From d8a9b18e74285996129b19fe40cf91557bd4f663 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 27 Sep 2023 12:56:59 -0400 Subject: [PATCH 01/10] remove MAR07785 for being a duplicate of MAR04908 --- .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 16 ---------------- model/reactions.tsv | 3 +-- 3 files changed, 2 insertions(+), 18 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 1938f667..53a45e22 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -230,3 +230,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00096" "" "BUP2" "" "" "" "BUP2" "MNXR96346" "" "" "" 0 "" "" "BUP2" "MAR02027" "" "r0193" "" "" "" "r0193" "MNXR105313" "" "" "" 0 "" "" "r0193" "MAR02006" "" "CPS_m" "" "" "" "r0034" "" "" "" "" 0 "" "" "r0034" +"MAR07785" "" "ATPtx" "" "" "" "ATPtx" "MNXR96140" "HMR_7785" "RCR20040" "" 0 "" "" "HMR_7785" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index a41283bd..df4e395f 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -201961,22 +201961,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR07785" - - name: "" - - metabolites: !!omap - - MAM01371c: -1 - - MAM01371x: 1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR07788" - name: "" diff --git a/model/reactions.tsv b/model/reactions.tsv index c79c8937..f94b661c 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -7043,7 +7043,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR07779" "" "NADPHtxu" "" "" "" "NADPHtxu" "MNXR101894" "HMR_7779" "RCR20311" "" 0 "" "" "HMR_7779" "MAR07782" "" "ADPtx" "" "" "" "ADPtx" "MNXR95484" "HMR_7782" "RCR20201" "" 0 "" "" "HMR_7782" "MAR07783" "" "AMPtp" "" "" "" "AMPtp" "MNXR95830" "HMR_7783" "RCR20046" "" 0 "" "" "HMR_7783" -"MAR07785" "" "ATPtx" "" "" "" "ATPtx" "MNXR96140" "HMR_7785" "RCR20040" "" 0 "" "" "HMR_7785" "MAR07788" "" "FADH2tx" "" "" "" "FADH2tx" "MNXR99212" "HMR_7788" "RCR20202" "" 0 "" "" "HMR_7788" "MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790" "MAR07797" "" "AKGtp" "" "" "" "AKGtp" "MNXR95663" "HMR_7797" "RCR20150" "" 0 "" "" "HMR_7797" @@ -9075,7 +9074,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04092" "" "EX_prostgh2_e" "" "" "" "EX_prostgh2[e]" "MNXR98873" "" "" "" 0 "" "" "EX_prostgh2[e]" "MAR04094" "" "EX_prostgi2_e" "" "" "" "EX_prostgi2[e]" "MNXR98874" "" "" "" 0 "" "" "EX_prostgi2[e]" "MAR04096" "" "EX_cdp_e" "" "" "" "EX_cdp[e]" "MNXR98331" "" "" "" 0 "" "" "EX_cdp[e]" -"MAR04098" "" "EX_dtdp_e" "" "" "" "EX_dtdp[e]" "MNXR98432" "" "" "" 0 "" "" "EX_dtdp[e]" +"MAR04098" "" "EX_dtdp_e" "" "" "" "EX_dtdp[e]" "MNXR98432" "" "" "" 0 "" "" "EX_dtdp[e];MAR07785" "MAR04100" "" "EX_HC00955_e" "" "" "" "EX_HC00955[e]" "MNXR98138" "" "" "" 0 "" "" "EX_HC00955[e]" "MAR04102" "" "" "" "" "" "EX_HC00002[e]" "" "" "" "" 0 "" "" "EX_HC00002[e]" "MAR04104" "" "" "" "" "" "EX_HC00003[e]" "" "" "" "" 0 "" "" "EX_HC00003[e]" From 27f64cb19ee4452c6fb337c5341792431028155b Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 27 Sep 2023 13:01:14 -0400 Subject: [PATCH 02/10] remove MAR07775 and MAR07788 --- .../deprecatedReactions.tsv | 2 ++ model/Human-GEM.yml | 32 ------------------- model/reactions.tsv | 2 -- 3 files changed, 2 insertions(+), 34 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 53a45e22..edcb6e07 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -231,3 +231,5 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR02027" "" "r0193" "" "" "" "r0193" "MNXR105313" "" "" "" 0 "" "" "r0193" "MAR02006" "" "CPS_m" "" "" "" "r0034" "" "" "" "" 0 "" "" "r0034" "MAR07785" "" "ATPtx" "" "" "" "ATPtx" "MNXR96140" "HMR_7785" "RCR20040" "" 0 "" "" "HMR_7785" +"MAR07775" "" "NADHtpu" "" "" "" "NADHtpu;NADtpu" "MNXR101881" "HMR_7775" "RCR20024" "" 0 "" "" "HMR_7775" +"MAR07788" "" "FADH2tx" "" "" "" "FADH2tx" "MNXR99212" "HMR_7788" "RCR20202" "" 0 "" "" "HMR_7788" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index df4e395f..8ce2f832 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -201881,22 +201881,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR07775" - - name: "" - - metabolites: !!omap - - MAM02553c: -1 - - MAM02553x: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR07777" - name: "" @@ -201961,22 +201945,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR07788" - - name: "" - - metabolites: !!omap - - MAM01803c: -1 - - MAM01803x: 1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR07790" - name: "" diff --git a/model/reactions.tsv b/model/reactions.tsv index f94b661c..50781e16 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -7038,12 +7038,10 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR07705" "" "GLYCLTtp" "" "" "" "GLYCLTtp" "MNXR100333" "HMR_7705" "RCR20712" "" 0 "" "" "HMR_7705" "MAR07707" "" "GLXtp" "" "" "" "GLXtp" "MNXR100306" "HMR_7707" "RCR20200" "" 0 "" "" "HMR_7707" "MAR07771" "" "NADtpu" "" "" "" "NADtx" "MNXR101881" "HMR_7771" "RCR20023" "" 0 "" "" "HMR_7771" -"MAR07775" "" "NADHtpu" "" "" "" "NADHtpu;NADtpu" "MNXR101881" "HMR_7775" "RCR20024" "" 0 "" "" "HMR_7775" "MAR07777" "" "NADPtxu" "" "" "" "NADPtxu" "MNXR101896" "HMR_7777" "RCR20713" "" 0 "" "" "HMR_7777" "MAR07779" "" "NADPHtxu" "" "" "" "NADPHtxu" "MNXR101894" "HMR_7779" "RCR20311" "" 0 "" "" "HMR_7779" "MAR07782" "" "ADPtx" "" "" "" "ADPtx" "MNXR95484" "HMR_7782" "RCR20201" "" 0 "" "" "HMR_7782" "MAR07783" "" "AMPtp" "" "" "" "AMPtp" "MNXR95830" "HMR_7783" "RCR20046" "" 0 "" "" "HMR_7783" -"MAR07788" "" "FADH2tx" "" "" "" "FADH2tx" "MNXR99212" "HMR_7788" "RCR20202" "" 0 "" "" "HMR_7788" "MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790" "MAR07797" "" "AKGtp" "" "" "" "AKGtp" "MNXR95663" "HMR_7797" "RCR20150" "" 0 "" "" "HMR_7797" "MAR08016" "" "LYStip" "" "" "" "LYStip" "MNXR101269" "HMR_8016" "RCR20033" "" 0 "" "" "HMR_8016" From e0ff4ddace7979d543e7c8562d10dc8812629174 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 27 Sep 2023 13:04:27 -0400 Subject: [PATCH 03/10] remove MAR04915, MAR07782, MAR07783, and MAR07790 --- .../deprecatedReactions.tsv | 5 ++ model/Human-GEM.yml | 80 ------------------- model/reactions.tsv | 5 -- 3 files changed, 5 insertions(+), 85 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index edcb6e07..80ca45d6 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -233,3 +233,8 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR07785" "" "ATPtx" "" "" "" "ATPtx" "MNXR96140" "HMR_7785" "RCR20040" "" 0 "" "" "HMR_7785" "MAR07775" "" "NADHtpu" "" "" "" "NADHtpu;NADtpu" "MNXR101881" "HMR_7775" "RCR20024" "" 0 "" "" "HMR_7775" "MAR07788" "" "FADH2tx" "" "" "" "FADH2tx" "MNXR99212" "HMR_7788" "RCR20202" "" 0 "" "" "HMR_7788" +"MAR04915" "" "COAtp" "" "r0864" "" "COAtp" "MNXR96815" "HMR_4915" "RCR20004" "" 0 "" "" "HMR_4915" +"MAR07771" "" "NADtpu" "" "" "" "NADtx" "MNXR101881" "HMR_7771" "RCR20023" "" 0 "" "" "HMR_7771" +"MAR07782" "" "ADPtx" "" "" "" "ADPtx" "MNXR95484" "HMR_7782" "RCR20201" "" 0 "" "" "HMR_7782" +"MAR07783" "" "AMPtp" "" "" "" "AMPtp" "MNXR95830" "HMR_7783" "RCR20046" "" 0 "" "" "HMR_7783" +"MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8ce2f832..958eb8fc 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -201523,22 +201523,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR04915" - - name: "" - - metabolites: !!omap - - MAM01597c: -1 - - MAM01597x: 1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "PMID:14598172" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR04924" - name: "" @@ -201865,22 +201849,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR07771" - - name: "" - - metabolites: !!omap - - MAM02552c: 1 - - MAM02552x: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR07777" - name: "" @@ -201913,54 +201881,6 @@ - subsystem: - "Transport reactions" - confidence_score: 0 - - !!omap - - id: "MAR07782" - - name: "" - - metabolites: !!omap - - MAM01285c: -1 - - MAM01285x: 1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - - !!omap - - id: "MAR07783" - - name: "" - - metabolites: !!omap - - MAM01334c: -1 - - MAM01334x: 1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - - !!omap - - id: "MAR07790" - - name: "" - - metabolites: !!omap - - MAM01802c: -1 - - MAM01802x: 1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "" - - references: "" - - subsystem: - - "Transport reactions" - - confidence_score: 0 - !!omap - id: "MAR07797" - name: "" diff --git a/model/reactions.tsv b/model/reactions.tsv index 50781e16..de4cd202 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -7016,7 +7016,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04890" "" "H2Otp" "" "r0852" "" "H2Otp" "MNXR98641" "HMR_4890" "RCR20016" "" 0 "RHEA:29670" "RHEA:29667" "HMR_4890" "MAR04900" "" "O2tp" "" "r0857" "" "O2tp" "MNXR102090" "HMR_4900" "RCR20059" "" 0 "" "" "HMR_4900" "MAR04908" "R00124" "r0860" "" "r0860" "" "r0860" "MNXR96123" "HMR_4908" "RCR20198" "" 0 "RHEA:35002" "RHEA:34999" "HMR_4908" -"MAR04915" "" "COAtp" "" "r0864" "" "COAtp" "MNXR96815" "HMR_4915" "RCR20004" "" 0 "" "" "HMR_4915" "MAR04924" "" "CO2tp" "" "r0869" "" "CO2tp" "MNXR96810" "HMR_4924" "RCR20149" "" 0 "" "" "HMR_4924" "MAR04930" "" "PYRt2p" "" "r0874" "" "PYRt2p" "MNXR103385" "HMR_4930" "RCR20123" "2.A.1.13.1;2.A.1.13.5" 0 "RHEA:64723" "RHEA:64720" "HMR_4930" "MAR04945" "" "" "RT0324" "" "" "FORMCOAtx" "" "HMR_4945" "RCR20306" "" 0 "" "" "HMR_4945" @@ -7037,12 +7036,8 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR07646" "" "DALAxt" "" "" "" "DALAxt" "MNXR95702" "HMR_7646" "RCR21081" "" 0 "" "" "HMR_7646" "MAR07705" "" "GLYCLTtp" "" "" "" "GLYCLTtp" "MNXR100333" "HMR_7705" "RCR20712" "" 0 "" "" "HMR_7705" "MAR07707" "" "GLXtp" "" "" "" "GLXtp" "MNXR100306" "HMR_7707" "RCR20200" "" 0 "" "" "HMR_7707" -"MAR07771" "" "NADtpu" "" "" "" "NADtx" "MNXR101881" "HMR_7771" "RCR20023" "" 0 "" "" "HMR_7771" "MAR07777" "" "NADPtxu" "" "" "" "NADPtxu" "MNXR101896" "HMR_7777" "RCR20713" "" 0 "" "" "HMR_7777" "MAR07779" "" "NADPHtxu" "" "" "" "NADPHtxu" "MNXR101894" "HMR_7779" "RCR20311" "" 0 "" "" "HMR_7779" -"MAR07782" "" "ADPtx" "" "" "" "ADPtx" "MNXR95484" "HMR_7782" "RCR20201" "" 0 "" "" "HMR_7782" -"MAR07783" "" "AMPtp" "" "" "" "AMPtp" "MNXR95830" "HMR_7783" "RCR20046" "" 0 "" "" "HMR_7783" -"MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790" "MAR07797" "" "AKGtp" "" "" "" "AKGtp" "MNXR95663" "HMR_7797" "RCR20150" "" 0 "" "" "HMR_7797" "MAR08016" "" "LYStip" "" "" "" "LYStip" "MNXR101269" "HMR_8016" "RCR20033" "" 0 "" "" "HMR_8016" "MAR08020" "" "THP2Ctp" "" "" "" "THP2Ctp" "MNXR104832" "HMR_8020" "RCR20714" "" 0 "" "" "HMR_8020" From 5748afdd9a55b222a5907821c8bf0e92009f9547 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 27 Sep 2023 13:23:15 -0400 Subject: [PATCH 04/10] edit MAR03473 to exchange AMP for ADP instead of ATP & update references --- 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 958eb8fc..600279f5 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -201299,17 +201299,17 @@ - id: "MAR03473" - name: "" - metabolites: !!omap + - MAM01285c: -1 + - MAM01285x: 1 - MAM01334c: 1 - MAM01334x: -1 - - MAM01371c: -1 - - MAM01371x: 1 - - lower_bound: 0 + - lower_bound: -1000 - upper_bound: 1000 - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" - - references: "PMID:16756494;PMID:9874197;PMID:12445829;PMID:14598172;PMID:18406340;PMID:9759482" + - references: "PMID:12445829;PMID:16756494;PMID:22185573" - subsystem: - "Transport reactions" - confidence_score: 0 From 77dfff27958a3393092bd9a48b2f9276eba3797d Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 27 Sep 2023 13:33:21 -0400 Subject: [PATCH 05/10] add reactions for solo transport of AMP and ADP by SLC25A17 --- model/Human-GEM.yml | 32 ++++++++++++++++++++++++++++++++ model/reactions.tsv | 2 ++ 2 files changed, 34 insertions(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 600279f5..6e3ce337 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -304688,6 +304688,38 @@ - subsystem: - "Miscellaneous" - confidence_score: 0 + - !!omap + - id: "MAR20115" + - name: "MAR20115" + - metabolites: !!omap + - MAM01334c: -1 + - MAM01334x: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - eccodes: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20116" + - name: "MAR20116" + - metabolites: !!omap + - MAM01285c: -1 + - MAM01285x: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - eccodes: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 - genes: - !!omap - id: "ENSG00000000419" diff --git a/model/reactions.tsv b/model/reactions.tsv index de4cd202..c5476208 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -12960,3 +12960,5 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR20112" "R04385" "" "" "" "" "" "MNXR96330" "" "" "" 0 "" "RHEA:13501" "" "MAR20113" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" "MAR20114" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20115" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20116" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" From 1f54fc095b54ccced73cb48801ae40cedb2127f9 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 27 Sep 2023 13:36:31 -0400 Subject: [PATCH 06/10] add peroxisomal FMN metabolite --- model/Human-GEM.yml | 8 ++++++++ model/metabolites.tsv | 1 + 2 files changed, 9 insertions(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 6e3ce337..b758eaaf 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -24961,6 +24961,14 @@ - charge: -2 - inchis: "" - metFrom: "HMRdatabase" + - !!omap + - id: "MAM01828x" + - name: "FMN" + - compartment: "x" + - formula: "C17H19N4O9P" + - charge: -2 + - inchis: "" + - metFrom: "" - !!omap - id: "MAM01829g" - name: "fn2m2masn" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index b7d4e67f..63fa75cc 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -3118,6 +3118,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "MAM01827l" "MAM01827" "" "C00393" "" "" "" "PROTEIN" "" "HC01852" "HC01852" "MNXM5157" "m01827l" "m01827l" "MAM01827e" "MAM01827" "" "C00393" "" "" "" "PROTEIN" "" "HC01852" "HC01852" "MNXM5157" "m01827s" "m01827s" "MAM01828c" "MAM01828" "fmn" "C00061" "HMDB0001520" "CHEBI:17621" "643976" "" "" "HC00064" "fmn" "MNXM119" "m01828c" "m01828c" +"MAM01828x" "MAM01828" "fmn" "C00061" "HMDB0001520" "CHEBI:17621" "643976" "" "" "" "" "MNXM119" "" "" "MAM01829g" "MAM01829" "fn2m2masn" "G00016" "" "CHEBI:32984" "" "" "" "" "fn2m2masn" "MNXM12419" "m01829g" "m01829g" "MAM01830c" "MAM01830" "fol" "C00504" "HMDB0000121" "CHEBI:27470" "6037" "" "" "HC00396" "fol" "MNXM617" "m01830c" "m01830c" "MAM01830m" "MAM01830" "fol" "C00504" "HMDB0000121" "CHEBI:27470" "6037" "" "" "HC00396" "fol" "MNXM617" "m01830m" "m01830m" From 40dac080526491dedc1531e3c0210093a45d7a74 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 27 Sep 2023 13:43:05 -0400 Subject: [PATCH 07/10] add peroxisomal hydrolysis of FAD to FMN + AMP by NUDT12 --- model/Human-GEM.yml | 17 +++++++++++++++++ model/reactions.tsv | 1 + 2 files changed, 18 insertions(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index b758eaaf..3fae32e8 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -304728,6 +304728,23 @@ - subsystem: - "Transport reactions" - confidence_score: 0 + - !!omap + - id: "MAR20117" + - name: "MAR20117" + - metabolites: !!omap + - MAM01334x: 1 + - MAM01802x: -1 + - MAM01828x: 1 + - MAM02040x: -1 + - lower_bound: 0 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000112874" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 - genes: - !!omap - id: "ENSG00000000419" diff --git a/model/reactions.tsv b/model/reactions.tsv index c5476208..1f3a19c3 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -12962,3 +12962,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR20114" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" "MAR20115" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" "MAR20116" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20117" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" From e1c400307addac76e92147ae9f9d826904d0db2e Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 27 Sep 2023 14:00:04 -0400 Subject: [PATCH 08/10] add other SLC25A17-mediated antiport reactions --- model/Human-GEM.yml | 238 ++++++++++++++++++++++++++++++++++++++++++++ model/reactions.tsv | 14 +++ 2 files changed, 252 insertions(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 3fae32e8..972ed4d4 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -304742,6 +304742,244 @@ - rxnNotes: "" - rxnFrom: "" - references: "PMID:22185573" + - subsystem: + - "Riboflavin metabolism" + - confidence_score: 0 + - !!omap + - id: "MAR20118" + - name: "MAR20118" + - metabolites: !!omap + - MAM01597c: 1 + - MAM01597x: -1 + - MAM01828c: -1 + - MAM01828x: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20119" + - name: "MAR20119" + - metabolites: !!omap + - MAM01802c: 1 + - MAM01802x: -1 + - MAM01828c: -1 + - MAM01828x: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20120" + - name: "MAR20120" + - metabolites: !!omap + - MAM01828c: -1 + - MAM01828x: 1 + - MAM02552c: 1 + - MAM02552x: -1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20121" + - name: "MAR20121" + - metabolites: !!omap + - MAM01334c: 1 + - MAM01334x: -1 + - MAM01828c: -1 + - MAM01828x: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20122" + - name: "MAR20122" + - metabolites: !!omap + - MAM01285c: 1 + - MAM01285x: -1 + - MAM01828c: -1 + - MAM01828x: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20123" + - name: "MAR20123" + - metabolites: !!omap + - MAM01597c: 1 + - MAM01597x: -1 + - MAM01802c: -1 + - MAM01802x: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20124" + - name: "MAR20124" + - metabolites: !!omap + - MAM01802c: -1 + - MAM01802x: 1 + - MAM02552c: 1 + - MAM02552x: -1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20125" + - name: "MAR20125" + - metabolites: !!omap + - MAM01334c: 1 + - MAM01334x: -1 + - MAM01802c: -1 + - MAM01802x: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20126" + - name: "MAR20126" + - metabolites: !!omap + - MAM01285c: 1 + - MAM01285x: -1 + - MAM01802c: -1 + - MAM01802x: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20127" + - name: "MAR20127" + - metabolites: !!omap + - MAM01597c: 1 + - MAM01597x: -1 + - MAM02552c: -1 + - MAM02552x: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20128" + - name: "MAR20128" + - metabolites: !!omap + - MAM01334c: 1 + - MAM01334x: -1 + - MAM02552c: -1 + - MAM02552x: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20129" + - name: "MAR20129" + - metabolites: !!omap + - MAM01285c: 1 + - MAM01285x: -1 + - MAM02552c: -1 + - MAM02552x: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20130" + - name: "MAR20130" + - metabolites: !!omap + - MAM01334c: -1 + - MAM01334x: 1 + - MAM01597c: 1 + - MAM01597x: -1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" + - subsystem: + - "Transport reactions" + - confidence_score: 0 + - !!omap + - id: "MAR20131" + - name: "MAR20131" + - metabolites: !!omap + - MAM01285c: -1 + - MAM01285x: 1 + - MAM01597c: 1 + - MAM01597x: -1 + - lower_bound: -1000 + - upper_bound: 1000 + - gene_reaction_rule: "ENSG00000100372" + - rxnNotes: "" + - rxnFrom: "" + - references: "PMID:22185573" - subsystem: - "Transport reactions" - confidence_score: 0 diff --git a/model/reactions.tsv b/model/reactions.tsv index 1f3a19c3..914232dd 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -12963,3 +12963,17 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR20115" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" "MAR20116" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" "MAR20117" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20118" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20119" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20120" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20121" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20122" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20123" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20124" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20125" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20126" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20127" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20128" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20129" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20130" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20131" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" From 4030753e8796ffceee196a433210be9f5aea0824 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 28 Sep 2023 20:03:08 -0400 Subject: [PATCH 09/10] fix: added missing eccodes entries to new reactions --- model/Human-GEM.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 972ed4d4..bcdc71e0 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -304741,6 +304741,7 @@ - gene_reaction_rule: "ENSG00000112874" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Riboflavin metabolism" @@ -304758,6 +304759,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304775,6 +304777,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304792,6 +304795,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304809,6 +304813,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304826,6 +304831,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304843,6 +304849,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304860,6 +304867,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304877,6 +304885,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304894,6 +304903,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304911,6 +304921,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304928,6 +304939,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304945,6 +304957,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304962,6 +304975,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" @@ -304979,6 +304993,7 @@ - gene_reaction_rule: "ENSG00000100372" - rxnNotes: "" - rxnFrom: "" + - eccodes: "" - references: "PMID:22185573" - subsystem: - "Transport reactions" From 3eb081774fe08db4969ff629a74880e52cfa9f15 Mon Sep 17 00:00:00 2001 From: haowang-bioinfo Date: Sun, 8 Oct 2023 23:09:02 +0200 Subject: [PATCH 10/10] fix: rebalance MAR20117 --- model/Human-GEM.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 295314c8..c6a46e87 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -304714,6 +304714,7 @@ - MAM01334x: 1 - MAM01802x: -1 - MAM01828x: 1 + - MAM02039x: 2 - MAM02040x: -1 - lower_bound: 0 - upper_bound: 1000