From 008b4439de3cdb6a102a3b7f5a78bd7f51d4b105 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer <33460176+Devlin-Moyer@users.noreply.github.com> Date: Mon, 23 Dec 2024 10:53:56 -0500 Subject: [PATCH] Fix Various Issues with Lipoic Acid Biosynthesis (#830) * feat: added new metabolite to represent mitochondrial octanoyl-[ACP] * feat: moved MAR06402 from c to m and removed apoA1 from reactants * fix: turned MAM00210c into MAM00210m since the only lipoylated human proteins are strictly mitochondrial * feat: added MAM20084m to represent a mitochondrial 4Fe4S iron-sulfur cluster * fix: noticed that KEGG IDs for MAM00077 metabolites in metabolites.tsv were in the BiGG ID column; moved them to the KEGG ID column * fix: moved MAR06403 from c to m and corrected various issues with the metabolites, stoichiometry, and GPR * fix: moved MAM00208c and MAM00209c from c to m since all lipoylated human proteins are strictly mitochondrial * fix: replaced [c] versions of remaining metabolites in MAR06404 with their [m] equivalents * feat: added MAM20085m to represent a mitochondrial 2Fe2S iron-sulfur cluster * feat: added MAR20184 to represent synthesis of 4Fe4S iron-sulfur clusters from 2Fe2S iron-sulfur clusters * chore: added row to reactions.tsv for MAR20184 * feat: added MAR20185 to represent de novo synthesis of 2Fe2S in mitochondria * feat: added MAM02042m to represent mitochondrial hydrosulfide * feat: added MAM20086m to represent mitochondrial S-sulfanylglutathione * feat: added MAR20186 to represent formation of GSSH from HS- and GSH by SQOR * feat: added SQOR to GPR of MAR06911 and reordered existing genes so they're sorted by the numeric bits of their IDs * feat: added MAR20187 to represent conversion of GSSH and O2 into GSH and sulfite by ETHE1 * feat: added MAM01098m to represent mitochondrial 5'deoxyadenosine * feat: added MAR20188 to represent transport of 5'deoxyadenosine from mitochondria to the cytosol * feat: added new genes to YAML file and genes.tsv for all genes in new reactions not already present * fix: added LYRM4 to YAML file and genes.tsv because I forgot it the first time * fix: accidentally wrote 'metfrom' instead of 'metFrom' for some of the new metabolite entries * fix: remove duplicate function getGenesFromGrRules is already in RAVEN * fix: remove exportHumanGEM use RAVEN's generic exportForGit instead * refactor: increaseHumanGEMVersion * chore: I/O of YAML file with latest RAVEN release * doc: update README.md * fix: testYamlConversion use new funcs * chore: add macaw test result * chore: add macaw test result * fix: name of gene essentiality job Github Action * chore: add macaw test result * fix: keep test-specific PR reference in sep. lines * chore: add macaw test result * chore: add macaw test result * fix: charge and empirical formula of GSSH to be consistent with GSH * fix: added missing proton in MAR20186 * fix: genes.tsv quote all content * fix: increaseHumanGEMVersion * fix: testYamlConversion * temporarily distribute YAML I/O functions until fully merged in new RAVEN release * fix: remove ENSG00000181562 and ENSG00000092529 from genes.tsv * chore: add macaw test result * fix: remove empty GPRs * refactor: increaseHumanGEMVersion * refactor: force specific IO functions * chore: add gene essentiality test result * feat: check RAVEN version increaseHumanGEMVersion * fix: genes.tsv missing " * fix: restore new genes in genes.tsv from earlier commit * chore: add macaw test result * chore: add macaw test result --------- Co-authored-by: Eduard Kerkhoven Co-authored-by: edkerk Co-authored-by: Devlin-Moyer --- data/testResults/README.md | 4 +- data/testResults/macaw_results.csv | 23 +-- data/testResults/macaw_summary.md | 6 +- model/Human-GEM.yml | 239 +++++++++++++++++++++++++---- model/genes.tsv | 15 ++ model/metabolites.tsv | 18 ++- model/reactions.tsv | 5 + 7 files changed, 258 insertions(+), 52 deletions(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 95c98d79..24c52291 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -4,7 +4,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/ The test results shown here were obtained by the GitHub Actions run in: -- **PR #942** (MACAW) +- **PR #830** (MACAW) - **PR #883** (gene essentiality) The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request. @@ -25,4 +25,4 @@ It is possible for a single reaction to fit in multiple of the above categories. ### Cell-line specific gene essentiality Evaluate gene essentiality predictions in 5 cell-line specific GEMs with experimental fitness data gathered from the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015). -Cell-line specific GEMs are constructed with tINIT2 for DLD1, GBM, HCT116, HeLa and RPE1 cell lines. Then, the `metabolicTasks_Essential.txt` list of tasks is used to identify essential genes in each of these models. The predicted gene essentiality is compared to results from a high-throughput CRISPR-Cas9 screen for identifying genes that affect fitness. Only the summary statistics of this comparison are kept. \ No newline at end of file +Cell-line specific GEMs are constructed with tINIT2 for DLD1, GBM, HCT116, HeLa and RPE1 cell lines. Then, the `metabolicTasks_Essential.txt` list of tasks is used to identify essential genes in each of these models. The predicted gene essentiality is compared to results from a high-throughput CRISPR-Cas9 screen for identifying genes that affect fitness. Only the summary statistics of this comparison are kept. diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv index 112e0ccf..0447ca0c 100644 --- a/data/testResults/macaw_results.csv +++ b/data/testResults/macaw_results.csv @@ -682,8 +682,8 @@ MAR05393,6 MAM02040c + MAM02981c --> 6 MAM01974c + MAM02980c,ok,ok,ok,ok,N/A MAR06409,MAM02039m + MAM02393m + MAM02553m <=> MAM01701m + MAM02552m,only when going forwards,ok,ok,ok,N/A MAR07702,MAM02007c + MAM02039c + MAM02555c <=> MAM01998c + MAM02554c,ok,ok,ok,ok,N/A MAR07703,MAM01998c + MAM02630c --> MAM02007c + MAM02041c,ok,ok,ok,ok,N/A -MAR08433,MAM00209c + MAM01986m + MAM02039m --> MAM01596m + MAM02878m,ok,ok,ok,ok,N/A -MAR08434,MAM02878m + MAM02980m --> MAM00208c + MAM01045m + MAM02039m + MAM02578m,ok,ok,ok,ok,N/A +MAR08433,MAM00209m + MAM01986m + MAM02039m --> MAM01596m + MAM02878m,ok,ok,ok,ok,N/A +MAR08434,MAM02878m + MAM02980m --> MAM00208m + MAM01045m + MAM02039m + MAM02578m,ok,ok,ok,ok,N/A MAR08439,MAM01708m + MAM01802m + MAM02040m --> MAM01803m + MAM01831m + MAM02880m,ok,ok,ok,ok,N/A MAR08440,MAM01394m + MAM02040m + MAM02552m --> MAM01393m + 2 MAM02039m + MAM02553m,ok,ok,ok,ok,N/A MAR08441,MAM01513m + MAM01802m --> MAM01394m + MAM01803m,ok,ok,ok,ok,N/A @@ -1659,9 +1659,9 @@ MAR02468,MAM00314r + MAM03109r --> MAM00323r + MAM02039r + MAM03106r,ok,ok,ok,ok MAR02469,MAM00314c + MAM03109c <=> MAM00327c + MAM02039c + MAM03106c,only when going backwards,ok,ok,ok,N/A MAR02470,MAM00314r + MAM03109r --> MAM00327r + MAM02039r + MAM03106r,ok,ok,ok,ok,N/A MAR06397,MAM02039c + MAM02394c + MAM02553c <=> MAM01702c + MAM02552c,ok,ok,ok,ok,N/A -MAR06402,MAM01350c + MAM02643c --> MAM00184c + MAM00210c,ok,ok,ok,ok,N/A -MAR06403,MAM00210c + 5 MAM02039c + 7 MAM02555c + 2 MAM02682c + 2 MAM02877c --> MAM00209c + 2 MAM01098c + 6 MAM02040c + 2 MAM02471c + 7 MAM02554c + 2 MAM02681c,ok,ok,ok,ok,N/A -MAR06404,MAM00209c + MAM02039c + MAM02553c <=> MAM00208c + MAM02552c,only when going forwards,ok,ok,ok,N/A +MAR06402,MAM02643m --> MAM00210m + MAM02484m,MAM02484m;MAM00210m;MAM02643m,ok,ok,ok,N/A +MAR06403,MAM00210m + 3 MAM02039m + MAM02555m + 2 MAM02877m + MAM20084m --> MAM00208m + 2 MAM01098m + 4 MAM01821m + 2 MAM02042m + 2 MAM02471m + MAM02554m,MAM00210m;MAM01098m;MAM02042m;MAM20084m,ok,ok,ok,N/A +MAR06404,MAM00209m + MAM02039m + MAM02553m <=> MAM00208m + MAM02552m,only when going forwards,ok,ok,ok,N/A MAR02472,MAM02039c + MAM02390c + MAM02555c + MAM02630c --> MAM00108c + 2 MAM02040c + MAM02554c,ok,ok,ok,ok,N/A MAR02475,MAM00108c + MAM02039c + MAM02444c --> MAM00811c + MAM01596c + MAM01597c,ok,ok,ok,ok,N/A MAR02478,MAM00811c + MAM02039c + MAM02555c --> MAM00708c + MAM02554c,ok,ok,ok,ok,N/A @@ -6593,7 +6593,7 @@ MAR09623,MAM01306c + MAM01659e --> MAM01306e + MAM01659c,ok,ok,ok,ok,N/A MAR09624,MAM01306c + MAM01789e --> MAM01306e + MAM01789c,ok,ok,ok,ok,N/A MAR09635,MAM02022c <=> MAM02022e,MAM02022c;MAM02022e,ok,ok,ok,N/A MAR09636,MAM02384c --> MAM02384e,ok,ok,ok,ok,N/A -MAR09637,MAM01098c <=> MAM01098e,only when going backwards,ok,ok,ok,N/A +MAR09637,MAM01098c <=> MAM01098e,MAM01098c;MAM01098e,ok,ok,ok,N/A MAR09638,MAM00969c <=> MAM00969e,ok,ok,ok,ok,N/A MAR09639,MAM01315c <=> MAM01315e,ok,ok,ok,ok,N/A MAR09640,MAM02328c <=> MAM02328e,ok,ok,ok,ok,N/A @@ -7814,7 +7814,7 @@ MAR09294,MAM01614e <=> ,ok,ok,ok,ok,N/A MAR09295,MAM01630e <=> ,ok,ok,ok,ok,N/A MAR09296,MAM01668e <=> ,ok,ok,ok,ok,N/A MAR09297,MAM01666e <=> ,ok,ok,ok,ok,N/A -MAR09298,MAM01098e <=> ,only when going backwards,ok,ok,ok,N/A +MAR09298,MAM01098e <=> ,MAM01098e,ok,ok,ok,N/A MAR09299,MAM01647e <=> ,MAM01647e,ok,ok,ok,N/A MAR09300,MAM01669e <=> ,ok,ok,ok,ok,N/A MAR09301,MAM01655e <=> ,ok,ok,ok,ok,N/A @@ -8018,7 +8018,7 @@ MAR09730,MAM01308e <=> ,ok,ok,ok,ok,N/A MAR09725,MAM02554c + MAM02555n <=> MAM02554n + MAM02555c,only when going forwards,ok,ok,ok,N/A MAR00031,0.19 MAM00240c + 0.0014 MAM00511c + 0.0024 MAM00560c + 0.0006 MAM00656c + 0.005 MAM01450c + 0.34 MAM01451c + 0.0008 MAM02629c + 0.0092 MAM02684c + 0.0034 MAM02685c + 0.0016 MAM02750c + 0.0002 MAM02808c + 0.0004 MAM02908c + 0.44 MAM02958c + 0.005 MAM10005c --> MAM02392c,ok,ok,ok,ok,N/A MAR00021,MAM01307c + MAM01365c + MAM01369c + MAM01370c + MAM01450c + MAM01451r + MAM01589c + MAM01602c + MAM01628c + MAM01721n + MAM01722n + MAM01974c + MAM01975c + MAM01986c + MAM02125c + MAM02184c + MAM02360c + MAM02392c + MAM02426c + MAM02471c + MAM02724c + MAM02733c + MAM02750c + MAM02770c + MAM02847c + MAM02896c + MAM02908c + MAM02993c + MAM03089c + MAM03101c + MAM03135c + MAM03161c --> MAM03970c,ok,ok,ok,ok,N/A -MAR00022,MAM00209c + MAM01401c + MAM01597c + MAM01600m + MAM01631m + MAM01803c + MAM02348c + MAM02553c + MAM02555c + MAM02842c + MAM02978c + MAM02980c + MAM03102m + 0.1 MAM03139c + 0.1 MAM03140c + 0.1 MAM03143c --> MAM01602c,ok,ok,ok,ok,N/A +MAR00022,MAM00209m + MAM01401c + MAM01597c + MAM01600m + MAM01631m + MAM01803c + MAM02348c + MAM02553c + MAM02555c + MAM02842c + MAM02978c + MAM02980c + MAM03102m + 0.1 MAM03139c + 0.1 MAM03140c + 0.1 MAM03143c --> MAM01602c,ok,ok,ok,ok,N/A MAR00023,MAM00291c + MAM00427c + MAM00427r + MAM01008c + MAM01008r + MAM01022c + MAM01022r + MAM01024c + MAM01024r + MAM01026r + MAM01028c + MAM01028r + MAM01030c + MAM01030r + MAM01031c + MAM01031r + MAM01032c + MAM01060c + MAM01232c + MAM02624c --> MAM03139c,ok,ok,ok,ok,N/A MAR00033,MAM00611c + MAM00611m + MAM00622c + MAM00622m --> MAM03140c,ok,ok,ok,ok,N/A MAR00034,MAM00766c + MAM01924c --> MAM03143c,ok,ok,ok,ok,N/A @@ -12951,7 +12951,7 @@ MAR20164,MAM01623c <=> MAM01623m,ok,ok,ok,ok,N/A MAR20165,MAM02034c <=> MAM02034m,ok,ok,ok,ok,N/A MAR20166,MAM03130c <=> MAM03130m,ok,ok,ok,ok,N/A MAR20167,MAM03103m + MAM20019c <=> MAM01828c + MAM03102m,ok,ok,ok,ok,N/A -MAR20168,MAM00209c --> MAM02393m,ok,ok,ok,ok,N/A +MAR20168,MAM00209m --> MAM02393m,ok,ok,ok,ok,N/A MAR20169,MAM01412c + MAM02040c --> MAM01410c + MAM01597c + MAM02039c,ok,ok,ok,ok,N/A MAR20170,MAM02040c + MAM02644c --> MAM01597c + MAM02039c + MAM02642c,ok,ok,ok,ok,N/A MAR20171,MAM01650c + MAM02040c --> MAM01597c + MAM01648c + MAM02039c,ok,ok,ok,ok,N/A @@ -12967,3 +12967,8 @@ MAR20180,MAM00077e <=> ,MAM00077e,ok,ok,ok,N/A MAR20181,MAM02983c + MAM02984m <=> MAM02983m + MAM02984c,ok,ok,ok,ok,N/A MAR20182,MAM01642c + MAM02983m <=> MAM01642m + MAM02983c,ok,ok,ok,ok,N/A MAR20183,MAM01642c + MAM02984m <=> MAM01642m + MAM02984c,ok,ok,ok,ok,N/A +MAR20184,2 MAM01371m + 2 MAM02040m + MAM02555m + 2 MAM20085m --> 2 MAM01285m + 3 MAM02039m + MAM02554m + 2 MAM02751m + MAM20084m,MAM20084m;MAM20085m,ok,ok,ok,N/A +MAR20185,2 MAM01628m + 2 MAM01821m + MAM02555m --> 2 MAM01307m + MAM02039m + MAM02554m + MAM20085m,MAM20085m,ok,ok,ok,N/A +MAR20186,MAM01802m + MAM02026m + MAM02039m + MAM02042m --> MAM01803m + MAM20086m,MAM02042m;MAM20086m,ok,ok,ok,N/A +MAR20187,MAM02040m + MAM02630m + MAM20086m --> MAM02026m + 2 MAM02039m + MAM02949m,MAM20086m,ok,ok,ok,N/A +MAR20188,MAM01098m <=> MAM01098c,MAM01098c;MAM01098m,ok,ok,ok,N/A diff --git a/data/testResults/macaw_summary.md b/data/testResults/macaw_summary.md index 26f5f7ab..94b1288d 100644 --- a/data/testResults/macaw_summary.md +++ b/data/testResults/macaw_summary.md @@ -1,7 +1,7 @@ Starting dead-end test... - - Found 1514 dead-end metabolites. - - Found 1319 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends. - - Found 1977 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends. + - Found 1523 dead-end metabolites. + - Found 1328 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends. + - Found 1975 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends. Starting duplicate test... - Skipping redox duplicates because no redox_pairs and/or proton_ids were provided. - Found 447 reactions that were some type of duplicate: diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 78429615..8e34d936 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -2868,23 +2868,23 @@ - charge: 0 - metFrom: "HMRdatabase" - !!omap - - id: "MAM00208c" + - id: "MAM00208m" - name: "[protein]-N6-(dihydrolipoyl)lysine" - compartment: "c" - formula: "C1375H2187N381O420S6" - charge: 0 - metFrom: "HMRdatabase" - !!omap - - id: "MAM00209c" + - id: "MAM00209m" - name: "[protein]-N6-(lipoyl)lysine" - - compartment: "c" + - compartment: "m" - formula: "C1375H2185N381O420S6" - charge: 0 - metFrom: "HMRdatabase" - !!omap - - id: "MAM00210c" + - id: "MAM00210m" - name: "[protein]-N6-(octanoyl)lysine" - - compartment: "c" + - compartment: "m" - formula: "C1375H2187N381O420S4" - charge: 0 - metFrom: "HMRdatabase" @@ -12152,6 +12152,13 @@ - formula: "C10H13N5O3" - charge: 0 - metFrom: "HMRdatabase" + - !!omap + - id: "MAM01098m" + - name: "5-deoxyadenosine" + - compartment: "m" + - formula: "C10H13N5O3" + - charge: 0 + - metFrom: "HMRdatabase" - !!omap - id: "MAM01099c" - name: "5-formiminotetrahydrofolate" @@ -24882,6 +24889,13 @@ - formula: "HS" - charge: -1 - metFrom: "HMRdatabase" + - !!omap + - id: "MAM02042m" + - name: "H2S" + - compartment: "m" + - formula: "HS" + - charge: -1 + - metFrom: "HMRdatabase" - !!omap - id: "MAM02042e" - name: "H2S" @@ -31908,6 +31922,14 @@ - formula: "C19H35N2O8PRS" - charge: -1 - metFrom: "HMRdatabase" + - !!omap + - id: "MAM02643m" + - name: "octanoyl-[ACP]" + - compartment: "m" + - formula: "C19H35N2O8PRS" + - charge: -1 + - inchis: "" + - metFrom: "" - !!omap - id: "MAM02644c" - name: "octanoyl-CoA" @@ -59997,6 +60019,27 @@ - formula: "C19H38O" - charge: 0 - inchis: "InChI=1S/C19H38O/c1-16(2)9-6-10-17(3)11-7-12-18(4)13-8-14-19(5)15-20/h15-19H,6-14H2,1-5H3" + - !!omap + - id: "MAM20084m" + - name: "4Fe4S iron-sulfur cluster" + - compartment: "m" + - formula: "S4Fe4" + - charge: 2 + - inchis: "InChI=1S/4Fe.4S/q;;2*+1;;;;" + - !!omap + - id: "MAM20085m" + - name: "2Fe2S iron-sulfur cluster" + - compartment: "m" + - formula: "S2Fe2" + - charge: 2 + - inchis: "InChI=1S/2Fe.2S/q2*+1;;" + - !!omap + - id: "MAM20086m" + - name: "GSSH" + - compartment: "m" + - formula: "C10H16N3O6S2" + - charge: -1 + - inchis: "InChI=1S/C10H17N3O6S2/c11-5(10(18)19)1-2-7(14)13-6(4-21-20)9(17)12-3-8(15)16/h5-6,20H,1-4,11H2,(H,12,17)(H,13,14)(H,15,16)(H,18,19)/t5-,6-/m0/s1" - reactions: - !!omap - id: "MAR03905" @@ -71766,7 +71809,7 @@ - !!omap - id: "MAR08433" - metabolites: !!omap - - MAM00209c: -1 + - MAM00209m: -1 - MAM01596m: 1 - MAM01986m: -1 - MAM02039m: -1 @@ -71785,7 +71828,7 @@ - !!omap - id: "MAR08434" - metabolites: !!omap - - MAM00208c: 1 + - MAM00208m: 1 - MAM01045m: 1 - MAM02039m: 1 - MAM02578m: 1 @@ -84253,7 +84296,7 @@ - MAM03103m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000140374 or ENSG00000105379 or ENSG00000171503 or ENSG00000100033 or ENSG00000250799 or ENSG00000115159 or ENSG00000102967 or ENSG00000016391" + - gene_reaction_rule: "ENSG00000016391 or ENSG00000100033 or ENSG00000102967 or ENSG00000105379 or ENSG00000115159 or ENSG00000137767 or ENSG00000140374 or ENSG00000171503 or ENSG00000250799" - rxnFrom: "HMRdatabase" - eccodes: "1.5.5.1" - references: "PMID:34428349" @@ -89685,15 +89728,15 @@ - id: "MAR06402" - name: "octanoyl-[acp]:protein N6-octanoyltransferase" - metabolites: !!omap - - MAM00184c: 1 - - MAM00210c: 1 - - MAM01350c: -1 - - MAM02643c: -1 + - MAM02484m: 1 + - MAM00210m: 1 + - MAM02643m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000175536" + - gene_reaction_rule: "ENSG00000004779 and ENSG00000140905 and ENSG00000175536" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.181" + - references: "PMID:24777537;PMID:28757203" - subsystem: - "Lipoic acid metabolism" - confidence_score: 0 @@ -89701,22 +89744,23 @@ - id: "MAR06403" - name: "[protein]-N6-(octanoyl)-L-lysine:an [Fe-S] cluster scaffold protein carrying a [4Fe-4S]2+ cluster sulfurtransferase" - metabolites: !!omap - - MAM00209c: 1 - - MAM00210c: -1 - - MAM01098c: 2 - - MAM02039c: -5 - - MAM02040c: 6 - - MAM02471c: 2 - - MAM02554c: 7 - - MAM02555c: -7 - - MAM02681c: 2 - - MAM02682c: -2 - - MAM02877c: -2 + - MAM00208m: 1 + - MAM00210m: -1 + - MAM01098m: 2 + - MAM01821m: 4 + - MAM02039m: -3 + - MAM02042m: 2 + - MAM02471m: 2 + - MAM02554m: 1 + - MAM02555m: -1 + - MAM02877m: -2 + - MAM20084m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000121897" + - gene_reaction_rule: "(ENSG00000121897 and ENSG00000137714 and ENSG00000140905 and ENSG00000161513 and ENSG00000135070) or (ENSG00000121897 and ENSG00000137714 and ENSG00000140905 and ENSG00000161513 and ENSG00000165898) or (ENSG00000121897 and ENSG00000137714 and ENSG00000140905 and ENSG00000161513 and ENSG00000169599)" - rxnFrom: "HMRdatabase" - eccodes: "2.8.1.8" + - references: "PMID:24777537;PMID:31493409;PMID:36281303;PMID:37453661" - subsystem: - "Lipoic acid metabolism" - confidence_score: 0 @@ -89724,11 +89768,11 @@ - id: "MAR06404" - name: "protein N6-(dihydrolipoyl)lysine:NAD+ oxidoreductase" - metabolites: !!omap - - MAM00208c: 1 - - MAM00209c: -1 - - MAM02039c: -1 - - MAM02552c: 1 - - MAM02553c: -1 + - MAM00208m: 1 + - MAM00209m: -1 + - MAM02039m: -1 + - MAM02552m: 1 + - MAM02553m: -1 - lower_bound: -1000 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000091140" @@ -187339,7 +187383,7 @@ - !!omap - id: "MAR00022" - metabolites: !!omap - - MAM00209c: -1 + - MAM00209m: -1 - MAM01401c: -1 - MAM01597c: -1 - MAM01600m: -1 @@ -260090,7 +260134,7 @@ - id: "MAR20168" - name: "MAR20168" - metabolites: !!omap - - MAM00209c: -1 + - MAM00209m: -1 - MAM02393m: 1 - lower_bound: 0 - upper_bound: 1000 @@ -260329,6 +260373,92 @@ - subsystem: - "Transport reactions" - confidence_score: 0 + - !!omap + - id: "MAR20184" + - name: "Synthesis of 4Fe4S from 2Fe2S" + - metabolites: !!omap + - MAM01285m: 2 + - MAM01371m: -2 + - MAM02039m: 3 + - MAM02040m: -2 + - MAM02554m: 1 + - MAM02555m: -1 + - MAM02751m: 2 + - MAM20084m: 1 + - MAM20085m: -2 + - lower_bound: 0 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100209 and ENSG00000109519 and ENSG00000113013 and ENSG00000135070 and ENSG00000161513 and ENSG00000165898 and ENSG00000181873 and ENSG00000182512 and ENSG00000267673" + - references: "PMID:31918395;PMID:31935115" + - subsystem: + - "Sulfur metabolism" + - confidence_score: 0 + - !!omap + - id: "MAR20185" + - name: "De novo synthesis of 2Fe2S" + - metabolites: !!omap + - MAM01307m: 2 + - MAM01628m: -2 + - MAM01821m: -2 + - MAM02039m: 1 + - MAM02554m: 1 + - MAM02555m: -1 + - MAM20085m: 1 + - lower_bound: 0 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000004779 and ENSG00000136003 and ENSG00000161513 and ENSG00000165060 and ENSG00000214113 and ENSG00000244005 and ENSG00000267673" + - references: "PMID:31918395;PMID:31935115" + - subsystem: + - "Sulfur metabolism" + - confidence_score: 0 + - !!omap + - id: "MAR20186" + - name: "Sulfide:glutathione,quinone oxidoreductase" + - metabolites: !!omap + - MAM01802m: -1 + - MAM01803m: 1 + - MAM02026m: -1 + - MAM02039m: -1 + - MAM02042m: -1 + - MAM20086m: 1 + - lower_bound: 0 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000137767" + - eccodes: "1.8.5.8" + - references: "PMID:25225291" + - subsystem: + - "Sulfur metabolism" + - confidence_score: 0 + - !!omap + - id: "MAR20187" + - name: "Persulfide dioxygenase" + - metabolites: !!omap + - MAM02026m: 1 + - MAM02039m: 2 + - MAM02040m: -1 + - MAM02630m: -1 + - MAM02949m: 1 + - MAM20086m: -1 + - lower_bound: 0 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000105755" + - eccodes: "1.13.11.18" + - references: "PMID:25225291" + - subsystem: + - "Sulfur metabolism" + - confidence_score: 0 + - !!omap + - id: "MAR20188" + - name: "Export of 5'-deoxyadenosine from mitochondria" + - metabolites: !!omap + - MAM01098c: 1 + - MAM01098m: -1 + - lower_bound: -1000 + - upper_bound: 1000 + - references: "PMID:34126623" + - subsystem: + - "Transport reactions" + - confidence_score: 0 - genes: - !!omap - id: "ENSG00000000419" @@ -261656,6 +261786,9 @@ - !!omap - id: "ENSG00000100197" - name: "CYP2D6" + - !!omap + - id: "ENSG00000100209" + - name: "HSCB" - !!omap - id: "ENSG00000100243" - name: "CYB5R3" @@ -262181,6 +262314,9 @@ - !!omap - id: "ENSG00000105701" - name: "FKBP8" + - !!omap + - id: "ENSG00000105755" + - name: "ETHE1" - !!omap - id: "ENSG00000105835" - name: "NAMPT" @@ -262412,6 +262548,9 @@ - !!omap - id: "ENSG00000109452" - name: "INPP4B" + - !!omap + - id: "ENSG00000109519" + - name: "GRPEL1" - !!omap - id: "ENSG00000109576" - name: "AADAT" @@ -262697,6 +262836,9 @@ - !!omap - id: "ENSG00000112992" - name: "NNT" + - !!omap + - id: "ENSG00000113013" + - name: "HSPA9" - !!omap - id: "ENSG00000113073" - name: "SLC4A9" @@ -264095,6 +264237,9 @@ - !!omap - id: "ENSG00000135069" - name: "PSAT1" + - !!omap + - id: "ENSG00000135070" + - name: "ISCA1" - !!omap - id: "ENSG00000135093" - name: "USP30" @@ -264176,6 +264321,9 @@ - !!omap - id: "ENSG00000135940" - name: "COX5B" + - !!omap + - id: "ENSG00000136003" + - name: "ISCU" - !!omap - id: "ENSG00000136010" - name: "ALDH1L2" @@ -264317,9 +264465,15 @@ - !!omap - id: "ENSG00000137563" - name: "GGH" + - !!omap + - id: "ENSG00000137714" + - name: "FDX1" - !!omap - id: "ENSG00000137731" - name: "FXYD2" + - !!omap + - id: "ENSG00000137767" + - name: "SQOR" - !!omap - id: "ENSG00000137770" - name: "CTDSPL2" @@ -266369,6 +266523,9 @@ - !!omap - id: "ENSG00000165841" - name: "CYP2C19" + - !!omap + - id: "ENSG00000165898" + - name: "ISCA2" - !!omap - id: "ENSG00000165970" - name: "SLC6A5" @@ -266762,6 +266919,9 @@ - !!omap - id: "ENSG00000169432" - name: "SCN9A" + - !!omap + - id: "ENSG00000169599" + - name: "NFU1" - !!omap - id: "ENSG00000169660" - name: "HEXD" @@ -267596,6 +267756,9 @@ - !!omap - id: "ENSG00000181867" - name: "FTMT" + - !!omap + - id: "ENSG00000181873" + - name: "IBA57" - !!omap - id: "ENSG00000181915" - name: "ADO" @@ -267635,6 +267798,9 @@ - !!omap - id: "ENSG00000182415" - name: "CDY2A" + - !!omap + - id: "ENSG00000182512" + - name: "GLRX5" - !!omap - id: "ENSG00000182551" - name: "ADI1" @@ -268550,6 +268716,9 @@ - !!omap - id: "ENSG00000214013" - name: "GANC" + - !!omap + - id: "ENSG00000214113" + - name: "LYRM4" - !!omap - id: "ENSG00000214160" - name: "ALG3" @@ -268760,6 +268929,9 @@ - !!omap - id: "ENSG00000243989" - name: "ACY1" + - !!omap + - id: "ENSG00000244005" + - name: "NFS1" - !!omap - id: "ENSG00000244038" - name: "DDOST" @@ -268865,6 +269037,9 @@ - !!omap - id: "ENSG00000266200" - name: "PNLIPRP2" + - !!omap + - id: "ENSG00000267673" + - name: "FDX2" - !!omap - id: "ENSG00000267855" - name: "NDUFA7" diff --git a/model/genes.tsv b/model/genes.tsv index 26405529..67ebb53b 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -2865,3 +2865,18 @@ "ENSG00000196407" "ENST00000368817.10;ENST00000453881.2" "ENSP00000357807.4;ENSP00000406809.2" "Q8N1Q8" "THEM5" "284486" "thioesterase superfamily member 5" "ACOT15" "Inner mitochondria" "SwissProt" "ENSG00000013306" "ENST00000377095;ENST00000225308;ENST00000590194;ENST00000537904;ENST00000586016;ENST00000588049;ENST00000592857;ENST00000588767;ENST00000585523;ENST00000586633;ENST00000585636;ENST00000593166;ENST00000591006;ENST00000588315;ENST00000585695;ENST00000592372;ENST00000591151" "ENSP00000366299;ENSP00000225308;ENSP00000467681;ENSP00000444540;ENSP00000466676;ENSP00000465182;ENSP00000467956;ENSP00000466615;ENSP00000466144;ENSP00000465594;ENSP00000465554" "Q9BZJ4" "SLC25A39" "51629" "solute carrier family 25 member 39" "" "" "" "ENSG00000075303" "ENST00000341119;ENST00000429674;ENST00000444363;ENST00000446236;ENST00000470328;ENST00000483810;ENST00000491499;ENST00000496348" "ENSP00000344831;ENSP00000401473;ENSP00000405566;ENSP00000407780" "Q8TBP6" "SLC25A40" "55972" "solute carrier family 25 member 40" "MCFP" "" "" +"ENSG00000100209" "ENST00000216027.8;ENST00000398941.6" "ENSP00000216027.3;ENSP00000381914.2" "Q8IWL3" "HSCB" "150274" "HscB mitochondrial iron-sulfur cluster cochaperone" "" "" "" +"ENSG00000105755" "ENST00000292147.7;ENST00000600651.5" "ENSP00000292147.1;ENSP00000469037.1" "O95571" "ETHE1" "23474" "ETHE1 persulfide dioxygenase" "" "" "" +"ENSG00000109519" "ENST00000264954.5;ENST00000706689.1" "ENSP00000264954.4;ENSP00000516503.1" "Q9HAV7" "GRPEL1" "80273" "GrpE like 1, mitochondrial" "" "" "" +"ENSG00000113013" "ENST00000297185.9;ENST00000677066.1;ENST00000678300.1;ENST00000678384.1;ENST00000678051.1;ENST00000677425.1;ENST00000677064.1;ENST00000507115.6" "ENSP00000297185.3;ENSP00000502902.1;ENSP00000503259.1;ENSP00000503992.1;ENSP00000503219.1;ENSP00000503066.1;ENSP00000503373.1;ENSP00000423759.2" "P38646" "HSPA9" "3313" "heat shock protein family A (Hsp70) member 9" "" "" "" +"ENSG00000135070" "ENST00000375991.9;ENST00000326094.4;ENST00000311534.6;ENST00000637705.1" "Q9BUE6" "ISCA1" "81689" "iron-sulfur cluster assembly 1" "" "" "" +"ENSG00000136003" "ENST00000311893.14;ENST00000535729.5;ENST00000539593.1;ENST00000392807.8;ENST00000431221.6;ENST00000547005.5" "ENSP00000310623.9;ENSP00000445598.1;ENSP00000443272.1;ENSP00000376554.4;ENSP00000411108.2;ENSP00000446606.1" "Q9H1K1" "ISCU" "23479" "iron-sulfur cluster assembly enzyme" "" "" "" +"ENSG00000137714" "ENST00000260270.3" "ENSP00000260270.2" "P10109" "FDX1" "2230" "ferredoxin 1" +"ENSG00000137767" "ENST00000260324.12;ENST00000568606.5;ENST00000566934.1;ENST00000561735.5;ENST00000561493.5;ENST00000563296.1;ENST00000565997.1;ENST00000565227.1" "ENSP00000260324.7;ENSP00000456019.1;ENSP00000454520.1;ENSP00000456075.1;ENSP00000457937.1;ENSP00000456979.1;ENSP00000454953.1;ENSP00000457592.1" "Q9Y6N5" "SQOR" "58472" "sulfide quinone oxidoreductase" "" "" "" +"ENSG00000165898" "ENST00000556816.6;ENST00000298818.12;ENST00000554924.1" "ENSP00000452007.1;ENSP00000298818.8;ENSP00000450523.1" "Q86U28" "ISCA2" "122961" "iron-sulfur cluster assembly 2" "" "" "" +"ENSG00000169599" "ENST00000410022.7;ENST00000394305.5;ENST00000303698.7;ENST00000484177.5;ENST00000450796.6;ENST00000462320.5" "ENSP00000387219.3;ENSP00000377842.1;ENSP00000306965.3;ENSP00000417693.1;ENSP00000415102.2;ENSP00000418598.1" "Q9UMS0" "NFU1" "27247" "NFU1 iron-sulfur cluster scaffold" "" "" "" +"ENSG00000181873" "ENST00000366711.4" "ENSP00000355672.3" "Q5T440" "IBA57" "200205" "iron-sulfur cluster assembly factor IBA57" "" "" "" +"ENSG00000182512" "ENST00000331334.5;ENST00000557731.1" "ENSP00000328570.4;ENSP00000451800.1" "Q86SX6" "GLRX5" "51218" "glutaredoxin 5" "" "" "" +"ENSG00000244005" "ENST00000374092.9;ENST00000374085.5;ENST00000397425.5;ENST00000541387.5;ENST00000306750.3;ENST00000419569.5" "ENSP00000363205.3;ENSP00000363198.1;ENSP00000380570.1;ENSP00000440897.1;ENSP00000304740.3;ENSP00000393482.1" "Q9Y697" "NFS1" "9054" "NFS1 cysteine desulfurase" "" "" "" +"ENSG00000267673" "ENST00000393708.3;ENST00000492239.5;ENST00000494368.5;ENST00000706663.1" "ENSP00000377311.5;ENSP00000488228.1;ENSP00000467188.1;ENSP00000516489.1" "Q6P4F2" "FDX2" "112812" "ferredoxin 2" "" "" "" +"ENSG00000214113" "ENST00000330636.9;ENST00000464010.5;ENST00000468929.5;ENST00000480566.5;ENST00000500576.4" "ENSP00000418787.1;ENSP00000420026.1;ENSP00000418321.1;ENSP00000419928.1;ENSP00000443900.3" "Q9HD34" "LYRM4" "57128" "LYR motif containing 4" "" "" "" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 109e0df2..5056c497 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -402,9 +402,9 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM00205r" "MAM00205" "Ser_Gly_Ala_X_Gly" "C02189" "" "" "" "" "" "" "Ser_Gly_Ala_X_Gly" "MNXM146222" "m00205r" "m00205r" "MAM00206c" "MAM00206" "" "C00585" "" "" "" "" "" "" "M00206" "MNXM7713" "m00206c" "m00206c" "MAM00207c" "MAM00207" "" "C03636" "" "" "" "" "" "" "M00207" "MNXM21326" "m00207c" "m00207c" -"MAM00208c" "MAM00208" "" "C16832" "" "" "" "" "" "" "M00208" "MNXM21289" "m00208c" "m00208c" -"MAM00209c" "MAM00209" "" "C16237" "" "" "" "" "" "" "M00209" "MNXM96070" "m00209c" "m00209c" -"MAM00210c" "MAM00210" "" "C16236" "" "" "" "" "" "" "M00210" "MNXM4090" "m00210c" "m00210c" +"MAM00208m" "MAM00208" "" "C16832" "" "" "" "" "" "" "M00208" "MNXM21289" "m00208c" "m00208c" +"MAM00209m" "MAM00209" "" "C16237" "" "" "" "" "" "" "M00209" "MNXM96070" "m00209c" "m00209c" +"MAM00210m" "MAM00210" "" "C16236" "" "" "" "" "" "" "M00210" "MNXM4090" "m00210c" "m00210c" "MAM00211c" "MAM00211" "Ntmelys" "C05546" "" "" "" "" "" "" "Ntmelys" "MNXM4790" "m00211c" "m00211c" "MAM00211n" "MAM00211" "Ntmelys" "C05546" "" "" "" "" "" "" "Ntmelys" "MNXM4790" "m00211n" "m00211n" "MAM00211r" "MAM00211" "Ntmelys" "C05546" "" "" "" "" "" "" "Ntmelys" "MNXM4790" "m00211r" "m00211r" @@ -1715,6 +1715,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01097m" "MAM01097" "" "" "" "" "" "" "CE5723" "" "CE5723" "MNXM37804" "m01097m" "m01097m" "MAM01098c" "MAM01098" "dad_5" "C05198" "" "" "" "" "" "" "dad_5" "MNXM316" "m01098c" "m01098c" "MAM01098e" "MAM01098" "dad_5" "C05198" "" "" "" "" "" "" "dad_5" "MNXM316" "m01098s" "m01098s" +"MAM01098m" "MAM01098" "dad_5" "C05198" "" "" "" "" "" "" "" "MNXM316" "" "" "MAM01099c" "MAM01099" "5forthf" "C00664" "" "CHEBI:15639" "530" "" "" "HC00483" "5forthf" "MNXM915" "m01099c" "m01099c" "MAM01100c" "MAM01100" "5fthf" "C03479" "HMDB0001562" "CHEBI:209153" "143" "" "" "HC01125" "5fthf" "MNXM1392" "m01100c" "m01100c" "MAM01100m" "MAM01100" "5fthf" "C03479" "HMDB0001562" "CHEBI:209153" "143" "" "" "HC01125" "5fthf" "MNXM1392" "m01100m" "m01100m" @@ -3521,6 +3522,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02041e" "MAM02041" "h2o2" "C00027" "HMDB0003125" "CHEBI:16240" "784" "" "" "HC00036" "h2o2" "MNXM22" "m02041s" "m02041s" "MAM02042c" "MAM02042" "" "C00283" "" "CHEBI:16136" "402" "" "" "HC00250" "HC00250" "MNXM162964;MNXM89582" "m02042c" "m02042c" "MAM02042e" "MAM02042" "" "C00283" "" "CHEBI:16136" "402" "" "" "HC00250" "HC00250" "MNXM162964;MNXM89582" "m02042s" "m02042s" +"MAM02042m" "MAM02042" "" "C00283" "" "CHEBI:16136" "402" "" "" "" "" "MNXM162964;MNXM89582" "" "" "MAM02043c" "MAM02043" "" "C05529" "" "CHEBI:5587" "24478" "" "" "HC01501" "HC01501" "MNXM164836;MNXM323" "m02043c" "m02043c" "MAM02044c" "MAM02044" "" "" "" "" "" "PROTEIN" "" "HC01939" "HC01939" "" "m02044c" "m02044c" "MAM02044l" "MAM02044" "" "" "" "" "" "PROTEIN" "" "HC01939" "HC01939" "" "m02044l" "m02044l" @@ -4514,6 +4516,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02642c" "MAM02642" "octa" "C06423" "HMDB0000482" "CHEBI:28837" "379" "LMFA01010008" "" "" "octa" "MNXM750" "m02642c" "m02642c" "MAM02642e" "MAM02642" "octa" "C06423" "HMDB0000482" "CHEBI:28837" "379" "LMFA01010008" "" "" "octa" "MNXM750" "m02642s" "m02642s" "MAM02643c" "MAM02643" "" "C05752" "" "" "" "" "" "HC01595" "HC01595" "MNXM979" "m02643c" "m02643c" +"MAM02643m" "MAM02643" "" "C05752" "" "" "" "" "" "" "" "MNXM979" "" "" "MAM02644c" "MAM02644" "occoa" "C01944" "HMDB0001070" "CHEBI:15533" "380" "" "" "HC00869" "occoa" "MNXM342" "m02644c" "m02644c" "MAM02644m" "MAM02644" "occoa" "C01944" "HMDB0001070" "CHEBI:15533" "380" "" "" "HC00869" "occoa" "MNXM342" "m02644m" "m02644m" "MAM02644x" "MAM02644" "occoa" "C01944" "HMDB0001070" "CHEBI:15533" "380" "" "" "HC00869" "occoa" "MNXM342" "m02644p" "m02644p" @@ -8451,6 +8454,9 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03884e" "MAM03884" "phyt" "C01607" "HMDB0000801" "CHEBI:16285" "26840" "" "" "" "phyt" "MNXM91275" "" "phyt_s" "MAM03884x" "MAM03884" "phyt" "C01607" "HMDB0000801" "CHEBI:16285" "26840" "" "" "" "phyt" "MNXM91275" "" "phyt_p" "MAM20083x" "MAM20083" "pristanal" "" "HMDB0001958" "CHEBI:49189" "14671060" "LMPR0104010012" "" "" "" "MNXM1947" "" "" -"MAM00077x" "MAM00077" "CE2416" "" "HMDB0000795" "CHEBI:51340" "123929" "LMPR0104010022" "CE2416" "" "" "MNXM747404" "m00077p" "m00077p" -"MAM00077c" "MAM00077" "CE2416" "" "HMDB0000795" "CHEBI:51340" "123929" "LMPR0104010022" "" "" "" "MNXM747404" "" "" -"MAM00077e" "MAM00077" "CE2416" "" "HMDB0000795" "CHEBI:51340" "123929" "LMPR0104010022" "" "" "" "MNXM747404" "" "" +"MAM00077x" "MAM00077" "" "CE2416" "HMDB0000795" "CHEBI:51340" "123929" "LMPR0104010022" "CE2416" "" "" "MNXM747404" "m00077p" "m00077p" +"MAM00077c" "MAM00077" "" "CE2416" "HMDB0000795" "CHEBI:51340" "123929" "LMPR0104010022" "" "" "" "MNXM747404" "" "" +"MAM00077e" "MAM00077" "" "CE2416" "HMDB0000795" "CHEBI:51340" "123929" "LMPR0104010022" "" "" "" "MNXM747404" "" "" +"MAM20084m" "MAM20084" "4fe4s" "" "" "CHEBI:33722" "6398953" "" "" "" "" "MNXM732007" "" "" +"MAM20085m" "MAM20085" "2fe2s" "" "" "CHEBI:33737" "5460691" "" "" "" "" "MNXM1107419" "" "" +"MAM20086m" "MAM20086" "" "C17267" "" "CHEBI:52857" "44176418" "" "" "" "" "MNXM2032" "" "" diff --git a/model/reactions.tsv b/model/reactions.tsv index 4fa8c7c9..0227b7c2 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -12967,3 +12967,8 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR20181" "" "" "" "" "" "" "" "" "" "2.A.29.16.1" 0 "RHEA:73386" "RHEA:73383" "" "MAR20182" "" "" "" "" "" "" "" "" "" "2.A.29.16.1" 0 "" "" "" "MAR20183" "" "" "" "" "" "" "" "" "" "2.A.29.16.1" 0 "" "" "" +"MAR20184" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20185" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20186" "R11929" "" "" "" "" "" "MNXR171837" "" "" "" 0 "RHEA:62609" "RHEA:62608" "" +"MAR20187" "R08678" "" "" "" "" "" "MNXR112193" "" "" "" 0 "RHEA:12982" "RHEA:12981" "" +"MAR20188" "" "" "" "" "" "" "" "" "" "" 0 "" "" ""