Merge pull request #725 from SysBioChalmers/fix/oxoadipate_dehydrogenase

Fix Oxoadipate Dehydrogenase
SysBioChalmers · Nov 18, 2023 · 7451de8 · 7451de8
2 parents af0862d + 2c314cd
commit 7451de8
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Showing 4 changed files with 12 additions and 36 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -259,5 +259,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR11292"	""	"HXAt3"	""	""	""	"HXAt3"	""	""	""	""	0	""	""	"HXAt3"
 "MAR11293"	""	"EX_hxa_e"	""	""	""	"EX_hxa[e]"	"MNXR98664"	""	""	""	0	""	""	"EX_hxa[e]"
 "MAR09949"	""	"FACOAE60"	""	""	""	"HXCOAc"	"MNXR99139"	""	""	""	0	""	""	"HXCOAc"
+"MAR04239"	"R01933"	"2OXOADOXm"	"R01933M"	"r0448"	""	"2OXOADOXm"	"MNXR94818"	"HMR_4239"	"RCR11332"	""	0	"RHEA:30796"	"RHEA:30795"	"HMR_4239"
 "MAR04940"	""	""	""	"r0885"	""	"r0885"	"MNXR105402"	"HMR_4940"	"RCR20265"	"2.A.29.2.7"	0	""	""	"HMR_4940"
 "MAR06391"	""	""	""	"r2520"	""	"r2520"	"MNXR106328"	"HMR_6391"	"RCR20063"	""	0	""	""	"HMR_6391"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -80915,26 +80915,6 @@
       - subsystem:
           - "Histidine metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR04239"
-      - name: "2-oxoadipate dehydrogenase complex"
-      - metabolites: !!omap
-          - MAM00670m: -1
-          - MAM01596m: 1
-          - MAM01597m: -1
-          - MAM01977m: 1
-          - MAM02552m: -1
-          - MAM02553m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000091140 and ENSG00000105953 and ENSG00000119689"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "1.2.4.2"
-      - references: "PMID:10676873"
-      - subsystem:
-          - "Lysine metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR04241"
       - name: "S-Adenosyl-L-methionine:histone-L-lysine N6-methyltransferase"
@@ -81022,11 +81002,11 @@
           - MAM02899m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000105953 or ENSG00000181192 or ENSG00000197444"
+      - gene_reaction_rule: "(ENSG00000105953 and ENSG00000119689) or (ENSG00000181192 and ENSG00000119689)"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.2.4.2"
-      - references: "PMID:10676873"
+      - references: "PMID:28757203;PMID:32160276"
       - subsystem:
           - "Lysine metabolism"
       - confidence_score: 0
@@ -81144,7 +81124,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.3.1.61"
-      - references: "PMID:9620315"
+      - references: "PMID:9620315;PMID:28757203;PMID:32160276"
       - subsystem:
           - "Lysine metabolism"
       - confidence_score: 0
@@ -94084,11 +94064,11 @@
           - MAM02984m: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000105953 or ENSG00000181192 or ENSG00000197444"
+      - gene_reaction_rule: "ENSG00000105953 or ENSG00000181192"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.2.4.2"
-      - references: "PMID:10676873;PMID:3207422"
+      - references: "PMID:10676873;PMID:3207422;PMID:32160276"
       - subsystem:
           - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
       - confidence_score: 0
@@ -94223,11 +94203,11 @@
           - MAM02984m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000105953 or ENSG00000181192 or ENSG00000197444"
+      - gene_reaction_rule: "ENSG00000105953 or ENSG00000181192"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.2.4.2"
-      - references: "PMID:10676873"
+      - references: "PMID:10676873;PMID:32160276"
       - subsystem:
           - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
       - confidence_score: 0
@@ -94245,7 +94225,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.3.1.61"
-      - references: "PMID:8076640;PMID:9620315"
+      - references: "PMID:8076640;PMID:9620315;PMID:32160276"
       - subsystem:
           - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
       - confidence_score: 0
@@ -313150,9 +313130,6 @@
     - !!omap
       - id: "ENSG00000197417"
       - name: "SHPK"
-    - !!omap
-      - id: "ENSG00000197444"
-      - name: "OGDHL"
     - !!omap
       - id: "ENSG00000197446"
       - name: "CYP2F1"

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -2607,7 +2607,6 @@ genes	geneENSTID	geneENSPID	geneUniProtID	geneSymbols	geneEntrezID	geneNames	gen
 "ENSG00000197408"	"ENST00000324071;ENST00000598834;ENST00000593831;ENST00000594187;ENST00000597612"	"ENSP00000324648;ENSP00000496294;ENSP00000470582"	"P20813"	"CYP2B6"	"1555"	"cytochrome P450 family 2 subfamily B member 6"	"CPB6;CYP2B;CYPIIB6"	"Endoplasmic reticulum;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000197416"	"ENST00000519696;ENST00000360464"	"ENSP00000427973;ENSP00000353650"	"A6NFH5"	"FABP12"	"646486"	"fatty acid binding protein 12"	""	"Cytosol"	"DeepLoc2"
 "ENSG00000197417"	"ENST00000225519"	"ENSP00000225519"	"Q9UHJ6"	"SHPK"	"23729"	"sedoheptulokinase"	"CARKL;SHK"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
-"ENSG00000197444"	"ENST00000374103;ENST00000419399;ENST00000432695;ENST00000490844;ENST00000496884;ENST00000471460"	"ENSP00000363216;ENSP00000401356;ENSP00000390240"	"Q9ULD0"	"OGDHL"	"55753"	"oxoglutarate dehydrogenase L"	"FLJ10851"	"Mitochondria;Nucleus"	"SwissProt;CellAtlas"
 "ENSG00000197446"	"ENST00000526093;ENST00000531409;ENST00000331105;ENST00000532164;ENST00000534009;ENST00000439903"	"ENSP00000333534;ENSP00000471416;ENSP00000470136;ENSP00000443424"	"P24903"	"CYP2F1"	"1572"	"cytochrome P450 family 2 subfamily F member 1"	"CYP2F"	"Endoplasmic reticulum"	"SwissProt"
 "ENSG00000197448"	"ENST00000436038;ENST00000409500;ENST00000443571;ENST00000358406;ENST00000442394;ENST00000479303;ENST00000494735;ENST00000473649;ENST00000489654"	"ENSP00000408341;ENSP00000386944;ENSP00000415813;ENSP00000351181;ENSP00000406802;ENSP00000431049"	"Q9Y2Q3"	"GSTK1"	"373156"	"glutathione S-transferase kappa 1"	"GST13"	"Peroxisome"	"SwissProt;CellAtlas"
 "ENSG00000197496"	"ENST00000359271;ENST00000486000;ENST00000611837"	"ENSP00000352216;ENSP00000478679"	"O95528"	"SLC2A10"	"81031"	"solute carrier family 2 member 10"	"GLUT10"	"Cytosol"	"SwissProt;CellAtlas"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -709,18 +709,17 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR08783"	"R02150"	"HISTASE"	""	""	""	"HISTASE"	"MNXR95850"	"HMR_8783"	"RCR11329"	""	0	""	"RHEA:25625"	"HMR_8783"
 "MAR08784"	"R04065"	"IMACTD"	""	""	""	"IMACTD"	"MNXR95745"	"HMR_8784"	"RCR11330"	""	0	"RHEA:31060"	"RHEA:31059"	"HMR_8784"
 "MAR08786"	"R04065"	"IMACTD_m"	""	""	""	"IMACTD_m"	"MNXR95745"	"HMR_8786"	"RCR11331"	""	0	"RHEA:31060"	"RHEA:31059"	"HMR_8786"
-"MAR04239"	"R01933"	"2OXOADOXm"	"R01933M"	"r0448"	""	"2OXOADOXm"	"MNXR94818"	"HMR_4239"	"RCR11332"	""	0	"RHEA:30796"	"RHEA:30795"	"HMR_4239"
 "MAR04241"	"R03938"	""	""	""	""	"HMR_4241"	"MNXR108541"	"HMR_4241"	"RCR14332"	""	0	""	"RHEA:10024"	"HMR_4241"
 "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"	""	"R01940M"	"r0451"	""	"r0451"	"MNXR102246;MNXR107241"	"HMR_4599"	"RCR10318"	""	0	""	"RHEA:12188"	"HMR_4599"
+"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"
 "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"
 "MAR04739"	"R03102"	"AASAD3m"	"R03102M"	""	""	"AASAD3m"	"MNXR95158"	"HMR_4739"	"RCR10527"	""	0	""	"RHEA:12308"	"HMR_4739"
 "MAR04740"	"R02317"	""	"RE1254C"	""	""	"RE1254C"	"MNXR95152"	"HMR_4740"	"RCR11337"	""	1	""	"RHEA:25121"	"HMR_4740"
-"MAR06415"	"R02571"	""	"R02571C"	"r0557"	""	"r0557"	"MNXR100213;MNXR107586"	"HMR_6415"	"RCR14333"	""	0	""	""	"HMR_6415"
+"MAR06415"	"R02571"	"2OXOADOXm"	"R02571C;R01933M"	"r0557;r0448"	""	"r0557;2OXOADOXm"	"MNXR100213;MNXR107586"	"HMR_6415;HMR_4239"	"RCR14333;RCR11332"	""	0	""	""	"HMR_6415;MAR04239;HMR_4239"
 "MAR06974"	""	""	""	"r1386"	""	""	""	"HMR_6974"	"RCR10159"	""	0	""	""	"HMR_6974"
 "MAR06975"	"R03875"	""	""	""	""	"HMR_6975"	"MNXR108494"	"HMR_6975"	"RCR11338"	""	0	""	"RHEA:51736"	"HMR_6975"
 "MAR06976"	"R04866"	""	""	""	""	"HMR_6976"	"MNXR109175"	"HMR_6976"	"RCR11339"	""	0	""	"RHEA:54196"	"HMR_6976"
@@ -1331,7 +1330,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04589"	"R01900"	""	"R01900C"	"r0426"	""	"r0426"	"MNXR105342;MNXR95387"	"HMR_4589"	"RCR10352"	""	0	""	"RHEA:22144"	"HMR_4589"
 "MAR04652"	"R00408;R02164"	"r0509;SUCD1m"	"R02164C"	"r0509"	""	"r0509;SUCD1m"	"MNXR107340;MNXR99636"	"HMR_4652;HMR_8743"	"RCR14481;RCR11674"	""	0	""	"RHEA:13713;RHEA:30343"	"HMR_4652;HMR_8743;MAR08743"
 "MAR06413"	"R03316"	""	"R03316M"	"r0620"	""	"r0620"	"MNXR105357;MNXR108089"	"HMR_6413"	"RCR11672"	""	0	""	""	"HMR_6413"
-"MAR06414"	"R02570"	""	"R02570C"	"r0556"	""	"r0556"	"MNXR107585;MNXR95656"	"HMR_6414"	"RCR14482"	""	0	""	"RHEA:15213"	"HMR_6414"
+"MAR06414"	"R02570"	""	"R02570C"	"r0556"	""	"r0556"	"MNXR107585;MNXR95656"	"HMR_6414"	"RCR14482"	""	0	"RHEA:15216"	"RHEA:15213"	"HMR_6414"
 "MAR07704"	"R00466"	"GLXO2p"	""	""	""	"GLXO2p"	"MNXR100305"	"HMR_7704"	"RCR10605"	""	0	""	"RHEA:14837"	"HMR_7704"
 "MAR07706"	"R00475"	"GLYCTO1p"	""	""	""	"GLYCTO1p"	"MNXR100338"	"HMR_7706"	"RCR11673"	""	0	""	"RHEA:25311"	"HMR_7706"
 "MAR08772"	""	"KHK2"	""	""	""	"KHK2"	"MNXR100937"	"HMR_8772"	"RCR11675"	""	0	""	""	"HMR_8772"