resolve the mentioned problem

Author: cheng-yu-zhang

Diff for: 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_ | 28-May-2022 | develop | 4069 | 2749 | 1163 |
+| _Saccharomyces cerevisiae_ | 29-May-2022 | develop | 4069 | 2749 | 1163 |
 
 # Installation & usage
 

Diff for: data/modelCuration/v8_6_0/newGPRsfromDBs.tsv

@@ -5,11 +5,11 @@ r_1616	NAN	(YGL101W or  YBR242W)	https://www.uniprot.org/uniprot/P53144; https:/
 r_1617	NAN	(YGL101W or  YBR242W)	https://www.uniprot.org/uniprot/P53144; https://www.uniprot.org/uniprot/P38331	https://www.yeastgenome.org/locus/S000000446; https://www.yeastgenome.org/locus/S000003069
 r_4584	NAN	(YOR317W or YER015W or YMR246W or YIL009W)	https://www.uniprot.org/uniprot/P30624; https://www.uniprot.org/uniprot/P39518; https://www.uniprot.org/uniprot/P47912; https://www.uniprot.org/uniprot/P39002	https://www.yeastgenome.org/locus/S000005844; https://www.yeastgenome.org/locus/S000000817; https://www.yeastgenome.org/locus/S000004860; https://www.yeastgenome.org/locus/S000001271
 r_4372	NAN	YGR247W	https://legacy.uniprot.org/uniprot/P53314	https://www.yeastgenome.org/locus/S000003479
-r_4378	NAN	(YBR299W or YGR292W)	https://legacy.uniprot.org/uniprot/P38158; https://legacy.uniprot.org/uniprot/P53341	https://www.yeastgenome.org/locus/S000000503; https://www.yeastgenome.org/locus/S000003524
+r_4378	(YBR299W or YGR292W)		https://legacy.uniprot.org/uniprot/P38158; https://legacy.uniprot.org/uniprot/P53341	https://www.yeastgenome.org/locus/S000000503; https://www.yeastgenome.org/locus/S000003524
 r_4388	NAN	YGR247W	https://legacy.uniprot.org/uniprot/P53314	https://www.yeastgenome.org/locus/S000003479
-r_4400	NAN	(YBR299W or  YGR292W)	https://legacy.uniprot.org/uniprot/P38158; https://legacy.uniprot.org/uniprot/P53341	https://www.yeastgenome.org/locus/S000000503; https://www.yeastgenome.org/locus/S000003524
+r_4400	NAN	(YBR299W or YGR292W)	https://legacy.uniprot.org/uniprot/P38158; https://legacy.uniprot.org/uniprot/P53341	https://www.yeastgenome.org/locus/S000000503; https://www.yeastgenome.org/locus/S000003524
 r_4412	NAN	YGR247W	https://legacy.uniprot.org/uniprot/P53314	https://www.yeastgenome.org/locus/S000003479
-r_4420	NAN	(YBR299W or  YGR292W)	https://legacy.uniprot.org/uniprot/P38158; https://legacy.uniprot.org/uniprot/P53341	https://www.yeastgenome.org/locus/S000000503; https://www.yeastgenome.org/locus/S000003524
+r_4420	NAN	(YBR299W or YGR292W)	https://legacy.uniprot.org/uniprot/P38158; https://legacy.uniprot.org/uniprot/P53341	https://www.yeastgenome.org/locus/S000000503; https://www.yeastgenome.org/locus/S000003524
 r_4566	NAN	YDR248C	https://legacy.uniprot.org/uniprot/Q03786	https://www.yeastgenome.org/locus/S000002656
 r_4570	NAN	(YIL074C or YER081W)	https://legacy.uniprot.org/uniprot/P40510; https://legacy.uniprot.org/uniprot/P40054	https://www.yeastgenome.org/locus/S000001336; https://www.yeastgenome.org/locus/S000000883
 r_4579	NAN	YMR108W	https://legacy.uniprot.org/uniprot/P07342	https://www.yeastgenome.org/locus/S000004714

Diff for: model/dependencies.txt

@@ -1,4 +1,4 @@
-MATLAB	9.10.0.1602886 (R2021a)
+MATLAB	9.11.0.1769968 (R2021b)
 libSBML	5.19.0
-RAVEN_toolbox	commit 12f905d
+RAVEN_toolbox	2.7.1
 COBRA_toolbox	unknown

Diff for: model/yeast-GEM.txt

@@ -3736,7 +3736,7 @@ r_4374	H2O[c] + 3-sulfino-L-alanine[c] => H+[c] + L-alanine[c] + sulphite[c]
 r_4375	H+[e] + 3-sulfino-L-alanine[e] <=> H+[c] + 3-sulfino-L-alanine[c] 		-1000.00	1000.00	  0.00
 r_4376	H2O[c] + 3'-AMP[c] => adenosine[c] + phosphate[c] 		  0.00	1000.00	  0.00
 r_4377	3'-AMP[e] <=> 3'-AMP[c] 		-1000.00	1000.00	  0.00
-r_4378	H2O[c] + 6-O-alpha-D-glucopyranosyl-D-fructofuranose[c] => D-fructose[c] + D-glucose[c] 	YBR299W or YGR292W	  0.00	1000.00	  0.00
+r_4378	H2O[c] + 6-O-alpha-D-glucopyranosyl-D-fructofuranose[c] => D-fructose[c] + D-glucose[c] 		  0.00	1000.00	  0.00
 r_4379	H+[e] + 6-O-alpha-D-glucopyranosyl-D-fructofuranose[e] <=> H+[c] + 6-O-alpha-D-glucopyranosyl-D-fructofuranose[c] 		-1000.00	1000.00	  0.00
 r_4380	coenzyme A[c] + H+[c] + N-acetyl-L-cysteine[c] <=> acetyl-CoA[c] + L-cysteine[c] 		-1000.00	1000.00	  0.00
 r_4381	H+[e] + N-acetyl-L-cysteine[e] <=> H+[c] + N-acetyl-L-cysteine[c] 		-1000.00	1000.00	  0.00

Diff for: model/yeast-GEM.xml

@@ -157504,12 +157504,6 @@
           <speciesReference species="M_s_0553" stoichiometry="1" constant="true"/>
           <speciesReference species="M_s_0563" stoichiometry="1" constant="true"/>
         </listOfProducts>
-        <fbc:geneProductAssociation>
-          <fbc:or>
-            <fbc:geneProductRef fbc:geneProduct="YBR299W"/>
-            <fbc:geneProductRef fbc:geneProduct="YGR292W"/>
-          </fbc:or>
-        </fbc:geneProductAssociation>
       </reaction>
       <reaction metaid="R_r_4379" sboTerm="SBO:0000655" id="R_r_4379" name="Palatinose transport in via proton symport" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
         <notes>

Diff for: model/yeast-GEM.yml

@@ -3,7 +3,7 @@
 - metaData:
     id: "yeastGEM_develop"
     name: "The Consensus Genome-Scale Metabolic Model of Yeast"
-    date: "2022-05-28"
+    date: "2022-05-29"
     givenName: "Eduard"
     familyName: "Kerkhoven"
     email: "[email protected]"
@@ -99312,7 +99312,6 @@
           - s_4108: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "YBR299W or YGR292W"
       - eccodes: "3.2.1.20"
       - subsystem:
       - annotation: !!omap