Merge pull request #723 from SysBioChalmers/fix/glutathione_transport

Fix Mitochondrial Glutathione Transport
SysBioChalmers · Nov 13, 2023 · af0862d · af0862d
2 parents ee82b6e + 39005dc
commit af0862d
Show file tree

Hide file tree

Showing 4 changed files with 13 additions and 46 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -259,3 +259,5 @@ 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"
+"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
@@ -86676,20 +86676,15 @@
       - id: "MAR08771"
       - name: ""
       - metabolites: !!omap
-          - MAM01285c: 1
-          - MAM01371c: -1
           - MAM02026c: -1
           - MAM02026m: 1
-          - MAM02039c: 1
-          - MAM02040c: -1
-          - MAM02751c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: ""
+      - gene_reaction_rule: "ENSG00000013306 or ENSG00000075303"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
-      - references: ""
+      - references: "PMID:25637873;PMID:34707288;PMID:35513392"
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
@@ -196414,24 +196409,6 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR04940"
-      - name: ""
-      - metabolites: !!omap
-          - MAM02026c: -1
-          - MAM02026m: 1
-          - MAM02751c: 1
-          - MAM02751m: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000183048"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: ""
-      - references: "PMID:15845418;PMID:16600197;PMID:9639574"
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR04944"
       - name: ""
@@ -198416,24 +198393,6 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR06391"
-      - name: ""
-      - metabolites: !!omap
-          - MAM01306c: -1
-          - MAM01306m: 1
-          - MAM02026c: 1
-          - MAM02026m: -1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000108528"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: ""
-      - references: "PMID:15845418"
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR06431"
       - name: ""
@@ -305505,6 +305464,9 @@
     - !!omap
       - id: "ENSG00000013288"
       - name: "MAN2B2"
+    - !!omap
+      - id: "ENSG00000013306"
+      - name: "SLC25A39"
     - !!omap
       - id: "ENSG00000013375"
       - name: "PGM3"
@@ -306099,6 +306061,9 @@
     - !!omap
       - id: "ENSG00000075239"
       - name: "ACAT1"
+    - !!omap
+      - id: "ENSG00000075303"
+      - name: "SLC25A40"
     - !!omap
       - id: "ENSG00000075415"
       - name: "SLC25A3"

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -2888,3 +2888,5 @@ genes	geneENSTID	geneENSPID	geneUniProtID	geneSymbols	geneEntrezID	geneNames	gen
 "ENSG00000114120"	"ENST00000324194;ENST00000446041;ENST00000507429;ENST00000453248;ENST00000513887;ENST00000648615;ENST00000502594;ENST00000512023;ENST00000512506;ENST00000631654"	"ENSP00000320688;ENSP00000401938;ENSP00000421470;ENSP00000391521;ENSP00000422265;ENSP00000497436;ENSP00000423319;ENSP00000424505;ENSP00000423711;ENSP00000487839"	"Q96CQ1"	"SLC25A36"	"55186"	"solute carrier family 25 member 36"	""	""	""
 "ENSG00000159445"	"ENST00000368814.8;ENST00000489410.1;ENST00000471464.5;ENST00000477437.1;ENST00000483207.5"	"ENSP00000357804.3;ENSP00000433304.1;ENSP00000431288.1"	"Q5T1C6"	"THEM4"	"117145"	"thioesterase superfamily member 4"	"CTMP"	"Cytosol;Inner mitochondria"	"SwissProt"
 "ENSG00000196407"	"ENST00000368817.10;ENST00000453881.2"	"ENSP00000357807.4;ENSP00000406809.2"	"Q8N1Q8"	"THEM5"	"284486"	"thioesterase superfamily member 5"	"ACOT15"	"Inner mitochondria"	"SwissProt"
+"ENSG00000013306"	"ENST00000377095;ENST00000225308;ENST00000590194;ENST00000537904;ENST00000586016;ENST00000588049;ENST00000592857;ENST00000588767;ENST00000585523;ENST00000586633;ENST00000585636;ENST00000593166;ENST00000591006;ENST00000588315;ENST00000585695;ENST00000592372;ENST00000591151"	"ENSP00000366299;ENSP00000225308;ENSP00000467681;ENSP00000444540;ENSP00000466676;ENSP00000465182;ENSP00000467956;ENSP00000466615;ENSP00000466144;ENSP00000465594;ENSP00000465554"	"Q9BZJ4"	"SLC25A39"	"51629"	"solute carrier family 25 member 39"	""	""	""
+"ENSG00000075303"	"ENST00000341119;ENST00000429674;ENST00000444363;ENST00000446236;ENST00000470328;ENST00000483810;ENST00000491499;ENST00000496348"	"ENSP00000344831;ENSP00000401473;ENSP00000405566;ENSP00000407780"	"Q8TBP6"	"SLC25A40"	"55972"	"solute carrier family 25 member 40"	"MCFP"	""	""
diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -1015,7 +1015,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04708"	"R02743"	""	"R02743C"	"r0568"	""	"r0568"	"MNXR105350"	"HMR_4708"	"RCR14413"	""	0	""	""	"HMR_4708"
 "MAR08769"	""	"GTMLTe"	""	""	""	"GTMLTe"	"MNXR100452"	"HMR_8769"	"RCR40314"	""	0	""	""	"HMR_8769"
 "MAR08770"	""	"GGLUCT"	""	""	""	"GGLUCT"	"MNXR100126"	"HMR_8770"	"RCR40168"	""	0	""	""	"HMR_8770"
-"MAR08771"	""	"GTHRDt"	""	""	""	"GTHRDt"	"MNXR100447"	"HMR_8771"	"RCR20224"	""	0	"RHEA:29792"	"RHEA:29791"	"HMR_8771"
+"MAR08771"	""	"GTHRDt"	""	"r0885;r2520"	""	"GTHRDt;r0885;r2520"	"MNXR100447;MNXR105402;MNXR106328"	"HMR_8771;HMR_4940;HMR_6391"	"RCR20224;RCR20265;RCR20063"	"2.A.29.2.7"	0	"RHEA:74821"	"RHEA:74819"	"HMR_8771;MAR04940;HMR_4940;MAR06391;HMR_6391"
 "MAR04078"	"R09076"	""	""	""	""	"HMR_4078"	""	"HMR_4078"	"RCR10551"	""	0	""	"RHEA:25804"	"HMR_4078"
 "MAR04079"	""	""	""	""	""	"HMR_4079"	""	"HMR_4079"	"RCR11506"	""	0	""	""	"HMR_4079"
 "MAR04174"	"R00489"	"ASP1DC"	"R00489C"	"r0128"	""	"ASP1DC"	"MNXR96077"	"HMR_4174"	"RCR10095"	""	0	""	"RHEA:19497"	"HMR_4174"
@@ -6725,7 +6725,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04914"	""	"COAtim"	""	"r0863"	""	"COAtm"	"MNXR96815"	"HMR_4914"	"RCR20001"	""	0	""	""	"HMR_4914"
 "MAR04922"	""	"CO2tm"	""	"r0868"	""	"CO2tm"	"MNXR96810"	"HMR_4922"	"RCR20011"	""	0	""	""	"HMR_4922"
 "MAR04926"	""	"PYRt2m"	""	"r0872"	""	"PYRt2m"	"MNXR103385"	"HMR_4926"	"RCR20136"	""	0	""	""	"HMR_4926"
-"MAR04940"	""	""	""	"r0885"	""	"r0885"	"MNXR105402"	"HMR_4940"	"RCR20265"	"2.A.29.2.7"	0	""	""	"HMR_4940"
 "MAR04944"	""	"FORtm"	""	"r0888"	""	"FORt2m"	"MNXR99620"	"HMR_4944"	"RCR20583"	""	0	"RHEA:29682"	"RHEA:29679"	"HMR_4944"
 "MAR04951"	""	"UREAtm"	""	"r0897"	""	"UREAtm"	"MNXR105156"	"HMR_4951"	"RCR20266"	""	0	"RHEA:32802"	"RHEA:32799"	"HMR_4951"
 "MAR04953"	""	"BALAtmr"	""	"r0900"	""	"BALAtmr"	"MNXR95682"	"HMR_4953"	"RCR20584"	""	0	""	""	"HMR_4953"
@@ -6836,7 +6835,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR06342"	""	"DNDPt58m"	""	"r2431"	""	"DNDPt58m"	"MNXR97671"	"HMR_6342"	"RCR20140"	"2.A.29.16.1"	0	""	""	"HMR_6342"
 "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"
 "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"