Merge pull request #655 from SysBioChalmers/fix/sodium_cotransport_gprs

Fix Sodium Cotransport GPRs
SysBioChalmers · Jul 6, 2023 · d3067b3 · d3067b3
2 parents ca1d328 + 6d45eb5
commit d3067b3
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Showing 3 changed files with 6 additions and 46 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -158,6 +158,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR20015"	"R02549"	"ABUTD;ABUTDm;R_ABUTD;R_ABUTDm"	""	""	""	""	"MNXR95191"	""	""	""	0	"RHEA:19105"	""	""
 "MAR20014"	"R03283"	"R_TMABADH;TMABADH"	""	""	""	""	"MNXR104876"	""	""	""	0	"RHEA:17985"	""	""
 "MAR20052"	""	"ALDD21;RE3076X;R_ALDD21;R_RE3076X"	""	""	""	""	"MNXR95747"	""	""	""	0	"RHEA:44016"	""	""
+"MAR05310"	""	"GLNtN1"	""	""	""	"GLNtN1"	"MNXR100263"	"HMR_5310"	"RCR41006"	""	0	""	""	"HMR_5310"
 "MAR00032"	""	""	""	""	""	"HMR_0032"	""	"HMR_0032"	"RCR14836"	""	0	""	""	"HMR_0032"
 "MAR02276"	""	"r0993"	""	""	""	"r0993"	"MNXR105414"	""	""	""	0	""	""	"r0993"
 "MAR02277"	""	"r0994"	""	""	""	"r0994"	"MNXR105415"	""	""	""	0	""	""	"r0994"
@@ -188,3 +189,4 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR03441"	""	"RE3150C"	""	""	""	"RE3150C"	"MNXR103806"	""	""	""	0	""	""	"RE3150C"
 "MAR10164"	""	""	""	""	""	"CE2516t"	""	""	""	""	0	""	""	"CE2516t"
 "MAR10433"	""	""	""	""	""	"EX_CE2516[e]"	""	""	""	""	0	""	""	"EX_CE2516[e]"
+"MAR09887"	""	"GLNB0AT3tc"	""	""	""	"GLNB0AT3tc"	""	""	""	""	0	""	""	"GLNB0AT3tc"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -172213,26 +172213,6 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR05310"
-      - name: ""
-      - metabolites: !!omap
-          - MAM01975c: 1
-          - MAM01975e: -1
-          - MAM02039c: -1
-          - MAM02039e: 1
-          - MAM02519c: 2
-          - MAM02519e: -2
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000017483 or ENSG00000188338"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: ""
-      - references: ""
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR05311"
       - name: ""
@@ -188970,9 +188950,9 @@
           - MAM02039e: 1
           - MAM02519c: 1
           - MAM02519e: -1
-      - lower_bound: 0
+      - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000017483 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209"
+      - gene_reaction_rule: "ENSG00000017483 or ENSG00000188338"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
@@ -248845,26 +248825,6 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR09887"
-      - name: "Glutamine Transport by B0At3"
-      - metabolites: !!omap
-          - MAM01442c: 1
-          - MAM01442e: -1
-          - MAM01975c: 1
-          - MAM01975e: -1
-          - MAM02519c: 1
-          - MAM02519e: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000147003 and ENSG00000164363"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: ""
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR09888"
       - name: "Glutamate Transport by B0At3"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -5397,7 +5397,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR05305"	""	"ALAt4"	""	"r1118"	""	"ALAt4"	"MNXR95692"	"HMR_5305"	"RCR41003"	"2.A.18.6.7"	0	""	""	"HMR_5305"
 "MAR05307"	""	"ALAtN1"	""	""	""	"ALAtN1"	"MNXR95705"	"HMR_5307"	"RCR41004"	""	0	""	""	"HMR_5307"
 "MAR05308"	""	"GLNt4"	""	"r1119"	""	"GLNt4"	"MNXR100261"	"HMR_5308"	"RCR41005"	"2.A.18.6.5"	0	""	""	"HMR_5308"
-"MAR05310"	""	"GLNtN1"	""	""	""	"GLNtN1"	"MNXR100263"	"HMR_5310"	"RCR41006"	""	0	""	""	"HMR_5310"
 "MAR05311"	""	"ASNt4"	""	"r1120"	""	"ASNt4"	"MNXR96057"	"HMR_5311"	"RCR41007"	"2.A.18.6.7"	0	""	""	"HMR_5311"
 "MAR05313"	""	"ASNtN1"	""	""	""	"ASNtN1"	"MNXR96068"	"HMR_5313"	"RCR41008"	""	0	""	""	"HMR_5313"
 "MAR05314"	""	"VALt4"	""	"r1121"	""	"VALt4"	"MNXR105189"	"HMR_5314"	"RCR41009"	"2.A.1.44.1"	0	""	""	"HMR_5314"
@@ -6275,7 +6274,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR06375"	""	"SERt4"	""	"r2474"	""	"SERt4"	"MNXR104346"	"HMR_6375"	"RCR41525"	"2.A.18.6.5"	0	""	""	"HMR_6375"
 "MAR06377"	""	"CYSt4"	""	"r2475"	""	"CYSt4"	"MNXR97028"	"HMR_6377"	"RCR41526"	"2.A.18.6.5"	0	""	""	"HMR_6377"
 "MAR06379"	""	"HOMt4"	""	"r2476"	""	"HOMt4"	"MNXR100677"	"HMR_6379"	"RCR41527"	"2.A.18.6.5"	0	""	""	"HMR_6379"
-"MAR06380"	""	"GLNt4"	""	"r2477"	""	""	"MNXR100261"	"HMR_6380"	"RCR41528"	"2.A.18.6.2"	0	""	""	"HMR_6380"
+"MAR06380"	""	"GLNt4;GLNtN1"	""	"r2477"	""	"GLNtN1"	"MNXR100261;MNXR100263"	"HMR_6380;HMR_5310"	"RCR41528;RCR41006"	"2.A.18.6.2"	0	""	""	"HMR_6380;HMR_5310;MAR05310"
 "MAR06381"	""	"SERt4"	""	"r2478"	""	""	"MNXR104346"	"HMR_6381"	"RCR41529"	"2.A.18.6.8"	0	""	""	"HMR_6381"
 "MAR06382"	""	"ASNt4"	""	"r2479"	""	""	"MNXR96057"	"HMR_6382"	"RCR41530"	"2.A.18.6.8"	0	""	""	"HMR_6382"
 "MAR06383"	""	"HOMt4"	""	"r2480"	""	""	"MNXR100677"	"HMR_6383"	"RCR41531"	"2.A.18.6.8"	0	""	""	"HMR_6383"
@@ -9504,7 +9503,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR06891"	""	"CYSTALArBATtc"	""	""	""	"CYSTALArBATtc"	"MNXR97011"	""	""	""	0	""	""	"CYSTALArBATtc"
 "MAR06892"	""	"CYSTLEUrBATtc"	""	""	""	"CYSTLEUrBATtc"	"MNXR97016"	""	""	""	0	""	""	"CYSTLEUrBATtc"
 "MAR06893"	""	"FOLt"	""	""	""	"FOLTle"	"MNXR99612"	""	""	""	0	""	""	"FOLTle"
-"MAR06896"	""	"GLNATB0tc"	""	""	""	"GLNATB0tc"	"MNXR100248"	""	""	""	0	""	""	"GLNATB0tc"
+"MAR06896"	""	"GLNATB0tc;GLNB0AT3tc"	""	""	""	"GLNATB0tc;GLNB0AT3tc"	"MNXR100248"	""	""	""	0	""	""	"GLNATB0tc;GLNB0AT3tc;MAR09887"
 "MAR06897"	""	"GLNyLATthc"	""	""	""	"GLNyLATthc"	"MNXR100264"	""	""	""	0	""	""	"GLNyLATthc"
 "MAR06898"	""	"GLYGLYCNc"	""	""	""	"GLYGLYCNc"	"MNXR100345"	""	""	""	0	""	""	"GLYGLYCNc"
 "MAR06899"	""	"GLYGLYPEPT1tc"	""	""	""	"GLYGLYPEPT1tc"	"MNXR100346"	""	""	""	0	""	""	"GLYGLYPEPT1tc"
@@ -9740,7 +9739,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR09884"	""	"FOLOAT2tc"	""	""	""	"FOLOAT2tc"	""	""	""	""	0	""	""	"FOLOAT2tc"
 "MAR09885"	""	"FOLOATPtc"	""	""	""	"FOLOATPtc"	""	""	""	""	0	""	""	"FOLOATPtc"
 "MAR09886"	""	"GABABGTtc"	""	""	""	"GABABGTtc"	""	""	""	""	0	""	""	"GABABGTtc"
-"MAR09887"	""	"GLNB0AT3tc"	""	""	""	"GLNB0AT3tc"	""	""	""	""	0	""	""	"GLNB0AT3tc"
 "MAR09888"	""	"GLUB0AT3tc"	""	""	""	"GLUB0AT3tc"	""	""	""	""	0	""	""	"GLUB0AT3tc"
 "MAR09889"	""	"GSNt2"	""	""	""	"GSNt2r"	"MNXR100434"	""	""	""	0	"RHEA:29586"	"RHEA:29583"	"GSNt2r"
 "MAR09890"	""	"H2OGLYAQPt"	""	""	""	"H2OGLYAQPt"	""	""	""	""	0	""	""	"H2OGLYAQPt"