Merge pull request #606 from Devlin-Moyer/fix/CLYBL_rxns

Fix Reactions Related To CLYBL
SysBioChalmers · Jun 8, 2023 · a279e97 · a279e97
2 parents 34dd975 + 1f66cd7
commit a279e97
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Showing 3 changed files with 24 additions and 38 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -103,6 +103,8 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04411"	""	"PIt8"	""	""	""	"PIt8"	"MNXR102875"	"HMR_4911"	"RCR40976"	""	0	""	""	"PIt8"
 "MAR08749"	""	"H2CO3D2"	""	""	""	"HMR_8749"	"MNXR100483"	"HMR_8749"	"RCR14128"	""	1	""	""	"HMR_8749"
 "MAR08750"	""	"H2CO3D2m"	""	""	""	"HMR_8750"	"MNXR100483"	"HMR_8750"	"RCR14129"	""	1	""	""	"HMR_8750"
+"MAR05294"	"R00362"	""	"R00362C"	"r1109"	""	"r1109"	"MNXR96731"	"HMR_5294"	"RCR11670"	""	0	"RHEA:10761"	"RHEA:10760"	"HMR_5294"
+"MAR11421"	""	"CITL"	""	""	""	"CITL"	"MNXR96731"	""	""	""	0	"RHEA:10761"	"RHEA:10760"	"CITL"
 "MAR00562"	""	"ETF"	""	""	""	"ETF"	"MNXR97965"	""	""	""	0	""	""	"ETF"
 "MAR00563"	""	"ETFQO"	""	""	""	"ETFQO"	"MNXR97966"	""	""	""	0	""	""	"ETFQO"
 "MAR05434"	""	"FAOXC3DC"	""	""	""	"FAOXC3DC"	""	""	""	""	0	""	""	"FAOXC3DC"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -94481,11 +94481,11 @@
           - MAM02819m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: ""
+      - gene_reaction_rule: "ENSG00000125246"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.1.3.25"
-      - references: ""
+      - references: "PMID:24334609"
       - subsystem:
           - "C5-branched dibasic acid metabolism"
       - confidence_score: 0
@@ -94881,23 +94881,6 @@
       - subsystem:
           - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR05294"
-      - name: "citrate oxaloacetate-lyase (forming acetate from the pro-S carboxymethyl group of citrate)"
-      - metabolites: !!omap
-          - MAM01252m: 1
-          - MAM01587m: -1
-          - MAM02633m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125246"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "4.1.-.-"
-      - references: "PMID:11741334"
-      - subsystem:
-          - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR06413"
       - name: ""
@@ -273978,23 +273961,6 @@
       - subsystem:
           - "Exchange/demand reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR11421"
-      - name: "Citrate Lyase"
-      - metabolites: !!omap
-          - MAM01252c: 1
-          - MAM01587c: -1
-          - MAM02633c: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125246"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: "4.1.3.6"
-      - references: "PMID:11741334"
-      - subsystem:
-          - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR11422"
       - name: "Exchange of Galactitol"
@@ -307323,6 +307289,25 @@
       - subsystem:
           - "Miscellaneous"
       - confidence_score: 0
+    - !!omap
+      - id: "MAR20111"
+      - name: "MAR20111"
+      - metabolties: !!omap
+          - MAM1261m: -1
+          - MAM01597m: 1
+          - MAM02007m: -1
+          - MAM02040m: -1
+          - MAM02439m: 1
+      - lower_bound: 0
+      - upper_bound: 1000
+      - gene_reaction_rule: "ENSG00000125246"
+      - rxnNotes: ""
+      - rxnFrom: ""
+      - eccodes: "2.3.3.9"
+      - references: "PMID:24334609"
+      - subsystem:
+          - "Miscellaneous"
+      - confidence_score: 0
 - genes:
     - !!omap
       - id: "ENSG00000000419"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -1344,7 +1344,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04465"	"R01392"	"HPYRRy"	"R01392C"	"r0327"	""	"HPYRRy"	"MNXR100336"	"HMR_4465"	"RCR11666"	""	0	""	"RHEA:18657"	"HMR_4465"
 "MAR04589"	"R01900"	""	"R01900C"	"r0426"	""	"r0426"	"MNXR105342;MNXR95387"	"HMR_4589"	"RCR10352"	""	0	""	"RHEA:22144"	"HMR_4589"
 "MAR04652"	"R02164"	"r0509"	"R02164C"	"r0509"	""	"r0509"	"MNXR107340"	"HMR_4652"	"RCR14481"	""	0	""	"RHEA:13713"	"HMR_4652"
-"MAR05294"	"R00362"	""	"R00362C"	"r1109"	""	"r1109"	"MNXR96731"	"HMR_5294"	"RCR11670"	""	0	"RHEA:10761"	"RHEA:10760"	"HMR_5294"
 "MAR06413"	"R03316"	""	"R03316M"	"r0620"	""	"r0620"	"MNXR105357;MNXR108089"	"HMR_6413"	"RCR11672"	""	0	""	""	"HMR_6413"
 "MAR06414"	"R02570"	""	"R02570C"	"r0556"	""	"r0556"	"MNXR107585;MNXR95656"	"HMR_6414"	"RCR14482"	""	0	""	"RHEA:15213"	"HMR_6414"
 "MAR07704"	"R00466"	"GLXO2p"	""	""	""	"GLXO2p"	"MNXR100305"	"HMR_7704"	"RCR10605"	""	0	""	"RHEA:14837"	"HMR_7704"
@@ -11205,7 +11204,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR11418"	""	"URIt2"	""	""	""	"URIt2r"	"MNXR105166"	""	""	""	0	"RHEA:29954"	"RHEA:29951"	"URIt2r"
 "MAR11419"	""	"EX_ind3ac_e"	""	""	""	"EX_ind3ac[e]"	"MNXR98679"	""	""	""	0	""	""	"EX_ind3ac[e]"
 "MAR11420"	""	"EX_nh4_e"	""	""	""	"EX_nh4[e]"	"MNXR98786"	""	""	""	0	""	""	"EX_nh4[e]"
-"MAR11421"	""	"CITL"	""	""	""	"CITL"	"MNXR96731"	""	""	""	0	"RHEA:10761"	"RHEA:10760"	"CITL"
 "MAR11422"	""	"EX_galt_e"	""	""	""	"EX_galt[e]"	"MNXR98554"	""	""	""	0	""	""	"EX_galt[e]"
 "MAR11423"	""	"EX_glcr_e"	""	""	""	"EX_glcr[e]"	"MNXR98575"	""	""	""	0	""	""	"EX_glcr[e]"
 "MAR11424"	""	"EX_glcur_e"	""	""	""	"EX_glcur[e]"	"MNXR98577"	""	""	""	0	""	""	"EX_glcur[e]"
@@ -13088,3 +13086,4 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR20108"	""	"HBZOPT10m;R_HBZOPT10m"	""	""	""	""	"MNXR100567"	""	""	""	0	"RHEA:44564"	""	""
 "MAR20109"	""	"HBZOPT10m;R_HBZOPT10m"	""	""	""	""	"MNXR100567"	""	""	""	0	"RHEA:44564"	""	""
 "MAR20110"	""	""	""	""	""	""	"MNXR102097"	""	""	""	0	"RHEA:15642"	"RHEA:15641"	""
+"MAR20111"	"R00472"	""	""	""	""	""	"MNXR188337"	""	""	""	0	"RHEA:18182"	"RHEA:18181"	""