Merge pull request #432 from SysBioChalmers/fix_issue381

Fix: Remove reaction MAR02517
SysBioChalmers · Nov 17, 2022 · 130e0e7 · 130e0e7
2 parents e2fff54 + d2132da
commit 130e0e7
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Showing 5 changed files with 6 additions and 58 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2184,3 +2184,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM10033s"	"MAM10033"	""	""	""	""	"5283821"	""	""	""	""	""	""	"m10033s"
 "MAM10034s"	"MAM10034"	""	""	""	""	"121933"	""	""	""	""	""	""	"m10034s"
 "MAM10041s"	"MAM10041"	""	""	""	""	"119046"	""	""	""	""	""	""	"m10041s"
+"MAM01596l"	"MAM01596"	"co2"	"C00011"	"HMDB01967"	"CHEBI:16526"	"280"	""	""	"HC00021"	"co2"	"MNXM13"	""	"m01596l"
+"MAM02444l"	"MAM02444"	"malcoa"	"C00083"	"HMDB01175"	"CHEBI:15531"	"10663"	"LMFA07050031"	""	"HC00086"	"malcoa"	"MNXM40"	""	"m02444l"
+"MAM02678l"	"MAM02678"	"pmtcoa"	"C00154"	"HMDB01338"	"CHEBI:15525"	"15667"	"LMFA07050002"	""	"HC00150"	"pmtcoa"	"MNXM88"	""	"m02678l"
+"MAM00890l"	"MAM00890"	"3ohodcoa"	"C16216"	"HMDB06498"	"CHEBI:50571"	"22833663"	""	""	""	"3ohodcoa"	"MNXM513"	""	"m00890l"
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -59,3 +59,4 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR06857"	""	"TETDECE1CRNe"	""	""	""	"TETDECE1CRNe"	""	""	""	""	0	""	""	"TETDECE1CRNe"
 "MAR06858"	""	"TIGCRNe"	""	""	""	"TIGCRNe"	"MNXR104864"	""	""	""	0	""	""	"TIGCRNe"
 "MAR07191"	""	"PNTOte"	""	""	""	"PNTORDe"	"MNXR103051"	""	""	""	0	""	""	"PNTORDe"
+"MAR02517"	""	"RE0580L"	""	""	""	"RE0580L"	"MNXR94939"	""	""	""	0	""	""	"RE0580L"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -46508,38 +46508,6 @@
       - charge: -1
       - inchis: ""
       - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM01596l"
-      - name: "CO2"
-      - compartment: "l"
-      - formula: "CO2"
-      - charge: 0
-      - inchis: "InChI=1S/CO2/c2-1-3"
-      - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM00890l"
-      - name: "3-oxooctadecanoyl-CoA"
-      - compartment: "l"
-      - formula: "C39H64N7O18P3S"
-      - charge: -4
-      - inchis: ""
-      - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM02678l"
-      - name: "palmitoyl-CoA"
-      - compartment: "l"
-      - formula: "C37H62N7O17P3S"
-      - charge: -4
-      - inchis: ""
-      - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM02444l"
-      - name: "malonyl-CoA"
-      - compartment: "l"
-      - formula: "C24H33N7O19P3S"
-      - charge: -5
-      - inchis: ""
-      - metFrom: "Recon3D"
     - !!omap
       - id: "MAM00890r"
       - name: "3-oxooctadecanoyl-CoA"
@@ -231044,26 +231012,6 @@
       - subsystem:
           - "Fatty acid biosynthesis"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR02517"
-      - name: ""
-      - metabolites: !!omap
-          - MAM00890l: 1
-          - MAM01596l: 1
-          - MAM01597l: 1
-          - MAM02039l: -1
-          - MAM02444l: -1
-          - MAM02678l: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000064601"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: "3.1.2.2"
-      - references: "PMID:10479480"
-      - subsystem:
-          - "Fatty acid biosynthesis"
-      - confidence_score: 0
     - !!omap
       - id: "MAR02519"
       - name: ""
@@ -231079,7 +231027,7 @@
       - gene_reaction_rule: "ENSG00000012660 or ENSG00000066322 or ENSG00000170522 or ENSG00000197977"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
-      - eccodes: "3.1.2.2"
+      - eccodes: "2.3.1.199"
       - references: "PMID:10479480"
       - subsystem:
           - "Fatty acid biosynthesis"

diff --git a/model/metabolites.tsv b/model/metabolites.tsv
@@ -5811,10 +5811,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM01373x"	"MAM01373"	""	"C08281"	"HMDB00944"	"CHEBI:28941"	"8215"	"LMFA01010022"	""	""	"docosac"	"MNXM162817;MNXM7102"	""	"m01373p"
 "MAM02385m"	"MAM02385"	"lgnc"	"C08320"	"HMDB02003"	"CHEBI:28866"	"11197"	"LMFA01010024"	""	"HC01788"	"lgnc"	"MNXM3297;MNXM8841"	""	"m02385m"
 "MAM02385x"	"MAM02385"	"lgnc"	"C08320"	"HMDB02003"	"CHEBI:28866"	"11197"	"LMFA01010024"	""	"HC01788"	"lgnc"	"MNXM3297;MNXM8841"	""	"m02385p"
-"MAM01596l"	"MAM01596"	"co2"	"C00011"	"HMDB01967"	"CHEBI:16526"	"280"	""	""	"HC00021"	"co2"	"MNXM13"	""	"m01596l"
-"MAM00890l"	"MAM00890"	"3ohodcoa"	"C16216"	"HMDB06498"	"CHEBI:50571"	"22833663"	""	""	""	"3ohodcoa"	"MNXM513"	""	"m00890l"
-"MAM02678l"	"MAM02678"	"pmtcoa"	"C00154"	"HMDB01338"	"CHEBI:15525"	"15667"	"LMFA07050002"	""	"HC00150"	"pmtcoa"	"MNXM88"	""	"m02678l"
-"MAM02444l"	"MAM02444"	"malcoa"	"C00083"	"HMDB01175"	"CHEBI:15531"	"10663"	"LMFA07050031"	""	"HC00086"	"malcoa"	"MNXM40"	""	"m02444l"
 "MAM00890r"	"MAM00890"	"3ohodcoa"	"C16216"	"HMDB06498"	"CHEBI:50571"	"22833663"	""	""	""	"3ohodcoa"	"MNXM513"	""	"m00890r"
 "MAM00793r"	"MAM00793"	""	""	""	""	"24906329"	""	"CE2248"	""	"CE2248"	"MNXM1309"	""	"m00793r"
 "MAM00057n"	"MAM00057"	"od2coa"	"C16218"	"HMDB06529"	"CHEBI:50570"	"53477850"	"LMFA07050055"	""	""	"od2coa"	"MNXM954"	""	"m00057n"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -8803,7 +8803,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR02506"	""	"RE0578X"	""	""	""	"RE0578X"	"MNXR103463"	""	""	""	0	""	""	"RE0578X"
 "MAR02507"	""	"RE0579M"	""	""	""	"RE0579M"	"MNXR103464"	""	""	""	0	""	""	"RE0579M"
 "MAR02508"	""	"RE0579X"	""	""	""	"RE0579X"	"MNXR103464"	""	""	""	0	""	""	"RE0579X"
-"MAR02517"	""	"RE0580L"	""	""	""	"RE0580L"	"MNXR94939"	""	""	""	0	""	""	"RE0580L"
 "MAR02519"	""	"RE0580R"	""	""	""	"RE0580R"	"MNXR94939"	""	""	""	0	""	""	"RE0580R"
 "MAR02521"	""	"RE0581R"	""	""	""	"RE0581R"	"MNXR103465"	""	""	""	0	"RHEA:35302"	"RHEA:35299"	"RE0581R"
 "MAR02523"	""	"RE0582N"	""	""	""	"RE0582N"	"MNXR103466"	""	""	""	0	"RHEA:35350"	"RHEA:35347"	"RE0582N"