diff --git a/README.md b/README.md index 6e0829df..a8c74980 100644 --- a/README.md +++ b/README.md @@ -39,21 +39,21 @@ This repository contains the current consensus genome-scale metabolic model of _ | Taxonomy | Latest update | Version | Reactions | Metabolites | Genes | |:-------|:--------------|:------|:------|:----------|:-----| -| _Saccharomyces cerevisiae_ | 14-Aug-2024 | 9.0.1 | 4130 | 2805 | 1162 | +| _Saccharomyces cerevisiae_ | 23-Nov-2024 | 9.0.2 | 4131 | 2806 | 1161 | ### Gene essentiality prediction -- Accuracy: 0.899 -- True non-essential genes: 953 -- True essential genes: 58 -- False non-essential genes: 100 -- False essential genes: 13 +- Accuracy: 0.903 +- True non-essential genes: 950 +- True essential genes: 65 +- False non-essential genes: 95 +- False essential genes: 14 ### Growth prediction - Correlation coefficient R2: 0.880 -![Growth curve](growth.png) +![Growth curve](data/testResults/growth.png) # Installation & usage diff --git a/code/increaseVersion.m b/code/increaseVersion.m index 2664753d..44f7eb0b 100644 --- a/code/increaseVersion.m +++ b/code/increaseVersion.m @@ -54,9 +54,7 @@ function increaseVersion(bumpType) disp('Running gene essentiality analysis') [new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(model); disp('Run growth analysis') -new.R2=growth(model); - -saveas(gcf,'../../growth.png'); +new.R2=growth(model,true); cd .. copyfile('../README.md','backup.md') @@ -134,7 +132,7 @@ function increaseVersion(bumpType) disp(['NOTE: File ' diff_i{3} ' is changing more than expected']) change = true; end - case {'history.md','README.md','growth.png','model/yeast-GEM.mat'} + case {'history.md','README.md','data/testResults/growth.png','model/yeast-GEM.mat','model/yeast-GEM.xlsx'} otherwise disp(['NOTE: File ' diff_i{3} ' is changing']) change = true; diff --git a/code/modelCuration/TEMPLATEcuration.m b/code/modelCuration/TEMPLATEcuration.m index f42dd6d5..d8d77ae2 100644 --- a/code/modelCuration/TEMPLATEcuration.m +++ b/code/modelCuration/TEMPLATEcuration.m @@ -48,7 +48,7 @@ % Show some metrics: cd ../modelTests disp('Run gene essentiality analysis') -[new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(model); +[new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(model,true); fprintf('Genes in model: %d\n',numel(model.genes)); fprintf('Gene essentiality accuracy: %.4f\n', new.accuracy); fprintf('True non-essential genes: %d\n', numel(new.tp)); @@ -56,7 +56,7 @@ fprintf('False non-essential genes: %d\n', numel(new.fp)); fprintf('False essential genes: %d\n', numel(new.fn)); fprintf('\nRun growth analysis\n') -R2=growth(model); +R2=growth(model,true); fprintf('R2 of growth prediction: %.4f\n', R2); % Save model: diff --git a/code/modelCuration/v9_0_2.m b/code/modelCuration/v9_0_2.m new file mode 100644 index 00000000..64581274 --- /dev/null +++ b/code/modelCuration/v9_0_2.m @@ -0,0 +1,161 @@ +% This scripts applies curations to be applied on yeast-GEM release 9.0.1, to +% get to yeast-GEM release 9.0.2. + +%% Load yeast-GEM 9.0.1 (requires local yeast-GEM git repository) +cd .. +codeDir=pwd(); +model = getEarlierModelVersion('9.0.1'); +model.id='yeastGEM_develop'; +model.version=''; +%dataDir=fullfile(pwd(),'..','data','modelCuration','v9.0.0'); % No dataDir required for these curations +cd modelCuration + +%% Issue #371. Implement auxotrophy-based curation, as proposed by Han +% et al., 2024 doi:10.1016/j.synbio.2024.07.006. Not all changes are +% implemented as proposed by the authors. + +% To resolve AAT2 causing asparate auxotrophy +model = setParam(model,'eq','r_0217',0); +rxnIdx = getIndexes(model,'r_0217','rxns'); +model.rxnNotes{rxnIdx} = 'No significant mitochondrial flux'; +model.rxnReferences{rxnIdx} = '10.1016/j.femsyr.2004.09.008'; + +% To resolve ALD2 and ALD3 causing pantothenic acid auxotrophy +model = changeGrRules(model,'r_0172','YMR170C or YMR169C',true); +rxnIdx = getIndexes(model,'r_0172','rxns'); +model.rxnReferences{rxnIdx} = '10.1093/genetics/163.1.69'; + +% To resolve CHO2 causing choline auxotrophy +CHO2rxns = {'r_2488','r_2489','r_2490','r_2491','r_2492','r_2493','r_2494','r_2495'}; +model = changeGrRules(model,CHO2rxns,'YGR157W',true); +rxnIdx = getIndexes(model,CHO2rxns,'rxns'); +model.rxnReferences(rxnIdx) = {'10.1016/0005-2760(90)90145-N'}; +% While the curation is correct, CHO2 and OPI3 are not strictly essential +% genes, choline auxotrophy is only in relation to the production of +% phosphocholines. If no cholines are available, the phospholipid +% composition would be different. But because of the fixed biomass +% composition in yeast-GEM, CHO2 and OPI3 act as essential genes. This +% causes false positives in the essentialGenes function, as the genes not +% truly essential. + +% To resolve CYS3 causing cysteine auxotrophy +model = setParam(model,'eq','r_0312',0); +rxnIdx = getIndexes(model,'r_0312','rxns'); +model.rxnNotes{rxnIdx} = 'Regulatory role only'; +model.rxnReferences{rxnIdx} = '10.1111/j.1574-6968.2003.tb11531.x'; + +% Han et al. suggest to block TUM1 reaction r_4703, to resolve CYS4 as +% causing cysteine auxotrophy. However, there is good evidence that this +% reaction is taking place (doi:10.1093/femsyr/fow100). Instead, make the +% reaction irreversible. +model = setParam(model,'lb','r_4703',0); + +% To resolve ERG10 causing ergosterol auxotrophy +model = removeReactions(model,'r_0559',true,true); % ERG13, mitochondrial +% only, see e.g. https://www.uniprot.org/uniprotkb/P54839/entry + +% To resolve GFA1 causing D-glucosamine auxotrophy: add chitin to +% carbohydrate pseudoreaction and adjust other reactions proportionally +rxn = getIndexes(model,'r_4048','rxns'); +met1 = getIndexes(model,'s_0509','mets');%chitin +met2 = getIndexes(model,'s_0001','mets');%(1->3)-beta-D-glucan +met3 = getIndexes(model,'s_0004','mets');%(1->6)-beta-D-glucan +met4 = getIndexes(model,'s_1107','mets');%mannan +met5 = getIndexes(model,'s_0773','mets');%glycogen +met6 = getIndexes(model,'s_1520','mets');%trehalose +model.S(met1, rxn) = -0.02361; +model.S(met2, rxn) = -0.73914; +model.S(met3, rxn) = -0.24696; +model.S(met4, rxn) = -0.70204; +model.S(met5, rxn) = -0.35689; +model.S(met6, rxn) = -0.13655; +% And change gene association +model = changeGrRules(model,'r_0477','YKL104C',true); + +% To resolve GSH1 causing glutatione auxotrophy: add glutathione to the +% cofactor pseudoreaction +rxn = getIndexes(model,'r_4598','rxns'); +met = getIndexes(model,'s_0750','mets'); +model.S(met, rxn) = -1e-06; +% The above change will make GSH1 and GSH2 essential genes. This will be +% reported in essentialGenes as false positives, as their essentiality is +% debated (see for instance doi:10.1016/S1567-1356(02)00081-8). We here +% argue that absence of glutathione very strongly affects cell growth and +% stress tolerance. + +% To resolve ERG13/20 causing ergosterol auxotrophy; and HEM1/2/3/4/12 +% causing heme auxotrophy. Heme transport and exchange should be present to +% allow uptake if supplemented +metsToAdd.metNames = 'heme a'; +metsToAdd.compartments = 'e'; +model = addMets(model,metsToAdd,true,'s_'); +model = addTransport(model,'c','e','heme a',true,false,'r_'); +model = addExchangeRxns(model,'out',model.mets(end)); +model.rxns(end) = generateNewIds(model,'rxns','r_',1); +model.rxnNames(end) = {'heme a exchange'}; +model.subSystems{end} = {'Exchange reaction'}; + +% To resolve MET3 causing methionine auxotrophy +rxnIdx = getIndexes(model,{'r_0223','r_0224','r_1026'},'rxns'); +model.eccodes(rxnIdx) = {'2.7.7.53','2.7.7.53','2.7.7.5'}; +% Han et al. suggest to block APA1 reaction r_1026, but their cited +% reference (doi:10.1007/BF00264692) contains no reasoning for this. +% Instead, there is good evidence for the function of this enzyme: +% (doi:10.1128/jb.171.12.6437-6445.1989), although the reaction is assayed +% in the reverse direction. So instead, invert the reaction (and keep it +% irreversible), this has the same effect for MET3 as blocking it. +model.S(:,rxnIdx(3)) = - model.S(:,rxnIdx(3)); + +% To resolve MET13 causing methionine auxotrophy +model = changeGrRules(model,'r_0080','(YGL125W and YPL023C) or YGL125W',true); + +% To resolve MET17 causing methionine auxotrophy +model = setParam(model,'lb','r_0815',0); + +% To resolve THI4 causing thiamine auxotrophy and HOM2 causing methionine +% and threonine auxotrophy +model = removeReactions(model,'r_2070',true,true); +model = removeReactions(model,'r_2071',true,true); +rxnsToAdd.rxns = generateNewIds(model,'rxns','r_',2); +rxnsToAdd.equations = {'s_3910 + s_0803 => s_0423 + s_0293 + s_0456 + s_0794', ... + 's_1003 + s_1198 + s_0841 => s_1216 + s_3910 + 3 s_0803 + s_0794'}; +rxnsToAdd.rxnNames = {'HET-P synthase (thiazole synthase)','adenylated thiazole synthase'}; +rxnsToAdd.lb = [0,0]; +rxnsToAdd.ub = [1000,1000]; +rxnsToAdd.eccodes = {'','2.4.2.60'}; +rxnsToAdd.subSystems= {'Thiamine metabolism','Thiamine metabolism'}; +rxnsToAdd.grRules = {'YGR144W','YGR144W'}; +rxnsToAdd.rxnMiriams{1} = struct('name',{{'kegg.reaction';'kegg.pathway';'metanetx.reaction'}},... + 'value',{{'R10685';'sce00730';'MNXR139808'}}); +rxnsToAdd.rxnMiriams{2} = struct('name',{{'kegg.reaction';'kegg.pathway';'metanetx.reaction'}},... + 'value',{{'R10711';'sce00730';'MNXR139812'}}); +rxnsToAdd.rxnReferences = {'10.1021/ja067606t','10.1021/ja067606t'}; +rxnsToAdd.rxnConfidenceScores = [3,3]; +model = addRxns(model,rxnsToAdd); + +% To resolve URA2 causing uracil auxotrophy +model = changeGrRules(model,'r_0250','YJL130C or (YJR109C and YOR303W)',true); + +%% Issue #372. Correct UniProt identifier of YCR024C and YCR024C-A +geneIdx = getIndexes(model,'YCR024C','genes'); +model.geneMiriams{geneIdx}.value = {'P25345'}; + +%% DO NOT CHANGE OR REMOVE THE CODE BELOW THIS LINE. +% Show some metrics: +cd(fullfile(codeDir,'modelTests')) +disp('Run gene essentiality analysis') +[new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(model,true); +fprintf('Genes in model: %d\n',numel(model.genes)); +fprintf('Gene essentiality accuracy: %.4f\n', new.accuracy); +fprintf('True non-essential genes: %d\n', numel(new.tp)); +fprintf('True essential genes: %d\n', numel(new.tn)); +fprintf('False non-essential genes: %d\n', numel(new.fp)); +fprintf('False essential genes: %d\n', numel(new.fn)); +fprintf('\nRun growth analysis\n') +R2=growth(model,true); +fprintf('R2 of growth prediction: %.4f\n', R2); + +% Save model: +cd .. +saveYeastModel(model) +cd modelCuration diff --git a/code/modelTests/essentialGenes.m b/code/modelTests/essentialGenes.m index 8b8e4735..5ffdab1e 100644 --- a/code/modelTests/essentialGenes.m +++ b/code/modelTests/essentialGenes.m @@ -1,4 +1,4 @@ -function [accuracy,tp,tn,fn,fp] = essentialGenes(model) +function [accuracy,tp,tn,fn,fp] = essentialGenes(model,writeOutput) % essentialGenes % Modify media + find essential genes in model. Adapted from: % https://doi.org/10.1371/journal.pcbi.1004530 @@ -12,11 +12,15 @@ % Usage: [accurancy,tp,tn,fn,fp] = essentialGenes % -if nargin<1; +if nargin<1 | isempty(model) cd .. model = loadYeastModel; cd modelTests end +if nargin<2 + writeOutput = false; +end + ko_tol = 1e-6; %constraints from genotype: check the genotype of the strains used in deletion experiment @@ -71,6 +75,19 @@ sqrt((n_tp + n_fp)*(n_tp + n_fn)*(n_tn + n_fp)*(n_tn + n_fn)); geoMean = (sensitivity * specificity)^.5; +if writeOutput + fid = fopen('../../data/testResults/essentialGenes.md','w'); + fprintf(fid,'%s\n','## False non-essential genes'); + fprintf(fid,'%s\n',fp{:}); + fprintf(fid,'%s\n','## False essential genes'); + fprintf(fid,'%s\n',fn{:}); + fprintf(fid,'%s\n','## True non-essential genes'); + fprintf(fid,'%s\n',tp{:}); + fprintf(fid,'%s\n','## True essential genes'); + fprintf(fid,'%s\n',tn{:}); + fclose(fid); +end + function model = complete_Y7(model) % change Y7 model medium to the Kennedy synthetic complete medium % NOTE: Y7 doesn't have exchange reactions for dihydrofolate, @@ -119,9 +136,10 @@ % Project (14 aug 11) % http://www-sequence.stanford.edu/group/yeast_deletion_project/downloads.html - genes = {'YAL001C';'YAL003W';'YAL025C';'YAL032C';'YAL033W';'YAL034W-a';'YAL035C-A';'YAL038W';'YAL041W';'YAL043C';'YAR007C';'YAR008W';'YAR019C';'YBL004W';'YBL014C';'YBL018C';'YBL020W';'YBL023C';'YBL026W';'YBL030C';'YBL034C';'YBL035C';'YBL040C';'YBL041W';'YBL050W';'YBL073W';'YBL074C';'YBL076C';'YBL077W';'YBL084C';'YBL092W';'YBL097W';'YBL105C';'YBR002C';'YBR004C';'YBR011C';'YBR029C';'YBR038W';'YBR049C';'YBR055C';'YBR060C';'YBR070C';'YBR079C';'YBR080C';'YBR087W';'YBR087W';'YBR088C';'YBR089W';'YBR091C';'YBR102C';'YBR109C';'YBR110W';'YBR123C';'YBR124W';'YBR135W';'YBR136W';'YBR140C';'YBR142W';'YBR143C';'YBR152W';'YBR153W';'YBR154C';'YBR155W';'YBR160W';'YBR167C';'YBR190W';'YBR192W';'YBR193C';'YBR196C';'YBR198C';'YBR202W';'YBR211C';'YBR233W-A';'YBR233W-A';'YBR234C';'YBR236C';'YBR237W';'YBR243C';'YBR247C';'YBR252W';'YBR253W';'YBR254C';'YBR256C';'YBR257W';'YBR265W';'YCL003W';'YCL017C';'YCL031C';'YCL031C';'YCL031C';'YCL043C';'YCL052C';'YCL053C';'YCL054W';'YCL059C';'YCR012W';'YCR012W';'YCR013C';'YCR013C';'YCR035C';'YCR052W';'YCR054C';'YCR057C';'YCR072C';'YCR093W';'YDL003W';'YDL004W';'YDL007W';'YDL008W';'YDL014W';'YDL015C';'YDL016C';'YDL017W';'YDL028C';'YDL029W';'YDL030W';'YDL031W';'YDL043C';'YDL045C';'YDL055C';'YDL058W';'YDL060W';'YDL064W';'YDL084W';'YDL087C';'YDL092W';'YDL097C';'YDL098C';'YDL102W';'YDL103C';'YDL105W';'YDL108W';'YDL111C';'YDL120W';'YDL126C';'YDL132W';'YDL139C';'YDL140C';'YDL141W';'YDL143W';'YDL145C';'YDL147W';'YDL148C';'YDL150W';'YDL152W';'YDL153C';'YDL163W';'YDL164C';'YDL165W';'YDL166C';'YDL193W';'YDL195W';'YDL196W';'YDL205C';'YDL207W';'YDL208W';'YDL209C';'YDL212W';'YDL217C';'YDL220C';'YDL221W';'YDL235C';'YDR002W';'YDR013W';'YDR016C';'YDR021W';'YDR023W';'YDR037W';'YDR041W';'YDR044W';'YDR045C';'YDR047W';'YDR050C';'YDR050C';'YDR052C';'YDR053W';'YDR054C';'YDR060W';'YDR062W';'YDR064W';'YDR081C';'YDR082W';'YDR086C';'YDR087C';'YDR088C';'YDR091C';'YDR113C';'YDR118W';'YDR141C';'YDR145W';'YDR160W';'YDR164C';'YDR166C';'YDR167W';'YDR168W';'YDR170C';'YDR172W';'YDR177W';'YDR180W';'YDR182W';'YDR187C';'YDR188W';'YDR189W';'YDR190C';'YDR196C';'YDR201W';'YDR208W';'YDR211W';'YDR212W';'YDR224C';'YDR224C';'YDR224C';'YDR228C';'YDR232W';'YDR235W';'YDR236C';'YDR238C';'YDR240C';'YDR243C';'YDR246W';'YDR267C';'YDR280W';'YDR288W';'YDR292C';'YDR299W';'YDR301W';'YDR302W';'YDR303C';'YDR308C';'YDR311W';'YDR320C-A';'YDR320C-A';'YDR324C';'YDR325W';'YDR327W';'YDR328C';'YDR331W';'YDR339C';'YDR341C';'YDR353W';'YDR355C';'YDR356W';'YDR361C';'YDR362C';'YDR365C';'YDR367W';'YDR373W';'YDR376W';'YDR381W';'YDR390C';'YDR394W';'YDR396W';'YDR397C';'YDR398W';'YDR404C';'YDR407C';'YDR412W';'YDR413C';'YDR416W';'YDR427W';'YDR427W';'YDR429C';'YDR434W';'YDR437W';'YDR449C';'YDR454C';'YDR460W';'YDR464W';'YDR468C';'YDR472W';'YDR473C';'YDR478W';'YDR487C';'YDR489W';'YDR498C';'YDR499W';'YDR510W';'YDR526C';'YDR527W';'YDR531W';'YEL002C';'YEL019C';'YEL026W';'YEL032W';'YEL034W';'YEL035C';'YEL055C';'YEL058W';'YER003C';'YER006W';'YER008C';'YER009W';'YER012W';'YER013W';'YER018C';'YER021W';'YER022W';'YER023W';'YER025W';'YER029C';'YER029C';'YER036C';'YER038C';'YER043C';'YER048W-A';'YER074W-A';'YER074W-A';'YER082C';'YER093C';'YER094C';'YER104W';'YER112W';'YER125W';'YER126C';'YER127W';'YER133W';'YER136W';'YER146W';'YER147C';'YER148W';'YER157W';'YER159C';'YER165W';'YER168C';'YER171W';'YER172C';'YFL002C';'YFL005W';'YFL008W';'YFL009W';'YFL017C';'YFL018W-A';'YFL022C';'YFL024C';'YFL029C';'YFL035C';'YFL035C-A';'YFL037W';'YFL038C';'YFL039C';'YFL045C';'YFR002W';'YFR003C';'YFR004W';'YFR005C';'YFR027W';'YFR028C';'YFR029W';'YFR031C';'YFR037C';'YFR042W';'YFR050C';'YFR051C';'YFR052W';'YGL001C';'YGL008C';'YGL011C';'YGL018C';'YGL022W';'YGL030W';'YGL040C';'YGL044C';'YGL044C';'YGL044C';'YGL047W';'YGL048C';'YGL055W';'YGL061C';'YGL065C';'YGL068W';'YGL069C';'YGL073W';'YGL074C';'YGL075C';'YGL091C';'YGL092W';'YGL093W';'YGL097W';'YGL097W';'YGL098W';'YGL099W';'YGL102C';'YGL103W';'YGL111W';'YGL112C';'YGL113W';'YGL116W';'YGL120C';'YGL122C';'YGL123W';'YGL128C';'YGL130W';'YGL137W';'YGL142C';'YGL145W';'YGL145W';'YGL145W';'YGL150C';'YGL155W';'YGL169W';'YGL171W';'YGL172W';'YGL201C';'YGL207W';'YGL225W';'YGL233W';'YGL238W';'YGL239C';'YGL239C';'YGL245W';'YGL247W';'YGR002C';'YGR005C';'YGR009C';'YGR013W';'YGR024C';'YGR029W';'YGR029W';'YGR029W';'YGR030C';'YGR046W';'YGR047C';'YGR048W';'YGR060W';'YGR065C';'YGR073C';'YGR074W';'YGR075C';'YGR082W';'YGR083C';'YGR090W';'YGR091W';'YGR094W';'YGR095C';'YGR098C';'YGR099W';'YGR103W';'YGR113W';'YGR114C';'YGR115C';'YGR116W';'YGR119C';'YGR120C';'YGR128C';'YGR140W';'YGR145W';'YGR147C';'YGR156W';'YGR158C';'YGR172C';'YGR175C';'YGR179C';'YGR185C';'YGR186W';'YGR190C';'YGR191W';'YGR195W';'YGR198W';'YGR211W';'YGR216C';'YGR218W';'YGR245C';'YGR246C';'YGR251W';'YGR253C';'YGR264C';'YGR265W';'YGR267C';'YGR274C';'YGR277C';'YGR278W';'YGR280C';'YHL015W';'YHR005C-A';'YHR007C';'YHR019C';'YHR020W';'YHR023W';'YHR024C';'YHR036W';'YHR040W';'YHR042W';'YHR058C';'YHR062C';'YHR065C';'YHR068W';'YHR069C';'YHR070W';'YHR072W';'YHR072W-A';'YHR072W-A';'YHR074W';'YHR083W';'YHR085W';'YHR088W';'YHR088W';'YHR088W';'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+ genes = 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%'YCL004W';... %removed by HA 2/7/2013 - doi: 10.1074/jbc.273.16.9829 %'YKL192C';... %removed by HA 2/7/2013 - http://dx.doi.org/10.1016/j.bbalip.2006.07.004 + %'YOL049W';'YJL101C'... %added by EJK 27/10/2024 - doi: 10.1007/BF02426954, very impaired growth in absence of glutathione }; genes = upper(genes); diff --git a/code/modelTests/growth.m b/code/modelTests/growth.m index 07caf9cd..7bc75afd 100644 --- a/code/modelTests/growth.m +++ b/code/modelTests/growth.m @@ -1,4 +1,4 @@ -function R2 = growth(model_origin) +function R2 = growth(model_origin,writeOutput) % This is for growth test: Fig S4c for yeast8 paper % here we use several chemostat data: 'N-limited aerobic' 'C-limited % aerobic' 'C-limited anaerobic' 'N-limited anaerobic' @@ -13,6 +13,9 @@ else cd ../otherChanges/ end +if nargin<2 + writeOutput = false; +end %Load chemostat data: fid = fopen('../../data/physiology/chemostatData_Tobias2013.tsv','r'); @@ -54,11 +57,21 @@ ylabel('In silico growth rate [1/h]','FontSize',14,'FontName','Helvetica') legend(b,'N-limited aerobic','C-limited aerobic','C-limited anaerobic','N-limited anaerobic','Location','northwest') -meanerror = sqrt(sum(([exp_data1(:,4);exp_data2(:,4);exp_data3(:,4);exp_data4(:,4)]-[mod_data1(:,4);mod_data2(:,4);mod_data3(:,4);mod_data4(:,4)]).^2)/32)/sqrt(32); -text(0.25,0.1,['SEM:',num2str(meanerror)]) +% meanerror = sqrt(sum(([exp_data1(:,4);exp_data2(:,4);exp_data3(:,4);exp_data4(:,4)]-[mod_data1(:,4);mod_data2(:,4);mod_data3(:,4);mod_data4(:,4)]).^2)/32)/sqrt(32); +% text(0.25,0.1,['SEM:',num2str(meanerror)]) hold off R2=corrcoef([exp_data1(:,4);exp_data2(:,4);exp_data3(:,4);exp_data4(:,4)],[mod_data1(:,4);mod_data2(:,4);mod_data3(:,4);mod_data4(:,4)]); R2=R2(2)^2; + +if writeOutput + saveas(gcf,'../../data/testResults/growth.png'); + fid = fopen('../../data/testResults/growth.md','w'); + fprintf(fid,'%s\n','## R2 of growth rate prediction'); + fprintf(fid,'%.4g\n\n',R2); + fprintf(fid,'%s\n','![Growth curve](growth.png)'); + fclose(fid); +end + end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% diff --git a/data/databases/model_metDeltaG.csv b/data/databases/model_metDeltaG.csv index dabf8125..ebe81da5 100644 --- a/data/databases/model_metDeltaG.csv +++ b/data/databases/model_metDeltaG.csv @@ -2804,3 +2804,4 @@ s_4328,-593.58 s_4329,-450.64 s_4330,-659.91 s_4331,-63.35 +s_4332,10000000 diff --git a/data/databases/model_rxnDeltaG.csv b/data/databases/model_rxnDeltaG.csv index 0f1e4b61..13d53174 100644 --- a/data/databases/model_rxnDeltaG.csv +++ b/data/databases/model_rxnDeltaG.csv @@ -442,7 +442,6 @@ r_0555,-27.78 r_0556,10000000 r_0557,15.51 r_0558,-9.81 -r_0559,-8.4 r_0560,-9.08 r_0561,-17.09 r_0562,-24.94 @@ -1467,8 +1466,6 @@ r_2066,10000000 r_2067,10000000 r_2068,10000000 r_2069,10000000 -r_2070,10000000 -r_2071,10000000 r_2072,0 r_2073,10000000 r_2074,-15.23 @@ -4129,3 +4126,7 @@ r_4775,NaN r_4776,NaN r_4777,NaN r_4778,NaN +r_4779,0 +r_4780,NaN +r_4781,NaN +r_4782,NaN diff --git a/data/testResults/essentialGenes.md b/data/testResults/essentialGenes.md new file mode 100644 index 00000000..39da7c0f --- /dev/null +++ b/data/testResults/essentialGenes.md @@ -0,0 +1,1128 @@ +## False non-essential genes +YAL038W +YBL030C +YBR002C +YBR004C +YBR011C +YBR038W +YBR070C +YBR110W +YBR153W +YBR192W +YBR196C +YBR243C +YBR252W +YBR256C +YBR265W +YCL017C +YCL052C +YCR012W +YDL004W +YDL015C +YDL120W +YDL166C +YDR023W +YDR050C +YDR062W +YDR208W +YDR236C +YDR302W +YDR353W +YDR367W +YDR373W +YDR376W +YDR437W +YDR487C +YER023W +YGL001C +YGL008C +YGL047W +YGL065C +YGL142C +YGL169W +YGL225W +YGR046W +YGR060W +YGR065C +YGR175C +YGR191W +YGR216C +YGR277C +YHR007C +YHR042W +YHR068W +YHR072W +YHR128W +YHR190W +YIL048W +YJL005W +YJL026W +YJL091C +YJL097W +YJR013W +YJR016C +YJR057W +YKL004W +YKL019W +YKL035W +YKL060C +YKL141W +YKL152C +YKL165C +YKL182W +YLL031C +YLR100W +YLR153C +YLR305C +YLR355C +YLR359W +YML125C +YMR013C +YMR108W +YMR281W +YMR296C +YMR298W +YMR301C +YNL036W +YNL038W +YNL267W +YOL066C +YOR143C +YOR149C +YPL076W +YPL175W +YPL231W +YPL252C +YPR035W +## False essential genes +YBR126C +YDR074W +YER014W +YER026C +YGR157W +YJR073C +YKL067W +YKR039W +YKR072C +YMR217W +YNL275W +YOL122C +YOR054C +YPL172C +## True non-essential genes +Q0045 +Q0080 +Q0085 +Q0105 +Q0130 +Q0250 +Q0275 +YAL012W +YAL022C +YAL023C +YAL026C +YAL035W +YAL039C +YAL044C +YAL054C +YAL060W +YAL062W +YAR015W +YAR035W +YAR071W +YBL011W +YBL013W +YBL015W +YBL033C +YBL039C +YBL042C +YBL045C +YBL064C +YBL068W +YBL080C +YBL091C +YBL098W +YBL099W +YBR001C +YBR003W +YBR006W +YBR018C +YBR019C +YBR020W +YBR021W +YBR022W +YBR023C +YBR026C +YBR034C +YBR035C +YBR036C +YBR039W +YBR041W +YBR042C +YBR046C +YBR058C-A +YBR068C +YBR069C +YBR084W +YBR085W +YBR092C +YBR093C +YBR097W +YBR111C +YBR115C +YBR117C +YBR121C +YBR127C +YBR128C +YBR132C +YBR145W +YBR147W +YBR149W +YBR159W +YBR161W +YBR166C +YBR176W +YBR177C +YBR180W +YBR183W +YBR199W +YBR204C +YBR205W +YBR208C +YBR213W +YBR218C +YBR221C +YBR222C +YBR229C +YBR235W +YBR244W +YBR248C +YBR249C +YBR263W +YBR281C +YBR291C +YBR293W +YBR294W +YBR295W +YBR296C +YBR298C +YBR299W +YCL004W +YCL005W-A +YCL009C +YCL018W +YCL025C +YCL030C +YCL035C +YCL038C +YCL040W +YCL047C +YCL050C +YCL064C +YCL069W +YCR005C +YCR010C +YCR011C +YCR024C +YCR024C-A +YCR028C +YCR034W +YCR036W +YCR037C +YCR048W +YCR053W +YCR068W +YCR075C +YCR083W +YCR098C +YCR105W +YCR107W +YDL022W +YDL024C +YDL040C +YDL042C +YDL052C +YDL066W +YDL067C +YDL078C +YDL080C +YDL085W +YDL090C +YDL093W +YDL095W +YDL100C +YDL131W +YDL142C +YDL168W +YDL171C +YDL174C +YDL178W +YDL182W +YDL185W +YDL198C +YDL210W +YDL215C +YDL219W +YDL236W +YDL238C +YDL243C +YDL245C +YDL247W +YDR001C +YDR007W +YDR009W +YDR017C +YDR019C +YDR035W +YDR036C +YDR038C +YDR039C +YDR040C +YDR046C +YDR051C +YDR058C +YDR071C +YDR072C +YDR093W +YDR098C +YDR105C +YDR127W +YDR135C +YDR147W +YDR148C +YDR158W +YDR173C +YDR178W +YDR191W +YDR204W +YDR226W +YDR231C +YDR234W +YDR242W +YDR256C +YDR261C +YDR268W +YDR270W +YDR272W +YDR284C +YDR287W +YDR294C +YDR297W +YDR298C +YDR300C +YDR305C +YDR315C +YDR321W +YDR322C-A +YDR342C +YDR343C +YDR345C +YDR352W +YDR354W +YDR368W +YDR377W +YDR380W +YDR384C +YDR399W +YDR400W +YDR402C +YDR403W +YDR408C +YDR410C +YDR428C +YDR440W +YDR441C +YDR452W +YDR453C +YDR456W +YDR481C +YDR483W +YDR497C +YDR502C +YDR503C +YDR508C +YDR513W +YDR516C +YDR529C +YDR530C +YDR533C +YDR536W +YDR538W +YDR539W +YEL004W +YEL006W +YEL017C-A +YEL021W +YEL024W +YEL027W +YEL029C +YEL031W +YEL038W +YEL039C +YEL041W +YEL042W +YEL046C +YEL047C +YEL051W +YEL063C +YEL066W +YEL069C +YEL071W +YER005W +YER010C +YER015W +YER019W +YER024W +YER037W +YER042W +YER052C +YER053C +YER055C +YER056C +YER060W +YER060W-A +YER061C +YER062C +YER065C +YER069W +YER070W +YER073W +YER081W +YER086W +YER087W +YER090W +YER091C +YER099C +YER119C +YER141W +YER152C +YER163C +YER170W +YER174C +YER175C +YER178W +YER183C +YFL001W +YFL011W +YFL018C +YFL030W +YFL053W +YFL055W +YFL058W +YFL059W +YFL060C +YFR015C +YFR019W +YFR021W +YFR025C +YFR030W +YFR033C +YFR044C +YFR047C +YFR049W +YFR053C +YGL006W +YGL009C +YGL012W +YGL017W +YGL026C +YGL027C +YGL037C +YGL038C +YGL062W +YGL063W +YGL067W +YGL077C +YGL080W +YGL084C +YGL125W +YGL148W +YGL154C +YGL156W +YGL167C +YGL184C +YGL186C +YGL187C +YGL191W +YGL196W +YGL202W +YGL205W +YGL224C +YGL234W +YGL248W +YGL253W +YGL255W +YGL256W +YGR007W +YGR010W +YGR012W +YGR019W +YGR020C +YGR032W +YGR036C +YGR038W +YGR043C +YGR055W +YGR061C +YGR062C +YGR087C +YGR088W +YGR096W +YGR106C +YGR110W +YGR121C +YGR124W +YGR138C +YGR143W +YGR144W +YGR154C +YGR155W +YGR170W +YGR171C +YGR177C +YGR180C +YGR183C +YGR192C +YGR193C +YGR194C +YGR202C +YGR204W +YGR208W +YGR209C +YGR227W +YGR234W +YGR240C +YGR243W +YGR244C +YGR247W +YGR248W +YGR254W +YGR255C +YGR256W +YGR260W +YGR282C +YGR286C +YGR287C +YGR289C +YGR292W +YHL003C +YHL011C +YHL016C +YHL032C +YHL036W +YHR001W-A +YHR002W +YHR008C +YHR011W +YHR013C +YHR018C +YHR025W +YHR026W +YHR037W +YHR039C-A +YHR043C +YHR044C +YHR046C +YHR051W +YHR063C +YHR067W +YHR091C +YHR092C +YHR094C +YHR096C +YHR100C +YHR104W +YHR106W +YHR109W +YHR116W +YHR119W +YHR123W +YHR137W +YHR144C +YHR162W +YHR163W +YHR174W +YHR183W +YHR201C +YHR208W +YHR215W +YHR216W +YIL002C +YIL006W +YIL009W +YIL010W +YIL013C +YIL020C +YIL023C +YIL043C +YIL053W +YIL066C +YIL074C +YIL094C +YIL099W +YIL107C +YIL111W +YIL116W +YIL124W +YIL125W +YIL134W +YIL145C +YIL155C +YIL160C +YIL162W +YIL172C +YIR027C +YIR028W +YIR029W +YIR031C +YIR032C +YIR034C +YIR037W +YIR038C +YJL003W +YJL012C +YJL045W +YJL046W +YJL052W +YJL060W +YJL068C +YJL071W +YJL088W +YJL100W +YJL121C +YJL126W +YJL129C +YJL130C +YJL133W +YJL134W +YJL137C +YJL139C +YJL153C +YJL155C +YJL166W +YJL168C +YJL196C +YJL198W +YJL200C +YJL212C +YJL214W +YJL216C +YJL219W +YJL221C +YJR001W +YJR009C +YJR010W +YJR019C +YJR024C +YJR025C +YJR040W +YJR048W +YJR049C +YJR051W +YJR069C +YJR077C +YJR078W +YJR095W +YJR103W +YJR104C +YJR105W +YJR109C +YJR110W +YJR121W +YJR130C +YJR131W +YJR133W +YJR137C +YJR139C +YJR143C +YJR148W +YJR152W +YJR153W +YJR155W +YJR158W +YJR159W +YJR160C +YKL001C +YKL008C +YKL016C +YKL026C +YKL029C +YKL055C +YKL069W +YKL080W +YKL085W +YKL087C +YKL094W +YKL103C +YKL106W +YKL120W +YKL127W +YKL132C +YKL140W +YKL146W +YKL148C +YKL150W +YKL174C +YKL181W +YKL184W +YKL188C +YKL192C +YKL194C +YKL211C +YKL212W +YKL215C +YKL216W +YKL217W +YKL218C +YKL220C +YKR009C +YKR031C +YKR043C +YKR052C +YKR053C +YKR058W +YKR061W +YKR066C +YKR067W +YKR069W +YKR076W +YKR080W +YKR089C +YKR093W +YKR097W +YLL001W +YLL012W +YLL015W +YLL018C-A +YLL028W +YLL041C +YLL043W +YLL048C +YLL051C +YLL052C +YLL057C +YLL060C +YLL061W +YLL062C +YLR011W +YLR017W +YLR020C +YLR027C +YLR028C +YLR038C +YLR043C +YLR044C +YLR047C +YLR056W +YLR057W +YLR058C +YLR070C +YLR081W +YLR089C +YLR092W +YLR099C +YLR109W +YLR130C +YLR133W +YLR134W +YLR138W +YLR142W +YLR143W +YLR146C +YLR151C +YLR155C +YLR157C +YLR158C +YLR160C +YLR164W +YLR172C +YLR174W +YLR180W +YLR189C +YLR201C +YLR209C +YLR214W +YLR231C +YLR237W +YLR239C +YLR240W +YLR244C +YLR245C +YLR258W +YLR260W +YLR284C +YLR285W +YLR286C +YLR295C +YLR299W +YLR300W +YLR303W +YLR304C +YLR307W +YLR308W +YLR328W +YLR342W +YLR348C +YLR350W +YLR351C +YLR354C +YLR360W +YLR372W +YLR377C +YLR382C +YLR386W +YLR395C +YLR410W +YLR420W +YLR432W +YLR438W +YLR447C +YLR450W +YML004C +YML008C +YML022W +YML035C +YML042W +YML054C +YML056C +YML059C +YML070W +YML075C +YML081C-A +YML086C +YML100W +YML106W +YML110C +YML120C +YML123C +YMR006C +YMR008C +YMR009W +YMR011W +YMR015C +YMR020W +YMR041C +YMR054W +YMR056C +YMR058W +YMR062C +YMR083W +YMR087W +YMR088C +YMR099C +YMR101C +YMR105C +YMR110C +YMR120C +YMR145C +YMR162C +YMR165C +YMR169C +YMR170C +YMR189W +YMR202W +YMR205C +YMR207C +YMR210W +YMR226C +YMR241W +YMR243C +YMR246W +YMR250W +YMR251W +YMR256C +YMR261C +YMR267W +YMR271C +YMR272C +YMR278W +YMR289W +YMR293C +YMR300C +YMR303C +YMR306W +YMR313C +YMR318C +YMR319C +YMR323W +YNL003C +YNL009W +YNL029C +YNL037C +YNL045W +YNL048W +YNL052W +YNL054W +YNL065W +YNL071W +YNL073W +YNL101W +YNL104C +YNL106C +YNL117W +YNL129W +YNL130C +YNL141W +YNL142W +YNL169C +YNL191W +YNL192W +YNL202W +YNL219C +YNL220W +YNL229C +YNL241C +YNL268W +YNL270C +YNL274C +YNL277W +YNL280C +YNL292W +YNL316C +YNL318C +YNL325C +YNL331C +YNL333W +YNL334C +YNR001C +YNR008W +YNR012W +YNR013C +YNR019W +YNR027W +YNR030W +YNR033W +YNR041C +YNR050C +YNR056C +YNR057C +YNR058W +YNR060W +YNR067C +YNR072W +YOL011W +YOL020W +YOL033W +YOL052C +YOL055C +YOL058W +YOL059W +YOL061W +YOL064C +YOL065C +YOL068C +YOL077W-A +YOL086C +YOL092W +YOL096C +YOL103W +YOL126C +YOL136C +YOL140W +YOL143C +YOL151W +YOL152W +YOL156W +YOL157C +YOL165C +YOR002W +YOR011W +YOR025W +YOR040W +YOR065W +YOR067C +YOR071C +YOR081C +YOR099W +YOR100C +YOR108W +YOR109W +YOR120W +YOR125C +YOR126C +YOR128C +YOR130C +YOR136W +YOR142W +YOR155C +YOR161C +YOR163W +YOR171C +YOR175C +YOR180C +YOR184W +YOR190W +YOR192C +YOR196C +YOR202W +YOR209C +YOR221C +YOR222W +YOR226C +YOR241W +YOR245C +YOR251C +YOR253W +YOR270C +YOR273C +YOR283W +YOR285W +YOR286W +YOR303W +YOR306C +YOR311C +YOR316C +YOR317W +YOR321W +YOR323C +YOR332W +YOR334W +YOR347C +YOR348C +YOR360C +YOR374W +YOR375C +YOR377W +YOR381W +YOR384W +YOR388C +YOR391C +YOR393W +YPL015C +YPL023C +YPL036W +YPL040C +YPL053C +YPL057C +YPL059W +YPL060W +YPL061W +YPL069C +YPL078C +YPL087W +YPL091W +YPL092W +YPL095C +YPL096C-A +YPL097W +YPL104W +YPL110C +YPL111W +YPL120W +YPL132W +YPL134C +YPL135W +YPL147W +YPL148C +YPL188W +YPL189W +YPL206C +YPL212C +YPL214C +YPL227C +YPL234C +YPL244C +YPL258C +YPL262W +YPL265W +YPL268W +YPL271W +YPL273W +YPL274W +YPL281C +YPR001W +YPR002W +YPR006C +YPR020W +YPR021C +YPR026W +YPR036W +YPR047W +YPR058W +YPR060C +YPR062W +YPR069C +YPR074C +YPR081C +YPR118W +YPR121W +YPR127W +YPR128C +YPR138C +YPR139C +YPR140W +YPR145W +YPR156C +YPR159W +YPR160W +YPR167C +YPR184W +YPR191W +YPR192W +YPR193C +## True essential genes +YBL076C +YBR029C +YDL045C +YDL055C +YDL103C +YDL141W +YDL205C +YDR037W +YDR044W +YDR047W +YDR196C +YDR232W +YDR341C +YDR454C +YDR531W +YEL058W +YER003C +YER043C +YFL017C +YFL022C +YFL045C +YGL040C +YGL055W +YGL245W +YGR094W +YGR185C +YGR264C +YGR267C +YHR019C +YHR020W +YHR074W +YIL078W +YIL083C +YJL101C +YJL167W +YKL024C +YKL088W +YKL104C +YLL018C +YLR060W +YML126C +YMR113W +YMR208W +YMR220W +YNL247W +YNL256W +YNR016C +YNR043W +YOL049W +YOL097C +YOL130W +YOR074C +YOR095C +YOR168W +YOR176W +YOR236W +YOR278W +YOR335C +YPL028W +YPL117C +YPL160W +YPR033C +YPR113W +YPR165W +YPR183W diff --git a/data/testResults/growth.md b/data/testResults/growth.md new file mode 100644 index 00000000..8212950e --- /dev/null +++ b/data/testResults/growth.md @@ -0,0 +1,4 @@ +## R2 of growth rate prediction +0.8798 + +![Growth curve](growth.png) diff --git a/data/testResults/growth.png b/data/testResults/growth.png new file mode 100644 index 00000000..d2905f3d Binary files /dev/null and b/data/testResults/growth.png differ diff --git a/growth.png b/growth.png deleted file mode 100644 index 31ade2b9..00000000 Binary files a/growth.png and /dev/null differ diff --git a/history.md b/history.md index 9e442cf1..e1c95dd2 100644 --- a/history.md +++ b/history.md @@ -1,5 +1,10 @@ # History +### yeast 9.0.2: +- Fixes: + - Curation based on auxotrophy predictions. (closes #371) + - Correct UniProt ID for YCR024C. (closes #372) + ### yeast 9.0.1: - Features: - Provide reference metabolite concentration from YMDB, which can be loaded with `code/missingFields/addYMDBconcentrations.m`. (PR #364) diff --git a/model/dependencies.txt b/model/dependencies.txt index b3712ef6..e7ad180d 100644 --- a/model/dependencies.txt +++ b/model/dependencies.txt @@ -1,4 +1,4 @@ MATLAB 24.1.0.2568132 (R2024a) Update 1 libSBML 5.20.2 -RAVEN_toolbox 2.9.3 +RAVEN_toolbox 2.10.2 COBRA_toolbox 3.4 diff --git a/model/yeast-GEM.mat b/model/yeast-GEM.mat index 33d5303b..f01658bb 100644 Binary files a/model/yeast-GEM.mat and b/model/yeast-GEM.mat differ diff --git a/model/yeast-GEM.txt b/model/yeast-GEM.txt index d84e9078..08be6e37 100755 --- a/model/yeast-GEM.txt +++ b/model/yeast-GEM.txt @@ -61,7 +61,7 @@ r_0076 CMP[c] + H2O[c] => cytidine[c] + phosphate[c] YER037W or YGL224C 0.00 r_0077 H2O[c] + IMP[c] => inosine[c] + phosphate[c] YOR155C 0.00 1000.00 0.00 r_0078 H2O[c] + UMP[c] => phosphate[c] + uridine[c] YER037W or YGL224C 0.00 1000.00 0.00 r_0079 5'-phosphoribosyl-N-formylglycineamide[c] + ATP[c] + H2O[c] + L-glutamine[c] => 5'-phosphoribosyl-N-formylglycineamidine[c] + ADP[c] + H+[c] + L-glutamate[c] + phosphate[c] YGR061C 0.00 1000.00 0.00 -r_0080 5,10-methylenetetrahydrofolate[c] + H+[c] + NADPH[c] => 5-methyltetrahydrofolate[c] + NADP(+)[c] YGL125W or YPL023C 0.00 1000.00 0.00 +r_0080 5,10-methylenetetrahydrofolate[c] + H+[c] + NADPH[c] => 5-methyltetrahydrofolate[c] + NADP(+)[c] (YGL125W and YPL023C) or YGL125W 0.00 1000.00 0.00 r_0081 H+[m] + L-glycine[m] + succinyl-CoA[m] => 5-aminolevulinate[m] + carbon dioxide[m] + coenzyme A[m] YDR232W 0.00 1000.00 0.00 r_0082 5-diphospho-1D-myo-inositol pentakisphosphate[c] + H2O[c] => H+[c] + myo-inositol hexakisphosphate[c] + phosphate[c] YOR163W 0.00 1000.00 0.00 r_0083 ATP[c] + myo-inositol hexakisphosphate[c] => 5-diphospho-1D-myo-inositol pentakisphosphate[c] + ADP[c] YDR017C 0.00 1000.00 0.00 @@ -149,7 +149,7 @@ r_0168 2-methylbutanal[c] + H+[c] + NADPH[c] => 2-methylbutanol[c] + NADP(+)[c] r_0169 H+[c] + NADH[c] + phenylacetaldehyde[c] => 2-phenylethanol[c] + NAD[c] YBR145W or YDL168W or YOL086C 0.00 1000.00 0.00 r_0170 H+[m] + NADH[m] + phenylacetaldehyde[m] => 2-phenylethanol[m] + NAD[m] YGL256W or YMR083W 0.00 1000.00 0.00 r_0171 H+[c] + NADPH[c] + phenylacetaldehyde[c] => 2-phenylethanol[c] + NADP(+)[c] YCR105W or YMR318C 0.00 1000.00 0.00 -r_0172 3-aminopropanal[c] + H2O[c] + NAD[c] => beta-alanine[c] + 2 H+[c] + NADH[c] YMR110C or YMR169C or YMR170C 0.00 1000.00 0.00 +r_0172 3-aminopropanal[c] + H2O[c] + NAD[c] => beta-alanine[c] + 2 H+[c] + NADH[c] YMR170C or YMR169C 0.00 1000.00 0.00 r_0173 acetaldehyde[c] + H2O[c] + NADP(+)[c] => acetate[c] + 2 H+[c] + NADPH[c] YPL061W 0.00 1000.00 0.00 r_0174 acetaldehyde[m] + H2O[m] + NAD[m] => acetate[m] + 2 H+[m] + NADH[m] YOR374W 0.00 1000.00 0.00 r_0175 acetaldehyde[m] + H2O[m] + NADP(+)[m] => acetate[m] + 2 H+[m] + NADPH[m] YER073W or YOR374W 0.00 1000.00 0.00 @@ -192,7 +192,7 @@ r_0213 ATP[m] + L-asparagine[m] + tRNA(Asn)[m] => AMP[m] + Asn-tRNA(Asn)[m] + di r_0214 carbamoyl phosphate[c] + L-aspartate[c] => H+[c] + N-carbamoyl-L-aspartate[c] + phosphate[c] YJL130C 0.00 1000.00 0.00 r_0215 ATP[c] + L-aspartate[c] => 4-phospho-L-aspartate[c] + ADP[c] YER052C 0.00 1000.00 0.00 r_0216 2-oxoglutarate[c] + L-aspartate[c] <=> L-glutamate[c] + oxaloacetate[c] YLR027C -1000.00 1000.00 0.00 -r_0217 L-glutamate[m] + oxaloacetate[m] => 2-oxoglutarate[m] + L-aspartate[m] YKL106W 0.00 1000.00 0.00 +r_0217 L-glutamate[m] + oxaloacetate[m] => 2-oxoglutarate[m] + L-aspartate[m] YKL106W 0.00 0.00 0.00 r_0218 2-oxoglutarate[p] + L-aspartate[p] <=> L-glutamate[p] + oxaloacetate[p] YLR027C -1000.00 1000.00 0.00 r_0219 4-phospho-L-aspartate[c] + H+[c] + NADPH[c] => L-aspartate 4-semialdehyde[c] + NADP(+)[c] + phosphate[c] YDR158W 0.00 1000.00 0.00 r_0220 ATP[c] + L-aspartate[c] + tRNA(Asp)[c] => AMP[c] + Asp-tRNA(Asp)[c] + diphosphate[c] YLL018C 0.00 1000.00 0.00 @@ -220,7 +220,7 @@ r_0242 episterol[c] + H+[c] + NADPH[c] + oxygen[c] => ergosta-5,7,24(28)-trien-3 r_0243 fecosterol[c] => episterol[c] YMR202W 0.00 1000.00 0.00 r_0244 ergosta-5,7,22,24(28)-tetraen-3beta-ol[er] + H+[er] + NADPH[er] => ergosterol[er] + NADP(+)[er] YGL012W 0.00 1000.00 0.00 r_0249 4-hydroxybenzoate[c] + nonaprenyl diphosphate[c] => diphosphate[c] + nonaprenyl 4-hydroxybenzoate[c] YDL090C and YKL019W 0.00 1000.00 0.00 -r_0250 2 ATP[c] + bicarbonate[c] + H2O[c] + L-glutamine[c] => 2 ADP[c] + carbamoyl phosphate[c] + 2 H+[c] + L-glutamate[c] + phosphate[c] YJL130C and YJR109C and YOR303W 0.00 1000.00 0.00 +r_0250 2 ATP[c] + bicarbonate[c] + H2O[c] + L-glutamine[c] => 2 ADP[c] + carbamoyl phosphate[c] + 2 H+[c] + L-glutamate[c] + phosphate[c] YJL130C or (YJR109C and YOR303W) 0.00 1000.00 0.00 r_0252 (R)-carnitine[c] + acetyl-CoA[c] => coenzyme A[c] + O-acetylcarnitine[c] YAR035W or YER024W 0.00 1000.00 0.00 r_0253 (R)-carnitine[p] + acetyl-CoA[p] => coenzyme A[p] + O-acetylcarnitine[p] YML042W 0.00 1000.00 0.00 r_0254 coenzyme A[m] + O-acetylcarnitine[m] => (R)-carnitine[m] + acetyl-CoA[m] YML042W 0.00 1000.00 0.00 @@ -275,7 +275,7 @@ r_0308 H2O[c] + L-cystathionine[c] => ammonium[c] + L-homocysteine[c] + pyruvate r_0309 L-homocysteine[c] + L-serine[c] => H2O[c] + L-cystathionine[c] YGR155W 0.00 1000.00 0.00 r_0310 H2O[c] + L-cystathionine[c] => 2-oxobutanoate[c] + ammonium[c] + L-cysteine[c] YAL012W 0.00 1000.00 0.00 r_0311 L-cysteine[c] + O-acetyl-L-homoserine[c] => acetate[c] + H+[c] + L-cystathionine[c] YJR130C 0.00 1000.00 0.00 -r_0312 hydrogen sulfide[c] + O-acetyl-L-serine[c] => acetate[c] + L-cysteine[c] YLR303W 0.00 1000.00 0.00 +r_0312 hydrogen sulfide[c] + O-acetyl-L-serine[c] => acetate[c] + L-cysteine[c] YLR303W 0.00 0.00 0.00 r_0313 ATP[c] + L-cysteine[c] + tRNA(Cys)[c] => AMP[c] + Cys-tRNA(Cys)[c] + diphosphate[c] YNL247W 0.00 1000.00 0.00 r_0314 cytidine[c] + H+[c] + H2O[c] => ammonium[c] + uridine[c] YLR245C 0.00 1000.00 0.00 r_0315 cytidine[c] + GTP[c] => CMP[c] + GDP[c] + H+[c] YNR012W 0.00 1000.00 0.00 @@ -369,7 +369,7 @@ r_0472 2-oxoglutarate[c] + H+[c] + L-glutamine[c] + NADH[c] => 2 L-glutamate[c] r_0473 H+[c] + L-gamma-glutamyl phosphate[c] + NADPH[c] => L-glutamic 5-semialdehyde[c] + NADP(+)[c] + phosphate[c] YOR323C 0.00 1000.00 0.00 r_0475 H2O[c] + L-glutamine[c] => ammonium[c] + L-glutamate[c] YFL060C or YNL334C 0.00 1000.00 0.00 r_0476 ammonium[c] + ATP[c] + L-glutamate[c] => ADP[c] + H+[c] + L-glutamine[c] + phosphate[c] YPR035W 0.00 1000.00 0.00 -r_0477 D-fructose 6-phosphate[c] + L-glutamine[c] => alpha-D-glucosamine 6-phosphate[c] + L-glutamate[c] YMR084W or YKL104C 0.00 1000.00 0.00 +r_0477 D-fructose 6-phosphate[c] + L-glutamine[c] => alpha-D-glucosamine 6-phosphate[c] + L-glutamate[c] YKL104C 0.00 1000.00 0.00 r_0478 ATP[c] + L-glutamine[c] + tRNA(Gln)[c] => AMP[c] + diphosphate[c] + Gln-tRNA(Gln)[c] YOR168W 0.00 1000.00 0.00 r_0479 ATP[c] + L-glutamate[c] + tRNA(Glu)[c] => AMP[c] + diphosphate[c] + Glu-tRNA(Glu)[c] YGL245W 0.00 1000.00 0.00 r_0480 ATP[m] + L-glutamate[m] + tRNA(Glu)[m] => AMP[m] + diphosphate[m] + Glu-tRNA(Glu)[m] YOL033W 0.00 1000.00 0.00 @@ -442,7 +442,6 @@ r_0555 4-hydroxybenzoate[m] + hexaprenyl diphosphate[m] => 3-hexaprenyl-4-hydrox r_0556 5-(2-hydroxyethyl)-4-methylthiazole[c] + ATP[c] => 4-methyl-5-(2-phosphonooxyethyl)thiazole[c] + ADP[c] + H+[c] YPL214C 0.00 1000.00 0.00 r_0557 H2O[c] + 4 porphobilinogen[c] => 4 ammonium[c] + preuroporphyrinogen[c] YDL205C 0.00 1000.00 0.00 r_0558 3-hydroxy-3-methylglutaryl-CoA[c] + 2 H+[c] + 2 NADPH[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W or YML075C 0.00 1000.00 0.00 -r_0559 acetoacetyl-CoA[c] + acetyl-CoA[c] + H2O[c] => 3-hydroxy-3-methylglutaryl-CoA[c] + coenzyme A[c] + H+[c] YML126C 0.00 1000.00 0.00 r_0560 acetoacetyl-CoA[m] + acetyl-CoA[m] + H2O[m] => 3-hydroxy-3-methylglutaryl-CoA[m] + coenzyme A[m] + H+[m] YML126C 0.00 1000.00 0.00 r_0561 4-amino-5-hydroxymethyl-2-methylpyrimidine[c] + ATP[c] => 4-amino-2-methyl-5-phosphomethylpyrimidine[c] + ADP[c] + H+[c] YOL055C or YPL258C or YPR121W 0.00 1000.00 0.00 r_0562 hypoxanthine[c] + PRPP[c] => diphosphate[c] + IMP[c] YDR399W 0.00 1000.00 0.00 @@ -654,7 +653,7 @@ r_0810 GDP[g] + H2O[g] => GMP[g] + H+[g] + phosphate[g] YEL042W 0.00 1000.00 r_0811 ATP[c] + UDP[c] => ADP[c] + UTP[c] YKL067W 0.00 1000.00 0.00 r_0812 methanethiol[c] + O-acetyl-L-homoserine[c] => acetate[c] + H+[c] + L-methionine[c] YLR303W 0.00 1000.00 0.00 r_0813 hydrogen sulfide[c] + O-acetyl-L-homoserine[c] => acetate[c] + L-homocysteine[c] YLR303W 0.00 1000.00 0.00 -r_0815 L-cysteine[c] + O-succinyl-L-homoserine[c] <=> H+[c] + L-cystathionine[c] + succinate[c] YLL058W or YML082W or YAL012W -1000.00 1000.00 0.00 +r_0815 L-cysteine[c] + O-succinyl-L-homoserine[c] => H+[c] + L-cystathionine[c] + succinate[c] YLL058W or YML082W or YAL012W 0.00 1000.00 0.00 r_0816 carbamoyl phosphate[c] + ornithine[c] => H+[c] + L-citrulline[c] + phosphate[c] YJL088W 0.00 1000.00 0.00 r_0817 H+[c] + ornithine[c] => carbon dioxide[c] + putrescine[c] YKL184W 0.00 1000.00 0.00 r_0818 L-glutamate[m] + N(2)-acetyl-L-ornithine[m] => N-acetyl-L-glutamate[m] + ornithine[m] YMR062C 0.00 1000.00 0.00 @@ -784,7 +783,7 @@ r_1022 ADP[m] + phosphate[m] + succinyl-CoA[m] => ATP[m] + coenzyme A[m] + succi r_1023 H2O[c] + NADP(+)[c] + succinic semialdehyde[c] => 2 H+[c] + NADPH[c] + succinate[c] YBR006W 0.00 1000.00 0.00 r_1024 H2O[e] + sucrose[e] => D-fructose[e] + D-glucose[e] YIL162W 0.00 1000.00 0.00 r_1025 ATP[c] + H+[c] + sulphate[c] => 5'-adenylyl sulfate[c] + diphosphate[c] YJR010W 0.00 1000.00 0.00 -r_1026 ADP[c] + H+[c] + sulphate[c] => 5'-adenylyl sulfate[c] + phosphate[c] YCL050C 0.00 1000.00 0.00 +r_1026 5'-adenylyl sulfate[c] + phosphate[c] => ADP[c] + H+[c] + sulphate[c] YCL050C 0.00 1000.00 0.00 r_1027 4 H+[c] + 3 NADPH[c] + sulphite[c] => 3 H2O[c] + hydrogen sulfide[c] + 3 NADP(+)[c] YFR030W and YJR137C 0.00 1000.00 0.00 r_1028 ATP[c] + H2O[c] + taurocholic acid[c] => ADP[c] + H+[c] + phosphate[c] + taurocholic acid[v] YLL048C 0.00 1000.00 0.00 r_1029 2-oxoglutarate[c] + oxygen[c] + taurine[c] => aminoacetaldehyde[c] + carbon dioxide[c] + H+[c] + succinate[c] + sulphite[c] YLL057C 0.00 1000.00 0.00 @@ -1467,8 +1466,6 @@ r_2066 TDP[e] => 0.00 1000.00 0.00 r_2067 thiamine[e] => 0.00 1000.00 0.00 r_2068 TMP[e] => 0.00 1000.00 0.00 r_2069 ATP[c] + TMP[c] => ADP[c] + TDP[c] 0.00 1000.00 0.00 -r_2070 H+[c] + L-cysteine[c] + L-glycine[c] + O-acetyl-L-homoserine[c] + ribose-5-phosphate[c] => 4-methyl-5-(2-phosphonooxyethyl)thiazole[c] + acetate[c] + ammonium[c] + carbon dioxide[c] + gamma-aminobutyrate[c] + 3 H2O[c] + pyruvate[c] 0.00 1000.00 0.00 -r_2071 D-xylulose 5-phosphate[c] + H+[c] + L-cysteine[c] + L-glycine[c] + O-acetyl-L-homoserine[c] => 4-methyl-5-(2-phosphonooxyethyl)thiazole[c] + acetate[c] + ammonium[c] + carbon dioxide[c] + gamma-aminobutyrate[c] + 3 H2O[c] + pyruvate[c] 0.00 1000.00 0.00 r_2072 L-threonine[c] => L-threonine[m] YDR508C 0.00 1000.00 0.00 r_2073 thymidine[e] => 0.00 1000.00 0.00 r_2074 ATP[c] + thymidine[c] => ADP[c] + dTMP[c] + H+[c] 0.00 1000.00 0.00 @@ -1865,14 +1862,14 @@ r_2484 phosphatidyl-L-serine (1-16:0, 2-18:1)[vm] => carbon dioxide[vm] + phosph r_2485 phosphatidyl-L-serine (1-16:1, 2-18:1)[vm] => carbon dioxide[vm] + phosphatidylethanolamine (1-16:1, 2-18:1)[vm] YGR170W 0.00 1000.00 0.00 r_2486 phosphatidyl-L-serine (1-18:0, 2-18:1)[vm] => carbon dioxide[vm] + phosphatidylethanolamine (1-18:0, 2-18:1)[vm] YGR170W 0.00 1000.00 0.00 r_2487 phosphatidyl-L-serine (1-18:1, 2-18:1)[vm] => carbon dioxide[vm] + phosphatidylethanolamine (1-18:1, 2-18:1)[vm] YGR170W 0.00 1000.00 0.00 -r_2488 phosphatidylethanolamine (1-16:0, 2-16:1)[erm] + S-adenosyl-L-methionine[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-16:0, 2-16:1)[erm] YGR157W or YJR073C 0.00 1000.00 0.00 -r_2489 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-16:1, 2-16:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-16:1, 2-16:1)[erm] YGR157W or YJR073C 0.00 1000.00 0.00 -r_2490 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-18:0, 2-16:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-18:0, 2-16:1)[erm] YGR157W or YJR073C 0.00 1000.00 0.00 -r_2491 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-18:1, 2-16:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-18:1, 2-16:1)[erm] YGR157W or YJR073C 0.00 1000.00 0.00 -r_2492 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-16:0, 2-18:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-16:0, 2-18:1)[erm] YGR157W or YJR073C 0.00 1000.00 0.00 -r_2493 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-16:1, 2-18:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-16:1, 2-18:1)[erm] YGR157W or YJR073C 0.00 1000.00 0.00 -r_2494 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-18:0, 2-18:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-18:0, 2-18:1)[erm] YGR157W or YJR073C 0.00 1000.00 0.00 -r_2495 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-18:1, 2-18:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-18:1, 2-18:1)[erm] YGR157W or YJR073C 0.00 1000.00 0.00 +r_2488 phosphatidylethanolamine (1-16:0, 2-16:1)[erm] + S-adenosyl-L-methionine[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-16:0, 2-16:1)[erm] YGR157W 0.00 1000.00 0.00 +r_2489 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-16:1, 2-16:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-16:1, 2-16:1)[erm] YGR157W 0.00 1000.00 0.00 +r_2490 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-18:0, 2-16:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-18:0, 2-16:1)[erm] YGR157W 0.00 1000.00 0.00 +r_2491 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-18:1, 2-16:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-18:1, 2-16:1)[erm] YGR157W 0.00 1000.00 0.00 +r_2492 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-16:0, 2-18:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-16:0, 2-18:1)[erm] YGR157W 0.00 1000.00 0.00 +r_2493 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-16:1, 2-18:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-16:1, 2-18:1)[erm] YGR157W 0.00 1000.00 0.00 +r_2494 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-18:0, 2-18:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-18:0, 2-18:1)[erm] YGR157W 0.00 1000.00 0.00 +r_2495 S-adenosyl-L-methionine[erm] + phosphatidylethanolamine (1-18:1, 2-18:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N-methylethanolamine (1-18:1, 2-18:1)[erm] YGR157W 0.00 1000.00 0.00 r_2496 S-adenosyl-L-methionine[erm] + phosphatidyl-N-methylethanolamine (1-16:0, 2-16:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N,N-dimethylethanolamine (1-16:0, 2-16:1)[erm] YJR073C 0.00 1000.00 0.00 r_2497 S-adenosyl-L-methionine[erm] + phosphatidyl-N-methylethanolamine (1-16:1, 2-16:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N,N-dimethylethanolamine (1-16:1, 2-16:1)[erm] YJR073C 0.00 1000.00 0.00 r_2498 S-adenosyl-L-methionine[erm] + phosphatidyl-N-methylethanolamine (1-18:0, 2-16:1)[erm] => H+[erm] + S-adenosyl-L-homocysteine[erm] + phosphatidyl-N,N-dimethylethanolamine (1-18:0, 2-16:1)[erm] YJR073C 0.00 1000.00 0.00 @@ -3414,7 +3411,7 @@ r_4044 melibiose[e] => 0.00 1000.00 0.00 r_4045 H2O[c] + uridine[c] => D-ribose[c] + uracil[c] YDR400W 0.00 1000.00 0.00 r_4046 ATP[c] + H2O[c] => ADP[c] + H+[c] + phosphate[c] 0.70 0.70 0.00 r_4047 0.52701 Ala-tRNA(Ala)[c] + 0.18459 Arg-tRNA(Arg)[c] + 0.11682 Asn-tRNA(Asn)[c] + 0.34173 Asp-tRNA(Asp)[c] + 0.0075813 Cys-tRNA(Cys)[c] + 0.12107 Gln-tRNA(Gln)[c] + 0.34667 Glu-tRNA(Glu)[c] + 0.33358 Gly-tRNA(Gly)[c] + 0.076157 His-tRNA(His)[c] + 0.22135 Ile-tRNA(Ile)[c] + 0.34047 Leu-tRNA(Leu)[c] + 0.32875 Lys-tRNA(Lys)[c] + 0.058238 Met-tRNA(Met)[c] + 0.15381 Phe-tRNA(Phe)[c] + 0.18919 Pro-tRNA(Pro)[c] + 0.21296 Ser-tRNA(Ser)[c] + 0.21986 Thr-tRNA(Thr)[c] + 0.032622 Trp-tRNA(Trp)[c] + 0.11716 Tyr-tRNA(Tyr)[c] + 0.30394 Val-tRNA(Val)[c] => 0.52701 tRNA(Ala)[c] + 0.18459 tRNA(Arg)[c] + 0.11682 tRNA(Asn)[c] + 0.34173 tRNA(Asp)[c] + 0.0075813 tRNA(Cys)[c] + 0.12107 tRNA(Gln)[c] + 0.34667 tRNA(Glu)[c] + 0.33358 tRNA(Gly)[c] + 0.076157 tRNA(His)[c] + 0.22135 tRNA(Ile)[c] + 0.34047 tRNA(Leu)[c] + 0.32875 tRNA(Lys)[c] + 0.058238 tRNA(Met)[c] + 0.15381 tRNA(Phe)[c] + 0.18919 tRNA(Pro)[c] + 0.21296 tRNA(Ser)[c] + 0.21986 tRNA(Thr)[c] + 0.032622 tRNA(Trp)[c] + 0.11716 tRNA(Tyr)[c] + 0.30394 tRNA(Val)[c] + protein[c] 0.00 1000.00 0.00 -r_4048 0.74851 (1->3)-beta-D-glucan[ce] + 0.25009 (1->6)-beta-D-glucan[ce] + 0.36141 glycogen[c] + 0.71094 mannan[c] + 0.13828 trehalose[c] => carbohydrate[c] 0.00 1000.00 0.00 +r_4048 0.73914 (1->3)-beta-D-glucan[ce] + 0.24696 (1->6)-beta-D-glucan[ce] + 0.02361 chitin[c] + 0.35689 glycogen[c] + 0.70204 mannan[c] + 0.13655 trehalose[c] => carbohydrate[c] 0.00 1000.00 0.00 r_4049 0.044535 AMP[c] + 0.043276 CMP[c] + 0.044535 GMP[c] + 0.057992 UMP[c] => RNA[c] 0.00 1000.00 0.00 r_4050 0.0036 dAMP[c] + 0.0024 dCMP[c] + 0.0024 dGMP[c] + 0.0036 dTMP[c] => DNA[c] 0.00 1000.00 0.00 r_4051 ceramide backbone[g] => ceramide backbone[c] 0.00 1000.00 0.00 @@ -3949,7 +3946,7 @@ r_4594 Cu2(+)[e] <=> -1000.00 1000.00 0.00 r_4595 Mn(2+)[e] <=> -1000.00 1000.00 0.00 r_4596 Zn(2+)[e] <=> -1000.00 1000.00 0.00 r_4597 Mg(2+)[e] <=> -1000.00 1000.00 0.00 -r_4598 0.00019 coenzyme A[c] + 1e-05 FAD[c] + 0.00265 NAD[c] + 0.00015 NADH[c] + 0.00057 NADP(+)[c] + 0.0027 NADPH[c] + 0.00099 riboflavin[c] + 1.2e-06 TDP[c] + 6.34e-05 THF[c] + 1e-06 heme a[c] => cofactor[c] 0.00 1000.00 0.00 +r_4598 0.00019 coenzyme A[c] + 1e-05 FAD[c] + 1e-06 glutathione[c] + 0.00265 NAD[c] + 0.00015 NADH[c] + 0.00057 NADP(+)[c] + 0.0027 NADPH[c] + 0.00099 riboflavin[c] + 1.2e-06 TDP[c] + 6.34e-05 THF[c] + 1e-06 heme a[c] => cofactor[c] 0.00 1000.00 0.00 r_4599 3.04e-05 iron(2+)[c] + 0.00363 potassium[c] + 0.00397 sodium[c] + 0.02 sulphate[c] + 0.00129 chloride[c] + 0.00273 Mn(2+)[c] + 0.000748 Zn(2+)[c] + 0.000217 Ca(2+)[c] + 0.0012425 Mg(2+)[c] + 0.000659 Cu2(+)[c] => ion[c] 0.00 1000.00 0.00 r_4600 Ca(2+)[e] <=> -1000.00 1000.00 0.00 r_4601 3-(4-hydroxyphenyl)pyruvate[c] + H+[c] <=> 3-(4-hydroxyphenyl)pyruvate[p] + H+[p] -1000.00 1000.00 0.00 @@ -4053,7 +4050,7 @@ r_4699 ethyl propionate[e] => 0.00 1000.00 0.00 r_4700 hydrogen sulfide[c] => hydrogen sulfide[e] YIL166C 0.00 1000.00 0.00 r_4701 H2O[m] + L-cysteine[m] <=> ammonium[m] + pyruvate[m] + hydrogen sulfide[m] YFR055W -1000.00 1000.00 0.00 r_4702 2-oxoglutarate[c] + L-cysteine[c] <=> L-glutamate[c] + 3-mercaptopyruvate[c] -1000.00 1000.00 0.00 -r_4703 TRX1[c] + 3-mercaptopyruvate[c] <=> hydrogen sulfide[c] + pyruvate[c] + TRX1 disulphide[c] YOR251C -1000.00 1000.00 0.00 +r_4703 TRX1[c] + 3-mercaptopyruvate[c] => hydrogen sulfide[c] + pyruvate[c] + TRX1 disulphide[c] YOR251C 0.00 1000.00 0.00 r_4704 alkanesulfonate[e] => alkanesulfonate[c] YIL166C 0.00 1000.00 0.00 r_4705 taurocholate[e] => taurocholate[c] YIL166C 0.00 1000.00 0.00 r_4706 2-oxoglutarate[c] + oxygen[c] + alkanesulfonate[c] <=> aminoacetaldehyde[c] + carbon dioxide[c] + succinate[c] + sulphite[c] YLL057C -1000.00 1000.00 0.00 @@ -4129,3 +4126,7 @@ r_4775 ATP[m] + GDP[m] => ADP[m] + GTP[m] YKL067W 0.00 1000.00 0.00 r_4776 ATP[m] + IDP[m] => ADP[m] + ITP[m] YKL067W 0.00 1000.00 0.00 r_4777 ATP[m] + dIDP[m] <=> ADP[m] + dITP[m] YKL067W -1000.00 1000.00 0.00 r_4778 ATP[m] + dUDP[m] <=> ADP[m] + dUTP[m] YKL067W -1000.00 1000.00 0.00 +r_4779 heme a[c] <=> heme a[e] -1000.00 1000.00 0.00 +r_4780 heme a[e] => 0.00 1000.00 0.00 +r_4781 H2O[c] + ADP-5-ethyl-4-methylthiazole-2-carboxylate[c] => 4-methyl-5-(2-phosphonooxyethyl)thiazole[c] + AMP[c] + carbon dioxide[c] + H+[c] YGR144W 0.00 1000.00 0.00 +r_4782 hydrogen sulfide[c] + L-glycine[c] + NAD[c] => H+[c] + 3 H2O[c] + nicotinamide[c] + ADP-5-ethyl-4-methylthiazole-2-carboxylate[c] YGR144W 0.00 1000.00 0.00 diff --git a/model/yeast-GEM.xlsx b/model/yeast-GEM.xlsx index ecad9c1d..bd635876 100644 Binary files a/model/yeast-GEM.xlsx and b/model/yeast-GEM.xlsx differ diff --git a/model/yeast-GEM.xml b/model/yeast-GEM.xml index dd4a04aa..7c0ab706 100644 --- a/model/yeast-GEM.xml +++ b/model/yeast-GEM.xml @@ -1,6 +1,6 @@ - + Saccharomyces cerevisiae - strain S288C @@ -8,7 +8,7 @@ - + @@ -24,10 +24,10 @@ - 2024-08-14T16:00:24Z + 2024-11-23T16:58:52Z - 2024-08-14T16:00:24Z + 2024-11-23T16:58:52Z @@ -63,10 +63,10 @@ - + - + @@ -79,10 +79,10 @@ - + - + @@ -95,10 +95,10 @@ - + - + @@ -111,10 +111,10 @@ - + - + @@ -127,10 +127,10 @@ - + - + @@ -143,10 +143,10 @@ - + - + @@ -159,10 +159,10 @@ - + - + @@ -175,10 +175,10 @@ - + - + @@ -191,10 +191,10 @@ - + - + @@ -207,10 +207,10 @@ - + - + @@ -223,10 +223,10 @@ - + - + @@ -239,10 +239,10 @@ - + - + @@ -253,10 +253,10 @@ - + - + @@ -267,10 +267,10 @@ - + - + @@ -283,10 +283,10 @@ - + - + @@ -299,10 +299,10 @@ - + - + @@ -315,10 +315,10 @@ - + - + @@ -331,10 +331,10 @@ - + - + @@ -347,10 +347,10 @@ - + - + @@ -363,10 +363,10 @@ - + - + @@ -379,10 +379,10 @@ - + - + @@ -395,10 +395,10 @@ - + - + @@ -411,10 +411,10 @@ - + - + @@ -427,10 +427,10 @@ - + - + @@ -443,10 +443,10 @@ - + - + @@ -459,10 +459,10 @@ - + - + @@ -475,10 +475,10 @@ - + - + @@ -491,10 +491,10 @@ - + - + @@ -507,10 +507,10 @@ - + - + @@ -523,10 +523,10 @@ - + - + @@ -539,10 +539,10 @@ - + - + @@ -555,10 +555,10 @@ - + - + @@ -571,10 +571,10 @@ - + - + @@ -587,10 +587,10 @@ - + - + @@ -603,10 +603,10 @@ - + - + @@ -619,10 +619,10 @@ - + - + @@ -635,10 +635,10 @@ - + - + @@ -651,10 +651,10 @@ - + - + @@ -667,10 +667,10 @@ - + - + @@ -683,10 +683,10 @@ - + - + @@ -697,10 +697,10 @@ - + - + @@ -713,10 +713,10 @@ - + - + @@ -729,10 +729,10 @@ - + - + @@ -745,10 +745,10 @@ - + - + @@ -761,10 +761,10 @@ - + - + @@ -777,10 +777,10 @@ - + - + @@ -793,10 +793,10 @@ - + - + @@ -809,10 +809,10 @@ - + - + @@ -825,10 +825,10 @@ - + - + @@ -841,10 +841,10 @@ - + - + @@ -857,10 +857,10 @@ - + - + @@ -873,10 +873,10 @@ - + - + @@ -889,10 +889,10 @@ - + - + @@ -905,10 +905,10 @@ - + - + @@ -921,10 +921,10 @@ - + - + @@ -937,10 +937,10 @@ - + - + @@ -953,10 +953,10 @@ - + - + @@ -969,10 +969,10 @@ - + - + @@ -985,10 +985,10 @@ - + - + @@ -1001,10 +1001,10 @@ - + - + @@ -1017,10 +1017,10 @@ - + - + @@ -1033,10 +1033,10 @@ - + - + @@ -1049,10 +1049,10 @@ - + - + @@ -1065,10 +1065,10 @@ - + - + @@ -1081,10 +1081,10 @@ - + - + @@ -1097,10 +1097,10 @@ - + - + @@ -1113,10 +1113,10 @@ - + - + @@ -1129,10 +1129,10 @@ - + - + @@ -1145,10 +1145,10 @@ - + - + @@ -1161,10 +1161,10 @@ - + - + @@ -1177,10 +1177,10 @@ - + - + @@ -1193,10 +1193,10 @@ - + - + @@ -1209,10 +1209,10 @@ - + - + @@ -1225,10 +1225,10 @@ - + - + @@ -1241,10 +1241,10 @@ - + - + @@ -1257,10 +1257,10 @@ - + - + @@ -1273,10 +1273,10 @@ - + - + @@ -1289,10 +1289,10 @@ - + - + @@ -1305,10 +1305,10 @@ - + - + @@ -1321,10 +1321,10 @@ - + - + @@ -1337,10 +1337,10 @@ - + - + @@ -1353,10 +1353,10 @@ - + - + @@ -1369,10 +1369,10 @@ - + - + @@ -1385,10 +1385,10 @@ - + - + @@ -1401,10 +1401,10 @@ - + - + @@ -1417,10 +1417,10 @@ - + - + @@ -1433,10 +1433,10 @@ - + - + @@ -1449,10 +1449,10 @@ - + - + @@ -1465,10 +1465,10 @@ - + - + @@ -1481,10 +1481,10 @@ - + - + @@ -1497,10 +1497,10 @@ - + - + @@ -1513,10 +1513,10 @@ - + - + @@ -1529,10 +1529,10 @@ - + - + @@ -1545,10 +1545,10 @@ - + - + @@ -1560,10 +1560,10 @@ - + - + @@ -1576,10 +1576,10 @@ - + - + @@ -1592,10 +1592,10 @@ - + - + @@ -1608,10 +1608,10 @@ - + - + @@ -1624,10 +1624,10 @@ - + - + @@ -1640,10 +1640,10 @@ - + - + @@ -1656,10 +1656,10 @@ - + - + @@ -1672,10 +1672,10 @@ - + - + @@ -1688,10 +1688,10 @@ - + - + @@ -1704,10 +1704,10 @@ - + - + @@ -1720,10 +1720,10 @@ - + - + @@ -1736,10 +1736,10 @@ - + - + @@ -1751,10 +1751,10 @@ - + - + @@ -1767,10 +1767,10 @@ - + - + @@ -1783,10 +1783,10 @@ - + - + @@ -1799,10 +1799,10 @@ - + - + @@ -1815,10 +1815,10 @@ - + - + @@ -1831,10 +1831,10 @@ - + - + @@ -1847,10 +1847,10 @@ - + - + @@ -1863,10 +1863,10 @@ - + - + @@ -1878,10 +1878,10 @@ - + - + @@ -1893,10 +1893,10 @@ - + - + @@ -1908,10 +1908,10 @@ - + - + @@ -1923,10 +1923,10 @@ - + - + @@ -1938,10 +1938,10 @@ - + - + @@ -1954,10 +1954,10 @@ - + - + @@ -1970,10 +1970,10 @@ - + - + @@ -1986,10 +1986,10 @@ - + - + @@ -2002,10 +2002,10 @@ - + - + @@ -2018,10 +2018,10 @@ - + - + @@ -2034,10 +2034,10 @@ - + - + @@ -2050,10 +2050,10 @@ - + - + @@ -2066,10 +2066,10 @@ - + - + @@ -2082,10 +2082,10 @@ - + - + @@ -2098,10 +2098,10 @@ - + - + @@ -2114,10 +2114,10 @@ - + - + @@ -2130,10 +2130,10 @@ - + - + @@ -2146,10 +2146,10 @@ - + - + @@ -2162,10 +2162,10 @@ - + - + @@ -2178,10 +2178,10 @@ - + - + @@ -2194,10 +2194,10 @@ - + - + @@ -2210,10 +2210,10 @@ - + - + @@ -2226,10 +2226,10 @@ - + - + @@ -2242,10 +2242,10 @@ - + - + @@ -2258,10 +2258,10 @@ - + - + @@ -2274,10 +2274,10 @@ - + - + @@ -2290,10 +2290,10 @@ - + - + @@ -2306,10 +2306,10 @@ - + - + @@ -2322,10 +2322,10 @@ - + - + @@ -2338,10 +2338,10 @@ - + - + @@ -2354,10 +2354,10 @@ - + - + @@ -2370,10 +2370,10 @@ - + - + @@ -2386,10 +2386,10 @@ - + - + @@ -2402,10 +2402,10 @@ - + - + @@ -2417,10 +2417,10 @@ - + - + @@ -2433,10 +2433,10 @@ - + - + @@ -2449,10 +2449,10 @@ - + - + @@ -2465,10 +2465,10 @@ - + - + @@ -2481,10 +2481,10 @@ - + - + @@ -2497,10 +2497,10 @@ - + - + @@ -2513,10 +2513,10 @@ - + - + @@ -2529,10 +2529,10 @@ - + - + @@ -2543,10 +2543,10 @@ - + - + @@ -2559,10 +2559,10 @@ - + - + @@ -2575,10 +2575,10 @@ - + - + @@ -2591,10 +2591,10 @@ - + - + @@ -2607,10 +2607,10 @@ - + - + @@ -2623,10 +2623,10 @@ - + - + @@ -2639,10 +2639,10 @@ - + - + @@ -2655,10 +2655,10 @@ - + - + @@ -2671,10 +2671,10 @@ - + - + @@ -2687,10 +2687,10 @@ - + - + @@ -2703,10 +2703,10 @@ - + - + @@ -2719,10 +2719,10 @@ - + - + @@ -2735,10 +2735,10 @@ - + - + @@ -2750,10 +2750,10 @@ - + - + @@ -2766,10 +2766,10 @@ - + - + @@ -2782,10 +2782,10 @@ - + - + @@ -2798,10 +2798,10 @@ - + - + @@ -2814,10 +2814,10 @@ - + - + @@ -2830,10 +2830,10 @@ - + - + @@ -2846,10 +2846,10 @@ - + - + @@ -2862,10 +2862,10 @@ - + - + @@ -2878,10 +2878,10 @@ - + - + @@ -2894,10 +2894,10 @@ - + - + @@ -2908,10 +2908,10 @@ - + - + @@ -2924,10 +2924,10 @@ - + - + @@ -2940,10 +2940,10 @@ - + - + @@ -2956,10 +2956,10 @@ - + - + @@ -2972,10 +2972,10 @@ - + - + @@ -2988,10 +2988,10 @@ - + - + @@ -3004,10 +3004,10 @@ - + - + @@ -3020,10 +3020,10 @@ - + - + @@ -3036,10 +3036,10 @@ - + - + @@ -3052,10 +3052,10 @@ - + - + @@ -3068,10 +3068,10 @@ - + - + @@ -3083,10 +3083,10 @@ - + - + @@ -3099,10 +3099,10 @@ - + - + @@ -3115,10 +3115,10 @@ - + - + @@ -3131,10 +3131,10 @@ - + - + @@ -3147,10 +3147,10 @@ - + - + @@ -3163,10 +3163,10 @@ - + - + @@ -3179,10 +3179,10 @@ - + - + @@ -3195,10 +3195,10 @@ - + - + @@ -3211,10 +3211,10 @@ - + - + @@ -3227,10 +3227,10 @@ - + - + @@ -3243,10 +3243,10 @@ - + - + @@ -3259,10 +3259,10 @@ - + - + @@ -3275,10 +3275,10 @@ - + - + @@ -3291,10 +3291,10 @@ - + - + @@ -3307,10 +3307,10 @@ - + - + @@ -3323,10 +3323,10 @@ - + - + @@ -3338,10 +3338,10 @@ - + - + @@ -3354,10 +3354,10 @@ - + - + @@ -3370,10 +3370,10 @@ - + - + @@ -3386,10 +3386,10 @@ - + - + @@ -3402,10 +3402,10 @@ - + - + @@ -3418,10 +3418,10 @@ - + - + @@ -3434,10 +3434,10 @@ - + - + @@ -3450,10 +3450,10 @@ - + - + @@ -3466,10 +3466,10 @@ - + - + @@ -3482,10 +3482,10 @@ - + - + @@ -3498,10 +3498,10 @@ - + - + @@ -3514,10 +3514,10 @@ - + - + @@ -3528,10 +3528,10 @@ - + - + @@ -3544,10 +3544,10 @@ - + - + @@ -3560,10 +3560,10 @@ - + - + @@ -3576,10 +3576,10 @@ - + - + @@ -3592,10 +3592,10 @@ - + - + @@ -3608,10 +3608,10 @@ - + - + @@ -3624,10 +3624,10 @@ - + - + @@ -3640,10 +3640,10 @@ - + - + @@ -3656,10 +3656,10 @@ - + - + @@ -3672,10 +3672,10 @@ - + - + @@ -3688,10 +3688,10 @@ - + - + @@ -3704,10 +3704,10 @@ - + - + @@ -3720,10 +3720,10 @@ - + - + @@ -3736,10 +3736,10 @@ - + - + @@ -3752,10 +3752,10 @@ - + - + @@ -3768,10 +3768,10 @@ - + - + @@ -3784,10 +3784,10 @@ - + - + @@ -3800,10 +3800,10 @@ - + - + @@ -3816,10 +3816,10 @@ - + - +
Saccharomyces cerevisiae - strain S288C