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cheng-yu-zhangcheng-yu-zhang
committedMay 30, 2022
remove r_4566 and make r_4232 reversible
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v9.0.2v8.6.1
1 parent bbd46f6 commit eab45b9

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‎README.md

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@@ -33,7 +33,7 @@ This repository contains the current consensus genome-scale metabolic model of _
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| Taxonomy | Latest update | Version | Reactions | Metabolites | Genes |
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|:-------|:--------------|:------|:------|:----------|:-----|
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| _Saccharomyces cerevisiae_ | 29-May-2022 | develop | 4069 | 2749 | 1163 |
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| _Saccharomyces cerevisiae_ | 30-May-2022 | develop | 4069 | 2749 | 1163 |
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# Installation & usage
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‎model/yeast-GEM.txt

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@@ -3595,7 +3595,7 @@ r_4227 H2O[c] + 2-Phenylacetamide[c] <=> ammonium[c] + phenylacetic acid[c] YDR
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r_4228 H2O[c] + (Indol-3-yl)acetamide[c] => ammonium[c] + indole-3-acetate[c] YDR242W 0.00 1000.00 0.00
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r_4230 ammonium[c] + Acrylic acid[c] <=> H2O[c] + Acrylamide[c] YDR242W -1000.00 1000.00 0.00
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r_4231 H2O[c] + Benzamide[c] <=> ammonium[c] + Benzoate[c] YDR242W -1000.00 1000.00 0.00
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r_4232 ATP[c] + D-gluconate[c] => 6-phospho-D-gluconate[c] + ADP[c] + H+[c] YDR248C 0.00 1000.00 0.00
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r_4232 ATP[c] + D-gluconate[c] <=> 6-phospho-D-gluconate[c] + ADP[c] + H+[c] YDR248C -1000.00 1000.00 0.00
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r_4233 S-adenosyl-L-methionine[c] + Protein C-terminal S-farnesyl-L-cysteine[c] <=> S-adenosyl-L-homocysteine[c] + Protein C-terminal S-farnesyl-L-cysteine methyl ester[c] YDR410C -1000.00 1000.00 0.00
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r_4234 UDP-N-acetyl-alpha-D-glucosamine[er] + 1-phosphatidyl-1D-myo-inositol[er] <=> H+[er] + UDP[er] + G00143[er] YDR437W and YGR216C and YNL038W and YPL076W and YPL175W and YPL096C-A -1000.00 1000.00 0.00
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r_4236 (R)-lactate[c] + H+[c] <=> H2O[c] + methylglyoxal[c] YDR533C or YMR322C or YOR391C or YPL280W -1000.00 1000.00 0.00
@@ -3924,7 +3924,7 @@ r_4562 uridine 2'-phosphate[e] => 0.00 1000.00 0.00
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r_4563 3'-UMP[e] => 0.00 1000.00 0.00
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r_4564 2',3'-cyclic CMP[e] => 0.00 1000.00 0.00
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r_4565 2',3'-cyclic UMP[e] => 0.00 1000.00 0.00
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r_4566 6-phospho-D-gluconate[c] + ADP[c] + H+[c] => ATP[c] + D-gluconate[c] YDR248C 0.00 1000.00 0.00
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r_4566 6-phospho-D-gluconate[c] + ADP[c] + H+[c] => ATP[c] + D-gluconate[c] YDR248C 0.00 0.00 0.00
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r_4567 6-phospho-D-gluconate[c] + H2O[c] => phosphate[c] + D-gluconate[c] 0.00 1000.00 0.00
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r_4568 H+[c] + phenylacetic acid[c] => 4-hydroxyphenyl acetate[c] 0.00 1000.00 0.00
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r_4569 acetate[c] + H+[c] + Hydroquinone[c] => H2O[c] + 4-hydroxyphenyl acetate[c] 0.00 1000.00 0.00

‎model/yeast-GEM.xml

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<fbc:geneProductRef fbc:geneProduct="YDR242W"/>
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</fbc:geneProductAssociation>
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</reaction>
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<reaction metaid="R_r_4232" sboTerm="SBO:0000176" id="R_r_4232" name="ATP:D-Gluconate 6-phosphotransferase" reversible="false" fast="false" fbc:lowerFluxBound="FB3N0" fbc:upperFluxBound="FB5N1000">
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<reaction metaid="R_r_4232" sboTerm="SBO:0000176" id="R_r_4232" name="ATP:D-Gluconate 6-phosphotransferase" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
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<notes>
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<body xmlns="http://www.w3.org/1999/xhtml">
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<p>Confidence Level: 2</p>
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<speciesReference species="M_s_4103" stoichiometry="1" constant="true"/>
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</listOfReactants>
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</reaction>
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<reaction metaid="R_r_4566" sboTerm="SBO:0000176" id="R_r_4566" name="ATP:D-Gluconate 6-phosphotransferase" reversible="false" fast="false" fbc:lowerFluxBound="FB3N0" fbc:upperFluxBound="FB5N1000">
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<reaction metaid="R_r_4566" sboTerm="SBO:0000176" id="R_r_4566" name="ATP:D-Gluconate 6-phosphotransferase" reversible="false" fast="false" fbc:lowerFluxBound="FB3N0" fbc:upperFluxBound="FB3N0">
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<notes>
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<body xmlns="http://www.w3.org/1999/xhtml">
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<p>Confidence Level: 0</p>

‎model/yeast-GEM.yml

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- metaData:
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id: "yeastGEM_develop"
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name: "The Consensus Genome-Scale Metabolic Model of Yeast"
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date: "2022-05-29"
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date: "2022-05-30"
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givenName: "Eduard"
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familyName: "Kerkhoven"
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email: "eduardk@chalmers.se"
@@ -96747,7 +96747,7 @@
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- s_0434: -1
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- s_0794: 1
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- s_3875: -1
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- lower_bound: 0
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- lower_bound: -1000
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- upper_bound: 1000
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- gene_reaction_rule: "YDR248C"
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- eccodes: "2.7.1.12"
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- s_0794: -1
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- s_3875: 1
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- lower_bound: 0
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- upper_bound: 1000
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- upper_bound: 0
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- gene_reaction_rule: "YDR248C"
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- eccodes: "2.7.1.12"
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- subsystem:

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