chore: generate new model files

SysBioChalmers · Dec 2, 2023 · 527644b · 527644b
1 parent a9185e1
commit 527644b
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diff --git a/README.md b/README.md
@@ -33,7 +33,7 @@ This repository contains the current consensus genome-scale metabolic model of _
 
 | Taxonomy | Latest update | Version | Reactions | Metabolites | Genes |
 |:-------|:--------------|:------|:------|:----------|:-----|
-| _Saccharomyces cerevisiae_ | 16-Oct-2023 | develop | 4131 | 2806 | 1163 |
+| _Saccharomyces cerevisiae_ | 02-Dec-2023 | develop | 4130 | 2805 | 1162 |
 
 # Installation & usage
 

diff --git a/code/modelCuration/v9_0_0.m b/code/modelCuration/v9_0_0.m
@@ -12,6 +12,7 @@
 codeDir=pwd();
 model = getEarlierModelVersion('8.7.1');
 model.id='yeastGEM_develop';
+model.version='';
 %dataDir=fullfile(pwd(),'..','data','modelCuration','v9.0.0'); % No dataDir required for these curations
 cd modelCuration
 
@@ -43,7 +44,7 @@
      'ATP[m] + H+[m] + nicotinate[m] + PRPP[m] => ADP[m] + diphosphate[m] + nicotinic acid D-ribonucleotide[m] + phosphate[m]'},3);
 
 % r_4196 (NADH:ferricytochrome-b5 oxidoreductase) is unbalanced, NAD is missing as product
-model = changeRxns(model,'r_4722','NADH[erm] + 2 Ferricytochrome b5[erm] <=> H+[erm] + 2 Ferrocytochrome b5[erm] + NAD[erm]',3);
+model = changeRxns(model,'r_4196','NADH[erm] + 2 Ferricytochrome b5[erm] <=> H+[erm] + 2 Ferrocytochrome b5[erm] + NAD[erm]',3);
 
 %% DO NOT CHANGE OR REMOVE THE CODE BELOW THIS LINE.
 % Show some metrics:

diff --git a/data/databases/model_metDeltaG.csv b/data/databases/model_metDeltaG.csv
@@ -2372,7 +2372,6 @@ s_3882,10000000
 s_3883,-356.59
 s_3884,10000000
 s_3885,10000000
-s_3886,10000000
 s_3887,10000000
 s_3888,83.01
 s_3889,10000000

diff --git a/data/databases/model_rxnDeltaG.csv b/data/databases/model_rxnDeltaG.csv
@@ -3602,7 +3602,6 @@ r_4236,16.42
 r_4237,10000000
 r_4238,10000000
 r_4239,10000000
-r_4240,10000000
 r_4241,10000000
 r_4242,10000000
 r_4243,10000000

diff --git a/model/dependencies.txt b/model/dependencies.txt
@@ -1,4 +1,4 @@
 MATLAB	9.12.0.2039608 (R2022a) Update 5
 libSBML	5.19.0
-RAVEN_toolbox	commit 2028181
+RAVEN_toolbox	2.8.6
 COBRA_toolbox	commit 28acb94
diff --git a/model/yeast-GEM.txt b/model/yeast-GEM.txt
@@ -3561,7 +3561,7 @@ r_4192	S-adenosyl-L-methionine[c] + [cytochrome c]-L-lysine[c] <=> H+[c] + S-ade
 r_4193	S-adenosyl-L-methionine[n] + L-lysine-[histone][n] <=> H+[n] + S-adenosyl-L-homocysteine[n] + N6-methyl-L-lysine-[histone][n] 	YHR119W or YDR440W or YJL168C	-1000.00	1000.00	  0.00
 r_4194	Zn(2+)[c] <=> Zn(2+)[er] 	YIL023C	-1000.00	1000.00	  0.00
 r_4195	Zn(2+)[m] <=> Zn(2+)[v] 	YMR243C or YOR316C	-1000.00	1000.00	  0.00
-r_4196	NADH[erm] + 2 Ferricytochrome b5[erm] <=> H+[erm] + 2 Ferrocytochrome b5[erm] 	YIL043C or YML125C	-1000.00	1000.00	  0.00
+r_4196	NADH[erm] + 2 Ferricytochrome b5[erm] <=> H+[erm] + NAD[erm] + 2 Ferrocytochrome b5[erm] 	YIL043C or YML125C	-1000.00	1000.00	  0.00
 r_4197	NADH[m] + 2 Ferricytochrome b5[m] <=> H+[m] + NAD[m] + 2 Ferrocytochrome b5[m] 	YIL043C or YKL150W or YML125C	-1000.00	1000.00	  0.00
 r_4198	NADP(+)[c] + (S)-benzoin[c] <=> H+[c] + NADPH[c] + benzil[c] 	YIR036C	-1000.00	1000.00	  0.00
 r_4199	RX[er] + glutathione[er] <=> HX[er] + R-S-glutathione[er] 	YIR038C	-1000.00	1000.00	  0.00
@@ -3602,7 +3602,6 @@ r_4236	(R)-lactate[c] + H+[c] <=> H2O[c] + methylglyoxal[c] 	YDR533C or YMR322C
 r_4237	H2O[v] + Ca(2+)[c] + ATP[v] => H+[v] + phosphate[v] + Ca(2+)[v] + ADP[v] 	YGL006W	  0.00	1000.00	  0.00
 r_4238	H2O[g] + Ca(2+)[c] + ATP[g] => H+[g] + phosphate[g] + Ca(2+)[g] + ADP[g] 	YGL167C	  0.00	1000.00	  0.00
 r_4239	Arg-tRNA(Arg)[c] + generic protein[c] <=> H+[c] + tRNA(Arg)[c] + L-Arginyl-protein[c] 	YGL017W	-1000.00	1000.00	  0.00
-r_4240	Protein asparagine[er] + G00008[er] <=> H+[er] + Dolichyl diphosphate[er] + G00009[er] 	YGL022W	-1000.00	1000.00	  0.00
 r_4241	H2O[er] + G00009[er] <=> G00171[er] + D-glucose[er] 	YGL027C	-1000.00	1000.00	  0.00
 r_4242	GDP-alpha-D-mannose[er] + G10694[er] <=> H+[er] + GDP[er] + G01813[er] 	YGL038C	-1000.00	1000.00	  0.00
 r_4243	GDP-alpha-D-mannose[er] + G00003[er] <=> H+[er] + GDP[er] + G00004[er] 	YGL065C	-1000.00	1000.00	  0.00
@@ -4073,7 +4072,7 @@ r_4718	H2O[c] + isobutyraldehyde[c] + NAD[c] <=> 2 H+[c] + NADH[c] + isobutyrate
 r_4719	2-methylbutanal[c] + H2O[c] + NAD[c] <=> 2 H+[c] + NADH[c] + 2-methylbutyrate[c] 	YOR374W or YPL061W	-1000.00	1000.00	  0.00
 r_4720	ethanol[c] + H+[c] + isobutyrate[c] <=> H2O[c] + ethyl isobutyrate[c] 	YOR126C	-1000.00	1000.00	  0.00
 r_4721	ethanol[c] + H+[c] + 2-methylbutyrate[c] <=> H2O[c] + ethyl 2-methylbutyrate[c] 	YOR126C	-1000.00	1000.00	  0.00
-r_4722	2 ATP[c] + H2O[c] => H+[c] + polyphosphate[v] 	YJL012C	  0.00	1000.00	  0.00
+r_4722	2 ATP[c] + H2O[c] => 2 ADP[c] + H+[c] + polyphosphate[v] 	YJL012C	  0.00	1000.00	  0.00
 r_4723	H2O[v] + polyphosphate[v] <=> H+[v] + 2 phosphate[v] 	YHR201C or YDR452W	-1000.00	1000.00	  0.00
 r_4724	H2O[m] + polyphosphate[m] <=> H+[m] + 2 phosphate[m] 	YHR201C or YDR452W	-1000.00	1000.00	  0.00
 r_4725	H2O[n] + polyphosphate[n] <=> H+[n] + 2 phosphate[n] 	YHR201C or YDR452W	-1000.00	1000.00	  0.00

diff --git a/model/yeast-GEM.xml b/model/yeast-GEM.xml
@@ -24,10 +24,10 @@
             </rdf:Bag>
           </dcterms:creator>
           <dcterms:created rdf:parseType="Resource">
-            <dcterms:W3CDTF>2023-10-16T02:22:19Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2023-12-02T23:21:12Z</dcterms:W3CDTF>
           </dcterms:created>
           <dcterms:modified rdf:parseType="Resource">
-            <dcterms:W3CDTF>2023-10-16T02:22:19Z</dcterms:W3CDTF>
+            <dcterms:W3CDTF>2023-12-02T23:21:12Z</dcterms:W3CDTF>
           </dcterms:modified>
           <bqbiol:is>
             <rdf:Bag>
@@ -33323,7 +33323,7 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="M_s_3765" sboTerm="SBO:0000247" id="M_s_3765" name="N-Acetyl-D-glucosaminyldiphosphodolichol" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C28H51NO12P2R">
+      <species metaid="M_s_3765" sboTerm="SBO:0000247" id="M_s_3765" name="N-Acetyl-D-glucosaminyldiphosphodolichol" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C28H51NO12P2">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
             <rdf:Description rdf:about="#M_s_3765">
@@ -33355,7 +33355,7 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="M_s_3767" sboTerm="SBO:0000247" id="M_s_3767" name="N,N&apos;-Chitobiosyldiphosphodolichol" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C36H64N2O17P2R">
+      <species metaid="M_s_3767" sboTerm="SBO:0000247" id="M_s_3767" name="N,N&apos;-Chitobiosyldiphosphodolichol" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C36H64N2O17P2">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
             <rdf:Description rdf:about="#meta_M_s_3767">
@@ -35064,20 +35064,6 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="M_s_3886" sboTerm="SBO:0000247" id="M_s_3886" name="Protein asparagine" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C4H6N2O2R">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-            <rdf:Description rdf:about="#M_s_3886">
-              <bqbiol:is>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:50347"/>
-                  <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C03021"/>
-                </rdf:Bag>
-              </bqbiol:is>
-            </rdf:Description>
-          </rdf:RDF>
-        </annotation>
-      </species>
       <species metaid="M_s_3887" sboTerm="SBO:0000247" id="M_s_3887" name="G00008" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2" fbc:chemicalFormula="C108H182N2O77P2R">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
@@ -35091,7 +35077,7 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="M_s_3888" sboTerm="SBO:0000247" id="M_s_3888" name="Dolichyl diphosphate" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-3" fbc:chemicalFormula="C20H35O7P2R">
+      <species metaid="M_s_3888" sboTerm="SBO:0000247" id="M_s_3888" name="Dolichyl diphosphate" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-3" fbc:chemicalFormula="C20H35O7P2">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
             <rdf:Description rdf:about="#M_s_3888">
@@ -35420,7 +35406,7 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="M_s_3911" sboTerm="SBO:0000247" id="M_s_3911" name="Dolichyl beta-D-glucosyl phosphate" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C26H46O9PR">
+      <species metaid="M_s_3911" sboTerm="SBO:0000247" id="M_s_3911" name="Dolichyl beta-D-glucosyl phosphate" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C26H46O9P">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
             <rdf:Description rdf:about="#M_s_3911">
@@ -35676,7 +35662,7 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="M_s_3932" sboTerm="SBO:0000247" id="M_s_3932" name="G00012" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C50H82N4O37">
+      <species metaid="M_s_3932" sboTerm="SBO:0000247" id="M_s_3932" name="G00012" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C50H82N4O37R">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
             <rdf:Description rdf:about="#M_s_3932">
@@ -36694,7 +36680,7 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="M_s_4002" sboTerm="SBO:0000247" id="M_s_4002" name="G00149" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0">
+      <species metaid="M_s_4002" sboTerm="SBO:0000247" id="M_s_4002" name="G00149" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C32H60N2O31P2R2">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
             <rdf:Description rdf:about="#M_s_4002">
@@ -36707,7 +36693,7 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="M_s_4003" sboTerm="SBO:0000247" id="M_s_4003" name="G00140" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0">
+      <species metaid="M_s_4003" sboTerm="SBO:0000247" id="M_s_4003" name="G00140" compartment="er" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C38H70N2O36P2R2">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
             <rdf:Description rdf:about="#M_s_4003">
@@ -152720,6 +152706,7 @@
         </listOfReactants>
         <listOfProducts>
           <speciesReference species="M_s_2783" stoichiometry="1" constant="true"/>
+          <speciesReference species="M_s_2820" stoichiometry="1" constant="true"/>
           <speciesReference species="M_s_4209" stoichiometry="2" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
@@ -154080,39 +154067,6 @@
           <fbc:geneProductRef fbc:geneProduct="YGL017W"/>
         </fbc:geneProductAssociation>
       </reaction>
-      <reaction metaid="R_r_4240" sboTerm="SBO:0000176" id="R_r_4240" name="Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 (Oligosaccharyl transferase subunit STT3) (EC 2.4.99.18)" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
-        <notes>
-          <body xmlns="http://www.w3.org/1999/xhtml">
-            <p>Confidence Level: 2</p>
-            <p>NOTES: added after new annotation (PR #142)</p>
-          </body>
-        </notes>
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-            <rdf:Description rdf:about="#R_r_4240">
-              <bqbiol:is>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="https://identifiers.org/ec-code/2.4.99.18"/>
-                  <rdf:li rdf:resource="https://identifiers.org/kegg.reaction/R05976"/>
-                  <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR109968"/>
-                </rdf:Bag>
-              </bqbiol:is>
-            </rdf:Description>
-          </rdf:RDF>
-        </annotation>
-        <listOfReactants>
-          <speciesReference species="M_s_3886" stoichiometry="1" constant="true"/>
-          <speciesReference species="M_s_3887" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="M_s_0795" stoichiometry="1" constant="true"/>
-          <speciesReference species="M_s_3888" stoichiometry="1" constant="true"/>
-          <speciesReference species="M_s_3889" stoichiometry="1" constant="true"/>
-        </listOfProducts>
-        <fbc:geneProductAssociation>
-          <fbc:geneProductRef fbc:geneProduct="YGL022W"/>
-        </fbc:geneProductAssociation>
-      </reaction>
       <reaction metaid="R_r_4241" sboTerm="SBO:0000176" id="R_r_4241" name="Mannosyl-oligosaccharide glucosidase (EC 3.2.1.106) (Processing A-glucosidase I) (Glucosidase I)" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
@@ -167259,6 +167213,7 @@
           <speciesReference species="M_s_0803" stoichiometry="1" constant="true"/>
         </listOfReactants>
         <listOfProducts>
+          <speciesReference species="M_s_0394" stoichiometry="2" constant="true"/>
           <speciesReference species="M_s_0794" stoichiometry="1" constant="true"/>
           <speciesReference species="M_s_4290" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -174039,19 +173994,6 @@
           </rdf:RDF>
         </annotation>
       </fbc:geneProduct>
-      <fbc:geneProduct metaid="YGL022W" sboTerm="SBO:0000243" fbc:id="YGL022W" fbc:label="STT3">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-            <rdf:Description rdf:about="#YGL022W">
-              <bqbiol:is>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="https://identifiers.org/uniprot/P39007"/>
-                </rdf:Bag>
-              </bqbiol:is>
-            </rdf:Description>
-          </rdf:RDF>
-        </annotation>
-      </fbc:geneProduct>
       <fbc:geneProduct metaid="YGL026C" sboTerm="SBO:0000243" fbc:id="YGL026C" fbc:label="TRP5">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
@@ -186254,7 +186196,6 @@
           <groups:member groups:idRef="R_r_4165"/>
           <groups:member groups:idRef="R_r_4166"/>
           <groups:member groups:idRef="R_r_4170"/>
-          <groups:member groups:idRef="R_r_4240"/>
           <groups:member groups:idRef="R_r_4241"/>
           <groups:member groups:idRef="R_r_4242"/>
           <groups:member groups:idRef="R_r_4243"/>