From 80ca5e3c582c6102958c3bbcfe9952bf3d887f09 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 25 Oct 2023 14:51:15 -0400 Subject: [PATCH 1/8] fix: removed LIPT1 from MAR01088 and MAR01091 --- model/Human-GEM.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 6c7c5541..572042ba 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -105524,7 +105524,7 @@ - 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.-" @@ -105543,7 +105543,7 @@ - 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.-" From d1f8b66b6c971e602d381ca08647135b384c85a5 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 25 Oct 2023 14:53:12 -0400 Subject: [PATCH 2/8] fix: remove MAR06398, MAR06399, and MAM02398c --- .../deprecatedMetabolites.tsv | 1 + .../deprecatedReactions.tsv | 2 + model/Human-GEM.yml | 46 ------------------- model/metabolites.tsv | 1 - model/reactions.tsv | 2 - 5 files changed, 3 insertions(+), 49 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 89187083..e4224e50 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2252,3 +2252,4 @@ 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" diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 2af418d9..ad68cf70 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" "" "" +"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" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 572042ba..87dec4a8 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -32657,14 +32657,6 @@ - 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" @@ -100667,44 +100659,6 @@ - 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" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index a87f5787..9e2662b2 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -4080,7 +4080,6 @@ 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" diff --git a/model/reactions.tsv b/model/reactions.tsv index 5de1d8ae..3be7341f 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -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" From 63c32a2841e8aefe317fe433eca85419d8b9da96 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 25 Oct 2023 14:56:05 -0400 Subject: [PATCH 3/8] fix: added new reaction to accurately represent activity of LIPT1 --- model/Human-GEM.yml | 16 ++++++++++++++++ model/reactions.tsv | 1 + 2 files changed, 17 insertions(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 87dec4a8..abf58e7a 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -305275,6 +305275,22 @@ - subsystem: - "Transport reactions" - confidence_score: 0 + - !!omap + - id: "MAR20167" + - name: "MAR20167" + - 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" diff --git a/model/reactions.tsv b/model/reactions.tsv index 3be7341f..bd2685d8 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -12995,3 +12995,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR20164" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" "MAR20165" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" "MAR20166" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20167" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" From 6c342dece1b769de3988ed26fede185ac626c8bc Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 25 Oct 2023 14:57:00 -0400 Subject: [PATCH 4/8] fix: change new reaction ID to not conflict with new DHODH reaction --- model/Human-GEM.yml | 4 ++-- model/reactions.tsv | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index abf58e7a..116211fa 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -305276,8 +305276,8 @@ - "Transport reactions" - confidence_score: 0 - !!omap - - id: "MAR20167" - - name: "MAR20167" + - id: "MAR20168" + - name: "MAR20168" - metabolites: !!omap - MAM00209c: -1 - MAM02393m: 1 diff --git a/model/reactions.tsv b/model/reactions.tsv index bd2685d8..13ae9f79 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -12995,4 +12995,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR20164" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" "MAR20165" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" "MAR20166" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" -"MAR20167" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" +"MAR20168" "" "" "" "" "" "" "" "" "" "" 0 "" "" "" From d9e40469687e94f930dfcfda7abe21d8ac4fb6ab Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 25 Oct 2023 16:00:57 -0400 Subject: [PATCH 5/8] fix: replace MAM02393m with MAM00209c in MAR08433 and MAM01701m with MAM00208c in MAR08434 --- model/Human-GEM.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 116211fa..64fc3cc5 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -80463,7 +80463,7 @@ - MAM01596m: 1 - MAM01986m: -1 - MAM02039m: -1 - - MAM02393m: -1 + - MAM00209c: -1 - MAM02878m: 1 - lower_bound: 0 - upper_bound: 1000 @@ -80480,7 +80480,7 @@ - name: "" - metabolites: !!omap - MAM01045m: 1 - - MAM01701m: 1 + - MAM00208c: 1 - MAM02039m: 1 - MAM02578m: 1 - MAM02878m: -1 From 4bf45c362ac4258005ed96eebeab30df506dc80d Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 25 Oct 2023 16:01:51 -0400 Subject: [PATCH 6/8] fix: removed protons from lipoamide transport reactions --- model/Human-GEM.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 64fc3cc5..a967c74b 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -270275,8 +270275,6 @@ - id: "MAR11346" - name: "Lipoamide Transport" - metabolites: !!omap - - MAM02039c: 1 - - MAM02039e: -1 - MAM02393c: 1 - MAM02393e: -1 - lower_bound: -1000 @@ -270512,8 +270510,6 @@ - id: "MAR11361" - name: "Transport of Lipoamide, Mitochondrial" - metabolites: !!omap - - MAM02039i: -1 - - MAM02039m: 1 - MAM02393c: -1 - MAM02393m: 1 - lower_bound: 0 From 66a2fff209d609816bd5cda7e9468ede3233ba61 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 25 Oct 2023 16:03:32 -0400 Subject: [PATCH 7/8] fix: remove MAR06408 and MAM01701c --- .../deprecatedMetabolites.tsv | 1 + .../deprecatedReactions.tsv | 1 + model/Human-GEM.yml | 26 ------------------- model/metabolites.tsv | 1 - model/reactions.tsv | 1 - 5 files changed, 2 insertions(+), 28 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index e4224e50..3c196da1 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2253,3 +2253,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "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" diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index ad68cf70..0457bfa9 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" "" "" "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" diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index a967c74b..3f6f0c0d 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -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" @@ -198450,24 +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: "" diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 9e2662b2..eef4c72d 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -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" diff --git a/model/reactions.tsv b/model/reactions.tsv index 13ae9f79..fbeef049 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -6837,7 +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" From 7e3fd1826a0f4efc14941fe413d2420dc4cf195d Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Thu, 26 Oct 2023 10:19:29 -0400 Subject: [PATCH 8/8] fix: make MAR11361 reversible --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 3f6f0c0d..50cc71b7 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -270486,7 +270486,7 @@ - metabolites: !!omap - MAM02393c: -1 - MAM02393m: 1 - - lower_bound: 0 + - lower_bound: -1000 - upper_bound: 1000 - gene_reaction_rule: "" - rxnNotes: ""