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Fix Representation of LIPT1 #714

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merged 8 commits into from
Oct 29, 2023
Merged

Fix Representation of LIPT1 #714

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80ca5e3
fix: removed LIPT1 from MAR01088 and MAR01091
Devlin-Moyer Oct 25, 2023
d1f8b66
fix: remove MAR06398, MAR06399, and MAM02398c
Devlin-Moyer Oct 25, 2023
63c32a2
fix: added new reaction to accurately represent activity of LIPT1
Devlin-Moyer Oct 25, 2023
6c342de
fix: change new reaction ID to not conflict with new DHODH reaction
Devlin-Moyer Oct 25, 2023
d9e4046
fix: replace MAM02393m with MAM00209c in MAR08433 and MAM01701m with …
Devlin-Moyer Oct 25, 2023
4bf45c3
fix: removed protons from lipoamide transport reactions
Devlin-Moyer Oct 25, 2023
66a2fff
fix: remove MAR06408 and MAM01701c
Devlin-Moyer Oct 25, 2023
7e3fd18
fix: make MAR11361 reversible
Devlin-Moyer Oct 26, 2023
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2 changes: 2 additions & 0 deletions data/deprecatedIdentifiers/deprecatedMetabolites.tsv
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Expand Up @@ -2252,3 +2252,5 @@ 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" "" ""
"MAM02398c" "MAM02398" "" "C16238" "" "" "23724672" "" "CE5656" "" "CE5656" "MNXM2392" "m02398c" "m02398c"
"MAM01701c" "MAM01701" "dhlam" "C00579" "HMDB0000985" "CHEBI:17694" "663" "" "" "HC00437" "dhlam" "MNXM1277" "m01701c" "m01701c"
3 changes: 3 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -253,3 +253,6 @@ 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" "" ""
"MAR06398" "R07770" "" "R07770C" "" "" "RE1944C" "MNXR101081" "HMR_6398" "RCR14489" "" 0 "" "RHEA:12913" "HMR_6398"
"MAR06399" "R07771" "" "R07771C" "" "" "HMR_6399" "MNXR111358" "HMR_6399" "RCR14490" "" 0 "" "RHEA:20473" "HMR_6399"
"MAR06408" "" "" "RT0295" "" "" "HMR_6408" "" "HMR_6408" "RCR21069" "" 0 "" "" "HMR_6408"
102 changes: 21 additions & 81 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -22849,14 +22849,6 @@
- charge: -2
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM01701c"
- name: "dihydrolipoamide"
- compartment: "c"
- formula: "C8H17NOS2"
- charge: 0
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM01701m"
- name: "dihydrolipoamide"
Expand Down Expand Up @@ -32657,14 +32649,6 @@
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02398c"
- name: "lipoyl-AMP"
- compartment: "c"
- formula: "C18H25N5O8PS2"
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02399c"
- name: "lipoyllysine"
Expand Down Expand Up @@ -80471,7 +80455,7 @@
- MAM01596m: 1
- MAM01986m: -1
- MAM02039m: -1
- MAM02393m: -1
- MAM00209c: -1
- MAM02878m: 1
- lower_bound: 0
- upper_bound: 1000
Expand All @@ -80488,7 +80472,7 @@
- name: ""
- metabolites: !!omap
- MAM01045m: 1
- MAM01701m: 1
- MAM00208c: 1
- MAM02039m: 1
- MAM02578m: 1
- MAM02878m: -1
Expand Down Expand Up @@ -100667,44 +100651,6 @@
- subsystem:
- "Lipoic acid metabolism"
- confidence_score: 0
- !!omap
- id: "MAR06398"
- name: ""
- metabolites: !!omap
- MAM01371c: -1
- MAM02039c: -1
- MAM02394c: -1
- MAM02398c: 1
- MAM02759c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000144182"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.7.63"
- references: "PMID:10103005"
- subsystem:
- "Lipoic acid metabolism"
- confidence_score: 0
- !!omap
- id: "MAR06399"
- name: ""
- metabolites: !!omap
- MAM00209c: 1
- MAM01334c: 1
- MAM01350c: -1
- MAM02039c: 1
- MAM02398c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000144182"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.7.63"
- references: ""
- subsystem:
- "Lipoic acid metabolism"
- confidence_score: 0
- !!omap
- id: "MAR06402"
- name: "octanoyl-[acp]:protein N6-octanoyltransferase"
Expand Down Expand Up @@ -105524,7 +105470,7 @@
- MAM02538c: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000023041 or ENSG00000054392 or ENSG00000087253 or ENSG00000090971 or ENSG00000097033 or ENSG00000099904 or ENSG00000100344 or ENSG00000102030 or ENSG00000102312 or ENSG00000102383 or ENSG00000103066 or ENSG00000104219 or ENSG00000106636 or ENSG00000109065 or ENSG00000110583 or ENSG00000111684 or ENSG00000121579 or ENSG00000122390 or ENSG00000123684 or ENSG00000125505 or ENSG00000133328 or ENSG00000135372 or ENSG00000136247 or ENSG00000141446 or ENSG00000143797 or ENSG00000144035 or ENSG00000144182 or ENSG00000153395 or ENSG00000153786 or ENSG00000156599 or ENSG00000159714 or ENSG00000160446 or ENSG00000163812 or ENSG00000163958 or ENSG00000167011 or ENSG00000171307 or ENSG00000171320 or ENSG00000172197 or ENSG00000172954 or ENSG00000173418 or ENSG00000174165 or ENSG00000175048 or ENSG00000175893 or ENSG00000176454 or ENSG00000177054 or ENSG00000177108 or ENSG00000177669 or ENSG00000180776 or ENSG00000184210 or ENSG00000184307 or ENSG00000184788 or ENSG00000186908 or ENSG00000188706 or ENSG00000188818 or ENSG00000203972 or ENSG00000204160 or ENSG00000206077 or ENSG00000243477"
- gene_reaction_rule: "ENSG00000023041 or ENSG00000054392 or ENSG00000087253 or ENSG00000090971 or ENSG00000097033 or ENSG00000099904 or ENSG00000100344 or ENSG00000102030 or ENSG00000102312 or ENSG00000102383 or ENSG00000103066 or ENSG00000104219 or ENSG00000106636 or ENSG00000109065 or ENSG00000110583 or ENSG00000111684 or ENSG00000121579 or ENSG00000122390 or ENSG00000123684 or ENSG00000125505 or ENSG00000133328 or ENSG00000135372 or ENSG00000136247 or ENSG00000141446 or ENSG00000143797 or ENSG00000144035 or ENSG00000153395 or ENSG00000153786 or ENSG00000156599 or ENSG00000159714 or ENSG00000160446 or ENSG00000163812 or ENSG00000163958 or ENSG00000167011 or ENSG00000171307 or ENSG00000171320 or ENSG00000172197 or ENSG00000172954 or ENSG00000173418 or ENSG00000174165 or ENSG00000175048 or ENSG00000175893 or ENSG00000176454 or ENSG00000177054 or ENSG00000177108 or ENSG00000177669 or ENSG00000180776 or ENSG00000184210 or ENSG00000184307 or ENSG00000184788 or ENSG00000186908 or ENSG00000188706 or ENSG00000188818 or ENSG00000203972 or ENSG00000204160 or ENSG00000206077 or ENSG00000243477"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.3.1.-"
Expand All @@ -105543,7 +105489,7 @@
- MAM02538n: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000023041 or ENSG00000054392 or ENSG00000087253 or ENSG00000090971 or ENSG00000097033 or ENSG00000099904 or ENSG00000100344 or ENSG00000102030 or ENSG00000102312 or ENSG00000102383 or ENSG00000103066 or ENSG00000104219 or ENSG00000106636 or ENSG00000109065 or ENSG00000110583 or ENSG00000111684 or ENSG00000121579 or ENSG00000122390 or ENSG00000123684 or ENSG00000125505 or ENSG00000133328 or ENSG00000135372 or ENSG00000136247 or ENSG00000141446 or ENSG00000143797 or ENSG00000144035 or ENSG00000144182 or ENSG00000153395 or ENSG00000153786 or ENSG00000156599 or ENSG00000159714 or ENSG00000160446 or ENSG00000163812 or ENSG00000163958 or ENSG00000167011 or ENSG00000171307 or ENSG00000171320 or ENSG00000172197 or ENSG00000172954 or ENSG00000173418 or ENSG00000174165 or ENSG00000175048 or ENSG00000175893 or ENSG00000176454 or ENSG00000177054 or ENSG00000177108 or ENSG00000177669 or ENSG00000180776 or ENSG00000184210 or ENSG00000184307 or ENSG00000184788 or ENSG00000186908 or ENSG00000188706 or ENSG00000188818 or ENSG00000203972 or ENSG00000204160 or ENSG00000206077 or ENSG00000243477"
- gene_reaction_rule: "ENSG00000023041 or ENSG00000054392 or ENSG00000087253 or ENSG00000090971 or ENSG00000097033 or ENSG00000099904 or ENSG00000100344 or ENSG00000102030 or ENSG00000102312 or ENSG00000102383 or ENSG00000103066 or ENSG00000104219 or ENSG00000106636 or ENSG00000109065 or ENSG00000110583 or ENSG00000111684 or ENSG00000121579 or ENSG00000122390 or ENSG00000123684 or ENSG00000125505 or ENSG00000133328 or ENSG00000135372 or ENSG00000136247 or ENSG00000141446 or ENSG00000143797 or ENSG00000144035 or ENSG00000153395 or ENSG00000153786 or ENSG00000156599 or ENSG00000159714 or ENSG00000160446 or ENSG00000163812 or ENSG00000163958 or ENSG00000167011 or ENSG00000171307 or ENSG00000171320 or ENSG00000172197 or ENSG00000172954 or ENSG00000173418 or ENSG00000174165 or ENSG00000175048 or ENSG00000175893 or ENSG00000176454 or ENSG00000177054 or ENSG00000177108 or ENSG00000177669 or ENSG00000180776 or ENSG00000184210 or ENSG00000184307 or ENSG00000184788 or ENSG00000186908 or ENSG00000188706 or ENSG00000188818 or ENSG00000203972 or ENSG00000204160 or ENSG00000206077 or ENSG00000243477"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.3.1.-"
Expand Down Expand Up @@ -198496,24 +198442,6 @@
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR06408"
- name: ""
- metabolites: !!omap
- MAM01701c: -1
- MAM01701m: 1
- MAM02039i: -1
- MAM02039m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: ""
- references: ""
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR06431"
- name: ""
Expand Down Expand Up @@ -270321,8 +270249,6 @@
- id: "MAR11346"
- name: "Lipoamide Transport"
- metabolites: !!omap
- MAM02039c: 1
- MAM02039e: -1
- MAM02393c: 1
- MAM02393e: -1
- lower_bound: -1000
Expand Down Expand Up @@ -270558,11 +270484,9 @@
- id: "MAR11361"
- name: "Transport of Lipoamide, Mitochondrial"
- metabolites: !!omap
- MAM02039i: -1
- MAM02039m: 1
- MAM02393c: -1
- MAM02393m: 1
- lower_bound: 0
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
Expand Down Expand Up @@ -305321,6 +305245,22 @@
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR20168"
- name: "MAR20168"
- metabolites: !!omap
- MAM00209c: -1
- MAM02393m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000144182"
- rxnNotes: ""
- rxnFrom: ""
- eccodes: ""
- references: "PMID:29987032"
- subsystem:
- "Miscellaneous"
- confidence_score: 0
- genes:
- !!omap
- id: "ENSG00000000419"
Expand Down
2 changes: 0 additions & 2 deletions model/metabolites.tsv
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Expand Up @@ -2854,7 +2854,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM01700l" "MAM01700" "dhf" "C00415" "" "CHEBI:15633" "98792" "" "" "HC00340" "dhf" "MNXM281" "m01700l" "m01700l"
"MAM01700m" "MAM01700" "dhf" "C00415" "" "CHEBI:15633" "98792" "" "" "HC00340" "dhf" "MNXM281" "m01700m" "m01700m"
"MAM01700e" "MAM01700" "dhf" "C00415" "" "CHEBI:15633" "98792" "" "" "HC00340" "dhf" "MNXM281" "m01700s" "m01700s"
"MAM01701c" "MAM01701" "dhlam" "C00579" "HMDB0000985" "CHEBI:17694" "663" "" "" "HC00437" "dhlam" "MNXM1277" "m01701c" "m01701c"
"MAM01701m" "MAM01701" "dhlam" "C00579" "HMDB0000985" "CHEBI:17694" "663" "" "" "HC00437" "dhlam" "MNXM1277" "m01701m" "m01701m"
"MAM01702c" "MAM01702" "" "C02147" "HMDB0012210" "CHEBI:18047" "421" "LMFA01130003" "" "" "C02147" "MNXM3585" "m01702c" "m01702c"
"MAM01704c" "MAM01704" "" "C04874" "" "CHEBI:17001" "65074" "" "" "HC01361" "HC01361" "MNXM993" "m01704c" "m01704c"
Expand Down Expand Up @@ -4080,7 +4079,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02396n" "MAM02396" "" "C06315" "HMDB0005082" "CHEBI:6499" "5280915" "LMFA03040002" "" "" "C06315" "MNXM12130" "m02396n" "m02396n"
"MAM02396x" "MAM02396" "" "C06315" "HMDB0005082" "CHEBI:6499" "5280915" "LMFA03040002" "" "" "C06315" "MNXM12130" "m02396p" "m02396p"
"MAM02396r" "MAM02396" "" "C06315" "HMDB0005082" "CHEBI:6499" "5280915" "LMFA03040002" "" "" "C06315" "MNXM12130" "m02396r" "m02396r"
"MAM02398c" "MAM02398" "" "C16238" "" "" "23724672" "" "CE5656" "" "CE5656" "MNXM2392" "m02398c" "m02398c"
"MAM02399c" "MAM02399" "" "" "" "" "53481572" "" "CE2102" "" "CE2102" "MNXM60228" "m02399c" "m02399c"
"MAM02401c" "MAM02401" "" "C03127" "" "CHEBI:29160" "" "" "" "" "M02401" "MNXM89832" "m02401c" "m02401c"
"MAM02402c" "MAM02402" "" "C03990" "HMDB0000761" "CHEBI:16325" "11740284" "LMST04010003" "" "HC02191" "HC02191" "MNXM886" "m02402c" "m02402c"
Expand Down
4 changes: 1 addition & 3 deletions model/reactions.tsv
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Expand Up @@ -1664,8 +1664,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR02469" "" "" "RE3264C" "" "" "RE3264C" "" "HMR_2469" "RCR11942" "" 0 "" "" "HMR_2469"
"MAR02470" "" "" "RE3264R" "" "" "RE3264R" "MNXR103858" "HMR_2470" "RCR11943" "" 0 "" "" "HMR_2470"
"MAR06397" "" "" "RE2882C" "" "" "HMR_6397" "" "HMR_6397" "RCR10619" "" 0 "" "" "HMR_6397"
"MAR06398" "R07770" "" "R07770C" "" "" "RE1944C" "MNXR101081" "HMR_6398" "RCR14489" "" 0 "" "RHEA:12913" "HMR_6398"
"MAR06399" "R07771" "" "R07771C" "" "" "HMR_6399" "MNXR111358" "HMR_6399" "RCR14490" "" 0 "" "RHEA:20473" "HMR_6399"
"MAR06402" "R07766;R07769" "" "R07766C;R07769C" "" "" "HMR_6402;HMR_6401" "MNXR111354" "HMR_6402;HMR_6401" "RCR11946;RCR11945" "" 0 "RHEA:17666" "RHEA:17665" "HMR_6402;HMR_6401;MAR06401"
"MAR06403" "R07767;R07768" "" "R07767C;R07768C" "" "" "HMR_6403;HMR_6400" "MNXR111355" "HMR_6403;HMR_6400" "RCR11947;RCR11948" "" 0 "RHEA:16586" "RHEA:16585" "HMR_6403;HMR_6400;MAR06400"
"MAR06404" "R08550" "" "R08550C" "" "" "HMR_6404" "MNXR112089" "HMR_6404" "RCR14491" "" 0 "" "" "HMR_6404"
Expand Down Expand Up @@ -6839,7 +6837,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR06343" "" "DNDPt42m" "" "r2432" "" "DNDPt42m" "MNXR97655" "HMR_6343" "RCR20276" "2.A.29.16.1" 0 "" "" "HMR_6343"
"MAR06389" "" "r2472" "" "r2472" "" "r2472" "MNXR100321" "HMR_6389" "RCR20616" "2.A.1.4.7" 0 "" "" "HMR_6389"
"MAR06391" "" "" "" "r2520" "" "r2520" "MNXR106328" "HMR_6391" "RCR20063" "" 0 "" "" "HMR_6391"
"MAR06408" "" "" "RT0295" "" "" "HMR_6408" "" "HMR_6408" "RCR21069" "" 0 "" "" "HMR_6408"
"MAR06431" "" "" "" "" "" "HMR_6431" "" "HMR_6431" "RCR20617" "" 0 "" "" "HMR_6431"
"MAR06438" "" "" "" "" "" "HMR_6438" "" "HMR_6438" "RCR20618" "" 0 "" "" "HMR_6438"
"MAR06446" "" "" "" "" "" "HMR_6446" "" "HMR_6446" "RCR20619" "" 0 "" "" "HMR_6446"
Expand Down Expand Up @@ -12997,3 +12994,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR20164" "" "" "" "" "" "" "" "" "" "" 0 "" "" ""
"MAR20165" "" "" "" "" "" "" "" "" "" "" 0 "" "" ""
"MAR20166" "" "" "" "" "" "" "" "" "" "" 0 "" "" ""
"MAR20168" "" "" "" "" "" "" "" "" "" "" 0 "" "" ""