diff --git a/ModelFiles/dependencies.txt b/ModelFiles/dependencies.txt index f6540b4c..8f8b1350 100644 --- a/ModelFiles/dependencies.txt +++ b/ModelFiles/dependencies.txt @@ -1,7 +1,7 @@ MATLAB 9.7.0.1190202 (R2019b) libSBML 5.17.0 RAVEN_toolbox 2.4.0 -COBRA_toolbox commit 8204bb7 +COBRA_toolbox commit 7a3f66f SBML_level 3 SBML_version 1 fbc_version 2 diff --git a/ModelFiles/txt/yeastGEM.txt b/ModelFiles/txt/yeastGEM.txt index 1005e58a..345db428 100644 --- a/ModelFiles/txt/yeastGEM.txt +++ b/ModelFiles/txt/yeastGEM.txt @@ -215,7 +215,7 @@ r_0237 s_0794[c] + s_1212[c] + s_1579[c] -> s_1207[c] + s_1569[c] YLR100W 0. r_0238 s_0296[c] + s_0794[c] + s_1212[c] + s_1275[c] -> s_0803[c] + s_1207[c] + s_1576[c] YGR060W 0.00 1000.00 0.00 r_0239 s_0794[c] + s_1212[c] + s_1275[c] + s_1576[c] -> 2 s_0803[c] + s_1207[c] + s_1577[c] YGR060W 0.00 1000.00 0.00 r_0240 s_1212[c] + s_1275[c] + s_1577[c] -> s_0803[c] + s_1207[c] + s_1578[c] YGR060W 0.00 1000.00 0.00 -r_0241 s_0122[c] + 5 s_0794[c] + 3 s_1275[c] + 6 s_3825[er] -> s_0297[c] + 4 s_0803[c] + 6 s_3824[er] YGR060W 0.00 1000.00 0.00 +r_0241 s_0122[c] + 5 s_0794[c] + 3 s_1275[c] + 6 s_4209[erm] -> s_0297[c] + 4 s_0803[c] + 6 s_4210[erm] YGR060W 0.00 1000.00 0.00 r_0242 s_0657[c] + s_0794[c] + s_1212[c] + s_1275[c] -> s_0664[c] + 2 s_0803[c] + s_1207[c] YLR056W 0.00 1000.00 0.00 r_0243 s_0700[c] -> s_0657[c] YMR202W 0.00 1000.00 0.00 r_0244 s_0663[er] + s_0795[er] + s_1213[er] -> s_0667[er] + s_1208[er] YGL012W 0.00 1000.00 0.00 @@ -3561,7 +3561,7 @@ r_4192 s_1416[c] + s_3816[c] <=> s_0794[c] + s_1413[c] + s_3817[c] YHR109W -10 r_4193 s_3818[n] + s_3819[n] <=> s_0800[n] + s_3820[n] + s_3821[n] ( YHR119W or YDR440W or YJL168C ) -1000.00 1000.00 0.00 r_4194 s_3822[c] <=> s_3823[er] YIL023C -1000.00 1000.00 0.00 r_4195 s_4026[m] <=> s_4027[v] ( YMR243C or YOR316C ) -1000.00 1000.00 0.00 -r_4196 s_1204[er] + 2 s_3824[er] <=> s_0795[er] + s_1199[er] + 2 s_3825[er] ( YIL043C or YML125C ) -1000.00 1000.00 0.00 +r_4196 s_2818[erm] + 2 s_4210[erm] <=> s_2783[erm] + 2 s_4209[erm] YIL043C or YML125C -1000.00 1000.00 0.00 r_4197 s_1205[m] + 2 s_3826[m] <=> s_0799[m] + s_1200[m] + 2 s_3827[m] ( YIL043C or YKL150W or YML125C ) -1000.00 1000.00 0.00 r_4198 s_1207[c] + s_3828[c] <=> s_0794[c] + s_1212[c] + s_3829[c] YIR036C -1000.00 1000.00 0.00 r_4199 s_3830[er] + s_3831[er] <=> s_3832[er] + s_3833[er] YIR038C -1000.00 1000.00 0.00 diff --git a/ModelFiles/xml/yeastGEM.xml b/ModelFiles/xml/yeastGEM.xml index 4730f4af..88e3537d 100644 --- a/ModelFiles/xml/yeastGEM.xml +++ b/ModelFiles/xml/yeastGEM.xml @@ -48227,56 +48227,6 @@ - - - -

NOTES: added after new annotation (PR #142); based on kegg and Rhea

- - - - - - - - - - - - - - - - - - - - - - - - - -

NOTES: added after new annotation (PR #142); based on kegg and Rhea

- - - - - - - - - - - - - - - - - - - - @@ -57724,6 +57674,32 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -66862,12 +66838,12 @@ - + - + @@ -188394,13 +188370,12 @@ - - + + - - - + + diff --git a/ModelFiles/yml/yeastGEM.yml b/ModelFiles/yml/yeastGEM.yml index 962c47e4..31a7cbd9 100644 --- a/ModelFiles/yml/yeastGEM.yml +++ b/ModelFiles/yml/yeastGEM.yml @@ -25099,28 +25099,6 @@ - kegg.compound: C00038 - metanetx.chemical: MNXM149 - sbo: SBO:0000247 - - !!omap - - id: s_3824 - - name: Ferricytochrome b5 - - compartment: er - - formula: Fe - - charge: 3 - - annotation: !!omap - - bigg.metabolite: ficytb5 - - chebi: CHEBI:18097 - - kegg.compound: C00996 - - metanetx.chemical: MNXM1083 - - sbo: SBO:0000247 - - !!omap - - id: s_3825 - - name: Ferrocytochrome b5 - - compartment: er - - formula: Fe - - charge: 2 - - annotation: !!omap - - bigg.metabolite: focytb5 - - kegg.compound: C00999 - - sbo: SBO:0000247 - !!omap - id: s_3826 - name: Ferricytochrome b5 @@ -29363,6 +29341,18 @@ - kegg.compound: C04039 - metanetx.chemical: MNXM734 - sbo: SBO:0000247 + - !!omap + - id: s_4209 + - name: Ferrocytochrome b5 + - compartment: erm + - annotation: !!omap + - sbo: SBO:0000247 + - !!omap + - id: s_4210 + - name: Ferricytochrome b5 + - compartment: erm + - annotation: !!omap + - sbo: SBO:0000247 - reactions: - !!omap - id: r_0001 @@ -34403,8 +34393,8 @@ - s_0794: -5 - s_0803: 4 - s_1275: -3 - - s_3824: 6 - - s_3825: -6 + - s_4209: -6 + - s_4210: 6 - lower_bound: 0 - upper_bound: 1000 - gene_reaction_rule: YGR060W @@ -92044,11 +92034,10 @@ - id: r_4196 - name: NADH:ferricytochrome-b5 oxidoreductase - metabolites: !!omap - - s_0795: 1 - - s_1199: 1 - - s_1204: -1 - - s_3824: -2 - - s_3825: 2 + - s_2783: 1 + - s_2818: -1 + - s_4209: 2 + - s_4210: -2 - lower_bound: -1000 - upper_bound: 1000 - gene_reaction_rule: YIL043C or YML125C diff --git a/README.md b/README.md index c04910b0..9a4669c7 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ This repository contains the current consensus genome-scale metabolic model of _ **GEM Category:** species; **Utilisation:** experimental data reconstruction, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** reconstruction, curated; **Model Source:** YeastMetabolicNetwork; **Omic Source:** genomics, metabolomics; **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** general metabolism; **Bioreactor**; **Strain:** S288C; **Condition:** aerobic, glucose-limited, defined media; -* Last update: 2020-07-15 +* Last update: 2020-08-08 * Main Model Descriptors: