diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml index 0db91dea..dfd9b1a4 100644 --- a/.github/workflows/continuous_integration.yml +++ b/.github/workflows/continuous_integration.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [ "3.10", "3.11", "3.12", "3.13" ] + python-version: [ "3.11", "3.12", "3.13" ] steps: - name: Checkout uses: actions/checkout@v4 @@ -27,7 +27,7 @@ jobs: run: uv sync --python "${{ matrix.python-version }}" --all-extras --dev - name: Run tests - run: uv run --python "${{ matrix.python-version }}" pytest --cov --junitxml=junit.xml -o junit_family=legacy + run: uv run --python "${{ matrix.python-version }}" pytest - name: Cache Clear run: uv cache prune --ci diff --git a/main/COMO.ipynb b/main/COMO.ipynb index abfe59ee..625d1163 100644 --- a/main/COMO.ipynb +++ b/main/COMO.ipynb @@ -53,7 +53,7 @@ " 3. Compare results between perturbed and unperturbed models (i.e., knocked-out models vs non-knocked-out models)\n", " 4. Integrate with disease genes and create a score of drug targets" ], - "id": "479b5fea813eb4c4" + "id": "227da2b778760c93" }, { "metadata": {}, @@ -223,7 +223,7 @@ " \n", "" ], - "id": "2ed670131b6f7ce2" + "id": "583a9cc77019b929" }, { "metadata": {}, @@ -239,12 +239,12 @@ "\n", " This is used to set the proper input and output paths for the rest of the notebook\n", "\n", + "\n", " Returns:\n", - " The directory to the COMO.ipynb notebook\n", + " The directory containing the `COMO.ipynb` notebook\n", "\n", " Raises:\n", - " FileNotFoundError: If the notebook directory cannot be determined\n", - "\n", + " FileNotFoundError: If the root directory could not be determined\n", " \"\"\"\n", " current_dir = Path().cwd()\n", "\n", @@ -256,7 +256,7 @@ " raise FileNotFoundError(\"Root directory could not be determined; unable to find 'COMO.ipynb'\")\n", " current_dir = current_dir.parent" ], - "id": "1a6e53c173aa9517" + "id": "18b794c4e630179e" }, { "metadata": {}, @@ -270,40 +270,36 @@ "from como.rnaseq_preprocess import rnaseq_preprocess\n", "\n", "taxon_id = 9606\n", - "context_names = [\"naiveB\"]\n", + "# context_names = [\"control1hr\", \"control6hr\", \"control15min\", \"control24hr\", \"indralin1hr\", \"indralin6hr\",\n", + "# \"indralin15min\", \"indralin24hr\", \"notreatment\"]\n", + "context_names = [\"notreatment\"]\n", "notebook_dir = get_notebook_dir()\n", "\n", - "gene_info_filepath = {context: Path(notebook_dir, \"data\", \"results\", context, \"gene_info.csv\") for context in\n", + "# Input Components\n", + "como_context_dir = {context: Path(notebook_dir / f\"data/COMO_input/{context}\") for context in context_names}\n", + "gene_info_filepath = {context: Path(notebook_dir / f\"data/results/{context}/gene_info.csv\") for context in\n", " context_names}\n", - "como_context_dir = {context: Path(notebook_dir, \"data\", \"COMO_input\", context) for context in context_names}\n", - "trna_matrix_filepath = {context: Path(notebook_dir, \"data\", \"results\", context, \"total-rna\", f\"totalrna_{context}.csv\")\n", - " for context in context_names}\n", - "mrna_matrix_filepath = {context: Path(notebook_dir, \"data\", \"results\", context, \"polya-rna\", f\"polyarna_{context}.csv\")\n", - " for context in context_names}\n", + "trna_matrix_filepath = {context: Path(notebook_dir / f\"data/results/{context}/total-rna/totalrna_{context}.csv\") for\n", + " context in\n", + " context_names}\n", + "mrna_matrix_filepath = {context: Path(notebook_dir / f\"data/results/{context}/mrna/mrna_{context}.csv\") for context in\n", + " context_names}\n", "proteomics_matrix_filepath = {\n", - " context: Path(notebook_dir, \"data\", \"data_matrices\", context, f\"protein_abundance_{context}.csv\") for context in\n", - " context_names\n", - "}\n", - "\n", - "output_trna_boolean_activity_filepath = {context: Path(notebook_dir, \"data\", \"results\", context,\n", - " f\"totalrna_{context}_boolean_activity.csv\") for context in\n", - " context_names}\n", - "output_mrna_boolean_activity_filepath = {\n", - " context: Path(notebook_dir, \"data\", \"results\", context, f\"polyarna_{context}_boolean_activity.csv\") for context in\n", - " context_names\n", - "}\n", - "\n", - "trna_metadata_filepath = Path(\"data/config_sheets/trna_config.xlsx\")\n", - "mrna_metadata_filepath = Path(\"data/config_sheets/mrna_config.xlsx\")\n", - "proteomics_metadata_filepath = Path(\"data/config_sheets/proteomics_config.xlsx\")\n", + " context: Path(notebook_dir / f\"data/data_matrices/{context}/protein_abundance_{context}.csv\") for context\n", + " in context_names}\n", "\n", "# No single-cell data is provided by default; COMO accepts single-cell data in CSV or h5ad format\n", "# If you are using single-cell data, adjust the following lines accordingly\n", - "scrna_matrix_filepath = {context: Path(f\"data/results/{context}/scrna/scrna_{context}.csv\") for context in\n", + "scrna_matrix_filepath = {context: Path(notebook_dir / f\"data/results/{context}/scrna/scrna_{context}.csv\") for context\n", + " in\n", " context_names}\n", - "# scrna_matrix_filepath = [Path(f\"data/results/{context}/scrna/scrna_{context}.h5ad\") for context in context_names]\n" + "# scrna_matrix_filepath = [Path(f\"data/results/{context}/scrna/scrna_{context}.h5ad\") for context in context_names]\n", + "\n", + "trna_metadata_filepath = Path(notebook_dir / \"data/config_sheets/trna_config.xlsx\")\n", + "mrna_metadata_filepath = Path(notebook_dir / \"data/config_sheets/mrna_config.xlsx\")\n", + "proteomics_metadata_filepath = Path(notebook_dir / \"data/config_sheets/proteomics_config.xlsx\")\n" ], - "id": "9ab22f2fc7fee5d1" + "id": "a1bfbaedc90f3090" }, { "metadata": {}, @@ -315,7 +311,7 @@ "- `taxon_id`: The [NCBI Taxon ID](https://www.ncbi.nlm.nih.gov/taxonomy) to use\n", "- `preprocess_mode`: This should be set to `\"create-matrix\"` if you are **not** providing a matrix, otherwise set it to `\"provide-matrix\"`" ], - "id": "25ac28c053dcf5c4" + "id": "abe71b54fcb24765" }, { "metadata": {}, @@ -334,13 +330,13 @@ " output_gene_info_filepath=gene_info_filepath[context],\n", " output_trna_metadata_filepath=trna_metadata_filepath,\n", " output_trna_count_matrix_filepath=trna_matrix_filepath[context],\n", - " output_mrna_metadata_filepath=mrna_metadata_filepath,\n", - " output_mrna_count_matrix_filepath=mrna_matrix_filepath[context],\n", + " # output_mrna_metadata_filepath=mrna_metadata_filepath,\n", + " # output_mrna_count_matrix_filepath=mrna_matrix_filepath[context],\n", " cache=True,\n", " log_level=\"INFO\",\n", " )" ], - "id": "db198ec6d4d97500" + "id": "fea7f4c6473d2e7a" }, { "metadata": {}, @@ -373,7 +369,7 @@ "\n", "This method is not recommended, as zFPKM is much more robust for a similar level of \"hands-off\" model building\n" ], - "id": "ce9d89e7703f70c7" + "id": "7588e085dca7726c" }, { "metadata": {}, @@ -394,7 +390,7 @@ "#### Single Cell RNA Sequencing\n", "While the Snakemake pipeline does not yet support single-cell alignment, and COMO does not yet support automated configuration file and counts matrix file creation for single-cell alignment output from STAR, it is possible to use single-cell data to create a model with COMO. Because normalization strategies can be applied to single-cell data in the same way it is applied to bulk RNA sequencing, `como/rnaseq_gen.py` can be used with a provided counts matrix and configuration file, from [Step 1](Step-1:-Initialize-and-Preprocess-RNA-seq-data), above. Just like `\"total\"` and `\"mRNA\"`, `como/rnaseq_gen.py` can be executed with `\"SC\"` as the \"`--library-prep`\" argument to help COMO differentiate it from any bulk RNA sequencing data if multiple strategies are being used." ], - "id": "e8aa695a4b89e2db" + "id": "2c157397f90cdf33" }, { "metadata": {}, @@ -413,7 +409,7 @@ "- `min_zfpkm`: The cutoff for Counts-Per-Million filtering\n", "- `prep_method`: The library method used for preparation. Options are: `\"total\"`, `\"mRNA\"`, or `\"SC\"`,\n" ], - "id": "68f67ce8ab353051" + "id": "ee2de748ea687a06" }, { "metadata": { @@ -436,12 +432,12 @@ "for context in context_names:\n", " if context not in trna_matrix_filepath:\n", " continue\n", - " output_zscore_norm_filepath = Path(notebook_dir, \"data\", \"results\", context, \"z_score_normalization.csv\")\n", + " output_zscore_norm_filepath = Path(get_notebook_dir() / f\"data/results/{context}/z_score_normalization.csv\")\n", " await rnaseq_gen(\n", " context_name=context,\n", " input_rnaseq_filepath=trna_matrix_filepath[context],\n", " input_gene_info_filepath=gene_info_filepath[context],\n", - " output_boolean_activity_filepath=output_trna_boolean_activity_filepath[context],\n", + " output_boolean_activity_filepath=trna_matrix_filepath[context],\n", " prep=RNAType.TRNA,\n", " taxon_id=taxon_id,\n", " input_metadata_filepath_or_df=trna_metadata_filepath,\n", @@ -454,21 +450,7 @@ " output_zscore_normalization_filepath=output_zscore_norm_filepath,\n", " )" ], - "id": "2cee097e1a352980", - "outputs": [ - { - "ename": "NameError", - "evalue": "name 'context_names' is not defined", - "output_type": "error", - "traceback": [ - "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", - "\u001B[0;31mNameError\u001B[0m Traceback (most recent call last)", - "Cell \u001B[0;32mIn[1], line 10\u001B[0m\n\u001B[1;32m 7\u001B[0m technique \u001B[38;5;241m=\u001B[39m FilteringTechnique\u001B[38;5;241m.\u001B[39mZFPKM\n\u001B[1;32m 8\u001B[0m cutoff \u001B[38;5;241m=\u001B[39m \u001B[38;5;241m-\u001B[39m\u001B[38;5;241m3\u001B[39m\n\u001B[0;32m---> 10\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m context \u001B[38;5;129;01min\u001B[39;00m \u001B[43mcontext_names\u001B[49m:\n\u001B[1;32m 11\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m context \u001B[38;5;129;01mnot\u001B[39;00m \u001B[38;5;129;01min\u001B[39;00m trna_matrix_filepath:\n\u001B[1;32m 12\u001B[0m \u001B[38;5;28;01mcontinue\u001B[39;00m\n", - "\u001B[0;31mNameError\u001B[0m: name 'context_names' is not defined" - ] - } - ], - "execution_count": 1 + "id": "16dbbffd7418b149" }, { "metadata": {}, @@ -488,7 +470,7 @@ "- `min_zfpkm`: The cutoff for Counts-Per-Million filtering\n", "- `prep_method`: The library method used for preparation. Options are: `\"total\"`, `\"mRNA\"`, or `\"SC\"`,\n" ], - "id": "2f2d8d87b47f6d5a" + "id": "381808e882528556" }, { "metadata": {}, @@ -513,9 +495,10 @@ " input_metadata_filepath_or_df=mrna_metadata_filepath,\n", " input_rnaseq_filepath=mrna_matrix_filepath[context],\n", " input_gene_info_filepath=gene_info_filepath[context],\n", - " output_boolean_activity_filepath=output_mrna_boolean_activity_filepath[context],\n", + " output_boolean_activity_filepath=mrna_matrix_filepath[context],\n", " prep=RNAType.MRNA,\n", " taxon_id=taxon_id,\n", + " input_metadata_filepath=mrna_metadata_filepath,\n", " replicate_ratio=replicate_ratio,\n", " high_replicate_ratio=high_confidence_replicate_ratio,\n", " batch_ratio=batch_ratio,\n", @@ -526,7 +509,7 @@ " f\"data/results/{context}/z_score_normalization.csv\"),\n", " )" ], - "id": "a6d8dd8355ef73a1" + "id": "653e0f1c879a3511" }, { "metadata": {}, @@ -546,7 +529,7 @@ "- `min_zfpkm`: The cutoff for Counts-Per-Million filtering\n", "- `prep_method`: The library method used for preparation. Options are: `\"total\"`, `\"mRNA\"`, or `\"scrna\"`,\n" ], - "id": "567295993b382a06" + "id": "76e24f90cd85cd12" }, { "metadata": {}, @@ -573,7 +556,7 @@ " output_boolean_activity_filepath=scrna_matrix_filepath[context],\n", " prep=RNAType.SCRNA,\n", " taxon_id=taxon_id,\n", - " input_metadata_filepath_or_df=scrna_matrix_filepath,\n", + " input_metadata_filepath=Path(\"./data/config_sheets/scrna_config.xlsx\"),\n", " replicate_ratio=replicate_ratio,\n", " high_replicate_ratio=high_confidence_replicate_ratio,\n", " batch_ratio=batch_ratio,\n", @@ -583,7 +566,7 @@ " output_zscore_normalization_filepath=None,\n", " )" ], - "id": "59a30ef35177f933" + "id": "338305e190a0195" }, { "metadata": {}, @@ -600,7 +583,7 @@ "- `high_batch_ratio`: The ratio required before a gene is considered \"high-confidence\" in the study\n", "- `quantile`: The cutoff Transcripts-Per-Million quantile for filtering" ], - "id": "6c859f0e5a054c41" + "id": "bbf5b896eda5357b" }, { "metadata": {}, @@ -627,7 +610,7 @@ " quantile=25,\n", " )" ], - "id": "eaef4b817dccf696" + "id": "ecf2b6e6c2e27f12" }, { "metadata": {}, @@ -653,7 +636,7 @@ "- `n_neighbors_context`: N nearest neighbors for context clustering. The default is `\"default\"`, which is the total number of contexts\n", "- `seed`: The random seed for clustering algorithm initialization. If not specified, `np.random.randint(0, 100000)` is used" ], - "id": "ddcb4aa5ee3b082f" + "id": "3a6b4ee9708c405b" }, { "metadata": {}, @@ -697,7 +680,7 @@ "\n", "!{cmd}" ], - "id": "46758ccca5f32fb1" + "id": "ec009ffb9e26ecc6" }, { "metadata": {}, @@ -737,7 +720,7 @@ "\n", "Each of the \"weights\" (`total_rna_weight`, `mrna_weight`, etc.) are used to place a significance on each method. Becuase there are many steps in the Dogma from transcription to translation, the gene expression as seen by total RNA or mRNA sequencing may not be representative of the gene's protein expression, and this its metabolic impact. Because of this, you are able to weight each source more (or less) than another." ], - "id": "32a97d01c869f864" + "id": "52eca3228ef747cd" }, { "metadata": {}, @@ -759,18 +742,23 @@ "merge_zfpkm_distrubution = True\n", "keep_transcriptomics_score = True\n", "\n", + "mrna_batches = {\"naiveB\": [\n", + " \"naiveB_S1R1\", \"naiveB_S1R2\", \"naiveB_S1R3\", \"naiveB_S1R4\",\n", + " \"naiveB_S2R1\", \"naiveB_S2R2\", \"naiveB_S2R3\", \"naiveB_S2R4\",\n", + "]}\n", + "trna_batches = {\"naiveB\": [\"naiveB_S3R1\", \"naiveB_S3R2\", \"naiveB_S3R3\"]}\n", + "\n", "for context in context_names:\n", " await merge_xomics(\n", - " taxon_id=taxon_id,\n", " context_name=context,\n", - " trna_metadata_filepath_or_df=trna_metadata_filepath,\n", - " mrna_metadata_filepath_or_df=mrna_metadata_filepath,\n", " trna_matrix_or_filepath=trna_matrix_filepath[context],\n", " mrna_matrix_or_filepath=mrna_matrix_filepath[context],\n", " scrna_matrix_or_filepath=None, # scrna_matrix_filepath[context],\n", " proteomic_matrix_or_filepath=None, # proteomics_matrix_filepath[context],\n", - " trna_boolean_matrix_or_filepath=output_trna_boolean_activity_filepath[context],\n", - " mrna_boolean_matrix_or_filepath=output_mrna_boolean_activity_filepath[context],\n", + " trna_batches=trna_batches,\n", + " mrna_batches=mrna_batches,\n", + " scrna_batches=None,\n", + " proteomic_batches=None,\n", " trna_weight=total_rna_weight,\n", " mrna_weight=mrna_weight,\n", " scrna_weight=single_cell_weight,\n", @@ -781,23 +769,18 @@ " force_activate_high_confidence=force_activate_high_confidence,\n", " adjust_for_na=adjust_for_na_sources,\n", " merge_zfpkm_distribution=merge_zfpkm_distrubution,\n", - " # TODO: Move these paths to be under `notebook_dir`\n", - " # Match variables defined above\n", - " output_merge_activity_filepath=Path(f\"{notebook_dir}/data/results/{context}/ActiveGenes_{context}_Merged.csv\"),\n", - " output_transcriptomic_details_filepath=Path(\n", - " f\"{notebook_dir}/data/results/{context}/TranscriptomicDetails_{context}.csv\"),\n", - " output_trna_activity_filepath=Path(\n", - " f\"{notebook_dir}/data/results/{context}/total-rna/trna_activity_{context}.csv\"),\n", - " output_mrna_activity_filepath=Path(f\"{notebook_dir}/data/results/{context}/mrna/mrna_activity_{context}.csv\"),\n", - " output_scrna_activity_filepath=Path(\n", - " f\"{notebook_dir}/data/results/{context}/scrna/scrna_activity_{context}.csv\"),\n", - " output_proteomic_activity_filepath=Path(\n", - " f\"{notebook_dir}/data/results/{context}/proteomics/proteomic_activity_{context}.csv\"),\n", - " output_final_model_scores_filepath=Path(f\"{notebook_dir}/data/results/{context}/model_scores_{context}.csv\"),\n", - " output_figure_dirpath=Path(f\"{notebook_dir}/data/results/{context}/figures\")\n", + " keep_transcriptomics_score=keep_transcriptomics_score,\n", + " output_merge_activity_filepath=Path(f\"data/results/{context}/ActiveGenes_{context}_Merged.csv\"),\n", + " output_transcriptomic_details_filepath=Path(f\"data/results/{context}/TranscriptomicDetails_{context}.csv\"),\n", + " output_trna_activity_filepath=Path(f\"data/results/{context}/total-rna/trna_activity_{context}.csv\"),\n", + " output_mrna_activity_filepath=Path(f\"data/results/{context}/mrna/mrna_activity_{context}.csv\"),\n", + " output_scrna_activity_filepath=Path(f\"data/results/{context}/scrna/scrna_activity_{context}.csv\"),\n", + " output_proteomic_activity_filepath=Path(f\"data/results/{context}/proteomics/proteomic_activity_{context}.csv\"),\n", + " output_final_model_scores_filepath=Path(f\"data/results/{context}/model_scores_{context}.csv\"),\n", + " output_figure_dirpath=Path(f\"data/results/{context}/figures\")\n", " )" ], - "id": "96934d1a17f86090" + "id": "d1a0a578865ea4a7" }, { "metadata": {}, @@ -864,7 +847,7 @@ "- `force_reactions_filename`: The filename of the force reactions to be used. Force reactions will (as the name implies) force the optimizer to use these reactions, **no matter their expression**\n", "- `exclude_reactions_filename`: The filename of reactions to exclude from the model, no matter their expression" ], - "id": "6294dc0a90e1281" + "id": "aff121ae1e86071b" }, { "metadata": {}, @@ -872,7 +855,7 @@ "outputs": [], "execution_count": null, "source": [ - "\n", + "import json\n", "from pathlib import Path\n", "\n", "from como.create_context_specific_model import create_context_specific_model\n", @@ -911,50 +894,10 @@ " algorithm=Algorithm.IMAT,\n", " solver=Solver.GUROBI,\n", " )\n", - "\n", - "# Load the output of step 1, which is a dictionary that specifies the merged list of active Gene IDs for each tissue\n", - "# step1_results_file = config.data_dir / \"results\" / \"step1_results_files.json\"\n", - "# with step1_results_file.open(\"r\") as json_file:\n", - "# context_gene_exp = json.load(json_file)\n", - "#\n", - "# for recon_algorithm in recon_algorithms:\n", - "# for context in context_gene_exp:\n", - "# objective = objective_dict[context]\n", - "#\n", - "# if recon_algorithm.upper() in [\"IMAT\", \"TINIT\"]:\n", - "# active_genes_filepath = config.data_dir / \"results\" / context / f\"model_scores_{context}.csv\"\n", - "# else:\n", - "# gene_expression_file = context_gene_exp[context]\n", - "# active_genes_filename = Path(gene_expression_file).name\n", - "# active_genes_filepath = config.data_dir / \"results\" / context / active_genes_filename\n", - "#\n", - "# general_model_filepath = config.data_dir / \"GeneralModelUpdatedV2.mat\"\n", - "# boundary_reactions_filepath = config.data_dir / \"boundary_rxns\" / f\"{context}_boundary_rxns.csv\"\n", - "# force_reactions_filepath = config.data_dir / \"force_rxns\" / f\"{context}_force_rxns.csv\"\n", - "# exclude_reactions_filepath = config.data_dir / \"exclude_rxns\" / f\"{context}_exclude_rxns.csv\"\n", - "#\n", - "# # fmt: off\n", - "# cmd = \" \".join(\n", - "# [\n", - "# \"python3\", \"como/create_context_specific_model.py\",\n", - "# \"--context\", context,\n", - "# \"--reference-model-filepath\", general_model_filepath,\n", - "# \"--active-genes-filepath\", active_genes_filepath,\n", - "# \"--objective\", objective,\n", - "# \"--boundary-reactions-filepath\", boundary_reactions_filepath,\n", - "# # \"--exclude-reactions-filepath\", exclude_reactions_filepath,\n", - "# \"--force-reactions-filepath\", force_reactions_filepath,\n", - "# \"--algorithm\", recon_algorithm,\n", - "# \"--low-threshold\", str(low_threshold),\n", - "# \"--high-threshold\", str(high_threshold),\n", - "# \"--solver\", solver,\n", - "# \"--output-filetypes\", output_filetypes,\n", - "# ]\n", - "# )\n", - "# # fmt: on\n", - "# !{cmd}" + " # fmt: on\n", + " !{cmd}" ], - "id": "f9b3b57f5e0e177e" + "id": "919e11a52790c5b" }, { "metadata": {}, @@ -979,7 +922,7 @@ "- `exampleTissue`: This is the name of the tissue context\n", "- `ALGORITHM`: This is the algorithm (`recon_algorithm`) used in the above model creation step\n" ], - "id": "41a3d196ee25c54a" + "id": "a039b13e7cfb5c45" }, { "metadata": {}, @@ -1057,7 +1000,7 @@ "\n", " !{cmd}" ], - "id": "b26399623722713c" + "id": "8993ff06e53c44ac" }, { "metadata": {}, @@ -1076,7 +1019,7 @@ "- `data_source`: The datasource you are using for disease analysis. This should be`\"rnaseq\"`\n", "- `taxon_id`: The [NCBI Taxon ID](https://www.ncbi.nlm.nih.gov/taxonomy) to use for disease analysis" ], - "id": "1a6ec8a4642fef1c" + "id": "b86824241ca2c785" }, { "metadata": {}, @@ -1088,7 +1031,7 @@ "\n", "disease_names = [\"arthritis\", \"lupus_a\", \"lupus_b\"]\n", "data_source = \"rnaseq\"\n", - "taxon_id = 9606\n", + "taxon_id = \"human\"\n", "\n", "for context_name in stringlist_to_list(context_names):\n", " disease_config_file = f\"disease_data_inputs_{context_name}.xlsx\"\n", @@ -1107,7 +1050,7 @@ "\n", " !{cmd}" ], - "id": "2b888b38e463c9d5" + "id": "a0e6b3bc29a2ee4c" }, { "metadata": {}, @@ -1142,7 +1085,7 @@ "\n", "- `solver`: The solver you would like to use. Available options are `\"gurobi\"` or `\"glpk\"`\n" ], - "id": "7c9a97233ba63a4a" + "id": "9898d75ab36fe5d7" }, { "metadata": {}, @@ -1190,7 +1133,7 @@ " tissue_specific_model_filepath = model_files[context]\n", " else:\n", " tissue_specific_model_filepath = (\n", - " config.data_dir / \"results\" / context / f\"{context}_SpecificModel_{recon_alg}.mat\"\n", + " config.data_dir / \"results\" / context / f\"{context}_SpecificModel_{recon_algorithm}.mat\"\n", " )\n", "\n", " # fmt: off\n", @@ -1213,16 +1156,10 @@ " cmd = \" \".join(cmd)\n", " !{cmd}" ], - "id": "be644a9283c83408" + "id": "7b79be19d1f47c81" } ], - "metadata": { - "kernelspec": { - "name": "python3", - "language": "python", - "display_name": "Python 3 (ipykernel)" - } - }, + "metadata": {}, "nbformat": 4, "nbformat_minor": 5 } diff --git a/main/como/__init__.py b/main/como/__init__.py index c84ef56e..cba3d35f 100644 --- a/main/como/__init__.py +++ b/main/como/__init__.py @@ -1,3 +1,4 @@ +from como import plot from como.data_types import AdjustmentMethod, Algorithm, CobraCompartments, FilteringTechnique, LogLevel, Solver from como.utils import stringlist_to_list diff --git a/main/como/combine_distributions.py b/main/como/combine_distributions.py index 535686ad..7549d1f6 100644 --- a/main/como/combine_distributions.py +++ b/main/como/combine_distributions.py @@ -23,7 +23,7 @@ ) -async def _combine_z_distribution_for_batch( +def _combine_z_distribution_for_batch( context_name: str, batch: _BatchEntry, matrix: pd.DataFrame, @@ -33,6 +33,21 @@ async def _combine_z_distribution_for_batch( weighted_z_floor: int, weighted_z_ceiling: int, ) -> pd.DataFrame: + """Combine z-score distributions across samples for a single batch. + + Args: + context_name: Name of the context (e.g., tissue or condition). + batch: Batch entry containing batch number and sample names. + matrix: DataFrame with 'ensembl_gene_id' and sample columns. + source: Source type (e.g., trna, mrna, scrna, proteomics). + output_combined_matrix_filepath: Path to save the combined z-score matrix. + output_figure_dirpath: Path to save the z-score distribution figure. + weighted_z_floor: Minimum z-score value after combining. + weighted_z_ceiling: Maximum z-score value after combining. + + Returns: + A pandas dataframe of the weighted z-distributions + """ output_combined_matrix_filepath.parent.mkdir(parents=True, exist_ok=True) output_figure_dirpath.mkdir(parents=True, exist_ok=True) @@ -80,7 +95,7 @@ async def _combine_z_distribution_for_batch( return weighted_matrix -async def _combine_z_distribution_for_source( +def _combine_z_distribution_for_source( merged_source_data: pd.DataFrame, context_name: str, num_replicates: int, @@ -88,7 +103,21 @@ async def _combine_z_distribution_for_source( output_figure_filepath: Path, weighted_z_floor: int = -6, weighted_z_ceiling: int = 6, -): +) -> pd.DataFrame: + """Combine z-score distributions across batches for a single source. + + Args: + merged_source_data: DataFrame with 'ensembl_gene_id' and batch columns. + context_name: Name of the context (e.g., tissue or condition). + num_replicates: Number of replicates (samples) for weighting. + output_combined_matrix_filepath: Path to save the combined z-score matrix. + output_figure_filepath: Path to save the z-score distribution figure. + weighted_z_floor: Minimum z-score value after combining. + weighted_z_ceiling: Maximum z-score value after combining. + + Returns: + A pandas dataframe of the weighted z-distributions + """ if _num_columns(merged_source_data) <= 2: logger.warning("A single source exists, returning matrix as-is because no additional combining can be done") merged_source_data.columns = ["ensembl_gene_id", "combine_z"] @@ -144,14 +173,10 @@ def _combine_z_distribution_for_context( return pd.DataFrame({"ensembl_gene_id": [], "combine_z": []}) z_matrices = [ - result.z_score_matrix.set_index("ensembl_gene_id").rename(columns=dict.fromkeys(result.z_score_matrix.columns[1:], result.type.value)) - for result in zscore_results + res.z_score_matrix.set_index("ensembl_gene_id").rename(columns=dict.fromkeys(res.z_score_matrix.columns[1:], res.type.value)) + for res in zscore_results ] - z_matrix = pd.DataFrame() - for matrix in z_matrices: - z_matrix = z_matrix.merge(right=matrix, left_index=True, right_index=True, how="outer") if not z_matrix.empty else matrix - z_matrix = z_matrix.reset_index(drop=False) - # z_matrix = pd.concat(z_matrices, axis=1, join="outer").reset_index() + z_matrix = pd.concat(z_matrices, axis=1, join="outer").reset_index() if _num_columns(z_matrix) <= 1: logger.trace(f"Only 1 source exists for '{context}', returning dataframe as-is becuase no data exists to combine") z_matrix.columns = ["ensembl_gene_id", "combine_z"] @@ -229,7 +254,7 @@ async def _begin_combining_distributions( matrix=matrix[[GeneIdentifier.ENSEMBL_GENE_ID.value, *batch.sample_names]], source=source, output_combined_matrix_filepath=( - output_filepaths[source.value].parent / f"{context_name}_{source.value}_batch{batch.batch_num}_combined_z_distribution_.csv" + output_filepaths[source.value].parent / f"{context_name}_{source.value}_batch{batch.batch_num}_combined_z_distribution.csv" ), output_figure_dirpath=output_figure_dirpath, weighted_z_floor=weighted_z_floor, @@ -243,7 +268,7 @@ async def _begin_combining_distributions( for df in batch_results: merged_batch_results = df if merged_batch_results.empty else merged_batch_results.merge(df, on="ensembl_gene_id", how="outer") - merged_source_results: pd.DataFrame = await _combine_z_distribution_for_source( + merged_source_results: pd.DataFrame = _combine_z_distribution_for_source( merged_source_data=merged_batch_results, context_name=context_name, num_replicates=sum(batch.num_samples for batch in batch_names[source.value]), diff --git a/main/como/create_context_specific_model.py b/main/como/create_context_specific_model.py index 6f004254..52a035ce 100644 --- a/main/como/create_context_specific_model.py +++ b/main/como/create_context_specific_model.py @@ -6,8 +6,10 @@ from collections.abc import Sequence from io import TextIOWrapper from pathlib import Path +from typing import Literal, TextIO, cast import cobra +import cobra.util.array import numpy as np import numpy.typing as npt import pandas as pd @@ -19,12 +21,20 @@ from troppo.methods.reconstruction.imat import IMAT, IMATProperties from troppo.methods.reconstruction.tINIT import tINIT, tINITProperties -from como.data_types import Algorithm, CobraCompartments, LogLevel, Solver, _BoundaryReactions, _BuildResults -from como.utils import _log_and_raise_error, _read_file, _set_up_logging, split_gene_expression_data +from como.data_types import Algorithm, BoundaryReactions, BuildResults, CobraCompartments, LogLevel, Solver +from como.utils import _log_and_raise_error, read_file, set_up_logging, split_gene_expression_data def _correct_bracket(rule: str, name: str) -> str: - """Correct GPR rules to format readable by.""" + """Correct GPR rules to format readable by. + + Args: + rule: GPR rule string from a COBRA model + name: Gene name string from a COBRA model + + Returns: + A corrected GPR rule string + """ rule_match = re.search(r"or|and", rule) name_match = re.search(r"or|and", name) if rule_match is None or name_match is None: @@ -53,7 +63,15 @@ def _correct_bracket(rule: str, name: str) -> str: def _gene_rule_logical(gpr_expression: str, level: int = 0) -> str: - """Create an expression from GPR rule which can be evaluated as true or false.""" + """Create an expression from GPR rule which can be evaluated as true or false. + + Args: + gpr_expression: GPR rule string from a COBRA model + level: Current recursion level (used for debugging) + + Returns: + An evaluable string where "and" is replaced with "min" and "or" is replaced with "max" + """ try: loc_r = gpr_expression.index(")") except ValueError: @@ -94,9 +112,9 @@ def _set_boundaries( upper_bounds: list[float], ) -> cobra.Model: # get boundary reactions - exchange_rxns = [rxn.id for rxn in model.reactions if re.search("EX_", rxn.id)] - sink_rxns = [rxn.id for rxn in model.reactions if re.search("sink_", rxn.id)] - demand_rxns = [rxn.id for rxn in model.reactions if re.search("DM_", rxn.id)] + exchange_rxns = [rxn.id for rxn in model.reactions if rxn.id.startswith("EX_")] + sink_rxns = [rxn.id for rxn in model.reactions if rxn.id.startswith("sink_")] + demand_rxns = [rxn.id for rxn in model.reactions if rxn.id.startswith("DM_")] # Allows all boundary reactions to be used if none are given allow_all_boundary_rxns = not boundary_reactions @@ -148,7 +166,15 @@ def _feasibility_test(model_cobra: cobra.Model, step: str): return incon_rxns, model_cobra_rm -def _build_with_gimme(cobra_model, s_matrix, lower_bounds, upper_bounds, idx_objective, expr_vector): +def _build_with_gimme( + reference_model: cobra.Model, + lower_bounds: Sequence[float | np.floating], + upper_bounds: Sequence[float | np.floating], + idx_objective: int, + expr_vector: npt.NDArray[np.floating], +): + model_reconstruction = reference_model.copy() + s_matrix: npt.NDArray[np.floating] = cobra.util.array.create_stoichiometric_matrix(model=model_reconstruction) # `Becker and Palsson (2008). Context-specific metabolic networks are # consistent with experiments. PLoS Comput. Biol. 4, e1000082.` properties = GIMMEProperties( @@ -160,18 +186,17 @@ def _build_with_gimme(cobra_model, s_matrix, lower_bounds, upper_bounds, idx_obj ) algorithm = GIMME(s_matrix, lower_bounds, upper_bounds, properties) gene_activity = algorithm.run() - context_cobra_model = cobra_model.copy() - reaction_ids = [r.id for r in context_cobra_model.reactions] + reaction_ids = [r.id for r in model_reconstruction.reactions] to_remove_ids = [reaction_ids[r] for r in np.where(gene_activity == 0)[0]] - context_cobra_model.remove_reactions(to_remove_ids, True) - psol = pfba(context_cobra_model) # noqa: F841 + model_reconstruction.remove_reactions(to_remove_ids, True) + psol = pfba(model_reconstruction) # noqa: F841 # reaction_ids = [r.id for r in context_cobra_model.reactions] # psol = context_cobra_model.optimize() # to_remove_ids = [reaction_ids[r] for r in np.where(abs(psol.fluxes) < 1e-8)[0]] # context_cobra_model.remove_reactions(to_remove_ids, True) - return context_cobra_model + return model_reconstruction def _build_with_fastcore(cobra_model, s_matrix, lower_bounds, upper_bounds, exp_idx_list, solver): @@ -193,45 +218,50 @@ def _build_with_fastcore(cobra_model, s_matrix, lower_bounds, upper_bounds, exp_ def _build_with_imat( - cobra_model: cobra.Model, - s_matrix: npt.NDArray, + reference_model: cobra.Model, lower_bounds: Sequence[float], upper_bounds: Sequence[float], expr_vector: npt.NDArray, expr_thresh: tuple[float, float], - force_reaction_indices: Sequence[int], + force_gene_indices: Sequence[int], solver: str, -) -> tuple[cobra.Model, pd.DataFrame]: - expr_vector = np.array(expr_vector) - properties = IMATProperties( +) -> cobra.Model: + properties: IMATProperties = IMATProperties( exp_vector=expr_vector, exp_thresholds=expr_thresh, - core=force_reaction_indices, + core=force_gene_indices, epsilon=0.01, solver=solver.upper(), ) - algorithm = IMAT(s_matrix, np.array(lower_bounds), np.array(upper_bounds), properties) - context_rxns: npt.NDArray = algorithm.run() - fluxes: pd.Series = algorithm.sol.to_series() - context_cobra_model = cobra_model.copy() - reaction_ids = [r.id for r in context_cobra_model.reactions] - remove_rxns = [reaction_ids[i] for i in range(s_matrix.shape[1]) if i not in context_rxns] - flux_df = pd.DataFrame(columns=["rxn", "flux"]) - for idx, (_, val) in enumerate(fluxes.items()): - if idx <= len(cobra_model.reactions) - 1: - r_id = str(context_cobra_model.reactions.get_by_id(reaction_ids[idx])).split(":")[0] - getattr(context_cobra_model.reactions, r_id).fluxes = val - flux_df.loc[len(flux_df.index)] = [r_id, val] + # Creating a copy of the model ensures we don't make any in-place modifications by accident + # Using cobra to create the stoichiometry matrix means we have less work to do + force_gene_indices = np.array(force_gene_indices, dtype=np.uint16) + model_reconstruction: cobra.Model = reference_model.copy() + s_matrix: npt.NDArray[np.floating] = cobra.util.array.create_stoichiometric_matrix(model=model_reconstruction) + algorithm: IMAT = IMAT(S=s_matrix, lb=np.array(lower_bounds), ub=np.array(upper_bounds), properties=properties) + rxns_from_imat: npt.NDArray[np.uint16] = algorithm.run().astype(np.uint16) - context_cobra_model.remove_reactions(remove_rxns, True) + # Collect all reaction IDs and their associated index (e.g., HEX1 is at index 123) + all_rxn_ids: npt.NDArray[str] = np.array([r.id for r in model_reconstruction.reactions], dtype=object) + all_rxn_indices: npt.NDArray[np.uint16] = np.array(range(len(model_reconstruction.reactions)), dtype=np.uint16) + + # Collect reactions to keep by creating a unique set of reactions from the iMAT algorithm and force-include reactions + # dtype is set to uint16 because indices will not be below 0 or be greater than 65,535 (max size of uint16), + # because only ~10,000 reactions exist in Recon3D + # Unsafe casting is OK because of these facts. + rxn_indices_to_keep: npt.NDArray[np.uint16] = np.unique(np.concatenate([rxns_from_imat, force_gene_indices], dtype=np.uint16)) + + # Reaction indices to exclude from the model are thus reactions that are not marked to be included in the model + # Assume unique is false because every value that is in `rxn_indices_to_keep` is included in `all_rxn_indices` + rxn_indices_to_remove: npt.NDArray[np.uint16] = np.setdiff1d(all_rxn_indices, rxn_indices_to_keep, assume_unique=False) + model_reconstruction.remove_reactions(reactions=all_rxn_ids[rxn_indices_to_remove].tolist(), remove_orphans=True) - return context_cobra_model, flux_df + return model_reconstruction def _build_with_tinit( - cobra_model: cobra.Model, - s_matrix, + reference_model: cobra.Model, lower_bounds, upper_bounds, expr_vector, @@ -246,6 +276,8 @@ def _build_with_tinit( allow_excretion=False, no_reverse_loops=True, ) + model_reconstruction = reference_model.copy() + s_matrix: npt.NDArray[np.floating] = cobra.util.array.create_stoichiometric_matrix(model=model_reconstruction).astype(np.float64) algorithm = tINIT(s_matrix, lower_bounds, upper_bounds, properties) algorithm.preprocessing() algorithm.build_problem() @@ -262,16 +294,40 @@ async def _map_expression_to_reaction( """Map gene ids to a reaction based on GPR (gene to protein to reaction) association rules. These rules should be defined in the general genome-scale metabolic model + + Args: + reference_model: A COBRA model object representing the general genome-scale metabolic model. + gene_expression_file: Path to a gene expression file (.csv, .tsv, .xlsx, or .xls) + recon_algorithm: Algorithm to use for reconstruction (GIMME, FASTCORE, iMAT, or tINIT) + low_thresh: Low expression threshold for algorithms that require it (iMAT, tINIT) + high_thresh: High expression threshold for algorithms that require it (iMAT, tINIT) + + Returns: + An ordered dictionary mapping reaction IDs to their corresponding expression values. + + Raises: + ValueError: If neither 'entrez_gene_id' nor 'ensembl_gene_id' columns are found in the gene expression file. """ - gene_activity = split_gene_expression_data(await _read_file(gene_expression_file), recon_algorithm=recon_algorithm) + expression_data = await read_file(gene_expression_file) + identifier_column = next((col for col in ("entrez_gene_id", "ensembl_gene_id") if col in expression_data.columns), "") + + if not identifier_column: + raise ValueError( + f"At least one column of 'entrez_gene_id' or 'ensembl_gene_id' could not be found in the gene expression file '{gene_expression_file}'" + ) + gene_activity = split_gene_expression_data( + expression_data, + identifier_column=cast(Literal["ensembl_gene_id", "entrez_gene_id"], identifier_column), + recon_algorithm=recon_algorithm, + ) reaction_expression = collections.OrderedDict() # fmt: off # Define a default expression value if a gene ID is not found default_expression = ( np.mean([low_thresh, high_thresh]) if recon_algorithm in {Algorithm.IMAT, Algorithm.TINIT} - else -1 if recon_algorithm in {Algorithm.GIMME} - else 0 if recon_algorithm in {Algorithm.FASTCORE} + else -1 if recon_algorithm == Algorithm.GIMME + else 0 if recon_algorithm == Algorithm.FASTCORE else 1 ) # fmt: on @@ -281,19 +337,19 @@ async def _map_expression_to_reaction( rxn: cobra.Reaction gene_reaction_rule = rxn.gene_reaction_rule - if gene_reaction_rule == "": + if not gene_reaction_rule: continue gene_ids = set(re.findall(r"\d+", gene_reaction_rule)) reaction_expression[rxn.id] = default_expression for gene_id in gene_ids: - activity = f"{gene_activity.at[gene_id, 'active']}" if gene_id in gene_activity.index else f"{default_expression!s}" + activity = gene_activity.at[gene_id, "active"] if gene_id in gene_activity.index else f"{default_expression!s}" # replace gene_id with activity, using optional whitespace before and after the gene id # Do not replace the whitespace (if it exists) before and after the gene ID gene_reaction_rule = re.sub(pattern=rf"\b{gene_id}\b", repl=activity, string=gene_reaction_rule) try: - # We are using eval here because ast.literal_eval is unable to process an evaluable such as `max(-4, -4)` + # We are using eval here because ast.literal_eval is unable to process an evaluable such as `max(-4, 0, 1)` # This isn't ideal, but ultimately the only other option is writing and maintaining a custom parsing engine, which is too much work evaluable_gene_rule = _gene_rule_logical(gene_reaction_rule).replace("{", "(").replace("}", ")") reaction_expression[rxn.id] = eval(evaluable_gene_rule) # noqa: S307 @@ -320,19 +376,40 @@ async def _build_model( # noqa: C901 low_thresh: float, high_thresh: float, output_flux_result_filepath: Path, -) -> _BuildResults: + *, + force_boundary_rxn_inclusion: bool, +) -> BuildResults: """Seed a context specific reference_model. Core reactions are determined from GPR associations with gene expression logicals. Core reactions that do not necessarily meet GPR association requirements can be forced if in the force reaction file. Metabolite exchange (media), sinks, and demands are determined from exchanges file. Reactions can also be force excluded even if they meet GPR association requirements using the force exclude file. + + Args: + general_model_file: Path to a COBRA model file (.xml, .mat, or .json) + gene_expression_file: Path to a gene expression file (.csv, .tsv, .xlsx, or .xls) + recon_algorithm: Algorithm to use for reconstruction (GIMME, FASTCORE, iMAT, or tINIT) + objective: Objective reaction ID in the general model + boundary_reactions: List of boundary reactions to set in the model + exclude_reactions: List of reactions to exclude from the model + force_reactions: List of reactions to force include in the model + lower_bounds: List of lower bounds corresponding to boundary reactions + upper_bounds: List of upper bounds corresponding to boundary reactions + solver: Solver to use (e.g., 'glpk', 'cplex', 'gurobi') + low_thresh: Low expression threshold for algorithms that require it (iMAT, tINIT) + high_thresh: High expression threshold for algorithms that require it (iMAT, tINIT) + output_flux_result_filepath: Path to save flux results (for iMAT only) + force_boundary_rxn_inclusion: If True, ensure that all boundary reactions are included in the final model. + + Returns: + A _BuildResults object containing the context-specific model, list of expression indices used, and a DataFrame of infeasible reactions. """ reference_model: cobra.Model match general_model_file.suffix: case ".mat": reference_model = cobra.io.load_matlab_model(general_model_file) - case ".xml": + case (".xml", ".sbml"): reference_model = cobra.io.read_sbml_model(general_model_file) case ".json": reference_model = cobra.io.load_json_model(general_model_file) @@ -346,7 +423,6 @@ async def _build_model( # noqa: C901 if objective not in force_reactions: force_reactions.append(objective) reference_model = _set_boundaries(reference_model, boundary_reactions, lower_bounds, upper_bounds) - reference_model.objective = objective reference_model.solver = solver.lower() # check number of unsolvable reactions for reference model under media assumptions @@ -374,8 +450,8 @@ async def _build_model( # noqa: C901 for rxn in force_reactions: if rxn not in reaction_ids: logger.warning( - f"The force reaction '{rxn}' was not found in the general reference_model. " - f"Check BiGG, or the relevant database for your general reference_model, for synonyms." + f"The force reaction '{rxn}' was not found in the reference model. " + f"Check BiGG, or the relevant database for your reference model, for synonyms." ) # collect list of reactions that are infeasible but active in expression data or user defined @@ -395,22 +471,31 @@ async def _build_model( # noqa: C901 expression_vector[i] = low_thresh - 0.1 if recon_algorithm in {Algorithm.TINIT, Algorithm.IMAT} else 0 objective_index = reaction_ids.index(objective) - force_reaction_indices = [reaction_ids.index(rxn) for rxn in force_reactions if rxn in reaction_ids] - expression_vector_indices = [i for (i, val) in enumerate(expression_vector) if val > 0] # type: ignore + + if force_boundary_rxn_inclusion: + all_forced: set[str] = {*force_reactions, *boundary_reactions} + force_reaction_indices: npt.NDArray[np.uint16] = np.array( + [reaction_ids.index(rxn) for rxn in all_forced if rxn in reaction_ids], dtype=np.uint16 + ) + else: + force_reaction_indices: npt.NDArray[np.uint16] = np.array( + [reaction_ids.index(rxn) for rxn in force_reactions if rxn in reaction_ids], dtype=np.uint16 + ) + + expression_vector_indices = [i for (i, val) in enumerate(expression_vector) if val > 0] expression_threshold = (low_thresh, high_thresh) match recon_algorithm: case Algorithm.GIMME: - context_model_cobra = _build_with_gimme( - cobra_model=reference_model, - s_matrix=s_matrix, + context_model_cobra: cobra.Model = _build_with_gimme( + reference_model=reference_model, lower_bounds=lower_bounds, upper_bounds=upper_bounds, idx_objective=objective_index, expr_vector=expression_vector, ) case Algorithm.FASTCORE: - context_model_cobra = _build_with_fastcore( + context_model_cobra: cobra.Model = _build_with_fastcore( cobra_model=reference_model, s_matrix=s_matrix, lower_bounds=lower_bounds, @@ -419,27 +504,26 @@ async def _build_model( # noqa: C901 solver=solver, ) case Algorithm.IMAT: - context_model_cobra: cobra.Model - context_model_cobra, flux_df = _build_with_imat( - cobra_model=reference_model, - s_matrix=s_matrix, + context_model_cobra: cobra.Model = _build_with_imat( + reference_model=reference_model, lower_bounds=lower_bounds, upper_bounds=upper_bounds, expr_vector=expression_vector, expr_thresh=expression_threshold, - force_reaction_indices=force_reaction_indices, + force_gene_indices=force_reaction_indices, solver=solver, ) - imat_reactions = flux_df.rxn - model_reactions = [reaction.id for reaction in context_model_cobra.reactions] - reaction_intersections = set(imat_reactions).intersection(model_reactions) - flux_df: pd.DataFrame = flux_df[~flux_df["rxn"].isin(reaction_intersections)] + context_model_cobra.objective = objective + flux_sol: cobra.Solution = context_model_cobra.optimize() + fluxes: pd.Series = flux_sol.fluxes + model_reactions: list[str] = [reaction.id for reaction in context_model_cobra.reactions] + reaction_intersections: set[str] = set(fluxes.index).intersection(model_reactions) + flux_df: pd.DataFrame = fluxes[~fluxes.index.isin(reaction_intersections)] flux_df.dropna(inplace=True) flux_df.to_csv(output_flux_result_filepath) case Algorithm.TINIT: - context_model_cobra = _build_with_tinit( - cobra_model=reference_model, - s_matrix=s_matrix, + context_model_cobra: cobra.Model = _build_with_tinit( + reference_model=reference_model, lower_bounds=lower_bounds, upper_bounds=upper_bounds, expr_vector=expression_vector, @@ -468,31 +552,32 @@ async def _build_model( # noqa: C901 axis=0, ) - return _BuildResults( + return BuildResults( model=context_model_cobra, expression_index_list=expression_vector_indices, infeasible_reactions=inconsistent_and_infeasible_reactions, ) -async def _create_df(path: Path) -> pd.DataFrame: - match path.suffix: - case ".csv" | ".tsv": - df = await _read_file(path, header=0, sep="," if path.suffix == ".csv" else "\t") - case ".xlsx" | ".xls": - df = await _read_file(path, header=0) - case _: - _log_and_raise_error( - f"File not found! Must be a csv, tsv, or Excel file. Searching for: {path}", - error=FileNotFoundError, - level=LogLevel.ERROR, - ) - df.columns = [c.lower() for c in df.columns] +async def _create_df(path: Path, *, lowercase_col_names: bool = False) -> pd.DataFrame: + if path.suffix not in {".csv", ".tsv"}: + raise ValueError(f"File must be a .csv or .tsv file, got '{path.suffix}'") + df: pd.DataFrame = await read_file(path=path, header=0, sep="," if path.suffix == ".csv" else "\t", h5ad_as_df=True) + + if not isinstance(df, pd.DataFrame): + _log_and_raise_error( + f"Expected a pandas.DataFrame, got {type(df)}", + error=TypeError, + level=LogLevel.ERROR, + ) + + if lowercase_col_names: + df.columns = [c.lower() for c in df.columns] return df -async def _collect_boundary_reactions(path: Path) -> _BoundaryReactions: - df: pd.DataFrame = await _create_df(path) +async def _collect_boundary_reactions(path: Path) -> BoundaryReactions: + df: pd.DataFrame = await _create_df(path, lowercase_col_names=True) for column in df.columns: if column not in [ "reaction", @@ -512,8 +597,8 @@ async def _collect_boundary_reactions(path: Path) -> _BoundaryReactions: reactions: list[str] = [""] * len(df) boundary_type: list[str] = df["reaction"].tolist() - reaction_abbreviation: list[str] = df["abbreviation"].astype(str).tolist() - reaction_compartment: list[str] = df["compartment"].astype(str).tolist() + reaction_abbreviation: list[str] = list(df["abbreviation"].astype(str)) + reaction_compartment: list[str] = list(df["compartment"].astype(str)) boundary_map = {"exchange": "EX", "demand": "DM", "sink": "SK"} for i in range(len(boundary_type)): boundary: str = boundary_type[i].lower() @@ -527,7 +612,7 @@ async def _collect_boundary_reactions(path: Path) -> _BoundaryReactions: shorthand_compartment = CobraCompartments.get_shorthand(reaction_compartment[i]) reactions[i] = f"{boundary_map.get(boundary)}_{reaction_abbreviation[i]}[{shorthand_compartment}]" - return _BoundaryReactions( + return BoundaryReactions( reactions=reactions, lower_bounds=df["minimum reaction rate"].tolist(), upper_bounds=df["maximum reaction rate"].tolist(), @@ -570,10 +655,38 @@ async def create_context_specific_model( # noqa: C901 high_threshold: float = -3, solver: Solver = Solver.GLPK, log_level: LogLevel = LogLevel.INFO, - log_location: str | TextIOWrapper = sys.stderr, + log_location: str | TextIO | TextIOWrapper = sys.stderr, + *, + force_boundary_rxn_inclusion: bool = True, ): - """Create a context-specific model using the provided data.""" - _set_up_logging(level=log_level, location=log_location) + """Create a context-specific model using the provided data. + + Args: + context_name: Name of the context-specific model. + reference_model: Path to the general genome-scale metabolic model file (.xml, .mat, or .json). + active_genes_filepath: Path to the gene expression data file (csv, tsv, or Excel). + output_infeasible_reactions_filepath: Path to save infeasible reactions (csv). + output_flux_result_filepath: Path to save flux results (csv). + output_model_filepaths: Path or list of paths to save the context-specific model (.xml, .mat, or .json). + output_filetypes: List of file types to save the model as ('xml', 'mat', 'json'). + output_fastcore_expression_index_filepath: Path to save Fastcore expression indices (txt). Required if using Fastcore. + objective: Objective function reaction ID. + boundary_rxns_filepath: Optional path to boundary reactions file (csv, tsv, or Excel). + exclude_rxns_filepath: Optional path to reactions to exclude file (csv, tsv, or Excel). + force_rxns_filepath: Optional path to reactions to force include file (csv, tsv, or Excel). + algorithm: Algorithm to use for reconstruction. One of Algorithm.GIMME, Algorithm.FASTCORE, Algorithm.IMAT, Algorithm.TINIT. + low_threshold: Low expression threshold for algorithms that require it. + high_threshold: High expression threshold for algorithms that require it. + solver: Solver to use. One of Solver.GLPK, Solver.CPLEX, Solver.GUROBI + log_level: Logging level. One of LogLevel.DEBUG, LogLevel.INFO, LogLevel.WARNING, LogLevel.ERROR, LogLevel.CRITICAL + log_location: Location for log output. Can be a file path or sys.stderr/sys.stdout. + force_boundary_rxn_inclusion: If True, ensure that all provided boundary reactions are included in the final model. + + Raises: + ImportError: If Gurobi solver is selected but gurobipy is not installed. + """ + boundary_rxns_filepath: Path | None = Path(boundary_rxns_filepath) if boundary_rxns_filepath else None + set_up_logging(level=log_level, location=log_location) output_model_filepaths = [output_model_filepaths] if isinstance(output_model_filepaths, Path) else output_model_filepaths for path in output_model_filepaths: if path.suffix not in {".mat", ".xml", ".sbml", ".json"}: @@ -655,7 +768,7 @@ async def create_context_specific_model( # noqa: C901 force_rxns: list[str] = [] if force_rxns_filepath: force_rxns_filepath: Path = Path(force_rxns_filepath) - df = await _create_df(force_rxns_filepath) + df = await _create_df(force_rxns_filepath, lowercase_col_names=True) if "abbreviation" not in df.columns: _log_and_raise_error( "The force reactions file should have a single column with a header named Abbreviation", @@ -680,14 +793,14 @@ async def create_context_specific_model( # noqa: C901 env = gp.Env() if env.getParam("WLSACCESSID") == "" or env.getParam("WLSSECRET") == "": logger.critical( - "You have requested to use the Gurobi solver but license information cannot be found. " + "Gurobi solver requested, but license information cannot be found. " "COMO will continue, but it is HIGHLY unlikely the resulting model will be valid." ) # remove gurobi-related information, it is no longer required del env, gp logger.info(f"Creating '{context_name}' model using '{algorithm.value}' reconstruction and '{solver.value}' solver") - build_results: _BuildResults = await _build_model( + build_results: BuildResults = await _build_model( general_model_file=reference_model, gene_expression_file=active_genes_filepath, recon_algorithm=algorithm, @@ -701,6 +814,7 @@ async def create_context_specific_model( # noqa: C901 low_thresh=low_threshold, high_thresh=high_threshold, output_flux_result_filepath=output_flux_result_filepath, + force_boundary_rxn_inclusion=force_boundary_rxn_inclusion, ) build_results.infeasible_reactions.dropna(inplace=True) diff --git a/main/como/data_types.py b/main/como/data_types.py index 977a5a20..8b439d47 100644 --- a/main/como/data_types.py +++ b/main/como/data_types.py @@ -139,12 +139,26 @@ class CobraCompartments: @classmethod def get_shorthand(cls, longhand: str) -> str | None: - """Get the short-hand compartment name from the long-hand name.""" + """Get the short-hand compartment name from the long-hand name. + + Args: + longhand: The long-hand compartment name (e.g., 'cytoplasm', 'extracellular'). + + Returns: + The short-hand compartment name if found, None otherwise. + """ return cls._REVERSE_LOOKUP.get(longhand.lower(), None) @classmethod def get_longhand(cls, shorthand: str) -> str | None: - """Get the long-hand compartment name from the short-hand name.""" + """Get the long-hand compartment name from the short-hand name. + + Args: + shorthand: The short-hand compartment name (e.g., 'c', 'e', 'm'). + + Returns: + The long-hand compartment name if found, None otherwise. + """ longhand = cls.SHORTHAND.get(shorthand.lower(), None) return longhand[0] if longhand else None @@ -192,8 +206,11 @@ class _BaseDataType: def __getitem__(self, value: str): """Access matrices using square bracket notation (e.g., `input_matrices['total_rna']`). - :param value: The name of the matrix to get ('trna', 'mrna', 'scrna', 'proteomics') - :returns: The DataFrame if it exists, None otherwise. + Args: + value: The name of the matrix to get ('trna', 'mrna', 'scrna', 'proteomics') + + Returns: + The DataFrame if it exists, None otherwise. """ self._validate_attribute(value) return getattr(self, value) @@ -209,7 +226,7 @@ def __setitem__(self, key, value): def _validate_attribute(self, key): if key not in {i.value for i in SourceTypes._member_map_.values()}: - # Unable to use como.utils._log_and_raise_error becuase it results in a circular import + # Unable to use como.utils._log_and_raise_error because it results in a circular import message = f"{key} is not a valid attribute of {SourceTypes.__name__}; got '{key}'" logger.warning(message) raise ValueError(message) diff --git a/main/como/knock_out_simulation.py b/main/como/knock_out_simulation.py index 936996c7..9e4e578a 100644 --- a/main/como/knock_out_simulation.py +++ b/main/como/knock_out_simulation.py @@ -74,7 +74,7 @@ def knock_out_simulation( drug_db = drug_db[drug_db["moa"].str.lower().str.contains("inhibitor")] drug_target_genes = pd.DataFrame(columns=["Gene ID"]) drug_target_genes["Gene ID"] = drug_db["Gene ID"].astype(str) - drug_target_genes.replace("-", np.nan, inplace=True) + drug_target_genes.replace("-", pd.NA, inplace=True) drug_target_genes.dropna(axis=0, inplace=True) drug_target_genes.to_csv(inhibitors_filepath, header=True, sep="\t", index=False) print(f"Inhibitors file written to: {inhibitors_filepath}") diff --git a/main/como/merge_xomics.py b/main/como/merge_xomics.py index c017bf4a..a89219ef 100644 --- a/main/como/merge_xomics.py +++ b/main/como/merge_xomics.py @@ -50,8 +50,17 @@ class _HighExpressionHeaderNames: # TODO: If function is no longer needed, remove? -async def _load_rnaseq_tests(filename, context_name, prep_method: RNAType) -> tuple[str, pd.DataFrame]: - """Load rnaseq results.""" +def _load_rnaseq_tests(filename, context_name, prep_method: RNAType) -> tuple[str, pd.DataFrame]: + """Load rnaseq results. + + Args: + filename: Name of the file to load + context_name: Name of the context (e.g., tissue or cell type) + prep_method: The RNA-seq library preparation method (e.g., mRNA, total RNA, single-cell RNA) + + Returns: + A tuple containing the context name and the loaded DataFrame± + """ logger.debug(f"Loading data for context '{context_name}' using preparation method '{prep_method.value}'") config = Config() @@ -90,8 +99,11 @@ def load_dummy_dict(): def _merge_logical_table(df: pd.DataFrame): """Merge rows of Logical Table belonging to the same entrez_gene_id. - :param df: pandas dataframe of logical table - :return: pandas dataframe of merged table + Args: + df: Pandas dataframe containing the logical table + + Returns: + pandas dataframe of merged table """ # step 1: get all plural ENTREZ_GENE_IDs in the input table, extract unique IDs df.dropna(subset=["entrez_gene_id"], inplace=True) @@ -115,7 +127,7 @@ def _merge_logical_table(df: pd.DataFrame): df = pd.concat([df, pd.DataFrame(duplicate_rows)], axis=0, ignore_index=True) df.drop(df[df["entrez_gene_id"] == i].index, inplace=True) - logger.trace(f"Shape after merging duplciated rows: {df.shape}") + logger.trace(f"Shape after merging duplicated rows: {df.shape}") full_entrez_id_sets: set[str] = set() entrez_dups_list: list[list[str]] = [] @@ -129,14 +141,14 @@ def _merge_logical_table(df: pd.DataFrame): logger.trace(f"Iterating through multi-entrez ids, index {i}") set1 = set(multiple_entrez_ids[i].split("//")) - multi_entrez_index.remove(i) + temp_multi_entrez_index.remove(i) for j in multi_entrez_index: set2 = set(multiple_entrez_ids[j].split("//")) intersect = set1.intersection(set2) if bool(intersect): set1 = set1.union(set2) - multi_entrez_index.remove(j) + temp_multi_entrez_index.remove(j) sortlist = list(set1) sortlist.sort(key=int) @@ -180,8 +192,12 @@ async def _get_transcriptmoic_details(merged_df: pd.DataFrame, taxon_id: int) -> The resulting dataframe will have its columns created in the order listed above It will return a pandas dataframe with this information - :param merged_df: A dataframe containing all active transcriptomic and proteomic genes - :return: A dataframe with the above-listed columns + Args: + merged_df: A dataframe containing all active transcriptomic and proteomic genes + taxon_id: The NCBI taxonomy ID of the organism + + Returns: + A dataframe with the above-listed columns """ # If _ExpressedHeaderNames.PROTEOMICS.value is in the dataframe, lower the required expression by 1 # We are only trying to get details for transcriptomic data diff --git a/main/como/migrations.py b/main/como/migrations.py index 61ac6abf..c1d291b1 100644 --- a/main/como/migrations.py +++ b/main/como/migrations.py @@ -2,5 +2,12 @@ def gene_info_migrations(df: pd.DataFrame) -> pd.DataFrame: - """Migrate gene info DataFrame to the latest version.""" + """Migrate gene info DataFrame to the latest version. + + Args: + df: The input DataFrame containing gene information. + + Returns: + The migrated DataFrame with updated column names. + """ return df.rename(columns={"hgnc_symbol": "gene_symbol"}) if "hgnc_symbol" in df.columns else df diff --git a/main/como/pipelines/__init__.py b/main/como/pipelines/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/main/como/pipelines/build_condition_heatmaps.py b/main/como/pipelines/build_condition_heatmaps.py new file mode 100644 index 00000000..16b970b8 --- /dev/null +++ b/main/como/pipelines/build_condition_heatmaps.py @@ -0,0 +1,283 @@ +"""Create heatmaps of conditions vs pathway flux. + +This pipeline will generate heatmaps showing the flux through various pathways +""" + +from __future__ import annotations + +import concurrent.futures +from collections import defaultdict +from functools import partial +from pathlib import Path + +import cobra +import matplotlib.pyplot as plt +import numpy as np +import numpy.typing as npt +import pandas as pd +from pandas._libs.missing import NAType + +from como.plot.heatmap import condition_vs_pathway + + +def find_possible_model_filepaths(search_dir: Path) -> list[Path]: + """Find potential files that could be constraint-based metabolic models. + + Args: + search_dir: The directory to search for models. + + Returns: + Potential filepaths that could be loaded as a `cobra.Model` object + """ + return [f for f in search_dir.rglob("*") if f.suffix in {".mat", ".json", ".sbml", ".xml"}] + + +def get_cobra_model_if_valid(filepath: Path) -> cobra.Model | None: + """Evaluate if a given filepath can be read as a `cobra.Model`. + + Args: + filepath: The filepath to read + + Returns: + a `cobra.Model` object if the file can be read, otherwise None + """ + if filepath.suffix == ".json": + return cobra.io.load_json_model(filepath) + elif filepath.suffix == ".mat": + return cobra.io.load_matlab_model(filepath) + elif filepath.suffix in {".yaml", ".yml"}: + return cobra.io.load_yaml_model(filepath) + elif filepath.suffix in {".xml", ".sbml"}: + return cobra.io.read_sbml_model(filepath) + return None + + +def get_model_flux(model: cobra.Model, objective: str = "biomass_maintenance", solver: str = "gurobi") -> pd.Series: + """Get the flux through a CBMM. + + Args: + model: A `cobra.Model` object + objective: The objective function to optimize + solver: The solver to use + + Returns: + A pandas Series of reaction fluxes indexed by reaction ID + """ + model.objective = objective + model.solver = solver + solution = model.optimize() + return solution.fluxes + + +def get_many_model_flux( + models: list[cobra.Model], + objective: str = "biomass_maintenance", + solver: str = "gurobi", + cores: int = 4, + process_pool: concurrent.futures.ProcessPoolExecutor | None = None, + colnames: list[str] | None = None, + na_value: NAType | int | float = NAType, +) -> pd.DataFrame: + """Get the flux through many CBMMs. + + Args: + models: A list of `cobra.Model` objects + objective: The objective function to optimize + solver: The solver to use + cores: The number of CPU cores to use + process_pool: An existing process pool to use + colnames: Column names to use for the resulting dataframe + na_value: Value to use for missing values in the dataframe + + Returns: + A pandas DataFrame of reaction fluxes indexed by condition (row) and reaction ID (column) + + Raises: + ValueError: If `colnames` is provided and its length does not match the number of models + """ + if colnames and len(colnames) != len(models): + raise ValueError("Length of colnames must match length of models") + + pool = process_pool or concurrent.futures.ProcessPoolExecutor(max_workers=cores) + shutdown = not process_pool # if the user provided a pool, do not shut it down + + func = partial(get_model_flux, objective=objective, solver=solver) + series: list[pd.Series] = list(pool.map(func, models)) + for i, series_obj in enumerate(series): + series_obj.name = colnames[i] if colnames else f"model_{i}" + df: pd.DataFrame = pd.concat(list(series), axis="columns") + + if shutdown: + pool.shutdown(wait=True) + + if na_value != NAType: # no need to replace values that are already pd.NA + df = df.fillna(na_value) + + df = df.T + return df + + +def group_reactions_by_pathway(models: cobra.Model | list[cobra.Model], flux_df: pd.DataFrame) -> pd.DataFrame: + """Group reactions by their subsystem/pathway and sum the fluxes. + + Args: + models: A cobra.Model or list of cobra.Models + flux_df: A dataframe of reaction fluxes, indexed by condition and with reaction IDs as columns + + Returns: + A dataframe of pathway fluxes, indexed by condition and with pathways as columns + """ + pathways_by_reaction: dict[str, set[str]] = defaultdict(set) + models = [models] if isinstance(models, cobra.Model) else models + + for model in models: + for reaction in model.reactions: + reaction: cobra.Reaction + pathways_by_reaction[reaction.subsystem].add(reaction.id) + pathways_by_reaction.pop("", None) # remove the empty pathway; faster than checking every reaction's subsystem + + # pathway_flux: pd.DataFrame = pd.DataFrame(index=flux_df.index, columns=list(pathways_by_reaction.keys())) + # for condition in flux_df.index: + # for pathway, reactions in pathways_by_reaction.items(): + # pathway_flux.loc[condition, pathway] = flux_df.loc[condition, list(reactions)].sum() + pathway_fluxes: dict[str, pd.Series[npt.NDArray[np.floating]]] = {} + for pathway, reactions in pathways_by_reaction.items(): + reactions_in_df = list(reactions.intersection(flux_df.columns)) + if reactions_in_df: + pathway_fluxes[pathway] = flux_df[reactions_in_df].sum(axis=1) + return pd.DataFrame(pathway_fluxes) + + +def build_condition_vs_pathway_heatmap( + data: pd.DataFrame | list[cobra.Model] | Path | list[Path], + save_filepath: Path | None = None, + objective: str = "biomass_maintenance", + solver: str = "gurobi", + process_pool: concurrent.futures.ProcessPoolExecutor | None = None, + cores: int = 4, + condition_names: list[str] | None = None, + na_value: NAType | int | float = NAType, + *, + search_path: bool = False, + copy_df_when_building_plot: bool = False, + exclude_zero_flux_pathways: bool = False, +) -> plt.Figure: + """Create a heatmap of conditions vs flux through pathways. + + If `data` is a pd.DataFrame: + - The index names wile used as conditions and placed on the Y-axis + - The column names will be used as pathways and placed on the X-axis. The columns should indicate pathways. + + If `data` is a Path and `search_path` is True: + - Models will be recursively discovered under the given path + - Models will be simulated with the given objective and solver + - A dataframe will be built from the resulting series based on the above rules + + If `data` is a list of Paths: + - Models will be read and simulated for each path + - A pd.DataFrame will be built from the resulting series based on the above rules + + If `data` is a list of cobra.Models: + - Models will be simulated with the given objective and solver + - A pd.DataFrame will be built from the resulting series based on the above rules + + Args: + data: The data to use for the heatmap + search_path: Whether to search the given path for models + save_filepath: The filepath to save the heatmap to + objective: The objective function to optimize + solver: The solver to use + process_pool: An existing process pool to use + cores: The number of CPU cores to use + condition_names: Column names to use for the resulting dataframe if `data` is a Path or list of Paths + na_value: Value to use for missing values in the flux dataframe + copy_df_when_building_plot: Whether to copy the dataframe when building the plot. + This can be useful if the dataframe is going to be reused later. + exclude_zero_flux_pathways: Whether to exclude pathways that have zero flux across all conditions + + Returns: + A matplotlib Figure object containing the heatmap + + Raises: + ValueError: If `search_path` is True and `data` is not a Path + """ + if not isinstance(data, Path) and search_path: + raise ValueError("If search_path is True, data must be a Path") + + flux_df: pd.DataFrame + if isinstance(data, pd.DataFrame): + return condition_vs_pathway( + data, + save_filepath=save_filepath, + copy_df=copy_df_when_building_plot, + exclude_zero_flux_pathways=exclude_zero_flux_pathways, + ) + elif isinstance(data, list) and isinstance(data[0], cobra.Model): + models = data + flux_df = get_many_model_flux( + models=data, + objective=objective, + solver=solver, + cores=cores, + process_pool=process_pool, + colnames=condition_names, + na_value=na_value, + ) + elif isinstance(data, Path): + if search_path: + possible_model_fps: list[Path] = find_possible_model_filepaths(data) + models = [] + for fp in possible_model_fps: + if isinstance(model := get_cobra_model_if_valid(fp), cobra.Model): + models.append(model) + flux_df = get_many_model_flux( + models, + objective=objective, + solver=solver, + cores=cores, + process_pool=process_pool, + colnames=condition_names, + na_value=na_value, + ) + else: + models = get_cobra_model_if_valid(data) + flux_df = pd.DataFrame(get_model_flux(models, objective=objective, solver=solver)) + elif isinstance(data, list) and isinstance(data[0], Path): + models = [get_cobra_model_if_valid(fp) for fp in data] + flux_df = get_many_model_flux( + models, + objective=objective, + solver=solver, + cores=cores, + process_pool=process_pool, + colnames=condition_names, + na_value=na_value, + ) + + flux_df = group_reactions_by_pathway(models=models, flux_df=flux_df) + return condition_vs_pathway(data=flux_df, save_filepath=save_filepath) + + +def _main(): + models = [ + Path("/home/joshl/projects/ImmunoMetabolism/data/model_build/A/A_pDCs/A_pDCs_model_imat.json"), + Path("/home/joshl/projects/ImmunoMetabolism/data/model_build/B/B_pDCs/B_pDCs_model_imat.json"), + Path("/home/joshl/projects/ImmunoMetabolism/data/model_build/C/C_pDCs/C_pDCs_model_imat.json"), + Path("/home/joshl/projects/ImmunoMetabolism/data/model_build/D/D_pDCs/D_pDCs_model_imat.json"), + Path("/home/joshl/projects/ImmunoMetabolism/data/model_build/E/E_pDCs/E_pDCs_model_imat.json"), + ] + save_path = Path( + f"/home/joshl/projects/ImmunoMetabolism/results/figures/{models[0].stem.removeprefix('A_').removesuffix('_model_imat')}_heatmap.png" + ) + + fig = build_condition_vs_pathway_heatmap( + data=models, + cores=5, + condition_names=["Age Group A", "Age Group B", "Age Group C", "Age Group D", "Age Group E"], + save_filepath=save_path, + ) + fig.show() + + +if __name__ == "__main__": + _main() diff --git a/main/como/plot/__init__.py b/main/como/plot/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/main/como/plot/heatmap.py b/main/como/plot/heatmap.py new file mode 100644 index 00000000..0d6e4e55 --- /dev/null +++ b/main/como/plot/heatmap.py @@ -0,0 +1,103 @@ +from __future__ import annotations + +import math +from pathlib import Path + +import matplotlib.colors as mcolors +import matplotlib.pyplot as plt +import numpy as np +import pandas as pd +import seaborn as sns +from matplotlib.ticker import FixedLocator + + +def condition_vs_pathway( + data: pd.DataFrame, + save_filepath: Path | None = None, + *, + copy_df: bool = False, + exclude_zero_flux_pathways: bool = False, +) -> plt.Figure: + """Build a heatmap of fluxes through pathways across conditions. + + Args: + data: Index values are conditions, column names are pathways + save_filepath: If provided, the resulting figure will be saved to this location + copy_df: Should the incoming dataframe be copied to prevent modifications to data? + exclude_zero_flux_pathways: Should pathways that have 0 flux across all rows be excluded? + + Returns: + The resulting `matpotlib.pyplt.Figure` object + """ + plot_df: pd.DataFrame = data.copy() if copy_df else data + plot_df = plot_df.astype(np.float32) + fig = plt.figure(figsize=(100, 40), dpi=175) + + if exclude_zero_flux_pathways: + # Select pathways that have at least one non-zero value + plot_df = plot_df.loc[:, plot_df.where(plot_df != 0).any(axis=0)] + + # Identify the second largest (pos or neg) value + # This is needed in order to set the upper & lower bounds for the graph, excluding +/- 1000-flux values + plot_df[plot_df > 1000] = 1001 + plot_df[plot_df < -1000] = -1001 + second_largest_positive = plot_df[plot_df > 0].stack().drop_duplicates().nlargest(2).iloc[-1] + second_largest_negative = plot_df[plot_df < 0].stack().drop_duplicates().nsmallest(2).iloc[-1] + vmax = max(abs(second_largest_negative), second_largest_positive) + + # Convert tick marks to reasonable values: + # max tick < 100: round to 10s place + # max tick < 1_000: round to 100s place + # max tick < 10_000: round to 1_000s place + base = 10 if vmax < 100 else 100 if vmax < 10_000 else 1000 + vmax_root = math.ceil(vmax / base) * base + + # Create 5 evenly spaced ticks along the legend + ticks = np.linspace(-vmax_root, vmax_root, 5) + + # Generate legend gradient + norm = mcolors.TwoSlopeNorm(vmin=-vmax_root, vcenter=0, vmax=vmax_root) + + # If a value falls outside of `vmax_root`, set it to the following colors + cmap = plt.get_cmap("coolwarm").copy() + cmap.set_over("#660033") + cmap.set_under("#000099") + + ax: plt.Axes = sns.heatmap( + data=plot_df, + linewidths=1.0, + linecolor="#686868", + center=0, + yticklabels=True, + xticklabels=True, + norm=norm, + cmap=cmap, + cbar_kws={"extend": "both", "label": f"Flux ratio (clipped at ±{vmax:.0f})"}, + ) + + plt.title("Metabolic Model Flux Sum through Pathways", fontsize=100) + + plt.xlabel("Pathway", fontsize=80) + ax.tick_params(axis="x", which="major", labelsize=55, labelrotation=90) + + plt.ylabel("Condition", fontsize=85) + ax.tick_params(axis="y", which="major", labelsize=55, labelrotation=0) + + cbar = ax.collections[0].colorbar + cbar.set_ticks(ticks) + cbar.ax.yaxis.set_major_locator(FixedLocator(ticks)) + cbar.update_ticks() + + # Add extended triangles that are detached from the colorbar (prevents very large pos/neg values from blowing out the legend) + cbar.ax.text(0.5, 1.06, "> +1000", ha="center", va="bottom", transform=cbar.ax.transAxes, fontsize=40) + cbar.ax.text(0.5, -0.06, "< -1000", ha="center", va="top", transform=cbar.ax.transAxes, fontsize=40) + cbar.ax.tick_params(labelsize=40) + cbar.set_label("Flux", rotation=270, labelpad=40) + + fig.tight_layout(h_pad=0.85) + + if save_filepath: + save_filepath.parent.mkdir(parents=True, exist_ok=True) + fig.savefig(save_filepath, transparent=False, bbox_inches="tight") + + return fig diff --git a/main/como/plot/z_score.py b/main/como/plot/z_score.py new file mode 100644 index 00000000..0822e63a --- /dev/null +++ b/main/como/plot/z_score.py @@ -0,0 +1,47 @@ +from pathlib import Path + +import pandas as pd +import seaborn as sns +from loguru import logger +from matplotlib import pyplot as plt + + +def z_score_distribution( + df: pd.DataFrame, + title: str, + output_filepath: Path, +): + """Graph a z-score distribution. + + :param df: The z-score data to graph + :param title: Title to add to graph + :param output_filepath: Output PNG filepath location + :return: None + """ + if output_filepath.suffix not in {".png", ".pdf", ".svg"}: + logger.warning(f"Expected .png, .pdf, or .svg suffix for output_png_filepath, got {output_filepath.suffix}. Defaulting to .pdf") + output_filepath = output_filepath.with_suffix(".pdf") + logger.trace("Graphing z-score distribution") + output_filepath.parent.mkdir(parents=True, exist_ok=True) + output_filepath.unlink(missing_ok=True) + + plt.figure(figsize=(10, 6)) + + if len(df["source"].unique()) == 1: + ax = sns.histplot(df, x="zscore", bins=100, kde=True) + sns.rugplot(df, x="zscore", ax=ax) + else: + sns.histplot(df, x="zscore", hue="source", bins=100, kde=True, element="step") + plt.legend(loc="upper right", frameon=False, title=None) + + plt.title(title) + plt.xlabel("Z-score") + plt.ylabel("Frequency") + plt.xticks(fontsize=12) + plt.yticks(fontsize=12) + plt.gca().spines["top"].set_visible(False) + plt.gca().spines["right"].set_visible(False) + plt.tight_layout() + plt.savefig(output_filepath) + plt.close() + logger.success(f"Saved z-score distribution graph to '{output_filepath}'") diff --git a/main/como/project.py b/main/como/project.py index b6a21bf9..19779940 100644 --- a/main/como/project.py +++ b/main/como/project.py @@ -9,8 +9,16 @@ class SingletonMeta(type): _instances: ClassVar[dict] = {} - def __call__(cls, *args, **kwargs): - """Validate that changes to the `__init__` argument do not affect the returned instance.""" + def __call__(cls, *args, **kwargs) -> SingletonMeta: + """Validate that changes to the `__init__` argument do not affect the returned instance. + + Args: + args: Positional arguments for the class constructor + kwargs: Keyword arguments for the class constructor + + Returns: + The singleton instance of the class + """ if cls not in cls._instances: instance = super().__call__(*args, **kwargs) cls._instances[cls] = instance @@ -56,7 +64,11 @@ def __init__( self.figures_dir.mkdir(parents=True, exist_ok=True) def update(self, **kwargs): - """Update a key in the config object.""" + """Update a key in the config object. + + Args: + kwargs: keyword argumentsto set for the singleton + """ for key, value in kwargs.items(): if hasattr(self, key): setattr(self, key, Path(value) if value else getattr(self, key)) @@ -64,18 +76,41 @@ def update(self, **kwargs): logger.warning(f"{key} is not a valid attribute of Config") def get_context_path(self, context_name: str, create: bool = True) -> Path: - """Get path for a specific context, optionally creating it.""" + """Get path for a specific context, optionally creating it. + + Args: + context_name: Name of the context (subdirectory). + create: Whether to create the directory if it doesn't exist. + + Returns: + Full path to the context directory. + """ path = self.result_dir / context_name if create: path.mkdir(parents=True, exist_ok=True) return path def get_r_path(self, path: Path) -> str: - """Convert a Path object to an R-compatible path string.""" + """Convert a Path object to an R-compatible path string. + + Args: + path: Path object to convert. + + Returns: + R-compatible path string. + """ return path.as_posix() def get_matrix_path(self, context_name: str, filename: str) -> Path: - """Get path for a matrix file in a specific context.""" + """Get path for a matrix file in a specific context. + + Arg: + context_name: Name of the context (subdirectory). + filename: Name of the matrix file. + + Returns: + Full path to the matrix file. + """ path = self.matrix_dir / context_name path.mkdir(parents=True, exist_ok=True) return path / filename diff --git a/main/como/proteomics/proteomics_preprocess.py b/main/como/proteomics/proteomics_preprocess.py index 4353a9f6..b2223da7 100644 --- a/main/como/proteomics/proteomics_preprocess.py +++ b/main/como/proteomics/proteomics_preprocess.py @@ -205,12 +205,23 @@ def _set_replicate_numbers(self): current_info.set_replicate(replicate_value) def _collect_cell_type_information(self, cell_type: str) -> list[FileInformation]: - """Collect all FileInformation objects of a given cell type.""" + """Collect all FileInformation objects of a given cell type. + + Arg: + cell_type: The cell type to collect information for. + + Returns: + A list of FileInformation objects matching the given cell type. + """ return [information for information in self.file_information if information.cell_type == cell_type] def parse_args() -> argparse.Namespace: - """Parse arguments from the command line.""" + """Parse arguments from the command line. + + Returns: + An argparse.Namespace object containing the parsed arguments. + """ parser = argparse.ArgumentParser( prog="proteomics_preprocess.py", description="Download and analyze proteomics data from proteomeXchange\n" diff --git a/main/como/proteomics_gen.py b/main/como/proteomics_gen.py index 945fa43e..012486a4 100644 --- a/main/como/proteomics_gen.py +++ b/main/como/proteomics_gen.py @@ -17,7 +17,14 @@ # Load Proteomics def process_proteomics_data(path: Path) -> pd.DataFrame: - """Load proteomics data from a given context and filename.""" + """Load proteomics data from a given context and filename. + + Args: + path: Path to the proteomics data file (CSV format). + + Returns: + pd.DataFrame: Processed proteomics data with 'gene_symbol' column exploded. + """ # Preprocess data, drop na, duplicate ';' in symbol, matrix: pd.DataFrame = pd.read_csv(path) if "gene_symbol" not in matrix.columns: @@ -35,7 +42,15 @@ def process_proteomics_data(path: Path) -> pd.DataFrame: # read map to convert to entrez async def load_gene_symbol_map(gene_symbols: list[str], entrez_map: Path | None = None): - """Add descirption....""" + """Load a mapping from gene symbols to Entrez IDs. + + Args: + gene_symbols (list[str]): List of gene symbols to map. + entrez_map (Path | None): Optional path to a CSV file containing precomputed mappings. + + Returns: + pd.DataFrame: DataFrame with gene symbols as index and corresponding Entrez IDs. + """ if entrez_map and entrez_map.exists(): df = pd.read_csv(entrez_map, index_col="gene_symbol") else: @@ -45,7 +60,7 @@ async def load_gene_symbol_map(gene_symbols: list[str], entrez_map: Path | None input_db=Input.GENE_SYMBOL, output_db=[Output.GENE_ID, Output.ENSEMBL_GENE_ID], ) - df.loc[df["gene_id"] == "-", ["gene_id"]] = np.nan + df.loc[df["gene_id"].isna(), ["gene_id"]] = np.nan df.to_csv(entrez_map, index_label="gene_symbol") return df[~df.index.duplicated()] @@ -122,8 +137,16 @@ def to_bool_context(context_name, group_ratio, hi_group_ratio, group_names): # read data from csv files -def load_proteomics_tests(filename, context_name): - """Load statistical test results.""" +def load_proteomics_tests(filename, context_name) -> tuple[str, pd.DataFrame]: + """Load statistical test results. + + Arg: + filename (str): The name of the file to load. + context_name (str): The context name for the data. + + Returns: + tuple: A tuple containing the context name and the loaded data as a pandas DataFrame. + """ config = Config() def load_empty_dict(): @@ -187,7 +210,7 @@ async def proteomics_gen( error=FileNotFoundError, level=LogLevel.ERROR, ) - if matrix_filepath.suffix not in {".csv"}: + if matrix_filepath.suffix != ".csv": _log_and_raise_error( f"Matrix file must be a csv file at {matrix_filepath}", error=FileNotFoundError, diff --git a/main/como/proteomics_preprocessing.py b/main/como/proteomics_preprocessing.py index 21f38a78..39d4c85c 100644 --- a/main/como/proteomics_preprocessing.py +++ b/main/como/proteomics_preprocessing.py @@ -29,7 +29,15 @@ class ZResult: def z_score_calc(abundance: pd.DataFrame, min_thresh: int) -> ZResult: - """Calculate Z-scores for protein abundance data.""" + """Calculate Z-scores for protein abundance data. + + Arg: + abundance: DataFrame with protein abundance data. + min_thresh: Minimum threshold for abundance values to be considered. + + Returns: + A ZResult object containing Z-score transformed data and related statistics. + """ values = abundance.values.copy() + 1 log_abundance_filt = np.log2(values[values > min_thresh]).reshape((len(abundance), len(abundance.columns))) log_abundance = np.log2(values) @@ -70,7 +78,17 @@ def z_score_calc(abundance: pd.DataFrame, min_thresh: int) -> ZResult: def lighten_color(red: int, green: int, blue: int, factor: float = 0.5) -> str: - """Lighten a color by a given factor.""" + """Lighten a color by a given factor. + + Args: + red: Red component (0-255). + green: Green component (0-255). + blue: Blue component (0-255). + factor: Factor by which to lighten the color (0.0 to 1.0). + + Returns: + A string representing the lightened color in RGB format. + """ # Convert RGB to HLS hue, lightness, saturation = colorsys.rgb_to_hls(red / 255.0, green / 255.0, blue / 255.0) @@ -84,7 +102,17 @@ def lighten_color(red: int, green: int, blue: int, factor: float = 0.5) -> str: # Plotting function def plot_gaussian_fit(z_results: ZResult, facet_titles: bool = True, x_min: int = -4) -> go.Figure: - """Plot Gaussian fit for Z-score transformed data.""" + """Plot Gaussian fit for Z-score transformed data. + + Arg: + z_results: The results from the Z-score calculation. + facet_titles: Whether to show titles for each facet. + x_min: Minimum x-axis value for the plots. + + Returns: + A Plotly Figure object containing the Gaussian fit plots. + + """ zfpkm = z_results.zfpkm x_range = z_results.x_range density = z_results.density diff --git a/main/como/rnaseq_gen.py b/main/como/rnaseq_gen.py index 058a6dc8..4f797658 100644 --- a/main/como/rnaseq_gen.py +++ b/main/como/rnaseq_gen.py @@ -8,15 +8,17 @@ from concurrent.futures import Future, ProcessPoolExecutor, as_completed from dataclasses import dataclass, field from enum import Enum +from io import TextIOWrapper from pathlib import Path -from typing import NamedTuple, TextIO +from typing import NamedTuple import matplotlib.pyplot as plt import numpy as np import numpy.typing as npt import pandas as pd import seaborn as sns -import sklearn.preprocessing +import sklearn +import sklearn.neighbors from fast_bioservices.pipeline import ensembl_to_gene_id_and_symbol, gene_symbol_to_ensembl_and_gene_id from loguru import logger from pandas import DataFrame @@ -130,9 +132,12 @@ def genefilter(data: pd.DataFrame | npt.NDArray, filter_func: Callable[[npt.NDAr This code is based on the `genefilter` function found in R's `genefilter` package: https://www.rdocumentation.org/packages/genefilter/versions/1.54.2/topics/genefilter - :param data: The data to filter - :param filter_func: THe function to filter the data by - :return: A NumPy array of the filtered data. + Arg: + data: The data to filter, either a Pandas DataFrame or a NumPy array. + filter_func: THe function to filter the data by + + Returns: + A NumPy array of the filtered data. """ if not isinstance(data, pd.DataFrame | npt.NDArray): _log_and_raise_error( @@ -153,12 +158,15 @@ async def _build_matrix_results( ) -> _ReadMatrixResults: """Read the counts matrix and returns the results. - :param matrix: The gene counts matrix to process - :param metadata_df: The configuration dataframe related to the current context - :param taxon: The NCBI Taxon ID - :return: A dataclass `ReadMatrixResults` + Arg: + matrix: The gene counts matrix to process + metadata_df: The configuration dataframe related to the current context + taxon: The NCBI Taxon ID + + Returns: + A dataclass `ReadMatrixResults` """ - matrix.dropna(inplace=True) + matrix.dropna(subset="ensembl_gene_id", inplace=True) conversion = await ensembl_to_gene_id_and_symbol(ids=matrix["ensembl_gene_id"].tolist(), taxon=taxon) conversion["ensembl_gene_id"] = conversion["ensembl_gene_id"].str.split(",") conversion = conversion.explode("ensembl_gene_id") @@ -222,7 +230,14 @@ async def _build_matrix_results( def calculate_tpm(metrics: NamedMetrics) -> NamedMetrics: - """Calculate the Transcripts Per Million (TPM) for each sample in the metrics dictionary.""" + """Calculate the Transcripts Per Million (TPM) for each sample in the metrics dictionary. + + Args: + metrics: A dictionary of study metrics to calculate TPM for. + + Returns: + A dictionary of study metrics with TPM calculated. + """ for sample in metrics: count_matrix = metrics[sample].count_matrix @@ -237,26 +252,38 @@ def calculate_tpm(metrics: NamedMetrics) -> NamedMetrics: return metrics -def _calculate_fpkm(metrics: NamedMetrics, scale: float = 1e6) -> NamedMetrics: - """Calculate the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) for each sample in the metrics dictionary.""" +def _calculate_fpkm(metrics: NamedMetrics, scale: int = 1e6) -> NamedMetrics: + """Calculate the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) for each sample in the metrics dictionary. + + Args: + metrics: A dictionary of study metrics to calculate FPKM for. + scale: The scaling factor for normalization (default is 1e6). + + Returns: + A dictionary of study metrics with FPKM calculated. + """ for study in metrics: - matrix_values: list[npt.NDArray[float]] = [] + matrix_values = [] + for sample in range(metrics[study].num_samples): layout = metrics[study].layout[sample] - count_matrix: npt.NDArray[int] = metrics[study].count_matrix.iloc[:, sample].values - - gene_lengths = metrics[study].fragment_lengths[sample] if layout == LayoutMethod.paired_end else metrics[study].gene_sizes.astype(int) + count_matrix: npt.NDArray[np.float32] = metrics[study].count_matrix.iloc[:, sample].values + gene_lengths = ( + metrics[study].fragment_lengths[sample].astype(np.float32) + if layout == LayoutMethod.paired_end + else metrics[study].gene_sizes.astype(np.float32) + ) gene_lengths_kb = gene_lengths / 1000.0 match layout: case LayoutMethod.paired_end: # FPKM - total_fragments: npt.NDArray[int] = count_matrix.sum(axis=0) + total_fragments = count_matrix.sum(axis=0) if total_fragments == 0: - fragments_per_kilobase_million: float = np.nan + fragments_per_kilobase_million = np.nan else: - counts_per_million: npt.NDArray[float] = total_fragments / scale - fragments_per_kilobase: npt.NDArray[float] = count_matrix / counts_per_million - fragments_per_kilobase_million: npt.NDArray[float] = fragments_per_kilobase / gene_lengths_kb + counts_per_million = total_fragments / scale + fragments_per_kilobase = count_matrix / gene_lengths_kb + fragments_per_kilobase_million = fragments_per_kilobase / counts_per_million matrix_values.append(fragments_per_kilobase_million) case LayoutMethod.single_end: # RPKM reads_per_kilobase = count_matrix / gene_lengths_kb @@ -297,6 +324,7 @@ def _zfpkm_calculation( Stabilize the variance in the data to make the distribution more symmetric; this is helpful for Gaussian fitting Kernel Density Estimation (kde) + - SciKit Learn: https://scikit-learn.org/stable/modules/density.html - Non-parametric method to estimate the probability density function (PDF) of a random variable - Estimates the distribution of log2-transformed FPKM values - Bandwidth parameter controls the smoothness of the density estimate @@ -379,7 +407,19 @@ def zfpkm_transform( bandwidth: float, update_every_percent: float = 0.1, ) -> tuple[dict[str, _ZFPKMResult], DataFrame]: - """Perform zFPKM calculation/transformation.""" + """Perform zFPKM calculation/transformation. + + Args: + fpkm_df: A DataFrame containing FPKM values with genes as rows and samples as columns. + peak_parameters: Parameters for peak identification in zFPKM calculation. + bandwidth: The bandwidth for kernel density estimation in zFPKM calculation. + update_every_percent: Frequency of progress updates as a decimal between 0 and 1 (e.g., 0.1 for every 10%). + + Returns: + A tuple containing: + - A dictionary of intermediate results for each sample. + - A DataFrame of zFPKM values with the same shape as the input fpkm_df. + """ if update_every_percent > 1: logger.warning(f"update_every_percent should be a decimal value between 0 and 1; got: {update_every_percent} - will convert to percentage") update_every_percent /= 100 @@ -485,7 +525,14 @@ def zfpkm_plot(results: dict[str, _ZFPKMResult], *, output_png_dirpath: Path, pl def calculate_z_score(metrics: NamedMetrics) -> NamedMetrics: - """Calculate the z-score for each sample in the metrics dictionary.""" + """Calculate the z-score for each sample in the metrics dictionary. + + Args: + metrics: A dictionary of study metrics to calculate z-scores for. + + Returns: + A dictionary of study metrics with z-scores calculated. + """ for sample in metrics: log_matrix = np.log(metrics[sample].normalization_matrix) z_matrix = pd.DataFrame(data=sklearn.preprocessing.scale(log_matrix, axis=1), columns=metrics[sample].sample_names) @@ -500,7 +547,17 @@ def cpm_filter( filtering_options: _FilteringOptions, prep: RNAType, ) -> NamedMetrics: - """Apply Counts Per Million (CPM) filtering to the count matrix for a given sample.""" + """Apply Counts Per Million (CPM) filtering to the count matrix for a given sample. + + Args: + context_name: The name of the context being processed. + metrics: A dictionary of study metrics to filter. + filtering_options: Options for filtering the count matrix. + prep: The RNA preparation type. + + Returns: + A dictionary of filtered study metrics. + """ config = Config() n_exp = filtering_options.replicate_ratio n_top = filtering_options.high_replicate_ratio @@ -533,14 +590,26 @@ def cpm_filter( top_samples = round(n_top * len(counts.columns)) # noqa: F841 test_bools = pd.DataFrame({"entrez_gene_ids": entrez_ids}) for i in range(len(counts_per_million.columns)): - cutoff = 10e6 / (np.median(np.sum(counts[:, i]))) if cut_off == "default" else (1e6 * cut_off) / np.median(np.sum(counts[:, i])) + median_sum = np.float64(np.median(np.sum(counts[:, i]))) + if cut_off == "default": # noqa: SIM108 + cutoff = np.float64(10e6) / median_sum + else: + cutoff = np.float64(1e6 * cut_off) / median_sum test_bools = test_bools.merge(counts_per_million[counts_per_million.iloc[:, i] > cutoff]) return metrics def tpm_quantile_filter(*, metrics: NamedMetrics, filtering_options: _FilteringOptions) -> NamedMetrics: - """Apply quantile-based filtering to the TPM matrix for a given sample.""" + """Apply quantile-based filtering to the TPM matrix for a given sample. + + Args: + metrics: A dictionary of study metrics to filter. + filtering_options: Options for filtering the count matrix. + + Returns: + A dictionary of filtered study metrics. + """ # TODO: Write the TPM matrix to disk n_exp = filtering_options.replicate_ratio @@ -590,9 +659,22 @@ def zfpkm_filter( force_zfpkm_plot: bool, peak_parameters: PeakIdentificationParameters, bandwidth: float, - output_png_dirpath: Path | None, + output_png_filepath: Path | None, ) -> NamedMetrics: - """Apply zFPKM filtering to the FPKM matrix for a given sample.""" + """Apply zFPKM filtering to the FPKM matrix for a given sample. + + Args: + metrics: A dictionary of study metrics to filter. + filtering_options: Options for filtering the count matrix. + calculate_fpkm: Whether to calculate FPKM from counts. + force_zfpkm_plot: Whether to force plotting of zFPKM results even if there are many samples. + peak_parameters: Parameters for peak identification in zFPKM calculation. + bandwidth: The bandwidth for kernel density estimation in zFPKM calculation. + output_png_filepath: Optional filepath to save the zFPKM plot. + + Returns: + A dictionary of filtered study metrics. + """ min_sample_expression = filtering_options.replicate_ratio high_confidence_sample_expression = filtering_options.high_replicate_ratio cut_off = filtering_options.cut_off @@ -646,7 +728,22 @@ def filter_counts( bandwidth: float, output_zfpkm_plot_dirpath: Path | None = None, ) -> NamedMetrics: - """Filter the count matrix based on the specified technique.""" + """Filter the count matrix based on the specified technique. + + Args: + context_name: The name of the context being processed. + metrics: A dictionary of study metrics to filter. + technique: The filtering technique to use. + filtering_options: Options for filtering the count matrix. + prep: The RNA preparation type. + force_zfpkm_plot: Whether to force plotting of zFPKM results even if there are many samples. + peak_parameters: Parameters for peak identification in zFPKM calculation. + bandwidth: The bandwidth for kernel density estimation in zFPKM calculation. + output_zfpkm_plot_dirpath: Optional filepath to save the zFPKM plot. + + Returns: + A dictionary of filtered study metrics. + """ match technique: case FilteringTechnique.CPM: return cpm_filter(context_name=context_name, metrics=metrics, filtering_options=filtering_options, prep=prep) diff --git a/main/como/rnaseq_preprocess.py b/main/como/rnaseq_preprocess.py index 1d73a5e8..b83678d1 100644 --- a/main/como/rnaseq_preprocess.py +++ b/main/como/rnaseq_preprocess.py @@ -5,7 +5,7 @@ import re import sys from dataclasses import asdict, dataclass, field -from io import StringIO, TextIOWrapper +from io import TextIOWrapper from itertools import chain from pathlib import Path from typing import Final, Literal, cast @@ -49,25 +49,30 @@ async def build_from_tab(cls, filepath: Path) -> _STARinformation: level=LogLevel.ERROR, ) - with filepath.open("r") as i_stream: - unmapped = i_stream.readline() - multimapping = i_stream.readline() - no_feature = i_stream.readline() - ambiguous = i_stream.readline() - - num_unmapped = [int(i) for i in unmapped.rstrip("\n").split("\t")[1:]] - num_multimapping = [int(i) for i in multimapping.rstrip("\n").split("\t")[1:]] - num_no_feature = [int(i) for i in no_feature.rstrip("\n").split("\t")[1:]] - num_ambiguous = [int(i) for i in ambiguous.rstrip("\n").split("\t")[1:]] - remainder = await asyncio.to_thread(i_stream.read) - - df = await _read_file(StringIO(remainder), sep="\t", header=None) - df.columns = [ - "ensembl_gene_id", - "unstranded_rna_counts", - "first_read_transcription_strand", - "second_read_transcription_strand", - ] + async with aiofiles.open(filepath) as i_stream: + # Cannot use `asyncio.gather()` here because the order of execution is not guaranteed + unmapped = await i_stream.readline() + multimapping = await i_stream.readline() + no_feature = await i_stream.readline() + ambiguous = await i_stream.readline() + + num_unmapped = [int(i) for i in unmapped.removesuffix("\n").split("\t")[1:]] + num_multimapping = [int(i) for i in multimapping.removesuffix("\n").split("\t")[1:]] + num_no_feature = [int(i) for i in no_feature.removesuffix("\n").split("\t")[1:]] + num_ambiguous = [int(i) for i in ambiguous.removesuffix("\n").split("\t")[1:]] + + df = await _read_file( + path=filepath, + sep="\t", + header=None, + skiprows=4, + names=[ + "ensembl_gene_id", + "unstranded_rna_counts", + "first_read_transcription_strand", + "second_read_transcription_strand", + ], + ) df = df[~df["ensembl_gene_id"].isna()] return _STARinformation( num_unmapped=num_unmapped, @@ -160,7 +165,20 @@ async def _read_text(path: Path | None, *, default: str, lower: bool = False) -> def _sample_name_from_filepath(file: Path) -> str: - return re.search(r".+_S\d+R\d+", file.stem).group() + return re.search(r".+_S\d+R\d+(r\d+)?", file.stem).group() + + +def _require_one(paths: list[Path], kind: Literal["layout", "strand", "preparation", "fragment"], label: str) -> Path | None: + if len(paths) == 1: + return paths[0] + if len(paths) == 0: + return None + _log_and_raise_error( + f"Multiple matching {kind} files for {label}, make sure there is only one copy for each replicate in COMO_input", + error=ValueError, + level=LogLevel.ERROR, + ) + return None # explicit return None to satisfy type-check def _require_one(paths: list[Path], kind: Literal["layout", "strand", "preparation", "fragment"], label: str) -> Path | None: @@ -220,8 +238,9 @@ def _organize_gene_counts_files(data_dir: Path) -> list[_StudyMetrics]: async def _process_first_multirun_sample(strand_file: Path, all_counts_files: list[Path]): sample_count = pd.DataFrame() - for file in all_counts_files: - star_information = await _STARinformation.build_from_tab(file) + all_star_information: list[_STARinformation] = await asyncio.gather(*[_STARinformation.build_from_tab(file) for file in all_counts_files]) + + for star_information in all_star_information: strand_information = strand_file.read_text().rstrip("\n").lower() if strand_information not in ("none", "first_read_transcription_strand", "second_read_transcription_strand"): @@ -238,16 +257,16 @@ async def _process_first_multirun_sample(strand_file: Path, all_counts_files: li strand_information = "unstranded_rna_counts" run_counts = star_information.count_matrix[["ensembl_gene_id", strand_information]] - run_counts.columns = pd.Index(["ensembl_gene_id", "counts"]) + run_counts.columns = ["ensembl_gene_id", "counts"] sample_count = run_counts if sample_count.empty else sample_count.merge(run_counts, on=["ensembl_gene_id", "counts"], how="outer") # Set na values to 0 sample_count = sample_count.fillna(value="0") - sample_count.iloc[:, 1:] = sample_count.iloc[:, 1:].apply(pd.to_numeric) + sample_count["counts"] = sample_count["counts"].astype(np.float64) - count_sums: pd.DataFrame = pd.DataFrame(sample_count.sum(axis=1, numeric_only=True)) - count_sums.insert(0, "ensembl_gene_id", sample_count["ensembl_gene_id"]) - count_sums.columns = pd.Index(["ensembl_gene_id", _sample_name_from_filepath(strand_file)]) + count_sums = sample_count.groupby("ensembl_gene_id", as_index=False)["counts"].mean() + count_sums["counts"] = np.ceil(count_sums["counts"].astype(np.uint32)) + count_sums.columns = ["ensembl_gene_id", _sample_name_from_filepath(strand_file)] return count_sums @@ -269,7 +288,7 @@ async def _process_standard_replicate(counts_file: Path, strand_file: Path, samp strand_information = "unstranded_rna_counts" sample_count = star_information.count_matrix[["ensembl_gene_id", strand_information]] - sample_count.columns = pd.Index(["ensembl_gene_id", sample_name]) + sample_count.columns = ["ensembl_gene_id", sample_name] return sample_count @@ -314,7 +333,8 @@ async def _create_sample_counts_matrix(metrics: _StudyMetrics) -> pd.DataFrame: # Remove run number "r\d+" from multi-run names if re.search(r"R\d+r1", metrics.sample_names[i]): new_sample_name = re.sub(r"r\d+", "", metrics.sample_names[i]) - counts.columns[i + 1 - adjusted_index] = new_sample_name + old_col_name = counts.columns[i + 1 - adjusted_index] + counts.rename(columns={old_col_name: new_sample_name}, inplace=True) return counts @@ -326,15 +346,24 @@ async def _write_counts_matrix( output_counts_matrix_filepath: Path, rna: RNAType, ) -> pd.DataFrame: - """Create a counts matrix file by reading gene counts table(s).""" + """Create a counts matrix file by reading gene counts table(s). + + Args: + config_df: Configuration DataFrame containing sample information. + como_context_dir: Path to the COMO_input directory containing gene count files. + output_counts_matrix_filepath: Path where the output counts matrix CSV will be saved. + rna: RNAType enum indicating whether to process 'trna' or 'mrna' samples. + + Returns: + A pandas DataFrame representing the final counts matrix. + """ study_metrics = _organize_gene_counts_files(data_dir=como_context_dir) counts: list[pd.DataFrame] = await asyncio.gather(*[_create_sample_counts_matrix(metric) for metric in study_metrics]) + rna_specific_sample_names = set(config_df.loc[config_df["library_prep"] == rna.value, "sample_name"].tolist()) - final_matrix = pd.DataFrame() - for count in counts: - final_matrix = count if final_matrix.empty else pd.merge(final_matrix, count, on="ensembl_gene_id", how="outer") - - rna_specific_sample_names = config_df.loc[config_df["library_prep"] == rna.value, "sample_name"].tolist() + final_matrix: pd.DataFrame = functools.reduce(lambda left, right: pd.merge(left, right, on="ensembl_gene_id", how="outer"), counts) + final_matrix.fillna(value=0, inplace=True) + final_matrix.iloc[:, 1:] = final_matrix.iloc[:, 1:].astype(np.uint64) final_matrix = final_matrix[["ensembl_gene_id", *rna_specific_sample_names]] output_counts_matrix_filepath.parent.mkdir(parents=True, exist_ok=True) @@ -357,9 +386,22 @@ async def _create_config_df( # noqa: C901 """Create configuration sheet. The configuration file created is based on the gene counts matrix. - If using zFPKM normalization technique, mean fragment lengths will be fetched + If using zFPKM normalization technique, mean fragment lengths will be fetched + + Args: + context_name: Name of the context, used as a prefix for sample names. + como_context_dir: Path to the COMO_input directory containing subdirectories for + gene counts, layouts, strandedness, fragment sizes, and prep methods. + gene_count_dirname: Name of the subdirectory containing gene count files. + layout_dirname: Name of the subdirectory containing layout files. + strandedness_dirname: Name of the subdirectory containing strandedness files. + fragment_sizes_dirname: Name of the subdirectory containing fragment size files. + prep_method_dirname: Name of the subdirectory containing library preparation method files. + + Returns: + A pandas DataFrame representing the configuration sheet. """ - label_regex: Final = re.compile(r"(?PS\d{1,3})(?PR\d{1,3})(?:(?Pr\d{1,3}))?") + label_regex: Final = re.compile(r"(?PS\d{1,3})(?PR\d{1,3})(?Pr\d{1,3})?") gene_counts: list[Path] = list((como_context_dir / gene_count_dirname).rglob("*.tab")) if not gene_counts: _log_and_raise_error( @@ -634,7 +676,7 @@ async def read_counts(file: Path) -> list[str]: ) except json.JSONDecodeError: _log_and_raise_error( - f"Got a JSO decode error for file '{counts_matrix_filepaths}'", + f"Got a JSON decode error for file '{counts_matrix_filepaths}'", error=ValueError, level=LogLevel.CRITICAL, ) @@ -647,11 +689,11 @@ async def read_counts(file: Path) -> list[str]: gene_data = await MyGene(cache=cache).query(items=list(genes), taxon=taxon, scopes="entrezgene") gene_info: pd.DataFrame = pd.DataFrame( data=None, - columns=pd.Index(data=["ensembl_gene_id", "gene_symbol", "entrez_gene_id", "size"]), - index=pd.Index(data=range(len(gene_data))), + columns=["ensembl_gene_id", "gene_symbol", "entrez_gene_id", "size"], + index=list(range(len(gene_data))), ) for i, data in enumerate(gene_data): - ensembl_ids = data.get("genomic_pos.ensemblgene", "-") + ensembl_ids = data.get("genomic_pos.ensemblgene", pd.NA) if isinstance(ensembl_ids, list): ensembl_ids = ensembl_ids[0] @@ -660,14 +702,16 @@ async def read_counts(file: Path) -> list[str]: end_pos = data.get("genomic_pos.end", 0) end_pos: int = int(sum(end_pos) / len(end_pos)) if isinstance(end_pos, list) else int(end_pos) - gene_info.at[i, "gene_symbol"] = data.get("symbol", "-") - gene_info.at[i, "entrez_gene_id"] = data.get("entrezgene", "-") + gene_info.at[i, "gene_symbol"] = data.get("symbol", pd.NA) + gene_info.at[i, "entrez_gene_id"] = data.get("entrezgene", pd.NA) gene_info.at[i, "ensembl_gene_id"] = ensembl_ids gene_info.at[i, "size"] = end_pos - start_pos - gene_info = gene_info[((gene_info["entrez_gene_id"] != "-") & (gene_info["ensembl_gene_id"] != "-") & (gene_info["gene_symbol"] != "-"))] + gene_info = gene_info[((~gene_info["entrez_gene_id"].isna()) & (~gene_info["ensembl_gene_id"].isna()) & (~gene_info["gene_symbol"].isna()))] gene_info.sort_values(by="ensembl_gene_id", inplace=True) gene_info.dropna(inplace=True) + + output_filepath.parent.mkdir(parents=True, exist_ok=True) gene_info.to_csv(output_filepath, index=False) logger.success(f"Gene Info file written at '{output_filepath}'") @@ -680,6 +724,7 @@ async def _process_como_input( rna: RNAType, ) -> None: config_df = await _create_config_df(context_name, como_context_dir=como_context_dir) + await _write_counts_matrix( config_df=config_df, como_context_dir=como_context_dir, @@ -701,7 +746,9 @@ async def _process( output_mrna_config_filepath: Path | None, output_trna_matrix_filepath: Path | None, output_mrna_matrix_filepath: Path | None, + *, cache: bool, + create_gene_info_only: bool, ): rna_types: list[tuple[RNAType, Path, Path]] = [] if output_trna_config_filepath: @@ -710,29 +757,31 @@ async def _process( rna_types.append((RNAType.MRNA, output_mrna_config_filepath, output_mrna_matrix_filepath)) # if provided, iterate through como-input specific directories - tasks = [] - for rna, output_config_filepath, output_matrix_filepath in rna_types: - tasks.append( - asyncio.create_task( - _process_como_input( - context_name=context_name, - output_config_filepath=output_config_filepath, - como_context_dir=como_context_dir, - output_counts_matrix_filepath=output_matrix_filepath, - rna=rna, + if not create_gene_info_only: + tasks = [] + for rna, output_config_filepath, output_matrix_filepath in rna_types: + tasks.append( + asyncio.create_task( + _process_como_input( + context_name=context_name, + output_config_filepath=output_config_filepath, + como_context_dir=como_context_dir, + output_counts_matrix_filepath=output_matrix_filepath, + rna=rna, + ) ) ) - ) - await asyncio.gather(*tasks) + await asyncio.gather(*tasks) # create the gene info filepath based on provided data - input_files = [] if input_matrix_filepath: input_files.extend(input_matrix_filepath) - output_trna_matrix_filepath and input_files.append(output_trna_matrix_filepath) - output_mrna_matrix_filepath and input_files.append(output_mrna_matrix_filepath) + if output_trna_matrix_filepath: + input_files.append(output_trna_matrix_filepath) + if output_mrna_matrix_filepath: + input_files.append(output_mrna_matrix_filepath) await _create_gene_info_file( counts_matrix_filepaths=input_files, @@ -755,6 +804,8 @@ async def rnaseq_preprocess( cache: bool = True, log_level: LogLevel | str = LogLevel.INFO, log_location: str | TextIOWrapper = sys.stderr, + *, + create_gene_info_only: bool = False, ) -> None: """Preprocesses RNA-seq data for downstream analysis. @@ -774,6 +825,7 @@ async def rnaseq_preprocess( :param cache: Should HTTP requests be cached :param log_level: The logging level :param log_location: The logging location + :param create_gene_info_only: If True, only create the gene info file and skip general preprocessing steps """ _set_up_logging(level=log_level, location=log_location) @@ -798,4 +850,30 @@ async def rnaseq_preprocess( output_trna_matrix_filepath=output_trna_count_matrix_filepath, output_mrna_matrix_filepath=output_mrna_count_matrix_filepath, cache=cache, + create_gene_info_only=create_gene_info_only, + ) + + +async def _main(): + context_name = "notreatment" + taxon = 9606 + como_context_dir = Path("/Users/joshl/Projects/COMO/main/data/COMO_input/notreatment") + output_gene_info_filepath = Path("/Users/joshl/Projects/COMO/main/data/results/notreatment/gene_info.csv") + output_trna_metadata_filepath = Path("/Users/joshl/Projects/COMO/main/data/config_sheets/trna_config.xlsx") + output_trna_count_matrix_filepath = Path("/Users/joshl/Projects/COMO/main/data/results/notreatment/total-rna/totalrna_notreatment.csv") + + await rnaseq_preprocess( + context_name=context_name, + taxon=taxon, + como_context_dir=como_context_dir, + input_matrix_filepath=None, + output_gene_info_filepath=output_gene_info_filepath, + output_trna_metadata_filepath=output_trna_metadata_filepath, + output_trna_count_matrix_filepath=output_trna_count_matrix_filepath, + cache=False, + log_level="INFO", ) + + +if __name__ == "__main__": + asyncio.run(_main()) diff --git a/main/como/stats/__init__.py b/main/como/stats/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/main/como/stats/_two_sample.py b/main/como/stats/_two_sample.py new file mode 100644 index 00000000..d856ebeb --- /dev/null +++ b/main/como/stats/_two_sample.py @@ -0,0 +1,60 @@ +from abc import ABC, abstractmethod +from collections.abc import Mapping +from concurrent.futures import ProcessPoolExecutor, as_completed +from typing import ClassVar, Generic, Literal, TypeVar + +import numpy as np +import numpy.typing as npt +import pandas as pd + +T_BASE_SAMPLE = TypeVar("T_BASE_SAMPLE", bound="BaseTwoSample") +T_ALTERNATIVE = Literal["greater", "less", "two-sided"] +KS_RESULT = tuple[np.floating, np.floating, np.floating, np.int8] +MW_RESULT = tuple[np.floating, np.floating] +TEST_RESULT = TypeVar("TEST_RESULT", KS_RESULT, MW_RESULT) + +__all__ = ["BaseTwoSample"] + + +class BaseTwoSample(ABC, Generic[TEST_RESULT]): + _fields: ClassVar[dict[str, type]] + + @staticmethod + @abstractmethod + def _worker(a: npt.NDArray[np.floating], b: npt.NDArray[np.floating], **kwargs) -> TEST_RESULT: ... + + @property + @abstractmethod + def df(self) -> pd.DataFrame: + """DataFrame representation of the results. + + Returns: + A DataFrame with columns corresponding to the fields in `_fields`. + """ + ... + + @classmethod + def _run( + cls: type[T_BASE_SAMPLE], + df1: pd.DataFrame, + df2: pd.DataFrame, + cores: int = 1, + worker_kwargs: dict | None = None, + ) -> tuple[list[str], Mapping[str, npt.NDArray[np.float64 | np.uint8]]]: + all_reactions = list(set(df1.columns) & set(df2.columns)) + array_a = df1[all_reactions].to_numpy(dtype=np.float64, copy=False) + array_b = df2[all_reactions].to_numpy(dtype=np.float64, copy=False) + n = len(all_reactions) + + results = {field: np.empty(n, dtype=np.dtype(dtype)) for field, dtype in cls._fields.items()} + + with ProcessPoolExecutor(max_workers=cores) as pool: + futures = {pool.submit(cls._worker, array_a[:, i], array_b[:, i], **(worker_kwargs or {})): i for i in range(n)} + for future in as_completed(futures): + col_idx: int = futures[future] + res: KS_RESULT | MW_RESULT = future.result() + + for (field, _), value in zip(cls._fields.items(), res, strict=True): + results[field][col_idx] = value + + return all_reactions, results diff --git a/main/como/stats/fisher_exact_test.py b/main/como/stats/fisher_exact_test.py new file mode 100644 index 00000000..068eb4c2 --- /dev/null +++ b/main/como/stats/fisher_exact_test.py @@ -0,0 +1,101 @@ +from dataclasses import dataclass +from typing import Annotated, Literal + +import cobra +import numpy as np +import scipy + + +@dataclass(frozen=True, kw_only=True, slots=True) +class FisherExactTest: + """Evalute Fisher's Exact Test for reaction presence. + + Fisher's Exact Test is a non-parametric statistical test used to determine if there are nonrandom associations between two variables. + It is useful in metabolic modeling because it can help assess whether the presence or absence of certain reactions in a metabolic model + is independent of a specific condition or treatment without assuming the distribution of the data. + + To calculate the Fisher's Exact Test, execute :func:`FisherExactTest.run`, which will return an instance of :class:`FisherExactTest` + + References: + [SciPy](https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html) + [Wikipedia](https://en.wikipedia.org/wiki/Fisher%27s_exact_test) + """ + + pathway: Annotated[str, "The pathway test"] + statistic: Annotated[float, "The odds ratio of the test"] + pvalue: Annotated[float, "The p-value of the test"] + a: Annotated[int, "Number of reactions in the pathway AND scenario model"] + b: Annotated[int, "Number of reactions in the pathway but NOT the scenario model"] + c: Annotated[int, "Number of reactions NOT in the pathway but ARE in the scenario model"] + d: Annotated[int, "Number of reactions NOT in the pathway NOR the scenario model"] + + @classmethod + def run( + cls: type["FisherExactTest"], + reference: cobra.Model, + scenario: cobra.Model, + pathway: str, + alternative: Literal["two-sided", "less", "greater"] = "two-sided", + ) -> "FisherExactTest": + """Perform a Fisher's Exact Test on two models with a known reference model. + + This test is based on the following assumptions: + - The general "reference" model was used to reconstruct the comprehensive and scenario models (such as Recon3D) + - A scenario-specific model exists that may not be representative of true biology + + --- + + Given the following contingency table for a set of conditions and N reactions: + - A: Reactions in `pathway` and the scenario-specific model + - B: Reactions in `pathway` but not the scenario-specific model + - C: Reactions in the scenario-specific model that are not a part of `pathway` + - D: Reactions not in `pathway` that are also not found in the scenario-specific model + + | Reaction Status | In scenario-specific model | Not in scenario-specific model | Row Total | + |:----------------:|:--------------------------:|:------------------------------:|:----------------------------:| + | In `pathway` | A | B | A + B | + | Not in `pathway` | C | D | C + D | + | Column Total | A + C | B + D | A + B + C + D (=N reactions) | + + A two-sided Fisher's exact test will ask the question: + > Is the inclusion or exclusion of this reaction in the patient model independent of its status in the reference model? + + If the scenario-specific dataset is "small", the reconstruction will likely have excluded/dropped some reactions + as a result of the limited data available. This means the Fisher's exact test may show **many apparent differences**. + However, this could be noise from undersampling and not indicative of the true underlying biology. + In practice, if only a few reactions fall into "condition A" (above), this suggests that the scenario-specific model is too sparse + and not reconstructed with enough data. + + Args: + reference: The general reference model that was used to build the model (e.g., Recon3D) + scenario: The scenario-specific model to test (e.g., built using a small cohort of single-cell RNA-seq data) + pathway: The pathway to investigate for a Fisher's Exact Test + alternative: The alternative hypothesis to test + + Returns: + The p-value indicating whether the reaction presence in the scenario model is independent of the reference model. + """ + scenario_rxn_ids: set[str] = {rxn.id for rxn in scenario.reactions} + + a = 0 # a reaction is in the given pathway and scenario model + b = 0 # a reaction is in the given pathway but not the scenario model + c = 0 # a reaction is not in the given pathway but is in the scenario model + d = 0 # a reaction is not in the given pathway OR the scenario model + + for rxn in reference.reactions: + in_pathway = rxn.subsystem == pathway + in_scenario = rxn.id in scenario_rxn_ids + + if in_pathway: + if in_scenario: + a += 1 + else: + b += 1 + else: + if in_scenario: + c += 1 + else: + d += 1 + + result = scipy.stats.fisher_exact(np.array([[a, b], [c, d]]), alternative=alternative) + return cls(statistic=result.statistic, pvalue=result.pvalue, pathway=pathway, a=a, b=b, c=c, d=d) diff --git a/main/como/stats/ks_test.py b/main/como/stats/ks_test.py new file mode 100644 index 00000000..9f3c1778 --- /dev/null +++ b/main/como/stats/ks_test.py @@ -0,0 +1,102 @@ +from dataclasses import dataclass +from typing import ClassVar, Literal + +import numpy as np +import numpy.typing as npt +import pandas as pd +from scipy.stats import ks_2samp + +from como.stats._two_sample import KS_RESULT, T_ALTERNATIVE, BaseTwoSample + +__all__ = ["KSTest"] + + +@dataclass(frozen=True, kw_only=True, slots=True) +class KSTest(BaseTwoSample[KS_RESULT]): + _fields: ClassVar[dict[str, type]] = { + "statistic": np.float64, + "pvalue": np.float64, + "statistic_location": np.float64, + "statistic_sign": np.uint8, + } + + reaction_ids: list[str] + statistic: npt.NDArray[np.float64] + pvalue: npt.NDArray[np.float64] + statistic_location: npt.NDArray[np.float64] + statistic_sign: npt.NDArray[np.int8] + + @staticmethod + def _worker(a: npt.NDArray[np.floating], b: npt.NDArray[np.floating], **kwargs) -> KS_RESULT: + """Calculate the KS statistic. + + Args: + a: First array + b: Second array + kwargs: Additional keyword arguments to pass to `ks_2samp` + + Returns: + A tuple of (statistic, pvalue, statistic_location, statistic_sign) + """ + res = ks_2samp(a, b, **kwargs) + return res.statistic, res.pvalue, res.statistic_location, res.statistic_sign + + @classmethod + def run( + cls, + df1: pd.DataFrame, + df2: pd.DataFrame, + alternative: T_ALTERNATIVE = "two-sided", + method: Literal["auto", "exact", "asymp"] = "auto", + axis: int = 0, + nan_policy: Literal["raise", "propagate", "omit"] = "propagate", + keepdims: bool = False, + cores: int = 1, + ) -> "KSTest": + """Run the KS test on two dataframes. + + Args: + df1: The first dataframe to process; obtained from running `cobra.sampling.sample`. + Columns should be reaction IDs and rows should be samples. + df2: The second dataframe to process; obtained from running `cobra.sampling.sample`. + Columns should be reaction IDs and rows should be samples. + alternative: The alternative hypothesis to test. + method: The method to use for calculating the p-value. + axis: The axis to perform the test along. + nan_policy: The policy to use for handling NaNs. + keepdims: Whether to keep the dimensions of the input arrays. + cores: The number of CPU cores to use for multiprocessing. + + Returns: + An instance of `KSTest` containing the results of the test. + """ + all_reactions, results = cls._run( + df1=df1, + df2=df2, + cores=cores, + worker_kwargs={"alternative": alternative, "method": method, "axis": axis, "nan_policy": nan_policy, "keepdims": keepdims}, + ) + return cls( + reaction_ids=all_reactions, + statistic=results["statistic"].astype(np.float64), + pvalue=results["pvalue"].astype(np.float64), + statistic_location=results["statistic_location"].astype(np.float64), + statistic_sign=results["statistic_sign"].astype(np.int8), + ) + + @property + def df(self) -> pd.DataFrame: + """DataFrame representation of the results. + + Returns: + A DataFrame with columns "statistic", "pvalue", "statistic_location", and "statistic_sign". + """ + return pd.DataFrame( + { + "statistic": self.statistic, + "pvalue": self.pvalue, + "statistic_location": self.statistic_location, + "statistic_sign": self.statistic_sign, + }, + index=pd.Index(name="reaction_id", data=self.reaction_ids), + ) diff --git a/main/como/stats/mann_whitney_test.py b/main/como/stats/mann_whitney_test.py new file mode 100644 index 00000000..98c8131d --- /dev/null +++ b/main/como/stats/mann_whitney_test.py @@ -0,0 +1,82 @@ +from dataclasses import dataclass +from typing import ClassVar, Literal + +import numpy as np +import numpy.typing as npt +import pandas as pd +from scipy.stats import PermutationMethod, mannwhitneyu + +from como.stats._two_sample import MW_RESULT, T_ALTERNATIVE, BaseTwoSample + +__all__ = ["MannWhitneyUTest"] + + +@dataclass(frozen=True, kw_only=True, slots=True) +class MannWhitneyUTest(BaseTwoSample[MW_RESULT]): + _fields: ClassVar[dict[str, type]] = {"statistic": np.float64, "pvalue": np.float64} + + reaction_ids: list[str] + statistic: npt.NDArray[np.float64] + pvalue: npt.NDArray[np.float64] + + @staticmethod + def _worker(a: npt.NDArray[np.floating], b: npt.NDArray[np.floating], **kwargs) -> MW_RESULT: + """Calculate the MWU statistic. + + Args: + a: First array + b: Second array + kwargs: Additional keyword arguments to pass to `mannwhitneyu` + + Returns: + A tuple of (statistic, pvalue) + """ + res = mannwhitneyu(x=a, y=b, **kwargs) + return np.float64(res.statistic), np.float64(res.pvalue) + + @classmethod + def run( + cls, + df1: pd.DataFrame, + df2: pd.DataFrame, + alternative: T_ALTERNATIVE = "two-sided", + use_continuity: bool = True, + axis: int = 0, + method: Literal["auto", "asymptotic", "exact"] | PermutationMethod = "auto", + cores: int = 1, + ) -> "MannWhitneyUTest": + """Run the MWU test on two dataframes. + + Args: + df1: The first dataframe to process; obtained from running `cobra.sampling.sample`. + Columns should be reaction IDs and rows should be samples. + df2: The second dataframe to process; obtained from running `cobra.sampling.sample`. + Columns should be reaction IDs and rows should be samples. + alternative: The alternative hypothesis to test. + use_continuity: Whether to apply a continuity correction when using the asymptotic method. + axis: The axis to perform the test along. + method: The method to use for calculating the p-value. + cores: The number of CPU cores to use for multiprocessing. + + Returns: + An instance of `MannWhitneyUTest` containing the results of the test. + """ + all_reactions, results = cls._run( + df1=df1, + df2=df2, + cores=cores, + worker_kwargs={"alternative": alternative, "use_continuity": use_continuity, "axis": axis, "method": method}, + ) + return cls(reaction_ids=all_reactions, statistic=results["statistic"].astype(np.float64), pvalue=results["pvalue"].astype(np.float64)) + + @property + def df(self) -> pd.DataFrame: + """DataFrame representation of the results. + + Returns: + A DataFrame with columns "statistic" and "pvalue". + """ + return pd.DataFrame( + {"statistic": self.statistic, "pvalue": self.pvalue}, + index=pd.Index(name="reaction_id", data=self.reaction_ids), + ) diff --git a/main/como/utils.py b/main/como/utils.py index 74716e24..ececc902 100644 --- a/main/como/utils.py +++ b/main/como/utils.py @@ -3,10 +3,9 @@ import contextlib import io import sys -import typing from collections.abc import Iterator from pathlib import Path -from typing import TextIO, TypeVar, cast, overload +from typing import Literal, NoReturn, TextIO, TypeVar, cast, overload import aiofiles import numpy.typing as npt @@ -66,34 +65,36 @@ def stringlist_to_list(stringlist: str | list[str]) -> list[str]: def split_gene_expression_data( expression_data: pd.DataFrame, + identifier_column: Literal["ensembl_gene_id", "entrez_gene_id"], recon_algorithm: Algorithm | None = None, - entrez_as_index: bool = True, -) -> pd.DataFrame: + *, + ensembl_as_index: bool = True, +): """Split the gene expression data into single-gene and multiple-gene names. - Args: + Arg: expression_data: The gene expression data to map + identifier_column: The column containing the gene identifiers, either 'ensembl_gene_id' recon_algorithm: The recon algorithm used to generate the gene expression data - entrez_as_index: Should the 'entrez_gene_id' column be set as the index + ensembl_as_index: Should the 'ensembl_gene_id' column be set as Returns: A pandas DataFrame with the split gene expression data - """ expression_data.columns = [c.lower() for c in expression_data.columns] if recon_algorithm in {Algorithm.IMAT, Algorithm.TINIT}: expression_data.rename(columns={"combine_z": "active"}, inplace=True) - expression_data = expression_data[["entrez_gene_id", "active"]] - single_gene_names = expression_data[~expression_data["entrez_gene_id"].astype(str).str.contains("//")] - multiple_gene_names = expression_data[expression_data["entrez_gene_id"].astype(str).str.contains("//")] - split_gene_names = multiple_gene_names.assign(entrez_gene_id=multiple_gene_names["entrez_gene_id"].astype(str).str.split("///")).explode( - "entrez_gene_id" + expression_data = cast(typ=pd.DataFrame, val=expression_data[[identifier_column, "active"]]) + single_gene_names = expression_data[~expression_data[identifier_column].astype(str).str.contains("//")] + multiple_gene_names = expression_data[expression_data[identifier_column].astype(str).str.contains("//")] + split_gene_names = multiple_gene_names.assign(ensembl_gene_id=multiple_gene_names[identifier_column].astype(str).str.split("///")).explode( + identifier_column ) gene_expressions = pd.concat([single_gene_names, split_gene_names], axis=0, ignore_index=True) - if entrez_as_index: - gene_expressions.set_index("entrez_gene_id", inplace=True) + if ensembl_as_index: + gene_expressions.set_index(identifier_column, inplace=True) return gene_expressions @@ -117,7 +118,7 @@ async def _format_determination( """Determine the data type of the given input values (i.e., Entrez Gene ID, Gene Symbol, etc.). Args: - biodbnet: The BioDBNet to use for deter + biodbnet: The BioDBNet to use for determination requested_output: The data type to generate (of type `Output`) input_values: The input values to determine taxon: The Taxon ID @@ -132,12 +133,29 @@ async def _format_determination( return coercion -@overload -async def _read_file(path: Path | io.StringIO, h5ad_as_df: bool = True, **kwargs) -> pd.DataFrame: ... - - -@overload -async def _read_file(path: Path | io.StringIO, h5ad_as_df: bool = False, **kwargs) -> pd.DataFrame | sc.AnnData: ... +async def get_missing_gene_data(values: list[str] | pd.DataFrame, taxon_id: int | str | Taxon) -> pd.DataFrame: + if isinstance(values, list): + gene_type = await determine_gene_type(values) + if all(v == "gene_symbol" for v in gene_type.values()): + return await gene_symbol_to_ensembl_and_gene_id(values, taxon=taxon_id) + elif all(v == "ensembl_gene_id" for v in gene_type.values()): + return await ensembl_to_gene_id_and_symbol(ids=values, taxon=taxon_id) + elif all(v == "entrez_gene_id" for v in gene_type.values()): + return await gene_id_to_ensembl_and_gene_symbol(ids=values, taxon=taxon_id) + else: + logger.critical("Gene data must be of the same type (i.e., all Ensembl, Entrez, or Gene Symbols)") + raise ValueError("Gene data must be of the same type (i.e., all Ensembl, Entrez, or Gene Symbols)") + else: + values: pd.DataFrame # Re-define type to assist in type hinting + if "gene_symbol" in values: + return await get_missing_gene_data(values["gene_symbol"].tolist(), taxon_id=taxon_id) + elif "entrez_gene_id" in values: + return await get_missing_gene_data(values["entrez_gene_id"].tolist(), taxon_id=taxon_id) + elif "ensembl_gene_id" in values: + return await get_missing_gene_data(values["ensembl_gene_id"].tolist(), taxon_id=taxon_id) + else: + logger.critical("Unable to find 'gene_symbol', 'entrez_gene_id', or 'ensembl_gene_id' in the input matrix.") + raise ValueError("Unable to find 'gene_symbol', 'entrez_gene_id', or 'ensembl_gene_id' in the input matrix.") @overload @@ -152,6 +170,10 @@ async def _read_file(path: pd.DataFrame, h5ad_as_df: bool, **kwargs) -> pd.DataF async def _read_file(path: sc.AnnData, h5ad_as_df: bool = False, **kwargs) -> sc.AnnData: ... +def _num_rows(item: pd.DataFrame | npt.NDArray) -> int: + return item.shape[0] + + @overload async def _read_file(path: sc.AnnData, h5ad_as_df: bool = True, **kwargs) -> pd.DataFrame: ... @@ -189,7 +211,7 @@ async def _read_file( _log_and_raise_error(f"File {path} does not exist", error=FileNotFoundError, level=LogLevel.CRITICAL) match path.suffix: - case ".csv" | ".tsv" | ".txt": + case ".csv" | ".tsv" | ".txt" | ".tab": kwargs.setdefault("sep", "," if path.suffix == ".csv" else "\t") # set sep if not defined async with aiofiles.open(path) as i_stream: content = await i_stream.read() @@ -212,31 +234,6 @@ async def _read_file( ) -async def get_missing_gene_data(values: list[str] | pd.DataFrame, taxon_id: int | str | Taxon) -> pd.DataFrame: - if isinstance(values, list): - gene_type = await determine_gene_type(values) - if all(v == "gene_symbol" for v in gene_type.values()): - return await gene_symbol_to_ensembl_and_gene_id(values, taxon=taxon_id) - elif all(v == "ensembl_gene_id" for v in gene_type.values()): - return await ensembl_to_gene_id_and_symbol(ids=values, taxon=taxon_id) - elif all(v == "entrez_gene_id" for v in gene_type.values()): - return await gene_id_to_ensembl_and_gene_symbol(ids=values, taxon=taxon_id) - else: - logger.critical("Gene data must be of the same type (i.e., all Ensembl, Entrez, or Gene Symbols)") - raise ValueError("Gene data must be of the same type (i.e., all Ensembl, Entrez, or Gene Symbols)") - else: - values: pd.DataFrame # Re-define type to assist in type hinting - if "gene_symbol" in values: - return await get_missing_gene_data(values["gene_symbol"].tolist(), taxon_id=taxon_id) - elif "entrez_gene_id" in values: - return await get_missing_gene_data(values["entrez_gene_id"].tolist(), taxon_id=taxon_id) - elif "ensembl_gene_id" in values: - return await get_missing_gene_data(values["ensembl_gene_id"].tolist(), taxon_id=taxon_id) - else: - logger.critical("Unable to find 'gene_symbol', 'entrez_gene_id', or 'ensembl_gene_id' in the input matrix.") - raise ValueError("Unable to find 'gene_symbol', 'entrez_gene_id', or 'ensembl_gene_id' in the input matrix.") - - @overload def _listify(value: list[T]) -> list[T]: ... @@ -289,14 +286,14 @@ def _log_and_raise_error( *, error: type[BaseException], level: LogLevel, -) -> typing.NoReturn: +) -> NoReturn: caller = logger.opt(depth=1) match level: case LogLevel.ERROR: caller.error(message) + raise error(message) case LogLevel.CRITICAL: caller.critical(message) + raise error(message) case _: raise ValueError(f"When raising an error, LogLevel.ERROR or LogLevel.CRITICAL must be used. Got: {level}") - - raise error(message) diff --git a/main/data/boundary_rxns/naiveB_boundary_rxns.csv b/main/data/boundary_rxns/naiveB_boundary_rxns.csv index 7130c9be..be3eec35 100644 --- a/main/data/boundary_rxns/naiveB_boundary_rxns.csv +++ b/main/data/boundary_rxns/naiveB_boundary_rxns.csv @@ -1,7 +1,7 @@ Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate -Exchange,glc_D,Extracellular,-100,1000 +Exchange,glc_D,Extracellular,-1000,100 Exchange,fe2,Extracellular,-1000,1000 -Exchange,gal,Extracellular,0,1000 +Exchange,gal,Extracellular,-1000,0 Exchange,zn2,Extracellular,-1000,1000 Exchange,ca2,Extracellular,-1000,1000 Exchange,na1,Extracellular,-1000,1000 @@ -16,55 +16,55 @@ Exchange,co2,Extracellular,-1000,1000 Exchange,nh4,Extracellular,-1000,1000 Exchange,no2,Extracellular,-1000,1000 Exchange,co,Extracellular,-1000,1000 -Exchange,asn_L,Extracellular,-1,1000 -Exchange,asp_L,Extracellular,-1,1000 -Exchange,glu_L,Extracellular,-1,1000 -Exchange,ile_L,Extracellular,-1,1000 -Exchange,leu_L,Extracellular,-1,1000 -Exchange,lys_L,Extracellular,-1,1000 -Exchange,met_L,Extracellular,-1,1000 -Exchange,pro_L,Extracellular,-1,1000 -Exchange,ser_L,Extracellular,-1,1000 -Exchange,val_L,Extracellular,-1,1000 -Exchange,gly,Extracellular,-1,1000 -Exchange,cys_L,Extracellular,-1,1000 -Exchange,ala_L,Extracellular,-1,1000 -Exchange,his_L,Extracellular,-1,1000 -Exchange,thr_L,Extracellular,-1,1000 -Exchange,gln_L,Extracellular,-1,1000 -Exchange,phe_L,Extracellular,-1,1000 -Exchange,tyr_L,Extracellular,-1,1000 -Exchange,arg_L,Extracellular,-1,1000 -Exchange,trp_L,Extracellular,-1,1000 -Exchange,eicostet,Extracellular,-1,1000 -Exchange,hdca,Extracellular,-1,1000 -Exchange,hdcea,Extracellular,-1,1000 -Exchange,lnlc,Extracellular,-1,1000 -Exchange,lnlnca,Extracellular,-1,1000 -Exchange,lnlncg,Extracellular,-1,1000 -Exchange,ocdca,Extracellular,-1,1000 -Exchange,ocdcea,Extracellular,-1,1000 -Exchange,thmmp,Extracellular,0,1000 -Exchange,thmtp,Extracellular,0,1000 -Exchange,ncam,Extracellular,0,1000 -Exchange,pnto_R,Extracellular,0,1000 -Exchange,pydxn,Extracellular,0,1000 -Exchange,pydx,Extracellular,0,1000 -Exchange,pydam,Extracellular,0,1000 -Exchange,btn,Extracellular,0,1000 -Exchange,fol,Extracellular,-10,1000 -Exchange,aqcobal,Extracellular,0,1000 -Exchange,vitd3,Extracellular,-1,1000 -Exchange,ascb_L,Extracellular,0,1000 -Exchange,retinol,Extracellular,-10,1000 -Exchange,retinal,Extracellular,-10,1000 -Exchange,ala_B,Extracellular,-1,1000 -Exchange,ala_D,Extracellular,-1,1000 +Exchange,asn_L,Extracellular,-1000,1 +Exchange,asp_L,Extracellular,-1000,1 +Exchange,glu_L,Extracellular,-1000,1 +Exchange,ile_L,Extracellular,-1000,1 +Exchange,leu_L,Extracellular,-1000,1 +Exchange,lys_L,Extracellular,-1000,1 +Exchange,met_L,Extracellular,-1000,1 +Exchange,pro_L,Extracellular,-1000,1 +Exchange,ser_L,Extracellular,-1000,1 +Exchange,val_L,Extracellular,-1000,1 +Exchange,gly,Extracellular,-1000,1 +Exchange,cys_L,Extracellular,-1000,1 +Exchange,ala_L,Extracellular,-1000,1 +Exchange,his_L,Extracellular,-1000,1 +Exchange,thr_L,Extracellular,-1000,1 +Exchange,gln_L,Extracellular,-1000,1 +Exchange,phe_L,Extracellular,-1000,1 +Exchange,tyr_L,Extracellular,-1000,1 +Exchange,arg_L,Extracellular,-1000,1 +Exchange,trp_L,Extracellular,-1000,1 +Exchange,eicostet,Extracellular,-1000,1 +Exchange,hdca,Extracellular,-1000,1 +Exchange,hdcea,Extracellular,-1000,1 +Exchange,lnlc,Extracellular,-1000,1 +Exchange,lnlnca,Extracellular,-1000,1 +Exchange,lnlncg,Extracellular,-1000,1 +Exchange,ocdca,Extracellular,-1000,1 +Exchange,ocdcea,Extracellular,-1000,1 +Exchange,thmmp,Extracellular,-1000,0 +Exchange,thmtp,Extracellular,-1000,0 +Exchange,ncam,Extracellular,-1000,0 +Exchange,pnto_R,Extracellular,-1000,0 +Exchange,pydxn,Extracellular,-1000,0 +Exchange,pydx,Extracellular,-1000,0 +Exchange,pydam,Extracellular,-1000,0 +Exchange,btn,Extracellular,-1000,0 +Exchange,fol,Extracellular,-1000,10 +Exchange,aqcobal,Extracellular,-1000,0 +Exchange,vitd3,Extracellular,-1000,1 +Exchange,ascb_L,Extracellular,-1000,0 +Exchange,retinol,Extracellular,-1000,10 +Exchange,retinal,Extracellular,-1000,10 +Exchange,ala_B,Extracellular,-1000,1 +Exchange,ala_D,Extracellular,-1000,1 Exchange,h2co3,Extracellular,-1000,1000 Exchange,h2o2,Extracellular,-1000,1000 Exchange,hco3,Extracellular,-1000,1000 -Exchange,orn,Extracellular,-1,1000 -Exchange,orn_D,Extracellular,-1,1000 +Exchange,orn,Extracellular,-1000,1 +Exchange,orn_D,Extracellular,-1000,1 Exchange,so4,Extracellular,-1000,1000 -Exchange,ribflv,Extracellular,-1,1000 -Exchange,Lcystin,Extracellular,-1,1000 \ No newline at end of file +Exchange,ribflv,Extracellular,-1000,1 +Exchange,Lcystin,Extracellular,-1000,1 diff --git a/main/data/boundary_rxns/smB_boundary_rxns.csv b/main/data/boundary_rxns/smB_boundary_rxns.csv index 0b08556e..9f0f9385 100644 --- a/main/data/boundary_rxns/smB_boundary_rxns.csv +++ b/main/data/boundary_rxns/smB_boundary_rxns.csv @@ -1,4 +1,4 @@ -Boundary,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate +Reaction,Abbreviation,Compartment,Minimum Reaction Rate,Maximum Reaction Rate Exchange,glc_D,Extracellular,-100,1000 Exchange,fe2,Extracellular,-1000,1000 Exchange,gal,Extracellular,0,1000 @@ -67,4 +67,4 @@ Exchange,orn,Extracellular,-1,1000 Exchange,orn_D,Extracellular,-1,1000 Exchange,so4,Extracellular,-1000,1000 Exchange,ribflv,Extracellular,-1,1000 -Exchange,Lcystin,Extracellular,-1,1000 \ No newline at end of file +Exchange,Lcystin,Extracellular,-1,1000 diff --git a/main/data/GeneralModelUpdatedV2.mat b/main/data/reference_models/GeneralModelUpdatedV2.mat similarity index 100% rename from main/data/GeneralModelUpdatedV2.mat rename to main/data/reference_models/GeneralModelUpdatedV2.mat diff --git a/main/data/reference_models/GeneralModelUpdatedV3.mat b/main/data/reference_models/GeneralModelUpdatedV3.mat new file mode 100644 index 00000000..f10c01e1 Binary files /dev/null and b/main/data/reference_models/GeneralModelUpdatedV3.mat differ diff --git a/main/data/iMM_madrid.mat b/main/data/reference_models/iMM_madrid.mat similarity index 100% rename from main/data/iMM_madrid.mat rename to main/data/reference_models/iMM_madrid.mat diff --git a/pyproject.toml b/pyproject.toml index 67c6b4f8..51f81319 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,42 +5,50 @@ build-backend = "hatchling.build" [project] name = "COMO" dynamic = ["version"] -requires-python = ">=3.10,<3.14" +requires-python = ">=3.11,<3.14" dependencies = [ - "aiofiles>=24.1.0", "aioftp>=0.23.1", + "anndata>=0.12.0", "cobamp@git+https://github.com/JoshLoecker/cobamp@master", "cobra>=0.28.0", "fast-bioservices>=0.3.9", - "kaleido==0.2.1", + "kaleido>=1.0.0", "loguru>=0.7.2", + "numpy>=2", "openpyxl>=3.1.5", "pandas>=1.3.5", - "plotly>=5.24.1", - "pydantic-settings", - "pydantic>=2.10.3", - "seaborn>=0.13.2", - "scanpy>=1.11.4", + "scanpy>=1.10.4", "scikit-learn>=1.5.2", - "scipy>=1.7.3", - "setuptools<60.0", - "statsmodels>=0.13.0", + "scipy>=1.13.0", + "seaborn>=0.13.2", + "setuptools>=78.1.1", + "statsmodels>=0.13.0; python_version < '3.12'", "statsmodels>=0.14.0; python_version >= '3.12'", "troppo@git+https://github.com/JoshLoecker/troppo@master", ] [project.optional-dependencies] -gurobi = ["gurobipy>=10.0.0"] +gurobi = [ + "gurobipy<14", +] interactive = [ "ipython>=8.0.0", "jupyterlab>=4.3.2" ] dev = [ - "hypothesis>=6.122.1", - "pytest-asyncio>=0.24.0", - "pytest-cov>=6.0.0", - "pytest>=8.3.3", - "ruff>=0.8.0", + "commitizen>=4.8.3", + "commitlint>=1.3.1", + "como", + "hatchling>=1.27.0", + "pandas-stubs>=2.3.2.250827", + "pre-commit>=4.2.0", + "pyright>=1.1.405", + "pytest>=8.4.1", + "pytest-asyncio>=1.1.0", + "pytest-cov>=6.2.1", + "ruff>=0.12.11", + "scipy-stubs>=1.16.1.1", + "types-aiofiles>=24.1.0.20250822", ] [tool.hatch.version] diff --git a/ruff.toml b/ruff.toml index 309140fa..4929a8e3 100644 --- a/ruff.toml +++ b/ruff.toml @@ -41,6 +41,9 @@ ignore = [ "F401", # allow unused imports ] +[lint.pydocstyle] +convention = "google" + [lint.per-file-ignores] "tests/*" = [ "D101", # allow undocumented public class diff --git a/tests/inputs/expected_ks_results.csv b/tests/inputs/expected_ks_results.csv new file mode 100644 index 00000000..b6640caf --- /dev/null +++ b/tests/inputs/expected_ks_results.csv @@ -0,0 +1,11 @@ +reaction_id,statistic,pvalue,statistic_location,statistic_sign +0,0.395,4.9525690933187676e-70,0.4804374873638153,1 +1,0.382,2.100275595200399e-65,0.6599260568618774,1 +2,0.416,7.105707649012374e-78,0.5388635396957397,1 +3,0.388,1.614348883239596e-67,0.460053950548172,1 +4,0.368,1.2990993761208528e-60,0.383552223443985,1 +5,0.382,2.100275595200399e-65,0.5969201326370239,1 +6,0.399,1.7223838690805776e-71,0.4544350504875183,1 +7,0.401,3.166572974357379e-72,0.5225677490234375,1 +8,0.385,1.8608981050282822e-66,0.6594884991645813,1 +9,0.355,2.435056842111727e-56,0.5130801200866699,1 diff --git a/tests/inputs/expected_mwu_results.csv b/tests/inputs/expected_mwu_results.csv new file mode 100644 index 00000000..2964651f --- /dev/null +++ b/tests/inputs/expected_mwu_results.csv @@ -0,0 +1,11 @@ +reaction_id,statistic,pvalue +0,246270.0,5.908986833278511e-86 +1,249044.0,3.9754187610805028e-84 +2,229206.0,1.2240591968361702e-97 +3,239091.0,8.876596072735212e-91 +4,251640.0,1.958199039053936e-82 +5,241101.0,2.051997493199763e-89 +6,234548.0,6.711468976164077e-94 +7,230278.0,6.983489755287457e-97 +8,239065.0,8.521868135307152e-91 +9,259912.0,3.698879057625339e-77 diff --git a/tests/inputs/naiveB_model.xml b/tests/inputs/naiveB_model.xml new file mode 100755 index 00000000..4de8cf9a --- /dev/null +++ b/tests/inputs/naiveB_model.xml @@ -0,0 +1,181471 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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References: We show in this study that the product of Slc6a18 called XT2 is a Na+- and Cl dependent neutral amino acid transporter and displays, compared with B0AT1, a lower K0.5 and a different substrate selectivity. Because of its broad transport selectivity for neutral amino acids, we suggest that it be renamed B0AT3. Exclusive to kidney, responsible for re-absorption of neutral amino acids (gly, ala, val, leu, ile, met, ser, cys, asn, gln, phe, tyr, trp, arg, glu).

+

Confidence Level: 0.0

+

NOTES: 4

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Used to make Ubiquinone-10 enzyme has not been identified yet. IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: PMID:486467 MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: as described in Bender (Nutritional biochmeistry of the vitamins, 2nd edition) MM

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM. activity measured in rat, 3-sulfinoalanine is substrate found in human brain

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM. activity measured in rat, 3-sulfinoalanine is substrate found in human brain

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: specific mechanism not known, proton dependence for trans-mit transport has been suggested, however directionality and stoichiometry has not yet been elucidated. see PMID: 12770731 and others NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: specific mechanism not known, proton dependence for trans-mit transport has been suggested, however directionality and stoichiometry has not yet been elucidated. see PMID: 12770731 and others NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD. Delta-aminolevulinic acid is produced in mitochondria then converted to PBG in the cytoplasm. Could not find anything on the transporter itself.

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: specific mechanism not known, proton dependence for trans-mit transport has been suggested, however directionality and stoichiometry has not yet been elucidated. see PMID: 12770731 and others NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: carrier-mediated transport - but which and how is unknown IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism. IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: carrier-mediated transport - but which and how is unknown IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism. IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC: 2.4.1.228 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: kh 1/6/03

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM. 2-Methyl-3-acetoacetyl-CoA excreted into urine for patients with disease deficiency

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD NJ - added peroxisomal version

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT, TDV changed name from "tm2" to "t2m" - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV (9/14/2004)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV-mitochondrial version JLR- also acts on propanoate AMF- made reaction to create AMP not ADP and changed EC

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: transport between cytosol and Golgi/ER presumed presumed facilitated transport, but unknown co-substrates, see PMID: 12739170, Hirabayashi et al NJ changed name from ACCOArt to ACCOAtr for consistency - NCD

+ +
+ + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - however must get to other intracellular compartments (e.g. lysosome for degradation) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - however must get to other intracellular compartments (e.g. lysosome for degradation) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: ATP dependent citrate lyase. Reaction is reversible in KEGG (new EC 2.3.3.8) NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC-2.5.1.56 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC-2.5.1.56 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: H symport into lysososome. See PMID: 2768261 and PMID: 10581036 ( for human evidence). Sialic acid storage disorders (due to transporter mutations) require import and export e.g. PMID: 2768266 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Assume NAD/NADH as acceptors Lumped long-chain acyl-CoA dehydrogenase (EC 1.3.99.13) This reaction is therefore equilivalent to trans-2-enoyl-CoA reductase (NAD) (EC 1.3.1.44)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF. Biochemical

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: INVALID ECO TERM: IFH

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: AMF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Added EC- JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: adenosine deaminase has been found on cell surface in human (Gonzales-Gronow et al, JBC, 2004,279,20993-20998). IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: most likely NOT physiological - detailed information about the peroxisomal transporters has not yet been achieved - this transport is most likely dependent on a concomitant energy consuming reaction (human ABC peroxisomal transporters: PEX family - check in future for new research articles describing biochemistry and stoichiometry) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: interaction between peroxisomes and ER (some enzymes on the outer membrane) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: FULLR corresponds to acyl/R groups in texts. NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC taken from Ligand TV. Genetic

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: tv Mendz pg. 201 Reversibility is unclear.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB based om PMID 10823827

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD. For NAD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: See also ALDH1 (1.2.1.3); r0177

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: cofactors + usage still not clear see version ALOX5b for ATP concomittant hydrolysis - literature notes in vitro requirement for Ca and ATP for activity in addition to Fe

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: cofactors + usage still not clear unknown mechanism - biochemistry supported by PMID: 2829172, 11160764

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Added by RS/TV (6/17/05)

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: "diffusion" NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: for MDR transport mechanism NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: specific mechanism not known, proton dependence for trans-mit transport has been suggested, however directionality and stoichiometry has not yet been elucidated. see PMID: 12770731 and others NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism, presumed diffusion NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: cytosolic conversion of pooled FA into palmitate (so subsequent transport into mit w/ FA oxidation can occur). Since Carbon stoichiometry normalized wrt C16 ratio between Rgroupcoa and pmtcoa is 1:1 HR fatty acid metabolism - R groups = acyl groups, Rtotal, Rtotal2, Rtotal3 correspond to three possible acyl groups added to glycerol R1 - C16 groups R2 - essential FA + associated derivatives R3 - non-essential, dietary FA (C18) R4 - monounsaturated FA R5 -other (C26, C24) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: cytosolic conversion of pooled FA into palmitate (so subsequent transport into mit w/ FA oxidation can occur). Since Carbon stoichiometry normalized wrt C16 ratio between Rgroupcoa and pmtcoa is 1:1 HR fatty acid metabolism - R groups = acyl groups, Rtotal, Rtotal2, Rtotal3 correspond to three possible acyl groups added to glycerol R1 - C16 groups R2 - essential FA + associated derivatives R3 - non-essential, dietary FA (C18) R4 - monounsaturated FA R5 -other (C26, C24) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB based om PMID 10823827

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: most likely NOT physiological - detailed information about the peroxisomal transporters has not yet been achieved - this transport is most likely dependent on a concomitant energy consuming reaction (human ABC peroxisomal transporters: PEX family - check in future for new research articles describing biochemistry and stoichiometry) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT, TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT, TDV

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism, however glucuronidated metabolites need to get out of the cell NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _01-25-05 based on Wang et al 1999, JBC, 274(21), 14875-14888. IT 03-07-05:replaced IT: now based on Balamurugan et al, 2005, Am J Physiol Renal Physiol, 288, F823-831,2005

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD ER version NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV (see C160CRN)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV C20:4 transport

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV C20:4 transport

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: interaction between peroxisomes and ER (some enzymes on the outer membrane) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD ER version NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD ER version NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD ER - NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 1.-.-.- NCD ER version NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: double check rxn specifics - see lit ref: Marijanovic, Molecular Endocrinology 2003 17:1715-1725 ER version NJ

+ +
+ + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: double check rxn specifics - see lit ref: Marijanovic, Molecular Endocrinology 2003 17:1715-1725 ER version NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: plasma membrane version (SR and ER versions also exist) stoichiometry actually varies (number of Ca/ATP transported). See PMID: 7876199 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: See PMID: 11946414 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: multiple EC EC 1.1.1.189 EC 1.1.1.197 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ - reversibility of enzyme found in lit by NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism, presumed diffusion NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: ER membrane - but on cytosolic surface NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: inner mitochondrial membrane NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: non-vesicular intracellular transport of ceramide

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: non-vesicular intracellular transport of ceramide

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: non-vesicular intracellular transport of glucocerebroside

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: non-vesicular intracellular transport of glucocerebroside

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - no strong evidence to indicate further lysosomal or golgi metabolism NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - no strong evidence to indicate further lysosomal or golgi metabolism NJ

+ +
+ + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0.0

+

NOTES: specific mechanism not known, proton dependence for trans-mit transport has been suggested, however directionality and stoichiometry has not yet been elucidated. see PMID: 12770731 and others NJ. NS: transport from lysozyme to mitochondria?

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: specific mechanism not known, proton dependence for trans-mit transport has been suggested, however directionality and stoichiometry has not yet been elucidated. see PMID: 12770731 and others NJ

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: specific mechanism not known, proton dependence for trans-mit transport has been suggested, however directionality and stoichiometry has not yet been elucidated. see PMID: 12770731 and others NJ

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: antiport with malate IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: antiport with PEP IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: kegg C02305 MJC SAB c

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: interaction between peroxisomes and ER (some enzymes on the outer membrane) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _2.1.1.114 IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _2.1.1.- IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _1.13.12.- IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _1.14.13.- IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: mechanism not currently elucidated NJ

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction occurs in the endosome during endocytosis, but has been compartmentalized as lysosomal. NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction occurs in the endosome during endocytosis, but has been compartmentalized as lysosomal. NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction occurs in the endosome during endocytosis, but has been compartmentalized as lysosomal. NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction occurs in the endosome during endocytosis, but has been compartmentalized as lysosomal. NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction occurs in the endosome during endocytosis, but has been compartmentalized as lysosomal. NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF old EC number (4.1.3.7) is obsolete -- transferred to 2.3.3.1 NCD. Biochemical

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: mm

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: reaction according to KEGG MM

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Merged CYSGLYexR and CYSGLYex - (May 2011) IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: adenosine deaminase has been found on cell surface in human (Gonzales-Gronow et al, JBC, 2004,279,20993-20998). IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT (2.7.1.74)

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT (2.7.1.74)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT (2.7.1.74)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: interaction between peroxisomes and ER (some enzymes on the outer membrane) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT rxn is done by 4.1.2.14 and 4.1.3.16 mitochondrial isozyme - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: ubiquinone precursor, transport by "diffusion" -> actually beleived to be flip-flop mechanism (PMID: 12840657). NJ

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: for homo sapiens, noted to actually be NADH-cyt b5, using NADH at present NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: for homo sapiens, noted to actually be NADH-cyt b5, using NADH at present NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: for homo sapiens, noted to actually be NADH-cyt b5, using NADH at present NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: FULLR corresponds to acyl/R groups in texts. NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Added EC- JLR IT

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: lanosterol -> cholesterol pathway FAD known to be cofactor, other details missing NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: lanosterol -> cholesterol pathway see paper refs Moebius et al PNAS 95:1899-1902 - check/re-check lit for more specific details (NADPH known to be cofactor - also NADH?, possibly rev?) NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: lanosterol -> cholesterol pathway see paper refs Moebius et al PNAS 95:1899-1902 - check/re-check lit for more specific details (NADPH known to be cofactor - also NADH?, possibly rev?) NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Used to make Ubiquinone-10 EC 2.1.1.114 IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD,IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _06-15-05 - EC 1.3.3.1 IT based on Bader et al, 1998, Prot. Expr. Purif 13,414-422 (I guess it is ubiquinone but i am not sure ) (needs FMN as cofactor) v(enzyme is located in inner-membrane of mitochondria, reaction take place in cytosol (Fig. 8 Rawls et al PMID: 10727948 )

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - however must get to other intracellular compartments (e.g. lysosome for degradation) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal version - NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: dmhptcoa is 'special' because its biochemical fat isn't known NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: added EC num; also EC 5.4.2.4 -- NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: enzyme has not been identified yet IT

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal version - NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: by analogy to other dimethyl transferase rxns. See PMID: 10586494, human interemidate (from C15 ->C50) not explicitly determined yet, however it is known to occur since this pathway is essential in Q10 synthesis. For human metabolism: may be associated w/ GeneID: 23590 TPRT - recheck lit in future IT and NJ

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: CoA transfer not explicitly in rxn (accounted for in Rtotal rxn -> ARTF) NJ

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _01-26-05 IT based on Lu et al JBC,1992,24,17102-17109

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _01-26-05 IT based on Lu et al JBC,1992,24,17102-17109

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: involved in lanosterol -> cholesterol pathway NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: involved in lanosterol -> cholesterol pathway NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM. based on assigned short chain enoyl-CoA hydratase activity

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB for mito

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB for x

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM. based on assigned short chain enoyl-CoA hydratase activity

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD SAB oaa -> asp-L

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: specific mechanism not known, proton dependence for trans-mit transport has been suggested, however directionality and stoichiometry has not yet been elucidated. see PMID: 12770731 and others NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: specific mechanism not known, proton dependence for trans-mit transport has been suggested, however directionality and stoichiometry has not yet been elucidated. see PMID: 12770731 and others NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV (5/4/05) Voet p.571

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV Ruzicka F, JBC, 1977

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: AR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV catalyzed by acyl-CoA synthetases

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: AR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV catalyzed by acyl-CoA synthetases

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV catalyzed by acyl-CoA synthetases

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ, RE1514C

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ, RE3114C

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: rev version so additional rxn doesn't need to be added to "unload" AA NJ. Merged GPR from FACOAL204 and FACOAL204i - (May 2011) IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: rev version so additional rxn doesn't need to be added to "unload" AA alternate to arachidonic acid (n-3 rather than n-6) NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: cytoplasmic version -NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion - but unidirectional uptake into ER (to avoid loops w/ NAD/NADP) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: most likely NOT physiological - detailed information about the peroxisomal transporters has not yet been achieved - this transport is most likely dependent on a concomitant energy consuming reaction (human ABC peroxisomal transporters: PEX family - check in future for new research articles describing biochemistry and stoichiometry) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion - but unidirectional output from ER (to avoid loops w/ NAD/NADP) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: most likely NOT physiological - detailed information about the peroxisomal transporters has not yet been achieved - this transport is most likely dependent on a concomitant energy consuming reaction (human ABC peroxisomal transporters: PEX family - check in future for new research articles describing biochemistry and stoichiometry) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: fatty acid elongation step NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: fatty acid elongation step NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: fatty acid elongation step NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: fatty acid elongation step NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: fatty acid omega hydroxylation NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV Other enzymes: 1.3.3.6, 4.2.1.74, 4.2.1.17, 1.1.1.35, 1.1.1.211

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV Other enzymes: 1.3.3.6, 4.2.1.74, 4.2.1.17, 1.1.1.35, 1.1.1.211

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _4 rounds of beta ox c16:0 -> c8:0, 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _4 rounds of beta ox - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) c16:0 -> c8:0, 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _4 rounds of beta ox, 1 loss of degree of unsat -> only 3 fad oxidized c16:1 -> c8:0 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _4 rounds of beta ox, 1 loss of degree of unsat -> only 3 fad oxidized c16:1 -> c8:0 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV Other enzymes: 1.3.3.6, 4.2.1.74, 4.2.1.17, 1.1.1.35, 1.1.1.211

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _5 rounds of beta ox, 1 loss of degree of unsat -> 4 fad oxidized c18:1 -> c8:0 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _5 rounds of beta ox, 1 loss of degree of unsat -> 4 fad oxidized c18:1 -> c8:0 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _5 rounds of beta ox, 1 loss of degree of unsat -> 4 fad oxidized c18:1 -> c8:0 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: c18:2,n-6 -> c8:0 - 5 rounds of beta ox, lose 2 degrees of unsat - only 3 fad oxidized 4 step FAO lumped also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: c18:2, transe -> c8:0 - 5 rounds of beta ox, lose 2 degrees of unsat - only 3 fad oxidized 4 step FAO lumped also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: c18:3, n-3 -> c8:0 - 5 rounds of beta ox, lose 3 degrees of unsat - only 2 fad oxidized 4 step FAO lumped also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _5 rounds of beta ox, 3 degrees loss of saturation -> only 2 fad oxidized to fadh2 - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) peroxisomal (very long chain FA) c18:3,n-6 -> c8:0, 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _5 rounds of beta ox, 3 degrees loss of saturation -> only 2 fad oxidized to fadh2 - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) peroxisomal (very long chain FA) c18:3,n-6 -> c8:0, 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _5 rounds of beta ox, 4 degrees loss of saturation -> only 1 fad oxidized to fadh2 peroxisomal (very long chain FA) c18:4,n-6 -> c8:0, 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _5 rounds of beta ox, 4 degrees loss of saturation -> only 1 fad oxidized to fadh2 - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) peroxisomal (very long chain FA) c18:4,n-6 -> c8:0, 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: c20:0 -> c18:0 4 step FAO lumped also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal (very long chain FA) - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) c20:0 -> c18:0 4 step FAO lumped also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: c20:3 -> c18:3 4 step FAO lumped also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV Other enzymes: 1.3.3.6, 4.2.1.74, 4.2.1.17, 1.1.1.35, 1.1.1.211

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _1 rounds of beta ox c20:4 -> c18:4 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _1 round beta ox, 1 degree loss of sat -> no fad oxidation peroxisomal (very long chain FA) c20:5,n-3 -> c18:4, n-3 - final '3' in abbreviation indicates omega3 FA 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _1 round beta ox, 1 degree loss of sat -> no fad oxidation - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) peroxisomal (very long chain FA) c20:5,n-3 -> c18:4, n-3 - final '3' in abbreviation indicates omega3 FA 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _1 round beta ox peroxisomal (very long chain FA) c22:4,n-6 -> c20:4, n-6 - final '6' in abbreviation indicates omega6 FA 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _1 round beta ox - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) peroxisomal (very long chain FA) c22:4,n-6 -> c20:4, n-6 - final '6' in abbreviation indicates omega6 FA 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _2 rounds of beta-ox, plus a loss of 2 degrees of desatuartion, so no fad is oxidized peroxisomal (very long chain FA) c22:5,n-6 -> c18:3, n-6 - final '6' in abbreviation indicates omega6 FA 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _2 rounds of beta-ox, plus a loss of 2 degrees of desatuartion, so no fad is oxidized - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) peroxisomal (very long chain FA) c22:5,n-6 -> c18:3, n-6 - final '6' in abbreviation indicates omega6 FA 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _1 round beta ox - c22:5,n-3 -> c20:5, n-3 - final '3' in abbreviation indicates omega3 FA 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _1 round beta ox - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) peroxisomal (very long chain FA) c22:5,n-3 -> c20:5, n-3 - final '3' in abbreviation indicates omega3 FA 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV Other enzymes: 1.3.3.6, 4.2.1.74, 4.2.1.17, 1.1.1.35, 1.1.1.211

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _1 round of beta-oxidation, loses degree of desat, so no fad peroxisomal (very long chain FA) c22:6,n-3 -> c20:5, n-3 4 step FAO lumped also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _1 round of beta-oxidation, loses degree of desat, so no fad - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) peroxisomal (very long chain FA) c22:6,n-3 -> c20:5, n-3 4 step FAO lumped also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal (very long chain FA) - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) c24:0 -> c20:0 4 step FAO lumped for 2 rounds also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal (very long chain FA) - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) c24:1 -> c18:1 - 3 rounds beta-ox 4 step FAO lumped also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal (very long chain FA) - in peroxisome, no fad, 1ste set of beta-ox is by acyl-coa oxidase (passes electrons directly to o2 -> h2o2) c26:0 -> c24:0 4 step FAO lumped also includes EC 1.1.1.35, 1.1.1.211, 1.3.3.6, 4.2.1.17, 4.2.1.74 -> into pmtcoa NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV (9/7/2004) Other enzymes: 1.3.3.6, 4.2.1.74, 4.2.1.17, 1.1.1.35, 1.1.1.211

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: electroneutral transport NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD; r0096

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD,IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: cholesterol precursor, transport by "diffusion" -> actually beleived to be flip-flop mechanism (PMID: 12840657). See also Krisans (PMID: 14713247, PMID: 12121718) for synthesis of cholesterol pathway (why FRDP needs to be transported between ER and peroxisome) NJ

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: cholesterol precursor, transport by "diffusion" -> actually beleived to be flip-flop mechanism (PMID: 12840657). See also Krisans (PMID: 14713247, PMID: 12121718) for synthesis of cholesterol pathway (why FRDP needs to be transported between ER and peroxisome) NJ

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism, however these blood groups need to make it to the extracellular surface of cells NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF. Biochemical

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Keratan sulfate II biosynthesis NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Keratan sulfate II biosynthesis NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Keratan sulfate II biosynthesis NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Keratan sulfate II biosynthesis NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Keratan sulfate II biosynthesis NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Keratan sulfate II biosynthesis NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Keratan sulfate II biosynthesis NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Keratan sulfate II biosynthesis NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: replaces old version which contains redundant metabolite (gly3p) NCD split compartmentation NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: spontaneous reaction NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB m TDV: name change from G5SDm

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: tv, jp NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB c

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - however must get to other intracellular compartments (e.g. lysosome for degradation) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - however must get to other intracellular compartments (e.g. lysosome for degradation) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - not known if it is energy dependent or not, recycling and IC transport is important to get it to other areas of the cell NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - not known if it is energy dependent or not, recycling and IC transport is important to get it to other areas of the cell (e.g. plasma membrane) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - intracellular transport occurs, most details are unknown - see for example Varki glycobiology text or numerous reviews (PMID: 8206147) - extracellular transport is also made available since metabolites can get to outer plasma membrane NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Both human and Escherichia coli enzymes can use NADH in place of NADPH to a slight extent. IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: REMOVES EITHER ONE OR TWO GLUTAMYL RESIDUES WITH A REACTION (WILL ONLY REPRESENT 1) - last step from 5-glutamyl to monoglutamyl is in one step IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: REMOVES EITHER ONE OR TWO GLUTAMYL RESIDUES WITH A REACTION (WILL ONLY REPRESENT 1) IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: REMOVES EITHER ONE OR TWO GLUTAMYL RESIDUES WITH A REACTION (WILL ONLY REPRESENT 1) IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: REMOVES EITHER ONE OR TWO GLUTAMYL RESIDUES WITH A REACTION (WILL ONLY REPRESENT 1) - last step from 5-glutamyl to monoglutamyl is in one step IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: REMOVES EITHER ONE OR TWO GLUTAMYL RESIDUES WITH A REACTION (WILL ONLY REPRESENT 1) - last step from 5-glutamyl to monoglutamyl is in one step IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: REMOVES EITHER ONE OR TWO GLUTAMYL RESIDUES WITH A REACTION (WILL ONLY REPRESENT 1) IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: REMOVES EITHER ONE OR TWO GLUTAMYL RESIDUES WITH A REACTION (WILL ONLY REPRESENT 1) IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: REMOVES EITHER ONE OR TWO GLUTAMYL RESIDUES WITH A REACTION (WILL ONLY REPRESENT 1) IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: REMOVES EITHER ONE OR TWO GLUTAMYL RESIDUES WITH A REACTION (WILL ONLY REPRESENT 1) IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Cleaves the gamma-glutamyl peptide bond of glutathione conjugates, but maybe not glutathione itself. Converts leukotriene C4 (LTC4) to leukotriene D4 (LTD4). NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Converts leukotriene E4 (LTE4) to leukotriene D4 (LTE4). NJ

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.226 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.226 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.226 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.226 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.225 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.225 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.225 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.225 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.223 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.224 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.224 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.224 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.4.1.224 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: H symport into lysososome. See PMID: 2768261 and PMID: 10581036 ( for human evidence). Sialic acid storage disorders (due to transporter mutations) require import and export e.g. PMID: 2768266 NJ renamed from GLCURlt to GLCURtly - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: lumped reaction, combination of 4-alpha-D-glucanotransferase (2.4.1.25) and amylo-alpha-1,6-glucosidase (3.2.1.33) NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV (6/7/2005) Study in rat liver (Soboll, 1991)

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB based om PMID 10823827

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB m

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB use of FAD is not certain

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism, needed to transport glu-L out of ER in conversion of leuktrC4-> leuktrD4 NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB c

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB irreversible

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV Biochim Biophys Acta. 1980 Jun 6;598(3):588-94

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP Note no proton generation by the the reaction NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - intracellular transport occurs, most details are unknown - see for example Varki glycobiology text or numerous reviews (PMID: 8206147) - extracellular transport is also made available since metabolites can get to outer plasma membrane NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal version - NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD, TV This EC (1.6.4.2) is obsolete. The new EC is 1.8.1.7. http://www.genome.ad.jp/dbget-bin/www_bget?ec:1.6.4.2

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD, TV This EC (1.6.4.2) is obsolete. The new EC is 1.8.1.7. http://www.genome.ad.jp/dbget-bin/www_bget?ec:1.6.4.2

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV (8-15-2003)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV (8-15-2003) Meister, A, Mitochondrial changes associated with glutathione deficiency, Biochimica et Biophysica Acta 1271 (1995) 35-42. The article reports that this is an active transport but doesn't not specify if it uses atp.

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism - NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD SAB e see Disussion section of PMID 15469854

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: tv

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: AMF

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: it

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: it

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Same as EC 1.1.1.157 SAB mito. some physiological

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Same as EC 1.1.1.157 SAB x

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM. inborn deficiency enzyme causes accumulation of substrate 3-hydroxy-2-methylbutyric acid

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Used to make Ubiquinone-10 EC 2.5.1.- IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: interaction between peroxisomes and ER (some enzymes on the outer membrane) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD New assignment: EC-2.3.3.10 EC-4.1.3.5 (created 1961, deleted 2002). Enzyme Commission Made irreversible to match KEGG data for S. aureus

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD New assignment: EC-2.3.3.10 EC-4.1.3.5 (created 1961, deleted 2002). Enzyme Commission mitochondrial enzyme NJ Made irreversible to match KEGG data for S. aureus

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV NJ added peroxisomal version - see Olivier Biochimica et Biophysica Act 1529 (2000) 89-102

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV (4/28/2004) There are conflicting data on how many moles of NADPH consumed per mole of Biliverdine (Tenhunen 1969, Ryter, 2000). Heme oxygenase is a well known enzyme

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The proton is located in the lysosome since it comes from oxidation of the NH3+ group in glucosamine. This reaction assumes that the other proton liberated from glucosamine reduces coa in the cytosol. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The proton is located in the lysosome since it comes from oxidation of the NH3+ group in glucosamine. This reaction assumes that the other proton liberated from glucosamine reduces coa in the cytosol. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The proton is located in the lysosome since it comes from oxidation of the NH3+ group in glucosamine. This reaction assumes that the other proton liberated from glucosamine reduces coa in the cytosol. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The proton is located in the lysosome since it comes from oxidation of the NH3+ group in glucosamine. This reaction assumes that the other proton liberated from glucosamine reduces coa in the cytosol. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: direct enzymatic rates quantified in human brain tissue

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: microsomal NAD as cofactor HSD type 2 recheck/confirm comparmentalization - type 1: cytosol, types 2,3: microsomes NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: see Russell bile acid synthesis review paper in human recon citation db adamanski et al Steroids (1997) 62:159 notes cofactor NADP/NADPH use

+ +
+ + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: see Russell bile acid synthesis review paper in human recon citation db adamanski et al Steroids (1997) 62:159 notes cofactor NADP/NADPH use

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Recombinant cDNA from human granulosa cells were purified and used in an enzyme assay, Km and Kcat values quantified

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: see PMID: 14643063 inferred use of O2 for oxidation - biochemical details have not yet been experimentally elucidated NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: kinetic studies done with recombinant human cDNA transfected into baculovirus

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction occurs in the endosome during endocytosis, but has been compartmentalized as lysosomal. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The reaction may be reversible. Strathern shows the reactions as irreversible. IF. Biochemical, Genetic

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Two reactions (ICDH1 and ICDH2) for isocitrate dehydrogenase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Strathern indicates this reaction as irreversible. It may be reversible. Location is the peroxisomal matrix (MIPS). IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The reaction may be reversible. Strathern shows the reaction as irreversible. IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: H symport into lysososome. See PMID: 2768261 and PMID: 10581036 (for human evidence). Sialic acid storage disorders (due to transporter mutations) require import and export e.g. PMID: 2768266 NJ renamed from GLCURlt to GLCURtly - NCD added IdoA reaction - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: AR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal version - NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Some enzymes in this group hydrolyse a-L-arabinosides; some animal enzymes also hydrolyse b-D-fucosides and b-D-glucosides; cf. EC 3.2.1.108 lactase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 1.2.1.1 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT. human enzymes overexpressed on E.coli, Pig Liver

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR- added irreversible form of LCAD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: this reaciton is only found in lactating mammary cells NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: described in PMID: 3346220 and KEGG MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: This follows the convention of L-LACtm Also see LDL_D.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism, presumed diffusion NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism, presumed diffusion NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD ER version - NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: phosphatidyl choline degradation NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: lanosterol -> cholesterol pathway NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: lanosterol -> cholesterol pathway NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Converts leukotriene C4 (LTC4) to leukotriene F4 (LTF4). NJ

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: previous EC 2.5.1.37 EC: 4.4.1.20 NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Converts leukotriene D4 (LTD4) to leukotriene E4 (LTE4). unknown compartmentalization, cytosolic by default NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV (9/14/2004) added "m" to denote compartmentalization - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV (9/14/2004) NJ added peroxismal and cytoplasmic reactions

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF. Biochemical

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR- Based on reaction given for B. subtilis (Sekowska A and A. Danchin paper(2002) )

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: excretion of 3-mercaptolactate-cysteine disulfide (PMID: 6945862) MM

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Human Y/N: Y

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal version NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: this rxn also represents the enzymatic conversion or non-enzymatic fragmentation of g3p to mthgxl - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR mitochondrial isoform - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV Also converts propanal to propanoyl-CoA

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: also EC 1.2.1.18 - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM. biochemical activity measured in rat, sequence similarity found in human

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction is specific to beta-N-acetylhexosaminidase A and cannot be catalyzed by beta-N-acetylhexosaminidase B (or presumably beta-N-acetylhexosaminidase S). This is also a lumped reaction, representing the cleavage of GalNAc4S or GalNAc6S and N-acetylgalactosamine 4-sulfatase or 6-sulfatase. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction is specific to beta-N-acetylhexosaminidase A and cannot be catalyzed by beta-N-acetylhexosaminidase B (or presumably beta-N-acetylhexosaminidase S). This is also a lumped reaction, representing the cleavage of GalNAc4S or GalNAc6S and N-acetylgalactosamine 4-sulfatase or 6-sulfatase. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction is specific to beta-N-acetylhexosaminidase A and cannot be catalyzed by beta-N-acetylhexosaminidase B (or presumably beta-N-acetylhexosaminidase S). This is also a lumped reaction, representing the cleavage of GalNAc4S or GalNAc6S and N-acetylgalactosamine 4-sulfatase or 6-sulfatase. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction is specific to beta-N-acetylhexosaminidase A and cannot be catalyzed by beta-N-acetylhexosaminidase B (or presumably beta-N-acetylhexosaminidase S). This is also a lumped reaction, representing the cleavage of GalNAc4S or GalNAc6S and N-acetylgalactosamine 4-sulfatase or 6-sulfatase. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction is specific to beta-N-acetylhexosaminidase A and cannot be catalyzed by beta-N-acetylhexosaminidase B (or presumably beta-N-acetylhexosaminidase S). This is also a lumped reaction, representing the cleavage of GalNAc4S or GalNAc6S and N-acetylgalactosamine 4-sulfatase or 6-sulfatase. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction is specific to beta-N-acetylhexosaminidase A and cannot be catalyzed by beta-N-acetylhexosaminidase B (or presumably beta-N-acetylhexosaminidase S). This is also a lumped reaction, representing the cleavage of GalNAc4S or GalNAc6S and N-acetylgalactosamine 4-sulfatase or 6-sulfatase. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction is specific to beta-N-acetylhexosaminidase A and cannot be catalyzed by beta-N-acetylhexosaminidase B (or presumably beta-N-acetylhexosaminidase S). This is also a lumped reaction, representing the cleavage of GalNAc4S or GalNAc6S and N-acetylgalactosamine 4-sulfatase or 6-sulfatase. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction is specific to beta-N-acetylhexosaminidase A and cannot be catalyzed by beta-N-acetylhexosaminidase B (or presumably beta-N-acetylhexosaminidase S). This is also a lumped reaction, representing the cleavage of GalNAc4S or GalNAc6S and N-acetylgalactosamine 4-sulfatase or 6-sulfatase. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction is specific to beta-N-acetylhexosaminidase A and cannot be catalyzed by beta-N-acetylhexosaminidase B (or presumably beta-N-acetylhexosaminidase S). This is also a lumped reaction, representing the cleavage of GalNAc4S or GalNAc6S and N-acetylgalactosamine 4-sulfatase or 6-sulfatase. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction is specific to beta-N-acetylhexosaminidase A and cannot be catalyzed by beta-N-acetylhexosaminidase B (or presumably beta-N-acetylhexosaminidase S). This is also a lumped reaction, representing the cleavage of GalNAc4S or GalNAc6S and N-acetylgalactosamine 4-sulfatase or 6-sulfatase. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Note that this reaction is specific to beta-N-acetylhexosaminidase A and cannot be catalyzed by beta-N-acetylhexosaminidase B (or presumably beta-N-acetylhexosaminidase S). This is also a lumped reaction, representing the cleavage of GalNAc4S or GalNAc6S and N-acetylgalactosamine 4-sulfatase or 6-sulfatase. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion - but unidirectional uptake into ER (to avoid loops w/ NAD/NADP) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion - but unidirectional uptake into ER (to avoid loops w/ NAD/NADP) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion - unidirectional to avoid NADP/NAD loops w/ free hydrogens NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion - but unidirectional output from ER (to avoid loops w/ NAD/NADP) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion - unidirectional to avoid NADP/NAD loops w/ potential for free H NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: it

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion - but unidirectional output from ER (to avoid loops w/ NAD/NADP) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Alpha-galactosidase B NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Alpha-galactosidase B NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 3.2.1.- This reaction is my best guess at how the GlcNAc-beta-1,6-GalNAc linkage is cleaved. NCD

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: AMF TDV (8/25/2005, stoichiometry changed)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions. . Presence in the nucleus

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions Presence in the nucleus

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions Presence in the nucleus

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions Presence in the nucleus

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions Presence in the nucleus

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Many nucleoside diphosphates (eight described) can act as acceptors. While many ribo- and deoxyribonucleoside triphosphates can act as donors, only ATP is chosen as a donor to minimize the number of total reactions Presence in the nucleus

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no gene or enzyme name known (in kegg) but reaction has to take place. IT

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: it

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: it

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: interaction between peroxisomes and ER (some enzymes on the outer membrane) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: interaction between peroxisomes and ER (some enzymes on the outer membrane) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: interaction between peroxisomes and ER (some enzymes on the outer membrane) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: kh 1/7/03 SAB m

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: reaction sequence mx steps, grouped into single reaction uses adrenal ferredoxin NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: further oxidation of omega hydroxy LTB4 (leukotriene B4) stoichiometry inferrered - explicity primary literature refs not found NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT. human enzymes overexpressed on E.coli

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: for PC secretion into bile NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: 12372595 - expression; 16436377 - biochemical, tissue-specific

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: See PMID: 10856717 - flippase activity NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: See PMID: 10856717 - flippase activity no detailed data on which compartment ATP hydrolysis occurs, so for the time being assumed to be cytosolic NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: 17888579 - kinetic characterization of human cytosolic form; 8325643 - homology to rat; 17211624 - immunohistochemistry for expression

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP Net reaction same as described in Lehringer 334 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from KEGG map. No enzyme assigned, so assumed this is a non-enzymatic reaction. NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV changed name to"tm" to indicate mitochondrial transport NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB m

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD FULLR corresponds to acyl/R groups in texts. NJ changed EC from 2.7.1.149 (pail5p) to 2.7.1.68 (pail4p) - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD FULLR corresponds to acyl/R groups in texts. NJ changed EC from 2.7.1.149 (pail5p) to 2.7.1.68 (pail4p) - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD Notice that contrary to some standards in texts, KEGG, etc, the Rtotal group accounts for the whole fatty acyl CoA (so the CHO only accounts for the core backbone), manner in which Rtotal was produced accounts for O and H balances. Formation of the Rtotal group (rxn flux)accounted for mass balance for CoA NJ changed EC from 2.7.1.149 (pail5p) to 2.7.1.68 (pail4p) - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Notice that contrary to some standards in texts, KEGG, etc, the Rtotal group accounts for the whole fatty acyl CoA (so the CHO only accounts for the core backbone), manner in which Rtotal was produced accounts for O and H balances. Formation of the Rtotal group (rxn flux)accounted for mass balance for CoA NJ changed EC from 2.7.1.149 (pail5p) to 2.7.1.68 (pail4p) - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: phosphatidyl choline degradation NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: phosphatidyl choline degradation NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal version - NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: interaction between peroxisomes and ER (some enzymes on the outer membrane) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 3.5.1- KEGG RXN R02973 RM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _01-25-05 based on Wang et al JBC, 1999,1 274(21), 14875-14888. IT 03-07-05:replaced IT: now based on Balamurugan et al, 2005, Am J Physiol Renal Physiol, 288, F823-831,2005

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV Short-chain fatty acid can diffuse through mitochondrial membrane

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD. Benzodiazepine receptor PBR see also 17168567

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: RS/TV (6/3/05) Peroxidases can act on a variety of substrates which are oxidized, not just methanol.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Mechanism not known, see PMID 11591435 for justification. NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Mechanism not known, see PMID 11591435 for justification. NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Mechanism not known, see PMID 11591435 for justification. NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: modified from TV version for hs NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: See PMID: 10856717 - flippase activity NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: See PMID: 10856717 - flippase activity no detailed data on which compartment ATP hydrolysis occurs, so for the time being assumed to be cytosolic NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: phosphatidylcholine as substrate NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: This reaction takes place in skin and needs UV 290-305. based on Vitamins, G.F.M. Ball,2004, Blackwell publishing, 1st ed (book) pg.194 IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR- added reversible form of PYNP2

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF changed name from "tm" to "t2m" - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - carnitine transporters not found, unknown mechanism intracellularly, however there must be a mechanism for FA transport NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.8.2- NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.8.2- NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.8.2- NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.8.2- NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.8.2.- NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: intracellular transport, mechanism details not presently known NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: intracellular transport, mechanism details not presently known NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SCP has two transcripts, second isoform specific to peroxisomes, first is specific for cyt and mit need to double check stoichiometry - reaction cofactors (additional coa + release of prop coa) from BM (Roche) Biochemical Pathways NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB based on PMID 12845534

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SGPL1 gene as per GeneCards states that hexadecanal is produced - the only way to do this and to maintain charge balance would be to have H2 gas as substrate - remarkably implausible. Due to lack of information to indicate otherwise, added water to breakdown components into ethamp and palmitate NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: AMF EC: 1.1.1.272

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SOAT11 and SOAT12 are templates, customized rxns can be formed particular ester moieties. NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport, may be vesicular/caveolar/other intracellular transport and extracellular export mechanisms must exist - see for example: PMID: 15585321 NJ

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism - reflects interaction between different stages of endosomes and cytoplasm NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism, however sphingosine manages to get in different compartments of cells. NOT presumed to be flip-flop. NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism, however sphingosine manages to get in different compartments of cells. NOT presumed to be flip-flop. NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - however must get to other intracellular compartments (e.g. lysosome for degradation) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - however must get to other intracellular compartments (e.g. lysosome for degradation) NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism, however sphs1p is known to have intracellular and extracellular activity and signal transduction functions (PMID: 10751414). NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism, however sphs1p is known to have intracellular and extracellular activity and signal transduction functions (PMID: 10751414 or PMID: 15585321). NJ

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TV (8-15-2003)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: This is a lumped reaction: Rxn 1: 2 frdp -> 2 ppi + presqualene diphosphate Rxn 2: presqualene diphosphate + NADPH -> squalene + NADP NCD ER version - NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: see PMID: 14643063 there are actually two types, but the difference between them lies in optimal pH function - grouped as one reaction at his point to eliminate redundancy. NADP known to be cofactor NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: there are actually two types, but the difference between them lies in optimal pH function - grouped as one reaction at his point to eliminate redundancy. NADP known to be cofactor NJ. human 5alpha-HSD activity determined in transfected COS cells using C-14 labelled testosterone as substrate

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD. Biochemical, Genetic

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MIPS: cofactor ATP IF changed EC from 6.2.1.4 to 6.2.1.5 - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT reaction involved in formation of 4-hydroxybenzoate from tyrosine.

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB based on PMID 10727395

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: TDV (2-6-2003)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD,IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _01-25-05 IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB see Kanai and Hediger 2004 (2003), PMID 14530974

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

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+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: also EC 2.7.6.2 - NCD

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: interaction between peroxisomes and ER (some enzymes on the outer membrane) NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Xia et al, 2003, JBC, 2141-2146

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Xia et al, 2003, JBC, 2141-2146

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB unlumped version of TRPHYDRO1

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: specific mechanism not known, proton dependence for trans-mit transport has been suggested, however directionality and stoichiometry has not yet been elucidated. see PMID: 12770731 and others NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

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+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

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+ + + +

Confidence Level: 0.0

+ +
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+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - there are UDPACGAL-translocators for ER and Golgi, however no info on lysosomal - poor support for this NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

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+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

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+ + + +

Confidence Level: 0.0

+

NOTES: JLR

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+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

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+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

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+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: unknown mechanism for transport - not known if it is energy dependent or not, recycling and IC transport is important to get it to other areas of the cell (e.g. plasma membrane) - translocators have been found for ER and Golgi - none found for lysosome yet so non-mechanistic transporter added - in future this will need to be revised _when_ a translocator is found NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
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+ + + +

Confidence Level: 0.0

+

NOTES: NCD

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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

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+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

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+ + + +

Confidence Level: 0.0

+

NOTES: NCD

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+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NJ

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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

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+ + + +

Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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+ + + +

Confidence Level: 0.0

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+ + + +

Confidence Level: 0.0

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+ + + +

Confidence Level: 0.0

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+ + + +

Confidence Level: 0.0

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+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

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+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB balanced

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

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+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

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+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: This reaction takes place in skin and needs body temperature based on Vitamins, G.F.M. Ball,2004, Blackwell publishing, 1st ed (book) pg.194 IT

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: from uniprot and lit - see human recon lit refs divalent cation requirement - unclear which one, reaction inhibited in the presence of EDTA (may just be MgATP or MgATP) - see Kelley and Vessey Biochimica et Biophysica Acta (1994) 1209: 51-55 temporarily will have H+ balance reaction NJ

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: details of metabolism, etc are unknown - allwoed to be exported presently - unknown mechanism NJ

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: cholesterol precursor, transport by "diffusion" -> actually beleived to be flip-flop mechanism (PMID: 12840657). NJ

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: immunocytochemistry, subcellular fractionation, and electron microscopy have demonstrated that xylosylation begins in the ER and continues in the early Golgi [Kearns, J Biol Chem 1993] PMID: 8496172 NCD

+ +
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+ + + +

Confidence Level: 0.0

+ +
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+ + + +

Confidence Level: 0.0

+

NOTES: NCD

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+ + + +

Confidence Level: 0.0

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NOTES: NCD

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+ + + +

Confidence Level: 0.0

+ +
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+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
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+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT - fixed proton

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+ + + +

Confidence Level: 0.0

+ +
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+ + + +

Confidence Level: 0.0

+

NOTES: IT - fixed proton

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+ + + +

Confidence Level: 0.0

+ +
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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: MM

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Hunt MC, Alexson SEH. (2008). Progress in Lipid Research 47: 405-21

+

Confidence Level: 0.0

+

NOTES: dicarboxylic coa synthetase, origin and gene not known

+ +
+ + + + + + + + + + +
+ + + +

References: Glatz JFC, Luiken JJFP, Bonen A. (2010). Physiological Reviews 90: 367-417, Kamp F, Hamilton JA. (2006). Prostaglandins, Leukotrienes and Essential Fatty Acids 75: 149-59, PMCID: PMC2785172, Evtodienko VY, Bondarenko DI, Antonenko YN. (1999). Biochimica et Biophysica Acta (BBA) - Biomembranes 1420: 95-103

+

Confidence Level: 0.0

+

NOTES: simple diffusion of fatty acids freely across membranes

+ +
+ + + + + + +
+ + + +

References: Westin M, Hunt M, Alexson S. (2008). Cellular and Molecular Life Sciences 65: 982-90,

+

Confidence Level: 0.0

+

NOTES: alternatively peroxisomal carnitine O-octanoyltransferase may convert adipoyl coa into adipoyl carnitine and excreted out. Thioesterases and CRAT/CROT show same substrate specificty and similar Vmax and Km values, however author suggested there is no competition as they are expressed differentially in different tissues.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Westin MAK, Hunt MC, Alexson SEH. (2005). Journal of Biological Chemistry 280: 38125-32

+

Confidence Level: 0.0

+

NOTES: human peroxisomal thioesterases are ACOT-4 and ACOT-8. ACOT 4 is specific for C4DC and C5DC, where as ACOT-8 catalyzes wide range of substrates. One proton added to the product for balancing

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Westin M, Hunt M, Alexson S. (2008). Cellular and Molecular Life Sciences 65: 982-90. doi:10.1006/mgme.2000.3055,doi:10.1006/bbrc.1999.1340,biochimica et biophysica acta 1546 (2001) 21-43

+

Confidence Level: 0.0

+

NOTES: acyl carnitines transported by CACT.

+ +
+ + + + + + + + + +
+ + + +

References: doi:10.1016/j.physletb.2003.10.071

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Westin MAK, Hunt MC, Alexson SEH. (2005). Journal of Biological Chemistry 280: 38125-32

+

Confidence Level: 0.0

+

NOTES: human peroxisomal thioesterases are ACOT-4 and ACOT-8. ACOT 4 is specific for C4DC and C5DC, where as ACOT-8 catalyzes wide range of substrates. One proton added to the product for balancing

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Hunt MC, Alexson SEH. (2008). Progress in Lipid Research 47: 405-21

+

Confidence Level: 0.0

+

NOTES: dicarboxylic coa synthetase, origin and gene not known

+ +
+ + + + + + + + + + +
+ + + +

References: Glatz JFC, Luiken JJFP, Bonen A. (2010). Physiological Reviews 90: 367-417, Kamp F, Hamilton JA. (2006). Prostaglandins, Leukotrienes and Essential Fatty Acids 75: 149-59, PMCID: PMC2785172, Evtodienko VY, Bondarenko DI, Antonenko YN. (1999). Biochimica et Biophysica Acta (BBA) - Biomembranes 1420: 95-103

+

Confidence Level: 0.0

+

NOTES: simple diffusion of fatty acids freely across membranes

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: biochemical and biophysical research communications 263,213-218(1999),biochimica et biophysica acta 1546(2001)21-43

+

Confidence Level: 0.0

+ +
+ + + + + + + + + +
+ + + +

References: PMCID: PMC2914534

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Biochemica et Biophysica Acta 1486(2000) 1-17, Eur. J. Biochem. 244, 1-14 (1997) FEBS 1997, Biochemica et Biophysica Acta 1546(2001) 21-43.

+

Confidence Level: 0.0

+

NOTES: CPT-2 reaction

+ +
+ + + + + + + + + + + +
+ + + +

References: Westin M, Hunt M, Alexson S. (2008). Cellular and Molecular Life Sciences 65: 982-90. doi:10.1006/mgme.2000.3055,doi:10.1006/bbrc.1999.1340,biochimica et biophysica acta 1546 (2001) 21-43

+

Confidence Level: 0.0

+

NOTES: acyl carnitines transported by CACT.

+ +
+ + + + + + + + + +
+ + + +

References: biochimica et biophysica acta 1546(2001)21-43

+

Confidence Level: 0.0

+

NOTES: should be noted that shortchain acylcarnitines are freely permeable accross membrane

+ +
+ + + + + + + + + +
+ + + +

References: biochimica et biophysica acta 1546(2001)21-43

+

Confidence Level: 0.0

+ +
+ + + + + + + + + +
+ + + +

References: the journal of biological chemistry volume280,no.1,issue of january,pp.738-744,2005

+

Confidence Level: 0.0

+

NOTES: crot shows activity for C6 to C10 fatty acylcoa, however some amont of activity for short chain fattyacylcoa also. The exit from peroxisomes can also be at the hexanoylcoa stage which is more frequently observed.however some levels of activity is also seen at the bytyrylcoa stage.

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: the journal of biological chemistry,vol 280, no1,issue of january 7,pp 738-744,2005

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

References: biochimica et biophysica acta 1546(2001)21-43

+

Confidence Level: 0.0

+

NOTES: short and medium chain acylcarnitines are also freely permeable accros the membrane.

+ +
+ + + + + + + + + +
+ + + +

References: Westin M, Hunt M, Alexson S. (2008). Cellular and Molecular Life Sciences 65: 982-90. doi:10.1006/mgme.2000.3055,doi:10.1006/bbrc.1999.1340,biochimica et biophysica acta 1546 (2001) 21-43

+

Confidence Level: 0.0

+

NOTES: acyl carnitines transported by CACT.

+ +
+ + + + + + + + + +
+ + + +

References: doi:10.1016/j.physletb.2003.10.071

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: doi:10.1016/j.physletb.2003.10.071

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + +
+ + + +

References: doi:10.1006/mgme.2000.3055,doi:10.1006/bbrc.1999.1340,biochimica et biophysica acta 1546 (2001) 21-43

+

Confidence Level: 0.0

+

NOTES: mentioned in recon1 as SCP22x. CACT activity has been reported in peroxisomes and they mediate transfer of acylcarnitine from peroxisomes to cytosol and then furher uptake into mitochondria.CACT are concentration dependant,uniport transporters acting in ping-pong mechanism. Synonym is CACT

+ +
+ + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: free fatty acids transported by simple diffusion, fatty acid transport proteins may be involved. Depends on the physiological concentration of these fatty acids.

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: free fatty acids transported by simple diffusion, fatty acid transport proteins may be involved. Depends on the physiological concentration of these fatty acids.

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: acyl coA dehydrogenase enzyme catalyzes this reaction in mitochondria.first step of beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal acyl coA oxidase reaction.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal beta oxidation reaction.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: PNAS August 1, 1992 vol. 89 no. 15 6673-6677, FEBS LETTERS vol.215 no.2 228-232

+

Confidence Level: 0.0

+

NOTES: delta3-cis->delta 2-trans isomerase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: 2,4-dienoyl coA reductase catalyzes this reaction in mitochondria.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: "Journal of Molecular Biology, Volume 342, Issue 4, 24 September 2004, Pages 1197-1208"

+

Confidence Level: 0.0

+

NOTES: cis-delta3->trans-delta2 isomerase

+ +
+ + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: 2,4-dienoyl coA reductase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: PNAS August 1, 1992 vol. 89 no. 15 6673-6677, FEBS LETTERS vol.215 no.2 228-232

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: one cycle of beta oxidation occurs in mitochondria

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: "Journal of Molecular Biology, Volume 342, Issue 4, 24 September 2004, Pages 1197-1208"

+

Confidence Level: 0.0

+

NOTES: delta3-cis/trans-->delta2-trans-enoyl coA isomerase enzyme catalyzes this reaction in mitochondria.

+ +
+ + + + + + + + + +
+ + + +

References: PNAS August 1, 1992 vol. 89 no. 15 6673-6677, FEBS LETTERS vol.215 no.2 228-232

+

Confidence Level: 0.0

+

NOTES: delta3-cis->delta 2-trans isomerase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: "Journal of Molecular Biology, Volume 342, Issue 4, 24 September 2004, Pages 1197-1208"

+

Confidence Level: 0.0

+

NOTES: cis-delta3->trans-delta2 isomerase

+ +
+ + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB00387

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: The Tohoku Journal of Experimental Medicine.Vol. 221 (2010) , No. 3 pp.191-195

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Westin M, Hunt M, Alexson S. (2008). Cellular and Molecular Life Sciences 65: 982-90. doi:10.1006/mgme.2000.3055,doi:10.1006/bbrc.1999.1340,biochimica et biophysica acta 1546 (2001) 21-43

+

Confidence Level: 0.0

+

NOTES: acyl carnitines transported by CACT.

+ +
+ + + + + + + + + +
+ + + +

References: Korman SH, Waterham HR, Gutman A, Jakobs C, Wanders RJA. (2005). Molecular Genetics and Metabolism 86: 337-43

+

Confidence Level: 0.0

+

NOTES: elevated in urine in C-12 dicarboxylic aciduria

+ +
+ + + + + + + + + + + + + + + +
+ + + +

References: Westin M, Hunt M, Alexson S. (2008). Cellular and Molecular Life Sciences 65: 982-90,

+

Confidence Level: 0.0

+

NOTES: alternatively peroxisomal carnitine O-octanoyltransferase may convert adipoyl coa into adipoyl carnitine and excreted out. Thioesterases and CRAT/CROT show same substrate specificty and similar Vmax and Km values, however author suggested there is no competition as they are expressed differentially in different tissues.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal beta oxidation reaction

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB02095,

+

Confidence Level: 0.0

+

NOTES: as a C3DC.HMDB02095,PMID: 12651823

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal beta oxidation reaction

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: PMCID: PMC2702680

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal acyl coA oxidase reaction.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: "Journal of Molecular Biology, Volume 342, Issue 4, 24 September 2004, Pages 1197-1208"

+

Confidence Level: 0.0

+ +
+ + + + + + + + + +
+ + + +

References: PNAS August 1, 1992 vol. 89 no. 15 6673-6677, FEBS LETTERS vol.215 no.2 228-232

+

Confidence Level: 0.0

+

NOTES: delta3-cis->delta 2-trans isomerase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: 2,4-dienoyl coA reductase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: PMCID: PMC2702680

+

Confidence Level: 0.0

+

NOTES: acyl coA dehydrogenase

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: "Journal of Molecular Biology, Volume 342, Issue 4, 24 September 2004, Pages 1197-1208"

+

Confidence Level: 0.0

+

NOTES: cis-delta3->trans-delta2 isomerase

+ +
+ + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: 2,4-dienoyl coA reductase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: to acetyl coA and accumulates and then combines with free carnitine and ultimately excreated in urine

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: PMCID:PMC1152672

+

Confidence Level: 0.0

+

NOTES: the enzyme is not yet charecterized at the molecular level.this evidence taken from mouse experiment.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: harpers biochemistry-25th edition-page no.242.

+

Confidence Level: 0.0

+

NOTES: "the dehydrogenase action can also be catalyzed by ACAD9 gene(Biochemical and Biophysical Research Communications,Volume 297, Issue 4, 4 October 2002, Pages 1033-1042)

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: journal of lipid research 1998 vol 39 pages 2161-2171

+

Confidence Level: 0.0

+

NOTES: peroxisomal beta oxidation reaction

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: "Journal of Molecular Biology, Volume 342, Issue 4, 24 September 2004, Pages 1197-1208 5.3.3.8

+

Confidence Level: 0.0

+

NOTES: cis-delta3->trans-delta2 isomerase

+ +
+ + + + + + + + + +
+ + + +

References: PNAS August 1, 1992 vol. 89 no. 15 6673-6677, FEBS LETTERS vol.215 no.2 228-232

+

Confidence Level: 0.0

+

NOTES: delta3-cis->delta 2-trans isomerase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: "Journal of Molecular Biology, Volume 342, Issue 4, 24 September 2004, Pages 1197-1208"

+

Confidence Level: 0.0

+

NOTES: cis-delta3->trans-delta2 isomerase

+ +
+ + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal acyl coA oxidase reaction.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: journal of lipid research 1998 vol 39 pages 2161-2171

+

Confidence Level: 0.0

+

NOTES: peroxisomal beta oxidation reaction

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: one cycle of beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: journal of lipid research 1998 vol 39 pages 2161-2171

+

Confidence Level: 0.0

+

NOTES: peroxisomal beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: PMCID: PMC2702680

+

Confidence Level: 0.0

+

NOTES: acyl coA dehydrogenase

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal acyl coA oxidase reaction.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: "Journal of Molecular Biology, Volume 342, Issue 4, 24 September 2004, Pages 1197-1208"

+

Confidence Level: 0.0

+

NOTES: cis-delta3->trans-delta2 isomerase

+ +
+ + + + + + + + + +
+ + + +

References: PNAS August 1, 1992 vol. 89 no. 15 6673-6677, FEBS LETTERS vol.215 no.2 228-232

+

Confidence Level: 0.0

+

NOTES: delta3-cis->delta 2-trans isomerase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: one cycle of beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: 2,4-dienoyl coA reductase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: 2,4-dienoyl coA reductase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: PMCID: PMC2702680

+

Confidence Level: 0.0

+

NOTES: acyl coA dehydrogenase

+ +
+ + + + + + + + + + + +
+ + + +

References: "Journal of Molecular Biology, Volume 342, Issue 4, 24 September 2004, Pages 1197-1208"

+

Confidence Level: 0.0

+

NOTES: cis-delta3->trans-delta2 isomerase

+ +
+ + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: 2,4-dienoyl coA reductase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: "Journal of Molecular Biology, Volume 342, Issue 4, 24 September 2004, Pages 1197-1208"

+

Confidence Level: 0.0

+

NOTES: cis-delta3->trans-delta2 isomerase

+ +
+ + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: PMCID:PMC1152672

+

Confidence Level: 0.0

+

NOTES: undergoes series of beta oxidation cycles to generate C8DC,C6DC,C4DC and acetate. The extra one proton was obtained in the product, from the aldehyde form of the omega-hydroxy palmitic acid (i.e. An intermediate not shown in this reaction). This was done in-order to balance the reaction and also to obtain the dicarboxylic form of the palmitic acid.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: first cycle of mitochondrial beta oxidation.

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: 2,4-dienoyl coA reductase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: "Journal of Molecular Biology, Volume 342, Issue 4, 24 September 2004, Pages 1197-1208"

+

Confidence Level: 0.0

+

NOTES: cis-delta3->trans-delta2 isomerase

+ +
+ + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: international journal of molecular medicine 19: 81-87, 2007.

+

Confidence Level: 0.0

+

NOTES: mitochondrial beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: peroxisomal beta oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: acyl coA binding protein is localized in cytosol, nucelus, golgi, E.R mitochondrial inter memebrane space. In mitochondria its released when the integrity of the organelle is compromised. It has wide role in lipid metabolism, also acts as a coA transporter between different cellular compartments. can transport accumulated acyl coAs from cutosol into mitochondria for beta oxidation or into cytosol for either transport into other compartemnts or for elliciting signalling cascades.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: free fatty acids transported by simple diffusion, fatty acid transport proteins may be involved. Depends on the physiological concentration of these fatty acids.

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: required for the production of short chain DC in peroxisomes. Alternatively C16 DC can also be produced from C18DC and other higher DC. Peroxisomes does not contain ACBP, so this reaction is irrerversible

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Biochemica et Biophysica Acta 1486(2000) 1-17, Eur. J. Biochem. 244, 1-14 (1997) FEBS 1997, Biochemica et Biophysica Acta 1546(2001) 21-43.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + +
+ + + +

References: Biochemica et Biophysica Acta 1486(2000) 1-17, Eur. J. Biochem. 244, 1-14 (1997) FEBS 1997, Biochemica et Biophysica Acta 1546(2001) 21-43.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + +
+ + + +

References: Biochemica et Biophysica Acta 1486(2000) 1-17, Eur. J. Biochem. 244, 1-14 (1997) FEBS 1997, Biochemica et Biophysica Acta 1546(2001) 21-43.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Westin MAK, Hunt MC, Alexson SEH. (2005). Journal of Biological Chemistry 280: 38125-32

+

Confidence Level: 0.0

+

NOTES: human peroxisomal thioesterases are ACOT-4 and ACOT-8. ACOT 4 is specific for C4DC and C5DC, where as ACOT-8 catalyzes wide range of substrates. One proton added to the product for balancing

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: already present in recon 1 but without coupled atp hydrolysis

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Hunt MC, Alexson SEH. (2008). Progress in Lipid Research 47: 405-21

+

Confidence Level: 0.0

+

NOTES: dicarboxylic coa synthetase, origin and gene not known

+ +
+ + + + + + + + + + +
+ + + +

References: Glatz JFC, Luiken JJFP, Bonen A. (2010). Physiological Reviews 90: 367-417, Kamp F, Hamilton JA. (2006). Prostaglandins, Leukotrienes and Essential Fatty Acids 75: 149-59, PMCID: PMC2785172, Evtodienko VY, Bondarenko DI, Antonenko YN. (1999). Biochimica et Biophysica Acta (BBA) - Biomembranes 1420: 95-103

+

Confidence Level: 0.0

+

NOTES: simple diffusion of fatty acids freely across membranes

+ +
+ + + + + + +
+ + + +

References: Westin M, Hunt M, Alexson S. (2008). Cellular and Molecular Life Sciences 65: 982-90,

+

Confidence Level: 0.0

+

NOTES: alternatively peroxisomal carnitine O-octanoyltransferase may convert adipoyl coa into adipoyl carnitine and excreted out. Thioesterases and CRAT/CROT show same substrate specificty and similar Vmax and Km values, however author suggested there is no competition as they are expressed differentially in different tissues.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Westin MAK, Hunt MC, Alexson SEH. (2005). Journal of Biological Chemistry 280: 38125-32

+

Confidence Level: 0.0

+

NOTES: human peroxisomal thioesterases are ACOT-4 and ACOT-8. ACOT 4 is specific for C4DC and C5DC, where as ACOT-8 catalyzes wide range of substrates. One proton added to the product for balancing

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Glatz JFC, Luiken JJFP, Bonen A. (2010). Physiological Reviews 90: 367-417, Kamp F, Hamilton JA. (2006). Prostaglandins, Leukotrienes and Essential Fatty Acids 75: 149-59, PMCID: PMC2785172, Evtodienko VY, Bondarenko DI, Antonenko YN. (1999). Biochimica et Biophysica Acta (BBA) - Biomembranes 1420: 95-103

+

Confidence Level: 0.0

+

NOTES: simple diffusion of fatty acids freely across membranes

+ +
+ + + + + + +
+ + + +

References: Westin M, Hunt M, Alexson S. (2008). Cellular and Molecular Life Sciences 65: 982-90. doi:10.1006/mgme.2000.3055,doi:10.1006/bbrc.1999.1340,biochimica et biophysica acta 1546 (2001) 21-43

+

Confidence Level: 0.0

+

NOTES: acyl carnitines transported by CACT.

+ +
+ + + + + + + + + +
+ + + +

References: Westin M, Hunt M, Alexson S. (2008). Cellular and Molecular Life Sciences 65: 982-90,

+

Confidence Level: 0.0

+

NOTES: alternatively peroxisomal carnitine O-octanoyltransferase may convert adipoyl coa into adipoyl carnitine and excreted out. Thioesterases and CRAT/CROT show same substrate specificty and similar Vmax and Km values, however author suggested there is no competition as they are expressed differentially in different tissues.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Hunt MC, Alexson SEH. (2008). Progress in Lipid Research 47: 405-21

+

Confidence Level: 0.0

+

NOTES: dicarboxylic coa synthetase, origin and gene not known

+ +
+ + + + + + + + + + +
+ + + +

References: Westin M, Hunt M, Alexson S. (2008). Cellular and Molecular Life Sciences 65: 982-90,

+

Confidence Level: 0.0

+

NOTES: alternatively peroxisomal carnitine O-octanoyltransferase may convert adipoyl coa into adipoyl carnitine and excreted out. Thioesterases and CRAT/CROT show same substrate specificty and similar Vmax and Km values, however author suggested there is no competition as they are expressed differentially in different tissues.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Westin MAK, Hunt MC, Alexson SEH. (2005). Journal of Biological Chemistry 280: 38125-32

+

Confidence Level: 0.0

+

NOTES: human peroxisomal thioesterases are ACOT-4 and ACOT-8. ACOT 4 is specific for C4DC and C5DC, where as ACOT-8 catalyzes wide range of substrates. One proton added to the product for balancing

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: PMCID: PMC1412501,

+

Confidence Level: 0.0

+

NOTES: Dipeptides and tripeptides enter the brush border of the intestinal mucosal cells, where they are hydrolyzed to free amino acids, which are then transported into hepatic portal vein. Peptides entering by transcellular or paracellular mechanisms elicit allergic reactions to food (Robert K. Murray, David A. Bender, Kathleen M. Botham, Peter J. kennelly, Victor W. Rodwell, P. Anthony Weil (2009) 28th edition, Harpers illustrated biochemistry,Mc Graw Hill, page 462). formation and hydrolysis of diglycine is a reversible process (David L. Nelson, Michael M. Cox, Lehniniger principles of biochemistry (2000), 3rd edition, worth publishers,page 69, figure 3a). CN1 is expressed in brain where as CN2 is more ubiquitously expressed (PMID: 12473676).

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: y+LAT1 and y+LAT2 transporters requires CD98 for sequesterization to the plasma membrane. Acts as an amino acid exchanger, with influx of neutral aminoa acids and efflux of cationic amino acid, requires Na+ for optimal activity. Can also operate with H+ in absence of Na+ (PMID: 11546643).

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: G.F.M. Ball (2006) Vitamins their role in the human body, Blackwell publishing, chapter 19, page 395-398,

+

Confidence Level: 0.0

+

NOTES: SVCT1 and SVCT2 differ in their tissue distribution, SVCT1 is more ubiquitously expressed, where as SVCT1 is confined to intestine, liver and kidney. The Na+ symport transport is energized by Na+/K+ ATPase, therefore its a secondary active transport ( G.F.M. Ball (2006) Vitamins their role in the human body, Blackwell publishing, chapter 19, page 395-398). Vitamin C is absorbed only in ascorbate form, can be oxidized into dehydroascorbate, and can then enter the blood stream (Sareen S. Gropper, Jack L. Smith, James L. Groff (2009) Advanced nutrition and human metabolism, Wadsworth cengage learning, 5th edition, page 312-313).

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: G.F.M. Ball (2006) Vitamins their role in the human body, Blackwell publishing, chapter 16, page 339-340.

+

Confidence Level: 0.0

+

NOTES: biotin release from the enterocytes along the baso-lateral membrane is carrier protein mediated, Na+ independant and eletroneutral (exact protein involved needs to be further investigated). However pantothenic acid seems to compete with biotin for uptake. also in the presence of pantothenate, more amount of biotin exits enterocytes (PMID: 10064315).

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

References: PMCID: PMC1665133,

+

Confidence Level: 0.0

+

NOTES: SNAT5 performs both symport with sodium and antiport with proton, for the net transport of neutral amino acid into the cell. Cellular localization has been reported in stomach, brain, liver, lung, small intestine, spleen, colon and kidney. (PMID: 12845534)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: y+LAT1 and y+LAT2 transporters requires CD98 for sequesterization to the plasma membrane. Acts as an amino acid exchanger, with influx of neutral aminoa acids and efflux of cationic amino acid, requires Na+ for optimal activity. Can also operate with H+ in absence of Na+ (PMID: 11546643).

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: PMCID: PMC1412501,

+

Confidence Level: 0.0

+

NOTES: Dipeptides and tripeptides enter the brush border of the intestinal mucosal cells, where they are hydrolyzed to free amino acids, which are then transported into hepatic portal vein. Peptides entering by transcellular or paracellular mechanisms elicit allergic reactions to food (Robert K. Murray, David A. Bender, Kathleen M. Botham, Peter J. kennelly, Victor W. Rodwell, P. Anthony Weil (2009) 28th edition, Harpers illustrated biochemistry,Mc Graw Hill, page 462). formation and hydrolysis of diglycine is a reversible process (David L. Nelson, Michael M. Cox, Lehniniger principles of biochemistry (2000), 3rd edition, worth publishers,page 69, figure 3a). CN1 is expressed in brain where as CN2 is more ubiquitously expressed (PMID: 12473676).

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: PMCID: PMC1665133,

+

Confidence Level: 0.0

+

NOTES: SNAT5 performs both symport with sodium and antiport with proton, for the net transport of neutral amino acid into the cell. Cellular localization has been reported in stomach, brain, liver, lung, small intestine, spleen, colon and kidney. (PMID: 12845534)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: PMCID: PMC1665133,

+

Confidence Level: 0.0

+

NOTES: SNAT5 performs both symport with sodium and antiport with proton, for the net transport of neutral amino acid into the cell. Cellular localization has been reported in stomach, brain, liver, lung, small intestine, spleen, colon and kidney. (PMID: 12845534)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: y+LAT1 and y+LAT2 transporters requires CD98 for sequesterization to the plasma membrane. Acts as an amino acid exchanger, with influx of neutral aminoa acids and efflux of cationic amino acid, requires Na+ for optimal activity. Can also operate with H+ in absence of Na+ (PMID: 11546643).

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: y+LAT1 and y+LAT2 transporters requires CD98 for sequesterization to the plasma membrane. Acts as an amino acid exchanger, with influx of neutral aminoa acids and efflux of cationic amino acid, requires Na+ for optimal activity. Can also operate with H+ in absence of Na+ (PMID: 11546643).

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: both pig(E.C. 3.4.11.5) and human (3.4.11.1) amino peptidase have similar amino acid sequence and catalytic properties (PMID: 1908238)

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: y+LAT1 and y+LAT2 transporters requires CD98 for sequesterization to the plasma membrane. Acts as an amino acid exchanger, with influx of neutral aminoa acids and efflux of cationic amino acid, requires Na+ for optimal activity. Can also operate with H+ in absence of Na+ (PMID: 11546643).

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0.0

+

NOTES: y+LAT1 and y+LAT2 transporters requires CD98 for sequesterization to the plasma membrane. Acts as an amino acid exchanger, with influx of neutral aminoa acids and efflux of cationic amino acid, requires Na+ for optimal activity. Can also operate with H+ in absence of Na+ (PMID: 11546643).

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

References: Sareen S. Gropper, jack L. Smith, James L. Groff (2009) Wadaworth cengage learning, Advanced nutrition and human metabolism, 5th edition, page 142-148.

+

Confidence Level: 0.0

+

NOTES: transported in chylomicrons into lymph

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: y+LAT1 and y+LAT2 transporters requires CD98 for sequesterization to the plasma membrane. Acts as an amino acid exchanger, with influx of neutral aminoa acids and efflux of cationic amino acid, requires Na+ for optimal activity. Can also operate with H+ in absence of Na+ (PMID: 11546643).

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: not much is known about the pantothenic acid exit across the basolateral membrane. Diffusion reaction is hypothetical. However, uptake of pantothenate by RBCs takes place by simple diffusion (G.F.M. Ball (2006) Vitamins their role in the human body, Blackwell publishing, chapter 15, page 329.).

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: ASCT1 helps in absorption of hydroxy-proline by aiding in its exit from the enterocytes into the blood stream. The ASCT1 transport system operates as an obligatory amino acid exchanger, Na+ depedant manner. Alaine is the preeferred susbstrate.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

References: no specific transporter for exit of D-alanine could be found, so diffusion mechanism is assumed.

+

Confidence Level: 0.0

+

NOTES: no specific transporter for exit of D-alanine could be found, so diffusion mechanism is assumed.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

References: Kim E. Barrett, Mark Donowitz (2001) Gastrointestinal transport: Molecular physiology, Academic press, A harcourt science and technology company, chapter 10, pages 389-391.

+

Confidence Level: 0.0

+

NOTES: ASCT-1 transport system operates at the basolateral surface, acts as an amino acid exchanger. Preferred substrates are small neutral amino acids, however shown to have transport proline and hydroxy-proline. At acidic ph also transports aspartate and glutamate. the ASCT-1 operates in a similar mechanism as ASCT-2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + +
+ + + +

References: Sareen S. Gropper, jack L. Smith, James L. Groff (2009) Wadaworth cengage learning, Advanced nutrition and human metabolism, 5th edition, page 143-144. charasuraisin, c. in short dissertation 19 (2008)

+

Confidence Level: 0.0

+

NOTES: re-formation of cholesterol ester within enterocytes, then exit in chylomicrons into the lymph.

+ +
+ + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: newly synthesized cholesterol may either be incorporated into membrane or transported out of enterocytes.

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

References: added during gap filling.

+

Confidence Level: 0.0

+

NOTES: added during gap filling.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

References: Davidson, N. O Magun, A. M. and Glickman, R. M. 2011. Enterocyte Lipid Absorption and Secretion. Comprehensive Physiology. 505?526, .

+

Confidence Level: 0.0

+

NOTES: Enterocytes stand next to liver in endogenous cholesterol synthesis. in rats they provide 25% of bodys cholesterol. the crypt epithelial cells synthesize maximum cholesterol when compared to other parts of the GI tract (PMCID: PMC292609). Reactions till farnesyl pyrophosphate operates in cytosol, however, further steps including squalene synthase operates in E.R (Harpers illustrated Biochemistry (2009) 28th edition, Lange medical publications, chapter 26, page 224-227). all the cholesterol synthesis enzymes have also been found in peroxisomes (PMID: 12121718), no evidence for enterocyte sub-cellular sites, so cytosolic reactions have been added according to Harper book. one proton added t product for elemental balancing.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Sareen S. Gropper, Jack L. Smith, James L. Groff (2009) Advanced nutrition and human metabolism, Wadsworth cengage learning, 5th edition, page 472-476.

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + +
+ + + +

References: required for cholesterol synthesis in E.R.

+

Confidence Level: 0.0

+

NOTES: required for cholesterol synthesis in E.R.

+ +
+ + + + + + +
+ + + +

References: Harpers illustrated Biochemistry (2009) 28th edition pages 174-183

+

Confidence Level: 0.0

+

NOTES: found in rats. HMP shunt reactions are cytosolic. Irreversible reaction, coefficient changed to 3

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: added during gap filling. No evidence found for such a reaction.

+

Confidence Level: 0.0

+

NOTES: added during gap filling. No evidence found for such a reaction.

+ +
+ + + + + + +
+ + + +

References: Kim E. Barrett, Mark Donowitz (2001) Gastrointestinal transport: Molecular physiology, Academic press, A harcourt science and technology company, chapter 10, pages 389-391.

+

Confidence Level: 0.0

+

NOTES: ASCT-1 transport system operates at the basolateral surface, acts as an amino acid exchanger. Preferred substrates are small neutral amino acids, however shown to have transport proline and hydroxy-proline. At acidic ph also transports aspartate and glutamate. the ASCT-1 operates in a similar mechanism as ASCT-2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

References: Harpers illustrated Biochemistry (2009) 28th edition pages 174-183

+

Confidence Level: 0.0

+

NOTES: coefficient changed to 3

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + +
+ + + +

References: Davidson, N. O Magun, A. M. and Glickman, R. M. 2011. Enterocyte Lipid Absorption and Secretion. Comprehensive Physiology. 505?526, .

+

Confidence Level: 0.0

+

NOTES: Enterocytes stand next to liver in endogenous cholesterol synthesis. in rats they provide 25% of bodys cholesterol. the crypt epithelial cells synthesize maximum cholesterol when compared to other parts of the GI tract (PMCID: PMC292609). Reactions till farnesyl pyrophosphate operates in cytosol, however, further steps including squalene synthase operates in E.R (Harpers illustrated Biochemistry (2009) 28th edition, Lange medical publications, chapter 26, page 224-227). all the cholesterol synthesis enzymes have also been found in peroxisomes (PMID: 12121718), no evidence for enterocyte sub-cellular sites, so cytosolic reactions have been added according to Harper book.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + +
+ + + +

References: PMCID: PMC1820816.

+

Confidence Level: 0.0

+

NOTES: for regeneration of nad in peroxisomes, for providing nad to the beta oxidation

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: added during gap-filling, no evidence for such a reaction. only assumed.

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: added during gap filling. Assumption that such a reaction can exist. Mamalian peroxisome do not contain malate dehydrogenase.

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Davidson, N. O Magun, A. M. and Glickman, R. M. 2011. Enterocyte Lipid Absorption and Secretion. Comprehensive Physiology. 505?526, .

+

Confidence Level: 0.0

+

NOTES: Enterocytes stand next to liver in endogenous cholesterol synthesis. in rats they provide 25% of bodys cholesterol. the crypt epithelial cells synthesize maximum cholesterol when compared to other parts of the GI tract (PMCID: PMC292609). Reactions till farnesyl pyrophosphate operates in cytosol, however, further steps including squalene synthase operates in E.R (Harpers illustrated Biochemistry (2009) 28th edition, Lange medical publications, chapter 26, page 224-227). all the cholesterol synthesis enzymes have also been found in peroxisomes (PMID: 12121718), no evidence for enterocyte sub-cellular sites, so cytosolic reactions have been added according to Harper book.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Sareen S. Gropper, Jack L. Smith, James L. Groff (2009) Advanced nutrition and human metabolism, Wadsworth cengage learning, 5th edition, page 350.

+

Confidence Level: 0.0

+

NOTES: absorbed folate undergoes conversion to 5-methyl-THF within the enterocytes.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +

References: Sareen S. Gropper, jack L. Smith, James L. Groff (2009) Wadaworth cengage learning, Advanced nutrition and human metabolism, 5th edition, page 194-196

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Harpers illustrated Biochemistry (2009) 28th edition pages 174-183

+

Confidence Level: 0.0

+

NOTES: coefficient changed to 3

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: feline leukemia virus subgroup receptor c is responsible for heme transport into the protal blood.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Davidson, N. O Magun, A. M. and Glickman, R. M. 2011. Enterocyte Lipid Absorption and Secretion. Comprehensive Physiology. 505?526, .

+

Confidence Level: 0.0

+

NOTES: Enterocytes stand next to liver in endogenous cholesterol synthesis. in rats they provide 25% of bodys cholesterol. the crypt epithelial cells synthesize maximum cholesterol when compared to other parts of the GI tract (PMCID: PMC292609). Reactions till farnesyl pyrophosphate operates in cytosol, however, further steps including squalene synthase operates in E.R (Harpers illustrated Biochemistry (2009) 28th edition, Lange medical publications, chapter 26, page 224-227). all the cholesterol synthesis enzymes have also been found in peroxisomes (PMID: 12121718), no evidence for enterocyte sub-cellular sites, so cytosolic reactions have been added according to Harper book. one proton added to substrate for elemental balancing.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + +
+ + + +

References: added during gap-filling.

+

Confidence Level: 0.0

+

NOTES: added during gap-filling.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: putriscine uptake by the cells via passive diffusion, reported to be more rapid at the basolateral side.

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

References: Harpers illustrated Biochemistry (2009) 28th edition pages 174-183

+

Confidence Level: 0.0

+

NOTES: coefficient changed to 2

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: HMDB01348

+

Confidence Level: 0.0

+

NOTES: Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hepatic cholesterol esterifying and cholesterol ester hydrolysing enzymes were characterized long ago in the rat [40]. This enzyme has maximal hydrolysing activity at pH 4.5-5.0, with some tailing to neutral pH. The hydrolase requires no co-factors, is stimulated by low concentrations of the surfactant Triton X-100, and is inhibited by sulfhydryl-blocking agents [21]. Stokke subsequently established that this acid cholesterol ester hydrolase (CEH) is of lysosomal origin in the calf, and presumably also in man [22].

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Phosphatidylinositol hydrolysis by phospholipase A2 and C activities in human peripheral blood neutrophils.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Phosphatidylinositol hydrolysis by phospholipase A2 and C activities in human peripheral blood neutrophils.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Lysophopshatidyl-choline (LPC) is derived from polar surface phosphatidylcholine (PC) of lipoproteins or from cell membrane-derived PC as a result of phospholipase A2 (PLA2) [8,9]. There is also a phospholipase A1 (PLA1), which is able to cleave the sn-1 ester bond [10]. Appreciable amounts of LPC are either formed in plasma by endothelial lipase [10] or by lecithin-cholesterol acyltransferase (LCAT) secreted from the liver to catalyse the transfer of fatty acids, preferentially linoleate which is in sn-2 position of phosphatidylcholine, to free cholesterol in plasma for the formation of cholesteryl esters [11]. Lysophospholipase substrates the reaction of LPC and water to carboxylate and glycerophosphocholine which is further converted to sn-glycerol-3-phosphate and choline by glycerophosphocholine phosphodiesterase. Glycerol-3-phosphate acyltransferase, located in both endoplasmic reticulum and mitochondrial, catalyses the formation of the lysoproduct LPA by the acylation of glycerol 3-phosphate. LPA may also be synthesized by PLA2 catalysed deacylation of phosphatidic acid (PA). PA is generated by the hydrolysis of PC by PC-specific phospholipase D (PLD) or the acylation of LPA by LPA acyl transferases. PA is an important metabolite involved in phospholipid biosynthesis and membrane remodeling. GPR association taken from Recon.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Hydrolysis of phosphatidylethanolamine by human pancreatic phospholipase A2.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: It seems likely that glycerol 1:2-cyclic phosphate has not previously been reported as a metabolic product of glycerylphosphorylcholine and glycerylphosphorylethanolamine decomposition because of its extreme acid-lability. This means that it is quickly hydrolysed in acid protein-denaturing agents, such as trichloroacetic acid. In addition, we have established that in tissues there is an Mg2+-dependent phosphodiesterase that can rapidly open the ring and produce glycerophosphate.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: sodium symport of acylcarnitine

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: It seems likely that glycerol 1:2-cyclic phosphate has not previously been reported as a metabolic product of glycerylphosphorylcholine and glycerylphosphorylethanolamine decomposition because of its extreme acid-lability. This means that it is quickly hydrolysed in acid protein-denaturing agents, such as trichloroacetic acid. In addition, we have established that in tissues there is an Mg2+-dependent phosphodiesterase that can rapidly open the ring and produce glycerophosphate.

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: acylarnitine transport by sodium symport

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: If these effects were truly competitive then 3-methylhistidine may be transferred across cell membranes by carrier(s) responsible for glutamine, asparagine and histidine transfer (system N) and/or systems L and ASC. If transport is via the glutamine carrier then the interference by leucine (a system L substrate) and cysteine (a typical ASC substrate) could be non-competitive as occurs in the case of the uptake of glutamine itself (Hundal et al. 1987).

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: If these effects were truly competitive then 3-methylhistidine may be transferred across cell membranes by carrier(s) responsible for glutamine, asparagine and histidine transfer (system N) and/or systems L and ASC. If transport is via the glutamine carrier then the interference by leucine (a system L substrate) and cysteine (a typical ASC substrate) could be non-competitive as occurs in the case of the uptake of glutamine itself (Hundal et al. 1987).

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: If these effects were truly competitive then 3-methylhistidine may be transferred across cell membranes by carrier(s) responsible for glutamine, asparagine and histidine transfer (system N) and/or systems L and ASC. If transport is via the glutamine carrier then the interference by leucine (a system L substrate) and cysteine (a typical ASC substrate) could be non-competitive as occurs in the case of the uptake of glutamine itself (Hundal et al. 1987).

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction,diffusion is assumed.

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction, diffusion assumed.

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction, transport mechanism similar to L-carnitine is assumed.

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction, transport mechanism similar to L-carnitine is assumed.

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction, transport mechanism similar to thymine is assumed.

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction,diffusion is assumed.

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: pentose sugar, same as ribose

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: pentose sugar, same as ribose

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction,diffusion is assumed.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction,diffusion is assumed.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction,diffusion is assumed.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction,diffusion is assumed.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Energy involved in long chain fatty acid efflux. We surmised that E. coli already possesses the ability to secrete FFA via native drug efflux pumps or other transport machinery and sought to identify the genes responsible in this study such that they could be overexpressed to allow improved production of FFA.

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Energy required for efflux of long chain fatty acids. We surmised that E. coli already possesses the ability to secrete FFA via native drug efflux pumps or other transport machinery and sought to identify the genes responsible in this study such that they could be overexpressed to allow improved production of FFA.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction,diffusion is assumed.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The transport of leukotriene C4 (LTC4) in membrane vesicles prepared from KCP-4 cells was facilitated by an ATP-dependent pump that appeared very similar to the GS-X pump. Transport mechanism similar to LTC4 is assumed.

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: ABC transport for very long chain fatty acids

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction,diffusion is assumed.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Glycolic acid (or hydroxyacetic acid) is the smallest alpha-hydroxy acid (AHA). In its pure form, glycolic acid is a colorless crystalline solid. Due to its excellent capability to penetrate skin, glycolic acid finds applications in skin care products, most often as a chemical peel. Glycolic acid is also used for tattoo removal. (HMDB00115). No evidence for such reaction, diffusion is assumed.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Competitive inhibition of malonate uptake by eosin and inorganic anions, strongly implies that a common route exists for both inorganic anions and organic dianions, namely the anion-exchange Band 3 protein. 14C-Malonate which is nonmetabolized in the erythrocyte, could be a useful probe for monitoring anion-exchange in reconstituted Band 3 systems.

+ +
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+ + + +

Confidence Level: 0.0

+

NOTES: Competitive inhibition of malonate uptake by eosin and inorganic anions, strongly implies that a common route exists for both inorganic anions and organic dianions, namely the anion-exchange Band 3 protein. 14C-Malonate which is nonmetabolized in the erythrocyte, could be a useful probe for monitoring anion-exchange in reconstituted Band 3 systems.

+ +
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+ + + +

Confidence Level: 0.0

+

NOTES: In agreement with these observations, brain mitochondrial swelling experiments indicate that MMA is an important inhibitor of succinate transport by the dicarboxylate carrier.

+ +
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+ + + +

Confidence Level: 0.0

+

NOTES: In agreement with these observations, brain mitochondrial swelling experiments indicate that MMA is an important inhibitor of succinate transport by the dicarboxylate carrier.

+ +
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+ + + +

Confidence Level: 0.0

+

NOTES: In agreement with these observations, brain mitochondrial swelling experiments indicate that MMA is an important inhibitor of succinate transport by the dicarboxylate carrier.

+ +
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+ + + +

Confidence Level: 0.0

+

NOTES: In agreement with these observations, brain mitochondrial swelling experiments indicate that MMA is an important inhibitor of succinate transport by the dicarboxylate carrier.

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+ + + +

Confidence Level: 0.0

+

NOTES: acylarnitine transport by diffusion

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+ + + +

Confidence Level: 0.0

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+ + + +

Confidence Level: 0.0

+

NOTES: The transport of leukotriene C4 (LTC4) in membrane vesicles prepared from KCP-4 cells was facilitated by an ATP-dependent pump that appeared very similar to the GS-X pump. Transport mechanism similar to LTC4 is assumed.

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+ + + +

Confidence Level: 0.0

+

NOTES: The transport of leukotriene C4 (LTC4) in membrane vesicles prepared from KCP-4 cells was facilitated by an ATP-dependent pump that appeared very similar to the GS-X pump. Transport mechanism similar to LTC4 is assumed.

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

+

NOTES: transport of long chain fatty acids by diffusion

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+ + + +

Confidence Level: 0.0

+

NOTES: no evidence for such reaction, diffusion is assumed.

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Confidence Level: 0.0

+

NOTES: curation of Harvey. Addition of new rxns to Recon for enabling accurate whole-body physiology. Genes/proteins for the metabolic reactions occurance in the respective organ come from Human proteome data by Kim et al. Corresponding metabolites needed to be mentioned with transport reactions.

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Confidence Level: 0.0

+

NOTES: curation of Harvey. Addition of new rxns to Recon for enabling accurate whole-body physiology. Genes/proteins for the metabolic reactions occurance in the respective organ come from Human proteome data by Kim et al. Corresponding metabolites needed to be mentioned with transport reactions.

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Confidence Level: 0.0

+

NOTES: curation of Harvey. Addition of new rxns to Recon for enabling accurate whole-body physiology. Genes/proteins for the metabolic reactions occurance in the respective organ come from Human proteome data by Kim et al. Corresponding metabolites needed to be mentioned with transport reactions.

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Confidence Level: 0.0

+

NOTES: curation of Harvey. Addition of new rxns to Recon for enabling accurate whole-body physiology. Genes/proteins for the metabolic reactions occurance in the respective organ come from Human proteome data by Kim et al. Corresponding metabolites needed to be mentioned with transport reactions.

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References: HMDB00115

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Confidence Level: 0.0

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NOTES: Glycolic acid (or hydroxyacetic acid) is the smallest alpha-hydroxy acid (AHA). In its pure form, glycolic acid is a colorless crystalline solid. Due to its excellent capability to penetrate skin, glycolic acid finds applications in skin care products, most often as a chemical peel. Glycolic acid is also used for tattoo removal.

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Confidence Level: 0.0

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NOTES: Phenylethylamine produces tyramine via alterantive dopamine biosysnthesis pathway

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Confidence Level: 0.0

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NOTES: Tyramine produces dopamine via alterantive dopamine biosynthesis pathway, via CYP2D catalysis

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Confidence Level: 0.0

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NOTES: Added during debugging the metabolomic data sets, to enable their uptake by kidney and flux consistency in blood circulation.

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Confidence Level: 0.0

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NOTES: Added during debugging the metabolomic data sets, to enable their uptake by kidney and flux consistency in blood circulation.

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NOTES: Added during debugging the metabolomic data sets, to enable their uptake by kidney and flux consistency in blood circulation.

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NOTES: Added during debugging the metabolomic data sets, to enable their uptake by kidney and flux consistency in blood circulation.

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NOTES: Added during debugging the metabolomic data sets, to enable their uptake by kidney and flux consistency in blood circulation.

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NOTES: Added during debugging the metabolomic data sets, to enable their uptake by kidney and flux consistency in blood circulation.

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NOTES: Added during debugging the metabolomic data sets, to enable their uptake by kidney only, and not other organs.

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NOTES: Added during debugging the metabolomic data sets, to enable their uptake by kidney only, and not other organs.

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NOTES: Added during debugging the metabolomic data sets, to enable their uptake by kidney only, and not other organs.

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NOTES: Added during debugging the metabolomic data sets, to enable their uptake by kidney only, and not other organs.

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Confidence Level: 0.0

+

NOTES: Added during debugging the metabolomic data sets, to enable their uptake by kidney only, and not other organs.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Added during debugging the metabolomic data sets, to enable their uptake by kidney only, and not other organs.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: No evidence found for such reaction, added for resolving deadend

+ +
+ + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from adipocyte model

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from adipocyte model

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from adipocyte model

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from adipocyte model

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from adipocyte model

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from adipocyte model

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from adipocyte model

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from adipocyte model

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from adipocyte model

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from RBC model

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from RBC model

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from RBC model

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from RBC model

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from RBC model

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from RBC model

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from RBC model

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR- reversible form of ACACT1

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: originally named AACTP NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP. Biochemical

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: r0277

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: tv renamed from CO2TPr to CO2t NCD

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: r0608, JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Human Y/N: Y

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: 6765112 - fluorescence of presence in human brain

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from RBC model

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Human Y/N: Y

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: EC 2.5.1.- NCD

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Needed in L-proline biosynthesis

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR - a reversible reaction that is otherwise identical to ZWF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Human Y/N: Y

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP. Same reaction as GAPDH, but localied to spermatids. NOTE: I think "glyceroyl" in this and many other reactions should be "glycerol There are "glyceroyl" compounds, but I don't think that is what is intended here.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: BRENDA also lists beta-Ala-His dipeptidase (E.C. 3.4.13.20) as another enzyme catalyzing this reaction, but no literature evidence found.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: most probable reaction. added during gap filling.

+

Confidence Level: 0.0

+

NOTES: most probable reaction. added during gap filling.

+ +
+ + + + + + + + +
+ + + +

References: Rubino A, Pierro M, Torretta GL, Vetrella M, Martino DD, Auricch S. (1969). Pediatric Research 3: 313-9

+

Confidence Level: 0.0

+

NOTES: prolidase 1 and 2 both have same E.C. Numbers, prolidase 1 has a substrate preference for glycylproline where as prolidase 2 catalyzes very slowly this reaction (PMID: 14580160).

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Human Y/N: Y

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Guanine and 6-mercaptopurine can replace hypoxanthine EC added (2.4.2.7 makes the same reaction) IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: tv

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: _2.6.1.42

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Human Y/N: Y

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Human Y/N: Y

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: tv renamed from O2TP to O2t to avoid confusion with transport reaction from cytosol to peroxisome NCD

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP Net reaction same as described in Lehringer 334

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from adipocyte model

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferase

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Specificity not completely determined. Can also catalyse ribosyltransferase reactions of the type catalysed by EC 2.4.2.5, nucleoside ribosyltransferasextsn

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP Two reactions for transketolase: TKT1 and TKT2

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP Two reactions for transketolase: TKT1 and TKT2

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP. 18840520 - expression data; 18456264 - protein purification; 2579079 - genetic, homology; 999837 - biochemical

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: used yeast system to overexpress gene to determine mutant kinetic properties

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Acts on a number of porphyrinogens, r0606

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from adipocyte model

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31. Not clear whether it is cytosolic but enzymes in this metabolism often are

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31. Rat

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: taken from adipocyte model

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Reaction from KEGG: an acylphosphate + H2O -> a carboxylate + phosphate

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: acetylglucosamine phosphate deacetylase; acetylaminodeoxyglucosephosphate acetylhydrolase; 2-acetamido-2-deoxy-D-glucose-6-phosphate amidohydrolase

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Only acetaldehyde considered for now. See also 1.2.1.4. Wide specificity, including oxidation of D-glucuronolactone to D-glucarate. Formerly EC 1.1.1.70; r0176

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR - Kegg R02705

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Previously EC 5.3.1.10

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: INVALID ECO TERM: IFH

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SMP Note no proton generation by the the reaction

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: D-Glucose, D-mannose, D-fructose, sorbitol and D-glucosamine can act as acceptors; ITP and dATP can act as donors. The liver isoenzyme has sometimes been called glucokinase. Same as 2.7.1.4

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Guanine (see GUAPRT) and 6-mercaptopurine can replace hypoxanthine

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB 2 H's on RHS are there to balance--not certain. enzymatic assay shows substrate used by aldehyde dehydrogenase in human liver

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR- added irreversible form of LCAD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Also see LDL_D

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IF

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Biochemical

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: IT

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Wide specificity for 5'-nucleotides Also see EC 3.1.3.31

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR- added proton to balance

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Previous EC number: 4.2.1.16. New EC number 4.3.1.19. Can't enter this

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: JLR

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: also EC 2.8.3.8 NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: SAB

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: NCD

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The authors conclude that mMpc1 and mMpc2 are essential components of the MPC in mammalian mitochondrial. Later it was determined that transport occurs primarily with symport of proton. Our current understanding is that two proteins, mitochondrial pyruvate carriers MPC1 and MPC2, form a hetero-oligomeric complex in the IMM to facilitate pyruvate transport. This step is required for mitochondrial pyruvate oxidation and carboxylation-critical reactions in intermediary metabolism that are dysregulated in several common diseases.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: Chalmers, R. A. and A. M. Lawson (1982). Organic Acids in Man: Analytical Chemistry, Biochemistry and Diagnosis of the Organic Acidurias. London, Chapman and Hall Ltd.

+

Confidence Level: 0.0

+

NOTES: A common clinical finding in maple syrup urine disease (MSUD) is increased concentrations in plasma and urine of valine, leucine, and isoleucine and their branched chain 2-keto- and 2-hydroxy acid metabolites. This is the result of partial, intermittent, or complete loss of activity of one or more components making up the branched chain 2-ketoacid dehydrogenase (BCKD) complex. Restricted oxidative decarboxylation of 2-ketoisovaleric, 2-ketoisocaproic, and 2-keto-3-methylvaleric acids to isobutyryl-CoA, isovaleryl-CoA, and 2-methylbutyryl-CoA, respectively, causes the accumulation of these 2-keto acids, and secondarily the amino acids, in tissues and fluids. The keto acids are also reduced to 2-hydroxyisovaleric, 2-hydroxyisocaproic, and 2-hydroxy-3-methylvaleric acids (probably by a L-lactate dehydrogenase), respectively, and these are also found increased in plasma and urine.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence found for such a transport reactions, diffusion is assumed. Dectected in saliva and urine (HMDB00317).

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

References: Chalmers, R. A. and A. M. Lawson (1982). Organic Acids in Man: Analytical Chemistry, Biochemistry and Diagnosis of the Organic Acidurias. London, Chapman and Hall Ltd.

+

Confidence Level: 0.0

+

NOTES: A common clinical finding in maple syrup urine disease (MSUD) is increased concentrations in plasma and urine of valine, leucine, and isoleucine and their branched chain 2-keto- and 2-hydroxy acid metabolites. This is the result of partial, intermittent, or complete loss of activity of one or more components making up the branched chain 2-ketoacid dehydrogenase (BCKD) complex. Restricted oxidative decarboxylation of 2-ketoisovaleric, 2-ketoisocaproic, and 2-keto-3-methylvaleric acids to isobutyryl-CoA, isovaleryl-CoA, and 2-methylbutyryl-CoA, respectively, causes the accumulation of these 2-keto acids, and secondarily the amino acids, in tissues and fluids. The keto acids are also reduced to 2-hydroxyisovaleric, 2-hydroxyisocaproic, and 2-hydroxy-3-methylvaleric acids (probably by a L-lactate dehydrogenase), respectively, and these are also found increased in plasma and urine.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence found for such a transport reactions, diffusion is assumed. Dectected in blood, csf, urine, feces, saliva and urine (HMDB00407).

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: In propionic acidemia, due to block in propionyl-CoA carboxylase reaction, during non-ketotic periods, when propionyl-CoA accumulation still occurs, two molecules of this substrate may condense via the action of a beta-ketothiolase to form 2-methyl-3-oxovaleryl-CoA, resulting ultimately in the excretion of 2-methyl-3-hydroxy-valeric acid and 2-methyl-3-oxovaleric acids in the urine.

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: In propionic acidemia, due to block in propionyl-CoA carboxylase reaction, during non-ketotic periods, when propionyl-CoA accumulation still occurs, two molecules of this substrate may condense via the action of a beta-ketothiolase to form 2-methyl-3-oxovaleryl-CoA, resulting ultimately in the excretion of 2-methyl-3-hydroxy-valeric acid and 2-methyl-3-oxovaleric acids in the urine.

+ +
+ + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence found for such a reaction, difussion is assumed, as detected in urine (HMDB00408).

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: In propionic acidemia, due to block in propionyl-CoA carboxylase reaction, during non-ketotic periods, when propionyl-CoA accumulation still occurs, two molecules of this substrate may condense via the action of a beta-ketothiolase to form 2-methyl-3-oxovaleryl-CoA, resulting ultimately in the excretion of 2-methyl-3-hydroxy-valeric acid and 2-methyl-3-oxovaleric acids in the urine.

+ +
+ + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence found for such a reaction, difussion is assumed, as detected in urine (HMDB29166).

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: An infant with glycogen storage disease and prolonged malnourishment showed a urinary organic acid profile during an episode of fasting hypoglycaemia with inappropriate hypoketotic dicarboxylic aciduria that was indistinguishable from that reported in long-chain L-3-hydroxyacyl-CoA dehydrogenase deficiency. Although there was a striking elevation of urinary 3-hydroxydecanedioic acid, the ratios between hydroxydicarboxylic acids were consistent with values reported to be indicate of medium-chain acyl-CoA dehydrogenase deficiency. We suspect that the fasting 3-hydroxydicarboxylic aciduria was attributable to secondarily impaired enzyme activities, the consequence of malnutrition, early infancy, and/or glycogen storage disease. Caution is advised in the interpretation of urinary organic acid patterns that indicate a 3-hydroxydicarboxylic aciduria, as well as an inappropriate hypoketotic dicarboxylic aciduria, as they may represent non-specific findings.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: An infant with glycogen storage disease and prolonged malnourishment showed a urinary organic acid profile during an episode of fasting hypoglycaemia with inappropriate hypoketotic dicarboxylic aciduria that was indistinguishable from that reported in long-chain L-3-hydroxyacyl-CoA dehydrogenase deficiency. Although there was a striking elevation of urinary 3-hydroxydecanedioic acid, the ratios between hydroxydicarboxylic acids were consistent with values reported to be indicate of medium-chain acyl-CoA dehydrogenase deficiency. We suspect that the fasting 3-hydroxydicarboxylic aciduria was attributable to secondarily impaired enzyme activities, the consequence of malnutrition, early infancy, and/or glycogen storage disease. Caution is advised in the interpretation of urinary organic acid patterns that indicate a 3-hydroxydicarboxylic aciduria, as well as an inappropriate hypoketotic dicarboxylic aciduria, as they may represent non-specific findings.

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence found for such reaction, but detected in blood and urine (HMDB00350)

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: no evidence found for such reaction, but detected in blood and urine (HMDB00350)

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The 3-OH-dicarboxylic acids with chain lengths longer than 10 are good substrates for ebta-oxidation

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The 3-OH-dicarboxylic acids with chain lengths longer than 10 are good substrates for ebta-oxidation

+ +
+ + + + + + + + + +
+ + + +

References: Chalmers, R. A. and A. M. Lawson (1982). Organic Acids in Man: Analytical Chemistry, Biochemistry and Diagnosis of the Organic Acidurias. London, Chapman and Hall Ltd

+

Confidence Level: 0.0

+

NOTES: no evidence found for such reaction, but detected in blood and urine (HMDB00325)

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

References: Chalmers, R. A. and A. M. Lawson (1982). Organic Acids in Man: Analytical Chemistry, Biochemistry and Diagnosis of the Organic Acidurias. London, Chapman and Hall Ltd

+

Confidence Level: 0.0

+

NOTES: no evidence found for such reaction, but detected in blood and urine (HMDB00325)

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

References: Chalmers, R. A. and A. M. Lawson (1982). Organic Acids in Man: Analytical Chemistry, Biochemistry and Diagnosis of the Organic Acidurias. London, Chapman and Hall Ltd .

+

Confidence Level: 0.0

+

NOTES: 5-OH-hexanoic acid, found in patients urine was considered to arise from the (w-1) oxidation of accumulating hexanoic acid, and a xenobiotic origin was also considered probable.

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

References: '

+

Confidence Level: 0.0

+

NOTES: transport mechanism similar to 4-Aminobutyrate (GABA) is assumed.

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The data also clearly demonstrate that the efficiency of Fe and Zn transfer across the epithelial barrier can be decreased by lesser phosphorylated derivatives of IPo- This effect is largely dependent on the degree of phosphorylation of inositol. Finally, the results raise the possibility that intestinal cells may take up inositol phosphate-metal complexes that require cellular metabolism before the micronutrients can be transferred across the basolateral surface to complete the process of absorption.

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The data also clearly demonstrate that the efficiency of Fe and Zn transfer across the epithelial barrier can be decreased by lesser phosphorylated derivatives of IPo- This effect is largely dependent on the degree of phosphorylation of inositol. Finally, the results raise the possibility that intestinal cells may take up inositol phosphate-metal complexes that require cellular metabolism before the micronutrients can be transferred across the basolateral surface to complete the process of absorption.

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: OMIM:171060,

+

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: '

+

Confidence Level: 0.0

+

NOTES: transport mechanism similar to 4-Aminobutyrate (GABA) is assumed.

+ +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: vescicular transport of phospholipids into the cell

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: vescicular transport of phospholipids into the cell

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: vescicular transport of phospholipids into the cell

+ +
+ + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: When situated in a membrane, sphingolipids first of all can diffuse as monomers in four directions. If we do not take into account the motions of the entire molecule that do not result in transport, like the rotation around their longitudinal axis and the wobble (279), sphingolipids can diffuse laterally in the two-dimensional plane of the membrane

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0.0

+

NOTES: ABC transport for very long chain fatty acids

+ +
+ + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Our studies indicate that several sex-steroid hormones are substrates for P-gp-mediated transport and are also able to induce P-gp expression at both the protein and mRNA level in vitro. Stimulation of P-gp ATPase catalytic activity by steroid hormones was also observed, suggesting physical interactions and identifying a need for further investigations to understand the in vivo effects of endogenous and synthetic steroid hormones on the expression and function of P-gp.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Radiolabeled Glucarate ([(99m)Tc]GLA) uptake is related to GLUT-5 transporter expression and transport.

+ +
+ + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Proton symport by monocarboxylic acid transporter (MCT1). Also known as SLC16A1. (Entrez Gene ID: 6566)

+ +
+ + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

References: 17502341

+

Confidence Level: 0.0

+

NOTES: Proton-coupled monocarboxylate transporter. Catalyzes the rapid transport across the plasma membrane of many monocarboxylates such as lactate, pyruvate, branched-chain oxo acids derived from leucine, valine and isoleucine, and the ketone bodies acetoacetate, beta-hydroxybutyrate and acetate.

+ +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: The results of the present study unequivocally prove the existence of a common Na+-dependent transport mechanism for Se-Met and Met in the jejunal BBM. SeMet and Met were actively transported across the BBM by a mechanism specific for neutral amino acids.

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0.0

+

NOTES: evidenced for carnitine and acetyl carnitine. evidenced in mouse colon, for carnitine, propionylcarnitine and acetylcarnitine

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: added folate transporter

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: No evidence found for such reaction, so diffusion assumed.

+ +
+ + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: No evidence found for such reaction, so diffusion assumed.

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Two isoforms of the human ornithine carrier, ORC1 and ORC2, have been identified by overexpression of the proteins in bacteria and by study of the transport properties of the purified proteins reconstituted into liposomes. Both transport L-isomers of ornithine, lysine, arginine, and citrulline by exchange and by unidirectional mechanisms, and they are inactivated by the same inhibitors. ORC2 has a broader specificity than ORC1, and L- and D-histidine, L-homoarginine, and D-isomers of ornithine, lysine, and ornithine are all substrates. Both proteins are expressed in a wide range of human tissues, but ORC1 is the predominant form. The highest levels of expression of both isoforms are in the liver. Five mutant forms of ORC1 associated with the human disease hyperornithinemia-hyperammonemia-homocitrullinuria were also made. The mutations abolish the transport properties of the protein. In patients with hyperornithinemia-hyperammonemia-homocitrullinuria, isoform ORC2 is unmodified, and its presence compensates partially for defective ORC1. Similar transporter for perxosime is assumed.

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Two isoforms of the human ornithine carrier, ORC1 and ORC2, have been identified by overexpression of the proteins in bacteria and by study of the transport properties of the purified proteins reconstituted into liposomes. Both transport L-isomers of ornithine, lysine, arginine, and citrulline by exchange and by unidirectional mechanisms, and they are inactivated by the same inhibitors. ORC2 has a broader specificity than ORC1, and L- and D-histidine, L-homoarginine, and D-isomers of ornithine, lysine, and ornithine are all substrates. Both proteins are expressed in a wide range of human tissues, but ORC1 is the predominant form. The highest levels of expression of both isoforms are in the liver. Five mutant forms of ORC1 associated with the human disease hyperornithinemia-hyperammonemia-homocitrullinuria were also made. The mutations abolish the transport properties of the protein. In patients with hyperornithinemia-hyperammonemia-homocitrullinuria, isoform ORC2 is unmodified, and its presence compensates partially for defective ORC1. Similar transporter for extracellular space is assumed.

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Our studies indicate that several sex-steroid hormones are substrates for P-gp-mediated transport and are also able to induce P-gp expression at both the protein and mRNA level in vitro. Stimulation of P-gp ATPase catalytic activity by steroid hormones was also observed, suggesting physical interactions and identifying a need for further investigations to understand the in vivo effects of endogenous and synthetic steroid hormones on the expression and function of P-gp. Transport mechanism similar to extracellular space is assumed.

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Confidence Level: 0.0

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Confidence Level: 0.0

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NOTES: Our studies indicate that several sex-steroid hormones are substrates for P-gp-mediated transport and are also able to induce P-gp expression at both the protein and mRNA level in vitro. Stimulation of P-gp ATPase catalytic activity by steroid hormones was also observed, suggesting physical interactions and identifying a need for further investigations to understand the in vivo effects of endogenous and synthetic steroid hormones on the expression and function of P-gp. Transport mechanism similar to extracellular space is assumed.

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Confidence Level: 0.0

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NOTES: Lipids, retinyl palmitate, squalene and non-cholesterol sterols were measured at baseline and after 3, 4, 6, 9, 12 and 24 h postprandially in plasma, chylomicron, VLDL and VLDL bottom and, in six randomly chosen subjects, also in IDL, LDL and HDL. In the fasting samples, squalene was mainly transported in LDL and HDL, whereas in squalene-supplemented postprandium most of squalene was carried in the triglyceride-rich lipoproteins. Postprandial squalene and retinyl palmitate curves closely resembled each other. After the squalene-enriched dietary fat load, squalene was significantly increased compared to control fat loads in plasma, chylomicrons, VLDL and IDL. Squalene addition increased significantly lathosterol/campesterol ratio in chylomicrons and VLDL at 12 h and in VLDL bottom at 9-12 h, and increased significantly VLDL lanosterol/campesterol ratio at 12 h, indicating enhanced cholesterol synthesis caused by squalene. Plasma plant sterol levels remained unchanged. In conclusion, a single oral dose of squalene representing a potential daily dietary amount increases cholesterol synthesis within 9-12 h detected in chylomicrons, VLDL and VLDL bottom.

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Confidence Level: 0.0

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NOTES: Lipids, retinyl palmitate, squalene and non-cholesterol sterols were measured at baseline and after 3, 4, 6, 9, 12 and 24 h postprandially in plasma, chylomicron, VLDL and VLDL bottom and, in six randomly chosen subjects, also in IDL, LDL and HDL. In the fasting samples, squalene was mainly transported in LDL and HDL, whereas in squalene-supplemented postprandium most of squalene was carried in the triglyceride-rich lipoproteins. Postprandial squalene and retinyl palmitate curves closely resembled each other. After the squalene-enriched dietary fat load, squalene was significantly increased compared to control fat loads in plasma, chylomicrons, VLDL and IDL. Squalene addition increased significantly lathosterol/campesterol ratio in chylomicrons and VLDL at 12 h and in VLDL bottom at 9-12 h, and increased significantly VLDL lanosterol/campesterol ratio at 12 h, indicating enhanced cholesterol synthesis caused by squalene. Plasma plant sterol levels remained unchanged. In conclusion, a single oral dose of squalene representing a potential daily dietary amount increases cholesterol synthesis within 9-12 h detected in chylomicrons, VLDL and VLDL bottom.

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Confidence Level: 0.0

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Confidence Level: 0.0

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NOTES: No evidence found for such reaction, so diffusion assumed.

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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NOTES: evidence in hepatocytes (basolateral membrane), passive excretion into urine of the fraction that is not excreted into bile

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Confidence Level: 0.0

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Confidence Level: 0.0

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NOTES: possible for acylcarnitine in various tissues

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Confidence Level: 0.0

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NOTES: no evidence found for specific transporter

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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NOTES: no evidence found for specific transporter

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Confidence Level: 0.0

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NOTES: Dopamine and its metabolites can undergo O-glucuronides before excretion. O-glucuronides occur in both CNS and periphery. Dopamine-4-O-glucuronide and Dopamine-3-O-glucuronide are formed in almost equal amounts. Glucuronidation is performed by ER-bound uridine diphosphoglucoronosyltransferases (UGTS)

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Confidence Level: 0.0

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NOTES: Dopamine and its metabolites can undergo O-glucuronides before excretion. O-glucuronides occur in both CNS and periphery. Dopamine-4-O-glucuronide and Dopamine-3-O-glucuronide are formed in almost equal amounts. Glucuronidation is performed by ER-bound uridine diphosphoglucoronosyltransferases (UGTS)

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Confidence Level: 0.0

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NOTES: dopamine glucuronides were found in the CSF

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Confidence Level: 0.0

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Confidence Level: 0.0

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NOTES: Dopamine glucuronides were found in the CSF. MRP1 can transport glucuronide conjugates

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Confidence Level: 0.0

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Confidence Level: 0.0

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NOTES: Comound was found in CSF, so it needs to be secreted. Gsh conjugate is transported out the cells and hydrolyzed by ggt and dipeptidases to the corresponding cys-dopamine. RLIP76 (10928) can catalyze transport of glutathione conjugates. RLIP76 is a multifunctional protein important for utilizing the energy currency adenosine triphosphate to transport various chemical materials outside

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References: ;PMID:

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References: ;UNIPROT:P06132

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Confidence Level: 0.0

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References: ;PMID:

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Confidence Level: 0.0

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Confidence Level: 0.0

+

NOTES: OATP2B1 is more significant for intestinal uptake of rosuvastatin, fluvastatin ; pravastatin. Atorvastatin, cerivastatin ; pitavastatin undergo more often passive diffusion. The intestinal permeability of atorvastatin is high at the physiologically relevant intestinal luminal pH of 6-6.5 ; predicts complete absoprtion (PMID: 14531725).

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+ + + +

Confidence Level: 0.0

+

NOTES: precise transporter has not been identified for heptic uptake. In rats sodium independant uptake is seen. In humans OATP1B1 ; OATP1B3 do not mediate ibuprofen uptake, however, these NSAIDs may influence allosterically the uptake of antibiotics ; statins. OAT1 transporter mediates ibuprofen uptake at the basolateral surface in renal epithelial cells (PMID: 18309312), dectected weakly in liver as well (PMID: 10462545). OAT1 transporter is an antiporter mediating uptake of organic anion (drugs) ; efflux of dicarboxylate ion (uric acid) (PMID: 12883891).

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Confidence Level: 0.0

+

NOTES: precise transporter has not been identified for heptic uptake. In rats sodium independant uptake is seen. In humans OATP1B1 ; OATP1B3 do not mediate ibuprofen uptake, however, these NSAIDs may influence allosterically the uptake of antibiotics ; statins. OAT1 transporter mediates ibuprofen uptake at the basolateral surface in renal epithelial cells (PMID: 18309312), dectected weakly in liver as well (PMID: 10462545). OAT1 transporter is an antiporter mediating uptake of organic anion (drugs) ; efflux of dicarboxylate ion (uric acid) (PMID: 12883891).

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+ + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0.0

+

NOTES: diffusion reaction assumed due to lack of specific transport protein

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+ + + +

Confidence Level: 0.0

+

NOTES: Losartan, an antagonist of the angiotensin II receptor (AT1-RA), ; its metabolite (EXP-3174) cis inhibited urate uptake ; the IC50 of losartan tended to be the same as that of probenecid consistent with the uricosuric property of losartan. URAT1 (GeneID:116085) is expresed in the renal cells ; losartan ; its active metabolite losartan-1374 was found to be its substrate, mediating antiport with organic anions (preferable chloride, can be substituted with bromide ; iodide).

+ +
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+ + + +

Confidence Level: 0.0

+

NOTES: diffusion reaction assumed due to lack of specific transport protein

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+ + + +

Confidence Level: 0.0

+

NOTES: Losartan, an antagonist of the angiotensin II receptor (AT1-RA), ; its metabolite (EXP-3174) cis inhibited urate uptake ; the IC50 of losartan tended to be the same as that of probenecid consistent with the uricosuric property of losartan. URAT1 (GeneID:116085) is expresed in the renal cells ; losartan ; its active metabolite losartan-1374 was found to be its substrate, mediating antiport with organic anions (preferable chloride, can be substituted with bromide ; iodide).

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: Losartan, an antagonist of the angiotensin II receptor (AT1-RA), ; its metabolite (EXP-3174) cis inhibited urate uptake ; the IC50 of losartan tended to be the same as that of probenecid consistent with the uricosuric property of losartan. URAT1 (GeneID:116085) is expresed in the renal cells ; losartan ; its active metabolite losartan-1374 was found to be its substrate, mediating antiport with organic anions (preferable chloride, can be substituted with bromide ; iodide).

+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + +

Confidence Level: 0.0

+

NOTES: diffusion reaction has been assumed since no conclusive evidence of a specific transport protein exists. Pgp has been shown to act as an efflux transporter in CaCo2 cells for losartan alone but not for its active metabolite losartan-1374. No PEPT1-specific uptake of valsartan ; losartan was found in HeLa cells.

+ +
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+ + + +

Confidence Level: 0.0

+

NOTES: a fraction of the intact drug passes through the small intestine at the proximal region, probably via a proton soupled carrier mediated transport, identity of the transport protein remains unknown.

+ +
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+ + + +

Confidence Level: 0.0

+

NOTES: transporter not identified, based on physiological evidence

+ +
+ + + + + + + + + + + + + + + + + +
+ + + +

References: Russel, F. G. M. (2010). Transporters: Importance in Drug Absorption, Distribution, ; Removal, Enzyme- ; Transporter-Based Drug-Drug Interactions. K. S. Pang, A. D. Rodrigues ; R. M. Peter, Springer New York: 27-49

+

Confidence Level: 0.0

+

NOTES: antiport transport for uptake of torasemide has been assumed, since, OATP1B1 mediates hepatic uptake of torasemide in an antipor manner, in exchange of bicarbonate.

+ +
+ + + + + + + + +
+ + + +

References: Russel, F. G. M. (2010). Transporters: Importance in Drug Absorption, Distribution, ; Removal, Enzyme- ; Transporter-Based Drug-Drug Interactions. K. S. Pang, A. D. Rodrigues ; R. M. Peter, Springer New York: 27-49, .

+

Confidence Level: 0.0

+

NOTES: In healthy volunteers ; patients with normal renal function, approximately 20% of a dose of torasemide is eliminated unchanged in the urine. The high renal clearance of torasemide indicates that the major part of torasemide is secreted by the proximal tubular anion carrier system. Hence, organic anion antiport mechanism has been assumed for hepatocytes. OAT4 located in the kidney, exchanges organic anions (efflux) for chloride (uptake). In another study, authors found that large variation in the renal clearance of torsemide, which was partially explained by genetic variation in the luminally expressed OAT4 rather than by polymorphisms in the genes coding for basolaterally located OAT1 ; OAT3.

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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Confidence Level: 0.0

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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
diff --git a/tests/unit/test_fisher_stats.py b/tests/unit/test_fisher_stats.py new file mode 100644 index 00000000..f607a931 --- /dev/null +++ b/tests/unit/test_fisher_stats.py @@ -0,0 +1,16 @@ +import cobra +import numpy as np +from como.stats.fisher_exact_test import FisherExactTest + + +def test_fisher_stats(): + reference_model = cobra.io.load_matlab_model("main/data/reference_models/GeneralModelUpdatedV3.mat") + scenario_model = cobra.io.read_sbml_model("tests/inputs/naiveB_model.xml") + real = FisherExactTest.run(reference=reference_model, scenario=scenario_model, pathway="Glycolysis/gluconeogenesis") + + assert real.statistic == np.float64(4.321708185053381) + assert real.pvalue == np.float64(1.2883495211648955e-05) + assert real.a == 32 + assert real.b == 10 + assert real.c == 4496 + assert real.d == 6072 diff --git a/tests/unit/test_ks_stats.py b/tests/unit/test_ks_stats.py new file mode 100644 index 00000000..08403d46 --- /dev/null +++ b/tests/unit/test_ks_stats.py @@ -0,0 +1,39 @@ +import numpy as np +import pandas as pd +import pytest +from como.stats.ks_test import KSTest + + +@pytest.fixture +def expected_result() -> pd.DataFrame: + df = pd.read_csv("tests/inputs/expected_ks_results.csv", index_col=0) + df["statistic_sign"] = df["statistic_sign"].astype(np.int8) + return df + + +@pytest.mark.parametrize("cores", [1, 2, 4]) +def test_ks_stats(expected_result: pd.DataFrame, cores: int): + seed = 123456789 + size = 1_000 + cols = 10 + gen = np.random.Generator(np.random.PCG64DXSM(seed=seed)) + + df1 = pd.DataFrame( + index=list(range(size)), + columns=list(range(cols)), + data=gen.normal(loc=0, size=size * cols).reshape(size, cols).astype(np.float32), + ) + df2 = pd.DataFrame( + index=list(range(size)), + columns=list(range(cols)), + data=gen.normal(loc=1, size=size * cols).reshape(size, cols).astype(np.float32), + ) + + real_result = KSTest.run(df1, df2, cores=cores) + real_df = real_result.df + # real_df.to_csv("/Users/joshl/Projects/COMO/tests/inputs/expected_ks_results.csv") + # assert False + assert len(expected_result.columns) == len(real_df.columns) + assert len(expected_result) == len(real_df) + assert all(col in real_df.columns for col in expected_result.columns) + pd.testing.assert_frame_equal(expected_result, real_df) diff --git a/tests/unit/test_mwu_stats.py b/tests/unit/test_mwu_stats.py new file mode 100644 index 00000000..9b1823e4 --- /dev/null +++ b/tests/unit/test_mwu_stats.py @@ -0,0 +1,36 @@ +import numpy as np +import pandas as pd +import pytest +from como.stats.mann_whitney_test import MannWhitneyUTest + + +@pytest.fixture +def expected_result() -> pd.DataFrame: + df = pd.read_csv("tests/inputs/expected_mwu_results.csv", index_col=0) + return df + + +@pytest.mark.parametrize("cores", [1, 2, 4]) +def test_mannwhitney_stats(expected_result: pd.DataFrame, cores: int): + seed = 123456789 + size = 1_000 + cols = 10 + gen = np.random.Generator(np.random.PCG64DXSM(seed=seed)) + + df1 = pd.DataFrame( + index=list(range(size)), + columns=list(range(cols)), + data=gen.normal(loc=0, size=size * cols).reshape(size, cols).astype(np.float32), + ) + df2 = pd.DataFrame( + index=list(range(size)), + columns=list(range(cols)), + data=gen.normal(loc=1, size=size * cols).reshape(size, cols).astype(np.float32), + ) + + real_result = MannWhitneyUTest.run(df1, df2, cores=cores) + real_df = real_result.df + assert len(expected_result.columns) == len(real_df.columns) + assert len(expected_result) == len(real_df) + assert all(col in real_df.columns for col in expected_result.columns) + pd.testing.assert_frame_equal(expected_result, real_df) diff --git a/tests/unit/test_rnaseq_preprocess.py b/tests/unit/test_rnaseq_preprocess.py index 56674d43..6b3419c2 100644 --- a/tests/unit/test_rnaseq_preprocess.py +++ b/tests/unit/test_rnaseq_preprocess.py @@ -7,7 +7,6 @@ from como.rnaseq_preprocess import ( _organize_gene_counts_files, _process_first_multirun_sample, - _process_standard_replicate, _sample_name_from_filepath, _STARinformation, _StudyMetrics, @@ -28,9 +27,10 @@ class TestSTARInformation: invalid_data = Path("main/data/COMO_input/naiveB/fragmentSizes/S1/naiveB_S1R1_fragment_size.txt").resolve() @pytest.mark.asyncio - async def test_build_from_tab_valid_file(self): + async def test_build_from_tab_valid_file(self) -> None: """Validate building STAR information object.""" star: _STARinformation = await _STARinformation.build_from_tab(TestSTARInformation.valid_data) + assert len(star.gene_names) == len(star.count_matrix) == 61541 assert len(star.num_unmapped) == 3 assert len(star.num_multimapping) == 3 @@ -40,7 +40,7 @@ async def test_build_from_tab_valid_file(self): @pytest.mark.asyncio async def test_build_from_tab_invalid_file(self): """Validate error on invalid file.""" - with pytest.raises(ValueError, match=r"Building STAR information requires a '.tab' file"): + with pytest.raises(ValueError, match=r"Building STAR information requires a '\.tab' file"): await _STARinformation.build_from_tab(TestSTARInformation.invalid_data) @@ -50,8 +50,8 @@ def test_sample_name_from_filepath(any_como_input_filepath: Path): def test_organize_gene_counts_files(como_input_data_directory: Path): - metrics: list[_StudyMetrics] = _organize_gene_counts_files(como_input_data_directory) - for metric in metrics: + metric: _StudyMetrics + for metric in _organize_gene_counts_files(como_input_data_directory): assert len(metric.sample_names) == metric.num_samples == len(metric.count_files) == len(metric.strand_files) for file in metric.count_files: @@ -70,7 +70,7 @@ async def test_process_first_multirun_sample(strand_filepath: Path, all_gene_cou result: pd.DataFrame = await _process_first_multirun_sample(strand_filepath, all_gene_count_filepaths) assert result.columns[0] == "ensembl_gene_id" assert len(result.columns) == 2 - assert result.columns[1] in strand_filepath.as_posix() + assert 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