Merge pull request #717 from SysBioChalmers/fix/hexanoate

Fix/hexanoate
SysBioChalmers · Oct 30, 2023 · 589821a · 589821a
2 parents 48eda9c + d4d0c50
commit 589821a
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diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2254,3 +2254,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM20023i"	"MAM20023"	"C00061"	""	""	"CHEBI:58210"	""	""	""	""	""	"MNXM1105928"	""	""
 "MAM02398c"	"MAM02398"	""	"C16238"	""	""	"23724672"	""	"CE5656"	""	"CE5656"	"MNXM2392"	"m02398c"	"m02398c"
 "MAM01701c"	"MAM01701"	"dhlam"	"C00579"	"HMDB0000985"	"CHEBI:17694"	"663"	""	""	"HC00437"	"dhlam"	"MNXM1277"	"m01701c"	"m01701c"
+"MAM03684c"	"MAM03684"	"hxa"	""	""	"CHEBI:17120"	""	""	""	""	"hxa"	"MNXM1653"	""	"hxa_c"
+"MAM03684m"	"MAM03684"	"hxa"	""	""	""	""	""	""	""	"hxa"	"MNXM1653"	""	"hxa_m"
+"MAM03684e"	"MAM03684"	"hxa"	""	""	""	""	""	""	""	"hxa"	"MNXM1653"	""	"hxa_s"
+"MAM03684x"	"MAM03684"	"hxa"	""	""	""	""	""	""	""	"hxa"	"MNXM1653"	""	"hxa_p"
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -256,3 +256,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR06398"	"R07770"	""	"R07770C"	""	""	"RE1944C"	"MNXR101081"	"HMR_6398"	"RCR14489"	""	0	""	"RHEA:12913"	"HMR_6398"
 "MAR06399"	"R07771"	""	"R07771C"	""	""	"HMR_6399"	"MNXR111358"	"HMR_6399"	"RCR14490"	""	0	""	"RHEA:20473"	"HMR_6399"
 "MAR06408"	""	""	"RT0295"	""	""	"HMR_6408"	""	"HMR_6408"	"RCR21069"	""	0	""	""	"HMR_6408"
+"MAR11292"	""	"HXAt3"	""	""	""	"HXAt3"	""	""	""	""	0	""	""	"HXAt3"
+"MAR11293"	""	"EX_hxa_e"	""	""	""	"EX_hxa[e]"	"MNXR98664"	""	""	""	0	""	""	"EX_hxa[e]"
+"MAR09949"	""	"FACOAE60"	""	""	""	"HXCOAc"	"MNXR99139"	""	""	""	0	""	""	"HXCOAc"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -29241,6 +29241,22 @@
       - charge: -1
       - inchis: ""
       - metFrom: "HMRdatabase"
+    - !!omap
+      - id: "MAM02120x"
+      - name: "hexanoic acid"
+      - compartment: "x"
+      - formula: "C6H11O2"
+      - charge: -1
+      - inchis: ""
+      - metFrom: "HMRdatabase"
+    - !!omap
+      - id: "MAM02120m"
+      - name: "hexanoic acid"
+      - compartment: "m"
+      - formula: "C6H11O2"
+      - charge: -1
+      - inchis: ""
+      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM02121c"
       - name: "hexanoyl-[ACP]"
@@ -53209,14 +53225,6 @@
       - charge: -1
       - inchis: ""
       - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM03684c"
-      - name: "Hexanoate (N-C6:0)"
-      - compartment: "c"
-      - formula: "C6H11O2"
-      - charge: -1
-      - inchis: ""
-      - metFrom: "Recon3D"
     - !!omap
       - id: "MAM03976c"
       - name: "Cia-5,8, Tetradecadienoic Acid"
@@ -54353,22 +54361,6 @@
       - charge: -1
       - inchis: ""
       - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM03684m"
-      - name: "Hexanoate (N-C6:0)"
-      - compartment: "m"
-      - formula: "C6H11O2"
-      - charge: -1
-      - inchis: ""
-      - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM03684x"
-      - name: "Hexanoate (N-C6:0)"
-      - compartment: "x"
-      - formula: "C6H11O2"
-      - charge: -1
-      - inchis: ""
-      - metFrom: "Recon3D"
     - !!omap
       - id: "MAM02169e"
       - name: "indoleacetate"
@@ -58633,14 +58625,6 @@
       - charge: 0
       - inchis: ""
       - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM03684e"
-      - name: "Hexanoate (N-C6:0)"
-      - compartment: "e"
-      - formula: "C6H11O2"
-      - charge: -1
-      - inchis: ""
-      - metFrom: "Recon3D"
     - !!omap
       - id: "MAM01954c"
       - name: "glcnac-alpha-1,4-core 1"
@@ -248691,25 +248675,6 @@
       - subsystem:
           - "Fatty acid oxidation"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR09949"
-      - name: "Acylcoa Hydrolase, Cytosolic"
-      - metabolites: !!omap
-          - MAM01597c: 1
-          - MAM02039c: 1
-          - MAM02040c: -1
-          - MAM02122c: -1
-          - MAM03684c: 1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: ""
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: "3.1.2.2"
-      - references: ""
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
     - !!omap
       - id: "MAR09950"
       - name: "Hydrolysis of Tetradecadienoyl Coenzyme A to Cis-5, 8-Tetradecadienoic Acid"
@@ -253804,16 +253769,16 @@
       - confidence_score: 0
     - !!omap
       - id: "MAR10374"
-      - name: "Acyl-Coenzyme A Hydrolase, Mitochondrial"
+      - name: "Hexanoyl-CoA hydrolase, Mitochondrial"
       - metabolites: !!omap
           - MAM01597m: 1
           - MAM02039m: 1
           - MAM02040m: -1
           - MAM02122m: -1
-          - MAM03684m: 1
+          - MAM02120m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: ""
+      - gene_reaction_rule: "ENSG00000123130"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: ""
@@ -253855,16 +253820,16 @@
       - confidence_score: 0
     - !!omap
       - id: "MAR10377"
-      - name: "Acylcoa Hydrolase, Peroxisome"
+      - name: "Hexanoyl-CoA hydrolase, Peroxisome"
       - metabolites: !!omap
           - MAM01597x: 1
           - MAM02039x: 1
           - MAM02040x: -1
           - MAM02122x: -1
-          - MAM03684x: 1
-      - lower_bound: -1000
+          - MAM02120x: 1
+      - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: ""
+      - gene_reaction_rule: "ENSG00000101473"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: ""
@@ -269331,8 +269296,8 @@
       - id: "MAR11290"
       - name: "Transport of Hexanoate (N-C6:0), Mitochondrial"
       - metabolites: !!omap
-          - MAM03684c: 1
-          - MAM03684m: -1
+          - MAM02120c: 1
+          - MAM02120m: -1
       - lower_bound: -1000
       - upper_bound: 1000
       - gene_reaction_rule: ""
@@ -269347,24 +269312,8 @@
       - id: "MAR11291"
       - name: "Transport of Hexanoate (N-C6:0), Peroxisome"
       - metabolites: !!omap
-          - MAM03684c: 1
-          - MAM03684x: -1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: ""
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: ""
-      - subsystem:
-          - "Transport reactions"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR11292"
-      - name: "Transport of Hexanoate (N-C6:0), Extracellular"
-      - metabolites: !!omap
-          - MAM03684c: -1
-          - MAM03684e: 1
+          - MAM02120c: 1
+          - MAM02120x: -1
       - lower_bound: -1000
       - upper_bound: 1000
       - gene_reaction_rule: ""
@@ -269375,21 +269324,6 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR11293"
-      - name: "Exchange of Hexanoate (N-C6:0)"
-      - metabolites: !!omap
-          - MAM03684e: -1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: ""
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: ""
-      - subsystem:
-          - "Exchange/demand reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR11294"
       - name: "Hydrolysis of Fatty Acyl Coenzyme A (14:1)"
@@ -302994,7 +302928,7 @@
           - MAM02040c: -1
           - MAM02554c: -1
           - MAM02555c: 1
-          - MAM03684c: 1
+          - MAM02120c: 1
           - MAM20037c: -1
       - lower_bound: 0
       - upper_bound: 1000

diff --git a/model/metabolites.tsv b/model/metabolites.tsv
@@ -3651,8 +3651,10 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02119l"	"MAM02119"	"6thf"	""	""	""	"169691"	""	""	""	"6thf"	"MNXM3616"	"m02119l"	"m02119l"
 "MAM02119m"	"MAM02119"	"6thf"	""	""	""	"169691"	""	""	""	"6thf"	"MNXM3616"	"m02119m"	"m02119m"
 "MAM02119e"	"MAM02119"	"6thf"	""	""	""	"169691"	""	""	""	"6thf"	"MNXM3616"	"m02119s"	"m02119s"
-"MAM02120c"	"MAM02120"	""	"C01585"	"HMDB0000535"	"CHEBI:17120;CHEBI:30776"	""	"LMFA01010006"	""	""	"caproic"	"MNXM1653"	"m02120c"	"m02120c"
-"MAM02120e"	"MAM02120"	""	"C01585"	"HMDB0000535"	"CHEBI:17120;CHEBI:30776"	""	"LMFA01010006"	""	""	"caproic"	"MNXM1653"	"m02120s"	"m02120s"
+"MAM02120c"	"MAM02120"	"hxa"	"C01585"	"HMDB0000535"	"CHEBI:17120;CHEBI:30776"	""	"LMFA01010006"	""	""	"caproic"	"MNXM1653"	"m02120c"	"m02120c"
+"MAM02120e"	"MAM02120"	"hxa"	"C01585"	"HMDB0000535"	"CHEBI:17120;CHEBI:30776"	""	"LMFA01010006"	""	""	"caproic"	"MNXM1653"	"m02120s"	"m02120s"
+"MAM02120x"	"MAM02120"	"hxa"	"C01585"	"HMDB0000535"	"CHEBI:17120;CHEBI:30776"	""	"LMFA01010006"	""	""	"caproic"	"MNXM1653"
+"MAM02120m"	"MAM02120"	"hxa"	"C01585"	"HMDB0000535"	"CHEBI:17120;CHEBI:30776"	""	"LMFA01010006"	""	""	"caproic"	"MNXM1653"
 "MAM02121c"	"MAM02121"	""	"C05749"	""	""	""	""	""	"HC01592"	"HC01592"	"MNXM23683"	"m02121c"	"m02121c"
 "MAM02122c"	"MAM02122"	""	"C05270"	"HMDB0002845"	"CHEBI:27540"	"440611"	"LMFA07050001"	""	"HC01409"	"hxcoa"	"MNXM162502;MNXM553"	"m02122c"	"m02122c"
 "MAM02122m"	"MAM02122"	""	"C05270"	"HMDB0002845"	"CHEBI:27540"	"440611"	"LMFA07050001"	""	"HC01409"	"hxcoa"	"MNXM162502;MNXM553"	"m02122m"	"m02122m"
@@ -6649,7 +6651,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM03814c"	"MAM03814"	"pchollinl_hs"	""	""	"CHEBI:28733"	""	""	""	""	"pchollinl_hs"	""	""	"pchollinl_hs_c"
 "MAM03856c"	"MAM03856"	"pelinl_hs"	""	""	"CHEBI:83058"	""	""	""	""	"pelinl_hs"	""	""	"pelinl_hs_c"
 "MAM03569c"	"MAM03569"	"eidi1114ac"	"C16525"	"HMDB0005060"	"CHEBI:603631"	"6439848"	""	""	""	"eidi1114ac"	""	""	"eidi1114ac_c"
-"MAM03684c"	"MAM03684"	"hxa"	""	""	"CHEBI:17120"	""	""	""	""	"hxa"	"MNXM1653"	""	"hxa_c"
 "MAM03976c"	"MAM03976"	"tetdeca511ac"	""	""	""	""	""	""	""	"tetdeca511ac"	""	""	"tetdeca511ac_c"
 "MAM03619c"	"MAM03619"	"glyc2p"	""	""	"CHEBI:58083"	""	""	""	""	"glyc2p"	"MNXM2527"	""	"glyc2p_c"
 "MAM03401c"	"MAM03401"	"aclys"	""	""	""	""	""	""	""	"aclys"	""	""	"aclys_c"
@@ -6792,8 +6793,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM03619e"	"MAM03619"	"glyc2p"	""	""	""	""	""	""	""	"glyc2p"	"MNXM2527"	""	"glyc2p_s"
 "MAM01998e"	"MAM01998"	"glyclt"	"C00160"	"HMDB0000115"	"CHEBI:17497"	"757"	""	""	""	"glyclt"	"MNXM222"	""	"m01998s"
 "MAM03232e"	"MAM03232"	"3hpppn"	""	""	""	""	""	""	""	"3hpppn"	"MNXM1634"	""	"3hpppn_s"
-"MAM03684m"	"MAM03684"	"hxa"	""	""	""	""	""	""	""	"hxa"	"MNXM1653"	""	"hxa_m"
-"MAM03684x"	"MAM03684"	"hxa"	""	""	""	""	""	""	""	"hxa"	"MNXM1653"	""	"hxa_p"
 "MAM02169e"	"MAM02169"	"ind3ac"	"C00954"	"HMDB0000197"	"CHEBI:16411"	"802"	""	""	""	"ind3ac"	"MNXM383"	""	"m02169s"
 "MAM02350e"	"MAM02350"	"Lcyst"	"C00506"	"HMDB0002757"	"CHEBI:21260"	"25701"	""	""	""	"Lcyst"	"MNXM713"	""	"m02350s"
 "MAM02413c"	"MAM02413"	"Lpipecol"	"C00408"	"HMDB0000716"	"CHEBI:30913"	"439227"	""	""	""	"Lpipecol"	"MNXM684"	""	"m02413c"
@@ -7327,7 +7326,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM04078c"	"MAM04078"	""	""	""	""	""	""	""	""	"xolest204_hs"	""	""	"xolest204_hs_c"
 "MAM04080c"	"MAM04080"	"xolest226_hs"	""	""	""	""	""	""	""	"xolest226_hs"	""	""	"xolest226_hs_c"
 "MAM02908e"	"MAM02908"	"sphmyln_hs"	"C00550"	""	"CHEBI:17636"	""	"LMSP03010000"	""	"HC02007"	"sphmyln_hs"	"MNXM5930"	""	"m02908s"
-"MAM03684e"	"MAM03684"	"hxa"	""	""	""	""	""	""	""	"hxa"	"MNXM1653"	""	"hxa_s"
 "MAM01954c"	"MAM01954"	"gncore1"	""	""	""	""	""	""	""	"gncore1"	"MNXM18091"	""	"m01954c"
 "MAM01954e"	"MAM01954"	"gncore1"	""	""	""	""	""	""	""	"gncore1"	"MNXM18091"	""	"m01954s"
 "MAM03394c"	"MAM03394"	"Lhcystin"	""	""	""	""	""	""	""	"Lhcystin"	""	""	"Lhcystin_c"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -9740,7 +9740,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR09946"	""	""	""	""	""	"XOLEST204CEH"	""	""	""	""	0	""	""	"XOLEST204CEH"
 "MAR09947"	""	"XOLEST226CEH"	""	""	""	"XOLEST226CEH"	""	""	""	""	0	""	""	"XOLEST226CEH"
 "MAR09948"	""	"CE4843HYDc"	""	""	""	"CE4843HYDc"	""	""	""	""	0	""	""	"CE4843HYDc"
-"MAR09949"	""	"FACOAE60"	""	""	""	"HXCOAc"	"MNXR99139"	""	""	""	0	""	""	"HXCOAc"
 "MAR09950"	""	"TETDECA511ACc"	""	""	""	"TETDECA511ACc"	""	""	""	""	0	""	""	"TETDECA511ACc"
 "MAR09951"	""	"GPDDACHOL"	""	""	""	"GPDDACHOL"	""	""	""	""	0	""	""	"GPDDACHOL"
 "MAR09952"	""	"ACLYSHYc"	""	""	""	"ACLYSHYc"	""	""	""	""	0	""	""	"ACLYSHYc"
@@ -10964,8 +10963,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR11289"	""	"PHEACGLYtm"	""	""	""	"PHEACGLYtm"	"MNXR157011"	""	""	""	0	""	""	"PHEACGLYtm"
 "MAR11290"	""	"HXAt1"	""	""	""	"HXAt1"	""	""	""	""	0	""	""	"HXAt1"
 "MAR11291"	""	"HXAt2"	""	""	""	"HXAt2"	""	""	""	""	0	""	""	"HXAt2"
-"MAR11292"	""	"HXAt3"	""	""	""	"HXAt3"	""	""	""	""	0	""	""	"HXAt3"
-"MAR11293"	""	"EX_hxa_e"	""	""	""	"EX_hxa[e]"	"MNXR98664"	""	""	""	0	""	""	"EX_hxa[e]"
 "MAR11294"	""	"TTDCEAc"	""	""	""	"TTDCEAc"	""	""	""	""	0	""	""	"TTDCEAc"
 "MAR11295"	""	"PACCOALm"	""	""	""	"PACCOALm"	""	""	""	""	0	""	""	"PACCOALm"
 "MAR11296"	""	"PACALDtm"	""	""	""	"PACALDtm"	"MNXR102312"	""	""	""	0	""	""	"PACALDtm"