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Fix/removed beta-D-glucose and related reactions #307

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Fix/removed beta-D-glucose and related reactions #307

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1b22fa4
Removed beta-D-glucose and related reactions
pranasag Aug 31, 2021
84ca924
Corrected .tsv files
pranasag Aug 31, 2021
e48cd1a
Revert "Corrected .tsv files"
pranasag Sep 1, 2021
aec4a88
Revert "Removed beta-D-glucose and related reactions"
pranasag Sep 1, 2021
b18df07
Removed only beta-D-G6P and related reactions
pranasag Sep 1, 2021
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78 changes: 0 additions & 78 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17956,14 +17956,6 @@
- charge: 0
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM01389c"
- name: "beta-D-glucose-6-phosphate"
- compartment: "c"
- formula: "C6H11O9P"
- charge: -2
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM01390c"
- name: "beta-D-mannosyldiacetylchitobiosyldiphosphodolichol"
Expand Down Expand Up @@ -67587,76 +67579,6 @@
- subsystem:
- "Glycolysis / Gluconeogenesis"
- confidence_score: 0
- !!omap
- id: "MAR07746"
- name: ""
- metabolites: !!omap
- MAM01285c: 1
- MAM01371c: -1
- MAM01388c: -1
- MAM01389c: 1
- MAM02039c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000106633 or ENSG00000156510 or ENSG00000156515 or ENSG00000159399 or ENSG00000160883"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.1.1;2.7.1.2"
- references: ""
- subsystem:
- "Glycolysis / Gluconeogenesis"
- confidence_score: 0
- !!omap
- id: "MAR07747"
- name: ""
- metabolites: !!omap
- MAM01285c: -1
- MAM01334c: 1
- MAM01388c: -1
- MAM01389c: 1
- MAM02039c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000159322"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.1.147"
- references: ""
- subsystem:
- "Glycolysis / Gluconeogenesis"
- confidence_score: 0
- !!omap
- id: "MAR07748"
- name: ""
- metabolites: !!omap
- MAM01389c: -1
- MAM01968c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000105220"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "5.3.1.9"
- references: ""
- subsystem:
- "Glycolysis / Gluconeogenesis"
- confidence_score: 0
- !!omap
- id: "MAR07749"
- name: ""
- metabolites: !!omap
- MAM01389c: -1
- MAM01845c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000105220"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "5.3.1.9"
- references: ""
- subsystem:
- "Glycolysis / Gluconeogenesis"
- confidence_score: 0
- !!omap
- id: "MAR08360"
- name: ""
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1 change: 0 additions & 1 deletion model/metabolites.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -2242,7 +2242,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM01386c" "MAM01386" "" "" "" "" "" "" "CE4722" "" "CE4722" "MNXM152651" "m01386c" "m01386c"
"MAM01387c" "MAM01387" "" "" "" "" "4424653" "" "CE2915" "" "CE2915" "MNXM163311" "m01387c" "m01387c"
"MAM01388c" "MAM01388" "" "C00221" "" "CHEBI:15903" "" "" "" "" "M01388" "MNXM105" "m01388c" "m01388c"
"MAM01389c" "MAM01389" "" "C01172" "" "CHEBI:17719" "" "" "" "" "M01389" "MNXM508" "m01389c" "m01389c"
"MAM01390c" "MAM01390" "mpdol__L" "C05860" "" "CHEBI:18396" "" "" "" "" "mpdol_L" "MNXM148107" "m01390c" "m01390c"
"MAM01391c" "MAM01391" "acgbgbside_hs" "" "" "" "" "" "" "" "acgbgbside_hs" "MNXM7110" "m01391c" "m01391c"
"MAM01391g" "MAM01391" "acgbgbside_hs" "" "" "" "" "" "" "" "acgbgbside_hs" "MNXM7110" "m01391g" "m01391g"
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4 changes: 0 additions & 4 deletions model/reactions.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -32,10 +32,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR06410" "R01699" "" "R01699M" "r0383" "" "r0383" "MNXR102427;MNXR107129" "HMR_6410" "RCR10446" "" 0 "" "" "HMR_6410"
"MAR06412" "R02569" "" "R02569C" "r0555" "" "r0555" "MNXR102430;MNXR107584" "HMR_6412" "RCR14187" "" 0 "" "" "HMR_6412"
"MAR07745" "R01602" "" "" "" "" "HMR_7745" "MNXR107082" "HMR_7745" "RCR10447" "" 0 "" "" "HMR_7745"
"MAR07746" "R01600" "" "" "" "" "HMR_7746" "MNXR107081" "HMR_7746" "RCR10448" "" 0 "" "" "HMR_7746"
"MAR07747" "R09086" "" "" "" "" "HMR_7747" "MNXR112530" "HMR_7747" "RCR10449" "" 0 "" "" "HMR_7747"
"MAR07748" "R02739" "" "" "" "" "HMR_7748" "MNXR99911" "HMR_7748" "RCR10277" "" 0 "" "" "HMR_7748"
"MAR07749" "R03321" "" "" "" "" "HMR_7749" "MNXR99910" "HMR_7749" "RCR14188" "" 0 "" "" "HMR_7749"
"MAR08360" "" "CAt7r" "" "" "" "CAT2p" "MNXR96461" "HMR_8360" "RCR11029" "" 0 "" "" "HMR_8360"
"MAR08652" "" "CBPS" "" "" "" "CBPPer" "MNXR96485" "HMR_8652" "RCR11030" "" 0 "" "" "HMR_8652"
"MAR08757" "" "ETOHtx" "" "" "" "ETOHMO" "MNXR97980" "HMR_8757" "RCR11031" "" 0 "" "" "HMR_8757"
Expand Down