fix: adjusted existing BCKDH and 2-OADH reactions to connect to new t…

…hiamine-dependent steps
SysBioChalmers · Dec 10, 2023 · 35b8fc1 · 35b8fc1
1 parent 271a14c
commit 35b8fc1
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Showing 2 changed files with 20 additions and 26 deletions.
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -70690,16 +70690,14 @@
       - metabolites: !!omap
           - MAM00671m: -1
           - MAM01596m: 1
-          - MAM01597m: -1
-          - MAM02552m: -1
-          - MAM02553m: 1
-          - MAM02774m: 1
+          - MAM02039m: -1
+          - MAM02984m: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000083123 and ENSG00000091140 and ENSG00000137992 and ENSG00000248098"
+      - gene_reaction_rule: "ENSG00000248098 and ENSG00000083123"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
-      - eccodes: "1.2.7.2"
+      - eccodes: "1.2.4.4"
       - references: "PMID:2649080;PMID:283398;PMID:3718468;PMID:9381974"
       - subsystem:
           - "Propanoate metabolism"
@@ -81043,11 +81041,10 @@
       - id: "MAR04599"
       - name: "2-Oxoadipate:lipoamde 2-oxidoreductase(decarboxylating and acceptor-succinylating)"
       - metabolites: !!omap
-          - MAM00670m: -1
-          - MAM01596m: 1
-          - MAM02039m: -1
           - MAM02393m: -1
           - MAM02899m: 1
+          - MAM02984m: 1
+          - MAM20077m: -1
       - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "(ENSG00000105953 and ENSG00000119689) or (ENSG00000181192 and ENSG00000119689)"
@@ -82450,11 +82447,10 @@
       - id: "MAR06419"
       - name: "(S)-3-Methyl-2-oxopentanoate:[dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-2-methylpropanoylating)"
       - metabolites: !!omap
-          - MAM00669m: -1
-          - MAM01596m: 1
-          - MAM02039m: -1
           - MAM02393m: -1
           - MAM02856m: 1
+          - MAM02984m: 1
+          - MAM20079m: -1
       - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000083123 and ENSG00000142046 and ENSG00000248098"
@@ -82487,11 +82483,10 @@
       - id: "MAR06421"
       - name: "4-methyl-2-oxopentanoate:[dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-2-methylpropanoylating)"
       - metabolites: !!omap
-          - MAM01013m: -1
-          - MAM01596m: 1
-          - MAM02039m: -1
           - MAM02393m: -1
           - MAM02858m: 1
+          - MAM02984m: 1
+          - MAM20080m: -1
       - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000083123 and ENSG00000142046 and ENSG00000248098"
@@ -87595,11 +87590,10 @@
       - id: "MAR06416"
       - name: "3-methyl-2-oxobutanoate:[dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-2-methylpropanoylating)"
       - metabolites: !!omap
-          - MAM00824m: -1
-          - MAM01596m: 1
-          - MAM02039m: -1
           - MAM02393m: -1
           - MAM02857m: 1
+          - MAM02984m: 1
+          - MAM20078m: -1
       - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000083123 and ENSG00000142046 and ENSG00000248098"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -160,7 +160,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR00153"	"R00925"	"ACS2"	""	"r0218"	""	"ACS2"	"MNXR106753;MNXR95222"	"HMR_0153"	"RCR10460"	""	0	"RHEA:20374"	"RHEA:20373"	"HMR_0153"
 "MAR03212"	"R00924"	"PPCOAOm"	""	"r0683"	""	"PPCOAOm;r0683"	"MNXR103101"	"HMR_3212;HMR_3211"	"RCR11088;RCR14348"	""	0	""	""	"HMR_3212;MAR03211"
 "MAR03797"	"R00925"	"ACCOALm"	""	"r0219"	""	"ACCOALm"	"MNXR106753;MNXR95222"	"HMR_3797"	"RCR14211"	""	0	"RHEA:20376"	"RHEA:20373"	"HMR_3797"
-"MAR03800"	""	"OBDHm"	""	"r1154"	""	"r1154"	"MNXR102133"	"HMR_3800"	"RCR10461"	""	0	""	""	"HMR_3800"
+"MAR03800"	"R10996"	"OBDHm"	""	"r1154"	""	"r1154"	"MNXR114300"	"HMR_3800"	"RCR10461"	""	0	""	""	"HMR_3800"
 "MAR04105"	"R00233"	"MCD"	""	"r0063"	""	"MCD"	"MNXR101412"	"HMR_4105"	"RCR10285"	""	0	"RHEA:18782"	"RHEA:18781"	"HMR_4105"
 "MAR04106"	"R00233"	"MCDm"	""	"r0064"	""	"MCDm"	"MNXR101412"	"HMR_4106"	"RCR11089"	""	0	"RHEA:18782"	"RHEA:18781"	"HMR_4106"
 "MAR04107"	"R00233"	"MCDp"	""	"r0065"	""	"MCDp"	"MNXR101412"	"HMR_4107"	"RCR14212"	""	0	"RHEA:18782"	"RHEA:18781"	"HMR_4107"
@@ -713,7 +713,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04288"	"R00716"	"SACCD3m"	"R00716M"	"r0180"	""	"SACCD3m"	"MNXR104238"	"HMR_4288"	"RCR11333"	""	0	""	"RHEA:19373"	"HMR_4288"
 "MAR04596"	"R01939"	""	"R01939C"	"r0450"	""	"AATAi"	"MNXR95160"	"HMR_4596"	"RCR10526"	""	0	""	"RHEA:12601"	"HMR_4596"
 "MAR04597"	"R01939"	""	"R01939M"	"r0450"	""	"r0450"	"MNXR95160"	"HMR_4597"	"RCR11334"	""	0	""	"RHEA:12601"	"HMR_4597"
-"MAR04599"	"R01940"	"2OXOADOXm"	"R01940M;R01933M"	"r0451;r0448"	""	"r0451;2OXOADOXm"	"MNXR102246;MNXR107241"	"HMR_4599;HMR_4239"	"RCR10318;RCR11332"	""	0	"RHEA:12189"	"RHEA:12188"	"HMR_4599;MAR04239;HMR_4239"
+"MAR04599"	"R13167"	"2OXOADOXm"	"R01940M;R01933M"	"r0451;r0448"	""	"r0451;2OXOADOXm"	""	"HMR_4599;HMR_4239"	"RCR10318;RCR11332"	""	0	""	""	"HMR_4599;MAR04239;HMR_4239"
 "MAR04667"	"R02313"	"r0525"	"R02313C"	"r0525"	""	"r0525"	"MNXR105347"	"HMR_4667"	"RCR11335"	""	0	""	"RHEA:24520"	"HMR_4667"
 "MAR04668"	"R02315"	"SACCD4m"	""	"r0526"	""	"SACCD4m"	"MNXR104236"	"HMR_4668"	"RCR11336"	""	0	""	"RHEA:10020"	"HMR_4668"
 "MAR04737"	"R03102"	""	"R03102M"	"r0594"	""	"r0594"	"MNXR95158"	"HMR_4737"	"RCR10319"	""	0	""	"RHEA:12308"	"HMR_4737"
@@ -787,9 +787,9 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR03795"	"R00922"	"MMSAD1m"	"R00922M"	"r0223"	""	"MMSAD1m"	"MNXR101662"	"HMR_3795"	"RCR10324"	""	0	""	"RHEA:20804"	"HMR_3795"
 "MAR04797"	"R03869"	""	"R03869C"	"r0642"	""	"r0642"	"MNXR105358;MNXR95762"	"HMR_4797"	"RCR10533"	""	0	""	"RHEA:31043"	"HMR_4797"
 "MAR06417"	"R02662"	""	"RE3326M"	"r0561"	""	"RE3326M;r0561"	"MNXR107649;MNXR97451"	"HMR_6417"	"RCR14349"	""	0	""	"RHEA:18865"	"HMR_6417"
-"MAR06419"	"R04225"	""	"R04225C"	"r0670"	""	"r0670"	"MNXR108745;MNXR94911"	"HMR_6419"	"RCR11381"	""	0	""	""	"HMR_6419"
+"MAR06419"	"R07604"	""	"R04225C"	"r0670"	""	"r0670"	"MNXR142264;MNXR183201"	"HMR_6419"	"RCR11381"	""	0	""	""	"HMR_6419"
 "MAR06420"	"R03174"	""	""	"r0604"	""	"r0604"	"MNXR108002;MNXR97450"	"HMR_6420"	"RCR14350"	""	0	""	""	"HMR_6420"
-"MAR06421"	"R01702;R01651"	"OIVD1m"	"R01702C;R03171M"	"r0386;r0601"	""	"r0386;OIVD1m"	"MNXR107132;MNXR95029;MNXR102172;MNXR107999"	"HMR_6421;HMR_3767"	"RCR11382;RCR14422"	""	0	""	"RHEA:25177"	"HMR_6421;HMR_3767;MAR03767_1"
+"MAR06421"	"R01702"	"OIVD1m"	"R01702C;R03171M"	"r0386;r0601"	""	"r0386;OIVD1m"	"MNXR144603;MNXR183200"	"HMR_6421;HMR_3767"	"RCR11382;RCR14422"	""	0	""	""	"HMR_6421;HMR_3767;MAR03767_1"
 "MAR06422"	"R04097;R01651"	"OIVD1m"	"R0317M"	"r0656;r0601"	""	"r0656;OIVD1m"	"MNXR108654;MNXR97452;MNXR102172;MNXR107999"	"HMR_6422;HMR_3767"	"RCR14351;RCR14422"	""	0	""	"RHEA:25177"	"HMR_6422;MAR03767_2"
 "MAR06923"	"R01090"	"LEUTA"	""	""	""	"LEUTA"	"MNXR96229"	"HMR_6923"	"RCR10325"	""	0	""	"RHEA:18321"	"HMR_6923"
 "MAR03765"	"R01090"	"LEUTAm"	"R01090C"	"r0262"	""	"LEUTAm"	"MNXR96229"	"HMR_3765"	"RCR11383"	""	0	""	"RHEA:18321"	"HMR_3765"
@@ -1060,7 +1060,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR03792"	"R02048"	""	"R02048M"	"r0483"	""	"3AIBTm;r0483"	"MNXR105346"	"HMR_3792"	"RCR11523"	""	0	""	""	"HMR_3792"
 "MAR03796"	"R00926"	""	"R00926C"	"r0221"	""	"r0221"	"MNXR105315;MNXR106754"	"HMR_3796"	"RCR10119"	""	0	""	""	"HMR_3796"
 "MAR03823"	"R04203"	"HACD9m"	"R04203M"	"r0664"	""	"HACD9m"	"MNXR100550"	"HMR_3823"	"RCR11524"	""	0	""	"RHEA:13281"	"HMR_3823"
-"MAR06416"	"R01701"	""	"R01701C"	"r0385"	""	"r0385"	"MNXR107131;MNXR94910"	"HMR_6416"	"RCR11525"	""	0	""	"RHEA:13457"	"HMR_6416"
+"MAR06416"	"R07600"	""	"R01701C"	"r0385"	""	"r0385"	"MNXR142260;MNXR183199"	"HMR_6416"	"RCR11525"	""	0	""	""	"HMR_6416"
 "MAR03986"	""	""	""	"r1374"	""	"r1374"	"MNXR105461"	"HMR_3986"	"RCR30265"	""	0	""	""	"HMR_3986"
 "MAR03988"	"R00022"	""	"R00022C"	"r0013"	""	"r0013"	"MNXR100746;MNXR95628"	"HMR_3988"	"RCR11526"	""	0	""	"RHEA:30671"	"HMR_3988"
 "MAR04124"	"R01384"	"UDPGLDCg"	"R01384C"	"r0326"	""	"HMR_4124"	"MNXR105068"	"HMR_4124"	"RCR11527"	""	0	""	"RHEA:23916"	"HMR_4124"
@@ -12994,9 +12994,9 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR20170"	""	""	""	""	""	""	""	""	""	""	0	"RHEA:30144"	"RHEA:30143"	""
 "MAR20171"	""	""	""	""	""	""	""	""	""	""	0	"RHEA:40060"	"RHEA:40059"	""
 "MAR20172"	""	""	""	""	""	""	""	""	""	""	0	""	""	""
-"MAR20173"	"R13167"	""	""	""	""	""	""	""	""	""	0	""	""	""
+"MAR20173"	"R13166"	""	""	""	""	""	""	""	""	""	0	""	""	""
 "MAR20174"	"R07599"	""	""	""	""	""	"MNXR145675"	""	""	""	0	""	""	""
 "MAR20175"	"R07603"	""	""	""	""	""	"MNXR145677"	""	""	""	0	""	""	""
 "MAR20176"	"R07601"	""	""	""	""	""	"MNXR145679"	""	""	""	0	""	""	""
-"MAR20177"	"R10996"	""	""	""	""	""	"MNXR114300"	""	""	""	0	""	""	""
-"MAR20178"	"R10997"	""	""	""	""	""	"MNXR114301"	""	""	""	0	""	""	""
+"MAR20177"	"R10997"	""	""	""	""	""	"MNXR114301"	""	""	""	0	""	""	""
+"MAR20178"	"R10998"	""	""	""	""	""	"MNXR114302"	""	""	""	0	""	""	""