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feat: add new ecModel
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@lylvsexinqing
lylvsexinqing committed Nov 16, 2020
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34 changes: 34 additions & 0 deletions result_ecYeast/Allchemicals-template.txt
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Expand Up @@ -759,6 +759,40 @@ Glycyrrhetinic acid Glycyrrhetinic acid_3 11-oxo-beta-amyrin 30-oxidase 11-Oxo-b
Glycyrrhetinic acid Glycyrrhetinic acid_4 Glycyrrhetinic acid transport Glycyrrhetinic acid[c] => Glycyrrhetinic acid[e] 0 0 1000
Glycyrrhetinic acid Glycyrrhetinic acid_5 Glycyrrhetinic acid exchange Glycyrrhetinic acid[e] => 1 0 1000

Taxa-4(20),11(12)-dien-6alpha-yl acetate Taxa-4(20),11(12)-dien-6alpha-yl acetate_1 Taxadiene synthase geranylgeranyl diphosphate[c] => diphosphate[c] + taxadiene[c] TASY 0 0 1000 Q2PRN4 0.16 97.962 4.2.3.17 0.1 YEP Glucose
Taxa-4(20),11(12)-dien-6alpha-yl acetate r_0904No1 phosphomevalonate kinase (No1) (R)-5-phosphomevalonic acid[c] + ATP[c] => (R)-5-diphosphomevalonic acid[c] + ADP[c] 0 0 1000 6.8 50.4544 2.7.4.2
Taxa-4(20),11(12)-dien-7alpha-yl acetate r_0735No1 mevalonate kinase (atp) (No1) (R)-mevalonate[c] + ATP[c] => (R)-5-phosphomevalonic acid[c] + ADP[c] + H+[c] 0 0 1000 43.8001 48.459 2.7.1.36
Taxa-4(20),11(12)-dien-8alpha-yl acetate r_0736No1 mevalonate kinase (ctp) (No1) (R)-mevalonate[c] + CTP[c] => (R)-5-phosphomevalonic acid[c] + CDP[c] + H+[c] 0 0 1000 43.8001 48.459 2.7.1.36
Taxa-4(20),11(12)-dien-9alpha-yl acetate r_0737No1 mevalonate kinase (gtp) (No1) (R)-mevalonate[c] + GTP[c] => (R)-5-phosphomevalonic acid[c] + GDP[c] + H+[c] 0 0 1000 43.8001 48.459 2.7.1.36
Taxa-4(20),11(12)-dien-10alpha-yl acetate r_0738No1 mevalonate kinase (UTP) (No1) (R)-mevalonate[c] + UTP[c] => (R)-5-phosphomevalonic acid[c] + H+[c] + UDP[c] 0 0 1000 43.8001 48.459 2.7.1.36
Taxa-4(20),11(12)-dien-11alpha-yl acetate r_0739No1 mevalonate pyrophoshate decarboxylase (No1) (R)-5-diphosphomevalonic acid[c] + ATP[c] => ADP[c] + carbon dioxide[c] + isopentenyl diphosphate[c] + phosphate[c] 0 0 1000 9.8 44.1154 4.1.1.33
Taxa-4(20),11(12)-dien-12alpha-yl acetate r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] 0 0 1000 2.2 40.4829 2.5.1.1
Taxa-4(20),11(12)-dien-13alpha-yl acetate r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] 0 0 1000 2.2 40.4829 2.5.1.1
Taxa-4(20),11(12)-dien-14alpha-yl acetate r_0667No1 isopentenyl-diphosphate D-isomerase (No1) isopentenyl diphosphate[c] => prenyl diphosphate(3-)[c] 0 0 1000 59800 33.3511 5.3.3.2
Taxa-4(20),11(12)-dien-15alpha-yl acetate r_0667_REVNo1 isopentenyl-diphosphate D-isomerase (reversible) (No1) prenyl diphosphate(3-)[c] => isopentenyl diphosphate[c] 0 0 1000 0.1212 33.3511 5.3.3.2
Taxa-4(20),11(12)-dien-16alpha-yl acetate Taxa-4(20),11(12)-dien-6alpha-yl acetate_2 geranylgeranyl diphosphate synthase farnesyl diphosphate[c] + isopentenyl diphosphate[c] => diphosphate[c] + geranylgeranyl diphosphate[c] crtE 0 0 1000 Q1L6K3 8.4 42.153 2.5.1.29
Taxa-4(20),11(12)-dien-17alpha-yl acetate Taxa-4(20),11(12)-dien-6alpha-yl acetate_3 Acetyl-CoA acetyltransferase acetyl-CoA[c] => coenzyme A[c] + acetoacetyl-CoA[c] mvaE 0 0 1000 Q9FD70 86.497 2.3.1.9
Taxa-4(20),11(12)-dien-18alpha-yl acetate Taxa-4(20),11(12)-dien-6alpha-yl acetate_4 Hydroxymethylglutaryl-CoA synthase acetyl-CoA[c] + acetoacetyl-CoA[c] + H2O[c] => 3-hydroxy-3-methylglutaryl-CoA[c] + coenzyme A[c] mvaS 0 0 1000 Q9FD71 7.025166667 42.151 2.3.3.10
Taxa-4(20),11(12)-dien-19alpha-yl acetate Taxa-4(20),11(12)-dien-6alpha-yl acetate_5 Taxadiene 5-alpha hydroxylase taxadiene[c] + oxygen[c] => Taxa-4(20),11-dien-5alpha-ol[c] + H2O[c] CYP725A4 0 0 1000 Q6WG30 56.558 1.14.99.37
Taxa-4(20),11(12)-dien-20alpha-yl acetate Taxa-4(20),11(12)-dien-6alpha-yl acetate_6 Taxadien-5-alpha-ol O-acetyltransferase Taxa-4(20),11-dien-5alpha-ol[c] + acetyl-CoA[c] => Taxa-4(20),11(12)-dien-5alpha-yl acetate[c] + coenzyme A[c] TAT 0 0 1000 Q9M6F0 29.59 49.08 2.3.1.162
Taxa-4(20),11(12)-dien-21alpha-yl acetate Taxa-4(20),11(12)-dien-6alpha-yl acetate_7 Taxa-4(20),11(12)-dien-5alpha-yl acetate transport Taxa-4(20),11(12)-dien-5alpha-yl acetate[c] => Taxa-4(20),11(12)-dien-6alpha-yl acetate[e] 0 0 1000
Taxa-4(20),11(12)-dien-22alpha-yl acetate Taxa-4(20),11(12)-dien-6alpha-yl acetate_8 Taxa-4(20),11(12)-dien-6alpha-yl acetate exchange Taxa-4(20),11(12)-dien-6alpha-yl acetate[e] => 1 0 1000

Vitamin A Vitamin A_1 geranylgeranyl diphosphate synthase farnesyl diphosphate[c] + isopentenyl diphosphate[c] => diphosphate[c] + geranylgeranyl diphosphate[c] crtE 0 0 1000 Q1L6K3 8.4 42.153 2.5.1.29 0.1 Min xylose YPL061W
Vitamin A Vitamin A_2 Bifunctional lycopene cyclase/phytoene synthase 2 geranylgeranyl diphosphate[c] => 2 diphosphate[c] + phytoene[c] crtYB 0 0 1000 Q7Z859 0.0834552 74.736 2.5.1.32
Vitamin A Vitamin A_3 Phytoene desaturase phytoene[c] => neurosporene[c] crtI 0 0 1000 Q7Z858 0.000314486 65.066 1.3.99.28
Vitamin A Vitamin A_4 Phytoene desaturase neurosporene[c] + oxygen[c] => 2 H2O[c] + lycopene[c] crtI 0 0 1000 Q7Z858 0.000314486 65.066 1.3.99.28
Vitamin A Vitamin A_5 Bifunctional lycopene cyclase/phytoene synthase lycopene[c] => ��-carotene[c] crtYB 0 0 1000 Q7Z859 0.4434336 74.736 5.5.1.19
Vitamin A Vitamin A_6 Beta-carotene 15,15'-dioxygenase ��-carotene[c] + oxygen[c] => 2 Retinal[c] blh 0 0 1000 Q4PNI0 0.037 31.037 1.13.11.63
Vitamin A Vitamin A_7 retinol dehydrogenase Retinal[c] + NADH[c] + H+[c] => Retinol[c] + NAD[c] ADH 0 0 1000 P00330 36.8487 1.1.1.1
Vitamin A Vitamin A_8 xylose reductase D-xylose[c] + H+[c] + NADH[c] => xylitol[c] + NAD[c] XYL1 0 0 1000 P31867 27.5 35.923 1.1.1.307
Vitamin A Vitamin A_9 xylose reductase D-xylose[c] + H+[c] + NADPH[c] => xylitol[c] + NADP(+)[c] XYL1 0 0 1000 P31867 27.5 35.923 1.1.1.307
Vitamin A Vitamin A_10 xylulose reductase xylitol[c] + NAD[c] => D-xylulose[c] + H+[c] + NADH[c] XYL2 0 0 1000 P22144 30.33 38.521 1.1.1.9
Vitamin A Vitamin A_11 xylulokinase ATP[c] + D-xylulose[c] => ADP[c] + D-xylulose 5-phosphate[c] + H+[c] XYL3 0 0 1000 Q9P938 1.144819177 69.397 2.7.1.17
Vitamin A Vitamin A_12 Vitamin A formation Retinal[c] + Retinol[c] => Vitamin A[c] 0 0 1000
Vitamin A Vitamin A_13 Vitamin A transport Vitamin A[c] => Vitamin A[e] 0 0 1000
Vitamin A Vitamin A_14 Vitamin A exchange Vitamin A[e] => 1 0 1000

Ergosterol 0.1 Min glucose
Glycine 0.1 Min glucose
Alanine 0.1 Min glucose
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Binary file modified result_ecYeast/Allchemicals-template.xlsx
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Binary file modified result_ecYeast/Data_Allchemicals.xlsx
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Binary file added result_ecYeast/ecModels/ecVitamin_A.mat
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134 changes: 116 additions & 18 deletions strain_design_ecYeast/Model_construction_others.asv
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Expand Up @@ -3103,32 +3103,130 @@ model=changeGeneAssociation(model,'newRxn1','TASY');
model=changeGeneAssociation(model,'newRxn2','crtE');
model=changeGeneAssociation(model,'newRxn3','mvaE');
model=changeGeneAssociation(model,'newRxn4','mvaS');
model=changeGeneAssociation(model,'newRxn5','CYP725A4 ');
model=changeGeneAssociation(model,'newRxn5','CYP725A4');
model=changeGeneAssociation(model,'newRxn6','TAT');
model.geneShortNames(1128)={'bAS'};
model.geneShortNames(1129)={'uni25647'};
model.geneShortNames(1130)={'CYP72A63'};
model.geneShortNames(1128)={'bAS'};
model.geneShortNames(1129)={'uni25647'};
model.geneShortNames(1130)={'CYP72A63'};

model.enzymes(964)={'Q9MB42'};
model.enzymes(965)={'A0A218KSA8'};
model.enzymes(966)={'H1A981'};
model.enzGenes(964)={'bAS'};
model.enzGenes(965)={'uni25647'};
model.enzGenes(966)={'CYP72A63'};
model.geneShortNames(1128)={'TASY'};
model.geneShortNames(1129)={'crtE'};
model.geneShortNames(1130)={'mvaE'};
model.geneShortNames(1131)={'mvaS'};
model.geneShortNames(1132)={'CYP725A4'};
model.geneShortNames(1133)={'TAT'};
model.enzymes(964)={'Q2PRN4'};
model.enzymes(965)={'Q1L6K3'};
model.enzymes(966)={'Q9FD70'};
model.enzymes(967)={'Q9FD71'};
model.enzymes(968)={'Q6WG30'};
model.enzymes(969)={'Q9M6F0'};
model.enzGenes(964)={'TASY'};
model.enzGenes(965)={'crtE'};
model.enzGenes(966)={'mvaE'};
model.enzGenes(967)={'mvaS'};
model.enzGenes(968)={'CYP725A4'};
model.enzGenes(969)={'TAT'};
model.metComps(4147)=1;
model.metComps(4148)=1;
model.metComps(4149)=1;
model.metComps(4150)=1;
model.metComps(4151)=1;
model.metComps(4152)=1;
model.metComps(4153)=3;



model.metComps(4153)=1;
model.metComps(4154)=1;
model.metComps(4155)=1;
model.metComps(4156)=3;
model=changeRxnBounds(model,'r_1714_REV',1000,'u');
model=changeRxnBounds(model,'r_2111',0.1,'l');
model=changeObjective(model,'newRxn8');
model=changeRxnBounds(model,'r_1710_REV',1,'u'); % add galactose
cd ../../strain_design_ecYeast
c_sourceID = 'D-glucose exchange (reversible)';
model = lychangeMedia_batch(model,c_sourceID,'YEP');
FBAsolution=optimizeCbModel(model)
cd ../result_ecYeast/ecModels
save ecTaxadien_5alpha_yl_acetate.mat model

% Vitamin A (xylose as carbon source)
cd ../../../ModelFiles/mat
load('ecYeastGEM_batch.mat');
model = ecModel_batch;
Kcat1=8.4*3600;
MW1=42.153;
Kcat2=0.08346*3600;
MW2=74.736;
Kcat3=0.0003*3600;
MW3=65.066;
Kcat4=0.4434*3600;
Kcat5=0.037*3600;
MW5=31.037;
MW6=36.8487;
Kcat7=27.5*3600;
MW7=35.923;
Kcat8=30.33*3600;
MW8=38.521;
Kcat9=1.1448*3600;
MW9=69.397;
model = addReaction(model,'newRxn1','metaboliteList',{'s_0190','s_0943','prot_Q1L6K3','s_0633','s_0189'},'stoichCoeffList',[-1 -1 -1/Kcat1 1 1],'reversible',false);
model = addReaction(model,'newRxn2','metaboliteList',{'s_0189','prot_Q7Z859','s_0633','s_4236'},'stoichCoeffList',[-2 -1/Kcat2 2 1],'reversible',false);
model = addReaction(model,'newRxn3','metaboliteList',{'s_4236','prot_Q7Z858','s_4237'},'stoichCoeffList',[-1 -1/Kcat3 1],'reversible',false);
model = addReaction(model,'newRxn4','metaboliteList',{'s_4237','s_1275','prot_Q7Z858','s_0803','s_4238'},'stoichCoeffList',[-1 -1 -1/Kcat3 2 1],'reversible',false);
model = addReaction(model,'newRxn5','metaboliteList',{'s_4238','prot_Q7Z859','s_4239'},'stoichCoeffList',[-1 -1/Kcat4 1],'reversible',false);
model = addReaction(model,'newRxn6','metaboliteList',{'s_4239','s_1275','prot_Q4PNI0','s_4416'},'stoichCoeffList',[-1 -1 -1/Kcat5 2],'reversible',false);
model = addReaction(model,'newRxn7','metaboliteList',{'s_4416','s_1203','s_0794','prot_P00330','s_4417','s_1198'},'stoichCoeffList',[-1 -1 -1 -1 1 1],'reversible',false);
model = addReaction(model,'newRxn8','metaboliteList',{'s_0578','s_0794','s_1203','prot_P31867','s_1566','s_1198'},'stoichCoeffList',[-1 -1 -1 -1/Kcat7 1 1],'reversible',false);
model = addReaction(model,'newRxn9','metaboliteList',{'s_0578','s_0794','s_1212','prot_P31867','s_1566','s_1207'},'stoichCoeffList',[-1 -1 -1 -1/Kcat7 1 1],'reversible',false);
model = addReaction(model,'newRxn10','metaboliteList',{'s_1566','s_1198','prot_P22144','s_0580','s_0794','s_1203'},'stoichCoeffList',[-1 -1 -1/Kcat8 1 1 1],'reversible',false);
model = addReaction(model,'newRxn11','metaboliteList',{'s_0434','s_0580','prot_Q9P938','s_0394','s_0581','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1 1],'reversible',false);
model = addReaction(model,'newRxn12','metaboliteList',{'s_4416','s_4417','s_4418'},'stoichCoeffList',[-1 -1 1],'reversible',false);
model = addReaction(model,'newRxn13','metaboliteList',{'s_4418','s_4419'},'stoichCoeffList',[-1 1],'reversible',false);
model = addReaction(model,'newRxn14','metaboliteList',{'s_4419'},'stoichCoeffList',[-1],'reversible',false);
model = addReaction(model,'newRxn15','metaboliteList',{'prot_pool','prot_Q1L6K3'},'stoichCoeffList',[-MW1 1],'reversible',false);
model = addReaction(model,'newRxn16','metaboliteList',{'prot_pool','prot_Q7Z859'},'stoichCoeffList',[-MW2 1],'reversible',false);
model = addReaction(model,'newRxn17','metaboliteList',{'prot_pool','prot_Q7Z858'},'stoichCoeffList',[-MW3 1],'reversible',false);
model = addReaction(model,'newRxn18','metaboliteList',{'prot_pool','prot_Q4PNI0'},'stoichCoeffList',[-MW5 1],'reversible',false);
model = addReaction(model,'newRxn19','metaboliteList',{'prot_pool','prot_P31867'},'stoichCoeffList',[-MW7 1],'reversible',false);
model = addReaction(model,'newRxn20','metaboliteList',{'prot_pool','prot_P22144'},'stoichCoeffList',[-MW8 1],'reversible',false);
model = addReaction(model,'newRxn21','metaboliteList',{'prot_pool','prot_Q9P938'},'stoichCoeffList',[-MW9 1],'reversible',false);
model = removeGenes(model,'YPL061W'); % delete ALD6
model=changeGeneAssociation(model,'newRxn1','crtE');
model=changeGeneAssociation(model,'newRxn2','crtYB');
model=changeGeneAssociation(model,'newRxn3','crtI');
model=changeGeneAssociation(model,'newRxn4','crtI');
model=changeGeneAssociation(model,'newRxn5','crtYB');
model=changeGeneAssociation(model,'newRxn6','blh');
model=changeGeneAssociation(model,'newRxn7','ADH');
model=changeGeneAssociation(model,'newRxn8','XYL1');
model=changeGeneAssociation(model,'newRxn9','XYL1');
model=changeGeneAssociation(model,'newRxn10','XYL2');
model=changeGeneAssociation(model,'newRxn11','XYL3');
model.geneShortNames(1127)={'crtE'};
model.geneShortNames(1128)={'crtYB'};
model.geneShortNames(1129)={'crtI'};
model.geneShortNames(1130)={'blh'};
model.geneShortNames(1131)={'ADH'};
model.geneShortNames(1132)={'XYL1'};
model.geneShortNames(1133)={'XYL2'};
model.geneShortNames(1134)={'XYL3'};
model.enzymes(964)={'Q2PRN4'};
model.enzymes(965)={'Q1L6K3'};
model.enzymes(966)={'Q9FD70'};
model.enzymes(967)={'Q9FD71'};
model.enzymes(968)={'Q6WG30'};
model.enzymes(969)={'Q9M6F0'};
model.enzGenes(964)={'TASY'};
model.enzGenes(965)={'crtE'};
model.enzGenes(966)={'mvaE'};
model.enzGenes(967)={'mvaS'};
model.enzGenes(968)={'CYP725A4'};
model.enzGenes(969)={'TAT'};
model.metComps(4147)=1;
model.metComps(4148)=1;
model.metComps(4149)=1;
model.metComps(4150)=1;
model.metComps(4151)=1;
model.metComps(4152)=1;
model.metComps(4153)=1;
model.metComps(4154)=1;
model.metComps(4155)=1;
model.metComps(4156)=3;



102 changes: 98 additions & 4 deletions strain_design_ecYeast/Model_construction_others.m
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Expand Up @@ -3103,7 +3103,7 @@ save ec(S)-reticuline.mat model
model=changeGeneAssociation(model,'newRxn2','crtE');
model=changeGeneAssociation(model,'newRxn3','mvaE');
model=changeGeneAssociation(model,'newRxn4','mvaS');
model=changeGeneAssociation(model,'newRxn5','CYP725A4 ');
model=changeGeneAssociation(model,'newRxn5','CYP725A4');
model=changeGeneAssociation(model,'newRxn6','TAT');
model.geneShortNames(1128)={'TASY'};
model.geneShortNames(1129)={'crtE'};
Expand Down Expand Up @@ -3144,9 +3144,103 @@ save ec(S)-reticuline.mat model
cd ../result_ecYeast/ecModels
save ecTaxadien_5alpha_yl_acetate.mat model




% Vitamin A (xylose as carbon source)
cd ../../../ModelFiles/mat
load('ecYeastGEM_batch.mat');
model = ecModel_batch;
Kcat1=8.4*3600;
MW1=42.153;
Kcat2=0.08346*3600;
MW2=74.736;
Kcat3=0.0003*3600;
MW3=65.066;
Kcat4=0.4434*3600;
Kcat5=0.037*3600;
MW5=31.037;
MW6=36.8487;
Kcat7=27.5*3600;
MW7=35.923;
Kcat8=30.33*3600;
MW8=38.521;
Kcat9=1.1448*3600;
MW9=69.397;
model = addReaction(model,'newRxn1','metaboliteList',{'s_0190','s_0943','prot_Q1L6K3','s_0633','s_0189'},'stoichCoeffList',[-1 -1 -1/Kcat1 1 1],'reversible',false);
model = addReaction(model,'newRxn2','metaboliteList',{'s_0189','prot_Q7Z859','s_0633','s_4236'},'stoichCoeffList',[-2 -1/Kcat2 2 1],'reversible',false);
model = addReaction(model,'newRxn3','metaboliteList',{'s_4236','prot_Q7Z858','s_4237'},'stoichCoeffList',[-1 -1/Kcat3 1],'reversible',false);
model = addReaction(model,'newRxn4','metaboliteList',{'s_4237','s_1275','prot_Q7Z858','s_0803','s_4238'},'stoichCoeffList',[-1 -1 -1/Kcat3 2 1],'reversible',false);
model = addReaction(model,'newRxn5','metaboliteList',{'s_4238','prot_Q7Z859','s_4239'},'stoichCoeffList',[-1 -1/Kcat4 1],'reversible',false);
model = addReaction(model,'newRxn6','metaboliteList',{'s_4239','s_1275','prot_Q4PNI0','s_4416'},'stoichCoeffList',[-1 -1 -1/Kcat5 2],'reversible',false);
model = addReaction(model,'newRxn7','metaboliteList',{'s_4416','s_1203','s_0794','prot_P00330','s_4417','s_1198'},'stoichCoeffList',[-1 -1 -1 -1 1 1],'reversible',false);
model = addReaction(model,'newRxn8','metaboliteList',{'s_0578','s_0794','s_1203','prot_P31867','s_1566','s_1198'},'stoichCoeffList',[-1 -1 -1 -1/Kcat7 1 1],'reversible',false);
model = addReaction(model,'newRxn9','metaboliteList',{'s_0578','s_0794','s_1212','prot_P31867','s_1566','s_1207'},'stoichCoeffList',[-1 -1 -1 -1/Kcat7 1 1],'reversible',false);
model = addReaction(model,'newRxn10','metaboliteList',{'s_1566','s_1198','prot_P22144','s_0580','s_0794','s_1203'},'stoichCoeffList',[-1 -1 -1/Kcat8 1 1 1],'reversible',false);
model = addReaction(model,'newRxn11','metaboliteList',{'s_0434','s_0580','prot_Q9P938','s_0394','s_0581','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1 1],'reversible',false);
model = addReaction(model,'newRxn12','metaboliteList',{'s_4416','s_4417','s_4418'},'stoichCoeffList',[-1 -1 1],'reversible',false);
model = addReaction(model,'newRxn13','metaboliteList',{'s_4418','s_4419'},'stoichCoeffList',[-1 1],'reversible',false);
model = addReaction(model,'newRxn14','metaboliteList',{'s_4419'},'stoichCoeffList',[-1],'reversible',false);
model = addReaction(model,'newRxn15','metaboliteList',{'prot_pool','prot_Q1L6K3'},'stoichCoeffList',[-MW1 1],'reversible',false);
model = addReaction(model,'newRxn16','metaboliteList',{'prot_pool','prot_Q7Z859'},'stoichCoeffList',[-MW2 1],'reversible',false);
model = addReaction(model,'newRxn17','metaboliteList',{'prot_pool','prot_Q7Z858'},'stoichCoeffList',[-MW3 1],'reversible',false);
model = addReaction(model,'newRxn18','metaboliteList',{'prot_pool','prot_Q4PNI0'},'stoichCoeffList',[-MW5 1],'reversible',false);
model = addReaction(model,'newRxn19','metaboliteList',{'prot_pool','prot_P31867'},'stoichCoeffList',[-MW7 1],'reversible',false);
model = addReaction(model,'newRxn20','metaboliteList',{'prot_pool','prot_P22144'},'stoichCoeffList',[-MW8 1],'reversible',false);
model = addReaction(model,'newRxn21','metaboliteList',{'prot_pool','prot_Q9P938'},'stoichCoeffList',[-MW9 1],'reversible',false);
model = removeGenes(model,'YPL061W'); % delete ALD6
model=changeGeneAssociation(model,'newRxn1','crtE');
model=changeGeneAssociation(model,'newRxn2','crtYB');
model=changeGeneAssociation(model,'newRxn3','crtI');
model=changeGeneAssociation(model,'newRxn4','crtI');
model=changeGeneAssociation(model,'newRxn5','crtYB');
model=changeGeneAssociation(model,'newRxn6','blh');
model=changeGeneAssociation(model,'newRxn7','ADH');
model=changeGeneAssociation(model,'newRxn8','XYL1');
model=changeGeneAssociation(model,'newRxn9','XYL1');
model=changeGeneAssociation(model,'newRxn10','XYL2');
model=changeGeneAssociation(model,'newRxn11','XYL3');
model.geneShortNames(1127)={'crtE'};
model.geneShortNames(1128)={'crtYB'};
model.geneShortNames(1129)={'crtI'};
model.geneShortNames(1130)={'blh'};
model.geneShortNames(1131)={'ADH'};
model.geneShortNames(1132)={'XYL1'};
model.geneShortNames(1133)={'XYL2'};
model.geneShortNames(1134)={'XYL3'};
model.enzymes(964)={'Q1L6K3'};
model.enzymes(965)={'Q7Z859'};
model.enzymes(966)={'Q7Z858'};
model.enzymes(967)={'Q4PNI0'};
model.enzymes(968)={'P31867'};
model.enzymes(969)={'P22144'};
model.enzymes(970)={'Q9P938'};
model.enzGenes(964)={'crtE'};
model.enzGenes(965)={'crtYB'};
model.enzGenes(966)={'crtI'};
model.enzGenes(967)={'blh'};
model.enzGenes(968)={'XYL1'};
model.enzGenes(969)={'XYL2'};
model.enzGenes(970)={'XYL3'};
model.metComps(4147)=1;
model.metComps(4148)=1;
model.metComps(4149)=1;
model.metComps(4150)=1;
model.metComps(4151)=1;
model.metComps(4152)=1;
model.metComps(4153)=1;
model.metComps(4154)=1;
model.metComps(4155)=1;
model.metComps(4156)=1;
model.metComps(4157)=1;
model.metComps(4158)=1;
model.metComps(4159)=1;
model.metComps(4160)=1;
model.metComps(4161)=3;
model=changeRxnBounds(model,'r_1714_REV',0,'u');
model=changeRxnBounds(model,'r_1718_REV',1000,'u');
model=changeRxnBounds(model,'r_2111',0.1,'l');
model=changeObjective(model,'newRxn14');
FBAsolution=optimizeCbModel(model)
cd ../../result_ecYeast/ecModels
save ecVitamin_A.mat model



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@IVANDOMENZAIN
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@lylvsexinqing and @hongzhonglu hello!

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