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Merge pull request #815 from SysBioChalmers/fix/thiamine_transport
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Fix Mitochondrial Thiamine Transport Reactions
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@feiranl
feiranl authored May 6, 2024
2 parents 56b345d + 37bda79 commit 9b68a73
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Showing 3 changed files with 62 additions and 95 deletions.
5 changes: 5 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -294,3 +294,8 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR00965" "" "FAOXC2252053m" "" "" "" "FAOXC2252053m" "MNXR99352" "" "" "" 0 "" "" "FAOXC2252053m"
"MAR04774" "R03237" "" "R03237C" "r0610" "" "r0610" "MNXR105355;MNXR108039" "HMR_4774" "RCR11046" "" 0 "" "" "HMR_4774"
"MAR04775" "R03239" "" "R03239C" "r0611" "" "r0611" "MNXR105356;MNXR108041" "HMR_4775" "RCR14197" "" 0 "" "" "HMR_4775"
"MAR01788" "" "THMMPtm" "" "" "" "THMMPtm" "MNXR104822" "" "" "" 0 "" "" "THMMPtm"
"MAR01789" "" "THMPPtm" "" "" "" "THMPPtm" "MNXR104824" "" "" "" 0 "" "" "THMPPtm"
"MAR04205" "" "" "RT0084" "" "" "HMR_4205" "" "HMR_4205" "RCR20258" "" 0 "" "" "HMR_4205"
"MAR08745" "" "THMMPtm" "" "" "" "" "MNXR104822" "HMR_8745" "RCR20669" "" 0 "" "" "HMR_8745"
"MAR08747" "" "THMPPtm" "" "" "" "" "MNXR104824" "HMR_8747" "RCR20670" "" 0 "" "" "HMR_8747"
144 changes: 54 additions & 90 deletions model/Human-GEM.yml
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Expand Up @@ -195689,24 +195689,6 @@
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR04205"
- name: ""
- metabolites: !!omap
- MAM02039i: -1
- MAM02039m: 1
- MAM02984c: -1
- MAM02984m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: ""
- references: ""
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR04237"
- name: ""
Expand Down Expand Up @@ -200003,42 +199985,6 @@
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR08745"
- name: ""
- metabolites: !!omap
- MAM02147c: -1
- MAM02147m: 1
- MAM02983c: 1
- MAM02983m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: ""
- references: ""
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR08747"
- name: ""
- metabolites: !!omap
- MAM02147c: 2
- MAM02147m: -2
- MAM02984c: -1
- MAM02984m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: ""
- references: ""
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR08776"
- name: ""
Expand Down Expand Up @@ -225748,42 +225694,6 @@
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR01788"
- name: "Thiamine Monophosphate Transport, Mitochondrial"
- metabolites: !!omap
- MAM02040c: 1
- MAM02040m: -1
- MAM02983c: -1
- MAM02983m: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: "PMID:12014993;PMID:9755848"
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR01789"
- name: "Thiamine Diphosphate Transport in via Anion Antiport, Mitochondria"
- metabolites: !!omap
- MAM02040c: 2
- MAM02040m: -2
- MAM02984c: -1
- MAM02984m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: "PMID:12014993"
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR01791"
- name: "Thiamine Transport in via Proton Symport, Mitochondrial"
Expand Down Expand Up @@ -304721,6 +304631,60 @@
- subsystem:
- "Exchange/demand reactions"
- confidence_score: 0
- !!omap
- id: "MAR20181"
- name: "Antiport of thiamine-diphosphate and thiamine-phosphate"
- metabolites: !!omap
- MAM02983c: -1
- MAM02983m: 1
- MAM02984c: 1
- MAM02984m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnNotes: ""
- rxnFrom: ""
- eccodes: ""
- references: "PMID:17035501"
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR20182"
- name: "Antiport of thiamine-phosphate and dATP"
- metabolites: !!omap
- MAM01642c: -1
- MAM01642m: 1
- MAM02983c: 1
- MAM02983m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnNotes: ""
- rxnFrom: ""
- eccodes: ""
- references: "PMID:17035501"
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR20183"
- name: "Antiport of thiamine-diphosphate and dATP"
- metabolites: !!omap
- MAM01642c: -1
- MAM01642m: 1
- MAM02984c: 1
- MAM02984m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnNotes: ""
- rxnFrom: ""
- eccodes: ""
- references: "PMID:17035501"
- subsystem:
- "Transport reactions"
- confidence_score: 0
- genes:
- !!omap
- id: "ENSG00000000419"
Expand Down
8 changes: 3 additions & 5 deletions model/reactions.tsv
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Expand Up @@ -6684,7 +6684,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR03954" "" "AACTtm" "" "" "" "AACTtm" "MNXR95150" "HMR_3954" "RCR20563" "" 0 "" "" "HMR_3954"
"MAR03971" "" "FUMtm" "" "" "" "FUMtm" "MNXR99716" "HMR_3971" "RCR20564" "" 0 "" "" "HMR_3971"
"MAR04184" "R00528" "" "" "r0140" "" "SULFOX" "MNXR106563" "HMR_4184" "RCR21060" "" 0 "" "RHEA:14281" "HMR_4184"
"MAR04205" "" "" "RT0084" "" "" "HMR_4205" "" "HMR_4205" "RCR20258" "" 0 "" "" "HMR_4205"
"MAR04237" "" "2OXOADPTm" "" "r0945" "" "2OXOADPTm" "MNXR94819" "HMR_4237" "RCR20259" "2.A.29.2.4" 0 "" "" "HMR_4237"
"MAR04266" "" "" "" "" "" "HMR_4266" "" "HMR_4266" "RCR20565" "" 0 "" "" "HMR_4266"
"MAR04367" "" "" "" "r0926" "" "r0926" "MNXR94974" "HMR_4367" "RCR20566" "" 0 "" "" "HMR_4367"
Expand Down Expand Up @@ -6930,8 +6929,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR08731" "" "SARCStm" "" "" "" "SARCStm" "MNXR104273" "HMR_8731" "RCR20666" "" 0 "" "" "HMR_8731"
"MAR08741" "" "FUMtm" "" "" "" "FUMSO3tm" "MNXR99716" "HMR_8741" "RCR20667" "" 0 "" "" "HMR_8741"
"MAR08742" "" "FUMTSULtm" "" "" "" "FUMSO4tm" "MNXR99710" "HMR_8742" "RCR20668" "" 0 "" "" "HMR_8742"
"MAR08745" "" "THMMPtm" "" "" "" "" "MNXR104822" "HMR_8745" "RCR20669" "" 0 "" "" "HMR_8745"
"MAR08747" "" "THMPPtm" "" "" "" "" "MNXR104824" "HMR_8747" "RCR20670" "" 0 "" "" "HMR_8747"
"MAR08776" "" "" "" "" "" "HMR_8776" "" "HMR_8776" "RCR20671" "" 0 "" "" "HMR_8776"
"MAR08785" "" "" "" "" "" "HMR_8785" "" "HMR_8785" "RCR20672" "" 0 "" "" "HMR_8785"
"MAR08848" "" "TCYNTtm" "" "" "" "TCYNTtm" "MNXR104749" "HMR_8848" "RCR20673" "" 0 "" "" "HMR_8848"
Expand Down Expand Up @@ -8477,8 +8474,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR01779" "" "THCHOLSTOICtm" "" "" "" "THCHOLSTOICtm" "MNXR104803" "" "" "" 0 "" "" "THCHOLSTOICtm"
"MAR01780" "" "THFt2" "" "" "" "THFt2" "MNXR104811" "" "" "" 0 "" "" "THFt2"
"MAR01782" "" "THMMPt4" "" "" "" "THMMPt4" "MNXR104822" "" "" "" 0 "" "" "THMMPt4"
"MAR01788" "" "THMMPtm" "" "" "" "THMMPtm" "MNXR104822" "" "" "" 0 "" "" "THMMPtm"
"MAR01789" "" "THMPPtm" "" "" "" "THMPPtm" "MNXR104824" "" "" "" 0 "" "" "THMPPtm"
"MAR01791" "" "THMt2m" "" "" "" "THMt2m" "MNXR104828" "" "" "" 0 "" "" "THMt2m"
"MAR01793" "" "THMTPt" "" "" "" "THMTPt" "MNXR104826" "" "" "" 0 "" "" "THMTPt"
"MAR01795" "" "TMNDNCCOAtx" "" "" "" "TMNDNCCOAtx" "MNXR104902" "" "" "" 0 "" "" "TMNDNCCOAtx"
Expand Down Expand Up @@ -12972,3 +12967,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR20178" "R10998" "" "" "" "" "" "MNXR114302" "" "" "" 0 "" "" ""
"MAR20179" "" "" "" "" "" "" "" "" "" "" 0 "" "" ""
"MAR20180" "" "" "" "" "" "" "" "" "" "" 0 "" "" ""
"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 "" "" ""

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