From 7635dd67b5b17bfa113c86774701d9304367f59a Mon Sep 17 00:00:00 2001 From: Pranas Grigaitis Date: Fri, 27 Oct 2023 16:05:06 +0200 Subject: [PATCH 1/7] Removed hexanoate, MAM03684c --- .../deprecatedMetabolites.tsv | 4 ++ .../deprecatedReactions.tsv | 2 + model/Human-GEM.yml | 51 ++++--------------- model/metabolites.tsv | 4 -- model/reactions.tsv | 2 - 5 files changed, 16 insertions(+), 47 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 89187083..46c89a90 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2252,3 +2252,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM20020r" "MAM20020" "C00061" "" "" "CHEBI:58210" "" "" "" "" "" "MNXM1105928" "" "" "MAM20022i" "MAM20022" "C01847" "" "" "CHEBI:57618" "" "" "" "" "" "MNXM1107623" "" "" "MAM20023i" "MAM20023" "C00061" "" "" "CHEBI:58210" "" "" "" "" "" "MNXM1105928" "" "" +"MAM03684c" "MAM03684" "hxa" "" "" "CHEBI:17120" "" "" "" "" "hxa" "MNXM1653" "" "hxa_c" +"MAM03684m" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_m" +"MAM03684e" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_s" +"MAM03684x" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_p" diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 2af418d9..d4bc21fc 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -253,3 +253,5 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00482" "R00848;R00849" "G3PD2m" "R00848C" "r0205" "" "HMR_0482;r0205" "MNXR99875;MNXR106713" "HMR_0482;HMR_0483" "RCR14578;RCR21050" "" 0 "" "RHEA:31283;RHEA:18977" "HMR_0482;HMR_0483;MAR00483" "MAR20012" "R02123" "HMR_6647;RADH;R_HMR_6647;R_RADH" "" "" "" "" "MNXR146215" "" "" "" 0 "RHEA:42080" "" "" "MAR20089" "R02701" "" "" "" "" "" "MNXR151808" "" "" "" 0 "RHEA:18533" "" "" +"MAR11292" "" "HXAt3" "" "" "" "HXAt3" "" "" "" "" 0 "" "" "HXAt3" +"MAR11293" "" "EX_hxa_e" "" "" "" "EX_hxa[e]" "MNXR98664" "" "" "" 0 "" "" "EX_hxa[e]" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 6c7c5541..cd6b197d 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -248771,8 +248771,8 @@ - MAM02039c: 1 - MAM02040c: -1 - MAM02122c: -1 - - MAM03684c: 1 - - lower_bound: -1000 + - MAM02120c: 1 + - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "" - rxnNotes: "" @@ -253882,7 +253882,7 @@ - MAM02039m: 1 - MAM02040m: -1 - MAM02122m: -1 - - MAM03684m: 1 + - MAM02120m: 1 - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "" @@ -253933,8 +253933,8 @@ - MAM02039x: 1 - MAM02040x: -1 - MAM02122x: -1 - - MAM03684x: 1 - - lower_bound: -1000 + - MAM02120x: 1 + - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: "" - rxnNotes: "" @@ -269403,8 +269403,8 @@ - id: "MAR11290" - name: "Transport of Hexanoate (N-C6:0), Mitochondrial" - metabolites: !!omap - - MAM03684c: 1 - - MAM03684m: -1 + - MAM02120c: 1 + - MAM02120m: -1 - lower_bound: -1000 - upper_bound: 1000 - gene_reaction_rule: "" @@ -269419,24 +269419,8 @@ - id: "MAR11291" - name: "Transport of Hexanoate (N-C6:0), Peroxisome" - metabolites: !!omap - - MAM03684c: 1 - - MAM03684x: -1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - - !!omap - - id: "MAR11292" - - name: "Transport of Hexanoate (N-C6:0), Extracellular" - - metabolites: !!omap - - MAM03684c: -1 - - MAM03684e: 1 + - MAM02120c: 1 + - MAM02120x: -1 - lower_bound: -1000 - upper_bound: 1000 - gene_reaction_rule: "" @@ -269447,21 +269431,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR11293" - - name: "Exchange of Hexanoate (N-C6:0)" - - metabolites: !!omap - - MAM03684e: -1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "" - - references: "" - - subsystem: - - "Exchange/demand reactions" - - confidence_score: 0 - !!omap - id: "MAR11294" - name: "Hydrolysis of Fatty Acyl Coenzyme A (14:1)" @@ -303070,7 +303039,7 @@ - MAM02040c: -1 - MAM02554c: -1 - MAM02555c: 1 - - MAM03684c: 1 + - MAM02120c: 1 - MAM20037c: -1 - lower_bound: 0 - upper_bound: 1000 diff --git a/model/metabolites.tsv b/model/metabolites.tsv index a87f5787..87419caf 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -6651,7 +6651,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03814c" "MAM03814" "pchollinl_hs" "" "" "CHEBI:28733" "" "" "" "" "pchollinl_hs" "" "" "pchollinl_hs_c" "MAM03856c" "MAM03856" "pelinl_hs" "" "" "CHEBI:83058" "" "" "" "" "pelinl_hs" "" "" "pelinl_hs_c" "MAM03569c" "MAM03569" "eidi1114ac" "C16525" "HMDB0005060" "CHEBI:603631" "6439848" "" "" "" "eidi1114ac" "" "" "eidi1114ac_c" -"MAM03684c" "MAM03684" "hxa" "" "" "CHEBI:17120" "" "" "" "" "hxa" "MNXM1653" "" "hxa_c" "MAM03976c" "MAM03976" "tetdeca511ac" "" "" "" "" "" "" "" "tetdeca511ac" "" "" "tetdeca511ac_c" "MAM03619c" "MAM03619" "glyc2p" "" "" "CHEBI:58083" "" "" "" "" "glyc2p" "MNXM2527" "" "glyc2p_c" "MAM03401c" "MAM03401" "aclys" "" "" "" "" "" "" "" "aclys" "" "" "aclys_c" @@ -6794,8 +6793,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM03619e" "MAM03619" "glyc2p" "" "" "" "" "" "" "" "glyc2p" "MNXM2527" "" "glyc2p_s" "MAM01998e" "MAM01998" "glyclt" "C00160" "HMDB0000115" "CHEBI:17497" "757" "" "" "" "glyclt" "MNXM222" "" "m01998s" "MAM03232e" "MAM03232" "3hpppn" "" "" "" "" "" "" "" "3hpppn" "MNXM1634" "" "3hpppn_s" -"MAM03684m" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_m" -"MAM03684x" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_p" "MAM02169e" "MAM02169" "ind3ac" "C00954" "HMDB0000197" "CHEBI:16411" "802" "" "" "" "ind3ac" "MNXM383" "" "m02169s" "MAM02350e" "MAM02350" "Lcyst" "C00506" "HMDB0002757" "CHEBI:21260" "25701" "" "" "" "Lcyst" "MNXM713" "" "m02350s" "MAM02413c" "MAM02413" "Lpipecol" "C00408" "HMDB0000716" "CHEBI:30913" "439227" "" "" "" "Lpipecol" "MNXM684" "" "m02413c" @@ -7329,7 +7326,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM04078c" "MAM04078" "" "" "" "" "" "" "" "" "xolest204_hs" "" "" "xolest204_hs_c" "MAM04080c" "MAM04080" "xolest226_hs" "" "" "" "" "" "" "" "xolest226_hs" "" "" "xolest226_hs_c" "MAM02908e" "MAM02908" "sphmyln_hs" "C00550" "" "CHEBI:17636" "" "LMSP03010000" "" "HC02007" "sphmyln_hs" "MNXM5930" "" "m02908s" -"MAM03684e" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_s" "MAM01954c" "MAM01954" "gncore1" "" "" "" "" "" "" "" "gncore1" "MNXM18091" "" "m01954c" "MAM01954e" "MAM01954" "gncore1" "" "" "" "" "" "" "" "gncore1" "MNXM18091" "" "m01954s" "MAM03394c" "MAM03394" "Lhcystin" "" "" "" "" "" "" "" "Lhcystin" "" "" "Lhcystin_c" diff --git a/model/reactions.tsv b/model/reactions.tsv index 5de1d8ae..bbdcc6bc 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -10967,8 +10967,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR11289" "" "PHEACGLYtm" "" "" "" "PHEACGLYtm" "MNXR157011" "" "" "" 0 "" "" "PHEACGLYtm" "MAR11290" "" "HXAt1" "" "" "" "HXAt1" "" "" "" "" 0 "" "" "HXAt1" "MAR11291" "" "HXAt2" "" "" "" "HXAt2" "" "" "" "" 0 "" "" "HXAt2" -"MAR11292" "" "HXAt3" "" "" "" "HXAt3" "" "" "" "" 0 "" "" "HXAt3" -"MAR11293" "" "EX_hxa_e" "" "" "" "EX_hxa[e]" "MNXR98664" "" "" "" 0 "" "" "EX_hxa[e]" "MAR11294" "" "TTDCEAc" "" "" "" "TTDCEAc" "" "" "" "" 0 "" "" "TTDCEAc" "MAR11295" "" "PACCOALm" "" "" "" "PACCOALm" "" "" "" "" 0 "" "" "PACCOALm" "MAR11296" "" "PACALDtm" "" "" "" "PACALDtm" "MNXR102312" "" "" "" 0 "" "" "PACALDtm" From c490f1d5e08375a3897ecac7fc9e7c0ed809da7e Mon Sep 17 00:00:00 2001 From: Pranas Grigaitis Date: Fri, 27 Oct 2023 16:09:40 +0200 Subject: [PATCH 2/7] Added missing [x] and [m] species --- model/metabolites.tsv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 87419caf..b081d728 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -3654,6 +3654,8 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02119e" "MAM02119" "6thf" "" "" "" "169691" "" "" "" "6thf" "MNXM3616" "m02119s" "m02119s" "MAM02120c" "MAM02120" "" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "m02120c" "m02120c" "MAM02120e" "MAM02120" "" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "m02120s" "m02120s" +"MAM02120x" "MAM02120" "" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" +"MAM02120m" "MAM02120" "" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "MAM02121c" "MAM02121" "" "C05749" "" "" "" "" "" "HC01592" "HC01592" "MNXM23683" "m02121c" "m02121c" "MAM02122c" "MAM02122" "" "C05270" "HMDB0002845" "CHEBI:27540" "440611" "LMFA07050001" "" "HC01409" "hxcoa" "MNXM162502;MNXM553" "m02122c" "m02122c" "MAM02122m" "MAM02122" "" "C05270" "HMDB0002845" "CHEBI:27540" "440611" "LMFA07050001" "" "HC01409" "hxcoa" "MNXM162502;MNXM553" "m02122m" "m02122m" From 4139c46f6795297b183ee38649c0885f4910918c Mon Sep 17 00:00:00 2001 From: Pranas Grigaitis Date: Fri, 27 Oct 2023 16:16:01 +0200 Subject: [PATCH 3/7] Added species MAM02120x and MAM02120m to Human-GEM.yml --- model/Human-GEM.yml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index cd6b197d..b307432f 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -29249,6 +29249,22 @@ - charge: -1 - inchis: "" - metFrom: "HMRdatabase" + - !!omap + - id: "MAM02120x" + - name: "hexanoic acid" + - compartment: "x" + - formula: "C6H11O2" + - charge: -1 + - inchis: "" + - metFrom: "HMRdatabase" + - !!omap + - id: "MAM02120m" + - name: "hexanoic acid" + - compartment: "m" + - formula: "C6H11O2" + - charge: -1 + - inchis: "" + - metFrom: "HMRdatabase" - !!omap - id: "MAM02121c" - name: "hexanoyl-[ACP]" From ca73f3e81d80b21e9de6dc4c84a878999991a1fd Mon Sep 17 00:00:00 2001 From: Pranas Grigaitis Date: Fri, 27 Oct 2023 16:27:18 +0200 Subject: [PATCH 4/7] Removed deprecated species from the model --- model/Human-GEM.yml | 32 -------------------------------- 1 file changed, 32 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index b307432f..3968a10b 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -53241,14 +53241,6 @@ - charge: -1 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03684c" - - name: "Hexanoate (N-C6:0)" - - compartment: "c" - - formula: "C6H11O2" - - charge: -1 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM03976c" - name: "Cia-5,8, Tetradecadienoic Acid" @@ -54385,22 +54377,6 @@ - charge: -1 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03684m" - - name: "Hexanoate (N-C6:0)" - - compartment: "m" - - formula: "C6H11O2" - - charge: -1 - - inchis: "" - - metFrom: "Recon3D" - - !!omap - - id: "MAM03684x" - - name: "Hexanoate (N-C6:0)" - - compartment: "x" - - formula: "C6H11O2" - - charge: -1 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM02169e" - name: "indoleacetate" @@ -58665,14 +58641,6 @@ - charge: 0 - inchis: "" - metFrom: "Recon3D" - - !!omap - - id: "MAM03684e" - - name: "Hexanoate (N-C6:0)" - - compartment: "e" - - formula: "C6H11O2" - - charge: -1 - - inchis: "" - - metFrom: "Recon3D" - !!omap - id: "MAM01954c" - name: "glcnac-alpha-1,4-core 1" From 85203eccca3cbebbd141648c2024d77daad1091d Mon Sep 17 00:00:00 2001 From: Pranas Grigaitis Date: Fri, 27 Oct 2023 16:43:04 +0200 Subject: [PATCH 5/7] Removed duplicate rxn MAR09949 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 19 ------------------- model/reactions.tsv | 1 - 3 files changed, 1 insertion(+), 20 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index d4bc21fc..a28b8e5f 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -255,3 +255,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR20089" "R02701" "" "" "" "" "" "MNXR151808" "" "" "" 0 "RHEA:18533" "" "" "MAR11292" "" "HXAt3" "" "" "" "HXAt3" "" "" "" "" 0 "" "" "HXAt3" "MAR11293" "" "EX_hxa_e" "" "" "" "EX_hxa[e]" "MNXR98664" "" "" "" 0 "" "" "EX_hxa[e]" +"MAR09949" "" "FACOAE60" "" "" "" "HXCOAc" "MNXR99139" "" "" "" 0 "" "" "HXCOAc" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 3968a10b..153d24ce 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -248747,25 +248747,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR09949" - - name: "Acylcoa Hydrolase, Cytosolic" - - metabolites: !!omap - - MAM01597c: 1 - - MAM02039c: 1 - - MAM02040c: -1 - - MAM02122c: -1 - - MAM02120c: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "3.1.2.2" - - references: "" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR09950" - name: "Hydrolysis of Tetradecadienoyl Coenzyme A to Cis-5, 8-Tetradecadienoic Acid" diff --git a/model/reactions.tsv b/model/reactions.tsv index bbdcc6bc..228b566d 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -9743,7 +9743,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR09946" "" "" "" "" "" "XOLEST204CEH" "" "" "" "" 0 "" "" "XOLEST204CEH" "MAR09947" "" "XOLEST226CEH" "" "" "" "XOLEST226CEH" "" "" "" "" 0 "" "" "XOLEST226CEH" "MAR09948" "" "CE4843HYDc" "" "" "" "CE4843HYDc" "" "" "" "" 0 "" "" "CE4843HYDc" -"MAR09949" "" "FACOAE60" "" "" "" "HXCOAc" "MNXR99139" "" "" "" 0 "" "" "HXCOAc" "MAR09950" "" "TETDECA511ACc" "" "" "" "TETDECA511ACc" "" "" "" "" 0 "" "" "TETDECA511ACc" "MAR09951" "" "GPDDACHOL" "" "" "" "GPDDACHOL" "" "" "" "" 0 "" "" "GPDDACHOL" "MAR09952" "" "ACLYSHYc" "" "" "" "ACLYSHYc" "" "" "" "" 0 "" "" "ACLYSHYc" From f924ff617d77b99e23e4ee3b46ff24b642fc6443 Mon Sep 17 00:00:00 2001 From: Pranas Grigaitis Date: Sun, 29 Oct 2023 11:44:09 +0100 Subject: [PATCH 6/7] Added BiGG ID for MAM02120 --- model/metabolites.tsv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/model/metabolites.tsv b/model/metabolites.tsv index b081d728..d71f1795 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -3652,10 +3652,10 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM02119l" "MAM02119" "6thf" "" "" "" "169691" "" "" "" "6thf" "MNXM3616" "m02119l" "m02119l" "MAM02119m" "MAM02119" "6thf" "" "" "" "169691" "" "" "" "6thf" "MNXM3616" "m02119m" "m02119m" "MAM02119e" "MAM02119" "6thf" "" "" "" "169691" "" "" "" "6thf" "MNXM3616" "m02119s" "m02119s" -"MAM02120c" "MAM02120" "" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "m02120c" "m02120c" -"MAM02120e" "MAM02120" "" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "m02120s" "m02120s" -"MAM02120x" "MAM02120" "" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" -"MAM02120m" "MAM02120" "" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" +"MAM02120c" "MAM02120" "hxa" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "m02120c" "m02120c" +"MAM02120e" "MAM02120" "hxa" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "m02120s" "m02120s" +"MAM02120x" "MAM02120" "hxa" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" +"MAM02120m" "MAM02120" "hxa" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "MAM02121c" "MAM02121" "" "C05749" "" "" "" "" "" "HC01592" "HC01592" "MNXM23683" "m02121c" "m02121c" "MAM02122c" "MAM02122" "" "C05270" "HMDB0002845" "CHEBI:27540" "440611" "LMFA07050001" "" "HC01409" "hxcoa" "MNXM162502;MNXM553" "m02122c" "m02122c" "MAM02122m" "MAM02122" "" "C05270" "HMDB0002845" "CHEBI:27540" "440611" "LMFA07050001" "" "HC01409" "hxcoa" "MNXM162502;MNXM553" "m02122m" "m02122m" From d4d0c50a9678e4ebabf32601dcdd3fcdc1e64337 Mon Sep 17 00:00:00 2001 From: Pranas Grigaitis Date: Mon, 30 Oct 2023 10:10:22 +0100 Subject: [PATCH 7/7] Added GPRs to MAR10377 and MAR10374 --- model/Human-GEM.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 64f626c4..e38bdb19 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -253769,7 +253769,7 @@ - confidence_score: 0 - !!omap - id: "MAR10374" - - name: "Acyl-Coenzyme A Hydrolase, Mitochondrial" + - name: "Hexanoyl-CoA hydrolase, Mitochondrial" - metabolites: !!omap - MAM01597m: 1 - MAM02039m: 1 @@ -253778,7 +253778,7 @@ - MAM02120m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "" + - gene_reaction_rule: "ENSG00000123130" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" @@ -253820,7 +253820,7 @@ - confidence_score: 0 - !!omap - id: "MAR10377" - - name: "Acylcoa Hydrolase, Peroxisome" + - name: "Hexanoyl-CoA hydrolase, Peroxisome" - metabolites: !!omap - MAM01597x: 1 - MAM02039x: 1 @@ -253829,7 +253829,7 @@ - MAM02120x: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "" + - gene_reaction_rule: "ENSG00000101473" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: ""