimethylamine
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of methane biosynthetic process from trimethylamine." [GOC:mengo_curators, GOC:TermGenie]
+is_a: GO:0033238 ! regulation of amine metabolic process
is_a: GO:0043457 ! regulation of cellular respiration
-is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
is_a: GO:1901577 ! regulation of alkane biosynthetic process
relationship: regulates GO:2001130 ! methane biosynthetic process from trimethylamine
@@ -428133,7 +431492,7 @@ synonym: "down regulation of methane biosynthetic process from trimethylamine" E
synonym: "down-regulation of methane biosynthetic process from trimethylamine" EXACT [GOC:TermGenie]
synonym: "downregulation of methane biosynthetic process from trimethylamine" EXACT [GOC:TermGenie]
synonym: "inhibition of methane biosynthetic process from trimethylamine" NARROW [GOC:TermGenie]
-is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
+is_a: GO:0033239 ! negative regulation of amine metabolic process
is_a: GO:1900330 ! regulation of methane biosynthetic process from trimethylamine
is_a: GO:1901578 ! negative regulation of alkane biosynthetic process
is_a: GO:1901856 ! negative regulation of cellular respiration
@@ -428148,7 +431507,7 @@ synonym: "activation of methane biosynthetic process from trimethylamine" NARROW
synonym: "up regulation of methane biosynthetic process from trimethylamine" EXACT [GOC:TermGenie]
synonym: "up-regulation of methane biosynthetic process from trimethylamine" EXACT [GOC:TermGenie]
synonym: "upregulation of methane biosynthetic process from trimethylamine" EXACT [GOC:TermGenie]
-is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
+is_a: GO:0033240 ! positive regulation of amine metabolic process
is_a: GO:1900330 ! regulation of methane biosynthetic process from trimethylamine
is_a: GO:1901579 ! positive regulation of alkane biosynthetic process
is_a: GO:1901857 ! positive regulation of cellular respiration
@@ -428241,6 +431600,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of methane biosynthetic process from formic acid." [GOC:mengo_curators, GOC:TermGenie]
is_a: GO:0010565 ! regulation of cellular ketone metabolic process
is_a: GO:0043457 ! regulation of cellular respiration
+is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
is_a: GO:1901577 ! regulation of alkane biosynthetic process
relationship: regulates GO:2001127 ! methane biosynthetic process from formic acid
@@ -428253,6 +431613,7 @@ synonym: "down regulation of methane biosynthetic process from formic acid" EXAC
synonym: "down-regulation of methane biosynthetic process from formic acid" EXACT [GOC:TermGenie]
synonym: "downregulation of methane biosynthetic process from formic acid" EXACT [GOC:TermGenie]
synonym: "inhibition of methane biosynthetic process from formic acid" NARROW [GOC:TermGenie]
+is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1900339 ! regulation of methane biosynthetic process from formic acid
is_a: GO:1901578 ! negative regulation of alkane biosynthetic process
@@ -428268,6 +431629,7 @@ synonym: "activation of methane biosynthetic process from formic acid" NARROW [G
synonym: "up regulation of methane biosynthetic process from formic acid" EXACT [GOC:TermGenie]
synonym: "up-regulation of methane biosynthetic process from formic acid" EXACT [GOC:TermGenie]
synonym: "upregulation of methane biosynthetic process from formic acid" EXACT [GOC:TermGenie]
+is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1900339 ! regulation of methane biosynthetic process from formic acid
is_a: GO:1901579 ! positive regulation of alkane biosynthetic process
@@ -428359,8 +431721,8 @@ id: GO:1900348
name: regulation of methane biosynthetic process from methylamine
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of methane biosynthetic process from methylamine." [GOC:mengo_curators, GOC:TermGenie]
+is_a: GO:0033238 ! regulation of amine metabolic process
is_a: GO:0043457 ! regulation of cellular respiration
-is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
is_a: GO:1901577 ! regulation of alkane biosynthetic process
relationship: regulates GO:2001128 ! methane biosynthetic process from methylamine
@@ -428373,7 +431735,7 @@ synonym: "down regulation of methane biosynthetic process from methylamine" EXAC
synonym: "down-regulation of methane biosynthetic process from methylamine" EXACT [GOC:TermGenie]
synonym: "downregulation of methane biosynthetic process from methylamine" EXACT [GOC:TermGenie]
synonym: "inhibition of methane biosynthetic process from methylamine" NARROW [GOC:TermGenie]
-is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
+is_a: GO:0033239 ! negative regulation of amine metabolic process
is_a: GO:1900348 ! regulation of methane biosynthetic process from methylamine
is_a: GO:1901578 ! negative regulation of alkane biosynthetic process
is_a: GO:1901856 ! negative regulation of cellular respiration
@@ -428388,7 +431750,7 @@ synonym: "activation of methane biosynthetic process from methylamine" NARROW [G
synonym: "up regulation of methane biosynthetic process from methylamine" EXACT [GOC:TermGenie]
synonym: "up-regulation of methane biosynthetic process from methylamine" EXACT [GOC:TermGenie]
synonym: "upregulation of methane biosynthetic process from methylamine" EXACT [GOC:TermGenie]
-is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
+is_a: GO:0033240 ! positive regulation of amine metabolic process
is_a: GO:1900348 ! regulation of methane biosynthetic process from methylamine
is_a: GO:1901579 ! positive regulation of alkane biosynthetic process
is_a: GO:1901857 ! positive regulation of cellular respiration
@@ -428657,61 +432019,57 @@ relationship: positively_regulates GO:0002213 ! defense response to insect
[Term]
id: GO:1900368
-name: regulation of RNA interference
+name: regulation of post-transcriptional gene silencing by RNA
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of RNA interference." [GOC:kmv, GOC:TermGenie, PMID:22412382]
-synonym: "regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie]
+def: "Any process that modulates the frequency, rate or extent of post-transcriptional gene silencing by RNA." [GOC:kmv, GOC:TermGenie, PMID:22412382]
+synonym: "regulation of PTGS" EXACT []
+synonym: "regulation of RNA interference" EXACT []
synonym: "regulation of RNAi" EXACT [GOC:TermGenie]
-is_a: GO:0060147 ! regulation of posttranscriptional gene silencing
+is_a: GO:0060147 ! regulation of post-transcriptional gene silencing
is_a: GO:0060966 ! regulation of gene silencing by RNA
-relationship: regulates GO:0016246 ! RNA interference
+relationship: regulates GO:0035194 ! ncRNA-mediated post-transcriptional gene silencing
[Term]
id: GO:1900369
-name: negative regulation of RNA interference
+name: negative regulation of post-transcriptional gene silencing by RNA
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of RNA interference." [GOC:kmv, GOC:TermGenie, PMID:22412382]
-synonym: "down regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of post-transcriptional gene silencing by RNA." [GOC:kmv, GOC:TermGenie, PMID:22412382]
synonym: "down regulation of RNA interference" EXACT [GOC:TermGenie]
synonym: "down regulation of RNAi" EXACT [GOC:TermGenie]
-synonym: "down-regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie]
synonym: "down-regulation of RNA interference" EXACT [GOC:TermGenie]
synonym: "down-regulation of RNAi" EXACT [GOC:TermGenie]
-synonym: "downregulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie]
synonym: "downregulation of RNA interference" EXACT [GOC:TermGenie]
synonym: "downregulation of RNAi" EXACT [GOC:TermGenie]
-synonym: "inhibition of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie]
synonym: "inhibition of RNA interference" NARROW [GOC:TermGenie]
synonym: "inhibition of RNAi" EXACT [GOC:TermGenie]
-synonym: "negative regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie]
+synonym: "negative regulation of posttranscriptional gene silencing by siRNA" NARROW [GOC:TermGenie]
+synonym: "negative regulation of PTGS" EXACT []
+synonym: "negative regulation of RNA interference" EXACT []
synonym: "negative regulation of RNAi" EXACT [GOC:TermGenie]
-is_a: GO:0060149 ! negative regulation of posttranscriptional gene silencing
+is_a: GO:0060149 ! negative regulation of post-transcriptional gene silencing
is_a: GO:0060967 ! negative regulation of gene silencing by RNA
-is_a: GO:1900368 ! regulation of RNA interference
-relationship: negatively_regulates GO:0016246 ! RNA interference
+is_a: GO:1900368 ! regulation of post-transcriptional gene silencing by RNA
+relationship: negatively_regulates GO:0035194 ! ncRNA-mediated post-transcriptional gene silencing
[Term]
id: GO:1900370
-name: positive regulation of RNA interference
+name: positive regulation of post-transcriptional gene silencing by RNA
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of RNA interference." [GOC:kmv, GOC:TermGenie, PMID:22412382]
-synonym: "activation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie]
+def: "Any process that activates or increases the frequency, rate or extent of post-transcriptional gene silencing by RNA." [GOC:kmv, GOC:TermGenie, PMID:22412382]
synonym: "activation of RNA interference" NARROW [GOC:TermGenie]
synonym: "activation of RNAi" EXACT [GOC:TermGenie]
-synonym: "positive regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie]
+synonym: "positive regulation of PTGS" EXACT []
+synonym: "positive regulation of RNA interference" EXACT []
synonym: "positive regulation of RNAi" EXACT [GOC:TermGenie]
-synonym: "up regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie]
synonym: "up regulation of RNA interference" EXACT [GOC:TermGenie]
synonym: "up regulation of RNAi" EXACT [GOC:TermGenie]
-synonym: "up-regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie]
synonym: "up-regulation of RNA interference" EXACT [GOC:TermGenie]
synonym: "up-regulation of RNAi" EXACT [GOC:TermGenie]
-synonym: "upregulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie]
synonym: "upregulation of RNA interference" EXACT [GOC:TermGenie]
synonym: "upregulation of RNAi" EXACT [GOC:TermGenie]
-is_a: GO:0060148 ! positive regulation of posttranscriptional gene silencing
-is_a: GO:1900368 ! regulation of RNA interference
-relationship: positively_regulates GO:0016246 ! RNA interference
+is_a: GO:0060148 ! positive regulation of post-transcriptional gene silencing
+is_a: GO:1900368 ! regulation of post-transcriptional gene silencing by RNA
+relationship: positively_regulates GO:0035194 ! ncRNA-mediated post-transcriptional gene silencing
[Term]
id: GO:1900371
@@ -429346,18 +432704,17 @@ relationship: positively_regulates GO:0006221 ! pyrimidine nucleotide biosynthet
[Term]
id: GO:1900400
-name: regulation of iron ion import into cell by regulation of transcription from RNA polymerase II promoter
+name: obsolete regulation of iron ion import into cell by regulation of transcription from RNA polymerase II promoter
namespace: biological_process
alt_id: GO:1900393
-def: "A regulation of transcription from RNA polymerase II promoter that results in regulation of iron ion import." [GOC:mah, GOC:TermGenie, PMID:18622392]
+def: "OBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in regulation of iron ion import." [GOC:mah, GOC:TermGenie, PMID:18622392]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "regulation of iron import by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie]
synonym: "regulation of iron ion import by regulation of transcription from RNA polymerase II promoter" RELATED []
synonym: "regulation of iron ion transport by regulation of transcription from RNA polymerase II promoter" BROAD []
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-is_a: GO:0034756 ! regulation of iron ion transport
-is_a: GO:0060341 ! regulation of cellular localization
-is_a: GO:0065008 ! regulation of biological quality
-relationship: regulates GO:0033212 ! iron import into cell
+is_obsolete: true
+consider: GO:0006357
+consider: GO:0033212
[Term]
id: GO:1900402
@@ -429383,23 +432740,23 @@ is_obsolete: true
[Term]
id: GO:1900404
-name: positive regulation of DNA repair by positive regulation of transcription from RNA polymerase II promoter
+name: obsolete positive regulation of DNA repair by positive regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "A positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of DNA repair." [GOC:mah, GOC:TermGenie, PMID:20299455]
+def: "OBSOLETE. A positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of DNA repair." [GOC:mah, GOC:TermGenie, PMID:20299455]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "activation of DNA repair by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie]
synonym: "stimulation of DNA repair by positive regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie]
synonym: "up regulation of DNA repair by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "up-regulation of DNA repair by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "upregulation of DNA repair by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
-is_a: GO:0045739 ! positive regulation of DNA repair
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
-relationship: positively_regulates GO:0100026 ! positive regulation of DNA repair by transcription from RNA polymerase II promoter
+is_obsolete: true
+consider: GO:0006281
[Term]
id: GO:1900405
name: obsolete regulation of cell separation after cytokinesis by regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "OBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in regulation of cell separation after cytokinesis." [GOC:mah, GOC:TermGenie, PMID:10491317, PMID:12665550]
+def: "OBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in regulation of cell separation after cytokinesis." [GOC:mah, GOC:TermGenie, PMID:10491317, PMID:12665550]
synonym: "regulation of cytokinetic cell separation by regulation of transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie]
is_obsolete: true
@@ -429562,9 +432919,9 @@ id: GO:1900419
name: regulation of cellular alcohol catabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of cellular alcohol catabolic process." [GOC:TermGenie]
-is_a: GO:0031329 ! regulation of cellular catabolic process
+is_a: GO:0009894 ! regulation of catabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
-relationship: regulates GO:0044109 ! cellular alcohol catabolic process
+relationship: regulates GO:0046164 ! alcohol catabolic process
[Term]
id: GO:1900420
@@ -429575,10 +432932,10 @@ synonym: "down regulation of cellular alcohol catabolic process" EXACT [GOC:Term
synonym: "down-regulation of cellular alcohol catabolic process" EXACT [GOC:TermGenie]
synonym: "downregulation of cellular alcohol catabolic process" EXACT [GOC:TermGenie]
synonym: "inhibition of cellular alcohol catabolic process" NARROW [GOC:TermGenie]
-is_a: GO:0031330 ! negative regulation of cellular catabolic process
+is_a: GO:0009895 ! negative regulation of catabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1900419 ! regulation of cellular alcohol catabolic process
-relationship: negatively_regulates GO:0044109 ! cellular alcohol catabolic process
+relationship: negatively_regulates GO:0046164 ! alcohol catabolic process
[Term]
id: GO:1900421
@@ -429589,10 +432946,10 @@ synonym: "activation of cellular alcohol catabolic process" NARROW [GOC:TermGeni
synonym: "up regulation of cellular alcohol catabolic process" EXACT [GOC:TermGenie]
synonym: "up-regulation of cellular alcohol catabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of cellular alcohol catabolic process" EXACT [GOC:TermGenie]
-is_a: GO:0031331 ! positive regulation of cellular catabolic process
+is_a: GO:0009896 ! positive regulation of catabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1900419 ! regulation of cellular alcohol catabolic process
-relationship: positively_regulates GO:0044109 ! cellular alcohol catabolic process
+relationship: positively_regulates GO:0046164 ! alcohol catabolic process
[Term]
id: GO:1900422
@@ -430186,22 +433543,26 @@ is_obsolete: true
[Term]
id: GO:1900463
-name: negative regulation of cellular response to alkaline pH by negative regulation of transcription from RNA polymerase II promoter
+name: obsolete negative regulation of cellular response to alkaline pH by negative regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular response to alkalinity by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:12509465, PMID:17023428]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of cellular response to alkalinity by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:12509465, PMID:17023428]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "negative regulation of cellular response to alkalinity by negative regulation of transcription from RNA polymerase II promoter" BROAD []
synonym: "negative regulation of cellular response to basic pH by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
-is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:1900068 ! negative regulation of cellular response to alkaline pH
+is_obsolete: true
+consider: GO:0000122
+consider: GO:0071469
[Term]
id: GO:1900464
-name: negative regulation of cellular hyperosmotic salinity response by negative regulation of transcription from RNA polymerase II promoter
+name: obsolete negative regulation of cellular hyperosmotic salinity response by negative regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular hyperosmotic salinity response by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:16278455]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of cellular hyperosmotic salinity response by stopping, preventing, or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dgf, GOC:TermGenie, PMID:16278455]
+comment: This term was obsoleted because it represents a GO-CAM model
synonym: "negative regulation of cellular response to hyperosmotic salt stress by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
-is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:1900070 ! negative regulation of cellular hyperosmotic salinity response
+is_obsolete: true
+consider: GO:0000122
+consider: GO:0071475
[Term]
id: GO:1900465
@@ -430264,6 +433625,7 @@ synonym: "regulation of phosphatidylserine anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of phosphatidylserine biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of phosphatidylserine formation" EXACT [GOC:TermGenie]
synonym: "regulation of phosphatidylserine synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0071071 ! regulation of phospholipid biosynthetic process
is_a: GO:0150178 ! regulation of phosphatidylserine metabolic process
relationship: regulates GO:0006659 ! phosphatidylserine biosynthetic process
@@ -430297,6 +433659,7 @@ synonym: "negative regulation of phosphatidylserine anabolism" EXACT [GOC:TermGe
synonym: "negative regulation of phosphatidylserine biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of phosphatidylserine formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of phosphatidylserine synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
is_a: GO:0071072 ! negative regulation of phospholipid biosynthetic process
is_a: GO:0150180 ! negative regulation of phosphatidylserine metabolic process
is_a: GO:1900468 ! regulation of phosphatidylserine biosynthetic process
@@ -430331,6 +433694,7 @@ synonym: "upregulation of phosphatidylserine biosynthesis" EXACT [GOC:TermGenie]
synonym: "upregulation of phosphatidylserine biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of phosphatidylserine formation" EXACT [GOC:TermGenie]
synonym: "upregulation of phosphatidylserine synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:0071073 ! positive regulation of phospholipid biosynthetic process
is_a: GO:0150179 ! positive regulation of phosphatidylserine metabolic process
is_a: GO:1900468 ! regulation of phosphatidylserine biosynthetic process
@@ -430571,7 +433935,7 @@ synonym: "upregulation of isopentenyl diphosphate anabolism, mevalonate pathway"
synonym: "upregulation of isopentenyl diphosphate biosynthetic process, mevalonate pathway" EXACT [GOC:TermGenie]
synonym: "upregulation of isopentenyl diphosphate formation, mevalonate pathway" EXACT [GOC:TermGenie]
synonym: "upregulation of isopentenyl diphosphate synthesis, mevalonate pathway" EXACT [GOC:TermGenie]
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0045828 ! positive regulation of isoprenoid metabolic process
is_a: GO:0051176 ! positive regulation of sulfur metabolic process
is_a: GO:0071073 ! positive regulation of phospholipid biosynthetic process
@@ -430739,7 +434103,7 @@ synonym: "downregulation of butyryl-CoA biosynthetic process from acetyl-CoA" EX
synonym: "inhibition of butyryl-CoA biosynthesis from acetyl-CoA" EXACT [GOC:TermGenie]
synonym: "inhibition of butyryl-CoA biosynthetic process from acetyl-CoA" NARROW [GOC:TermGenie]
synonym: "negative regulation of butyryl-CoA biosynthesis from acetyl-CoA" EXACT [GOC:TermGenie]
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0045717 ! negative regulation of fatty acid biosynthetic process
is_a: GO:0051175 ! negative regulation of sulfur metabolic process
is_a: GO:1900372 ! negative regulation of purine nucleotide biosynthetic process
@@ -430760,7 +434124,7 @@ synonym: "up-regulation of butyryl-CoA biosynthesis from acetyl-CoA" EXACT [GOC:
synonym: "up-regulation of butyryl-CoA biosynthetic process from acetyl-CoA" EXACT [GOC:TermGenie]
synonym: "upregulation of butyryl-CoA biosynthesis from acetyl-CoA" EXACT [GOC:TermGenie]
synonym: "upregulation of butyryl-CoA biosynthetic process from acetyl-CoA" EXACT [GOC:TermGenie]
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0045723 ! positive regulation of fatty acid biosynthetic process
is_a: GO:0051176 ! positive regulation of sulfur metabolic process
is_a: GO:1900373 ! positive regulation of purine nucleotide biosynthetic process
@@ -430775,7 +434139,7 @@ def: "Any process that modulates the frequency, rate or extent of butyryl-CoA ca
synonym: "regulation of butyryl-CoA catabolism to butanol" EXACT [GOC:TermGenie]
is_a: GO:0019217 ! regulation of fatty acid metabolic process
is_a: GO:0033121 ! regulation of purine nucleotide catabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0042762 ! regulation of sulfur metabolic process
is_a: GO:0046890 ! regulation of lipid biosynthetic process
is_a: GO:0050994 ! regulation of lipid catabolic process
@@ -430797,7 +434161,7 @@ synonym: "inhibition of butyryl-CoA catabolic process to butanol" NARROW [GOC:Te
synonym: "inhibition of butyryl-CoA catabolism to butanol" EXACT [GOC:TermGenie]
synonym: "negative regulation of butyryl-CoA catabolism to butanol" EXACT [GOC:TermGenie]
is_a: GO:0033122 ! negative regulation of purine nucleotide catabolic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0045922 ! negative regulation of fatty acid metabolic process
is_a: GO:0050995 ! negative regulation of lipid catabolic process
is_a: GO:0051055 ! negative regulation of lipid biosynthetic process
@@ -430821,7 +434185,7 @@ synonym: "up-regulation of butyryl-CoA catabolism to butanol" EXACT [GOC:TermGen
synonym: "upregulation of butyryl-CoA catabolic process to butanol" EXACT [GOC:TermGenie]
synonym: "upregulation of butyryl-CoA catabolism to butanol" EXACT [GOC:TermGenie]
is_a: GO:0033123 ! positive regulation of purine nucleotide catabolic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0045923 ! positive regulation of fatty acid metabolic process
is_a: GO:0046889 ! positive regulation of lipid biosynthetic process
is_a: GO:0050996 ! positive regulation of lipid catabolic process
@@ -430837,7 +434201,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of butyryl-CoA catabolic process to butyrate." [GOC:mengo_curators, GOC:TermGenie]
synonym: "regulation of butyryl-CoA catabolism to butyrate" EXACT [GOC:TermGenie]
is_a: GO:0033121 ! regulation of purine nucleotide catabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0042304 ! regulation of fatty acid biosynthetic process
is_a: GO:0042762 ! regulation of sulfur metabolic process
is_a: GO:0050994 ! regulation of lipid catabolic process
@@ -430858,7 +434222,7 @@ synonym: "inhibition of butyryl-CoA catabolic process to butyrate" NARROW [GOC:T
synonym: "inhibition of butyryl-CoA catabolism to butyrate" EXACT [GOC:TermGenie]
synonym: "negative regulation of butyryl-CoA catabolism to butyrate" EXACT [GOC:TermGenie]
is_a: GO:0033122 ! negative regulation of purine nucleotide catabolic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0045717 ! negative regulation of fatty acid biosynthetic process
is_a: GO:0050995 ! negative regulation of lipid catabolic process
is_a: GO:0051175 ! negative regulation of sulfur metabolic process
@@ -430880,7 +434244,7 @@ synonym: "up-regulation of butyryl-CoA catabolism to butyrate" EXACT [GOC:TermGe
synonym: "upregulation of butyryl-CoA catabolic process to butyrate" EXACT [GOC:TermGenie]
synonym: "upregulation of butyryl-CoA catabolism to butyrate" EXACT [GOC:TermGenie]
is_a: GO:0033123 ! positive regulation of purine nucleotide catabolic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0045723 ! positive regulation of fatty acid biosynthetic process
is_a: GO:0050996 ! positive regulation of lipid catabolic process
is_a: GO:0051176 ! positive regulation of sulfur metabolic process
@@ -431016,7 +434380,7 @@ name: regulation of pentose catabolic process to ethanol
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of pentose catabolic process to ethanol." [GOC:mengo_curators, GOC:TermGenie]
synonym: "regulation of pentose catabolism to ethanol" EXACT [GOC:TermGenie]
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
is_a: GO:1902930 ! regulation of alcohol biosynthetic process
relationship: regulates GO:0044576 ! pentose catabolic process to ethanol
@@ -431035,7 +434399,7 @@ synonym: "inhibition of pentose catabolic process to ethanol" NARROW [GOC:TermGe
synonym: "inhibition of pentose catabolism to ethanol" EXACT [GOC:TermGenie]
synonym: "negative regulation of pentose catabolism to ethanol" EXACT [GOC:TermGenie]
is_a: GO:0009895 ! negative regulation of catabolic process
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:1900509 ! regulation of pentose catabolic process to ethanol
is_a: GO:1902931 ! negative regulation of alcohol biosynthetic process
relationship: negatively_regulates GO:0044576 ! pentose catabolic process to ethanol
@@ -431055,7 +434419,7 @@ synonym: "up-regulation of pentose catabolism to ethanol" EXACT [GOC:TermGenie]
synonym: "upregulation of pentose catabolic process to ethanol" EXACT [GOC:TermGenie]
synonym: "upregulation of pentose catabolism to ethanol" EXACT [GOC:TermGenie]
is_a: GO:0009896 ! positive regulation of catabolic process
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:1900509 ! regulation of pentose catabolic process to ethanol
is_a: GO:1902932 ! positive regulation of alcohol biosynthetic process
relationship: positively_regulates GO:0044576 ! pentose catabolic process to ethanol
@@ -431447,8 +434811,8 @@ name: fumonisin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving fumonisin." [GOC:TermGenie]
synonym: "fumonisin metabolism" RELATED []
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0019748 ! secondary metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
[Term]
id: GO:1900540
@@ -431458,7 +434822,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of fumonisi
synonym: "fumonisin breakdown" EXACT []
synonym: "fumonisin catabolism" EXACT []
synonym: "fumonisin degradation" RELATED []
-is_a: GO:0016054 ! organic acid catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:0090487 ! secondary metabolite catabolic process
is_a: GO:1900539 ! fumonisin metabolic process
@@ -431471,8 +434835,8 @@ synonym: "fumonisin anabolism" EXACT []
synonym: "fumonisin biosynthesis" EXACT []
synonym: "fumonisin formation" EXACT []
synonym: "fumonisin synthesis" EXACT []
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0044550 ! secondary metabolite biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:1900539 ! fumonisin metabolic process
[Term]
@@ -431581,7 +434945,7 @@ is_obsolete: true
id: GO:1900548
name: heme B catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of heme b, a Fe(II) porphyrin complex readily isolated from the hemoglobin of beef blood, but also found in other proteins including other hemoglobins, myoglobins, cytochromes P-450, catalases, peroxidases as well as b type cytochromes." [GOC:TermGenie, GOC:yaf, PMID:28352909, UniPathway:UPA00684]
+def: "The chemical reactions and pathways resulting in the breakdown of heme b, a Fe(II) porphyrin complex readily isolated from the hemoglobin of beef blood, but also found in other proteins including other hemoglobins, myoglobins, cytochromes P-450, catalases, peroxidases as well as b type cytochromes." [GOC:TermGenie, GOC:yaf, PMID:28352909]
synonym: "heme B breakdown" EXACT [GOC:TermGenie]
synonym: "heme B catabolism" EXACT [GOC:TermGenie]
synonym: "heme B degradation" EXACT [GOC:TermGenie]
@@ -431681,6 +435045,7 @@ synonym: "emericellamide metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006629 ! lipid metabolic process
is_a: GO:0019748 ! secondary metabolic process
is_a: GO:0050761 ! depsipeptide metabolic process
+is_a: GO:0072338 ! lactam metabolic process
is_a: GO:1901334 ! lactone metabolic process
[Term]
@@ -431693,6 +435058,7 @@ synonym: "emericellamide catabolism" EXACT [GOC:TermGenie]
synonym: "emericellamide degradation" EXACT [GOC:TermGenie]
is_a: GO:0016042 ! lipid catabolic process
is_a: GO:0050762 ! depsipeptide catabolic process
+is_a: GO:0072340 ! lactam catabolic process
is_a: GO:0090487 ! secondary metabolite catabolic process
is_a: GO:1900555 ! emericellamide metabolic process
is_a: GO:1901335 ! lactone catabolic process
@@ -431709,6 +435075,7 @@ synonym: "emericellamide synthesis" EXACT [GOC:TermGenie]
is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:0044550 ! secondary metabolite biosynthetic process
is_a: GO:0050763 ! depsipeptide biosynthetic process
+is_a: GO:0072339 ! lactam biosynthetic process
is_a: GO:1900555 ! emericellamide metabolic process
is_a: GO:1901336 ! lactone biosynthetic process
@@ -431790,32 +435157,27 @@ is_a: GO:1901360 ! organic cyclic compound metabolic process
[Term]
id: GO:1900565
-name: chanoclavine-I catabolic process
+name: obsolete chanoclavine-I catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of chanoclavine-I." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of chanoclavine-I." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "chanoclavine-I breakdown" EXACT [GOC:TermGenie]
synonym: "chanoclavine-I catabolism" EXACT [GOC:TermGenie]
synonym: "chanoclavine-I degradation" EXACT [GOC:TermGenie]
-is_a: GO:0034310 ! primary alcohol catabolic process
-is_a: GO:0046700 ! heterocycle catabolic process
-is_a: GO:1900564 ! chanoclavine-I metabolic process
-is_a: GO:1900806 ! ergot alkaloid catabolic process
-is_a: GO:1901361 ! organic cyclic compound catabolic process
+is_obsolete: true
[Term]
id: GO:1900566
-name: chanoclavine-I biosynthetic process
+name: obsolete chanoclavine-I biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of chanoclavine-I." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of chanoclavine-I." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "chanoclavine-I anabolism" EXACT [GOC:TermGenie]
synonym: "chanoclavine-I biosynthesis" EXACT [GOC:TermGenie]
synonym: "chanoclavine-I formation" EXACT [GOC:TermGenie]
synonym: "chanoclavine-I synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0018130 ! heterocycle biosynthetic process
-is_a: GO:0034309 ! primary alcohol biosynthetic process
-is_a: GO:0035837 ! ergot alkaloid biosynthetic process
-is_a: GO:1900564 ! chanoclavine-I metabolic process
-is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+is_obsolete: true
+replaced_by: GO:1900809
[Term]
id: GO:1900567
@@ -431825,32 +435187,31 @@ def: "The chemical reactions and pathways involving chanoclavine-I aldehyde." [G
synonym: "chanoclavine-I aldehyde metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006081 ! cellular aldehyde metabolic process
is_a: GO:0035836 ! ergot alkaloid metabolic process
+is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:0120254 ! olefinic compound metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
[Term]
id: GO:1900568
-name: chanoclavine-I aldehyde catabolic process
+name: obsolete chanoclavine-I aldehyde catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of chanoclavine-I aldehyde." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of chanoclavine-I aldehyde." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "chanoclavine-I aldehyde breakdown" EXACT [GOC:TermGenie]
synonym: "chanoclavine-I aldehyde catabolism" EXACT [GOC:TermGenie]
synonym: "chanoclavine-I aldehyde degradation" EXACT [GOC:TermGenie]
-is_a: GO:0046185 ! aldehyde catabolic process
-is_a: GO:0120256 ! olefinic compound catabolic process
-is_a: GO:1900567 ! chanoclavine-I aldehyde metabolic process
-is_a: GO:1900806 ! ergot alkaloid catabolic process
-is_a: GO:1901361 ! organic cyclic compound catabolic process
+is_obsolete: true
[Term]
id: GO:1900569
name: chanoclavine-I aldehyde biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of chanoclavine-I aldehyde." [GOC:di, GOC:TermGenie]
+def: "The chemical reactions and pathways resulting in the formation of chanoclavine-I aldehyde. Chanoclavine-I aldehyde is at a branching point in the biosynthetic pathways of fumigaclavine C and ergotamine." [GOC:di, GOC:TermGenie]
synonym: "chanoclavine-I aldehyde anabolism" EXACT [GOC:TermGenie]
synonym: "chanoclavine-I aldehyde biosynthesis" EXACT [GOC:TermGenie]
synonym: "chanoclavine-I aldehyde formation" EXACT [GOC:TermGenie]
synonym: "chanoclavine-I aldehyde synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0035837 ! ergot alkaloid biosynthetic process
is_a: GO:0046184 ! aldehyde biosynthetic process
is_a: GO:0120255 ! olefinic compound biosynthetic process
@@ -431937,10 +435298,10 @@ name: gerfelin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving gerfelin." [GOC:di, GOC:TermGenie]
synonym: "gerfelin metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0009712 ! catechol-containing compound metabolic process
is_a: GO:0018904 ! ether metabolic process
is_a: GO:0019748 ! secondary metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0042537 ! benzene-containing compound metabolic process
[Term]
@@ -431951,8 +435312,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of gerfelin
synonym: "gerfelin breakdown" EXACT [GOC:TermGenie]
synonym: "gerfelin catabolism" EXACT [GOC:TermGenie]
synonym: "gerfelin degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0019614 ! catechol-containing compound catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:0090487 ! secondary metabolite catabolic process
is_a: GO:1900576 ! gerfelin metabolic process
is_a: GO:1901502 ! ether catabolic process
@@ -431967,8 +435328,8 @@ synonym: "gerfelin biosynthesis" EXACT [GOC:TermGenie]
synonym: "gerfelin formation" EXACT [GOC:TermGenie]
synonym: "gerfelin synthesis" EXACT [GOC:TermGenie]
is_a: GO:0009713 ! catechol-containing compound biosynthetic process
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0044550 ! secondary metabolite biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:1900576 ! gerfelin metabolic process
is_a: GO:1901503 ! ether biosynthetic process
@@ -432244,9 +435605,9 @@ name: endocrocin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving endocrocin." [GOC:di, GOC:TermGenie]
synonym: "endocrocin metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0018958 ! phenol-containing compound metabolic process
is_a: GO:0019748 ! secondary metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:1901661 ! quinone metabolic process
[Term]
@@ -432257,8 +435618,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of endocroc
synonym: "endocrocin breakdown" EXACT [GOC:TermGenie]
synonym: "endocrocin catabolism" EXACT [GOC:TermGenie]
synonym: "endocrocin degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0019336 ! phenol-containing compound catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:0090487 ! secondary metabolite catabolic process
is_a: GO:1900600 ! endocrocin metabolic process
is_a: GO:1901662 ! quinone catabolic process
@@ -432272,9 +435633,9 @@ synonym: "endocrocin anabolism" EXACT [GOC:TermGenie]
synonym: "endocrocin biosynthesis" EXACT [GOC:TermGenie]
synonym: "endocrocin formation" EXACT [GOC:TermGenie]
synonym: "endocrocin synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0044550 ! secondary metabolite biosynthetic process
is_a: GO:0046189 ! phenol-containing compound biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:1900600 ! endocrocin metabolic process
is_a: GO:1901663 ! quinone biosynthetic process
@@ -432286,7 +435647,7 @@ def: "The chemical reactions and pathways involving tensidol A." [GOC:di, GOC:Te
synonym: "tensidol A metabolism" EXACT [GOC:TermGenie]
is_a: GO:0019748 ! secondary metabolic process
is_a: GO:0042180 ! cellular ketone metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
is_a: GO:1901564 ! organonitrogen compound metabolic process
@@ -432329,10 +435690,10 @@ name: tensidol B metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving tensidol B." [GOC:di, GOC:TermGenie]
synonym: "tensidol B metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0019748 ! secondary metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0042180 ! cellular ketone metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
@@ -432344,8 +435705,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of tensidol
synonym: "tensidol B breakdown" EXACT [GOC:TermGenie]
synonym: "tensidol B catabolism" EXACT [GOC:TermGenie]
synonym: "tensidol B degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0042182 ! ketone catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:0046700 ! heterocycle catabolic process
is_a: GO:0090487 ! secondary metabolite catabolic process
is_a: GO:1900606 ! tensidol B metabolic process
@@ -432360,11 +435721,11 @@ synonym: "tensidol B anabolism" EXACT [GOC:TermGenie]
synonym: "tensidol B biosynthesis" EXACT [GOC:TermGenie]
synonym: "tensidol B formation" EXACT [GOC:TermGenie]
synonym: "tensidol B synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0042181 ! ketone biosynthetic process
is_a: GO:0043604 ! amide biosynthetic process
is_a: GO:0044550 ! secondary metabolite biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:1900606 ! tensidol B metabolic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
@@ -432522,9 +435883,10 @@ consider: GO:0019722
[Term]
id: GO:1900622
-name: positive regulation of transcription from RNA polymerase II promoter by calcium-mediated signaling
+name: obsolete positive regulation of transcription from RNA polymerase II promoter by calcium-mediated signaling
namespace: biological_process
-def: "Calcium-mediated signaling that results in positive regulation of transcription from an RNA polymerase II promoter." [GOC:bf, GOC:BHF, GOC:dgf, GOC:TermGenie, PMID:9407035, PMID:9407036]
+def: "OBSOLETE. Calcium-mediated signaling that results in positive regulation of transcription from an RNA polymerase II promoter." [GOC:bf, GOC:BHF, GOC:dgf, GOC:TermGenie, PMID:9407035, PMID:9407036]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "activation of global transcription from RNA polymerase II promoter by calcium-mediated signaling" RELATED [GOC:TermGenie]
synonym: "activation of transcription from RNA polymerase II promoter by calcium-mediated signaling" EXACT [GOC:TermGenie]
synonym: "calcineurin-dependent transcription activation" NARROW [PMID:9407036]
@@ -432542,8 +435904,9 @@ synonym: "up-regulation of global transcription from RNA polymerase II promoter
synonym: "up-regulation of transcription from RNA polymerase II promoter by calcium-mediated signaling" EXACT [GOC:TermGenie]
synonym: "upregulation of global transcription from RNA polymerase II promoter by calcium-mediated signaling" RELATED [GOC:TermGenie]
synonym: "upregulation of transcription from RNA polymerase II promoter by calcium-mediated signaling" EXACT [GOC:TermGenie]
-is_a: GO:0019722 ! calcium-mediated signaling
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
+is_obsolete: true
+consider: GO:0019722
+consider: GO:0045944
[Term]
id: GO:1900623
@@ -432913,22 +436276,22 @@ relationship: positively_regulates GO:1900560 ! austinol biosynthetic process
[Term]
id: GO:1900643
-name: regulation of chanoclavine-I biosynthetic process
+name: obsolete regulation of chanoclavine-I biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of chanoclavine-I biosynthetic process." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of chanoclavine-I biosynthetic process." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "regulation of chanoclavine-I anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of chanoclavine-I biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of chanoclavine-I formation" EXACT [GOC:TermGenie]
synonym: "regulation of chanoclavine-I synthesis" EXACT [GOC:TermGenie]
-is_a: GO:1900822 ! regulation of ergot alkaloid biosynthetic process
-is_a: GO:1902930 ! regulation of alcohol biosynthetic process
-relationship: regulates GO:1900566 ! chanoclavine-I biosynthetic process
+is_obsolete: true
[Term]
id: GO:1900644
-name: negative regulation of chanoclavine-I biosynthetic process
+name: obsolete negative regulation of chanoclavine-I biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of chanoclavine-I biosynthetic process." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of chanoclavine-I biosynthetic process." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "down regulation of chanoclavine-I anabolism" EXACT [GOC:TermGenie]
synonym: "down regulation of chanoclavine-I biosynthesis" EXACT [GOC:TermGenie]
synonym: "down regulation of chanoclavine-I biosynthetic process" EXACT [GOC:TermGenie]
@@ -432953,16 +436316,14 @@ synonym: "negative regulation of chanoclavine-I anabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of chanoclavine-I biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of chanoclavine-I formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of chanoclavine-I synthesis" EXACT [GOC:TermGenie]
-is_a: GO:1900643 ! regulation of chanoclavine-I biosynthetic process
-is_a: GO:1900823 ! negative regulation of ergot alkaloid biosynthetic process
-is_a: GO:1902931 ! negative regulation of alcohol biosynthetic process
-relationship: negatively_regulates GO:1900566 ! chanoclavine-I biosynthetic process
+is_obsolete: true
[Term]
id: GO:1900645
-name: positive regulation of chanoclavine-I biosynthetic process
+name: obsolete positive regulation of chanoclavine-I biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of chanoclavine-I biosynthetic process." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of chanoclavine-I biosynthetic process." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "activation of chanoclavine-I anabolism" EXACT [GOC:TermGenie]
synonym: "activation of chanoclavine-I biosynthesis" EXACT [GOC:TermGenie]
synonym: "activation of chanoclavine-I biosynthetic process" NARROW [GOC:TermGenie]
@@ -432987,10 +436348,7 @@ synonym: "upregulation of chanoclavine-I biosynthesis" EXACT [GOC:TermGenie]
synonym: "upregulation of chanoclavine-I biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of chanoclavine-I formation" EXACT [GOC:TermGenie]
synonym: "upregulation of chanoclavine-I synthesis" EXACT [GOC:TermGenie]
-is_a: GO:1900643 ! regulation of chanoclavine-I biosynthetic process
-is_a: GO:1900824 ! positive regulation of ergot alkaloid biosynthetic process
-is_a: GO:1902932 ! positive regulation of alcohol biosynthetic process
-relationship: positively_regulates GO:1900566 ! chanoclavine-I biosynthetic process
+is_obsolete: true
[Term]
id: GO:1900646
@@ -433001,6 +436359,7 @@ synonym: "regulation of chanoclavine-I aldehyde anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of chanoclavine-I aldehyde biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of chanoclavine-I aldehyde formation" EXACT [GOC:TermGenie]
synonym: "regulation of chanoclavine-I aldehyde synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:1900822 ! regulation of ergot alkaloid biosynthetic process
relationship: regulates GO:1900569 ! chanoclavine-I aldehyde biosynthetic process
@@ -433033,6 +436392,7 @@ synonym: "negative regulation of chanoclavine-I aldehyde anabolism" EXACT [GOC:T
synonym: "negative regulation of chanoclavine-I aldehyde biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of chanoclavine-I aldehyde formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of chanoclavine-I aldehyde synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
is_a: GO:1900646 ! regulation of chanoclavine-I aldehyde biosynthetic process
is_a: GO:1900823 ! negative regulation of ergot alkaloid biosynthetic process
relationship: negatively_regulates GO:1900569 ! chanoclavine-I aldehyde biosynthetic process
@@ -433066,6 +436426,7 @@ synonym: "upregulation of chanoclavine-I aldehyde biosynthesis" EXACT [GOC:TermG
synonym: "upregulation of chanoclavine-I aldehyde biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of chanoclavine-I aldehyde formation" EXACT [GOC:TermGenie]
synonym: "upregulation of chanoclavine-I aldehyde synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:1900646 ! regulation of chanoclavine-I aldehyde biosynthetic process
is_a: GO:1900824 ! positive regulation of ergot alkaloid biosynthetic process
relationship: positively_regulates GO:1900569 ! chanoclavine-I aldehyde biosynthetic process
@@ -433323,8 +436684,9 @@ synonym: "regulation of emericellamide biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of emericellamide formation" EXACT [GOC:TermGenie]
synonym: "regulation of emericellamide synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031326 ! regulation of cellular biosynthetic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0046890 ! regulation of lipid biosynthetic process
+is_a: GO:0062012 ! regulation of small molecule metabolic process
is_a: GO:1900376 ! regulation of secondary metabolite biosynthetic process
relationship: regulates GO:1900557 ! emericellamide biosynthetic process
@@ -433358,8 +436720,9 @@ synonym: "negative regulation of emericellamide biosynthesis" EXACT [GOC:TermGen
synonym: "negative regulation of emericellamide formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of emericellamide synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0051055 ! negative regulation of lipid biosynthetic process
+is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1900377 ! negative regulation of secondary metabolite biosynthetic process
is_a: GO:1900658 ! regulation of emericellamide biosynthetic process
relationship: negatively_regulates GO:1900557 ! emericellamide biosynthetic process
@@ -433394,8 +436757,9 @@ synonym: "upregulation of emericellamide biosynthetic process" EXACT [GOC:TermGe
synonym: "upregulation of emericellamide formation" EXACT [GOC:TermGenie]
synonym: "upregulation of emericellamide synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0046889 ! positive regulation of lipid biosynthetic process
+is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1900378 ! positive regulation of secondary metabolite biosynthetic process
is_a: GO:1900658 ! regulation of emericellamide biosynthetic process
relationship: positively_regulates GO:1900557 ! emericellamide biosynthetic process
@@ -434121,7 +437485,7 @@ synonym: "regulation of gliotoxin biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of gliotoxin formation" EXACT [GOC:TermGenie]
synonym: "regulation of gliotoxin synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031326 ! regulation of cellular biosynthetic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0042762 ! regulation of sulfur metabolic process
is_a: GO:1900376 ! regulation of secondary metabolite biosynthetic process
relationship: regulates GO:2001310 ! gliotoxin biosynthetic process
@@ -434156,7 +437520,7 @@ synonym: "negative regulation of gliotoxin biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of gliotoxin formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of gliotoxin synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0051175 ! negative regulation of sulfur metabolic process
is_a: GO:1900377 ! negative regulation of secondary metabolite biosynthetic process
is_a: GO:1900689 ! regulation of gliotoxin biosynthetic process
@@ -434192,7 +437556,7 @@ synonym: "upregulation of gliotoxin biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of gliotoxin formation" EXACT [GOC:TermGenie]
synonym: "upregulation of gliotoxin synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0051176 ! positive regulation of sulfur metabolic process
is_a: GO:1900378 ! positive regulation of secondary metabolite biosynthetic process
is_a: GO:1900689 ! regulation of gliotoxin biosynthetic process
@@ -434539,7 +437903,7 @@ synonym: "regulation of siderophore biosynthetic process, peptide modification"
synonym: "regulation of siderophore formation" EXACT [GOC:TermGenie]
synonym: "regulation of siderophore synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031326 ! regulation of cellular biosynthetic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:1900376 ! regulation of secondary metabolite biosynthetic process
relationship: regulates GO:0019290 ! siderophore biosynthetic process
@@ -434593,7 +437957,7 @@ synonym: "negative regulation of siderophore biosynthetic process, peptide modif
synonym: "negative regulation of siderophore formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of siderophore synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:1900377 ! negative regulation of secondary metabolite biosynthetic process
is_a: GO:1900704 ! regulation of siderophore biosynthetic process
relationship: negatively_regulates GO:0019290 ! siderophore biosynthetic process
@@ -434648,7 +438012,7 @@ synonym: "upregulation of siderophore biosynthetic process, peptide modification
synonym: "upregulation of siderophore formation" EXACT [GOC:TermGenie]
synonym: "upregulation of siderophore synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:1900378 ! positive regulation of secondary metabolite biosynthetic process
is_a: GO:1900704 ! regulation of siderophore biosynthetic process
relationship: positively_regulates GO:0019290 ! siderophore biosynthetic process
@@ -434663,7 +438027,7 @@ synonym: "regulation of tensidol A biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of tensidol A formation" EXACT [GOC:TermGenie]
synonym: "regulation of tensidol A synthesis" EXACT [GOC:TermGenie]
is_a: GO:0010566 ! regulation of ketone biosynthetic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:1900376 ! regulation of secondary metabolite biosynthetic process
relationship: regulates GO:1900605 ! tensidol A biosynthetic process
@@ -434697,7 +438061,7 @@ synonym: "negative regulation of tensidol A biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of tensidol A formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of tensidol A synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1900377 ! negative regulation of secondary metabolite biosynthetic process
is_a: GO:1900707 ! regulation of tensidol A biosynthetic process
@@ -434733,7 +438097,7 @@ synonym: "upregulation of tensidol A biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of tensidol A formation" EXACT [GOC:TermGenie]
synonym: "upregulation of tensidol A synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1900378 ! positive regulation of secondary metabolite biosynthetic process
is_a: GO:1900707 ! regulation of tensidol A biosynthetic process
@@ -434749,7 +438113,7 @@ synonym: "regulation of tensidol B biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of tensidol B formation" EXACT [GOC:TermGenie]
synonym: "regulation of tensidol B synthesis" EXACT [GOC:TermGenie]
is_a: GO:0010566 ! regulation of ketone biosynthetic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:1900376 ! regulation of secondary metabolite biosynthetic process
relationship: regulates GO:1900608 ! tensidol B biosynthetic process
@@ -434783,7 +438147,7 @@ synonym: "negative regulation of tensidol B biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of tensidol B formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of tensidol B synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1900377 ! negative regulation of secondary metabolite biosynthetic process
is_a: GO:1900710 ! regulation of tensidol B biosynthetic process
@@ -434819,7 +438183,7 @@ synonym: "upregulation of tensidol B biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of tensidol B formation" EXACT [GOC:TermGenie]
synonym: "upregulation of tensidol B synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1900378 ! positive regulation of secondary metabolite biosynthetic process
is_a: GO:1900710 ! regulation of tensidol B biosynthetic process
@@ -435654,7 +439018,6 @@ synonym: "H2malo transport" RELATED [GOC:TermGenie]
synonym: "HOOC-CH2-COOH transport" RELATED [GOC:TermGenie]
synonym: "propanedioic acid transport" EXACT [GOC:TermGenie]
is_a: GO:0006835 ! dicarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
[Term]
id: GO:1900753
@@ -435684,7 +439047,6 @@ synonym: "(p-hydroxyphenyl)acetate transport" EXACT [GOC:TermGenie]
synonym: "2-(4-hydroxyphenyl)ethanoate transport" EXACT [GOC:TermGenie]
synonym: "4-hydroxybenzeneacetate transport" EXACT [GOC:TermGenie]
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
[Term]
@@ -435737,8 +439099,8 @@ synonym: "inhibition of new yellow enzyme" RELATED [GOC:TermGenie]
synonym: "negative regulation of D-amino-acid:oxygen oxidoreductase (deaminating)" EXACT [GOC:TermGenie]
synonym: "negative regulation of L-amino acid:O2 oxidoreductase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of new yellow enzyme" RELATED [GOC:TermGenie]
-is_a: GO:0051354 ! negative regulation of oxidoreductase activity
is_a: GO:1900757 ! regulation of D-amino-acid oxidase activity
+is_a: GO:1902283 ! negative regulation of primary amine oxidase activity
[Term]
id: GO:1900759
@@ -435933,23 +439295,12 @@ is_a: GO:1900767 ! fonsecin metabolic process
is_a: GO:1900787 ! naphtho-gamma-pyrone biosynthetic process
is_a: GO:1901503 ! ether biosynthetic process
-[Term]
-id: GO:1900770
-name: fumitremorgin B metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving fumitremorgin B." [GOC:di, GOC:TermGenie]
-synonym: "fumitremorgin B metabolism" EXACT [GOC:TermGenie]
-synonym: "Lanosulin metabolic process" RELATED [GOC:TermGenie]
-synonym: "Lanosulin metabolism" RELATED [GOC:TermGenie]
-is_a: GO:0019748 ! secondary metabolic process
-is_a: GO:0035834 ! indole alkaloid metabolic process
-is_a: GO:1901376 ! organic heteropentacyclic compound metabolic process
-
[Term]
id: GO:1900771
-name: fumitremorgin B catabolic process
+name: obsolete fumitremorgin B catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of fumitremorgin B." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of fumitremorgin B." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "fumitremorgin B breakdown" EXACT [GOC:TermGenie]
synonym: "fumitremorgin B catabolism" EXACT [GOC:TermGenie]
synonym: "fumitremorgin B degradation" EXACT [GOC:TermGenie]
@@ -435957,47 +439308,36 @@ synonym: "Lanosulin breakdown" RELATED [GOC:TermGenie]
synonym: "Lanosulin catabolic process" RELATED [GOC:TermGenie]
synonym: "Lanosulin catabolism" RELATED [GOC:TermGenie]
synonym: "Lanosulin degradation" RELATED [GOC:TermGenie]
-is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:0090487 ! secondary metabolite catabolic process
-is_a: GO:1900770 ! fumitremorgin B metabolic process
-is_a: GO:1901377 ! organic heteropentacyclic compound catabolic process
+is_obsolete: true
[Term]
id: GO:1900772
name: fumitremorgin B biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of fumitremorgin B." [GOC:di, GOC:TermGenie]
+alt_id: GO:1900770
+def: "The chemical reactions and pathways resulting in the formation of the indole alkaloid fumitremorgin B." [GOC:di, GOC:TermGenie, PMID:18683158]
synonym: "fumitremorgin B anabolism" EXACT [GOC:TermGenie]
synonym: "fumitremorgin B biosynthesis" EXACT [GOC:TermGenie]
synonym: "fumitremorgin B formation" EXACT [GOC:TermGenie]
+synonym: "fumitremorgin B metabolic process" BROAD []
+synonym: "fumitremorgin B metabolism" EXACT [GOC:TermGenie]
synonym: "fumitremorgin B synthesis" EXACT [GOC:TermGenie]
synonym: "Lanosulin anabolism" RELATED [GOC:TermGenie]
synonym: "Lanosulin biosynthesis" RELATED [GOC:TermGenie]
synonym: "Lanosulin biosynthetic process" RELATED [GOC:TermGenie]
synonym: "Lanosulin formation" RELATED [GOC:TermGenie]
+synonym: "Lanosulin metabolic process" RELATED [GOC:TermGenie]
+synonym: "Lanosulin metabolism" RELATED [GOC:TermGenie]
synonym: "Lanosulin synthesis" RELATED [GOC:TermGenie]
is_a: GO:0035835 ! indole alkaloid biosynthetic process
-is_a: GO:0044550 ! secondary metabolite biosynthetic process
-is_a: GO:1900770 ! fumitremorgin B metabolic process
is_a: GO:1901378 ! organic heteropentacyclic compound biosynthetic process
-[Term]
-id: GO:1900773
-name: fumiquinazoline metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving fumiquinazoline." [GOC:di, GOC:TermGenie]
-synonym: "fumiquinazoline metabolism" EXACT [GOC:TermGenie]
-synonym: "fumiquinazolines metabolic process" RELATED [GOC:TermGenie]
-synonym: "fumiquinazolines metabolism" RELATED [GOC:TermGenie]
-is_a: GO:0035834 ! indole alkaloid metabolic process
-is_a: GO:0046483 ! heterocycle metabolic process
-is_a: GO:1901360 ! organic cyclic compound metabolic process
-
[Term]
id: GO:1900774
-name: fumiquinazoline catabolic process
+name: obsolete fumiquinazoline catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of fumiquinazoline." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of fumiquinazoline." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "fumiquinazoline breakdown" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline catabolism" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline degradation" EXACT [GOC:TermGenie]
@@ -436005,125 +439345,108 @@ synonym: "fumiquinazolines breakdown" RELATED [GOC:TermGenie]
synonym: "fumiquinazolines catabolic process" RELATED [GOC:TermGenie]
synonym: "fumiquinazolines catabolism" RELATED [GOC:TermGenie]
synonym: "fumiquinazolines degradation" RELATED [GOC:TermGenie]
-is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:0046700 ! heterocycle catabolic process
-is_a: GO:1900773 ! fumiquinazoline metabolic process
-is_a: GO:1901361 ! organic cyclic compound catabolic process
-
-[Term]
-id: GO:1900775
-name: fumiquinazoline biosynthetic process
-namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of fumiquinazoline." [GOC:di, GOC:TermGenie]
-synonym: "fumiquinazoline anabolism" EXACT [GOC:TermGenie]
-synonym: "fumiquinazoline biosynthesis" EXACT [GOC:TermGenie]
-synonym: "fumiquinazoline formation" EXACT [GOC:TermGenie]
-synonym: "fumiquinazoline synthesis" EXACT [GOC:TermGenie]
-synonym: "fumiquinazolines anabolism" RELATED [GOC:TermGenie]
-synonym: "fumiquinazolines biosynthesis" RELATED [GOC:TermGenie]
-synonym: "fumiquinazolines biosynthetic process" RELATED [GOC:TermGenie]
-synonym: "fumiquinazolines formation" RELATED [GOC:TermGenie]
-synonym: "fumiquinazolines synthesis" RELATED [GOC:TermGenie]
-is_a: GO:0018130 ! heterocycle biosynthetic process
-is_a: GO:0035835 ! indole alkaloid biosynthetic process
-is_a: GO:1900773 ! fumiquinazoline metabolic process
-is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+is_obsolete: true
[Term]
id: GO:1900776
-name: fumiquinazoline A metabolic process
+name: obsolete fumiquinazoline A metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving fumiquinazoline A." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways involving fumiquinazoline A." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "fumiquinazoline A metabolism" EXACT [GOC:TermGenie]
-is_a: GO:1900773 ! fumiquinazoline metabolic process
+is_obsolete: true
[Term]
id: GO:1900777
-name: fumiquinazoline A catabolic process
+name: obsolete fumiquinazoline A catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of fumiquinazoline A." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of fumiquinazoline A." [GOC:di, GOC:TermGenie]
+comment: This ter was obsoleted because there is no evidence that this process exists.
synonym: "fumiquinazoline A breakdown" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline A catabolism" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline A degradation" EXACT [GOC:TermGenie]
-is_a: GO:1900774 ! fumiquinazoline catabolic process
-is_a: GO:1900776 ! fumiquinazoline A metabolic process
+is_obsolete: true
[Term]
id: GO:1900778
-name: fumiquinazoline A biosynthetic process
+name: obsolete fumiquinazoline A biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of fumiquinazoline A." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of fumiquinazoline A." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "fumiquinazoline A anabolism" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline A biosynthesis" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline A formation" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline A synthesis" EXACT [GOC:TermGenie]
-is_a: GO:1900775 ! fumiquinazoline biosynthetic process
-is_a: GO:1900776 ! fumiquinazoline A metabolic process
-
-[Term]
-id: GO:1900779
-name: fumiquinazoline C metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving fumiquinazoline C." [GOC:di, GOC:TermGenie]
-synonym: "fumiquinazoline C metabolism" EXACT [GOC:TermGenie]
-is_a: GO:1900773 ! fumiquinazoline metabolic process
+is_obsolete: true
+replaced_by: GO:1900781
[Term]
id: GO:1900780
-name: fumiquinazoline C catabolic process
+name: obsolete fumiquinazoline C catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of fumiquinazoline C." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of fumiquinazoline C." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "fumiquinazoline C breakdown" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline C catabolism" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline C degradation" EXACT [GOC:TermGenie]
-is_a: GO:1900774 ! fumiquinazoline catabolic process
-is_a: GO:1900779 ! fumiquinazoline C metabolic process
+is_obsolete: true
[Term]
id: GO:1900781
name: fumiquinazoline C biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of fumiquinazoline C." [GOC:di, GOC:TermGenie]
+alt_id: GO:1900773
+alt_id: GO:1900775
+alt_id: GO:1900779
+def: "The chemical reactions and pathways resulting in the formation of the indole alkaloid fumiquinazoline C." [GOC:di, GOC:TermGenie, PMID:20225828]
+synonym: "fumiquinazoline biosynthesis" EXACT [GOC:TermGenie]
+synonym: "fumiquinazoline biosynthetic process" BROAD []
synonym: "fumiquinazoline C anabolism" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline C biosynthesis" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline C formation" EXACT [GOC:TermGenie]
+synonym: "fumiquinazoline C metabolic process" BROAD []
+synonym: "fumiquinazoline C metabolism" BROAD [GOC:TermGenie]
synonym: "fumiquinazoline C synthesis" EXACT [GOC:TermGenie]
-is_a: GO:1900775 ! fumiquinazoline biosynthetic process
-is_a: GO:1900779 ! fumiquinazoline C metabolic process
+synonym: "fumiquinazoline metabolic process" BROAD []
+synonym: "fumiquinazoline metabolism" BROAD [GOC:TermGenie]
+synonym: "fumiquinazolines synthesis" RELATED [GOC:TermGenie]
+is_a: GO:0018130 ! heterocycle biosynthetic process
+is_a: GO:0035835 ! indole alkaloid biosynthetic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
[Term]
id: GO:1900782
-name: fumiquinazoline F metabolic process
+name: obsolete fumiquinazoline F metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving fumiquinazoline F." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways involving fumiquinazoline F." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "fumiquinazoline F metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0042430 ! indole-containing compound metabolic process
-is_a: GO:1900773 ! fumiquinazoline metabolic process
+is_obsolete: true
+consider: GO:1900781
[Term]
id: GO:1900783
-name: fumiquinazoline F catabolic process
+name: obsolete fumiquinazoline F catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of fumiquinazoline F." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of fumiquinazoline F." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "fumiquinazoline F breakdown" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline F catabolism" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline F degradation" EXACT [GOC:TermGenie]
-is_a: GO:0042436 ! indole-containing compound catabolic process
-is_a: GO:1900774 ! fumiquinazoline catabolic process
-is_a: GO:1900782 ! fumiquinazoline F metabolic process
+is_obsolete: true
[Term]
id: GO:1900784
-name: fumiquinazoline F biosynthetic process
+name: obsolete fumiquinazoline F biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of fumiquinazoline F." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of fumiquinazoline F." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "fumiquinazoline F anabolism" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline F biosynthesis" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline F formation" EXACT [GOC:TermGenie]
synonym: "fumiquinazoline F synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0042435 ! indole-containing compound biosynthetic process
-is_a: GO:1900775 ! fumiquinazoline biosynthetic process
-is_a: GO:1900782 ! fumiquinazoline F metabolic process
+is_obsolete: true
+replaced_by: GO:1900781
[Term]
id: GO:1900785
@@ -436181,10 +439504,7 @@ def: "The chemical reactions and pathways involving pseurotin A." [GOC:di, GOC:T
synonym: "pseurotin A metabolism" EXACT [GOC:TermGenie]
synonym: "Pseurotin metabolic process" RELATED [GOC:TermGenie]
synonym: "Pseurotin metabolism" RELATED [GOC:TermGenie]
-is_a: GO:0043603 ! cellular amide metabolic process
-is_a: GO:0046483 ! heterocycle metabolic process
-is_a: GO:1901360 ! organic cyclic compound metabolic process
-is_a: GO:1901564 ! organonitrogen compound metabolic process
+is_a: GO:0072338 ! lactam metabolic process
[Term]
id: GO:1900789
@@ -436198,7 +439518,7 @@ synonym: "Pseurotin breakdown" RELATED [GOC:TermGenie]
synonym: "Pseurotin catabolic process" RELATED [GOC:TermGenie]
synonym: "Pseurotin catabolism" RELATED [GOC:TermGenie]
synonym: "Pseurotin degradation" RELATED [GOC:TermGenie]
-is_a: GO:0046700 ! heterocycle catabolic process
+is_a: GO:0072340 ! lactam catabolic process
is_a: GO:1900788 ! pseurotin A metabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
@@ -436217,11 +439537,8 @@ synonym: "Pseurotin biosynthesis" RELATED [GOC:TermGenie]
synonym: "Pseurotin biosynthetic process" RELATED [GOC:TermGenie]
synonym: "Pseurotin formation" RELATED [GOC:TermGenie]
synonym: "Pseurotin synthesis" RELATED [GOC:TermGenie]
-is_a: GO:0018130 ! heterocycle biosynthetic process
-is_a: GO:0043604 ! amide biosynthetic process
+is_a: GO:0072339 ! lactam biosynthetic process
is_a: GO:1900788 ! pseurotin A metabolic process
-is_a: GO:1901362 ! organic cyclic compound biosynthetic process
-is_a: GO:1901566 ! organonitrogen compound biosynthetic process
[Term]
id: GO:1900791
@@ -436263,51 +439580,32 @@ is_a: GO:0044550 ! secondary metabolite biosynthetic process
is_a: GO:0046189 ! phenol-containing compound biosynthetic process
is_a: GO:1900791 ! shamixanthone metabolic process
-[Term]
-id: GO:1900794
-name: terrequinone A metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving terrequinone A." [GOC:di, GOC:TermGenie]
-synonym: "terrequinone A metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0009820 ! alkaloid metabolic process
-is_a: GO:0019748 ! secondary metabolic process
-is_a: GO:0046483 ! heterocycle metabolic process
-is_a: GO:0120254 ! olefinic compound metabolic process
-is_a: GO:1901360 ! organic cyclic compound metabolic process
-is_a: GO:1901615 ! organic hydroxy compound metabolic process
-is_a: GO:1901661 ! quinone metabolic process
-
[Term]
id: GO:1900795
-name: terrequinone A catabolic process
+name: obsolete terrequinone A catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of terrequinone A." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of terrequinone A." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "terrequinone A breakdown" EXACT [GOC:TermGenie]
synonym: "terrequinone A catabolism" EXACT [GOC:TermGenie]
synonym: "terrequinone A degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:0046700 ! heterocycle catabolic process
-is_a: GO:0090487 ! secondary metabolite catabolic process
-is_a: GO:0120256 ! olefinic compound catabolic process
-is_a: GO:1900794 ! terrequinone A metabolic process
-is_a: GO:1901361 ! organic cyclic compound catabolic process
-is_a: GO:1901616 ! organic hydroxy compound catabolic process
-is_a: GO:1901662 ! quinone catabolic process
+is_obsolete: true
[Term]
id: GO:1900796
name: terrequinone A biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of terrequinone A." [GOC:di, GOC:TermGenie]
+alt_id: GO:1900794
+def: "The chemical reactions and pathways resulting in the formation of terrequinone A." [GOC:di, GOC:TermGenie, PMID:17291795, PMID:17704773]
synonym: "terrequinone A anabolism" EXACT [GOC:TermGenie]
synonym: "terrequinone A biosynthesis" EXACT [GOC:TermGenie]
synonym: "terrequinone A formation" EXACT [GOC:TermGenie]
+synonym: "terrequinone A metabolic process" BROAD []
+synonym: "terrequinone A metabolism" BROAD [GOC:TermGenie]
synonym: "terrequinone A synthesis" EXACT [GOC:TermGenie]
is_a: GO:0009821 ! alkaloid biosynthetic process
is_a: GO:0018130 ! heterocycle biosynthetic process
-is_a: GO:0044550 ! secondary metabolite biosynthetic process
is_a: GO:0120255 ! olefinic compound biosynthetic process
-is_a: GO:1900794 ! terrequinone A metabolic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
is_a: GO:1901617 ! organic hydroxy compound biosynthetic process
is_a: GO:1901663 ! quinone biosynthetic process
@@ -436355,8 +439653,8 @@ name: cspyrone B1 metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving cspyrone B1." [GOC:di, GOC:TermGenie]
synonym: "cspyrone B1 metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0019748 ! secondary metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0042180 ! cellular ketone metabolic process
is_a: GO:1901334 ! lactone metabolic process
@@ -436368,8 +439666,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of cspyrone
synonym: "cspyrone B1 breakdown" EXACT [GOC:TermGenie]
synonym: "cspyrone B1 catabolism" EXACT [GOC:TermGenie]
synonym: "cspyrone B1 degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0042182 ! ketone catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:0090487 ! secondary metabolite catabolic process
is_a: GO:1900800 ! cspyrone B1 metabolic process
is_a: GO:1901335 ! lactone catabolic process
@@ -436383,38 +439681,18 @@ synonym: "cspyrone B1 anabolism" EXACT [GOC:TermGenie]
synonym: "cspyrone B1 biosynthesis" EXACT [GOC:TermGenie]
synonym: "cspyrone B1 formation" EXACT [GOC:TermGenie]
synonym: "cspyrone B1 synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0042181 ! ketone biosynthetic process
is_a: GO:0044550 ! secondary metabolite biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:1900800 ! cspyrone B1 metabolic process
is_a: GO:1901336 ! lactone biosynthetic process
-[Term]
-id: GO:1900803
-name: brevianamide F metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving brevianamide F." [GOC:di, GOC:TermGenie]
-synonym: "brevianamide F metabolism" EXACT [GOC:TermGenie]
-synonym: "cyclo-(Trp-Pro) metabolism" RELATED [GOC:TermGenie]
-synonym: "cyclo-L-Trp-L-Pro metabolic process" RELATED [GOC:TermGenie]
-synonym: "cyclo-L-Trp-L-Pro metabolism" RELATED [GOC:TermGenie]
-synonym: "cyclo-L-tryptophanyl-L-proline metabolic process" RELATED [GOC:TermGenie]
-synonym: "cyclo-L-tryptophanyl-L-proline metabolism" RELATED [GOC:TermGenie]
-synonym: "L-prolyl-L-tryptophan anhydride metabolic process" RELATED [GOC:TermGenie]
-synonym: "L-prolyl-L-tryptophan anhydride metabolism" RELATED [GOC:TermGenie]
-synonym: "L-tryptophyl-L-proline cyclic anhydride metabolic process" RELATED [GOC:TermGenie]
-synonym: "L-tryptophyl-L-proline cyclic anhydride metabolism" RELATED [GOC:TermGenie]
-synonym: "tryptophan-proline diketopiperazine metabolic process" RELATED [GOC:TermGenie]
-synonym: "tryptophan-proline diketopiperazine metabolism" RELATED [GOC:TermGenie]
-is_a: GO:0006518 ! peptide metabolic process
-is_a: GO:0019748 ! secondary metabolic process
-is_a: GO:0042430 ! indole-containing compound metabolic process
-
[Term]
id: GO:1900804
-name: brevianamide F catabolic process
+name: obsolete brevianamide F catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of brevianamide F." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of brevianamide F." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "brevianamide F breakdown" EXACT [GOC:TermGenie]
synonym: "brevianamide F catabolism" EXACT [GOC:TermGenie]
synonym: "brevianamide F degradation" EXACT [GOC:TermGenie]
@@ -436442,19 +439720,18 @@ synonym: "tryptophan-proline diketopiperazine breakdown" RELATED [GOC:TermGenie]
synonym: "tryptophan-proline diketopiperazine catabolic process" RELATED [GOC:TermGenie]
synonym: "tryptophan-proline diketopiperazine catabolism" RELATED [GOC:TermGenie]
synonym: "tryptophan-proline diketopiperazine degradation" RELATED [GOC:TermGenie]
-is_a: GO:0042436 ! indole-containing compound catabolic process
-is_a: GO:0043171 ! peptide catabolic process
-is_a: GO:0090487 ! secondary metabolite catabolic process
-is_a: GO:1900803 ! brevianamide F metabolic process
+is_obsolete: true
[Term]
id: GO:1900805
name: brevianamide F biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of brevianamide F." [GOC:di, GOC:TermGenie]
+alt_id: GO:1900803
+def: "The chemical reactions and pathways resulting in the formation of brevianamide F. Brevianamide F is the biosynthetic precursor of a large family of biologically active prenylated tryptophan-proline 2,5-diketopiperazines that are produced by some fungi." [GOC:di, GOC:TermGenie, PMID:16755625, PMID:17464044]
synonym: "brevianamide F anabolism" EXACT [GOC:TermGenie]
synonym: "brevianamide F biosynthesis" EXACT [GOC:TermGenie]
synonym: "brevianamide F formation" EXACT [GOC:TermGenie]
+synonym: "brevianamide F metabolic process" NARROW []
synonym: "brevianamide F synthesis" EXACT [GOC:TermGenie]
synonym: "C16H17N3O2 anabolism" RELATED [GOC:TermGenie]
synonym: "C16H17N3O2 biosynthesis" RELATED [GOC:TermGenie]
@@ -436491,16 +439768,16 @@ synonym: "tryptophan-proline diketopiperazine biosynthesis" RELATED [GOC:TermGen
synonym: "tryptophan-proline diketopiperazine biosynthetic process" RELATED [GOC:TermGenie]
synonym: "tryptophan-proline diketopiperazine formation" RELATED [GOC:TermGenie]
synonym: "tryptophan-proline diketopiperazine synthesis" RELATED [GOC:TermGenie]
+is_a: GO:0035835 ! indole alkaloid biosynthetic process
is_a: GO:0042435 ! indole-containing compound biosynthetic process
is_a: GO:0043043 ! peptide biosynthetic process
-is_a: GO:0044550 ! secondary metabolite biosynthetic process
-is_a: GO:1900803 ! brevianamide F metabolic process
[Term]
id: GO:1900806
-name: ergot alkaloid catabolic process
+name: obsolete ergot alkaloid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of ergot alkaloid." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of ergot alkaloid." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "ergot alkaloid breakdown" EXACT [GOC:TermGenie]
synonym: "ergot alkaloid catabolism" EXACT [GOC:TermGenie]
synonym: "ergot alkaloid degradation" EXACT [GOC:TermGenie]
@@ -436508,42 +439785,33 @@ synonym: "ergot alkaloids breakdown" RELATED [GOC:TermGenie]
synonym: "ergot alkaloids catabolic process" RELATED [GOC:TermGenie]
synonym: "ergot alkaloids catabolism" RELATED [GOC:TermGenie]
synonym: "ergot alkaloids degradation" RELATED [GOC:TermGenie]
-is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:0035836 ! ergot alkaloid metabolic process
-is_a: GO:0090487 ! secondary metabolite catabolic process
-
-[Term]
-id: GO:1900807
-name: fumigaclavine C metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving fumigaclavine C." [GOC:di, GOC:TermGenie]
-synonym: "fumigaclavine C metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0035836 ! ergot alkaloid metabolic process
-is_a: GO:1900619 ! acetate ester metabolic process
+is_obsolete: true
[Term]
id: GO:1900808
-name: fumigaclavine C catabolic process
+name: obsolete fumigaclavine C catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of fumigaclavine C." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of fumigaclavine C." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "fumigaclavine C breakdown" EXACT [GOC:TermGenie]
synonym: "fumigaclavine C catabolism" EXACT [GOC:TermGenie]
synonym: "fumigaclavine C degradation" EXACT [GOC:TermGenie]
-is_a: GO:1900806 ! ergot alkaloid catabolic process
-is_a: GO:1900807 ! fumigaclavine C metabolic process
+is_obsolete: true
[Term]
id: GO:1900809
name: fumigaclavine C biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of fumigaclavine C." [GOC:di, GOC:TermGenie]
+alt_id: GO:1900807
+def: "The chemical reactions and pathways resulting in the formation of fumigaclavine C, a fungal ergot alkaloid." [GOC:di, GOC:TermGenie, PMID:15933009, PMID:23435153, PMID:26972831]
synonym: "fumigaclavine C anabolism" EXACT [GOC:TermGenie]
synonym: "fumigaclavine C biosynthesis" EXACT [GOC:TermGenie]
synonym: "fumigaclavine C formation" EXACT [GOC:TermGenie]
+synonym: "fumigaclavine C metabolic process" BROAD []
+synonym: "fumigaclavine C metabolism" BROAD [GOC:TermGenie]
synonym: "fumigaclavine C synthesis" EXACT [GOC:TermGenie]
is_a: GO:0035837 ! ergot alkaloid biosynthetic process
is_a: GO:1900620 ! acetate ester biosynthetic process
-is_a: GO:1900807 ! fumigaclavine C metabolic process
[Term]
id: GO:1900810
@@ -436607,9 +439875,9 @@ name: monodictyphenone metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving monodictyphenone." [GOC:di, GOC:TermGenie]
synonym: "monodictyphenone metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0018958 ! phenol-containing compound metabolic process
is_a: GO:0019748 ! secondary metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0042180 ! cellular ketone metabolic process
is_a: GO:0042537 ! benzene-containing compound metabolic process
@@ -436621,9 +439889,9 @@ def: "The chemical reactions and pathways resulting in the breakdown of monodict
synonym: "monodictyphenone breakdown" EXACT [GOC:TermGenie]
synonym: "monodictyphenone catabolism" EXACT [GOC:TermGenie]
synonym: "monodictyphenone degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0019336 ! phenol-containing compound catabolic process
is_a: GO:0042182 ! ketone catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:0090487 ! secondary metabolite catabolic process
is_a: GO:1900813 ! monodictyphenone metabolic process
@@ -436636,10 +439904,10 @@ synonym: "monodictyphenone anabolism" EXACT [GOC:TermGenie]
synonym: "monodictyphenone biosynthesis" EXACT [GOC:TermGenie]
synonym: "monodictyphenone formation" EXACT [GOC:TermGenie]
synonym: "monodictyphenone synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0042181 ! ketone biosynthetic process
is_a: GO:0044550 ! secondary metabolite biosynthetic process
is_a: GO:0046189 ! phenol-containing compound biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:1900813 ! monodictyphenone metabolic process
[Term]
@@ -436649,13 +439917,11 @@ namespace: biological_process
def: "The chemical reactions and pathways involving ochratoxin A." [GOC:di, GOC:TermGenie]
synonym: "Ochratoxin A metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006575 ! cellular modified amino acid metabolic process
-is_a: GO:0006629 ! lipid metabolic process
is_a: GO:0019748 ! secondary metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
-is_a: GO:1901568 ! fatty acid derivative metabolic process
[Term]
id: GO:1900817
@@ -436665,14 +439931,12 @@ def: "The chemical reactions and pathways resulting in the breakdown of ochratox
synonym: "ochratoxin A breakdown" EXACT [GOC:TermGenie]
synonym: "ochratoxin A catabolism" EXACT [GOC:TermGenie]
synonym: "ochratoxin A degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016042 ! lipid catabolic process
is_a: GO:0042219 ! cellular modified amino acid catabolic process
is_a: GO:0046700 ! heterocycle catabolic process
is_a: GO:0072329 ! monocarboxylic acid catabolic process
is_a: GO:0090487 ! secondary metabolite catabolic process
is_a: GO:1900816 ! ochratoxin A metabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
-is_a: GO:1901569 ! fatty acid derivative catabolic process
[Term]
id: GO:1900818
@@ -436683,7 +439947,6 @@ synonym: "Ochratoxin A anabolism" EXACT [GOC:TermGenie]
synonym: "Ochratoxin A biosynthesis" EXACT [GOC:TermGenie]
synonym: "Ochratoxin A formation" EXACT [GOC:TermGenie]
synonym: "Ochratoxin A synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
is_a: GO:0043604 ! amide biosynthetic process
@@ -436691,7 +439954,6 @@ is_a: GO:0044550 ! secondary metabolite biosynthetic process
is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
is_a: GO:1900816 ! ochratoxin A metabolic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
-is_a: GO:1901570 ! fatty acid derivative biosynthetic process
[Term]
id: GO:1900819
@@ -436742,7 +440004,6 @@ synonym: "regulation of ergot alkaloid anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of ergot alkaloid biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of ergot alkaloid formation" EXACT [GOC:TermGenie]
synonym: "regulation of ergot alkaloid synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
is_a: GO:1900376 ! regulation of secondary metabolite biosynthetic process
relationship: regulates GO:0035837 ! ergot alkaloid biosynthetic process
@@ -436776,7 +440037,6 @@ synonym: "negative regulation of ergot alkaloid anabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of ergot alkaloid biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of ergot alkaloid formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of ergot alkaloid synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
is_a: GO:1900377 ! negative regulation of secondary metabolite biosynthetic process
is_a: GO:1900822 ! regulation of ergot alkaloid biosynthetic process
@@ -436811,7 +440071,6 @@ synonym: "upregulation of ergot alkaloid biosynthesis" EXACT [GOC:TermGenie]
synonym: "upregulation of ergot alkaloid biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of ergot alkaloid formation" EXACT [GOC:TermGenie]
synonym: "upregulation of ergot alkaloid synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
is_a: GO:1900378 ! positive regulation of secondary metabolite biosynthetic process
is_a: GO:1900822 ! regulation of ergot alkaloid biosynthetic process
@@ -437132,7 +440391,8 @@ synonym: "regulation of Pseurotin biosynthetic process" RELATED [GOC:TermGenie]
synonym: "regulation of Pseurotin formation" RELATED [GOC:TermGenie]
synonym: "regulation of Pseurotin synthesis" RELATED [GOC:TermGenie]
is_a: GO:0031326 ! regulation of cellular biosynthetic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
+is_a: GO:0062012 ! regulation of small molecule metabolic process
relationship: regulates GO:1900790 ! pseurotin A biosynthetic process
[Term]
@@ -437144,7 +440404,8 @@ synonym: "down regulation of pseurotin A biosynthetic process" EXACT [GOC:TermGe
synonym: "down-regulation of pseurotin A biosynthetic process" EXACT [GOC:TermGenie]
synonym: "downregulation of pseurotin A biosynthetic process" EXACT [GOC:TermGenie]
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
+is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1900849 ! regulation of pseurotin A biosynthetic process
relationship: negatively_regulates GO:1900790 ! pseurotin A biosynthetic process
@@ -437157,59 +440418,45 @@ synonym: "up regulation of pseurotin A biosynthetic process" EXACT [GOC:TermGeni
synonym: "up-regulation of pseurotin A biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of pseurotin A biosynthetic process" EXACT [GOC:TermGenie]
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
+is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1900849 ! regulation of pseurotin A biosynthetic process
relationship: positively_regulates GO:1900790 ! pseurotin A biosynthetic process
-[Term]
-id: GO:1900852
-name: regulation of terrequinone A biosynthetic process
-namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of terrequinone A biosynthetic process." [GOC:di, GOC:TermGenie]
-synonym: "regulation of terrequinone A anabolism" EXACT [GOC:TermGenie]
-synonym: "regulation of terrequinone A biosynthesis" EXACT [GOC:TermGenie]
-synonym: "regulation of terrequinone A formation" EXACT [GOC:TermGenie]
-synonym: "regulation of terrequinone A synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0010566 ! regulation of ketone biosynthetic process
-is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
-is_a: GO:1900376 ! regulation of secondary metabolite biosynthetic process
-relationship: regulates GO:1900796 ! terrequinone A biosynthetic process
-
[Term]
id: GO:1900853
-name: negative regulation of terrequinone A biosynthetic process
+name: obsolete negative regulation of terrequinone A biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of terrequinone A biosynthetic process." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of terrequinone A biosynthetic process." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "down regulation of terrequinone A biosynthetic process" EXACT [GOC:TermGenie]
synonym: "down-regulation of terrequinone A biosynthetic process" EXACT [GOC:TermGenie]
synonym: "downregulation of terrequinone A biosynthetic process" EXACT [GOC:TermGenie]
-is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
-is_a: GO:0062014 ! negative regulation of small molecule metabolic process
-is_a: GO:1900377 ! negative regulation of secondary metabolite biosynthetic process
-is_a: GO:1900852 ! regulation of terrequinone A biosynthetic process
-relationship: negatively_regulates GO:1900796 ! terrequinone A biosynthetic process
+is_obsolete: true
[Term]
id: GO:1900854
name: positive regulation of terrequinone A biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of terrequinone A biosynthetic process." [GOC:di, GOC:TermGenie]
+alt_id: GO:1900852
+def: "Any process that activates or increases the frequency, rate or extent of terrequinone A biosynthetic process." [GOC:di, GOC:TermGenie, PMID:24066102]
+synonym: "regulation of terrequinone A biosynthetic process" BROAD []
synonym: "up regulation of terrequinone A biosynthetic process" EXACT [GOC:TermGenie]
synonym: "up-regulation of terrequinone A biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of terrequinone A biosynthetic process" EXACT [GOC:TermGenie]
+is_a: GO:0010566 ! regulation of ketone biosynthetic process
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1900378 ! positive regulation of secondary metabolite biosynthetic process
-is_a: GO:1900852 ! regulation of terrequinone A biosynthetic process
relationship: positively_regulates GO:1900796 ! terrequinone A biosynthetic process
[Term]
id: GO:1900855
-name: regulation of fumitremorgin B biosynthetic process
+name: obsolete regulation of fumitremorgin B biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of fumitremorgin B biosynthetic process." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of fumitremorgin B biosynthetic process." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "regulation of fumitremorgin B anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of fumitremorgin B biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of fumitremorgin B formation" EXACT [GOC:TermGenie]
@@ -437219,80 +440466,63 @@ synonym: "regulation of Lanosulin biosynthesis" RELATED [GOC:TermGenie]
synonym: "regulation of Lanosulin biosynthetic process" RELATED [GOC:TermGenie]
synonym: "regulation of Lanosulin formation" RELATED [GOC:TermGenie]
synonym: "regulation of Lanosulin synthesis" RELATED [GOC:TermGenie]
-is_a: GO:0031326 ! regulation of cellular biosynthetic process
-is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
-is_a: GO:1900376 ! regulation of secondary metabolite biosynthetic process
-relationship: regulates GO:1900772 ! fumitremorgin B biosynthetic process
+is_obsolete: true
[Term]
id: GO:1900856
-name: negative regulation of fumitremorgin B biosynthetic process
+name: obsolete negative regulation of fumitremorgin B biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of fumitremorgin B biosynthetic process." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of fumitremorgin B biosynthetic process." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "down regulation of fumitremorgin B biosynthetic process" EXACT [GOC:TermGenie]
synonym: "down-regulation of fumitremorgin B biosynthetic process" EXACT [GOC:TermGenie]
synonym: "downregulation of fumitremorgin B biosynthetic process" EXACT [GOC:TermGenie]
-is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
-is_a: GO:1900377 ! negative regulation of secondary metabolite biosynthetic process
-is_a: GO:1900855 ! regulation of fumitremorgin B biosynthetic process
-relationship: negatively_regulates GO:1900772 ! fumitremorgin B biosynthetic process
+is_obsolete: true
[Term]
id: GO:1900857
-name: positive regulation of fumitremorgin B biosynthetic process
+name: obsolete positive regulation of fumitremorgin B biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of fumitremorgin B biosynthetic process." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of fumitremorgin B biosynthetic process." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "up regulation of fumitremorgin B biosynthetic process" EXACT [GOC:TermGenie]
synonym: "up-regulation of fumitremorgin B biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of fumitremorgin B biosynthetic process" EXACT [GOC:TermGenie]
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
-is_a: GO:1900378 ! positive regulation of secondary metabolite biosynthetic process
-is_a: GO:1900855 ! regulation of fumitremorgin B biosynthetic process
-relationship: positively_regulates GO:1900772 ! fumitremorgin B biosynthetic process
+is_obsolete: true
[Term]
id: GO:1900858
-name: regulation of brevianamide F biosynthetic process
+name: obsolete regulation of brevianamide F biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of brevianamide F biosynthetic process." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of brevianamide F biosynthetic process." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "regulation of brevianamide F anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of brevianamide F biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of brevianamide F formation" EXACT [GOC:TermGenie]
synonym: "regulation of brevianamide F synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0031326 ! regulation of cellular biosynthetic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
-is_a: GO:1900376 ! regulation of secondary metabolite biosynthetic process
-relationship: regulates GO:1900805 ! brevianamide F biosynthetic process
+is_obsolete: true
[Term]
id: GO:1900859
-name: negative regulation of brevianamide F biosynthetic process
+name: obsolete negative regulation of brevianamide F biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of brevianamide F biosynthetic process." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of brevianamide F biosynthetic process." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "down regulation of brevianamide F biosynthetic process" EXACT [GOC:TermGenie]
synonym: "down-regulation of brevianamide F biosynthetic process" EXACT [GOC:TermGenie]
synonym: "downregulation of brevianamide F biosynthetic process" EXACT [GOC:TermGenie]
-is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
-is_a: GO:1900377 ! negative regulation of secondary metabolite biosynthetic process
-is_a: GO:1900858 ! regulation of brevianamide F biosynthetic process
-relationship: negatively_regulates GO:1900805 ! brevianamide F biosynthetic process
+is_obsolete: true
[Term]
id: GO:1900860
-name: positive regulation of brevianamide F biosynthetic process
+name: obsolete positive regulation of brevianamide F biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of brevianamide F biosynthetic process." [GOC:di, GOC:TermGenie]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of brevianamide F biosynthetic process." [GOC:di, GOC:TermGenie]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "up regulation of brevianamide F biosynthetic process" EXACT [GOC:TermGenie]
synonym: "up-regulation of brevianamide F biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of brevianamide F biosynthetic process" EXACT [GOC:TermGenie]
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
-is_a: GO:1900378 ! positive regulation of secondary metabolite biosynthetic process
-is_a: GO:1900858 ! regulation of brevianamide F biosynthetic process
-relationship: positively_regulates GO:1900805 ! brevianamide F biosynthetic process
+is_obsolete: true
[Term]
id: GO:1900861
@@ -437356,7 +440586,6 @@ name: glycolate transport
namespace: biological_process
def: "The directed movement of a glycolate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:pr, GOC:TermGenie]
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
[Term]
@@ -438336,8 +441565,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of glycine import into a cell." [GOC:TermGenie]
synonym: "regulation of glycine import" BROAD []
is_a: GO:0010958 ! regulation of amino acid import across plasma membrane
-is_a: GO:1903959 ! regulation of anion transmembrane transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
relationship: regulates GO:1903804 ! glycine import across plasma membrane
[Term]
@@ -438350,10 +441577,9 @@ synonym: "down-regulation of glycine import" EXACT [GOC:TermGenie]
synonym: "downregulation of glycine import" EXACT [GOC:TermGenie]
synonym: "inhibition of glycine import" NARROW [GOC:TermGenie]
synonym: "negative regulation of glycine import" BROAD []
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:0051956 ! negative regulation of amino acid transport
is_a: GO:1900923 ! regulation of glycine import across plasma membrane
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
-is_a: GO:1904063 ! negative regulation of cation transmembrane transport
relationship: negatively_regulates GO:1903804 ! glycine import across plasma membrane
[Term]
@@ -438366,10 +441592,9 @@ synonym: "positive regulation of glycine import" BROAD []
synonym: "up regulation of glycine import" EXACT [GOC:TermGenie]
synonym: "up-regulation of glycine import" EXACT [GOC:TermGenie]
synonym: "upregulation of glycine import" EXACT [GOC:TermGenie]
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:0051957 ! positive regulation of amino acid transport
is_a: GO:1900923 ! regulation of glycine import across plasma membrane
-is_a: GO:1903961 ! positive regulation of anion transmembrane transport
-is_a: GO:1904064 ! positive regulation of cation transmembrane transport
relationship: positively_regulates GO:1903804 ! glycine import across plasma membrane
[Term]
@@ -438380,8 +441605,6 @@ def: "Any process that modulates the frequency, rate or extent of L-threonine im
synonym: "regulation of L-threonine import" BROAD []
synonym: "regulation of L-threonine uptake" EXACT [GOC:TermGenie]
is_a: GO:0010958 ! regulation of amino acid import across plasma membrane
-is_a: GO:1903959 ! regulation of anion transmembrane transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
relationship: regulates GO:1903807 ! L-threonine import across plasma membrane
[Term]
@@ -438398,10 +441621,9 @@ synonym: "downregulation of L-threonine uptake" RELATED [GOC:TermGenie]
synonym: "inhibition of L-threonine import" NARROW [GOC:TermGenie]
synonym: "inhibition of L-threonine uptake" NARROW [GOC:TermGenie]
synonym: "negative regulation of L-threonine uptake" RELATED [GOC:TermGenie]
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:0051956 ! negative regulation of amino acid transport
is_a: GO:1900926 ! regulation of L-threonine import across plasma membrane
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
-is_a: GO:1904063 ! negative regulation of cation transmembrane transport
relationship: negatively_regulates GO:1903807 ! L-threonine import across plasma membrane
[Term]
@@ -438419,10 +441641,9 @@ synonym: "up-regulation of L-threonine import" EXACT [GOC:TermGenie]
synonym: "up-regulation of L-threonine uptake" RELATED [GOC:TermGenie]
synonym: "upregulation of L-threonine import" EXACT [GOC:TermGenie]
synonym: "upregulation of L-threonine uptake" RELATED [GOC:TermGenie]
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:0051957 ! positive regulation of amino acid transport
is_a: GO:1900926 ! regulation of L-threonine import across plasma membrane
-is_a: GO:1903961 ! positive regulation of anion transmembrane transport
-is_a: GO:1904064 ! positive regulation of cation transmembrane transport
relationship: positively_regulates GO:1903807 ! L-threonine import across plasma membrane
[Term]
@@ -438433,8 +441654,6 @@ def: "Any process that modulates the frequency, rate or extent of L-tyrosine imp
synonym: "regulation of L-tyrosine import" BROAD []
synonym: "regulation of L-tyrosine uptake" EXACT [GOC:TermGenie]
is_a: GO:0010958 ! regulation of amino acid import across plasma membrane
-is_a: GO:1903959 ! regulation of anion transmembrane transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
relationship: regulates GO:1903808 ! L-tyrosine import across plasma membrane
[Term]
@@ -438452,10 +441671,9 @@ synonym: "inhibition of L-tyrosine import" NARROW [GOC:TermGenie]
synonym: "inhibition of L-tyrosine uptake" RELATED [GOC:TermGenie]
synonym: "negative regulation of L-tyrosine import" BROAD []
synonym: "negative regulation of L-tyrosine uptake" RELATED [GOC:TermGenie]
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:0051956 ! negative regulation of amino acid transport
is_a: GO:1900929 ! regulation of L-tyrosine import across plasma membrane
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
-is_a: GO:1904063 ! negative regulation of cation transmembrane transport
relationship: negatively_regulates GO:1903808 ! L-tyrosine import across plasma membrane
[Term]
@@ -438473,10 +441691,9 @@ synonym: "up-regulation of L-tyrosine import" EXACT [GOC:TermGenie]
synonym: "up-regulation of L-tyrosine uptake" RELATED [GOC:TermGenie]
synonym: "upregulation of L-tyrosine import" EXACT [GOC:TermGenie]
synonym: "upregulation of L-tyrosine uptake" RELATED [GOC:TermGenie]
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:0051957 ! positive regulation of amino acid transport
is_a: GO:1900929 ! regulation of L-tyrosine import across plasma membrane
-is_a: GO:1903961 ! positive regulation of anion transmembrane transport
-is_a: GO:1904064 ! positive regulation of cation transmembrane transport
relationship: positively_regulates GO:1903808 ! L-tyrosine import across plasma membrane
[Term]
@@ -439702,7 +442919,7 @@ relationship: positively_regulates GO:0002047 ! phenazine biosynthetic process
id: GO:1900983
name: vindoline metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving vindoline." [GOC:TermGenie, GOC:yaf, MetaCyc:PWY-5292, UniPathway:UPA00365]
+def: "The chemical reactions and pathways involving vindoline." [GOC:TermGenie, GOC:yaf, PMID:23864440]
synonym: "vindoline metabolism" EXACT [GOC:TermGenie]
is_a: GO:0046447 ! terpenoid indole alkaloid metabolic process
is_a: GO:1900619 ! acetate ester metabolic process
@@ -439711,100 +442928,82 @@ is_a: GO:1902644 ! tertiary alcohol metabolic process
[Term]
id: GO:1900984
-name: vindoline catabolic process
+name: obsolete vindoline catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of vindoline." [GOC:TermGenie, GOC:yaf, MetaCyc:PWY-5292, UniPathway:UPA00365]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of vindoline." [GOC:TermGenie, GOC:yaf, MetaCyc:PWY-5292]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "vindoline breakdown" EXACT [GOC:TermGenie]
synonym: "vindoline catabolism" EXACT [GOC:TermGenie]
synonym: "vindoline degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:0046164 ! alcohol catabolic process
-is_a: GO:1900983 ! vindoline metabolic process
-is_a: GO:1901377 ! organic heteropentacyclic compound catabolic process
+is_obsolete: true
[Term]
id: GO:1900985
name: vindoline biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of vindoline." [GOC:TermGenie, GOC:yaf, MetaCyc:PWY-5292, UniPathway:UPA00365]
+def: "The chemical reactions and pathways resulting in the formation of vindoline." [GOC:TermGenie, GOC:yaf, PMID:12228585]
synonym: "vindoline anabolism" EXACT [GOC:TermGenie]
synonym: "vindoline biosynthesis" EXACT [GOC:TermGenie]
synonym: "vindoline formation" EXACT [GOC:TermGenie]
synonym: "vindoline synthesis" EXACT [GOC:TermGenie]
+xref: MetaCyc:PWY-5292
is_a: GO:0009709 ! terpenoid indole alkaloid biosynthetic process
is_a: GO:1900620 ! acetate ester biosynthetic process
is_a: GO:1900983 ! vindoline metabolic process
is_a: GO:1901378 ! organic heteropentacyclic compound biosynthetic process
is_a: GO:1902645 ! tertiary alcohol biosynthetic process
-[Term]
-id: GO:1900986
-name: ajmaline metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving ajmaline." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00310]
-synonym: "ajmaline metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0046447 ! terpenoid indole alkaloid metabolic process
-is_a: GO:1901615 ! organic hydroxy compound metabolic process
-
[Term]
id: GO:1900987
-name: ajmaline catabolic process
+name: obsolete ajmaline catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of ajmaline." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00310]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of ajmaline." [GOC:TermGenie, GOC:yaf]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "ajmaline breakdown" EXACT [GOC:TermGenie]
synonym: "ajmaline catabolism" EXACT [GOC:TermGenie]
synonym: "ajmaline degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:1900986 ! ajmaline metabolic process
-is_a: GO:1901616 ! organic hydroxy compound catabolic process
+is_obsolete: true
[Term]
id: GO:1900988
name: ajmaline biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of ajmaline." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00310]
+alt_id: GO:1900986
+def: "The chemical reactions and pathways resulting in the formation of ajmaline." [GOC:TermGenie, GOC:yaf]
synonym: "ajmaline anabolism" EXACT [GOC:TermGenie]
synonym: "ajmaline biosynthesis" EXACT [GOC:TermGenie]
synonym: "ajmaline formation" EXACT [GOC:TermGenie]
+synonym: "ajmaline metabolic process" BROAD []
+synonym: "ajmaline metabolism" BROAD [GOC:TermGenie]
synonym: "ajmaline synthesis" EXACT [GOC:TermGenie]
is_a: GO:0009709 ! terpenoid indole alkaloid biosynthetic process
-is_a: GO:1900986 ! ajmaline metabolic process
is_a: GO:1901617 ! organic hydroxy compound biosynthetic process
-[Term]
-id: GO:1900989
-name: scopolamine metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving scopolamine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00725]
-synonym: "scopolamine metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0046448 ! tropane alkaloid metabolic process
-is_a: GO:0097176 ! epoxide metabolic process
-
[Term]
id: GO:1900990
-name: scopolamine catabolic process
+name: obsolete scopolamine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of scopolamine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00725]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of scopolamine." [GOC:TermGenie, GOC:yaf]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "scopolamine breakdown" EXACT [GOC:TermGenie]
synonym: "scopolamine catabolism" EXACT [GOC:TermGenie]
synonym: "scopolamine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:0046700 ! heterocycle catabolic process
-is_a: GO:1900989 ! scopolamine metabolic process
-is_a: GO:1901361 ! organic cyclic compound catabolic process
-is_a: GO:1901502 ! ether catabolic process
+is_obsolete: true
[Term]
id: GO:1900991
name: scopolamine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of scopolamine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00725]
+alt_id: GO:1900989
+def: "The chemical reactions and pathways resulting in the formation of scopolamine." [GOC:TermGenie, GOC:yaf, PMID:16720272, PMID:18251710, PMID:32879484]
synonym: "scopolamine anabolism" EXACT [GOC:TermGenie]
synonym: "scopolamine biosynthesis" EXACT [GOC:TermGenie]
synonym: "scopolamine formation" EXACT [GOC:TermGenie]
+synonym: "scopolamine metabolic process" BROAD []
+synonym: "scopolamine metabolism" BROAD [GOC:TermGenie]
synonym: "scopolamine synthesis" EXACT [GOC:TermGenie]
is_a: GO:0009710 ! tropane alkaloid biosynthetic process
-is_a: GO:1900989 ! scopolamine metabolic process
+is_a: GO:0097176 ! epoxide metabolic process
is_a: GO:1901503 ! ether biosynthetic process
[Term]
@@ -439840,7 +443039,7 @@ is_a: GO:1901805 ! beta-glucoside catabolic process
id: GO:1900994
name: (-)-secologanin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of (-)-secologanin." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00328]
+def: "The chemical reactions and pathways resulting in the formation of (-)-secologanin." [GOC:TermGenie, GOC:yaf, PMID:24104568]
synonym: "(-)-secologanin anabolism" EXACT [GOC:TermGenie]
synonym: "(-)-secologanin biosynthesis" EXACT [GOC:TermGenie]
synonym: "(-)-secologanin formation" EXACT [GOC:TermGenie]
@@ -440021,29 +443220,33 @@ namespace: biological_process
def: "The chemical reactions and pathways involving (S)-scoulerine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00319]
synonym: "(S)-scoulerine metabolism" EXACT [GOC:TermGenie]
is_a: GO:0033076 ! isoquinoline alkaloid metabolic process
+is_a: GO:0046483 ! heterocycle metabolic process
+is_a: GO:1901360 ! organic cyclic compound metabolic process
[Term]
id: GO:1901008
-name: (S)-scoulerine catabolic process
+name: obsolete (S)-scoulerine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of (S)-scoulerine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00319]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of (S)-scoulerine." [GOC:TermGenie, GOC:yaf]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "(S)-scoulerine breakdown" EXACT [GOC:TermGenie]
synonym: "(S)-scoulerine catabolism" EXACT [GOC:TermGenie]
synonym: "(S)-scoulerine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0071274 ! isoquinoline alkaloid catabolic process
-is_a: GO:1901007 ! (S)-scoulerine metabolic process
+is_obsolete: true
[Term]
id: GO:1901009
name: (S)-scoulerine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of (S)-scoulerine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00319]
+def: "The chemical reactions and pathways resulting in the formation of (S)-scoulerine." [GOC:TermGenie, GOC:yaf, PMID:15672841]
synonym: "(S)-scoulerine anabolism" EXACT [GOC:TermGenie]
synonym: "(S)-scoulerine biosynthesis" EXACT [GOC:TermGenie]
synonym: "(S)-scoulerine formation" EXACT [GOC:TermGenie]
synonym: "(S)-scoulerine synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0033075 ! isoquinoline alkaloid biosynthetic process
is_a: GO:1901007 ! (S)-scoulerine metabolic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
[Term]
id: GO:1901010
@@ -440052,62 +443255,60 @@ namespace: biological_process
def: "The chemical reactions and pathways involving (S)-reticuline." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00306]
synonym: "(S)-reticuline metabolism" EXACT [GOC:TermGenie]
is_a: GO:0046445 ! benzyl isoquinoline alkaloid metabolic process
+is_a: GO:0046483 ! heterocycle metabolic process
+is_a: GO:1901360 ! organic cyclic compound metabolic process
+is_a: GO:1901615 ! organic hydroxy compound metabolic process
[Term]
id: GO:1901011
-name: (S)-reticuline catabolic process
+name: obsolete (S)-reticuline catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of (S)-reticuline." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00306]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of (S)-reticuline." [GOC:TermGenie, GOC:yaf]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "(S)-reticuline breakdown" EXACT [GOC:TermGenie]
synonym: "(S)-reticuline catabolism" EXACT [GOC:TermGenie]
synonym: "(S)-reticuline degradation" EXACT [GOC:TermGenie]
-is_a: GO:0071274 ! isoquinoline alkaloid catabolic process
-is_a: GO:1901010 ! (S)-reticuline metabolic process
+is_obsolete: true
[Term]
id: GO:1901012
name: (S)-reticuline biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of (S)-reticuline." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00306]
+def: "The chemical reactions and pathways resulting in the formation of (S)-reticuline." [GOC:TermGenie, GOC:yaf, PMID:22725256]
synonym: "(S)-reticuline anabolism" EXACT [GOC:TermGenie]
synonym: "(S)-reticuline biosynthesis" EXACT [GOC:TermGenie]
synonym: "(S)-reticuline formation" EXACT [GOC:TermGenie]
synonym: "(S)-reticuline synthesis" EXACT [GOC:TermGenie]
is_a: GO:0009708 ! benzyl isoquinoline alkaloid biosynthetic process
+is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:1901010 ! (S)-reticuline metabolic process
-
-[Term]
-id: GO:1901013
-name: 3alpha(S)-strictosidine metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving 3alpha(S)-strictosidine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00311]
-synonym: "3alpha(S)-strictosidine metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0035834 ! indole alkaloid metabolic process
-is_a: GO:1901804 ! beta-glucoside metabolic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+is_a: GO:1901617 ! organic hydroxy compound biosynthetic process
[Term]
id: GO:1901014
-name: 3alpha(S)-strictosidine catabolic process
+name: obsolete 3alpha(S)-strictosidine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 3alpha(S)-strictosidine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00311]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of 3alpha(S)-strictosidine." [GOC:TermGenie, GOC:yaf]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "3alpha(S)-strictosidine breakdown" EXACT [GOC:TermGenie]
synonym: "3alpha(S)-strictosidine catabolism" EXACT [GOC:TermGenie]
synonym: "3alpha(S)-strictosidine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:1901013 ! 3alpha(S)-strictosidine metabolic process
-is_a: GO:1901805 ! beta-glucoside catabolic process
+is_obsolete: true
[Term]
id: GO:1901015
name: 3alpha(S)-strictosidine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 3alpha(S)-strictosidine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00311]
+alt_id: GO:1901013
+def: "The chemical reactions and pathways resulting in the formation of 3alpha(S)-strictosidine." [GOC:TermGenie, GOC:yaf]
synonym: "3alpha(S)-strictosidine anabolism" EXACT [GOC:TermGenie]
synonym: "3alpha(S)-strictosidine biosynthesis" EXACT [GOC:TermGenie]
synonym: "3alpha(S)-strictosidine formation" EXACT [GOC:TermGenie]
+synonym: "3alpha(S)-strictosidine metabolic process" BROAD []
+synonym: "3alpha(S)-strictosidine metabolism" EXACT [GOC:TermGenie]
synonym: "3alpha(S)-strictosidine synthesis" EXACT [GOC:TermGenie]
is_a: GO:0035835 ! indole alkaloid biosynthetic process
-is_a: GO:1901013 ! 3alpha(S)-strictosidine metabolic process
is_a: GO:1901806 ! beta-glucoside biosynthetic process
[Term]
@@ -440116,7 +443317,7 @@ name: regulation of potassium ion transmembrane transporter activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of potassium ion transmembrane transporter activity." [GOC:BHF, GOC:TermGenie]
synonym: "regulation of potassium transporter activity" EXACT [GOC:TermGenie]
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
is_a: GO:1901379 ! regulation of potassium ion transmembrane transport
[Term]
@@ -440160,7 +443361,7 @@ id: GO:1901019
name: regulation of calcium ion transmembrane transporter activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of calcium ion transmembrane transporter activity." [GOC:BHF, GOC:TermGenie]
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
is_a: GO:1903169 ! regulation of calcium ion transmembrane transport
[Term]
@@ -440193,7 +443394,7 @@ is_a: GO:1904427 ! positive regulation of calcium ion transmembrane transport
id: GO:1901022
name: 4-hydroxyphenylacetate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving 4-hydroxyphenylacetate." [GOC:TermGenie, GOC:yaf, MetaCyc:RXN-8505, UniPathway:UPA00208]
+def: "The chemical reactions and pathways involving 4-hydroxyphenylacetate." [GOC:TermGenie, GOC:yaf, MetaCyc:RXN-8505]
synonym: "4-hydroxyphenylacetate metabolism" EXACT [GOC:TermGenie]
is_a: GO:0018958 ! phenol-containing compound metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
@@ -440202,7 +443403,7 @@ is_a: GO:0032787 ! monocarboxylic acid metabolic process
id: GO:1901023
name: 4-hydroxyphenylacetate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 4-hydroxyphenylacetate." [GOC:TermGenie, GOC:yaf, MetaCyc:RXN-8505, UniPathway:UPA00208]
+def: "The chemical reactions and pathways resulting in the breakdown of 4-hydroxyphenylacetate." [GOC:TermGenie, GOC:yaf, MetaCyc:RXN-8505, PMID:8550403]
synonym: "4-hydroxyphenylacetate breakdown" EXACT [GOC:TermGenie]
synonym: "4-hydroxyphenylacetate catabolism" EXACT [GOC:TermGenie]
synonym: "4-hydroxyphenylacetate degradation" EXACT [GOC:TermGenie]
@@ -440214,7 +443415,7 @@ is_a: GO:1901022 ! 4-hydroxyphenylacetate metabolic process
id: GO:1901024
name: 4-hydroxyphenylacetate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 4-hydroxyphenylacetate." [GOC:TermGenie, GOC:yaf, MetaCyc:RXN-8505, UniPathway:UPA00208]
+def: "The chemical reactions and pathways resulting in the formation of 4-hydroxyphenylacetate." [GOC:TermGenie, GOC:yaf, MetaCyc:RXN-8505]
synonym: "4-hydroxyphenylacetate anabolism" EXACT [GOC:TermGenie]
synonym: "4-hydroxyphenylacetate biosynthesis" EXACT [GOC:TermGenie]
synonym: "4-hydroxyphenylacetate formation" EXACT [GOC:TermGenie]
@@ -440278,6 +443479,7 @@ synonym: "inhibition of MOMP" NARROW [GOC:TermGenie]
synonym: "negative regulation of mitochondrial outer membrane permeabilization" BROAD []
synonym: "negative regulation of MOMP" EXACT [GOC:TermGenie]
is_a: GO:0010823 ! negative regulation of mitochondrion organization
+is_a: GO:0035795 ! negative regulation of mitochondrial membrane permeability
is_a: GO:1901028 ! regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway
is_a: GO:2001234 ! negative regulation of apoptotic signaling pathway
relationship: negatively_regulates GO:0097345 ! mitochondrial outer membrane permeabilization
@@ -440299,6 +443501,7 @@ synonym: "up-regulation of MOMP" EXACT [GOC:TermGenie]
synonym: "upregulation of mitochondrial outer membrane permeabilization" EXACT [GOC:TermGenie]
synonym: "upregulation of MOMP" EXACT [GOC:TermGenie]
is_a: GO:0010822 ! positive regulation of mitochondrion organization
+is_a: GO:0035794 ! positive regulation of mitochondrial membrane permeability
is_a: GO:0051050 ! positive regulation of transport
is_a: GO:1901028 ! regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway
relationship: positively_regulates GO:0097345 ! mitochondrial outer membrane permeabilization
@@ -440411,8 +443614,6 @@ def: "Any process that modulates the frequency, rate or extent of L-glutamine im
synonym: "regulation of L-glutamine import" BROAD []
synonym: "regulation of L-glutamine uptake" EXACT [GOC:TermGenie]
is_a: GO:0010958 ! regulation of amino acid import across plasma membrane
-is_a: GO:1903959 ! regulation of anion transmembrane transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
is_a: GO:2000485 ! regulation of glutamine transport
relationship: regulates GO:1903803 ! L-glutamine import across plasma membrane
@@ -440431,9 +443632,8 @@ synonym: "inhibition of L-glutamine import" NARROW [GOC:TermGenie]
synonym: "inhibition of L-glutamine uptake" EXACT [GOC:TermGenie]
synonym: "negative regulation of L-glutamine import" BROAD []
synonym: "negative regulation of L-glutamine uptake" EXACT [GOC:TermGenie]
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:1901034 ! regulation of L-glutamine import across plasma membrane
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
-is_a: GO:1904063 ! negative regulation of cation transmembrane transport
is_a: GO:2000486 ! negative regulation of glutamine transport
relationship: negatively_regulates GO:1903803 ! L-glutamine import across plasma membrane
@@ -440452,9 +443652,8 @@ synonym: "up-regulation of L-glutamine import" EXACT [GOC:TermGenie]
synonym: "up-regulation of L-glutamine uptake" EXACT [GOC:TermGenie]
synonym: "upregulation of L-glutamine import" EXACT [GOC:TermGenie]
synonym: "upregulation of L-glutamine uptake" EXACT [GOC:TermGenie]
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:1901034 ! regulation of L-glutamine import across plasma membrane
-is_a: GO:1903961 ! positive regulation of anion transmembrane transport
-is_a: GO:1904064 ! positive regulation of cation transmembrane transport
is_a: GO:2000487 ! positive regulation of glutamine transport
relationship: positively_regulates GO:1903803 ! L-glutamine import across plasma membrane
@@ -440545,7 +443744,7 @@ relationship: part_of GO:0071630 ! nuclear protein quality control by the ubiqui
[Term]
id: GO:1901045
-name: negative regulation of oviposition
+name: negative regulation of egg-laying behavior
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of oviposition." [GOC:kmv, GOC:TermGenie]
synonym: "down regulation of egg laying" BROAD [GOC:TermGenie]
@@ -440562,15 +443761,15 @@ synonym: "inhibition of egg-laying" BROAD [GOC:TermGenie]
synonym: "inhibition of oviposition" NARROW [GOC:TermGenie]
synonym: "negative regulation of egg laying" BROAD [GOC:TermGenie]
synonym: "negative regulation of egg-laying" BROAD [GOC:TermGenie]
-is_a: GO:0046662 ! regulation of oviposition
+synonym: "negative regulation of oviposition" EXACT []
+is_a: GO:0046662 ! regulation of egg-laying behavior
is_a: GO:0048521 ! negative regulation of behavior
-is_a: GO:0051241 ! negative regulation of multicellular organismal process
is_a: GO:2000242 ! negative regulation of reproductive process
-relationship: negatively_regulates GO:0018991 ! oviposition
+relationship: negatively_regulates GO:0018991 ! egg-laying behavior
[Term]
id: GO:1901046
-name: positive regulation of oviposition
+name: positive regulation of egg-laying behavior
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of oviposition." [GOC:kmv, GOC:TermGenie]
synonym: "activation of egg laying" BROAD [GOC:TermGenie]
@@ -440578,6 +443777,7 @@ synonym: "activation of egg-laying" BROAD [GOC:TermGenie]
synonym: "activation of oviposition" NARROW [GOC:TermGenie]
synonym: "positive regulation of egg laying" BROAD [GOC:TermGenie]
synonym: "positive regulation of egg-laying" BROAD [GOC:TermGenie]
+synonym: "positive regulation of oviposition" EXACT []
synonym: "up regulation of egg laying" BROAD [GOC:TermGenie]
synonym: "up regulation of egg-laying" BROAD [GOC:TermGenie]
synonym: "up regulation of oviposition" EXACT [GOC:TermGenie]
@@ -440587,28 +443787,27 @@ synonym: "up-regulation of oviposition" EXACT [GOC:TermGenie]
synonym: "upregulation of egg laying" BROAD [GOC:TermGenie]
synonym: "upregulation of egg-laying" BROAD [GOC:TermGenie]
synonym: "upregulation of oviposition" EXACT [GOC:TermGenie]
-is_a: GO:0046662 ! regulation of oviposition
+is_a: GO:0046662 ! regulation of egg-laying behavior
is_a: GO:0048520 ! positive regulation of behavior
-is_a: GO:0051240 ! positive regulation of multicellular organismal process
is_a: GO:2000243 ! positive regulation of reproductive process
-relationship: positively_regulates GO:0018991 ! oviposition
+relationship: positively_regulates GO:0018991 ! egg-laying behavior
[Term]
id: GO:1901047
-name: insulin receptor signaling pathway involved in determination of adult lifespan
+name: obsolete insulin receptor signaling pathway involved in determination of adult lifespan
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of the insulin receptor binding to insulin that controls viability and duration in the adult phase of the life-cycle." [GOC:kmv, GOC:TermGenie, PMID:9360933]
+def: "OBSOLETE. The series of molecular signals generated as a consequence of the insulin receptor binding to insulin that controls viability and duration in the adult phase of the life-cycle." [GOC:kmv, GOC:TermGenie, PMID:9360933]
+comment: This term was obsoleted because it represents a pathway and a readout.
synonym: "daf-2 receptor signaling pathway of determination of adult lifespan" NARROW [GOC:TermGenie]
synonym: "insulin receptor signaling pathway of determination of adult lifespan" EXACT [GOC:TermGenie]
synonym: "insulin receptor signalling pathway of determination of adult lifespan" EXACT [GOC:TermGenie]
-is_a: GO:0008286 ! insulin receptor signaling pathway
-relationship: part_of GO:0008340 ! determination of adult lifespan
+is_obsolete: true
[Term]
id: GO:1901048
name: transforming growth factor beta receptor signaling pathway involved in regulation of multicellular organism growth
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription, that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size." [GOC:kmv, GOC:TermGenie, PMID:9847239]
+def: "The series of molecular signals initiated by an extracellular ligand binding to a transforming growth factor beta receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription, that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size." [GOC:kmv, GOC:TermGenie, PMID:9847239]
synonym: "TGF-beta receptor signaling pathway of regulation of body growth" EXACT [GOC:TermGenie]
synonym: "TGF-beta receptor signaling pathway of regulation of body size" EXACT [GOC:TermGenie]
synonym: "TGF-beta receptor signaling pathway of regulation of multicellular organism growth" EXACT [GOC:TermGenie]
@@ -440630,44 +443829,37 @@ synonym: "transforming growth factor beta receptor signalling pathway of regulat
is_a: GO:0007179 ! transforming growth factor beta receptor signaling pathway
relationship: part_of GO:0040014 ! regulation of multicellular organism growth
-[Term]
-id: GO:1901049
-name: atropine metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving atropine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00303]
-synonym: "atropine metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0046448 ! tropane alkaloid metabolic process
-
[Term]
id: GO:1901050
-name: atropine catabolic process
+name: obsolete atropine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of atropine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00303]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of atropine." [GOC:TermGenie, GOC:yaf]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "atropine breakdown" EXACT [GOC:TermGenie]
synonym: "atropine catabolism" EXACT [GOC:TermGenie]
synonym: "atropine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:0046700 ! heterocycle catabolic process
-is_a: GO:1901049 ! atropine metabolic process
-is_a: GO:1901361 ! organic cyclic compound catabolic process
+is_obsolete: true
[Term]
id: GO:1901051
name: atropine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of atropine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00303]
+alt_id: GO:1901049
+def: "The chemical reactions and pathways resulting in the formation of atropine. Atropine is the racemic mixture of hyoscyamine." [GOC:TermGenie, GOC:yaf, PMID:2879005, PMID:33572199]
synonym: "atropine anabolism" EXACT [GOC:TermGenie]
synonym: "atropine biosynthesis" EXACT [GOC:TermGenie]
synonym: "atropine formation" EXACT [GOC:TermGenie]
+synonym: "atropine metabolic process" BROAD []
+synonym: "atropine metabolism" BROAD [GOC:TermGenie]
synonym: "atropine synthesis" EXACT [GOC:TermGenie]
+synonym: "hyoscyamine biosynthetic process" EXACT []
is_a: GO:0009710 ! tropane alkaloid biosynthetic process
-is_a: GO:1901049 ! atropine metabolic process
[Term]
id: GO:1901052
name: sarcosine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving sarcosine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00292]
+def: "The chemical reactions and pathways involving sarcosine." [GOC:TermGenie, GOC:yaf, PMID:17951379]
synonym: "sarcosine metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006575 ! cellular modified amino acid metabolic process
is_a: GO:1901605 ! alpha-amino acid metabolic process
@@ -440676,11 +443868,11 @@ is_a: GO:1901605 ! alpha-amino acid metabolic process
id: GO:1901053
name: sarcosine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of sarcosine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00292]
+def: "The chemical reactions and pathways resulting in the breakdown of sarcosine." [GOC:TermGenie, GOC:yaf, PMID:17951379]
synonym: "sarcosine breakdown" EXACT [GOC:TermGenie]
synonym: "sarcosine catabolism" EXACT [GOC:TermGenie]
synonym: "sarcosine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0042219 ! cellular modified amino acid catabolic process
is_a: GO:1901052 ! sarcosine metabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
@@ -440689,7 +443881,7 @@ is_a: GO:1901606 ! alpha-amino acid catabolic process
id: GO:1901054
name: sarcosine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of sarcosine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00292]
+def: "The chemical reactions and pathways resulting in the formation of sarcosine." [GOC:TermGenie, GOC:yaf, PMID:31402327]
synonym: "sarcosine anabolism" EXACT [GOC:TermGenie]
synonym: "sarcosine biosynthesis" EXACT [GOC:TermGenie]
synonym: "sarcosine formation" EXACT [GOC:TermGenie]
@@ -440704,7 +443896,8 @@ name: trimethylenediamine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving trimethylenediamine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00010]
synonym: "trimethylenediamine metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006595 ! polyamine metabolic process
+is_a: GO:0006807 ! nitrogen compound metabolic process
+is_a: GO:0071704 ! organic substance metabolic process
[Term]
id: GO:1901056
@@ -440714,8 +443907,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of trimethy
synonym: "trimethylenediamine breakdown" EXACT [GOC:TermGenie]
synonym: "trimethylenediamine catabolism" EXACT [GOC:TermGenie]
synonym: "trimethylenediamine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0006598 ! polyamine catabolic process
is_a: GO:1901055 ! trimethylenediamine metabolic process
+is_a: GO:1901575 ! organic substance catabolic process
[Term]
id: GO:1901057
@@ -440726,8 +443919,8 @@ synonym: "trimethylenediamine anabolism" EXACT [GOC:TermGenie]
synonym: "trimethylenediamine biosynthesis" EXACT [GOC:TermGenie]
synonym: "trimethylenediamine formation" EXACT [GOC:TermGenie]
synonym: "trimethylenediamine synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0006596 ! polyamine biosynthetic process
is_a: GO:1901055 ! trimethylenediamine metabolic process
+is_a: GO:1901576 ! organic substance biosynthetic process
[Term]
id: GO:1901058
@@ -441076,20 +444269,20 @@ is_a: GO:0009820 ! alkaloid metabolic process
[Term]
id: GO:1901084
-name: pyrrolizidine alkaloid catabolic process
+name: obsolete pyrrolizidine alkaloid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pyrrolizidine alkaloid." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00329]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of pyrrolizidine alkaloid." [GOC:TermGenie, GOC:yaf]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "pyrrolizidine alkaloid breakdown" EXACT [GOC:TermGenie]
synonym: "pyrrolizidine alkaloid catabolism" EXACT [GOC:TermGenie]
synonym: "pyrrolizidine alkaloid degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:1901083 ! pyrrolizidine alkaloid metabolic process
+is_obsolete: true
[Term]
id: GO:1901085
name: pyrrolizidine alkaloid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyrrolizidine alkaloid." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00329]
+def: "The chemical reactions and pathways resulting in the formation of pyrrolizidine alkaloid." [GOC:TermGenie, GOC:yaf, PMID:30001795]
synonym: "pyrrolizidine alkaloid anabolism" EXACT [GOC:TermGenie]
synonym: "pyrrolizidine alkaloid biosynthesis" EXACT [GOC:TermGenie]
synonym: "pyrrolizidine alkaloid formation" EXACT [GOC:TermGenie]
@@ -441448,7 +444641,7 @@ is_a: GO:1901101 ! gramicidin S metabolic process
id: GO:1901103
name: gramicidin S biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of gramicidin S." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00102]
+def: "The chemical reactions and pathways resulting in the formation of gramicidin S." [GOC:TermGenie, GOC:yaf, PMID:7534306]
synonym: "gramicidin S anabolism" EXACT [GOC:TermGenie]
synonym: "gramicidin S biosynthesis" EXACT [GOC:TermGenie]
synonym: "gramicidin S formation" EXACT [GOC:TermGenie]
@@ -441539,11 +444732,7 @@ name: actinorhodin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving actinorhodin." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00173]
synonym: "actinorhodin metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0018958 ! phenol-containing compound metabolic process
-is_a: GO:0030638 ! polyketide metabolic process
is_a: GO:0043648 ! dicarboxylic acid metabolic process
-is_a: GO:0046483 ! heterocycle metabolic process
-is_a: GO:1901661 ! quinone metabolic process
[Term]
id: GO:1901111
@@ -441553,12 +444742,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of actinorh
synonym: "actinorhodin breakdown" EXACT [GOC:TermGenie]
synonym: "actinorhodin catabolism" EXACT [GOC:TermGenie]
synonym: "actinorhodin degradation" EXACT [GOC:TermGenie]
-is_a: GO:0019336 ! phenol-containing compound catabolic process
-is_a: GO:0030640 ! polyketide catabolic process
is_a: GO:0043649 ! dicarboxylic acid catabolic process
-is_a: GO:0046700 ! heterocycle catabolic process
is_a: GO:1901110 ! actinorhodin metabolic process
-is_a: GO:1901662 ! quinone catabolic process
[Term]
id: GO:1901112
@@ -441569,12 +444754,8 @@ synonym: "actinorhodin anabolism" EXACT [GOC:TermGenie]
synonym: "actinorhodin biosynthesis" EXACT [GOC:TermGenie]
synonym: "actinorhodin formation" EXACT [GOC:TermGenie]
synonym: "actinorhodin synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0018130 ! heterocycle biosynthetic process
-is_a: GO:0030639 ! polyketide biosynthetic process
is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
-is_a: GO:0046189 ! phenol-containing compound biosynthetic process
is_a: GO:1901110 ! actinorhodin metabolic process
-is_a: GO:1901663 ! quinone biosynthetic process
[Term]
id: GO:1901113
@@ -441815,6 +444996,7 @@ def: "The chemical reactions and pathways involving carbohydrate derivative." [G
subset: goslim_agr
subset: goslim_generic
subset: goslim_mouse
+subset: prokaryote_subset
synonym: "carbohydrate derivative metabolism" EXACT [GOC:TermGenie]
is_a: GO:0071704 ! organic substance metabolic process
@@ -441937,7 +445119,6 @@ namespace: molecular_function
def: "Binding to salicylic acid." [GOC:TermGenie, PMID:22699612]
synonym: "salicylic acid receptor" NARROW [PMID:22699612]
is_a: GO:0033293 ! monocarboxylic acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
[Term]
@@ -441950,7 +445131,8 @@ synonym: "ribostamycin metabolism" EXACT [GOC:yaf]
synonym: "vistamycin metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006790 ! sulfur compound metabolic process
is_a: GO:0006807 ! nitrogen compound metabolic process
-is_a: GO:0016137 ! glycoside metabolic process
+is_a: GO:0019751 ! polyol metabolic process
+is_a: GO:0030647 ! aminoglycoside antibiotic metabolic process
[Term]
id: GO:1901151
@@ -441964,8 +445146,9 @@ synonym: "ribostamycin degradation" EXACT [GOC:yaf]
synonym: "vistamycin breakdown" EXACT [GOC:TermGenie]
synonym: "vistamycin catabolism" EXACT [GOC:TermGenie]
synonym: "vistamycin degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016139 ! glycoside catabolic process
+is_a: GO:0030649 ! aminoglycoside antibiotic catabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
+is_a: GO:0046174 ! polyol catabolic process
is_a: GO:1901150 ! vistamycin metabolic process
[Term]
@@ -441982,8 +445165,9 @@ synonym: "vistamycin anabolism" EXACT [GOC:TermGenie]
synonym: "vistamycin biosynthesis" EXACT [GOC:TermGenie]
synonym: "vistamycin formation" EXACT [GOC:TermGenie]
synonym: "vistamycin synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0016138 ! glycoside biosynthetic process
+is_a: GO:0030648 ! aminoglycoside antibiotic biosynthetic process
is_a: GO:0044272 ! sulfur compound biosynthetic process
+is_a: GO:0046173 ! polyol biosynthetic process
is_a: GO:1901150 ! vistamycin metabolic process
[Term]
@@ -442862,9 +446046,10 @@ relationship: positively_regulates GO:0003207 ! cardiac chamber formation
[Term]
id: GO:1901213
-name: regulation of transcription from RNA polymerase II promoter involved in heart development
+name: obsolete regulation of transcription from RNA polymerase II promoter involved in heart development
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the development of the heart over time." [GOC:BHF, GOC:TermGenie]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the development of the heart over time." [GOC:BHF, GOC:TermGenie]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "global transcription regulation from Pol II promoter involved in cardiac development" RELATED [GOC:TermGenie]
synonym: "global transcription regulation from Pol II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie]
synonym: "global transcription regulation from Pol II promoter involved in heart development" RELATED [GOC:TermGenie]
@@ -442882,8 +446067,7 @@ synonym: "regulation of transcription from RNA polymerase II promoter involved i
synonym: "regulation of transcription from RNA polymerase II promoter, global involved in cardiac development" RELATED [GOC:TermGenie]
synonym: "regulation of transcription from RNA polymerase II promoter, global involved in dorsal vessel development" RELATED [GOC:TermGenie]
synonym: "regulation of transcription from RNA polymerase II promoter, global involved in heart development" RELATED [GOC:TermGenie]
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-relationship: part_of GO:0007507 ! heart development
+is_obsolete: true
[Term]
id: GO:1901214
@@ -442943,31 +446127,28 @@ relationship: positively_regulates GO:0070997 ! neuron death
[Term]
id: GO:1901217
-name: regulation of holin activity
+name: obsolete regulation of holin activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of holin activity." [GOC:bm, GOC:TermGenie]
-is_a: GO:0022898 ! regulation of transmembrane transporter activity
-is_a: GO:0043903 ! regulation of biological process involved in symbiotic interaction
-is_a: GO:0050792 ! regulation of viral process
-relationship: regulates GO:0019076 ! viral release from host cell
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of holin activity." [GOC:bm, GOC:TermGenie]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0098772
[Term]
id: GO:1901218
-name: negative regulation of holin activity
+name: obsolete negative regulation of holin activity
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of holin activity." [GOC:bm, GOC:TermGenie]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of holin activity." [GOC:bm, GOC:TermGenie]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "antiholin activity" EXACT []
synonym: "down regulation of holin activity" EXACT [GOC:TermGenie]
synonym: "down-regulation of holin activity" EXACT [GOC:TermGenie]
synonym: "downregulation of holin activity" EXACT [GOC:TermGenie]
synonym: "inhibition of holin activity" NARROW [GOC:TermGenie]
synonym: "phage antiholin" NARROW [GOC:bm]
-is_a: GO:0032410 ! negative regulation of transporter activity
-is_a: GO:0034763 ! negative regulation of transmembrane transport
-is_a: GO:0048525 ! negative regulation of viral process
-is_a: GO:0051711 ! negative regulation of killing of cells of another organism
-is_a: GO:1901217 ! regulation of holin activity
-relationship: negatively_regulates GO:0019076 ! viral release from host cell
+is_obsolete: true
+consider: GO:0140313
+consider: GO:0140678
[Term]
id: GO:1901219
@@ -443310,9 +446491,10 @@ consider: GO:0045944
[Term]
id: GO:1901227
-name: negative regulation of transcription from RNA polymerase II promoter involved in heart development
+name: obsolete negative regulation of transcription from RNA polymerase II promoter involved in heart development
namespace: biological_process
-def: "Any negative regulation of transcription from RNA polymerase II promoter that is involved in heart development." [GOC:BHF, GOC:TermGenie]
+def: "OBSOLETE. Any negative regulation of transcription from RNA polymerase II promoter that is involved in heart development." [GOC:BHF, GOC:TermGenie]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "down regulation of global transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie]
synonym: "down regulation of global transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie]
synonym: "down regulation of global transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie]
@@ -443348,14 +446530,14 @@ synonym: "negative regulation of transcription from Pol II promoter involved in
synonym: "negative regulation of transcription from Pol II promoter involved in heart development" EXACT [GOC:TermGenie]
synonym: "negative regulation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie]
synonym: "negative regulation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie]
-is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:1901213 ! regulation of transcription from RNA polymerase II promoter involved in heart development
+is_obsolete: true
[Term]
id: GO:1901228
-name: positive regulation of transcription from RNA polymerase II promoter involved in heart development
+name: obsolete positive regulation of transcription from RNA polymerase II promoter involved in heart development
namespace: biological_process
-def: "Any positive regulation of transcription from RNA polymerase II promoter that is involved in heart development." [GOC:BHF, GOC:TermGenie]
+def: "OBSOLETE. Any positive regulation of transcription from RNA polymerase II promoter that is involved in heart development." [GOC:BHF, GOC:TermGenie]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "activation of global transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie]
synonym: "activation of global transcription from RNA polymerase II promoter involved in dorsal vessel development" RELATED [GOC:TermGenie]
synonym: "activation of global transcription from RNA polymerase II promoter involved in heart development" RELATED [GOC:TermGenie]
@@ -443397,8 +446579,7 @@ synonym: "upregulation of global transcription from RNA polymerase II promoter i
synonym: "upregulation of transcription from RNA polymerase II promoter involved in cardiac development" RELATED [GOC:TermGenie]
synonym: "upregulation of transcription from RNA polymerase II promoter involved in dorsal vessel development" NARROW [GOC:TermGenie]
synonym: "upregulation of transcription from RNA polymerase II promoter involved in heart development" EXACT [GOC:TermGenie]
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
-is_a: GO:1901213 ! regulation of transcription from RNA polymerase II promoter involved in heart development
+is_obsolete: true
[Term]
id: GO:1901229
@@ -443518,6 +446699,7 @@ xref: EC:7.3.2.6
xref: RHEA:35027
is_a: GO:0043225 ! ATPase-coupled inorganic anion transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:1901239
@@ -443528,7 +446710,7 @@ def: "Enables the transfer of malonate(1-) from one side of a membrane to the ot
synonym: "malonic acid uptake transmembrane transporter activity" RELATED []
xref: RHEA:33115
is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:1901241
@@ -443537,7 +446719,6 @@ namespace: molecular_function
def: "Enables the transfer of 4-hydroxyphenylacetate from one side of a membrane to the other." [GOC:TermGenie, PMID:9315705]
xref: RHEA:33175
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:1901618 ! organic hydroxy compound transmembrane transporter activity
[Term]
@@ -443550,7 +446731,6 @@ synonym: "doxorubicin transmembrane-transporting ATPase activity" RELATED []
xref: TC:3.A.1.105.1
is_a: GO:0015101 ! organic cation transmembrane transporter activity
is_a: GO:0015665 ! alcohol transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
is_a: GO:1901505 ! carbohydrate derivative transmembrane transporter activity
@@ -443942,7 +447122,6 @@ name: lipooligosaccharide metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving lipooligosaccharide." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00501]
synonym: "lipooligosaccharide metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0009311 ! oligosaccharide metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
[Term]
@@ -443953,7 +447132,6 @@ def: "The chemical reactions and pathways resulting in the breakdown of lipoolig
synonym: "lipooligosaccharide breakdown" EXACT [GOC:TermGenie]
synonym: "lipooligosaccharide catabolism" EXACT [GOC:TermGenie]
synonym: "lipooligosaccharide degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009313 ! oligosaccharide catabolic process
is_a: GO:1901136 ! carbohydrate derivative catabolic process
is_a: GO:1901269 ! lipooligosaccharide metabolic process
@@ -443966,7 +447144,6 @@ synonym: "lipooligosaccharide anabolism" EXACT [GOC:TermGenie]
synonym: "lipooligosaccharide biosynthesis" EXACT [GOC:TermGenie]
synonym: "lipooligosaccharide formation" EXACT [GOC:TermGenie]
synonym: "lipooligosaccharide synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0009312 ! oligosaccharide biosynthetic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
is_a: GO:1901269 ! lipooligosaccharide metabolic process
@@ -444076,7 +447253,7 @@ synonym: "fructosyllysine breakdown" EXACT [GOC:TermGenie]
synonym: "fructosyllysine catabolic process" EXACT []
synonym: "fructosyllysine catabolism" EXACT [GOC:TermGenie]
synonym: "fructosyllysine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0030392 ! fructosamine catabolic process
is_a: GO:0030393 ! fructoselysine metabolic process
@@ -444090,7 +447267,7 @@ synonym: "fructosyllysine biosynthesis" EXACT [GOC:TermGenie]
synonym: "fructosyllysine biosynthetic process" EXACT []
synonym: "fructosyllysine formation" EXACT [GOC:TermGenie]
synonym: "fructosyllysine synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
+is_a: GO:0008652 ! amino acid biosynthetic process
is_a: GO:0030391 ! fructosamine biosynthetic process
is_a: GO:0030393 ! fructoselysine metabolic process
@@ -444439,7 +447616,7 @@ synonym: "negative regulation of spermidine biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of spermidine formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of spermidine synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0033239 ! negative regulation of cellular amine metabolic process
+is_a: GO:0033239 ! negative regulation of amine metabolic process
is_a: GO:1901304 ! regulation of spermidine biosynthetic process
relationship: negatively_regulates GO:0008295 ! spermidine biosynthetic process
@@ -444473,25 +447650,25 @@ synonym: "upregulation of spermidine biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of spermidine formation" EXACT [GOC:TermGenie]
synonym: "upregulation of spermidine synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0033240 ! positive regulation of cellular amine metabolic process
+is_a: GO:0033240 ! positive regulation of amine metabolic process
is_a: GO:1901304 ! regulation of spermidine biosynthetic process
relationship: positively_regulates GO:0008295 ! spermidine biosynthetic process
[Term]
id: GO:1901308
-name: regulation of sterol regulatory element binding protein cleavage
+name: obsolete regulation of sterol regulatory element binding protein cleavage
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of sterol regulatory element binding protein cleavage." [GOC:TermGenie]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of sterol regulatory element binding protein cleavage." [GOC:TermGenie]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "regulation of SREBP cleavage" EXACT [GOC:TermGenie]
-is_a: GO:0032268 ! regulation of cellular protein metabolic process
-is_a: GO:0070613 ! regulation of protein processing
-relationship: regulates GO:0035103 ! sterol regulatory element binding protein cleavage
+is_obsolete: true
[Term]
id: GO:1901309
-name: negative regulation of sterol regulatory element binding protein cleavage
+name: obsolete negative regulation of sterol regulatory element binding protein cleavage
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of sterol regulatory element binding protein cleavage." [GOC:TermGenie, PMID:15899885, PMID:16525117]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of sterol regulatory element binding protein cleavage." [GOC:TermGenie, PMID:15899885, PMID:16525117]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of SREBP cleavage" EXACT [GOC:TermGenie]
synonym: "down regulation of sterol regulatory element binding protein cleavage" EXACT [GOC:TermGenie]
synonym: "down-regulation of SREBP cleavage" EXACT [GOC:TermGenie]
@@ -444502,16 +447679,14 @@ synonym: "inhibition of SREBP cleavage" EXACT [GOC:TermGenie]
synonym: "inhibition of SREBP processing" EXACT [GOC:bf]
synonym: "inhibition of sterol regulatory element binding protein cleavage" NARROW [GOC:TermGenie]
synonym: "negative regulation of SREBP cleavage" EXACT [GOC:TermGenie]
-is_a: GO:0010955 ! negative regulation of protein processing
-is_a: GO:1901308 ! regulation of sterol regulatory element binding protein cleavage
-is_a: GO:2000639 ! negative regulation of SREBP signaling pathway
-relationship: negatively_regulates GO:0035103 ! sterol regulatory element binding protein cleavage
+is_obsolete: true
[Term]
id: GO:1901310
-name: positive regulation of sterol regulatory element binding protein cleavage
+name: obsolete positive regulation of sterol regulatory element binding protein cleavage
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of sterol regulatory element binding protein cleavage." [GOC:TermGenie, PMID:15899885, PMID:16525117]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of sterol regulatory element binding protein cleavage." [GOC:TermGenie, PMID:15899885, PMID:16525117]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of SREBP cleavage" EXACT [GOC:TermGenie]
synonym: "activation of sterol regulatory element binding protein cleavage" NARROW [GOC:TermGenie]
synonym: "positive regulation of SREBP cleavage" EXACT [GOC:TermGenie]
@@ -444521,9 +447696,7 @@ synonym: "up-regulation of SREBP cleavage" EXACT [GOC:TermGenie]
synonym: "up-regulation of sterol regulatory element binding protein cleavage" EXACT [GOC:TermGenie]
synonym: "upregulation of SREBP cleavage" EXACT [GOC:TermGenie]
synonym: "upregulation of sterol regulatory element binding protein cleavage" EXACT [GOC:TermGenie]
-is_a: GO:0010954 ! positive regulation of protein processing
-is_a: GO:1901308 ! regulation of sterol regulatory element binding protein cleavage
-relationship: positively_regulates GO:0035103 ! sterol regulatory element binding protein cleavage
+is_obsolete: true
[Term]
id: GO:1901311
@@ -444695,9 +447868,9 @@ synonym: "upregulation of trehalose breakdown" EXACT [GOC:TermGenie]
synonym: "upregulation of trehalose catabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of trehalose catabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of trehalose degradation" EXACT [GOC:TermGenie]
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
-is_a: GO:0031331 ! positive regulation of cellular catabolic process
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
+is_a: GO:0009896 ! positive regulation of catabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:0090062 ! regulation of trehalose metabolic process
relationship: positively_regulates GO:0005993 ! trehalose catabolic process
@@ -444775,7 +447948,9 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tacrolimus stimulus." [GOC:TermGenie]
synonym: "response to FK506" EXACT [CHEBI:61057]
synonym: "response to tacrolimus hydrate" EXACT [CHEBI:61057]
-is_a: GO:0042221 ! response to chemical
+is_a: GO:0010243 ! response to organonitrogen compound
+is_a: GO:0014070 ! response to organic cyclic compound
+is_a: GO:1901700 ! response to oxygen-containing compound
[Term]
id: GO:1901328
@@ -445092,7 +448267,6 @@ id: GO:1901349
name: glucosinolate transport
namespace: biological_process
def: "The directed movement of a glucosinolate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:TermGenie]
-is_a: GO:0006820 ! anion transport
is_a: GO:0071705 ! nitrogen compound transport
is_a: GO:0072348 ! sulfur compound transport
is_a: GO:1901264 ! carbohydrate derivative transport
@@ -445123,6 +448297,7 @@ synonym: "regulation of phosphatidylglycerol anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of phosphatidylglycerol biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of phosphatidylglycerol formation" EXACT [GOC:TermGenie]
synonym: "regulation of phosphatidylglycerol synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0071071 ! regulation of phospholipid biosynthetic process
relationship: regulates GO:0006655 ! phosphatidylglycerol biosynthetic process
@@ -445155,6 +448330,7 @@ synonym: "negative regulation of phosphatidylglycerol anabolism" EXACT [GOC:Term
synonym: "negative regulation of phosphatidylglycerol biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of phosphatidylglycerol formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of phosphatidylglycerol synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
is_a: GO:0071072 ! negative regulation of phospholipid biosynthetic process
is_a: GO:1901351 ! regulation of phosphatidylglycerol biosynthetic process
relationship: negatively_regulates GO:0006655 ! phosphatidylglycerol biosynthetic process
@@ -445188,6 +448364,7 @@ synonym: "upregulation of phosphatidylglycerol biosynthesis" EXACT [GOC:TermGeni
synonym: "upregulation of phosphatidylglycerol biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of phosphatidylglycerol formation" EXACT [GOC:TermGenie]
synonym: "upregulation of phosphatidylglycerol synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:0071073 ! positive regulation of phospholipid biosynthetic process
is_a: GO:1901351 ! regulation of phosphatidylglycerol biosynthetic process
relationship: positively_regulates GO:0006655 ! phosphatidylglycerol biosynthetic process
@@ -445198,6 +448375,7 @@ name: response to L-canavanine
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a L-canavanine stimulus." [GOC:TermGenie]
is_a: GO:0043200 ! response to amino acid
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1901355
@@ -445329,6 +448507,7 @@ name: response to L-cysteine
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a L-cysteine stimulus." [GOC:TermGenie]
is_a: GO:0043200 ! response to amino acid
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1901369
@@ -445352,7 +448531,7 @@ id: GO:1901370
name: response to glutathione
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glutathione stimulus." [GOC:TermGenie]
-is_a: GO:1901652 ! response to peptide
+is_a: GO:0010033 ! response to organic substance
[Term]
id: GO:1901371
@@ -445450,7 +448629,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of potassium ion transmembrane transport." [GOC:BHF, GOC:TermGenie]
synonym: "regulation of potassium ion membrane transport" EXACT []
is_a: GO:0043266 ! regulation of potassium ion transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
+is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport
relationship: regulates GO:0071805 ! potassium ion transmembrane transport
[Term]
@@ -445661,6 +448840,8 @@ synonym: "regulation of TGF-B activation" EXACT [GOC:TermGenie]
synonym: "regulation of TGF-beta activation" EXACT [GOC:TermGenie]
synonym: "regulation of TGFB activation" EXACT [GOC:TermGenie]
synonym: "regulation of TGFbeta activation" EXACT [GOC:TermGenie]
+is_a: GO:0010646 ! regulation of cell communication
+is_a: GO:0023051 ! regulation of signaling
is_a: GO:0071634 ! regulation of transforming growth factor beta production
relationship: regulates GO:0036363 ! transforming growth factor beta activation
@@ -445703,6 +448884,8 @@ synonym: "negative regulation of TGF-B activation" EXACT [GOC:TermGenie]
synonym: "negative regulation of TGF-beta activation" EXACT [GOC:TermGenie]
synonym: "negative regulation of TGFB activation" EXACT [GOC:TermGenie]
synonym: "negative regulation of TGFbeta activation" EXACT [GOC:TermGenie]
+is_a: GO:0010648 ! negative regulation of cell communication
+is_a: GO:0023057 ! negative regulation of signaling
is_a: GO:0071635 ! negative regulation of transforming growth factor beta production
is_a: GO:1901388 ! regulation of transforming growth factor beta activation
relationship: negatively_regulates GO:0036363 ! transforming growth factor beta activation
@@ -445746,6 +448929,8 @@ synonym: "upregulation of TGF-beta activation" EXACT [GOC:TermGenie]
synonym: "upregulation of TGFB activation" EXACT [GOC:TermGenie]
synonym: "upregulation of TGFbeta activation" EXACT [GOC:TermGenie]
synonym: "upregulation of transforming growth factor beta activation" EXACT [GOC:TermGenie]
+is_a: GO:0010647 ! positive regulation of cell communication
+is_a: GO:0023056 ! positive regulation of signaling
is_a: GO:0071636 ! positive regulation of transforming growth factor beta production
is_a: GO:1901388 ! regulation of transforming growth factor beta activation
relationship: positively_regulates GO:0036363 ! transforming growth factor beta activation
@@ -446112,22 +449297,23 @@ relationship: positively_regulates GO:0033015 ! tetrapyrrole catabolic process
[Term]
id: GO:1901407
-name: regulation of phosphorylation of RNA polymerase II C-terminal domain
+name: obsolete regulation of phosphorylation of RNA polymerase II C-terminal domain
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain." [GOC:TermGenie]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain." [GOC:TermGenie]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "regulation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie]
synonym: "regulation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie]
synonym: "regulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie]
synonym: "regulation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie]
-is_a: GO:0001932 ! regulation of protein phosphorylation
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-relationship: regulates GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain
+is_obsolete: true
+consider: GO:0006357
[Term]
id: GO:1901408
-name: negative regulation of phosphorylation of RNA polymerase II C-terminal domain
+name: obsolete negative regulation of phosphorylation of RNA polymerase II C-terminal domain
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain." [GOC:TermGenie]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain." [GOC:TermGenie]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie]
synonym: "down regulation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie]
synonym: "down regulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie]
@@ -446152,15 +449338,15 @@ synonym: "negative regulation of CTD domain phosphorylation of RNA polymerase II
synonym: "negative regulation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie]
synonym: "negative regulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie]
synonym: "negative regulation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie]
-is_a: GO:0001933 ! negative regulation of protein phosphorylation
-is_a: GO:1901407 ! regulation of phosphorylation of RNA polymerase II C-terminal domain
-relationship: negatively_regulates GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain
+is_obsolete: true
+consider: GO:0006357
[Term]
id: GO:1901409
-name: positive regulation of phosphorylation of RNA polymerase II C-terminal domain
+name: obsolete positive regulation of phosphorylation of RNA polymerase II C-terminal domain
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain." [GOC:TermGenie]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain." [GOC:TermGenie]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of CTD domain phosphorylation of RNA polymerase II" EXACT [GOC:TermGenie]
synonym: "activation of generation of hyperphosphorylated CTD of RNA polymerase II" EXACT [GOC:TermGenie]
synonym: "activation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie]
@@ -446185,9 +449371,7 @@ synonym: "upregulation of generation of hyperphosphorylated CTD of RNA polymeras
synonym: "upregulation of generation of II(0) form of RNA polymerase II" EXACT [GOC:TermGenie]
synonym: "upregulation of hyperphosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie]
synonym: "upregulation of phosphorylation of RNA polymerase II C-terminal domain" EXACT [GOC:TermGenie]
-is_a: GO:0001934 ! positive regulation of protein phosphorylation
-is_a: GO:1901407 ! regulation of phosphorylation of RNA polymerase II C-terminal domain
-relationship: positively_regulates GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain
+is_obsolete: true
[Term]
id: GO:1901410
@@ -446280,7 +449464,7 @@ synonym: "regulation of tetrapyrrole biosynthesis from glycine and succinyl-CoA"
synonym: "regulation of tetrapyrrole formation from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
synonym: "regulation of tetrapyrrole synthesis from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
is_a: GO:0006521 ! regulation of cellular amino acid metabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0042762 ! regulation of sulfur metabolic process
is_a: GO:1900542 ! regulation of purine nucleotide metabolic process
is_a: GO:1901463 ! regulation of tetrapyrrole biosynthetic process
@@ -446315,7 +449499,7 @@ synonym: "negative regulation of tetrapyrrole anabolism from glycine and succiny
synonym: "negative regulation of tetrapyrrole biosynthesis from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
synonym: "negative regulation of tetrapyrrole formation from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
synonym: "negative regulation of tetrapyrrole synthesis from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0045763 ! negative regulation of cellular amino acid metabolic process
is_a: GO:0051175 ! negative regulation of sulfur metabolic process
is_a: GO:1900543 ! negative regulation of purine nucleotide metabolic process
@@ -446352,8 +449536,8 @@ synonym: "upregulation of tetrapyrrole biosynthesis from glycine and succinyl-Co
synonym: "upregulation of tetrapyrrole biosynthetic process from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
synonym: "upregulation of tetrapyrrole formation from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
synonym: "upregulation of tetrapyrrole synthesis from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
-is_a: GO:0045764 ! positive regulation of cellular amino acid metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
+is_a: GO:0045764 ! positive regulation of amino acid metabolic process
is_a: GO:0051176 ! positive regulation of sulfur metabolic process
is_a: GO:1900544 ! positive regulation of purine nucleotide metabolic process
is_a: GO:1901413 ! regulation of tetrapyrrole biosynthetic process from glycine and succinyl-CoA
@@ -446458,7 +449642,9 @@ name: response to formic acid
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a formic acid stimulus." [GOC:mengo_curators, GOC:TermGenie]
is_a: GO:0010033 ! response to organic substance
+is_a: GO:1901698 ! response to nitrogen compound
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1901426
@@ -447251,18 +450437,16 @@ def: "The directed movement of pyruvate across a membrane." [GOC:TermGenie]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "pyruvate membrane transport" EXACT []
is_a: GO:0006848 ! pyruvate transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:1901477
-name: benomyl transmembrane transport
+name: obsolete benomyl transmembrane transport
namespace: biological_process
-def: "The directed movement of benomyl across a membrane." [GOC:TermGenie]
-comment: Note that this term is not intended for use in annotating lateral movement within membranes.
+def: "OBSOLETE. The directed movement of benomyl across a membrane." [GOC:TermGenie]
+comment: Note that this term is not intended for use in annotating lateral movement within membranes.\nThis term is out of scope for GO.
synonym: "benomyl membrane transport" EXACT []
-is_a: GO:0015900 ! benomyl transport
-is_a: GO:0055085 ! transmembrane transport
+is_obsolete: true
[Term]
id: GO:1901478
@@ -447275,13 +450459,13 @@ is_a: GO:1901474 ! azole transmembrane transporter activity
[Term]
id: GO:1901479
-name: benomyl transmembrane transporter activity
+name: obsolete benomyl transmembrane transporter activity
namespace: molecular_function
alt_id: GO:0015242
-def: "Enables the transfer of benomyl from one side of a membrane to the other." [GOC:TermGenie]
+def: "OBSOLETE. Enables the transfer of benomyl from one side of a membrane to the other." [GOC:TermGenie]
+comment: The reason for obsoletion is that these terms are beyond the scope of GO.
synonym: "benomyl transporter activity" RELATED []
-is_a: GO:0042887 ! amide transmembrane transporter activity
-is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
+is_obsolete: true
[Term]
id: GO:1901480
@@ -447291,7 +450475,6 @@ def: "Enables the transfer of oleate from one side of a membrane to the other."
synonym: "oleate transporter activity" RELATED []
xref: RHEA:33655
is_a: GO:0005324 ! long-chain fatty acid transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015245 ! fatty acid transmembrane transporter activity
[Term]
@@ -447547,7 +450730,7 @@ synonym: "up-regulation of cysteine metabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of cysteine metabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of cysteine metabolism" EXACT [GOC:TermGenie]
is_a: GO:0031337 ! positive regulation of sulfur amino acid metabolic process
-is_a: GO:0045764 ! positive regulation of cellular amino acid metabolic process
+is_a: GO:0045764 ! positive regulation of amino acid metabolic process
is_a: GO:1901494 ! regulation of cysteine metabolic process
relationship: positively_regulates GO:0006534 ! cysteine metabolic process
@@ -447915,6 +451098,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hypochlorite stimulus." [GOC:pr, GOC:TermGenie, PMID:22223481]
is_a: GO:0000302 ! response to reactive oxygen species
is_a: GO:0010035 ! response to inorganic substance
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1901531
@@ -448034,8 +451218,7 @@ synonym: "changes in DNA methylation involved in embryogenesis" EXACT [GOC:TermG
synonym: "changes in DNA methylation involved in embryonal development" RELATED [GOC:TermGenie]
synonym: "DNA methylation or demethylation involved in embryogenesis" EXACT [GOC:TermGenie]
synonym: "DNA methylation or demethylation involved in embryonal development" EXACT [GOC:TermGenie]
-is_a: GO:0044728 ! DNA methylation or demethylation
-relationship: part_of GO:0009790 ! embryo development
+is_a: GO:0040029 ! epigenetic regulation of gene expression
[Term]
id: GO:1901539
@@ -448168,7 +451351,6 @@ subset: goslim_synapse
synonym: "regulation of synaptic vesicle lumen pH reduction" EXACT [GOC:TermGenie]
synonym: "regulation of synaptic vesicle lumen proton loading" EXACT syngo_official_label []
is_a: GO:0010155 ! regulation of proton transport
-is_a: GO:0065008 ! regulation of biological quality
relationship: regulates GO:0097401 ! synaptic vesicle lumen acidification
[Term]
@@ -448253,7 +451435,6 @@ namespace: biological_process
def: "The directed movement of malonic acid across a membrane." [GOC:al, GOC:TermGenie]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "malonic acid membrane transport" EXACT []
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1900752 ! malonic acid transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
@@ -448269,10 +451450,12 @@ is_a: GO:1901700 ! response to oxygen-containing compound
[Term]
id: GO:1901555
-name: response to paclitaxel
+name: obsolete response to paclitaxel
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a paclitaxel stimulus." [GOC:TermGenie]
-is_a: GO:0033993 ! response to lipid
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a paclitaxel stimulus." [GOC:TermGenie]
+comment: This term was obsoleted because it represents a response to xenobiotic stimulus, and GO terms are not created for every xenobiotic.
+is_obsolete: true
+replaced_by: GO:0009410
[Term]
id: GO:1901556
@@ -448317,12 +451500,11 @@ is_a: GO:0014074 ! response to purine-containing compound
[Term]
id: GO:1901561
-name: response to benomyl
+name: obsolete response to benomyl
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a benomyl stimulus." [GOC:TermGenie]
-is_a: GO:0010243 ! response to organonitrogen compound
-is_a: GO:0014070 ! response to organic cyclic compound
-is_a: GO:1901700 ! response to oxygen-containing compound
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a benomyl stimulus." [GOC:TermGenie]
+comment: This term is out of scope for GO.
+is_obsolete: true
[Term]
id: GO:1901562
@@ -448330,6 +451512,7 @@ name: response to paraquat
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a paraquat stimulus." [GOC:TermGenie]
is_a: GO:0010033 ! response to organic substance
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1901563
@@ -448378,7 +451561,7 @@ id: GO:1901567
name: fatty acid derivative binding
namespace: molecular_function
def: "Binding to fatty acid derivative." [GOC:pr, GOC:TermGenie]
-is_a: GO:0005488 ! binding
+is_a: GO:0008289 ! lipid binding
[Term]
id: GO:1901568
@@ -448386,7 +451569,7 @@ name: fatty acid derivative metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving fatty acid derivative." [GOC:pr, GOC:TermGenie]
synonym: "fatty acid derivative metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0071704 ! organic substance metabolic process
+is_a: GO:0006629 ! lipid metabolic process
[Term]
id: GO:1901569
@@ -448396,8 +451579,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of fatty ac
synonym: "fatty acid derivative breakdown" EXACT [GOC:TermGenie]
synonym: "fatty acid derivative catabolism" EXACT [GOC:TermGenie]
synonym: "fatty acid derivative degradation" EXACT [GOC:TermGenie]
+is_a: GO:0016042 ! lipid catabolic process
is_a: GO:1901568 ! fatty acid derivative metabolic process
-is_a: GO:1901575 ! organic substance catabolic process
[Term]
id: GO:1901570
@@ -448408,15 +451591,15 @@ synonym: "fatty acid derivative anabolism" EXACT [GOC:TermGenie]
synonym: "fatty acid derivative biosynthesis" EXACT [GOC:TermGenie]
synonym: "fatty acid derivative formation" EXACT [GOC:TermGenie]
synonym: "fatty acid derivative synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:1901568 ! fatty acid derivative metabolic process
-is_a: GO:1901576 ! organic substance biosynthetic process
[Term]
id: GO:1901571
name: fatty acid derivative transport
namespace: biological_process
def: "The directed movement of a fatty acid derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:pr, GOC:TermGenie]
-is_a: GO:0071702 ! organic substance transport
+is_a: GO:0006869 ! lipid transport
[Term]
id: GO:1901572
@@ -448570,6 +451753,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of telomeric RNA transcription from RNA pol II promoter." [GOC:TermGenie]
synonym: "regulation of telomeric RNA transcription from Pol II promoter" EXACT [GOC:TermGenie]
is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
+is_a: GO:0140747 ! regulation of ncRNA transcription
relationship: regulates GO:0097394 ! telomeric repeat-containing RNA transcription by RNA polymerase II
[Term]
@@ -448610,12 +451794,13 @@ relationship: positively_regulates GO:0097394 ! telomeric repeat-containing RNA
[Term]
id: GO:1901583
-name: tetrapeptide transmembrane transport
+name: tetrapeptide import across plasma membrane
namespace: biological_process
-def: "The directed movement of tetrapeptide across a membrane." [GOC:TermGenie]
+def: "The directed movement of a tetrapeptide from outside of a cell, across the plasma membrane and into the cytosol." [GOC:TermGenie, PMID:22226946]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "tetrapeptide membrane transport" EXACT []
-is_a: GO:0035672 ! oligopeptide transmembrane transport
+synonym: "tetrapeptide transmembrane transport" BROAD []
+is_a: GO:0140205 ! oligopeptide import across plasma membrane
[Term]
id: GO:1901584
@@ -448813,7 +451998,6 @@ namespace: molecular_function
def: "Binding to dethiobiotin." [GOC:TermGenie]
is_a: GO:0033218 ! amide binding
is_a: GO:0033293 ! monocarboxylic acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -448823,7 +452007,6 @@ name: dethiobiotin transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of dethiobiotin from one side of a membrane to the other." [GOC:TermGenie]
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0042887 ! amide transmembrane transporter activity
[Term]
@@ -448832,7 +452015,7 @@ name: alpha-amino acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving an alpha-amino acid." [GOC:TermGenie]
synonym: "alpha-amino acid metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0006520 ! amino acid metabolic process
[Term]
id: GO:1901606
@@ -448842,7 +452025,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of an alpha
synonym: "alpha-amino acid breakdown" EXACT [GOC:TermGenie]
synonym: "alpha-amino acid catabolism" EXACT [GOC:TermGenie]
synonym: "alpha-amino acid degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016054 ! organic acid catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
is_a: GO:1901605 ! alpha-amino acid metabolic process
@@ -448855,7 +452038,7 @@ synonym: "alpha-amino acid anabolism" EXACT [GOC:TermGenie]
synonym: "alpha-amino acid biosynthesis" EXACT [GOC:TermGenie]
synonym: "alpha-amino acid formation" EXACT [GOC:TermGenie]
synonym: "alpha-amino acid synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
+is_a: GO:0008652 ! amino acid biosynthetic process
is_a: GO:1901605 ! alpha-amino acid metabolic process
[Term]
@@ -448882,7 +452065,6 @@ synonym: "inhibition of microtubule-based vesicle localization" EXACT [GOC:TermG
synonym: "inhibition of vesicle transport along microtubule" NARROW [GOC:TermGenie]
synonym: "negative regulation of microtubule-based vesicle localization" EXACT [GOC:TermGenie]
is_a: GO:0032387 ! negative regulation of intracellular transport
-is_a: GO:0051271 ! negative regulation of cellular component movement
is_a: GO:1901608 ! regulation of vesicle transport along microtubule
relationship: negatively_regulates GO:0047496 ! vesicle transport along microtubule
@@ -448901,7 +452083,6 @@ synonym: "up-regulation of vesicle transport along microtubule" EXACT [GOC:TermG
synonym: "upregulation of microtubule-based vesicle localization" EXACT [GOC:TermGenie]
synonym: "upregulation of vesicle transport along microtubule" EXACT [GOC:TermGenie]
is_a: GO:0032388 ! positive regulation of intracellular transport
-is_a: GO:0051272 ! positive regulation of cellular component movement
is_a: GO:1901608 ! regulation of vesicle transport along microtubule
relationship: positively_regulates GO:0047496 ! vesicle transport along microtubule
@@ -449407,7 +452588,7 @@ id: GO:1901645
name: regulation of synoviocyte proliferation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of synoviocyte proliferation." [GOC:TermGenie]
-is_a: GO:0042127 ! regulation of cell population proliferation
+is_a: GO:0050678 ! regulation of epithelial cell proliferation
relationship: regulates GO:0002941 ! synoviocyte proliferation
[Term]
@@ -449419,7 +452600,7 @@ synonym: "down regulation of synoviocyte proliferation" EXACT [GOC:TermGenie]
synonym: "down-regulation of synoviocyte proliferation" EXACT [GOC:TermGenie]
synonym: "downregulation of synoviocyte proliferation" EXACT [GOC:TermGenie]
synonym: "inhibition of synoviocyte proliferation" NARROW [GOC:TermGenie]
-is_a: GO:0008285 ! negative regulation of cell population proliferation
+is_a: GO:0050680 ! negative regulation of epithelial cell proliferation
is_a: GO:1901645 ! regulation of synoviocyte proliferation
relationship: negatively_regulates GO:0002941 ! synoviocyte proliferation
@@ -449432,7 +452613,7 @@ synonym: "activation of synoviocyte proliferation" NARROW [GOC:TermGenie]
synonym: "up regulation of synoviocyte proliferation" EXACT [GOC:TermGenie]
synonym: "up-regulation of synoviocyte proliferation" EXACT [GOC:TermGenie]
synonym: "upregulation of synoviocyte proliferation" EXACT [GOC:TermGenie]
-is_a: GO:0008284 ! positive regulation of cell population proliferation
+is_a: GO:0050679 ! positive regulation of epithelial cell proliferation
is_a: GO:1901645 ! regulation of synoviocyte proliferation
relationship: positively_regulates GO:0002941 ! synoviocyte proliferation
@@ -449495,12 +452676,11 @@ relationship: positively_regulates GO:0032187 ! actomyosin contractile ring loca
[Term]
id: GO:1901651
-name: regulation of mitotic chromosome decondensation
+name: obsolete regulation of mitotic chromosome decondensation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of mitotic chromosome decondensation." [GOC:TermGenie]
-is_a: GO:0010564 ! regulation of cell cycle process
-is_a: GO:0033044 ! regulation of chromosome organization
-relationship: regulates GO:0007083 ! mitotic chromosome decondensation
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of mitotic chromosome decondensation." [GOC:TermGenie]
+comment: This term was obsoleted because it is a spontaneous process.
+is_obsolete: true
[Term]
id: GO:1901652
@@ -449581,7 +452761,6 @@ name: calcium ion export
namespace: biological_process
def: "The directed movement of calcium ion out of a cell or organelle." [GOC:TermGenie]
is_a: GO:0006816 ! calcium ion transport
-is_a: GO:0070839 ! metal ion export
[Term]
id: GO:1901661
@@ -450133,19 +453312,22 @@ relationship: regulates GO:0090307 ! mitotic spindle assembly
[Term]
id: GO:1901674
-name: regulation of histone H3-K27 acetylation
+name: obsolete regulation of histone H3-K27 acetylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone H3-K27 acetylation." [GOC:BHF, GOC:TermGenie]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone H3-K27 acetylation." [GOC:BHF, GOC:TermGenie]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "regulation of histone H3 acetylation at K27" EXACT [GOC:TermGenie]
synonym: "regulation of histone H3K27 acetylation" EXACT [GOC:TermGenie]
-is_a: GO:0035065 ! regulation of histone acetylation
-relationship: regulates GO:0043974 ! histone H3-K27 acetylation
+is_obsolete: true
+consider: GO:0031507
+consider: GO:0045815
[Term]
id: GO:1901675
-name: negative regulation of histone H3-K27 acetylation
+name: obsolete negative regulation of histone H3-K27 acetylation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K27 acetylation." [GOC:BHF, GOC:TermGenie]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K27 acetylation." [GOC:BHF, GOC:TermGenie]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of histone H3 acetylation at K27" EXACT [GOC:TermGenie]
synonym: "down regulation of histone H3-K27 acetylation" EXACT [GOC:TermGenie]
synonym: "down regulation of histone H3K27 acetylation" EXACT [GOC:TermGenie]
@@ -450160,15 +453342,15 @@ synonym: "inhibition of histone H3-K27 acetylation" NARROW [GOC:TermGenie]
synonym: "inhibition of histone H3K27 acetylation" EXACT [GOC:TermGenie]
synonym: "negative regulation of histone H3 acetylation at K27" EXACT [GOC:TermGenie]
synonym: "negative regulation of histone H3K27 acetylation" EXACT [GOC:TermGenie]
-is_a: GO:0035067 ! negative regulation of histone acetylation
-is_a: GO:1901674 ! regulation of histone H3-K27 acetylation
-relationship: negatively_regulates GO:0043974 ! histone H3-K27 acetylation
+is_obsolete: true
+consider: GO:0031507
[Term]
id: GO:1901676
-name: positive regulation of histone H3-K27 acetylation
+name: obsolete positive regulation of histone H3-K27 acetylation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of histone H3-K27 acetylation." [GOC:BHF, GOC:TermGenie]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of histone H3-K27 acetylation." [GOC:BHF, GOC:TermGenie]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of histone H3 acetylation at K27" EXACT [GOC:TermGenie]
synonym: "activation of histone H3-K27 acetylation" NARROW [GOC:TermGenie]
synonym: "activation of histone H3K27 acetylation" EXACT [GOC:TermGenie]
@@ -450183,9 +453365,8 @@ synonym: "up-regulation of histone H3K27 acetylation" EXACT [GOC:TermGenie]
synonym: "upregulation of histone H3 acetylation at K27" EXACT [GOC:TermGenie]
synonym: "upregulation of histone H3-K27 acetylation" EXACT [GOC:TermGenie]
synonym: "upregulation of histone H3K27 acetylation" EXACT [GOC:TermGenie]
-is_a: GO:0035066 ! positive regulation of histone acetylation
-is_a: GO:1901674 ! regulation of histone H3-K27 acetylation
-relationship: positively_regulates GO:0043974 ! histone H3-K27 acetylation
+is_obsolete: true
+consider: GO:0045815
[Term]
id: GO:1901678
@@ -450233,7 +453414,7 @@ id: GO:1901683
name: arsenate ion transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of an arsenate ion from one side of a membrane to the other." [GOC:TermGenie]
-is_a: GO:0008509 ! anion transmembrane transporter activity
+is_a: GO:0022857 ! transmembrane transporter activity
[Term]
id: GO:1901684
@@ -450241,7 +453422,7 @@ name: arsenate ion transmembrane transport
namespace: biological_process
def: "The process in which arsenate is transported across a membrane." [GOC:TermGenie]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:1901685
@@ -450446,8 +453627,7 @@ id: GO:1901707
name: leptomycin B binding
namespace: molecular_function
def: "Binding to leptomycin B." [GOC:TermGenie]
-is_a: GO:0008289 ! lipid binding
-is_a: GO:0043177 ! organic acid binding
+is_a: GO:0005504 ! fatty acid binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -450455,7 +453635,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:1901708
name: (+)-3'-hydroxylarreatricin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of (+)-3'-hydroxylarreatricin." [GOC:TermGenie, pmid:12960376]
+def: "The chemical reactions and pathways resulting in the formation of (+)-3'-hydroxylarreatricin." [GOC:TermGenie, PMID:12960376]
synonym: "(+)-3'-hydroxylarreatricin anabolism" EXACT [GOC:TermGenie]
synonym: "(+)-3'-hydroxylarreatricin biosynthesis" EXACT [GOC:TermGenie]
synonym: "(+)-3'-hydroxylarreatricin formation" EXACT [GOC:TermGenie]
@@ -450467,7 +453647,7 @@ is_a: GO:0018130 ! heterocycle biosynthetic process
id: GO:1901709
name: (+)-larreatricin metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving (+)-larreatricin." [GOC:TermGenie, pmid:12960376]
+def: "The chemical reactions and pathways involving (+)-larreatricin." [GOC:TermGenie, PMID:12960376]
synonym: "(+)-larreatricin metabolism" EXACT [GOC:TermGenie]
is_a: GO:0009806 ! lignan metabolic process
is_a: GO:0018958 ! phenol-containing compound metabolic process
@@ -450515,7 +453695,7 @@ synonym: "negative regulation of homoserine biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of homoserine formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of homoserine synthesis" EXACT [GOC:TermGenie]
is_a: GO:1901710 ! regulation of homoserine biosynthetic process
-is_a: GO:2000283 ! negative regulation of cellular amino acid biosynthetic process
+is_a: GO:2000283 ! negative regulation of amino acid biosynthetic process
relationship: negatively_regulates GO:0009090 ! homoserine biosynthetic process
[Term]
@@ -450548,7 +453728,7 @@ synonym: "upregulation of homoserine biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of homoserine formation" EXACT [GOC:TermGenie]
synonym: "upregulation of homoserine synthesis" EXACT [GOC:TermGenie]
is_a: GO:1901710 ! regulation of homoserine biosynthetic process
-is_a: GO:2000284 ! positive regulation of cellular amino acid biosynthetic process
+is_a: GO:2000284 ! positive regulation of amino acid biosynthetic process
relationship: positively_regulates GO:0009090 ! homoserine biosynthetic process
[Term]
@@ -450580,7 +453760,7 @@ synonym: "negative regulation of urea breakdown" EXACT [GOC:TermGenie]
synonym: "negative regulation of urea catabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of urea decomposition" EXACT [GOC:TermGenie]
synonym: "negative regulation of urea degradation" EXACT [GOC:TermGenie]
-is_a: GO:0034252 ! negative regulation of cellular amide catabolic process
+is_a: GO:0034252 ! negative regulation of amide catabolic process
is_a: GO:0034254 ! regulation of urea catabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1903315 ! negative regulation of nitrogen cycle metabolic process
@@ -450615,7 +453795,7 @@ synonym: "upregulation of urea catabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of urea catabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of urea decomposition" EXACT [GOC:TermGenie]
synonym: "upregulation of urea degradation" EXACT [GOC:TermGenie]
-is_a: GO:0034253 ! positive regulation of cellular amide catabolic process
+is_a: GO:0034253 ! positive regulation of amide catabolic process
is_a: GO:0034254 ! regulation of urea catabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1903316 ! positive regulation of nitrogen cycle metabolic process
@@ -450753,7 +453933,7 @@ synonym: "upregulation of gamma-aminobutyric acid catabolic process" EXACT [GOC:
synonym: "upregulation of gamma-aminobutyric acid catabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of gamma-aminobutyric acid degradation" EXACT [GOC:TermGenie]
is_a: GO:0031331 ! positive regulation of cellular catabolic process
-is_a: GO:0045764 ! positive regulation of cellular amino acid metabolic process
+is_a: GO:0045764 ! positive regulation of amino acid metabolic process
is_a: GO:1901715 ! regulation of gamma-aminobutyric acid catabolic process
relationship: positively_regulates GO:0009450 ! gamma-aminobutyric acid catabolic process
@@ -450765,76 +453945,6 @@ def: "OBSOLETE. A regulation of transcription from RNA polymerase II promoter th
comment: The term was obsoleted because it is better represented by a GO-CAM model.
is_obsolete: true
-[Term]
-id: GO:1901719
-name: regulation of NMS complex assembly
-namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of NMS complex assembly. The NMS complex is involved in chromosome segregation." [GOC:TermGenie, GOC:vw, PMID:22561345]
-synonym: "regulation of KMN complex assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "regulation of KMN network assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "regulation of NMS complex assembly involved in kinetochore assembly" EXACT []
-synonym: "regulation of NMS complex association involved in chromosome segregation" EXACT [GOC:TermGenie]
-is_a: GO:0090234 ! regulation of kinetochore assembly
-relationship: regulates GO:0044768 ! NMS complex assembly
-
-[Term]
-id: GO:1901720
-name: negative regulation of NMS complex assembly
-namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of NMS complex assembly. The NMS complex is involved in chromosome segregation." [GOC:TermGenie, GOC:vw, PMID:22561345]
-synonym: "down regulation of KMN complex assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "down regulation of KMN network assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "down regulation of NMS complex association involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "down regulation of NMS complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "down-regulation of KMN complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "down-regulation of KMN network assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "down-regulation of NMS complex association involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "down-regulation of NMS complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "downregulation of KMN complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "downregulation of KMN network assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "downregulation of NMS complex association involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "downregulation of NMS complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "inhibition of KMN complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "inhibition of KMN network assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "inhibition of NMS complex association involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "inhibition of NMS complex interaction involved in chromosome segregation" NARROW [GOC:TermGenie]
-synonym: "negative regulation of KMN complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "negative regulation of KMN network assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "negative regulation of NMS complex assembly involved in kinetochore assembly" EXACT []
-synonym: "negative regulation of NMS complex association involved in chromosome segregation" EXACT [GOC:TermGenie]
-is_a: GO:1901719 ! regulation of NMS complex assembly
-is_a: GO:1905560 ! negative regulation of kinetochore assembly
-relationship: negatively_regulates GO:0044768 ! NMS complex assembly
-
-[Term]
-id: GO:1901721
-name: positive regulation of NMS complex assembly
-namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of NMS complex assembly. The NMS complex is involved in chromosome segregation." [GOC:TermGenie, GOC:vw, PMID:22561345]
-synonym: "activation of KMN complex assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "activation of KMN network assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "activation of NMS complex association involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "activation of NMS complex interaction involved in chromosome segregation" NARROW [GOC:TermGenie]
-synonym: "positive regulation of KMN complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "positive regulation of KMN network assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "positive regulation of NMS complex assembly involved in kinetochore assembly" EXACT []
-synonym: "positive regulation of NMS complex association involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "up regulation of KMN complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "up regulation of KMN network assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "up regulation of NMS complex association involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "up regulation of NMS complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "up-regulation of KMN complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "up-regulation of KMN network assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "up-regulation of NMS complex association involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "up-regulation of NMS complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "upregulation of KMN complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "upregulation of KMN network assembly involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "upregulation of NMS complex association involved in chromosome segregation" EXACT [GOC:TermGenie]
-synonym: "upregulation of NMS complex interaction involved in chromosome segregation" EXACT [GOC:TermGenie]
-is_a: GO:1901719 ! regulation of NMS complex assembly
-is_a: GO:1905561 ! positive regulation of kinetochore assembly
-relationship: positively_regulates GO:0044768 ! NMS complex assembly
-
[Term]
id: GO:1901722
name: regulation of cell proliferation involved in kidney development
@@ -450911,7 +454021,7 @@ def: "The chemical reactions and pathways involving monensin A." [GOC:TermGenie,
synonym: "monensin A metabolism" EXACT [GOC:TermGenie]
synonym: "monensin metabolism" EXACT [GOC:yaf]
is_a: GO:0006066 ! alcohol metabolic process
-is_a: GO:0006082 ! organic acid metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
@@ -450926,8 +454036,8 @@ synonym: "monensin A degradation" EXACT [GOC:TermGenie]
synonym: "monensin breakdown" EXACT [GOC:yaf]
synonym: "monensin catabolism" EXACT [GOC:yaf]
synonym: "monensin degradation" EXACT [GOC:yaf]
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0046164 ! alcohol catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:0046700 ! heterocycle catabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
is_a: GO:1901728 ! monensin A metabolic process
@@ -450945,9 +454055,9 @@ synonym: "monensin anabolism" EXACT [GOC:yaf]
synonym: "monensin biosynthesis" EXACT [GOC:yaf]
synonym: "monensin formation" EXACT [GOC:yaf]
synonym: "monensin synthesis" EXACT [GOC:yaf]
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0046165 ! alcohol biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
is_a: GO:1901728 ! monensin A metabolic process
@@ -451210,9 +454320,8 @@ name: leukotriene A4 metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving leukotriene A4." [GOC:TermGenie, GOC:yaf]
synonym: "leukotriene A4 metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006629 ! lipid metabolic process
+is_a: GO:0001676 ! long-chain fatty acid metabolic process
is_a: GO:0006691 ! leukotriene metabolic process
-is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:0097176 ! epoxide metabolic process
is_a: GO:1901568 ! fatty acid derivative metabolic process
@@ -451224,10 +454333,9 @@ def: "The chemical reactions and pathways resulting in the breakdown of leukotri
synonym: "leukotriene A4 breakdown" EXACT [GOC:TermGenie]
synonym: "leukotriene A4 catabolism" EXACT [GOC:TermGenie]
synonym: "leukotriene A4 degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016042 ! lipid catabolic process
is_a: GO:0036100 ! leukotriene catabolic process
+is_a: GO:0042758 ! long-chain fatty acid catabolic process
is_a: GO:0046700 ! heterocycle catabolic process
-is_a: GO:0072329 ! monocarboxylic acid catabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
is_a: GO:1901502 ! ether catabolic process
is_a: GO:1901523 ! icosanoid catabolic process
@@ -451244,10 +454352,9 @@ synonym: "leukotriene A4 biosynthesis" EXACT [GOC:TermGenie]
synonym: "leukotriene A4 formation" EXACT [GOC:TermGenie]
synonym: "leukotriene A4 synthesis" EXACT [GOC:TermGenie]
synonym: "LTA4 biosynthesis" EXACT []
-is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0019370 ! leukotriene biosynthetic process
-is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
+is_a: GO:0042759 ! long-chain fatty acid biosynthetic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
is_a: GO:1901503 ! ether biosynthetic process
is_a: GO:1901570 ! fatty acid derivative biosynthetic process
@@ -451289,6 +454396,7 @@ synonym: "vitamin D3 formation" EXACT [GOC:yaf]
synonym: "vitamin D3 synthesis" EXACT [GOC:yaf]
is_a: GO:0042368 ! vitamin D biosynthetic process
is_a: GO:0070640 ! vitamin D3 metabolic process
+is_a: GO:0120178 ! steroid hormone biosynthetic process
is_a: GO:1902653 ! secondary alcohol biosynthetic process
[Term]
@@ -451485,7 +454593,7 @@ def: "The chemical reactions and pathways involving lincomycin." [GOC:TermGenie,
synonym: "lincomycin metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006575 ! cellular modified amino acid metabolic process
is_a: GO:0016143 ! S-glycoside metabolic process
-is_a: GO:0043603 ! cellular amide metabolic process
+is_a: GO:0043603 ! amide metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
@@ -451818,8 +454926,9 @@ synonym: "inhibition of proteasome-mediated protein catabolic process" EXACT [GO
synonym: "inhibition of proteasome-mediated protein catabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of proteasome-mediated protein catabolic process" EXACT [GOC:TermGenie]
synonym: "negative regulation of proteasome-mediated protein catabolism" EXACT [GOC:TermGenie]
+is_a: GO:0042177 ! negative regulation of protein catabolic process
is_a: GO:0061136 ! regulation of proteasomal protein catabolic process
-is_a: GO:1903051 ! negative regulation of proteolysis involved in cellular protein catabolic process
+is_a: GO:1903051 ! negative regulation of proteolysis involved in protein catabolic process
relationship: negatively_regulates GO:0010498 ! proteasomal protein catabolic process
[Term]
@@ -451841,8 +454950,9 @@ synonym: "up-regulation of proteasome-mediated protein catabolism" EXACT [GOC:Te
synonym: "upregulation of proteasomal protein catabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of proteasome-mediated protein catabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of proteasome-mediated protein catabolism" EXACT [GOC:TermGenie]
+is_a: GO:0045732 ! positive regulation of protein catabolic process
is_a: GO:0061136 ! regulation of proteasomal protein catabolic process
-is_a: GO:1903052 ! positive regulation of proteolysis involved in cellular protein catabolic process
+is_a: GO:1903052 ! positive regulation of proteolysis involved in protein catabolic process
relationship: positively_regulates GO:0010498 ! proteasomal protein catabolic process
[Term]
@@ -452284,6 +455394,7 @@ def: "Any process that modulates the frequency, rate or extent of transcription
synonym: "regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter" EXACT []
synonym: "regulation of transcription of nuclear rRNA large Pol I transcript" EXACT [GOC:TermGenie]
is_a: GO:0006356 ! regulation of transcription by RNA polymerase I
+is_a: GO:0140747 ! regulation of ncRNA transcription
relationship: regulates GO:0042790 ! nucleolar large rRNA transcription by RNA polymerase I
[Term]
@@ -453034,7 +456145,7 @@ relationship: positively_regulates GO:0051261 ! protein depolymerization
id: GO:1901882
name: 4-hydroxycoumarin metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving 4-hydroxycoumarin." [GOC:TermGenie, pmid:19757094]
+def: "The chemical reactions and pathways involving 4-hydroxycoumarin." [GOC:TermGenie, PMID:19757094]
synonym: "4-hydroxycoumarin metabolism" EXACT [GOC:TermGenie]
is_a: GO:0009804 ! coumarin metabolic process
@@ -453042,7 +456153,7 @@ is_a: GO:0009804 ! coumarin metabolic process
id: GO:1901883
name: 4-hydroxycoumarin catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 4-hydroxycoumarin." [GOC:TermGenie, pmid:19757094]
+def: "The chemical reactions and pathways resulting in the breakdown of 4-hydroxycoumarin." [GOC:TermGenie, PMID:19757094]
synonym: "4-hydroxycoumarin breakdown" EXACT [GOC:TermGenie]
synonym: "4-hydroxycoumarin catabolism" EXACT [GOC:TermGenie]
synonym: "4-hydroxycoumarin degradation" EXACT [GOC:TermGenie]
@@ -453053,7 +456164,7 @@ is_a: GO:1901882 ! 4-hydroxycoumarin metabolic process
id: GO:1901884
name: 4-hydroxycoumarin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 4-hydroxycoumarin." [GOC:TermGenie, pmid:19757094]
+def: "The chemical reactions and pathways resulting in the formation of 4-hydroxycoumarin." [GOC:TermGenie, PMID:19757094]
synonym: "4-hydroxycoumarin anabolism" EXACT [GOC:TermGenie]
synonym: "4-hydroxycoumarin biosynthesis" EXACT [GOC:TermGenie]
synonym: "4-hydroxycoumarin formation" EXACT [GOC:TermGenie]
@@ -453065,7 +456176,7 @@ is_a: GO:1901882 ! 4-hydroxycoumarin metabolic process
id: GO:1901885
name: 2-hydroxybenzoyl-CoA metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving 2-hydroxybenzoyl-CoA." [GOC:TermGenie, pmid:19757094]
+def: "The chemical reactions and pathways involving 2-hydroxybenzoyl-CoA." [GOC:TermGenie, PMID:19757094]
synonym: "2-hydroxybenzoyl-CoA metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006637 ! acyl-CoA metabolic process
is_a: GO:0018958 ! phenol-containing compound metabolic process
@@ -453074,7 +456185,7 @@ is_a: GO:0018958 ! phenol-containing compound metabolic process
id: GO:1901886
name: 2-hydroxybenzoyl-CoA catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 2-hydroxybenzoyl-CoA." [GOC:TermGenie, pmid:19757094]
+def: "The chemical reactions and pathways resulting in the breakdown of 2-hydroxybenzoyl-CoA." [GOC:TermGenie, PMID:19757094]
synonym: "2-hydroxybenzoyl-CoA breakdown" EXACT [GOC:TermGenie]
synonym: "2-hydroxybenzoyl-CoA catabolism" EXACT [GOC:TermGenie]
synonym: "2-hydroxybenzoyl-CoA degradation" EXACT [GOC:TermGenie]
@@ -453089,7 +456200,7 @@ is_a: GO:1901885 ! 2-hydroxybenzoyl-CoA metabolic process
id: GO:1901887
name: 2-hydroxybenzoyl-CoA biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 2-hydroxybenzoyl-CoA." [GOC:TermGenie, pmid:19757094]
+def: "The chemical reactions and pathways resulting in the formation of 2-hydroxybenzoyl-CoA." [GOC:TermGenie, PMID:19757094]
synonym: "2-hydroxybenzoyl-CoA anabolism" EXACT [GOC:TermGenie]
synonym: "2-hydroxybenzoyl-CoA biosynthesis" EXACT [GOC:TermGenie]
synonym: "2-hydroxybenzoyl-CoA formation" EXACT [GOC:TermGenie]
@@ -453198,7 +456309,7 @@ is_a: GO:1901019 ! regulation of calcium ion transmembrane transporter activity
id: GO:1901895
name: negative regulation of ATPase-coupled calcium transmembrane transporter activity
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of an ATPase-coupled calcium transmembrane transporter activity." [GOC:BHF, GOC:rl, GOC:TermGenie, PMID:19708671]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of an ATPase-coupled calcium transmembrane transporter activity." [GOC:BHF, GOC:rl, GOC:TermGenie, PMID:19708671]
synonym: "down regulation of ATP phosphohydrolase (Ca2+-transporting)" EXACT [GOC:TermGenie]
synonym: "down regulation of Ca(2+)-transporting ATPase activity" EXACT [GOC:TermGenie]
synonym: "down regulation of Ca2+-pumping ATPase activity" EXACT [GOC:TermGenie]
@@ -453383,7 +456494,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to cell division site." [GOC:dph, GOC:TermGenie, PMID:22573892]
synonym: "regulation of protein localisation to cell division site" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0072741 ! protein localization to cell division site
[Term]
@@ -453434,6 +456544,7 @@ def: "Any process that results in a change in state or activity of a cell or an
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0014075 ! response to amine
is_a: GO:0045472 ! response to ether
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1901906
@@ -453611,12 +456722,14 @@ relationship: part_of GO:0032147 ! activation of protein kinase activity
[Term]
id: GO:1901921
-name: phosphorylation of RNA polymerase II C-terminal domain involved in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex
+name: obsolete phosphorylation of RNA polymerase II C-terminal domain involved in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex
namespace: biological_process
-def: "Any phosphorylation of RNA polymerase II C-terminal domain that is involved in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex." [GOC:TermGenie, PMID:10594013]
+def: "OBSOLETE. Any phosphorylation of RNA polymerase II C-terminal domain that is involved in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex." [GOC:TermGenie, PMID:10594013]
+comment: This term was obsoleted because it represents both a molecular function and a biological process.
synonym: "CTD domain phosphorylation of RNA polymerase II involved in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex" EXACT [GOC:TermGenie]
-is_a: GO:0070816 ! phosphorylation of RNA polymerase II C-terminal domain
-relationship: part_of GO:0034402 ! recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex
+is_obsolete: true
+consider: GO:0008353
+consider: GO:0031124
[Term]
id: GO:1901922
@@ -453666,7 +456779,7 @@ is_a: GO:0072479 ! response to mitotic cell cycle spindle assembly checkpoint si
id: GO:1901926
name: cadinene metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving cadinene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways involving cadinene." [GOC:TermGenie, PMID:22867794]
synonym: "cadinene metabolism" EXACT [GOC:TermGenie]
is_a: GO:0051761 ! sesquiterpene metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
@@ -453675,7 +456788,7 @@ is_a: GO:1901360 ! organic cyclic compound metabolic process
id: GO:1901927
name: cadinene catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of cadinene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways resulting in the breakdown of cadinene." [GOC:TermGenie, PMID:22867794]
synonym: "cadinene breakdown" EXACT [GOC:TermGenie]
synonym: "cadinene catabolism" EXACT [GOC:TermGenie]
synonym: "cadinene degradation" EXACT [GOC:TermGenie]
@@ -453687,7 +456800,7 @@ is_a: GO:1901926 ! cadinene metabolic process
id: GO:1901928
name: cadinene biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of cadinene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways resulting in the formation of cadinene." [GOC:TermGenie, PMID:22867794]
synonym: "cadinene anabolism" EXACT [GOC:TermGenie]
synonym: "cadinene biosynthesis" EXACT [GOC:TermGenie]
synonym: "cadinene formation" EXACT [GOC:TermGenie]
@@ -453700,7 +456813,7 @@ is_a: GO:1901926 ! cadinene metabolic process
id: GO:1901929
name: alpha-copaene metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving alpha-copaene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways involving alpha-copaene." [GOC:TermGenie, PMID:22867794]
synonym: "alpha-copaene metabolism" EXACT [GOC:TermGenie]
is_a: GO:0051761 ! sesquiterpene metabolic process
@@ -453708,7 +456821,7 @@ is_a: GO:0051761 ! sesquiterpene metabolic process
id: GO:1901930
name: alpha-copaene catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of alpha-copaene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways resulting in the breakdown of alpha-copaene." [GOC:TermGenie, PMID:22867794]
synonym: "alpha-copaene breakdown" EXACT [GOC:TermGenie]
synonym: "alpha-copaene catabolism" EXACT [GOC:TermGenie]
synonym: "alpha-copaene degradation" EXACT [GOC:TermGenie]
@@ -453719,7 +456832,7 @@ is_a: GO:1901929 ! alpha-copaene metabolic process
id: GO:1901931
name: alpha-copaene biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of alpha-copaene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways resulting in the formation of alpha-copaene." [GOC:TermGenie, PMID:22867794]
synonym: "alpha-copaene anabolism" EXACT [GOC:TermGenie]
synonym: "alpha-copaene biosynthesis" EXACT [GOC:TermGenie]
synonym: "alpha-copaene formation" EXACT [GOC:TermGenie]
@@ -453731,7 +456844,7 @@ is_a: GO:1901929 ! alpha-copaene metabolic process
id: GO:1901932
name: bicyclogermacrene metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving bicyclogermacrene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways involving bicyclogermacrene." [GOC:TermGenie, PMID:22867794]
synonym: "bicyclogermacrene metabolism" EXACT [GOC:TermGenie]
is_a: GO:0051761 ! sesquiterpene metabolic process
@@ -453739,7 +456852,7 @@ is_a: GO:0051761 ! sesquiterpene metabolic process
id: GO:1901933
name: bicyclogermacrene catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of bicyclogermacrene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways resulting in the breakdown of bicyclogermacrene." [GOC:TermGenie, PMID:22867794]
synonym: "bicyclogermacrene breakdown" EXACT [GOC:TermGenie]
synonym: "bicyclogermacrene catabolism" EXACT [GOC:TermGenie]
synonym: "bicyclogermacrene degradation" EXACT [GOC:TermGenie]
@@ -453750,7 +456863,7 @@ is_a: GO:1901932 ! bicyclogermacrene metabolic process
id: GO:1901934
name: bicyclogermacrene biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of bicyclogermacrene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways resulting in the formation of bicyclogermacrene." [GOC:TermGenie, PMID:22867794]
synonym: "bicyclogermacrene anabolism" EXACT [GOC:TermGenie]
synonym: "bicyclogermacrene biosynthesis" EXACT [GOC:TermGenie]
synonym: "bicyclogermacrene formation" EXACT [GOC:TermGenie]
@@ -453762,7 +456875,7 @@ is_a: GO:1901932 ! bicyclogermacrene metabolic process
id: GO:1901935
name: beta-caryophyllene metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving beta-caryophyllene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways involving beta-caryophyllene." [GOC:TermGenie, PMID:22867794]
synonym: "beta-caryophyllene metabolism" EXACT [GOC:TermGenie]
is_a: GO:0051761 ! sesquiterpene metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
@@ -453771,7 +456884,7 @@ is_a: GO:1901360 ! organic cyclic compound metabolic process
id: GO:1901936
name: beta-caryophyllene catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of beta-caryophyllene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways resulting in the breakdown of beta-caryophyllene." [GOC:TermGenie, PMID:22867794]
synonym: "beta-caryophyllene breakdown" EXACT [GOC:TermGenie]
synonym: "beta-caryophyllene catabolism" EXACT [GOC:TermGenie]
synonym: "beta-caryophyllene degradation" EXACT [GOC:TermGenie]
@@ -453783,7 +456896,7 @@ is_a: GO:1901935 ! beta-caryophyllene metabolic process
id: GO:1901937
name: beta-caryophyllene biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of beta-caryophyllene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways resulting in the formation of beta-caryophyllene." [GOC:TermGenie, PMID:22867794]
synonym: "beta-caryophyllene anabolism" EXACT [GOC:TermGenie]
synonym: "beta-caryophyllene biosynthesis" EXACT [GOC:TermGenie]
synonym: "beta-caryophyllene formation" EXACT [GOC:TermGenie]
@@ -453796,7 +456909,7 @@ is_a: GO:1901935 ! beta-caryophyllene metabolic process
id: GO:1901938
name: (-)-exo-alpha-bergamotene metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving (-)-exo-alpha-bergamotene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways involving (-)-exo-alpha-bergamotene." [GOC:TermGenie, PMID:22867794]
synonym: "(-)-exo-alpha-bergamotene metabolism" EXACT [GOC:TermGenie]
is_a: GO:0051761 ! sesquiterpene metabolic process
is_a: GO:1900673 ! olefin metabolic process
@@ -453806,7 +456919,7 @@ is_a: GO:1901360 ! organic cyclic compound metabolic process
id: GO:1901939
name: (-)-exo-alpha-bergamotene catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of (-)-exo-alpha-bergamotene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways resulting in the breakdown of (-)-exo-alpha-bergamotene." [GOC:TermGenie, PMID:22867794]
synonym: "(-)-exo-alpha-bergamotene breakdown" EXACT [GOC:TermGenie]
synonym: "(-)-exo-alpha-bergamotene catabolism" EXACT [GOC:TermGenie]
synonym: "(-)-exo-alpha-bergamotene degradation" EXACT [GOC:TermGenie]
@@ -453819,7 +456932,7 @@ is_a: GO:1901938 ! (-)-exo-alpha-bergamotene metabolic process
id: GO:1901940
name: (-)-exo-alpha-bergamotene biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of (-)-exo-alpha-bergamotene." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways resulting in the formation of (-)-exo-alpha-bergamotene." [GOC:TermGenie, PMID:22867794]
synonym: "(-)-exo-alpha-bergamotene anabolism" EXACT [GOC:TermGenie]
synonym: "(-)-exo-alpha-bergamotene biosynthesis" EXACT [GOC:TermGenie]
synonym: "(-)-exo-alpha-bergamotene formation" EXACT [GOC:TermGenie]
@@ -453833,7 +456946,7 @@ is_a: GO:1901938 ! (-)-exo-alpha-bergamotene metabolic process
id: GO:1901941
name: (+)-epi-alpha-bisabolol metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving (+)-epi-alpha-bisabolol." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways involving (+)-epi-alpha-bisabolol." [GOC:TermGenie, PMID:22867794]
synonym: "(+)-epi-alpha-bisabolol metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006714 ! sesquiterpenoid metabolic process
@@ -453841,7 +456954,7 @@ is_a: GO:0006714 ! sesquiterpenoid metabolic process
id: GO:1901942
name: (+)-epi-alpha-bisabolol catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of (+)-epi-alpha-bisabolol." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways resulting in the breakdown of (+)-epi-alpha-bisabolol." [GOC:TermGenie, PMID:22867794]
synonym: "(+)-epi-alpha-bisabolol breakdown" EXACT [GOC:TermGenie]
synonym: "(+)-epi-alpha-bisabolol catabolism" EXACT [GOC:TermGenie]
synonym: "(+)-epi-alpha-bisabolol degradation" EXACT [GOC:TermGenie]
@@ -453852,7 +456965,7 @@ is_a: GO:1901941 ! (+)-epi-alpha-bisabolol metabolic process
id: GO:1901943
name: (+)-epi-alpha-bisabolol biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of (+)-epi-alpha-bisabolol." [GOC:TermGenie, pmid:22867794]
+def: "The chemical reactions and pathways resulting in the formation of (+)-epi-alpha-bisabolol." [GOC:TermGenie, PMID:22867794]
synonym: "(+)-epi-alpha-bisabolol anabolism" EXACT [GOC:TermGenie]
synonym: "(+)-epi-alpha-bisabolol biosynthesis" EXACT [GOC:TermGenie]
synonym: "(+)-epi-alpha-bisabolol formation" EXACT [GOC:TermGenie]
@@ -453864,7 +456977,7 @@ is_a: GO:1901941 ! (+)-epi-alpha-bisabolol metabolic process
id: GO:1901944
name: miltiradiene metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving miltiradiene." [GOC:TermGenie, pmid:22027823]
+def: "The chemical reactions and pathways involving miltiradiene." [GOC:TermGenie, PMID:22027823]
synonym: "miltiradiene metabolism" EXACT [GOC:TermGenie]
is_a: GO:0042214 ! terpene metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
@@ -453873,7 +456986,7 @@ is_a: GO:1901360 ! organic cyclic compound metabolic process
id: GO:1901945
name: miltiradiene catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of miltiradiene." [GOC:TermGenie, pmid:22027823]
+def: "The chemical reactions and pathways resulting in the breakdown of miltiradiene." [GOC:TermGenie, PMID:22027823]
synonym: "miltiradiene breakdown" EXACT [GOC:TermGenie]
synonym: "miltiradiene catabolism" EXACT [GOC:TermGenie]
synonym: "miltiradiene degradation" EXACT [GOC:TermGenie]
@@ -453885,7 +456998,7 @@ is_a: GO:1901944 ! miltiradiene metabolic process
id: GO:1901946
name: miltiradiene biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of miltiradiene." [GOC:TermGenie, pmid:22027823]
+def: "The chemical reactions and pathways resulting in the formation of miltiradiene." [GOC:TermGenie, PMID:22027823]
synonym: "miltiradiene anabolism" EXACT [GOC:TermGenie]
synonym: "miltiradiene biosynthesis" EXACT [GOC:TermGenie]
synonym: "miltiradiene formation" EXACT [GOC:TermGenie]
@@ -453898,7 +457011,7 @@ is_a: GO:1901944 ! miltiradiene metabolic process
id: GO:1901947
name: 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate." [GOC:TermGenie, pmid:22027823]
+def: "The chemical reactions and pathways involving 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate." [GOC:TermGenie, PMID:22027823]
synonym: "5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006644 ! phospholipid metabolic process
is_a: GO:0016101 ! diterpenoid metabolic process
@@ -453908,7 +457021,7 @@ is_a: GO:1901360 ! organic cyclic compound metabolic process
id: GO:1901948
name: 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate." [GOC:TermGenie, pmid:22027823]
+def: "The chemical reactions and pathways resulting in the breakdown of 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate." [GOC:TermGenie, PMID:22027823]
synonym: "5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate breakdown" EXACT [GOC:TermGenie]
synonym: "5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate catabolism" EXACT [GOC:TermGenie]
synonym: "5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate degradation" EXACT [GOC:TermGenie]
@@ -453921,7 +457034,7 @@ is_a: GO:1901947 ! 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate me
id: GO:1901949
name: 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate." [GOC:TermGenie, pmid:22027823]
+def: "The chemical reactions and pathways resulting in the formation of 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate." [GOC:TermGenie, PMID:22027823]
synonym: "5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate anabolism" EXACT [GOC:TermGenie]
synonym: "5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate biosynthesis" EXACT [GOC:TermGenie]
synonym: "5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate formation" EXACT [GOC:TermGenie]
@@ -454125,7 +457238,7 @@ def: "The directed movement of S-adenosyl-L-methionine across a membrane." [GOC:
synonym: "S-adenosylmethionine transmembrane transport" EXACT []
synonym: "SAM transmembrane transport" EXACT []
is_a: GO:0015805 ! S-adenosyl-L-methionine transport
-is_a: GO:0098655 ! cation transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:1901963
@@ -454295,19 +457408,15 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:1901974
name: glycerate transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of glycerate from one side of a membrane to the other." [GOC:TermGenie, pmid:23382251]
-is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0015144 ! carbohydrate transmembrane transporter activity
+def: "Enables the transfer of glycerate from one side of a membrane to the other." [GOC:TermGenie, PMID:23382251]
is_a: GO:0042879 ! aldonate transmembrane transporter activity
[Term]
id: GO:1901975
name: glycerate transmembrane transport
namespace: biological_process
-def: "The process in which glycerate is transported across a membrane." [GOC:TermGenie, pmid:23382251]
-is_a: GO:0034219 ! carbohydrate transmembrane transport
+def: "The process in which glycerate is transported across a membrane." [GOC:TermGenie, PMID:23382251]
is_a: GO:0042873 ! aldonate transmembrane transport
-is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
id: GO:1901976
@@ -454691,7 +457800,7 @@ name: regulation of amyloid-beta formation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of amyloid-beta formation." [GOC:dph, GOC:TermGenie, PMID:17098871]
synonym: "regulation of beta-amyloid formation" EXACT []
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:1902991 ! regulation of amyloid precursor protein catabolic process
relationship: regulates GO:0034205 ! amyloid-beta formation
@@ -454705,7 +457814,7 @@ synonym: "positive regulation of beta-amyloid formation" EXACT []
synonym: "up regulation of beta-amyloid formation" EXACT [GOC:TermGenie]
synonym: "up-regulation of beta-amyloid formation" EXACT [GOC:TermGenie]
synonym: "upregulation of beta-amyloid formation" EXACT [GOC:TermGenie]
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:1902003 ! regulation of amyloid-beta formation
is_a: GO:1902993 ! positive regulation of amyloid precursor protein catabolic process
relationship: positively_regulates GO:0034205 ! amyloid-beta formation
@@ -454754,7 +457863,7 @@ synonym: "negative regulation of proline formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of proline synthesis" EXACT [GOC:TermGenie]
is_a: GO:1902005 ! regulation of proline biosynthetic process
is_a: GO:2000215 ! negative regulation of proline metabolic process
-is_a: GO:2000283 ! negative regulation of cellular amino acid biosynthetic process
+is_a: GO:2000283 ! negative regulation of amino acid biosynthetic process
relationship: negatively_regulates GO:0006561 ! proline biosynthetic process
[Term]
@@ -454974,8 +458083,6 @@ id: GO:1902022
name: L-lysine transport
namespace: biological_process
def: "The directed movement of a L-lysine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:kmv, GOC:TermGenie, PMID:22822152]
-is_a: GO:0006812 ! cation transport
-is_a: GO:0006865 ! amino acid transport
is_a: GO:0015807 ! L-amino acid transport
[Term]
@@ -454983,8 +458090,8 @@ id: GO:1902024
name: L-histidine transport
namespace: biological_process
def: "The directed movement of a L-histidine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:kmv, GOC:TermGenie, PMID:22822152]
-is_a: GO:0006812 ! cation transport
is_a: GO:0015801 ! aromatic amino acid transport
+is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0015817 ! histidine transport
[Term]
@@ -454994,7 +458101,8 @@ namespace: biological_process
def: "The directed movement of nitrate into a cell or organelle." [GOC:TermGenie, PMID:22658680]
synonym: "nitrate influx" EXACT []
synonym: "nitrate uptake" EXACT []
-is_a: GO:0015706 ! nitrate transport
+is_a: GO:0015698 ! inorganic anion transport
+is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:1902026
@@ -455019,19 +458127,21 @@ relationship: positively_regulates GO:0001502 ! cartilage condensation
[Term]
id: GO:1902028
-name: regulation of histone H3-K18 acetylation
+name: obsolete regulation of histone H3-K18 acetylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone H3-K18 acetylation." [GOC:TermGenie, PMID:22110608]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone H3-K18 acetylation." [GOC:TermGenie, PMID:22110608]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "regulation of histone H3 acetylation at K18" EXACT [GOC:TermGenie]
synonym: "regulation of histone H3K18 acetylation" EXACT [GOC:TermGenie]
-is_a: GO:0035065 ! regulation of histone acetylation
-relationship: regulates GO:0043971 ! histone H3-K18 acetylation
+is_obsolete: true
+consider: GO:0043993
[Term]
id: GO:1902029
-name: positive regulation of histone H3-K18 acetylation
+name: obsolete positive regulation of histone H3-K18 acetylation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of histone H3-K18 acetylation." [GOC:TermGenie, PMID:22110608]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of histone H3-K18 acetylation." [GOC:TermGenie, PMID:22110608]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of histone H3 acetylation at K18" EXACT [GOC:TermGenie]
synonym: "activation of histone H3-K18 acetylation" NARROW [GOC:TermGenie]
synonym: "activation of histone H3K18 acetylation" EXACT [GOC:TermGenie]
@@ -455046,15 +458156,15 @@ synonym: "up-regulation of histone H3K18 acetylation" EXACT [GOC:TermGenie]
synonym: "upregulation of histone H3 acetylation at K18" EXACT [GOC:TermGenie]
synonym: "upregulation of histone H3-K18 acetylation" EXACT [GOC:TermGenie]
synonym: "upregulation of histone H3K18 acetylation" EXACT [GOC:TermGenie]
-is_a: GO:0035066 ! positive regulation of histone acetylation
-is_a: GO:1902028 ! regulation of histone H3-K18 acetylation
-relationship: positively_regulates GO:0043971 ! histone H3-K18 acetylation
+is_obsolete: true
+consider: GO:0043993
[Term]
id: GO:1902030
-name: negative regulation of histone H3-K18 acetylation
+name: obsolete negative regulation of histone H3-K18 acetylation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K18 acetylation." [GOC:TermGenie, PMID:22110608]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K18 acetylation." [GOC:TermGenie, PMID:22110608]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of histone H3 acetylation at K18" EXACT [GOC:TermGenie]
synonym: "down regulation of histone H3-K18 acetylation" EXACT [GOC:TermGenie]
synonym: "down regulation of histone H3K18 acetylation" EXACT [GOC:TermGenie]
@@ -455069,9 +458179,7 @@ synonym: "inhibition of histone H3-K18 acetylation" NARROW [GOC:TermGenie]
synonym: "inhibition of histone H3K18 acetylation" EXACT [GOC:TermGenie]
synonym: "negative regulation of histone H3 acetylation at K18" EXACT [GOC:TermGenie]
synonym: "negative regulation of histone H3K18 acetylation" EXACT [GOC:TermGenie]
-is_a: GO:0035067 ! negative regulation of histone acetylation
-is_a: GO:1902028 ! regulation of histone H3-K18 acetylation
-relationship: negatively_regulates GO:0043971 ! histone H3-K18 acetylation
+is_obsolete: true
[Term]
id: GO:1902031
@@ -455096,7 +458204,7 @@ synonym: "regulation of reduced NADP metabolic process" EXACT [GOC:TermGenie]
synonym: "regulation of reduced NADP metabolism" EXACT [GOC:TermGenie]
synonym: "regulation of reduced nicotinamide adenine dinucleotide phosphate metabolic process" EXACT [GOC:TermGenie]
synonym: "regulation of reduced nicotinamide adenine dinucleotide phosphate metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0019222 ! regulation of metabolic process
+is_a: GO:1900542 ! regulation of purine nucleotide metabolic process
relationship: regulates GO:0006739 ! NADP metabolic process
[Term]
@@ -455498,7 +458606,6 @@ name: (25S)-Delta(4)-dafachronate binding
namespace: molecular_function
def: "Binding to (25S)-Delta(4)-dafachronate." [GOC:TermGenie, PMID:16529801]
is_a: GO:0031406 ! carboxylic acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:1990239 ! steroid hormone binding
[Term]
@@ -455507,7 +458614,6 @@ name: (25S)-Delta(7)-dafachronate binding
namespace: molecular_function
def: "Binding to (25S)-Delta(7)-dafachronate." [GOC:TermGenie, PMID:16529801]
is_a: GO:0031406 ! carboxylic acid binding
-is_a: GO:0043177 ! organic acid binding
is_a: GO:1990239 ! steroid hormone binding
[Term]
@@ -455696,8 +458802,7 @@ name: betaine aldehyde metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving betaine aldehyde." [GOC:di, GOC:TermGenie, PMID:23563483]
synonym: "betaine aldehyde metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006807 ! nitrogen compound metabolic process
-is_a: GO:0071704 ! organic substance metabolic process
+is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
id: GO:1902062
@@ -455707,7 +458812,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of betaine
synonym: "betaine aldehyde breakdown" EXACT [GOC:TermGenie]
synonym: "betaine aldehyde catabolism" EXACT [GOC:TermGenie]
synonym: "betaine aldehyde degradation" EXACT [GOC:TermGenie]
-is_a: GO:1901575 ! organic substance catabolic process
+is_a: GO:1901565 ! organonitrogen compound catabolic process
is_a: GO:1902061 ! betaine aldehyde metabolic process
[Term]
@@ -455719,14 +458824,15 @@ synonym: "betaine aldehyde anabolism" EXACT [GOC:TermGenie]
synonym: "betaine aldehyde biosynthesis" EXACT [GOC:TermGenie]
synonym: "betaine aldehyde formation" EXACT [GOC:TermGenie]
synonym: "betaine aldehyde synthesis" EXACT [GOC:TermGenie]
-is_a: GO:1901576 ! organic substance biosynthetic process
+is_a: GO:1901566 ! organonitrogen compound biosynthetic process
is_a: GO:1902061 ! betaine aldehyde metabolic process
[Term]
id: GO:1902064
-name: regulation of transcription from RNA polymerase II promoter involved in spermatogenesis
+name: obsolete regulation of transcription from RNA polymerase II promoter involved in spermatogenesis
namespace: biological_process
-def: "Any regulation of transcription from RNA polymerase II promoter that is involved in spermatogenesis." [GOC:kmv, GOC:TermGenie, PMID:22570621]
+def: "OBSOLETE. Any regulation of transcription from RNA polymerase II promoter that is involved in spermatogenesis." [GOC:kmv, GOC:TermGenie, PMID:22570621]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "global transcription regulation from Pol II promoter involved in generation of spermatozoa" RELATED [GOC:TermGenie]
synonym: "global transcription regulation from Pol II promoter involved in spermatogenesis" RELATED [GOC:TermGenie]
synonym: "regulation of gene-specific transcription from RNA polymerase II promoter involved in generation of spermatozoa" RELATED [GOC:TermGenie]
@@ -455738,9 +458844,7 @@ synonym: "regulation of transcription from Pol II promoter involved in spermatog
synonym: "regulation of transcription from RNA polymerase II promoter involved in generation of spermatozoa" EXACT [GOC:TermGenie]
synonym: "regulation of transcription from RNA polymerase II promoter, global involved in generation of spermatozoa" RELATED [GOC:TermGenie]
synonym: "regulation of transcription from RNA polymerase II promoter, global involved in spermatogenesis" RELATED [GOC:TermGenie]
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-is_a: GO:0022414 ! reproductive process
-relationship: part_of GO:0007283 ! spermatogenesis
+is_obsolete: true
[Term]
id: GO:1902065
@@ -455748,6 +458852,7 @@ name: response to L-glutamate
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an L-glutamate stimulus." [GOC:TermGenie, PMID:23574009]
is_a: GO:0043200 ! response to amino acid
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1902066
@@ -455933,7 +459038,7 @@ name: regulation of calcium ion import into sarcoplasmic reticulum
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of calcium ion import into sarcoplasmic reticulum." [GOC:BHF, GOC:rl, GOC:TermGenie, PMID:8349590]
is_a: GO:0032386 ! regulation of intracellular transport
-is_a: GO:0090279 ! regulation of calcium ion import
+is_a: GO:0051924 ! regulation of calcium ion transport
relationship: regulates GO:1990036 ! calcium ion import into sarcoplasmic reticulum
[Term]
@@ -455946,7 +459051,7 @@ synonym: "down-regulation of calcium ion import into sarcoplasmic reticulum" EXA
synonym: "downregulation of calcium ion import into sarcoplasmic reticulum" EXACT [GOC:TermGenie]
synonym: "inhibition of calcium ion import into sarcoplasmic reticulum" NARROW [GOC:TermGenie]
is_a: GO:0032387 ! negative regulation of intracellular transport
-is_a: GO:0090281 ! negative regulation of calcium ion import
+is_a: GO:0051926 ! negative regulation of calcium ion transport
is_a: GO:1902080 ! regulation of calcium ion import into sarcoplasmic reticulum
relationship: negatively_regulates GO:1990036 ! calcium ion import into sarcoplasmic reticulum
@@ -455960,7 +459065,7 @@ synonym: "up regulation of calcium ion import into sarcoplasmic reticulum" EXACT
synonym: "up-regulation of calcium ion import into sarcoplasmic reticulum" EXACT [GOC:TermGenie]
synonym: "upregulation of calcium ion import into sarcoplasmic reticulum" EXACT [GOC:TermGenie]
is_a: GO:0032388 ! positive regulation of intracellular transport
-is_a: GO:0090280 ! positive regulation of calcium ion import
+is_a: GO:0051928 ! positive regulation of calcium ion transport
is_a: GO:1902080 ! regulation of calcium ion import into sarcoplasmic reticulum
relationship: positively_regulates GO:1990036 ! calcium ion import into sarcoplasmic reticulum
@@ -455993,7 +459098,7 @@ name: fumagillin metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving fumagillin." [GOC:di, GOC:TermGenie, PMID:23488861]
synonym: "fumagillin metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006082 ! organic acid metabolic process
+is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:0097176 ! epoxide metabolic process
[Term]
@@ -456004,8 +459109,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of fumagill
synonym: "fumagillin breakdown" EXACT [GOC:TermGenie]
synonym: "fumagillin catabolism" EXACT [GOC:TermGenie]
synonym: "fumagillin degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0046700 ! heterocycle catabolic process
+is_a: GO:0072329 ! monocarboxylic acid catabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
is_a: GO:1901502 ! ether catabolic process
is_a: GO:1902084 ! fumagillin metabolic process
@@ -456019,9 +459124,9 @@ synonym: "fumagillin anabolism" EXACT [GOC:TermGenie]
synonym: "fumagillin biosynthesis" EXACT [GOC:TermGenie]
synonym: "fumagillin formation" EXACT [GOC:TermGenie]
synonym: "fumagillin synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0019748 ! secondary metabolic process
+is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
is_a: GO:1901503 ! ether biosynthetic process
is_a: GO:1902084 ! fumagillin metabolic process
@@ -456343,7 +459448,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of leukocyte differentiation." [GOC:add, GOC:TermGenie]
synonym: "regulation of immune cell differentiation" EXACT [GOC:TermGenie]
synonym: "regulation of leucocyte differentiation" EXACT [GOC:TermGenie]
-is_a: GO:0045595 ! regulation of cell differentiation
is_a: GO:1903706 ! regulation of hemopoiesis
relationship: regulates GO:0002521 ! leukocyte differentiation
@@ -456366,7 +459470,6 @@ synonym: "inhibition of leucocyte differentiation" NARROW [GOC:TermGenie]
synonym: "inhibition of leukocyte differentiation" NARROW [GOC:TermGenie]
synonym: "negative regulation of immune cell differentiation" EXACT [GOC:TermGenie]
synonym: "negative regulation of leucocyte differentiation" EXACT [GOC:TermGenie]
-is_a: GO:0045596 ! negative regulation of cell differentiation
is_a: GO:1902105 ! regulation of leukocyte differentiation
is_a: GO:1903707 ! negative regulation of hemopoiesis
relationship: negatively_regulates GO:0002521 ! leukocyte differentiation
@@ -456390,7 +459493,6 @@ synonym: "up-regulation of leukocyte differentiation" EXACT [GOC:TermGenie]
synonym: "upregulation of immune cell differentiation" EXACT [GOC:TermGenie]
synonym: "upregulation of leucocyte differentiation" EXACT [GOC:TermGenie]
synonym: "upregulation of leukocyte differentiation" EXACT [GOC:TermGenie]
-is_a: GO:0045597 ! positive regulation of cell differentiation
is_a: GO:1902105 ! regulation of leukocyte differentiation
is_a: GO:1903708 ! positive regulation of hemopoiesis
relationship: positively_regulates GO:0002521 ! leukocyte differentiation
@@ -456523,11 +459625,11 @@ is_a: GO:1902111 ! response to diethyl maleate
[Term]
id: GO:1902113
-name: nucleotide phosphorylation involved in DNA repair
+name: obsolete nucleotide phosphorylation involved in DNA repair
namespace: biological_process
-def: "Any nucleotide phosphorylation that is involved in DNA repair." [GOC:TermGenie, PMID:11729194]
-is_a: GO:0046939 ! nucleotide phosphorylation
-relationship: part_of GO:0006281 ! DNA repair
+def: "OBSOLETE. Any nucleotide phosphorylation that is involved in DNA repair." [GOC:TermGenie, PMID:11729194]
+comment: The reason for obsoletion is that this term represents a single step MF.
+is_obsolete: true
[Term]
id: GO:1902114
@@ -456622,7 +459724,6 @@ def: "Binding to lithocholic acid." [GOC:bf, GOC:TermGenie, PMID:20371703]
synonym: "LCA binding" EXACT [PMID:20371703]
is_a: GO:0005496 ! steroid binding
is_a: GO:0032052 ! bile acid binding
-is_a: GO:0043177 ! organic acid binding
[Term]
id: GO:1902122
@@ -456632,7 +459733,6 @@ def: "Binding to chenodeoxycholic acid." [GOC:bf, GOC:TermGenie, PMID:10334992]
synonym: "CDCA binding" EXACT [CHEBI:16755]
is_a: GO:0005496 ! steroid binding
is_a: GO:0032052 ! bile acid binding
-is_a: GO:0043177 ! organic acid binding
[Term]
id: GO:1902123
@@ -457111,7 +460211,7 @@ def: "Any process that modulates the frequency, rate or extent of cyclic nucleot
synonym: "regulation of cyclic nucleotide activated ion channel activity" EXACT [GOC:TermGenie]
synonym: "regulation of cyclic nucleotide gated ion channel activity" EXACT [GOC:TermGenie]
synonym: "regulation of cyclic nucleotide-activated ion channel activity" EXACT [GOC:TermGenie]
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
[Term]
id: GO:1902160
@@ -457429,19 +460529,14 @@ is_a: GO:1901360 ! organic cyclic compound metabolic process
[Term]
id: GO:1902180
-name: verruculogen catabolic process
+name: obsolete verruculogen catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of verruculogen." [GOC:di, GOC:TermGenie, PMID:23649274]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of verruculogen." [GOC:di, GOC:TermGenie, PMID:23649274]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "verruculogen breakdown" EXACT [GOC:TermGenie]
synonym: "verruculogen catabolism" EXACT [GOC:TermGenie]
synonym: "verruculogen degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009822 ! alkaloid catabolic process
-is_a: GO:0019439 ! aromatic compound catabolic process
-is_a: GO:0034313 ! diol catabolic process
-is_a: GO:0046700 ! heterocycle catabolic process
-is_a: GO:1901361 ! organic cyclic compound catabolic process
-is_a: GO:1901502 ! ether catabolic process
-is_a: GO:1902179 ! verruculogen metabolic process
+is_obsolete: true
[Term]
id: GO:1902181
@@ -457454,7 +460549,6 @@ synonym: "verruculogen formation" EXACT [GOC:TermGenie]
synonym: "verruculogen synthesis" EXACT [GOC:TermGenie]
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0019438 ! aromatic compound biosynthetic process
-is_a: GO:0019748 ! secondary metabolic process
is_a: GO:0034312 ! diol biosynthetic process
is_a: GO:0035835 ! indole alkaloid biosynthetic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
@@ -457650,7 +460744,7 @@ is_a: GO:1902192 ! 2-methylbut-2-enoyl-CoA(4-) metabolic process
id: GO:1902195
name: isovaleryl-CoA(4-) metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving isovaleryl-CoA(4-)." [GOC:TermGenie, pmid:11231285]
+def: "The chemical reactions and pathways involving isovaleryl-CoA(4-)." [GOC:TermGenie, PMID:11231285]
synonym: "isovaleryl-CoA(4-) metabolism" EXACT [GOC:TermGenie]
is_a: GO:0035337 ! fatty-acyl-CoA metabolic process
@@ -457658,7 +460752,7 @@ is_a: GO:0035337 ! fatty-acyl-CoA metabolic process
id: GO:1902196
name: isovaleryl-CoA(4-) catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of isovaleryl-CoA(4-)." [GOC:TermGenie, pmid:11231285]
+def: "The chemical reactions and pathways resulting in the breakdown of isovaleryl-CoA(4-)." [GOC:TermGenie, PMID:11231285]
synonym: "isovaleryl-CoA(4-) breakdown" EXACT [GOC:TermGenie]
synonym: "isovaleryl-CoA(4-) catabolism" EXACT [GOC:TermGenie]
synonym: "isovaleryl-CoA(4-) degradation" EXACT [GOC:TermGenie]
@@ -457669,7 +460763,7 @@ is_a: GO:1902195 ! isovaleryl-CoA(4-) metabolic process
id: GO:1902197
name: isovaleryl-CoA(4-) biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of isovaleryl-CoA(4-)." [GOC:TermGenie, pmid:11231285]
+def: "The chemical reactions and pathways resulting in the formation of isovaleryl-CoA(4-)." [GOC:TermGenie, PMID:11231285]
synonym: "isovaleryl-CoA(4-) anabolism" EXACT [GOC:TermGenie]
synonym: "isovaleryl-CoA(4-) biosynthesis" EXACT [GOC:TermGenie]
synonym: "isovaleryl-CoA(4-) formation" EXACT [GOC:TermGenie]
@@ -457681,7 +460775,7 @@ is_a: GO:1902195 ! isovaleryl-CoA(4-) metabolic process
id: GO:1902198
name: 3-methylbut-2-enoyl-CoA(4-) metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving 3-methylbut-2-enoyl-CoA(4-)." [GOC:TermGenie, pmid:11231285]
+def: "The chemical reactions and pathways involving 3-methylbut-2-enoyl-CoA(4-)." [GOC:TermGenie, PMID:11231285]
synonym: "3-methylbut-2-enoyl-CoA(4-) metabolism" EXACT [GOC:TermGenie]
is_a: GO:0035337 ! fatty-acyl-CoA metabolic process
@@ -457689,7 +460783,7 @@ is_a: GO:0035337 ! fatty-acyl-CoA metabolic process
id: GO:1902199
name: 3-methylbut-2-enoyl-CoA(4-) catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 3-methylbut-2-enoyl-CoA(4-)." [GOC:TermGenie, pmid:11231285]
+def: "The chemical reactions and pathways resulting in the breakdown of 3-methylbut-2-enoyl-CoA(4-)." [GOC:TermGenie, PMID:11231285]
synonym: "3-methylbut-2-enoyl-CoA(4-) breakdown" EXACT [GOC:TermGenie]
synonym: "3-methylbut-2-enoyl-CoA(4-) catabolism" EXACT [GOC:TermGenie]
synonym: "3-methylbut-2-enoyl-CoA(4-) degradation" EXACT [GOC:TermGenie]
@@ -457700,7 +460794,7 @@ is_a: GO:1902198 ! 3-methylbut-2-enoyl-CoA(4-) metabolic process
id: GO:1902200
name: 3-methylbut-2-enoyl-CoA(4-) biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 3-methylbut-2-enoyl-CoA(4-)." [GOC:TermGenie, pmid:11231285]
+def: "The chemical reactions and pathways resulting in the formation of 3-methylbut-2-enoyl-CoA(4-)." [GOC:TermGenie, PMID:11231285]
synonym: "3-methylbut-2-enoyl-CoA(4-) anabolism" EXACT [GOC:TermGenie]
synonym: "3-methylbut-2-enoyl-CoA(4-) biosynthesis" EXACT [GOC:TermGenie]
synonym: "3-methylbut-2-enoyl-CoA(4-) formation" EXACT [GOC:TermGenie]
@@ -458073,6 +461167,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of erythros
synonym: "erythrose 4-phosphate/phosphoenolpyruvate family amino acid breakdown" EXACT [GOC:TermGenie]
synonym: "erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolism" EXACT [GOC:TermGenie]
synonym: "erythrose 4-phosphate/phosphoenolpyruvate family amino acid degradation" EXACT [GOC:TermGenie]
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
is_a: GO:1902221 ! erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process
@@ -458173,7 +461268,7 @@ name: regulation of intrinsic apoptotic signaling pathway in response to DNA dam
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of intrinsic apoptotic signaling pathway in response to DNA damage." [GOC:BHF, GOC:mtg_apoptosis, GOC:rl, GOC:TermGenie, PMID:15314165]
synonym: "regulation of DNA damage response, signal transduction resulting in induction of apoptosis" RELATED [GOC:TermGenie]
-is_a: GO:2001020 ! regulation of response to DNA damage stimulus
+is_a: GO:0080135 ! regulation of cellular response to stress
is_a: GO:2001242 ! regulation of intrinsic apoptotic signaling pathway
relationship: regulates GO:0008630 ! intrinsic apoptotic signaling pathway in response to DNA damage
@@ -458192,7 +461287,6 @@ synonym: "inhibition of DNA damage response, signal transduction resulting in in
synonym: "inhibition of intrinsic apoptotic signaling pathway in response to DNA damage" NARROW [GOC:TermGenie]
synonym: "negative regulation of DNA damage response, signal transduction resulting in induction of apoptosis" RELATED [GOC:TermGenie]
is_a: GO:1902229 ! regulation of intrinsic apoptotic signaling pathway in response to DNA damage
-is_a: GO:2001021 ! negative regulation of response to DNA damage stimulus
is_a: GO:2001243 ! negative regulation of intrinsic apoptotic signaling pathway
relationship: negatively_regulates GO:0008630 ! intrinsic apoptotic signaling pathway in response to DNA damage
@@ -458211,7 +461305,6 @@ synonym: "up-regulation of intrinsic apoptotic signaling pathway in response to
synonym: "upregulation of DNA damage response, signal transduction resulting in induction of apoptosis" RELATED [GOC:TermGenie]
synonym: "upregulation of intrinsic apoptotic signaling pathway in response to DNA damage" EXACT [GOC:TermGenie]
is_a: GO:1902229 ! regulation of intrinsic apoptotic signaling pathway in response to DNA damage
-is_a: GO:2001022 ! positive regulation of response to DNA damage stimulus
is_a: GO:2001244 ! positive regulation of intrinsic apoptotic signaling pathway
relationship: positively_regulates GO:0008630 ! intrinsic apoptotic signaling pathway in response to DNA damage
@@ -458419,7 +461512,7 @@ relationship: positively_regulates GO:1990127 ! intrinsic apoptotic signaling pa
id: GO:1902241
name: copal-8-ol diphosphate(3-) metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving copal-8-ol diphosphate(3-)." [GOC:TermGenie, pmid:22672125]
+def: "The chemical reactions and pathways involving copal-8-ol diphosphate(3-)." [GOC:TermGenie, PMID:22672125]
synonym: "copal-8-ol diphosphate(3-) metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006644 ! phospholipid metabolic process
is_a: GO:0016101 ! diterpenoid metabolic process
@@ -458428,7 +461521,7 @@ is_a: GO:0016101 ! diterpenoid metabolic process
id: GO:1902242
name: copal-8-ol diphosphate(3-) catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of copal-8-ol diphosphate(3-)." [GOC:TermGenie, pmid:22672125]
+def: "The chemical reactions and pathways resulting in the breakdown of copal-8-ol diphosphate(3-)." [GOC:TermGenie, PMID:22672125]
synonym: "copal-8-ol diphosphate(3-) breakdown" EXACT [GOC:TermGenie]
synonym: "copal-8-ol diphosphate(3-) catabolism" EXACT [GOC:TermGenie]
synonym: "copal-8-ol diphosphate(3-) degradation" EXACT [GOC:TermGenie]
@@ -458440,7 +461533,7 @@ is_a: GO:1902241 ! copal-8-ol diphosphate(3-) metabolic process
id: GO:1902243
name: copal-8-ol diphosphate(3-) biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of copal-8-ol diphosphate(3-)." [GOC:TermGenie, pmid:22672125]
+def: "The chemical reactions and pathways resulting in the formation of copal-8-ol diphosphate(3-)." [GOC:TermGenie, PMID:22672125]
synonym: "copal-8-ol diphosphate(3-) anabolism" EXACT [GOC:TermGenie]
synonym: "copal-8-ol diphosphate(3-) biosynthesis" EXACT [GOC:TermGenie]
synonym: "copal-8-ol diphosphate(3-) formation" EXACT [GOC:TermGenie]
@@ -458453,7 +461546,7 @@ is_a: GO:1902241 ! copal-8-ol diphosphate(3-) metabolic process
id: GO:1902244
name: cis-abienol metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving cis-abienol." [GOC:TermGenie, pmid:22672125]
+def: "The chemical reactions and pathways involving cis-abienol." [GOC:TermGenie, PMID:22672125]
synonym: "cis-abienol metabolism" EXACT [GOC:TermGenie]
is_a: GO:0016101 ! diterpenoid metabolic process
is_a: GO:1902644 ! tertiary alcohol metabolic process
@@ -458462,7 +461555,7 @@ is_a: GO:1902644 ! tertiary alcohol metabolic process
id: GO:1902245
name: cis-abienol catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of cis-abienol." [GOC:TermGenie, pmid:22672125]
+def: "The chemical reactions and pathways resulting in the breakdown of cis-abienol." [GOC:TermGenie, PMID:22672125]
synonym: "cis-abienol breakdown" EXACT [GOC:TermGenie]
synonym: "cis-abienol catabolism" EXACT [GOC:TermGenie]
synonym: "cis-abienol degradation" EXACT [GOC:TermGenie]
@@ -458474,7 +461567,7 @@ is_a: GO:1902244 ! cis-abienol metabolic process
id: GO:1902246
name: cis-abienol biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of cis-abienol." [GOC:TermGenie, pmid:22672125]
+def: "The chemical reactions and pathways resulting in the formation of cis-abienol." [GOC:TermGenie, PMID:22672125]
synonym: "cis-abienol anabolism" EXACT [GOC:TermGenie]
synonym: "cis-abienol biosynthesis" EXACT [GOC:TermGenie]
synonym: "cis-abienol formation" EXACT [GOC:TermGenie]
@@ -458487,7 +461580,7 @@ is_a: GO:1902645 ! tertiary alcohol biosynthetic process
id: GO:1902247
name: geranylgeranyl diphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of geranylgeranyl diphosphate." [GOC:TermGenie, pmid:22672125]
+def: "The chemical reactions and pathways resulting in the breakdown of geranylgeranyl diphosphate." [GOC:TermGenie, PMID:22672125]
synonym: "geranylgeranyl diphosphate breakdown" EXACT [GOC:TermGenie]
synonym: "geranylgeranyl diphosphate catabolism" EXACT [GOC:TermGenie]
synonym: "geranylgeranyl diphosphate degradation" EXACT [GOC:TermGenie]
@@ -458775,17 +461868,16 @@ namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of abscisic acid within an organism or cell." [GOC:TermGenie, PMID:23252460]
synonym: "2-cis-abscisate homeostasis" RELATED []
synonym: "ABA homeostasis" RELATED []
-is_a: GO:0055081 ! anion homeostasis
is_a: GO:0055088 ! lipid homeostasis
[Term]
id: GO:1902266
-name: cellular abscisic acid homeostasis
+name: intracellular abscisic acid homeostasis
namespace: biological_process
-def: "Any biological process involved in the maintenance of an internal steady state of abscisic acid at the level of the cell." [GOC:TermGenie, PMID:23252460]
+def: "A homeostatic process involved in the maintenance of a steady state level of abscisic acid within a cell." [GOC:TermGenie, PMID:23252460]
synonym: "cellular 2-cis-abscisate homeostasis" EXACT []
synonym: "cellular ABA homeostasis" RELATED []
-is_a: GO:0030002 ! cellular anion homeostasis
+is_a: GO:0055082 ! intracellular chemical homeostasis
is_a: GO:1902265 ! abscisic acid homeostasis
[Term]
@@ -458842,7 +461934,7 @@ id: GO:1902272
name: regulation of (R)-carnitine transmembrane transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of (R)-carnitine transmembrane transport." [GOC:TermGenie, PMID:23755272]
-is_a: GO:1904062 ! regulation of cation transmembrane transport
+is_a: GO:0034762 ! regulation of transmembrane transport
relationship: regulates GO:1902270 ! (R)-carnitine transmembrane transport
[Term]
@@ -458854,8 +461946,8 @@ synonym: "down regulation of (R)-carnitine transmembrane transport" EXACT [GOC:T
synonym: "down-regulation of (R)-carnitine transmembrane transport" EXACT [GOC:TermGenie]
synonym: "downregulation of (R)-carnitine transmembrane transport" EXACT [GOC:TermGenie]
synonym: "inhibition of (R)-carnitine transmembrane transport" NARROW [GOC:TermGenie]
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:1902272 ! regulation of (R)-carnitine transmembrane transport
-is_a: GO:1904063 ! negative regulation of cation transmembrane transport
relationship: negatively_regulates GO:1902270 ! (R)-carnitine transmembrane transport
[Term]
@@ -458867,16 +461959,19 @@ synonym: "activation of (R)-carnitine transmembrane transport" NARROW [GOC:TermG
synonym: "up regulation of (R)-carnitine transmembrane transport" EXACT [GOC:TermGenie]
synonym: "up-regulation of (R)-carnitine transmembrane transport" EXACT [GOC:TermGenie]
synonym: "upregulation of (R)-carnitine transmembrane transport" EXACT [GOC:TermGenie]
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:1902272 ! regulation of (R)-carnitine transmembrane transport
-is_a: GO:1904064 ! positive regulation of cation transmembrane transport
relationship: positively_regulates GO:1902270 ! (R)-carnitine transmembrane transport
[Term]
id: GO:1902275
name: regulation of chromatin organization
namespace: biological_process
+alt_id: GO:0001672
alt_id: GO:1903308
def: "Any process that modulates the frequency, rate or extent of chromatin organization." [GO_REF:0000058, GOC:bf, GOC:TermGenie, GOC:vw, PMID:18314879]
+synonym: "regulation of chromatin assembly or disassembly" RELATED []
+synonym: "regulation of chromatin assembly/disassembly" RELATED []
synonym: "regulation of chromatin modification" RELATED []
synonym: "regulation of chromatin organisation" EXACT [GOC:TermGenie]
synonym: "regulation of establishment or maintenance of chromatin architecture" EXACT [GOC:TermGenie]
@@ -459176,7 +462271,7 @@ def: "Any maintenance of fidelity that is involved in cell cycle DNA replication
synonym: "maintenance of fidelity during DNA-dependent DNA replication involved in cell cycle DNA replication" RELATED [GOC:TermGenie]
synonym: "maintenance of fidelity involved in cell cycle DNA replication" EXACT []
is_a: GO:0022402 ! cell cycle process
-is_a: GO:0045005 ! DNA-dependent DNA replication maintenance of fidelity
+is_a: GO:0045005 ! DNA-templated DNA replication maintenance of fidelity
relationship: part_of GO:0044786 ! cell cycle DNA replication
[Term]
@@ -459218,7 +462313,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of sodium ion transmembrane transport." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:18591664]
synonym: "regulation of sodium ion membrane transport" EXACT [GOC:TermGenie]
is_a: GO:0002028 ! regulation of sodium ion transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
+is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport
relationship: regulates GO:0035725 ! sodium ion transmembrane transport
[Term]
@@ -459301,7 +462396,7 @@ def: "Any process that modulates the frequency, rate or extent of copper ion tra
synonym: "regulation of copper cation transmembrane transport" EXACT [GOC:TermGenie]
synonym: "regulation of copper ion membrane transport" EXACT [GOC:TermGenie]
is_a: GO:0010959 ! regulation of metal ion transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
+is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport
relationship: regulates GO:0035434 ! copper ion transmembrane transport
[Term]
@@ -459354,7 +462449,7 @@ relationship: positively_regulates GO:0035434 ! copper ion transmembrane transpo
id: GO:1902314
name: hydroquinone binding
namespace: molecular_function
-def: "Binding to hydroquinone." [GOC:bhm, GOC:TermGenie, pmid:15667223]
+def: "Binding to hydroquinone." [GOC:bhm, GOC:TermGenie, PMID:15667223]
synonym: "quinol binding" EXACT []
is_a: GO:0097159 ! organic cyclic compound binding
@@ -459435,8 +462530,7 @@ synonym: "methyl-branched fatty acid anabolism" EXACT [GOC:TermGenie]
synonym: "methyl-branched fatty acid biosynthesis" EXACT [GOC:TermGenie]
synonym: "methyl-branched fatty acid formation" EXACT [GOC:TermGenie]
synonym: "methyl-branched fatty acid synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0008610 ! lipid biosynthetic process
-is_a: GO:0016053 ! organic acid biosynthetic process
+is_a: GO:0006633 ! fatty acid biosynthetic process
is_a: GO:0097089 ! methyl-branched fatty acid metabolic process
[Term]
@@ -459448,9 +462542,7 @@ synonym: "regulation of methyl-branched fatty acid anabolism" EXACT [GOC:TermGen
synonym: "regulation of methyl-branched fatty acid biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of methyl-branched fatty acid formation" EXACT [GOC:TermGenie]
synonym: "regulation of methyl-branched fatty acid synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0031326 ! regulation of cellular biosynthetic process
-is_a: GO:0046890 ! regulation of lipid biosynthetic process
-is_a: GO:0062012 ! regulation of small molecule metabolic process
+is_a: GO:0042304 ! regulation of fatty acid biosynthetic process
relationship: regulates GO:1902321 ! methyl-branched fatty acid biosynthetic process
[Term]
@@ -459482,9 +462574,7 @@ synonym: "negative regulation of methyl-branched fatty acid anabolism" EXACT [GO
synonym: "negative regulation of methyl-branched fatty acid biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of methyl-branched fatty acid formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of methyl-branched fatty acid synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0051055 ! negative regulation of lipid biosynthetic process
-is_a: GO:0062014 ! negative regulation of small molecule metabolic process
+is_a: GO:0045717 ! negative regulation of fatty acid biosynthetic process
is_a: GO:1902322 ! regulation of methyl-branched fatty acid biosynthetic process
relationship: negatively_regulates GO:1902321 ! methyl-branched fatty acid biosynthetic process
@@ -459517,9 +462607,7 @@ synonym: "upregulation of methyl-branched fatty acid biosynthesis" EXACT [GOC:Te
synonym: "upregulation of methyl-branched fatty acid biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of methyl-branched fatty acid formation" EXACT [GOC:TermGenie]
synonym: "upregulation of methyl-branched fatty acid synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0046889 ! positive regulation of lipid biosynthetic process
-is_a: GO:0062013 ! positive regulation of small molecule metabolic process
+is_a: GO:0045723 ! positive regulation of fatty acid biosynthetic process
is_a: GO:1902322 ! regulation of methyl-branched fatty acid biosynthetic process
relationship: positively_regulates GO:1902321 ! methyl-branched fatty acid biosynthetic process
@@ -459666,7 +462754,6 @@ namespace: biological_process
def: "The directed movement of fructose from vacuole to cytoplasm." [GOC:TermGenie, PMID:23583552]
synonym: "fructose transport from vacuole to cytoplasm" EXACT []
is_a: GO:0015755 ! fructose transmembrane transport
-is_a: GO:0033231 ! carbohydrate export
is_a: GO:0034486 ! vacuolar transmembrane transport
[Term]
@@ -459795,19 +462882,20 @@ relationship: negatively_regulates GO:0030261 ! chromosome condensation
[Term]
id: GO:1902341
-name: xylitol transport
+name: xylitol transmembrane transport
namespace: biological_process
-def: "The directed movement of a xylitol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Xylitol is a polyalcohol (pentane-1,2,3,4,5-pentol), produced by hydrogenation of xylose." [GOC:TermGenie, PMID:23475614]
-is_a: GO:0008643 ! carbohydrate transport
-is_a: GO:0015791 ! polyol transport
+def: "The directed movement of a xylitol across a membrane. Xylitol is a polyalcohol (pentane-1,2,3,4,5-pentol), produced by hydrogenation of xylose." [GOC:TermGenie, PMID:23475614]
+synonym: "xylitol transport" BROAD []
+is_a: GO:0015791 ! polyol transmembrane transport
+is_a: GO:0034219 ! carbohydrate transmembrane transport
[Term]
id: GO:1902342
-name: xylitol export
+name: obsolete xylitol export
namespace: biological_process
-def: "The directed movement of xylitol out of a cell or organelle." [GOC:TermGenie, PMID:23475614]
-is_a: GO:0033231 ! carbohydrate export
-is_a: GO:1902341 ! xylitol transport
+def: "OBSOLETE. The directed movement of xylitol out of a cell or organelle." [GOC:TermGenie, PMID:23475614]
+comment: This term was obsoleted because there is is no specific process for xylitol export.
+is_obsolete: true
[Term]
id: GO:1902343
@@ -459890,6 +462978,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chloroquine stimulus." [GOC:kmv, GOC:TermGenie, PMID:23922869]
is_a: GO:0010243 ! response to organonitrogen compound
is_a: GO:0014070 ! response to organic cyclic compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1902350
@@ -459898,6 +462987,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chloroquine stimulus." [GOC:kmv, GOC:TermGenie, PMID:23922869]
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0071417 ! cellular response to organonitrogen compound
+is_a: GO:1902075 ! cellular response to salt
is_a: GO:1902349 ! response to chloroquine
[Term]
@@ -459949,7 +463039,6 @@ name: oxaloacetate(2-) transmembrane transport
namespace: biological_process
def: "The directed movement of oxaloacetate(2-) across a membrane." [GOC:dph, GOC:TermGenie, PMID:18682385]
is_a: GO:0015729 ! oxaloacetate transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -459958,7 +463047,6 @@ name: 2-isopropylmalate(2-) transmembrane transport
namespace: biological_process
def: "The process in which 2-isopropylmalate(2-) is transported across a membrane." [GOC:dph, GOC:TermGenie, GOC:vw, PMID:18682385]
is_a: GO:0034659 ! isopropylmalate transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -460033,7 +463121,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to spindle pole body." [GOC:TermGenie, PMID:21131906]
synonym: "regulation of protein localisation to spindle pole body" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0071988 ! protein localization to spindle pole body
[Term]
@@ -460050,7 +463137,6 @@ synonym: "downregulation of protein localization to spindle pole body" EXACT [GO
synonym: "inhibition of protein localisation to spindle pole body" NARROW [GOC:TermGenie]
synonym: "inhibition of protein localization to spindle pole body" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to spindle pole body" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1902363 ! regulation of protein localization to spindle pole body
is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:0071988 ! protein localization to spindle pole body
@@ -460069,7 +463155,6 @@ synonym: "up-regulation of protein localisation to spindle pole body" EXACT [GOC
synonym: "up-regulation of protein localization to spindle pole body" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localisation to spindle pole body" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to spindle pole body" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1902363 ! regulation of protein localization to spindle pole body
is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:0071988 ! protein localization to spindle pole body
@@ -460408,7 +463493,7 @@ is_a: GO:0060699 ! regulation of endoribonuclease activity
id: GO:1902381
name: 11-oxo-beta-amyrin metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving 11-oxo-beta-amyrin." [GOC:TermGenie, pmid:22128119]
+def: "The chemical reactions and pathways involving 11-oxo-beta-amyrin." [GOC:TermGenie, PMID:22128119]
synonym: "11-oxo-beta-amyrin metabolism" EXACT [GOC:TermGenie]
is_a: GO:0019742 ! pentacyclic triterpenoid metabolic process
is_a: GO:0042180 ! cellular ketone metabolic process
@@ -460417,7 +463502,7 @@ is_a: GO:0042180 ! cellular ketone metabolic process
id: GO:1902382
name: 11-oxo-beta-amyrin catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 11-oxo-beta-amyrin." [GOC:TermGenie, pmid:22128119]
+def: "The chemical reactions and pathways resulting in the breakdown of 11-oxo-beta-amyrin." [GOC:TermGenie, PMID:22128119]
synonym: "11-oxo-beta-amyrin breakdown" EXACT [GOC:TermGenie]
synonym: "11-oxo-beta-amyrin catabolism" EXACT [GOC:TermGenie]
synonym: "11-oxo-beta-amyrin degradation" EXACT [GOC:TermGenie]
@@ -460429,7 +463514,7 @@ is_a: GO:1902381 ! 11-oxo-beta-amyrin metabolic process
id: GO:1902383
name: 11-oxo-beta-amyrin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 11-oxo-beta-amyrin." [GOC:TermGenie, pmid:22128119]
+def: "The chemical reactions and pathways resulting in the formation of 11-oxo-beta-amyrin." [GOC:TermGenie, PMID:22128119]
synonym: "11-oxo-beta-amyrin anabolism" EXACT [GOC:TermGenie]
synonym: "11-oxo-beta-amyrin biosynthesis" EXACT [GOC:TermGenie]
synonym: "11-oxo-beta-amyrin formation" EXACT [GOC:TermGenie]
@@ -460442,7 +463527,7 @@ is_a: GO:1902381 ! 11-oxo-beta-amyrin metabolic process
id: GO:1902384
name: glycyrrhetinate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving glycyrrhetinate." [GOC:TermGenie, pmid:22128119]
+def: "The chemical reactions and pathways involving glycyrrhetinate." [GOC:TermGenie, PMID:22128119]
synonym: "glycyrrhetinate metabolism" EXACT [GOC:TermGenie]
is_a: GO:0019742 ! pentacyclic triterpenoid metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
@@ -460453,7 +463538,7 @@ is_a: GO:1901615 ! organic hydroxy compound metabolic process
id: GO:1902385
name: glycyrrhetinate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of glycyrrhetinate." [GOC:TermGenie, pmid:22128119]
+def: "The chemical reactions and pathways resulting in the breakdown of glycyrrhetinate." [GOC:TermGenie, PMID:22128119]
synonym: "glycyrrhetinate breakdown" EXACT [GOC:TermGenie]
synonym: "glycyrrhetinate catabolism" EXACT [GOC:TermGenie]
synonym: "glycyrrhetinate degradation" EXACT [GOC:TermGenie]
@@ -460467,7 +463552,7 @@ is_a: GO:1902384 ! glycyrrhetinate metabolic process
id: GO:1902386
name: glycyrrhetinate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of glycyrrhetinate." [GOC:TermGenie, pmid:22128119]
+def: "The chemical reactions and pathways resulting in the formation of glycyrrhetinate." [GOC:TermGenie, PMID:22128119]
synonym: "glycyrrhetinate anabolism" EXACT [GOC:TermGenie]
synonym: "glycyrrhetinate biosynthesis" EXACT [GOC:TermGenie]
synonym: "glycyrrhetinate formation" EXACT [GOC:TermGenie]
@@ -460668,12 +463753,11 @@ is_a: GO:1902410 ! mitotic cytokinetic process
[Term]
id: GO:1902408
-name: mitotic cytokinesis, site selection
+name: mitotic cytokinesis, division site positioning
namespace: biological_process
-def: "Any cytokinesis, site selection that is involved in mitotic cell cycle." [GOC:mtg_cell_cycle, GOC:TermGenie]
-synonym: "site selection involved in cell cycle cytokinesis involved in mitotic cell cycle" EXACT [GOC:TermGenie]
-synonym: "site selection involved in cytokinesis involved in mitotic cell cycle" EXACT [GOC:TermGenie]
-is_a: GO:0007105 ! cytokinesis, site selection
+def: "The process in which a contractile ring is positioned in a specific location during the mitotic cell cycle. This process is critical for both for both symmetric and asymmetric cell divisions." [PMID:26553932, PMID:28162898]
+synonym: "mitotic cytokinesis, site selection" EXACT []
+is_a: GO:0007105 ! cytokinesis, division site positioning
is_a: GO:1902410 ! mitotic cytokinetic process
[Term]
@@ -460953,7 +464037,7 @@ synonym: "down-regulation of beta-amyloid formation" EXACT [GOC:TermGenie]
synonym: "downregulation of beta-amyloid formation" EXACT [GOC:TermGenie]
synonym: "inhibition of beta-amyloid formation" NARROW [GOC:TermGenie]
synonym: "negative regulation of beta-amyloid formation" EXACT []
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:1902003 ! regulation of amyloid-beta formation
is_a: GO:1902992 ! negative regulation of amyloid precursor protein catabolic process
relationship: negatively_regulates GO:0034205 ! amyloid-beta formation
@@ -461037,7 +464121,6 @@ synonym: "down-regulation of male mating behavior" EXACT [GOC:TermGenie]
synonym: "downregulation of male mating behavior" EXACT [GOC:TermGenie]
synonym: "inhibition of male mating behavior" NARROW [GOC:TermGenie]
is_a: GO:0048521 ! negative regulation of behavior
-is_a: GO:0051241 ! negative regulation of multicellular organismal process
is_a: GO:1902435 ! regulation of male mating behavior
is_a: GO:2000242 ! negative regulation of reproductive process
relationship: negatively_regulates GO:0060179 ! male mating behavior
@@ -461052,7 +464135,6 @@ synonym: "up regulation of male mating behavior" EXACT [GOC:TermGenie]
synonym: "up-regulation of male mating behavior" EXACT [GOC:TermGenie]
synonym: "upregulation of male mating behavior" EXACT [GOC:TermGenie]
is_a: GO:0048520 ! positive regulation of behavior
-is_a: GO:0051240 ! positive regulation of multicellular organismal process
is_a: GO:1902435 ! regulation of male mating behavior
is_a: GO:2000243 ! positive regulation of reproductive process
relationship: positively_regulates GO:0060179 ! male mating behavior
@@ -461064,6 +464146,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vanadate(3-) stimulus." [GOC:di, GOC:TermGenie, PMID:7489911]
is_a: GO:0010035 ! response to inorganic substance
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1902439
@@ -461071,6 +464154,7 @@ name: cellular response to vanadate(3-)
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vanadate(3-) stimulus." [GOC:di, GOC:TermGenie, PMID:7489911]
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
is_a: GO:1902438 ! response to vanadate(3-)
[Term]
@@ -461301,7 +464385,7 @@ def: "A process in which a protein is transported to, or maintained in, a locati
synonym: "protein localisation in cell leading edge" EXACT [GOC:TermGenie]
synonym: "protein localisation to cell leading edge" EXACT [GOC:TermGenie]
synonym: "protein localization in cell leading edge" EXACT [GOC:TermGenie]
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
[Term]
id: GO:1902464
@@ -461348,12 +464432,13 @@ relationship: regulates GO:1902405 ! mitotic actomyosin contractile ring localiz
[Term]
id: GO:1902472
-name: regulation of mitotic cytokinesis, site selection
+name: regulation of mitotic cytokinesis, division site positioning
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of mitotic cytokinesis, site selection." [GOC:TermGenie, PMID:19959363, PMID:21246752, PMID:22786806]
+def: "Any process that modulates the frequency, rate or extent of mitotic cytokinesis, division site positioning." [PMID:9852154]
+synonym: "regulation of mitotic cytokinesis, site selection" EXACT []
is_a: GO:1903436 ! regulation of mitotic cytokinetic process
is_a: GO:2000073 ! regulation of cytokinesis, site selection
-relationship: regulates GO:1902408 ! mitotic cytokinesis, site selection
+relationship: regulates GO:1902408 ! mitotic cytokinesis, division site positioning
[Term]
id: GO:1902473
@@ -461388,6 +464473,7 @@ name: L-alpha-amino acid transmembrane transport
namespace: biological_process
def: "The directed movement of L-alpha-amino acid across a membrane." [GOC:kmv, GOC:TermGenie, PMID:14668347]
is_a: GO:0003333 ! amino acid transmembrane transport
+is_a: GO:0015807 ! L-amino acid transport
[Term]
id: GO:1902476
@@ -461395,6 +464481,7 @@ name: chloride transmembrane transport
namespace: biological_process
def: "The process in which chloride is transported across a membrane." [GOC:TermGenie, GOC:vw]
is_a: GO:0006821 ! chloride transport
+is_a: GO:0098656 ! monoatomic anion transmembrane transport
is_a: GO:0098661 ! inorganic anion transmembrane transport
[Term]
@@ -461458,8 +464545,8 @@ name: L-cysteine binding
namespace: molecular_function
def: "Binding to L-cysteine." [GOC:bhm, GOC:TermGenie, PMID:12941942]
is_a: GO:0016597 ! amino acid binding
-is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0043169 ! cation binding
+is_a: GO:0072341 ! modified amino acid binding
is_a: GO:1901681 ! sulfur compound binding
[Term]
@@ -461574,7 +464661,6 @@ namespace: cellular_component
def: "A transmembrane protein complex which enables the transfer of a substance from one side of a membrane to the other." [GOC:bhm, GOC:TermGenie, PMID:18024586]
is_a: GO:0098796 ! membrane protein complex
is_a: GO:1990351 ! transporter complex
-relationship: part_of GO:0016021 ! integral component of membrane
[Term]
id: GO:1902496
@@ -462487,7 +465573,7 @@ comment: An example is IRE1 in S. cerevisiae (UniProt ID P32361) in PMID:1819122
synonym: "Ire1 complex dimer" RELATED []
synonym: "Ire1 complex homodimer" RELATED []
synonym: "Ire1 complex homooligomer" RELATED []
-is_a: GO:1902494 ! catalytic complex
+is_a: GO:1905348 ! endonuclease complex
[Term]
id: GO:1902556
@@ -462522,7 +465608,6 @@ is_a: GO:0015868 ! purine ribonucleotide transport
is_a: GO:0051503 ! adenine nucleotide transport
is_a: GO:0072348 ! sulfur compound transport
is_a: GO:0072530 ! purine-containing compound transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1901679 ! nucleotide transmembrane transport
[Term]
@@ -462533,14 +465618,13 @@ def: "The process in which 3'-phospho-5'-adenylyl sulfate is transported across
synonym: "3'-phosphoadenosine 5'-phosphosulfate transmembrane transport" EXACT [PMID:24296033]
is_a: GO:0046963 ! 3'-phosphoadenosine 5'-phosphosulfate transport
is_a: GO:0072530 ! purine-containing compound transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1901679 ! nucleotide transmembrane transport
[Term]
id: GO:1902560
name: GMP reductase complex
namespace: cellular_component
-def: "An oxidoreductase complex which is capable of GMP reductase activity. It catalyses the irreversible reaction: GMP + 2 H(+) + NADPH => IMP + NADP(+) + NH(4)(+)." [GOC:bhm, GOC:TermGenie, PMID:12009299]
+def: "An oxidoreductase complex which is capable of GMP reductase activity. It catalyses the irreversible reaction: GMP + 2 H+ + NADPH => IMP + NADP+ + NH4." [GOC:bhm, GOC:TermGenie, PMID:12009299]
comment: An example of this is GMPR2 in human (UniProt Symbol Q9P2T1) in PMID:12009299 (inferred from direct assay).
synonym: "GMP reductase" NARROW []
synonym: "GMPR1 complex" NARROW []
@@ -462783,7 +465867,7 @@ synonym: "negative regulation of DNA replication involved in S phase" EXACT [GOC
synonym: "negative regulation of DNA replication involved in S-phase" EXACT [GOC:TermGenie]
is_a: GO:0010948 ! negative regulation of cell cycle process
is_a: GO:0033262 ! regulation of nuclear cell cycle DNA replication
-is_a: GO:2000104 ! negative regulation of DNA-dependent DNA replication
+is_a: GO:2000104 ! negative regulation of DNA-templated DNA replication
relationship: negatively_regulates GO:0033260 ! nuclear DNA replication
[Term]
@@ -462971,6 +466055,7 @@ synonym: "hydrogen transmembrane transport" EXACT []
synonym: "hydrogen transport" BROAD []
synonym: "passive proton transport, down the electrochemical gradient" NARROW []
synonym: "proton transport" BROAD []
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -462997,7 +466082,7 @@ name: carnitine transmembrane transport
namespace: biological_process
def: "The directed movement of carnitine across a membrane." [GO_REF:0000069, GOC:pr, GOC:TermGenie]
is_a: GO:0015879 ! carnitine transport
-is_a: GO:0098655 ! cation transmembrane transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:1902604
@@ -463007,7 +466092,6 @@ def: "The directed movement of N-(4-aminobenzoyl)-L-glutamate across a membrane.
synonym: "N-(4-aminobenzoyl)-L-glutamate transmembrane transport" EXACT []
is_a: GO:0015814 ! p-aminobenzoyl-glutamate transport
is_a: GO:0035442 ! dipeptide transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -463192,13 +466276,16 @@ name: response to fluoride
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fluoride stimulus." [GO_REF:0000071, GOC:kmv, GOC:TermGenie, PMID:8138152]
is_a: GO:0010035 ! response to inorganic substance
+is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1902618
name: cellular response to fluoride
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fluoride stimulus." [GO_REF:0000071, GOC:kmv, GOC:TermGenie, PMID:8138152]
-is_a: GO:0070887 ! cellular response to chemical stimulus
+is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
is_a: GO:1902617 ! response to fluoride
[Term]
@@ -463284,7 +466371,7 @@ def: "The aggregation, arrangement and bonding together of a set of components t
synonym: "66S preribosome assembly" NARROW [GOC:TermGenie]
synonym: "66S preribosome formation" NARROW [GOC:TermGenie]
synonym: "preribosome, large subunit precursor formation" EXACT [GOC:TermGenie]
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
[Term]
id: GO:1902627
@@ -463715,8 +466802,7 @@ name: calcium ion import into cytosol
namespace: biological_process
def: "The directed movement of calcium ion into a cytosol." [GO_REF:0000075, GOC:TermGenie, GOC:vw]
synonym: "calcium import into cytosol" BROAD []
-is_a: GO:0060402 ! calcium ion transport into cytosol
-is_a: GO:0070509 ! calcium ion import
+is_a: GO:0006816 ! calcium ion transport
[Term]
id: GO:1902657
@@ -463902,8 +466988,8 @@ def: "Any process that modulates the frequency, rate or extent of axon guidance.
synonym: "regulation of axon chemotaxis" RELATED [GOC:TermGenie]
synonym: "regulation of axon growth cone guidance" NARROW [GOC:TermGenie]
synonym: "regulation of axon pathfinding" EXACT [GOC:TermGenie]
+is_a: GO:0010975 ! regulation of neuron projection development
is_a: GO:0050920 ! regulation of chemotaxis
-is_a: GO:0051270 ! regulation of cellular component movement
relationship: regulates GO:0007411 ! axon guidance
[Term]
@@ -463930,8 +467016,8 @@ synonym: "inhibition of axon pathfinding" NARROW [GOC:TermGenie]
synonym: "negative regulation of axon chemotaxis" RELATED [GOC:TermGenie]
synonym: "negative regulation of axon growth cone guidance" NARROW [GOC:TermGenie]
synonym: "negative regulation of axon pathfinding" EXACT [GOC:TermGenie]
+is_a: GO:0010977 ! negative regulation of neuron projection development
is_a: GO:0050922 ! negative regulation of chemotaxis
-is_a: GO:0051271 ! negative regulation of cellular component movement
is_a: GO:1902667 ! regulation of axon guidance
relationship: negatively_regulates GO:0007411 ! axon guidance
@@ -463959,7 +467045,7 @@ synonym: "upregulation of axon chemotaxis" RELATED [GOC:TermGenie]
synonym: "upregulation of axon growth cone guidance" NARROW [GOC:TermGenie]
synonym: "upregulation of axon guidance" EXACT [GOC:TermGenie]
synonym: "upregulation of axon pathfinding" EXACT [GOC:TermGenie]
-is_a: GO:0051272 ! positive regulation of cellular component movement
+is_a: GO:0010976 ! positive regulation of neuron projection development
is_a: GO:1902667 ! regulation of axon guidance
relationship: positively_regulates GO:0007411 ! axon guidance
@@ -464209,8 +467295,7 @@ def: "Any process that modulates the frequency, rate or extent of replication fo
synonym: "regulation of replication fork arrest at ribosomal DNA repeats" EXACT [GOC:TermGenie]
synonym: "regulation of replication fork blocking at rDNA repeats" EXACT [GOC:TermGenie]
is_a: GO:0033044 ! regulation of chromosome organization
-is_a: GO:0051052 ! regulation of DNA metabolic process
-is_a: GO:0090329 ! regulation of DNA-dependent DNA replication
+is_a: GO:0090329 ! regulation of DNA-templated DNA replication
relationship: regulates GO:0031582 ! replication fork arrest at rDNA repeats
[Term]
@@ -464342,7 +467427,7 @@ synonym: "regulation of oxidized NAD metabolic process" EXACT [GOC:TermGenie]
synonym: "regulation of oxidized NAD metabolism" EXACT [GOC:TermGenie]
synonym: "regulation of oxidized nicotinamide adenine dinucleotide metabolic process" EXACT [GOC:TermGenie]
synonym: "regulation of oxidized nicotinamide adenine dinucleotide metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0019222 ! regulation of metabolic process
+is_a: GO:1900542 ! regulation of purine nucleotide metabolic process
relationship: regulates GO:0019674 ! NAD metabolic process
[Term]
@@ -464404,7 +467489,7 @@ synonym: "negative regulation of oxidized NAD metabolic process" EXACT [GOC:Term
synonym: "negative regulation of oxidized NAD metabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of oxidized nicotinamide adenine dinucleotide metabolic process" EXACT [GOC:TermGenie]
synonym: "negative regulation of oxidized nicotinamide adenine dinucleotide metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0009892 ! negative regulation of metabolic process
+is_a: GO:1900543 ! negative regulation of purine nucleotide metabolic process
is_a: GO:1902688 ! regulation of NAD metabolic process
relationship: negatively_regulates GO:0019674 ! NAD metabolic process
@@ -464467,7 +467552,7 @@ synonym: "upregulation of oxidized NAD metabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of oxidized NAD metabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of oxidized nicotinamide adenine dinucleotide metabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of oxidized nicotinamide adenine dinucleotide metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0009893 ! positive regulation of metabolic process
+is_a: GO:1900544 ! positive regulation of purine nucleotide metabolic process
is_a: GO:1902688 ! regulation of NAD metabolic process
relationship: positively_regulates GO:0019674 ! NAD metabolic process
@@ -464594,86 +467679,86 @@ is_a: GO:1902639 ! propan-2-ol metabolic process
[Term]
id: GO:1902702
-name: hexose catabolic process to propan-2-ol
+name: obsolete hexose catabolic process to propan-2-ol
namespace: biological_process
alt_id: GO:1990283
-def: "The chemical reactions and pathways resulting in the breakdown of hexose to propan-2-ol." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of hexose to propan-2-ol." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744]
+comment: This term was obsoleted because there is no evidence that this pathway exists.
synonym: "hexose breakdown to propan-2-ol" EXACT [GOC:TermGenie]
synonym: "hexose catabolic process to isopropanol" EXACT [GOC:tt]
synonym: "hexose catabolic process to isopropyl alcohol" EXACT [GOC:tt]
synonym: "hexose catabolism to propan-2-ol" EXACT [GOC:TermGenie]
synonym: "hexose degradation to propan-2-ol" EXACT [GOC:TermGenie]
synonym: "solventogenesis" RELATED [GOC:tt]
-is_a: GO:0019320 ! hexose catabolic process
-is_a: GO:1902639 ! propan-2-ol metabolic process
+is_obsolete: true
[Term]
id: GO:1902703
-name: hexose catabolic process to butan-1-ol
+name: obsolete hexose catabolic process to butan-1-ol
namespace: biological_process
alt_id: GO:1990284
-def: "The chemical reactions and pathways resulting in the breakdown of hexose to butan-1-ol." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of hexose to butan-1-ol." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744]
+comment: This term was obsoleted because there is no evidence that this pathway exists.
synonym: "hexose breakdown to butan-1-ol" EXACT [GOC:TermGenie]
synonym: "hexose catabolic process to 1-butanol" EXACT [GOC:tt]
synonym: "hexose catabolic process to butanol" EXACT [GOC:tt]
synonym: "hexose catabolism to butan-1-ol" EXACT [GOC:TermGenie]
synonym: "hexose degradation to butan-1-ol" EXACT [GOC:TermGenie]
synonym: "solventogenesis" BROAD [GOC:tt]
-is_a: GO:0019320 ! hexose catabolic process
-is_a: GO:0071270 ! 1-butanol metabolic process
+is_obsolete: true
[Term]
id: GO:1902704
-name: hexose catabolic process to acetone
+name: obsolete hexose catabolic process to acetone
namespace: biological_process
alt_id: GO:1990285
-def: "The chemical reactions and pathways resulting in the breakdown of hexose to acetone." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of hexose to acetone." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744]
+comment: This term was obsoleted because there is no evidence that this pathway exists.
synonym: "hexose breakdown to acetone" EXACT [GOC:TermGenie]
synonym: "hexose catabolic process to 2-propanone" EXACT [GOC:tt]
synonym: "hexose catabolism to acetone" EXACT [GOC:TermGenie]
synonym: "hexose degradation to acetone" EXACT [GOC:TermGenie]
synonym: "solventogenesis" BROAD [GOC:tt]
-is_a: GO:0019320 ! hexose catabolic process
-is_a: GO:0043443 ! acetone metabolic process
+is_obsolete: true
[Term]
id: GO:1902705
-name: hexose catabolic process to butyrate
+name: obsolete hexose catabolic process to butyrate
namespace: biological_process
alt_id: GO:1990287
-def: "The chemical reactions and pathways resulting in the breakdown of hexose to butyrate." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of hexose to butyrate." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744]
+comment: This term was obsoleted because there is no evidence that this pathway exists.
synonym: "acidogenesis" BROAD [GOC:tt]
synonym: "hexose breakdown to butyrate" EXACT [GOC:TermGenie]
synonym: "hexose catabolism to butyrate" EXACT [GOC:TermGenie]
synonym: "hexose degradation to butyrate" EXACT [GOC:TermGenie]
-is_a: GO:0019320 ! hexose catabolic process
-is_a: GO:0019605 ! butyrate metabolic process
+is_obsolete: true
[Term]
id: GO:1902706
-name: hexose catabolic process to acetate
+name: obsolete hexose catabolic process to acetate
namespace: biological_process
alt_id: GO:1990286
-def: "The chemical reactions and pathways resulting in the breakdown of hexose to acetate." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of hexose to acetate." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744]
+comment: This term was obsoleted because there is no evidence that this pathway exists.
synonym: "acidogenesis" BROAD [GOC:tt]
synonym: "hexose breakdown to acetate" EXACT [GOC:TermGenie]
synonym: "hexose catabolism to acetate" EXACT [GOC:TermGenie]
synonym: "hexose degradation to acetate" EXACT [GOC:TermGenie]
-is_a: GO:0006083 ! acetate metabolic process
-is_a: GO:0019320 ! hexose catabolic process
+is_obsolete: true
[Term]
id: GO:1902707
-name: hexose catabolic process to ethanol
+name: obsolete hexose catabolic process to ethanol
namespace: biological_process
alt_id: GO:1990282
-def: "The chemical reactions and pathways resulting in the breakdown of hexose to ethanol." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of hexose to ethanol." [GO_REF:0000093, GOC:mengo_curators, GOC:TermGenie, PMID:18727018, PMID:19539744]
+comment: This term was obsoleted because there is no evidence that this pathway exists.
synonym: "hexose breakdown to ethanol" EXACT [GOC:TermGenie]
synonym: "hexose catabolism to ethanol" EXACT [GOC:TermGenie]
synonym: "hexose degradation to ethanol" EXACT [GOC:TermGenie]
synonym: "solventogenesis" BROAD [GOC:tt]
-is_a: GO:0006067 ! ethanol metabolic process
-is_a: GO:0019320 ! hexose catabolic process
+is_obsolete: true
[Term]
id: GO:1902708
@@ -465657,24 +468742,26 @@ is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:1902794
-name: siRNA-independent facultative heterochromatin assembly
+name: siRNA-independent facultative heterochromatin formation
namespace: biological_process
-def: "The assembly of facultative heterochromatin to form a heterochromatin domain, enriched in histone H3 methylated on lysine 9 (H3K9me), by a process independent of small interfering RNAs." [GO_REF:0000079, GOC:TermGenie, PMID:22144463, PMID:24210919]
+def: "The formation of facultative heterochromatin into a heterochromatin domain, enriched in histone H3 methylated on lysine 9 (H3K9me), by a process independent of small interfering RNAs." [PMID:22144463, PMID:24210919]
synonym: "heterochromatin island assembly" EXACT []
synonym: "heterochromatin island formation" EXACT [GOC:TermGenie]
-is_a: GO:0140718 ! facultative heterochromatin assembly
+synonym: "siRNA-independent facultative heterochromatin assembly" EXACT []
+is_a: GO:0140718 ! facultative heterochromatin formation
[Term]
id: GO:1902795
-name: siRNA-dependent facultative heterochromatin assembly
+name: siRNA-mediated facultative heterochromatin formation
namespace: biological_process
-def: "The assembly of facultative heterochromatin to form a heterochromatin domain, enriched in histone H3 methylated on lysine 9 (H3K9me), by a process mediated by a small interfering RNA." [GO_REF:0000079, GOC:TermGenie, PMID:23151475, PMID:24210919]
+def: "The formation of facultative heterochromatin into a heterochromatin domain, enriched in histone H3 methylated on lysine 9 (H3K9me), by a process mediated by a small interfering RNA." [GO_REF:0000079, GOC:TermGenie, PMID:23151475, PMID:24210919]
synonym: "heterochromatin domain assembly" EXACT []
synonym: "heterochromatin domain formation" EXACT [GOC:TermGenie]
synonym: "HOOD assembly" EXACT [GOC:TermGenie]
synonym: "HOOD formation" EXACT [GOC:TermGenie]
-is_a: GO:0031048 ! heterochromatin assembly by small RNA
-is_a: GO:0140718 ! facultative heterochromatin assembly
+synonym: "siRNA-dependent facultative heterochromatin assembly" EXACT []
+synonym: "siRNA-dependent facultative heterochromatin formation" EXACT []
+is_a: GO:0031048 ! small ncRNA-mediated heterochromatin formation
[Term]
id: GO:1902796
@@ -465819,25 +468906,27 @@ is_a: GO:1905779 ! positive regulation of exonuclease activity
[Term]
id: GO:1902801
-name: regulation of siRNA-independent facultative heterochromatin assembly
+name: regulation of siRNA-independent facultative heterochromatin formation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of siRNA-independent facultative heterochromatin assembly." [GO_REF:0000058, GOC:TermGenie, PMID:24210919]
synonym: "regulation of heterochromatin island assembly" EXACT []
synonym: "regulation of heterochromatin island formation" EXACT [GOC:TermGenie]
-is_a: GO:0031445 ! regulation of heterochromatin assembly
-relationship: regulates GO:1902794 ! siRNA-independent facultative heterochromatin assembly
+synonym: "regulation of siRNA-independent facultative heterochromatin assembly" EXACT []
+is_a: GO:0031445 ! regulation of heterochromatin formation
+relationship: regulates GO:1902794 ! siRNA-independent facultative heterochromatin formation
[Term]
id: GO:1902802
-name: regulation of siRNA-dependent facultative heterochromatin assembly
+name: regulation of siRNA-dependent facultative heterochromatin formation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of siRNA-dependent facultative heterochromatin assembly." [GO_REF:0000058, GOC:TermGenie, PMID:24210919]
+def: "Any process that modulates the frequency, rate or extent of siRNA-dependent facultative heterochromatin formation." [GO_REF:0000058, GOC:TermGenie, PMID:24210919]
synonym: "regulation of heterochromatin domain assembly" EXACT []
synonym: "regulation of heterochromatin domain formation" EXACT [GOC:TermGenie]
synonym: "regulation of HOOD assembly" EXACT [GOC:TermGenie]
synonym: "regulation of HOOD formation" EXACT [GOC:TermGenie]
-is_a: GO:0010964 ! regulation of heterochromatin assembly by small RNA
-relationship: regulates GO:1902795 ! siRNA-dependent facultative heterochromatin assembly
+synonym: "regulation of siRNA-dependent facultative heterochromatin assembly" EXACT []
+is_a: GO:0010964 ! regulation of small non-coding RNA-mediated heterochromatin formation
+relationship: regulates GO:1902795 ! siRNA-mediated facultative heterochromatin formation
[Term]
id: GO:1902803
@@ -465847,7 +468936,6 @@ def: "Any process that modulates the frequency, rate or extent of synaptic vesic
synonym: "regulation of synaptic vesicle fission" RELATED [GOC:TermGenie]
synonym: "regulation of synaptic vesicle fusion" RELATED [GOC:TermGenie]
is_a: GO:0051049 ! regulation of transport
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0048489 ! synaptic vesicle transport
[Term]
@@ -465869,7 +468957,6 @@ synonym: "inhibition of synaptic vesicle fusion" RELATED [GOC:TermGenie]
synonym: "inhibition of synaptic vesicle transport" NARROW [GOC:TermGenie]
synonym: "negative regulation of synaptic vesicle fission" RELATED [GOC:TermGenie]
synonym: "negative regulation of synaptic vesicle fusion" RELATED [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0051051 ! negative regulation of transport
is_a: GO:1902803 ! regulation of synaptic vesicle transport
relationship: negatively_regulates GO:0048489 ! synaptic vesicle transport
@@ -465893,7 +468980,6 @@ synonym: "up-regulation of synaptic vesicle transport" EXACT [GOC:TermGenie]
synonym: "upregulation of synaptic vesicle fission" RELATED [GOC:TermGenie]
synonym: "upregulation of synaptic vesicle fusion" RELATED [GOC:TermGenie]
synonym: "upregulation of synaptic vesicle transport" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:0051050 ! positive regulation of transport
is_a: GO:1902803 ! regulation of synaptic vesicle transport
relationship: positively_regulates GO:0048489 ! synaptic vesicle transport
@@ -466041,7 +469127,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to microtubule." [GO_REF:0000058, GOC:TermGenie, GOC:vw, PMID:23087209]
synonym: "regulation of protein localisation to microtubule" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0035372 ! protein localization to microtubule
[Term]
@@ -466058,7 +469143,6 @@ synonym: "downregulation of protein localization to microtubule" EXACT [GOC:Term
synonym: "inhibition of protein localisation to microtubule" NARROW [GOC:TermGenie]
synonym: "inhibition of protein localization to microtubule" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to microtubule" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1902816 ! regulation of protein localization to microtubule
is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:0035372 ! protein localization to microtubule
@@ -466318,7 +469402,6 @@ synonym: "negative regulation of nuclear migration, microtubule-mediated" EXACT
synonym: "negative regulation of transport of nucleus by microtubules" EXACT [GOC:TermGenie]
synonym: "negative regulation of transport of nucleus, microtubule-mediated" EXACT [GOC:TermGenie]
is_a: GO:0032387 ! negative regulation of intracellular transport
-is_a: GO:0051271 ! negative regulation of cellular component movement
is_a: GO:1902838 ! regulation of nuclear migration along microtubule
relationship: negatively_regulates GO:0030473 ! nuclear migration along microtubule
@@ -466372,7 +469455,6 @@ synonym: "upregulation of nuclear migration, microtubule-mediated" EXACT [GOC:Te
synonym: "upregulation of transport of nucleus by microtubules" EXACT [GOC:TermGenie]
synonym: "upregulation of transport of nucleus, microtubule-mediated" EXACT [GOC:TermGenie]
is_a: GO:0032388 ! positive regulation of intracellular transport
-is_a: GO:0051272 ! positive regulation of cellular component movement
is_a: GO:1902838 ! regulation of nuclear migration along microtubule
relationship: positively_regulates GO:0030473 ! nuclear migration along microtubule
@@ -466380,7 +469462,7 @@ relationship: positively_regulates GO:0030473 ! nuclear migration along microtub
id: GO:1902841
name: regulation of netrin-activated signaling pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of netrin-activated signaling pathway." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:24004945]
+def: "Any process that modulates the frequency, rate or extent of netrin-activated signaling pathway." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:24004945]
synonym: "regulation of netrin signaling pathway" EXACT [GOC:TermGenie]
synonym: "regulation of netrin-activated signal transduction pathway" EXACT [GOC:TermGenie]
synonym: "regulation of netrin-activated signalling pathway" EXACT [GOC:TermGenie]
@@ -466392,7 +469474,7 @@ relationship: regulates GO:0038007 ! netrin-activated signaling pathway
id: GO:1902842
name: negative regulation of netrin-activated signaling pathway
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of netrin-activated signaling pathway." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:24004945]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of netrin-activated signaling pathway." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:24004945]
synonym: "down regulation of netrin signaling pathway" EXACT [GOC:TermGenie]
synonym: "down regulation of netrin-activated signal transduction pathway" EXACT [GOC:TermGenie]
synonym: "down regulation of netrin-activated signaling pathway" EXACT [GOC:TermGenie]
@@ -466425,7 +469507,7 @@ relationship: negatively_regulates GO:0038007 ! netrin-activated signaling pathw
id: GO:1902843
name: positive regulation of netrin-activated signaling pathway
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of netrin-activated signaling pathway." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:24004945]
+def: "Any process that activates or increases the frequency, rate or extent of netrin-activated signaling pathway." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:24004945]
synonym: "activation of netrin signaling pathway" NARROW [GOC:TermGenie]
synonym: "activation of netrin-activated signal transduction pathway" NARROW [GOC:TermGenie]
synonym: "activation of netrin-activated signaling pathway" NARROW [GOC:TermGenie]
@@ -466674,8 +469756,7 @@ name: propionyl-CoA metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving propionyl-CoA." [GO_REF:0000068, GOC:mengo_curators, GOC:TermGenie, PMID:15514053]
synonym: "propionyl-CoA metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006629 ! lipid metabolic process
-is_a: GO:0006637 ! acyl-CoA metabolic process
+is_a: GO:0035337 ! fatty-acyl-CoA metabolic process
[Term]
id: GO:1902859
@@ -466685,11 +469766,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of propiony
synonym: "propionyl-CoA breakdown" EXACT [GOC:TermGenie]
synonym: "propionyl-CoA catabolism" EXACT [GOC:TermGenie]
synonym: "propionyl-CoA degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009154 ! purine ribonucleotide catabolic process
-is_a: GO:0016042 ! lipid catabolic process
-is_a: GO:0034031 ! ribonucleoside bisphosphate catabolic process
-is_a: GO:0034034 ! purine nucleoside bisphosphate catabolic process
-is_a: GO:0044273 ! sulfur compound catabolic process
+is_a: GO:0036115 ! fatty-acyl-CoA catabolic process
is_a: GO:1902858 ! propionyl-CoA metabolic process
[Term]
@@ -466701,8 +469778,7 @@ synonym: "propionyl-CoA anabolism" EXACT [GOC:TermGenie]
synonym: "propionyl-CoA biosynthesis" EXACT [GOC:TermGenie]
synonym: "propionyl-CoA formation" EXACT [GOC:TermGenie]
synonym: "propionyl-CoA synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0008610 ! lipid biosynthetic process
-is_a: GO:0071616 ! acyl-CoA biosynthetic process
+is_a: GO:0046949 ! fatty-acyl-CoA biosynthetic process
is_a: GO:1902858 ! propionyl-CoA metabolic process
[Term]
@@ -467236,7 +470312,8 @@ synonym: "regulation of miRNA gene transcription" EXACT []
synonym: "regulation of pri-miRNA transcription by RNA polymerase II" EXACT []
synonym: "regulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT []
synonym: "regulation of primary miRNA gene transcription" EXACT []
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
+is_a: GO:2000628 ! regulation of miRNA metabolic process
relationship: regulates GO:0061614 ! miRNA transcription
[Term]
@@ -467253,8 +470330,9 @@ synonym: "negative regulation of miRNA gene transcription" EXACT []
synonym: "negative regulation of pri-miRNA transcription by RNA polymerase II" EXACT []
synonym: "negative regulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT []
synonym: "negative regulation of primary miRNA gene transcription" EXACT []
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
is_a: GO:1902893 ! regulation of miRNA transcription
+is_a: GO:2000629 ! negative regulation of miRNA metabolic process
relationship: negatively_regulates GO:0061614 ! miRNA transcription
[Term]
@@ -467271,15 +470349,16 @@ synonym: "positive regulation of primary miRNA gene transcription" EXACT []
synonym: "up regulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "up-regulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "upregulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
is_a: GO:1902893 ! regulation of miRNA transcription
+is_a: GO:2000630 ! positive regulation of miRNA metabolic process
relationship: positively_regulates GO:0061614 ! miRNA transcription
[Term]
id: GO:1902896
name: terminal web assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form a terminal web." [GO_REF:0000079, GOC:kmv, GOC:TermGenie, pmid:21949650]
+def: "The aggregation, arrangement and bonding together of a set of components to form a terminal web." [GO_REF:0000079, GOC:kmv, GOC:TermGenie, PMID:21949650]
synonym: "terminal web formation" EXACT [GOC:TermGenie]
is_a: GO:0030866 ! cortical actin cytoskeleton organization
is_a: GO:0140694 ! non-membrane-bounded organelle assembly
@@ -467303,7 +470382,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving fatty acid methyl ester." [GO_REF:0000068, GOC:mengo_curators, GOC:TermGenie, PMID:16570218]
synonym: "FAME metabolic process" EXACT []
synonym: "fatty acid methyl ester metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006629 ! lipid metabolic process
+is_a: GO:1901568 ! fatty acid derivative metabolic process
[Term]
id: GO:1902899
@@ -467315,24 +470394,25 @@ synonym: "fatty acid methyl ester anabolism" EXACT [GOC:TermGenie]
synonym: "fatty acid methyl ester biosynthesis" EXACT [GOC:TermGenie]
synonym: "fatty acid methyl ester formation" EXACT [GOC:TermGenie]
synonym: "fatty acid methyl ester synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0008610 ! lipid biosynthetic process
+is_a: GO:1901570 ! fatty acid derivative biosynthetic process
is_a: GO:1902898 ! fatty acid methyl ester metabolic process
[Term]
id: GO:1902900
name: gut granule assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form a gut granule." [GO_REF:0000079, GOC:kmv, GOC:TermGenie, pmid:17202409]
-synonym: "gut granule biogenesis" EXACT [pmid:17202409]
+def: "The aggregation, arrangement and bonding together of a set of components to form a gut granule." [GO_REF:0000079, GOC:kmv, GOC:TermGenie, PMID:17202409]
+synonym: "gut granule biogenesis" EXACT [PMID:17202409]
synonym: "gut granule formation" EXACT [GOC:TermGenie]
is_a: GO:0016050 ! vesicle organization
is_a: GO:0070925 ! organelle assembly
[Term]
id: GO:1902901
-name: positive regulation of transcription from RNA polymerase II promoter involved in stress response to cadmium ion
+name: obsolete positive regulation of transcription from RNA polymerase II promoter involved in stress response to cadmium ion
namespace: biological_process
-def: "Any positive regulation of transcription from RNA polymerase II promoter that is involved in stress response to cadmium ion." [GO_REF:0000060, GOC:kmv, GOC:TermGenie, pmid:17888400]
+def: "OBSOLETE. Any positive regulation of transcription from RNA polymerase II promoter that is involved in stress response to cadmium ion." [GO_REF:0000060, GOC:kmv, GOC:TermGenie, PMID:17888400]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "activation of global transcription from RNA polymerase II promoter involved in response to cadmium ion stress" RELATED [GOC:TermGenie]
synonym: "activation of global transcription from RNA polymerase II promoter involved in response to cadmium toxicity" RELATED [GOC:TermGenie]
synonym: "activation of global transcription from RNA polymerase II promoter involved in stress response to cadmium ion" RELATED [GOC:TermGenie]
@@ -467374,8 +470454,9 @@ synonym: "upregulation of global transcription from RNA polymerase II promoter i
synonym: "upregulation of transcription from RNA polymerase II promoter involved in response to cadmium ion stress" EXACT [GOC:TermGenie]
synonym: "upregulation of transcription from RNA polymerase II promoter involved in response to cadmium toxicity" RELATED [GOC:TermGenie]
synonym: "upregulation of transcription from RNA polymerase II promoter involved in stress response to cadmium ion" EXACT [GOC:TermGenie]
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
-relationship: part_of GO:1990170 ! stress response to cadmium ion
+is_obsolete: true
+consider: GO:0045944
+consider: GO:1990170
[Term]
id: GO:1902902
@@ -467485,8 +470566,8 @@ id: GO:1902908
name: regulation of melanosome transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of melanosome transport." [GO_REF:0000058, GOC:als, GOC:TermGenie, PMID:23334344]
+is_a: GO:0050794 ! regulation of cellular process
is_a: GO:0051049 ! regulation of transport
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0032402 ! melanosome transport
[Term]
@@ -467714,8 +470795,7 @@ synonym: "poly(hydroxyalkanoate) anabolism from fatty acid" EXACT [GOC:TermGenie
synonym: "poly(hydroxyalkanoate) biosynthesis from fatty acid" EXACT [GOC:TermGenie]
synonym: "poly(hydroxyalkanoate) formation from fatty acid" EXACT [GOC:TermGenie]
synonym: "poly(hydroxyalkanoate) synthesis from fatty acid" EXACT [GOC:TermGenie]
-is_a: GO:0006082 ! organic acid metabolic process
-is_a: GO:0006629 ! lipid metabolic process
+is_a: GO:0006631 ! fatty acid metabolic process
is_a: GO:1901441 ! poly(hydroxyalkanoate) biosynthetic process
[Term]
@@ -467902,8 +470982,6 @@ name: regulation of intracellular calcium activated chloride channel activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of intracellular calcium activated chloride channel activity." [GO_REF:0000059, GOC:als, GOC:TermGenie, PMID:22946059]
is_a: GO:0010359 ! regulation of anion channel activity
-is_a: GO:1903795 ! regulation of inorganic anion transmembrane transport
-is_a: GO:2001225 ! regulation of chloride transport
[Term]
id: GO:1902939
@@ -467916,8 +470994,6 @@ synonym: "downregulation of intracellular calcium activated chloride channel act
synonym: "inhibition of intracellular calcium activated chloride channel activity" NARROW [GOC:TermGenie]
is_a: GO:0010360 ! negative regulation of anion channel activity
is_a: GO:1902938 ! regulation of intracellular calcium activated chloride channel activity
-is_a: GO:1903796 ! negative regulation of inorganic anion transmembrane transport
-is_a: GO:2001226 ! negative regulation of chloride transport
[Term]
id: GO:1902940
@@ -467930,7 +471006,6 @@ synonym: "up-regulation of intracellular calcium activated chloride channel acti
synonym: "upregulation of intracellular calcium activated chloride channel activity" EXACT [GOC:TermGenie]
is_a: GO:1901529 ! positive regulation of anion channel activity
is_a: GO:1902938 ! regulation of intracellular calcium activated chloride channel activity
-is_a: GO:1903797 ! positive regulation of inorganic anion transmembrane transport
[Term]
id: GO:1902941
@@ -469391,7 +472466,7 @@ synonym: "negative regulation of lysine biosynthetic process, aminoadipic pathwa
synonym: "negative regulation of lysine formation via aminoadipic acid" EXACT [GOC:TermGenie]
synonym: "negative regulation of lysine synthesis via aminoadipic acid" EXACT [GOC:TermGenie]
is_a: GO:1902986 ! regulation of lysine biosynthetic process via aminoadipic acid
-is_a: GO:2000283 ! negative regulation of cellular amino acid biosynthetic process
+is_a: GO:2000283 ! negative regulation of amino acid biosynthetic process
relationship: negatively_regulates GO:0019878 ! lysine biosynthetic process via aminoadipic acid
[Term]
@@ -469957,7 +473032,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of glycoprotein metabolic process." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:23544079]
comment: human serum amyloid P component (SAP) P02743 inhibits viral neuraminidase, NA (exo-alpha-sialidase activity) and thus the metabolism of glycoproteins, demonstrated in Figure 4A PMID:23544079, (IDA), the negative regulation term would be applied to this protein
synonym: "regulation of glycoprotein metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0031323 ! regulation of cellular metabolic process
is_a: GO:0051246 ! regulation of protein metabolic process
relationship: regulates GO:0009100 ! glycoprotein metabolic process
@@ -469976,7 +473050,6 @@ synonym: "downregulation of glycoprotein metabolism" EXACT [GOC:TermGenie]
synonym: "inhibition of glycoprotein metabolic process" NARROW [GOC:TermGenie]
synonym: "inhibition of glycoprotein metabolism" NARROW [GOC:TermGenie]
synonym: "negative regulation of glycoprotein metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0031324 ! negative regulation of cellular metabolic process
is_a: GO:0051248 ! negative regulation of protein metabolic process
is_a: GO:1903018 ! regulation of glycoprotein metabolic process
relationship: negatively_regulates GO:0009100 ! glycoprotein metabolic process
@@ -469996,7 +473069,6 @@ synonym: "up-regulation of glycoprotein metabolic process" EXACT [GOC:TermGenie]
synonym: "up-regulation of glycoprotein metabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of glycoprotein metabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of glycoprotein metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0031325 ! positive regulation of cellular metabolic process
is_a: GO:0051247 ! positive regulation of protein metabolic process
is_a: GO:1903018 ! regulation of glycoprotein metabolic process
relationship: positively_regulates GO:0009100 ! glycoprotein metabolic process
@@ -470117,7 +473189,6 @@ synonym: "up regulation of opsonization" EXACT [GOC:TermGenie]
synonym: "up-regulation of opsonization" EXACT [GOC:TermGenie]
synonym: "upregulation of opsonization" EXACT [GOC:TermGenie]
is_a: GO:0002699 ! positive regulation of immune effector process
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:0050766 ! positive regulation of phagocytosis
is_a: GO:1903027 ! regulation of opsonization
relationship: positively_regulates GO:0008228 ! opsonization
@@ -470157,7 +473228,7 @@ is_a: GO:1904528 ! positive regulation of microtubule binding
id: GO:1903034
name: regulation of response to wounding
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of response to wounding." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:19164535]
+def: "Any process that modulates the frequency, rate or extent of response to wounding." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:19164535]
synonym: "regulation of physiological response to wounding" EXACT [GOC:TermGenie]
is_a: GO:0080134 ! regulation of response to stress
relationship: regulates GO:0009611 ! response to wounding
@@ -470166,7 +473237,7 @@ relationship: regulates GO:0009611 ! response to wounding
id: GO:1903035
name: negative regulation of response to wounding
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:19164535]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:19164535]
synonym: "down regulation of physiological response to wounding" EXACT [GOC:TermGenie]
synonym: "down regulation of response to wounding" EXACT [GOC:TermGenie]
synonym: "down-regulation of physiological response to wounding" EXACT [GOC:TermGenie]
@@ -470184,7 +473255,7 @@ relationship: negatively_regulates GO:0009611 ! response to wounding
id: GO:1903036
name: positive regulation of response to wounding
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of response to wounding." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:19164535]
+def: "Any process that activates or increases the frequency, rate or extent of response to wounding." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:19164535]
synonym: "activation of physiological response to wounding" NARROW [GOC:TermGenie]
synonym: "activation of response to wounding" NARROW [GOC:TermGenie]
synonym: "positive regulation of physiological response to wounding" EXACT [GOC:TermGenie]
@@ -470370,9 +473441,9 @@ is_a: GO:2001258 ! negative regulation of cation channel activity
[Term]
id: GO:1903050
-name: regulation of proteolysis involved in cellular protein catabolic process
+name: regulation of proteolysis involved in protein catabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of proteolysis involved in cellular protein catabolic process." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:18307834]
+def: "Any process that modulates the frequency, rate or extent of proteolysis involved in cellular catabolic process." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:18307834]
comment: overexpression of cathepsin C propeptide significantly increased the degradation of intestinal alkaline phosphatase (IAP)
synonym: "regulation of peptidolysis during cellular protein catabolic process" RELATED [GOC:TermGenie]
synonym: "regulation of peptidolysis during cellular protein catabolism" RELATED [GOC:TermGenie]
@@ -470380,15 +473451,15 @@ synonym: "regulation of peptidolysis involved in cellular protein catabolic proc
synonym: "regulation of peptidolysis involved in cellular protein catabolism" EXACT [GOC:TermGenie]
synonym: "regulation of proteolysis during cellular protein catabolic process" RELATED [GOC:TermGenie]
synonym: "regulation of proteolysis during cellular protein catabolism" RELATED [GOC:TermGenie]
+synonym: "regulation of proteolysis involved in cellular protein catabolic process" EXACT []
is_a: GO:0030162 ! regulation of proteolysis
-is_a: GO:1903362 ! regulation of cellular protein catabolic process
-relationship: regulates GO:0051603 ! proteolysis involved in cellular protein catabolic process
+relationship: regulates GO:0051603 ! proteolysis involved in protein catabolic process
[Term]
id: GO:1903051
-name: negative regulation of proteolysis involved in cellular protein catabolic process
+name: negative regulation of proteolysis involved in protein catabolic process
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of proteolysis involved in cellular protein catabolic process." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:18307834]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of proteolysis involved in protein catabolic process." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:18307834]
comment: Overexpression of cathepsin C propeptide significantly increased the degradation of intestinal alkaline phosphatase (IAP).
synonym: "down regulation of peptidolysis during cellular protein catabolic process" RELATED [GOC:TermGenie]
synonym: "down regulation of peptidolysis during cellular protein catabolism" RELATED [GOC:TermGenie]
@@ -470424,16 +473495,16 @@ synonym: "negative regulation of peptidolysis involved in cellular protein catab
synonym: "negative regulation of peptidolysis involved in cellular protein catabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of proteolysis during cellular protein catabolic process" RELATED [GOC:TermGenie]
synonym: "negative regulation of proteolysis during cellular protein catabolism" RELATED [GOC:TermGenie]
+synonym: "negative regulation of proteolysis involved in cellular protein catabolic process" EXACT []
is_a: GO:0045861 ! negative regulation of proteolysis
-is_a: GO:1903050 ! regulation of proteolysis involved in cellular protein catabolic process
-is_a: GO:1903363 ! negative regulation of cellular protein catabolic process
-relationship: negatively_regulates GO:0051603 ! proteolysis involved in cellular protein catabolic process
+is_a: GO:1903050 ! regulation of proteolysis involved in protein catabolic process
+relationship: negatively_regulates GO:0051603 ! proteolysis involved in protein catabolic process
[Term]
id: GO:1903052
-name: positive regulation of proteolysis involved in cellular protein catabolic process
+name: positive regulation of proteolysis involved in protein catabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of proteolysis involved in cellular protein catabolic process." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:18307834]
+def: "Any process that activates or increases the frequency, rate or extent of proteolysis involved in protein catabolic process." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:18307834]
comment: overexpression of cathepsin C propeptide significantly increased the degradation of intestinal alkaline phosphatase (IAP)
synonym: "activation of peptidolysis during cellular protein catabolic process" RELATED [GOC:TermGenie]
synonym: "activation of peptidolysis during cellular protein catabolism" RELATED [GOC:TermGenie]
@@ -470448,6 +473519,7 @@ synonym: "positive regulation of peptidolysis involved in cellular protein catab
synonym: "positive regulation of peptidolysis involved in cellular protein catabolism" EXACT [GOC:TermGenie]
synonym: "positive regulation of proteolysis during cellular protein catabolic process" RELATED [GOC:TermGenie]
synonym: "positive regulation of proteolysis during cellular protein catabolism" RELATED [GOC:TermGenie]
+synonym: "positive regulation of proteolysis involved in cellular protein catabolic process" EXACT []
synonym: "up regulation of peptidolysis during cellular protein catabolic process" RELATED [GOC:TermGenie]
synonym: "up regulation of peptidolysis during cellular protein catabolism" RELATED [GOC:TermGenie]
synonym: "up regulation of peptidolysis involved in cellular protein catabolic process" EXACT [GOC:TermGenie]
@@ -470470,9 +473542,8 @@ synonym: "upregulation of proteolysis during cellular protein catabolic process"
synonym: "upregulation of proteolysis during cellular protein catabolism" RELATED [GOC:TermGenie]
synonym: "upregulation of proteolysis involved in cellular protein catabolic process" EXACT [GOC:TermGenie]
is_a: GO:0045862 ! positive regulation of proteolysis
-is_a: GO:1903050 ! regulation of proteolysis involved in cellular protein catabolic process
-is_a: GO:1903364 ! positive regulation of cellular protein catabolic process
-relationship: positively_regulates GO:0051603 ! proteolysis involved in cellular protein catabolic process
+is_a: GO:1903050 ! regulation of proteolysis involved in protein catabolic process
+relationship: positively_regulates GO:0051603 ! proteolysis involved in protein catabolic process
[Term]
id: GO:1903053
@@ -470596,9 +473667,9 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein lipidation." [GO_REF:0000058, GOC:rph, GOC:TermGenie, PMID:21909394]
synonym: "regulation of lipid:protein modification" EXACT [GOC:TermGenie]
synonym: "regulation of protein amino acid lipidation" EXACT [GOC:TermGenie]
+is_a: GO:0010556 ! regulation of macromolecule biosynthetic process
is_a: GO:0031399 ! regulation of protein modification process
is_a: GO:0050746 ! regulation of lipoprotein metabolic process
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
relationship: regulates GO:0006497 ! protein lipidation
[Term]
@@ -470620,10 +473691,10 @@ synonym: "inhibition of protein amino acid lipidation" NARROW [GOC:TermGenie]
synonym: "inhibition of protein lipidation" NARROW [GOC:TermGenie]
synonym: "negative regulation of lipid:protein modification" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein amino acid lipidation" EXACT [GOC:TermGenie]
+is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process
is_a: GO:0031400 ! negative regulation of protein modification process
is_a: GO:0050748 ! negative regulation of lipoprotein metabolic process
is_a: GO:1903059 ! regulation of protein lipidation
-is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process
relationship: negatively_regulates GO:0006497 ! protein lipidation
[Term]
@@ -470701,7 +473772,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to cell tip." [GO_REF:0000058, GOC:TermGenie, PMID:24554432]
synonym: "regulation of protein localisation to cell tip" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:1990151 ! protein localization to cell tip
[Term]
@@ -470718,7 +473788,6 @@ synonym: "downregulation of protein localization to cell tip" EXACT [GOC:TermGen
synonym: "inhibition of protein localisation to cell tip" NARROW [GOC:TermGenie]
synonym: "inhibition of protein localization to cell tip" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to cell tip" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903066 ! regulation of protein localization to cell tip
is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:1990151 ! protein localization to cell tip
@@ -470737,7 +473806,6 @@ synonym: "up-regulation of protein localisation to cell tip" EXACT [GOC:TermGeni
synonym: "up-regulation of protein localization to cell tip" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localisation to cell tip" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to cell tip" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903066 ! regulation of protein localization to cell tip
is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:1990151 ! protein localization to cell tip
@@ -471116,7 +474184,7 @@ relationship: positively_regulates GO:0038118 ! C-C chemokine receptor CCR7 sign
id: GO:1903083
name: protein localization to condensed chromosome
namespace: biological_process
-def: "A process in which a protein is transported to, or maintained in, a location within a condensed chromosome." [GO_REF:0000087, GOC:kmv, GOC:TermGenie, pmid:12707312]
+def: "A process in which a protein is transported to, or maintained in, a location within a condensed chromosome." [GO_REF:0000087, GOC:kmv, GOC:TermGenie, PMID:12707312]
synonym: "protein localisation in condensed chromosome" EXACT [GOC:TermGenie]
synonym: "protein localisation to condensed chromosome" EXACT [GOC:TermGenie]
synonym: "protein localization in condensed chromosome" EXACT [GOC:TermGenie]
@@ -471126,7 +474194,7 @@ is_a: GO:0034502 ! protein localization to chromosome
id: GO:1903084
name: protein localization to condensed nuclear chromosome
namespace: biological_process
-def: "A process in which a protein is transported to, or maintained in, a location within a condensed nuclear chromosome." [GO_REF:0000087, GOC:kmv, GOC:TermGenie, pmid:12707312]
+def: "A process in which a protein is transported to, or maintained in, a location within a condensed nuclear chromosome." [GO_REF:0000087, GOC:kmv, GOC:TermGenie, PMID:12707312]
synonym: "protein localisation in condensed nuclear chromosome" EXACT [GOC:TermGenie]
synonym: "protein localisation to condensed nuclear chromosome" EXACT [GOC:TermGenie]
synonym: "protein localization in condensed nuclear chromosome" EXACT [GOC:TermGenie]
@@ -471223,7 +474291,6 @@ namespace: biological_process
def: "The process in which pyridoxal is transported across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:15701794]
is_a: GO:0031920 ! pyridoxal transport
is_a: GO:0035461 ! vitamin transmembrane transport
-is_a: GO:0098655 ! cation transmembrane transport
[Term]
id: GO:1903091
@@ -471232,7 +474299,6 @@ namespace: biological_process
def: "The process in which pyridoxamine is transported across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:15701794]
is_a: GO:0031922 ! pyridoxamine transport
is_a: GO:0035461 ! vitamin transmembrane transport
-is_a: GO:0098655 ! cation transmembrane transport
[Term]
id: GO:1903092
@@ -471275,7 +474341,7 @@ is_a: GO:1902555 ! endoribonuclease complex
id: GO:1903096
name: protein localization to meiotic spindle midzone
namespace: biological_process
-def: "A process in which a protein is transported to, or maintained in, a location within a meiotic spindle midzone." [GO_REF:0000087, GOC:kmv, GOC:TermGenie, pmid:12707312]
+def: "A process in which a protein is transported to, or maintained in, a location within a meiotic spindle midzone." [GO_REF:0000087, GOC:kmv, GOC:TermGenie, PMID:12707312]
synonym: "protein localisation in meiotic spindle midzone" EXACT [GOC:TermGenie]
synonym: "protein localisation to meiotic spindle midzone" EXACT [GOC:TermGenie]
synonym: "protein localization in meiotic spindle midzone" EXACT [GOC:TermGenie]
@@ -471283,9 +474349,10 @@ is_a: GO:1905359 ! protein localization to meiotic spindle
[Term]
id: GO:1903097
-name: regulation of CENP-A containing nucleosome assembly
+name: obsolete regulation of CENP-A containing nucleosome assembly
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of the formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres." [GO_REF:0000058, GOC:TermGenie, PMID:24710126]
+def: "OBSOLETE. Any process that modulates the rate, frequency or extent of the formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres." [GO_REF:0000058, GOC:TermGenie, PMID:24710126]
+comment: This term has been obsoleted because this process is not known to be regulated.
synonym: "regulation of CenH3-containing nucleosome assembly at centromere" RELATED [GOC:TermGenie]
synonym: "regulation of CENP-A deposition" RELATED [GOC:TermGenie]
synonym: "regulation of CENP-A loading" RELATED [GOC:TermGenie]
@@ -471294,16 +474361,15 @@ synonym: "regulation of centromere-specific histone exchange" EXACT [GOC:TermGen
synonym: "regulation of centromere-specific nucleosome assembly" EXACT [GOC:TermGenie]
synonym: "regulation of centromeric DNA replication-independent nucleosome assembly" EXACT [GOC:TermGenie]
synonym: "regulation of DNA replication-independent nucleosome assembly at centromere" EXACT [GOC:TermGenie]
-is_a: GO:0010847 ! regulation of chromatin assembly
-is_a: GO:0090230 ! regulation of centromere complex assembly
-is_a: GO:1900049 ! regulation of histone exchange
-relationship: regulates GO:0034080 ! CENP-A containing chromatin assembly
+is_obsolete: true
+consider: GO:0034080
[Term]
id: GO:1903098
-name: negative regulation of CENP-A containing nucleosome assembly
+name: obsolete negative regulation of CENP-A containing nucleosome assembly
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of the formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres." [GO_REF:0000058, GOC:TermGenie, PMID:24710126]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of the formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres." [GO_REF:0000058, GOC:TermGenie, PMID:24710126]
+comment: This term has been obsoleted because this process is not known to be regulated.
synonym: "down regulation of CenH3-containing nucleosome assembly at centromere" RELATED [GOC:TermGenie]
synonym: "down regulation of CENP-A containing nucleosome assembly at centromere" EXACT [GOC:TermGenie]
synonym: "down regulation of CENP-A deposition" RELATED [GOC:TermGenie]
@@ -471348,17 +474414,14 @@ synonym: "negative regulation of centromere-specific histone exchange" EXACT [GO
synonym: "negative regulation of centromere-specific nucleosome assembly" EXACT [GOC:TermGenie]
synonym: "negative regulation of centromeric DNA replication-independent nucleosome assembly" EXACT [GOC:TermGenie]
synonym: "negative regulation of DNA replication-independent nucleosome assembly at centromere" EXACT [GOC:TermGenie]
-is_a: GO:0031333 ! negative regulation of protein-containing complex assembly
-is_a: GO:0045798 ! negative regulation of chromatin assembly or disassembly
-is_a: GO:1900050 ! negative regulation of histone exchange
-is_a: GO:1903097 ! regulation of CENP-A containing nucleosome assembly
-relationship: negatively_regulates GO:0034080 ! CENP-A containing chromatin assembly
+is_obsolete: true
[Term]
id: GO:1903099
-name: positive regulation of CENP-A containing nucleosome assembly
+name: obsolete positive regulation of CENP-A containing nucleosome assembly
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres." [GO_REF:0000058, GOC:TermGenie, PMID:24710126]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres." [GO_REF:0000058, GOC:TermGenie, PMID:24710126]
+comment: This term has been obsoleted because this process is not known to be regulated.
synonym: "activation of CenH3-containing nucleosome assembly at centromere" RELATED [GOC:TermGenie]
synonym: "activation of CENP-A containing nucleosome assembly at centromere" NARROW [GOC:TermGenie]
synonym: "activation of CENP-A deposition" RELATED [GOC:TermGenie]
@@ -471403,11 +474466,7 @@ synonym: "upregulation of centromere-specific histone exchange" EXACT [GOC:TermG
synonym: "upregulation of centromere-specific nucleosome assembly" EXACT [GOC:TermGenie]
synonym: "upregulation of centromeric DNA replication-independent nucleosome assembly" EXACT [GOC:TermGenie]
synonym: "upregulation of DNA replication-independent nucleosome assembly at centromere" EXACT [GOC:TermGenie]
-is_a: GO:0031334 ! positive regulation of protein-containing complex assembly
-is_a: GO:0045799 ! positive regulation of chromatin assembly or disassembly
-is_a: GO:1900051 ! positive regulation of histone exchange
-is_a: GO:1903097 ! regulation of CENP-A containing nucleosome assembly
-relationship: positively_regulates GO:0034080 ! CENP-A containing chromatin assembly
+is_obsolete: true
[Term]
id: GO:1903100
@@ -471450,20 +474509,21 @@ is_a: GO:1902495 ! transmembrane transporter complex
[Term]
id: GO:1903104
-name: regulation of insulin receptor signaling pathway involved in determination of adult lifespan
+name: obsolete regulation of insulin receptor signaling pathway involved in determination of adult lifespan
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of insulin receptor signaling pathway involved in determination of adult lifespan." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:19853560]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of insulin receptor signaling pathway involved in determination of adult lifespan." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:19853560]
+comment: This term was obsoleted because it should be represented as a GO-CAM model.
synonym: "regulation of daf-2 receptor signaling pathway of determination of adult lifespan" NARROW [GOC:TermGenie]
synonym: "regulation of insulin receptor signaling pathway of determination of adult lifespan" EXACT [GOC:TermGenie]
synonym: "regulation of insulin receptor signalling pathway of determination of adult lifespan" EXACT [GOC:TermGenie]
-is_a: GO:0046626 ! regulation of insulin receptor signaling pathway
-relationship: regulates GO:1901047 ! insulin receptor signaling pathway involved in determination of adult lifespan
+is_obsolete: true
[Term]
id: GO:1903105
-name: negative regulation of insulin receptor signaling pathway involved in determination of adult lifespan
+name: obsolete negative regulation of insulin receptor signaling pathway involved in determination of adult lifespan
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of insulin receptor signaling pathway involved in determination of adult lifespan." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:19853560]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of insulin receptor signaling pathway involved in determination of adult lifespan." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:19853560]
+comment: This term was obsoleted because it should be represented as a GO-CAM model.
synonym: "down regulation of daf-2 receptor signaling pathway of determination of adult lifespan" NARROW [GOC:TermGenie]
synonym: "down regulation of insulin receptor signaling pathway involved in determination of adult lifespan" EXACT [GOC:TermGenie]
synonym: "down regulation of insulin receptor signaling pathway of determination of adult lifespan" EXACT [GOC:TermGenie]
@@ -471483,17 +474543,14 @@ synonym: "inhibition of insulin receptor signalling pathway of determination of
synonym: "negative regulation of daf-2 receptor signaling pathway of determination of adult lifespan" NARROW [GOC:TermGenie]
synonym: "negative regulation of insulin receptor signaling pathway of determination of adult lifespan" EXACT [GOC:TermGenie]
synonym: "negative regulation of insulin receptor signalling pathway of determination of adult lifespan" EXACT [GOC:TermGenie]
-is_a: GO:0046627 ! negative regulation of insulin receptor signaling pathway
-is_a: GO:0051093 ! negative regulation of developmental process
-is_a: GO:0051241 ! negative regulation of multicellular organismal process
-is_a: GO:1903104 ! regulation of insulin receptor signaling pathway involved in determination of adult lifespan
-relationship: negatively_regulates GO:1901047 ! insulin receptor signaling pathway involved in determination of adult lifespan
+is_obsolete: true
[Term]
id: GO:1903106
-name: positive regulation of insulin receptor signaling pathway involved in determination of adult lifespan
+name: obsolete positive regulation of insulin receptor signaling pathway involved in determination of adult lifespan
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of insulin receptor signaling pathway involved in determination of adult lifespan." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:19853560]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of insulin receptor signaling pathway involved in determination of adult lifespan." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:19853560]
+comment: This term was obsoleted because it should be represented as a GO-CAM model.
synonym: "activation of daf-2 receptor signaling pathway of determination of adult lifespan" NARROW [GOC:TermGenie]
synonym: "activation of insulin receptor signaling pathway involved in determination of adult lifespan" NARROW [GOC:TermGenie]
synonym: "activation of insulin receptor signaling pathway of determination of adult lifespan" NARROW [GOC:TermGenie]
@@ -471513,11 +474570,7 @@ synonym: "upregulation of daf-2 receptor signaling pathway of determination of a
synonym: "upregulation of insulin receptor signaling pathway involved in determination of adult lifespan" EXACT [GOC:TermGenie]
synonym: "upregulation of insulin receptor signaling pathway of determination of adult lifespan" EXACT [GOC:TermGenie]
synonym: "upregulation of insulin receptor signalling pathway of determination of adult lifespan" EXACT [GOC:TermGenie]
-is_a: GO:0046628 ! positive regulation of insulin receptor signaling pathway
-is_a: GO:0051094 ! positive regulation of developmental process
-is_a: GO:0051240 ! positive regulation of multicellular organismal process
-is_a: GO:1903104 ! regulation of insulin receptor signaling pathway involved in determination of adult lifespan
-relationship: positively_regulates GO:1901047 ! insulin receptor signaling pathway involved in determination of adult lifespan
+is_obsolete: true
[Term]
id: GO:1903107
@@ -471535,7 +474588,7 @@ name: regulation of mitochondrial transcription
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of transcription occuring in the mitochondrion." [GO_REF:0000058, GOC:TermGenie, PMID:21357609]
synonym: "regulation of transcription from mitochondrial promoter" EXACT []
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
is_a: GO:0062125 ! regulation of mitochondrial gene expression
relationship: regulates GO:0006390 ! mitochondrial transcription
@@ -471553,7 +474606,7 @@ synonym: "up-regulation of mitochondrial transcription" EXACT [GOC:TermGenie]
synonym: "up-regulation of transcription from mitochondrial promoter" EXACT [GOC:TermGenie]
synonym: "upregulation of mitochondrial transcription" EXACT [GOC:TermGenie]
synonym: "upregulation of transcription from mitochondrial promoter" EXACT [GOC:TermGenie]
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
is_a: GO:1903108 ! regulation of mitochondrial transcription
relationship: positively_regulates GO:0006390 ! mitochondrial transcription
@@ -471616,7 +474669,6 @@ name: regulation of actin filament-based movement
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of actin filament-based movement." [GO_REF:0000058, GOC:TermGenie, PMID:24798735]
is_a: GO:0032970 ! regulation of actin filament-based process
-is_a: GO:0051270 ! regulation of cellular component movement
relationship: regulates GO:0030048 ! actin filament-based movement
[Term]
@@ -471628,15 +474680,16 @@ synonym: "activation of actin filament-based movement" NARROW [GOC:TermGenie]
synonym: "up regulation of actin filament-based movement" EXACT [GOC:TermGenie]
synonym: "up-regulation of actin filament-based movement" EXACT [GOC:TermGenie]
synonym: "upregulation of actin filament-based movement" EXACT [GOC:TermGenie]
-is_a: GO:0051272 ! positive regulation of cellular component movement
+is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903115 ! regulation of actin filament-based movement
relationship: positively_regulates GO:0030048 ! actin filament-based movement
[Term]
id: GO:1903117
-name: regulation of actin filament organization involved in cytokinetic actomyosin contractile ring assembly
+name: obsolete regulation of actin filament organization involved in cytokinetic actomyosin contractile ring assembly
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of actin filament organization involved in cytokinetic actomyosin contractile ring assembly." [GO_REF:0000058, GOC:TermGenie, PMID:24798735]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of actin filament organization involved in cytokinetic actomyosin contractile ring assembly." [GO_REF:0000058, GOC:TermGenie, PMID:24798735]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
synonym: "regulation of actin filament organisation of constriction ring assembly" RELATED [GOC:TermGenie]
synonym: "regulation of actin filament organisation of contractile ring assembly" EXACT [GOC:TermGenie]
synonym: "regulation of actin filament organisation of cytokinesis, actomyosin contractile ring assembly" EXACT [GOC:TermGenie]
@@ -471658,16 +474711,16 @@ synonym: "regulation of regulation of actin filament localization of cytokinesis
synonym: "regulation of regulation of actin filament localization of cytokinesis, actomyosin ring biosynthesis" RELATED [GOC:TermGenie]
synonym: "regulation of regulation of actin filament localization of cytokinesis, actomyosin ring formation" RELATED [GOC:TermGenie]
synonym: "regulation of regulation of actin filament localization of cytokinesis, contractile ring assembly" RELATED [GOC:TermGenie]
-is_a: GO:0010564 ! regulation of cell cycle process
-is_a: GO:0110053 ! regulation of actin filament organization
-relationship: regulates GO:2000689 ! actomyosin contractile ring assembly actin filament organization
+is_obsolete: true
[Term]
id: GO:1903118
-name: urate homeostasis
+name: obsolete urate homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of urate within an organism or cell." [GO_REF:0000072, GOC:dph, GOC:TermGenie, PMID:22306318]
-is_a: GO:0048878 ! chemical homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of urate within an organism or cell." [GO_REF:0000072, GOC:dph, GOC:TermGenie, PMID:22306318]
+comment: This term was obsoleted because this process does not exist: urea is a waste product, there are no biological processes to maintain its level, although some mutants accumulate excesses.
+is_obsolete: true
+consider: GO:0003014
[Term]
id: GO:1903119
@@ -471852,6 +474905,7 @@ synonym: "copper(2+)binding" EXACT [CHEBI:29036]
synonym: "Cu(2+) binding" EXACT [CHEBI:29036]
synonym: "Cu(II) binding" EXACT [PMID:24567322]
is_a: GO:0005507 ! copper ion binding
+is_a: GO:1901681 ! sulfur compound binding
[Term]
id: GO:1903136
@@ -472358,7 +475412,7 @@ comment: human HRC regulates RYR2 and thus regulates transmembrane transport of
synonym: "regulation of calcium ion membrane transport" EXACT [GOC:TermGenie]
synonym: "regulation of transmembrane calcium transport" EXACT [GOC:TermGenie]
is_a: GO:0051924 ! regulation of calcium ion transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
+is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport
relationship: regulates GO:0070588 ! calcium ion transmembrane transport
[Term]
@@ -472388,18 +475442,20 @@ relationship: negatively_regulates GO:0070588 ! calcium ion transmembrane transp
[Term]
id: GO:1903171
-name: carbon dioxide homeostasis
+name: obsolete carbon dioxide homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of carbon dioxide within an organism or cell." [GO_REF:0000072, GOC:mr, GOC:TermGenie, PMID:16571594]
-is_a: GO:0048878 ! chemical homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal steady state of carbon dioxide within an organism or cell." [GO_REF:0000072, GOC:mr, GOC:TermGenie, PMID:16571594]
+comment: The reason for obsoletion is that there is no evidence that this process exists.
+is_obsolete: true
+replaced_by: GO:0160061
[Term]
id: GO:1903172
-name: cellular carbon dioxide homeostasis
+name: obsolete cellular carbon dioxide homeostasis
namespace: biological_process
-def: "Any biological process involved in the maintenance of an internal steady state of carbon dioxide at the level of the cell." [GO_REF:0000072, GOC:mr, GOC:TermGenie, PMID:16571594]
-is_a: GO:0055082 ! cellular chemical homeostasis
-is_a: GO:1903171 ! carbon dioxide homeostasis
+def: "OBSOLETE. Any biological process involved in the maintenance of an internal steady state of carbon dioxide at the level of the cell." [GO_REF:0000072, GOC:mr, GOC:TermGenie, PMID:16571594]
+comment: The reason for obsoletion is that there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:1903173
@@ -472408,7 +475464,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving fatty alcohol." [GO_REF:0000068, GOC:mengo_curators, GOC:TermGenie, PMID:24036493]
synonym: "fatty alcohol metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006066 ! alcohol metabolic process
-is_a: GO:0006629 ! lipid metabolic process
+is_a: GO:1901568 ! fatty acid derivative metabolic process
[Term]
id: GO:1903174
@@ -472418,8 +475474,8 @@ def: "The chemical reactions and pathways resulting in the breakdown of fatty al
synonym: "fatty alcohol breakdown" EXACT [GOC:TermGenie]
synonym: "fatty alcohol catabolism" EXACT [GOC:TermGenie]
synonym: "fatty alcohol degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016042 ! lipid catabolic process
is_a: GO:0046164 ! alcohol catabolic process
+is_a: GO:1901569 ! fatty acid derivative catabolic process
is_a: GO:1903173 ! fatty alcohol metabolic process
[Term]
@@ -472431,8 +475487,8 @@ synonym: "fatty alcohol anabolism" EXACT [GOC:TermGenie]
synonym: "fatty alcohol biosynthesis" EXACT [GOC:TermGenie]
synonym: "fatty alcohol formation" EXACT [GOC:TermGenie]
synonym: "fatty alcohol synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:0046165 ! alcohol biosynthetic process
+is_a: GO:1901570 ! fatty acid derivative biosynthetic process
is_a: GO:1903173 ! fatty alcohol metabolic process
[Term]
@@ -472633,7 +475689,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving L-dopa." [GO_REF:0000068, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:8822146]
synonym: "L-dopa metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006575 ! cellular modified amino acid metabolic process
-is_a: GO:0009072 ! aromatic amino acid family metabolic process
+is_a: GO:0009072 ! aromatic amino acid metabolic process
is_a: GO:1901605 ! alpha-amino acid metabolic process
[Term]
@@ -472794,7 +475850,7 @@ synonym: "negative regulation of L-dopa biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of L-dopa formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of L-dopa synthesis" EXACT [GOC:TermGenie]
is_a: GO:1903195 ! regulation of L-dopa biosynthetic process
-is_a: GO:2000283 ! negative regulation of cellular amino acid biosynthetic process
+is_a: GO:2000283 ! negative regulation of amino acid biosynthetic process
relationship: negatively_regulates GO:1903185 ! L-dopa biosynthetic process
[Term]
@@ -472827,7 +475883,7 @@ synonym: "upregulation of L-dopa biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of L-dopa formation" EXACT [GOC:TermGenie]
synonym: "upregulation of L-dopa synthesis" EXACT [GOC:TermGenie]
is_a: GO:1903195 ! regulation of L-dopa biosynthetic process
-is_a: GO:2000284 ! positive regulation of cellular amino acid biosynthetic process
+is_a: GO:2000284 ! positive regulation of amino acid biosynthetic process
relationship: positively_regulates GO:1903185 ! L-dopa biosynthetic process
[Term]
@@ -473057,30 +476113,16 @@ relationship: positively_regulates GO:0036473 ! cell death in response to oxidat
[Term]
id: GO:1903210
-name: glomerular visceral epithelial cell apoptotic process
+name: podocyte apoptotic process
namespace: biological_process
def: "Any apoptotic process in a glomerular visceral epithelial cell." [GO_REF:0000085, GOC:TermGenie, PMID:23515840]
synonym: "glomerular podocyte apoptosis" NARROW [GOC:TermGenie]
synonym: "glomerular podocyte apoptotic process" EXACT [GOC:TermGenie]
synonym: "glomerular visceral epithelial cell apoptosis" NARROW [GOC:TermGenie]
+synonym: "glomerular visceral epithelial cell apoptotic process" EXACT []
synonym: "podocyte apoptosis" NARROW [GOC:TermGenie]
-synonym: "podocyte apoptotic process" EXACT [GOC:TermGenie]
is_a: GO:1904019 ! epithelial cell apoptotic process
-[Term]
-id: GO:1903211
-name: mitotic recombination involved in replication fork processing
-namespace: biological_process
-def: "Any mitotic recombination that is involved in replication fork processing." [GO_REF:0000060, GOC:mah, GOC:TermGenie, PMID:23093942]
-synonym: "mitotic recombination involved in collapsed replication fork processing" EXACT [GOC:TermGenie]
-synonym: "mitotic recombination involved in recovery from replication fork arrest" EXACT [GOC:TermGenie]
-synonym: "mitotic recombination involved in recovery from replication fork stalling" EXACT [GOC:TermGenie]
-synonym: "mitotic recombination involved in replication fork restart" RELATED [GOC:TermGenie]
-synonym: "mitotic recombination involved in replication restart" RELATED [GOC:TermGenie]
-is_a: GO:0006312 ! mitotic recombination
-is_a: GO:1903047 ! mitotic cell cycle process
-relationship: part_of GO:1990426 ! mitotic recombination-dependent replication fork processing
-
[Term]
id: GO:1903212
name: protein localization to mating-type region heterochromatin
@@ -473165,7 +476207,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein processing involved in protein targeting to mitochondrion." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:21370995]
synonym: "regulation of mitochondrial processing" BROAD [GOC:TermGenie]
synonym: "regulation of mitochondrial protein processing during import" RELATED [GOC:TermGenie]
-is_a: GO:0032268 ! regulation of cellular protein metabolic process
is_a: GO:0070613 ! regulation of protein processing
relationship: regulates GO:0006627 ! protein processing involved in protein targeting to mitochondrion
@@ -473319,18 +476360,19 @@ is_a: GO:1903218 ! regulation of malate dehydrogenase (decarboxylating) (NADP+)
[Term]
id: GO:1903221
-name: regulation of mitotic recombination involved in replication fork processing
+name: regulation of mitotic recombination-dependent replication fork processing
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of mitotic recombination involved in replication fork processing. Regulation of mitotic recombination contributes to replication fork processing by preventing recombination between inappropriate homologous sequences." [GO_REF:0000058, GOC:TermGenie, PMID:23093942]
+def: "Any process that modulates the frequency, rate or extent of mitotic recombination-dependent replication fork processing. Regulation of mitotic recombination prevents recombination between inappropriate homologous sequences." [GO_REF:0000058, GOC:TermGenie, PMID:23093942]
synonym: "prevention of genomic instability induced by DNA replication fork arrest" RELATED [PMID:23093942]
synonym: "regulation of mitotic recombination involved in collapsed replication fork processing" EXACT [GOC:TermGenie]
synonym: "regulation of mitotic recombination involved in recovery from replication fork arrest" EXACT [GOC:TermGenie]
synonym: "regulation of mitotic recombination involved in recovery from replication fork stalling" EXACT [GOC:TermGenie]
+synonym: "regulation of mitotic recombination involved in replication fork processing" EXACT []
synonym: "regulation of mitotic recombination involved in replication fork restart" RELATED [GOC:TermGenie]
synonym: "regulation of mitotic recombination involved in replication restart" RELATED [GOC:TermGenie]
-is_a: GO:0000019 ! regulation of mitotic recombination
is_a: GO:0010564 ! regulation of cell cycle process
-relationship: regulates GO:1903211 ! mitotic recombination involved in replication fork processing
+is_a: GO:0051052 ! regulation of DNA metabolic process
+relationship: regulates GO:1990426 ! mitotic recombination-dependent replication fork processing
[Term]
id: GO:1903222
@@ -473339,7 +476381,6 @@ namespace: biological_process
def: "The process in which quinolinic acid is transported across a membrane." [GO_REF:0000069, GOC:di, GOC:TermGenie, PMID:23457190]
is_a: GO:0006835 ! dicarboxylic acid transport
is_a: GO:0071705 ! nitrogen compound transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -473463,15 +476504,27 @@ is_obsolete: true
[Term]
id: GO:1903231
-name: mRNA binding involved in posttranscriptional gene silencing
+name: mRNA base-pairing translational repressor activity
namespace: molecular_function
-def: "Any mRNA binding that is involved in posttranscriptional gene silencing." [GO_REF:0000061, GOC:BHF, GOC:BHF_miRNA, GOC:jl, GOC:TermGenie]
+alt_id: GO:0150100
+def: "A translation repressor activity that acts by base-pairing with an mRNA. The binding can result in targeting the mRNA for degradation or interfering with mRNA translation, hence resulting in posttranscriptional gene silencing." [GOC:BHF, GOC:BHF_miRNA, PMID:18197166, PMID:20533884]
+comment: This term is intended for microRNAs that act by base-pairing with a target mRNA.
+synonym: "mRNA base-pairing post-transcriptional repressor activity" RELATED []
+synonym: "mRNA base-pairing posttranscriptional repressor activity" EXACT []
synonym: "mRNA binding involved in cosuppression" RELATED [GOC:TermGenie]
synonym: "mRNA binding involved in post-transcriptional gene silencing" EXACT [GOC:TermGenie]
+synonym: "mRNA binding involved in posttranscriptional gene silencing" EXACT []
synonym: "mRNA binding involved in PTGS" EXACT [GOC:TermGenie]
synonym: "mRNA binding involved in quelling" EXACT [GOC:TermGenie]
+synonym: "mRNA binding translation repressor activity" BROAD []
+synonym: "RNA binding involved in cosuppression" BROAD []
+synonym: "RNA binding involved in post-transcriptional gene silencing" BROAD []
+synonym: "RNA binding involved in posttranscriptional gene silencing" BROAD []
+synonym: "RNA binding involved in PTGS" BROAD []
+synonym: "RNA binding involved in quelling" BROAD []
+synonym: "translational inhibitor activity via mRNA base-pairing" EXACT []
is_a: GO:0003729 ! mRNA binding
-is_a: GO:0150100 ! RNA binding involved in posttranscriptional gene silencing
+is_a: GO:0030371 ! translation repressor activity
[Term]
id: GO:1903232
@@ -473780,7 +476833,7 @@ synonym: "negative regulation of citrulline biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of citrulline formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of citrulline synthesis" EXACT [GOC:TermGenie]
is_a: GO:1903248 ! regulation of citrulline biosynthetic process
-is_a: GO:2000283 ! negative regulation of cellular amino acid biosynthetic process
+is_a: GO:2000283 ! negative regulation of amino acid biosynthetic process
relationship: negatively_regulates GO:0019240 ! citrulline biosynthetic process
[Term]
@@ -473813,7 +476866,7 @@ synonym: "upregulation of citrulline biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of citrulline formation" EXACT [GOC:TermGenie]
synonym: "upregulation of citrulline synthesis" EXACT [GOC:TermGenie]
is_a: GO:1903248 ! regulation of citrulline biosynthetic process
-is_a: GO:2000284 ! positive regulation of cellular amino acid biosynthetic process
+is_a: GO:2000284 ! positive regulation of amino acid biosynthetic process
relationship: positively_regulates GO:0019240 ! citrulline biosynthetic process
[Term]
@@ -473832,6 +476885,7 @@ def: "The chemical reactions and pathways involving hercynylcysteine sulfoxide."
synonym: "hercynylcysteine sulfoxide metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006790 ! sulfur compound metabolic process
is_a: GO:0052701 ! cellular modified histidine metabolic process
+is_a: GO:1901605 ! alpha-amino acid metabolic process
[Term]
id: GO:1903253
@@ -473844,6 +476898,7 @@ synonym: "hercynylcysteine sulfoxide formation" EXACT [GOC:TermGenie]
synonym: "hercynylcysteine sulfoxide synthesis" EXACT [GOC:TermGenie]
is_a: GO:0044272 ! sulfur compound biosynthetic process
is_a: GO:0052703 ! cellular modified histidine biosynthetic process
+is_a: GO:1901607 ! alpha-amino acid biosynthetic process
is_a: GO:1903252 ! hercynylcysteine sulfoxide metabolic process
[Term]
@@ -473854,6 +476909,7 @@ def: "The chemical reactions and pathways involving hercynylselenocysteine." [GO
synonym: "hercynylselenocysteine metabolism" EXACT [GOC:TermGenie]
is_a: GO:0001887 ! selenium compound metabolic process
is_a: GO:0052701 ! cellular modified histidine metabolic process
+is_a: GO:1901605 ! alpha-amino acid metabolic process
[Term]
id: GO:1903255
@@ -473865,6 +476921,7 @@ synonym: "hercynylselenocysteine biosynthesis" EXACT [GOC:TermGenie]
synonym: "hercynylselenocysteine formation" EXACT [GOC:TermGenie]
synonym: "hercynylselenocysteine synthesis" EXACT [GOC:TermGenie]
is_a: GO:0052703 ! cellular modified histidine biosynthetic process
+is_a: GO:1901607 ! alpha-amino acid biosynthetic process
is_a: GO:1903254 ! hercynylselenocysteine metabolic process
[Term]
@@ -474032,7 +477089,7 @@ synonym: "upregulation of ornithine catabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of ornithine catabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of ornithine degradation" EXACT [GOC:TermGenie]
is_a: GO:0031331 ! positive regulation of cellular catabolic process
-is_a: GO:0045764 ! positive regulation of cellular amino acid metabolic process
+is_a: GO:0045764 ! positive regulation of amino acid metabolic process
is_a: GO:1903266 ! regulation of ornithine catabolic process
relationship: positively_regulates GO:0006593 ! ornithine catabolic process
@@ -474044,7 +477101,7 @@ def: "A protein complex which is capable of ornithine carbamoyltransferase inhib
comment: An example of this is ARGI in Saccharomyces cerevisiae (P00812) in PMID:12679340 (inferred from direct assay).
synonym: "ornithine carbamoyltransferase arginase complex" NARROW []
synonym: "OTC-ARGI complex" NARROW []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:1903270
@@ -474665,8 +477722,8 @@ synonym: "negative regulation of hexokinase type III activity" NARROW [GOC:TermG
synonym: "negative regulation of hexokinase type IV" RELATED [GOC:TermGenie]
synonym: "negative regulation of hexokinase type IV (glucokinase) activity" NARROW [GOC:TermGenie]
synonym: "negative regulation of hexokinase type IV glucokinase activity" EXACT [GOC:TermGenie]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
is_a: GO:0033673 ! negative regulation of kinase activity
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:1903299 ! regulation of hexokinase activity
[Term]
@@ -475533,10 +478590,7 @@ id: GO:1903352
name: L-ornithine transmembrane transport
namespace: biological_process
def: "The directed movement of L-ornithine across a membrane." [GO_REF:0000069, GOC:krc, GOC:TermGenie, PMID:8195186]
-is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0015822 ! ornithine transport
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -475588,13 +478642,14 @@ relationship: positively_regulates GO:0097628 ! distal tip cell migration
[Term]
id: GO:1903357
-name: regulation of transcription initiation from RNA polymerase I promoter
+name: regulation of transcription initiation by RNA polymerase I
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of transcription initiation from RNA polymerase I promoter." [GO_REF:0000058, GOC:TermGenie, PMID:9092673]
+synonym: "regulation of transcription initiation from RNA polymerase I promoter" EXACT []
synonym: "regulation of transcription initiation from RNA polymerase I promoter for nuclear large rRNA transcript" NARROW []
is_a: GO:0006356 ! regulation of transcription by RNA polymerase I
-is_a: GO:2000142 ! regulation of DNA-templated transcription, initiation
-relationship: regulates GO:0006361 ! transcription initiation from RNA polymerase I promoter
+is_a: GO:2000142 ! regulation of DNA-templated transcription initiation
+relationship: regulates GO:0006361 ! transcription initiation at RNA polymerase I promoter
[Term]
id: GO:1903358
@@ -475639,97 +478694,6 @@ synonym: "protein localization in basolateral plasma membrane" EXACT [GOC:TermGe
is_a: GO:0072657 ! protein localization to membrane
is_a: GO:1990778 ! protein localization to cell periphery
-[Term]
-id: GO:1903362
-name: regulation of cellular protein catabolic process
-namespace: biological_process
-alt_id: GO:2000598
-def: "Any process that modulates the frequency, rate or extent of cellular protein catabolic process." [GO_REF:0000058, GOC:kmv, GOC:obol, GOC:TermGenie, PMID:24785082]
-synonym: "regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
-synonym: "regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
-synonym: "regulation of cellular protein degradation" EXACT [GOC:TermGenie]
-synonym: "regulation of cyclin breakdown" NARROW [GOC:obol]
-synonym: "regulation of cyclin catabolic process" NARROW []
-synonym: "regulation of cyclin catabolism" NARROW [GOC:obol]
-synonym: "regulation of cyclin degradation" NARROW [GOC:obol]
-synonym: "regulation of degradation of cyclin" NARROW [GOC:obol]
-is_a: GO:0031329 ! regulation of cellular catabolic process
-is_a: GO:0032268 ! regulation of cellular protein metabolic process
-is_a: GO:0042176 ! regulation of protein catabolic process
-relationship: regulates GO:0044257 ! cellular protein catabolic process
-
-[Term]
-id: GO:1903363
-name: negative regulation of cellular protein catabolic process
-namespace: biological_process
-alt_id: GO:2000599
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of cellular protein catabolic process." [GO_REF:0000058, GOC:kmv, GOC:obol, GOC:TermGenie, PMID:24785082]
-synonym: "down regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
-synonym: "down regulation of cellular protein catabolic process" EXACT [GOC:TermGenie]
-synonym: "down regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
-synonym: "down regulation of cellular protein degradation" EXACT [GOC:TermGenie]
-synonym: "down-regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
-synonym: "down-regulation of cellular protein catabolic process" EXACT [GOC:TermGenie]
-synonym: "down-regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
-synonym: "down-regulation of cellular protein degradation" EXACT [GOC:TermGenie]
-synonym: "downregulation of cellular protein breakdown" EXACT [GOC:TermGenie]
-synonym: "downregulation of cellular protein catabolic process" EXACT [GOC:TermGenie]
-synonym: "downregulation of cellular protein catabolism" EXACT [GOC:TermGenie]
-synonym: "downregulation of cellular protein degradation" EXACT [GOC:TermGenie]
-synonym: "inhibition of cellular protein breakdown" NARROW [GOC:TermGenie]
-synonym: "inhibition of cellular protein catabolic process" NARROW [GOC:TermGenie]
-synonym: "inhibition of cellular protein catabolism" NARROW [GOC:TermGenie]
-synonym: "inhibition of cellular protein degradation" NARROW [GOC:TermGenie]
-synonym: "negative regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
-synonym: "negative regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
-synonym: "negative regulation of cellular protein degradation" EXACT [GOC:TermGenie]
-synonym: "negative regulation of cyclin breakdown" NARROW [GOC:obol]
-synonym: "negative regulation of cyclin catabolic process" NARROW []
-synonym: "negative regulation of cyclin catabolism" NARROW [GOC:obol]
-synonym: "negative regulation of cyclin degradation" NARROW [GOC:obol]
-synonym: "negative regulation of degradation of cyclin" NARROW [GOC:obol]
-is_a: GO:0031330 ! negative regulation of cellular catabolic process
-is_a: GO:0032269 ! negative regulation of cellular protein metabolic process
-is_a: GO:0042177 ! negative regulation of protein catabolic process
-is_a: GO:1903362 ! regulation of cellular protein catabolic process
-relationship: negatively_regulates GO:0044257 ! cellular protein catabolic process
-
-[Term]
-id: GO:1903364
-name: positive regulation of cellular protein catabolic process
-namespace: biological_process
-alt_id: GO:2000600
-def: "Any process that activates or increases the frequency, rate or extent of cellular protein catabolic process." [GO_REF:0000058, GOC:kmv, GOC:obol, GOC:TermGenie, PMID:24785082]
-synonym: "activation of cellular protein breakdown" NARROW [GOC:TermGenie]
-synonym: "activation of cellular protein catabolic process" NARROW [GOC:TermGenie]
-synonym: "activation of cellular protein catabolism" NARROW [GOC:TermGenie]
-synonym: "activation of cellular protein degradation" NARROW [GOC:TermGenie]
-synonym: "positive regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
-synonym: "positive regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
-synonym: "positive regulation of cellular protein degradation" EXACT [GOC:TermGenie]
-synonym: "positive regulation of cyclin breakdown" NARROW [GOC:obol]
-synonym: "positive regulation of cyclin catabolic process" NARROW []
-synonym: "positive regulation of cyclin catabolism" NARROW [GOC:obol]
-synonym: "positive regulation of cyclin degradation" NARROW [GOC:obol]
-synonym: "positive regulation of degradation of cyclin" NARROW [GOC:obol]
-synonym: "up regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
-synonym: "up regulation of cellular protein catabolic process" EXACT [GOC:TermGenie]
-synonym: "up regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
-synonym: "up regulation of cellular protein degradation" EXACT [GOC:TermGenie]
-synonym: "up-regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
-synonym: "up-regulation of cellular protein catabolic process" EXACT [GOC:TermGenie]
-synonym: "up-regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
-synonym: "up-regulation of cellular protein degradation" EXACT [GOC:TermGenie]
-synonym: "upregulation of cellular protein breakdown" EXACT [GOC:TermGenie]
-synonym: "upregulation of cellular protein catabolic process" EXACT [GOC:TermGenie]
-synonym: "upregulation of cellular protein catabolism" EXACT [GOC:TermGenie]
-synonym: "upregulation of cellular protein degradation" EXACT [GOC:TermGenie]
-is_a: GO:0031331 ! positive regulation of cellular catabolic process
-is_a: GO:0032270 ! positive regulation of cellular protein metabolic process
-is_a: GO:0045732 ! positive regulation of protein catabolic process
-is_a: GO:1903362 ! regulation of cellular protein catabolic process
-relationship: positively_regulates GO:0044257 ! cellular protein catabolic process
-
[Term]
id: GO:1903365
name: regulation of fear response
@@ -475881,16 +478845,16 @@ relationship: positively_regulates GO:0071786 ! endoplasmic reticulum tubular ne
[Term]
id: GO:1903374
-name: subarachnoid space development
+name: obsolete subarachnoid space development
namespace: biological_process
-def: "The process whose specific outcome is the progression of a subarachnoid space over time, from its formation to the mature structure." [GO_REF:0000094, GOC:cjm, GOC:TermGenie, Wikipedia:Subarachnoid_space]
+def: "OBSOLETE. The process whose specific outcome is the progression of a subarachnoid space over time, from its formation to the mature structure." [GO_REF:0000094, GOC:cjm, GOC:TermGenie, Wikipedia:Subarachnoid_space]
+comment: This term was obsoleted because it does not represent a real process. While subarachnoid space is a valid anatomical structure, it is formed by the development of the structures that surround it.
synonym: "cavitas subarachnoidea development" RELATED [GOC:TermGenie]
synonym: "cavum subarachnoideale development" RELATED [GOC:TermGenie]
synonym: "spatium leptomeningeum development" RELATED [GOC:TermGenie]
synonym: "spatium subarachnoideum development" RELATED [GOC:TermGenie]
synonym: "subarachnoid cavity development" RELATED [GOC:TermGenie]
-is_a: GO:0048856 ! anatomical structure development
-relationship: part_of GO:0007417 ! central nervous system development
+is_obsolete: true
[Term]
id: GO:1903375
@@ -476280,20 +479244,22 @@ relationship: positively_regulates GO:1990344 ! secondary cell septum biogenesis
[Term]
id: GO:1903398
-name: regulation of m7G(5')pppN diphosphatase activity
+name: obsolete regulation of m7G(5')pppN diphosphatase activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of m7G(5')pppN diphosphatase activity." [GO_REF:0000059, GOC:TermGenie, PMID:22323607]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of m7G(5')pppN diphosphatase activity." [GO_REF:0000059, GOC:TermGenie, PMID:22323607]
+comment: This term was obsoleted because the obsoleted EC was obsoleted.
synonym: "regulation of 7-methylguanosine-5'-triphospho-5'-polynucleotide 7-methylguanosine-5'-phosphohydrolase activity" EXACT [GOC:TermGenie]
synonym: "regulation of decapase activity" RELATED [GOC:TermGenie]
synonym: "regulation of M(7)G(5')pppN pyrophosphatase activity" EXACT [GOC:TermGenie]
synonym: "regulation of m7G(5')pppN pyrophosphatase activity" EXACT [GOC:TermGenie]
-is_a: GO:0051336 ! regulation of hydrolase activity
+is_obsolete: true
[Term]
id: GO:1903399
-name: positive regulation of m7G(5')pppN diphosphatase activity
+name: obsolete positive regulation of m7G(5')pppN diphosphatase activity
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of m7G(5')pppN diphosphatase activity." [GO_REF:0000059, GOC:TermGenie, PMID:22323607]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of m7G(5')pppN diphosphatase activity." [GO_REF:0000059, GOC:TermGenie, PMID:22323607]
+comment: This term was obsoleted because the obsoleted EC was obsoleted.
synonym: "activation of 7-methylguanosine-5'-triphospho-5'-polynucleotide 7-methylguanosine-5'-phosphohydrolase activity" NARROW [GOC:TermGenie]
synonym: "activation of decapase activity" RELATED [GOC:TermGenie]
synonym: "activation of M(7)G(5')pppN pyrophosphatase activity" NARROW [GOC:TermGenie]
@@ -476318,16 +479284,13 @@ synonym: "upregulation of decapase activity" RELATED [GOC:TermGenie]
synonym: "upregulation of M(7)G(5')pppN pyrophosphatase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of m7G(5')pppN diphosphatase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of m7G(5')pppN pyrophosphatase activity" EXACT [GOC:TermGenie]
-is_a: GO:0051345 ! positive regulation of hydrolase activity
-is_a: GO:1903398 ! regulation of m7G(5')pppN diphosphatase activity
+is_obsolete: true
[Term]
id: GO:1903401
name: L-lysine transmembrane transport
namespace: biological_process
def: "The directed movement of L-lysine across a membrane." [GO_REF:0000069, GOC:krc, GOC:TermGenie, PMID:8195186]
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902022 ! L-lysine transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
@@ -476734,6 +479697,7 @@ namespace: biological_process
def: "The process in which fluoride is transported across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:24173035]
synonym: "fluoride membrane transport" EXACT []
synonym: "transmembrane fluoride transport" EXACT []
+is_a: GO:0098656 ! monoatomic anion transmembrane transport
is_a: GO:0098661 ! inorganic anion transmembrane transport
[Term]
@@ -476741,7 +479705,9 @@ id: GO:1903425
name: fluoride transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of fluoride from one side of a membrane to the other." [GO_REF:0000070, GOC:TermGenie, PMID:24173035]
+is_a: GO:0008509 ! monoatomic anion transmembrane transporter activity
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
+is_a: GO:1901702 ! salt transmembrane transporter activity
[Term]
id: GO:1903426
@@ -477443,7 +480409,7 @@ name: regulation of mitotic DNA replication initiation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA replication initiation involved in mitotic DNA replication." [GO_REF:0000058, GOC:mtg_cell_cycle, GOC:TermGenie, PMID:1234]
synonym: "regulation of DNA replication initiation involved in mitotic cell cycle DNA replication" EXACT [GOC:TermGenie]
-is_a: GO:0030174 ! regulation of DNA-dependent DNA replication initiation
+is_a: GO:0030174 ! regulation of DNA-templated DNA replication initiation
is_a: GO:1903463 ! regulation of mitotic cell cycle DNA replication
relationship: regulates GO:1902975 ! mitotic DNA replication initiation
@@ -477461,7 +480427,7 @@ synonym: "downregulation of DNA replication initiation involved in mitotic DNA r
synonym: "inhibition of DNA replication initiation involved in mitotic cell cycle DNA replication" NARROW [GOC:TermGenie]
synonym: "inhibition of DNA replication initiation involved in mitotic DNA replication" NARROW [GOC:TermGenie]
synonym: "negative regulation of DNA replication initiation involved in mitotic cell cycle DNA replication" EXACT [GOC:TermGenie]
-is_a: GO:0032297 ! negative regulation of DNA-dependent DNA replication initiation
+is_a: GO:0032297 ! negative regulation of DNA-templated DNA replication initiation
is_a: GO:1903464 ! negative regulation of mitotic cell cycle DNA replication
is_a: GO:1903466 ! regulation of mitotic DNA replication initiation
relationship: negatively_regulates GO:1902975 ! mitotic DNA replication initiation
@@ -477480,7 +480446,7 @@ synonym: "up-regulation of DNA replication initiation involved in mitotic cell c
synonym: "up-regulation of DNA replication initiation involved in mitotic DNA replication" EXACT [GOC:TermGenie]
synonym: "upregulation of DNA replication initiation involved in mitotic cell cycle DNA replication" EXACT [GOC:TermGenie]
synonym: "upregulation of DNA replication initiation involved in mitotic DNA replication" EXACT [GOC:TermGenie]
-is_a: GO:0032298 ! positive regulation of DNA-dependent DNA replication initiation
+is_a: GO:0032298 ! positive regulation of DNA-templated DNA replication initiation
is_a: GO:1903465 ! positive regulation of mitotic cell cycle DNA replication
is_a: GO:1903466 ! regulation of mitotic DNA replication initiation
relationship: positively_regulates GO:1902975 ! mitotic DNA replication initiation
@@ -477627,15 +480593,15 @@ is_a: GO:1903479 ! mitotic actomyosin contractile ring assembly actin filament o
[Term]
id: GO:1903478
-name: actin filament bundle convergence involved in mitotic contractile ring assembly
+name: obsolete actin filament bundle convergence involved in mitotic contractile ring assembly
namespace: biological_process
-def: "Any actin filament bundle convergence that is involved in mitotic actomyosin contractile ring assembly." [GO_REF:0000060, GOC:mtg_cell_cycle, GOC:TermGenie, GOC:vw]
+def: "OBSOLETE. Any actin filament bundle convergence that is involved in mitotic actomyosin contractile ring assembly." [GO_REF:0000060, GOC:mtg_cell_cycle, GOC:TermGenie, GOC:vw]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
synonym: "actin filament bundle convergence involved in actomyosin contractile ring assembly involved in cytokinesis after mitosis" EXACT [GOC:TermGenie]
synonym: "actin filament bundle convergence involved in contractile ring assembly involved in mitotic cytokinesis" EXACT [GOC:TermGenie]
synonym: "actin filament bundle convergence involved in cytokinesis, actomyosin contractile ring assembly involved in mitotic cytokinesis" EXACT [GOC:TermGenie]
synonym: "actin filament bundle convergence involved in mitotic actomyosin contractile ring assembly" EXACT []
-is_a: GO:0071520 ! actomyosin contractile ring assembly actin filament bundle convergence
-is_a: GO:1903479 ! mitotic actomyosin contractile ring assembly actin filament organization
+is_obsolete: true
[Term]
id: GO:1903479
@@ -477651,19 +480617,20 @@ relationship: part_of GO:1903475 ! mitotic actomyosin contractile ring assembly
[Term]
id: GO:1903480
-name: regulation of actin filament organization involved in mitotic actomyosin contractile ring assembly
+name: obsolete regulation of actin filament organization involved in mitotic actomyosin contractile ring assembly
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of actin filament organization involved in mitotic actomyosin contractile ring assembly." [GO_REF:0000058, GOC:mtg_cell_cycle, GOC:TermGenie]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of actin filament organization involved in mitotic actomyosin contractile ring assembly." [GO_REF:0000058, GOC:mtg_cell_cycle, GOC:TermGenie]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
synonym: "regulation of actin filament organisation involved in contractile ring assembly involved in mitotic cytokinesis" EXACT [GOC:TermGenie]
synonym: "regulation of actin filament organisation involved in mitotic actomyosin contractile ring assembly" EXACT [GOC:TermGenie]
-is_a: GO:1903117 ! regulation of actin filament organization involved in cytokinetic actomyosin contractile ring assembly
-relationship: regulates GO:1903479 ! mitotic actomyosin contractile ring assembly actin filament organization
+is_obsolete: true
[Term]
id: GO:1903481
-name: negative regulation of actin filament organization involved in mitotic actomyosin contractile ring assembly
+name: obsolete negative regulation of actin filament organization involved in mitotic actomyosin contractile ring assembly
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of actin filament organization involved in mitotic actomyosin contractile ring assembly." [GO_REF:0000058, GOC:mtg_cell_cycle, GOC:TermGenie]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of actin filament organization involved in mitotic actomyosin contractile ring assembly." [GO_REF:0000058, GOC:mtg_cell_cycle, GOC:TermGenie]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
synonym: "down regulation of actin filament organisation involved in contractile ring assembly involved in mitotic cytokinesis" EXACT [GOC:TermGenie]
synonym: "down regulation of actin filament organisation involved in mitotic actomyosin contractile ring assembly" EXACT [GOC:TermGenie]
synonym: "down regulation of actin filament organization involved in mitotic actomyosin contractile ring assembly" EXACT [GOC:TermGenie]
@@ -477678,16 +480645,14 @@ synonym: "inhibition of actin filament organisation involved in mitotic actomyos
synonym: "inhibition of actin filament organization involved in mitotic actomyosin contractile ring assembly" NARROW [GOC:TermGenie]
synonym: "negative regulation of actin filament organisation involved in contractile ring assembly involved in mitotic cytokinesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of actin filament organisation involved in mitotic actomyosin contractile ring assembly" EXACT [GOC:TermGenie]
-is_a: GO:1902904 ! negative regulation of supramolecular fiber organization
-is_a: GO:1903480 ! regulation of actin filament organization involved in mitotic actomyosin contractile ring assembly
-is_a: GO:1903500 ! negative regulation of mitotic actomyosin contractile ring assembly
-relationship: negatively_regulates GO:1903479 ! mitotic actomyosin contractile ring assembly actin filament organization
+is_obsolete: true
[Term]
id: GO:1903482
-name: positive regulation of actin filament organization involved in mitotic actomyosin contractile ring assembly
+name: obsolete positive regulation of actin filament organization involved in mitotic actomyosin contractile ring assembly
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of actin filament organization involved in mitotic actomyosin contractile ring assembly." [GO_REF:0000058, GOC:mtg_cell_cycle, GOC:TermGenie]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of actin filament organization involved in mitotic actomyosin contractile ring assembly." [GO_REF:0000058, GOC:mtg_cell_cycle, GOC:TermGenie]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
synonym: "activation of actin filament organisation involved in contractile ring assembly involved in mitotic cytokinesis" NARROW [GOC:TermGenie]
synonym: "activation of actin filament organisation involved in mitotic actomyosin contractile ring assembly" NARROW [GOC:TermGenie]
synonym: "activation of actin filament organization involved in mitotic actomyosin contractile ring assembly" NARROW [GOC:TermGenie]
@@ -477702,10 +480667,7 @@ synonym: "up-regulation of actin filament organization involved in mitotic actom
synonym: "upregulation of actin filament organisation involved in contractile ring assembly involved in mitotic cytokinesis" EXACT [GOC:TermGenie]
synonym: "upregulation of actin filament organisation involved in mitotic actomyosin contractile ring assembly" EXACT [GOC:TermGenie]
synonym: "upregulation of actin filament organization involved in mitotic actomyosin contractile ring assembly" EXACT [GOC:TermGenie]
-is_a: GO:0090068 ! positive regulation of cell cycle process
-is_a: GO:1902905 ! positive regulation of supramolecular fiber organization
-is_a: GO:1903480 ! regulation of actin filament organization involved in mitotic actomyosin contractile ring assembly
-relationship: positively_regulates GO:1903479 ! mitotic actomyosin contractile ring assembly actin filament organization
+is_obsolete: true
[Term]
id: GO:1903483
@@ -477877,6 +480839,7 @@ def: "Any process that results in a change in state or activity of a cell or an
is_a: GO:0010243 ! response to organonitrogen compound
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1903494
@@ -478126,7 +481089,6 @@ name: calcium ion transport from cytosol to endoplasmic reticulum
namespace: biological_process
def: "The directed movement of calcium ion from cytosol to endoplasmic reticulum." [GO_REF:0000078, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:16402920]
is_a: GO:0046967 ! cytosol to endoplasmic reticulum transport
-is_a: GO:0060401 ! cytosolic calcium ion transport
is_a: GO:0070588 ! calcium ion transmembrane transport
[Term]
@@ -478400,8 +481362,6 @@ synonym: "regulation of lactose anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of lactose biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of lactose formation" EXACT [GOC:TermGenie]
synonym: "regulation of lactose synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
-is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0043255 ! regulation of carbohydrate biosynthetic process
relationship: regulates GO:0005989 ! lactose biosynthetic process
@@ -478434,8 +481394,8 @@ synonym: "negative regulation of lactose anabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of lactose biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of lactose formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of lactose synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
-is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
+is_a: GO:0009890 ! negative regulation of biosynthetic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:1903534 ! regulation of lactose biosynthetic process
relationship: negatively_regulates GO:0005989 ! lactose biosynthetic process
@@ -478468,8 +481428,8 @@ synonym: "upregulation of lactose biosynthesis" EXACT [GOC:TermGenie]
synonym: "upregulation of lactose biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of lactose formation" EXACT [GOC:TermGenie]
synonym: "upregulation of lactose synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
+is_a: GO:0009891 ! positive regulation of biosynthetic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:1903534 ! regulation of lactose biosynthetic process
relationship: positively_regulates GO:0005989 ! lactose biosynthetic process
@@ -478497,7 +481457,7 @@ relationship: regulates GO:1903537 ! meiotic cell cycle process involved in oocy
id: GO:1903539
name: protein localization to postsynaptic membrane
namespace: biological_process
-def: "A process in which a protein is transported to, or maintained in, a location within a postsynaptic membrane." [GO_REF:0000087, GOC:kmv, GOC:TermGenie, pmid:9753322]
+def: "A process in which a protein is transported to, or maintained in, a location within a postsynaptic membrane." [GO_REF:0000087, GOC:kmv, GOC:TermGenie, PMID:9753322]
synonym: "protein localisation in postsynaptic membrane" EXACT [GOC:TermGenie]
synonym: "protein localisation to postsynaptic membrane" EXACT [GOC:TermGenie]
synonym: "protein localization in postsynaptic membrane" EXACT [GOC:TermGenie]
@@ -478509,7 +481469,7 @@ is_a: GO:1990778 ! protein localization to cell periphery
id: GO:1903540
name: establishment of protein localization to postsynaptic membrane
namespace: biological_process
-def: "The directed movement of a protein to a specific location in a postsynaptic membrane." [GO_REF:0000087, GOC:kmv, GOC:TermGenie, pmid:9753322]
+def: "The directed movement of a protein to a specific location in a postsynaptic membrane." [GO_REF:0000087, GOC:kmv, GOC:TermGenie, PMID:9753322]
synonym: "establishment of protein localisation in postsynaptic membrane" EXACT [GOC:TermGenie]
synonym: "establishment of protein localisation to postsynaptic membrane" EXACT [GOC:TermGenie]
synonym: "establishment of protein localization in postsynaptic membrane" EXACT [GOC:TermGenie]
@@ -478526,7 +481486,6 @@ synonym: "regulation of exosomal secretory pathway" EXACT [GOC:TermGenie]
synonym: "regulation of extracellular vesicular exosome secretion" EXACT [GOC:TermGenie]
synonym: "regulation of secretion of exosome" EXACT [GOC:TermGenie]
is_a: GO:0017157 ! regulation of exocytosis
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:1990182 ! exosomal secretion
[Term]
@@ -478602,6 +481561,7 @@ name: response to butyrate
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a butyrate stimulus." [GO_REF:0000071, GOC:mr, GOC:TermGenie, PMID:9734870]
is_a: GO:0070542 ! response to fatty acid
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1903545
@@ -478609,6 +481569,7 @@ name: cellular response to butyrate
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a butyrate stimulus." [GO_REF:0000071, GOC:mr, GOC:TermGenie, PMID:9734870]
is_a: GO:0071398 ! cellular response to fatty acid
+is_a: GO:1902075 ! cellular response to salt
is_a: GO:1903544 ! response to butyrate
[Term]
@@ -478728,7 +481689,7 @@ relationship: positively_regulates GO:0071971 ! extracellular exosome assembly
id: GO:1903554
name: G protein-coupled receptor signaling pathway involved in defense response to Gram-negative bacterium
namespace: biological_process
-def: "Any G protein-coupled receptor signaling pathway that is involved in defense response to Gram-negative bacterium." [GO_REF:0000060, GOC:kmv, GOC:TermGenie, pmid:25303524]
+def: "A G protein-coupled receptor signaling pathway that is involved in the defense response to Gram-negative bacterium." [GO_REF:0000060, GOC:kmv, GOC:TermGenie, PMID:25303524]
synonym: "G protein coupled receptor protein signaling pathway involved in defence response to Gram-negative bacteria" EXACT [GOC:TermGenie]
synonym: "G protein coupled receptor protein signaling pathway involved in defence response to Gram-negative bacterium" EXACT [GOC:TermGenie]
synonym: "G protein coupled receptor protein signaling pathway involved in defense response to Gram-negative bacteria" EXACT [GOC:TermGenie]
@@ -478840,7 +481801,7 @@ relationship: positively_regulates GO:0071706 ! tumor necrosis factor superfamil
id: GO:1903558
name: 3-cyano-L-alanine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving 3-cyano-L-alanine." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, pmid:24100226, pmid:24843024]
+def: "The chemical reactions and pathways involving 3-cyano-L-alanine." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, PMID:24100226, PMID:24843024]
synonym: "3-cyano-L-alanine metabolism" EXACT [GOC:TermGenie]
is_a: GO:0033052 ! cyanoamino acid metabolic process
is_a: GO:1901605 ! alpha-amino acid metabolic process
@@ -478849,11 +481810,11 @@ is_a: GO:1901605 ! alpha-amino acid metabolic process
id: GO:1903559
name: 3-cyano-L-alanine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 3-cyano-L-alanine." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, pmid:24100226, pmid:24843024]
+def: "The chemical reactions and pathways resulting in the breakdown of 3-cyano-L-alanine." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, PMID:24100226, PMID:24843024]
synonym: "3-cyano-L-alanine breakdown" EXACT [GOC:TermGenie]
synonym: "3-cyano-L-alanine catabolism" EXACT [GOC:TermGenie]
synonym: "3-cyano-L-alanine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0050899 ! nitrile catabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
is_a: GO:1903558 ! 3-cyano-L-alanine metabolic process
@@ -478862,7 +481823,7 @@ is_a: GO:1903558 ! 3-cyano-L-alanine metabolic process
id: GO:1903560
name: 3-cyano-L-alanine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 3-cyano-L-alanine." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, pmid:24100226, pmid:24843024]
+def: "The chemical reactions and pathways resulting in the formation of 3-cyano-L-alanine." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, PMID:24100226, PMID:24843024]
synonym: "3-cyano-L-alanine anabolism" EXACT [GOC:TermGenie]
synonym: "3-cyano-L-alanine biosynthesis" EXACT [GOC:TermGenie]
synonym: "3-cyano-L-alanine formation" EXACT [GOC:TermGenie]
@@ -478916,7 +481877,6 @@ name: regulation of protein localization to cilium
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to cilium." [GO_REF:0000058, GOC:cilia, GOC:krc, GOC:TermGenie, PMID:22072986]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0061512 ! protein localization to cilium
[Term]
@@ -478928,7 +481888,6 @@ synonym: "down regulation of protein localization to cilium" EXACT [GOC:TermGeni
synonym: "down-regulation of protein localization to cilium" EXACT [GOC:TermGenie]
synonym: "downregulation of protein localization to cilium" EXACT [GOC:TermGenie]
synonym: "inhibition of protein localization to cilium" NARROW [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903564 ! regulation of protein localization to cilium
is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:0061512 ! protein localization to cilium
@@ -478942,7 +481901,6 @@ synonym: "activation of protein localization to cilium" NARROW [GOC:TermGenie]
synonym: "up regulation of protein localization to cilium" EXACT [GOC:TermGenie]
synonym: "up-regulation of protein localization to cilium" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to cilium" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903564 ! regulation of protein localization to cilium
is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:0061512 ! protein localization to cilium
@@ -479183,7 +482141,7 @@ name: regulation of ATP metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of ATP metabolic process." [GO_REF:0000058, GOC:TermGenie, PMID:20695849]
synonym: "regulation of ATP metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0019222 ! regulation of metabolic process
+is_a: GO:1900542 ! regulation of purine nucleotide metabolic process
relationship: regulates GO:0046034 ! ATP metabolic process
[Term]
@@ -479200,7 +482158,7 @@ synonym: "downregulation of ATP metabolism" EXACT [GOC:TermGenie]
synonym: "inhibition of ATP metabolic process" NARROW [GOC:TermGenie]
synonym: "inhibition of ATP metabolism" NARROW [GOC:TermGenie]
synonym: "negative regulation of ATP metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0009892 ! negative regulation of metabolic process
+is_a: GO:1900543 ! negative regulation of purine nucleotide metabolic process
is_a: GO:1903578 ! regulation of ATP metabolic process
relationship: negatively_regulates GO:0046034 ! ATP metabolic process
@@ -479218,7 +482176,7 @@ synonym: "up-regulation of ATP metabolic process" EXACT [GOC:TermGenie]
synonym: "up-regulation of ATP metabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of ATP metabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of ATP metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0009893 ! positive regulation of metabolic process
+is_a: GO:1900544 ! positive regulation of purine nucleotide metabolic process
is_a: GO:1903578 ! regulation of ATP metabolic process
relationship: positively_regulates GO:0046034 ! ATP metabolic process
@@ -479295,7 +482253,6 @@ synonym: "inhibition of histone deubiquitinylation" NARROW [GOC:TermGenie]
synonym: "inhibition of histone deubiquitylation" NARROW [GOC:TermGenie]
synonym: "negative regulation of histone deubiquitinylation" EXACT [GOC:TermGenie]
synonym: "negative regulation of histone deubiquitylation" EXACT [GOC:TermGenie]
-is_a: GO:0031057 ! negative regulation of histone modification
is_a: GO:0090086 ! negative regulation of protein deubiquitination
is_a: GO:1903584 ! regulation of histone deubiquitination
relationship: negatively_regulates GO:0016578 ! histone deubiquitination
@@ -479319,7 +482276,6 @@ synonym: "up-regulation of histone deubiquitylation" EXACT [GOC:TermGenie]
synonym: "upregulation of histone deubiquitination" EXACT [GOC:TermGenie]
synonym: "upregulation of histone deubiquitinylation" EXACT [GOC:TermGenie]
synonym: "upregulation of histone deubiquitylation" EXACT [GOC:TermGenie]
-is_a: GO:0031058 ! positive regulation of histone modification
is_a: GO:1903003 ! positive regulation of protein deubiquitination
is_a: GO:1903584 ! regulation of histone deubiquitination
relationship: positively_regulates GO:0016578 ! histone deubiquitination
@@ -479526,7 +482482,6 @@ id: GO:1903593
name: regulation of histamine secretion by mast cell
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of histamine secretion by mast cell." [GO_REF:0000058, GOC:als, GOC:TermGenie, PMID:18253931]
-is_a: GO:0043269 ! regulation of ion transport
is_a: GO:0046883 ! regulation of hormone secretion
is_a: GO:0050727 ! regulation of inflammatory response
is_a: GO:0051239 ! regulation of multicellular organismal process
@@ -479541,7 +482496,6 @@ synonym: "down regulation of histamine secretion by mast cell" EXACT [GOC:TermGe
synonym: "down-regulation of histamine secretion by mast cell" EXACT [GOC:TermGenie]
synonym: "downregulation of histamine secretion by mast cell" EXACT [GOC:TermGenie]
synonym: "inhibition of histamine secretion by mast cell" NARROW [GOC:TermGenie]
-is_a: GO:0043271 ! negative regulation of ion transport
is_a: GO:0046888 ! negative regulation of hormone secretion
is_a: GO:0050728 ! negative regulation of inflammatory response
is_a: GO:1903593 ! regulation of histamine secretion by mast cell
@@ -479556,11 +482510,9 @@ synonym: "activation of histamine secretion by mast cell" NARROW [GOC:TermGenie]
synonym: "up regulation of histamine secretion by mast cell" EXACT [GOC:TermGenie]
synonym: "up-regulation of histamine secretion by mast cell" EXACT [GOC:TermGenie]
synonym: "upregulation of histamine secretion by mast cell" EXACT [GOC:TermGenie]
-is_a: GO:0043270 ! positive regulation of ion transport
is_a: GO:0043306 ! positive regulation of mast cell degranulation
is_a: GO:0046887 ! positive regulation of hormone secretion
is_a: GO:0050729 ! positive regulation of inflammatory response
-is_a: GO:0051240 ! positive regulation of multicellular organismal process
is_a: GO:1903593 ! regulation of histamine secretion by mast cell
relationship: positively_regulates GO:0002553 ! histamine secretion by mast cell
@@ -479961,13 +482913,14 @@ is_obsolete: true
[Term]
id: GO:1903617
-name: positive regulation of mitotic cytokinesis, site selection
+name: positive regulation of mitotic cytokinesis, division site positioning
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of mitotic cytokinesis, site selection." [GO_REF:0000058, GOC:TermGenie, PMID:21246752]
-is_a: GO:1902472 ! regulation of mitotic cytokinesis, site selection
+def: "Any process that activates or increases the frequency, rate or extent of mitotic cytokinesis, division site positioning." [PMID:21246752, PMID:9852154]
+synonym: "positive regulation of mitotic cytokinesis, site selection" EXACT []
+is_a: GO:1902472 ! regulation of mitotic cytokinesis, division site positioning
is_a: GO:1903438 ! positive regulation of mitotic cytokinetic process
is_a: GO:2000076 ! positive regulation of cytokinesis, site selection
-relationship: positively_regulates GO:1902408 ! mitotic cytokinesis, site selection
+relationship: positively_regulates GO:1902408 ! mitotic cytokinesis, division site positioning
[Term]
id: GO:1903618
@@ -480379,7 +483332,6 @@ synonym: "regulation of protein import into mitochondrial outer membrane" EXACT
synonym: "regulation of protein transport into mitochondrial outer membrane" EXACT [GOC:TermGenie]
is_a: GO:0010821 ! regulation of mitochondrion organization
is_a: GO:1903214 ! regulation of protein targeting to mitochondrion
-is_a: GO:1904589 ! regulation of protein import
is_a: GO:1905475 ! regulation of protein localization to membrane
relationship: regulates GO:0045040 ! protein insertion into mitochondrial outer membrane
@@ -480410,7 +483362,6 @@ synonym: "negative regulation of protein transport into mitochondrial outer memb
is_a: GO:0010823 ! negative regulation of mitochondrion organization
is_a: GO:1903215 ! negative regulation of protein targeting to mitochondrion
is_a: GO:1903636 ! regulation of protein insertion into mitochondrial outer membrane
-is_a: GO:1904590 ! negative regulation of protein import
is_a: GO:1905476 ! negative regulation of protein localization to membrane
relationship: negatively_regulates GO:0045040 ! protein insertion into mitochondrial outer membrane
@@ -480441,7 +483392,6 @@ synonym: "upregulation of protein transport into mitochondrial outer membrane" E
is_a: GO:0010822 ! positive regulation of mitochondrion organization
is_a: GO:1903636 ! regulation of protein insertion into mitochondrial outer membrane
is_a: GO:1903955 ! positive regulation of protein targeting to mitochondrion
-is_a: GO:1904591 ! positive regulation of protein import
is_a: GO:1905477 ! positive regulation of protein localization to membrane
relationship: positively_regulates GO:0045040 ! protein insertion into mitochondrial outer membrane
@@ -480663,19 +483613,23 @@ relationship: regulates GO:0048870 ! cell motility
[Term]
id: GO:1903654
-name: phosphorylation of RNA polymerase II C-terminal domain serine 5 residues involved in positive regulation of transcription elongation from RNA polymerase II promoter
+name: obsolete phosphorylation of RNA polymerase II C-terminal domain serine 5 residues involved in positive regulation of transcription elongation from RNA polymerase II promoter
namespace: biological_process
-def: "Any phosphorylation of RNA polymerase II C-terminal domain serine 5 residues that is involved in positive regulation of transcription elongation from RNA polymerase II promoter." [GO_REF:0000060, GOC:TermGenie, PMID:19328067]
-is_a: GO:0071620 ! phosphorylation of RNA polymerase II C-terminal domain serine 5 residues
-relationship: part_of GO:0032968 ! positive regulation of transcription elongation from RNA polymerase II promoter
+def: "OBSOLETE. Any phosphorylation of RNA polymerase II C-terminal domain serine 5 residues that is involved in positive regulation of transcription elongation from RNA polymerase II promoter." [GO_REF:0000060, GOC:TermGenie, PMID:19328067]
+comment: This term was obsoleted because it represents both a molecular function and a biological process.
+is_obsolete: true
+consider: GO:0006368
+consider: GO:0140836
[Term]
id: GO:1903655
-name: phosphorylation of RNA polymerase II C-terminal domain serine 2 residues involved in positive regulation of transcription elongation from RNA polymerase II promoter
+name: obsolete phosphorylation of RNA polymerase II C-terminal domain serine 2 residues involved in positive regulation of transcription elongation from RNA polymerase II promoter
namespace: biological_process
-def: "Any phosphorylation of RNA polymerase II C-terminal domain serine 2 residues that is involved in positive regulation of transcription elongation from RNA polymerase II promoter." [GO_REF:0000060, GOC:TermGenie, PMID:19328067]
-is_a: GO:0071619 ! phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
-relationship: part_of GO:0032968 ! positive regulation of transcription elongation from RNA polymerase II promoter
+def: "OBSOLETE. Any phosphorylation of RNA polymerase II C-terminal domain serine 2 residues that is involved in positive regulation of transcription elongation from RNA polymerase II promoter." [GO_REF:0000060, GOC:TermGenie, PMID:19328067]
+comment: This term was obsoleted because it represents both a molecular function and a biological process.
+is_obsolete: true
+consider: GO:0006368
+consider: GO:0140834
[Term]
id: GO:1903656
@@ -480872,6 +483826,7 @@ name: L-altrarate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving L-altrarate." [GO_REF:0000068, GOC:TermGenie, PMID:17649980]
synonym: "L-altrarate(1-) metabolism" EXACT [GOC:TermGenie]
+is_a: GO:0005975 ! carbohydrate metabolic process
is_a: GO:0019577 ! aldaric acid metabolic process
[Term]
@@ -480882,6 +483837,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of L-altrar
synonym: "L-altrarate(1-) breakdown" EXACT [GOC:TermGenie]
synonym: "L-altrarate(1-) catabolism" EXACT [GOC:TermGenie]
synonym: "L-altrarate(1-) degradation" EXACT [GOC:TermGenie]
+is_a: GO:0016052 ! carbohydrate catabolic process
is_a: GO:0019579 ! aldaric acid catabolic process
is_a: GO:1903662 ! L-altrarate metabolic process
@@ -481203,8 +484159,6 @@ synonym: "methionine import" BROAD []
synonym: "methionine import into cell" EXACT []
is_a: GO:0015821 ! methionine transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:1903693
@@ -481360,9 +484314,9 @@ is_a: GO:0060575 ! intestinal epithelial cell differentiation
[Term]
id: GO:1903704
-name: negative regulation of production of siRNA involved in RNA interference
+name: negative regulation of siRNA processing
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of production of siRNA involved in RNA interference." [GO_REF:0000058, GOC:BHF, GOC:nc, GOC:TermGenie, PMID:19701182]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of siRNA processing." [GO_REF:0000058, GOC:BHF, GOC:nc, GOC:TermGenie, PMID:19701182]
synonym: "down regulation of production of guide RNAs involved in RNA interference" EXACT [GOC:TermGenie]
synonym: "down regulation of production of siRNA involved in RNA interference" EXACT [GOC:TermGenie]
synonym: "down regulation of RNA interference, production of guide RNAs" EXACT [GOC:TermGenie]
@@ -481380,26 +484334,32 @@ synonym: "inhibition of production of siRNA involved in RNA interference" NARROW
synonym: "inhibition of RNA interference, production of guide RNAs" NARROW [GOC:TermGenie]
synonym: "inhibition of RNA interference, production of siRNA" NARROW [GOC:TermGenie]
synonym: "negative regulation of production of guide RNAs involved in RNA interference" EXACT [GOC:TermGenie]
+synonym: "negative regulation of production of siRNA involved in post-transcriptional gene silencing by RNA" RELATED []
+synonym: "negative regulation of production of siRNA involved in PTGS" EXACT []
+synonym: "negative regulation of production of siRNA involved in RNA interference" EXACT []
synonym: "negative regulation of RNA interference, production of guide RNAs" EXACT [GOC:TermGenie]
synonym: "negative regulation of RNA interference, production of siRNA" EXACT [GOC:TermGenie]
-is_a: GO:0010629 ! negative regulation of gene expression
+synonym: "negative regulation of siRNA production" RELATED []
is_a: GO:0051253 ! negative regulation of RNA metabolic process
-is_a: GO:0090065 ! regulation of production of siRNA involved in RNA interference
-is_a: GO:1900369 ! negative regulation of RNA interference
-relationship: negatively_regulates GO:0030422 ! production of siRNA involved in RNA interference
+is_a: GO:0070921 ! regulation of siRNA processing
+relationship: negatively_regulates GO:0030422 ! siRNA processing
[Term]
id: GO:1903705
-name: positive regulation of production of siRNA involved in RNA interference
+name: positive regulation of siRNA processing
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of production of siRNA involved in RNA interference." [GO_REF:0000058, GOC:BHF, GOC:nc, GOC:TermGenie, PMID:19701182]
+def: "Any process that activates or increases the frequency, rate or extent of siRNA processing." [GO_REF:0000058, GOC:BHF, GOC:nc, GOC:TermGenie, PMID:19701182]
synonym: "activation of production of guide RNAs involved in RNA interference" NARROW [GOC:TermGenie]
synonym: "activation of production of siRNA involved in RNA interference" NARROW [GOC:TermGenie]
synonym: "activation of RNA interference, production of guide RNAs" NARROW [GOC:TermGenie]
synonym: "activation of RNA interference, production of siRNA" NARROW [GOC:TermGenie]
synonym: "positive regulation of production of guide RNAs involved in RNA interference" EXACT [GOC:TermGenie]
+synonym: "positive regulation of production of siRNA involved in post-transcriptional gene silencing by RNA" RELATED []
+synonym: "positive regulation of production of siRNA involved in PTGS" EXACT []
+synonym: "positive regulation of production of siRNA involved in RNA interference" EXACT []
synonym: "positive regulation of RNA interference, production of guide RNAs" EXACT [GOC:TermGenie]
synonym: "positive regulation of RNA interference, production of siRNA" EXACT [GOC:TermGenie]
+synonym: "positive regulation of siRNA production" RELATED []
synonym: "up regulation of production of guide RNAs involved in RNA interference" EXACT [GOC:TermGenie]
synonym: "up regulation of production of siRNA involved in RNA interference" EXACT [GOC:TermGenie]
synonym: "up regulation of RNA interference, production of guide RNAs" EXACT [GOC:TermGenie]
@@ -481413,8 +484373,8 @@ synonym: "upregulation of production of siRNA involved in RNA interference" EXAC
synonym: "upregulation of RNA interference, production of guide RNAs" EXACT [GOC:TermGenie]
synonym: "upregulation of RNA interference, production of siRNA" EXACT [GOC:TermGenie]
is_a: GO:0051254 ! positive regulation of RNA metabolic process
-is_a: GO:0090065 ! regulation of production of siRNA involved in RNA interference
-relationship: positively_regulates GO:0030422 ! production of siRNA involved in RNA interference
+is_a: GO:0070921 ! regulation of siRNA processing
+relationship: positively_regulates GO:0030422 ! siRNA processing
[Term]
id: GO:1903706
@@ -481427,6 +484387,7 @@ synonym: "regulation of blood cell formation" EXACT [GOC:TermGenie]
synonym: "regulation of haemopoiesis" EXACT [GOC:TermGenie]
synonym: "regulation of hematopoiesis" EXACT [GOC:TermGenie]
is_a: GO:0002682 ! regulation of immune system process
+is_a: GO:0060284 ! regulation of cell development
is_a: GO:2000026 ! regulation of multicellular organismal development
relationship: regulates GO:0030097 ! hemopoiesis
@@ -481461,7 +484422,7 @@ synonym: "negative regulation of blood cell formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of haemopoiesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of hematopoiesis" EXACT [GOC:TermGenie]
is_a: GO:0002683 ! negative regulation of immune system process
-is_a: GO:0051093 ! negative regulation of developmental process
+is_a: GO:0010721 ! negative regulation of cell development
is_a: GO:0051241 ! negative regulation of multicellular organismal process
is_a: GO:1903706 ! regulation of hemopoiesis
relationship: negatively_regulates GO:0030097 ! hemopoiesis
@@ -481497,7 +484458,7 @@ synonym: "upregulation of haemopoiesis" EXACT [GOC:TermGenie]
synonym: "upregulation of hematopoiesis" EXACT [GOC:TermGenie]
synonym: "upregulation of hemopoiesis" EXACT [GOC:TermGenie]
is_a: GO:0002684 ! positive regulation of immune system process
-is_a: GO:0051094 ! positive regulation of developmental process
+is_a: GO:0010720 ! positive regulation of cell development
is_a: GO:0051240 ! positive regulation of multicellular organismal process
is_a: GO:1903706 ! regulation of hemopoiesis
relationship: positively_regulates GO:0030097 ! hemopoiesis
@@ -481514,7 +484475,6 @@ synonym: "glandular part of endometrium development" RELATED [GOC:TermGenie]
synonym: "set of uterine glands development" RELATED [GOC:TermGenie]
synonym: "uterine glands development" EXACT [GOC:TermGenie]
synonym: "uterine glands set development" EXACT [GOC:TermGenie]
-is_a: GO:0048608 ! reproductive structure development
is_a: GO:0048732 ! gland development
[Term]
@@ -481523,7 +484483,6 @@ name: spermine transmembrane transport
namespace: biological_process
def: "The process in which spermine is transported across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:15637075]
is_a: GO:0000296 ! spermine transport
-is_a: GO:0098655 ! cation transmembrane transport
is_a: GO:1902047 ! polyamine transmembrane transport
[Term]
@@ -481532,7 +484491,6 @@ name: spermidine transmembrane transport
namespace: biological_process
def: "The process in which spermidine is transported across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:15637075]
is_a: GO:0015848 ! spermidine transport
-is_a: GO:0098655 ! cation transmembrane transport
is_a: GO:1902047 ! polyamine transmembrane transport
[Term]
@@ -481542,8 +484500,6 @@ namespace: biological_process
def: "The directed movement of cysteine across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:17435223]
is_a: GO:0003333 ! amino acid transmembrane transport
is_a: GO:0042883 ! cysteine transport
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:1903713
@@ -481863,7 +484819,7 @@ relationship: part_of GO:0071072 ! negative regulation of phospholipid biosynthe
id: GO:1903742
name: regulation of anterograde synaptic vesicle transport
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of anterograde synaptic vesicle transport." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:25329901]
+def: "Any process that modulates the frequency, rate or extent of anterograde synaptic vesicle transport." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:25329901]
subset: goslim_synapse
is_a: GO:1901608 ! regulation of vesicle transport along microtubule
is_a: GO:1902803 ! regulation of synaptic vesicle transport
@@ -481873,7 +484829,7 @@ relationship: regulates GO:0048490 ! anterograde synaptic vesicle transport
id: GO:1903743
name: negative regulation of anterograde synaptic vesicle transport
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of anterograde synaptic vesicle transport." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:25329901]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of anterograde synaptic vesicle transport." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:25329901]
synonym: "down regulation of anterograde synaptic vesicle transport" EXACT [GOC:TermGenie]
synonym: "down-regulation of anterograde synaptic vesicle transport" EXACT [GOC:TermGenie]
synonym: "downregulation of anterograde synaptic vesicle transport" EXACT [GOC:TermGenie]
@@ -481887,7 +484843,7 @@ relationship: negatively_regulates GO:0048490 ! anterograde synaptic vesicle tra
id: GO:1903744
name: positive regulation of anterograde synaptic vesicle transport
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of anterograde synaptic vesicle transport." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:25329901]
+def: "Any process that activates or increases the frequency, rate or extent of anterograde synaptic vesicle transport." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:25329901]
synonym: "activation of anterograde synaptic vesicle transport" NARROW [GOC:TermGenie]
synonym: "up regulation of anterograde synaptic vesicle transport" EXACT [GOC:TermGenie]
synonym: "up-regulation of anterograde synaptic vesicle transport" EXACT [GOC:TermGenie]
@@ -481901,7 +484857,7 @@ relationship: positively_regulates GO:0048490 ! anterograde synaptic vesicle tra
id: GO:1903745
name: negative regulation of pharyngeal pumping
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of pharyngeal pumping." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:25329901]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of pharyngeal pumping." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:25329901]
synonym: "down regulation of pharyngeal pumping" EXACT [GOC:TermGenie]
synonym: "down regulation of pumping behavior" RELATED [GOC:TermGenie]
synonym: "down-regulation of pharyngeal pumping" EXACT [GOC:TermGenie]
@@ -481919,7 +484875,7 @@ relationship: negatively_regulates GO:0043050 ! pharyngeal pumping
id: GO:1903746
name: positive regulation of pharyngeal pumping
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of pharyngeal pumping." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:25329901]
+def: "Any process that activates or increases the frequency, rate or extent of pharyngeal pumping." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, PMID:25329901]
synonym: "activation of pharyngeal pumping" NARROW [GOC:TermGenie]
synonym: "activation of pumping behavior" RELATED [GOC:TermGenie]
synonym: "positive regulation of pumping behavior" RELATED [GOC:TermGenie]
@@ -481940,7 +484896,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of establishment of protein localization to mitochondrion." [GO_REF:0000058, GOC:TermGenie, PMID:16857185]
synonym: "regulation of establishment of protein localisation to mitochondrion" EXACT [GOC:TermGenie]
synonym: "regulation of establishment of protein localization in mitochondrion" EXACT [GOC:TermGenie]
-is_a: GO:0060341 ! regulation of cellular localization
is_a: GO:0070201 ! regulation of establishment of protein localization
relationship: regulates GO:0072655 ! establishment of protein localization to mitochondrion
@@ -481963,7 +484918,6 @@ synonym: "inhibition of establishment of protein localization in mitochondrion"
synonym: "inhibition of establishment of protein localization to mitochondrion" NARROW [GOC:TermGenie]
synonym: "negative regulation of establishment of protein localisation to mitochondrion" EXACT [GOC:TermGenie]
synonym: "negative regulation of establishment of protein localization in mitochondrion" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903747 ! regulation of establishment of protein localization to mitochondrion
is_a: GO:1904950 ! negative regulation of establishment of protein localization
relationship: negatively_regulates GO:0072655 ! establishment of protein localization to mitochondrion
@@ -481987,7 +484941,6 @@ synonym: "up-regulation of establishment of protein localization to mitochondrio
synonym: "upregulation of establishment of protein localisation to mitochondrion" EXACT [GOC:TermGenie]
synonym: "upregulation of establishment of protein localization in mitochondrion" EXACT [GOC:TermGenie]
synonym: "upregulation of establishment of protein localization to mitochondrion" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903747 ! regulation of establishment of protein localization to mitochondrion
is_a: GO:1904951 ! positive regulation of establishment of protein localization
relationship: positively_regulates GO:0072655 ! establishment of protein localization to mitochondrion
@@ -482547,7 +485500,6 @@ name: regulation of cardiac conduction
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of cardiac conduction." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rph, GOC:TermGenie, PMID:12967627]
is_a: GO:0008016 ! regulation of heart contraction
-is_a: GO:0023051 ! regulation of signaling
relationship: regulates GO:0061337 ! cardiac conduction
[Term]
@@ -482559,8 +485511,7 @@ synonym: "down regulation of cardiac conduction" EXACT [GOC:TermGenie]
synonym: "down-regulation of cardiac conduction" EXACT [GOC:TermGenie]
synonym: "downregulation of cardiac conduction" EXACT [GOC:TermGenie]
synonym: "inhibition of cardiac conduction" NARROW [GOC:TermGenie]
-is_a: GO:0023057 ! negative regulation of signaling
-is_a: GO:0051241 ! negative regulation of multicellular organismal process
+is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:1903779 ! regulation of cardiac conduction
relationship: negatively_regulates GO:0061337 ! cardiac conduction
@@ -482573,8 +485524,7 @@ synonym: "activation of cardiac conduction" NARROW [GOC:TermGenie]
synonym: "up regulation of cardiac conduction" EXACT [GOC:TermGenie]
synonym: "up-regulation of cardiac conduction" EXACT [GOC:TermGenie]
synonym: "upregulation of cardiac conduction" EXACT [GOC:TermGenie]
-is_a: GO:0023056 ! positive regulation of signaling
-is_a: GO:0051240 ! positive regulation of multicellular organismal process
+is_a: GO:0048518 ! positive regulation of biological process
is_a: GO:1903779 ! regulation of cardiac conduction
relationship: positively_regulates GO:0061337 ! cardiac conduction
@@ -482617,10 +485567,7 @@ id: GO:1903785
name: L-valine transmembrane transport
namespace: biological_process
def: "The directed movement of L-valine across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:20944394]
-is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0015829 ! valine transport
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -482633,8 +485580,7 @@ synonym: "regulation of glutathione biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of glutathione formation" EXACT [GOC:TermGenie]
synonym: "regulation of glutathione synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031326 ! regulation of cellular biosynthetic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
-is_a: GO:0042762 ! regulation of sulfur metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
relationship: regulates GO:0006750 ! glutathione biosynthetic process
[Term]
@@ -482667,8 +485613,7 @@ synonym: "negative regulation of glutathione biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of glutathione formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of glutathione synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
-is_a: GO:0051175 ! negative regulation of sulfur metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:1903786 ! regulation of glutathione biosynthetic process
relationship: negatively_regulates GO:0006750 ! glutathione biosynthetic process
@@ -482702,8 +485647,7 @@ synonym: "upregulation of glutathione biosynthetic process" EXACT [GOC:TermGenie
synonym: "upregulation of glutathione formation" EXACT [GOC:TermGenie]
synonym: "upregulation of glutathione synthesis" EXACT [GOC:TermGenie]
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
-is_a: GO:0051176 ! positive regulation of sulfur metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:1903786 ! regulation of glutathione biosynthetic process
relationship: positively_regulates GO:0006750 ! glutathione biosynthetic process
@@ -482737,29 +485681,31 @@ is_a: GO:1904082 ! pyrimidine nucleobase transmembrane transport
[Term]
id: GO:1903792
-name: negative regulation of anion transport
+name: negative regulation of monoatomic anion transport
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of anion transport." [GO_REF:0000058, GOC:TermGenie, PMID:11336802]
synonym: "down regulation of anion transport" EXACT [GOC:TermGenie]
synonym: "down-regulation of anion transport" EXACT [GOC:TermGenie]
synonym: "downregulation of anion transport" EXACT [GOC:TermGenie]
synonym: "inhibition of anion transport" NARROW [GOC:TermGenie]
-is_a: GO:0043271 ! negative regulation of ion transport
-is_a: GO:0044070 ! regulation of anion transport
-relationship: negatively_regulates GO:0006820 ! anion transport
+synonym: "negative regulation of anion transport" BROAD []
+is_a: GO:0043271 ! negative regulation of monoatomic ion transport
+is_a: GO:0044070 ! regulation of monoatomic anion transport
+relationship: negatively_regulates GO:0006820 ! monoatomic anion transport
[Term]
id: GO:1903793
-name: positive regulation of anion transport
+name: positive regulation of monoatomic anion transport
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of anion transport." [GO_REF:0000058, GOC:TermGenie, PMID:11336802]
synonym: "activation of anion transport" NARROW [GOC:TermGenie]
+synonym: "positive regulation of anion transport" BROAD []
synonym: "up regulation of anion transport" EXACT [GOC:TermGenie]
synonym: "up-regulation of anion transport" EXACT [GOC:TermGenie]
synonym: "upregulation of anion transport" EXACT [GOC:TermGenie]
-is_a: GO:0043270 ! positive regulation of ion transport
-is_a: GO:0044070 ! regulation of anion transport
-relationship: positively_regulates GO:0006820 ! anion transport
+is_a: GO:0043270 ! positive regulation of monoatomic ion transport
+is_a: GO:0044070 ! regulation of monoatomic anion transport
+relationship: positively_regulates GO:0006820 ! monoatomic anion transport
[Term]
id: GO:1903794
@@ -482776,7 +485722,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of inorganic anion transmembrane transport." [GO_REF:0000058, GOC:TermGenie, PMID:11336802]
synonym: "regulation of inorganic anion membrane transport" EXACT [GOC:TermGenie]
synonym: "regulation of transmembrane inorganic anion transport" EXACT [GOC:TermGenie]
-is_a: GO:1903959 ! regulation of anion transmembrane transport
+is_a: GO:0034762 ! regulation of transmembrane transport
relationship: regulates GO:0098661 ! inorganic anion transmembrane transport
[Term]
@@ -482798,8 +485744,8 @@ synonym: "inhibition of inorganic anion transmembrane transport" NARROW [GOC:Ter
synonym: "inhibition of transmembrane inorganic anion transport" NARROW [GOC:TermGenie]
synonym: "negative regulation of inorganic anion membrane transport" EXACT [GOC:TermGenie]
synonym: "negative regulation of transmembrane inorganic anion transport" EXACT [GOC:TermGenie]
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:1903795 ! regulation of inorganic anion transmembrane transport
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
relationship: negatively_regulates GO:0098661 ! inorganic anion transmembrane transport
[Term]
@@ -482821,15 +485767,15 @@ synonym: "up-regulation of transmembrane inorganic anion transport" EXACT [GOC:T
synonym: "upregulation of inorganic anion membrane transport" EXACT [GOC:TermGenie]
synonym: "upregulation of inorganic anion transmembrane transport" EXACT [GOC:TermGenie]
synonym: "upregulation of transmembrane inorganic anion transport" EXACT [GOC:TermGenie]
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:1903795 ! regulation of inorganic anion transmembrane transport
-is_a: GO:1903961 ! positive regulation of anion transmembrane transport
relationship: positively_regulates GO:0098661 ! inorganic anion transmembrane transport
[Term]
id: GO:1903798
-name: regulation of production of miRNAs involved in gene silencing by miRNA
+name: regulation of miRNA processing
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA." [GO_REF:0000058, GOC:BHF, GOC:BHF_miRNA, GOC:rph, GOC:TermGenie, PMID:22269326]
+def: "Any process that modulates the frequency, rate or extent of microRNA processing." [GO_REF:0000058, GOC:BHF, GOC:BHF_miRNA, GOC:rph, GOC:TermGenie, PMID:22269326]
synonym: "regulation of gene silencing by miRNA, production of miRNAs" EXACT [GOC:TermGenie]
synonym: "regulation of microRNA biogenesis" RELATED [GOC:TermGenie]
synonym: "regulation of microRNA biosynthesis" RELATED [GOC:TermGenie]
@@ -482839,17 +485785,15 @@ synonym: "regulation of microRNA metabolism" RELATED [GOC:TermGenie]
synonym: "regulation of microRNA processing" BROAD [GOC:TermGenie]
synonym: "regulation of microRNA-mediated gene silencing, production of microRNAs" EXACT [GOC:TermGenie]
synonym: "regulation of miRNA biogenesis" RELATED [GOC:TermGenie]
-synonym: "regulation of miRNA processing" EXACT [GOC:TermGenie]
-synonym: "regulation of miRNA-mediated gene silencing, production of miRNAs" EXACT [GOC:TermGenie]
-synonym: "regulation of production of microRNAs involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
-is_a: GO:0070920 ! regulation of production of small RNA involved in gene silencing by RNA
-relationship: regulates GO:0035196 ! production of miRNAs involved in gene silencing by miRNA
+synonym: "regulation of miRNA maturation" NARROW []
+is_a: GO:0070920 ! regulation of regulatory ncRNA processing
+relationship: regulates GO:0035196 ! miRNA processing
[Term]
id: GO:1903799
-name: negative regulation of production of miRNAs involved in gene silencing by miRNA
+name: negative regulation of miRNA processing
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA." [GO_REF:0000058, GOC:BHF, GOC:BHF_miRNA, GOC:rph, GOC:TermGenie, PMID:22269326]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of microRNA processing." [GO_REF:0000058, GOC:BHF, GOC:BHF_miRNA, GOC:rph, GOC:TermGenie, PMID:22269326]
synonym: "down regulation of gene silencing by miRNA, production of miRNAs" EXACT [GOC:TermGenie]
synonym: "down regulation of microRNA biogenesis" RELATED [GOC:TermGenie]
synonym: "down regulation of microRNA biosynthesis" RELATED [GOC:TermGenie]
@@ -482906,20 +485850,21 @@ synonym: "negative regulation of microRNA metabolic process" RELATED [GOC:TermGe
synonym: "negative regulation of microRNA metabolism" RELATED [GOC:TermGenie]
synonym: "negative regulation of microRNA-mediated gene silencing, production of microRNAs" EXACT [GOC:TermGenie]
synonym: "negative regulation of miRNA biogenesis" RELATED [GOC:TermGenie]
-synonym: "negative regulation of miRNA processing" EXACT [GOC:TermGenie]
+synonym: "negative regulation of miRNA maturation" NARROW []
synonym: "negative regulation of miRNA-mediated gene silencing, production of miRNAs" EXACT [GOC:TermGenie]
synonym: "negative regulation of production of microRNAs involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
+synonym: "negative regulation of production of miRNAs involved in gene silencing by miRNA" RELATED []
is_a: GO:0010629 ! negative regulation of gene expression
is_a: GO:0051253 ! negative regulation of RNA metabolic process
-is_a: GO:0060965 ! negative regulation of gene silencing by miRNA
-is_a: GO:1903798 ! regulation of production of miRNAs involved in gene silencing by miRNA
-relationship: negatively_regulates GO:0035196 ! production of miRNAs involved in gene silencing by miRNA
+is_a: GO:0060965 ! negative regulation of miRNA-mediated gene silencing
+is_a: GO:1903798 ! regulation of miRNA processing
+relationship: negatively_regulates GO:0035196 ! miRNA processing
[Term]
id: GO:1903800
-name: positive regulation of production of miRNAs involved in gene silencing by miRNA
+name: positive regulation of miRNA processing
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA." [GO_REF:0000058, GOC:BHF, GOC:BHF_miRNA, GOC:rph, GOC:TermGenie, PMID:22269326]
+def: "Any process that activates or increases the frequency, rate or extent of microRNA processing." [GO_REF:0000058, GOC:BHF, GOC:BHF_miRNA, GOC:rph, GOC:TermGenie, PMID:22269326]
synonym: "activation of gene silencing by miRNA, production of miRNAs" NARROW [GOC:TermGenie]
synonym: "activation of microRNA biogenesis" RELATED [GOC:TermGenie]
synonym: "activation of microRNA biosynthesis" RELATED [GOC:TermGenie]
@@ -482940,50 +485885,15 @@ synonym: "positive regulation of microRNA metabolic process" RELATED [GOC:TermGe
synonym: "positive regulation of microRNA metabolism" RELATED [GOC:TermGenie]
synonym: "positive regulation of microRNA-mediated gene silencing, production of microRNAs" EXACT [GOC:TermGenie]
synonym: "positive regulation of miRNA biogenesis" RELATED [GOC:TermGenie]
-synonym: "positive regulation of miRNA processing" EXACT [GOC:TermGenie]
+synonym: "positive regulation of miRNA maturation" NARROW []
synonym: "positive regulation of miRNA-mediated gene silencing, production of miRNAs" EXACT [GOC:TermGenie]
synonym: "positive regulation of production of microRNAs involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
-synonym: "up regulation of gene silencing by miRNA, production of miRNAs" EXACT [GOC:TermGenie]
-synonym: "up regulation of microRNA biogenesis" RELATED [GOC:TermGenie]
-synonym: "up regulation of microRNA biosynthesis" RELATED [GOC:TermGenie]
-synonym: "up regulation of microRNA biosynthetic process" RELATED [GOC:TermGenie]
-synonym: "up regulation of microRNA metabolic process" RELATED [GOC:TermGenie]
-synonym: "up regulation of microRNA metabolism" RELATED [GOC:TermGenie]
-synonym: "up regulation of microRNA-mediated gene silencing, production of microRNAs" EXACT [GOC:TermGenie]
-synonym: "up regulation of miRNA biogenesis" RELATED [GOC:TermGenie]
-synonym: "up regulation of miRNA processing" EXACT [GOC:TermGenie]
-synonym: "up regulation of miRNA-mediated gene silencing, production of miRNAs" EXACT [GOC:TermGenie]
-synonym: "up regulation of production of microRNAs involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
-synonym: "up regulation of production of miRNAs involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
-synonym: "up-regulation of gene silencing by miRNA, production of miRNAs" EXACT [GOC:TermGenie]
-synonym: "up-regulation of microRNA biogenesis" RELATED [GOC:TermGenie]
-synonym: "up-regulation of microRNA biosynthesis" RELATED [GOC:TermGenie]
-synonym: "up-regulation of microRNA biosynthetic process" RELATED [GOC:TermGenie]
-synonym: "up-regulation of microRNA metabolic process" RELATED [GOC:TermGenie]
-synonym: "up-regulation of microRNA metabolism" RELATED [GOC:TermGenie]
-synonym: "up-regulation of microRNA-mediated gene silencing, production of microRNAs" EXACT [GOC:TermGenie]
-synonym: "up-regulation of miRNA biogenesis" RELATED [GOC:TermGenie]
-synonym: "up-regulation of miRNA processing" EXACT [GOC:TermGenie]
-synonym: "up-regulation of miRNA-mediated gene silencing, production of miRNAs" EXACT [GOC:TermGenie]
-synonym: "up-regulation of production of microRNAs involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
-synonym: "up-regulation of production of miRNAs involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
-synonym: "upregulation of gene silencing by miRNA, production of miRNAs" EXACT [GOC:TermGenie]
-synonym: "upregulation of microRNA biogenesis" RELATED [GOC:TermGenie]
-synonym: "upregulation of microRNA biosynthesis" RELATED [GOC:TermGenie]
-synonym: "upregulation of microRNA biosynthetic process" RELATED [GOC:TermGenie]
-synonym: "upregulation of microRNA metabolic process" RELATED [GOC:TermGenie]
-synonym: "upregulation of microRNA metabolism" RELATED [GOC:TermGenie]
-synonym: "upregulation of microRNA-mediated gene silencing, production of microRNAs" EXACT [GOC:TermGenie]
-synonym: "upregulation of miRNA biogenesis" RELATED [GOC:TermGenie]
-synonym: "upregulation of miRNA processing" EXACT [GOC:TermGenie]
-synonym: "upregulation of miRNA-mediated gene silencing, production of miRNAs" EXACT [GOC:TermGenie]
-synonym: "upregulation of production of microRNAs involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
-synonym: "upregulation of production of miRNAs involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
+synonym: "positive regulation of production of miRNAs involved in gene silencing by miRNA" RELATED []
is_a: GO:0010628 ! positive regulation of gene expression
is_a: GO:0051254 ! positive regulation of RNA metabolic process
-is_a: GO:1903798 ! regulation of production of miRNAs involved in gene silencing by miRNA
-is_a: GO:2000637 ! positive regulation of gene silencing by miRNA
-relationship: positively_regulates GO:0035196 ! production of miRNAs involved in gene silencing by miRNA
+is_a: GO:1903798 ! regulation of miRNA processing
+is_a: GO:2000637 ! positive regulation of miRNA-mediated gene silencing
+relationship: positively_regulates GO:0035196 ! miRNA processing
[Term]
id: GO:1903801
@@ -482996,9 +485906,6 @@ synonym: "L-leucine import into cell" EXACT []
synonym: "L-leucine uptake" NARROW []
synonym: "leucine import" BROAD []
synonym: "leucine uptake" EXACT []
-is_a: GO:0015807 ! L-amino acid transport
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:0098713 ! leucine import across plasma membrane
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
@@ -483012,10 +485919,7 @@ synonym: "L-glutamine import" BROAD []
synonym: "L-glutamine import into cell" EXACT []
synonym: "L-glutamine uptake" EXACT [GOC:bf]
is_a: GO:0006868 ! glutamine transport
-is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -483028,8 +485932,6 @@ synonym: "glycine import" BROAD []
synonym: "glycine import into cell" EXACT []
is_a: GO:0015816 ! glycine transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -483053,10 +485955,7 @@ def: "The directed movement of L-isoleucine from outside of a cell, across the p
synonym: "isoleucine import" BROAD []
synonym: "L-isoleucine import" BROAD []
synonym: "L-isoleucine import into cell" EXACT []
-is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
is_a: GO:1903714 ! isoleucine transmembrane transport
@@ -483069,11 +485968,8 @@ def: "The directed movement of L-threonine from outside of a cell, across the pl
synonym: "L-threonine import" BROAD []
synonym: "L-threonine import into cell" EXACT []
synonym: "L-threonine uptake" EXACT [GOC:bf]
-is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0015826 ! threonine transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -483085,11 +485981,8 @@ def: "The directed movement of L-tyrosine from outside of a cell, across the pla
synonym: "L-tyrosine import" BROAD []
synonym: "L-tyrosine import into cell" EXACT []
synonym: "L-tyrosine uptake" EXACT [GOC:bf]
-is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0015828 ! tyrosine transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -483114,10 +486007,7 @@ def: "The directed movement of L-asparagine from outside of a cell, across the p
synonym: "asparagine import" BROAD []
synonym: "L-asparagine import into cell" EXACT []
is_a: GO:0006867 ! asparagine transport
-is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
is_a: GO:1903713 ! asparagine transmembrane transport
@@ -483332,9 +486222,7 @@ synonym: "arginine transport" BROAD []
synonym: "L-arginine import" NARROW []
synonym: "L-arginine transport" BROAD []
synonym: "L-arginine uptake" NARROW []
-is_a: GO:0015807 ! L-amino acid transport
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0072337 ! modified amino acid transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
is_a: GO:1990822 ! basic amino acid transmembrane transport
@@ -483354,7 +486242,7 @@ synonym: "inhibition of cellular protein localization" NARROW [GOC:TermGenie]
synonym: "negative regulation of cellular protein localisation" EXACT [GOC:TermGenie]
synonym: "negative regulation of cellular protein localization" EXACT []
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0048519 ! negative regulation of biological process
+is_a: GO:0048523 ! negative regulation of cellular process
relationship: negatively_regulates GO:0008104 ! protein localization
[Term]
@@ -483371,7 +486259,7 @@ synonym: "up-regulation of cellular protein localization" EXACT [GOC:TermGenie]
synonym: "upregulation of cellular protein localisation" EXACT [GOC:TermGenie]
synonym: "upregulation of cellular protein localization" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0048518 ! positive regulation of biological process
+is_a: GO:0048522 ! positive regulation of cellular process
relationship: positively_regulates GO:0008104 ! protein localization
[Term]
@@ -483380,6 +486268,7 @@ name: magnesium ion transmembrane transport
namespace: biological_process
def: "The directed movement of magnesium ion across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:11254124]
is_a: GO:0015693 ! magnesium ion transport
+is_a: GO:0098655 ! monoatomic cation transmembrane transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -483545,7 +486434,6 @@ synonym: "up-regulation of cellular response to transforming growth factor beta
synonym: "upregulation of cellular response to TGF-beta stimulus" EXACT [GOC:TermGenie]
synonym: "upregulation of cellular response to TGFbeta stimulus" EXACT [GOC:TermGenie]
synonym: "upregulation of cellular response to transforming growth factor beta stimulus" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:0048584 ! positive regulation of response to stimulus
is_a: GO:1903844 ! regulation of cellular response to transforming growth factor beta stimulus
relationship: positively_regulates GO:0071560 ! cellular response to transforming growth factor beta stimulus
@@ -483790,7 +486678,6 @@ synonym: "upregulation of oxidative phosphorylation" EXACT [GOC:TermGenie]
synonym: "upregulation of respiratory-chain phosphorylation" EXACT [GOC:TermGenie]
is_a: GO:0002082 ! regulation of oxidative phosphorylation
is_a: GO:1901857 ! positive regulation of cellular respiration
-is_a: GO:1903580 ! positive regulation of ATP metabolic process
relationship: positively_regulates GO:0006119 ! oxidative phosphorylation
[Term]
@@ -485334,14 +488221,16 @@ id: GO:1903927
name: response to cyanide
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cyanide stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:21854848]
-is_a: GO:0010033 ! response to organic substance
+is_a: GO:0010243 ! response to organonitrogen compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1903928
name: cellular response to cyanide
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cyanide stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:21854848]
-is_a: GO:0070887 ! cellular response to chemical stimulus
+is_a: GO:0071417 ! cellular response to organonitrogen compound
+is_a: GO:1902075 ! cellular response to salt
is_a: GO:1903927 ! response to cyanide
[Term]
@@ -485749,12 +488638,13 @@ is_a: GO:1990204 ! oxidoreductase complex
[Term]
id: GO:1903959
-name: regulation of anion transmembrane transport
+name: regulation of monoatomic anion transmembrane transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of anion transmembrane transport." [GO_REF:0000058, GOC:TermGenie, GOC:vw]
-is_a: GO:0034765 ! regulation of ion transmembrane transport
-is_a: GO:0044070 ! regulation of anion transport
-relationship: regulates GO:0098656 ! anion transmembrane transport
+synonym: "regulation of anion transmembrane transport" BROAD []
+is_a: GO:0034765 ! regulation of monoatomic ion transmembrane transport
+is_a: GO:0044070 ! regulation of monoatomic anion transport
+relationship: regulates GO:0098656 ! monoatomic anion transmembrane transport
[Term]
id: GO:1903960
@@ -485765,10 +488655,10 @@ synonym: "down regulation of anion transmembrane transport" EXACT [GOC:TermGenie
synonym: "down-regulation of anion transmembrane transport" EXACT [GOC:TermGenie]
synonym: "downregulation of anion transmembrane transport" EXACT [GOC:TermGenie]
synonym: "inhibition of anion transmembrane transport" NARROW [GOC:TermGenie]
-is_a: GO:0034766 ! negative regulation of ion transmembrane transport
-is_a: GO:1903792 ! negative regulation of anion transport
-is_a: GO:1903959 ! regulation of anion transmembrane transport
-relationship: negatively_regulates GO:0098656 ! anion transmembrane transport
+is_a: GO:0034766 ! negative regulation of monoatomic ion transmembrane transport
+is_a: GO:1903792 ! negative regulation of monoatomic anion transport
+is_a: GO:1903959 ! regulation of monoatomic anion transmembrane transport
+relationship: negatively_regulates GO:0098656 ! monoatomic anion transmembrane transport
[Term]
id: GO:1903961
@@ -485779,10 +488669,10 @@ synonym: "activation of anion transmembrane transport" NARROW [GOC:TermGenie]
synonym: "up regulation of anion transmembrane transport" EXACT [GOC:TermGenie]
synonym: "up-regulation of anion transmembrane transport" EXACT [GOC:TermGenie]
synonym: "upregulation of anion transmembrane transport" EXACT [GOC:TermGenie]
-is_a: GO:0034767 ! positive regulation of ion transmembrane transport
-is_a: GO:1903793 ! positive regulation of anion transport
-is_a: GO:1903959 ! regulation of anion transmembrane transport
-relationship: positively_regulates GO:0098656 ! anion transmembrane transport
+is_a: GO:0034767 ! positive regulation of monoatomic ion transmembrane transport
+is_a: GO:1903793 ! positive regulation of monoatomic anion transport
+is_a: GO:1903959 ! regulation of monoatomic anion transmembrane transport
+relationship: positively_regulates GO:0098656 ! monoatomic anion transmembrane transport
[Term]
id: GO:1903962
@@ -485793,7 +488683,6 @@ comment: An example of this is S100A9 in human (P06702) in PMID:15642721 (inferr
synonym: "arachidonate transporter activity" RELATED []
synonym: "arachidonic acid transporter activity" RELATED []
is_a: GO:0005324 ! long-chain fatty acid transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015245 ! fatty acid transmembrane transporter activity
[Term]
@@ -485802,7 +488691,6 @@ name: arachidonate transport
namespace: biological_process
def: "The directed movement of an arachidonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GO_REF:0000065, GOC:bhm, GOC:TermGenie, PMID:15642721]
synonym: "arachidonic acid transport" EXACT []
-is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0015909 ! long-chain fatty acid transport
is_a: GO:0071715 ! icosanoid transport
@@ -485813,8 +488701,7 @@ namespace: biological_process
def: "The chemical reactions and pathways involving monounsaturated fatty acid." [GO_REF:0000068, GOC:hjd, GOC:TermGenie, PMID:16443825]
comment: For example, stearoyl-coenzyme A desaturase (Scd) catalyzes the desaturation of saturated fatty acids to monounsaturated fatty acids in mammals and yeast.
synonym: "monounsaturated fatty acid metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006082 ! organic acid metabolic process
-is_a: GO:0006629 ! lipid metabolic process
+is_a: GO:0006631 ! fatty acid metabolic process
[Term]
id: GO:1903965
@@ -485824,8 +488711,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of monounsa
synonym: "monounsaturated fatty acid breakdown" EXACT [GOC:TermGenie]
synonym: "monounsaturated fatty acid catabolism" EXACT [GOC:TermGenie]
synonym: "monounsaturated fatty acid degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016042 ! lipid catabolic process
-is_a: GO:0016054 ! organic acid catabolic process
+is_a: GO:0009062 ! fatty acid catabolic process
is_a: GO:1903964 ! monounsaturated fatty acid metabolic process
[Term]
@@ -485838,8 +488724,7 @@ synonym: "monounsaturated fatty acid anabolism" EXACT [GOC:TermGenie]
synonym: "monounsaturated fatty acid biosynthesis" EXACT [GOC:TermGenie]
synonym: "monounsaturated fatty acid formation" EXACT [GOC:TermGenie]
synonym: "monounsaturated fatty acid synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0008610 ! lipid biosynthetic process
-is_a: GO:0016053 ! organic acid biosynthetic process
+is_a: GO:0006633 ! fatty acid biosynthetic process
is_a: GO:1903964 ! monounsaturated fatty acid metabolic process
[Term]
@@ -486138,7 +489023,6 @@ synonym: "ferrous iron export across plasma membrane" NARROW []
synonym: "iron cation export" RELATED []
synonym: "iron(2+) export" RELATED []
is_a: GO:0034755 ! iron ion transmembrane transport
-is_a: GO:0070839 ! metal ion export
is_a: GO:0140115 ! export across plasma membrane
[Term]
@@ -486538,18 +489422,21 @@ is_a: GO:1904005 ! regulation of phospholipase D activity
[Term]
id: GO:1904008
-name: response to monosodium glutamate
+name: obsolete response to monosodium glutamate
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosodium glutamate stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:20704590]
-is_a: GO:1902074 ! response to salt
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosodium glutamate stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:20704590]
+comment: This term was obsoleted because GCI patterns make it equivalent to response to L-glutamate; GO:1902065.
+is_obsolete: true
+consider: GO:1902065
[Term]
id: GO:1904009
-name: cellular response to monosodium glutamate
+name: obsolete cellular response to monosodium glutamate
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosodium glutamate stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:20704590]
-is_a: GO:1902075 ! cellular response to salt
-is_a: GO:1904008 ! response to monosodium glutamate
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosodium glutamate stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:20704590]
+comment: This term was obsoleted because GCI patterns make it equivalent to cellular response to L-glutamate; GO:1905232.
+is_obsolete: true
+consider: GO:1905232
[Term]
id: GO:1904010
@@ -486697,8 +489584,6 @@ synonym: "regulation of homolactic fermentation" EXACT [GOC:TermGenie]
is_a: GO:0010906 ! regulation of glucose metabolic process
is_a: GO:0043465 ! regulation of fermentation
is_a: GO:0043470 ! regulation of carbohydrate catabolic process
-is_a: GO:1902688 ! regulation of NAD metabolic process
-is_a: GO:1903578 ! regulation of ATP metabolic process
relationship: regulates GO:0019661 ! glucose catabolic process to lactate via pyruvate
[Term]
@@ -486744,8 +489629,6 @@ is_a: GO:0009895 ! negative regulation of catabolic process
is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1901003 ! negative regulation of fermentation
-is_a: GO:1902689 ! negative regulation of NAD metabolic process
-is_a: GO:1903579 ! negative regulation of ATP metabolic process
is_a: GO:1904023 ! regulation of glucose catabolic process to lactate via pyruvate
relationship: negatively_regulates GO:0019661 ! glucose catabolic process to lactate via pyruvate
@@ -486790,8 +489673,7 @@ synonym: "upregulation of homolactate fermentation" EXACT [GOC:TermGenie]
synonym: "upregulation of homolactic fermentation" EXACT [GOC:TermGenie]
is_a: GO:0009896 ! positive regulation of catabolic process
is_a: GO:0010907 ! positive regulation of glucose metabolic process
-is_a: GO:1902690 ! positive regulation of NAD metabolic process
-is_a: GO:1903580 ! positive regulation of ATP metabolic process
+is_a: GO:0031325 ! positive regulation of cellular metabolic process
is_a: GO:1904023 ! regulation of glucose catabolic process to lactate via pyruvate
relationship: positively_regulates GO:0019661 ! glucose catabolic process to lactate via pyruvate
@@ -487412,11 +490294,12 @@ relationship: positively_regulates GO:0045475 ! locomotor rhythm
[Term]
id: GO:1904062
-name: regulation of cation transmembrane transport
+name: regulation of monoatomic cation transmembrane transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of cation transmembrane transport." [GO_REF:0000058, GOC:TermGenie, PMID:15304482]
-is_a: GO:0034765 ! regulation of ion transmembrane transport
-relationship: regulates GO:0098655 ! cation transmembrane transport
+synonym: "regulation of cation transmembrane transport" BROAD []
+is_a: GO:0034765 ! regulation of monoatomic ion transmembrane transport
+relationship: regulates GO:0098655 ! monoatomic cation transmembrane transport
[Term]
id: GO:1904063
@@ -487427,9 +490310,9 @@ synonym: "down regulation of cation transmembrane transport" EXACT [GOC:TermGeni
synonym: "down-regulation of cation transmembrane transport" EXACT [GOC:TermGenie]
synonym: "downregulation of cation transmembrane transport" EXACT [GOC:TermGenie]
synonym: "inhibition of cation transmembrane transport" NARROW [GOC:TermGenie]
-is_a: GO:0034766 ! negative regulation of ion transmembrane transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
-relationship: negatively_regulates GO:0098655 ! cation transmembrane transport
+is_a: GO:0034766 ! negative regulation of monoatomic ion transmembrane transport
+is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport
+relationship: negatively_regulates GO:0098655 ! monoatomic cation transmembrane transport
[Term]
id: GO:1904064
@@ -487440,15 +490323,15 @@ synonym: "activation of cation transmembrane transport" NARROW [GOC:TermGenie]
synonym: "up regulation of cation transmembrane transport" EXACT [GOC:TermGenie]
synonym: "up-regulation of cation transmembrane transport" EXACT [GOC:TermGenie]
synonym: "upregulation of cation transmembrane transport" EXACT [GOC:TermGenie]
-is_a: GO:0034767 ! positive regulation of ion transmembrane transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
-relationship: positively_regulates GO:0098655 ! cation transmembrane transport
+is_a: GO:0034767 ! positive regulation of monoatomic ion transmembrane transport
+is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport
+relationship: positively_regulates GO:0098655 ! monoatomic cation transmembrane transport
[Term]
id: GO:1904065
name: G protein-coupled acetylcholine receptor signaling pathway involved in positive regulation of acetylcholine secretion, neurotransmission
namespace: biological_process
-def: "Any G protein-coupled acetylcholine receptor signaling pathway that is involved in positive regulation of acetylcholine secretion, neurotransmission." [GO_REF:0000060, GOC:kmv, GOC:TermGenie, pmid:22588719]
+def: "Any G protein-coupled acetylcholine receptor signaling pathway that is involved in positive regulation of acetylcholine secretion, neurotransmission." [GO_REF:0000060, GOC:kmv, GOC:TermGenie, PMID:22588719]
synonym: "acetylcholine receptor signalling, muscarinic pathway involved in activation of acetylcholine secretion" NARROW [GOC:TermGenie]
synonym: "acetylcholine receptor signalling, muscarinic pathway involved in positive regulation of acetylcholine secretion, neurotransmission" EXACT [GOC:TermGenie]
synonym: "acetylcholine receptor signalling, muscarinic pathway involved in stimulation of acetylcholine secretion" NARROW [GOC:TermGenie]
@@ -487474,7 +490357,7 @@ relationship: part_of GO:0014057 ! positive regulation of acetylcholine secretio
id: GO:1904066
name: G protein-coupled receptor signaling pathway involved in dauer larval development
namespace: biological_process
-def: "Any G protein-coupled receptor signaling pathway that is involved in dauer larval development." [GO_REF:0000060, GOC:kmv, GOC:TermGenie, pmid:22665789]
+def: "Any G protein-coupled receptor signaling pathway that is involved in dauer larval development." [GO_REF:0000060, GOC:kmv, GOC:TermGenie, PMID:22665789]
synonym: "G protein coupled receptor protein signaling pathway involved in dauer larval development" EXACT [GOC:TermGenie]
synonym: "G protein coupled receptor protein signalling pathway involved in dauer larval development" EXACT [GOC:TermGenie]
synonym: "G-protein coupled receptor protein signal transduction involved in dauer larval development" EXACT [GOC:TermGenie]
@@ -487497,7 +490380,7 @@ is_a: GO:0097367 ! carbohydrate derivative binding
id: GO:1904068
name: G protein-coupled receptor signaling pathway involved in social behavior
namespace: biological_process
-def: "Any G protein-coupled receptor signaling pathway that is involved in social behavior." [GO_REF:0000060, GOC:kmv, GOC:TermGenie, pmid:22665789]
+def: "Any G protein-coupled receptor signaling pathway that is involved in social behavior." [GO_REF:0000060, GOC:kmv, GOC:TermGenie, PMID:22665789]
synonym: "G protein coupled receptor protein signaling pathway involved in cooperative behavior" RELATED [GOC:TermGenie]
synonym: "G protein coupled receptor protein signaling pathway involved in social behavior" EXACT [GOC:TermGenie]
synonym: "G protein coupled receptor protein signaling pathway involved in social behaviour" EXACT [GOC:TermGenie]
@@ -487535,7 +490418,7 @@ relationship: part_of GO:0035176 ! social behavior
id: GO:1904069
name: ascaroside metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving ascaroside." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, pmid:25775534]
+def: "The chemical reactions and pathways involving ascaroside." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, PMID:25775534]
synonym: "ascaroside metabolism" EXACT [GOC:TermGenie]
is_a: GO:0016137 ! glycoside metabolic process
@@ -487543,7 +490426,7 @@ is_a: GO:0016137 ! glycoside metabolic process
id: GO:1904070
name: ascaroside biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of ascaroside." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, pmid:25775534]
+def: "The chemical reactions and pathways resulting in the formation of ascaroside." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, PMID:25775534]
synonym: "ascaroside anabolism" EXACT [GOC:TermGenie]
synonym: "ascaroside biosynthesis" EXACT [GOC:TermGenie]
synonym: "ascaroside formation" EXACT [GOC:TermGenie]
@@ -487555,7 +490438,7 @@ is_a: GO:1904069 ! ascaroside metabolic process
id: GO:1904071
name: presynaptic active zone assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form a presynaptic active zone. The presynaptic active zone is a specialized region of the plasma membrane and cell cortex of a presynaptic neuron; encompasses a region of the plasma membrane where synaptic vesicles dock and fuse, and a specialized cortical cytoskeletal matrix." [GO_REF:0000079, GOC:pr, GOC:TermGenie, PMID:10769383]
+def: "The aggregation, arrangement and bonding together of a set of components to form a presynaptic active zone. The presynaptic active zone is a specialized region of the plasma membrane and cell cortex of a presynaptic neuron; encompasses a region of the plasma membrane where synaptic vesicles dock and fuse, and a specialized cortical cytoskeletal matrix." [GO_REF:0000079, GOC:pr, GOC:TermGenie, PMID:10769383]
synonym: "pre-synaptic active zone assembly" EXACT [GOC:TermGenie]
synonym: "pre-synaptic active zone component assembly" NARROW [GOC:TermGenie]
synonym: "pre-synaptic active zone component formation" NARROW [GOC:TermGenie]
@@ -487963,13 +490846,14 @@ relationship: positively_regulates GO:0055113 ! epiboly involved in gastrulation
[Term]
id: GO:1904089
-name: negative regulation of neuron apoptotic process by negative regulation of transcription from RNA polymerase II promoter
+name: obsolete negative regulation of neuron apoptotic process by negative regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "A negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of neuron apoptotic process." [GO_REF:0000063, GOC:kmv, GOC:TermGenie, PMID:20150917]
+def: "OBSOLETE. A negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of neuron apoptotic process." [GO_REF:0000063, GOC:kmv, GOC:TermGenie, PMID:20150917]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "negative regulation of neuron apoptosis by negative regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie]
synonym: "negative regulation of programmed cell death, neurons by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
-is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:0043524 ! negative regulation of neuron apoptotic process
+is_obsolete: true
+consider: GO:0000122
[Term]
id: GO:1904090
@@ -487982,57 +490866,16 @@ is_a: GO:0032991 ! protein-containing complex
[Term]
id: GO:1904091
-name: peptidyl carrier protein activity
+name: non-ribosomal peptide synthetase activity
namespace: molecular_function
-def: "Binding an amino-acid derived peptidyl group and presenting it for processing or offloading to a cognate enzyme. Covalently binds the peptidyl group via a phosphopantetheine prosthetic group and mediates protein-protein interactions with the enzyme conferring specificity. Peptidyl carrier protein (PCP) is involved in nonribosomal peptide biosynthetic process." [GO_REF:0000061, GOC:pr, GOC:TermGenie, GOC:vw, PMID:17502372]
+def: "Catalysis of a multistep reaction that produce non-ribosomal peptides. The key chain-building reaction, a C-N bond-forming reaction, involves the generation of the characteristic peptide bond by nucleophilic attack of the amino group of an amino-acyl donor unit covalently bound to a downstream peptidyl carrier protein module (amino acyl-S-PCP) on the acyl group of an upstream electrophilic acyl- or peptidyl acyl-S-PCP chain, catalyzed by a condensation (C) domain. Supplementing these core chain-elongation domains are variable numbers of auxiliary domains that are responsible for modification of the growing polypeptide chain by a small set of iterated reactions including epimerization, N-methylation, and heterocyclization." [PMID:10631508, PMID:17502372]
comment: Examples are the ferrichrome synthetase Sib1 in S. pombe and the peptidyl carrier protein (PCP) module in bacterial nonribosomal peptide synthases (NRPSs), which holds the peptidyl group and acts as a swinging arm, limiting diffusion until the peptide comes into contact with the next enzymatic module in the NRPS process.
-synonym: "Oligopeptid binding involved in non-ribosomal peptide biosynthesis" RELATED [GOC:TermGenie]
-synonym: "Oligopeptid binding involved in non-ribosomal peptide biosynthetic process" RELATED [GOC:TermGenie]
-synonym: "Oligopeptid binding involved in non-ribosomal peptide formation" RELATED [GOC:TermGenie]
-synonym: "Oligopeptid binding involved in non-ribosomal peptide synthesis" RELATED [GOC:TermGenie]
-synonym: "Oligopeptid binding involved in nonribosomal peptide anabolism" RELATED [GOC:TermGenie]
-synonym: "Oligopeptid binding involved in nonribosomal peptide biosynthesis" RELATED [GOC:TermGenie]
-synonym: "Oligopeptid binding involved in nonribosomal peptide biosynthetic process" RELATED [GOC:TermGenie]
-synonym: "Oligopeptid binding involved in nonribosomal peptide formation" RELATED [GOC:TermGenie]
-synonym: "Oligopeptid binding involved in nonribosomal peptide synthesis" RELATED [GOC:TermGenie]
-synonym: "Oligopeptid binding involved in nonribosomal peptide synthetase" RELATED [GOC:TermGenie]
-synonym: "oligopeptide binding involved in non-ribosomal peptide biosynthesis" EXACT [GOC:TermGenie]
-synonym: "oligopeptide binding involved in non-ribosomal peptide biosynthetic process" EXACT [GOC:TermGenie]
-synonym: "oligopeptide binding involved in non-ribosomal peptide formation" EXACT [GOC:TermGenie]
-synonym: "oligopeptide binding involved in non-ribosomal peptide synthesis" EXACT [GOC:TermGenie]
-synonym: "oligopeptide binding involved in nonribosomal peptide anabolism" EXACT [GOC:TermGenie]
-synonym: "oligopeptide binding involved in nonribosomal peptide biosynthesis" EXACT [GOC:TermGenie]
-synonym: "oligopeptide binding involved in nonribosomal peptide biosynthetic process" EXACT [GOC:pr]
-synonym: "oligopeptide binding involved in nonribosomal peptide formation" EXACT [GOC:TermGenie]
-synonym: "oligopeptide binding involved in nonribosomal peptide synthesis" EXACT [GOC:TermGenie]
-synonym: "oligopeptide binding involved in nonribosomal peptide synthetase" RELATED [GOC:TermGenie]
-synonym: "oligopeptides binding involved in non-ribosomal peptide biosynthesis" EXACT [GOC:TermGenie]
-synonym: "oligopeptides binding involved in non-ribosomal peptide biosynthetic process" EXACT [GOC:TermGenie]
-synonym: "oligopeptides binding involved in non-ribosomal peptide formation" EXACT [GOC:TermGenie]
-synonym: "oligopeptides binding involved in non-ribosomal peptide synthesis" EXACT [GOC:TermGenie]
-synonym: "oligopeptides binding involved in nonribosomal peptide anabolism" EXACT [GOC:TermGenie]
-synonym: "oligopeptides binding involved in nonribosomal peptide biosynthesis" EXACT [GOC:TermGenie]
-synonym: "oligopeptides binding involved in nonribosomal peptide biosynthetic process" EXACT [GOC:TermGenie]
-synonym: "oligopeptides binding involved in nonribosomal peptide formation" EXACT [GOC:TermGenie]
-synonym: "oligopeptides binding involved in nonribosomal peptide synthesis" EXACT [GOC:TermGenie]
-synonym: "oligopeptides binding involved in nonribosomal peptide synthetase" RELATED [GOC:TermGenie]
-synonym: "oligopeptido binding involved in non-ribosomal peptide biosynthesis" RELATED [GOC:TermGenie]
-synonym: "oligopeptido binding involved in non-ribosomal peptide biosynthetic process" RELATED [GOC:TermGenie]
-synonym: "oligopeptido binding involved in non-ribosomal peptide formation" RELATED [GOC:TermGenie]
-synonym: "oligopeptido binding involved in non-ribosomal peptide synthesis" RELATED [GOC:TermGenie]
-synonym: "oligopeptido binding involved in nonribosomal peptide anabolism" RELATED [GOC:TermGenie]
-synonym: "oligopeptido binding involved in nonribosomal peptide biosynthesis" RELATED [GOC:TermGenie]
-synonym: "oligopeptido binding involved in nonribosomal peptide biosynthetic process" RELATED [GOC:TermGenie]
-synonym: "oligopeptido binding involved in nonribosomal peptide formation" RELATED [GOC:TermGenie]
-synonym: "oligopeptido binding involved in nonribosomal peptide synthesis" RELATED [GOC:TermGenie]
-synonym: "oligopeptido binding involved in nonribosomal peptide synthetase" RELATED [GOC:TermGenie]
synonym: "PCP" RELATED []
-synonym: "peptidyl binding involved in nonribosomal peptide biosynthesis" EXACT [GOC:pr]
-synonym: "peptidyl binding involved in nonribosomal peptide biosynthetic process" EXACT [GOC:pr]
synonym: "peptidyl carrier protein" RELATED [GOC:pr]
+synonym: "peptidyl carrier protein activity" RELATED []
synonym: "peptidyl carrier protein activity involved in nonribosomal peptide biosynthesis" EXACT []
synonym: "peptidyl carrier protein activity involved in nonribosomal peptide biosynthetic process" EXACT [GOC:pr]
-is_a: GO:0140414 ! phosphopantetheine-dependent carrier activity
+is_a: GO:0003824 ! catalytic activity
[Term]
id: GO:1904092
@@ -488268,7 +491111,6 @@ synonym: "upregulation of cholesterol import" EXACT [GOC:TermGenie]
synonym: "upregulation of cholesterol uptake" EXACT [GOC:TermGenie]
is_a: GO:0032376 ! positive regulation of cholesterol transport
is_a: GO:0060620 ! regulation of cholesterol import
-is_a: GO:2000911 ! positive regulation of sterol import
relationship: positively_regulates GO:0070508 ! cholesterol import
[Term]
@@ -488350,7 +491192,7 @@ synonym: "downregulation of muscle filament sliding" EXACT [GOC:TermGenie]
synonym: "inhibition of muscle filament sliding" NARROW [GOC:TermGenie]
is_a: GO:0032971 ! regulation of muscle filament sliding
is_a: GO:0045932 ! negative regulation of muscle contraction
-is_a: GO:0051271 ! negative regulation of cellular component movement
+is_a: GO:0048523 ! negative regulation of cellular process
relationship: negatively_regulates GO:0030049 ! muscle filament sliding
[Term]
@@ -489069,37 +491911,43 @@ relationship: positively_regulates GO:0032060 ! bleb assembly
[Term]
id: GO:1904173
-name: regulation of histone demethylase activity (H3-K4 specific)
+name: obsolete regulation of histone demethylase activity (H3-K4 specific)
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone demethylase activity (H3-K4 specific)." [GO_REF:0000059, GOC:dph, GOC:TermGenie, PMID:24843136]
-is_a: GO:0031056 ! regulation of histone modification
-is_a: GO:0050790 ! regulation of catalytic activity
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone demethylase activity (H3-K4 specific)." [GO_REF:0000059, GOC:dph, GOC:TermGenie, PMID:24843136]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0006338
+consider: GO:0031507
+consider: GO:0045815
+consider: GO:0140673
[Term]
id: GO:1904174
-name: negative regulation of histone demethylase activity (H3-K4 specific)
+name: obsolete negative regulation of histone demethylase activity (H3-K4 specific)
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone demethylase activity (H3-K4 specific)." [GO_REF:0000059, GOC:dph, GOC:TermGenie, PMID:24843136]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone demethylase activity (H3-K4 specific)." [GO_REF:0000059, GOC:dph, GOC:TermGenie, PMID:24843136]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of histone demethylase activity (H3-K4 specific)" EXACT [GOC:TermGenie]
synonym: "down-regulation of histone demethylase activity (H3-K4 specific)" EXACT [GOC:TermGenie]
synonym: "downregulation of histone demethylase activity (H3-K4 specific)" EXACT [GOC:TermGenie]
synonym: "inhibition of histone demethylase activity (H3-K4 specific)" NARROW [GOC:TermGenie]
-is_a: GO:0031057 ! negative regulation of histone modification
-is_a: GO:0043086 ! negative regulation of catalytic activity
-is_a: GO:1904173 ! regulation of histone demethylase activity (H3-K4 specific)
+is_obsolete: true
+consider: GO:0031507
[Term]
id: GO:1904175
-name: positive regulation of histone demethylase activity (H3-K4 specific)
+name: obsolete positive regulation of histone demethylase activity (H3-K4 specific)
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of histone demethylase activity (H3-K4 specific)." [GO_REF:0000059, GOC:dph, GOC:TermGenie, PMID:24843136]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of histone demethylase activity (H3-K4 specific)." [GO_REF:0000059, GOC:dph, GOC:TermGenie, PMID:24843136]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of histone demethylase activity (H3-K4 specific)" NARROW [GOC:TermGenie]
synonym: "up regulation of histone demethylase activity (H3-K4 specific)" EXACT [GOC:TermGenie]
synonym: "up-regulation of histone demethylase activity (H3-K4 specific)" EXACT [GOC:TermGenie]
synonym: "upregulation of histone demethylase activity (H3-K4 specific)" EXACT [GOC:TermGenie]
-is_a: GO:0031058 ! positive regulation of histone modification
-is_a: GO:0043085 ! positive regulation of catalytic activity
-is_a: GO:1904173 ! regulation of histone demethylase activity (H3-K4 specific)
+is_obsolete: true
+consider: GO:0006338
+consider: GO:0045815
+consider: GO:0140673
[Term]
id: GO:1904176
@@ -489267,6 +492115,7 @@ synonym: "regulation of viral transformation" EXACT [GOC:TermGenie]
synonym: "regulation of viral transformation of host cell" EXACT [GOC:TermGenie]
is_a: GO:0043903 ! regulation of biological process involved in symbiotic interaction
is_a: GO:0050792 ! regulation of viral process
+is_a: GO:0050794 ! regulation of cellular process
relationship: regulates GO:0019087 ! transformation of host cell by virus
[Term]
@@ -489463,6 +492312,7 @@ name: iodide transmembrane transport
namespace: biological_process
def: "The process in which iodide is transported across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:20392814]
is_a: GO:0015705 ! iodide transport
+is_a: GO:0098656 ! monoatomic anion transmembrane transport
is_a: GO:0098661 ! inorganic anion transmembrane transport
[Term]
@@ -489470,7 +492320,7 @@ id: GO:1904201
name: regulation of iodide transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of iodide transport." [GO_REF:0000058, GOC:TermGenie, PMID:20392814]
-is_a: GO:0044070 ! regulation of anion transport
+is_a: GO:0044070 ! regulation of monoatomic anion transport
relationship: regulates GO:0015705 ! iodide transport
[Term]
@@ -489482,7 +492332,7 @@ synonym: "down regulation of iodide transport" EXACT [GOC:TermGenie]
synonym: "down-regulation of iodide transport" EXACT [GOC:TermGenie]
synonym: "downregulation of iodide transport" EXACT [GOC:TermGenie]
synonym: "inhibition of iodide transport" NARROW [GOC:TermGenie]
-is_a: GO:1903792 ! negative regulation of anion transport
+is_a: GO:1903792 ! negative regulation of monoatomic anion transport
is_a: GO:1904201 ! regulation of iodide transport
relationship: negatively_regulates GO:0015705 ! iodide transport
@@ -489495,7 +492345,7 @@ synonym: "activation of iodide transport" NARROW [GOC:TermGenie]
synonym: "up regulation of iodide transport" EXACT [GOC:TermGenie]
synonym: "up-regulation of iodide transport" EXACT [GOC:TermGenie]
synonym: "upregulation of iodide transport" EXACT [GOC:TermGenie]
-is_a: GO:1903793 ! positive regulation of anion transport
+is_a: GO:1903793 ! positive regulation of monoatomic anion transport
is_a: GO:1904201 ! regulation of iodide transport
relationship: positively_regulates GO:0015705 ! iodide transport
@@ -489559,7 +492409,7 @@ synonym: "membrane protein proteolysis involved in protein dislocation from ER"
synonym: "membrane protein proteolysis involved in protein retrotranslocation, ER to cytosol" EXACT [GOC:TermGenie]
synonym: "membrane protein proteolysis involved in retrograde protein transport, endoplasmic reticulum to cytosol" EXACT [GOC:TermGenie]
is_a: GO:0033619 ! membrane protein proteolysis
-is_a: GO:0051603 ! proteolysis involved in cellular protein catabolic process
+is_a: GO:0051603 ! proteolysis involved in protein catabolic process
relationship: part_of GO:0030970 ! retrograde protein transport, ER to cytosol
[Term]
@@ -489568,6 +492418,7 @@ name: regulation of iodide transmembrane transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of iodide transmembrane transport." [GO_REF:0000058, GOC:TermGenie, PMID:20392814]
is_a: GO:1903795 ! regulation of inorganic anion transmembrane transport
+is_a: GO:1903959 ! regulation of monoatomic anion transmembrane transport
is_a: GO:1904201 ! regulation of iodide transport
relationship: regulates GO:1904200 ! iodide transmembrane transport
@@ -489581,6 +492432,7 @@ synonym: "down-regulation of iodide transmembrane transport" EXACT [GOC:TermGeni
synonym: "downregulation of iodide transmembrane transport" EXACT [GOC:TermGenie]
synonym: "inhibition of iodide transmembrane transport" NARROW [GOC:TermGenie]
is_a: GO:1903796 ! negative regulation of inorganic anion transmembrane transport
+is_a: GO:1903960 ! negative regulation of anion transmembrane transport
is_a: GO:1904202 ! negative regulation of iodide transport
is_a: GO:1904212 ! regulation of iodide transmembrane transport
relationship: negatively_regulates GO:1904200 ! iodide transmembrane transport
@@ -489595,6 +492447,7 @@ synonym: "up regulation of iodide transmembrane transport" EXACT [GOC:TermGenie]
synonym: "up-regulation of iodide transmembrane transport" EXACT [GOC:TermGenie]
synonym: "upregulation of iodide transmembrane transport" EXACT [GOC:TermGenie]
is_a: GO:1903797 ! positive regulation of inorganic anion transmembrane transport
+is_a: GO:1903961 ! positive regulation of anion transmembrane transport
is_a: GO:1904203 ! positive regulation of iodide transport
is_a: GO:1904212 ! regulation of iodide transmembrane transport
relationship: positively_regulates GO:1904200 ! iodide transmembrane transport
@@ -489608,7 +492461,6 @@ synonym: "regulation of chloroplast stroma protein import" EXACT [GOC:TermGenie]
synonym: "regulation of protein transport into chloroplast stroma" EXACT [GOC:TermGenie]
is_a: GO:0034762 ! regulation of transmembrane transport
is_a: GO:1903533 ! regulation of protein targeting
-is_a: GO:1904589 ! regulation of protein import
relationship: regulates GO:0045037 ! protein import into chloroplast stroma
[Term]
@@ -489633,7 +492485,6 @@ synonym: "upregulation of protein transport into chloroplast stroma" EXACT [GOC:
is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:0090316 ! positive regulation of intracellular protein transport
is_a: GO:1904215 ! regulation of protein import into chloroplast stroma
-is_a: GO:1904591 ! positive regulation of protein import
relationship: positively_regulates GO:0045037 ! protein import into chloroplast stroma
[Term]
@@ -491352,7 +494203,7 @@ def: "Any process that modulates the frequency, rate or extent of an iron transm
synonym: "regulation of iron cation channel activity" EXACT [GOC:TermGenie]
synonym: "regulation of iron channel activity" EXACT []
synonym: "regulation of iron-specific channel activity" EXACT [GOC:TermGenie]
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
is_a: GO:0034759 ! regulation of iron ion transmembrane transport
[Term]
@@ -491406,14 +494257,17 @@ is_a: GO:1904254 ! regulation of iron ion transmembrane transporter activity
[Term]
id: GO:1904257
-name: zinc ion import into Golgi apparatus
+name: zinc ion import into Golgi lumen
namespace: biological_process
-def: "The directed import of zinc(2+) from the cytosol across the Golgi membrane into the Golgi apparatus." [GO_REF:0000075, GOC:TermGenie, PMID:25732056]
+def: "The directed import of zinc(2+) from the cytosol across the Golgi membrane into the Golgi lumen." [GO_REF:0000075, GOC:TermGenie, PMID:25732056]
+synonym: "cytosol to Golgi apparatus zinc transport" EXACT []
synonym: "zinc II ion import across Golgi membrane" EXACT []
synonym: "zinc ion import across Golgi membrane" EXACT []
+synonym: "zinc ion import into Golgi apparatus" EXACT []
synonym: "zinc ion import into Golgi membrane" RELATED []
synonym: "zinc(2+) import across Golgi membrane" EXACT []
is_a: GO:0062111 ! zinc ion import into organelle
+is_a: GO:0140820 ! cytosol to Golgi apparatus transport
[Term]
id: GO:1904258
@@ -491614,7 +494468,7 @@ synonym: "regulation of wax anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of wax biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of wax formation" EXACT [GOC:TermGenie]
synonym: "regulation of wax synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0009889 ! regulation of biosynthetic process
+is_a: GO:0046890 ! regulation of lipid biosynthetic process
relationship: regulates GO:0010025 ! wax biosynthetic process
[Term]
@@ -491646,7 +494500,7 @@ synonym: "negative regulation of wax anabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of wax biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of wax formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of wax synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0009890 ! negative regulation of biosynthetic process
+is_a: GO:0051055 ! negative regulation of lipid biosynthetic process
is_a: GO:1904276 ! regulation of wax biosynthetic process
relationship: negatively_regulates GO:0010025 ! wax biosynthetic process
@@ -491679,7 +494533,7 @@ synonym: "upregulation of wax biosynthesis" EXACT [GOC:TermGenie]
synonym: "upregulation of wax biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of wax formation" EXACT [GOC:TermGenie]
synonym: "upregulation of wax synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0009891 ! positive regulation of biosynthetic process
+is_a: GO:0046889 ! positive regulation of lipid biosynthetic process
is_a: GO:1904276 ! regulation of wax biosynthetic process
relationship: positively_regulates GO:0010025 ! wax biosynthetic process
@@ -491690,7 +494544,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase V." [GO_REF:0000058, GOC:TermGenie, PMID:24726328]
synonym: "regulation of transcription from RNA pol V promoter" EXACT [GOC:TermGenie]
synonym: "regulation of transcription from RNA polymerase V promoter" EXACT []
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
+is_a: GO:0006355 ! regulation of DNA-templated transcription
relationship: regulates GO:0001060 ! transcription by RNA polymerase V
[Term]
@@ -491708,7 +494562,7 @@ synonym: "inhibition of transcription from RNA pol V promoter" NARROW [GOC:TermG
synonym: "inhibition of transcription from RNA polymerase V promoter" NARROW [GOC:TermGenie]
synonym: "negative regulation of transcription from RNA pol V promoter" EXACT [GOC:TermGenie]
synonym: "negative regulation of transcription from RNA polymerase V promoter" EXACT []
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
is_a: GO:1904279 ! regulation of transcription by RNA polymerase V
relationship: negatively_regulates GO:0001060 ! transcription by RNA polymerase V
@@ -491727,7 +494581,7 @@ synonym: "up-regulation of transcription from RNA pol V promoter" EXACT [GOC:Ter
synonym: "up-regulation of transcription from RNA polymerase V promoter" EXACT [GOC:TermGenie]
synonym: "upregulation of transcription from RNA pol V promoter" EXACT [GOC:TermGenie]
synonym: "upregulation of transcription from RNA polymerase V promoter" EXACT [GOC:TermGenie]
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
is_a: GO:1904279 ! regulation of transcription by RNA polymerase V
relationship: positively_regulates GO:0001060 ! transcription by RNA polymerase V
@@ -492132,6 +494986,7 @@ name: response to methamphetamine hydrochloride
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a methamphetamine hydrochloride stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:22174933]
synonym: "response to methamphetamine HCL" EXACT []
+is_a: GO:0014075 ! response to amine
is_a: GO:1902074 ! response to salt
[Term]
@@ -492140,18 +494995,20 @@ name: cellular response to methamphetamine hydrochloride
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a methamphetamine hydrochloride stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:22174933]
synonym: "cellular response to methamphetamine HCL" EXACT []
+is_a: GO:0071418 ! cellular response to amine stimulus
is_a: GO:1902075 ! cellular response to salt
is_a: GO:1904313 ! response to methamphetamine hydrochloride
[Term]
id: GO:1904315
-name: transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential
+name: transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential
namespace: molecular_function
def: "Any transmitter-gated ion channel activity that is involved in regulation of postsynaptic membrane potential." [GO_REF:0000061, GOC:TermGenie, PMID:20200227]
subset: goslim_synapse
synonym: "ionotropic neurotransmitter receptor activity involved in regulation of post-synaptic membrane potential" NARROW [GOC:TermGenie]
synonym: "ionotropic neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential" NARROW [GOC:TermGenie]
-is_a: GO:0022824 ! transmitter-gated ion channel activity
+synonym: "transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential" BROAD []
+is_a: GO:0022824 ! transmitter-gated monoatomic ion channel activity
is_a: GO:0099529 ! neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential
[Term]
@@ -492348,7 +495205,7 @@ synonym: "inhibition of MFB contraction" NARROW [GOC:TermGenie]
synonym: "inhibition of myofibroblast contraction" NARROW [GOC:TermGenie]
synonym: "negative regulation of MF contraction" EXACT [GOC:TermGenie]
synonym: "negative regulation of MFB contraction" EXACT [GOC:TermGenie]
-is_a: GO:0051271 ! negative regulation of cellular component movement
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1904328 ! regulation of myofibroblast contraction
relationship: negatively_regulates GO:1990764 ! myofibroblast contraction
@@ -492452,7 +495309,7 @@ namespace: biological_process
def: "The directed movement of heme from outside of a cell, across the plasma membrane and into the cytosol." [GO_REF:0000075, GOC:TermGenie, PMID:25733668]
synonym: "heme assimilation" BROAD []
is_a: GO:0035351 ! heme transmembrane transport
-is_a: GO:0098739 ! import across plasma membrane
+is_a: GO:0098711 ! iron ion import across plasma membrane
is_a: GO:0140420 ! heme import into cell
[Term]
@@ -492645,7 +495502,7 @@ synonym: "regulation of vacuolar protein breakdown" RELATED [GOC:TermGenie]
synonym: "regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie]
synonym: "regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie]
synonym: "regulation of vacuolar protein degradation" RELATED [GOC:TermGenie]
-is_a: GO:1903362 ! regulation of cellular protein catabolic process
+is_a: GO:0042176 ! regulation of protein catabolic process
relationship: regulates GO:0007039 ! protein catabolic process in the vacuole
[Term]
@@ -492677,7 +495534,7 @@ synonym: "negative regulation of vacuolar protein breakdown" RELATED [GOC:TermGe
synonym: "negative regulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie]
synonym: "negative regulation of vacuolar protein catabolism" RELATED [GOC:TermGenie]
synonym: "negative regulation of vacuolar protein degradation" RELATED [GOC:TermGenie]
-is_a: GO:1903363 ! negative regulation of cellular protein catabolic process
+is_a: GO:0042177 ! negative regulation of protein catabolic process
is_a: GO:1904350 ! regulation of protein catabolic process in the vacuole
relationship: negatively_regulates GO:0007039 ! protein catabolic process in the vacuole
@@ -492710,7 +495567,7 @@ synonym: "upregulation of vacuolar protein breakdown" RELATED [GOC:TermGenie]
synonym: "upregulation of vacuolar protein catabolic process" RELATED [GOC:TermGenie]
synonym: "upregulation of vacuolar protein catabolism" RELATED [GOC:TermGenie]
synonym: "upregulation of vacuolar protein degradation" RELATED [GOC:TermGenie]
-is_a: GO:1903364 ! positive regulation of cellular protein catabolic process
+is_a: GO:0045732 ! positive regulation of protein catabolic process
is_a: GO:1904350 ! regulation of protein catabolic process in the vacuole
relationship: positively_regulates GO:0007039 ! protein catabolic process in the vacuole
@@ -492800,7 +495657,8 @@ namespace: biological_process
alt_id: GO:0075006
def: "Any process that modulates the frequency, rate or extent of spore germination." [GO_REF:0000058, GOC:TermGenie, PMID:14718564, PMID:8798577]
synonym: "modulation of spore germination on or near host" NARROW []
-is_a: GO:0045595 ! regulation of cell differentiation
+is_a: GO:0050793 ! regulation of developmental process
+is_a: GO:0050794 ! regulation of cellular process
relationship: regulates GO:0009847 ! spore germination
[Term]
@@ -492814,7 +495672,8 @@ synonym: "down-regulation of spore germination" EXACT [GOC:TermGenie]
synonym: "downregulation of spore germination" EXACT [GOC:TermGenie]
synonym: "inhibition of spore germination" NARROW [GOC:TermGenie]
synonym: "negative regulation of spore germination on or near host" NARROW []
-is_a: GO:0045596 ! negative regulation of cell differentiation
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:0051093 ! negative regulation of developmental process
is_a: GO:1904359 ! regulation of spore germination
relationship: negatively_regulates GO:0009847 ! spore germination
@@ -492829,7 +495688,8 @@ synonym: "positive regulation of spore germination on or near host" NARROW []
synonym: "up regulation of spore germination" EXACT [GOC:TermGenie]
synonym: "up-regulation of spore germination" EXACT [GOC:TermGenie]
synonym: "upregulation of spore germination" EXACT [GOC:TermGenie]
-is_a: GO:0045597 ! positive regulation of cell differentiation
+is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:0051094 ! positive regulation of developmental process
is_a: GO:1904359 ! regulation of spore germination
relationship: positively_regulates GO:0009847 ! spore germination
@@ -492989,7 +495849,6 @@ name: regulation of protein localization to cell periphery
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to cell periphery." [GO_REF:0000058, GOC:TermGenie, PMID:18216290]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:1990778 ! protein localization to cell periphery
[Term]
@@ -493001,7 +495860,6 @@ synonym: "down regulation of protein localization to cell periphery" EXACT [GOC:
synonym: "down-regulation of protein localization to cell periphery" EXACT [GOC:TermGenie]
synonym: "downregulation of protein localization to cell periphery" EXACT [GOC:TermGenie]
synonym: "inhibition of protein localization to cell periphery" NARROW [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1904375 ! regulation of protein localization to cell periphery
relationship: negatively_regulates GO:1990778 ! protein localization to cell periphery
@@ -493015,7 +495873,6 @@ synonym: "activation of protein localization to cell periphery" NARROW [GOC:Term
synonym: "up regulation of protein localization to cell periphery" EXACT [GOC:TermGenie]
synonym: "up-regulation of protein localization to cell periphery" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to cell periphery" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1904375 ! regulation of protein localization to cell periphery
relationship: positively_regulates GO:1990778 ! protein localization to cell periphery
@@ -493165,7 +496022,8 @@ synonym: "downregulation of pasRNA transcription" NARROW [GOC:TermGenie]
synonym: "inhibition of ncRNA transcription associated with protein coding gene TSS/TES" NARROW [GOC:TermGenie]
synonym: "inhibition of pasRNA transcription" NARROW [GOC:TermGenie]
synonym: "negative regulation of pasRNA transcription" NARROW [GOC:TermGenie]
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
+is_a: GO:0140747 ! regulation of ncRNA transcription
relationship: negatively_regulates GO:0098790 ! ncRNA transcription associated with protein coding gene TSS/TES
[Term]
@@ -493328,6 +496186,7 @@ name: heparan sulfate binding
namespace: molecular_function
def: "Binding to heparan sulfate." [GO_REF:0000067, GOC:TermGenie, PMID:8567685]
is_a: GO:0005539 ! glycosaminoglycan binding
+is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:1901681 ! sulfur compound binding
[Term]
@@ -493829,7 +496688,6 @@ synonym: "regulation of ferrous iron import across plasma membrane" RELATED []
synonym: "regulation of ferrous iron import into cell" RELATED []
is_a: GO:0034759 ! regulation of iron ion transmembrane transport
is_a: GO:0060341 ! regulation of cellular localization
-is_a: GO:0065008 ! regulation of biological quality
relationship: regulates GO:0098711 ! iron ion import across plasma membrane
[Term]
@@ -494021,7 +496879,6 @@ id: GO:1904448
name: regulation of aspartate secretion
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of aspartate secretion." [GO_REF:0000058, GOC:TermGenie, PMID:2342602]
-is_a: GO:0044070 ! regulation of anion transport
is_a: GO:0051955 ! regulation of amino acid transport
is_a: GO:1903530 ! regulation of secretion by cell
relationship: regulates GO:0061528 ! aspartate secretion
@@ -494037,7 +496894,6 @@ synonym: "downregulation of aspartate secretion" EXACT [GOC:TermGenie]
synonym: "inhibition of aspartate secretion" NARROW [GOC:TermGenie]
is_a: GO:0051956 ! negative regulation of amino acid transport
is_a: GO:1903531 ! negative regulation of secretion by cell
-is_a: GO:1903792 ! negative regulation of anion transport
is_a: GO:1904448 ! regulation of aspartate secretion
relationship: negatively_regulates GO:0061528 ! aspartate secretion
@@ -494052,7 +496908,6 @@ synonym: "up-regulation of aspartate secretion" EXACT [GOC:TermGenie]
synonym: "upregulation of aspartate secretion" EXACT [GOC:TermGenie]
is_a: GO:0051957 ! positive regulation of amino acid transport
is_a: GO:1903532 ! positive regulation of secretion by cell
-is_a: GO:1903793 ! positive regulation of anion transport
is_a: GO:1904448 ! regulation of aspartate secretion
relationship: positively_regulates GO:0061528 ! aspartate secretion
@@ -494063,11 +496918,11 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of hydrogen:potassium-exchanging ATPase activity." [GO_REF:0000059, GOC:TermGenie, PMID:11897793]
synonym: "regulation of (K+ + H+)-ATPase activity" EXACT [GOC:TermGenie]
synonym: "regulation of ATP phosphohydrolase (H+/K+-exchanging)" EXACT [GOC:TermGenie]
-synonym: "regulation of gastric H(+)/K(+) ATPase activity" NARROW [GOC:TermGenie]
+synonym: "regulation of gastric H+/K(+) ATPase activity" NARROW [GOC:TermGenie]
synonym: "regulation of gastric H+/K+ ATPase" NARROW [GOC:TermGenie]
-synonym: "regulation of H(+)/K(+)-ATPase activity" EXACT [GOC:TermGenie]
-synonym: "regulation of H(+)/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "regulation of H+-K+-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "regulation of H+/K(+)-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "regulation of H+/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "regulation of H+/K+-ATPase activity" EXACT [GOC:TermGenie]
synonym: "regulation of H+/K+-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "regulation of H,K-ATPase activity" EXACT [GOC:TermGenie]
@@ -494086,11 +496941,11 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of hydrogen:potassium-exchanging ATPase activity." [GO_REF:0000059, GOC:TermGenie, PMID:11897793]
synonym: "down regulation of (K+ + H+)-ATPase activity" EXACT [GOC:TermGenie]
synonym: "down regulation of ATP phosphohydrolase (H+/K+-exchanging)" EXACT [GOC:TermGenie]
-synonym: "down regulation of gastric H(+)/K(+) ATPase activity" NARROW [GOC:TermGenie]
+synonym: "down regulation of gastric H+/K(+) ATPase activity" NARROW [GOC:TermGenie]
synonym: "down regulation of gastric H+/K+ ATPase" NARROW [GOC:TermGenie]
-synonym: "down regulation of H(+)/K(+)-ATPase activity" EXACT [GOC:TermGenie]
-synonym: "down regulation of H(+)/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "down regulation of H+-K+-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "down regulation of H+/K(+)-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "down regulation of H+/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "down regulation of H+/K+-ATPase activity" EXACT [GOC:TermGenie]
synonym: "down regulation of H+/K+-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "down regulation of H,K-ATPase activity" EXACT [GOC:TermGenie]
@@ -494099,11 +496954,11 @@ synonym: "down regulation of hydrogen:potassium exchanging ATPase activity" EXAC
synonym: "down regulation of hydrogen:potassium-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "down-regulation of (K+ + H+)-ATPase activity" EXACT [GOC:TermGenie]
synonym: "down-regulation of ATP phosphohydrolase (H+/K+-exchanging)" EXACT [GOC:TermGenie]
-synonym: "down-regulation of gastric H(+)/K(+) ATPase activity" NARROW [GOC:TermGenie]
+synonym: "down-regulation of gastric H+/K(+) ATPase activity" NARROW [GOC:TermGenie]
synonym: "down-regulation of gastric H+/K+ ATPase" NARROW [GOC:TermGenie]
-synonym: "down-regulation of H(+)/K(+)-ATPase activity" EXACT [GOC:TermGenie]
-synonym: "down-regulation of H(+)/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "down-regulation of H+-K+-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "down-regulation of H+/K(+)-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "down-regulation of H+/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "down-regulation of H+/K+-ATPase activity" EXACT [GOC:TermGenie]
synonym: "down-regulation of H+/K+-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "down-regulation of H,K-ATPase activity" EXACT [GOC:TermGenie]
@@ -494112,11 +496967,11 @@ synonym: "down-regulation of hydrogen:potassium exchanging ATPase activity" EXAC
synonym: "down-regulation of hydrogen:potassium-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "downregulation of (K+ + H+)-ATPase activity" EXACT [GOC:TermGenie]
synonym: "downregulation of ATP phosphohydrolase (H+/K+-exchanging)" EXACT [GOC:TermGenie]
-synonym: "downregulation of gastric H(+)/K(+) ATPase activity" NARROW [GOC:TermGenie]
+synonym: "downregulation of gastric H+/K(+) ATPase activity" NARROW [GOC:TermGenie]
synonym: "downregulation of gastric H+/K+ ATPase" NARROW [GOC:TermGenie]
-synonym: "downregulation of H(+)/K(+)-ATPase activity" EXACT [GOC:TermGenie]
-synonym: "downregulation of H(+)/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "downregulation of H+-K+-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "downregulation of H+/K(+)-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "downregulation of H+/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "downregulation of H+/K+-ATPase activity" EXACT [GOC:TermGenie]
synonym: "downregulation of H+/K+-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "downregulation of H,K-ATPase activity" EXACT [GOC:TermGenie]
@@ -494125,11 +496980,11 @@ synonym: "downregulation of hydrogen:potassium exchanging ATPase activity" EXACT
synonym: "downregulation of hydrogen:potassium-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "inhibition of (K+ + H+)-ATPase activity" NARROW [GOC:TermGenie]
synonym: "inhibition of ATP phosphohydrolase (H+/K+-exchanging)" NARROW [GOC:TermGenie]
-synonym: "inhibition of gastric H(+)/K(+) ATPase activity" NARROW [GOC:TermGenie]
+synonym: "inhibition of gastric H+/K(+) ATPase activity" NARROW [GOC:TermGenie]
synonym: "inhibition of gastric H+/K+ ATPase" NARROW [GOC:TermGenie]
-synonym: "inhibition of H(+)/K(+)-ATPase activity" NARROW [GOC:TermGenie]
-synonym: "inhibition of H(+)/K(+)-exchanging ATPase activity" NARROW [GOC:TermGenie]
synonym: "inhibition of H+-K+-ATPase activity" NARROW [GOC:TermGenie]
+synonym: "inhibition of H+/K(+)-ATPase activity" NARROW [GOC:TermGenie]
+synonym: "inhibition of H+/K(+)-exchanging ATPase activity" NARROW [GOC:TermGenie]
synonym: "inhibition of H+/K+-ATPase activity" NARROW [GOC:TermGenie]
synonym: "inhibition of H+/K+-exchanging ATPase activity" NARROW [GOC:TermGenie]
synonym: "inhibition of H,K-ATPase activity" NARROW [GOC:TermGenie]
@@ -494138,11 +496993,11 @@ synonym: "inhibition of hydrogen:potassium exchanging ATPase activity" NARROW [G
synonym: "inhibition of hydrogen:potassium-exchanging ATPase activity" NARROW [GOC:TermGenie]
synonym: "negative regulation of (K+ + H+)-ATPase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of ATP phosphohydrolase (H+/K+-exchanging)" EXACT [GOC:TermGenie]
-synonym: "negative regulation of gastric H(+)/K(+) ATPase activity" NARROW [GOC:TermGenie]
+synonym: "negative regulation of gastric H+/K(+) ATPase activity" NARROW [GOC:TermGenie]
synonym: "negative regulation of gastric H+/K+ ATPase" NARROW [GOC:TermGenie]
-synonym: "negative regulation of H(+)/K(+)-ATPase activity" EXACT [GOC:TermGenie]
-synonym: "negative regulation of H(+)/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of H+-K+-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "negative regulation of H+/K(+)-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "negative regulation of H+/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of H+/K+-ATPase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of H+/K+-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of H,K-ATPase activity" EXACT [GOC:TermGenie]
@@ -494160,11 +497015,11 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of hydrogen:potassium-exchanging ATPase activity." [GO_REF:0000059, GOC:TermGenie, PMID:11897793]
synonym: "activation of (K+ + H+)-ATPase activity" NARROW [GOC:TermGenie]
synonym: "activation of ATP phosphohydrolase (H+/K+-exchanging)" NARROW [GOC:TermGenie]
-synonym: "activation of gastric H(+)/K(+) ATPase activity" NARROW [GOC:TermGenie]
+synonym: "activation of gastric H+/K(+) ATPase activity" NARROW [GOC:TermGenie]
synonym: "activation of gastric H+/K+ ATPase" NARROW [GOC:TermGenie]
-synonym: "activation of H(+)/K(+)-ATPase activity" NARROW [GOC:TermGenie]
-synonym: "activation of H(+)/K(+)-exchanging ATPase activity" NARROW [GOC:TermGenie]
synonym: "activation of H+-K+-ATPase activity" NARROW [GOC:TermGenie]
+synonym: "activation of H+/K(+)-ATPase activity" NARROW [GOC:TermGenie]
+synonym: "activation of H+/K(+)-exchanging ATPase activity" NARROW [GOC:TermGenie]
synonym: "activation of H+/K+-ATPase activity" NARROW [GOC:TermGenie]
synonym: "activation of H+/K+-exchanging ATPase activity" NARROW [GOC:TermGenie]
synonym: "activation of H,K-ATPase activity" NARROW [GOC:TermGenie]
@@ -494173,11 +497028,11 @@ synonym: "activation of hydrogen:potassium exchanging ATPase activity" NARROW [G
synonym: "activation of hydrogen:potassium-exchanging ATPase activity" NARROW [GOC:TermGenie]
synonym: "positive regulation of (K+ + H+)-ATPase activity" EXACT [GOC:TermGenie]
synonym: "positive regulation of ATP phosphohydrolase (H+/K+-exchanging)" EXACT [GOC:TermGenie]
-synonym: "positive regulation of gastric H(+)/K(+) ATPase activity" NARROW [GOC:TermGenie]
+synonym: "positive regulation of gastric H+/K(+) ATPase activity" NARROW [GOC:TermGenie]
synonym: "positive regulation of gastric H+/K+ ATPase" NARROW [GOC:TermGenie]
-synonym: "positive regulation of H(+)/K(+)-ATPase activity" EXACT [GOC:TermGenie]
-synonym: "positive regulation of H(+)/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "positive regulation of H+-K+-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "positive regulation of H+/K(+)-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "positive regulation of H+/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "positive regulation of H+/K+-ATPase activity" EXACT [GOC:TermGenie]
synonym: "positive regulation of H+/K+-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "positive regulation of H,K-ATPase activity" EXACT [GOC:TermGenie]
@@ -494186,11 +497041,11 @@ synonym: "positive regulation of hydrogen:potassium exchanging ATPase activity"
synonym: "positive regulation of hydrogen:potassium-exchanging ATPase activity" EXACT []
synonym: "up regulation of (K+ + H+)-ATPase activity" EXACT [GOC:TermGenie]
synonym: "up regulation of ATP phosphohydrolase (H+/K+-exchanging)" EXACT [GOC:TermGenie]
-synonym: "up regulation of gastric H(+)/K(+) ATPase activity" NARROW [GOC:TermGenie]
+synonym: "up regulation of gastric H+/K(+) ATPase activity" NARROW [GOC:TermGenie]
synonym: "up regulation of gastric H+/K+ ATPase" NARROW [GOC:TermGenie]
-synonym: "up regulation of H(+)/K(+)-ATPase activity" EXACT [GOC:TermGenie]
-synonym: "up regulation of H(+)/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "up regulation of H+-K+-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "up regulation of H+/K(+)-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "up regulation of H+/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "up regulation of H+/K+-ATPase activity" EXACT [GOC:TermGenie]
synonym: "up regulation of H+/K+-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "up regulation of H,K-ATPase activity" EXACT [GOC:TermGenie]
@@ -494199,11 +497054,11 @@ synonym: "up regulation of hydrogen:potassium exchanging ATPase activity" EXACT
synonym: "up regulation of hydrogen:potassium-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "up-regulation of (K+ + H+)-ATPase activity" EXACT [GOC:TermGenie]
synonym: "up-regulation of ATP phosphohydrolase (H+/K+-exchanging)" EXACT [GOC:TermGenie]
-synonym: "up-regulation of gastric H(+)/K(+) ATPase activity" NARROW [GOC:TermGenie]
+synonym: "up-regulation of gastric H+/K(+) ATPase activity" NARROW [GOC:TermGenie]
synonym: "up-regulation of gastric H+/K+ ATPase" NARROW [GOC:TermGenie]
-synonym: "up-regulation of H(+)/K(+)-ATPase activity" EXACT [GOC:TermGenie]
-synonym: "up-regulation of H(+)/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "up-regulation of H+-K+-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "up-regulation of H+/K(+)-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "up-regulation of H+/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "up-regulation of H+/K+-ATPase activity" EXACT [GOC:TermGenie]
synonym: "up-regulation of H+/K+-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "up-regulation of H,K-ATPase activity" EXACT [GOC:TermGenie]
@@ -494212,11 +497067,11 @@ synonym: "up-regulation of hydrogen:potassium exchanging ATPase activity" EXACT
synonym: "up-regulation of hydrogen:potassium-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of (K+ + H+)-ATPase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of ATP phosphohydrolase (H+/K+-exchanging)" EXACT [GOC:TermGenie]
-synonym: "upregulation of gastric H(+)/K(+) ATPase activity" NARROW [GOC:TermGenie]
+synonym: "upregulation of gastric H+/K(+) ATPase activity" NARROW [GOC:TermGenie]
synonym: "upregulation of gastric H+/K+ ATPase" NARROW [GOC:TermGenie]
-synonym: "upregulation of H(+)/K(+)-ATPase activity" EXACT [GOC:TermGenie]
-synonym: "upregulation of H(+)/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of H+-K+-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "upregulation of H+/K(+)-ATPase activity" EXACT [GOC:TermGenie]
+synonym: "upregulation of H+/K(+)-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of H+/K+-ATPase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of H+/K+-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of H,K-ATPase activity" EXACT [GOC:TermGenie]
@@ -494618,28 +497473,28 @@ is_a: GO:0048732 ! gland development
[Term]
id: GO:1904486
-name: response to 17alpha-ethynylestradiol
+name: obsolete response to 17alpha-ethynylestradiol
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a 17alpha-ethynylestradiol stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:18805421]
-is_a: GO:0014070 ! response to organic cyclic compound
-is_a: GO:0033993 ! response to lipid
-is_a: GO:1901700 ! response to oxygen-containing compound
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a 17alpha-ethynylestradiol stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:18805421]
+comment: The reason for obsoletion is that this term represent an assay and not a real GO process.
+is_obsolete: true
+replaced_by: GO:0043627
[Term]
id: GO:1904487
-name: cellular response to 17alpha-ethynylestradiol
+name: obsolete cellular response to 17alpha-ethynylestradiol
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a 17alpha-ethynylestradiol stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:18805421]
-is_a: GO:0071396 ! cellular response to lipid
-is_a: GO:0071407 ! cellular response to organic cyclic compound
-is_a: GO:1901701 ! cellular response to oxygen-containing compound
-is_a: GO:1904486 ! response to 17alpha-ethynylestradiol
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a 17alpha-ethynylestradiol stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:18805421]
+comment: The reason for obsoletion is that this term represent an assay and not a real GO process.
+is_obsolete: true
+replaced_by: GO:0071391
[Term]
id: GO:1904488
-name: regulation of reactive oxygen species metabolic process by positive regulation of transcription from RNA polymerase II promoter
+name: obsolete regulation of reactive oxygen species metabolic process by positive regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "A positive regulation of transcription from RNA polymerase II promoter that results in regulation of reactive oxygen species metabolic process." [GO_REF:0000063, GOC:kmv, GOC:TermGenie, PMID:25961505]
+def: "OBSOLETE. A positive regulation of transcription from RNA polymerase II promoter that results in regulation of reactive oxygen species metabolic process." [GO_REF:0000063, GOC:kmv, GOC:TermGenie, PMID:25961505]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "regulation of reactive oxygen species metabolic process by activation of global transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie]
synonym: "regulation of reactive oxygen species metabolic process by activation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "regulation of reactive oxygen species metabolic process by positive regulation of gene-specific transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie]
@@ -494684,14 +497539,15 @@ synonym: "regulation of ROS metabolic process by up-regulation of global transcr
synonym: "regulation of ROS metabolic process by up-regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "regulation of ROS metabolic process by upregulation of global transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie]
synonym: "regulation of ROS metabolic process by upregulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
-is_a: GO:2000377 ! regulation of reactive oxygen species metabolic process
+is_obsolete: true
+replaced_by: GO:0045944
[Term]
id: GO:1904489
-name: regulation of reactive oxygen species metabolic process by negative regulation of transcription from RNA polymerase II promoter
+name: obsolete regulation of reactive oxygen species metabolic process by negative regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "A negative regulation of transcription from RNA polymerase II promoter that results in regulation of reactive oxygen species metabolic process." [GO_REF:0000063, GOC:kmv, GOC:TermGenie, PMID:25961505]
+def: "OBSOLETE. A negative regulation of transcription from RNA polymerase II promoter that results in regulation of reactive oxygen species metabolic process." [GO_REF:0000063, GOC:kmv, GOC:TermGenie, PMID:25961505]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "regulation of reactive oxygen species metabolic process by down regulation of global transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie]
synonym: "regulation of reactive oxygen species metabolic process by down regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "regulation of reactive oxygen species metabolic process by down-regulation of global transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie]
@@ -494730,14 +497586,15 @@ synonym: "regulation of ROS metabolic process by negative regulation of global t
synonym: "regulation of ROS metabolic process by negative regulation of transcription from Pol II promoter" EXACT [GOC:TermGenie]
synonym: "regulation of ROS metabolic process by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "regulation of ROS metabolic process by negative regulation of transcription from RNA polymerase II promoter, global" RELATED [GOC:TermGenie]
-is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:2000377 ! regulation of reactive oxygen species metabolic process
+is_obsolete: true
+consider: GO:0000122
[Term]
id: GO:1904490
-name: negative regulation of mitochondrial unfolded protein response by negative regulation of transcription from RNA polymerase II promoter
+name: obsolete negative regulation of mitochondrial unfolded protein response by negative regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "A negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of mitochondrial unfolded protein response." [GO_REF:0000063, GOC:kmv, GOC:TermGenie, PMID:25961505]
+def: "OBSOLETE. A negative regulation of transcription from RNA polymerase II promoter that results in negative regulation of mitochondrial unfolded protein response." [GO_REF:0000063, GOC:kmv, GOC:TermGenie, PMID:25961505]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "negative regulation of mitochondrial unfolded protein response by down regulation of global transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie]
synonym: "negative regulation of mitochondrial unfolded protein response by down regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "negative regulation of mitochondrial unfolded protein response by down-regulation of global transcription from RNA polymerase II promoter" RELATED [GOC:TermGenie]
@@ -494763,10 +497620,8 @@ synonym: "negative regulation of mtUPR by negative regulation of global transcri
synonym: "negative regulation of mtUPR by negative regulation of transcription from Pol II promoter" EXACT [GOC:TermGenie]
synonym: "negative regulation of mtUPR by negative regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "negative regulation of mtUPR by negative regulation of transcription from RNA polymerase II promoter, global" RELATED [GOC:TermGenie]
-is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:0048585 ! negative regulation of response to stimulus
-is_a: GO:0080135 ! regulation of cellular response to stress
-relationship: negatively_regulates GO:0034514 ! mitochondrial unfolded protein response
+is_obsolete: true
+consider: GO:0000122
[Term]
id: GO:1904491
@@ -494917,7 +497772,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of telomere maintenance in response to DNA damage." [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:22579284]
synonym: "regulation of DNA damage response, telomere maintenance" EXACT [GOC:TermGenie]
is_a: GO:0032204 ! regulation of telomere maintenance
-is_a: GO:2001020 ! regulation of response to DNA damage stimulus
+is_a: GO:0080135 ! regulation of cellular response to stress
relationship: regulates GO:0043247 ! telomere maintenance in response to DNA damage
[Term]
@@ -494935,8 +497790,8 @@ synonym: "inhibition of DNA damage response, telomere maintenance" NARROW [GOC:T
synonym: "inhibition of telomere maintenance in response to DNA damage" NARROW [GOC:TermGenie]
synonym: "negative regulation of DNA damage response, telomere maintenance" EXACT [GOC:TermGenie]
is_a: GO:0032205 ! negative regulation of telomere maintenance
+is_a: GO:0048585 ! negative regulation of response to stimulus
is_a: GO:1904505 ! regulation of telomere maintenance in response to DNA damage
-is_a: GO:2001021 ! negative regulation of response to DNA damage stimulus
relationship: negatively_regulates GO:0043247 ! telomere maintenance in response to DNA damage
[Term]
@@ -494954,8 +497809,8 @@ synonym: "up-regulation of telomere maintenance in response to DNA damage" EXACT
synonym: "upregulation of DNA damage response, telomere maintenance" EXACT [GOC:TermGenie]
synonym: "upregulation of telomere maintenance in response to DNA damage" EXACT [GOC:TermGenie]
is_a: GO:0032206 ! positive regulation of telomere maintenance
+is_a: GO:0048584 ! positive regulation of response to stimulus
is_a: GO:1904505 ! regulation of telomere maintenance in response to DNA damage
-is_a: GO:2001022 ! positive regulation of response to DNA damage stimulus
relationship: positively_regulates GO:0043247 ! telomere maintenance in response to DNA damage
[Term]
@@ -495051,7 +497906,7 @@ synonym: "regulation of initiation of meiotic DNA synthesis" RELATED [GOC:TermGe
synonym: "regulation of initiation of premeiotic DNA synthesis" RELATED [GOC:TermGenie]
synonym: "regulation of meiotic DNA replication initiation" RELATED [GOC:TermGenie]
synonym: "regulation of premeiotic DNA replication initiation" EXACT [GOC:TermGenie]
-is_a: GO:0030174 ! regulation of DNA-dependent DNA replication initiation
+is_a: GO:0030174 ! regulation of DNA-templated DNA replication initiation
is_a: GO:0033262 ! regulation of nuclear cell cycle DNA replication
is_a: GO:0051445 ! regulation of meiotic cell cycle
relationship: regulates GO:1902974 ! meiotic DNA replication initiation
@@ -495085,7 +497940,7 @@ synonym: "negative regulation of initiation of meiotic DNA synthesis" RELATED [G
synonym: "negative regulation of initiation of premeiotic DNA synthesis" RELATED [GOC:TermGenie]
synonym: "negative regulation of meiotic DNA replication initiation" RELATED [GOC:TermGenie]
synonym: "negative regulation of premeiotic DNA replication initiation" EXACT [GOC:TermGenie]
-is_a: GO:0032297 ! negative regulation of DNA-dependent DNA replication initiation
+is_a: GO:0032297 ! negative regulation of DNA-templated DNA replication initiation
is_a: GO:0051447 ! negative regulation of meiotic cell cycle
is_a: GO:1902576 ! negative regulation of nuclear cell cycle DNA replication
is_a: GO:1904512 ! regulation of initiation of premeiotic DNA replication
@@ -495121,7 +497976,7 @@ synonym: "upregulation of initiation of premeiotic DNA synthesis" RELATED [GOC:T
synonym: "upregulation of meiotic DNA replication initiation" RELATED [GOC:TermGenie]
synonym: "upregulation of premeiotic DNA replication initiation" EXACT [GOC:TermGenie]
is_a: GO:0010571 ! positive regulation of nuclear cell cycle DNA replication
-is_a: GO:0032298 ! positive regulation of DNA-dependent DNA replication initiation
+is_a: GO:0032298 ! positive regulation of DNA-templated DNA replication initiation
is_a: GO:1904512 ! regulation of initiation of premeiotic DNA replication
is_a: GO:2000243 ! positive regulation of reproductive process
relationship: positively_regulates GO:1902974 ! meiotic DNA replication initiation
@@ -495156,10 +498011,12 @@ is_a: GO:0006915 ! apoptotic process
[Term]
id: GO:1904517
-name: MgATP(2-) binding
+name: obsolete MgATP(2-) binding
namespace: molecular_function
-def: "Binding to MgATP(2-)." [GO_REF:0000067, GOC:bhm, GOC:TermGenie, PMID:20086079]
-is_a: GO:0005488 ! binding
+def: "OBSOLETE. Binding to MgATP(2-)." [GO_REF:0000067, GOC:bhm, GOC:TermGenie, PMID:20086079]
+comment: This term was obsolsted because it is equivalent to GO:0005524 ; ATP binding.
+is_obsolete: true
+replaced_by: GO:0005524
[Term]
id: GO:1904518
@@ -495447,7 +498304,7 @@ id: GO:1904536
name: regulation of mitotic telomere tethering at nuclear periphery
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of mitotic telomere tethering at nuclear periphery." [GO_REF:0000058, GOC:TermGenie, PMID:22959349]
-is_a: GO:0060341 ! regulation of cellular localization
+is_a: GO:0032879 ! regulation of localization
relationship: regulates GO:0044820 ! mitotic telomere tethering at nuclear periphery
[Term]
@@ -495459,7 +498316,7 @@ synonym: "down regulation of mitotic telomere tethering at nuclear periphery" EX
synonym: "down-regulation of mitotic telomere tethering at nuclear periphery" EXACT [GOC:TermGenie]
synonym: "downregulation of mitotic telomere tethering at nuclear periphery" EXACT [GOC:TermGenie]
synonym: "inhibition of mitotic telomere tethering at nuclear periphery" NARROW [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:1904536 ! regulation of mitotic telomere tethering at nuclear periphery
relationship: negatively_regulates GO:0044820 ! mitotic telomere tethering at nuclear periphery
@@ -495746,11 +498603,8 @@ id: GO:1904555
name: L-proline transmembrane transport
namespace: biological_process
def: "The directed movement of L-proline across a membrane." [GO_REF:0000069, GOC:kmv, GOC:TermGenie]
-is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0015824 ! proline transport
is_a: GO:0035524 ! proline transmembrane transport
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -495758,10 +498612,7 @@ id: GO:1904556
name: L-tryptophan transmembrane transport
namespace: biological_process
def: "The directed movement of L-tryptophan across a membrane." [GO_REF:0000069, GOC:kmv, GOC:TermGenie]
-is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0015827 ! tryptophan transport
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -495770,8 +498621,6 @@ name: L-alanine transmembrane transport
namespace: biological_process
def: "The directed movement of L-alanine across a membrane." [GO_REF:0000069, GOC:kmv, GOC:TermGenie]
is_a: GO:0015808 ! L-alanine transport
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -495975,37 +498824,39 @@ is_a: GO:1904573 ! regulation of selenocysteine insertion sequence binding
[Term]
id: GO:1904576
-name: response to tunicamycin
+name: obsolete response to tunicamycin
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tunicamycin stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:23106379]
-is_a: GO:0042221 ! response to chemical
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tunicamycin stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:23106379]
+comment: This term was obsoleted because it represents an experimental condition to cause endoplasmic reticulum stress.
+is_obsolete: true
+consider: GO:0034976
[Term]
id: GO:1904577
-name: cellular response to tunicamycin
+name: obsolete cellular response to tunicamycin
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tunicamycin stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:23106379]
-is_a: GO:0070887 ! cellular response to chemical stimulus
-is_a: GO:1904576 ! response to tunicamycin
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tunicamycin stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:23106379]
+comment: This term was obsoleted because it represents an experimental condition to cause endoplasmic reticulum stress.
+is_obsolete: true
+consider: GO:0034976
[Term]
id: GO:1904578
-name: response to thapsigargin
+name: obsolete response to thapsigargin
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thapsigargin stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:23106379]
-is_a: GO:0014070 ! response to organic cyclic compound
-is_a: GO:0033993 ! response to lipid
-is_a: GO:1901700 ! response to oxygen-containing compound
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thapsigargin stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:23106379]
+comment: This term was obsoleted because it represents an experimental condition to cause endoplasmic reticulum stress.
+is_obsolete: true
+consider: GO:0034976
[Term]
id: GO:1904579
-name: cellular response to thapsigargin
+name: obsolete cellular response to thapsigargin
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thapsigargin stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:23106379]
-is_a: GO:0071396 ! cellular response to lipid
-is_a: GO:0071407 ! cellular response to organic cyclic compound
-is_a: GO:1901701 ! cellular response to oxygen-containing compound
-is_a: GO:1904578 ! response to thapsigargin
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thapsigargin stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:23106379]
+comment: This term was obsoleted because it represents an experimental condition to cause endoplasmic reticulum stress.
+is_obsolete: true
+consider: GO:0034976
[Term]
id: GO:1904580
@@ -496235,7 +499086,7 @@ synonym: "regulation of RNA polymerase II transcription termination" EXACT [GOC:
synonym: "regulation of RNA polymerase II transcription termination factor activity" RELATED [GOC:TermGenie]
synonym: "regulation of transcription termination from Pol II promoter" EXACT [GOC:TermGenie]
synonym: "regulation of transcription termination from RNA polymerase II promoter" EXACT [GOC:TermGenie]
-is_a: GO:0031554 ! regulation of DNA-templated transcription, termination
+is_a: GO:0031554 ! regulation of termination of DNA-templated transcription
relationship: regulates GO:0006369 ! termination of RNA polymerase II transcription
[Term]
@@ -496272,7 +499123,7 @@ synonym: "upregulation of RNA polymerase II transcription termination factor act
synonym: "upregulation of termination of RNA polymerase II transcription" EXACT [GOC:TermGenie]
synonym: "upregulation of transcription termination from Pol II promoter" EXACT [GOC:TermGenie]
synonym: "upregulation of transcription termination from RNA polymerase II promoter" EXACT [GOC:TermGenie]
-is_a: GO:0060566 ! positive regulation of DNA-templated transcription, termination
+is_a: GO:0060566 ! positive regulation of termination of DNA-templated transcription
is_a: GO:1904594 ! regulation of termination of RNA polymerase II transcription
relationship: positively_regulates GO:0006369 ! termination of RNA polymerase II transcription
@@ -496280,7 +499131,7 @@ relationship: positively_regulates GO:0006369 ! termination of RNA polymerase II
id: GO:1904596
name: regulation of connective tissue replacement involved in inflammatory response wound healing
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of connective tissue replacement involved in inflammatory response wound healing." [GO_REF:0000058, GOC:krc, GOC:TermGenie, PMID:18245812]
+def: "Any process that modulates the frequency, rate or extent of wound healing connective tissue replacement, which may be replaced with fibrotic material, that occurs as part of an inflammatory response." [GO_REF:0000058, GOC:krc, GOC:TermGenie, PMID:18245812]
synonym: "regulation of connective tissue replacement during inflammatory response" RELATED [GOC:TermGenie]
synonym: "regulation of fibrosis during inflammatory response" NARROW [GOC:TermGenie]
is_a: GO:1905203 ! regulation of connective tissue replacement
@@ -496290,7 +499141,7 @@ relationship: regulates GO:0002248 ! connective tissue replacement involved in i
id: GO:1904597
name: negative regulation of connective tissue replacement involved in inflammatory response wound healing
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of connective tissue replacement involved in inflammatory response wound healing." [GO_REF:0000058, GOC:krc, GOC:TermGenie, PMID:18245812]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of wound healing connective tissue replacement, which may be replaced with fibrotic material, that occurs as part of an inflammatory response." [GO_REF:0000058, GOC:krc, GOC:TermGenie, PMID:18245812]
synonym: "down regulation of connective tissue replacement during inflammatory response" RELATED [GOC:TermGenie]
synonym: "down regulation of connective tissue replacement involved in inflammatory response wound healing" EXACT [GOC:TermGenie]
synonym: "down regulation of fibrosis during inflammatory response" NARROW [GOC:TermGenie]
@@ -496313,7 +499164,7 @@ relationship: negatively_regulates GO:0002248 ! connective tissue replacement in
id: GO:1904598
name: positive regulation of connective tissue replacement involved in inflammatory response wound healing
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of connective tissue replacement involved in inflammatory response wound healing." [GO_REF:0000058, GOC:krc, GOC:TermGenie, PMID:18245812]
+def: "Any process that activates or increases the frequency, rate or extent of wound healing connective tissue replacement, which may be replaced with fibrotic material, that occurs as part of an inflammatory response." [GO_REF:0000058, GOC:krc, GOC:TermGenie, PMID:18245812]
synonym: "activation of connective tissue replacement during inflammatory response" RELATED [GOC:TermGenie]
synonym: "activation of connective tissue replacement involved in inflammatory response wound healing" NARROW [GOC:TermGenie]
synonym: "activation of fibrosis during inflammatory response" NARROW [GOC:TermGenie]
@@ -496341,9 +499192,10 @@ is_a: GO:0097367 ! carbohydrate derivative binding
[Term]
id: GO:1904600
-name: actin fusion focus assembly
+name: mating projection actin fusion focus assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form an actin fusion focus." [GO_REF:0000079, GOC:TermGenie, PMID:25825517]
+synonym: "actin fusion focus assembly" BROAD []
synonym: "actin fusion focus formation" EXACT [GOC:TermGenie]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0010927 ! cellular component assembly involved in morphogenesis
@@ -496352,14 +499204,13 @@ relationship: part_of GO:0031382 ! mating projection formation
[Term]
id: GO:1904601
-name: protein localization to actin fusion focus
+name: protein transport to mating projection actin fusion focus
namespace: biological_process
-def: "A process in which a protein is transported to, or maintained in, a location within an actin fusion focus." [GO_REF:0000087, GOC:TermGenie, PMID:25825517]
+def: "A process in which a protein is transported to a location within an actin fusion focus." [GO_REF:0000087, GOC:TermGenie, PMID:25825517]
synonym: "protein localisation in actin fusion focus" EXACT [GOC:TermGenie]
synonym: "protein localisation to actin fusion focus" EXACT [GOC:TermGenie]
synonym: "protein localization in actin fusion focus" EXACT [GOC:TermGenie]
-is_a: GO:1903119 ! protein localization to actin cytoskeleton
-is_a: GO:1903260 ! protein localization to mating projection tip
+is_a: GO:0015031 ! protein transport
[Term]
id: GO:1904602
@@ -496373,6 +499224,7 @@ synonym: "5-hydroxytryptamine receptor 3 complex" EXACT []
synonym: "5HT3 receptor complex" EXACT []
synonym: "serotonin receptor complex" BROAD []
is_a: GO:0034703 ! cation channel complex
+is_a: GO:0098665 ! serotonin receptor complex
is_a: GO:0098878 ! neurotransmitter receptor complex
[Term]
@@ -496442,18 +499294,21 @@ is_a: GO:0006915 ! apoptotic process
[Term]
id: GO:1904608
-name: response to monosodium L-glutamate
+name: obsolete response to monosodium L-glutamate
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosodium L-glutamate stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:21389115]
-is_a: GO:1904008 ! response to monosodium glutamate
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosodium L-glutamate stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:21389115]
+comment: This term was obsoleted because GCI patterns make it equivalent to response to L-glutamate; GO:1902065.
+is_obsolete: true
+replaced_by: GO:1902065
[Term]
id: GO:1904609
-name: cellular response to monosodium L-glutamate
+name: obsolete cellular response to monosodium L-glutamate
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosodium L-glutamate stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:21389115]
-is_a: GO:1904009 ! cellular response to monosodium glutamate
-is_a: GO:1904608 ! response to monosodium L-glutamate
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosodium L-glutamate stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:21389115]
+comment: This term was obsoleted because GCI patterns make it equivalent to cellular response to L-glutamate; GO:1905232.
+is_obsolete: true
+consider: GO:1905232
[Term]
id: GO:1904610
@@ -496570,7 +499425,6 @@ id: GO:1904624
name: regulation of glycine secretion, neurotransmission
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of glycine secretion, neurotransmission." [GO_REF:0000058, GOC:TermGenie, PMID:22988142]
-is_a: GO:0044070 ! regulation of anion transport
is_a: GO:0046928 ! regulation of neurotransmitter secretion
is_a: GO:0051955 ! regulation of amino acid transport
is_a: GO:0060092 ! regulation of synaptic transmission, glycinergic
@@ -496588,7 +499442,6 @@ synonym: "inhibition of glycine secretion, neurotransmission" NARROW [GOC:TermGe
is_a: GO:0046929 ! negative regulation of neurotransmitter secretion
is_a: GO:0051956 ! negative regulation of amino acid transport
is_a: GO:0060093 ! negative regulation of synaptic transmission, glycinergic
-is_a: GO:1903792 ! negative regulation of anion transport
is_a: GO:1904624 ! regulation of glycine secretion, neurotransmission
relationship: negatively_regulates GO:0061537 ! glycine secretion, neurotransmission
@@ -496604,7 +499457,6 @@ synonym: "upregulation of glycine secretion, neurotransmission" EXACT [GOC:TermG
is_a: GO:0001956 ! positive regulation of neurotransmitter secretion
is_a: GO:0051957 ! positive regulation of amino acid transport
is_a: GO:0060094 ! positive regulation of synaptic transmission, glycinergic
-is_a: GO:1903793 ! positive regulation of anion transport
is_a: GO:1904624 ! regulation of glycine secretion, neurotransmission
relationship: positively_regulates GO:0061537 ! glycine secretion, neurotransmission
@@ -496669,20 +499521,20 @@ is_a: GO:1904631 ! response to glucoside
[Term]
id: GO:1904633
-name: regulation of glomerular visceral epithelial cell apoptotic process
+name: regulation of podocyte apoptotic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of glomerular visceral epithelial cell apoptotic process." [GO_REF:0000058, GOC:TermGenie, PMID:23692924]
synonym: "regulation of glomerular podocyte apoptosis" NARROW [GOC:TermGenie]
synonym: "regulation of glomerular podocyte apoptotic process" EXACT [GOC:TermGenie]
synonym: "regulation of glomerular visceral epithelial cell apoptosis" NARROW [GOC:TermGenie]
+synonym: "regulation of glomerular visceral epithelial cell apoptotic process" EXACT []
synonym: "regulation of podocyte apoptosis" NARROW [GOC:TermGenie]
-synonym: "regulation of podocyte apoptotic process" EXACT [GOC:TermGenie]
is_a: GO:1904035 ! regulation of epithelial cell apoptotic process
-relationship: regulates GO:1903210 ! glomerular visceral epithelial cell apoptotic process
+relationship: regulates GO:1903210 ! podocyte apoptotic process
[Term]
id: GO:1904634
-name: negative regulation of glomerular visceral epithelial cell apoptotic process
+name: negative regulation of podocyte apoptotic process
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of glomerular visceral epithelial cell apoptotic process." [GO_REF:0000058, GOC:TermGenie, PMID:23692924]
synonym: "down regulation of glomerular podocyte apoptosis" NARROW [GOC:TermGenie]
@@ -496712,15 +499564,15 @@ synonym: "inhibition of podocyte apoptotic process" NARROW [GOC:TermGenie]
synonym: "negative regulation of glomerular podocyte apoptosis" NARROW [GOC:TermGenie]
synonym: "negative regulation of glomerular podocyte apoptotic process" EXACT [GOC:TermGenie]
synonym: "negative regulation of glomerular visceral epithelial cell apoptosis" NARROW [GOC:TermGenie]
-synonym: "negative regulation of podocyte apoptosis" NARROW [GOC:TermGenie]
-synonym: "negative regulation of podocyte apoptotic process" EXACT [GOC:TermGenie]
+synonym: "negative regulation of glomerular visceral epithelial cell apoptotic process" EXACT []
+synonym: "negative regulation of podocyte apoptosis" EXACT [GOC:TermGenie]
is_a: GO:1904036 ! negative regulation of epithelial cell apoptotic process
-is_a: GO:1904633 ! regulation of glomerular visceral epithelial cell apoptotic process
-relationship: negatively_regulates GO:1903210 ! glomerular visceral epithelial cell apoptotic process
+is_a: GO:1904633 ! regulation of podocyte apoptotic process
+relationship: negatively_regulates GO:1903210 ! podocyte apoptotic process
[Term]
id: GO:1904635
-name: positive regulation of glomerular visceral epithelial cell apoptotic process
+name: positive regulation of podocyte apoptotic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of glomerular visceral epithelial cell apoptotic process." [GO_REF:0000058, GOC:TermGenie, PMID:23692924]
synonym: "activation of glomerular podocyte apoptosis" NARROW [GOC:TermGenie]
@@ -496732,8 +499584,8 @@ synonym: "activation of podocyte apoptotic process" NARROW [GOC:TermGenie]
synonym: "positive regulation of glomerular podocyte apoptosis" NARROW [GOC:TermGenie]
synonym: "positive regulation of glomerular podocyte apoptotic process" EXACT [GOC:TermGenie]
synonym: "positive regulation of glomerular visceral epithelial cell apoptosis" NARROW [GOC:TermGenie]
+synonym: "positive regulation of glomerular visceral epithelial cell apoptotic process" EXACT []
synonym: "positive regulation of podocyte apoptosis" NARROW [GOC:TermGenie]
-synonym: "positive regulation of podocyte apoptotic process" EXACT [GOC:TermGenie]
synonym: "up regulation of glomerular podocyte apoptosis" NARROW [GOC:TermGenie]
synonym: "up regulation of glomerular podocyte apoptotic process" EXACT [GOC:TermGenie]
synonym: "up regulation of glomerular visceral epithelial cell apoptosis" NARROW [GOC:TermGenie]
@@ -496753,8 +499605,8 @@ synonym: "upregulation of glomerular visceral epithelial cell apoptotic process"
synonym: "upregulation of podocyte apoptosis" NARROW [GOC:TermGenie]
synonym: "upregulation of podocyte apoptotic process" EXACT [GOC:TermGenie]
is_a: GO:1904037 ! positive regulation of epithelial cell apoptotic process
-is_a: GO:1904633 ! regulation of glomerular visceral epithelial cell apoptotic process
-relationship: positively_regulates GO:1903210 ! glomerular visceral epithelial cell apoptotic process
+is_a: GO:1904633 ! regulation of podocyte apoptotic process
+relationship: positively_regulates GO:1903210 ! podocyte apoptotic process
[Term]
id: GO:1904636
@@ -497254,11 +500106,11 @@ is_a: GO:0015867 ! ATP transport
[Term]
id: GO:1904670
-name: actin filament polymerization involved in mitotic actomyosin contractile ring assembly
+name: obsolete actin filament polymerization involved in mitotic actomyosin contractile ring assembly
namespace: biological_process
-def: "Any actin filament polymerization that is involved in mitotic actomyosin contractile ring assembly." [GO_REF:0000060, GOC:TermGenie, PMID:24127216]
-is_a: GO:0030041 ! actin filament polymerization
-is_a: GO:1903479 ! mitotic actomyosin contractile ring assembly actin filament organization
+def: "OBSOLETE. Any actin filament polymerization that is involved in mitotic actomyosin contractile ring assembly." [GO_REF:0000060, GOC:TermGenie, PMID:24127216]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:1904671
@@ -497371,6 +500223,7 @@ namespace: biological_process
alt_id: GO:0097357
def: "The directed movement of myo-inositol from outside of a cell, across the plasma membrane and into the cytosol." [GO_REF:0000075, GOC:TermGenie, PMID:9560432]
synonym: "myo-inositol import into cell" EXACT []
+is_a: GO:0015791 ! polyol transmembrane transport
is_a: GO:0015798 ! myo-inositol transport
is_a: GO:0098657 ! import into cell
is_a: GO:0098739 ! import across plasma membrane
@@ -498275,7 +501128,7 @@ id: GO:1904726
name: regulation of replicative senescence
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of replicative senescence." [GO_REF:0000058, GOC:BHF, GOC:BHF_miRNA, GOC:rph, GOC:TermGenie, PMID:23496142]
-is_a: GO:0090342 ! regulation of cell aging
+is_a: GO:0031323 ! regulation of cellular metabolic process
relationship: regulates GO:0090399 ! replicative senescence
[Term]
@@ -498287,7 +501140,7 @@ synonym: "down regulation of replicative senescence" EXACT [GOC:TermGenie]
synonym: "down-regulation of replicative senescence" EXACT [GOC:TermGenie]
synonym: "downregulation of replicative senescence" EXACT [GOC:TermGenie]
synonym: "inhibition of replicative senescence" NARROW [GOC:TermGenie]
-is_a: GO:0090344 ! negative regulation of cell aging
+is_a: GO:0031324 ! negative regulation of cellular metabolic process
is_a: GO:1904726 ! regulation of replicative senescence
relationship: negatively_regulates GO:0090399 ! replicative senescence
@@ -498300,7 +501153,7 @@ synonym: "activation of replicative senescence" NARROW [GOC:TermGenie]
synonym: "up regulation of replicative senescence" EXACT [GOC:TermGenie]
synonym: "up-regulation of replicative senescence" EXACT [GOC:TermGenie]
synonym: "upregulation of replicative senescence" EXACT [GOC:TermGenie]
-is_a: GO:0090343 ! positive regulation of cell aging
+is_a: GO:0031325 ! positive regulation of cellular metabolic process
is_a: GO:1904726 ! regulation of replicative senescence
relationship: positively_regulates GO:0090399 ! replicative senescence
@@ -498692,15 +501545,15 @@ is_a: GO:0014909 ! smooth muscle cell migration
[Term]
id: GO:1904739
-name: regulation of synapse organization by posttranscriptional regulation of gene expression
+name: obsolete regulation of synapse organization by posttranscriptional regulation of gene expression
namespace: biological_process
-def: "A posttranscriptional regulation of gene expression that results in regulation of synapse organization." [GO_REF:0000063, GOC:rb, GOC:TermGenie, PMID:20729808]
+def: "OBSOLETE. A posttranscriptional regulation of gene expression that results in regulation of synapse organization." [GO_REF:0000063, GOC:rb, GOC:TermGenie, PMID:20729808]
+comment: This term was obsoleted because it represents a precomposed term and should be represented as a GO-CAM model.
synonym: "regulation of synapse development by posttranscriptional regulation of gene expression" EXACT [GOC:TermGenie]
synonym: "regulation of synapse morphogenesis by posttranscriptional regulation of gene expression" RELATED [GOC:TermGenie]
synonym: "regulation of synapse organisation by posttranscriptional regulation of gene expression" EXACT [GOC:TermGenie]
synonym: "regulation of synapse organization and biogenesis by posttranscriptional regulation of gene expression" RELATED [GOC:TermGenie]
-is_a: GO:0010608 ! posttranscriptional regulation of gene expression
-is_a: GO:0050807 ! regulation of synapse organization
+is_obsolete: true
[Term]
id: GO:1904740
@@ -499427,9 +502280,10 @@ is_a: GO:0032984 ! protein-containing complex disassembly
[Term]
id: GO:1904765
-name: positive regulation of transcription from RNA polymerase II promoter in response to maltose
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to maltose
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a maltose stimulus." [GO_REF:0000060, GOC:TermGenie, PMID:24224056]
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a maltose stimulus." [GO_REF:0000060, GOC:TermGenie, PMID:24224056]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "activation of global transcription from RNA polymerase II promoter involved in cellular response to maltose stimulus" RELATED [GOC:TermGenie]
synonym: "activation of transcription from RNA polymerase II promoter involved in cellular response to maltose stimulus" EXACT [GOC:TermGenie]
synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter involved in cellular response to maltose stimulus" RELATED [GOC:TermGenie]
@@ -499445,14 +502299,15 @@ synonym: "up-regulation of global transcription from RNA polymerase II promoter
synonym: "up-regulation of transcription from RNA polymerase II promoter involved in cellular response to maltose stimulus" EXACT [GOC:TermGenie]
synonym: "upregulation of global transcription from RNA polymerase II promoter involved in cellular response to maltose stimulus" RELATED [GOC:TermGenie]
synonym: "upregulation of transcription from RNA polymerase II promoter involved in cellular response to maltose stimulus" EXACT [GOC:TermGenie]
-is_a: GO:1901522 ! positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus
-relationship: part_of GO:0071328 ! cellular response to maltose stimulus
+is_obsolete: true
+replaced_by: GO:0045944
[Term]
id: GO:1904766
-name: negative regulation of macroautophagy by TORC1 signaling
+name: obsolete negative regulation of macroautophagy by TORC1 signaling
namespace: biological_process
-def: "A TORC1 signaling that results in negative regulation of macroautophagy." [GO_REF:0000063, GOC:autophagy, GOC:dph, GOC:TermGenie, PMID:23602450]
+def: "OBSOLETE. A TORC1 signaling that results in negative regulation of macroautophagy." [GO_REF:0000063, GOC:autophagy, GOC:dph, GOC:TermGenie, PMID:23602450]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "negative regulation of autophagy in response to cellular starvation by TORC1 signal transduction" EXACT [GOC:TermGenie]
synonym: "negative regulation of autophagy in response to cellular starvation by TORC1 signaling" EXACT [GOC:TermGenie]
synonym: "negative regulation of macroautophagy by TORC1 signal transduction" EXACT [GOC:TermGenie]
@@ -499460,8 +502315,7 @@ synonym: "negative regulation of non-specific autophagy by TORC1 signal transduc
synonym: "negative regulation of non-specific autophagy by TORC1 signaling" EXACT [GOC:TermGenie]
synonym: "negative regulation of starvation-induced autophagy by TORC1 signal transduction" EXACT [GOC:TermGenie]
synonym: "negative regulation of starvation-induced autophagy by TORC1 signaling" EXACT [GOC:TermGenie]
-is_a: GO:0016242 ! negative regulation of macroautophagy
-is_a: GO:0038202 ! TORC1 signaling
+is_obsolete: true
[Term]
id: GO:1904767
@@ -499470,7 +502324,6 @@ namespace: molecular_function
def: "Binding to octanoic acid." [GO_REF:0000067, GOC:kmv, GOC:TermGenie, PMID:19828452]
synonym: "caprylic acid binding" EXACT [CHEBI:28837]
is_a: GO:0005504 ! fatty acid binding
-is_a: GO:0043177 ! organic acid binding
[Term]
id: GO:1904768
@@ -499486,7 +502339,6 @@ namespace: molecular_function
def: "Binding to isopentadecanoic acid." [GO_REF:0000067, GOC:kmv, GOC:TermGenie, PMID:19828452]
synonym: "13-methylmyristic acid binding" EXACT [CHEBI:39250]
is_a: GO:0036041 ! long-chain fatty acid binding
-is_a: GO:0043177 ! organic acid binding
[Term]
id: GO:1904770
@@ -499748,7 +502600,6 @@ def: "Any process that modulates the frequency, rate or extent of protein locali
comment: An example is cdk-2 in C. elegans (UniProt ID O61847) in PMID:17115027 (inferred from mutant phenotype).
synonym: "regulation of protein localisation to centrosome" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0071539 ! protein localization to centrosome
[Term]
@@ -499766,7 +502617,6 @@ synonym: "downregulation of protein localization to centrosome" EXACT [GOC:TermG
synonym: "inhibition of protein localisation to centrosome" NARROW [GOC:TermGenie]
synonym: "inhibition of protein localization to centrosome" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to centrosome" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1904779 ! regulation of protein localization to centrosome
relationship: negatively_regulates GO:0071539 ! protein localization to centrosome
@@ -499786,7 +502636,6 @@ synonym: "up-regulation of protein localisation to centrosome" EXACT [GOC:TermGe
synonym: "up-regulation of protein localization to centrosome" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localisation to centrosome" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to centrosome" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1904779 ! regulation of protein localization to centrosome
relationship: positively_regulates GO:0071539 ! protein localization to centrosome
@@ -499810,9 +502659,9 @@ synonym: "inhibition of NMDA glutamate receptor activity" NARROW [GOC:TermGenie]
synonym: "inhibition of NMDA receptor" NARROW [GOC:TermGenie]
synonym: "negative regulation of N-methyl-D-aspartate selective glutamate receptor activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of NMDA receptor" EXACT [GOC:TermGenie]
+is_a: GO:0032413 ! negative regulation of ion transmembrane transporter activity
is_a: GO:2000272 ! negative regulation of signaling receptor activity
is_a: GO:2000310 ! regulation of NMDA receptor activity
-is_a: GO:2001258 ! negative regulation of cation channel activity
[Term]
id: GO:1904783
@@ -499833,9 +502682,9 @@ synonym: "up-regulation of NMDA receptor" EXACT [GOC:TermGenie]
synonym: "upregulation of N-methyl-D-aspartate selective glutamate receptor activity" EXACT [GOC:TermGenie]
synonym: "upregulation of NMDA glutamate receptor activity" EXACT [GOC:TermGenie]
synonym: "upregulation of NMDA receptor" EXACT [GOC:TermGenie]
+is_a: GO:0032414 ! positive regulation of ion transmembrane transporter activity
is_a: GO:2000273 ! positive regulation of signaling receptor activity
is_a: GO:2000310 ! regulation of NMDA receptor activity
-is_a: GO:2001259 ! positive regulation of cation channel activity
[Term]
id: GO:1904784
@@ -499846,7 +502695,7 @@ comment: The aggregation, arrangement and bonding together of a set of component
synonym: "NALP1 inflammasome complex assembly" EXACT [GOC:TermGenie]
synonym: "NALP1 inflammasome complex formation" EXACT [GOC:TermGenie]
synonym: "NLRP1 inflammasome complex formation" EXACT [GOC:TermGenie]
-is_a: GO:0140632 ! inflammasome complex assembly
+is_a: GO:0140632 ! canonical inflammasome complex assembly
[Term]
id: GO:1904785
@@ -500151,7 +503000,7 @@ name: RITS complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a RITS complex." [GO_REF:0000079, GOC:TermGenie, PMID:26443059]
synonym: "RITS complex formation" EXACT [GOC:TermGenie]
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
[Term]
id: GO:1904803
@@ -500292,7 +503141,6 @@ def: "Any process that modulates the frequency, rate or extent of protein locali
synonym: "regulation of protein localisation to chromosome, telomeric region" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization to telomere" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0070198 ! protein localization to chromosome, telomeric region
[Term]
@@ -500314,7 +503162,6 @@ synonym: "inhibition of protein localization to chromosome, telomeric region" NA
synonym: "inhibition of protein localization to telomere" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to chromosome, telomeric region" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization to telomere" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1904814 ! regulation of protein localization to chromosome, telomeric region
relationship: negatively_regulates GO:0070198 ! protein localization to chromosome, telomeric region
@@ -500338,7 +503185,6 @@ synonym: "up-regulation of protein localization to telomere" EXACT [GOC:TermGeni
synonym: "upregulation of protein localisation to chromosome, telomeric region" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to chromosome, telomeric region" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to telomere" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1904814 ! regulation of protein localization to chromosome, telomeric region
relationship: positively_regulates GO:0070198 ! protein localization to chromosome, telomeric region
@@ -501945,8 +504791,7 @@ name: transmembrane L-lysine transport from lysosomal lumen to cytosol
namespace: biological_process
def: "The directed movement of L-lysine from the lysosomal lumen across the lysosomal membrane and into the cytosol." [GO_REF:0000078, GOC:kmv, GOC:TermGenie, PMID:22822152]
is_a: GO:0007041 ! lysosomal transport
-is_a: GO:0034486 ! vacuolar transmembrane transport
-is_a: GO:1903401 ! L-lysine transmembrane transport
+is_a: GO:0089707 ! L-lysine transmembrane export from vacuole
[Term]
id: GO:1904917
@@ -501955,11 +504800,7 @@ namespace: biological_process
def: "The directed movement of L-arginine across a membrane from lysosomal lumen to cytosol." [GO_REF:0000078, GOC:kmv, GOC:TermGenie, PMID:22822152]
synonym: "transmembrane L-arginine transport from lysosomal lumen to cytosol" EXACT []
is_a: GO:0007041 ! lysosomal transport
-is_a: GO:0015807 ! L-amino acid transport
-is_a: GO:0034486 ! vacuolar transmembrane transport
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
-is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
+is_a: GO:1990818 ! L-arginine transmembrane export from vacuole
[Term]
id: GO:1904918
@@ -501967,7 +504808,7 @@ name: transmembrane L-histidine transport from lysosomal lumen to cytosol
namespace: biological_process
def: "The directed movement of L-histidine from the lysosomal lumen across the lysosomal membrane and into the cytosol." [GO_REF:0000078, GOC:kmv, GOC:TermGenie, PMID:22822152]
is_a: GO:0007041 ! lysosomal transport
-is_a: GO:0034486 ! vacuolar transmembrane transport
+is_a: GO:0032974 ! amino acid transmembrane export from vacuole
is_a: GO:0089709 ! L-histidine transmembrane transport
[Term]
@@ -501977,8 +504818,7 @@ namespace: biological_process
def: "The directed movement of L-cystine from the lysosomal lumen across the lysosomal membrane and into the cytosol." [GO_REF:0000078, GOC:kmv, GOC:TermGenie, PMID:22822152]
is_a: GO:0007041 ! lysosomal transport
is_a: GO:0015811 ! L-cystine transport
-is_a: GO:0034486 ! vacuolar transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0034489 ! neutral amino acid transmembrane export from vacuole
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
@@ -502579,7 +505419,6 @@ namespace: biological_process
def: "The process in which folic acid is transported from the cytosol into the mitochondrial matrix." [GO_REF:0000075, GOC:BHF, GOC:rph, GOC:TermGenie, PMID:15140890]
synonym: "folic acid import into mitochondrion" RELATED []
is_a: GO:0098838 ! folate transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1904948
@@ -502663,7 +505502,7 @@ id: GO:1904952
name: hydroxycinnamic acid transport
namespace: biological_process
def: "The directed movement of a hydroxycinnamic acid into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GO_REF:0000065, GOC:TermGenie, PMID:26744218]
-is_a: GO:0015849 ! organic acid transport
+is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:1904953
@@ -502918,7 +505757,7 @@ synonym: "regulation of indophenolase" NARROW [GOC:TermGenie]
synonym: "regulation of NADH cytochrome c oxidase" EXACT [GOC:TermGenie]
synonym: "regulation of warburg's respiratory enzyme activity" RELATED [GOC:TermGenie]
is_a: GO:0010155 ! regulation of proton transport
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
is_a: GO:1904732 ! regulation of electron transfer activity
[Term]
@@ -503421,11 +506260,7 @@ namespace: biological_process
def: "The process in which glycine is transported from the cytosol into the mitochondrial matrix." [GO_REF:0000078, GOC:TermGenie, PMID:26821380]
synonym: "transmembrane glycine transport from cytosol to mitochondrion" EXACT []
is_a: GO:0015816 ! glycine transport
-is_a: GO:0043090 ! amino acid import
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1904984
@@ -503843,8 +506678,6 @@ synonym: "regulation of L-lysine import into cell" EXACT []
synonym: "regulation of lysine import" BROAD []
synonym: "regulation of lysine uptake" EXACT [GOC:dph, GOC:tb]
is_a: GO:0010958 ! regulation of amino acid import across plasma membrane
-is_a: GO:1903959 ! regulation of anion transmembrane transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
relationship: regulates GO:0097639 ! L-lysine import across plasma membrane
[Term]
@@ -503860,9 +506693,8 @@ synonym: "inhibition of L-lysine import into cell" NARROW [GOC:TermGenie]
synonym: "negative regulation of L-lysine import into cell" EXACT []
synonym: "negative regulation of lysine import" BROAD []
synonym: "negative regulation of lysine uptake" EXACT [GOC:dph, GOC:tb]
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:0051956 ! negative regulation of amino acid transport
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
-is_a: GO:1904063 ! negative regulation of cation transmembrane transport
is_a: GO:1905008 ! regulation of L-lysine import across plasma membrane
relationship: negatively_regulates GO:0097639 ! L-lysine import across plasma membrane
@@ -503876,9 +506708,8 @@ synonym: "positive regulation of L-lysine import into cell" EXACT []
synonym: "up regulation of L-lysine import into cell" EXACT [GOC:TermGenie]
synonym: "up-regulation of L-lysine import into cell" EXACT [GOC:TermGenie]
synonym: "upregulation of L-lysine import into cell" EXACT [GOC:TermGenie]
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:0051957 ! positive regulation of amino acid transport
-is_a: GO:1903961 ! positive regulation of anion transmembrane transport
-is_a: GO:1904064 ! positive regulation of cation transmembrane transport
is_a: GO:1905008 ! regulation of L-lysine import across plasma membrane
relationship: positively_regulates GO:0097639 ! L-lysine import across plasma membrane
@@ -503898,8 +506729,9 @@ name: regulation of 'de novo' NAD biosynthetic process from tryptophan
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of 'de novo' NAD biosynthetic process from tryptophan." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:12140278, PMID:19843166]
synonym: "regulation of de novo NAD biosynthetic process from tryptophan" RELATED [GOC:TermGenie]
-is_a: GO:0030808 ! regulation of nucleotide biosynthetic process
is_a: GO:0090357 ! regulation of tryptophan metabolic process
+is_a: GO:1900371 ! regulation of purine nucleotide biosynthetic process
+is_a: GO:1902688 ! regulation of NAD metabolic process
relationship: regulates GO:0034354 ! 'de novo' NAD biosynthetic process from tryptophan
[Term]
@@ -503916,8 +506748,9 @@ synonym: "downregulation of de novo NAD biosynthetic process from tryptophan" RE
synonym: "inhibition of 'de novo' NAD biosynthetic process from tryptophan" NARROW [GOC:TermGenie]
synonym: "inhibition of de novo NAD biosynthetic process from tryptophan" RELATED [GOC:TermGenie]
synonym: "negative regulation of de novo NAD biosynthetic process from tryptophan" RELATED [GOC:TermGenie]
-is_a: GO:0030809 ! negative regulation of nucleotide biosynthetic process
is_a: GO:0045763 ! negative regulation of cellular amino acid metabolic process
+is_a: GO:1900372 ! negative regulation of purine nucleotide biosynthetic process
+is_a: GO:1902689 ! negative regulation of NAD metabolic process
is_a: GO:1905012 ! regulation of 'de novo' NAD biosynthetic process from tryptophan
relationship: negatively_regulates GO:0034354 ! 'de novo' NAD biosynthetic process from tryptophan
@@ -503935,8 +506768,9 @@ synonym: "up-regulation of 'de novo' NAD biosynthetic process from tryptophan" E
synonym: "up-regulation of de novo NAD biosynthetic process from tryptophan" RELATED [GOC:TermGenie]
synonym: "upregulation of 'de novo' NAD biosynthetic process from tryptophan" EXACT [GOC:TermGenie]
synonym: "upregulation of de novo NAD biosynthetic process from tryptophan" RELATED [GOC:TermGenie]
-is_a: GO:0030810 ! positive regulation of nucleotide biosynthetic process
is_a: GO:0090358 ! positive regulation of tryptophan metabolic process
+is_a: GO:1900373 ! positive regulation of purine nucleotide biosynthetic process
+is_a: GO:1902690 ! positive regulation of NAD metabolic process
is_a: GO:1905012 ! regulation of 'de novo' NAD biosynthetic process from tryptophan
relationship: positively_regulates GO:0034354 ! 'de novo' NAD biosynthetic process from tryptophan
@@ -504413,7 +507247,7 @@ relationship: positively_regulates GO:0086045 ! membrane depolarization during A
[Term]
id: GO:1905030
-name: voltage-gated ion channel activity involved in regulation of postsynaptic membrane potential
+name: voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential
namespace: molecular_function
def: "Any voltage-gated ion channel activity that is involved in regulation of postsynaptic membrane potential." [GO_REF:0000061, GOC:TermGenie, ISBN:9780071120005]
subset: goslim_synapse
@@ -504422,7 +507256,8 @@ synonym: "voltage gated ion channel activity involved in regulation of postsynap
synonym: "voltage-dependent ion channel activity involved in regulation of post-synaptic membrane potential" EXACT [GOC:TermGenie]
synonym: "voltage-dependent ion channel activity involved in regulation of postsynaptic membrane potential" EXACT [GOC:TermGenie]
synonym: "voltage-gated ion channel activity involved in regulation of post-synaptic membrane potential" EXACT [GOC:TermGenie]
-is_a: GO:0005244 ! voltage-gated ion channel activity
+synonym: "voltage-gated ion channel activity involved in regulation of postsynaptic membrane potential" BROAD []
+is_a: GO:0005244 ! voltage-gated monoatomic ion channel activity
[Term]
id: GO:1905031
@@ -504442,7 +507277,7 @@ synonym: "down regulation of membrane repolarization during cardiac muscle cell
synonym: "down-regulation of membrane repolarization during cardiac muscle cell action potential" EXACT [GOC:TermGenie]
synonym: "downregulation of membrane repolarization during cardiac muscle cell action potential" EXACT [GOC:TermGenie]
synonym: "inhibition of membrane repolarization during cardiac muscle cell action potential" NARROW [GOC:TermGenie]
-is_a: GO:0034766 ! negative regulation of ion transmembrane transport
+is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:1905031 ! regulation of membrane repolarization during cardiac muscle cell action potential
relationship: negatively_regulates GO:0086013 ! membrane repolarization during cardiac muscle cell action potential
@@ -504455,7 +507290,7 @@ synonym: "activation of membrane repolarization during cardiac muscle cell actio
synonym: "up regulation of membrane repolarization during cardiac muscle cell action potential" EXACT [GOC:TermGenie]
synonym: "up-regulation of membrane repolarization during cardiac muscle cell action potential" EXACT [GOC:TermGenie]
synonym: "upregulation of membrane repolarization during cardiac muscle cell action potential" EXACT [GOC:TermGenie]
-is_a: GO:0034767 ! positive regulation of ion transmembrane transport
+is_a: GO:0048518 ! positive regulation of biological process
is_a: GO:1905031 ! regulation of membrane repolarization during cardiac muscle cell action potential
relationship: positively_regulates GO:0086013 ! membrane repolarization during cardiac muscle cell action potential
@@ -504519,6 +507354,7 @@ id: GO:1905039
name: carboxylic acid transmembrane transport
namespace: biological_process
def: "The process in which carboxylic acid is transported across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:10869563]
+is_a: GO:0046942 ! carboxylic acid transport
is_a: GO:1903825 ! organic acid transmembrane transport
[Term]
@@ -504729,12 +507565,13 @@ is_a: GO:0048763 ! calcium-induced calcium release activity
[Term]
id: GO:1905055
-name: calcium:cation antiporter activity involved in regulation of presynaptic cytosolic calcium ion concentration
+name: calcium:monoatomic cation antiporter activity involved in regulation of presynaptic cytosolic calcium ion concentration
namespace: molecular_function
def: "Any calcium:cation antiporter activity that is involved in regulation of presynaptic cytosolic calcium ion concentration." [GO_REF:0000061, GOC:TermGenie, PMID:22972962, PMID:23255722]
subset: goslim_synapse
synonym: "calcium ion antiporter activity involved in regulation of presynaptic cytosolic calcium levels" EXACT syngo_official_label []
-is_a: GO:0015368 ! calcium:cation antiporter activity
+synonym: "calcium:cation antiporter activity involved in regulation of presynaptic cytosolic calcium ion concentration" BROAD []
+is_a: GO:0015368 ! calcium:monoatomic cation antiporter activity
[Term]
id: GO:1905056
@@ -504805,12 +507642,13 @@ is_a: GO:0005388 ! P-type calcium transporter activity
[Term]
id: GO:1905060
-name: calcium:cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration
+name: calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration
namespace: molecular_function
def: "Any calcium:cation antiporter activity that is involved in regulation of postsynaptic cytosolic calcium ion concentration." [GO_REF:0000061, GOC:TermGenie, PMID:18024055]
subset: goslim_synapse
+synonym: "calcium:cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration" BROAD []
synonym: "calcium:cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion levels" EXACT syngo_official_label []
-is_a: GO:0015368 ! calcium:cation antiporter activity
+is_a: GO:0015368 ! calcium:monoatomic cation antiporter activity
[Term]
id: GO:1905061
@@ -504994,9 +507832,10 @@ is_a: GO:0150147 ! cell-cell junction disassembly
id: GO:1905072
name: cardiac jelly development
namespace: biological_process
-def: "The process whose specific outcome is the progression of cardiac jelly over time, from its formation to the mature structure." [GO_REF:0000094, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:19703439]
+def: "The process whose specific outcome is the progression of cardiac jelly over time, from its formation to the mature structure. The cardiac jelly is an acellular gelatinous matrix secreted by the myocardium and plays a central role in the septation of the heart." [GO_REF:0000094, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:10645959, PMID:16314491, PMID:19703439]
synonym: "heart cardiac jelly development" EXACT [GOC:TermGenie]
is_a: GO:0009888 ! tissue development
+relationship: part_of GO:0007507 ! heart development
[Term]
id: GO:1905073
@@ -505440,13 +508279,14 @@ relationship: positively_regulates GO:0097314 ! apoptosome assembly
[Term]
id: GO:1905103
-name: integral component of lysosomal membrane
+name: obsolete integral component of lysosomal membrane
namespace: cellular_component
-def: "The component of the lysosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GO_REF:0000064, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:26134396]
+def: "OBSOLETE. The component of the lysosome membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GO_REF:0000064, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:26134396]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral component of lysosome membrane" EXACT [GOC:bf]
synonym: "integral to lysosomal membrane" NARROW []
-is_a: GO:0031166 ! integral component of vacuolar membrane
-relationship: part_of GO:0005765 ! lysosomal membrane
+is_obsolete: true
+replaced_by: GO:0005765
[Term]
id: GO:1905104
@@ -505939,7 +508779,6 @@ synonym: "downregulation of axonal protein transport" NARROW [GOC:TermGenie]
synonym: "inhibition of axo-dendritic protein transport" NARROW [GOC:TermGenie]
synonym: "inhibition of axonal protein transport" NARROW [GOC:TermGenie]
synonym: "negative regulation of axonal protein transport" NARROW [GOC:TermGenie]
-is_a: GO:0051271 ! negative regulation of cellular component movement
is_a: GO:0090317 ! negative regulation of intracellular protein transport
is_a: GO:1905126 ! regulation of axo-dendritic protein transport
relationship: negatively_regulates GO:0099640 ! axo-dendritic protein transport
@@ -505958,7 +508797,6 @@ synonym: "up-regulation of axo-dendritic protein transport" EXACT [GOC:TermGenie
synonym: "up-regulation of axonal protein transport" NARROW [GOC:TermGenie]
synonym: "upregulation of axo-dendritic protein transport" EXACT [GOC:TermGenie]
synonym: "upregulation of axonal protein transport" NARROW [GOC:TermGenie]
-is_a: GO:0051272 ! positive regulation of cellular component movement
is_a: GO:0090316 ! positive regulation of intracellular protein transport
is_a: GO:1905126 ! regulation of axo-dendritic protein transport
relationship: positively_regulates GO:0099640 ! axo-dendritic protein transport
@@ -505977,6 +508815,7 @@ id: GO:1905130
name: carcinine import across plasma membrane
namespace: biological_process
def: "The directed movement of carcinine from outside of a cell, across the plasma membrane and into the cytosol." [GO_REF:0000075, GOC:dph, GOC:TermGenie, PMID:26653853, PMID:26713872]
+is_a: GO:0015695 ! organic cation transport
is_a: GO:0042886 ! amide transport
is_a: GO:0045117 ! azole transmembrane transport
is_a: GO:0072337 ! modified amino acid transport
@@ -505988,6 +508827,7 @@ id: GO:1905131
name: carcinine transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of carcinine from one side of a membrane to the other." [GO_REF:0000070, GOC:dph, GOC:TermGenie, PMID:26653853, PMID:26713872]
+is_a: GO:0015101 ! organic cation transmembrane transporter activity
is_a: GO:0042887 ! amide transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
is_a: GO:1901474 ! azole transmembrane transporter activity
@@ -506062,7 +508902,6 @@ synonym: "biotin import" RELATED []
synonym: "biotin import into cell" EXACT []
is_a: GO:0015878 ! biotin transport
is_a: GO:0035461 ! vitamin transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:0098657 ! import into cell
is_a: GO:0098739 ! import across plasma membrane
is_a: GO:1905039 ! carboxylic acid transmembrane transport
@@ -506078,7 +508917,6 @@ synonym: "dethiobiotin import" RELATED []
synonym: "dethiobiotin import into cell" EXACT []
is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0042886 ! amide transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:0098657 ! import into cell
is_a: GO:0098739 ! import across plasma membrane
is_a: GO:1905039 ! carboxylic acid transmembrane transport
@@ -506198,17 +509036,18 @@ id: GO:1905144
name: response to acetylcholine
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetylcholine stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:21238497]
-is_a: GO:0010033 ! response to organic substance
-is_a: GO:1901698 ! response to nitrogen compound
+is_a: GO:0010243 ! response to organonitrogen compound
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1905145
name: cellular response to acetylcholine
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetylcholine stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:21238497]
-is_a: GO:1901699 ! cellular response to nitrogen compound
+is_a: GO:0071417 ! cellular response to organonitrogen compound
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
is_a: GO:1905144 ! response to acetylcholine
[Term]
@@ -506407,7 +509246,7 @@ id: GO:1905158
name: obsolete regulation of Factor XII activation
namespace: biological_process
def: "OBSOLETE. Any process that modulates the frequency, rate or extent of Factor XII activation." [GO_REF:0000058, GOC:TermGenie, PMID:617517]
-comment: This term was accidentally approved after TermGenie review. It should not have been approved.
+comment: This term was accidentally approved after TermGenie review. It should not have been approved.
synonym: "regulation of Hageman factor activation" EXACT [GOC:TermGenie]
is_obsolete: true
@@ -506416,7 +509255,7 @@ id: GO:1905159
name: obsolete negative regulation of Factor XII activation
namespace: biological_process
def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of Factor XII activation." [GO_REF:0000058, GOC:TermGenie, PMID:617517]
-comment: This term was accidentally approved after TermGenie review. It should not have been approved.
+comment: This term was accidentally approved after TermGenie review. It should not have been approved.
synonym: "down regulation of Factor XII activation" EXACT [GOC:TermGenie]
synonym: "down regulation of Hageman factor activation" EXACT [GOC:TermGenie]
synonym: "down-regulation of Factor XII activation" EXACT [GOC:TermGenie]
@@ -506433,7 +509272,7 @@ id: GO:1905160
name: obsolete positive regulation of Factor XII activation
namespace: biological_process
def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of Factor XII activation." [GO_REF:0000058, GOC:TermGenie, PMID:617517]
-comment: This term was accidentally approved after TermGenie review. It should not have been approved.
+comment: This term was accidentally approved after TermGenie review. It should not have been approved.
synonym: "activation of Factor XII activation" NARROW [GOC:TermGenie]
synonym: "activation of Hageman factor activation" NARROW [GOC:TermGenie]
synonym: "positive regulation of Hageman factor activation" EXACT [GOC:TermGenie]
@@ -506668,7 +509507,6 @@ synonym: "regulation of protein localisation to phagosome" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in phagocytic vesicle" EXACT [GOC:TermGenie]
synonym: "regulation of protein recruitment to phagosome" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:1905161 ! protein localization to phagocytic vesicle
[Term]
@@ -506705,7 +509543,6 @@ synonym: "negative regulation of protein localisation to phagocytic vesicle" EXA
synonym: "negative regulation of protein localisation to phagosome" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in phagocytic vesicle" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein recruitment to phagosome" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905169 ! regulation of protein localization to phagocytic vesicle
relationship: negatively_regulates GO:1905161 ! protein localization to phagocytic vesicle
@@ -506744,7 +509581,6 @@ synonym: "upregulation of protein localisation to phagosome" EXACT [GOC:TermGeni
synonym: "upregulation of protein localization in phagocytic vesicle" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to phagocytic vesicle" EXACT [GOC:TermGenie]
synonym: "upregulation of protein recruitment to phagosome" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905169 ! regulation of protein localization to phagocytic vesicle
relationship: positively_regulates GO:1905161 ! protein localization to phagocytic vesicle
@@ -507376,13 +510212,15 @@ is_a: GO:0009653 ! anatomical structure morphogenesis
[Term]
id: GO:1905224
-name: clathrin-coated pit assembly
+name: obsolete clathrin-coated pit assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form a clathrin-coated pit." [GO_REF:0000079, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:26589353]
+def: "OBSOLETE. The aggregation, arrangement and bonding together of a set of components to form a clathrin-coated pit." [GO_REF:0000079, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:26589353]
+comment: The reason for obsoletion is this term is describing a process similar to that of clathrin coat assembly.
synonym: "clathrin-coated pit formation" EXACT [GOC:TermGenie]
synonym: "coated pit assembly" EXACT [GOC:TermGenie]
synonym: "coated pit formation" EXACT [GOC:TermGenie]
-is_a: GO:0071709 ! membrane assembly
+is_obsolete: true
+replaced_by: GO:0048268
[Term]
id: GO:1905225
@@ -507460,6 +510298,7 @@ def: "Any process that results in a change in state or activity of a cell (in te
synonym: "cellular response to L-glutamate(1-)" RELATED []
is_a: GO:0071230 ! cellular response to amino acid stimulus
is_a: GO:1902065 ! response to L-glutamate
+is_a: GO:1902075 ! cellular response to salt
[Term]
id: GO:1905233
@@ -507585,6 +510424,7 @@ synonym: "response to Liothyronine" EXACT []
synonym: "response to Liothyroninum" EXACT []
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0043200 ! response to amino acid
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1905243
@@ -507596,6 +510436,7 @@ synonym: "cellular response to Liothyronine" EXACT []
synonym: "cellular response to Liothyroninum" EXACT []
is_a: GO:0071230 ! cellular response to amino acid stimulus
is_a: GO:0071407 ! cellular response to organic cyclic compound
+is_a: GO:1902075 ! cellular response to salt
is_a: GO:1905242 ! response to 3,3',5-triiodo-L-thyronine
[Term]
@@ -507921,20 +510762,27 @@ relationship: part_of GO:0008033 ! tRNA processing
id: GO:1905268
name: negative regulation of chromatin organization
namespace: biological_process
+alt_id: GO:0045798
alt_id: GO:1903309
def: "Any process that stops, prevents or reduces the frequency, rate or extent of chromatin organization." [GO_REF:0000058, GOC:pr, GOC:TermGenie, GOC:vw, PMID:654321]
+synonym: "down regulation of chromatin assembly or disassembly" RELATED []
synonym: "down regulation of chromatin organisation" EXACT [GOC:TermGenie]
synonym: "down regulation of chromatin organization" EXACT [GOC:TermGenie]
synonym: "down regulation of establishment or maintenance of chromatin architecture" EXACT [GOC:TermGenie]
+synonym: "down-regulation of chromatin assembly or disassembly" RELATED []
synonym: "down-regulation of chromatin organisation" EXACT [GOC:TermGenie]
synonym: "down-regulation of chromatin organization" EXACT [GOC:TermGenie]
synonym: "down-regulation of establishment or maintenance of chromatin architecture" EXACT [GOC:TermGenie]
+synonym: "downregulation of chromatin assembly or disassembly" RELATED []
synonym: "downregulation of chromatin organisation" EXACT [GOC:TermGenie]
synonym: "downregulation of chromatin organization" EXACT [GOC:TermGenie]
synonym: "downregulation of establishment or maintenance of chromatin architecture" EXACT [GOC:TermGenie]
+synonym: "inhibition of chromatin assembly or disassembly" NARROW []
synonym: "inhibition of chromatin organisation" NARROW [GOC:TermGenie]
synonym: "inhibition of chromatin organization" NARROW [GOC:TermGenie]
synonym: "inhibition of establishment or maintenance of chromatin architecture" NARROW [GOC:TermGenie]
+synonym: "negative regulation of chromatin assembly or disassembly" RELATED []
+synonym: "negative regulation of chromatin assembly/disassembly" EXACT []
synonym: "negative regulation of chromatin modification" RELATED []
synonym: "negative regulation of chromatin organisation" EXACT [GOC:TermGenie]
synonym: "negative regulation of establishment or maintenance of chromatin architecture" EXACT [GOC:TermGenie]
@@ -507946,20 +510794,28 @@ relationship: negatively_regulates GO:0006325 ! chromatin organization
id: GO:1905269
name: positive regulation of chromatin organization
namespace: biological_process
+alt_id: GO:0045799
alt_id: GO:1903310
def: "Any process that activates or increases the frequency, rate or extent of chromatin organization." [GO_REF:0000058, GOC:pr, GOC:TermGenie, GOC:vw, PMID:654321]
+synonym: "activation of chromatin assembly or disassembly" NARROW []
synonym: "activation of chromatin organisation" NARROW [GOC:TermGenie]
synonym: "activation of chromatin organization" NARROW [GOC:TermGenie]
synonym: "activation of establishment or maintenance of chromatin architecture" NARROW [GOC:TermGenie]
+synonym: "positive regulation of chromatin assembly or disassembly" RELATED []
+synonym: "positive regulation of chromatin assembly/disassembly" RELATED []
synonym: "positive regulation of chromatin modification" RELATED []
synonym: "positive regulation of chromatin organisation" EXACT [GOC:TermGenie]
synonym: "positive regulation of establishment or maintenance of chromatin architecture" EXACT [GOC:TermGenie]
+synonym: "stimulation of chromatin assembly or disassembly" NARROW []
+synonym: "up regulation of chromatin assembly or disassembly" RELATED []
synonym: "up regulation of chromatin organisation" EXACT [GOC:TermGenie]
synonym: "up regulation of chromatin organization" EXACT [GOC:TermGenie]
synonym: "up regulation of establishment or maintenance of chromatin architecture" EXACT [GOC:TermGenie]
+synonym: "up-regulation of chromatin assembly or disassembly" RELATED []
synonym: "up-regulation of chromatin organisation" EXACT [GOC:TermGenie]
synonym: "up-regulation of chromatin organization" EXACT [GOC:TermGenie]
synonym: "up-regulation of establishment or maintenance of chromatin architecture" EXACT [GOC:TermGenie]
+synonym: "upregulation of chromatin assembly or disassembly" EXACT []
synonym: "upregulation of chromatin organisation" EXACT [GOC:TermGenie]
synonym: "upregulation of chromatin organization" EXACT [GOC:TermGenie]
synonym: "upregulation of establishment or maintenance of chromatin architecture" EXACT [GOC:TermGenie]
@@ -508827,7 +511683,7 @@ name: telomerase holoenzyme complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a telomerase holoenzyme complex." [GO_REF:0000079, GOC:TermGenie, PMID:26305931]
synonym: "telomerase holoenzyme complex formation" EXACT [GOC:TermGenie]
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
[Term]
id: GO:1905324
@@ -509030,7 +511886,6 @@ comment: Q9H211 in Human in PMID:22581055
synonym: "regulation of condensin localization to kinetochore" NARROW [GOC:TermGenie]
synonym: "regulation of protein localisation to kinetochore" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0034501 ! protein localization to kinetochore
[Term]
@@ -509053,7 +511908,6 @@ synonym: "inhibition of protein localisation to kinetochore" NARROW [GOC:TermGen
synonym: "inhibition of protein localization to kinetochore" NARROW [GOC:TermGenie]
synonym: "negative regulation of condensin localization to kinetochore" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to kinetochore" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905340 ! regulation of protein localization to kinetochore
relationship: negatively_regulates GO:0034501 ! protein localization to kinetochore
@@ -509078,7 +511932,6 @@ synonym: "up-regulation of protein localization to kinetochore" EXACT [GOC:TermG
synonym: "upregulation of condensin localization to kinetochore" NARROW [GOC:TermGenie]
synonym: "upregulation of protein localisation to kinetochore" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to kinetochore" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905340 ! regulation of protein localization to kinetochore
relationship: positively_regulates GO:0034501 ! protein localization to kinetochore
@@ -509132,7 +511985,7 @@ def: "A protein complex which is capable of endodeoxyribonuclease activity." [GO
comment: An example of this is MUS81 in human (Q96NY9) in PMID:18413719 (inferred from direct assay).
synonym: "Mus81-Eme1 complex" NARROW []
synonym: "Mus81-Eme2 complex" NARROW []
-is_a: GO:1902494 ! catalytic complex
+is_a: GO:1905348 ! endonuclease complex
[Term]
id: GO:1905348
@@ -509594,6 +512447,7 @@ def: "Any process that modulates the frequency, rate or extent of snRNA transcri
synonym: "regulation of snRNA transcription from Pol II promoter" EXACT [GOC:TermGenie]
synonym: "regulation of snRNA transcription from RNA polymerase II promoter" EXACT []
is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
+is_a: GO:0140747 ! regulation of ncRNA transcription
relationship: regulates GO:0042795 ! snRNA transcription by RNA polymerase II
[Term]
@@ -510080,7 +512934,7 @@ id: GO:1905407
name: regulation of creatine transmembrane transporter activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of creatine transmembrane transporter activity." [GO_REF:0000059, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:25531585]
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
+is_a: GO:0022898 ! regulation of transmembrane transporter activity
[Term]
id: GO:1905408
@@ -510091,7 +512945,7 @@ synonym: "down regulation of creatine transmembrane transporter activity" EXACT
synonym: "down-regulation of creatine transmembrane transporter activity" EXACT [GOC:TermGenie]
synonym: "downregulation of creatine transmembrane transporter activity" EXACT [GOC:TermGenie]
synonym: "inhibition of creatine transmembrane transporter activity" NARROW [GOC:TermGenie]
-is_a: GO:0032413 ! negative regulation of ion transmembrane transporter activity
+is_a: GO:0032410 ! negative regulation of transporter activity
is_a: GO:1905407 ! regulation of creatine transmembrane transporter activity
[Term]
@@ -510103,7 +512957,7 @@ synonym: "activation of creatine transmembrane transporter activity" NARROW [GOC
synonym: "up regulation of creatine transmembrane transporter activity" EXACT [GOC:TermGenie]
synonym: "up-regulation of creatine transmembrane transporter activity" EXACT [GOC:TermGenie]
synonym: "upregulation of creatine transmembrane transporter activity" EXACT [GOC:TermGenie]
-is_a: GO:0032414 ! positive regulation of ion transmembrane transporter activity
+is_a: GO:0032411 ! positive regulation of transporter activity
is_a: GO:1905407 ! regulation of creatine transmembrane transporter activity
[Term]
@@ -511030,37 +513884,36 @@ relationship: positively_regulates GO:0099082 ! retrograde trans-synaptic signal
[Term]
id: GO:1905435
-name: regulation of histone H3-K4 trimethylation
+name: obsolete regulation of histone H3-K4 trimethylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone H3-K4 trimethylation." [GO_REF:0000058, GOC:TermGenie, PMID:27541139]
-is_a: GO:0051569 ! regulation of histone H3-K4 methylation
-relationship: regulates GO:0080182 ! histone H3-K4 trimethylation
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone H3-K4 trimethylation." [GO_REF:0000058, GOC:TermGenie, PMID:27541139]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0042800
[Term]
id: GO:1905436
-name: negative regulation of histone H3-K4 trimethylation
+name: obsolete negative regulation of histone H3-K4 trimethylation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K4 trimethylation." [GO_REF:0000058, GOC:TermGenie, PMID:27541139]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K4 trimethylation." [GO_REF:0000058, GOC:TermGenie, PMID:27541139]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of histone H3-K4 trimethylation" EXACT [GOC:TermGenie]
synonym: "down-regulation of histone H3-K4 trimethylation" EXACT [GOC:TermGenie]
synonym: "downregulation of histone H3-K4 trimethylation" EXACT [GOC:TermGenie]
synonym: "inhibition of histone H3-K4 trimethylation" NARROW [GOC:TermGenie]
-is_a: GO:0051572 ! negative regulation of histone H3-K4 methylation
-is_a: GO:1905435 ! regulation of histone H3-K4 trimethylation
-relationship: negatively_regulates GO:0080182 ! histone H3-K4 trimethylation
+is_obsolete: true
[Term]
id: GO:1905437
-name: positive regulation of histone H3-K4 trimethylation
+name: obsolete positive regulation of histone H3-K4 trimethylation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of histone H3-K4 trimethylation." [GO_REF:0000058, GOC:TermGenie, PMID:27541139]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of histone H3-K4 trimethylation." [GO_REF:0000058, GOC:TermGenie, PMID:27541139]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of histone H3-K4 trimethylation" NARROW [GOC:TermGenie]
synonym: "up regulation of histone H3-K4 trimethylation" EXACT [GOC:TermGenie]
synonym: "up-regulation of histone H3-K4 trimethylation" EXACT [GOC:TermGenie]
synonym: "upregulation of histone H3-K4 trimethylation" EXACT [GOC:TermGenie]
-is_a: GO:0051571 ! positive regulation of histone H3-K4 methylation
-is_a: GO:1905435 ! regulation of histone H3-K4 trimethylation
-relationship: positively_regulates GO:0080182 ! histone H3-K4 trimethylation
+is_obsolete: true
[Term]
id: GO:1905438
@@ -511100,15 +513953,15 @@ name: response to chondroitin 6'-sulfate
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chondroitin 6'-sulfate stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:22365850]
is_a: GO:0010243 ! response to organonitrogen compound
-is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:0034284 ! response to monosaccharide
[Term]
id: GO:1905440
name: cellular response to chondroitin 6'-sulfate
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chondroitin 6'-sulfate stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:22365850]
+is_a: GO:0071326 ! cellular response to monosaccharide stimulus
is_a: GO:0071417 ! cellular response to organonitrogen compound
-is_a: GO:1901701 ! cellular response to oxygen-containing compound
is_a: GO:1905439 ! response to chondroitin 6'-sulfate
[Term]
@@ -511117,15 +513970,15 @@ name: response to chondroitin 4'-sulfate
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chondroitin 4'-sulfate stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:22365850]
is_a: GO:0010243 ! response to organonitrogen compound
-is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:0034284 ! response to monosaccharide
[Term]
id: GO:1905442
name: cellular response to chondroitin 4'-sulfate
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chondroitin 4'-sulfate stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:22365850]
+is_a: GO:0071326 ! cellular response to monosaccharide stimulus
is_a: GO:0071417 ! cellular response to organonitrogen compound
-is_a: GO:1901701 ! cellular response to oxygen-containing compound
is_a: GO:1905441 ! response to chondroitin 4'-sulfate
[Term]
@@ -511555,21 +514408,22 @@ relationship: positively_regulates GO:0044806 ! G-quadruplex DNA unwinding
[Term]
id: GO:1905468
-name: regulation of clathrin-coated pit assembly
+name: obsolete regulation of clathrin-coated pit assembly
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of clathrin-coated pit assembly." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of clathrin-coated pit assembly." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie]
+comment: The reason for obsoletion is this term is describing a process similar to that of regulation of clathrin coat assembly.
synonym: "regulation of clathrin-coated pit formation" EXACT [GOC:TermGenie]
synonym: "regulation of coated pit assembly" EXACT [GOC:TermGenie]
synonym: "regulation of coated pit formation" EXACT [GOC:TermGenie]
-is_a: GO:0044087 ! regulation of cellular component biogenesis
-is_a: GO:0051128 ! regulation of cellular component organization
-relationship: regulates GO:1905224 ! clathrin-coated pit assembly
+is_obsolete: true
+replaced_by: GO:1905443
[Term]
id: GO:1905469
-name: negative regulation of clathrin-coated pit assembly
+name: obsolete negative regulation of clathrin-coated pit assembly
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of clathrin-coated pit assembly." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:26589353]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of clathrin-coated pit assembly." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:26589353]
+comment: The reason for obsoletion is this term is describing a process similar to that of negative regulation of clathrin coat assembly.
synonym: "down regulation of clathrin-coated pit assembly" EXACT [GOC:TermGenie]
synonym: "down regulation of clathrin-coated pit formation" EXACT [GOC:TermGenie]
synonym: "down regulation of coated pit assembly" EXACT [GOC:TermGenie]
@@ -511589,15 +514443,15 @@ synonym: "inhibition of coated pit formation" NARROW [GOC:TermGenie]
synonym: "negative regulation of clathrin-coated pit formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of coated pit assembly" EXACT [GOC:TermGenie]
synonym: "negative regulation of coated pit formation" EXACT [GOC:TermGenie]
-is_a: GO:0051129 ! negative regulation of cellular component organization
-is_a: GO:1905468 ! regulation of clathrin-coated pit assembly
-relationship: negatively_regulates GO:1905224 ! clathrin-coated pit assembly
+is_obsolete: true
+replaced_by: GO:1905444
[Term]
id: GO:1905470
-name: positive regulation of clathrin-coated pit assembly
+name: obsolete positive regulation of clathrin-coated pit assembly
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of clathrin-coated pit assembly." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of clathrin-coated pit assembly." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie]
+comment: The reason for obsoletion is this term is describing a process similar to that of positive regulation of clathrin coat assembly.
synonym: "activation of clathrin-coated pit assembly" NARROW [GOC:TermGenie]
synonym: "activation of clathrin-coated pit formation" NARROW [GOC:TermGenie]
synonym: "activation of coated pit assembly" NARROW [GOC:TermGenie]
@@ -511617,26 +514471,25 @@ synonym: "upregulation of clathrin-coated pit assembly" EXACT [GOC:TermGenie]
synonym: "upregulation of clathrin-coated pit formation" EXACT [GOC:TermGenie]
synonym: "upregulation of coated pit assembly" EXACT [GOC:TermGenie]
synonym: "upregulation of coated pit formation" EXACT [GOC:TermGenie]
-is_a: GO:0044089 ! positive regulation of cellular component biogenesis
-is_a: GO:0051130 ! positive regulation of cellular component organization
-is_a: GO:1905468 ! regulation of clathrin-coated pit assembly
-relationship: positively_regulates GO:1905224 ! clathrin-coated pit assembly
+is_obsolete: true
+replaced_by: GO:1905445
[Term]
id: GO:1905471
-name: regulation of histone H3-K79 dimethylation
+name: obsolete regulation of histone H3-K79 dimethylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone H3-K79 dimethylation." [GO_REF:0000058, GOC:TermGenie, PMID:27541139]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone H3-K79 dimethylation." [GO_REF:0000058, GOC:TermGenie, PMID:27541139]
+comment: This term was obsoleted because it represents regulation of a molecular function.
synonym: "regulation of histone H3 K79 dimethylation" EXACT [GOC:TermGenie]
synonym: "regulation of histone lysine H3 K79 dimethylation" EXACT [GOC:TermGenie]
-is_a: GO:2001160 ! regulation of histone H3-K79 methylation
-relationship: regulates GO:0097725 ! histone H3-K79 dimethylation
+is_obsolete: true
[Term]
id: GO:1905472
-name: negative regulation of histone H3-K79 dimethylation
+name: obsolete negative regulation of histone H3-K79 dimethylation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K79 dimethylation." [GO_REF:0000058, GOC:TermGenie, PMID:27541139]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K79 dimethylation." [GO_REF:0000058, GOC:TermGenie, PMID:27541139]
+comment: This term was obsoleted because it represents regulation of a molecular function.
synonym: "down regulation of histone H3 K79 dimethylation" EXACT [GOC:TermGenie]
synonym: "down regulation of histone H3-K79 dimethylation" EXACT [GOC:TermGenie]
synonym: "down regulation of histone lysine H3 K79 dimethylation" EXACT [GOC:TermGenie]
@@ -511651,15 +514504,14 @@ synonym: "inhibition of histone H3-K79 dimethylation" NARROW [GOC:TermGenie]
synonym: "inhibition of histone lysine H3 K79 dimethylation" NARROW [GOC:TermGenie]
synonym: "negative regulation of histone H3 K79 dimethylation" EXACT [GOC:TermGenie]
synonym: "negative regulation of histone lysine H3 K79 dimethylation" EXACT [GOC:TermGenie]
-is_a: GO:1905471 ! regulation of histone H3-K79 dimethylation
-is_a: GO:2001161 ! negative regulation of histone H3-K79 methylation
-relationship: negatively_regulates GO:0097725 ! histone H3-K79 dimethylation
+is_obsolete: true
[Term]
id: GO:1905473
-name: positive regulation of histone H3-K79 dimethylation
+name: obsolete positive regulation of histone H3-K79 dimethylation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of histone H3-K79 dimethylation." [GO_REF:0000058, GOC:TermGenie, PMID:27541139]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of histone H3-K79 dimethylation." [GO_REF:0000058, GOC:TermGenie, PMID:27541139]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of histone H3 K79 dimethylation" NARROW [GOC:TermGenie]
synonym: "activation of histone H3-K79 dimethylation" NARROW [GOC:TermGenie]
synonym: "activation of histone lysine H3 K79 dimethylation" NARROW [GOC:TermGenie]
@@ -511674,9 +514526,8 @@ synonym: "up-regulation of histone lysine H3 K79 dimethylation" EXACT [GOC:TermG
synonym: "upregulation of histone H3 K79 dimethylation" EXACT [GOC:TermGenie]
synonym: "upregulation of histone H3-K79 dimethylation" EXACT [GOC:TermGenie]
synonym: "upregulation of histone lysine H3 K79 dimethylation" EXACT [GOC:TermGenie]
-is_a: GO:1905471 ! regulation of histone H3-K79 dimethylation
-is_a: GO:2001162 ! positive regulation of histone H3-K79 methylation
-relationship: positively_regulates GO:0097725 ! histone H3-K79 dimethylation
+is_obsolete: true
+consider: GO:0140673
[Term]
id: GO:1905474
@@ -511700,7 +514551,6 @@ def: "Any process that modulates the frequency, rate or extent of protein locali
synonym: "regulation of protein localisation in membrane" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in membrane" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0072657 ! protein localization to membrane
[Term]
@@ -511722,7 +514572,6 @@ synonym: "inhibition of protein localization in membrane" NARROW [GOC:TermGenie]
synonym: "inhibition of protein localization to membrane" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation in membrane" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in membrane" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905475 ! regulation of protein localization to membrane
relationship: negatively_regulates GO:0072657 ! protein localization to membrane
@@ -511746,7 +514595,6 @@ synonym: "up-regulation of protein localization to membrane" EXACT [GOC:TermGeni
synonym: "upregulation of protein localisation in membrane" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization in membrane" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to membrane" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905475 ! regulation of protein localization to membrane
relationship: positively_regulates GO:0072657 ! protein localization to membrane
@@ -512143,7 +514991,6 @@ name: acetyl-CoA binding
namespace: molecular_function
def: "Binding to acetyl-CoA, an acyl-CoA having acetyl as its S-acetyl component." [GO_REF:0000067, GOC:bc, GOC:krc, GOC:PARL, GOC:TermGenie, PMID:24927529]
synonym: "acetyl-coenzyme A binding" EXACT []
-is_a: GO:0043168 ! anion binding
is_a: GO:0120227 ! acyl-CoA binding
[Term]
@@ -512785,7 +515632,7 @@ name: polysome binding
namespace: molecular_function
def: "Binding to a polysome." [GOC:bc, GOC:PARL, GOC:TermGenie, PMID:18426977]
synonym: "polyribosome binding" EXACT [GOC:TermGenie]
-is_a: GO:0043021 ! ribonucleoprotein complex binding
+is_a: GO:0043022 ! ribosome binding
[Term]
id: GO:1905539
@@ -512819,8 +515666,6 @@ def: "Any process that modulates the frequency, rate or extent of L-arginine imp
synonym: "regulation of L-arginine import" BROAD []
synonym: "regulation of L-arginine import into cell" EXACT []
is_a: GO:0010958 ! regulation of amino acid import across plasma membrane
-is_a: GO:1903959 ! regulation of anion transmembrane transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
relationship: regulates GO:0097638 ! L-arginine import across plasma membrane
[Term]
@@ -512833,9 +515678,8 @@ synonym: "down regulation of L-arginine import into cell" EXACT [GOC:TermGenie]
synonym: "downregulation of L-arginine import into cell" EXACT [GOC:TermGenie]
synonym: "inhibition of L-arginine import into cell" NARROW [GOC:TermGenie]
synonym: "negative regulation of L-arginine import into cell" EXACT []
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:0051956 ! negative regulation of amino acid transport
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
-is_a: GO:1904063 ! negative regulation of cation transmembrane transport
is_a: GO:1905541 ! regulation of L-arginine import across plasma membrane
relationship: negatively_regulates GO:0097638 ! L-arginine import across plasma membrane
@@ -513142,7 +515986,6 @@ synonym: "regulation of protein localisation in endoplasmic reticulum" EXACT [GO
synonym: "regulation of protein localization in endoplasmic reticulum" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in ER" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0070972 ! protein localization to endoplasmic reticulum
[Term]
@@ -513169,7 +516012,6 @@ synonym: "inhibition of protein localization to endoplasmic reticulum" NARROW [G
synonym: "negative regulation of protein localisation in endoplasmic reticulum" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in endoplasmic reticulum" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in ER" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905550 ! regulation of protein localization to endoplasmic reticulum
relationship: negatively_regulates GO:0070972 ! protein localization to endoplasmic reticulum
@@ -513198,7 +516040,6 @@ synonym: "upregulation of protein localisation in endoplasmic reticulum" EXACT [
synonym: "upregulation of protein localization in endoplasmic reticulum" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization in ER" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to endoplasmic reticulum" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905550 ! regulation of protein localization to endoplasmic reticulum
relationship: positively_regulates GO:0070972 ! protein localization to endoplasmic reticulum
@@ -513339,6 +516180,7 @@ relationship: positively_regulates GO:0007077 ! mitotic nuclear membrane disasse
id: GO:1905560
name: negative regulation of kinetochore assembly
namespace: biological_process
+alt_id: GO:1901720
def: "Any process that stops, prevents or reduces the frequency, rate or extent of kinetochore assembly." [GO_REF:0000058, GOC:TermGenie, PMID:18765790]
synonym: "down regulation of centromere and kinetochore complex maturation" NARROW [GOC:TermGenie]
synonym: "down regulation of centromere/kinetochore complex maturation" NARROW [GOC:TermGenie]
@@ -513365,6 +516207,7 @@ synonym: "negative regulation of centromere and kinetochore complex maturation"
synonym: "negative regulation of centromere/kinetochore complex maturation" NARROW [GOC:TermGenie]
synonym: "negative regulation of chromosome-kinetochore attachment" NARROW [GOC:TermGenie]
synonym: "negative regulation of kinetochore formation" RELATED [GOC:TermGenie]
+synonym: "negative regulation of NMS complex assembly" NARROW []
is_a: GO:0031333 ! negative regulation of protein-containing complex assembly
is_a: GO:0090234 ! regulation of kinetochore assembly
is_a: GO:1902116 ! negative regulation of organelle assembly
@@ -513375,6 +516218,7 @@ relationship: negatively_regulates GO:0051382 ! kinetochore assembly
id: GO:1905561
name: positive regulation of kinetochore assembly
namespace: biological_process
+alt_id: GO:1901721
def: "Any process that activates or increases the frequency, rate or extent of kinetochore assembly." [GO_REF:0000058, GOC:TermGenie, PMID:18765790]
synonym: "activation of centromere and kinetochore complex maturation" NARROW [GOC:TermGenie]
synonym: "activation of centromere/kinetochore complex maturation" NARROW [GOC:TermGenie]
@@ -513385,6 +516229,7 @@ synonym: "positive regulation of centromere and kinetochore complex maturation"
synonym: "positive regulation of centromere/kinetochore complex maturation" NARROW [GOC:TermGenie]
synonym: "positive regulation of chromosome-kinetochore attachment" NARROW [GOC:TermGenie]
synonym: "positive regulation of kinetochore formation" RELATED [GOC:TermGenie]
+synonym: "positive regulation of NMS complex assembly" NARROW []
synonym: "up regulation of centromere and kinetochore complex maturation" NARROW [GOC:TermGenie]
synonym: "up regulation of centromere/kinetochore complex maturation" NARROW [GOC:TermGenie]
synonym: "up regulation of chromosome-kinetochore attachment" NARROW [GOC:TermGenie]
@@ -513864,9 +516709,8 @@ synonym: "up-regulation of L-arginine uptake" EXACT [GOC:TermGenie]
synonym: "upregulation of L-arginine import" EXACT [GOC:TermGenie]
synonym: "upregulation of L-arginine import into cell" EXACT [GOC:TermGenie]
synonym: "upregulation of L-arginine uptake" EXACT [GOC:TermGenie]
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:0051957 ! positive regulation of amino acid transport
-is_a: GO:1903961 ! positive regulation of anion transmembrane transport
-is_a: GO:1904064 ! positive regulation of cation transmembrane transport
is_a: GO:1905541 ! regulation of L-arginine import across plasma membrane
relationship: positively_regulates GO:0097638 ! L-arginine import across plasma membrane
@@ -514280,9 +517124,10 @@ relationship: positively_regulates GO:0080186 ! developmental vegetative growth
[Term]
id: GO:1905616
-name: regulation of miRNA-mediated gene silencing by inhibition of translation
+name: obsolete regulation of miRNA-mediated gene silencing by inhibition of translation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of miRNA-mediated gene silencing by inhibition of translation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23409027]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of miRNA-mediated gene silencing by inhibition of translation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23409027]
+comment: This term was obsoleted because it represents regulation of a regulatory process and has been used incorrectly
synonym: "regulation of down regulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
synonym: "regulation of down-regulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
synonym: "regulation of downregulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
@@ -514291,15 +517136,16 @@ synonym: "regulation of inhibition of translation involved in gene silencing by
synonym: "regulation of miRNA mediated inhibition of translation" EXACT []
synonym: "regulation of miRNA-mediated gene silencing, negative regulation of translation" RELATED [GOC:TermGenie]
synonym: "regulation of negative regulation of translation involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
-is_a: GO:0006417 ! regulation of translation
-is_a: GO:0060964 ! regulation of gene silencing by miRNA
-relationship: regulates GO:0035278 ! miRNA-mediated gene silencing by inhibition of translation
+is_obsolete: true
+consider: GO:0035278
+consider: GO:0060964
[Term]
id: GO:1905617
-name: negative regulation of miRNA-mediated gene silencing by inhibition of translation
+name: obsolete negative regulation of miRNA-mediated gene silencing by inhibition of translation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of miRNA-mediated gene silencing by inhibition of translation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23409027]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of miRNA-mediated gene silencing by inhibition of translation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23409027]
+comment: This term was obsoleted because it represents regulation of a regulatory process and has been used incorrectly
synonym: "down regulation of down regulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
synonym: "down regulation of down-regulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
synonym: "down regulation of downregulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
@@ -514340,16 +517186,16 @@ synonym: "negative regulation of inhibition of translation involved in gene sile
synonym: "negative regulation of miRNA mediated inhibition of translation" EXACT []
synonym: "negative regulation of miRNA-mediated gene silencing, negative regulation of translation" RELATED [GOC:TermGenie]
synonym: "negative regulation of negative regulation of translation involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
-is_a: GO:0045727 ! positive regulation of translation
-is_a: GO:0060965 ! negative regulation of gene silencing by miRNA
-is_a: GO:1905616 ! regulation of miRNA-mediated gene silencing by inhibition of translation
-relationship: negatively_regulates GO:0035278 ! miRNA-mediated gene silencing by inhibition of translation
+is_obsolete: true
+consider: GO:0035278
+consider: GO:0060965
[Term]
id: GO:1905618
-name: positive regulation of miRNA-mediated gene silencing by inhibition of translation
+name: obsolete positive regulation of miRNA-mediated gene silencing by inhibition of translation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of miRNA-mediated gene silencing by inhibition of translation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23409027]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of miRNA-mediated gene silencing by inhibition of translation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23409027]
+comment: This term was obsoleted because it represents regulation of a regulatory process and has been used incorrectly
synonym: "activation of down regulation of translation involved in gene silencing by miRNA" NARROW [GOC:TermGenie]
synonym: "activation of down-regulation of translation involved in gene silencing by miRNA" NARROW [GOC:TermGenie]
synonym: "activation of downregulation of translation involved in gene silencing by miRNA" NARROW [GOC:TermGenie]
@@ -514390,9 +517236,9 @@ synonym: "upregulation of inhibition of translation involved in gene silencing b
synonym: "upregulation of miRNA mediated inhibition of translation" EXACT [GOC:TermGenie]
synonym: "upregulation of miRNA-mediated gene silencing, negative regulation of translation" RELATED [GOC:TermGenie]
synonym: "upregulation of negative regulation of translation involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
-is_a: GO:1905616 ! regulation of miRNA-mediated gene silencing by inhibition of translation
-is_a: GO:2000637 ! positive regulation of gene silencing by miRNA
-relationship: positively_regulates GO:0035278 ! miRNA-mediated gene silencing by inhibition of translation
+is_obsolete: true
+consider: GO:0035278
+consider: GO:2000637
[Term]
id: GO:1905619
@@ -514493,8 +517339,6 @@ name: regulation of L-methionine import across plasma membrane
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of L-methionine import across plasma membrane." [GO_REF:0000058, GOC:TermGenie, PMID:17556368]
is_a: GO:0010958 ! regulation of amino acid import across plasma membrane
-is_a: GO:1903959 ! regulation of anion transmembrane transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
relationship: regulates GO:1905544 ! L-methionine import across plasma membrane
[Term]
@@ -514502,9 +517346,8 @@ id: GO:1905625
name: negative regulation of L-methionine import across plasma membrane
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of L-methionine import across plasma membrane." [GO_REF:0000058, GOC:TermGenie, PMID:17556368]
+is_a: GO:0034763 ! negative regulation of transmembrane transport
is_a: GO:0051956 ! negative regulation of amino acid transport
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
-is_a: GO:1904063 ! negative regulation of cation transmembrane transport
is_a: GO:1905624 ! regulation of L-methionine import across plasma membrane
relationship: negatively_regulates GO:1905544 ! L-methionine import across plasma membrane
@@ -514513,9 +517356,8 @@ id: GO:1905626
name: positive regulation of L-methionine import across plasma membrane
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of L-methionine import across plasma membrane." [GO_REF:0000058, GOC:TermGenie, PMID:17556368]
+is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:0051957 ! positive regulation of amino acid transport
-is_a: GO:1903961 ! positive regulation of anion transmembrane transport
-is_a: GO:1904064 ! positive regulation of cation transmembrane transport
is_a: GO:1905624 ! regulation of L-methionine import across plasma membrane
relationship: positively_regulates GO:1905544 ! L-methionine import across plasma membrane
@@ -514643,7 +517485,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to chromatin." [GO_REF:0000058, GOC:TermGenie, PMID:20889714]
synonym: "regulation of protein localisation to chromatin" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0071168 ! protein localization to chromatin
[Term]
@@ -515006,8 +517847,6 @@ name: regulation of calcium ion import across plasma membrane
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of calcium ion import across plasma membrane." [GO_REF:0000058, GOC:bhm, GOC:TermGenie, PMID:17640527]
comment: An example of this is PPP3CA in human (Q08209) in 17640527 (inferred from direct assay).
-is_a: GO:0010522 ! regulation of calcium ion transport into cytosol
-is_a: GO:0090279 ! regulation of calcium ion import
is_a: GO:1903169 ! regulation of calcium ion transmembrane transport
relationship: regulates GO:0098703 ! calcium ion import across plasma membrane
@@ -515021,8 +517860,6 @@ synonym: "activation of calcium ion import across plasma membrane" NARROW [GOC:T
synonym: "up regulation of calcium ion import across plasma membrane" EXACT [GOC:TermGenie]
synonym: "up-regulation of calcium ion import across plasma membrane" EXACT [GOC:TermGenie]
synonym: "upregulation of calcium ion import across plasma membrane" EXACT [GOC:TermGenie]
-is_a: GO:0010524 ! positive regulation of calcium ion transport into cytosol
-is_a: GO:0090280 ! positive regulation of calcium ion import
is_a: GO:1904427 ! positive regulation of calcium ion transmembrane transport
is_a: GO:1905664 ! regulation of calcium ion import across plasma membrane
relationship: positively_regulates GO:0098703 ! calcium ion import across plasma membrane
@@ -515035,7 +517872,6 @@ def: "Any process that modulates the frequency, rate or extent of protein locali
synonym: "regulation of protein localisation in endosome" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in endosome" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0036010 ! protein localization to endosome
[Term]
@@ -515057,7 +517893,6 @@ synonym: "inhibition of protein localization in endosome" NARROW [GOC:TermGenie]
synonym: "inhibition of protein localization to endosome" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation in endosome" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in endosome" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905666 ! regulation of protein localization to endosome
relationship: negatively_regulates GO:0036010 ! protein localization to endosome
@@ -515081,7 +517916,6 @@ synonym: "up-regulation of protein localization to endosome" EXACT [GOC:TermGeni
synonym: "upregulation of protein localisation in endosome" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization in endosome" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to endosome" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905666 ! regulation of protein localization to endosome
relationship: positively_regulates GO:0036010 ! protein localization to endosome
@@ -515340,7 +518174,7 @@ synonym: "regulation of DGK activity" EXACT [GOC:TermGenie]
synonym: "regulation of diacylglycerol:ATP kinase activity" NARROW [GOC:TermGenie]
synonym: "regulation of diglyceride kinase activity" EXACT [GOC:TermGenie]
synonym: "regulation of sn-1,2-diacylglycerol kinase activity" EXACT [GOC:TermGenie]
-is_a: GO:0043549 ! regulation of kinase activity
+is_a: GO:0043550 ! regulation of lipid kinase activity
[Term]
id: GO:1905688
@@ -515406,7 +518240,7 @@ synonym: "negative regulation of DGK activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of diacylglycerol:ATP kinase activity" NARROW [GOC:TermGenie]
synonym: "negative regulation of diglyceride kinase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of sn-1,2-diacylglycerol kinase activity" EXACT [GOC:TermGenie]
-is_a: GO:0033673 ! negative regulation of kinase activity
+is_a: GO:0090219 ! negative regulation of lipid kinase activity
is_a: GO:1905687 ! regulation of diacylglycerol kinase activity
[Term]
@@ -515473,7 +518307,7 @@ synonym: "upregulation of diacylglycerol kinase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of diacylglycerol:ATP kinase activity" NARROW [GOC:TermGenie]
synonym: "upregulation of diglyceride kinase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of sn-1,2-diacylglycerol kinase activity" EXACT [GOC:TermGenie]
-is_a: GO:0033674 ! positive regulation of kinase activity
+is_a: GO:0090218 ! positive regulation of lipid kinase activity
is_a: GO:1905687 ! regulation of diacylglycerol kinase activity
[Term]
@@ -515515,6 +518349,7 @@ synonym: "regulation of phosphatidic acid anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of phosphatidic acid biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of phosphatidic acid formation" EXACT [GOC:TermGenie]
synonym: "regulation of phosphatidic acid synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0071071 ! regulation of phospholipid biosynthetic process
relationship: regulates GO:0006654 ! phosphatidic acid biosynthetic process
@@ -515547,6 +518382,7 @@ synonym: "negative regulation of phosphatidic acid anabolism" EXACT [GOC:TermGen
synonym: "negative regulation of phosphatidic acid biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of phosphatidic acid formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of phosphatidic acid synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
is_a: GO:0071072 ! negative regulation of phospholipid biosynthetic process
is_a: GO:1905693 ! regulation of phosphatidic acid biosynthetic process
relationship: negatively_regulates GO:0006654 ! phosphatidic acid biosynthetic process
@@ -515580,6 +518416,7 @@ synonym: "upregulation of phosphatidic acid biosynthesis" EXACT [GOC:TermGenie]
synonym: "upregulation of phosphatidic acid biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of phosphatidic acid formation" EXACT [GOC:TermGenie]
synonym: "upregulation of phosphatidic acid synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:0071073 ! positive regulation of phospholipid biosynthetic process
is_a: GO:1905693 ! regulation of phosphatidic acid biosynthetic process
relationship: positively_regulates GO:0006654 ! phosphatidic acid biosynthetic process
@@ -515716,32 +518553,29 @@ relationship: positively_regulates GO:1904862 ! inhibitory synapse assembly
[Term]
id: GO:1905705
-name: cellular response to paclitaxel
+name: obsolete cellular response to paclitaxel
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a paclitaxel stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:18472094]
-is_a: GO:0071396 ! cellular response to lipid
-is_a: GO:1901555 ! response to paclitaxel
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a paclitaxel stimulus." [GO_REF:0000071, GOC:TermGenie, PMID:18472094]
+comment: This term was obsoleted because it represents a response to xenobiotic stimulus, and GO terms are not created for every xenobiotic.
+is_obsolete: true
+replaced_by: GO:0009410
[Term]
id: GO:1905706
name: regulation of mitochondrial ATP synthesis coupled proton transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of mitochondrial ATP synthesis coupled proton transport." [GO_REF:0000058, GOC:TermGenie, PMID:12809520, PMID:15294286]
-is_a: GO:0010155 ! regulation of proton transport
-is_a: GO:0032386 ! regulation of intracellular transport
is_a: GO:2001169 ! regulation of ATP biosynthetic process
-relationship: regulates GO:0042776 ! mitochondrial ATP synthesis coupled proton transport
+relationship: regulates GO:0042776 ! proton motive force-driven mitochondrial ATP synthesis
[Term]
id: GO:1905707
name: negative regulation of mitochondrial ATP synthesis coupled proton transport
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of mitochondrial ATP synthesis coupled proton transport." [GO_REF:0000058, GOC:TermGenie, PMID:12809520, PMID:15294286]
-is_a: GO:0032387 ! negative regulation of intracellular transport
-is_a: GO:1904063 ! negative regulation of cation transmembrane transport
is_a: GO:1905706 ! regulation of mitochondrial ATP synthesis coupled proton transport
is_a: GO:2001170 ! negative regulation of ATP biosynthetic process
-relationship: negatively_regulates GO:0042776 ! mitochondrial ATP synthesis coupled proton transport
+relationship: negatively_regulates GO:0042776 ! proton motive force-driven mitochondrial ATP synthesis
[Term]
id: GO:1905708
@@ -515988,8 +518822,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of L-proline import across plasma membrane." [GO_REF:0000058, GOC:TermGenie, PMID:24344203]
is_a: GO:0070881 ! regulation of proline transport
is_a: GO:1902834 ! regulation of proline import across plasma membrane
-is_a: GO:1903959 ! regulation of anion transmembrane transport
-is_a: GO:1904062 ! regulation of cation transmembrane transport
relationship: regulates GO:1904271 ! L-proline import across plasma membrane
[Term]
@@ -515998,8 +518830,6 @@ name: negative regulation of L-proline import across plasma membrane
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of L-proline import across plasma membrane." [GO_REF:0000058, GOC:TermGenie, PMID:24344203]
is_a: GO:1902835 ! negative regulation of proline import across plasma membrane
-is_a: GO:1903960 ! negative regulation of anion transmembrane transport
-is_a: GO:1904063 ! negative regulation of cation transmembrane transport
is_a: GO:1905735 ! regulation of L-proline import across plasma membrane
relationship: negatively_regulates GO:1904271 ! L-proline import across plasma membrane
@@ -516009,8 +518839,6 @@ name: positive regulation of L-proline import across plasma membrane
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of L-proline import across plasma membrane." [GO_REF:0000058, GOC:TermGenie, PMID:24344203]
is_a: GO:1902836 ! positive regulation of proline import across plasma membrane
-is_a: GO:1903961 ! positive regulation of anion transmembrane transport
-is_a: GO:1904064 ! positive regulation of cation transmembrane transport
is_a: GO:1905735 ! regulation of L-proline import across plasma membrane
relationship: positively_regulates GO:1904271 ! L-proline import across plasma membrane
@@ -516021,8 +518849,9 @@ namespace: biological_process
def: "Any mitochondrial calcium release that is involved in positive regulation of presynaptic cytosolic calcium concentration." [GO_REF:0000060, GOC:TermGenie, PMID:26644474]
synonym: "calcium ion transmembrane export from mitochondrion involved in positive regulation of presynaptic cytosolic calcium concentration" EXACT [GOC:TermGenie]
synonym: "mitochondrial calcium release involved in positive regulation of presynaptic cytosolic calcium concentration" EXACT []
+is_a: GO:0051649 ! establishment of localization in cell
is_a: GO:0099093 ! calcium export from the mitochondrion
-is_a: GO:0099533 ! positive regulation of presynaptic cytosolic calcium concentration
+relationship: part_of GO:0099533 ! positive regulation of presynaptic cytosolic calcium concentration
[Term]
id: GO:1905742
@@ -516807,6 +519636,7 @@ def: "Any process that results in a change in state or activity of a cell or an
synonym: "response to 3'-deoxy-N,N-dimethyl-3'-(O-methyl-L-tyrosinamido)adenosine" EXACT []
is_a: GO:0014074 ! response to purine-containing compound
is_a: GO:1901700 ! response to oxygen-containing compound
+is_a: GO:1902074 ! response to salt
[Term]
id: GO:1905795
@@ -516817,6 +519647,7 @@ synonym: "cellular response to 3'-deoxy-N,N-dimethyl-3'-(O-methyl-L-tyrosinamido
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0071417 ! cellular response to organonitrogen compound
is_a: GO:1901701 ! cellular response to oxygen-containing compound
+is_a: GO:1902075 ! cellular response to salt
is_a: GO:1905794 ! response to puromycin
[Term]
@@ -516844,7 +519675,6 @@ synonym: "inhibition of intraciliary anterograde transport" NARROW [GOC:TermGeni
synonym: "inhibition of intraflagellar anterograde transport" NARROW [GOC:TermGenie]
synonym: "negative regulation of intraflagellar anterograde transport" EXACT [GOC:TermGenie]
is_a: GO:0032387 ! negative regulation of intracellular transport
-is_a: GO:0051271 ! negative regulation of cellular component movement
is_a: GO:1905796 ! regulation of intraciliary anterograde transport
relationship: negatively_regulates GO:0035720 ! intraciliary anterograde transport
@@ -516864,7 +519694,6 @@ synonym: "upregulation of intraciliary anterograde transport" EXACT [GOC:TermGen
synonym: "upregulation of intraflagellar anterograde transport" EXACT [GOC:TermGenie]
is_a: GO:0010638 ! positive regulation of organelle organization
is_a: GO:0032388 ! positive regulation of intracellular transport
-is_a: GO:0051272 ! positive regulation of cellular component movement
is_a: GO:1905796 ! regulation of intraciliary anterograde transport
relationship: positively_regulates GO:0035720 ! intraciliary anterograde transport
@@ -516893,7 +519722,6 @@ synonym: "inhibition of intraciliary retrograde transport" NARROW [GOC:TermGenie
synonym: "inhibition of intraflagellar retrograde transport" NARROW [GOC:TermGenie]
synonym: "negative regulation of intraflagellar retrograde transport" EXACT [GOC:TermGenie]
is_a: GO:0032387 ! negative regulation of intracellular transport
-is_a: GO:0051271 ! negative regulation of cellular component movement
is_a: GO:1905799 ! regulation of intraciliary retrograde transport
relationship: negatively_regulates GO:0035721 ! intraciliary retrograde transport
@@ -516912,7 +519740,6 @@ synonym: "up-regulation of intraflagellar retrograde transport" EXACT [GOC:TermG
synonym: "upregulation of intraciliary retrograde transport" EXACT [GOC:TermGenie]
synonym: "upregulation of intraflagellar retrograde transport" EXACT [GOC:TermGenie]
is_a: GO:0032388 ! positive regulation of intracellular transport
-is_a: GO:0051272 ! positive regulation of cellular component movement
is_a: GO:1905799 ! regulation of intraciliary retrograde transport
relationship: positively_regulates GO:0035721 ! intraciliary retrograde transport
@@ -517225,7 +520052,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of chromosome separation." [GO_REF:0000058, GOC:bhm, GOC:TermGenie, PMID:21795393]
synonym: "regulation of chromatid release" RELATED [GOC:TermGenie]
synonym: "regulation of rDNA separation" NARROW [GOC:TermGenie]
-is_a: GO:0010564 ! regulation of cell cycle process
is_a: GO:0051983 ! regulation of chromosome segregation
relationship: regulates GO:0051304 ! chromosome separation
@@ -517248,7 +520074,6 @@ synonym: "inhibition of chromosome separation" NARROW [GOC:TermGenie]
synonym: "inhibition of rDNA separation" NARROW [GOC:TermGenie]
synonym: "negative regulation of chromatid release" RELATED [GOC:TermGenie]
synonym: "negative regulation of rDNA separation" NARROW [GOC:TermGenie]
-is_a: GO:0010948 ! negative regulation of cell cycle process
is_a: GO:0051985 ! negative regulation of chromosome segregation
is_a: GO:1905818 ! regulation of chromosome separation
relationship: negatively_regulates GO:0051304 ! chromosome separation
@@ -517374,7 +520199,7 @@ synonym: "up-regulation of selenocysteine metabolic process" EXACT [GOC:TermGeni
synonym: "up-regulation of selenocysteine metabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of selenocysteine metabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of selenocysteine metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0045764 ! positive regulation of cellular amino acid metabolic process
+is_a: GO:0045764 ! positive regulation of amino acid metabolic process
is_a: GO:1905825 ! regulation of selenocysteine metabolic process
relationship: positively_regulates GO:0016259 ! selenocysteine metabolic process
@@ -517386,7 +520211,7 @@ def: "Any process that modulates the frequency, rate or extent of prostaglandin
synonym: "regulation of prostaglandin breakdown" EXACT [GOC:TermGenie]
synonym: "regulation of prostaglandin catabolism" EXACT [GOC:TermGenie]
synonym: "regulation of prostaglandin degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009894 ! regulation of catabolic process
+is_a: GO:0050994 ! regulation of lipid catabolic process
relationship: regulates GO:1905344 ! prostaglandin catabolic process
[Term]
@@ -517413,7 +520238,7 @@ synonym: "inhibition of prostaglandin degradation" NARROW [GOC:TermGenie]
synonym: "negative regulation of prostaglandin breakdown" EXACT [GOC:TermGenie]
synonym: "negative regulation of prostaglandin catabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of prostaglandin degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009895 ! negative regulation of catabolic process
+is_a: GO:0050995 ! negative regulation of lipid catabolic process
is_a: GO:1905828 ! regulation of prostaglandin catabolic process
relationship: negatively_regulates GO:1905344 ! prostaglandin catabolic process
@@ -517441,7 +520266,7 @@ synonym: "upregulation of prostaglandin breakdown" EXACT [GOC:TermGenie]
synonym: "upregulation of prostaglandin catabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of prostaglandin catabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of prostaglandin degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009896 ! positive regulation of catabolic process
+is_a: GO:0050996 ! positive regulation of lipid catabolic process
is_a: GO:1905828 ! regulation of prostaglandin catabolic process
relationship: positively_regulates GO:1905344 ! prostaglandin catabolic process
@@ -517797,7 +520622,7 @@ name: negative regulation of pentose-phosphate shunt
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of pentose-phosphate shunt." [GO_REF:0000058, GOC:TermGenie, PMID:19015259]
is_a: GO:0043456 ! regulation of pentose-phosphate shunt
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
+is_a: GO:1900543 ! negative regulation of purine nucleotide metabolic process
relationship: negatively_regulates GO:0006098 ! pentose-phosphate shunt
[Term]
@@ -517806,7 +520631,7 @@ name: positive regulation of pentose-phosphate shunt
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of pentose-phosphate shunt." [GO_REF:0000058, GOC:TermGenie, PMID:19015259]
is_a: GO:0043456 ! regulation of pentose-phosphate shunt
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
+is_a: GO:1900544 ! positive regulation of purine nucleotide metabolic process
relationship: positively_regulates GO:0006098 ! pentose-phosphate shunt
[Term]
@@ -518084,7 +520909,6 @@ namespace: biological_process
def: "The process whose specific outcome is the progression of an epididymis over time, from its formation to the mature structure." [GO_REF:0000094, GOC:TermGenie, PMID:12388089]
synonym: "epididymus development" EXACT [GOC:TermGenie]
is_a: GO:0035295 ! tube development
-is_a: GO:0048608 ! reproductive structure development
[Term]
id: GO:1905868
@@ -518141,7 +520965,6 @@ synonym: "regulation of protein localisation in cell leading edge" EXACT [GOC:Te
synonym: "regulation of protein localisation to cell leading edge" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in cell leading edge" EXACT [GOC:TermGenie]
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:1902463 ! protein localization to cell leading edge
[Term]
@@ -518168,7 +520991,6 @@ synonym: "inhibition of protein localization to cell leading edge" NARROW [GOC:T
synonym: "negative regulation of protein localisation in cell leading edge" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localisation to cell leading edge" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in cell leading edge" EXACT [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905871 ! regulation of protein localization to cell leading edge
relationship: negatively_regulates GO:1902463 ! protein localization to cell leading edge
@@ -518197,7 +521019,6 @@ synonym: "upregulation of protein localisation in cell leading edge" EXACT [GOC:
synonym: "upregulation of protein localisation to cell leading edge" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization in cell leading edge" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to cell leading edge" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905871 ! regulation of protein localization to cell leading edge
relationship: positively_regulates GO:1902463 ! protein localization to cell leading edge
@@ -518422,8 +521243,7 @@ def: "The process in which (2R,4S)-2-methyltetrahydrofuran-2,3,3,4-tetrol (autoi
synonym: "(2R,4S)-2-methyltetrahydrofuran-2,3,3,4-tetrol transmembrane transport" EXACT [PMID:15601708]
synonym: "AI-2 transmembrane transport" EXACT [PMID:15601708]
synonym: "autoinducer 2 transmembrane transport" EXACT [PMID:15601708]
-is_a: GO:0015791 ! polyol transport
-is_a: GO:0055085 ! transmembrane transport
+is_a: GO:0015791 ! polyol transmembrane transport
[Term]
id: GO:1905888
@@ -518475,77 +521295,73 @@ relationship: regulates GO:0090731 ! cellular response to very-low-density lipop
[Term]
id: GO:1905891
-name: regulation of cellular response to thapsigargin
+name: obsolete regulation of cellular response to thapsigargin
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of cellular response to thapsigargin." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:21803450]
-is_a: GO:0048583 ! regulation of response to stimulus
-is_a: GO:0050794 ! regulation of cellular process
-relationship: regulates GO:1904579 ! cellular response to thapsigargin
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of cellular response to thapsigargin." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:21803450]
+comment: This term was obsoleted because it represents an experimental condition to cause endoplasmic reticulum stress.
+is_obsolete: true
+consider: GO:0034976
[Term]
id: GO:1905892
-name: negative regulation of cellular response to thapsigargin
+name: obsolete negative regulation of cellular response to thapsigargin
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to thapsigargin." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:21803450]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to thapsigargin." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:21803450]
+comment: This term was obsoleted because it represents an experimental condition to cause endoplasmic reticulum stress.
synonym: "down regulation of cellular response to thapsigargin" EXACT [GOC:TermGenie]
synonym: "down-regulation of cellular response to thapsigargin" EXACT [GOC:TermGenie]
synonym: "downregulation of cellular response to thapsigargin" EXACT [GOC:TermGenie]
synonym: "inhibition of cellular response to thapsigargin" NARROW [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
-is_a: GO:0048585 ! negative regulation of response to stimulus
-is_a: GO:1905891 ! regulation of cellular response to thapsigargin
-relationship: negatively_regulates GO:1904579 ! cellular response to thapsigargin
+is_obsolete: true
+consider: GO:0034976
[Term]
id: GO:1905893
-name: positive regulation of cellular response to thapsigargin
+name: obsolete positive regulation of cellular response to thapsigargin
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of cellular response to thapsigargin." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:21803450]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of cellular response to thapsigargin." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:21803450]
+comment: This term was obsoleted because it represents an experimental condition to cause endoplasmic reticulum stress.
synonym: "activation of cellular response to thapsigargin" NARROW [GOC:TermGenie]
synonym: "up regulation of cellular response to thapsigargin" EXACT [GOC:TermGenie]
synonym: "up-regulation of cellular response to thapsigargin" EXACT [GOC:TermGenie]
synonym: "upregulation of cellular response to thapsigargin" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
-is_a: GO:0048584 ! positive regulation of response to stimulus
-is_a: GO:1905891 ! regulation of cellular response to thapsigargin
-relationship: positively_regulates GO:1904579 ! cellular response to thapsigargin
+is_obsolete: true
+consider: GO:0034976
[Term]
id: GO:1905894
-name: regulation of cellular response to tunicamycin
+name: obsolete regulation of cellular response to tunicamycin
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of cellular response to tunicamycin." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:21803450]
-is_a: GO:0048583 ! regulation of response to stimulus
-is_a: GO:0050794 ! regulation of cellular process
-relationship: regulates GO:1904577 ! cellular response to tunicamycin
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of cellular response to tunicamycin." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:21803450]
+comment: This term was obsoleted because it represents an experimental condition to cause endoplasmic reticulum stress.
+is_obsolete: true
+consider: GO:0034976
[Term]
id: GO:1905895
-name: negative regulation of cellular response to tunicamycin
+name: obsolete negative regulation of cellular response to tunicamycin
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to tunicamycin." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:21803450]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to tunicamycin." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:21803450]
+comment: This term was obsoleted because it represents an experimental condition to cause endoplasmic reticulum stress.
synonym: "down regulation of cellular response to tunicamycin" EXACT [GOC:TermGenie]
synonym: "down-regulation of cellular response to tunicamycin" EXACT [GOC:TermGenie]
synonym: "downregulation of cellular response to tunicamycin" EXACT [GOC:TermGenie]
synonym: "inhibition of cellular response to tunicamycin" NARROW [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
-is_a: GO:0048585 ! negative regulation of response to stimulus
-is_a: GO:1905894 ! regulation of cellular response to tunicamycin
-relationship: negatively_regulates GO:1904577 ! cellular response to tunicamycin
+is_obsolete: true
+consider: GO:0034976
[Term]
id: GO:1905896
-name: positive regulation of cellular response to tunicamycin
+name: obsolete positive regulation of cellular response to tunicamycin
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of cellular response to tunicamycin." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:21803450]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of cellular response to tunicamycin." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:21803450]
+comment: This term was obsoleted because it represents an experimental condition to cause endoplasmic reticulum stress.
synonym: "activation of cellular response to tunicamycin" NARROW [GOC:TermGenie]
synonym: "up regulation of cellular response to tunicamycin" EXACT [GOC:TermGenie]
synonym: "up-regulation of cellular response to tunicamycin" EXACT [GOC:TermGenie]
synonym: "upregulation of cellular response to tunicamycin" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
-is_a: GO:0048584 ! positive regulation of response to stimulus
-is_a: GO:1905894 ! regulation of cellular response to tunicamycin
-relationship: positively_regulates GO:1904577 ! cellular response to tunicamycin
+is_obsolete: true
+consider: GO:0034976
[Term]
id: GO:1905897
@@ -518669,7 +521485,7 @@ id: GO:1905906
name: regulation of amyloid fibril formation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of amyloid fibril formation." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:23106396]
-comment: Although deposition of amyloid fibrils is associated with diseases, e.g. Alzheimer's disease, amyloid formation is a normal process. Disease occurs when the balance between amyloid formation and clearance is disrupted (reviewed e.g. in PMID:29654159 and PMID:28937655). An example of a normal amyloid complex is composed of human RIP1 and RIP3 kinases (PMID:22817896).
+comment: Although deposition of amyloid fibrils is associated with diseases, e.g. Alzheimer's disease, amyloid formation is a normal process. Disease occurs when the balance between amyloid formation and clearance is disrupted (reviewed e.g. in PMID:29654159 and PMID:28937655). An example of a normal amyloid complex is composed of human RIP1 and RIP3 kinases (PMID:22817896).
synonym: "regulation of amyloid fibril assembly" RELATED [GOC:TermGenie]
synonym: "regulation of amyloid structure assembly" RELATED [GOC:TermGenie]
synonym: "regulation of amyloid structure formation" RELATED [GOC:TermGenie]
@@ -518682,7 +521498,7 @@ id: GO:1905907
name: negative regulation of amyloid fibril formation
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of amyloid fibril formation." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:23106396]
-comment: Although deposition of amyloid fibrils is associated with diseases, e.g. Alzheimer's disease, amyloid formation is a normal process. Disease occurs when the balance between amyloid formation and clearance is disrupted (reviewed e.g. in PMID:29654159 and PMID:28937655). An example of a normal amyloid complex is composed of human RIP1 and RIP3 kinases (PMID:22817896).
+comment: Although deposition of amyloid fibrils is associated with diseases, e.g. Alzheimer's disease, amyloid formation is a normal process. Disease occurs when the balance between amyloid formation and clearance is disrupted (reviewed e.g. in PMID:29654159 and PMID:28937655). An example of a normal amyloid complex is composed of human RIP1 and RIP3 kinases (PMID:22817896).
synonym: "down regulation of amyloid fibril assembly" RELATED [GOC:TermGenie]
synonym: "down regulation of amyloid fibril formation" EXACT [GOC:TermGenie]
synonym: "down regulation of amyloid structure assembly" RELATED [GOC:TermGenie]
@@ -518712,7 +521528,7 @@ id: GO:1905908
name: positive regulation of amyloid fibril formation
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of amyloid fibril formation." [GO_REF:0000058, GOC:aruk, GOC:bc, GOC:TermGenie, PMID:23106396]
-comment: Although deposition of amyloid fibrils is associated with diseases, e.g. Alzheimer's disease, amyloid formation is a normal process. Disease occurs when the balance between amyloid formation and clearance is disrupted (reviewed e.g. in PMID:29654159 and PMID:28937655). An example of a normal amyloid complex is composed of human RIP1 and RIP3 kinases (PMID:22817896).
+comment: Although deposition of amyloid fibrils is associated with diseases, e.g. Alzheimer's disease, amyloid formation is a normal process. Disease occurs when the balance between amyloid formation and clearance is disrupted (reviewed e.g. in PMID:29654159 and PMID:28937655). An example of a normal amyloid complex is composed of human RIP1 and RIP3 kinases (PMID:22817896).
synonym: "activation of amyloid fibril assembly" RELATED [GOC:TermGenie]
synonym: "activation of amyloid fibril formation" NARROW [GOC:TermGenie]
synonym: "activation of amyloid structure assembly" RELATED [GOC:TermGenie]
@@ -519361,7 +522177,6 @@ synonym: "ATPase-coupled cGMP transmembrane transporter activity" EXACT []
is_a: GO:0001409 ! guanine nucleotide transmembrane transporter activity
is_a: GO:0005346 ! purine ribonucleotide transmembrane transporter activity
is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
[Term]
@@ -519374,8 +522189,6 @@ synonym: "down regulation of calcium ion import across plasma membrane" EXACT [G
synonym: "down-regulation of calcium ion import across plasma membrane" EXACT [GOC:TermGenie]
synonym: "downregulation of calcium ion import across plasma membrane" EXACT [GOC:TermGenie]
synonym: "inhibition of calcium ion import across plasma membrane" NARROW [GOC:TermGenie]
-is_a: GO:0010523 ! negative regulation of calcium ion transport into cytosol
-is_a: GO:0090281 ! negative regulation of calcium ion import
is_a: GO:1903170 ! negative regulation of calcium ion transmembrane transport
is_a: GO:1905664 ! regulation of calcium ion import across plasma membrane
relationship: negatively_regulates GO:0098703 ! calcium ion import across plasma membrane
@@ -519533,7 +522346,7 @@ id: GO:1990000
name: amyloid fibril formation
namespace: biological_process
def: "The generation of amyloid fibrils, insoluble fibrous protein aggregates exhibiting beta sheet structure, from proteins." [GOC:cvs, GOC:jj, GOC:ppm, GOC:sj, PMID:21148556, PMID:22817896, PMID:28937655, PMID:29654159]
-comment: Although deposition of amyloid fibrils is associated with diseases, e.g. Alzheimer's disease, amyloid formation is a normal process. Disease occurs when the balance between amyloid formation and clearance is disrupted (reviewed e.g. in PMID:29654159 and PMID:28937655). An example of a normal amyloid complex is composed of human RIP1 and RIP3 kinases (PMID:22817896).
+comment: Although deposition of amyloid fibrils is associated with diseases, e.g. Alzheimer's disease, amyloid formation is a normal process. Disease occurs when the balance between amyloid formation and clearance is disrupted (reviewed e.g. in PMID:29654159 and PMID:28937655). An example of a normal amyloid complex is composed of human RIP1 and RIP3 kinases (PMID:22817896).
synonym: "amyloid fibril assembly" RELATED []
synonym: "amyloid structure assembly" RELATED []
synonym: "amyloid structure formation" RELATED []
@@ -519558,18 +522371,18 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
[Term]
id: GO:1990003
-name: inosine-diphosphatase activity
+name: IDP phosphatase activity
namespace: molecular_function
alt_id: GO:0090450
-def: "Catalysis of the reaction: IDP + H2O = IMP + phosphate." [PMID:20385596, PMID:22849572, RHEA:35207]
-synonym: "IDP phosphatase activity" EXACT []
+def: "Catalysis of the reaction: IDP + H2O = IMP + H+ + phosphate." [PMID:20385596, PMID:22849572, RHEA:35207]
+synonym: "IDP diphosphatase activity" BROAD []
synonym: "IDPase activity" EXACT []
synonym: "inosine diphosphatase activity" EXACT []
+synonym: "inosine-diphosphatase activity" EXACT []
xref: EC:3.6.1.64
xref: Reactome:R-HSA-2509816 "NUDT16 hydrolyses IDP to IMP"
xref: RHEA:35207
-is_a: GO:0017110 ! nucleoside-diphosphatase activity
-is_a: GO:0098519 ! nucleotide phosphatase activity, acting on free nucleotides
+is_a: GO:0017110 ! nucleoside diphosphate phosphatase activity
[Term]
id: GO:1990004
@@ -519846,10 +522659,8 @@ namespace: biological_process
def: "The directed movement of calcium ions from inside of a cell, across the plasma membrane and into the extracellular region." [GOC:mah, PMID:2145281]
synonym: "calcium ion efflux from cell" EXACT [GOC:vw, PMID:2145281]
synonym: "calcium ion export from cell" EXACT []
-is_a: GO:0060401 ! cytosolic calcium ion transport
is_a: GO:0070588 ! calcium ion transmembrane transport
is_a: GO:0140115 ! export across plasma membrane
-is_a: GO:1901660 ! calcium ion export
[Term]
id: GO:1990036
@@ -519858,7 +522669,6 @@ namespace: biological_process
def: "The directed movement of calcium ions into a sarcoplasmic reticulum." [GOC:BHF, PMID:17286271]
is_a: GO:0046907 ! intracellular transport
is_a: GO:0070296 ! sarcoplasmic reticulum calcium ion transport
-is_a: GO:0070509 ! calcium ion import
[Term]
id: GO:1990037
@@ -520080,7 +522890,6 @@ def: "Protein complex facilitating ATP-dependent maltose transport through inner
synonym: "maltose ABC transporter complex" EXACT []
synonym: "maltose ATP-binding cassette transporter complex" EXACT []
is_a: GO:0043190 ! ATP-binding cassette (ABC) transporter complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:1990061
@@ -520105,7 +522914,7 @@ namespace: cellular_component
def: "Protein complex which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. In E. coli it is composed of BamABCDE, of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE. BamA interacts directly with BamB and the BamCDE subcomplex." [GOC:bhm, PMID:20378773]
synonym: "OMP complex" EXACT []
is_a: GO:0098796 ! membrane protein complex
-relationship: part_of GO:0031246 ! intrinsic component of periplasmic side of cell outer membrane
+relationship: part_of GO:0031241 ! periplasmic side of cell outer membrane
[Term]
id: GO:1990064
@@ -520217,7 +523026,7 @@ relationship: part_of GO:0009838 ! abscission
id: GO:1990077
name: primosome complex
namespace: cellular_component
-def: "Any of a family of protein complexes that form at the origin of replication or stalled replication forks and function in replication primer synthesis in all organisms. Early complexes initiate double-stranded DNA unwinding. The core unit consists of a replicative helicase and a primase. The helicase further unwinds the DNA and recruits the polymerase machinery. The primase synthesizes RNA primers that act as templates for complementary stand replication by the polymerase machinery. The primosome contains a number of associated proteins and protein complexes and contributes to the processes of replication initiation, lagging strand elongation, and replication restart." [GOC:bhm, GOC:mah, PMID:21856207]
+def: "Any of a family of protein complexes that form at the origin of replication or stalled replication forks and function in replication primer synthesis in all organisms. Early complexes initiate double-stranded DNA unwinding. The core unit consists of a replicative helicase and a primase. The helicase further unwinds the DNA and recruits the polymerase machinery. The primase synthesizes RNA primers that act as templates for complementary stand replication by the polymerase machinery. The primosome contains a number of associated proteins and protein complexes and contributes to the processes of replication initiation, lagging strand elongation, and replication restart." [GOC:bhm, GOC:mah, PMID:21856207]
synonym: "primosome" EXACT []
is_a: GO:0032993 ! protein-DNA complex
relationship: part_of GO:0030894 ! replisome
@@ -520297,10 +523106,18 @@ is_a: GO:1904019 ! epithelial cell apoptotic process
[Term]
id: GO:1990088
-name: [methyl-Co(III) methanol-specific corrinoid protein]:coenzyme M methyltransferase activity
+name: [methyl-Co(III) methanol-specific corrinoid protein]:coenzyme M methyltransferase
namespace: molecular_function
-def: "Catalysis of the reaction: a [methyl-Co(III) methanol-specific corrinoid protein] + coenzyme M = methyl-CoM + a [Co(I) methanol-specific corrinoid protein]." [GOC:hjd, PMID:10077852]
+alt_id: GO:0043851
+def: "Catalysis of the reaction: a [methyl-Co(III) methanol-specific corrinoid protein] + coenzyme M = methyl-coenzyme M + a [Co(I) methanol-specific corrinoid protein] + H+." [GOC:hjd, PMID:10077852, RHEA:45208]
+comment: This function is the second step in the pathway of methanogenesis from methanol.
+synonym: "methanol-specific methylcobalamin: coenzyme M methyltransferase activity" EXACT []
+synonym: "methanol-specific methylcobalamin:coenzyme M methyltransferase activity" EXACT []
+synonym: "methanol-specific methylcobalamin:CoM methyltransferase activity" EXACT []
+synonym: "methylcobamide:coenzyme M methyltransferase activity" BROAD []
+synonym: "methylcobamide:CoM methyltransferase activity" BROAD []
xref: EC:2.1.1.246
+xref: MetaCyc:RXN-8096
xref: RHEA:45208
is_a: GO:0008168 ! methyltransferase activity
@@ -520310,7 +523127,6 @@ name: response to nerve growth factor
namespace: biological_process
def: "A process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nerve growth factor stimulus." [PMID:22399805]
synonym: "response to nerve growth factor stimulus" EXACT [GOC:dos]
-is_a: GO:0009719 ! response to endogenous stimulus
is_a: GO:0070848 ! response to growth factor
[Term]
@@ -520320,7 +523136,6 @@ namespace: biological_process
def: "A process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nerve growth factor stimulus." [PMID:22399805, Wikipedia:Nerve_growth_factor]
synonym: "cellular response to NGF" EXACT [GOC:bf, Wikipedia:Nerve_growth_factor]
is_a: GO:0071363 ! cellular response to growth factor stimulus
-is_a: GO:0071495 ! cellular response to endogenous stimulus
is_a: GO:1990089 ! response to nerve growth factor
[Term]
@@ -520359,19 +523174,23 @@ is_obsolete: true
[Term]
id: GO:1990095
-name: positive regulation of transcription from RNA polymerase II promoter in response to reactive oxygen species
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to reactive oxygen species
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals." [GOC:kmv, PMID:16166371]
-is_a: GO:0036091 ! positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress
-relationship: part_of GO:0034614 ! cellular response to reactive oxygen species
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals." [GOC:kmv, PMID:16166371]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0034599
+consider: GO:0045944
[Term]
id: GO:1990096
-name: positive regulation of transcription from RNA polymerase II promoter in response to superoxide
+name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to superoxide
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion." [GOC:kmv, PMID:12869585, PMID:16166371]
-is_a: GO:1990095 ! positive regulation of transcription from RNA polymerase II promoter in response to reactive oxygen species
-relationship: part_of GO:0071451 ! cellular response to superoxide
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion." [GOC:kmv, PMID:12869585, PMID:16166371]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0034599
+consider: GO:0045944
[Term]
id: GO:1990097
@@ -520429,7 +523248,7 @@ is_a: GO:1990077 ! primosome complex
id: GO:1990102
name: DnaA-DiaA complex
namespace: cellular_component
-def: "A protein-DNA complex containing a tetramer of DiaA attached to multiple DnaA molecule bound to oriC DNA. Regulates timely initiation of chromosomal replication during the cell cycle by stimulating assembly of DnaA-oriC complexes, conformational changes in ATP-DnaA initiation complexes, and unwinding of oriC duplex DNA." [GOC:bhm, PMID:15326179, PMID:17699754]
+def: "A protein-DNA complex containing a tetramer of DiaA attached to multiple DnaA molecule bound to oriC DNA. Regulates timely initiation of chromosomal replication during the cell cycle by stimulating assembly of DnaA-oriC complexes, conformational changes in ATP-DnaA initiation complexes, and unwinding of oriC duplex DNA." [GOC:bhm, PMID:15326179, PMID:17699754]
synonym: "DnaA-DiaA-DNA complex" EXACT [GOC:bhm]
is_a: GO:1990077 ! primosome complex
@@ -520479,10 +523298,10 @@ is_a: GO:0016579 ! protein deubiquitination
id: GO:1990109
name: rejection of pollen from other species
namespace: biological_process
-def: "The process involved in the rejection of pollen of one species by cells in the stigma of another species." [PMID:21205670]
+def: "The recognition and rejection of pollen of one species by cells in the stigma of another species." [PMID:21205670]
synonym: "unilateral interspecific incompatibility" EXACT []
is_a: GO:0022414 ! reproductive process
-is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms
+is_a: GO:0048544 ! recognition of pollen
relationship: part_of GO:0009875 ! pollen-pistil interaction
[Term]
@@ -520578,7 +523397,7 @@ synonym: "messenger ribonucleoprotein assembly" RELATED []
synonym: "mRNA-protein complex assembly" EXACT [GOC:bf]
synonym: "mRNP assembly" EXACT [GOC:rb]
synonym: "mRNP complex assembly" EXACT [GOC:bf]
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
[Term]
id: GO:1990121
@@ -520614,7 +523433,7 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:1990127
name: intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of osmotic stress, and ends when the execution phase of apoptosis is triggered." [GOC:krc, GOC:mtg_apoptosis, PMID:16571598]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of osmotic stress, and ends when the execution phase of apoptosis is triggered." [GOC:krc, GOC:mtg_apoptosis, PMID:16571598]
is_a: GO:0008627 ! intrinsic apoptotic signaling pathway in response to osmotic stress
is_a: GO:0072332 ! intrinsic apoptotic signaling pathway by p53 class mediator
@@ -520641,7 +523460,7 @@ id: GO:1990130
name: GATOR1 complex
namespace: cellular_component
def: "A GTPase-activating protein (GAP) complex that regulates TORC1 signaling by interacting with the Rag GTPase. In human, the GATOR1 complex consists of DEPDC5, NPRL2, and NPRL3. In S. cerevisiae, this complex is referred to as SEACIT and contains the Iml1p, Npr2p, and Npr3p proteins." [GOC:krc, GOC:rb, PMID:21900499, PMID:23723238, PMID:23974112, PMID:25934700, PMID:28199306, PMID:29199950]
-comment: The Rag GTPase complex corresponds to Gtr1-Gtr2 GTPase complex ; GO:1990131.
+comment: The Rag GTPase complex corresponds to Gtr1-Gtr2 GTPase complex ; GO:1990131.
synonym: "IML1 complex" EXACT []
synonym: "SEACIT complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
@@ -520652,7 +523471,7 @@ id: GO:1990131
name: Gtr1-Gtr2 GTPase complex
namespace: cellular_component
def: "A heterodimer GTPase complex. In S. cerevisiae, this complex contains Gtr1p and Gtr2p proteins." [GOC:rb, PMID:10388807, PMID:16143306]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1905360 ! GTPase complex
[Term]
id: GO:1990132
@@ -520667,7 +523486,7 @@ is_obsolete: true
id: GO:1990133
name: molybdopterin cofactor (Moco) biosynthesis adenylyltransferase complex
namespace: cellular_component
-def: "A heterodimeric protein complex which adenylates two molecules of the sulfur carrier subunit of the molybdopterin (MPT) cofactor synthase using ATP as part of molybdopterin cofactor (Moco) biosynthesis. In E. coli the subunits are MoeB and MoaD; Moco biosynthesis and its constituent molecules are evolutionarily conserved." [GOC:bhm, pmid:11713534, pmid:16669776]
+def: "A heterodimeric protein complex which adenylates two molecules of the sulfur carrier subunit of the molybdopterin (MPT) cofactor synthase using ATP as part of molybdopterin cofactor (Moco) biosynthesis. In E. coli the subunits are MoeB and MoaD; Moco biosynthesis and its constituent molecules are evolutionarily conserved." [GOC:bhm, PMID:11713534, PMID:16669776]
is_a: GO:1902503 ! adenylyltransferase complex
relationship: part_of GO:0005829 ! cytosol
@@ -520738,14 +523557,6 @@ def: "A heterodimeric protein complex which catalyses sulfur transfer from the s
synonym: "molybdopterin cofactor (Moco) biosynthesis sulfurtransferase complex" RELATED []
is_a: GO:1990228 ! sulfurtransferase complex
-[Term]
-id: GO:1990142
-name: envenomation resulting in hemolysis in another organism
-namespace: biological_process
-def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with hemolysis in the bitten organism." [PMID:21590705]
-synonym: "envenomation resulting in hemolysis in other organism" EXACT []
-is_a: GO:0044649 ! envenomation resulting in cytolysis in another organism
-
[Term]
id: GO:1990143
name: CoA-synthesizing protein complex
@@ -520753,13 +523564,13 @@ namespace: cellular_component
def: "A multisubunit complex likely involved in the synthesis of coenzyme A (CoA). In S. cerevisiae, the complex consists of at least Cab2, Cab3, Cab4 and Cab5 but may also include Sis2 and Vhs3. The latter subunits are shared by the GO:0071513 phosphopantothenoylcysteine decarboxylase complex that catalyses the third step of the coenzyme A (CoA) biosynthetic pathway." [GOC:rb, PMID:23789928]
synonym: "CoA-SPC" EXACT []
synonym: "coenzyme A-synthesizing protein complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:1990144
name: intrinsic apoptotic signaling pathway in response to hypoxia
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to hypoxia (lowered oxygen tension). Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. The pathway ends when the execution phase of apoptosis is triggered." [GOC:BHF, GOC:mtg_apoptosis, GOC:rl, PMID:20436456]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to hypoxia (lowered oxygen tension). Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. The pathway ends when the execution phase of apoptosis is triggered." [GOC:BHF, GOC:mtg_apoptosis, GOC:rl, PMID:20436456]
is_a: GO:0097193 ! intrinsic apoptotic signaling pathway
relationship: part_of GO:0071456 ! cellular response to hypoxia
@@ -520776,7 +523587,7 @@ id: GO:1990146
name: protein localization to rhabdomere
namespace: biological_process
def: "A process in which a protein is transported to, or maintained in, a location within a rhabdomere." [GOC:sart, PMID:8335687]
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
[Term]
id: GO:1990147
@@ -520824,7 +523635,7 @@ name: protein localization to cell tip
namespace: biological_process
def: "A process in which a protein is transported to, or maintained in, a location at the cell tip." [PMID:22768263]
synonym: "protein localisation to cell tip" EXACT [GOC:mah]
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
[Term]
id: GO:1990153
@@ -520845,7 +523656,6 @@ synonym: "EIIA(Glc)-MalFGK2 complex" EXACT [PMID:23770568]
synonym: "EIIA(Glc)-maltose transporter complex" EXACT [PMID:23770568]
synonym: "maltose transporter inhibitor complex" RELATED [GOC:bhm]
is_a: GO:0043190 ! ATP-binding cassette (ABC) transporter complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:1990155
@@ -520908,17 +523718,21 @@ is_a: GO:0033202 ! DNA helicase complex
[Term]
id: GO:1990162
-name: histone deacetylase activity (H3-K4 specific)
+name: histone H3K4 deacetylase activity
namespace: molecular_function
def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 4) + H2O = histone H3 L-lysine (position 4) + acetate. This reaction represents the removal of an acetyl group from lysine at position 4 of the histone H3 protein." [GOC:al, PMID:23771057, PMID:28450737]
+synonym: "histone deacetylase activity (H3-K4 specific)" EXACT []
+synonym: "histone H3-K4 deacetylase activity" EXACT []
is_a: GO:0004407 ! histone deacetylase activity
[Term]
id: GO:1990164
-name: histone H2A phosphorylation
+name: obsolete histone H2A phosphorylation
namespace: biological_process
-def: "The modification of histone H2A by the addition of a phosphate group." [GOC:mah, PMID:23080121]
-is_a: GO:0016572 ! histone phosphorylation
+def: "OBSOLETE. The modification of histone H2A by the addition of a phosphate group." [GOC:mah, PMID:23080121]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0035173
[Term]
id: GO:1990165
@@ -521008,7 +523822,7 @@ name: phosphodiesterase decapping endonuclease activity
namespace: molecular_function
def: "Catalysis of the removal of the cap from an unmethylated 5'-end capped RNA resulting in the release of the entire cap structure (GpppN) and a 5' monophosphorylated RNA." [GOC:dgf, PMID:20802481]
synonym: "G(5')pppN pyrophosphatase activity" RELATED []
-is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0016891 ! RNA endonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:1990175
@@ -521148,14 +523962,14 @@ is_a: GO:0003682 ! chromatin binding
[Term]
id: GO:1990189
-name: peptide-serine-N-acetyltransferase activity
+name: peptide-serine-alpha-N-acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + N-terminal L-serine in peptide = CoA + N-acetyl-L-serine-peptide." [GOC:al, PMID:23912279]
is_a: GO:0004596 ! peptide alpha-N-acetyltransferase activity
[Term]
id: GO:1990190
-name: peptide-glutamate-N-acetyltransferase activity
+name: peptide-glutamate-alpha-N-acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + N-terminal L-glutamate in peptide = CoA + N-acetyl-L-glutamate-peptide." [GOC:al, PMID:23912279]
is_a: GO:0004596 ! peptide alpha-N-acetyltransferase activity
@@ -521195,7 +524009,7 @@ name: cytoplasmic U snRNP body assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic U snRNP body." [PMID:19464282]
synonym: "U body assembly" RELATED []
-is_a: GO:0022618 ! ribonucleoprotein complex assembly
+is_a: GO:0022618 ! protein-RNA complex assembly
[Term]
id: GO:1990195
@@ -521334,21 +524148,24 @@ def: "A transmembrane protein complex capable of transporting positively charged
synonym: "EmrE complex" NARROW []
is_a: GO:0098797 ! plasma membrane protein complex
is_a: GO:1902495 ! transmembrane transporter complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:1990208
-name: positive regulation by symbiont of RNA levels in host
+name: obsolete positive regulation by symbiont of RNA levels in host
namespace: biological_process
-def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of the RNA levels in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:12182338, PMID:18703740]
-is_a: GO:0052018 ! modulation by symbiont of RNA levels in host
+def: "OBSOLETE. Any process in which an organism activates, maintains or increases the frequency, rate or extent of the RNA levels in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:12182338, PMID:18703740]
+comment: This term was obsoleted because it represents a readout.
+is_obsolete: true
+consider: GO:0052167
[Term]
id: GO:1990209
-name: negative regulation by symbiont of RNA levels in host
+name: obsolete negative regulation by symbiont of RNA levels in host
namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the RNA levels in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:ml, PMID:18703740]
-is_a: GO:0052018 ! modulation by symbiont of RNA levels in host
+def: "OBSOLETE. Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the RNA levels in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:ml, PMID:18703740]
+comment: This term was obsoleted because it represents a readout.
+is_obsolete: true
+consider: GO:0052167
[Term]
id: GO:1990210
@@ -521447,7 +524264,7 @@ def: "A protein complex capable of cysteine desulfurase activity decomposing L-c
synonym: "IscS" NARROW [GOC:bhm, GOC:dph]
synonym: "NifS" NARROW [GOC:bhm, GOC:dph]
synonym: "SufS complex" NARROW []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005829 ! cytosol
[Term]
@@ -521538,7 +524355,7 @@ relationship: part_of GO:0005829 ! cytosol
id: GO:1990231
name: STING complex
namespace: cellular_component
-def: "A protein dimer containing two STING monomers. It binds cyclic purine di-nucleotides. Activation of the sting complex by 2',5'-3'-5'-cyclic GMP-AMP activates nuclear transcription factor kB (NF-kB) and interferon regulatory factor 3 (IRF3) which then induce transcription of the genes encoding type I IFN and cytokines active in the innate immune response." [GOC:bhm, PMID:22705373, PMID:23706668, PMID:23910378]
+def: "A protein dimer containing two STING monomers. It binds cyclic purine di-nucleotides. Activation of the sting complex by 2',5'-3'-5'-cyclic GMP-AMP activates nuclear transcription factor kB (NF-kB) and interferon regulatory factor 3 (IRF3) which then induce transcription of the genes encoding type I IFN and cytokines active in the innate immune response." [GOC:bhm, PMID:22705373, PMID:23706668, PMID:23910378]
synonym: "stimulator of interferon genes complex" EXACT [GOC:bhm, PMID:22705373, PMID:23910378]
is_a: GO:0098796 ! membrane protein complex
relationship: part_of GO:0030659 ! cytoplasmic vesicle membrane
@@ -521590,11 +524407,12 @@ is_a: GO:0051170 ! import into nucleus
[Term]
id: GO:1990238
-name: double-stranded DNA endodeoxyribonuclease activity
+name: double-stranded DNA endonuclease activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of ester linkages within a double-stranded deoxyribonucleic acid molecule by creating internal breaks." [GOC:PG, PMID:22885404]
+def: "Catalysis of the hydrolysis of ester linkages within a double-stranded DNA molecule by creating internal breaks." [PMID:22885404]
+synonym: "double-stranded DNA endodeoxyribonuclease activity" EXACT []
synonym: "dsDNA-specific endodeoxyribonuclease activity" RELATED []
-is_a: GO:0004520 ! endodeoxyribonuclease activity
+is_a: GO:0004520 ! DNA endonuclease activity
[Term]
id: GO:1990239
@@ -521631,21 +524449,24 @@ is_a: GO:0035976 ! transcription factor AP-1 complex
[Term]
id: GO:1990244
-name: histone kinase activity (H2A-T120 specific)
+name: histone H2AT120 kinase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a phosphate group to the threonine-120 residue of histone H2A." [PMID:24140421]
+def: "Catalysis of the reaction: histone H2A-threonine (position 120) + ATP = histone H2A-phosphothreonine (position 120) + ADP. This reaction is the addition of a phosphate group to the threonine residue at position 120 of histone H2A." [PMID:24140421]
+synonym: "histone H2A-T120 kinase activity" EXACT []
+synonym: "histone kinase activity (H2A-T120 specific)" EXACT []
synonym: "histone threonine kinase activity (H2A-T120 specific)" EXACT []
-is_a: GO:0035184 ! histone threonine kinase activity
+is_a: GO:0140995 ! histone H2A kinase activity
[Term]
id: GO:1990245
-name: histone H2A-T120 phosphorylation
+name: obsolete histone H2A-T120 phosphorylation
namespace: biological_process
-def: "The modification of histone H2A by the addition of a phosphate group to a threonine residue at position 120 of the histone." [PMID:24140421]
+def: "OBSOLETE. The modification of histone H2A by the addition of a phosphate group to a threonine residue at position 120 of the histone." [PMID:24140421]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H2A phosphorylation at T120" EXACT []
synonym: "histone H2AT120 phosphorylation" EXACT []
-is_a: GO:0035405 ! histone-threonine phosphorylation
-is_a: GO:1990164 ! histone H2A phosphorylation
+is_obsolete: true
+consider: GO:1990244
[Term]
id: GO:1990246
@@ -521666,11 +524487,13 @@ is_a: GO:0003723 ! RNA binding
[Term]
id: GO:1990248
-name: regulation of transcription from RNA polymerase II promoter in response to DNA damage
+name: obsolete regulation of transcription from RNA polymerase II promoter in response to DNA damage
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of DNA damage." [PMID:15660129]
-is_a: GO:0006974 ! cellular response to DNA damage stimulus
-is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter in response to stress
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of DNA damage." [PMID:15660129]
+comment: This term was obsoleted becausee it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0006357
+consider: GO:0006974
[Term]
id: GO:1990249
@@ -521751,19 +524574,26 @@ is_a: GO:0018364 ! peptidyl-glutamine methylation
[Term]
id: GO:1990259
-name: histone-glutamine methyltransferase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-glutamine = S-adenosyl-L-homocysteine + (histone)-N5-methyl-glutamine." [PMID:24352239]
+name: histone H2AQ104 methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + (histone H2A)-glutamine (position 104) = S-adenosyl-L-homocysteine + (histone H2A)-N5-methyl-glutamine (position 104). Note that this corresponds to Q105 in yeast." [PMID:24352239]
+synonym: "histone glutamine methylase activity" EXACT []
+synonym: "histone glutamine methyltransferase activity" EXACT []
+synonym: "histone glutamine N-methyltransferase activity" BROAD []
+synonym: "histone-glutamine methyltransferase activity" EXACT []
+synonym: "histone-glutamine N-methyltransferase activity" EXACT []
is_a: GO:0036009 ! protein-glutamine N-methyltransferase activity
-is_a: GO:0042054 ! histone methyltransferase activity
+is_a: GO:0140940 ! histone H2A methyltransferase activity
[Term]
id: GO:1990260
-name: negative regulation of transcription from RNA polymerase II promoter by transcription factor localization involved in response to DNA damage checkpoint signaling
+name: obsolete negative regulation of transcription from RNA polymerase II promoter by transcription factor localization involved in response to DNA damage checkpoint signaling
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter using a mechanism that involves the localization of a transcription factor and initiated in response to the DNA damage checkpoint signaling." [PMID:24006488]
-is_a: GO:0010621 ! negative regulation of transcription by transcription factor localization
-relationship: part_of GO:0072423 ! response to DNA damage checkpoint signaling
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter using a mechanism that involves the localization of a transcription factor and initiated in response to the DNA damage checkpoint signaling." [PMID:24006488]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0000122
+consider: GO:0006974
[Term]
id: GO:1990261
@@ -521778,7 +524608,7 @@ is_a: GO:0006401 ! RNA catabolic process
id: GO:1990262
name: anti-Mullerian hormone signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by the binding of anti-Mullerian hormone to its receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:hjd, PMID:23624077]
+def: "The series of molecular signals initiated by the binding of anti-Mullerian hormone to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:hjd, PMID:23624077]
comment: An example of this is Amhr2 in M. musculus (Q8K592) a receptor for anti-mullerian hormone, described in PMID:23624077.
is_a: GO:0007166 ! cell surface receptor signaling pathway
@@ -521868,7 +524698,6 @@ synonym: "PDGF-DD-receptor alpha-beta complex" NARROW []
synonym: "PDGF-DD-receptor beta complex" NARROW []
synonym: "receptor-ligand complex" BROAD []
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:1990271
@@ -521889,9 +524718,10 @@ is_a: GO:0016500 ! protein-hormone receptor activity
[Term]
id: GO:1990273
-name: snRNA 5'-end processing
+name: snRNA capping
namespace: biological_process
-def: "Any process involved in forming the mature 5' end of an snRNA molecule." [PMID:22740346]
+def: "The addition of a methylphosphate cap at the 5'-end of 7SK snRNA (7SK RNA). Capping 7SK RNA stabilizes it." [PMID:22740346]
+synonym: "snRNA 5'-end processing" BROAD []
is_a: GO:0016180 ! snRNA processing
is_a: GO:0034471 ! ncRNA 5'-end processing
@@ -521926,12 +524756,13 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
[Term]
id: GO:1990277
-name: parasexual conjugation with cellular fusion
+name: parasexual reproduction with cellular fusion
namespace: biological_process
-def: "A conjugation process that results in the union of cellular and genetic information from compatible mating types, without the formation of zygotes. An example of this process is found in Candida albicans." [GOC:di]
+def: "A type of reproduction in which new individuals are produced from two individuals, with the fusion of two somatic cells." [GOC:di, PMID:26210747]
synonym: "mating" BROAD []
-is_a: GO:0000746 ! conjugation
-is_a: GO:0140253 ! cell-cell fusion
+synonym: "parasexual conjugation with cellular fusion" EXACT []
+xref: Wikipedia:Parasexual_cycle
+is_a: GO:0000003 ! reproduction
[Term]
id: GO:1990278
@@ -522122,7 +524953,7 @@ is_a: GO:0071375 ! cellular response to peptide hormone stimulus
id: GO:1990315
name: Mcs4 RR-MAPKKK complex
namespace: cellular_component
-def: "A protein complex that consists of a phospho relay component and a MAPK cascade component. The complex is involved in signaling oxidative stress and osmostress." [PMID:24255738]
+def: "A protein complex that consists of a phospho relay component and a MAPK cascade component. The complex is involved in signaling oxidative stress and osmostress." [PMID:24255738]
comment: In S. pombe it consists of Mpr1, Tdh1, Mcs4, Win1, Wis4 and Wis1.
is_a: GO:0032991 ! protein-containing complex
@@ -522436,11 +525267,11 @@ is_a: GO:0071267 ! L-methionine salvage
[Term]
id: GO:1990356
-name: sumoylated E2 ligase complex
+name: obsolete sumoylated E2 ligase complex
namespace: cellular_component
-def: "A protein complex consisting of a SUMO (small ubiquitin-related modifier) protein bound to a SUMO-conjugating E2 ligase. Sumoylation of the E2 ligase is an intermediate step required for the formation of covalent bonds between a SUMO protein and its ultimate protein target. SUMO is transferred to the E2 ligase by a SUMO-activating E1 enzyme. Sumoylation of the target protein is either facilitated directly by the sumoylated E2 ligase or aided by an optional E3 ligase." [GOC:bhm, PMID:18691969]
-comment: An example of this is UBC9 in human (UniProt symbol P63279) in PMID:18691969 (inferred from direct assay).
-is_a: GO:0032991 ! protein-containing complex
+def: "OBSOLETE. A protein complex consisting of a SUMO (small ubiquitin-related modifier) protein bound to a SUMO-conjugating E2 ligase. Sumoylation of the E2 ligase is an intermediate step required for the formation of covalent bonds between a SUMO protein and its ultimate protein target. SUMO is transferred to the E2 ligase by a SUMO-activating E1 enzyme. Sumoylation of the target protein is either facilitated directly by the sumoylated E2 ligase or aided by an optional E3 ligase." [GOC:bhm, PMID:18691969]
+comment: This term was obsoleted because it is represents a complex with a modified (sumoylated) subunit; this is out of the scope of GO.
+is_obsolete: true
[Term]
id: GO:1990357
@@ -522461,7 +525292,7 @@ is_a: GO:1902494 ! catalytic complex
id: GO:1990359
name: stress response to zinc ion
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis caused by a zinc ion stimulus." [GOC:kmv, pmid:17888400]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis caused by a zinc ion stimulus." [GOC:kmv, PMID:17888400]
synonym: "response to zinc ion stress" EXACT []
synonym: "response to zinc toxicity" RELATED []
synonym: "stress response to zinc" BROAD []
@@ -522622,12 +525453,14 @@ is_a: GO:0150104 ! transport across blood-brain barrier
[Term]
id: GO:1990380
-name: Lys48-specific deubiquitinase activity
+name: K48-linked deubiquitinase activity
namespace: molecular_function
-def: "Hydrolysis of Lys48-linked ubiquitin unit(s) from a ubiquitinated protein." [GOC:bf, GOC:PARL, PMID:22970133]
-synonym: "K48-specific deubiquitinase activity" EXACT [PMID:22970133]
+def: "Hydrolysis of a ubiquitin unit from a ubiquitinated protein linked via the Lys48 residue of ubiquitin." [GOC:bf, GOC:PARL, PMID:22970133]
+synonym: "K48-specific deubiquitinase activity" EXACT []
synonym: "K48-specific deubiquitinating activity" EXACT [PMID:22970133]
+synonym: "Lys48-specific deubiquitinase activity" EXACT [PMID:22970133]
xref: Reactome:R-HSA-5690870 "OTUD7B,TNFAIP3 deubiquitinate TRAF6"
+xref: Reactome:R-HSA-9711058 "SARS-CoV-1 nsp3 deubiquinates K48-linked pUb IkBA"
is_a: GO:0101005 ! deubiquitinase activity
[Term]
@@ -522719,7 +525552,7 @@ namespace: cellular_component
def: "A protein complex involved in DNA repair processes including direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [GOC:bhm, PMID:17217467, PMID:20551348, PMID:22749910, PMID:24192350]
synonym: "DNA damage repair complex" EXACT []
synonym: "WHY1 complex" NARROW []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:1990392
@@ -522728,7 +525561,6 @@ namespace: cellular_component
def: "A trimeric cell-cell fusion complex that serves as a scaffold for zippering up the extracellular domains, bringing the transmembrane segments into close proximity such that they can continue zippering within the two membranes into one. Two prefusion monomers cluster at the surface of adjacent cells. Parallel EFF-1 interactions occur across cells and a third monomer, which can come from either cell, adds on to make an intermediate, extended trimer." [GOC:bhm, PMID:24725407]
comment: An example of this is eff-1 in C. elegans (G5ECA1) in PMID:24725407 (inferred from direct assay).
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:1990393
@@ -522784,7 +525616,6 @@ synonym: "silver efflux system" NARROW []
is_a: GO:0098797 ! plasma membrane protein complex
is_a: GO:1903113 ! copper ion transmembrane transporter complex
is_a: GO:1903114 ! silver ion transmembrane transporter complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:1990399
@@ -522828,10 +525659,13 @@ is_a: GO:0048568 ! embryonic organ development
[Term]
id: GO:1990404
-name: protein ADP-ribosylase activity
+name: NAD+-protein ADP-ribosyltransferase activity
namespace: molecular_function
-def: "The transfer, from NAD, of ADP-ribose to a protein amino acid residue." [PMID:1899243, RESID:AA0040, RESID:AA0168, RESID:AA0169, RESID:AA0231, RESID:AA0237, RESID:AA0295, wikipedia:ADP-ribosylation]
+def: "Catalysis of the reaction: amino acyl-[protein] + NAD+ = H+ + (ADP-D-ribosyl)-amino acyl-[protein] + nicotinamide." [PMID:1899243]
+synonym: "protein ADP-ribosylase activity" EXACT []
+synonym: "protein ADP-ribosyltransferase activity" BROAD []
synonym: "ribosylase activity" BROAD []
+xref: Wikipedia:ADP-ribosylation
is_a: GO:0016763 ! pentosyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -522869,7 +525703,7 @@ is_a: GO:0097644 ! calcitonin family binding
id: GO:1990408
name: calcitonin gene-related peptide receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by an extracellular calcitonin gene-related peptide (CGRP) combining with a calcitonin gene-related peptide receptor on the surface of the target cell. Calcitonin gene-related peptide receptors may form dimers, trimers or tetramers." [GOC:bhm, PMID:10882736]
+def: "The series of molecular signals initiated by an extracellular calcitonin gene-related peptide (CGRP) combining with a calcitonin gene-related peptide receptor on the surface of the target cell. Calcitonin gene-related peptide receptors may form dimers, trimers or tetramers." [GOC:bhm, PMID:10882736]
comment: An example of a protein that could be annotated to this term is CALCRL in human (Q16602) in PMID:10882736.
synonym: "calcitonin-gene-related peptide receptor signaling pathway" EXACT []
synonym: "calcitonin-gene-related polypeptide receptor signaling pathway" EXACT []
@@ -522889,7 +525723,7 @@ is_a: GO:0097644 ! calcitonin family binding
id: GO:1990410
name: adrenomedullin receptor signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by an extracellular adrenomedullin combining with a dimeric adrenomedullin receptor on the surface of the target cell." [GOC:bhm, PMID:10882736]
+def: "The series of molecular signals initiated by an extracellular adrenomedullin combining with a dimeric adrenomedullin receptor on the surface of the target cell." [GOC:bhm, PMID:10882736]
comment: An example of a protein that could be annotated to this term is CALCRL in human (Q16602) in PMID:10882736.
synonym: "AM receptor signaling pathway" EXACT []
is_a: GO:0097646 ! calcitonin family receptor signaling pathway
@@ -522991,6 +525825,7 @@ name: protein arginine kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + a protein arginine = ADP + protein arginine phosphate." [GOC:imk, PMID:22517742]
comment: This reaction occurs in bacterial species e.g. Bacillus subtilis.
+synonym: "protein-arginine kinase activity" EXACT []
is_a: GO:0004672 ! protein kinase activity
[Term]
@@ -523008,9 +525843,16 @@ relationship: part_of GO:0033017 ! sarcoplasmic reticulum membrane
id: GO:1990426
name: mitotic recombination-dependent replication fork processing
namespace: biological_process
+alt_id: GO:1903211
def: "Replication fork processing that includes recombination between DNA near the arrested fork and homologous sequences. Proteins involved in homologous recombination are required for replication restart." [GOC:mah, PMID:23093942]
synonym: "homologous recombination dependent replication fork recovery" RELATED [PMID:23093942]
synonym: "homologous recombination-dependent replication fork processing" EXACT []
+synonym: "mitotic recombination involved in collapsed replication fork processing" EXACT [GOC:TermGenie]
+synonym: "mitotic recombination involved in recovery from replication fork arrest" EXACT [GOC:TermGenie]
+synonym: "mitotic recombination involved in recovery from replication fork stalling" EXACT [GOC:TermGenie]
+synonym: "mitotic recombination involved in replication fork processing" RELATED []
+synonym: "mitotic recombination involved in replication fork restart" RELATED [GOC:TermGenie]
+synonym: "mitotic recombination involved in replication restart" RELATED [GOC:TermGenie]
is_a: GO:0031297 ! replication fork processing
is_a: GO:1990505 ! mitotic DNA replication maintenance of fidelity
@@ -523057,7 +525899,7 @@ namespace: biological_process
def: "The process of forming the mature 3' end of a priRNA molecule." [PMID:24095277]
synonym: "primal small RNA 3'-end processing" EXACT []
synonym: "priRNA 3' end processing" EXACT []
-is_a: GO:0043628 ! ncRNA 3'-end processing
+is_a: GO:0043628 ! regulatory ncRNA 3'-end processing
[Term]
id: GO:1990432
@@ -523066,7 +525908,7 @@ namespace: biological_process
def: "The process of forming the mature 3' end of a siRNA molecule." [PMID:24095277]
synonym: "siRNA 3' end processing" EXACT []
synonym: "small interfering RNA 3'-end processing" EXACT []
-is_a: GO:0043628 ! ncRNA 3'-end processing
+is_a: GO:0043628 ! regulatory ncRNA 3'-end processing
[Term]
id: GO:1990433
@@ -523096,7 +525938,7 @@ is_a: GO:1990427 ! stereocilia tip-link density
id: GO:1990436
name: obsolete MAPK cascade involved in oxidative stress signaling pathway
namespace: biological_process
-def: "OBSOLETE. A series of molecular signals in which a MAP kinase cascade activated by oxidative stress relays one or more of the signals, MAP kinase cascades involve at least three protein kinase activities and culminate in the phosphorylation and activation of a MAP kinase. Just FYI in pombe the osmotic stress and oxidative stress MAPK cascade involve many of the same proteins, but the pathways are slightly different, therefore Im req this term." [PMID:10398679]
+def: "OBSOLETE. The series of molecular signals in which a MAP kinase cascade activated by oxidative stress relays one or more of the signals, MAP kinase cascades involve at least three protein kinase activities and culminate in the phosphorylation and activation of a MAP kinase. Just FYI in pombe the osmotic stress and oxidative stress MAPK cascade involve many of the same proteins, but the pathways are slightly different, therefore Im req this term." [PMID:10398679]
comment: This term was obsoleted at the TermGenie Gatekeeper stage.
synonym: "MAPK cascade involved in oxidative stress signaling pathway" EXACT []
is_obsolete: true
@@ -523158,7 +526000,7 @@ is_a: GO:0097201 ! negative regulation of transcription from RNA polymerase II p
id: GO:1990442
name: intrinsic apoptotic signaling pathway in response to nitrosative stress
namespace: biological_process
-def: "A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to nitrosative stress; a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions." [GOC:bf, GOC:PARL, PMID:23985028]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to nitrosative stress; a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions." [GOC:bf, GOC:PARL, PMID:23985028]
synonym: "nitrosative stress-induced apoptosis" RELATED [PMID:23985028]
synonym: "nitrosative stress-induced intrinsic apoptotic signaling pathway" EXACT [GOC:bf]
is_a: GO:0071500 ! cellular response to nitrosative stress
@@ -523373,7 +526215,7 @@ is_a: GO:0016901 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:1990465
name: aldehyde oxygenase (deformylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction a long-chain aldehyde + O(2) + 2 NADPH = an alkane + formate + H(2)O + 2 NADP(+)." [GOC:mengo_curators, PMID:22947199, RHEA:21440]
+def: "Catalysis of the reaction a long-chain aldehyde + O2 + 2 NADPH = an alkane + formate + H2O + 2 NADP+." [GOC:mengo_curators, PMID:22947199, RHEA:21440]
xref: EC:4.1.99.5
xref: RHEA:21440
is_a: GO:0016830 ! carbon-carbon lyase activity
@@ -523410,6 +526252,7 @@ comment: An example of this is cuff in Drosophila melanogaster (Q9V629) in PMID:
synonym: "RDC complex" EXACT []
synonym: "rhi-del-cuff complex" EXACT []
is_a: GO:0140513 ! nuclear protein-containing complex
+is_a: GO:1990923 ! PET complex
relationship: part_of GO:0043073 ! germ cell nucleus
[Term]
@@ -523466,7 +526309,7 @@ relationship: part_of GO:0098794 ! postsynapse
id: GO:1990476
name: synaptic vesicle, resting pool
namespace: cellular_component
-def: "A synaptic vesicle belonging to the pool that remain unreleased even after prolonged stimulation causes a saturating degree of vesicular turnover. 50-80% of the total number of synaptic vesicles at a resting terminal bouton are in this pool." [GOC:pad, PMID:22745285]
+def: "A synaptic vesicle belonging to the pool that remain unreleased even after prolonged stimulation causes a saturating degree of vesicular turnover. 50-80% of the total number of synaptic vesicles at a resting terminal bouton are in this pool." [GOC:pad, PMID:22745285]
synonym: "reserve pool of synaptic vesicles" EXACT [PMID:15611727]
synonym: "resting pool of synaptic vesicles" EXACT []
is_a: GO:0008021 ! synaptic vesicle
@@ -523736,9 +526579,10 @@ relationship: part_of GO:1902969 ! mitotic DNA replication
[Term]
id: GO:1990506
-name: mitotic DNA-dependent DNA replication
+name: mitotic DNA-templated DNA replication
namespace: biological_process
def: "A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands during the mitotic cell cycle." [PMID:16120966]
+synonym: "mitotic DNA-dependent DNA replication" EXACT []
is_a: GO:1902969 ! mitotic DNA replication
[Term]
@@ -523772,14 +526616,6 @@ synonym: "PYM-mago-RNA-binding protein 8A complex" EXACT []
synonym: "wibg-mago-tsu complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
-[Term]
-id: GO:1990511
-name: piRNA biosynthetic process
-namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of piRNAs, Piwi-associated RNAs, a class of 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism." [GOC:kmv, PMID:24696457]
-synonym: "Piwi-associated RNA biosynthetic process" EXACT []
-is_a: GO:0034587 ! piRNA metabolic process
-
[Term]
id: GO:1990512
name: Cry-Per complex
@@ -523844,7 +526680,6 @@ synonym: "mitochondrial pyrimidine nucleotide import" EXACT []
is_a: GO:0006864 ! pyrimidine nucleotide transport
is_a: GO:0072531 ! pyrimidine-containing compound transmembrane transport
is_a: GO:1901679 ! nucleotide transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990520
@@ -523856,10 +526691,11 @@ is_a: GO:1905369 ! endopeptidase complex
[Term]
id: GO:1990521
-name: m7G(5')pppN diphosphatase activator activity
+name: obsolete m7G(5')pppN diphosphatase activator activity
namespace: molecular_function
-def: "Binds to and increases the activity of m7G(5')pppN diphosphatase." [PMID:22323607]
-is_a: GO:0008047 ! enzyme activator activity
+def: "OBSOLETE. Binds to and increases the activity of m7G(5')pppN diphosphatase." [PMID:22323607]
+comment: This term was obsoleted because the obsoleted EC was obsoleted.
+is_obsolete: true
[Term]
id: GO:1990522
@@ -523884,7 +526720,6 @@ namespace: cellular_component
def: "A protein complex located in the inner membrane of mitochondria that is involved in the assembly of the peripheral (or stator) stalk of the mitochondrial proton-transporting ATP synthase (also known as the F1F0 ATP synthase). In budding yeast, this complex includes Ina22p and Ina17p." [GOC:rn, PMID:24942160]
synonym: "INAC" EXACT []
is_a: GO:0098800 ! inner mitochondrial membrane protein complex
-relationship: part_of GO:0031304 ! intrinsic component of mitochondrial inner membrane
[Term]
id: GO:1990525
@@ -523922,8 +526757,8 @@ name: glycosylphosphatidylinositol-mannosyltransferase I complex
namespace: cellular_component
def: "A protein complex that is involved in the transfer of the four mannoses in the GPI-anchor precursor. In yeast S. cerevisiae this complex consists of Pbn1p and Gpi14p and in rat this complex consists of PIG-X and PIG-M." [GOC:dph, GOC:rb, PMID:15635094]
synonym: "GPI-MT-I complex" RELATED []
+is_a: GO:0031501 ! mannosyltransferase complex
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
-is_a: GO:1990234 ! transferase complex
[Term]
id: GO:1990530
@@ -524015,8 +526850,11 @@ is_a: GO:0016413 ! O-acetyltransferase activity
id: GO:1990539
name: fructose import across plasma membrane
namespace: biological_process
+alt_id: GO:0032445
def: "The directed movement of fructose substance from outside of a cell, across the plasma membrane and into the cytosol." [PMID:10735857]
-is_a: GO:0032445 ! fructose import
+synonym: "fructose import" RELATED []
+synonym: "fructose uptake" EXACT [GOC:dph, GOC:tb]
+is_a: GO:0015755 ! fructose transmembrane transport
is_a: GO:0140271 ! hexose import across plasma membrane
[Term]
@@ -524025,13 +526863,13 @@ name: mitochondrial manganese ion transmembrane transport
namespace: biological_process
def: "The process in which a manganese ion is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:12890866]
is_a: GO:0071421 ! manganese ion transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990542
name: mitochondrial transmembrane transport
namespace: biological_process
def: "The process in which a solute is transported from one side of a membrane to the other into, out of or within a mitochondrion." [PMID:20533899]
+is_a: GO:0006839 ! mitochondrial transport
is_a: GO:0055085 ! transmembrane transport
[Term]
@@ -524040,7 +526878,6 @@ name: mitochondrial S-adenosyl-L-methionine transmembrane transport
namespace: biological_process
def: "The process in which S-adenosyl-L-methionine is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:14609944]
is_a: GO:1901962 ! S-adenosyl-L-methionine transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990544
@@ -524049,9 +526886,7 @@ namespace: biological_process
def: "The process in which ATP is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:18485069]
is_a: GO:0015867 ! ATP transport
is_a: GO:0072530 ! purine-containing compound transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1901679 ! nucleotide transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990545
@@ -524059,7 +526894,6 @@ name: mitochondrial thiamine pyrophosphate transmembrane transport
namespace: biological_process
def: "The process in which thiamine pyrophosphate is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:12411483]
is_a: GO:0030974 ! thiamine pyrophosphate transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990546
@@ -524067,7 +526901,6 @@ name: mitochondrial tricarboxylic acid transmembrane transport
namespace: biological_process
def: "The process in which a tricarboxylic acid is transported across a mitochondrial membrane, into or out of the mitochondrion." [GOC:vw]
is_a: GO:0035674 ! tricarboxylic acid transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990547
@@ -524075,7 +526908,6 @@ name: mitochondrial phosphate ion transmembrane transport
namespace: biological_process
def: "The process in which a phosphate ion is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:9099701]
is_a: GO:0035435 ! phosphate ion transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990548
@@ -524083,7 +526915,6 @@ name: mitochondrial FAD transmembrane transport
namespace: biological_process
def: "The process in which FAD is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:14555654]
is_a: GO:0035350 ! FAD transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990549
@@ -524091,7 +526922,6 @@ name: mitochondrial NAD transmembrane transport
namespace: biological_process
def: "The process in which NAD is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:16291748]
is_a: GO:0035352 ! NAD transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990550
@@ -524101,9 +526931,7 @@ alt_id: GO:1990552
def: "The process in which alpha-ketoglutarate is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:11013234, PMID:20371607]
synonym: "mitochondrial 2-oxoglutarate transmembrane transport" EXACT []
is_a: GO:0015742 ! alpha-ketoglutarate transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990551
@@ -524111,9 +526939,7 @@ name: mitochondrial 2-oxoadipate transmembrane transport
namespace: biological_process
def: "The process in which 2-oxoadipate is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:11013234]
is_a: GO:0006835 ! dicarboxylic acid transport
-is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990553
@@ -524121,7 +526947,6 @@ name: mitochondrial 5'-adenylyl sulfate transmembrane transport
namespace: biological_process
def: "The process in which 5'-adenylyl sulfate is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:24296033]
is_a: GO:1902558 ! 5'-adenylyl sulfate transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990554
@@ -524129,7 +526954,6 @@ name: mitochondrial 3'-phospho-5'-adenylyl sulfate transmembrane transport
namespace: biological_process
def: "The process in which 3'-phospho-5'-adenylyl sulfate is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:24296033]
is_a: GO:1902559 ! 3'-phospho-5'-adenylyl sulfate transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990555
@@ -524137,7 +526961,6 @@ name: mitochondrial oxaloacetate transmembrane transport
namespace: biological_process
def: "The process in which oxaloacetate is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:10428783]
is_a: GO:1902356 ! oxaloacetate(2-) transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990556
@@ -524145,7 +526968,6 @@ name: mitochondrial isopropylmalate transmembrane transport
namespace: biological_process
def: "The process in which 2-isopropylmalate(2-) is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:10428783]
is_a: GO:1902357 ! 2-isopropylmalate(2-) transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990557
@@ -524153,7 +526975,6 @@ name: mitochondrial sulfate transmembrane transport
namespace: biological_process
def: "The process in which sulfate is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:10428783]
is_a: GO:1902358 ! sulfate transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990558
@@ -524161,7 +526982,6 @@ name: mitochondrial malonate(1-) transmembrane transport
namespace: biological_process
def: "The process in which malonate(1-) is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:10428783]
is_a: GO:1901553 ! malonic acid transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990559
@@ -524169,7 +526989,6 @@ name: mitochondrial coenzyme A transmembrane transport
namespace: biological_process
def: "The process in which coenzyme A is transported across a mitochondrial membrane, into or out of the mitochondrion." [PMID:11158296]
is_a: GO:0035349 ! coenzyme A transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990560
@@ -524223,7 +527042,7 @@ name: HSP90-CDC37 chaperone complex
namespace: cellular_component
def: "A protein kinase chaperone complex required for the proper folding, maturation and stabilization of target proteins (mostly signalling protein kinases, some steroid hormone receptors), usually during or immediately after completion of translation. The highly conserved, phosphorylated CDC37-Ser13 (vertebrates) or cdc37-Ser14 (yeast) is essential for complex assembly and target protein binding. CDC37-Ser13 (Ser14) is phosphorylated by Casein kinase II (CK2), which in turn is a target of CDC37 creating a positive feedback loop. Complex binding also prevents rapid ubiquitin-dependent proteosomal degradation of target proteins." [GOC:bhm, GOC:pad, GOC:PARL, PMID:21855797, PMID:22939624]
comment: An example of this is HSP90AB1 in human (UniProt symbol P08238) in PMID:21855797 (inferred from direct assay).
-is_a: GO:0101031 ! chaperone complex
+is_a: GO:0101031 ! protein folding chaperone complex
relationship: part_of GO:0005737 ! cytoplasm
[Term]
@@ -524262,7 +527081,6 @@ def: "The process in which UDP-N-acetylglucosamine is transported across a membr
synonym: "UDP-N-acetylglucosamine transport" RELATED []
is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:1990570
@@ -524322,7 +527140,6 @@ def: "The process in which L-ornithine is transported across a mitochondrial mem
synonym: "mitochondrial ornithine transmembrane transport" BROAD []
synonym: "mitochondrial ornithine transport" RELATED []
is_a: GO:1903352 ! L-ornithine transmembrane transport
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:1990576
@@ -524346,7 +527163,7 @@ namespace: cellular_component
def: "The membrane of the perinuclear endoplasmic reticulum, which is the portion of endoplasmic reticulum, the intracellular network of tubules and cisternae, that occurs near the nucleus." [PMID:25454947]
synonym: "perinuclear ER membrane" EXACT []
is_a: GO:0031090 ! organelle membrane
-relationship: part_of GO:0042175 ! nuclear outer membrane-endoplasmic reticulum membrane network
+relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
relationship: part_of GO:0097038 ! perinuclear endoplasmic reticulum
[Term]
@@ -524392,7 +527209,7 @@ is_obsolete: true
id: GO:1990583
name: phospholipase D activator activity
namespace: molecular_function
-def: "Increases the activity of the enzyme phospholipase D." [PMID:7972129]
+def: "Binds to and increases the activity of the enzyme phospholipase D." [PMID:7972129]
is_a: GO:0016004 ! phospholipase activator activity
[Term]
@@ -524482,7 +527299,7 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:1990594
name: L-altrarate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O." [PMID:17649980]
+def: "Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate + H2O." [PMID:17649980]
synonym: "L-talarate dehydratase activity" EXACT []
xref: RHEA:44028
is_a: GO:0016836 ! hydro-lyase activity
@@ -524496,10 +527313,12 @@ is_a: GO:0004930 ! G protein-coupled receptor activity
[Term]
id: GO:1990596
-name: histone H3-K4 deacetylation
+name: obsolete histone H3-K4 deacetylation
namespace: biological_process
-def: "The modification of histone H3 by the removal of an acetyl group from lysine at position 4 of the histone." [PMID:20299449]
-is_a: GO:0070932 ! histone H3 deacetylation
+def: "OBSOLETE. The modification of histone H3 by the removal of an acetyl group from lysine at position 4 of the histone." [PMID:20299449]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:1990162
[Term]
id: GO:1990597
@@ -524523,7 +527342,7 @@ id: GO:1990600
name: single-stranded DNA endodeoxyribonuclease activator activity
namespace: molecular_function
def: "Increases the activity of a single-stranded DNA endodeoxyribonuclease activator activity." [PMID:25203555]
-is_a: GO:0008047 ! enzyme activator activity
+is_a: GO:0140656 ! endodeoxyribonuclease activator activity
[Term]
id: GO:1990601
@@ -524606,7 +527425,7 @@ id: GO:1990609
name: glutamate-cysteine ligase regulator activity
namespace: molecular_function
def: "Binds to and modulates the activity of glutamate-cysteine ligase." [PMID:8103521]
-is_a: GO:0030234 ! enzyme regulator activity
+is_a: GO:0055103 ! ligase regulator activity
[Term]
id: GO:1990610
@@ -524630,15 +527449,6 @@ name: Sad1-Kms1 LINC complex
namespace: cellular_component
def: "A LINC complex implicated in the connection of DNA double strand breaks to the cytoskeleton during DNA double-strand break repair." [GOC:vw, PMID:24943839, PMID:24947240]
is_a: GO:0034993 ! meiotic nuclear membrane microtubule tethering complex
-is_a: GO:1990391 ! DNA repair complex
-
-[Term]
-id: GO:1990613
-name: mitochondrial membrane fusion
-namespace: biological_process
-def: "The joining of two lipid bilayers that surround the mitochondria." [PMID:12052774]
-is_a: GO:0007006 ! mitochondrial membrane organization
-is_a: GO:0090174 ! organelle membrane fusion
[Term]
id: GO:1990615
@@ -524656,7 +527466,6 @@ namespace: biological_process
def: "The directed movement of magnesium ions out of mitochondrial matrix into the cytosol by means of some agent such as a transporter or pore." [PMID:25585246]
synonym: "magnesium ion efflux from mitochondrion" EXACT []
is_a: GO:0045016 ! mitochondrial magnesium ion transmembrane transport
-is_a: GO:0070839 ! metal ion export
[Term]
id: GO:1990617
@@ -524721,7 +527530,8 @@ synonym: "ATF3-CHOP complex" EXACT [GOC:bf]
synonym: "CHOP-ATF3 heterodimer" EXACT [GOC:bf]
synonym: "CHOP-ATF3 heterodimeric complex" EXACT [GOC:bf]
synonym: "GADD153-ATF3 complex" EXACT [GOC:bf]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0005667 ! transcription regulator complex
+is_a: GO:0140513 ! nuclear protein-containing complex
[Term]
id: GO:1990623
@@ -524755,7 +527565,7 @@ namespace: biological_process
def: "The membrane organization process that joins two mitochondrial outer membranes to form a single membrane." [GOC:vw, PMID:21385840]
synonym: "mitochondrion outer membrane fusion" EXACT []
is_a: GO:0007008 ! outer mitochondrial membrane organization
-is_a: GO:1990613 ! mitochondrial membrane fusion
+relationship: part_of GO:0008053 ! mitochondrial fusion
[Term]
id: GO:1990627
@@ -524764,7 +527574,7 @@ namespace: biological_process
def: "The membrane organization process that joins two mitochondrial inner membranes to form a single membrane." [GOC:vw, PMID:17055438]
synonym: "mitochondrion inner membrane fusion" EXACT []
is_a: GO:0007007 ! inner mitochondrial membrane organization
-is_a: GO:1990613 ! mitochondrial membrane fusion
+relationship: part_of GO:0008053 ! mitochondrial fusion
[Term]
id: GO:1990628
@@ -524842,8 +527652,11 @@ is_a: GO:0030425 ! dendrite
id: GO:1990636
name: reproductive senescence
namespace: biological_process
-def: "A natural reduction in reproductive capacity with aging, often taking the form of a switch from regular reproductive cycles to irregular and infrequent ones." [PMID:24914937, PMID:25523082]
-is_a: GO:0010259 ! multicellular organism aging
+def: "A life cycle stage during which the reproductive capacity and fitness of an organism declines." [PMID:24914937, PMID:25523082, PMID:27353257]
+comment: Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase.
+subset: gocheck_do_not_annotate
+synonym: "ovarian senescence" NARROW []
+is_a: GO:0044848 ! biological phase
[Term]
id: GO:1990637
@@ -525040,7 +527853,7 @@ synonym: "sequestration of manganese ion" EXACT []
synonym: "storage of manganese ion" EXACT []
is_a: GO:0051238 ! sequestering of metal ion
is_a: GO:0051651 ! maintenance of location in cell
-relationship: part_of GO:0030026 ! cellular manganese ion homeostasis
+relationship: part_of GO:0030026 ! intracellular manganese ion homeostasis
[Term]
id: GO:1990660
@@ -525170,12 +527983,13 @@ relationship: part_of GO:0048219 ! inter-Golgi cisterna vesicle-mediated transpo
[Term]
id: GO:1990673
-name: intrinsic component of endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane
+name: obsolete intrinsic component of endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane
namespace: cellular_component
-def: "The component of the ERGIC membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+def: "OBSOLETE. The component of the ERGIC membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic component of endoplasmic reticulum-Golgi intermediate compartment membrane" EXACT []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:0033116 ! endoplasmic reticulum-Golgi intermediate compartment membrane
+is_obsolete: true
+replaced_by: GO:0033116
[Term]
id: GO:1990674
@@ -525347,30 +528161,33 @@ relationship: part_of GO:0000301 ! retrograde transport, vesicle recycling withi
[Term]
id: GO:1990693
-name: intrinsic component of Golgi cis cisterna membrane
+name: obsolete intrinsic component of Golgi cis cisterna membrane
namespace: cellular_component
-def: "The component of the Golgi cis cisterna membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+def: "OBSOLETE. The component of the Golgi cis cisterna membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic component of cis-Golgi cisterna membrane" EXACT []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:1990674 ! Golgi cis cisterna membrane
+is_obsolete: true
+replaced_by: GO:1990674
[Term]
id: GO:1990694
-name: intrinsic component of Golgi medial cisterna membrane
+name: obsolete intrinsic component of Golgi medial cisterna membrane
namespace: cellular_component
-def: "The component of the Golgi medial cisterna membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+def: "OBSOLETE. The component of the Golgi medial cisterna membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic component of medial-Golgi cisterna membrane" EXACT []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:1990675 ! Golgi medial cisterna membrane
+is_obsolete: true
+replaced_by: GO:1990675
[Term]
id: GO:1990695
-name: intrinsic component of Golgi trans cisterna membrane
+name: obsolete intrinsic component of Golgi trans cisterna membrane
namespace: cellular_component
-def: "The component of the Golgi trans cisterna membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+def: "OBSOLETE. The component of the Golgi trans cisterna membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "intrinsic component of trans-Golgi cisterna membrane" EXACT []
-is_a: GO:0031300 ! intrinsic component of organelle membrane
-relationship: part_of GO:1990676 ! Golgi trans cisterna membrane
+is_obsolete: true
+replaced_by: GO:1990676
[Term]
id: GO:1990696
@@ -525415,41 +528232,45 @@ relationship: part_of GO:0007000 ! nucleolus organization
[Term]
id: GO:1990701
-name: integral component of endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane
+name: obsolete integral component of endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane
namespace: cellular_component
-def: "The component of the ERGIC membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+def: "OBSOLETE. The component of the ERGIC membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral component of endoplasmic reticulum-Golgi intermediate compartment membrane" EXACT []
synonym: "integral component of ER-Golgi intermediate compartment membrane" EXACT []
synonym: "integral component of ERGIC membrane" EXACT []
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:1990673 ! intrinsic component of endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane
+is_obsolete: true
+replaced_by: GO:0033116
[Term]
id: GO:1990702
-name: integral component of Golgi cis cisterna membrane
+name: obsolete integral component of Golgi cis cisterna membrane
namespace: cellular_component
-def: "The component of the Golgi cis membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+def: "OBSOLETE. The component of the Golgi cis membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral component of cis-Golgi cisterna membrane" EXACT []
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:1990693 ! intrinsic component of Golgi cis cisterna membrane
+is_obsolete: true
+replaced_by: GO:1990674
[Term]
id: GO:1990703
-name: integral component of Golgi medial cisterna membrane
+name: obsolete integral component of Golgi medial cisterna membrane
namespace: cellular_component
-def: "The component of the Golgi medial membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+def: "OBSOLETE. The component of the Golgi medial membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral component of medial-Golgi cisterna membrane" EXACT []
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:1990694 ! intrinsic component of Golgi medial cisterna membrane
+is_obsolete: true
+replaced_by: GO:1990675
[Term]
id: GO:1990704
-name: integral component of Golgi trans cisterna membrane
+name: obsolete integral component of Golgi trans cisterna membrane
namespace: cellular_component
-def: "The component of the Golgi trans membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+def: "OBSOLETE. The component of the Golgi trans membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral component of trans-Golgi cisterna membrane" EXACT []
-is_a: GO:0031301 ! integral component of organelle membrane
-is_a: GO:1990695 ! intrinsic component of Golgi trans cisterna membrane
+is_obsolete: true
+replaced_by: GO:1990676
[Term]
id: GO:1990705
@@ -525491,7 +528312,7 @@ def: "A homodimeric mismatch repair complex involved in binding to and correctin
comment: An example of this is MutS in E. coli (UniProt symbol P23909) in PMID:21666597 (inferred from physical interaction).
synonym: "MutS mismatch repair complex" EXACT []
is_a: GO:0032300 ! mismatch repair complex
-is_a: GO:1902494 ! catalytic complex
+is_a: GO:1990391 ! DNA repair complex
[Term]
id: GO:1990711
@@ -525649,14 +528470,6 @@ synonym: "MAD1-MAD2 complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0005737 ! cytoplasm
-[Term]
-id: GO:1990729
-name: primary miRNA modification
-namespace: biological_process
-def: "The covalent alteration of one or more nucleotides within a primary miRNA molecule to produce a primary miRNA molecule with a sequence that differs from that coded genetically." [PMID:25799998]
-is_a: GO:0009451 ! RNA modification
-is_a: GO:0031053 ! primary miRNA processing
-
[Term]
id: GO:1990730
name: VCP-NSFL1C complex
@@ -525668,9 +528481,10 @@ relationship: part_of GO:0005737 ! cytoplasm
[Term]
id: GO:1990731
-name: UV-damage excision repair, DNA incision
+name: obsolete UV-damage excision repair, DNA incision
namespace: biological_process
-def: "A process that results in the endonucleolytic cleavage of the damaged strand of DNA immediately 5' of a UV-induced damage site, and is the first part of a DNA repair process that acts on both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone 6-4 photoproducts (6-4PPs)." [PMID:10704216]
+def: "OBSOLETE. A process that results in the endonucleolytic cleavage of the damaged strand of DNA immediately 5' of a UV-induced damage site, and is the first part of a DNA repair process that acts on both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone 6-4 photoproducts (6-4PPs)." [PMID:10704216]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "alternative excision repair, DNA incision" RELATED [PMID:10704216]
synonym: "DNA incision involved in AER" RELATED [PMID:10704216]
synonym: "DNA incision involved in alternative excision repair" RELATED [PMID:10704216]
@@ -525681,8 +528495,8 @@ synonym: "DNA incision involved in UVER" EXACT []
synonym: "nucleic acid cleavage involved in UV-damage excision repair" EXACT []
synonym: "UV-damaged DNA endonuclease-dependent excision repair, DNA incision" EXACT []
synonym: "UVDE-dependent excision repair, DNA incision" EXACT []
-is_a: GO:0090305 ! nucleic acid phosphodiester bond hydrolysis
-relationship: part_of GO:0070914 ! UV-damage excision repair
+is_obsolete: true
+replaced_by: GO:0070914
[Term]
id: GO:1990732
@@ -525789,17 +528603,9 @@ id: GO:1990743
name: protein sialylation
namespace: biological_process
def: "A protein modification process that results in the addition of a sialic acid unit to the end of an oligosaccharide chain in a glycoprotein." [PMID:21930713]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0036211 ! protein modification process
is_a: GO:0097503 ! sialylation
-[Term]
-id: GO:1990744
-name: primary miRNA methylation
-namespace: biological_process
-def: "The posttranscriptional addition of methyl groups to specific residues in an primary miRNA molecule." [PMID:25799998]
-is_a: GO:0001510 ! RNA methylation
-is_a: GO:1990729 ! primary miRNA modification
-
[Term]
id: GO:1990745
name: EARP complex
@@ -525892,7 +528698,7 @@ namespace: molecular_function
def: "The binding activity of a molecule that brings together a ubiquitin ligase and its substrate. Usually mediated by F-box BTB/POZ domain proteins." [PMID:24658274]
synonym: "protein binding, bridging involved in substrate recognition for ubiquitination" EXACT []
synonym: "ubiquitin ligase substrate adaptor" EXACT []
-is_a: GO:0030674 ! protein-macromolecule adaptor activity
+is_a: GO:0140767 ! enzyme-substrate adaptor activity
[Term]
id: GO:1990757
@@ -525913,12 +528719,14 @@ is_a: GO:0051315 ! attachment of mitotic spindle microtubules to kinetochore
[Term]
id: GO:1990760
-name: osmolarity-sensing cation channel activity
+name: osmolarity-sensing monoatomic cation channel activity
namespace: molecular_function
-def: "Enables the transmembrane transfer of a cation by a channel that opens when a change in the osmolarity occurs in the extracellular space of the cell in which the cation channel resides." [PMID:18279313]
+def: "Enables the transmembrane transfer of a monoatomic cation by a channel that opens when a change in the osmolarity occurs in the extracellular space of the cell in which the cation channel resides." [PMID:18279313]
+synonym: "osmolarity-sensing cation channel activity" BROAD []
is_a: GO:0005034 ! osmosensor activity
-is_a: GO:0005261 ! cation channel activity
-is_a: GO:0022836 ! gated channel activity
+is_a: GO:0005261 ! monoatomic cation channel activity
+is_a: GO:0022839 ! monoatomic ion gated channel activity
+is_a: GO:0022890 ! inorganic cation transmembrane transporter activity
[Term]
id: GO:1990761
@@ -526051,7 +528859,7 @@ id: GO:1990778
name: protein localization to cell periphery
namespace: biological_process
def: "A process in which a protein is transported to, or maintained in, the cell periphery." [PMID:18216290]
-is_a: GO:0034613 ! cellular protein localization
+is_a: GO:0008104 ! protein localization
[Term]
id: GO:1990779
@@ -526064,7 +528872,6 @@ synonym: "GPIb-IX-V complex" EXACT []
synonym: "GPIb-V-IX complex" EXACT []
is_a: GO:0090665 ! glycoprotein complex
is_a: GO:0098802 ! plasma membrane signaling receptor complex
-relationship: part_of GO:0005887 ! integral component of plasma membrane
[Term]
id: GO:1990780
@@ -526160,7 +528967,6 @@ def: "Any process that results in a change in state or activity of a cell or an
synonym: "response to astrocyte-derived trophic factor" EXACT []
synonym: "response to ATF" EXACT []
synonym: "response to GDNF" EXACT []
-is_a: GO:0009719 ! response to endogenous stimulus
is_a: GO:0070848 ! response to growth factor
[Term]
@@ -526180,7 +528986,6 @@ synonym: "cellular response to astrocyte-derived trophic factor" EXACT []
synonym: "cellular response to ATF" EXACT []
synonym: "cellular response to GDNF" EXACT []
is_a: GO:0071363 ! cellular response to growth factor stimulus
-is_a: GO:0071495 ! cellular response to endogenous stimulus
is_a: GO:1990790 ! response to glial cell derived neurotrophic factor
[Term]
@@ -526305,7 +529110,7 @@ relationship: part_of GO:0035869 ! ciliary transition zone
id: GO:1990806
name: ligand-gated ion channel signaling pathway
namespace: biological_process
-def: "A series of molecular signals initiated by activation of a ligand-gated ion channel on the surface of a cell. The pathway begins with binding of an extracellular ligand to a ligand-gated ion channel and ends with a molecular function that directly regulates a downstream cellular process, e.g. transcription." [GOC:bhm, PMID:25869137]
+def: "The series of molecular signals initiated by activation of a ligand-gated ion channel on the surface of a cell. The pathway begins with binding of an extracellular ligand to a ligand-gated ion channel and ends with a molecular function that directly regulates a downstream cellular process, e.g. transcription." [GOC:bhm, PMID:25869137]
synonym: "ligand-gated ion channel signalling pathway" EXACT []
is_a: GO:0007165 ! signal transduction
@@ -526365,6 +529170,7 @@ namespace: biological_process
def: "The process in which the association between sister chromatids of a replicated chromosome centromeric region is maintained during homologous chromosome segregation after cohesin is cleaved by separase along the arm regions." [PMID:14730319, PMID:25533956]
synonym: "protection of centromeric cohesion during meiotic anaphase I" EXACT []
is_a: GO:0035875 ! maintenance of meiotic sister chromatid cohesion, centromeric
+is_a: GO:1903046 ! meiotic cell cycle process
relationship: part_of GO:0051455 ! monopolar spindle attachment to meiosis I kinetochore
[Term]
@@ -526395,27 +529201,36 @@ is_a: GO:0044232 ! organelle membrane contact site
[Term]
id: GO:1990817
-name: RNA adenylyltransferase activity
+name: poly(A) RNA polymerase activity
namespace: molecular_function
-def: "Catalysis of the template-independent extension of the 3'- end of an RNA strand by addition of one adenosine molecule at a time. Cannot initiate a chain 'de novo'. The primer, depending on the source of the enzyme, may be an RNA, or oligo(A) bearing a 3'-OH terminal group." [GOC:vw]
-is_a: GO:0004652 ! polynucleotide adenylyltransferase activity
+def: "Catalysis of the reaction: ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide. The primer may be an RNA or DNA fragment, or oligo(A) bearing a 3'-OH terminal group." [PMID:13965521, RHEA:11332]
+synonym: "NTP polymerase activity" BROAD [EC:2.7.7.19]
+synonym: "poly(A) polymerase activity" RELATED [EC:2.7.7.19]
+synonym: "polynucleotide adenylyltransferase activity" EXACT []
+synonym: "RNA adenylating enzyme" EXACT [EC:2.7.7.19]
+synonym: "RNA adenyltransferase activity" EXACT []
+synonym: "RNA adenylyltransferase activity" EXACT []
+xref: EC:2.7.7.19
+xref: MetaCyc:POLYNUCLEOTIDE-ADENYLYLTRANSFERASE-RXN
+xref: Reactome:R-HSA-72185 "mRNA polyadenylation"
+xref: RHEA:11332
+is_a: GO:0070566 ! adenylyltransferase activity
[Term]
id: GO:1990818
name: L-arginine transmembrane export from vacuole
namespace: biological_process
def: "The directed movement of L-arginine out of the vacuole, across the vacuolar membrane." [PMID:26083598]
-is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0032974 ! amino acid transmembrane export from vacuole
-is_a: GO:0098655 ! cation transmembrane transport
-is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:0072337 ! modified amino acid transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
id: GO:1990819
-name: actin fusion focus
+name: mating projection actin fusion focus
namespace: cellular_component
def: "A focus at the mating projection tip where the cell wall is degraded during conjugation with cellular fusion. Actin filaments form an aster-like structure from this location." [PMID:25825517]
+synonym: "actin fusion focus" BROAD []
is_a: GO:0110165 ! cellular anatomical entity
relationship: part_of GO:0015629 ! actin cytoskeleton
relationship: part_of GO:0043332 ! mating projection tip
@@ -526563,7 +529378,7 @@ id: GO:1990838
name: poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends
namespace: molecular_function
def: "Catalysis of 3' exonucleolytic cleavage of poly(U), to form poly(U)-N containing a 3' uridine cyclic phosphate (U>P)." [PMID:23022480]
-is_a: GO:0000175 ! 3'-5'-exoribonuclease activity
+is_a: GO:0000175 ! 3'-5'-RNA exonuclease activity
[Term]
id: GO:1990839
@@ -526695,11 +529510,11 @@ is_a: GO:0098840 ! protein transport along microtubule
[Term]
id: GO:1990853
-name: histone H2A SQE motif phosphorylation
+name: obsolete histone H2A SQE motif phosphorylation
namespace: biological_process
-def: "The modification of histone H2A by the addition of an phosphate group to the serine residue in the SQE motif of the histone." [DOI:10.1038/35052000, PMID:15226425]
-is_a: GO:0018105 ! peptidyl-serine phosphorylation
-is_a: GO:1990164 ! histone H2A phosphorylation
+def: "OBSOLETE. The modification of histone H2A by the addition of an phosphate group to the serine residue in the SQE motif of the histone." [DOI:10.1038/35052000, PMID:15226425]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:1990854
@@ -526777,7 +529592,7 @@ namespace: cellular_component
def: "A protein complex that resides in the inner nuclear membrane and anchors telomeres to the nuclear envelope. In fission yeast, it is composed of Bqt3 and Bqt4." [PMID:19948484]
is_a: GO:0098796 ! membrane protein complex
is_a: GO:0140513 ! nuclear protein-containing complex
-relationship: part_of GO:0005639 ! integral component of nuclear inner membrane
+relationship: part_of GO:0005637 ! nuclear inner membrane
[Term]
id: GO:1990863
@@ -526883,11 +529698,12 @@ is_obsolete: true
[Term]
id: GO:1990873
-name: intrinsic component of plasma membrane of cell tip
+name: obsolete intrinsic component of plasma membrane of cell tip
namespace: cellular_component
-def: "The component of the plasma membrane surrounding the cell tip consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the plasma membrane surrounding the cell tip or some other covalently attached group such as a GPI anchor that is similarly embedded in the plasma membrane surrounding the cell tip." [PMID:20624220]
-is_a: GO:0031226 ! intrinsic component of plasma membrane
-relationship: part_of GO:0031520 ! plasma membrane of cell tip
+def: "OBSOLETE. The component of the plasma membrane surrounding the cell tip consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the plasma membrane surrounding the cell tip or some other covalently attached group such as a GPI anchor that is similarly embedded in the plasma membrane surrounding the cell tip." [PMID:20624220]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0031520
[Term]
id: GO:1990874
@@ -526922,12 +529738,14 @@ relationship: part_of GO:0005643 ! nuclear pore
[Term]
id: GO:1990877
-name: Lst4-Lst7 complex
-namespace: cellular_component
-def: "A heterodimeric complex that functions as a GTPase-Activating Protein (GAP) Complex for members of the Rag family of GTPases. In the budding yeast, this complex contains Lst4 and Lst7, while the orthologous mammalian complex contains Follicular (FLCN) and either follicular interaction protein 1 (FNIP1) or FNIP2." [GOC:rn, PMID:24095279, PMID:26387955]
-synonym: "FLCN-FNIP1 complex" RELATED []
-synonym: "FLCN-FNIP2 complex" RELATED []
-synonym: "FNIP-Folliculin RagC/D GAP complex" RELATED []
+name: FNIP-folliculin RagC/D GAP
+namespace: cellular_component
+def: "A heterodimeric complex that functions as a GTPase-Activating Protein (GAP) Complex for members of the Rag family of GTPases. In the budding yeast, this complex contains Lst4 and Lst7, while the orthologous mammalian complex contains follicular (FLCN) and either follicular interacting protein 1 (FNIP1) or FNIP2." [GOC:rn, PMID:24095279, PMID:26387955, PMID:34805795]
+synonym: "BFC complex" EXACT [PMID:34805795]
+synonym: "FLCN-FNIP1 complex" EXACT []
+synonym: "FLCN-FNIP2 complex" EXACT []
+synonym: "FNIP-Folliculin RagC/D GAP complex" EXACT []
+synonym: "Lst4-Lst7 complex" EXACT []
is_a: GO:1902773 ! GTPase activator complex
[Term]
@@ -526953,7 +529771,7 @@ name: cellular detoxification of copper ion
namespace: biological_process
def: "Any process that reduces or removes the toxicity of copper ions in a cell. These include transport of copper cations away from sensitive areas and to compartments or complexes whose purpose is sequestration." [PMID:10369673]
is_a: GO:0010273 ! detoxification of copper ion
-is_a: GO:1990748 ! cellular detoxification
+is_a: GO:0140961 ! cellular detoxification of metal ion
relationship: part_of GO:0071280 ! cellular response to copper ion
[Term]
@@ -527056,7 +529874,7 @@ id: GO:1990894
name: obsolete positive regulation of induction of conjugation with cellular fusion by regulation of transcription from RNA polymerase II promoter
namespace: biological_process
def: "OBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in positive regulation of induction of conjugation with cellular fusion." [PMID:22144909]
-comment: This term was obsoleted during the TG review process. It should have been created using a template.
+comment: This term was obsoleted during the TG review process. It should have been created using a template.
is_obsolete: true
[Term]
@@ -527086,21 +529904,19 @@ is_obsolete: true
[Term]
id: GO:1990898
-name: meiotic DNA double-strand break clipping
+name: obsolete meiotic DNA double-strand break clipping
namespace: biological_process
-def: "The process by which SPO11/Rec12-oligonucleotide complexes are removed from 5' DNA double-strand breaks induced during meiosis. Proteins involved in this process include the MRX/MRN complex and Sae2/Ctp1/RBBP8(CtIP)." [PMID:26130711]
-is_a: GO:0044260 ! cellular macromolecule metabolic process
-is_a: GO:1903046 ! meiotic cell cycle process
-relationship: part_of GO:0010705 ! meiotic DNA double-strand break processing involved in reciprocal meiotic recombination
+def: "OBSOLETE. The process by which SPO11/Rec12-oligonucleotide complexes are removed from 5' DNA double-strand breaks induced during meiosis. Proteins involved in this process include the MRX/MRN complex and Sae2/Ctp1/RBBP8(CtIP)." [PMID:26130711]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:1990899
-name: meiotic DNA double-strand break resectioning
+name: obsolete meiotic DNA double-strand break resectioning
namespace: biological_process
-def: "The process following clipping in double-strand break processing of SPO11 induced breaks, where long-tract single-stranded 3'-end DNA is generated from naked (SPO11 has been removed) 5' ends." [PMID:26130711]
-is_a: GO:0044260 ! cellular macromolecule metabolic process
-is_a: GO:1903046 ! meiotic cell cycle process
-relationship: part_of GO:0010705 ! meiotic DNA double-strand break processing involved in reciprocal meiotic recombination
+def: "OBSOLETE. The process following clipping in double-strand break processing of SPO11 induced breaks, where long-tract single-stranded 3'-end DNA is generated from naked (SPO11 has been removed) 5' ends." [PMID:26130711]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:1990900
@@ -527225,12 +530041,12 @@ relationship: part_of GO:0097524 ! sperm plasma membrane
[Term]
id: GO:1990914
-name: integral component of periplasmic side of plasma membrane
+name: obsolete integral component of periplasmic side of plasma membrane
namespace: cellular_component
-def: "The component of the plasma membrane consisting of the gene products that penetrate only the periplasmic side of the membrane." [GOC:bhm, PMID:15919996]
-comment: An example of this is hyaA in E. coli (P69739) in PMID:23260654 (inferred from direct assay).
-is_a: GO:0031237 ! intrinsic component of periplasmic side of plasma membrane
-is_a: GO:0071575 ! integral component of external side of plasma membrane
+def: "OBSOLETE. The component of the plasma membrane consisting of the gene products that penetrate only the periplasmic side of the membrane." [GOC:bhm, PMID:15919996]
+comment: This term was obsoleted because it represents protein topology, not a cellular component.
+is_obsolete: true
+replaced_by: GO:0098567
[Term]
id: GO:1990915
@@ -527279,10 +530095,12 @@ is_a: GO:0043495 ! protein-membrane adaptor activity
[Term]
id: GO:1990920
-name: proteasome localization to nuclear periphery
+name: obsolete proteasome localization to nuclear periphery
namespace: biological_process
-def: "Any process in which the proteasome is transported to, or maintained at the nuclear periphery." [PMID:11084332]
-is_a: GO:0031144 ! proteasome localization
+def: "OBSOLETE. Any process in which the proteasome is transported to, or maintained at the nuclear periphery." [PMID:11084332]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:1990919
[Term]
id: GO:1990921
@@ -527323,7 +530141,7 @@ is_obsolete: true
id: GO:1990926
name: short-term synaptic potentiation
namespace: biological_process
-def: "The process by which synaptic transmission, induced by the arrival of a spike (action potential) at a synapse, acts to increase the amount of neurotransmitter released in response to the arrival of subsequent spikes. This effect is seen when a train of closely space spikes arrives at a synapse with a low initial release probability. It occurs in a timeframe of tens to hundreds of milliseconds." [GOC:dos, GOC:sp, ISBN:9780071120005, PMID:11826273, PMID:26738595]
+def: "The process by which synaptic transmission, induced by the arrival of a spike (action potential) at a synapse, acts to increase the amount of neurotransmitter released in response to the arrival of subsequent spikes. This effect is seen when a train of closely space spikes arrives at a synapse with a low initial release probability. It occurs in a timeframe of tens to hundreds of milliseconds." [GOC:dos, GOC:sp, ISBN:9780071120005, PMID:11826273, PMID:26738595]
comment: The mechanism of short term potentiation is thought to be either increased influx of calcium into the presynapse (Zucker and Regeh, 2002 PMID:11826273) increased sensitivity to calcium (Jackman et al., 2016 PMID:26738595) or both.
synonym: "synaptic facilitation" EXACT [ISBN:9780071120005, PMID:11826273, PMID:26738595]
is_a: GO:0048167 ! regulation of synaptic plasticity
@@ -527384,7 +530202,7 @@ id: GO:1990933
name: microtubule cytoskeleton attachment to nuclear envelope
namespace: biological_process
def: "A process in which the microtubule cytoskeleton is attached to the nuclear envelope." [PMID:14655046, PMID:20507227]
-is_a: GO:0007010 ! cytoskeleton organization
+is_a: GO:0000226 ! microtubule cytoskeleton organization
[Term]
id: GO:1990934
@@ -527459,7 +530277,6 @@ synonym: "microtubule sliding involved in mitotic metaphase chromosome recapture
synonym: "microtubule sliding involved in sister kinetochore recapture" EXACT [GOC:TermGenie]
synonym: "sister kinetochore recapture" EXACT []
is_a: GO:0051303 ! establishment of chromosome localization
-is_a: GO:1903047 ! mitotic cell cycle process
relationship: part_of GO:0007080 ! mitotic metaphase plate congression
[Term]
@@ -527605,7 +530422,7 @@ name: xenobiotic detoxification by transmembrane export across the plasma membra
namespace: biological_process
def: "A process that reduces or removes the toxicity of a xenobiotic by exporting it outside the cell." [PMID:28355133]
synonym: "drug transmembrane export" NARROW []
-is_a: GO:0046618 ! xenobiotic export
+is_a: GO:0046618 ! xenobiotic export from cell
is_a: GO:0140115 ! export across plasma membrane
relationship: part_of GO:0098754 ! detoxification
@@ -527639,7 +530456,7 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:1990965
name: cytosylglucuronate decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cytosylglucuronic acid + H(+) = cytosylarabinopyranose + CO(2)." [GOC:pr, GOC:tb, PMID:23874663]
+def: "Catalysis of the reaction: cytosylglucuronic acid + H+ = cytosylarabinopyranose + CO2." [GOC:pr, GOC:tb, PMID:23874663]
comment: This enzymatic activity was shown to be involved in the bacterial blasticidin S biosynthetic pathway.
is_a: GO:0016831 ! carboxy-lyase activity
@@ -527650,7 +530467,6 @@ namespace: biological_process
def: "The process of generating ATP in the nucleus from poly-ADP-D-ribose. Nuclear ATP generation is required for extensive chromatin remodeling events that are energy-consuming." [PMID:27257257]
is_a: GO:0043170 ! macromolecule metabolic process
is_a: GO:0046034 ! ATP metabolic process
-is_a: GO:1901135 ! carbohydrate derivative metabolic process
[Term]
id: GO:1990967
@@ -527832,8 +530648,8 @@ name: regulation of DNA damage checkpoint
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of a DNA damage checkpoint." [GOC:obol]
synonym: "regulation of DNA damage response, signal transduction resulting in cell cycle arrest" RELATED [GOC:obol]
+is_a: GO:0080135 ! regulation of cellular response to stress
is_a: GO:1901976 ! regulation of cell cycle checkpoint
-is_a: GO:2001020 ! regulation of response to DNA damage stimulus
relationship: regulates GO:0000077 ! DNA damage checkpoint signaling
[Term]
@@ -527844,7 +530660,6 @@ def: "Any process that stops, prevents, or reduces the frequency, rate or extent
synonym: "negative regulation of DNA damage response, signal transduction resulting in cell cycle arrest" RELATED [GOC:obol]
is_a: GO:1901977 ! negative regulation of cell cycle checkpoint
is_a: GO:2000001 ! regulation of DNA damage checkpoint
-is_a: GO:2001021 ! negative regulation of response to DNA damage stimulus
relationship: negatively_regulates GO:0000077 ! DNA damage checkpoint signaling
[Term]
@@ -527855,7 +530670,6 @@ def: "Any process that activates or increases the frequency, rate or extent of a
synonym: "positive regulation of DNA damage response, signal transduction resulting in cell cycle arrest" RELATED [GOC:obol]
is_a: GO:1901978 ! positive regulation of cell cycle checkpoint
is_a: GO:2000001 ! regulation of DNA damage checkpoint
-is_a: GO:2001022 ! positive regulation of response to DNA damage stimulus
relationship: positively_regulates GO:0000077 ! DNA damage checkpoint signaling
[Term]
@@ -527900,7 +530714,6 @@ def: "Any process that modulates the frequency, rate or extent of protein locali
synonym: "regulation of protein localisation at cell surface" EXACT [GOC:mah]
synonym: "regulation of protein localization at cell surface" EXACT []
is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0034394 ! protein localization to cell surface
[Term]
@@ -527910,7 +530723,6 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to the cell surface." [GOC:obol]
synonym: "negative regulation of protein localisation at cell surface" EXACT [GOC:mah]
synonym: "negative regulation of protein localization at cell surface" EXACT []
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:2000008 ! regulation of protein localization to cell surface
relationship: negatively_regulates GO:0034394 ! protein localization to cell surface
@@ -527922,7 +530734,6 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of protein localization to the cell surface." [GOC:obol]
synonym: "positive regulation of protein localisation at cell surface" EXACT [GOC:mah]
synonym: "positive regulation of protein localization at cell surface" EXACT []
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:2000008 ! regulation of protein localization to cell surface
relationship: positively_regulates GO:0034394 ! protein localization to cell surface
@@ -528418,7 +531229,8 @@ synonym: "regulation of protein ubiquitinylation during ubiquitin-dependent prot
synonym: "regulation of protein ubiquitinylation during ubiquitin-dependent protein catabolism" EXACT [GOC:obol]
synonym: "regulation of protein ubiquitylation during ubiquitin-dependent protein catabolic process" EXACT [GOC:obol]
synonym: "regulation of protein ubiquitylation during ubiquitin-dependent protein catabolism" EXACT [GOC:obol]
-is_a: GO:1903050 ! regulation of proteolysis involved in cellular protein catabolic process
+is_a: GO:0009894 ! regulation of catabolic process
+is_a: GO:1903050 ! regulation of proteolysis involved in protein catabolic process
relationship: regulates GO:0006511 ! ubiquitin-dependent protein catabolic process
[Term]
@@ -528436,7 +531248,8 @@ synonym: "negative regulation of protein ubiquitinylation during ubiquitin-depen
synonym: "negative regulation of protein ubiquitinylation during ubiquitin-dependent protein catabolism" NARROW [GOC:obol]
synonym: "negative regulation of protein ubiquitylation during ubiquitin-dependent protein catabolic process" NARROW [GOC:obol]
synonym: "negative regulation of protein ubiquitylation during ubiquitin-dependent protein catabolism" NARROW [GOC:obol]
-is_a: GO:1903051 ! negative regulation of proteolysis involved in cellular protein catabolic process
+is_a: GO:0009895 ! negative regulation of catabolic process
+is_a: GO:1903051 ! negative regulation of proteolysis involved in protein catabolic process
is_a: GO:2000058 ! regulation of ubiquitin-dependent protein catabolic process
relationship: negatively_regulates GO:0006511 ! ubiquitin-dependent protein catabolic process
@@ -528454,7 +531267,8 @@ synonym: "positive regulation of protein ubiquitinylation during ubiquitin-depen
synonym: "positive regulation of protein ubiquitinylation during ubiquitin-dependent protein catabolism" NARROW [GOC:obol]
synonym: "positive regulation of protein ubiquitylation during ubiquitin-dependent protein catabolic process" NARROW [GOC:obol]
synonym: "positive regulation of protein ubiquitylation during ubiquitin-dependent protein catabolism" NARROW [GOC:obol]
-is_a: GO:1903052 ! positive regulation of proteolysis involved in cellular protein catabolic process
+is_a: GO:0009896 ! positive regulation of catabolic process
+is_a: GO:1903052 ! positive regulation of proteolysis involved in protein catabolic process
is_a: GO:2000058 ! regulation of ubiquitin-dependent protein catabolic process
relationship: positively_regulates GO:0006511 ! ubiquitin-dependent protein catabolic process
@@ -528586,8 +531400,9 @@ name: regulation of cytokinesis, site selection
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of site selection that occurs as part of cytokinesis." [GOC:mtg_cell_cycle, GOC:obol]
synonym: "regulation of site selection involved in cell cycle cytokinesis" EXACT []
+is_a: GO:0032879 ! regulation of localization
is_a: GO:0032954 ! regulation of cytokinetic process
-relationship: regulates GO:0007105 ! cytokinesis, site selection
+relationship: regulates GO:0007105 ! cytokinesis, division site positioning
[Term]
id: GO:2000074
@@ -528607,7 +531422,7 @@ def: "Any process that stops, prevents, or reduces the frequency, rate or extent
synonym: "negative regulation of site selection involved in cell cycle cytokinesis" EXACT []
is_a: GO:0032466 ! negative regulation of cytokinesis
is_a: GO:2000073 ! regulation of cytokinesis, site selection
-relationship: negatively_regulates GO:0007105 ! cytokinesis, site selection
+relationship: negatively_regulates GO:0007105 ! cytokinesis, division site positioning
[Term]
id: GO:2000076
@@ -528617,7 +531432,7 @@ def: "Any process that activates or increases the frequency, rate or extent of s
synonym: "positive regulation of site selection involved in cell cycle cytokinesis" EXACT []
is_a: GO:0032467 ! positive regulation of cytokinesis
is_a: GO:2000073 ! regulation of cytokinesis, site selection
-relationship: positively_regulates GO:0007105 ! cytokinesis, site selection
+relationship: positively_regulates GO:0007105 ! cytokinesis, division site positioning
[Term]
id: GO:2000077
@@ -528926,21 +531741,23 @@ relationship: positively_regulates GO:0002174 ! mammary stem cell proliferation
[Term]
id: GO:2000104
-name: negative regulation of DNA-dependent DNA replication
+name: negative regulation of DNA-templated DNA replication
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent DNA replication." [GOC:mah]
+synonym: "negative regulation of DNA-dependent DNA replication" EXACT []
is_a: GO:0008156 ! negative regulation of DNA replication
-is_a: GO:0090329 ! regulation of DNA-dependent DNA replication
-relationship: negatively_regulates GO:0006261 ! DNA-dependent DNA replication
+is_a: GO:0090329 ! regulation of DNA-templated DNA replication
+relationship: negatively_regulates GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:2000105
-name: positive regulation of DNA-dependent DNA replication
+name: positive regulation of DNA-templated DNA replication
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of DNA-dependent DNA replication." [GOC:mah]
+def: "Any process that activates or increases the frequency, rate or extent of DNA-templated DNA replication." [GOC:mah]
+synonym: "positive regulation of DNA-dependent DNA replication" EXACT []
is_a: GO:0045740 ! positive regulation of DNA replication
-is_a: GO:0090329 ! regulation of DNA-dependent DNA replication
-relationship: positively_regulates GO:0006261 ! DNA-dependent DNA replication
+is_a: GO:0090329 ! regulation of DNA-templated DNA replication
+relationship: positively_regulates GO:0006261 ! DNA-templated DNA replication
[Term]
id: GO:2000106
@@ -529011,32 +531828,31 @@ relationship: positively_regulates GO:0071888 ! macrophage apoptotic process
[Term]
id: GO:2000112
-name: regulation of cellular macromolecule biosynthetic process
+name: obsolete regulation of cellular macromolecule biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process." [GOC:obol]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process." [GOC:obol]
+comment: This term was obsoleted because it is not different from its parent, regulation of macromolecule biosynthetic process ; GO:0010556.
synonym: "regulation of cellular biopolymer biosynthetic process" EXACT [GOC:obol]
synonym: "regulation of cellular macromolecule anabolism" EXACT [GOC:obol]
synonym: "regulation of cellular macromolecule biosynthesis" EXACT [GOC:obol]
synonym: "regulation of cellular macromolecule formation" EXACT [GOC:obol]
synonym: "regulation of cellular macromolecule synthesis" EXACT [GOC:obol]
-is_a: GO:0010556 ! regulation of macromolecule biosynthetic process
-is_a: GO:0031326 ! regulation of cellular biosynthetic process
-relationship: regulates GO:0034645 ! cellular macromolecule biosynthetic process
+is_obsolete: true
+replaced_by: GO:0010556
[Term]
id: GO:2000113
-name: negative regulation of cellular macromolecule biosynthetic process
+name: obsolete negative regulation of cellular macromolecule biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process." [GOC:obol]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process." [GOC:obol]
+comment: This term was obsoleted because it is not different from its parent, negative regulation of macromolecule biosynthetic process ; GO:0010558.
synonym: "negative regulation of cellular biopolymer biosynthetic process" EXACT [GOC:obol]
synonym: "negative regulation of cellular macromolecule anabolism" EXACT [GOC:obol]
synonym: "negative regulation of cellular macromolecule biosynthesis" EXACT [GOC:obol]
synonym: "negative regulation of cellular macromolecule formation" EXACT [GOC:obol]
synonym: "negative regulation of cellular macromolecule synthesis" EXACT [GOC:obol]
-is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process
-is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
-relationship: negatively_regulates GO:0034645 ! cellular macromolecule biosynthetic process
+is_obsolete: true
+replaced_by: GO:0010558
[Term]
id: GO:2000114
@@ -529088,7 +531904,7 @@ id: GO:2000119
name: negative regulation of sodium-dependent phosphate transport
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of sodium-dependent phosphate transport." [GOC:BHF]
-is_a: GO:1903792 ! negative regulation of anion transport
+is_a: GO:0051051 ! negative regulation of transport
is_a: GO:2000118 ! regulation of sodium-dependent phosphate transport
relationship: negatively_regulates GO:0044341 ! sodium-dependent phosphate transport
@@ -529097,7 +531913,7 @@ id: GO:2000120
name: positive regulation of sodium-dependent phosphate transport
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of sodium-dependent phosphate transport." [GOC:BHF]
-is_a: GO:1903793 ! positive regulation of anion transport
+is_a: GO:0051050 ! positive regulation of transport
is_a: GO:2000118 ! regulation of sodium-dependent phosphate transport
relationship: positively_regulates GO:0044341 ! sodium-dependent phosphate transport
@@ -529309,40 +532125,43 @@ relationship: positively_regulates GO:0071935 ! octopamine signaling pathway inv
[Term]
id: GO:2000142
-name: regulation of DNA-templated transcription, initiation
+name: regulation of DNA-templated transcription initiation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA-templated transcription initiation." [GOC:mah, GOC:txnOH]
synonym: "regulation of DNA-dependent transcription, initiation" EXACT [GOC:txnOH]
+synonym: "regulation of DNA-templated transcription, initiation" EXACT []
synonym: "regulation of initiation of DNA-dependent transcription" EXACT [GOC:jh2]
synonym: "regulation of transcription initiation, DNA-dependent" EXACT [GOC:jh2]
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
-relationship: regulates GO:0006352 ! DNA-templated transcription, initiation
+is_a: GO:0006355 ! regulation of DNA-templated transcription
+relationship: regulates GO:0006352 ! DNA-templated transcription initiation
[Term]
id: GO:2000143
-name: negative regulation of DNA-templated transcription, initiation
+name: negative regulation of DNA-templated transcription initiation
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-templated transcription initiation." [GOC:mah, GOC:txnOH]
synonym: "negative regulation of DNA-dependent transcription, initiation" EXACT [GOC:txnOH]
+synonym: "negative regulation of DNA-templated transcription, initiation" EXACT []
synonym: "negative regulation of initiation of DNA-dependent transcription" EXACT [GOC:jh2]
synonym: "negative regulation of transcription initiation, DNA-dependent" EXACT [GOC:jh2]
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
-is_a: GO:2000142 ! regulation of DNA-templated transcription, initiation
-relationship: negatively_regulates GO:0006352 ! DNA-templated transcription, initiation
+is_a: GO:0045892 ! negative regulation of DNA-templated transcription
+is_a: GO:2000142 ! regulation of DNA-templated transcription initiation
+relationship: negatively_regulates GO:0006352 ! DNA-templated transcription initiation
[Term]
id: GO:2000144
-name: positive regulation of DNA-templated transcription, initiation
+name: positive regulation of DNA-templated transcription initiation
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of DNA-templated transcription initiation." [GOC:mah, GOC:txnOH]
synonym: "positive regulation of DNA-dependent transcription, initiation" EXACT [GOC:txnOH]
+synonym: "positive regulation of DNA-templated transcription, initiation" EXACT []
synonym: "positive regulation of initiation of DNA-dependent transcription" EXACT [GOC:jh2]
synonym: "positive regulation of transcription initiation, DNA-dependent" EXACT [GOC:jh2]
synonym: "transactivation" RELATED [PMID:11158542]
synonym: "transcriptional transactivation" RELATED [PMID:11580863]
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
-is_a: GO:2000142 ! regulation of DNA-templated transcription, initiation
-relationship: positively_regulates GO:0006352 ! DNA-templated transcription, initiation
+is_a: GO:0045893 ! positive regulation of DNA-templated transcription
+is_a: GO:2000142 ! regulation of DNA-templated transcription initiation
+relationship: positively_regulates GO:0006352 ! DNA-templated transcription initiation
[Term]
id: GO:2000145
@@ -529353,7 +532172,7 @@ synonym: "regulation of cell locomotion" EXACT [GOC:obol]
synonym: "regulation of cell movement" RELATED [GOC:obol]
synonym: "regulation of movement of a cell" EXACT [GOC:obol]
is_a: GO:0040012 ! regulation of locomotion
-is_a: GO:0051270 ! regulation of cellular component movement
+is_a: GO:0050794 ! regulation of cellular process
relationship: regulates GO:0048870 ! cell motility
[Term]
@@ -529365,7 +532184,7 @@ synonym: "negative regulation of cell locomotion" EXACT [GOC:obol]
synonym: "negative regulation of cell movement" RELATED [GOC:obol]
synonym: "negative regulation of movement of a cell" EXACT [GOC:obol]
is_a: GO:0040013 ! negative regulation of locomotion
-is_a: GO:0051271 ! negative regulation of cellular component movement
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:2000145 ! regulation of cell motility
relationship: negatively_regulates GO:0048870 ! cell motility
@@ -529378,7 +532197,7 @@ synonym: "positive regulation of cell locomotion" EXACT [GOC:obol]
synonym: "positive regulation of cell movement" RELATED [GOC:obol]
synonym: "positive regulation of movement of a cell" EXACT [GOC:obol]
is_a: GO:0040017 ! positive regulation of locomotion
-is_a: GO:0051272 ! positive regulation of cellular component movement
+is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:2000145 ! regulation of cell motility
relationship: positively_regulates GO:0048870 ! cell motility
@@ -530063,6 +532882,7 @@ synonym: "regulation of glutamate metabolism" EXACT [GOC:obol]
synonym: "regulation of glutamic acid metabolic process" EXACT [GOC:obol]
synonym: "regulation of glutamic acid metabolism" EXACT [GOC:obol]
is_a: GO:0000820 ! regulation of glutamine family amino acid metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
relationship: regulates GO:0006536 ! glutamate metabolic process
[Term]
@@ -530073,6 +532893,7 @@ def: "Any process that stops, prevents, or reduces the frequency, rate or extent
synonym: "negative regulation of glutamate metabolism" EXACT [GOC:obol]
synonym: "negative regulation of glutamic acid metabolic process" EXACT [GOC:obol]
synonym: "negative regulation of glutamic acid metabolism" EXACT [GOC:obol]
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0045763 ! negative regulation of cellular amino acid metabolic process
is_a: GO:2000211 ! regulation of glutamate metabolic process
relationship: negatively_regulates GO:0006536 ! glutamate metabolic process
@@ -530085,7 +532906,8 @@ def: "Any process that activates or increases the frequency, rate or extent of g
synonym: "positive regulation of glutamate metabolism" EXACT [GOC:obol]
synonym: "positive regulation of glutamic acid metabolic process" EXACT [GOC:obol]
synonym: "positive regulation of glutamic acid metabolism" EXACT [GOC:obol]
-is_a: GO:0045764 ! positive regulation of cellular amino acid metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
+is_a: GO:0045764 ! positive regulation of amino acid metabolic process
is_a: GO:2000211 ! regulation of glutamate metabolic process
relationship: positively_regulates GO:0006536 ! glutamate metabolic process
@@ -530114,7 +532936,7 @@ name: positive regulation of proline metabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of proline metabolic process." [GOC:sl]
synonym: "positive regulation of proline metabolism" EXACT [GOC:obol]
-is_a: GO:0045764 ! positive regulation of cellular amino acid metabolic process
+is_a: GO:0045764 ! positive regulation of amino acid metabolic process
is_a: GO:2000214 ! regulation of proline metabolic process
relationship: positively_regulates GO:0006560 ! proline metabolic process
@@ -530541,8 +533363,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein activation cascade." [GOC:mah]
synonym: "regulation of protein activation pathway" EXACT [GOC:obol]
synonym: "regulation of protein activitory cascade" EXACT [GOC:obol]
-is_a: GO:0048583 ! regulation of response to stimulus
-is_a: GO:0051246 ! regulation of protein metabolic process
+is_a: GO:1903317 ! regulation of protein maturation
relationship: regulates GO:0072376 ! protein activation cascade
[Term]
@@ -530552,8 +533373,7 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein activation cascade." [GOC:mah]
synonym: "negative regulation of protein activation pathway" EXACT [GOC:obol]
synonym: "negative regulation of protein activitory cascade" EXACT [GOC:obol]
-is_a: GO:0048585 ! negative regulation of response to stimulus
-is_a: GO:0051248 ! negative regulation of protein metabolic process
+is_a: GO:1903318 ! negative regulation of protein maturation
is_a: GO:2000257 ! regulation of protein activation cascade
relationship: negatively_regulates GO:0072376 ! protein activation cascade
@@ -530564,8 +533384,7 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of protein activation cascade." [GOC:mah]
synonym: "positive regulation of protein activation pathway" EXACT [GOC:obol]
synonym: "positive regulation of protein activitory cascade" EXACT [GOC:obol]
-is_a: GO:0048584 ! positive regulation of response to stimulus
-is_a: GO:0051247 ! positive regulation of protein metabolic process
+is_a: GO:1903319 ! positive regulation of protein maturation
is_a: GO:2000257 ! regulation of protein activation cascade
relationship: positively_regulates GO:0072376 ! protein activation cascade
@@ -530754,8 +533573,9 @@ synonym: "regulation of DNA anabolism" EXACT [GOC:obol]
synonym: "regulation of DNA biosynthesis" EXACT [GOC:obol]
synonym: "regulation of DNA formation" EXACT [GOC:obol]
synonym: "regulation of DNA synthesis" EXACT [GOC:obol]
+is_a: GO:0010556 ! regulation of macromolecule biosynthetic process
+is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0051052 ! regulation of DNA metabolic process
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
relationship: regulates GO:0071897 ! DNA biosynthetic process
[Term]
@@ -530767,8 +533587,9 @@ synonym: "negative regulation of DNA anabolism" EXACT [GOC:obol]
synonym: "negative regulation of DNA biosynthesis" EXACT [GOC:obol]
synonym: "negative regulation of DNA formation" EXACT [GOC:obol]
synonym: "negative regulation of DNA synthesis" EXACT [GOC:obol]
+is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process
+is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
is_a: GO:0051053 ! negative regulation of DNA metabolic process
-is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process
is_a: GO:2000278 ! regulation of DNA biosynthetic process
relationship: negatively_regulates GO:0071897 ! DNA biosynthetic process
@@ -530782,12 +533603,12 @@ relationship: regulates GO:0048364 ! root development
[Term]
id: GO:2000281
-name: regulation of histone H3-T3 phosphorylation
+name: obsolete regulation of histone H3-T3 phosphorylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone H3-T3 phosphorylation." [GOC:obol]
-is_a: GO:0010799 ! regulation of peptidyl-threonine phosphorylation
-is_a: GO:0033127 ! regulation of histone phosphorylation
-relationship: regulates GO:0072355 ! histone H3-T3 phosphorylation
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone H3-T3 phosphorylation." [GOC:obol]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0030291
[Term]
id: GO:2000282
@@ -530801,37 +533622,37 @@ synonym: "regulation of cellular amino acid formation" EXACT [GOC:obol]
synonym: "regulation of cellular amino acid synthesis" EXACT [GOC:obol]
is_a: GO:0006521 ! regulation of cellular amino acid metabolic process
is_a: GO:0031326 ! regulation of cellular biosynthetic process
-relationship: regulates GO:0008652 ! cellular amino acid biosynthetic process
+relationship: regulates GO:0008652 ! amino acid biosynthetic process
[Term]
id: GO:2000283
-name: negative regulation of cellular amino acid biosynthetic process
-namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of cellular amino acid biosynthetic process." [GOC:obol]
-synonym: "negative regulation of amino acid biosynthetic process" EXACT [GOC:obol]
-synonym: "negative regulation of cellular amino acid anabolism" EXACT [GOC:obol]
-synonym: "negative regulation of cellular amino acid biosynthesis" EXACT [GOC:obol]
-synonym: "negative regulation of cellular amino acid formation" EXACT [GOC:obol]
-synonym: "negative regulation of cellular amino acid synthesis" EXACT [GOC:obol]
+name: negative regulation of amino acid biosynthetic process
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of an amino acid biosynthetic process." [GOC:obol]
+synonym: "negative regulation of amino acid anabolism" EXACT [GOC:obol]
+synonym: "negative regulation of amino acid biosynthesis" EXACT [GOC:obol]
+synonym: "negative regulation of amino acid formation" EXACT [GOC:obol]
+synonym: "negative regulation of amino acid synthesis" EXACT [GOC:obol]
+synonym: "negative regulation of cellular amino acid biosynthetic process" EXACT [GOC:obol]
is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
is_a: GO:0045763 ! negative regulation of cellular amino acid metabolic process
is_a: GO:2000282 ! regulation of cellular amino acid biosynthetic process
-relationship: negatively_regulates GO:0008652 ! cellular amino acid biosynthetic process
+relationship: negatively_regulates GO:0008652 ! amino acid biosynthetic process
[Term]
id: GO:2000284
-name: positive regulation of cellular amino acid biosynthetic process
+name: positive regulation of amino acid biosynthetic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of cellular amino acid biosynthetic process." [GOC:obol]
-synonym: "positive regulation of amino acid biosynthetic process" EXACT [GOC:obol]
-synonym: "positive regulation of cellular amino acid anabolism" EXACT [GOC:obol]
-synonym: "positive regulation of cellular amino acid biosynthesis" EXACT [GOC:obol]
-synonym: "positive regulation of cellular amino acid formation" EXACT [GOC:obol]
-synonym: "positive regulation of cellular amino acid synthesis" EXACT [GOC:obol]
+synonym: "positive regulation of amino acid anabolism" EXACT [GOC:obol]
+synonym: "positive regulation of amino acid biosynthesis" EXACT [GOC:obol]
+synonym: "positive regulation of amino acid formation" EXACT [GOC:obol]
+synonym: "positive regulation of amino acid synthesis" EXACT [GOC:obol]
+synonym: "positive regulation of cellular amino acid biosynthetic process" EXACT [GOC:obol]
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0045764 ! positive regulation of cellular amino acid metabolic process
+is_a: GO:0045764 ! positive regulation of amino acid metabolic process
is_a: GO:2000282 ! regulation of cellular amino acid biosynthetic process
-relationship: positively_regulates GO:0008652 ! cellular amino acid biosynthetic process
+relationship: positively_regulates GO:0008652 ! amino acid biosynthetic process
[Term]
id: GO:2000285
@@ -531013,7 +533834,6 @@ id: GO:2000301
name: negative regulation of synaptic vesicle exocytosis
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of synaptic vesicle exocytosis." [GOC:obol]
-is_a: GO:0046929 ! negative regulation of neurotransmitter secretion
is_a: GO:1903306 ! negative regulation of regulated secretory pathway
is_a: GO:2000300 ! regulation of synaptic vesicle exocytosis
relationship: negatively_regulates GO:0016079 ! synaptic vesicle exocytosis
@@ -531037,7 +533857,7 @@ synonym: "regulation of ceramide anabolism" EXACT [GOC:obol]
synonym: "regulation of ceramide biosynthesis" EXACT [GOC:obol]
synonym: "regulation of ceramide formation" EXACT [GOC:obol]
synonym: "regulation of ceramide synthesis" EXACT [GOC:obol]
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0090153 ! regulation of sphingolipid biosynthetic process
relationship: regulates GO:0046513 ! ceramide biosynthetic process
@@ -531050,7 +533870,7 @@ synonym: "positive regulation of ceramide anabolism" EXACT [GOC:obol]
synonym: "positive regulation of ceramide biosynthesis" EXACT [GOC:obol]
synonym: "positive regulation of ceramide formation" EXACT [GOC:obol]
synonym: "positive regulation of ceramide synthesis" EXACT [GOC:obol]
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0090154 ! positive regulation of sphingolipid biosynthetic process
is_a: GO:2000303 ! regulation of ceramide biosynthetic process
relationship: positively_regulates GO:0046513 ! ceramide biosynthetic process
@@ -531116,8 +533936,8 @@ name: regulation of NMDA receptor activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of N-methyl-D-aspartate selective glutamate receptor activity." [GOC:BHF]
synonym: "regulation of N-methyl-D-aspartate selective glutamate receptor activity" EXACT []
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
is_a: GO:0099601 ! regulation of neurotransmitter receptor activity
-is_a: GO:2001257 ! regulation of cation channel activity
[Term]
id: GO:2000311
@@ -531125,8 +533945,8 @@ name: regulation of AMPA receptor activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of AMPA selective glutamate receptor activity." [GOC:BHF]
synonym: "regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity" EXACT []
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
is_a: GO:0099601 ! regulation of neurotransmitter receptor activity
-is_a: GO:2001257 ! regulation of cation channel activity
[Term]
id: GO:2000312
@@ -532043,7 +534863,6 @@ def: "Any process that modulates the frequency, rate or extent of ubiquitin-depe
synonym: "regulation of ubiquitin-mediated endocytosis" EXACT [GOC:obol]
is_a: GO:0030100 ! regulation of endocytosis
is_a: GO:0051223 ! regulation of protein transport
-is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0070086 ! ubiquitin-dependent endocytosis
[Term]
@@ -532542,7 +535361,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of toll-like receptor 15 signaling pathway." [GOC:obol]
synonym: "regulation of TLR15 signaling pathway" EXACT [GOC:obol]
synonym: "regulation of toll-like receptor 15 signalling pathway" EXACT [GOC:mah]
-is_a: GO:0034121 ! regulation of toll-like receptor signaling pathway
+is_a: GO:0062207 ! regulation of pattern recognition receptor signaling pathway
relationship: regulates GO:0035681 ! toll-like receptor 15 signaling pathway
[Term]
@@ -532552,7 +535371,8 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of toll-like receptor 15 signaling pathway." [GOC:obol]
synonym: "negative regulation of TLR15 signaling pathway" EXACT [GOC:obol]
synonym: "negative regulation of toll-like receptor 15 signalling pathway" EXACT [GOC:mah]
-is_a: GO:0034122 ! negative regulation of toll-like receptor signaling pathway
+is_a: GO:0002683 ! negative regulation of immune system process
+is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:2000440 ! regulation of toll-like receptor 15 signaling pathway
relationship: negatively_regulates GO:0035681 ! toll-like receptor 15 signaling pathway
@@ -532563,7 +535383,7 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of toll-like receptor 15 signaling pathway." [GOC:obol]
synonym: "positive regulation of TLR15 signaling pathway" EXACT [GOC:obol]
synonym: "positive regulation of toll-like receptor 15 signalling pathway" EXACT [GOC:mah]
-is_a: GO:0034123 ! positive regulation of toll-like receptor signaling pathway
+is_a: GO:0062208 ! positive regulation of pattern recognition receptor signaling pathway
is_a: GO:2000440 ! regulation of toll-like receptor 15 signaling pathway
relationship: positively_regulates GO:0035681 ! toll-like receptor 15 signaling pathway
@@ -532923,22 +535743,22 @@ relationship: positively_regulates GO:0038003 ! G protein-coupled opioid recepto
[Term]
id: GO:2000477
-name: regulation of metanephric glomerular visceral epithelial cell development
+name: regulation of metanephric podocyte development
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of metanephric glomerular visceral epithelial cell development." [GOC:obol]
-synonym: "regulation of metanephric podocyte development" RELATED [GOC:obol]
+synonym: "regulation of metanephric glomerular visceral epithelial cell development" EXACT []
is_a: GO:0060284 ! regulation of cell development
-relationship: regulates GO:0072249 ! metanephric glomerular visceral epithelial cell development
+relationship: regulates GO:0072249 ! metanephric podocyte development
[Term]
id: GO:2000478
-name: positive regulation of metanephric glomerular visceral epithelial cell development
+name: positive regulation of metanephric podocyte development
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of metanephric glomerular visceral epithelial cell development." [GOC:obol]
-synonym: "positive regulation of metanephric podocyte development" RELATED [GOC:obol]
+synonym: "positive regulation of metanephric glomerular visceral epithelial cell development" EXACT []
is_a: GO:0010720 ! positive regulation of cell development
-is_a: GO:2000477 ! regulation of metanephric glomerular visceral epithelial cell development
-relationship: positively_regulates GO:0072249 ! metanephric glomerular visceral epithelial cell development
+is_a: GO:2000477 ! regulation of metanephric podocyte development
+relationship: positively_regulates GO:0072249 ! metanephric podocyte development
[Term]
id: GO:2000479
@@ -533002,7 +535822,6 @@ name: regulation of glutamine transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of glutamine transport." [GOC:obol]
synonym: "regulation of L-glutamine transport" RELATED [GOC:obol]
-is_a: GO:0044070 ! regulation of anion transport
is_a: GO:0051955 ! regulation of amino acid transport
relationship: regulates GO:0006868 ! glutamine transport
@@ -533013,7 +535832,6 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of glutamine transport." [GOC:obol]
synonym: "negative regulation of L-glutamine transport" RELATED [GOC:obol]
is_a: GO:0051956 ! negative regulation of amino acid transport
-is_a: GO:1903792 ! negative regulation of anion transport
is_a: GO:2000485 ! regulation of glutamine transport
relationship: negatively_regulates GO:0006868 ! glutamine transport
@@ -533024,7 +535842,6 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of glutamine transport." [GOC:obol]
synonym: "positive regulation of L-glutamine transport" RELATED [GOC:obol]
is_a: GO:0051957 ! positive regulation of amino acid transport
-is_a: GO:1903793 ! positive regulation of anion transport
is_a: GO:2000485 ! regulation of glutamine transport
relationship: positively_regulates GO:0006868 ! glutamine transport
@@ -533039,7 +535856,7 @@ synonym: "positive regulation of brassinosteroid formation" EXACT [GOC:obol]
synonym: "positive regulation of brassinosteroid synthesis" EXACT [GOC:obol]
is_a: GO:0010422 ! regulation of brassinosteroid biosynthetic process
is_a: GO:0010893 ! positive regulation of steroid biosynthetic process
-is_a: GO:0046886 ! positive regulation of hormone biosynthetic process
+is_a: GO:0032352 ! positive regulation of hormone metabolic process
relationship: positively_regulates GO:0016132 ! brassinosteroid biosynthetic process
[Term]
@@ -533493,8 +536310,9 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein geranylgeranylation." [GOC:obol]
synonym: "regulation of C-terminal protein geranylgeranylation" RELATED [GOC:obol]
synonym: "regulation of protein amino acid geranylgeranylation" EXACT [GOC:obol]
+is_a: GO:0010556 ! regulation of macromolecule biosynthetic process
+is_a: GO:0031323 ! regulation of cellular metabolic process
is_a: GO:0031399 ! regulation of protein modification process
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
relationship: regulates GO:0018344 ! protein geranylgeranylation
[Term]
@@ -533504,6 +536322,7 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein geranylgeranylation." [GOC:obol]
synonym: "negative regulation of C-terminal protein geranylgeranylation" RELATED [GOC:obol]
synonym: "negative regulation of protein amino acid geranylgeranylation" EXACT [GOC:obol]
+is_a: GO:0031324 ! negative regulation of cellular metabolic process
is_a: GO:0031400 ! negative regulation of protein modification process
is_a: GO:2000539 ! regulation of protein geranylgeranylation
relationship: negatively_regulates GO:0018344 ! protein geranylgeranylation
@@ -533515,6 +536334,7 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of protein geranylgeranylation." [GOC:obol]
synonym: "positive regulation of C-terminal protein geranylgeranylation" RELATED [GOC:obol]
synonym: "positive regulation of protein amino acid geranylgeranylation" EXACT [GOC:obol]
+is_a: GO:0031325 ! positive regulation of cellular metabolic process
is_a: GO:0031401 ! positive regulation of protein modification process
is_a: GO:2000539 ! regulation of protein geranylgeranylation
relationship: positively_regulates GO:0018344 ! protein geranylgeranylation
@@ -534307,22 +537127,22 @@ relationship: positively_regulates GO:0043970 ! histone H3-K9 acetylation
[Term]
id: GO:2000618
-name: regulation of histone H4-K16 acetylation
+name: obsolete regulation of histone H4-K16 acetylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone H4-K16 acetylation." [GOC:BHF]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone H4-K16 acetylation." [GOC:BHF]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "regulation of histone H4 acetylation at K16" EXACT [GOC:obol]
-is_a: GO:0090239 ! regulation of histone H4 acetylation
-relationship: regulates GO:0043984 ! histone H4-K16 acetylation
+is_obsolete: true
+consider: GO:0031452
[Term]
id: GO:2000619
-name: negative regulation of histone H4-K16 acetylation
+name: obsolete negative regulation of histone H4-K16 acetylation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone H4-K16 acetylation." [GOC:BHF]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone H4-K16 acetylation." [GOC:BHF]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "negative regulation of histone H4 acetylation at K16" EXACT [GOC:obol]
-is_a: GO:0090241 ! negative regulation of histone H4 acetylation
-is_a: GO:2000618 ! regulation of histone H4-K16 acetylation
-relationship: negatively_regulates GO:0043984 ! histone H4-K16 acetylation
+is_obsolete: true
[Term]
id: GO:2000620
@@ -534331,7 +537151,6 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of histone H4-K16 acetylation." [GOC:BHF]
synonym: "positive regulation of histone H4 acetylation at K16" EXACT [GOC:obol]
is_a: GO:0090240 ! positive regulation of histone H4 acetylation
-is_a: GO:2000618 ! regulation of histone H4-K16 acetylation
relationship: positively_regulates GO:0043984 ! histone H4-K16 acetylation
[Term]
@@ -534339,8 +537158,7 @@ id: GO:2000621
name: regulation of DNA replication termination
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA replication termination." [GOC:obol]
-is_a: GO:0051052 ! regulation of DNA metabolic process
-is_a: GO:0090329 ! regulation of DNA-dependent DNA replication
+is_a: GO:0090329 ! regulation of DNA-templated DNA replication
relationship: regulates GO:0006274 ! DNA replication termination
[Term]
@@ -534453,8 +537271,9 @@ id: GO:2000631
name: regulation of pre-miRNA processing
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of pre-microRNA processing." [GOC:dph, GOC:sl]
+synonym: "regulation of miRNA maturation" EXACT []
synonym: "regulation of pre-microRNA processing" EXACT []
-is_a: GO:0051252 ! regulation of RNA metabolic process
+is_a: GO:1903798 ! regulation of miRNA processing
relationship: regulates GO:0031054 ! pre-miRNA processing
[Term]
@@ -534462,8 +537281,9 @@ id: GO:2000632
name: negative regulation of pre-miRNA processing
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of pre-microRNA processing." [GOC:dph, GOC:sl]
+synonym: "negative regulation of miRNA maturation" EXACT []
synonym: "negative regulation of pre-microRNA processing" EXACT [GOC:obol]
-is_a: GO:0051253 ! negative regulation of RNA metabolic process
+is_a: GO:1903799 ! negative regulation of miRNA processing
is_a: GO:2000631 ! regulation of pre-miRNA processing
relationship: negatively_regulates GO:0031054 ! pre-miRNA processing
@@ -534472,8 +537292,9 @@ id: GO:2000633
name: positive regulation of pre-miRNA processing
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of pre-microRNA processing." [GOC:dph, GOC:sl]
+synonym: "positive regulation of miRNA maturation" EXACT []
synonym: "positive regulation of pre-microRNA processing" EXACT [GOC:obol]
-is_a: GO:0051254 ! positive regulation of RNA metabolic process
+is_a: GO:1903800 ! positive regulation of miRNA processing
is_a: GO:2000631 ! regulation of pre-miRNA processing
relationship: positively_regulates GO:0031054 ! pre-miRNA processing
@@ -534484,7 +537305,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of primary microRNA processing." [GOC:dph, GOC:sl]
synonym: "regulation of pri-miRNA processing" EXACT [GOC:obol]
synonym: "regulation of primary microRNA processing" EXACT [GOC:obol]
-is_a: GO:0051252 ! regulation of RNA metabolic process
+is_a: GO:1903798 ! regulation of miRNA processing
relationship: regulates GO:0031053 ! primary miRNA processing
[Term]
@@ -534494,7 +537315,7 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of primary microRNA processing." [GOC:dph, GOC:sl]
synonym: "negative regulation of pri-miRNA processing" EXACT [GOC:obol]
synonym: "negative regulation of primary microRNA processing" EXACT [GOC:obol]
-is_a: GO:0051253 ! negative regulation of RNA metabolic process
+is_a: GO:1903799 ! negative regulation of miRNA processing
is_a: GO:2000634 ! regulation of primary miRNA processing
relationship: negatively_regulates GO:0031053 ! primary miRNA processing
@@ -534505,21 +537326,21 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of primary microRNA processing." [GOC:dph, GOC:sl]
synonym: "positive regulation of pri-miRNA processing" EXACT [GOC:obol]
synonym: "positive regulation of primary microRNA processing" EXACT [GOC:obol]
-is_a: GO:0051254 ! positive regulation of RNA metabolic process
+is_a: GO:1903800 ! positive regulation of miRNA processing
is_a: GO:2000634 ! regulation of primary miRNA processing
relationship: positively_regulates GO:0031053 ! primary miRNA processing
[Term]
id: GO:2000637
-name: positive regulation of gene silencing by miRNA
+name: positive regulation of miRNA-mediated gene silencing
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of gene silencing by miRNA." [GOC:dph]
+def: "A process that activates or increases the frequency, rate or extent of gene silencing by a microRNA (miRNA)." [GOC:dph]
synonym: "positive regulation of gene silencing by microRNA" RELATED [GOC:pr]
+synonym: "positive regulation of gene silencing by miRNA" EXACT []
synonym: "positive regulation of microRNA-mediated gene silencing" EXACT [GOC:obol]
-synonym: "positive regulation of miRNA-mediated gene silencing" EXACT [GOC:obol]
-is_a: GO:0060148 ! positive regulation of posttranscriptional gene silencing
-is_a: GO:0060964 ! regulation of gene silencing by miRNA
-relationship: positively_regulates GO:0035195 ! gene silencing by miRNA
+is_a: GO:0060964 ! regulation of miRNA-mediated gene silencing
+is_a: GO:1900370 ! positive regulation of post-transcriptional gene silencing by RNA
+relationship: positively_regulates GO:0035195 ! miRNA-mediated gene silencing
[Term]
id: GO:2000638
@@ -534643,7 +537464,7 @@ name: regulation of sodium ion transmembrane transporter activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity." [GOC:obol]
synonym: "regulation of sodium transporter activity" EXACT [GOC:obol]
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
is_a: GO:1902305 ! regulation of sodium ion transmembrane transport
[Term]
@@ -534687,7 +537508,8 @@ name: regulation of genetic imprinting
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of genetic imprinting." [GOC:BHF]
synonym: "regulation of DNA imprinting" EXACT [GOC:obol]
-is_a: GO:0031445 ! regulation of heterochromatin assembly
+is_a: GO:0010468 ! regulation of gene expression
+is_a: GO:1902275 ! regulation of chromatin organization
relationship: regulates GO:0071514 ! genomic imprinting
[Term]
@@ -535207,37 +538029,6 @@ is_a: GO:0044089 ! positive regulation of cellular component biogenesis
is_a: GO:2000705 ! regulation of dense core granule biogenesis
relationship: positively_regulates GO:0061110 ! dense core granule biogenesis
-[Term]
-id: GO:2000708
-name: myosin filament organization involved in cytokinetic actomyosin contractile ring assembly
-namespace: biological_process
-def: "A myosin filament organization process that contributes to actomyosin contractile ring assembly during cytokinesis." [GOC:mah]
-synonym: "myosin filament assembly or disassembly of constriction ring assembly" RELATED [GOC:obol]
-synonym: "myosin filament assembly or disassembly of contractile ring assembly" RELATED [GOC:obol]
-synonym: "myosin filament assembly or disassembly of cytokinesis, actomyosin contractile ring assembly" RELATED [GOC:obol]
-synonym: "myosin filament assembly or disassembly of cytokinesis, actomyosin contractile ring formation" RELATED [GOC:obol]
-synonym: "myosin filament assembly or disassembly of cytokinesis, actomyosin ring biosynthesis" RELATED [GOC:obol]
-synonym: "myosin filament assembly or disassembly of cytokinesis, actomyosin ring formation" RELATED [GOC:obol]
-synonym: "myosin filament assembly or disassembly of cytokinesis, contractile ring assembly" RELATED [GOC:obol]
-synonym: "myosin filament organisation involved in cytokinetic actomyosin contractile ring assembly" EXACT [GOC:mah]
-synonym: "myosin filament organization of constriction ring assembly" RELATED [GOC:obol]
-synonym: "myosin filament organization of contractile ring assembly" EXACT [GOC:obol]
-synonym: "myosin filament organization of cytokinesis, actomyosin contractile ring assembly" EXACT [GOC:obol]
-synonym: "myosin filament organization of cytokinesis, actomyosin contractile ring formation" RELATED [GOC:obol]
-synonym: "myosin filament organization of cytokinesis, actomyosin ring biosynthesis" RELATED [GOC:obol]
-synonym: "myosin filament organization of cytokinesis, actomyosin ring formation" RELATED [GOC:obol]
-synonym: "myosin filament organization of cytokinesis, contractile ring assembly" RELATED [GOC:obol]
-synonym: "myosin polymerization or depolymerization of constriction ring assembly" RELATED [GOC:obol]
-synonym: "myosin polymerization or depolymerization of contractile ring assembly" RELATED [GOC:obol]
-synonym: "myosin polymerization or depolymerization of cytokinesis, actomyosin contractile ring assembly" RELATED [GOC:obol]
-synonym: "myosin polymerization or depolymerization of cytokinesis, actomyosin contractile ring formation" RELATED [GOC:obol]
-synonym: "myosin polymerization or depolymerization of cytokinesis, actomyosin ring biosynthesis" RELATED [GOC:obol]
-synonym: "myosin polymerization or depolymerization of cytokinesis, actomyosin ring formation" RELATED [GOC:obol]
-synonym: "myosin polymerization or depolymerization of cytokinesis, contractile ring assembly" RELATED [GOC:obol]
-is_a: GO:0022402 ! cell cycle process
-is_a: GO:0031033 ! myosin filament organization
-relationship: part_of GO:0000915 ! actomyosin contractile ring assembly
-
[Term]
id: GO:2000709
name: regulation of maintenance of meiotic sister chromatid cohesion, centromeric
@@ -535376,9 +538167,10 @@ relationship: positively_regulates GO:0071960 ! maintenance of mitotic sister ch
[Term]
id: GO:2000721
-name: positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation
+name: obsolete positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation
namespace: biological_process
-def: "Any positive regulation of transcription from RNA polymerase II promoter that is involved in smooth muscle cell differentiation." [GOC:BHF]
+def: "OBSOLETE. Any positive regulation of transcription from RNA polymerase II promoter that is involved in smooth muscle cell differentiation." [GOC:BHF]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "activation of global transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" RELATED [GOC:obol]
synonym: "activation of global transcription from RNA polymerase II promoter of smooth muscle cell differentiation" RELATED [GOC:obol]
synonym: "activation of transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" EXACT [GOC:obol]
@@ -535407,8 +538199,9 @@ synonym: "up-regulation of transcription from RNA polymerase II promoter of nons
synonym: "up-regulation of transcription from RNA polymerase II promoter of smooth muscle cell differentiation" EXACT [GOC:obol]
synonym: "upregulation of global transcription from RNA polymerase II promoter of nonstriated muscle cell differentiation" RELATED [GOC:obol]
synonym: "upregulation of global transcription from RNA polymerase II promoter of smooth muscle cell differentiation" EXACT [GOC:obol]
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
-relationship: part_of GO:0051145 ! smooth muscle cell differentiation
+is_obsolete: true
+consider: GO:0045944
+consider: GO:0051145
[Term]
id: GO:2000722
@@ -535509,7 +538302,7 @@ synonym: "regulation of RNA polymerase I transcription termination" EXACT [GOC:o
synonym: "regulation of transcription termination from Pol I promoter" EXACT [GOC:obol]
synonym: "regulation of transcription termination from RNA polymerase I promoter" EXACT [GOC:obol]
is_a: GO:0006356 ! regulation of transcription by RNA polymerase I
-is_a: GO:0031554 ! regulation of DNA-templated transcription, termination
+is_a: GO:0031554 ! regulation of termination of DNA-templated transcription
relationship: regulates GO:0006363 ! termination of RNA polymerase I transcription
[Term]
@@ -535521,7 +538314,7 @@ synonym: "negative regulation of RNA polymerase I transcription termination" EXA
synonym: "negative regulation of transcription termination from Pol I promoter" EXACT [GOC:obol]
synonym: "negative regulation of transcription termination from RNA polymerase I promoter" EXACT [GOC:obol]
is_a: GO:0016479 ! negative regulation of transcription by RNA polymerase I
-is_a: GO:0060567 ! negative regulation of DNA-templated transcription, termination
+is_a: GO:0060567 ! negative regulation of termination of DNA-templated transcription
is_a: GO:2000730 ! regulation of termination of RNA polymerase I transcription
relationship: negatively_regulates GO:0006363 ! termination of RNA polymerase I transcription
@@ -535534,7 +538327,7 @@ synonym: "positive regulation of RNA polymerase I transcription termination" EXA
synonym: "positive regulation of transcription termination from Pol I promoter" EXACT [GOC:obol]
synonym: "positive regulation of transcription termination from RNA polymerase I promoter" EXACT [GOC:obol]
is_a: GO:0045943 ! positive regulation of transcription by RNA polymerase I
-is_a: GO:0060566 ! positive regulation of DNA-templated transcription, termination
+is_a: GO:0060566 ! positive regulation of termination of DNA-templated transcription
is_a: GO:2000730 ! regulation of termination of RNA polymerase I transcription
relationship: positively_regulates GO:0006363 ! termination of RNA polymerase I transcription
@@ -535722,17 +538515,18 @@ relationship: positively_regulates GO:0035882 ! defecation rhythm
[Term]
id: GO:2000749
-name: positive regulation of rDNA heterochromatin assembly
+name: positive regulation of rDNA heterochromatin formation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of assembly of rDNA heterochromatin." [PMID:10899127]
+def: "Any process that activates or increases the frequency, rate or extent of rDNA heterochromatin formation." [PMID:10899127]
synonym: "positive regulation of chromatin silencing at rDNA" BROAD []
synonym: "positive regulation of chromatin silencing at ribosomal DNA" BROAD [GOC:obol]
synonym: "positive regulation of heterochromatic silencing at rDNA" BROAD [GOC:obol]
synonym: "positive regulation of rDNA chromatin silencing" BROAD [GOC:obol]
+synonym: "positive regulation of rDNA heterochromatin assembly" EXACT []
synonym: "positive regulation of ribosomal DNA heterochromatin assembly" EXACT []
-is_a: GO:0031453 ! positive regulation of heterochromatin assembly
-is_a: GO:0061187 ! regulation of ribosomal DNA heterochromatin assembly
-relationship: positively_regulates GO:0000183 ! rDNA heterochromatin assembly
+is_a: GO:0031453 ! positive regulation of heterochromatin formation
+is_a: GO:0061187 ! regulation of rDNA heterochromatin formation
+relationship: positively_regulates GO:0000183 ! rDNA heterochromatin formation
[Term]
id: GO:2000750
@@ -535745,16 +538539,17 @@ relationship: negatively_regulates GO:0061246 ! establishment or maintenance of
[Term]
id: GO:2000751
-name: histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore
+name: obsolete histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore
namespace: biological_process
-def: "Any histone H3-T3 phosphorylation that is involved in chromosome passenger complex localization to kinetochore." [GOC:obol]
+def: "OBSOLETE. Any histone H3-T3 phosphorylation that is involved in chromosome passenger complex localization to kinetochore." [GOC:obol]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "histone H3-T3 phosphorylation of chromosomal passenger complex localization to kinetochore" EXACT [GOC:obol]
synonym: "histone H3-T3 phosphorylation of chromosome passenger complex localisation to kinetochore" RELATED [GOC:obol]
synonym: "histone H3-T3 phosphorylation of chromosome passenger complex localization to kinetochore" EXACT [GOC:obol]
synonym: "histone H3-T3 phosphorylation of CPC complex localization to kinetochore" EXACT [GOC:obol]
synonym: "histone H3-T3 phosphorylation of CPC localization to kinetochore" EXACT [GOC:obol]
-is_a: GO:0072355 ! histone H3-T3 phosphorylation
-relationship: part_of GO:0072356 ! chromosome passenger complex localization to kinetochore
+is_obsolete: true
+consider: GO:0072354
[Term]
id: GO:2000752
@@ -535765,7 +538560,7 @@ synonym: "regulation of glucosylceramide breakdown" EXACT [GOC:obol]
synonym: "regulation of glucosylceramide catabolism" EXACT [GOC:obol]
synonym: "regulation of glucosylceramide degradation" EXACT [GOC:obol]
is_a: GO:0031329 ! regulation of cellular catabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0050994 ! regulation of lipid catabolic process
is_a: GO:1905038 ! regulation of membrane lipid metabolic process
relationship: regulates GO:0006680 ! glucosylceramide catabolic process
@@ -535779,7 +538574,7 @@ synonym: "positive regulation of glucosylceramide breakdown" EXACT [GOC:obol]
synonym: "positive regulation of glucosylceramide catabolism" EXACT [GOC:obol]
synonym: "positive regulation of glucosylceramide degradation" EXACT [GOC:obol]
is_a: GO:0031331 ! positive regulation of cellular catabolic process
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0050996 ! positive regulation of lipid catabolic process
is_a: GO:2000752 ! regulation of glucosylceramide catabolic process
relationship: positively_regulates GO:0006680 ! glucosylceramide catabolic process
@@ -535792,7 +538587,7 @@ def: "Any process that modulates the frequency, rate or extent of sphingomyelin
synonym: "regulation of sphingomyelin breakdown" EXACT [GOC:obol]
synonym: "regulation of sphingomyelin catabolism" EXACT [GOC:obol]
synonym: "regulation of sphingomyelin degradation" EXACT [GOC:obol]
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0060696 ! regulation of phospholipid catabolic process
is_a: GO:1905038 ! regulation of membrane lipid metabolic process
relationship: regulates GO:0006685 ! sphingomyelin catabolic process
@@ -535805,7 +538600,7 @@ def: "Any process that activates or increases the frequency, rate or extent of s
synonym: "positive regulation of sphingomyelin breakdown" EXACT [GOC:obol]
synonym: "positive regulation of sphingomyelin catabolism" EXACT [GOC:obol]
synonym: "positive regulation of sphingomyelin degradation" EXACT [GOC:obol]
-is_a: GO:0034250 ! positive regulation of cellular amide metabolic process
+is_a: GO:0034250 ! positive regulation of amide metabolic process
is_a: GO:0060697 ! positive regulation of phospholipid catabolic process
is_a: GO:2000754 ! regulation of sphingomyelin catabolic process
relationship: positively_regulates GO:0006685 ! sphingomyelin catabolic process
@@ -535968,8 +538763,7 @@ id: GO:2000772
name: regulation of cellular senescence
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of cellular senescence." [GOC:BHF]
-is_a: GO:0080135 ! regulation of cellular response to stress
-is_a: GO:0090342 ! regulation of cell aging
+is_a: GO:0031323 ! regulation of cellular metabolic process
relationship: regulates GO:0090398 ! cellular senescence
[Term]
@@ -535977,8 +538771,7 @@ id: GO:2000773
name: negative regulation of cellular senescence
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of cellular senescence." [GOC:BHF]
-is_a: GO:0048585 ! negative regulation of response to stimulus
-is_a: GO:0090344 ! negative regulation of cell aging
+is_a: GO:0031324 ! negative regulation of cellular metabolic process
is_a: GO:2000772 ! regulation of cellular senescence
relationship: negatively_regulates GO:0090398 ! cellular senescence
@@ -535987,8 +538780,7 @@ id: GO:2000774
name: positive regulation of cellular senescence
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of cellular senescence." [GOC:BHF]
-is_a: GO:0048584 ! positive regulation of response to stimulus
-is_a: GO:0090343 ! positive regulation of cell aging
+is_a: GO:0031325 ! positive regulation of cellular metabolic process
is_a: GO:2000772 ! regulation of cellular senescence
relationship: positively_regulates GO:0090398 ! cellular senescence
@@ -536004,16 +538796,17 @@ is_obsolete: true
[Term]
id: GO:2000776
-name: histone H4 acetylation involved in response to DNA damage stimulus
+name: obsolete histone H4 acetylation involved in response to DNA damage stimulus
namespace: biological_process
-def: "Any histone H4 acetylation that is involved in a response to DNA damage stimulus." [GOC:mah]
+def: "OBSOLETE. Any histone H4 acetylation that is involved in a response to DNA damage stimulus." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function and is a precomposed term.
synonym: "histone H4 acetylation of cellular DNA damage response" EXACT [GOC:obol]
synonym: "histone H4 acetylation of cellular response to DNA damage stimulus" EXACT [GOC:obol]
synonym: "histone H4 acetylation of DNA damage response" EXACT [GOC:obol]
synonym: "histone H4 acetylation of response to DNA damage stimulus" EXACT [GOC:obol]
synonym: "histone H4 acetylation of response to genotoxic stress" EXACT [GOC:obol]
-is_a: GO:0043967 ! histone H4 acetylation
-relationship: part_of GO:0006974 ! cellular response to DNA damage stimulus
+is_obsolete: true
+consider: GO:0140861
[Term]
id: GO:2000777
@@ -536316,7 +539109,7 @@ id: GO:2000807
name: regulation of synaptic vesicle clustering
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of synaptic vesicle clustering." [PMID:21513708]
-is_a: GO:0060341 ! regulation of cellular localization
+is_a: GO:0032879 ! regulation of localization
relationship: regulates GO:0097091 ! synaptic vesicle clustering
[Term]
@@ -536324,7 +539117,6 @@ id: GO:2000808
name: negative regulation of synaptic vesicle clustering
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of synaptic vesicle clustering." [PMID:21513708]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0051051 ! negative regulation of transport
is_a: GO:2000807 ! regulation of synaptic vesicle clustering
relationship: negatively_regulates GO:0097091 ! synaptic vesicle clustering
@@ -536334,7 +539126,6 @@ id: GO:2000809
name: positive regulation of synaptic vesicle clustering
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of synaptic vesicle clustering." [PMID:21513708]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:0051050 ! positive regulation of transport
is_a: GO:2000807 ! regulation of synaptic vesicle clustering
relationship: positively_regulates GO:0097091 ! synaptic vesicle clustering
@@ -536424,15 +539215,15 @@ relationship: negatively_regulates GO:0051306 ! mitotic sister chromatid separat
[Term]
id: GO:2000817
-name: regulation of histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore
+name: obsolete regulation of histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore
namespace: biological_process
-def: "Any regulation of histone H3-T3 phosphorylation that is involved in chromosome passenger complex localization to kinetochore." [GOC:obol]
+def: "OBSOLETE. Any regulation of histone H3-T3 phosphorylation that is involved in chromosome passenger complex localization to kinetochore." [GOC:obol]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "regulation of histone H3-T3 phosphorylation involved in chromosomal passenger complex localization to kinetochore" EXACT [GOC:obol]
synonym: "regulation of histone H3-T3 phosphorylation involved in chromosome passenger complex localisation to kinetochore" RELATED [GOC:obol]
synonym: "regulation of histone H3-T3 phosphorylation involved in CPC complex localization to kinetochore" EXACT [GOC:obol]
synonym: "regulation of histone H3-T3 phosphorylation involved in CPC localization to kinetochore" EXACT [GOC:obol]
-is_a: GO:2000281 ! regulation of histone H3-T3 phosphorylation
-relationship: part_of GO:0072356 ! chromosome passenger complex localization to kinetochore
+is_obsolete: true
[Term]
id: GO:2000818
@@ -536902,8 +539693,7 @@ name: regulation of estradiol secretion
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of estradiol secretion." [GOC:sl]
synonym: "regulation of oestradiol secretion" EXACT [GOC:obol]
-is_a: GO:0032368 ! regulation of lipid transport
-is_a: GO:0046883 ! regulation of hormone secretion
+is_a: GO:2000831 ! regulation of steroid hormone secretion
relationship: regulates GO:0035938 ! estradiol secretion
[Term]
@@ -536912,8 +539702,7 @@ name: negative regulation of estradiol secretion
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of estradiol secretion." [GOC:sl]
synonym: "negative regulation of oestradiol secretion" EXACT [GOC:obol]
-is_a: GO:0032369 ! negative regulation of lipid transport
-is_a: GO:0046888 ! negative regulation of hormone secretion
+is_a: GO:2000832 ! negative regulation of steroid hormone secretion
is_a: GO:2000864 ! regulation of estradiol secretion
relationship: negatively_regulates GO:0035938 ! estradiol secretion
@@ -536923,8 +539712,7 @@ name: positive regulation of estradiol secretion
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of estradiol secretion." [GOC:sl]
synonym: "positive regulation of oestradiol secretion" EXACT [GOC:obol]
-is_a: GO:0032370 ! positive regulation of lipid transport
-is_a: GO:0046887 ! positive regulation of hormone secretion
+is_a: GO:2000833 ! positive regulation of steroid hormone secretion
is_a: GO:2000864 ! regulation of estradiol secretion
relationship: positively_regulates GO:0035938 ! estradiol secretion
@@ -536935,8 +539723,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of estrone secretion." [GOC:sl]
synonym: "regulation of 3-hydroxy-1,3,5(10)-estratrien-17-one secretion" EXACT [GOC:obol]
synonym: "regulation of folliculin secretion" EXACT [GOC:obol]
-is_a: GO:0032368 ! regulation of lipid transport
-is_a: GO:0046883 ! regulation of hormone secretion
+is_a: GO:2000831 ! regulation of steroid hormone secretion
relationship: regulates GO:0035943 ! estrone secretion
[Term]
@@ -536946,8 +539733,7 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of estrone secretion." [GOC:sl]
synonym: "negative regulation of 3-hydroxy-1,3,5(10)-estratrien-17-one secretion" EXACT [GOC:obol]
synonym: "negative regulation of folliculin secretion" EXACT [GOC:obol]
-is_a: GO:0032369 ! negative regulation of lipid transport
-is_a: GO:0046888 ! negative regulation of hormone secretion
+is_a: GO:2000832 ! negative regulation of steroid hormone secretion
is_a: GO:2000867 ! regulation of estrone secretion
relationship: negatively_regulates GO:0035943 ! estrone secretion
@@ -536958,8 +539744,7 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of estrone secretion." [GOC:sl]
synonym: "positive regulation of 3-hydroxy-1,3,5(10)-estratrien-17-one secretion" EXACT [GOC:obol]
synonym: "positive regulation of folliculin secretion" EXACT [GOC:obol]
-is_a: GO:0032370 ! positive regulation of lipid transport
-is_a: GO:0046887 ! positive regulation of hormone secretion
+is_a: GO:2000833 ! positive regulation of steroid hormone secretion
is_a: GO:2000867 ! regulation of estrone secretion
relationship: positively_regulates GO:0035943 ! estrone secretion
@@ -536994,17 +539779,17 @@ relationship: positively_regulates GO:0042701 ! progesterone secretion
[Term]
id: GO:2000873
-name: regulation of histone H4 acetylation involved in response to DNA damage stimulus
+name: obsolete regulation of histone H4 acetylation involved in response to DNA damage stimulus
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone H4 acetylation involved in response to DNA damage stimulus." [GOC:mah]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone H4 acetylation involved in response to DNA damage stimulus." [GOC:mah]
+comment: This term was obsoleted because it represents a molecular function and is a precomposed term.
synonym: "regulation of histone H4 acetylation involved in cellular DNA damage response" EXACT [GOC:obol]
synonym: "regulation of histone H4 acetylation involved in cellular response to DNA damage stimulus" EXACT [GOC:obol]
synonym: "regulation of histone H4 acetylation involved in DNA damage response" EXACT [GOC:obol]
synonym: "regulation of histone H4 acetylation involved in response to DNA damage" EXACT [GOC:bf]
synonym: "regulation of histone H4 acetylation involved in response to genotoxic stress" EXACT [GOC:obol]
-is_a: GO:0090239 ! regulation of histone H4 acetylation
-is_a: GO:2001020 ! regulation of response to DNA damage stimulus
-relationship: regulates GO:2000776 ! histone H4 acetylation involved in response to DNA damage stimulus
+is_obsolete: true
+consider: GO:0140861
[Term]
id: GO:2000874
@@ -537012,8 +539797,8 @@ name: regulation of glyoxylate cycle
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of glyoxylate cycle." [GOC:dgf]
synonym: "regulation of glyoxylate bypass" EXACT [GOC:obol]
+is_a: GO:0006109 ! regulation of carbohydrate metabolic process
is_a: GO:0010565 ! regulation of cellular ketone metabolic process
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
relationship: regulates GO:0006097 ! glyoxylate cycle
[Term]
@@ -537022,7 +539807,8 @@ name: negative regulation of glyoxylate cycle
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of glyoxylate cycle." [GOC:dgf]
synonym: "negative regulation of glyoxylate bypass" EXACT [GOC:obol]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
+is_a: GO:0031324 ! negative regulation of cellular metabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:2000874 ! regulation of glyoxylate cycle
relationship: negatively_regulates GO:0006097 ! glyoxylate cycle
@@ -537033,7 +539819,8 @@ name: positive regulation of glyoxylate cycle
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of glyoxylate cycle." [GOC:dgf]
synonym: "positive regulation of glyoxylate bypass" EXACT [GOC:obol]
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
+is_a: GO:0031325 ! positive regulation of cellular metabolic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:2000874 ! regulation of glyoxylate cycle
relationship: positively_regulates GO:0006097 ! glyoxylate cycle
@@ -537082,7 +539869,7 @@ def: "Any process that modulates the frequency, rate or extent of starch catabol
synonym: "regulation of starch breakdown" EXACT [GOC:obol]
synonym: "regulation of starch catabolism" EXACT [GOC:obol]
synonym: "regulation of starch degradation" EXACT [GOC:obol]
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
is_a: GO:2000904 ! regulation of starch metabolic process
relationship: regulates GO:0005983 ! starch catabolic process
@@ -537094,7 +539881,7 @@ def: "Any process that stops, prevents or reduces the frequency, rate or extent
synonym: "negative regulation of starch breakdown" EXACT [GOC:obol]
synonym: "negative regulation of starch catabolism" EXACT [GOC:obol]
synonym: "negative regulation of starch degradation" EXACT [GOC:obol]
-is_a: GO:0031330 ! negative regulation of cellular catabolic process
+is_a: GO:0009895 ! negative regulation of catabolic process
is_a: GO:2000881 ! regulation of starch catabolic process
is_a: GO:2000905 ! negative regulation of starch metabolic process
relationship: negatively_regulates GO:0005983 ! starch catabolic process
@@ -537107,7 +539894,7 @@ def: "Any process that activates or increases the frequency, rate or extent of s
synonym: "positive regulation of starch breakdown" EXACT [GOC:obol]
synonym: "positive regulation of starch catabolism" EXACT [GOC:obol]
synonym: "positive regulation of starch degradation" EXACT [GOC:obol]
-is_a: GO:0031331 ! positive regulation of cellular catabolic process
+is_a: GO:0009896 ! positive regulation of catabolic process
is_a: GO:2000881 ! regulation of starch catabolic process
is_a: GO:2000906 ! positive regulation of starch metabolic process
relationship: positively_regulates GO:0005983 ! starch catabolic process
@@ -537302,7 +540089,6 @@ name: regulation of starch metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of starch metabolic process." [GOC:obol]
synonym: "regulation of starch metabolism" EXACT [GOC:obol]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:0032881 ! regulation of polysaccharide metabolic process
relationship: regulates GO:0005982 ! starch metabolic process
@@ -537313,7 +540099,7 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of starch metabolic process." [GOC:obol]
synonym: "negative regulation of starch metabolism" EXACT [GOC:obol]
is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:2000904 ! regulation of starch metabolic process
relationship: negatively_regulates GO:0005982 ! starch metabolic process
@@ -537324,7 +540110,7 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of starch metabolic process." [GOC:obol]
synonym: "positive regulation of starch metabolism" EXACT [GOC:obol]
is_a: GO:0010604 ! positive regulation of macromolecule metabolic process
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:2000904 ! regulation of starch metabolic process
relationship: positively_regulates GO:0005982 ! starch metabolic process
@@ -537575,7 +540361,7 @@ name: regulation of cellobiose metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of cellobiose metabolic process." [GOC:mengo_curators]
synonym: "regulation of cellobiose metabolism" EXACT [GOC:obol]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
+is_a: GO:0006109 ! regulation of carbohydrate metabolic process
relationship: regulates GO:2000891 ! cellobiose metabolic process
[Term]
@@ -537584,7 +540370,7 @@ name: negative regulation of cellobiose metabolic process
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of cellobiose metabolic process." [GOC:mengo_curators]
synonym: "negative regulation of cellobiose metabolism" EXACT [GOC:obol]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:2000930 ! regulation of cellobiose metabolic process
relationship: negatively_regulates GO:2000891 ! cellobiose metabolic process
@@ -537594,7 +540380,7 @@ name: positive regulation of cellobiose metabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of cellobiose metabolic process." [GOC:mengo_curators]
synonym: "positive regulation of cellobiose metabolism" EXACT [GOC:obol]
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:2000930 ! regulation of cellobiose metabolic process
relationship: positively_regulates GO:2000891 ! cellobiose metabolic process
@@ -537677,7 +540463,6 @@ name: negative regulation of plant-type cell wall cellulose catabolic process
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of plant-type cell wall cellulose catabolic process." [GOC:mengo_curators]
synonym: "negative regulation of plant-type cell wall polysaccharide breakdown" EXACT [GOC:obol]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
is_a: GO:2000939 ! regulation of plant-type cell wall cellulose catabolic process
is_a: GO:2000967 ! negative regulation of cell wall polysaccharide catabolic process
relationship: negatively_regulates GO:0044348 ! plant-type cell wall cellulose catabolic process
@@ -537688,7 +540473,6 @@ name: positive regulation of plant-type cell wall cellulose catabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of plant-type cell wall cellulose catabolic process." [GOC:mengo_curators]
synonym: "positive regulation of plant-type cell wall polysaccharide breakdown" EXACT [GOC:obol]
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
is_a: GO:2000939 ! regulation of plant-type cell wall cellulose catabolic process
is_a: GO:2000968 ! positive regulation of cell wall polysaccharide catabolic process
relationship: positively_regulates GO:0044348 ! plant-type cell wall cellulose catabolic process
@@ -537763,7 +540547,6 @@ name: regulation of xyloglucan metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of xyloglucan metabolic process." [GOC:mengo_curators]
synonym: "regulation of xyloglucan metabolism" EXACT [GOC:obol]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:0010981 ! regulation of cell wall macromolecule metabolic process
is_a: GO:0032881 ! regulation of polysaccharide metabolic process
relationship: regulates GO:0010411 ! xyloglucan metabolic process
@@ -537775,7 +540558,7 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of xyloglucan metabolic process." [GOC:mengo_curators]
synonym: "negative regulation of xyloglucan metabolism" EXACT [GOC:obol]
is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:2000948 ! regulation of xyloglucan metabolic process
relationship: negatively_regulates GO:0010411 ! xyloglucan metabolic process
@@ -537786,7 +540569,7 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of xyloglucan metabolic process." [GOC:mengo_curators]
synonym: "positive regulation of xyloglucan metabolism" EXACT [GOC:obol]
is_a: GO:0010604 ! positive regulation of macromolecule metabolic process
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:2000948 ! regulation of xyloglucan metabolic process
relationship: positively_regulates GO:0010411 ! xyloglucan metabolic process
@@ -537953,7 +540736,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of cell wall polysaccharide catabolic process." [GOC:mengo_curators]
synonym: "regulation of cell wall polysaccharide breakdown" EXACT [GOC:obol]
is_a: GO:0010981 ! regulation of cell wall macromolecule metabolic process
-is_a: GO:0031329 ! regulation of cellular catabolic process
is_a: GO:0032881 ! regulation of polysaccharide metabolic process
is_a: GO:0043470 ! regulation of carbohydrate catabolic process
relationship: regulates GO:0044347 ! cell wall polysaccharide catabolic process
@@ -537964,8 +540746,8 @@ name: negative regulation of cell wall polysaccharide catabolic process
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of cell wall polysaccharide catabolic process." [GOC:mengo_curators]
synonym: "negative regulation of cell wall polysaccharide breakdown" EXACT [GOC:obol]
+is_a: GO:0009895 ! negative regulation of catabolic process
is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
-is_a: GO:0031330 ! negative regulation of cellular catabolic process
is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:2000966 ! regulation of cell wall polysaccharide catabolic process
relationship: negatively_regulates GO:0044347 ! cell wall polysaccharide catabolic process
@@ -537976,8 +540758,8 @@ name: positive regulation of cell wall polysaccharide catabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of cell wall polysaccharide catabolic process." [GOC:mengo_curators]
synonym: "positive regulation of cell wall polysaccharide breakdown" EXACT [GOC:obol]
+is_a: GO:0009896 ! positive regulation of catabolic process
is_a: GO:0010604 ! positive regulation of macromolecule metabolic process
-is_a: GO:0031331 ! positive regulation of cellular catabolic process
is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:2000966 ! regulation of cell wall polysaccharide catabolic process
relationship: positively_regulates GO:0044347 ! cell wall polysaccharide catabolic process
@@ -537988,9 +540770,9 @@ name: positive regulation of AMPA receptor activity
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of AMPA selective glutamate receptor activity." [PMID:21423165]
synonym: "positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity" BROAD []
+is_a: GO:0032414 ! positive regulation of ion transmembrane transporter activity
is_a: GO:2000273 ! positive regulation of signaling receptor activity
is_a: GO:2000311 ! regulation of AMPA receptor activity
-is_a: GO:2001259 ! positive regulation of cation channel activity
[Term]
id: GO:2000970
@@ -538239,7 +541021,6 @@ name: regulation of hemicellulose catabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of hemicellulose catabolic process." [GOC:mengo_curators]
synonym: "regulation of hemicellulose catabolism" EXACT [GOC:obol]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:2000966 ! regulation of cell wall polysaccharide catabolic process
relationship: regulates GO:2000895 ! hemicellulose catabolic process
@@ -538249,7 +541030,6 @@ name: negative regulation of hemicellulose catabolic process
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of hemicellulose catabolic process." [GOC:mengo_curators]
synonym: "negative regulation of hemicellulose catabolism" EXACT [GOC:obol]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
is_a: GO:2000967 ! negative regulation of cell wall polysaccharide catabolic process
is_a: GO:2000988 ! regulation of hemicellulose catabolic process
relationship: negatively_regulates GO:2000895 ! hemicellulose catabolic process
@@ -538260,7 +541040,6 @@ name: positive regulation of hemicellulose catabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of hemicellulose catabolic process." [GOC:mengo_curators]
synonym: "positive regulation of hemicellulose catabolism" EXACT [GOC:obol]
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
is_a: GO:2000968 ! positive regulation of cell wall polysaccharide catabolic process
is_a: GO:2000988 ! regulation of hemicellulose catabolic process
relationship: positively_regulates GO:2000895 ! hemicellulose catabolic process
@@ -538304,7 +541083,6 @@ def: "Any process that modulates the frequency, rate or extent of mannan catabol
synonym: "regulation of mannan breakdown" EXACT [GOC:obol]
synonym: "regulation of mannan catabolism" EXACT [GOC:obol]
synonym: "regulation of mannan degradation" EXACT [GOC:obol]
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
is_a: GO:2000924 ! regulation of cellodextrin metabolic process
is_a: GO:2000966 ! regulation of cell wall polysaccharide catabolic process
relationship: regulates GO:0046355 ! mannan catabolic process
@@ -538317,7 +541095,6 @@ def: "Any process that stops, prevents or reduces the frequency, rate or extent
synonym: "negative regulation of mannan breakdown" EXACT [GOC:obol]
synonym: "negative regulation of mannan catabolism" EXACT [GOC:obol]
synonym: "negative regulation of mannan degradation" EXACT [GOC:obol]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
is_a: GO:2000925 ! negative regulation of cellodextrin metabolic process
is_a: GO:2000967 ! negative regulation of cell wall polysaccharide catabolic process
is_a: GO:2000994 ! regulation of mannan catabolic process
@@ -538331,7 +541108,6 @@ def: "Any process that activates or increases the frequency, rate or extent of m
synonym: "positive regulation of mannan breakdown" EXACT [GOC:obol]
synonym: "positive regulation of mannan catabolism" EXACT [GOC:obol]
synonym: "positive regulation of mannan degradation" EXACT [GOC:obol]
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
is_a: GO:2000926 ! positive regulation of cellodextrin metabolic process
is_a: GO:2000968 ! positive regulation of cell wall polysaccharide catabolic process
is_a: GO:2000994 ! regulation of mannan catabolic process
@@ -538346,7 +541122,7 @@ synonym: "regulation of cellulose breakdown" EXACT [GOC:obol]
synonym: "regulation of cellulose catabolism" EXACT [GOC:obol]
synonym: "regulation of cellulose degradation" EXACT [GOC:obol]
is_a: GO:0032950 ! regulation of beta-glucan metabolic process
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
relationship: regulates GO:0030245 ! cellulose catabolic process
[Term]
@@ -538357,9 +541133,9 @@ def: "Any process that stops, prevents or reduces the frequency, rate or extent
synonym: "negative regulation of cellulose breakdown" EXACT [GOC:obol]
synonym: "negative regulation of cellulose catabolism" EXACT [GOC:obol]
synonym: "negative regulation of cellulose degradation" EXACT [GOC:obol]
+is_a: GO:0009895 ! negative regulation of catabolic process
is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
-is_a: GO:0031330 ! negative regulation of cellular catabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:2000997 ! regulation of cellulose catabolic process
relationship: negatively_regulates GO:0030245 ! cellulose catabolic process
@@ -538371,9 +541147,9 @@ def: "Any process that activates or increases the frequency, rate or extent of c
synonym: "positive regulation of cellulose breakdown" EXACT [GOC:obol]
synonym: "positive regulation of cellulose catabolism" EXACT [GOC:obol]
synonym: "positive regulation of cellulose degradation" EXACT [GOC:obol]
+is_a: GO:0009896 ! positive regulation of catabolic process
is_a: GO:0010604 ! positive regulation of macromolecule metabolic process
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
-is_a: GO:0031331 ! positive regulation of cellular catabolic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:2000997 ! regulation of cellulose catabolic process
relationship: positively_regulates GO:0030245 ! cellulose catabolic process
@@ -538385,9 +541161,8 @@ def: "Any process that modulates the frequency, rate or extent of xylan cataboli
synonym: "regulation of xylan breakdown" EXACT [GOC:obol]
synonym: "regulation of xylan catabolism" EXACT [GOC:obol]
synonym: "regulation of xylan degradation" EXACT [GOC:obol]
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
is_a: GO:2000924 ! regulation of cellodextrin metabolic process
-is_a: GO:2000966 ! regulation of cell wall polysaccharide catabolic process
+is_a: GO:2000988 ! regulation of hemicellulose catabolic process
relationship: regulates GO:0045493 ! xylan catabolic process
[Term]
@@ -538398,9 +541173,8 @@ def: "Any process that stops, prevents or reduces the frequency, rate or extent
synonym: "negative regulation of xylan breakdown" EXACT [GOC:obol]
synonym: "negative regulation of xylan catabolism" EXACT [GOC:obol]
synonym: "negative regulation of xylan degradation" EXACT [GOC:obol]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
is_a: GO:2000925 ! negative regulation of cellodextrin metabolic process
-is_a: GO:2000967 ! negative regulation of cell wall polysaccharide catabolic process
+is_a: GO:2000989 ! negative regulation of hemicellulose catabolic process
is_a: GO:2001000 ! regulation of xylan catabolic process
relationship: negatively_regulates GO:0045493 ! xylan catabolic process
@@ -538412,9 +541186,8 @@ def: "Any process that activates or increases the frequency, rate or extent of x
synonym: "positive regulation of xylan breakdown" EXACT [GOC:obol]
synonym: "positive regulation of xylan catabolism" EXACT [GOC:obol]
synonym: "positive regulation of xylan degradation" EXACT [GOC:obol]
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
is_a: GO:2000926 ! positive regulation of cellodextrin metabolic process
-is_a: GO:2000968 ! positive regulation of cell wall polysaccharide catabolic process
+is_a: GO:2000990 ! positive regulation of hemicellulose catabolic process
is_a: GO:2001000 ! regulation of xylan catabolic process
relationship: positively_regulates GO:0045493 ! xylan catabolic process
@@ -538427,7 +541200,7 @@ synonym: "regulation of pectin breakdown" EXACT [GOC:obol]
synonym: "regulation of pectin catabolism" EXACT [GOC:obol]
synonym: "regulation of pectin degradation" EXACT [GOC:obol]
is_a: GO:0032881 ! regulation of polysaccharide metabolic process
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
relationship: regulates GO:0045490 ! pectin catabolic process
[Term]
@@ -538440,7 +541213,7 @@ synonym: "negative regulation of pectin catabolism" EXACT [GOC:obol]
synonym: "negative regulation of pectin degradation" EXACT [GOC:obol]
is_a: GO:0009895 ! negative regulation of catabolic process
is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:2001003 ! regulation of pectin catabolic process
relationship: negatively_regulates GO:0045490 ! pectin catabolic process
@@ -538454,7 +541227,7 @@ synonym: "positive regulation of pectin catabolism" EXACT [GOC:obol]
synonym: "positive regulation of pectin degradation" EXACT [GOC:obol]
is_a: GO:0009896 ! positive regulation of catabolic process
is_a: GO:0010604 ! positive regulation of macromolecule metabolic process
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:2001003 ! regulation of pectin catabolic process
relationship: positively_regulates GO:0045490 ! pectin catabolic process
@@ -538479,8 +541252,8 @@ synonym: "negative regulation of cellulose anabolism" EXACT [GOC:obol]
synonym: "negative regulation of cellulose biosynthesis" EXACT [GOC:obol]
synonym: "negative regulation of cellulose formation" EXACT [GOC:obol]
synonym: "negative regulation of cellulose synthesis" EXACT [GOC:obol]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
-is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process
+is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:2001006 ! regulation of cellulose biosynthetic process
relationship: negatively_regulates GO:0030244 ! cellulose biosynthetic process
@@ -538494,8 +541267,7 @@ synonym: "positive regulation of cellulose biosynthesis" EXACT [GOC:obol]
synonym: "positive regulation of cellulose formation" EXACT [GOC:obol]
synonym: "positive regulation of cellulose synthesis" EXACT [GOC:obol]
is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:2001006 ! regulation of cellulose biosynthetic process
relationship: positively_regulates GO:0030244 ! cellulose biosynthetic process
@@ -538594,7 +541366,6 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of retrograde axon cargo transport." [GOC:obol]
synonym: "negative regulation of retrograde axonal transport" EXACT [GOC:obol]
is_a: GO:0032387 ! negative regulation of intracellular transport
-is_a: GO:0051271 ! negative regulation of cellular component movement
is_a: GO:2001017 ! regulation of retrograde axon cargo transport
relationship: negatively_regulates GO:0008090 ! retrograde axonal transport
@@ -538605,49 +541376,47 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of retrograde axon cargo transport." [GOC:obol]
synonym: "positive regulation of retrograde axonal transport" EXACT [GOC:obol]
is_a: GO:0032388 ! positive regulation of intracellular transport
-is_a: GO:0051272 ! positive regulation of cellular component movement
is_a: GO:2001017 ! regulation of retrograde axon cargo transport
relationship: positively_regulates GO:0008090 ! retrograde axonal transport
[Term]
id: GO:2001020
-name: regulation of response to DNA damage stimulus
+name: obsolete regulation of response to DNA damage stimulus
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of response to DNA damage stimulus." [GOC:obol]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of response to DNA damage stimulus." [GOC:obol]
+comment: The reason for obsoletion is that the meaning of the term is ambiguous; genes annotated to these terms all seem to be part of the response.
synonym: "regulation of cellular DNA damage response" EXACT [GOC:obol]
synonym: "regulation of cellular response to DNA damage stimulus" EXACT [GOC:obol]
synonym: "regulation of DNA damage response" EXACT [GOC:obol]
synonym: "regulation of response to genotoxic stress" EXACT [GOC:obol]
-is_a: GO:0080135 ! regulation of cellular response to stress
-relationship: regulates GO:0006974 ! cellular response to DNA damage stimulus
+is_obsolete: true
+replaced_by: GO:0006974
[Term]
id: GO:2001021
-name: negative regulation of response to DNA damage stimulus
+name: obsolete negative regulation of response to DNA damage stimulus
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of response to DNA damage stimulus." [GOC:obol]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of response to DNA damage stimulus." [GOC:obol]
+comment: The reason for obsoletion is that the meaning of the term is ambiguous; genes annotated to these terms all seem to be part of the response.
synonym: "negative regulation of cellular DNA damage response" EXACT [GOC:obol]
synonym: "negative regulation of cellular response to DNA damage stimulus" EXACT [GOC:obol]
synonym: "negative regulation of DNA damage response" EXACT [GOC:obol]
synonym: "negative regulation of response to genotoxic stress" EXACT [GOC:obol]
-is_a: GO:0048523 ! negative regulation of cellular process
-is_a: GO:0048585 ! negative regulation of response to stimulus
-is_a: GO:2001020 ! regulation of response to DNA damage stimulus
-relationship: negatively_regulates GO:0006974 ! cellular response to DNA damage stimulus
+is_obsolete: true
+replaced_by: GO:0006974
[Term]
id: GO:2001022
-name: positive regulation of response to DNA damage stimulus
+name: obsolete positive regulation of response to DNA damage stimulus
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of response to DNA damage stimulus." [GOC:obol]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of response to DNA damage stimulus." [GOC:obol]
+comment: The reason for obsoletion is that the meaning of the term is ambiguous; genes annotated to these terms all seem to be part of the response.
synonym: "positive regulation of cellular DNA damage response" EXACT [GOC:obol]
synonym: "positive regulation of cellular response to DNA damage stimulus" EXACT [GOC:obol]
synonym: "positive regulation of DNA damage response" EXACT [GOC:obol]
synonym: "positive regulation of response to genotoxic stress" EXACT [GOC:obol]
-is_a: GO:0048522 ! positive regulation of cellular process
-is_a: GO:0048584 ! positive regulation of response to stimulus
-is_a: GO:2001020 ! regulation of response to DNA damage stimulus
-relationship: positively_regulates GO:0006974 ! cellular response to DNA damage stimulus
+is_obsolete: true
+replaced_by: GO:0006974
[Term]
id: GO:2001023
@@ -538719,8 +541488,8 @@ synonym: "regulation of cellular glucuronide biosynthesis" EXACT [GOC:obol]
synonym: "regulation of cellular glucuronide biosynthetic process" EXACT [GOC:obol]
synonym: "regulation of cellular glucuronoside biosynthesis" EXACT [GOC:obol]
synonym: "regulation of cellular glucuronoside biosynthetic process" EXACT [GOC:obol]
+is_a: GO:0006109 ! regulation of carbohydrate metabolic process
is_a: GO:0010565 ! regulation of cellular ketone metabolic process
-is_a: GO:0010675 ! regulation of cellular carbohydrate metabolic process
relationship: regulates GO:0052695 ! cellular glucuronidation
[Term]
@@ -538732,7 +541501,8 @@ synonym: "negative regulation of cellular glucuronide biosynthesis" EXACT [GOC:o
synonym: "negative regulation of cellular glucuronide biosynthetic process" EXACT [GOC:obol]
synonym: "negative regulation of cellular glucuronoside biosynthesis" EXACT [GOC:obol]
synonym: "negative regulation of cellular glucuronoside biosynthetic process" EXACT [GOC:obol]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
+is_a: GO:0031324 ! negative regulation of cellular metabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:2001029 ! regulation of cellular glucuronidation
relationship: negatively_regulates GO:0052695 ! cellular glucuronidation
@@ -538746,7 +541516,8 @@ synonym: "positive regulation of cellular glucuronide biosynthesis" EXACT [GOC:o
synonym: "positive regulation of cellular glucuronide biosynthetic process" EXACT [GOC:obol]
synonym: "positive regulation of cellular glucuronoside biosynthesis" EXACT [GOC:obol]
synonym: "positive regulation of cellular glucuronoside biosynthetic process" EXACT [GOC:obol]
-is_a: GO:0010676 ! positive regulation of cellular carbohydrate metabolic process
+is_a: GO:0031325 ! positive regulation of cellular metabolic process
+is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:2001029 ! regulation of cellular glucuronidation
relationship: positively_regulates GO:0052695 ! cellular glucuronidation
@@ -539203,10 +541974,11 @@ is_a: GO:0030247 ! polysaccharide binding
[Term]
id: GO:2001086
-name: laminarabiose transport
+name: obsolete laminarabiose transport
namespace: biological_process
-def: "The directed movement of a laminarabioseacetate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mengo_curators]
-is_a: GO:0015766 ! disaccharide transport
+def: "OBSOLETE. The directed movement of a laminarabioseacetate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mengo_curators]
+comment: This term has been obsoleted because it does not represent an evolved process.
+is_obsolete: true
[Term]
id: GO:2001087
@@ -539421,7 +542193,6 @@ name: positive regulation of cellular response to hepatocyte growth factor stimu
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of cellular response to hepatocyte growth factor stimulus." [GOC:obol]
synonym: "positive regulation of cellular response to HGF stimulus" EXACT [GOC:obol]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:0048584 ! positive regulation of response to stimulus
is_a: GO:2001112 ! regulation of cellular response to hepatocyte growth factor stimulus
relationship: positively_regulates GO:0035729 ! cellular response to hepatocyte growth factor stimulus
@@ -539679,7 +542450,6 @@ name: nicotinate transport
namespace: biological_process
def: "The directed movement of a nicotinateacetate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:obol]
is_a: GO:0015718 ! monocarboxylic acid transport
-is_a: GO:0015849 ! organic acid transport
is_a: GO:0071705 ! nitrogen compound transport
[Term]
@@ -539793,8 +542563,7 @@ def: "Any process that modulates the frequency, rate or extent of glucose catabo
synonym: "regulation of ethanol fermentation" EXACT [GOC:obol]
synonym: "regulation of glucose fermentation to ethanol" EXACT [GOC:obol]
is_a: GO:0043465 ! regulation of fermentation
-is_a: GO:0043471 ! regulation of cellular carbohydrate catabolic process
-is_a: GO:1903578 ! regulation of ATP metabolic process
+is_a: GO:0043470 ! regulation of carbohydrate catabolic process
relationship: regulates GO:0019655 ! glycolytic fermentation to ethanol
[Term]
@@ -539804,9 +542573,8 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of glucose catabolic process to ethanol." [GOC:obol]
synonym: "negative regulation of ethanol fermentation" EXACT [GOC:obol]
synonym: "negative regulation of glucose fermentation to ethanol" EXACT [GOC:obol]
-is_a: GO:0010677 ! negative regulation of cellular carbohydrate metabolic process
+is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:1901003 ! negative regulation of fermentation
-is_a: GO:1903579 ! negative regulation of ATP metabolic process
is_a: GO:2001154 ! regulation of glycolytic fermentation to ethanol
relationship: negatively_regulates GO:0019655 ! glycolytic fermentation to ethanol
@@ -539818,7 +542586,9 @@ def: "Any process that modulates the frequency, rate or extent of proline catabo
synonym: "regulation of proline breakdown to glutamate" EXACT [GOC:obol]
synonym: "regulation of proline degradation to glutamate" EXACT [GOC:obol]
synonym: "regulation of proline oxidation" RELATED [GOC:obol]
-is_a: GO:0033241 ! regulation of cellular amine catabolic process
+is_a: GO:0031329 ! regulation of cellular catabolic process
+is_a: GO:0033241 ! regulation of amine catabolic process
+is_a: GO:0034251 ! regulation of amide catabolic process
is_a: GO:2000211 ! regulation of glutamate metabolic process
is_a: GO:2000214 ! regulation of proline metabolic process
relationship: regulates GO:0010133 ! proline catabolic process to glutamate
@@ -539831,7 +542601,9 @@ def: "Any process that stops, prevents or reduces the frequency, rate or extent
synonym: "negative regulation of proline breakdown to glutamate" EXACT [GOC:obol]
synonym: "negative regulation of proline degradation to glutamate" EXACT [GOC:obol]
synonym: "negative regulation of proline oxidation" RELATED [GOC:obol]
-is_a: GO:0033242 ! negative regulation of cellular amine catabolic process
+is_a: GO:0031330 ! negative regulation of cellular catabolic process
+is_a: GO:0033242 ! negative regulation of amine catabolic process
+is_a: GO:0034252 ! negative regulation of amide catabolic process
is_a: GO:2000212 ! negative regulation of glutamate metabolic process
is_a: GO:2000215 ! negative regulation of proline metabolic process
is_a: GO:2001156 ! regulation of proline catabolic process to glutamate
@@ -539845,7 +542617,9 @@ def: "Any process that activates or increases the frequency, rate or extent of p
synonym: "positive regulation of proline breakdown to glutamate" EXACT [GOC:obol]
synonym: "positive regulation of proline degradation to glutamate" EXACT [GOC:obol]
synonym: "positive regulation of proline oxidation" RELATED [GOC:obol]
-is_a: GO:0033243 ! positive regulation of cellular amine catabolic process
+is_a: GO:0031331 ! positive regulation of cellular catabolic process
+is_a: GO:0033243 ! positive regulation of amine catabolic process
+is_a: GO:0034253 ! positive regulation of amide catabolic process
is_a: GO:2000213 ! positive regulation of glutamate metabolic process
is_a: GO:2000216 ! positive regulation of proline metabolic process
is_a: GO:2001156 ! regulation of proline catabolic process to glutamate
@@ -539864,64 +542638,68 @@ relationship: regulates GO:0032258 ! cytoplasm to vacuole transport by the Cvt p
[Term]
id: GO:2001160
-name: regulation of histone H3-K79 methylation
+name: obsolete regulation of histone H3-K79 methylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone H3-K79 methylation." [PMID:12876294]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone H3-K79 methylation." [PMID:12876294]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "regulation of histone H3 K79 methylation" EXACT [GOC:obol]
synonym: "regulation of histone H3K79me" EXACT [GOC:obol]
synonym: "regulation of histone lysine H3 K79 methylation" EXACT [GOC:obol]
-is_a: GO:0031060 ! regulation of histone methylation
-relationship: regulates GO:0034729 ! histone H3-K79 methylation
+is_obsolete: true
+consider: GO:0140673
+consider: GO:0140861
[Term]
id: GO:2001161
-name: negative regulation of histone H3-K79 methylation
+name: obsolete negative regulation of histone H3-K79 methylation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K79 methylation." [PMID:12876294]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K79 methylation." [PMID:12876294]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "negative regulation of histone H3 K79 methylation" EXACT [GOC:obol]
synonym: "negative regulation of histone H3K79me" EXACT [GOC:obol]
synonym: "negative regulation of histone lysine H3 K79 methylation" EXACT [GOC:obol]
-is_a: GO:0031061 ! negative regulation of histone methylation
-is_a: GO:2001160 ! regulation of histone H3-K79 methylation
-relationship: negatively_regulates GO:0034729 ! histone H3-K79 methylation
+is_obsolete: true
+consider: GO:0006338
[Term]
id: GO:2001162
-name: positive regulation of histone H3-K79 methylation
+name: obsolete positive regulation of histone H3-K79 methylation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of histone H3-K79 methylation." [PMID:12876294]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of histone H3-K79 methylation." [PMID:12876294]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "positive regulation of histone H3 K79 methylation" EXACT [GOC:obol]
synonym: "positive regulation of histone H3K79me" EXACT [GOC:obol]
synonym: "positive regulation of histone lysine H3 K79 methylation" EXACT [GOC:obol]
-is_a: GO:0031062 ! positive regulation of histone methylation
-is_a: GO:2001160 ! regulation of histone H3-K79 methylation
-relationship: positively_regulates GO:0034729 ! histone H3-K79 methylation
+is_obsolete: true
+consider: GO:0140673
+consider: GO:0140861
[Term]
id: GO:2001163
-name: regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
+name: obsolete regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues." [PMID:15149594]
-is_a: GO:1901407 ! regulation of phosphorylation of RNA polymerase II C-terminal domain
-relationship: regulates GO:0071619 ! phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues." [PMID:15149594]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0006357
[Term]
id: GO:2001164
-name: negative regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
+name: obsolete negative regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues." [PMID:15149594]
-is_a: GO:1901408 ! negative regulation of phosphorylation of RNA polymerase II C-terminal domain
-is_a: GO:2001163 ! regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
-relationship: negatively_regulates GO:0071619 ! phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues." [PMID:15149594]
+comment: This term was obsoleted because it represents both a molecular function and a biological process.
+is_obsolete: true
+consider: GO:0006357
[Term]
id: GO:2001165
-name: positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
+name: obsolete positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues." [PMID:15149594]
-is_a: GO:1901409 ! positive regulation of phosphorylation of RNA polymerase II C-terminal domain
-is_a: GO:2001163 ! regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
-relationship: positively_regulates GO:0071619 ! phosphorylation of RNA polymerase II C-terminal domain serine 2 residues
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues." [PMID:15149594]
+comment: This term has been obsoleted because it represents both a molecular function and a biological process.
+is_obsolete: true
+consider: GO:0006357
[Term]
id: GO:2001166
@@ -539933,12 +542711,11 @@ relationship: regulates GO:0033523 ! histone H2B ubiquitination
[Term]
id: GO:2001167
-name: negative regulation of histone H2B ubiquitination
+name: obsolete negative regulation of histone H2B ubiquitination
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone H2B ubiquitination." [PMID:12876293]
-is_a: GO:0033183 ! negative regulation of histone ubiquitination
-is_a: GO:2001166 ! regulation of histone H2B ubiquitination
-relationship: negatively_regulates GO:0033523 ! histone H2B ubiquitination
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone H2B ubiquitination." [PMID:12876293]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:2001168
@@ -540001,7 +542778,6 @@ def: "Any process that activates or increases the frequency, rate or extent of g
synonym: "positive regulation of ethanol fermentation" EXACT [GOC:obol]
synonym: "positive regulation of glucose fermentation to ethanol" EXACT [GOC:obol]
is_a: GO:0031325 ! positive regulation of cellular metabolic process
-is_a: GO:1903580 ! positive regulation of ATP metabolic process
is_a: GO:2001154 ! regulation of glycolytic fermentation to ethanol
relationship: positively_regulates GO:0019655 ! glycolytic fermentation to ethanol
@@ -540018,27 +542794,25 @@ relationship: regulates GO:0071894 ! histone H2B conserved C-terminal lysine ubi
[Term]
id: GO:2001174
-name: negative regulation of histone H2B conserved C-terminal lysine ubiquitination
+name: obsolete negative regulation of histone H2B conserved C-terminal lysine ubiquitination
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone H2B conserved C-terminal lysine ubiquitination." [PMID:17576814]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone H2B conserved C-terminal lysine ubiquitination." [PMID:17576814]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "negative regulation of budding yeast H2B K123 ubiquitination" RELATED [GOC:obol]
synonym: "negative regulation of fission yeast H2B K119 ubiquitination" RELATED [GOC:obol]
synonym: "negative regulation of mammalian H2B K120 ubiquitination" RELATED [GOC:obol]
-is_a: GO:2001167 ! negative regulation of histone H2B ubiquitination
-is_a: GO:2001173 ! regulation of histone H2B conserved C-terminal lysine ubiquitination
-relationship: negatively_regulates GO:0071894 ! histone H2B conserved C-terminal lysine ubiquitination
+is_obsolete: true
[Term]
id: GO:2001175
-name: positive regulation of histone H2B conserved C-terminal lysine ubiquitination
+name: obsolete positive regulation of histone H2B conserved C-terminal lysine ubiquitination
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of histone H2B conserved C-terminal lysine ubiquitination." [PMID:17576814]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of histone H2B conserved C-terminal lysine ubiquitination." [PMID:17576814]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "positive regulation of budding yeast H2B K123 ubiquitination" RELATED [GOC:obol]
synonym: "positive regulation of fission yeast H2B K119 ubiquitination" RELATED [GOC:obol]
synonym: "positive regulation of mammalian H2B K120 ubiquitination" RELATED [GOC:obol]
-is_a: GO:2001168 ! positive regulation of histone H2B ubiquitination
-is_a: GO:2001173 ! regulation of histone H2B conserved C-terminal lysine ubiquitination
-relationship: positively_regulates GO:0071894 ! histone H2B conserved C-terminal lysine ubiquitination
+is_obsolete: true
[Term]
id: GO:2001176
@@ -540205,7 +542979,7 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of lysine biosynthetic process via alpha-aminoadipate and saccharopine." [GOC:obol]
synonym: "positive regulation of lysine biosynthesis via aminoadipic acid and saccharopine" EXACT [GOC:obol]
synonym: "positive regulation of lysine biosynthetic process via aminoadipic acid and saccharopine" EXACT [GOC:obol]
-is_a: GO:2000284 ! positive regulation of cellular amino acid biosynthetic process
+is_a: GO:2000284 ! positive regulation of amino acid biosynthetic process
is_a: GO:2001194 ! regulation of lysine biosynthetic process via alpha-aminoadipate and saccharopine
relationship: positively_regulates GO:0051975 ! lysine biosynthetic process via alpha-aminoadipate and saccharopine
@@ -540250,7 +543024,7 @@ name: regulation of osteoclast development
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of osteoclast development." [GOC:obol]
synonym: "regulation of osteoclast cell development" EXACT [GOC:obol]
-is_a: GO:0060284 ! regulation of cell development
+is_a: GO:1903706 ! regulation of hemopoiesis
relationship: regulates GO:0036035 ! osteoclast development
[Term]
@@ -540259,7 +543033,6 @@ name: negative regulation of osteoclast development
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of osteoclast development." [GOC:obol]
synonym: "negative regulation of osteoclast cell development" EXACT [GOC:obol]
-is_a: GO:0010721 ! negative regulation of cell development
is_a: GO:0045671 ! negative regulation of osteoclast differentiation
is_a: GO:2001204 ! regulation of osteoclast development
relationship: negatively_regulates GO:0036035 ! osteoclast development
@@ -540270,19 +543043,19 @@ name: positive regulation of osteoclast development
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of osteoclast development." [GOC:obol]
synonym: "positive regulation of osteoclast cell development" EXACT [GOC:obol]
-is_a: GO:0010720 ! positive regulation of cell development
is_a: GO:0045672 ! positive regulation of osteoclast differentiation
is_a: GO:2001204 ! regulation of osteoclast development
relationship: positively_regulates GO:0036035 ! osteoclast development
[Term]
id: GO:2001207
-name: regulation of transcription elongation from RNA polymerase I promoter
+name: regulation of transcription elongation by RNA polymerase I
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of transcription elongation from RNA polymerase I promoter." [PMID:20299458]
synonym: "regulation of RNA elongation from Pol I promoter" EXACT [GOC:obol]
-is_a: GO:0032784 ! regulation of DNA-templated transcription, elongation
-relationship: regulates GO:0006362 ! transcription elongation from RNA polymerase I promoter
+synonym: "regulation of transcription elongation from RNA polymerase I promoter" EXACT []
+is_a: GO:0032784 ! regulation of DNA-templated transcription elongation
+relationship: regulates GO:0006362 ! transcription elongation by RNA polymerase I
[Term]
id: GO:2001208
@@ -540293,19 +543066,20 @@ synonym: "negative regulation of RNA elongation from Pol I promoter" EXACT [GOC:
synonym: "negative regulation of transcription elongation from RNA polymerase I promoter" EXACT []
is_a: GO:0016479 ! negative regulation of transcription by RNA polymerase I
is_a: GO:0032785 ! negative regulation of DNA-templated transcription, elongation
-is_a: GO:2001207 ! regulation of transcription elongation from RNA polymerase I promoter
-relationship: negatively_regulates GO:0006362 ! transcription elongation from RNA polymerase I promoter
+is_a: GO:2001207 ! regulation of transcription elongation by RNA polymerase I
+relationship: negatively_regulates GO:0006362 ! transcription elongation by RNA polymerase I
[Term]
id: GO:2001209
-name: positive regulation of transcription elongation from RNA polymerase I promoter
+name: positive regulation of transcription elongation by RNA polymerase I
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of transcription elongation from RNA polymerase I promoter." [PMID:20299458]
synonym: "positive regulation of RNA elongation from Pol I promoter" EXACT [GOC:obol]
+synonym: "positive regulation of transcription elongation from RNA polymerase I promoter" EXACT []
is_a: GO:0032786 ! positive regulation of DNA-templated transcription, elongation
is_a: GO:0045943 ! positive regulation of transcription by RNA polymerase I
-is_a: GO:2001207 ! regulation of transcription elongation from RNA polymerase I promoter
-relationship: positively_regulates GO:0006362 ! transcription elongation from RNA polymerase I promoter
+is_a: GO:2001207 ! regulation of transcription elongation by RNA polymerase I
+relationship: positively_regulates GO:0006362 ! transcription elongation by RNA polymerase I
[Term]
id: GO:2001210
@@ -540318,7 +543092,7 @@ synonym: "regulation of isopentenyl diphosphate anabolism, mevalonate pathway" E
synonym: "regulation of isopentenyl diphosphate formation, mevalonate pathway" EXACT [GOC:obol]
synonym: "regulation of isopentenyl diphosphate synthesis, mevalonate pathway" EXACT [GOC:obol]
is_a: GO:0019747 ! regulation of isoprenoid metabolic process
-is_a: GO:0034248 ! regulation of cellular amide metabolic process
+is_a: GO:0034248 ! regulation of amide metabolic process
is_a: GO:0042762 ! regulation of sulfur metabolic process
is_a: GO:0071071 ! regulation of phospholipid biosynthetic process
is_a: GO:1900542 ! regulation of purine nucleotide metabolic process
@@ -540334,7 +543108,7 @@ synonym: "negative regulation of acetate-mevalonate pathway" EXACT [GOC:obol]
synonym: "negative regulation of isopentenyl diphosphate anabolism, mevalonate pathway" EXACT [GOC:obol]
synonym: "negative regulation of isopentenyl diphosphate formation, mevalonate pathway" EXACT [GOC:obol]
synonym: "negative regulation of isopentenyl diphosphate synthesis, mevalonate pathway" EXACT [GOC:obol]
-is_a: GO:0034249 ! negative regulation of cellular amide metabolic process
+is_a: GO:0034249 ! negative regulation of amide metabolic process
is_a: GO:0045827 ! negative regulation of isoprenoid metabolic process
is_a: GO:0051175 ! negative regulation of sulfur metabolic process
is_a: GO:0071072 ! negative regulation of phospholipid biosynthetic process
@@ -540481,7 +543255,7 @@ id: GO:2001225
name: regulation of chloride transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of chloride transport." [GOC:dph]
-is_a: GO:0044070 ! regulation of anion transport
+is_a: GO:0044070 ! regulation of monoatomic anion transport
relationship: regulates GO:0006821 ! chloride transport
[Term]
@@ -540489,7 +543263,7 @@ id: GO:2001226
name: negative regulation of chloride transport
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of chloride transport." [GOC:dph]
-is_a: GO:1903792 ! negative regulation of anion transport
+is_a: GO:1903792 ! negative regulation of monoatomic anion transport
is_a: GO:2001225 ! regulation of chloride transport
relationship: negatively_regulates GO:0006821 ! chloride transport
@@ -540713,6 +543487,7 @@ synonym: "regulation of phosphatidylcholine anabolism" EXACT [GOC:obol]
synonym: "regulation of phosphatidylcholine biosynthesis" EXACT [GOC:obol]
synonym: "regulation of phosphatidylcholine formation" EXACT [GOC:obol]
synonym: "regulation of phosphatidylcholine synthesis" EXACT [GOC:obol]
+is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0071071 ! regulation of phospholipid biosynthetic process
is_a: GO:0150172 ! regulation of phosphatidylcholine metabolic process
relationship: regulates GO:0006656 ! phosphatidylcholine biosynthetic process
@@ -540726,6 +543501,7 @@ synonym: "negative regulation of phosphatidylcholine anabolism" EXACT [GOC:obol]
synonym: "negative regulation of phosphatidylcholine biosynthesis" EXACT [GOC:obol]
synonym: "negative regulation of phosphatidylcholine formation" EXACT [GOC:obol]
synonym: "negative regulation of phosphatidylcholine synthesis" EXACT [GOC:obol]
+is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
is_a: GO:0071072 ! negative regulation of phospholipid biosynthetic process
is_a: GO:0150174 ! negative regulation of phosphatidylcholine metabolic process
is_a: GO:2001245 ! regulation of phosphatidylcholine biosynthetic process
@@ -540740,6 +543516,7 @@ synonym: "positive regulation of phosphatidylcholine anabolism" EXACT [GOC:obol]
synonym: "positive regulation of phosphatidylcholine biosynthesis" EXACT [GOC:obol]
synonym: "positive regulation of phosphatidylcholine formation" EXACT [GOC:obol]
synonym: "positive regulation of phosphatidylcholine synthesis" EXACT [GOC:obol]
+is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:0071073 ! positive regulation of phospholipid biosynthetic process
is_a: GO:0150173 ! positive regulation of phosphatidylcholine metabolic process
is_a: GO:2001245 ! regulation of phosphatidylcholine biosynthetic process
@@ -540808,29 +543585,30 @@ relationship: positively_regulates GO:0051276 ! chromosome organization
[Term]
id: GO:2001253
-name: regulation of histone H3-K36 trimethylation
+name: obsolete regulation of histone H3-K36 trimethylation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone H3-K36 trimethylation." [PMID:17948059]
-is_a: GO:0000414 ! regulation of histone H3-K36 methylation
-relationship: regulates GO:0097198 ! histone H3-K36 trimethylation
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone H3-K36 trimethylation." [PMID:17948059]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0140673
[Term]
id: GO:2001254
-name: negative regulation of histone H3-K36 trimethylation
+name: obsolete negative regulation of histone H3-K36 trimethylation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K36 trimethylation." [PMID:17948059]
-is_a: GO:0000415 ! negative regulation of histone H3-K36 methylation
-is_a: GO:2001253 ! regulation of histone H3-K36 trimethylation
-relationship: negatively_regulates GO:0097198 ! histone H3-K36 trimethylation
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K36 trimethylation." [PMID:17948059]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0006338
[Term]
id: GO:2001255
-name: positive regulation of histone H3-K36 trimethylation
+name: obsolete positive regulation of histone H3-K36 trimethylation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of histone H3-K36 trimethylation." [PMID:17948059]
-is_a: GO:0000416 ! positive regulation of histone H3-K36 methylation
-is_a: GO:2001253 ! regulation of histone H3-K36 trimethylation
-relationship: positively_regulates GO:0097198 ! histone H3-K36 trimethylation
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of histone H3-K36 trimethylation." [PMID:17948059]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0140673
[Term]
id: GO:2001256
@@ -540851,8 +543629,8 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of cation channel activity." [GOC:BHF]
synonym: "regulation of cation diffusion facilitator activity" EXACT [GOC:obol]
synonym: "regulation of nonselective cation channel activity" EXACT [GOC:obol]
-is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
-is_a: GO:1904062 ! regulation of cation transmembrane transport
+is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity
+is_a: GO:1904062 ! regulation of monoatomic cation transmembrane transport
[Term]
id: GO:2001258
@@ -541055,7 +543833,7 @@ synonym: "negative regulation of leucine anabolism" EXACT [GOC:obol]
synonym: "negative regulation of leucine biosynthesis" EXACT [GOC:obol]
synonym: "negative regulation of leucine formation" EXACT [GOC:obol]
synonym: "negative regulation of leucine synthesis" EXACT [GOC:obol]
-is_a: GO:2000283 ! negative regulation of cellular amino acid biosynthetic process
+is_a: GO:2000283 ! negative regulation of amino acid biosynthetic process
is_a: GO:2001276 ! regulation of leucine biosynthetic process
relationship: negatively_regulates GO:0009098 ! leucine biosynthetic process
@@ -541068,7 +543846,7 @@ synonym: "positive regulation of leucine anabolism" EXACT [GOC:obol]
synonym: "positive regulation of leucine biosynthesis" EXACT [GOC:obol]
synonym: "positive regulation of leucine formation" EXACT [GOC:obol]
synonym: "positive regulation of leucine synthesis" EXACT [GOC:obol]
-is_a: GO:2000284 ! positive regulation of cellular amino acid biosynthetic process
+is_a: GO:2000284 ! positive regulation of amino acid biosynthetic process
is_a: GO:2001276 ! regulation of leucine biosynthetic process
relationship: positively_regulates GO:0009098 ! leucine biosynthetic process
@@ -541241,7 +544019,7 @@ is_a: GO:1901376 ! organic heteropentacyclic compound metabolic process
id: GO:2001292
name: codeine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of codeine, an alkaloid found in the opium poppy, Papaver somniferum var. album. Codeine has analgesic, anti-tussive and anti-diarrhoeal properties." [GOC:yaf, UniPathway:UPA00318]
+def: "The chemical reactions and pathways resulting in the breakdown of codeine, an alkaloid found in the opium poppy, Papaver somniferum var. album. Codeine has analgesic, anti-tussive and anti-diarrhoeal properties." [GOC:yaf, PMID:8845855]
synonym: "codeine breakdown" EXACT [GOC:obol]
synonym: "codeine catabolism" EXACT [GOC:obol]
synonym: "codeine degradation" EXACT [GOC:obol]
@@ -541300,7 +544078,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of N(omega)
synonym: "N(omega)-methyl-L-arginine breakdown" EXACT [GOC:obol]
synonym: "N(omega)-methyl-L-arginine catabolism" EXACT [GOC:obol]
synonym: "N(omega)-methyl-L-arginine degradation" EXACT [GOC:obol]
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0042219 ! cellular modified amino acid catabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
is_a: GO:2001296 ! N(omega)-methyl-L-arginine metabolic process
@@ -541322,6 +544100,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of N(omega)
synonym: "N(omega),N(omega)-dimethyl-L-arginine breakdown" EXACT [GOC:obol]
synonym: "N(omega),N(omega)-dimethyl-L-arginine catabolism" EXACT [GOC:obol]
synonym: "N(omega),N(omega)-dimethyl-L-arginine degradation" EXACT [GOC:obol]
+is_a: GO:0009063 ! amino acid catabolic process
is_a: GO:0042219 ! cellular modified amino acid catabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
is_a: GO:2001298 ! N(omega),N(omega)-dimethyl-L-arginine metabolic process
@@ -541354,6 +544133,7 @@ def: "The chemical reactions and pathways involving lipoxin A4. Lipoxin A4 is a
synonym: "lipoxin A4 metabolism" EXACT [GOC:obol]
synonym: "LXA4 metabolic process" EXACT [GOC:obol]
synonym: "LXA4 metabolism" EXACT [GOC:obol]
+is_a: GO:0001676 ! long-chain fatty acid metabolic process
is_a: GO:0033559 ! unsaturated fatty acid metabolic process
is_a: GO:1901615 ! organic hydroxy compound metabolic process
is_a: GO:2001300 ! lipoxin metabolic process
@@ -541373,6 +544153,7 @@ synonym: "LXA4 biosynthetic process" EXACT [GOC:obol]
synonym: "LXA4 formation" EXACT [GOC:obol]
synonym: "LXA4 synthesis" EXACT [GOC:obol]
is_a: GO:0006636 ! unsaturated fatty acid biosynthetic process
+is_a: GO:0042759 ! long-chain fatty acid biosynthetic process
is_a: GO:1901617 ! organic hydroxy compound biosynthetic process
is_a: GO:2001301 ! lipoxin biosynthetic process
is_a: GO:2001302 ! lipoxin A4 metabolic process
@@ -541385,6 +544166,7 @@ def: "The chemical reactions and pathways involving lipoxin B4. Lipoxin B4 is a
synonym: "lipoxin B4 metabolism" EXACT [GOC:obol]
synonym: "LXB4 metabolic process" EXACT [GOC:obol]
synonym: "LXB4 metabolism" EXACT [GOC:obol]
+is_a: GO:0001676 ! long-chain fatty acid metabolic process
is_a: GO:0033559 ! unsaturated fatty acid metabolic process
is_a: GO:1901615 ! organic hydroxy compound metabolic process
is_a: GO:2001300 ! lipoxin metabolic process
@@ -541417,6 +544199,7 @@ synonym: "LXB4 biosynthetic process" EXACT [GOC:obol]
synonym: "LXB4 formation" EXACT [GOC:obol]
synonym: "LXB4 synthesis" EXACT [GOC:obol]
is_a: GO:0006636 ! unsaturated fatty acid biosynthetic process
+is_a: GO:0042759 ! long-chain fatty acid biosynthetic process
is_a: GO:1901617 ! organic hydroxy compound biosynthetic process
is_a: GO:2001301 ! lipoxin biosynthetic process
is_a: GO:2001304 ! lipoxin B4 metabolic process
diff --git a/src/.DS_Store b/src/.DS_Store
index 047067a..5d6a7f3 100644
Binary files a/src/.DS_Store and b/src/.DS_Store differ
diff --git a/src/App.js b/src/App.js
index 5790d8b..4b9bbcb 100644
--- a/src/App.js
+++ b/src/App.js
@@ -20,6 +20,9 @@ import UploadFilesModal from "./components/upload-files-modal";
import UploadGOFilesModal from "./components/upload-go-files-modal";
import GOResultModal from "./components/go-result-modal";
import TreeResultModal from "./components/tree-result-modal";
+import CollapseModal from "./components/collapse-depth-modal";
+import FilterSNPsModal from "./components/filter-SNP-modal";
+import ApplyFilterModal from "./components/apply-filter-modal";
//import ResizableModal from "./components/resizable";
// import { PushSpinner } from "react-spinners-kit";
@@ -31,45 +34,24 @@ import * as d3 from "d3";
import * as d3v5 from "d3v5";
import * as $ from "jquery";
import * as _ from "lodash";
-
import "bootstrap";
import HeatmapView from "./components/heatmap-view";
+//import { ThreeSixty } from "@material-ui/icons";
+
class App extends Component {
+ zoom = null;
state = {};
+ tx = 0;
+ ty = 0;
chosenMD = "";
- // Create vertical zoom for all components
- verticalZoom = (e) => {
- if (!e.ctrlKey) {
- for (let id of [
- "#heatmap-container",
- "#md-container",
- "#zoom-phylotree",
- "#container-labels",
- "#guidelines-container",
- ]) {
- if (d3v5.select(id).node()) {
- let selection = d3v5.select(id);
- let transform = selection.attr("transform") || "translate(0,0)scale(1,1)";
- transform = d3.transform(transform);
- let horizontalZoom = { x: transform.translate[0], k: transform.scale[0] };
- let transformY = { y: transform.translate[1], k: transform.scale[1] };
- let scale = transformY.k + e.deltaY * -0.001;
- scale = Math.min(Math.max(0.8, scale), 10);
- //TODO if scale is smaller than one, allow movement
- let scaleDifference = Math.min(
- 0,
- this.svgContainer.offsetHeight - this.svgContainer.offsetHeight * transformY.k
- );
- let translateY = Math.max(transformY.y, scaleDifference);
- let transformString = `translate(${horizontalZoom.x},${translateY})scale(${horizontalZoom.k},${scale})`;
- selection.attr("transform", `${transformString}`);
- }
- }
- }
- };
+ numSNPs=0
+
+ /**
+ Panning in vertical direction
+ **/
verticalDrag = (ev) => {
- if (this.state.dragActive) {
+ if (this.state.dragActive && !ev.ctrlKey && !ev.shiftKey){
for (let id of [
"#heatmap-container",
"#md-container",
@@ -85,15 +67,34 @@ class App extends Component {
let transformY = { y: transform.translate[1], k: transform.scale[1] };
let translateY = transformY.y + ev.movementY;
- let scaleDifference = Math.min(
- 0,
- this.svgContainer.offsetHeight - this.svgContainer.offsetHeight * transformY.k
- );
- translateY = Math.max(Math.min(0, translateY), scaleDifference);
- let transformString = `translate(${horizontalZoom.x},${translateY})scale(${horizontalZoom.k},${transformY.k})`;
+ let transformString = `translate(${horizontalZoom.x},${translateY})scale(${horizontalZoom.k},${1})`;
selection.attr("transform", `${transformString}`);
}
}
+ }
+ };
+
+ /**
+ Semantic zoom in vertical direction
+ **/
+ verticalZoom = (e) => {
+ if (!e.ctrlKey&&!e.shiftKey) {
+
+ var which_function = this.tree.spacing_x;
+
+ //Restrict zooming if tree gets small
+ if(this.tree.size()[0]< 1049 && e.deltaY >0) {
+ this.tree.size([928, this.tree.size()[1]]).update()
+ which_function(which_function()-e.deltaY/100).update()
+ this.setState({treeSize:this.tree.size()[0]}) //*1.0075
+ }
+ else{
+ this.tree.size([this.tree.size()[0]-e.deltaY, this.tree.size()[1]]).update()
+ which_function(which_function()-e.deltaY/100).update()
+ this.setState({treeSize:this.tree.size()[0]})
+ //d3.select("#tree-display").attr("height",this.state.treeSize)
+ }
+
}
};
@@ -152,27 +153,34 @@ class App extends Component {
tree = this.tree.branch_length(this.tree_branch_upgma);
initialState = {
- // resetClick: 0,
isLoaded: false,
dragActive: false,
hiddenNodes: [],
+ filteredNodes:[],
cladeNumber: 0,
mdinfo: [],
availableSNPs: [],
collapsedClades: [],
selectedNodes: [],
+ nodesToCollapse: [],
visualizedMD: [],
visualizedSNPs: [],
SNPTable: {},
selectedNodeId: null,
ordinalModalShow: false,
renameModalShow: false,
+ collapsedModalShow: false,
+ filterSNPModalShow:false,
+ applyFilterModalShow:false,
createdFilters: [],
nameOfFilters: [],
activeFilters: [],
orderChanged: false,
loadAnimationShow: false,
cladogram: false,
+ yscale: 1,
+ selectedLabels:[],
+
//-------------------------------------------------
// added for holding preprocessed statistical data
@@ -185,6 +193,7 @@ class App extends Component {
all_snps: [],
node_to_snps: {},
tree_size: 0,
+ tree_depth: 0,
tree_snps: 0,
in_gene_tree: 0,
subtree_size: 0,
@@ -269,6 +278,8 @@ class App extends Component {
tree_size: json.tree_size,
tree_snps: json.num_snps,
all_snps: json.all_snps,
+ yscale: 1,
+ selectedLabels:[],
});
}
$("#welcome-modal-button").text("Close");
@@ -276,25 +287,33 @@ class App extends Component {
}
};
- resetZoom = function () {
+ /**
+ * Resets the zoom to the original state of the visualization.
+ */
+ resetZoom = () => {
+ var which_function = this.tree.spacing_x;
+ this.tree.size([929, 691])
+ which_function(which_function()-20).update()
+ this.setState({treeSize:this.tree.size()[0]})
+ this.tree.update();
+ this.tree.trigger_refresh();
+
for (let id of [
- "#heatmap-container",
- "#md-container",
- "#zoom-phylotree",
- "#container-labels",
- "#guidelines-container",
- ]) {
- if (d3v5.select(id).node()) {
- let selection = d3v5.select(id);
+ "#heatmap-container",
+ "#md-container",
+ "#zoom-phylotree",
+ "#container-labels",
+ "#guidelines-container",
+ ]) {
+ let selection = d3.select(id);
let transformString = `translate(${0},${0})scale(${1},${1})`;
selection.attr("transform", `${transformString}`);
- }
}
};
+
/**
* Resets the view to the original state of the visualization.
*/
-
resetApp = () => {
this.setState({
hiddenNodes: [],
@@ -317,6 +336,9 @@ class App extends Component {
visualizedSNPs: [],
SNPTable: {},
selectedNodeId: null,
+ yscale: 1,
+ treeSize: 929,
+ selectedLabels :[],
});
this.resetZoom();
const all_nodes = this.tree.get_nodes();
@@ -332,6 +354,9 @@ class App extends Component {
node["own-collapse"] = false;
this.handleDecollapse(node, false);
}
+ if(node["just-collapsed"]){
+ node["just-collapsed"]=false;
+ }
});
this.handleShowNodes(root[0]);
this.tree.update();
@@ -344,6 +369,7 @@ class App extends Component {
* @param {string} exampleName - Name of the example data to load.
*/
handleExampleLoad = async (exampleName) => {
+ this.resetApp()
this.setState(this.initialState);
this.handleLoadingToggle(true);
@@ -683,6 +709,7 @@ class App extends Component {
* @param formData
*/
handleSubmit = async (formData) => {
+ this.resetApp()
this.handleLoadingToggle(true);
let response = await fetch(`/api/upload`, {
method: "post",
@@ -727,6 +754,10 @@ class App extends Component {
this.sortSnpData();
};
+ handleInitialSizes = (treeMargin, treeSize ) =>{
+ this.setState({treeMargin:treeMargin,treeSize:treeSize})
+ }
+
/**
* Verifies if the node is a visible End-node
* @param {Object} node of Phylotree library
@@ -804,7 +835,7 @@ class App extends Component {
};
handleMDChange = (ev) => {
this.setState({
- visualizedMD: ev.map(({ value }) => value),
+ visualizedMD: ev.map(({ value }) => value)
});
};
updateSNPTable = (nodeID, supportSNPTable, nonSupportSNPTable) => {
@@ -839,6 +870,7 @@ class App extends Component {
document.body.style.cursor = "";
}, 5);
};
+
handleHideSNPs = (list_of_snps) => {
const curr = this.state.visualizedSNPs;
var next = curr.filter((snp) => !list_of_snps.includes(snp));
@@ -893,8 +925,26 @@ class App extends Component {
});
};
handleDeleteAllFilters = () => {
- this.handleShowNodes(this.tree.get_nodes()[0]);
this.setState({ createdFilters: [], nameOfFilters: [] });
+ if(this.state.hidden){
+ this.handleShowNodes(this.tree.get_nodes()[0]);
+ }
+ else{
+ const all_nodes = this.tree.get_nodes();
+ const root = [all_nodes[0]];
+ const descendants = root.concat(this.tree.select_all_descendants(root[0], true, true));
+ this.tree.modify_selection(descendants, undefined, undefined, undefined, "false");
+ all_nodes.forEach((node) => {
+ if (node["own-collapse"]) {
+ node["show-name"] = "";
+ node["own-collapse"] = false;
+ this.handleDecollapse(node, false);
+ }
+ });
+ this.handleShowNodes(root[0]);
+ this.tree.update();
+ this.tree.trigger_refresh();
+ }
};
handleFilterCloseModal = (save, filter, name) => {
let newFilters = [...this.state.createdFilters, filter];
@@ -946,6 +996,7 @@ class App extends Component {
if (!node["hidden-t"]) {
node["hidden-t"] = true;
this.tree.modify_selection([node], "notshown", true, true, "true");
+
}
}
this.handleHide(nodeList);
@@ -960,8 +1011,8 @@ class App extends Component {
this.handleShowOnHeatmap(this.tree.descendants(node));
}
- handleApplyAllFilter = () => {
- let root = this.tree.get_nodes()[0];
+ handleFindNodesToFilter = () => {
+ let root = this.tree.get_nodes()[0]; //get root
this.tempShowNodes(root);
let taxaDataModified = _.keyBy(this.state.taxamd, "Information");
let resultingNodes = this.tree
@@ -971,12 +1022,66 @@ class App extends Component {
let filterResult = this.testForFilters(node, this.state.createdFilters, taxaDataModified);
return !filterResult;
});
- this.handleHideMultipleNodes(resultingNodes);
+ return resultingNodes
+ }
+
+ handleApplyAllFilter = () => {
+ this.handleApplyFilterModalOpen();
};
+ handleApplyFilterModalOpen = () =>{
+ this.setState({applyFilterModalShow:true});
+ }
+ handleApplyFilterModalClose = (save, hide, collapseAll) =>{
+ if(save){
+ let resultingNodes = this.handleFindNodesToFilter();
+ if(hide){
+ this.setState({hidden:true})
+ this.handleHideMultipleNodes(resultingNodes);
+ this.setState({applyFilterModalShow:false});
+ return
+ }
+ else{
+ this.setState({hidden:false})
+ var nodesToCollapse = this.handleFindNodesToFilterForCollapse(resultingNodes, collapseAll)
+ this.setState({filteredNodes:nodesToCollapse})
+ document.body.style.cursor = "wait";
+ setTimeout(()=>{
+ this.handleCollapseMultipleNodes(nodesToCollapse)
+ document.body.style.cursor = "default";
+ });
+ }
+ }
+ this.setState({applyFilterModalShow:false});
+ }
+
+ handleFindNodesToFilterForCollapse = (leafnodeList, collapseAll) =>{
+ var nodesToCollapse = [];
+ leafnodeList.forEach(function(node, i){
+ var pathToRoot = this.tree.path_to_root(node)
+ pathToRoot.shift(); //remove first element
+ var previousNode;
+ pathToRoot.every((parentNode)=>{
+ var descendingLeaves = this.tree.select_all_descendants(parentNode,true,false) //select terminal nodes
+ if(!descendingLeaves.every(elem => leafnodeList.includes(elem) )){
+ if(previousNode !== undefined){
+ nodesToCollapse.push(previousNode)
+ }
+ else if (collapseAll){
+ nodesToCollapse.push(parentNode)
+ }
+ return false
+ }
+ previousNode = parentNode;
+ return true;
+ })
+ },this)
+ return nodesToCollapse
+ }
handleRenameOpenModal = (node) => {
this.setState({ renameModalShow: true, changingCladeNode: node });
};
+
handleRenameCloseModal = (save, node, name) => {
name = name.replace(/[^a-zA-Z0-9_-]/g, "_");
let given_names = this.tree
@@ -1012,6 +1117,132 @@ class App extends Component {
});
}
};
+ handleCollapseOpenModal =()=>{
+ this.setState({collapsedModalShow:true, tree_depth:this.tree.get_max_depth_of_tree()});
+ }
+
+ handleCollapseModalSelection =(value)=>{
+ this.tree.modify_selection(
+ this.tree.select_all_descendants(this.tree.get_nodes()[0], true, true),
+ undefined,
+ undefined,
+ undefined,
+ "false"
+ );
+ var selectedNodes = this.handlefindNodesByDepth(parseInt(value));
+ this.setState({nodesToCollapse:selectedNodes})
+
+ selectedNodes.forEach((node)=>{
+ this.tree.modify_selection(
+ this.tree.select_all_descendants(node, true, true),
+ undefined,
+ undefined,
+ undefined,
+ "true"
+ );
+ });
+ }
+ handleCollapseCloseModal=(save)=>{
+ if(save){
+ this.tree.modify_selection(
+ this.tree.select_all_descendants(this.tree.get_nodes()[0], true, true),
+ undefined,
+ undefined,
+ undefined,
+ "false"
+ );
+ this.setState({collapsedModalShow:false})
+ document.body.style.cursor = "wait";
+ setTimeout(()=>{
+ this.handleCollapseMultipleNodes(this.state.nodesToCollapse)
+ document.body.style.cursor = "default";
+ });
+ return
+ }
+ else{
+ this.tree.modify_selection(
+ this.tree.select_all_descendants(this.tree.get_nodes()[0], true, true),
+ undefined,
+ undefined,
+ undefined,
+ "false"
+ );
+ this.setState({collapsedModalShow:false})
+ }
+ }
+
+ handleFilterSNPsOpenModal =()=>{
+ this.setState({filterSNPModalShow:true});
+ }
+
+ handleFilterSNPsModalSelection =(value)=>{
+ this.tree.modify_selection(
+ this.tree.select_all_descendants(this.tree.get_nodes()[0], true, true),
+ undefined,
+ undefined,
+ undefined,
+ "false"
+ );
+ var selectedNodes = this.handleFilterNodesBySNPContent(parseInt(value));
+ this.setState({nodesToCollapse:selectedNodes})
+
+ selectedNodes.forEach((node)=>{
+ this.tree.modify_selection(
+ this.tree.select_all_descendants(node, true, true),
+ undefined,
+ undefined,
+ undefined,
+ "true"
+ );
+ });
+ }
+ handleFilterSNPsCloseModal=(save)=>{
+ if(save){
+ this.tree.modify_selection(
+ this.tree.select_all_descendants(this.tree.get_nodes()[0], true, true),
+ undefined,
+ undefined,
+ undefined,
+ "false"
+ );
+ this.setState({filterSNPModalShow:false})
+ document.body.style.cursor = "wait";
+ setTimeout(()=>{
+ this.handleCollapseMultipleNodes(this.state.nodesToCollapse)
+ document.body.style.cursor = "default";
+ });
+ return
+ }
+ else{
+ this.tree.modify_selection(
+ this.tree.select_all_descendants(this.tree.get_nodes()[0], true, true),
+ undefined,
+ undefined,
+ undefined,
+ "false"
+ );
+ this.setState({filterSNPModalShow:false})
+ }
+ }
+ handleRemoveFilterSNPs = ()=>{
+
+ const all_nodes = this.tree.get_nodes();
+ const root = [all_nodes[0]];
+ const descendants = root.concat(this.tree.select_all_descendants(root[0], true, true));
+ this.tree.modify_selection(descendants, undefined, undefined, undefined, "false");
+ all_nodes.forEach((node) => {
+ if (node["own-collapse"]) {
+ node["show-name"] = "";
+ node["own-collapse"] = false;
+ this.handleDecollapse(node, false);
+ }
+ });
+ this.handleShowNodes(root[0]);
+ this.tree.update();
+ this.tree.trigger_refresh();
+
+ }
+
handleColorChange = (metadataName) => {
this.chosenMD = metadataName;
this.setState({ colorScaleModalShow: true });
@@ -1039,23 +1270,63 @@ class App extends Component {
nodes: nodes,
});
};
+ handlefindNodesByDepth(depth){
+ const nodes = this.tree.get_nodes();
+ var nodes_to_collapse = [];
+ nodes.forEach(function(node){
+ if(!d3.layout.phylotree.is_leafnode(node)&&node.name!=="root"){
+ if(node.depth === depth){
+ nodes_to_collapse.push(node);
+ }
+ }
+ });
+ return nodes_to_collapse
+ }
+
+ handleFilterNodesBySNPContent(percentage){
+ const nodes = this.tree.get_nodes();
+ var nodes_to_collapse = [];
+ nodes.forEach(function(node){
+ if(!d3.layout.phylotree.is_leafnode(node)&&node.name!=="root"){
+ if(node["percent-support-SNPs"] <= percentage){
+ nodes_to_collapse.push(node);
+ }
+ }
+ });
+ return nodes_to_collapse
+ }
+
+ handleCollapseMultipleNodes(nodeList){
+ if(nodeList.length !== 0){
+ nodeList.forEach(function(node){
+ if(!node["hidden"] && !node["own-collapse"] && !node["notshown"]){
+ node["own-collapse"] = true;
+ node["show-name"] = this.handleCollapse(node);
+ node["just-collapsed"]=true;
+ }
+ },this)
+ this.handleSelection(this.tree.get_selection());
+ }
+ this.tree.trigger_refresh();
+ }
handleCollapse = (cladeNode) => {
let collapsedNodes = this.tree.descendants(cladeNode).filter(d3.layout.phylotree.is_leafnode);
-
let clade = {
name: "Clade_" + this.state.cladeNumber,
showname: "Clade_" + this.state.cladeNumber,
cladeParent: cladeNode,
cladeLeaves: collapsedNodes,
};
- cladeNode.name = clade.name;
+ cladeNode.name = clade.name;
cladeNode["show-name"] = clade.name;
let actualNumber = this.state.cladeNumber;
let jointNodes = this.state.collapsedClades.concat([clade]);
+
this.tree.toggle_collapse(cladeNode).update();
this.setState({ collapsedClades: jointNodes, cladeNumber: actualNumber + 1 });
+
return clade.name;
};
handleDecollapse = (cladeNode, should_update = true) => {
@@ -1082,6 +1353,7 @@ class App extends Component {
this.handleShowOnHeatmap(this.tree.descendants(node));
this.handleSelection(this.tree.get_selection());
};
+
handleShowOnHeatmap = (showNodes) => {
let namesShowNodes = showNodes.map(({ name }) => name);
let filteredNodes = this.state.hiddenNodes.filter((n) => {
@@ -1090,6 +1362,14 @@ class App extends Component {
this.setState({ hiddenNodes: filteredNodes });
};
+ handleLabelSelection = (list)=>{
+ this.setState({selectedLabels : list});
+ }
+ clearLabelSelection = ()=>{
+ this.setState({selectedLabels : []})
+ }
+
+
handleSelection = (selection) => {
let filteredSelection = selection.filter((node) => {
return (
@@ -1104,8 +1384,18 @@ class App extends Component {
this.setState({ cladogram: !this.state.cladogram });
this.tree.placenodes();
this.tree.update();
- // this.tree.update();
};
+ handleMouseDown = () =>{
+ this.setState({ dragActive: true })
+ const all_nodes = this.tree.get_nodes();
+ all_nodes.forEach((node) => {
+ if(node["just-collapsed"]){
+ node["just-collapsed"]=false;
+ }
+ });
+ this.tree.trigger_refresh();
+
+ }
componentDidMount() {
d3.select("body")
@@ -1114,7 +1404,6 @@ class App extends Component {
.attr("class", "tooltip")
.attr("id", "tooltip")
.style("display", "none");
-
this.handleInitTool();
}
@@ -1135,16 +1424,18 @@ class App extends Component {
className='parent-svgs'
ref={(el) => (this.svgContainer = el)}
onWheel={this.verticalZoom}
- onMouseDown={() => this.setState({ dragActive: true })}
+ onMouseDown={this.handleMouseDown}
onMouseMove={this.verticalDrag}
onMouseUp={() => this.setState({ dragActive: false })}
>
-
+