diff --git a/ComplementaryData/modelCuration/Metabolomics_newRxnMatrix.tsv b/ComplementaryData/modelCuration/Metabolomics_newRxnMatrix.tsv new file mode 100644 index 00000000..05a0265e --- /dev/null +++ b/ComplementaryData/modelCuration/Metabolomics_newRxnMatrix.tsv @@ -0,0 +1,96 @@ +ID coefficient standard_name type compartment +MNXR111769 1 2-hydroxyglutarate reactant cytoplasm +MNXR111769 1 NAD reactant cytoplasm +MNXR111769 1 H+ product cytoplasm +MNXR111769 1 NADH product cytoplasm +MNXR111769 1 2-oxoglutarate product cytoplasm +MNXR134240 1 2-hydroxyglutarate reactant cytoplasm +MNXR134240 3 H+ product cytoplasm +MNXR134240 1 glyoxylate product cytoplasm +MNXR134240 1 propionyl-CoA product cytoplasm +MNXR95862 1 beta-alanine reactant cytoplasm +MNXR95862 1 2-oxoglutarate reactant cytoplasm +MNXR95862 1 3-oxopropanoate product cytoplasm +MNXR95862 1 L-glutamate product cytoplasm +MNXR101665 1 coenzyme A reactant cytoplasm +MNXR101665 1 3-oxopropanoate reactant cytoplasm +MNXR101665 1 NAD reactant cytoplasm +MNXR101665 1 NADH product cytoplasm +MNXR101665 1 carbon dioxide product cytoplasm +MNXR101665 1 acetyl-CoA product cytoplasm +MNXR106650 1 coenzyme A reactant cytoplasm +MNXR106650 1 3-oxopropanoate reactant cytoplasm +MNXR106650 1 NADP(+) reactant cytoplasm +MNXR106650 1 carbon dioxide product cytoplasm +MNXR106650 1 acetyl-CoA product cytoplasm +MNXR106650 1 NADPH product cytoplasm +MNXR110693 1 H+ reactant cytoplasm +MNXR110693 1 3-oxopropanoate reactant cytoplasm +MNXR110693 1 carbon dioxide product cytoplasm +MNXR110693 1 acetaldehyde product cytoplasm +MNXR100904 1 (R)-2,3-dihydroxy-3-methylbutanoate reactant cytoplasm +MNXR100904 1 NADP(+) reactant cytoplasm +MNXR100904 1 H+ product cytoplasm +MNXR100904 1 3-hydroxy-3-methyl-2-oxobutanoate product cytoplasm +MNXR100904 1 NADPH product cytoplasm +MNXR137278 1 3-methyl-2-oxobutanoate reactant cytoplasm +MNXR137278 1 3-hydroxy-3-methyl-2-oxobutanoate product cytoplasm +MNXR137279 1 2-acetyllactic acid reactant cytoplasm +MNXR137279 1 NADPH reactant cytoplasm +MNXR137279 1 H+ product cytoplasm +MNXR137279 1 3-hydroxy-3-methyl-2-oxobutanoate product cytoplasm +MNXR137279 1 NADP(+) product cytoplasm +MNXR95271 1 H+ reactant cytoplasm +MNXR95271 2 pyruvate reactant cytoplasm +MNXR95271 1 (2S)-2-acetolactate product cytoplasm +MNXR95271 1 carbon dioxide product cytoplasm +MNXR100390 1 H+ reactant cytoplasm +MNXR100390 1 6-phospho-D-gluconate reactant cytoplasm +MNXR100390 1 ADP reactant cytoplasm +MNXR100390 1 ATP product cytoplasm +MNXR100390 1 D-gluconate product cytoplasm +MNXR97523 1 (R)-2,3-dihydroxy-3-methylbutanoate reactant cytoplasm +MNXR97523 1 NADP(+) reactant cytoplasm +MNXR97523 1 H+ product cytoplasm +MNXR97523 1 (2S)-2-acetolactate product cytoplasm +MNXR97523 1 NADPH product cytoplasm +MNXR106779 1 (2R,3S)-3-methylmalate reactant cytoplasm +MNXR106779 1 NAD reactant cytoplasm +MNXR106779 1 NADH product cytoplasm +MNXR106779 1 carbon dioxide product cytoplasm +MNXR106779 1 2-oxobutanoate product cytoplasm +MNXR121603 1 H2O reactant cytoplasm +MNXR121603 1 glyoxylate reactant cytoplasm +MNXR121603 1 propionyl-CoA reactant cytoplasm +MNXR121603 1 H+ product cytoplasm +MNXR121603 1 coenzyme A product cytoplasm +MNXR121603 1 (2R,3S)-3-methylmalate product cytoplasm +MNXR99136 1 H2O reactant cytoplasm +MNXR99136 1 trans-2,cis-9-octadecadienoyl-CoA reactant cytoplasm +MNXR99136 1 H+ product cytoplasm +MNXR99136 1 coenzyme A product cytoplasm +MNXR99136 1 (9Z,12Z)-octadecadienoate product cytoplasm +MNXR99175 1 coenzyme A reactant cytoplasm +MNXR99175 1 (9Z,12Z)-octadecadienoate reactant cytoplasm +MNXR99175 1 ATP reactant cytoplasm +MNXR99175 1 diphosphate product cytoplasm +MNXR99175 1 AMP product cytoplasm +MNXR99175 1 trans-2,cis-9-octadecadienoyl-CoA product cytoplasm +MNXR100010 1 stachyose reactant cytoplasm +MNXR100010 1 H2O reactant cytoplasm +MNXR100010 1 D-galactose product cytoplasm +MNXR100010 1 raffinose product cytoplasm +MNXR122225 2 raffinose product cytoplasm +MNXR122225 1 stachyose reactant cytoplasm +MNXR122225 1 sucrose reactant cytoplasm +MNXR123213 1 6-phospho-D-gluconate reactant cytoplasm +MNXR123213 1 D-gluconate product cytoplasm +MNXR123213 1 phosphate product cytoplasm +MNXR110535 1 H+ reactant cytoplasm +MNXR110535 1 phenylacetic acid reactant cytoplasm +MNXR110535 1 4-hydroxyphenyl acetate product cytoplasm +MNXR110621 1 H+ reactant cytoplasm +MNXR110621 1 acetate reactant cytoplasm +MNXR110621 1 Hydroquinone reactant cytoplasm +MNXR110621 1 H2O product cytoplasm +MNXR110621 1 4-hydroxyphenyl acetate product cytoplasm diff --git a/ComplementaryData/modelCuration/Metabolomics_newRxnMetAnnotation.tsv b/ComplementaryData/modelCuration/Metabolomics_newRxnMetAnnotation.tsv new file mode 100644 index 00000000..9251889c --- /dev/null +++ b/ComplementaryData/modelCuration/Metabolomics_newRxnMetAnnotation.tsv @@ -0,0 +1,15 @@ +NewMetName Charged formula Charge compartment KEGG ID CHEBI ID Remark Ref +2-hydroxyglutarate [cytoplasm] C5H6O5 -2 cytoplasm C02630 CHEBI:11596 MNXM1210 DOI: 10.1002/biot.201500613; DOI: 10.1021/ac302881e; DOI: 10.1186/jbiol54 +propionyl-CoA [cytoplasm] C24H36N7O17P3S -4 cytoplasm C00100 CHEBI:57392 MNXM86 exist in model, but in another compartment +3-oxopropanoate [cytoplasm] C3H3O3 -1 cytoplasm C00222 CHEBI:33190 MNXM244 DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x +(R)-2,3-dihydroxy-3-methylbutanoate [cytoplasm] C5H9O4 -1 cytoplasm C04272 CHEBI:49072 MNXM114097 exist in model, but in another compartment +3-hydroxy-3-methyl-2-oxobutanoate [cytoplasm] C5H7O4 -1 cytoplasm C04181 CHEBI:11812 MNXM1638 DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x +2-acetyllactic acid [cytoplasm] C5H7O4 -1 cytoplasm C00900 CHEBI:57774 MNXM426 exist in model, but in another compartment +(2S)-2-acetolactate [cytoplasm] C5H7O4 -1 cytoplasm C06010 CHEBI:58476 MNXM114079 DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x +(2R,3S)-3-methylmalate [cytoplasm] C5H6O5 -2 cytoplasm C06032 CHEBI:58511 MNXM2512 DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x +trans-2,cis-9-octadecadienoyl-CoA [cytoplasm] C39H62N7O17P3S -4 cytoplasm C02050 CHEBI:57383 MNXM638 exist in model, but in another compartment +(9Z,12Z)-octadecadienoate [cytoplasm] C18H31O2 -1 cytoplasm C01595 CHEBI:30245 MNXM293 DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x; DOI: 10.1016/j.procbio.2017.04.003; DOI: 10.1038/srep42659 +stachyose [cytoplasm] C24H42O21 0 cytoplasm C01613 CHEBI:17164 MNXM1503 DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x +raffinose [cytoplasm] C18H32O16 0 cytoplasm C00492 CHEBI:16634 MNXM621 exist in model, but in another compartment +4-hydroxyphenyl acetate [cytoplasm] C8H8O3 0 cytoplasm C00642 CHEBI:18101 MNXM3863 DOI: 10.1186/s12918-016-0350-8; DOI: 10.1007/s11306-017-1195-x +Hydroquinone [cytoplasm] C6H6O2 0 cytoplasm C00530 CHEBI:17594 MNXM376 exist in model, but in another compartment diff --git a/ComplementaryData/modelCuration/Metabolomics_newRxnProp.tsv b/ComplementaryData/modelCuration/Metabolomics_newRxnProp.tsv new file mode 100644 index 00000000..bc885bfd --- /dev/null +++ b/ComplementaryData/modelCuration/Metabolomics_newRxnProp.tsv @@ -0,0 +1,22 @@ +RxnID rev RxnName EC rxnID_kegg Source +MNXR100390 0 ATP:D-Gluconate 6-phosphotransferase 2.7.1.12 R01737 rhea:19433 +MNXR123213 0 6-phosphogluconate phosphatase 3.1.3.-;3.1.3.2;3.1.3.29 metacyc:RXN0-5185 +MNXR110535 0 R06790 R06790 seed:rxn04605 +MNXR110621 0 Carboxylic ester hydrolases 3.1.1.-;3.1.1.2 rhea:47384 +MNXR111769 1 phosphoglycerate dehydrogenase 1.1.1.95 R08198 rhea:13449 +MNXR134240 1 seed:rxn00681 seed:rxn00681 +MNXR95862 1 beta-alanine:2-oxoglutarate aminotransferase 2.6.1.19;2.6.1.55 R00908 rhea:30699 +MNXR101665 0 3-Oxopropanoate:NAD+ oxidoreductase (decarboxylating, CoA-acetylating) 1.2.1.-;1.2.1.18;1.2.1.27 R00705 rhea:22992 +MNXR106650 0 3-Oxopropanoate:NADP+ oxidoreductase (decarboxylating, CoA-acetylating) 1.2.1.-;1.2.1.18 R00706 rhea:22988 +MNXR110693 0 3-oxopropanoate carboxy-lyase 4.1.1.-;4.2.1.155 R06973 rhea:45160 +MNXR100904 1 (R)-2,3-Dihydroxy-3-methylbutanoate:NADP+ oxidoreductase (isomerizing) 1.1.1.86 R04440 rhea:31139 +MNXR137278 0 Dihydroxy-acid dehydratase, mitochondrial seed:rxn13007 +MNXR137279 0 Ketol-acid reductoisomerase, mitochondrial seed:rxn13008 +MNXR95271 0 pyruvate:pyruvate acetaldehydetransferase (decarboxylating); (S)-2-acetolactate pyruvate-lyase (carboxylating) 2.2.1.6 R00226 rhea:25249 +MNXR97523 1 (R)-2,3-dihydroxy-3-methylbutanoate:NADP+ oxidoreductase (isomerizing) 1.1.1.383;1.1.1.86 R04439 rhea:22068 +MNXR106779 0 (2R,3S)-3-methylmalate:NAD+ oxidoreductase 1.1.1.-;1.1.1.85 R00994 rhea:32715 +MNXR121603 0 malate/β-methylmalate synthase 2.3.3.- metacyc:RXN-18333 +MNXR99136 0 palmitoyl-CoA hydrolase 3.1.2.-;3.1.2.2 rhea:40143 +MNXR99175 0 long-chain-fatty-acid---CoA ligase 6.2.1.3 rhea:33651 +MNXR100010 0 a-galactosidase (stachyose) 3.2.1.22 seed:rxn02596 +MNXR122225 0 stachyose synthase 2.4.1.- metacyc:RXN-8287 diff --git a/ComplementaryData/modelCuration/Biolog_Substrate.tsv b/ComplementaryData/physiology/Biolog_Substrate.tsv similarity index 100% rename from ComplementaryData/modelCuration/Biolog_Substrate.tsv rename to ComplementaryData/physiology/Biolog_Substrate.tsv diff --git a/ComplementaryData/physiology/biomassComposition_Forster2003.tsv b/ComplementaryData/physiology/biomassComposition_Forster2003.tsv new file mode 100644 index 00000000..06a18b45 --- /dev/null +++ b/ComplementaryData/physiology/biomassComposition_Forster2003.tsv @@ -0,0 +1,38 @@ +model_id name abundance_mmol/gDW MW_g/mol group +s_0001[ce] (1->3)-beta-D-glucan 0.8506 180.16 carbohydrate +s_0004[ce] (1->6)-beta-D-glucan 0.2842 180.16 carbohydrate +s_0404[c] alanine 0.4588 89.09 protein +s_0423[c] AMP 0.046 347.22 RNA +s_0428[c] arginine 0.1607 174.2 protein +s_0430[c] asparagine 0.1017 132.12 protein +s_0432[c] aspartic acid 0.2975 133.11 protein +s_0509[c] chitin 0.000001 221.21 carbohydrate +s_0526[c] CMP 0.0447 323.2 RNA +s_0542[c] cysteine 0.0066 121.16 protein +s_0584[c] dAMP 0.0036 331.22 DNA +s_0589[c] dCMP 0.0024 307.2 DNA +s_0615[c] dGMP 0.0024 345.21 DNA +s_0649[c] dTMP 0.0036 322.21 DNA +s_0747[c] glutamine 0.1054 146.14 protein +s_0748[c] glutamic acid 0.3018 147.13 protein +s_0757[c] glycine 0.2904 75.07 protein +s_0773[c] glycogen 0.5185 180.16 carbohydrate +s_0782[c] GMP 0.046 363.22 RNA +s_0832[c] histidine 0.0663 155.15 protein +s_0847[c] isoleucine 0.1927 131.17 protein +s_1077[c] leucine 0.2964 131.17 protein +s_1099[c] lysine 0.2862 146.19 protein +s_1107[c] mannan 0.8079 180.16 carbohydrate +s_1148[c] methionine 0.0507 149.21 protein +s_1314[c] Phenylalanine 0.1339 165.19 protein +s_1379[c] proline 0.1647 115.13 protein +s_1405[c] riboflavin 0.00099 376.36 other +s_1428[c] serine 0.1854 105.09 protein +s_1467[c] sulphate 0.02 96.06 other +s_1491[c] threonine 0.1914 119.12 protein +s_1520[c] trehalose 0.0234 342.296 carbohydrate +s_1527[c] tryptophan 0.0284 204.23 protein +s_1533[c] tyrosine 0.102 181.19 protein +s_1545[c] UMP 0.0599 324.18 RNA +s_1561[c] valine 0.2646 117.15 protein +s_3714[c] heme a 0.000001 852.83 other diff --git a/ComplementaryData/physiology/biomassComposition_Lahtvee2017.tsv b/ComplementaryData/physiology/biomassComposition_Lahtvee2017.tsv new file mode 100644 index 00000000..5ff428c4 --- /dev/null +++ b/ComplementaryData/physiology/biomassComposition_Lahtvee2017.tsv @@ -0,0 +1,9 @@ +model_id name abundance_g/gDW +s_1520[c] trehalose 0.050958 +s_0773[c] glycogen 0.0666 +s_3717[c] protein 0.46 +s_3719[c] RNA 0.061 +s_3740[c] C16:0chain 0.00808584 +s_3741[c] C16:1chain 0.02373021 +s_3742[c] C18:0chain 0.002266316 +s_3743[c] C18:1chain 0.008706639 diff --git a/ComplementaryData/physiology/chemostatData_VanHoek1998.tsv b/ComplementaryData/physiology/chemostatData_VanHoek1998.tsv new file mode 100644 index 00000000..fee00763 --- /dev/null +++ b/ComplementaryData/physiology/chemostatData_VanHoek1998.tsv @@ -0,0 +1,5 @@ +Drate GlucoseUptake O2uptake CO2production +0.025 0.30 0.80 0.80 +0.05 0.60 1.30 1.40 +0.10 1.10 2.50 2.70 +0.15 1.70 3.90 4.20 diff --git a/ComplementaryScripts/increaseVersion.m b/ComplementaryScripts/increaseVersion.m index 88542d1a..e18ed12a 100644 --- a/ComplementaryScripts/increaseVersion.m +++ b/ComplementaryScripts/increaseVersion.m @@ -1,10 +1,19 @@ -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% increaseVersion(bumpType) -% -% Benjamín J. Sánchez -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - function increaseVersion(bumpType) +% increaseVersion +% Upgrades the model to a new version. Run this function after merging +% changes to the master branch for making a new release. +% +% bumpType One of the following 3 strings: "major", "minor" or +% "patch", indicating the type of increase of version to be +% performed. +% +% NOTE: This function requires a git wrapper added to the MATLAB search +% path: https://github.com/manur/MATLAB-git +% +% Usage: increaseVersion(bumpType) +% +% Benjamin Sanchez, 2018-09-25 +% %Check if in master: currentBranch = git('rev-parse --abbrev-ref HEAD'); @@ -74,7 +83,7 @@ function increaseVersion(bumpType) 'then merge to master, and try again.']) end -%Allow .mat & .xls storage: +%Allow .mat & .xlsx storage: copyfile('../.gitignore','backup') fin = fopen('backup','r'); fout = fopen('../.gitignore','w'); @@ -95,6 +104,14 @@ function increaseVersion(bumpType) %Convert to RAVEN format and store model as .xlsx: model = ravenCobraWrapper(model); +model.annotation.defaultLB = -1000; +model.annotation.defaultUB = +1000; +model.annotation.taxonomy = 'taxonomy/559292'; +model.annotation.givenName = 'Benjamin'; +model.annotation.familyName = 'Sanchez'; +model.annotation.email = 'bensan@chalmers.se'; +model.annotation.organization = 'Chalmers University of Technology'; +model.annotation.note = 'Saccharomyces cerevisiae - strain S288C'; exportToExcelFormat(model,'../ModelFiles/xlsx/yeastGEM.xlsx'); %Update version file: @@ -103,5 +120,3 @@ function increaseVersion(bumpType) fclose(fid); end - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \ No newline at end of file diff --git a/ComplementaryScripts/modelCuration/SubstrateUsage.m b/ComplementaryScripts/modelCuration/SubstrateUsage.m index f373a820..7dfadb0c 100644 --- a/ComplementaryScripts/modelCuration/SubstrateUsage.m +++ b/ComplementaryScripts/modelCuration/SubstrateUsage.m @@ -2,7 +2,7 @@ % SubstrateUsage % % Automatically adds exchange reactions for every metabolite in -% ComplementaryData/modelCuration/Biolog_substrate.tsv and checks whether +% ComplementaryData/physiology/Biolog_substrate.tsv and checks whether % it can be used as a "solo" substrate. % % NOTE: requires COBRA @@ -15,7 +15,7 @@ model = loadYeastModel; % Load data: -fid2 = fopen('../ComplementaryData/modelCuration/Biolog_substrate.tsv'); +fid2 = fopen('../ComplementaryData/physiology/Biolog_substrate.tsv'); substrate = textscan(fid2,'%s %s %s %s %s %s','Delimiter','\t','HeaderLines',1); SubBiologName = substrate{1}; SubModelName = substrate{2}; @@ -139,7 +139,7 @@ % Update results from model: cd .. -fid2 = fopen('../ComplementaryData/modelCuration/Biolog_substrate.tsv','w'); +fid2 = fopen('../ComplementaryData/physiology/Biolog_substrate.tsv','w'); formatSpec = '%s\t%s\t%s\t%s\t%s\n'; fprintf(fid2,formatSpec,'Substrate','Name_in_Model','Substrate_type','Growth_Biolog','Growth_Model'); for i = 1:length(FBAresult) diff --git a/ComplementaryScripts/modelCuration/addMetabolomicsRxnToGEM.m b/ComplementaryScripts/modelCuration/addMetabolomicsRxnToGEM.m new file mode 100644 index 00000000..1edda7a1 --- /dev/null +++ b/ComplementaryScripts/modelCuration/addMetabolomicsRxnToGEM.m @@ -0,0 +1,151 @@ +% This Function is for adding Metabolomics related metabolites/reactions into model. +% Input: model, Metabolomics_newRxnMatrix.tsv,Metabolomics_newRxnProp.tsv,Metabolomics_newRxnMetAnnotation.tsv. +% Extract model info from .tsv format. +% Before run the codes below, the file should be manually editted. +% COBRA required. +% New reaction should be in .tsv format. +% +% Feiran Li 2018.08.31 +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%newreaction: +% Load model +cd .. +model = loadYeastModel; +%load rxn matrix +fid = fopen('../ComplementaryData/modelCuration/Metabolomics_newRxnMatrix.tsv'); +newreaction = textscan(fid,'%s %s %s %s %s','Delimiter','\t','HeaderLines',1); +matrix.rxnIDs = newreaction{1}; +matrix.metcoef = cellfun(@str2num, newreaction{2}); +matrix.metIDs = newreaction{3}; +matrix.mettype = newreaction{4}; +matrix.metcompartments = newreaction{5}; +fclose(fid); +%load rxn prop, which include rxn rev, rxn names, rxn ec numbers, rxn +%KEGGID and rxn notes. +fid = fopen('../ComplementaryData/modelCuration/Metabolomics_newRxnProp.tsv','r'); +rev = textscan(fid,'%s %s %s %s %s %s %s','Delimiter','\t','HeaderLines',1); +newrxn.ID = rev{1}; +newrxn.Rev = cellfun(@str2num, rev{2}); +newrxn.rxnNames = rev{3}; +newrxn.rxnECNumbers = rev{4}; +newrxn.rxnKEGGID = rev{5}; +newrxn.rxnNotes = rev{6}; +newrxn.rxnMetaNetXID = newrxn.ID; +for i = 1:length(newrxn.rxnMetaNetXID) + if ~startsWith(newrxn.rxnMetaNetXID{i},'MNXR') + newrxn.rxnMetaNetXID{i} = ''; + end +end + +fclose(fid); + +% Change coefficients for reactants: +for i=1:length(matrix.rxnIDs) + if strcmp(matrix.mettype(i),'reactant') + matrix.metcoef(i) = matrix.metcoef(i)*-1; + end +end + +% Change compartments: +CONValldata = cat(2,model.compNames,model.comps); +lbracket = ' [' ; +llbracket = '['; +rbrackets = ']'; +space = ' '; +[m, n] = size(CONValldata); +for i = 1:m + aa = CONValldata(i,1); + aa = char(aa); + for j=1:length(matrix.rxnIDs) + bb = matrix.metcompartments(j,1); + bb = char(bb); + if strcmp(bb,aa) + matrix.Newcomps(j,1) = CONValldata(i,2); + end + end +end +for i=1:length(matrix.rxnIDs) + matrix.metnames(i) = strcat(matrix.metIDs(i),lbracket,matrix.metcompartments(i),rbrackets); + matrix.Newcomps(i) = strcat(llbracket,matrix.Newcomps(i),rbrackets); +end + +% Map mets to model.metnames, get s_index for new mets: +cd otherChanges +for j = 1:length(matrix.metnames) + [~,metindex] = ismember(matrix.metnames(j),model.metNames); + if metindex ~= 0 + matrix.mets(j) = model.mets(metindex); + elseif metindex == 0 + newID = getNewIndex(model.mets); + matrix.mets(j) = strcat('s_',newID,matrix.Newcomps(j)); + model = addMetabolite(model,char(matrix.mets(j)), ... + 'metName',matrix.metnames(j)); + end +end + + +% Add metabolite data: +fid = fopen('../../ComplementaryData/modelCuration/Metabolomics_newRxnMetAnnotation.tsv'); +newmet_annot = textscan(fid,'%s %s %s %s %s %s %s %s','Delimiter','\t','HeaderLines',1); +newmet.metNames = newmet_annot{1}; +newmet.metFormulas = newmet_annot{2}; +newmet.metCharges = cellfun(@str2num, newmet_annot{3}); +newmet.metKEGGID = newmet_annot{5}; +newmet.metChEBIID = newmet_annot{6}; +newmet.metMetaNetXID = newmet_annot{7}; + + +fclose(fid); +for i = 1:length(newmet.metNames) + [~,metID] = ismember(newmet.metNames(i),model.metNames); + if metID ~= 0 + model.metFormulas{metID} = newmet.metFormulas{i}; + model.metCharges(metID) = newmet.metCharges(i); + model.metKEGGID{metID} = newmet.metKEGGID{i}; + model.metChEBIID{metID} = newmet.metChEBIID{i}; + model.metMetaNetXID{metID} = newmet.metMetaNetXID{i}; + model.metNotes{metID} = ''; + model.metNotes{metID} = 'added from metabolomics data'; + end +end + +% Add new reactions according to rev ID: Met Coef needs to be a column, not +% a row. Coef should be a double, which was converted at the import section +EnergyResults = {}; +MassChargeresults = {}; +RedoxResults = {}; +if ~isfield(model,'rxnMetaNetXID') + model.rxnMetaNetXID = cell(size(model.rxns)); +end +for i = 1:length(newrxn.ID) + newID = getNewIndex(model.rxns); + j = find(strcmp(matrix.rxnIDs,newrxn.ID{i})); + Met = matrix.mets(j); + Coef = transpose(matrix.metcoef(j)); + [model,rxnIndex] = addReaction(model, ['r_' newID],... + 'reactionName', newrxn.ID{i},... + 'metaboliteList',Met,... + 'stoichCoeffList',Coef,... + 'reversible',newrxn.Rev(i,1),... + 'checkDuplicate',1); + [EnergyResults,RedoxResults] = CheckEnergyProduction(model,{['r_' newID]},EnergyResults,RedoxResults); + [MassChargeresults] = CheckBalanceforSce(model,{['r_' newID]},MassChargeresults); + if isempty(rxnIndex) + rxnIndex = strcmp(model.rxns,['r_' newID]); + end + % Add rxn annotation: + model.rxnNames{rxnIndex} = newrxn.rxnNames{i}; + model.rxnECNumbers(rxnIndex) = newrxn.rxnECNumbers(i); + model.rxnKEGGID(rxnIndex) = newrxn.rxnKEGGID(i); + model.rxnMetaNetXID(rxnIndex) = newrxn.rxnMetaNetXID(i); + model.rxnConfidenceScores(rxnIndex) = 0; %reactions added for metabolomics data + model.rxnNotes{rxnIndex} = 'metabolites observed in metabolomics data'; +end + + +% Save model: +cd .. +saveYeastModel(model) +cd modelCuration + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + diff --git a/ComplementaryScripts/modelCuration/calculateContent.m b/ComplementaryScripts/modelCuration/calculateContent.m deleted file mode 100644 index ff154374..00000000 --- a/ComplementaryScripts/modelCuration/calculateContent.m +++ /dev/null @@ -1,62 +0,0 @@ -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% [Ptot,Ctot] = calculateContent(model) -% -% Benjamín J. Sánchez -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - -function [Ptot,Ctot] = calculateContent(model) - -% MW aminoacids [g/mol]: -aas = {'s_0404[c]' 89.09 % A Alanine ala - 's_0542[c]' 121.16 % C Cysteine cys - 's_0432[c]' 133.11 % D Aspartic acid asp - 's_0748[c]' 147.13 % E Glutamic acid glu - 's_1314[c]' 165.19 % F Phenylalanine phe - 's_0757[c]' 75.07 % G Glycine gly - 's_0832[c]' 155.15 % H Histidine his - 's_0847[c]' 131.17 % I Isoleucine ile - 's_1099[c]' 146.19 % K Lysine lys - 's_1077[c]' 131.17 % L Leucine leu - 's_1148[c]' 149.21 % M Methionine met - 's_0430[c]' 132.12 % N Asparagine asn - 's_1379[c]' 115.13 % P Proline pro - 's_0747[c]' 146.14 % Q Glutamine gln - 's_0428[c]' 174.2 % R Arginine arg - 's_1428[c]' 105.09 % S Serine ser - 's_1491[c]' 119.12 % T Threonine thr - 's_1561[c]' 117.15 % V Valine val - 's_1527[c]' 204.23 % W Tryptophan trp - 's_1533[c]' 181.19}; % Y Tyrosine tyr - -% MW carbohidrates [g/mol]: -carbs = {'s_0001[ce]' 180.16 % (1->3)-beta-D-glucan - 's_0004[ce]' 180.16 % (1->6)-beta-D-glucan - 's_0509[c]' 221.21 % chitin - 's_0773[c]' 180.16 % glycogen - 's_1107[c]' 180.16 % mannan - 's_1520[c]' 342.296}; % trehalose - -%Initialize protein and carb content: -Ptot = 0; -Ctot = 0; - -%Count protein/carb content in the corresponding pseudo-rxn: -protPos = strcmp(model.metNames,'protein [cytoplasm]'); -carbPos = strcmp(model.metNames,'carbohydrate [cytoplasm]'); -protRxn = model.S(protPos,:) == 1; -carbRxn = model.S(carbPos,:) == 1; -for i = 1:length(model.mets) - posP = strcmp(aas(:,1),model.mets{i}); - posC = strcmp(carbs(:,1),model.mets{i}); - if sum(posP) == 1 - Sprot = abs(model.S(i,protRxn)); % mmol/gDW - Ptot = Ptot + Sprot*aas{posP,2}/1000; % mmol/gDW * g/mmol = g/gDW - elseif sum(posC) == 1 - Scarb = abs(model.S(i,carbRxn)); % mmol/gDW - Ctot = Ctot + Scarb*carbs{posC,2}/1000; % mmol/gDW * g/mmol = g/gDW - end -end - -end - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \ No newline at end of file diff --git a/ComplementaryScripts/modelCuration/changeBiomass.m b/ComplementaryScripts/modelCuration/changeBiomass.m deleted file mode 100644 index 95573dba..00000000 --- a/ComplementaryScripts/modelCuration/changeBiomass.m +++ /dev/null @@ -1,57 +0,0 @@ -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% model = changeBiomass(model,P,GAM,NGAM) -% -% Benjamín J. Sánchez -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - -function model = changeBiomass(model,P,GAM,NGAM) - -%Get current contents and calculate conversion factors for proteins and carbs: -[Pbase,Cbase] = calculateContent(model); -Pfactor = P/Pbase; -Cfactor = (Cbase+Pbase-P)/Cbase; %Assumption: change in protein is balanced with a change in carbohydrate -fullGAM = GAM + 16.965*Pfactor + 5.210*Cfactor; - -%Change biomass composition: -protPos = strcmp(model.metNames,'protein [cytoplasm]'); -carbPos = strcmp(model.metNames,'carbohydrate [cytoplasm]'); -bioRxn = model.S(protPos,:) == -1; -protRxn = model.S(protPos,:) == 1; -carbRxn = model.S(carbPos,:) == 1; -for i = 1:length(model.mets) - Sbio = model.S(i,bioRxn); - Sprot = model.S(i,protRxn); - Scarb = model.S(i,carbRxn); - if Sbio ~= 0 - name = model.metNames{i}; - isATP = strcmpi(name,'ATP [cytoplasm]'); - isADP = strcmpi(name,'ADP [cytoplasm]'); - isH2O = strcmpi(name,'H2O [cytoplasm]'); - isH = strcmpi(name,'H+ [cytoplasm]'); - isP = strcmpi(name,'phosphate [cytoplasm]'); - - %Variable ATP growth related maintenance (GAM): - if isATP || isADP || isH2O || isH || isP - model.S(i,bioRxn) = sign(Sbio)*round(fullGAM,4); - end - - elseif Sprot ~= 0 && Sprot ~= 1 - %Variable aa content in biomass eq: - model.S(i,protRxn) = round(Sprot*Pfactor,4); - - elseif Scarb ~= 0 && Scarb ~= 1 - %Variable carb content in biomass eq: - model.S(i,carbRxn) = round(Scarb*Cfactor,4); - end -end - -%Add/change NGAM reaction: -% ATP + H2O -> ADP + H+ + PO4 -mets = {'s_0434[c]','s_0803[c]','s_0394[c]','s_0794[c]','s_1322[c]'}; -coefs = [-1,-1,1,1,1]; -model = addReaction(model,{'r_4046','non-growth associated maintenance reaction'}, ... - mets,coefs,false,NGAM,NGAM); - -end - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \ No newline at end of file diff --git a/ComplementaryScripts/modelCuration/fitGAM.m b/ComplementaryScripts/modelCuration/fitGAM.m new file mode 100644 index 00000000..480628f3 --- /dev/null +++ b/ComplementaryScripts/modelCuration/fitGAM.m @@ -0,0 +1,116 @@ +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% model = fitGAM(model) +% +% Benjamin Sanchez. Last update: 2018-09-04 +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +function model = fitGAM(model) + +%Load chemostat data: +fid = fopen('../../ComplementaryData/physiology/chemostatData_VanHoek1998.tsv','r'); +exp_data = textscan(fid,'%f32 %f32 %f32 %f32','Delimiter','\t','HeaderLines',1); +exp_data = [exp_data{1} exp_data{2} exp_data{3} exp_data{4}]; +fclose(fid); + +%GAMs to span: +disp('Estimating GAM:') +GAM = 30:5:70; + +%1st iteration: +GAM = iteration(model,GAM,exp_data); + +%2nd iteration: +GAM = iteration(model,GAM-10:1:GAM+10,exp_data); + +%3rd iteration: +GAM = iteration(model,GAM-1:0.1:GAM+1,exp_data); + +model = changeGAM(model,GAM); + +%Plot fit: +mod_data = simulateChemostat(model,exp_data); +figure +hold on +cols = [0,1,0;0,0,1;1,0,0]; +b = zeros(1,length(exp_data(1,:))-1); +for i = 1:length(exp_data(1,:))-1 + b(i) = plot(mod_data(:,1),mod_data(:,i+1),'Color',cols(i,:),'LineWidth',2); + plot(exp_data(:,1),exp_data(:,i+1),'o','Color',cols(i,:),'MarkerFaceColor',cols(i,:)) +end +title('GAM fitting for growth on glucose minimal media') +xlabel('Dilution rate [1/h]') +ylabel('Exchange fluxes [mmol/gDWh]') +legend(b,'Glucose consumption','O2 consumption','CO2 production','Location','northwest') +hold off + +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +function GAM = iteration(model,GAM,exp_data) + +fitting = ones(size(GAM))*1000; + +for i = 1:length(GAM) + %Modify GAM: + model_i = changeGAM(model,GAM(i)); + + %Simulate model and calculate fitting: + mod_data = simulateChemostat(model_i,exp_data); + R = (mod_data - exp_data)./exp_data; + fitting(i) = sqrt(sum(sum(R.^2))); + disp(['GAM = ' num2str(GAM(i)) ' -> Error = ' num2str(fitting(i))]) +end + +%Choose best: +[~,best] = min(fitting); + +if best == 1 || best == length(GAM) + error('GAM found is sub-optimal: please expand GAM search bounds.') +else + GAM = GAM(best); +end + +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +function model = changeGAM(model,GAM) + +bioPos = strcmp(model.rxnNames,'biomass pseudoreaction'); +for i = 1:length(model.mets) + S_ix = model.S(i,bioPos); + isGAM = sum(strcmp({'ATP [cytoplasm]','ADP [cytoplasm]','H2O [cytoplasm]', ... + 'H+ [cytoplasm]','phosphate [cytoplasm]'},model.metNames{i})) == 1; + if S_ix ~= 0 && isGAM + model.S(i,bioPos) = sign(S_ix)*GAM; + end +end + +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +function mod_data = simulateChemostat(model,exp_data) + +%Relevant positions: +pos(1) = find(strcmp(model.rxnNames,'growth')); +pos(2) = find(strcmp(model.rxnNames,'D-glucose exchange')); +pos(3) = find(strcmp(model.rxnNames,'oxygen exchange')); +pos(4) = find(strcmp(model.rxnNames,'carbon dioxide exchange')); + +%Simulate chemostats: +mod_data = zeros(size(exp_data)); +for i = 1:length(exp_data(:,1)) + %Fix biomass and minimize glucose: + model = changeRxnBounds(model,model.rxns(pos(1)),exp_data(i,1),'l'); + model = changeRxnBounds(model,model.rxns(pos(2)),-10,'l'); + model = changeObjective(model,model.rxns(pos(2)),+1); + sol = optimizeCbModel(model); + %Store relevant variables: + mod_data(i,:) = abs(sol.x(pos)'); +end + +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% diff --git a/ComplementaryScripts/modelCuration/scaleBioMass.m b/ComplementaryScripts/modelCuration/scaleBioMass.m new file mode 100644 index 00000000..3aaa8a3f --- /dev/null +++ b/ComplementaryScripts/modelCuration/scaleBioMass.m @@ -0,0 +1,121 @@ +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% scaleBioMass +% Corrects the stoichiometry coefficients of all pseudo-rxns in an +% iterative fashion: +% 1. Switch back to original model's abundance values (Forster et al. 2003) +% 2. Improve with data from a more recent study (Lahtvee et al. 2017) +% compatible with the current 8% lipid fraction +% 3. Rescale carbohydrate fraction (total) to have biomass add up to 1 +% 4. GAM is fitted to simulate chemostat data of S. cerevisiae at low +% growth rates (Van Hoek et al. 1988) +% +% Function adapted from SLIMEr: https://github.com/SysBioChalmers/SLIMEr +% +% Benjamin Sanchez. Last update: 2018-09-07 +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +function scaleBioMass + +%Load model: +initCobraToolbox +cd .. +model = loadYeastModel; +cd modelCuration + +%Load data from Forster 2003: +fid = fopen('../../ComplementaryData/physiology/biomassComposition_Forster2003.tsv'); +Forster2003 = textscan(fid,'%s %s %f32 %f32 %s','Delimiter','\t','HeaderLines',1); +data.mets = Forster2003{1}; +data.abundances = double(Forster2003{3}); +data.MWs = double(Forster2003{4}); +data.groups = Forster2003{5}; +fclose(fid); + +%Compute current composition: +sumBioMass(model,data); + +%Switch to Forster 2003 data: +for i = 1:length(data.mets) + %Find positions: + rxnName = [data.groups{i} ' pseudoreaction']; + rxnName = strrep(rxnName,'other','biomass'); + rxnPos = strcmp(model.rxnNames,rxnName); + metPos = strcmp(model.mets,data.mets{i}); + %Extra changes in protein pseudoreaction: + if strcmp(data.groups{i},'protein') + oldVal = abs(model.S(metPos,rxnPos)); + metPos = abs(model.S(:,rxnPos)) == oldVal; + if sum(metPos) ~= 2 + error('did not found tRNA(aa) pair') + end + end + %Change stoichiometry: + model.S(metPos,rxnPos) = sign(model.S(metPos,rxnPos))*data.abundances(i); +end +[~,P,~,R,~,~,~] = sumBioMass(model,data); + +%Correct with data from Lahtvee 2017: +fid = fopen('../../ComplementaryData/physiology/biomassComposition_Lahtvee2017.tsv'); +Lahtvee2017 = textscan(fid,'%s %s %f32 %f32 %s','Delimiter','\t','HeaderLines',1); +data2.mets = Lahtvee2017{1}; +data2.names = Lahtvee2017{2}; +data2.abundances = double(Lahtvee2017{3}); +fclose(fid); +for i = 1:length(data2.mets) + metID = data2.mets{i}; + metName = data2.names{i}; + abundance = data2.abundances(i); + if strcmp(metName,'protein') %protein fraction + fP = abundance/P; %ratio to scale + model = rescalePseudoReaction(model,'protein',fP); + + elseif strcmp(metName,'RNA') %RNA fraction + fR = abundance/R; %ratio to scale + model = rescalePseudoReaction(model,'RNA',fR); + + else %Some extra carbohydrates: + modelPos = strcmp(model.mets,metID); + compPos = strcmp(data.mets,metID); + rxnPos = strcmp(model.rxnNames,'carbohydrate pseudoreaction'); + if model.S(modelPos,rxnPos) < 0 + MW = data.MWs(compPos)-18; + model.S(modelPos,rxnPos) = -abundance/MW*1000; + end + end +end +[X,~,C,~,~,~,~] = sumBioMass(model,data); + +%Balance out mass with carbohydrate content: +delta = X - 1; %difference to balance +fC = (C - delta)/C; +model = rescalePseudoReaction(model,'carbohydrate',fC); +sumBioMass(model,data); + +%Fit GAM: +model = fitGAM(model); +sumBioMass(model,data); + +%Finally, save model: +cd .. +saveYeastModel(model) +cd modelCuration + +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +function model = rescalePseudoReaction(model,metName,f) + +rxnName = [metName ' pseudoreaction']; +rxnPos = strcmp(model.rxnNames,rxnName); +for i = 1:length(model.mets) + S_ir = model.S(i,rxnPos); + isProd = strcmp(model.metNames{i},[metName ' [cytoplasm]']); + if S_ir ~= 0 && ~isProd + model.S(i,rxnPos) = f*S_ir; + end +end + +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% diff --git a/ComplementaryScripts/modelCuration/sumBioMass.m b/ComplementaryScripts/modelCuration/sumBioMass.m new file mode 100644 index 00000000..9b3963c7 --- /dev/null +++ b/ComplementaryScripts/modelCuration/sumBioMass.m @@ -0,0 +1,82 @@ +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% [X,P,C,R,D,L,N] = sumBioMass(model) +% Calculates breakdown of biomass +% +% model metabolic model in COBRA format +% data structure with at least the following 2 fields: +% mets Cell array with metabolite ids +% MWs Numeric array with molecular weights for each metabolite +% +% X Total biomass fraction [gDW/gDW] +% P Protein fraction [g/gDW] +% C Carbohydrate fraction [g/gDW] +% R RNA fraction [g/gDW] +% D DNA fraction [g/gDW] +% L Lipid fraction [g/gDW] +% N Other mets [g/gDW] +% +% Function adapted from SLIMEr: https://github.com/SysBioChalmers/SLIMEr +% +% Benjamin Sanchez. Last update: 2018-09-04 +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +function [X,P,C,R,D,L,N] = sumBioMass(model,data) + +%Get main fractions: +[P,X] = getFraction(model,data,'P',0); +[C,X] = getFraction(model,data,'C',X); +[R,X] = getFraction(model,data,'R',X); +[D,X] = getFraction(model,data,'D',X); +[L,X] = getFraction(model,data,'L',X); +[N,X] = getFraction(model,data,'N',X); + +disp(['X -> ' num2str(X) ' gDW/gDW']) + +% Simulate growth: +sol = optimizeCbModel(model); +disp(['Growth = ' num2str(sol.f) ' 1/h']) +disp(' ') + +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +function [F,X] = getFraction(model,data,compType,X) + +%Define pseudoreaction name: +rxnName = [compType ' pseudoreaction']; +rxnName = strrep(rxnName,'P','protein'); +rxnName = strrep(rxnName,'C','carbohydrate'); +rxnName = strrep(rxnName,'N','biomass'); +rxnName = strrep(rxnName,'L','lipid backbone'); +rxnName = strrep(rxnName,'R','RNA'); +rxnName = strrep(rxnName,'D','DNA'); + +%Add up fraction: +rxnPos = strcmp(model.rxnNames,rxnName); +isSub = model.S(:,rxnPos) < 0; %substrates in pseudo-rxn +if strcmp(compType,'L') + F = -sum(model.S(isSub,rxnPos)); %g/gDW +else + F = 0; + %Add up all components: + for i = 1:length(model.mets) + pos = strcmp(data.mets,model.mets{i}); + if isSub(i) && sum(pos) == 1 + if strcmp(compType,'N') + MW = data.MWs(pos); + else + MW = data.MWs(pos)-18; + end + abundance = -model.S(i,rxnPos)*MW/1000; + F = F + abundance; + end + end +end +X = X + F; + +disp([compType ' -> ' num2str(F) ' g/gDW']) + +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% diff --git a/ModelFiles/dependencies.txt b/ModelFiles/dependencies.txt index 341091c9..dea80f6f 100644 --- a/ModelFiles/dependencies.txt +++ b/ModelFiles/dependencies.txt @@ -1,7 +1,7 @@ MATLAB 9.4.0.813654 (R2018a) libSBML 5.17.0 RAVEN_toolbox 2.0.2 -COBRA_toolbox commit 75d530c +COBRA_toolbox commit d7ce7d6 SBML_level 3 SBML_version 1 fbc_version 2 diff --git a/ModelFiles/txt/yeastGEM.txt b/ModelFiles/txt/yeastGEM.txt index 70ebd3a2..a9734202 100644 --- a/ModelFiles/txt/yeastGEM.txt +++ b/ModelFiles/txt/yeastGEM.txt @@ -3412,11 +3412,11 @@ r_4038 s_3713[erm] <=> s_1524[c] -1000.00 1000.00 0.00 r_4040 s_0811[m] <=> s_3714[c] -1000.00 1000.00 0.00 r_4043 s_3715[e] -> 0.00 1000.00 0.00 r_4044 s_3716[e] -> 0.00 1000.00 0.00 -r_4041 61.9779 s_0434[c] + 61.9779 s_0803[c] + s_1096[c] + 0.00099 s_1405[c] + 0.02 s_1467[c] + 1e-06 s_3714[c] + s_3717[c] + s_3718[c] + s_3719[c] + s_3720[c] -> 61.9779 s_0394[c] + s_0450[c] + 61.9779 s_0794[c] + 61.9779 s_1322[c] 0.00 1000.00 0.00 +r_4041 55.4 s_0434[c] + 55.4 s_0803[c] + s_1096[c] + 0.00099 s_1405[c] + 0.02 s_1467[c] + 1e-06 s_3714[c] + s_3717[c] + s_3718[c] + s_3719[c] + s_3720[c] -> 55.4 s_0394[c] + s_0450[c] + 55.4 s_0794[c] + 55.4 s_1322[c] 0.00 1000.00 0.00 r_4046 s_0434[c] + s_0803[c] -> s_0394[c] + s_0794[c] + s_1322[c] 0.70 0.70 0.00 -r_4047 0.452121 s_0404[c] + 0.158399 s_0428[c] + 0.100172 s_0430[c] + 0.293183 s_0432[c] + 0.00646965 s_0542[c] + 0.103838 s_0747[c] + 0.297388 s_0748[c] + 0.286174 s_0757[c] + 0.0653434 s_0832[c] + 0.189884 s_0847[c] + 0.292105 s_1077[c] + 0.282077 s_1099[c] + 0.0499241 s_1148[c] + 0.131981 s_1314[c] + 0.16228 s_1379[c] + 0.18266 s_1428[c] + 0.18859 s_1491[c] + 0.0280351 s_1527[c] + 0.100495 s_1533[c] + 0.260727 s_1561[c] -> 0.452121 s_1582[c] + 0.158399 s_1583[c] + 0.100172 s_1585[c] + 0.293183 s_1587[c] + 0.00646965 s_1589[c] + 0.103838 s_1590[c] + 0.297388 s_1591[c] + 0.286174 s_1593[c] + 0.0653434 s_1594[c] + 0.189884 s_1596[c] + 0.292105 s_1598[c] + 0.282077 s_1600[c] + 0.0499241 s_1602[c] + 0.131981 s_1604[c] + 0.16228 s_1606[c] + 0.18266 s_1607[c] + 0.18859 s_1608[c] + 0.0280351 s_1610[c] + 0.100495 s_1612[c] + 0.260727 s_1614[c] + s_3717[c] 0.00 1000.00 0.00 -r_4048 0.716087 s_0001[ce] + 0.239185 s_0004[ce] + 0.285686 s_0773[c] + 0.680151 s_1107[c] + 0.115049 s_1520[c] -> s_3718[c] 0.00 1000.00 0.00 -r_4049 0.0421665 s_0423[c] + 0.0409749 s_0526[c] + 0.0421665 s_0782[c] + 0.0549082 s_1545[c] -> s_3719[c] 0.00 1000.00 0.00 +r_4047 0.527012 s_0404[c] + 0.184592 s_0428[c] + 0.11682 s_0430[c] + 0.341731 s_0432[c] + 0.00758126 s_0542[c] + 0.12107 s_0747[c] + 0.34667 s_0748[c] + 0.333575 s_0757[c] + 0.0761572 s_0832[c] + 0.22135 s_0847[c] + 0.340467 s_1077[c] + 0.328751 s_1099[c] + 0.0582379 s_1148[c] + 0.153808 s_1314[c] + 0.189187 s_1379[c] + 0.212964 s_1428[c] + 0.219857 s_1491[c] + 0.0326224 s_1527[c] + 0.117165 s_1533[c] + 0.30394 s_1561[c] -> 0.527012 s_1582[c] + 0.184592 s_1583[c] + 0.11682 s_1585[c] + 0.341731 s_1587[c] + 0.00758126 s_1589[c] + 0.12107 s_1590[c] + 0.34667 s_1591[c] + 0.333575 s_1593[c] + 0.0761572 s_1594[c] + 0.22135 s_1596[c] + 0.340467 s_1598[c] + 0.328751 s_1600[c] + 0.0582379 s_1602[c] + 0.153808 s_1604[c] + 0.189187 s_1606[c] + 0.212964 s_1607[c] + 0.219857 s_1608[c] + 0.0326224 s_1610[c] + 0.117165 s_1612[c] + 0.30394 s_1614[c] + s_3717[c] 0.00 1000.00 0.00 +r_4048 0.758415 s_0001[ce] + 0.253399 s_0004[ce] + 0.366195 s_0773[c] + 0.720342 s_1107[c] + 0.140105 s_1520[c] -> s_3718[c] 0.00 1000.00 0.00 +r_4049 0.0445348 s_0423[c] + 0.0432762 s_0526[c] + 0.0445348 s_0782[c] + 0.0579921 s_1545[c] -> s_3719[c] 0.00 1000.00 0.00 r_4050 0.0036 s_0584[c] + 0.0024 s_0589[c] + 0.0024 s_0615[c] + 0.0036 s_0649[c] -> s_3720[c] 0.00 1000.00 0.00 r_4051 s_3721[g] -> s_3722[c] 0.00 1000.00 0.00 r_4052 s_0859[g] -> s_3723[c] 0.00 1000.00 0.00 @@ -3927,3 +3927,24 @@ r_4562 s_4082[e] -> 0.00 1000.00 0.00 r_4563 s_4084[e] -> 0.00 1000.00 0.00 r_4564 s_4127[e] -> 0.00 1000.00 0.00 r_4565 s_4103[e] -> 0.00 1000.00 0.00 +r_4566 s_0340[c] + s_0394[c] + s_0794[c] -> s_0434[c] + s_3875[c] 0.00 1000.00 0.00 +r_4567 s_0340[c] -> s_1322[c] + s_3875[c] 0.00 1000.00 0.00 +r_4568 s_0794[c] + s_1321[c] -> s_4194[c] 0.00 1000.00 0.00 +r_4569 s_0362[c] + s_0794[c] + s_4195[c] -> s_0803[c] + s_4194[c] 0.00 1000.00 0.00 +r_4570 s_1198[c] + s_4182[c] <=> s_0180[c] + s_0794[c] + s_1203[c] -1000.00 1000.00 0.00 +r_4571 s_4182[c] <=> s_0779[c] + 3 s_0794[c] + s_4183[c] -1000.00 1000.00 0.00 +r_4572 s_0180[c] + s_0441[c] <=> s_0991[c] + s_4184[c] -1000.00 1000.00 0.00 +r_4573 s_0529[c] + s_1198[c] + s_4184[c] -> s_0373[c] + s_0456[c] + s_1203[c] 0.00 1000.00 0.00 +r_4574 s_0529[c] + s_1207[c] + s_4184[c] -> s_0373[c] + s_0456[c] + s_1212[c] 0.00 1000.00 0.00 +r_4575 s_0794[c] + s_4184[c] -> s_0359[c] + s_0456[c] 0.00 1000.00 0.00 +r_4576 s_1207[c] + s_4185[c] <=> s_0794[c] + s_1212[c] + s_4186[c] -1000.00 1000.00 0.00 +r_4577 s_0232[c] -> s_4186[c] 0.00 1000.00 0.00 +r_4578 s_1212[c] + s_4187[c] -> s_0794[c] + s_1207[c] + s_4186[c] 0.00 1000.00 0.00 +r_4579 s_0794[c] + 2 s_1399[c] -> s_0456[c] + s_4188[c] 0.00 1000.00 0.00 +r_4580 s_1207[c] + s_4185[c] <=> s_0794[c] + s_1212[c] + s_4188[c] -1000.00 1000.00 0.00 +r_4581 s_1198[c] + s_4189[c] -> s_0178[c] + s_0456[c] + s_1203[c] 0.00 1000.00 0.00 +r_4582 s_0779[c] + s_0803[c] + s_4183[c] -> s_0529[c] + s_0794[c] + s_4189[c] 0.00 1000.00 0.00 +r_4583 s_0803[c] + s_4190[c] -> s_0529[c] + s_0794[c] + s_4191[c] 0.00 1000.00 0.00 +r_4584 s_0434[c] + s_0529[c] + s_4191[c] -> s_0423[c] + s_0633[c] + s_4190[c] 0.00 1000.00 0.00 +r_4585 s_0803[c] + s_4192[c] -> s_0558[c] + s_4193[c] 0.00 1000.00 0.00 +r_4586 s_3998[c] + s_4192[c] -> 2 s_4193[c] 0.00 1000.00 0.00 diff --git a/ModelFiles/xml/yeastGEM.xml b/ModelFiles/xml/yeastGEM.xml index 71b34029..185b4e93 100644 --- a/ModelFiles/xml/yeastGEM.xml +++ b/ModelFiles/xml/yeastGEM.xml @@ -49125,6 +49125,356 @@ + + + +

NOTES: added from metabolomics data

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NOTES: added from metabolomics data

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NOTES: added from metabolomics data

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NOTES: added from metabolomics data

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NOTES: added from metabolomics data

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NOTES: added from metabolomics data

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NOTES: added from metabolomics data

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NOTES: added from metabolomics data

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NOTES: added from metabolomics data

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NOTES: added from metabolomics data

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NOTES: added from metabolomics data

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NOTES: added from metabolomics data

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NOTES: added from metabolomics data

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NOTES: added from metabolomics data

+ + + + + + + + + + + + + + + + + + + + + @@ -168369,22 +168719,22 @@ - - + + - - - + + + - + - - + + @@ -168432,48 +168782,48 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -168495,11 +168845,11 @@ - - - - - + + + + + @@ -168523,10 +168873,10 @@ - - - - + + + + @@ -168550,10 +168900,10 @@ - - - - + + + + @@ -183935,6 +184285,728 @@ + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

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Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

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Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

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Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Confidence Level: 0

+

NOTES: metabolites observed in metabolomics data

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Confidence Level: 0

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NOTES: metabolites observed in metabolomics data

+ + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/ModelFiles/yml/yeastGEM.yml b/ModelFiles/yml/yeastGEM.yml index 871ba080..9ca7efd6 100644 --- a/ModelFiles/yml/yeastGEM.yml +++ b/ModelFiles/yml/yeastGEM.yml @@ -25245,6 +25245,160 @@ - kegg.compound: C01904 - metanetx.chemical: MNXM1018 - sbo: SBO:0000247 + - !!omap + - id: s_4182 + - name: 2-hydroxyglutarate + - compartment: c + - formula: C5H6O5 + - charge: -2 + - annotation: !!omap + - chebi: CHEBI:11596 + - kegg.compound: C02630 + - metanetx.chemical: MNXM1210 + - sbo: SBO:0000247 + - !!omap + - id: s_4183 + - name: propionyl-CoA + - compartment: c + - formula: C24H36N7O17P3S + - charge: -4 + - annotation: !!omap + - chebi: CHEBI:57392 + - kegg.compound: C00100 + - metanetx.chemical: MNXM86 + - sbo: SBO:0000247 + - !!omap + - id: s_4184 + - name: 3-oxopropanoate + - compartment: c + - formula: C3H3O3 + - charge: -1 + - annotation: !!omap + - chebi: CHEBI:33190 + - kegg.compound: C00222 + - metanetx.chemical: MNXM244 + - sbo: SBO:0000247 + - !!omap + - id: s_4185 + - name: (R)-2,3-dihydroxy-3-methylbutanoate + - compartment: c + - formula: C5H9O4 + - charge: -1 + - annotation: !!omap + - chebi: CHEBI:49072 + - kegg.compound: C04272 + - metanetx.chemical: MNXM114097 + - sbo: SBO:0000247 + - !!omap + - id: s_4186 + - name: 3-hydroxy-3-methyl-2-oxobutanoate + - compartment: c + - formula: C5H7O4 + - charge: -1 + - annotation: !!omap + - chebi: CHEBI:11812 + - kegg.compound: C04181 + - metanetx.chemical: MNXM1638 + - sbo: SBO:0000247 + - !!omap + - id: s_4187 + - name: 2-acetyllactic acid + - compartment: c + - formula: C5H7O4 + - charge: -1 + - annotation: !!omap + - chebi: CHEBI:57774 + - kegg.compound: C00900 + - metanetx.chemical: MNXM426 + - sbo: SBO:0000247 + - !!omap + - id: s_4188 + - name: (2S)-2-acetolactate + - compartment: c + - formula: C5H7O4 + - charge: -1 + - annotation: !!omap + - chebi: CHEBI:58476 + - kegg.compound: C06010 + - metanetx.chemical: MNXM114079 + - sbo: SBO:0000247 + - !!omap + - id: s_4189 + - name: (2R,3S)-3-methylmalate + - compartment: c + - formula: C5H6O5 + - charge: -2 + - annotation: !!omap + - chebi: CHEBI:58511 + - kegg.compound: C06032 + - metanetx.chemical: MNXM2512 + - sbo: SBO:0000247 + - !!omap + - id: s_4190 + - name: trans-2,cis-9-octadecadienoyl-CoA + - compartment: c + - formula: C39H62N7O17P3S + - charge: -4 + - annotation: !!omap + - chebi: CHEBI:57383 + - kegg.compound: C02050 + - metanetx.chemical: MNXM638 + - sbo: SBO:0000247 + - !!omap + - id: s_4191 + - name: (9Z,12Z)-octadecadienoate + - compartment: c + - formula: C18H31O2 + - charge: -1 + - annotation: !!omap + - chebi: CHEBI:30245 + - kegg.compound: C01595 + - metanetx.chemical: MNXM293 + - sbo: SBO:0000247 + - !!omap + - id: s_4192 + - name: stachyose + - compartment: c + - formula: C24H42O21 + - charge: 0 + - annotation: !!omap + - chebi: CHEBI:17164 + - kegg.compound: C01613 + - metanetx.chemical: MNXM1503 + - sbo: SBO:0000247 + - !!omap + - id: s_4193 + - name: raffinose + - compartment: c + - formula: C18H32O16 + - charge: 0 + - annotation: !!omap + - chebi: CHEBI:16634 + - kegg.compound: C00492 + - metanetx.chemical: MNXM621 + - sbo: SBO:0000247 + - !!omap + - id: s_4194 + - name: 4-hydroxyphenyl acetate + - compartment: c + - formula: C8H8O3 + - charge: 0 + - annotation: !!omap + - chebi: CHEBI:18101 + - kegg.compound: C00642 + - metanetx.chemical: MNXM3863 + - sbo: SBO:0000247 + - !!omap + - id: s_4195 + - name: Hydroquinone + - compartment: c + - formula: C6H6O2 + - charge: 0 + - annotation: !!omap + - chebi: CHEBI:17594 + - kegg.compound: C00530 + - metanetx.chemical: MNXM376 + - sbo: SBO:0000247 - reactions: - !!omap - id: r_0001 @@ -82733,13 +82887,13 @@ - id: r_4041 - name: biomass pseudoreaction - metabolites: !!omap - - s_0394: 61.9779 - - s_0434: -61.9779 + - s_0394: 55.4 + - s_0434: -55.4 - s_0450: 1 - - s_0794: 61.9779 - - s_0803: -61.9779 + - s_0794: 55.4 + - s_0803: -55.4 - s_1096: -1 - - s_1322: 61.9779 + - s_1322: 55.4 - s_1405: -0.00099 - s_1467: -0.02 - s_3714: -1e-06 @@ -82826,46 +82980,46 @@ - id: r_4047 - name: protein pseudoreaction - metabolites: !!omap - - s_0404: -0.45212 - - s_0428: -0.1584 - - s_0430: -0.10017 - - s_0432: -0.29318 - - s_0542: -0.0064696 - - s_0747: -0.10384 - - s_0748: -0.29739 - - s_0757: -0.28617 - - s_0832: -0.065343 - - s_0847: -0.18988 - - s_1077: -0.2921 - - s_1099: -0.28208 - - s_1148: -0.049924 - - s_1314: -0.13198 - - s_1379: -0.16228 - - s_1428: -0.18266 - - s_1491: -0.18859 - - s_1527: -0.028035 - - s_1533: -0.1005 - - s_1561: -0.26073 - - s_1582: 0.45212 - - s_1583: 0.1584 - - s_1585: 0.10017 - - s_1587: 0.29318 - - s_1589: 0.0064696 - - s_1590: 0.10384 - - s_1591: 0.29739 - - s_1593: 0.28617 - - s_1594: 0.065343 - - s_1596: 0.18988 - - s_1598: 0.2921 - - s_1600: 0.28208 - - s_1602: 0.049924 - - s_1604: 0.13198 - - s_1606: 0.16228 - - s_1607: 0.18266 - - s_1608: 0.18859 - - s_1610: 0.028035 - - s_1612: 0.1005 - - s_1614: 0.26073 + - s_0404: -0.52701 + - s_0428: -0.18459 + - s_0430: -0.11682 + - s_0432: -0.34173 + - s_0542: -0.0075813 + - s_0747: -0.12107 + - s_0748: -0.34667 + - s_0757: -0.33358 + - s_0832: -0.076157 + - s_0847: -0.22135 + - s_1077: -0.34047 + - s_1099: -0.32875 + - s_1148: -0.058238 + - s_1314: -0.15381 + - s_1379: -0.18919 + - s_1428: -0.21296 + - s_1491: -0.21986 + - s_1527: -0.032622 + - s_1533: -0.11716 + - s_1561: -0.30394 + - s_1582: 0.52701 + - s_1583: 0.18459 + - s_1585: 0.11682 + - s_1587: 0.34173 + - s_1589: 0.0075813 + - s_1590: 0.12107 + - s_1591: 0.34667 + - s_1593: 0.33358 + - s_1594: 0.076157 + - s_1596: 0.22135 + - s_1598: 0.34047 + - s_1600: 0.32875 + - s_1602: 0.058238 + - s_1604: 0.15381 + - s_1606: 0.18919 + - s_1607: 0.21296 + - s_1608: 0.21986 + - s_1610: 0.032622 + - s_1612: 0.11716 + - s_1614: 0.30394 - s_3717: 1 - lower_bound: 0 - upper_bound: 1000 @@ -82876,11 +83030,11 @@ - id: r_4048 - name: carbohydrate pseudoreaction - metabolites: !!omap - - s_0001: -0.71609 - - s_0004: -0.23919 - - s_0773: -0.28569 - - s_1107: -0.68015 - - s_1520: -0.11505 + - s_0001: -0.75841 + - s_0004: -0.2534 + - s_0773: -0.36619 + - s_1107: -0.72034 + - s_1520: -0.1401 - s_3718: 1 - lower_bound: 0 - upper_bound: 1000 @@ -82891,10 +83045,10 @@ - id: r_4049 - name: RNA pseudoreaction - metabolites: !!omap - - s_0423: -0.042167 - - s_0526: -0.040975 - - s_0782: -0.042167 - - s_1545: -0.054908 + - s_0423: -0.044535 + - s_0526: -0.043276 + - s_0782: -0.044535 + - s_1545: -0.057992 - s_3719: 1 - lower_bound: 0 - upper_bound: 1000 @@ -90056,6 +90210,359 @@ - upper_bound: 1000 - annotation: !!omap - sbo: SBO:0000627 + - !!omap + - id: r_4566 + - name: ATP:D-Gluconate 6-phosphotransferase + - metabolites: !!omap + - s_0340: -1 + - s_0394: -1 + - s_0434: 1 + - s_0794: -1 + - s_3875: 1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: 2.7.1.12 + - kegg.reaction: R01737 + - metanetx.reaction: MNXR100390 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4567 + - name: 6-phosphogluconate phosphatase + - metabolites: !!omap + - s_0340: -1 + - s_1322: 1 + - s_3875: 1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: + - 3.1.3.- + - 3.1.3.2 + - 3.1.3.29 + - metanetx.reaction: MNXR123213 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4568 + - name: R06790 + - metabolites: !!omap + - s_0794: -1 + - s_1321: -1 + - s_4194: 1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - kegg.reaction: R06790 + - metanetx.reaction: MNXR110535 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4569 + - name: Carboxylic ester hydrolases + - metabolites: !!omap + - s_0362: -1 + - s_0794: -1 + - s_0803: 1 + - s_4194: 1 + - s_4195: -1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: + - 3.1.1.- + - 3.1.1.2 + - metanetx.reaction: MNXR110621 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4570 + - name: phosphoglycerate dehydrogenase + - metabolites: !!omap + - s_0180: 1 + - s_0794: 1 + - s_1198: -1 + - s_1203: 1 + - s_4182: -1 + - lower_bound: -1000 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: 1.1.1.95 + - kegg.reaction: R08198 + - metanetx.reaction: MNXR111769 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4571 + - name: seed:rxn00681 + - metabolites: !!omap + - s_0779: 1 + - s_0794: 3 + - s_4182: -1 + - s_4183: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - annotation: !!omap + - metanetx.reaction: MNXR134240 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4572 + - name: beta-alanine:2-oxoglutarate aminotransferase + - metabolites: !!omap + - s_0180: -1 + - s_0441: -1 + - s_0991: 1 + - s_4184: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: + - 2.6.1.19 + - 2.6.1.55 + - kegg.reaction: R00908 + - metanetx.reaction: MNXR95862 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4573 + - name: 3-Oxopropanoate:NAD+ oxidoreductase (decarboxylating, CoA-acetylating) + - metabolites: !!omap + - s_0373: 1 + - s_0456: 1 + - s_0529: -1 + - s_1198: -1 + - s_1203: 1 + - s_4184: -1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: + - 1.2.1.- + - 1.2.1.18 + - 1.2.1.27 + - kegg.reaction: R00705 + - metanetx.reaction: MNXR101665 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4574 + - name: 3-Oxopropanoate:NADP+ oxidoreductase (decarboxylating, CoA-acetylating) + - metabolites: !!omap + - s_0373: 1 + - s_0456: 1 + - s_0529: -1 + - s_1207: -1 + - s_1212: 1 + - s_4184: -1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: + - 1.2.1.- + - 1.2.1.18 + - kegg.reaction: R00706 + - metanetx.reaction: MNXR106650 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4575 + - name: 3-oxopropanoate carboxy-lyase + - metabolites: !!omap + - s_0359: 1 + - s_0456: 1 + - s_0794: -1 + - s_4184: -1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: + - 4.1.1.- + - 4.2.1.155 + - kegg.reaction: R06973 + - metanetx.reaction: MNXR110693 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4576 + - name: (R)-2,3-Dihydroxy-3-methylbutanoate:NADP+ oxidoreductase (isomerizing) + - metabolites: !!omap + - s_0794: 1 + - s_1207: -1 + - s_1212: 1 + - s_4185: -1 + - s_4186: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: 1.1.1.86 + - kegg.reaction: R04440 + - metanetx.reaction: MNXR100904 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4577 + - name: Dihydroxy-acid dehydratase, mitochondrial + - metabolites: !!omap + - s_0232: -1 + - s_4186: 1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - metanetx.reaction: MNXR137278 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4578 + - name: Ketol-acid reductoisomerase, mitochondrial + - metabolites: !!omap + - s_0794: 1 + - s_1207: 1 + - s_1212: -1 + - s_4186: 1 + - s_4187: -1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - metanetx.reaction: MNXR137279 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4579 + - name: pyruvate:pyruvate acetaldehydetransferase (decarboxylating); (S)-2-acetolactate pyruvate-lyase (carboxylating) + - metabolites: !!omap + - s_0456: 1 + - s_0794: -1 + - s_1399: -2 + - s_4188: 1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: 2.2.1.6 + - kegg.reaction: R00226 + - metanetx.reaction: MNXR95271 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4580 + - name: (R)-2,3-dihydroxy-3-methylbutanoate:NADP+ oxidoreductase (isomerizing) + - metabolites: !!omap + - s_0794: 1 + - s_1207: -1 + - s_1212: 1 + - s_4185: -1 + - s_4188: 1 + - lower_bound: -1000 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: + - 1.1.1.383 + - 1.1.1.86 + - kegg.reaction: R04439 + - metanetx.reaction: MNXR97523 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4581 + - name: (2R,3S)-3-methylmalate:NAD+ oxidoreductase + - metabolites: !!omap + - s_0178: 1 + - s_0456: 1 + - s_1198: -1 + - s_1203: 1 + - s_4189: -1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: + - 1.1.1.- + - 1.1.1.85 + - kegg.reaction: R00994 + - metanetx.reaction: MNXR106779 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4582 + - name: malate/β-methylmalate synthase + - metabolites: !!omap + - s_0529: 1 + - s_0779: -1 + - s_0794: 1 + - s_0803: -1 + - s_4183: -1 + - s_4189: 1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: 2.3.3.- + - metanetx.reaction: MNXR121603 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4583 + - name: palmitoyl-CoA hydrolase + - metabolites: !!omap + - s_0529: 1 + - s_0794: 1 + - s_0803: -1 + - s_4190: -1 + - s_4191: 1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: + - 3.1.2.- + - 3.1.2.2 + - metanetx.reaction: MNXR99136 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4584 + - name: long-chain-fatty-acid---CoA ligase + - metabolites: !!omap + - s_0423: 1 + - s_0434: -1 + - s_0529: -1 + - s_0633: 1 + - s_4190: 1 + - s_4191: -1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: 6.2.1.3 + - metanetx.reaction: MNXR99175 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4585 + - name: a-galactosidase (stachyose) + - metabolites: !!omap + - s_0558: 1 + - s_0803: -1 + - s_4192: -1 + - s_4193: 1 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: 3.2.1.22 + - metanetx.reaction: MNXR100010 + - sbo: SBO:0000176 + - confidence_score: 0 + - !!omap + - id: r_4586 + - name: stachyose synthase + - metabolites: !!omap + - s_3998: -1 + - s_4192: -1 + - s_4193: 2 + - lower_bound: 0 + - upper_bound: 1000 + - annotation: !!omap + - ec-code: 2.4.1.- + - metanetx.reaction: MNXR122225 + - sbo: SBO:0000176 + - confidence_score: 0 - genes: - !!omap - id: Q0045 diff --git a/README.md b/README.md index 626cc6b1..fc016b1d 100644 --- a/README.md +++ b/README.md @@ -10,13 +10,13 @@ This repository contains the current consensus genome-scale metabolic model of _ **GEM Category:** Species; **Utilisation:** predictive simulation, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** curated, reconstruction; **Model Source:** [Yeast 7.6](https://sourceforge.net/projects/yeast/); **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** General Metabolism; **Condition:** aerobic, glucose-limited, defined media, maximization of growth. -* Last update: 2018-09-05 +* Last update: 2018-09-11 * Main Model Descriptors: |Taxonomy | Template Model | Reactions | Metabolites| Genes | |:-------:|:--------------:|:---------:|:----------:|:-----:| -|_Saccharomyces cerevisiae_|[Yeast 7.6](https://sourceforge.net/projects/yeast/)|3928|2666|1133| +|_Saccharomyces cerevisiae_|[Yeast 7.6](https://sourceforge.net/projects/yeast/)|3949|2680|1133| This repository is administered by Benjamín J. Sánchez ([@BenjaSanchez](https://github.com/benjasanchez)), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology. @@ -75,6 +75,7 @@ The model is available in `.xml`, `.txt`, `.yml`, `.mat` and `.xlsx` (the last 2 * `databases`: Yeast data from different databases (KEGG, SGD, swissprot, etc). * `modelCuration`: Data files used for performing curations to the model. Mostly lists of new rxns, mets or genes added (or fixed) in the model. +* `physiology`: Data on yeast growth under different conditions, biomass composition, gene essentiality experiments, etc. ## Contributors