Merge pull request #807 from SysBioChalmers/fix/tagatose

Remove Tagatose-1,6-Bisphosphate
SysBioChalmers · Apr 24, 2024 · be23d02 · be23d02
2 parents 56279d7 + 3a16284
commit be23d02
Show file tree

Hide file tree

Showing 5 changed files with 9 additions and 55 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2271,3 +2271,4 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM03203m"	"MAM03203"	"3ddecdicoa"	""	""	""	"5280771"	""	""	""	"3ddecdicoa"	""	""	"3ddecdicoa_m"
 "MAM02698m"	"MAM02698"	"2ddecdicoa"	""	""	""	"5280770"	""	""	""	"2ddecdicoa"	""	""	"2ddecdicoa_m"
 "MAM03650m"	"MAM03650"	"hexddcoa"	""	""	""	""	""	""	""	"hexddcoa"	""	""	"hexddcoa_m"
+"MAM02955c"	"MAM02955"	""	"C03785"	""	"CHEBI:4250"	"440117"	""	""	"HC01180"	"HC01180"	"MNXM1324;MNXM164715"	"m02955c"	"m02955c"
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -295,3 +295,5 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR05075"	""	"FAOXC122m"	""	""	""	"FAOXC122m;HMR_3422"	""	"HMR_3422"	"RCR12667"	""	0	""	""	"FAOXC122m;HMR_3422;MAR03422"
 "MAR05072"	""	"FAOXC122C101m"	""	""	""	"FAOXC122C101m;HMR_3422"	""	"HMR_3422"	"RCR12667"	""	0	""	""	"FAOXC122C101m;HMR_3422;MAR03422"
 "MAR00965"	""	"FAOXC2252053m"	""	""	""	"FAOXC2252053m"	"MNXR99352"	""	""	""	0	""	""	"FAOXC2252053m"
+"MAR04774"	"R03237"	""	"R03237C"	"r0610"	""	"r0610"	"MNXR105355;MNXR108039"	"HMR_4774"	"RCR11046"	""	0	""	""	"HMR_4774"
+"MAR04775"	"R03239"	""	"R03239C"	"r0611"	""	"r0611"	"MNXR105356;MNXR108041"	"HMR_4775"	"RCR14197"	""	0	""	""	"HMR_4775"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -40793,14 +40793,6 @@
       - charge: 0
       - inchis: ""
       - metFrom: "HMRdatabase"
-    - !!omap
-      - id: "MAM02955c"
-      - name: "tagatose-1,6-bisphosphate"
-      - compartment: "c"
-      - formula: "C6H10O12P2"
-      - charge: -4
-      - inchis: ""
-      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM02956e"
       - name: "TAG-chylomicron pool"
@@ -68998,44 +68990,6 @@
       - subsystem:
           - "Galactose metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR04774"
-      - name: "CTP:D-tagatose 6-phosphate 1-phosphotransferase"
-      - metabolites: !!omap
-          - MAM01424c: -1
-          - MAM01623c: 1
-          - MAM01746c: 1
-          - MAM02039c: -1
-          - MAM02955c: -1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000067057 or ENSG00000141959 or ENSG00000152556"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "2.7.1.11"
-      - references: "PMID:131802;PMID:1810251;PMID:193556;PMID:2987258;PMID:6091737"
-      - subsystem:
-          - "Galactose metabolism"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR04775"
-      - name: "ITP:D-tagatose 6-phosphate 1-phosphotransferase"
-      - metabolites: !!omap
-          - MAM01746c: -1
-          - MAM02039c: 1
-          - MAM02161c: 1
-          - MAM02193c: -1
-          - MAM02955c: 1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000067057 or ENSG00000141959 or ENSG00000152556"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "2.7.1.11"
-      - references: "PMID:131802;PMID:1810251"
-      - subsystem:
-          - "Galactose metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR04831"
       - name: "Lactose:(acceptor) 3-oxidoreductase"
@@ -69107,7 +69061,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.1.3"
-      - references: ""
+      - references: "PMID:33715524"
       - subsystem:
           - "Galactose metabolism"
       - confidence_score: 0
@@ -69124,7 +69078,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.1.2.13"
-      - references: ""
+      - references: "PMID:33715524"
       - subsystem:
           - "Galactose metabolism"
       - confidence_score: 0
@@ -191976,7 +191930,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
-      - references: ""
+      - references: "PMID:33715524"
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
@@ -215766,7 +215720,7 @@
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: ""
-      - references: ""
+      - references: "PMID:33715524"
       - subsystem:
           - "Exchange/demand reactions"
       - confidence_score: 0
@@ -222350,7 +222304,7 @@
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "4.1.2.13"
-      - references: "PMID:2996495;PMID:6284103;PMID:6298387"
+      - references: "PMID:33715524"
       - subsystem:
           - "Galactose metabolism"
       - confidence_score: 0
@@ -223360,7 +223314,7 @@
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "2.7.1.3"
-      - references: "PMID:2996495;PMID:6284103;PMID:6298387"
+      - references: "PMID:33715524"
       - subsystem:
           - "Galactose metabolism"
       - confidence_score: 0

diff --git a/model/metabolites.tsv b/model/metabolites.tsv
@@ -5097,7 +5097,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02952e"	"MAM02952"	""	"C03642"	""	"CHEBI:17864"	"440071"	"LMST05020003"	""	"HC02198"	"HC02198"	"MNXM162796;MNXM1950"	"m02952s"	"m02952s"
 "MAM02953c"	"MAM02953"	"ts3"	""	"HMDB0006560"	""	"5283713"	""	""	""	"ts3"	"MNXM21968"	"m02953c"	"m02953c"
 "MAM02954c"	"MAM02954"	""	"C11148"	""	"CHEBI:28888"	""	""	""	""	"M02954"	"MNXM3722"	"m02954c"	"m02954c"
-"MAM02955c"	"MAM02955"	""	"C03785"	""	"CHEBI:4250"	"440117"	""	""	"HC01180"	"HC01180"	"MNXM1324;MNXM164715"	"m02955c"	"m02955c"
 "MAM02956e"	"MAM02956"	""	"C00422"	""	"CHEBI:17855"	""	"LMGL03010000"	""	""	"M02956"	"MNXM248"	"m02956s"	"m02956s"
 "MAM02957e"	"MAM02957"	""	"C00422"	""	"CHEBI:17855"	""	"LMGL03010000"	""	""	"M02957"	"MNXM248"	"m02957s"	"m02957s"
 "MAM02958c"	"MAM02958"	""	"C00422"	""	"CHEBI:17855"	""	"LMGL03010000"	""	""	"M02958"	"MNXM248"	"m02958c"	"m02958c"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -76,8 +76,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04414"	"R01092"	""	"R01092C"	"r0265"	""	"GALK"	"MNXR99985"	"HMR_4414"	"RCR10454"	""	0	""	"RHEA:13553"	"HMR_4414"
 "MAR04415"	"R01100"	"LACZe"	"R01100C"	"r0266"	""	"LACZe"	"MNXR101000"	"HMR_4415"	"RCR30497"	""	0	""	"RHEA:10076"	"HMR_4415"
 "MAR04416"	"R01104"	""	"R01104C"	"r0627"	""	"r0627"	"MNXR100115"	"HMR_4416"	"RCR30257"	""	0	""	""	"HMR_4416"
-"MAR04774"	"R03237"	""	"R03237C"	"r0610"	""	"r0610"	"MNXR105355;MNXR108039"	"HMR_4774"	"RCR11046"	""	0	""	""	"HMR_4774"
-"MAR04775"	"R03239"	""	"R03239C"	"r0611"	""	"r0611"	"MNXR105356;MNXR108041"	"HMR_4775"	"RCR14197"	""	0	""	""	"HMR_4775"
 "MAR04831"	"R01680"	""	""	""	""	"HMR_4831"	"MNXR107115"	"HMR_4831"	"RCR30498"	""	0	""	""	"HMR_4831"
 "MAR04832"	"R04783"	""	"R04783C"	"r0737"	""	"r0737"	"MNXR105374;MNXR109113"	"HMR_4832"	"RCR30499"	""	0	""	""	"HMR_4832"
 "MAR07674"	"R00503"	"UGALGTg"	""	""	""	"UGALGTg"	"MNXR105080"	"HMR_7674"	"RCR11047"	""	0	""	"RHEA:12404"	"HMR_7674"