diff --git a/ComplementaryData/modelCuration/GapfillingnewRxnProp.tsv b/ComplementaryData/modelCuration/GapfillingnewRxnProp.tsv index 89dbcca3..527cb206 100644 --- a/ComplementaryData/modelCuration/GapfillingnewRxnProp.tsv +++ b/ComplementaryData/modelCuration/GapfillingnewRxnProp.tsv @@ -1,29 +1,29 @@ -rxnID rev GPR standard_name EC rxnID_kegg rxnID_MNX Source;reason -MNXR94845 1 3-(4-hydroxyphenyl)pyruvate transport MNXR94845 seed:rxn09802; unknown transporter -MNXR95431 1 acetate transport MNXR95431 rhea:27814; unknown transporter -MNXR95481 1 ADP-ribose transport MNXR95481 bigg:ADPRIBt; unknown transporter -MNXR99646 1 farnesyl diphosphate transport MNXR99646 seed:rxn13290; unknown transporter -MNXR101858 1 nicotinate transport MNXR101858 seed:rxn12806; unknown transporter -MNXR135002 1 O-phosphoethanolamine transport MNXR135002 seed:rxn05716; unknown transporter -MNXR102871 1 phosphate transport MNXR102871 rhea:32823; bigg:PItg; unknown transporter -MNXR106312 0 propionyl-CoA transport MNXR106312 bigg:r2499; unknown transporter -MNXR105076 1 UDP transport MNXR105076 bigg:UDPtg; unknown transporter -MNXR105076_2 1 UDP transport MNXR105076 bigg:UDPtg; unknown transporter -MNXR105127 1 UMP transport MNXR105127 rhea:27926; unknown transporter -MNXR104921 1 TRX1 disulphide transport MNXR104921 seed:rxn13406; unknown transporter -MNXR99110 1 oleate transport MNXR99110 rhea:33655; unknown transporter -MNXR95426 1 (R)-acetoin transport MNXR95426 bigg:ACTNt2r; unknown transporter -MNXR100259 1 L-glutamine transport MNXR100259 seed:rxn08625; bigg:GLNtm; unknown transporter -MNXR105127_2 1 UMP transport MNXR105127 rhea:27926; unknown transporter -MNXR95809 1 S-adenosyl-L-methionine transport MNXR95809 seed:rxn09784; bigg:AMETtn; unknown transporter -MNXR100449 1 glutathione transport MNXR100449 seed:rxn08677; unknown transporter -MNXR96123 1 ATP transport 2.7.4.6 MNXR96123 rhea:34999; unknown transporter -MNXR101385 1 D-mannose 6-phosphate transport MNXR101385 seed:rxn08880; unknown transporter -MNXR95416 1 O-acetyl-L-serine transport MNXR95416 rhea:29659; bigg:ACSERtmi; unknown transporter -MNXR100494 1 hydrogen sulfide transport MNXR100494 seed:rxn08689; unknown transporter -MNXR97002 1 L-cysteinylglycine transport MNXR97002 seed:rxn05529; unknown transporter -MNXR96123_2 1 ATP transport 2.7.4.6 MNXR96123 rhea:34999; unknown transporter -MNXR104966 1 thiosulfate transport MNXR104966 rhea:32807; unknown transporter -MNXR104460 1 sulphite transport MNXR104460 seed:rxn09260; unknown transporter -MNXR105071 1 UDP-D-glucose transport MNXR105071 seed:rxn09353; unknown transporter -MNXR105021 1 UDP-N-acetyl-alpha-D-glucosamine transport MNXR105021 seed:rxn09342; unknown transporter +rxnID rev GPR standard_name EC rxnID_kegg rxnID_MNX bigg Source;reason +MNXR94845 1 3-(4-hydroxyphenyl)pyruvate transport MNXR94845 seed:rxn09802; unknown transporter +MNXR95431 1 acetate transport MNXR95431 rhea:27814; unknown transporter +MNXR95481 1 ADP-ribose transport MNXR95481 ADPRIBt unknown transporter +MNXR99646 1 farnesyl diphosphate transport MNXR99646 seed:rxn13290; unknown transporter +MNXR101858 1 nicotinate transport MNXR101858 seed:rxn12806; unknown transporter +MNXR135002 1 O-phosphoethanolamine transport MNXR135002 seed:rxn05716; unknown transporter +MNXR102871 1 phosphate transport MNXR102871 PItg rhea:32823; unknown transporter +MNXR106312 0 propionyl-CoA transport MNXR106312 r2499 unknown transporter +MNXR105076 1 UDP transport MNXR105076 UDPtg unknown transporter +MNXR105076_2 1 UDP transport MNXR105076 UDPtg unknown transporter +MNXR105127 1 UMP transport MNXR105127 rhea:27926; unknown transporter +MNXR104921 1 TRX1 disulphide transport MNXR104921 seed:rxn13406; unknown transporter +MNXR99110 1 oleate transport MNXR99110 rhea:33655; unknown transporter +MNXR95426 1 (R)-acetoin transport MNXR95426 ACTNt2r unknown transporter +MNXR100259 1 L-glutamine transport MNXR100259 GLNtm seed:rxn08625; unknown transporter +MNXR105127_2 1 UMP transport MNXR105127 rhea:27926; unknown transporter +MNXR95809 1 S-adenosyl-L-methionine transport MNXR95809 AMETtn seed:rxn09784;unknown transporter +MNXR100449 1 glutathione transport MNXR100449 seed:rxn08677; unknown transporter +MNXR96123 1 ATP transport 2.7.4.6 MNXR96123 rhea:34999; unknown transporter +MNXR101385 1 D-mannose 6-phosphate transport MNXR101385 seed:rxn08880; unknown transporter +MNXR95416 1 O-acetyl-L-serine transport MNXR95416 ACSERtmi rhea:29659;unknown transporter +MNXR100494 1 hydrogen sulfide transport MNXR100494 seed:rxn08689; unknown transporter +MNXR97002 1 L-cysteinylglycine transport MNXR97002 seed:rxn05529; unknown transporter +MNXR96123_2 1 ATP transport 2.7.4.6 MNXR96123 rhea:34999; unknown transporter +MNXR104966 1 thiosulfate transport MNXR104966 rhea:32807; unknown transporter +MNXR104460 1 sulphite transport MNXR104460 seed:rxn09260; unknown transporter +MNXR105071 1 UDP-D-glucose transport MNXR105071 seed:rxn09353; unknown transporter +MNXR105021 1 UDP-N-acetyl-alpha-D-glucosamine transport MNXR105021 seed:rxn09342; unknown transporter \ No newline at end of file diff --git a/ComplementaryScripts/modelCuration/CheckEnergyProduction.m b/ComplementaryScripts/modelCuration/CheckEnergyProduction.m index 1f3e8e34..cbbff528 100755 --- a/ComplementaryScripts/modelCuration/CheckEnergyProduction.m +++ b/ComplementaryScripts/modelCuration/CheckEnergyProduction.m @@ -19,9 +19,9 @@ mets,coefs,false,0,1000); model_test = changeObjective(model_test,'GenerateATP', 1); sol = optimizeCbModel(model_test); - if sol.obj <= 360 && sol.obj > 0 %later can be changed to the experimental value + if sol.f <= 360 && sol.f > 0 %later can be changed to the experimental value energyResults = [energyResults; model.rxns(rxnID),'pass',num2str(sol.obj)]; - elseif sol.obj > 360 + elseif sol.f > 360 energyResults = [energyResults; model.rxns(rxnID),'Fail',num2str(sol.obj)]; else energyResults = [energyResults; model.rxns(rxnID),'error','error']; @@ -37,7 +37,7 @@ mets,coefs,false,0,1000); model_test = changeObjective(model_test, model_test.rxns(end), 1); sol = optimizeCbModel(model_test); - if sol.obj <= 120 && sol.obj > 0 %later can be changed to the experimental value + if sol.f <= 120 && sol.f > 0 %later can be changed to the experimental value redoxResults = [redoxResults; model.rxns(rxnID),'pass',num2str(sol.obj)]; elseif sol.obj > 120 redoxResults = [redoxResults; model.rxns(rxnID),'Fail',num2str(sol.obj)]; diff --git a/ComplementaryScripts/modelCuration/addGapfillingRxnToGEM.m b/ComplementaryScripts/modelCuration/addGapfillingRxnToGEM.m index df3fbc69..b7915d6e 100644 --- a/ComplementaryScripts/modelCuration/addGapfillingRxnToGEM.m +++ b/ComplementaryScripts/modelCuration/addGapfillingRxnToGEM.m @@ -21,15 +21,16 @@ % Load rxn properties data: fid = fopen('../ComplementaryData/modelCuration/GapfillingnewRxnProp.tsv','r'); -rev = textscan(fid,'%s %s %s %s %s %s %s %s','Delimiter','\t','HeaderLines',1); +rev = textscan(fid,'%s %s %s %s %s %s %s %s %s','Delimiter','\t','HeaderLines',1); newrxn.ID = rev{1}; newrxn.Rev = cellfun(@str2num, rev{2}); newrxn.GPR = rev{3}; newrxn.rxnNames = rev{4}; newrxn.rxnECNumbers = rev{5}; newrxn.rxnKEGGID = rev{6}; -newrxn.rxnNotes = rev{7}; -newrxn.rxnMetaNetXID = rev{8}; +newrxn.rxnMetaNetXID = rev{7}; +newrxn.rxnBiGGID = rev{8}; +newrxn.rxnNotes = rev{9}; for i = 1:length(newrxn.rxnMetaNetXID) if ~startsWith(newrxn.rxnMetaNetXID{i},'MNXR') newrxn.rxnMetaNetXID{i} = ''; @@ -113,6 +114,7 @@ model.rxnECNumbers(rxnIndex) = newrxn.rxnECNumbers(i); model.rxnKEGGID(rxnIndex) = newrxn.rxnKEGGID(i); model.rxnMetaNetXID(rxnIndex) = newrxn.rxnMetaNetXID(i); + model.rxnBiGGID(rxnIndex) = newrxn.rxnBiGGID(i); model.rxnConfidenceScores(rxnIndex) = 0; model.rxnNotes{rxnIndex} = ['NOTES: added after Gapfilling (PR #185); ',newrxn.rxnNotes{i}]; end diff --git a/ModelFiles/xml/yeastGEM.xml b/ModelFiles/xml/yeastGEM.xml index ffa9925c..f34adeb3 100644 --- a/ModelFiles/xml/yeastGEM.xml +++ b/ModelFiles/xml/yeastGEM.xml @@ -193691,7 +193691,7 @@

Confidence Level: 1

-

NOTES: added after the Biolog update (PR #149); bigg:EX_glyc2p_e;glycerol 2-phosphate(2-)_P Source | MetaNetX ID curated (PR #220)

+

NOTES: added after the Biolog update (PR #149); bigg:GLYC2Ptex;glycerol 2-phosphate(2-)_P Source | MetaNetX ID curated (PR #220)

 @@ -194144,7 +194144,7 @@

Confidence Level: 1

-

NOTES: added after the Biolog update (PR #149); bigg:RE2034C;2-aminobutanoate_N Source

+

NOTES: added after the Biolog update (PR #149); 2-aminobutanoate_N Source

 @@ -195447,7 +195447,7 @@

Confidence Level: 2

-

NOTES: added after the Biolog update (PR #149); bigg:TAGAT_Dt;D-tagatose_C Source

+

NOTES: added after the Biolog update (PR #149); D-tagatose_C Source

 @@ -195534,7 +195534,7 @@

Confidence Level: 1

-

NOTES: added after the Biolog update (PR #149); bigg:RE2640C;N(alpha)-acetyl-L-methionine_S Source

+

NOTES: added after the Biolog update (PR #149); N(alpha)-acetyl-L-methionine_S Source

 @@ -197335,7 +197335,7 @@

Confidence Level: 1

-

NOTES: added after the Biolog update (PR #149); bigg:EX_g6p_e;D-glucose 6-phosphate_P Source | MetaNetX ID curated (PR #220)

+

NOTES: added after the Biolog update (PR #149); bigg:G6Ptex;D-glucose 6-phosphate_P Source | MetaNetX ID curated (PR #220)

 @@ -197591,7 +197591,7 @@

Confidence Level: 1

-

NOTES: added after the Biolog update (PR #149); bigg:CHOLPtg;choline phosphate_P Source

+

NOTES: added after the Biolog update (PR #149); choline phosphate_P Source

 @@ -198669,7 +198669,7 @@

Confidence Level: NaN

-

NOTES: added after the Biolog update (PR #149); bigg:EX_meoh_e;methyl alpha-D-glucopyranoside_C Source | MetaNetX ID curated (PR #220)

+

NOTES: added after the Biolog update (PR #149); methyl alpha-D-glucopyranoside_C Source | MetaNetX ID curated (PR #220)

 @@ -201734,12 +201734,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR94845

+

NOTES: added after Gapfilling (PR #185); seed:rxn09802; unknown transporter

 + + + + + @@ -201761,12 +201766,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR95431

+

NOTES: added after Gapfilling (PR #185); rhea:27814; unknown transporter

 + + + + + @@ -201786,12 +201796,18 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR95481

+

NOTES: added after Gapfilling (PR #185); unknown transporter

 + + + + + + @@ -201811,12 +201827,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR99646

+

NOTES: added after Gapfilling (PR #185); seed:rxn13290; unknown transporter

 + + + + + @@ -201836,12 +201857,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR101858

+

NOTES: added after Gapfilling (PR #185); seed:rxn12806; unknown transporter

 + + + + + @@ -201863,12 +201889,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR135002

+

NOTES: added after Gapfilling (PR #185); seed:rxn05716; unknown transporter

 + + + + + @@ -201890,12 +201921,18 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR102871

+

NOTES: added after Gapfilling (PR #185); rhea:32823; unknown transporter

 + + + + + + @@ -201915,12 +201952,18 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR106312

+

NOTES: added after Gapfilling (PR #185); unknown transporter

 + + + + + + @@ -201945,12 +201988,18 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR105076

+

NOTES: added after Gapfilling (PR #185); unknown transporter

 + + + + + + @@ -201970,12 +202019,18 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR105076

+

NOTES: added after Gapfilling (PR #185); unknown transporter

 + + + + + + @@ -201995,12 +202050,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR105127

+

NOTES: added after Gapfilling (PR #185); rhea:27926; unknown transporter

 + + + + + @@ -202020,12 +202080,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR104921

+

NOTES: added after Gapfilling (PR #185); seed:rxn13406; unknown transporter

 + + + + + @@ -202045,12 +202110,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR99110

+

NOTES: added after Gapfilling (PR #185); rhea:33655; unknown transporter

 + + + + + @@ -202070,12 +202140,18 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR95426

+

NOTES: added after Gapfilling (PR #185); unknown transporter

 + + + + + + @@ -202097,12 +202173,18 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR100259

+

NOTES: added after Gapfilling (PR #185); seed:rxn08625; unknown transporter

 + + + + + + @@ -202122,12 +202204,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR105127

+

NOTES: added after Gapfilling (PR #185); rhea:27926; unknown transporter

 + + + + + @@ -202147,12 +202234,18 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR95809

+

NOTES: added after Gapfilling (PR #185); seed:rxn09784;unknown transporter

 + + + + + + @@ -202172,12 +202265,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR100449

+

NOTES: added after Gapfilling (PR #185); seed:rxn08677; unknown transporter

 + + + + + @@ -202197,7 +202295,7 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR96123

+

NOTES: added after Gapfilling (PR #185); rhea:34999; unknown transporter

 @@ -202206,6 +202304,7 @@ + @@ -202229,12 +202328,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR101385

+

NOTES: added after Gapfilling (PR #185); seed:rxn08880; unknown transporter

 + + + + + @@ -202254,12 +202358,18 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR95416

+

NOTES: added after Gapfilling (PR #185); rhea:29659;unknown transporter

 + + + + + + @@ -202279,12 +202389,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR100494

+

NOTES: added after Gapfilling (PR #185); seed:rxn08689; unknown transporter

 + + + + + @@ -202304,12 +202419,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR97002

+

NOTES: added after Gapfilling (PR #185); seed:rxn05529; unknown transporter

 + + + + + @@ -202331,7 +202451,7 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR96123

+

NOTES: added after Gapfilling (PR #185); rhea:34999; unknown transporter

 @@ -202340,6 +202460,7 @@ + @@ -202363,12 +202484,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR104966

+

NOTES: added after Gapfilling (PR #185); rhea:32807; unknown transporter

 + + + + + @@ -202388,12 +202514,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR104460

+

NOTES: added after Gapfilling (PR #185); seed:rxn09260; unknown transporter

 + + + + + @@ -202413,12 +202544,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR105071

+

NOTES: added after Gapfilling (PR #185); seed:rxn09353; unknown transporter

 + + + + + @@ -202438,12 +202574,17 @@

Confidence Level: 0

-

NOTES: added after Gapfilling (PR #185); MNXR105021

+

NOTES: added after Gapfilling (PR #185); seed:rxn09342; unknown transporter

 + + + + + diff --git a/ModelFiles/yml/yeastGEM.yml b/ModelFiles/yml/yeastGEM.yml index 46ff7f86..27bb5bb8 100644 --- a/ModelFiles/yml/yeastGEM.yml +++ b/ModelFiles/yml/yeastGEM.yml @@ -98044,6 +98044,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR94845 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98055,6 +98056,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR95431 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98066,6 +98068,8 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - bigg.reaction: ADPRIBt + - metanetx.reaction: MNXR95481 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98077,6 +98081,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR99646 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98090,6 +98095,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR101858 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98103,6 +98109,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR135002 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98114,6 +98121,8 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - bigg.reaction: PItg + - metanetx.reaction: MNXR102871 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98130,6 +98139,8 @@ - lower_bound: 0 - upper_bound: 1000 - annotation: !!omap + - bigg.reaction: r2499 + - metanetx.reaction: MNXR106312 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98141,6 +98152,8 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - bigg.reaction: UDPtg + - metanetx.reaction: MNXR105076 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98152,6 +98165,8 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - bigg.reaction: UDPtg + - metanetx.reaction: MNXR105076 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98163,6 +98178,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR105127 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98174,6 +98190,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR104921 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98185,6 +98202,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR99110 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98198,6 +98216,8 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - bigg.reaction: ACTNt2r + - metanetx.reaction: MNXR95426 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98209,6 +98229,8 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - bigg.reaction: GLNtm + - metanetx.reaction: MNXR100259 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98220,6 +98242,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR105127 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98231,6 +98254,8 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - bigg.reaction: AMETtn + - metanetx.reaction: MNXR95809 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98242,6 +98267,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR100449 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98256,6 +98282,7 @@ - upper_bound: 1000 - annotation: !!omap - ec-code: 2.7.4.6 + - metanetx.reaction: MNXR96123 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98267,6 +98294,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR101385 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98278,6 +98306,8 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - bigg.reaction: ACSERtmi + - metanetx.reaction: MNXR95416 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98289,6 +98319,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR100494 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98302,6 +98333,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR97002 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98316,6 +98348,7 @@ - upper_bound: 1000 - annotation: !!omap - ec-code: 2.7.4.6 + - metanetx.reaction: MNXR96123 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98327,6 +98360,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR104966 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98338,6 +98372,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR104460 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98349,6 +98384,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR105071 - sbo: SBO:0000655 - confidence_score: 0 - !!omap @@ -98360,6 +98396,7 @@ - lower_bound: -1000 - upper_bound: 1000 - annotation: !!omap + - metanetx.reaction: MNXR105021 - sbo: SBO:0000655 - confidence_score: 0 - genes: diff --git a/README.md b/README.md index 413b606c..276746c8 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ This repository contains the current consensus genome-scale metabolic model of _ **GEM Category:** species; **Utilisation:** experimental data reconstruction, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** reconstruction, curated; **Model Source:** YeastMetabolicNetwork; **Omic Source:** genomics, metabolomics; **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** general metabolism; **Bioreactor**; **Strain:** S288C; **Condition:** aerobic, glucose-limited, defined media; -* Last update: 2020-06-12 +* Last update: 2020-06-19 * Main Model Descriptors: