Merge pull request #708 from SysBioChalmers/fix/refineTrpRxnGPRs

fix: refine Trp metabolism reactions and GPRs
SysBioChalmers · Oct 16, 2023 · 4d59404 · 4d59404
2 parents dc5ce9c + ca672c9
commit 4d59404
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Showing 5 changed files with 15 additions and 58 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2247,3 +2247,4 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02757l"	"MAM02757"	""	""	""	""	""	""	""	""	"M02757"	""	"m02757l"	"m02757l"
 "MAM02757n"	"MAM02757"	""	""	""	""	""	""	""	""	"M02757"	""	"m02757n"	"m02757n"
 "MAM01816n"	"MAM01816"	""	""	""	""	""	"PROTEIN"	""	""	"M01816"	""	"m01816n"	"m01816n"
+"MAM00926c"	"MAM00926"	"4aphdob"	"C01252"	"HMDB0000978"	"CHEBI:17442"	"472"	""	""	""	"4aphdob"	"MNXM163204"	"m00926c"	"m00926c"
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -238,4 +238,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR07771"	""	"NADtpu"	""	""	""	"NADtx"	"MNXR101881"	"HMR_7771"	"RCR20023"	""	0	""	""	"HMR_7771"
 "MAR07782"	""	"ADPtx"	""	""	""	"ADPtx"	"MNXR95484"	"HMR_7782"	"RCR20201"	""	0	""	""	"HMR_7782"
 "MAR07783"	""	"AMPtp"	""	""	""	"AMPtp"	"MNXR95830"	"HMR_7783"	"RCR20046"	""	0	""	""	"HMR_7783"
-"MAR07790"	""	"FADtx"	""	""	""	"FADtx"	"MNXR99217"	"HMR_7790"	"RCR20203"	""	0	""	""	"HMR_7790"
+"MAR07790"	""	"FADtx"	""	""	""	"FADtx"	"MNXR99217"	"HMR_7790"	"RCR20203"	""	0	""	""	"HMR_7790"
+"MAR08564"	""	"KYNAKGAT"	""	""	""	"KYNAKGAT"	"MNXR100948"	"HMR_8564"	"RCR11356"	""	0	""	""	"HMR_8564"
+"MAR08565"	"R03445"	"KYNATESYN"	""	""	""	"KYNATESYN"	"MNXR100949"	"HMR_8565"	"RCR11357"	""	0	""	"RHEA:42452"	"HMR_8565"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -11729,14 +11729,6 @@
       - charge: -1
       - inchis: ""
       - metFrom: "HMRdatabase"
-    - !!omap
-      - id: "MAM00926c"
-      - name: "4-(2-aminophenyl)-2,4-dioxobutanoate"
-      - compartment: "c"
-      - formula: "C10H8NO4"
-      - charge: -1
-      - inchis: ""
-      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM00927c"
       - name: "4-(methylnitrosamino)-1-(1-oxido-3-pyridinyl)-1-butanone"
@@ -81699,41 +81691,6 @@
       - subsystem:
           - "Tryptophan metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR08564"
-      - name: ""
-      - metabolites: !!omap
-          - MAM00926c: 1
-          - MAM01306c: -1
-          - MAM01974c: 1
-          - MAM02319c: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000109576 or ENSG00000137944 or ENSG00000171097"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "2.6.1.7"
-      - references: ""
-      - subsystem:
-          - "Tryptophan metabolism"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR08565"
-      - name: ""
-      - metabolites: !!omap
-          - MAM00926c: -1
-          - MAM00990c: 1
-          - MAM02040c: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: ""
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: ""
-      - references: ""
-      - subsystem:
-          - "Tryptophan metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR08566"
       - name: ""
@@ -82834,14 +82791,14 @@
       - id: "MAR04222"
       - name: ""
       - metabolites: !!omap
-          - MAM00990c: -1
-          - MAM01306c: 1
-          - MAM01974c: -1
-          - MAM02040c: -1
-          - MAM02319c: 1
-      - lower_bound: -1000
+          - MAM00990c: 1
+          - MAM01306c: -1
+          - MAM01974c: 1
+          - MAM02040c: 1
+          - MAM02319c: -1
+      - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000109576 or ENSG00000137944 or ENSG00000171097"
+      - gene_reaction_rule: "ENSG00000137944 or ENSG00000171097"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.6.1.7"
@@ -218228,7 +218185,7 @@
           - MAM02553m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124 or ENSG00000159423"
+      - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.5.1.12"
@@ -230344,7 +230301,7 @@
           - MAM01974m: 1
           - MAM02040m: 1
           - MAM02319m: -1
-      - lower_bound: -1000
+      - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000109576 or ENSG00000137944"
       - rxnNotes: ""

diff --git a/model/metabolites.tsv b/model/metabolites.tsv
@@ -1464,7 +1464,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM00923c"	"MAM00923"	"cala"	"C02642"	"HMDB0000026"	"CHEBI:18261"	"111"	""	""	"HC00975"	"cala"	"MNXM802"	"m00923c"	"m00923c"
 "MAM00924c"	"MAM00924"	"42A3HP24DB"	"C05645"	""	""	"440741"	""	""	"HC01547"	"42A3HP24DB"	"MNXM163203;MNXM4997"	"m00924c"	"m00924c"
 "MAM00925c"	"MAM00925"	""	""	""	""	"10948689"	""	"CE3086"	""	"CE3086"	"MNXM166294"	"m00925c"	"m00925c"
-"MAM00926c"	"MAM00926"	"4aphdob"	"C01252"	"HMDB0000978"	"CHEBI:17442"	"472"	""	""	""	"4aphdob"	"MNXM163204"	"m00926c"	"m00926c"
 "MAM00927c"	"MAM00927"	""	"C19602"	""	""	""	""	""	""	"M00927"	"MNXM14691"	"m00927c"	"m00927c"
 "MAM00928c"	"MAM00928"	""	"C19605"	""	""	""	""	""	""	"M00928"	"MNXM14692"	"m00928c"	"m00928c"
 "MAM00929c"	"MAM00929"	""	"C19574"	""	""	""	""	""	""	"M00929"	"MNXM4356"	"m00929c"	"m00929c"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -748,8 +748,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR08091"	""	"3HXKYNDCL"	""	""	""	"3HXKYNDCL"	"MNXR94906"	"HMR_8091"	"RCR11354"	""	0	""	""	"HMR_8091"
 "MAR08092"	"R04907"	"3HXKYNOXDA"	""	""	""	"3HXKYNOXDA"	"MNXR94907"	"HMR_8092"	"RCR11355"	""	0	""	""	"HMR_8092"
 "MAR08563"	"R02678"	"ALDD20xm"	""	""	""	"ALDD20xm"	"MNXR95744"	"HMR_8563"	"RCR10320"	""	0	""	"RHEA:30867"	"HMR_8563"
-"MAR08564"	""	"KYNAKGAT"	""	""	""	"KYNAKGAT"	"MNXR100948"	"HMR_8564"	"RCR11356"	""	0	""	""	"HMR_8564"
-"MAR08565"	"R03445"	"KYNATESYN"	""	""	""	"KYNATESYN"	"MNXR100949"	"HMR_8565"	"RCR11357"	""	0	""	"RHEA:42452"	"HMR_8565"
 "MAR08566"	""	"MELATNOX"	""	""	""	"MELATNOX"	"MNXR101458"	"HMR_8566"	"RCR11358"	""	0	""	""	"HMR_8566"
 "MAR03935"	"R06982"	"r1377"	""	"r1377"	""	"r1377"	"MNXR105462;MNXR99239"	"HMR_3935"	"RCR11359"	""	0	""	"RHEA:22488"	"HMR_3935"
 "MAR04681"	"R00699"	""	""	""	""	"PHYCBOXL"	"MNXR102650"	"HMR_4681"	"RCR10321"	""	0	""	"RHEA:19717"	"HMR_4681"
@@ -808,7 +806,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04218"	"R03936"	"LFORKYNHYD"	"R03936C"	"r0646"	""	"LFORKYNHYD"	"MNXR101060;MNXR108539"	"HMR_4218"	"RCR11391"	""	0	""	""	"HMR_4218"
 "MAR04219"	"R00988"	""	"R00988C"	"r0239"	""	"r0239"	"MNXR105316;MNXR106774"	"HMR_4219"	"RCR11392"	""	0	""	""	"HMR_4219"
 "MAR04220"	"R01960"	"KYN3OX"	"R01960C"	"r0455"	""	"KYN3OX"	"MNXR100947"	"HMR_4220"	"RCR11393"	""	0	"RHEA:20548"	"RHEA:20545"	"HMR_4220"
-"MAR04222"	""	""	"RE1233C"	""	""	"RE1233C"	""	"HMR_4222"	"RCR11394"	""	0	""	""	"HMR_4222"
+"MAR04222"	""	""	"RE1233C"	""	""	"RE1233C"	""	"HMR_4222"	"RCR11394"	""	0	"RHEA:65561"	"RHEA:65560"	"HMR_4222;MAR08564+MAR08565"
 "MAR04224"	"R00987"	"KYN"	"R00987C"	"r0238"	""	"KYN"	"MNXR100946"	"HMR_4224"	"RCR11395"	""	0	""	"RHEA:16813"	"HMR_4224"
 "MAR04225"	"R02668"	"HKYNH"	"R02668C"	"r0563"	""	"HKYNH"	"MNXR100656"	"HMR_4225"	"RCR10534"	""	0	""	"RHEA:25143"	"HMR_4225"
 "MAR04227"	"R02670"	""	""	""	""	"HMR_4227"	"MNXR107655"	"HMR_4227"	"RCR14355"	""	0	""	""	"HMR_4227"
@@ -8726,7 +8724,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR02751"	""	"RE1134M"	""	""	""	"RE1134M"	"MNXR102255"	""	""	""	0	""	""	"RE1134M"
 "MAR02756"	""	""	""	""	""	"RE1135G"	""	""	""	""	0	""	""	"RE1135G"
 "MAR02763"	""	""	""	""	""	"RE1135L"	""	""	""	""	0	""	""	"RE1135L"
-"MAR02765"	""	""	""	""	""	"RE1233M"	""	""	""	""	0	""	""	"RE1233M"
+"MAR02765"	""	""	""	""	""	"RE1233M"	""	""	""	""	0	"RHEA:65561"	"RHEA:65560"	"RE1233M"
 "MAR02767"	""	"RE1309M"	""	""	""	"RE1309M"	"MNXR103507"	""	""	""	0	""	""	"RE1309M"
 "MAR02779"	""	"RE1342C"	""	""	""	"RE1342C"	"MNXR103511"	""	""	""	0	""	""	"RE1342C"
 "MAR02781"	""	"RE1447M"	""	""	""	"RE1447M"	"MNXR102717"	""	""	""	0	""	""	"RE1447M"