Merge pull request #551 from Devlin-Moyer/develop

fix: sedoheptulose kinase/phosphatase reactions
SysBioChalmers · May 6, 2023 · 757585f · 757585f
2 parents 2df1146 + 9ed8d58
commit 757585f
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Showing 3 changed files with 26 additions and 26 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -81,3 +81,4 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR05297"	"R08549"	"AKGDm"	""	"r1114"	""	"AKGDm"	"MNXR95655"	"HMR_5297"	"RCR11671"	""	0	""	""	"HMR_5297"
 "MAR06410"	"R01699"	""	"R01699M"	"r0383"	""	"r0383"	"MNXR102427;MNXR107129"	"HMR_6410"	"RCR10446"	""	0	""	"RHEA:19189"	"HMR_6410"
 "MAR06411"	"R01700"	""	""	"r0384"	""	"r0384"	"MNXR107130;MNXR95657"	"HMR_6411"	"RCR10353"	""	0	""	""	"HMR_6411"
+"MAR04568"	""	""	""	"r0409"	""	"r0409"	"MNXR105339"	"HMR_4568"	"RCR11109"	""	0	""	""	"HMR_4568"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -71242,12 +71242,12 @@
       - id: "MAR04567"
       - name: "ATP:Sedoheptulose 7-phosphate 1-phosphotransferase"
       - metabolites: !!omap
-          - MAM01285c: -1
-          - MAM01371c: 1
-          - MAM02039c: -1
-          - MAM02883c: -1
-          - MAM02884c: 1
-      - lower_bound: -1000
+          - MAM01285c: 1
+          - MAM01371c: -1
+          - MAM02039c: 1
+          - MAM02883c: 1
+          - MAM02884c: -1
+      - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000067057 or ENSG00000141959 or ENSG00000152556"
       - rxnNotes: ""
@@ -71257,25 +71257,6 @@
       - subsystem:
           - "Pentose phosphate pathway"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR04568"
-      - name: ""
-      - metabolites: !!omap
-          - MAM02039c: -1
-          - MAM02883c: -1
-          - MAM02884c: 1
-          - MAM03106c: -1
-          - MAM03130c: 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:11945275"
-      - subsystem:
-          - "Pentose phosphate pathway"
-      - confidence_score: 0
     - !!omap
       - id: "MAR09799"
       - name: "ATP:sedoheptulose 7-phosphate"
@@ -306608,6 +306589,24 @@
       - subsystem:
           - "Glycolysis / Gluconeogenesis"
       - confidence_score: 0
+    - !!omap
+      - id: "MAR20070"
+      - name: "MAR20070"
+      - metabolites: !!omap
+          - MAM02883c: -1
+          - MAM02040c: -1
+          - MAM02884c: 1
+          - MAM02751c: 1
+      - lower_bound: 0
+      - upper_bound: 1000
+      - gene_reaction_rule: "ENSG00000130957 or ENSG00000165140"
+      - rxnNotes: "https://doi.org/10.1007/BF02702726"
+      - rxnFrom: ""
+      - eccodes: "3.1.3.11"
+      - references: "PMID:6998788"
+      - subsystem:
+          - "Pentose Phosphate Pathway"
+      - confidence_score: 0
 - genes:
     - !!omap
       - id: "ENSG00000000419"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -198,7 +198,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04501"	"R01641"	"TKT1"	"R01641C"	"r0370"	""	"TKT1"	"MNXR104868;MNXR107105"	"HMR_4501"	"RCR14218"	""	0	""	"RHEA:10508"	"HMR_4501"
 "MAR04565"	"R08575"	"TALA"	"R01827C"	"r0406"	""	"TALA"	"MNXR104715"	"HMR_4565"	"RCR14219"	""	0	""	""	"HMR_4565"
 "MAR04567"	"R01843"	""	""	"r0408"	""	"r0408"	"MNXR102510;MNXR105338"	"HMR_4567"	"RCR10468"	""	0	""	"RHEA:31443"	"HMR_4567"
-"MAR04568"	""	""	""	"r0409"	""	"r0409"	"MNXR105339"	"HMR_4568"	"RCR11109"	""	0	""	""	"HMR_4568"
 "MAR09799"	"R01844"	""	""	""	""	"HMR_9799"	"MNXR107202"	"HMR_9799"	"RCR14220"	""	0	""	"RHEA:23844"	"HMR_9799"
 "MAR09800"	"R03819"	""	""	""	""	"HMR_9800"	"MNXR108451"	"HMR_9800"	"RCR14221"	""	0	""	""	"HMR_9800"
 "MAR04623"	"R02035"	"PGLer"	"R02035C"	"r0478"	""	"PGLer"	"MNXR102539"	"HMR_4623"	"RCR10469"	""	0	""	"RHEA:12556"	"HMR_4623"
@@ -13072,3 +13071,4 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR20067"	""	""	""	""	""	""	"MNXR133799"	""	""	""	0	"RHEA:55936"	""	""
 "MAR20068"	""	""	""	""	""	""	"MNXR171534"	""	""	""	0	"RHEA:60632"	""	""
 "MAR20069"	""	""	""	""	""	""	""	""	""	""	0	""	""	""
+"MAR20070"	""	""	""	""	""	""	""	""	""	""	0	""	""	""