diff --git a/ComplementaryData/Amorphadiene_GEM/newpathway_newRxnMatrix.tsv b/ComplementaryData/Amorphadiene_GEM/newpathway_newRxnMatrix.tsv new file mode 100644 index 0000000..4d27260 --- /dev/null +++ b/ComplementaryData/Amorphadiene_GEM/newpathway_newRxnMatrix.tsv @@ -0,0 +1,7 @@ +rxnID coefficient Metabolite standard name Metabolite_type compartment +MNXR111232 1 farnesyl diphosphate reactant cytoplasm +MNXR111232 1 diphosphate product cytoplasm +MNXR111232 1 amorphadiene product cytoplasm +Amorphadiene transport 1 amorphadiene reactant cytoplasm +Amorphadiene transport 1 amorphadiene product extracellular +Amorphadiene exchange 1 amorphadiene reactant extracellular diff --git a/ComplementaryData/Amorphadiene_GEM/newpathway_newRxnMetAnnotation.tsv b/ComplementaryData/Amorphadiene_GEM/newpathway_newRxnMetAnnotation.tsv new file mode 100644 index 0000000..e4a9cc5 --- /dev/null +++ b/ComplementaryData/Amorphadiene_GEM/newpathway_newRxnMetAnnotation.tsv @@ -0,0 +1,3 @@ +NewMetName Charged formula Charge compartment KEGG ID CHEBI ID Remark +amorphadiene [cytoplasm] C15H24 0 cytoplasm CHEBI:52026 MNXM3912 +amorphadiene [extracellular] C15H24 0 extracellular CHEBI:52026 MNXM3912 diff --git a/ComplementaryData/Amorphadiene_GEM/newpathway_newRxnProp.tsv b/ComplementaryData/Amorphadiene_GEM/newpathway_newRxnProp.tsv new file mode 100644 index 0000000..8187029 --- /dev/null +++ b/ComplementaryData/Amorphadiene_GEM/newpathway_newRxnProp.tsv @@ -0,0 +1,4 @@ +rxnID rev GPR rxn_name_seed EC rxnID_kegg Source;reason +MNXR111232 0 amorphadiene synthase 4.2.3.24 R07630 rhea:26446 +Amorphadiene transport 0 Amorphadiene transport NA +Amorphadiene exchange 0 Amorphadiene exchange NA diff --git a/result_ecYeast/Allchemicals-template.txt b/result_ecYeast/Allchemicals-template.txt index f0ac6ba..3aa795a 100644 --- a/result_ecYeast/Allchemicals-template.txt +++ b/result_ecYeast/Allchemicals-template.txt @@ -1,701 +1,962 @@ -Chemicals rxns rxnNames formulas grRules c lb ub proteins kcats MWs EC_number ¦Ì qO2 ATP Medium Carbon source deletion -Lactic acid Lactic acid_1 L-lactate dehydrogenase pyruvate[c] + NADH[c] + H+[c] => (S)-lactate[c] + NAD[c] LDHA 0 0 1000 P19858 7.0146 36.598 1.1.1.27 0.29 YEP glucose YDL022W,YML054C,YLR044C,YOL086C,YPL061W -Lactic acid Lactic acid_2 acetaldehyde dehydrogenase acetaldehyde[c] + coenzyme A[c] + NAD[c] => acetyl-CoA[c] + NADH[c] + H+[c] EutE 0 0 1000 P77445 15.7 49.022 1.2.1.10 -Lactic acid Lactic acid_3 L-lactate transport (S)-lactate[c] => (S)-lactate[e] 0 0 1000 -Lactic acid Lactic acid_4 L-lactate exchange (S)-lactate[e] => 1 0 1000 - -Malate r_0958No1 pyruvate carboxylase (No1) pmet_r_0958[c] => ADP[c] + H+[c] + oxaloacetate[c] + phosphate[c] YBR218C 0 0 1000 P32327 0.52 130.166 0.1 Min glucose YLR044C,YLR134W,YGR087C,YDL078C -Malate r_0958No2 pyruvate carboxylase (No2) pmet_r_0958[c] => ADP[c] + H+[c] + oxaloacetate[c] + phosphate[c] YGL062W 0 0 1000 P11154 0.52 130.098 -Malate r_0714_REVNo1 malate dehydrogenase, cytoplasmic (reversible) (No1) H+[c] + NADH[c] + oxaloacetate[c] => (S)-malate[c] + NAD[c] YOL126C 0 0 1000 P22133 20.70467083 40.7305 -Malate r_1901_REV L-malate transport (reversible) (S)-malate[c] => (S)-malate[e] mae1 0 0 1000 P50537 49.304 2.A.16.2.1 - -cis,cis-muconic acid cis,cis-muconic acid_1 dehydroshikimate dehydratase 3-dehydroshikimate[c] => 3,4-Dihydroxybenzoate[c] + H2O[c] Pa_5_5120 0 0 1000 3DSD 121.44 40.48 4.2.1.118 0.1 YEP glucose YDR035W,YBR249C,YNL241C -cis,cis-muconic acid cis,cis-muconic acid_2 protocatechuic acid decarboxylase 3,4-Dihydroxybenzoate[c] + H+[c] => carbon dioxide[c] + Catechol[c] ECL_01944 0 0 1000 A0A0H3CJN8 90 53.541 4.1.1.63 -cis,cis-muconic acid cis,cis-muconic acid_3 catechol 1,2-dioxygenase Catechol[c] + oxygen[c] => 2 H+[c] + cis,cis-muconate[c] HQD2 0 0 1000 P86029 157.7333333 33.8 1.13.11.1 -cis,cis-muconic acid cis,cis-muconic acid_4 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.082809792 39.7487 2.5.1.54 -cis,cis-muconic acid cis,cis-muconic acid_5 cis,cis-muconic acid transport cis,cis-muconate[c] => cis,cis-muconate[e] 0 0 1000 -cis,cis-muconic acid cis,cis-muconic acid_6 cis,cis-muconic acid exchange cis,cis-muconate[e] => 1 0 1000 - -Resveratrol Resveratrol_1 tyrosine ammonia-lyase L-tyrosine[c] => ammonium[c] + trans-4-coumarate[c] Haur_4629 0 0 1000 A9B0P2 0.076 56.397 4.3.1.23 0.15 Min glucose -Resveratrol Resveratrol_2 4-coumaryl-CoA ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => AMP[c] + diphosphate[c] + 4-coumaroyl-CoA[c] 4CL1 0 0 1000 Q42524 12.719375 61.053 6.2.1.12 -Resveratrol Resveratrol_3 resveratrol synthase 3 H+[c] + 4-coumaroyl-CoA[c] + 3 malonyl-CoA[c] => 4 coenzyme A[c] + 4 carbon dioxide[c] + resveratrol[c] VST1 0 0 1000 P28343 0.003 42.84 2.3.1.95 -Resveratrol Resveratrol_4 resveratrol transport resveratrol[c] => resveratrol[e] 0 0 1000 -Resveratrol Resveratrol_5 resveratrol exchange resveratrol[e] => 1 0 1000 - -Genistein Genistein_1 Phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL 0 0 1000 P45730 22 77.919 4.3.1.24 0.1 YEP glucose -Genistein Genistein_2 Cinnamate-4-hydroxylase H+[c] + oxygen[c] + cinnamate[c] + NADPH[c] => H2O[c] + NADP(+)[c] + trans-4-coumarate[c] C4H 0 0 1000 C0LUU6 161.8 58.011 1.14.13.11 -Genistein Genistein_3 4-coumarate:CoA ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => diphosphate[c] + AMP[c] + 4-coumaroyl-CoA[c] 4CL 0 0 1000 C0LUU7 0.101656667 60.994 6.2.1.12 -Genistein Genistein_4 Isoflavone synthase naringenin[c] => 3 H+[c] + genistein[c] IFS 0 0 Inf Q9M6D6 58.93 1.14.14.87 -Genistein Genistein_5 Chalcone synthase 2 H+[c] + 4-coumaroyl-CoA[c] + 3 malonyl-CoA[c] => 4 coenzyme A[c] + 3 carbon dioxide[c] + naringenin chalcone[c] CHS 0 0 1000 Q6X0M9 0.006019133 42.488 2.3.1.74 -Genistein Genistein_6 Chalcone isomerase H+[c] + naringenin chalcone[c] => naringenin[c] CHI 0 0 1000 C0LUV0 139.8476667 24.679 5.5.1.6 -Genistein Genistein_7 Flavanone 3-hydroxylase naringenin[c] + oxygen[c] + 2-oxoglutarate[c] => carbon dioxide[c] + succinate[c] + dihydrokaempferol[c] F3H 0 0 0 Q53B69 42.673 1.14.11.9 -Genistein Genistein_8 Flavonoid 3'-hydroxylase H+[c] + oxygen[c] + NADPH[c] + dihydrokaempferol[c] => dihydroquercetin[c] + H2O[c] + NADP(+)[c] F3'H 0 0 0 Q8W3Y5 12.5 56.982 1.14.13.21 -Genistein Genistein_9 Flavonol synthase dihydrokaempferol[c] + 2-oxoglutarate[c] + oxygen[c] => H+[c] + carbon dioxide[c] + H2O[c] + succinate[c] + kaempferol[c] FLS 0 0 0 C0LUV3 6.6 40.041 1.14.11.23 -Genistein Genistein_10 Flavonol synthase dihydroquercetin[c] + 2-oxoglutarate[c] + oxygen[c] => H+[c] + carbon dioxide[c] + H2O[c] + succinate[c] + quercetin[c] FLS 0 0 0 C0LUV3 3.9 40.041 1.14.11.23 -Genistein Genistein_11 quercetin transport quercetin[c] => quercetin[e] 0 0 1000 -Genistein Genistein_12 quercetin exchange quercetin[e] => 0 0 1000 -Genistein Genistein_13 kaempferol transport kaempferol[c] => kaempferol[e] 0 0 1000 -Genistein Genistein_14 kaempferol exchange kaempferol[e] => 0 0 1000 -Genistein Genistein_15 genisteinl transport genistein[c] => genistein[e] 0 0 1000 -Genistein Genistein_16 genistein exchange genistein[e] => 1 0 1000 - -Kaempferol Kaempferol_1 Phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL 0 0 1000 P45730 22 77.919 4.3.1.24 0.1 YEP glucose -Kaempferol Kaempferol_2 Cinnamate-4-hydroxylase H+[c] + oxygen[c] + cinnamate[c] + NADPH[c] => H2O[c] + NADP(+)[c] + trans-4-coumarate[c] C4H 0 0 1000 C0LUU6 161.8 58.011 1.14.13.11 -Kaempferol Kaempferol_3 4-coumarate:CoA ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => diphosphate[c] + AMP[c] + 4-coumaroyl-CoA[c] 4CL 0 0 1000 C0LUU7 0.101656667 60.994 6.2.1.12 -Kaempferol Kaempferol_4 Isoflavone synthase naringenin[c] => 3 H+[c] + genistein[c] IFS 0 0 0 Q9M6D6 58.93 1.14.14.87 -Kaempferol Kaempferol_5 Chalcone synthase 2 H+[c] + 4-coumaroyl-CoA[c] + 3 malonyl-CoA[c] => 4 coenzyme A[c] + 3 carbon dioxide[c] + naringenin chalcone[c] CHS 0 0 1000 Q6X0M9 0.006019133 42.488 2.3.1.74 -Kaempferol Kaempferol_6 Chalcone isomerase H+[c] + naringenin chalcone[c] => naringenin[c] CHI 0 0 1000 C0LUV0 139.8476667 24.679 5.5.1.6 -Kaempferol Kaempferol_7 Flavanone 3-hydroxylase naringenin[c] + oxygen[c] + 2-oxoglutarate[c] => carbon dioxide[c] + succinate[c] + dihydrokaempferol[c] F3H 0 0 1000 Q53B69 42.673 1.14.11.9 -Kaempferol Kaempferol_8 Flavonoid 3'-hydroxylase H+[c] + oxygen[c] + NADPH[c] + dihydrokaempferol[c] => dihydroquercetin[c] + H2O[c] + NADP(+)[c] F3'H 0 0 1000 Q8W3Y5 12.5 56.982 1.14.13.21 -Kaempferol Kaempferol_9 Flavonol synthase dihydrokaempferol[c] + 2-oxoglutarate[c] + oxygen[c] => H+[c] + carbon dioxide[c] + H2O[c] + succinate[c] + kaempferol[c] FLS 0 0 Inf C0LUV3 6.6 40.041 1.14.11.23 -Kaempferol Kaempferol_10 Flavonol synthase dihydroquercetin[c] + 2-oxoglutarate[c] + oxygen[c] => H+[c] + carbon dioxide[c] + H2O[c] + succinate[c] + quercetin[c] FLS 0 0 0 C0LUV3 3.9 40.041 1.14.11.23 -Kaempferol Kaempferol_11 quercetin transport quercetin[c] => quercetin[e] 0 0 1000 -Kaempferol Kaempferol_12 quercetin exchange quercetin[e] => 0 0 1000 -Kaempferol Kaempferol_13 kaempferol transport kaempferol[c] => kaempferol[e] 0 0 1000 -Kaempferol Kaempferol_14 kaempferol exchange kaempferol[e] => 1 0 1000 -Kaempferol Kaempferol_15 genisteinl transport genistein[c] => genistein[e] 0 0 1000 -Kaempferol Kaempferol_16 genistein exchange genistein[e] => 0 0 1000 - -Quercetin Quercetin_1 Phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL 0 0 1000 P45730 22 77.919 4.3.1.24 0.1 YEP glucose -Quercetin Quercetin_2 Cinnamate-4-hydroxylase H+[c] + oxygen[c] + cinnamate[c] + NADPH[c] => H2O[c] + NADP(+)[c] + trans-4-coumarate[c] C4H 0 0 1000 C0LUU6 161.8 58.011 1.14.13.11 -Quercetin Quercetin_3 4-coumarate:CoA ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => diphosphate[c] + AMP[c] + 4-coumaroyl-CoA[c] 4CL 0 0 1000 C0LUU7 0.101656667 60.994 6.2.1.12 -Quercetin Quercetin_4 Isoflavone synthase naringenin[c] => 3 H+[c] + genistein[c] IFS 0 0 0 Q9M6D6 58.93 1.14.14.87 -Quercetin Quercetin_5 Chalcone synthase 2 H+[c] + 4-coumaroyl-CoA[c] + 3 malonyl-CoA[c] => 4 coenzyme A[c] + 3 carbon dioxide[c] + naringenin chalcone[c] CHS 0 0 1000 Q6X0M9 0.006019133 42.488 2.3.1.74 -Quercetin Quercetin_6 Chalcone isomerase H+[c] + naringenin chalcone[c] => naringenin[c] CHI 0 0 1000 C0LUV0 139.8476667 24.679 5.5.1.6 -Quercetin Quercetin_7 Flavanone 3-hydroxylase naringenin[c] + oxygen[c] + 2-oxoglutarate[c] => carbon dioxide[c] + succinate[c] + dihydrokaempferol[c] F3H 0 0 1000 Q53B69 42.673 1.14.11.9 -Quercetin Quercetin_8 Flavonoid 3'-hydroxylase H+[c] + oxygen[c] + NADPH[c] + dihydrokaempferol[c] => dihydroquercetin[c] + H2O[c] + NADP(+)[c] F3'H 0 0 1000 Q8W3Y5 12.5 56.982 1.14.13.21 -Quercetin Quercetin_9 Flavonol synthase dihydrokaempferol[c] + 2-oxoglutarate[c] + oxygen[c] => H+[c] + carbon dioxide[c] + H2O[c] + succinate[c] + kaempferol[c] FLS 0 0 0 C0LUV3 6.6 40.041 1.14.11.23 -Quercetin Quercetin_10 Flavonol synthase dihydroquercetin[c] + 2-oxoglutarate[c] + oxygen[c] => H+[c] + carbon dioxide[c] + H2O[c] + succinate[c] + quercetin[c] FLS 0 0 1000 C0LUV3 3.9 40.041 1.14.11.23 -Quercetin Quercetin_11 quercetin transport quercetin[c] => quercetin[e] 0 0 1000 -Quercetin Quercetin_12 quercetin exchange quercetin[e] => 1 0 1000 -Quercetin Quercetin_13 kaempferol transport kaempferol[c] => kaempferol[e] 0 0 1000 -Quercetin Quercetin_14 kaempferol exchange kaempferol[e] => 0 0 1000 -Quercetin Quercetin_15 genisteinl transport genistein[c] => genistein[e] 0 0 1000 -Quercetin Quercetin_16 genistein exchange genistein[e] => 0 0 1000 - -Trans-cinnamate Trans-cinnamate_1 phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL 0 0 1000 P11544 25.7 76.88 4.3.1.24 0.1 YEP glucose -Trans-cinnamate Trans-cinnamate_2 cinnamate transport cinnamate[c] => cinnamate[e] 0 0 1000 -Trans-cinnamate Trans-cinnamate_3 cinnamate exchange cinnamate[e] => 1 0 1000 - -p-coumaric acid p-coumaric acid_1 tyrosine ammonia-lyase L-tyrosine[c] => ammonium[c] + p-coumaric acid[c] TAL 0 0 1000 A5FKY3 0.023 56.649 4.3.1.23 0.1 YEP glucose YDR380W,YLR134W -p-coumaric acid p-coumaric acid_2 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.215305458 39.7487 2.5.1.54 -p-coumaric acid p-coumaric acid_3 chorismate mutase chorismate[c] => prephenate[c] ARO7G141S 0 0 1000 P32178ly 0.1338606 29.7468 5.4.99.5 -p-coumaric acid p-coumaric acid_4 shikimate kinase ATP[c] + shikimate[c] => 3-phosphoshikimic acid[c] + ADP[c] + H+[c] aroL 0 0 1000 P0A6E1 31.91833333 19.151 2.7.1.71 -p-coumaric acid p-coumaric acid_5 p-coumaric acid transport p-coumaric acid[c] => p-coumaric acid[e] 0 0 1000 -p-coumaric acid p-coumaric acid_6 p-coumaric acid exchange p-coumaric acid[e] => 1 0 1000 - -Artemisinic acid Artemisinic acid_1 amorphadiene synthase farnesyl diphosphate[c] => diphosphate[c] + amorpha-4,11-diene[c] ADS 0 0 1000 Q9AR04 0.186 63.933 4.2.3.24 0.1 YEP glucose -Artemisinic acid Artemisinic acid_2 Amorpha-4,11-diene 12-monooxygenase 2 H+[c] + amorpha-4,11-diene[c] + 3 oxygen[c] + 3 NADPH[c] => 4 H2O[c] + 3 NADP(+)[c] + artemisinic acid[c] CYP71AV1 0 0 1000 Q1PS23 7.74 55.725 1.14.14.114 -Artemisinic acid Artemisinic acid_3 artemisinic acid transport artemisinic acid[c] => artemisinic acid[e] 0 0 1000 -Artemisinic acid Artemisinic acid_4 artemisinic acid exchange artemisinic acid[e] => 1 0 1000 -Artemisinic acid r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 -Artemisinic acid r_0558No2 hydroxymethylglutaryl CoA reductase (No2) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YML075C 0 0 1000 P12683 92.4996 115.624 1.1.1.34 -Artemisinic acid r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 - -¦Â-Carotene ¦Â-Carotene_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 YEP glucose -¦Â-Carotene ¦Â-Carotene_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 -¦Â-Carotene ¦Â-Carotene_3 Phytoene desaturase phytoene[c] => neurosporene[c] crtI 0 0 1000 Q7Z858 0.000314486 65.066 1.3.99.28 -¦Â-Carotene ¦Â-Carotene_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 -¦Â-Carotene ¦Â-Carotene_5 Bifunctional lycopene cyclase/phytoene synthase lycopene[c] => ¦Â-carotene[c] crtYB 0 0 1000 Q7Z859 0.4434336 74.736 5.5.1.19 -¦Â-Carotene ¦Â-Carotene_6 ¦Â-carotene transport ¦Â-carotene[c] => ¦Â-carotene[e] 0 0 1000 -¦Â-Carotene ¦Â-Carotene_7 ¦Â-carotene exchange ¦Â-carotene[e] => 1 0 1000 -¦Â-Carotene r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 - -Linalool Linalool_1 monoterpene synthase geranyl diphosphate[c] + H2O[c] => diphosphate[c] + linalool[c] NES1 0 0 1000 H9M5U5 0.044 65.381 4.2.3.25 0.09 Min glucose -Linalool Linalool_2 Limonene synthase geranyl diphosphate[c] => diphosphate[c] + Limonene[c] ClLIS1 0 0 1000 Q8L5K3 0.186 70.348 4.2.3.20 -Linalool Linalool_3 linalool transport linalool[c] => linalool[e] 0 0 1000 -Linalool Linalool_4 linalool exchange linalool[e] => 1 0 1000 -Linalool Linalool_5 limonene transport Limonene[c] => Limonene[e] 0 0 1000 -Linalool Linalool_6 limonene exchange Limonene[e] => 0 0 1000 -Linalool r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 0.55 40.4829 - -Limonene Limonene_1 monoterpene synthase geranyl diphosphate[c] + H2O[c] => diphosphate[c] + linalool[c] NES1 0 0 1000 H9M5U5 0.044 65.381 4.2.3.25 0.1 Min glucose -Limonene Limonene_2 Limonene synthase geranyl diphosphate[c] => diphosphate[c] + Limonene[c] ClLIS1 0 0 1000 Q8L5K3 0.186 70.348 4.2.3.20 -Limonene Limonene_3 linalool transport linalool[c] => linalool[e] 0 0 1000 -Limonene Limonene_4 linalool exchange linalool[e] => 0 0 1000 -Limonene Limonene_5 limonene transport Limonene[c] => Limonene[e] 0 0 1000 -Limonene Limonene_6 limonene exchange Limonene[e] => 1 0 1000 -Limonene r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 0.55 40.4829 - -4-hydroxymandelic 4-hydroxymandelic_1 hydroxymandelate synthase 3-(4-hydroxyphenyl)pyruvate[c] + oxygen[c] => carbon dioxide[c] + 4-hydroxymandelic[c] hmaS 0 0 1000 Q5J1Q8 3.7 36.597 1.13.11.46 0.1 Min glucose YNL316C,YER090W,YDR380W,YLR134W,YGL202W -4-hydroxymandelic 4-hydroxymandelic_2 hydroxymandelate synthase keto-phenylpyruvate[c] + oxygen[c] => carbon dioxide[c] + mandelic[c] + H+[c] hmaS 0 0 1000 Q5J1Q8 0.88 36.597 1.13.11.46 -4-hydroxymandelic 4-hydroxymandelic_3 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.215305458 39.7487 2.5.1.54 -4-hydroxymandelic 4-hydroxymandelic_4 4-hydroxymandelic transport 4-hydroxymandelic[c] => 4-hydroxymandelic[e] 0 0 1000 -4-hydroxymandelic 4-hydroxymandelic_5 4-hydroxymandelic exchange 4-hydroxymandelic[e] => 1 0 1000 -4-hydroxymandelic 4-hydroxymandelic_6 mandelic transport mandelic[c] => mandelic[e] 0 0 1000 -4-hydroxymandelic 4-hydroxymandelic_7 mandelic exchange mandelic[e] => 0 0 1000 -4-hydroxymandelic 4-hydroxymandelic_8 anthranilate transport anthranilate[e] => anthranilate[c] 0 0 1000 -4-hydroxymandelic 4-hydroxymandelic_9 anthranilate exchange => anthranilate[e] 0 0 1 -4-hydroxymandelic r_0997No1 shikimate dehydrogenase ATP[c] + shikimate[c] => 3-phosphoshikimic acid[c] + ADP[c] + H+[c] YDR127W 0 0 1000 P08566 120 174.753 -4-hydroxymandelic r_1903_REV 0 0 1 - -mandelic mandelic_1 hydroxymandelate synthase 3-(4-hydroxyphenyl)pyruvate[c] + oxygen[c] => carbon dioxide[c] + 4-hydroxymandelic[c] hmaS 0 0 1000 Q5J1Q8 3.7 36.597 1.13.11.46 0.1 Min glucose YBR166C,YER090W,YDR380W,YLR134W,YGL202W -mandelic mandelic_2 hydroxymandelate synthase keto-phenylpyruvate[c] + oxygen[c] => carbon dioxide[c] + mandelic[c] + H+[c] hmaS 0 0 1000 Q5J1Q8 0.88 36.597 1.13.11.46 -mandelic mandelic_3 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.215305458 39.7487 2.5.1.54 -mandelic mandelic_4 4-hydroxymandelic transport 4-hydroxymandelic[c] => 4-hydroxymandelic[e] 0 0 1000 -mandelic mandelic_5 4-hydroxymandelic exchange 4-hydroxymandelic[e] => 0 0 1000 -mandelic mandelic_6 mandelic transport mandelic[c] => mandelic[e] 0 0 1000 -mandelic mandelic_7 mandelic exchange mandelic[e] => 1 0 1000 -mandelic mandelic_8 anthranilate transport anthranilate[e] => anthranilate[c] 0 0 1000 -mandelic mandelic_9 anthranilate exchange => anthranilate[e] 0 0 1 -mandelic r_0997No1 shikimate dehydrogenase ATP[c] + shikimate[c] => 3-phosphoshikimic acid[c] + ADP[c] + H+[c] YDR127W 0 0 1000 P08566 120 174.753 -mandelic r_1913_REV 0 0 1 - -Oleanolic acid Oleanolic acid_1 Beta-amyrin synthase (S)-2,3-epoxysqualene[c] => ¦Â-amyrin[c] GgbAS1 0 0 1000 Q9MB42 0.77 87.516 5.4.99.39 0.1 YEP glucose YBR020W -Oleanolic acid Oleanolic acid_2 Beta-amyrin 28-monooxygenase 2 H+[c] + ¦Â-amyrin[c] + 3 oxygen[c] + 3 NADPH[c] => 4 H2O[c] + Oleanolic acid[c] + 3 NADP(+)[c] CYP716A12 0 0 1000 Q2MJ20 54.713 1.14.13.201 -Oleanolic acid Oleanolic acid_3 oleanolic acid transport Oleanolic acid[c] => Oleanolic acid[e] 0 0 1000 -Oleanolic acid Oleanolic acid_4 oleanolic acid exchange Oleanolic acid[e] => 1 0 1000 -Oleanolic acid r_0558No2 hydroxymethylglutaryl CoA reductase (No2) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YML075C 0 0 1000 P12683 92.4996 -Oleanolic acid r_1010No1 squalene epoxidase (NAD) (No1) H+[er] + NADH[er] + oxygen[er] + squalene[er] => (S)-2,3-epoxysqualene[er] + H2O[er] + NAD[er] YGR175C 0 0 1000 P32476 0.152 -Oleanolic acid r_1011No1 squalene epoxidase (NADP) (No1) H+[er] + NADPH[er] + oxygen[er] + squalene[er] => (S)-2,3-epoxysqualene[er] + H2O[er] + NADP(+)[er] YGR175C 0 0 1000 P32476 0.152 -Oleanolic acid r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 3.3 - -Fumaric acid Fumaric acid_1 malate dehydrogenase H+[c] + NADH[c] + oxaloacetate[c] => (S)-malate[c] + NAD[c] RoMDH 0 0 1000 D6R7B7 24.026625 35.595 1.1.1.37 0.1 Min glucose block r_0714_REVNo1 (Mdh2p is known to be subject to glucose catabolite inactivation) -Fumaric acid r_0958No1 pyruvate carboxylase (No1) pmet_r_0958[c] => ADP[c] + H+[c] + oxaloacetate[c] + phosphate[c] YBR218C 0 0 1000 P32327 72.48055072 130.166 -Fumaric acid r_0958No2 pyruvate carboxylase (No2) pmet_r_0958[c] => ADP[c] + H+[c] + oxaloacetate[c] + phosphate[c] YGL062W 0 0 1000 P11154 72.48041459 130.098 -Fumaric acid r_1798 1 0 Inf -Fumaric acid r_0714_REVNo1 0 0 0 - -Pyruvate Pyruvate_1 NADH oxidase oxygen[c] + 3 H+[c] + NADH[c] => 2 H2O[c] + NAD[c] noxE 0 0 1000 A2RIB7 57.4246 48.872 1.6.99.3 0.2 YEP glucose YLR044C,YLR134W,YGR087C -Pyruvate Pyruvate_2 transhydrogenase NADP(+)[c] + NADH[c] => NADPH[c] + NAD[c] udhA 0 0 1000 P27306 167.9 51.56 1.6.1.1 -Pyruvate Pyruvate_2_REV transhydrogenase NADPH[c] + NAD[c] => NADP(+)[c] + NADH[c] udhA 0 0 1000 P27306 9.1304 51.56 1.6.1.1 -Pyruvate r_2033 1 0 Inf - -Adipic acid Adipic acid_1 dehydroshikimate dehydratase 3-dehydroshikimate[c] => 3,4-Dihydroxybenzoate[c] + H2O[c] Pa_5_5120 0 0 1000 3DSD 121.44 40.48 4.2.1.118 0.1 YEP glucose YDR035W,YBR249C,YNL241C -Adipic acid Adipic acid_2 protocatechuic acid decarboxylase 3,4-Dihydroxybenzoate[c] + H+[c] => carbon dioxide[c] + Catechol[c] ECL_01944 0 0 1000 A0A0H3CJN8 90 53.541 4.1.1.63 -Adipic acid Adipic acid_3 catechol 1,2-dioxygenase Catechol[c] + oxygen[c] => 2 H+[c] + cis,cis-muconate[c] HQD2 0 0 1000 P86029 157.7333333 33.8 1.13.11.1 -Adipic acid Adipic acid_4 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.082809792 39.7487 2.5.1.54 -Adipic acid Adipic acid_5 cis,cis-muconic acid transport cis,cis-muconate[c] => cis,cis-muconate[e] 0 0 1000 -Adipic acid Adipic acid_6 cis,cis-muconic acid exchange cis,cis-muconate[e] => 0 0 1000 -Adipic acid Adipic acid_7 enoate reductase cis,cis-muconate[c] + NADH[c] + 3 H+[c] => Adipic acid[c] + NAD[c] ERBC 0 0 1000 G2TQU6 8.376025 72.835 1.3.1.31 0.1 YEP glucose -Adipic acid Adipic acid_8 adipic acid transport Adipic acid[c] => Adipic acid[e] 0 0 1000 -Adipic acid Adipic acid_9 adipic acid exchange Adipic acid[e] => 1 0 1000 -Adipic acid r_2189_REV 0 0 1 -Adipic acid r_1757_REV 0 0 1 -Adipic acid r_2038_REV 0 0 1 -Adipic acid r_1807_REV 0 0 1 - -Isobutanol r_0016No1 2-aceto-2-hydroxybutanoate synthase (No1) pmet_r_0016[m] + 1.72533e-05 prot_P25605 => (S)-2-acetyl-2-hydroxybutanoate[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 32.2 0.1 YEP glucose YPL061W,YHR208W -Isobutanol r_0016No2 2-aceto-2-hydroxybutanoate synthase (No2) pmet_r_0016[m] => (S)-2-acetyl-2-hydroxybutanoate[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 32.2 -Isobutanol r_0097No1 acetolactate synthase (No1) 3.45066e-05 prot_P25605 + pmet_r_0097[m] => 2-acetyllactic acid[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 16.1 -Isobutanol r_0097No2 acetolactate synthase (No2) pmet_r_0097[m] => 2-acetyllactic acid[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 16.1 -Isobutanol r_0352No1 dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylbutanoate) (No1) (R)-2,3-dihydroxy-3-methylbutanoate[m] => 3-methyl-2-oxobutanoate[m] + H2O[m] YJR016C 0 0 1000 P39522 50 -Isobutanol r_0353No1 dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylpentanoate) (No1) (2R,3R)-2,3-dihydroxy-3-methylpentanoate[m] => (S)-3-methyl-2-oxopentanoate[m] + H2O[m] YJR016C 0 0 1000 P39522 50 -Isobutanol r_0096No1 acetohydroxy acid isomeroreductase (No1) 2-acetyllactic acid[m] + H+[m] + NADPH[m] => (R)-2,3-dihydroxy-3-methylbutanoate[m] + NADP(+)[m] YLR355C 0 0 1000 P06168 36.6 -Isobutanol r_0669No1 ketol-acid reductoisomerase (2-aceto-2-hydroxybutanoate) (No1) (S)-2-acetyl-2-hydroxybutanoate[m] + H+[m] + NADPH[m] => (2R,3R)-2,3-dihydroxy-3-methylpentanoate[m] + NADP(+)[m] YLR355C 0 0 1000 P06168 1.96 -Isobutanol r_0854No1 phenylpyruvate decarboxylase (No1) H+[c] + keto-phenylpyruvate[c] => carbon dioxide[c] + phenylacetaldehyde[c] YDR380W 0 0 1000 Q06408 1140 -Isobutanol r_0163No1 alcohol dehydrogenase (ethanol to acetaldehyde) (No1) ethanol[c] + NAD[c] => acetaldehyde[c] + H+[c] + NADH[c] YMR303C 0 0 1000 P00331 286 -Isobutanol r_1866 1 0 Inf - -3-Methyl-1-Butanol r_0016No1 2-aceto-2-hydroxybutanoate synthase (No1) pmet_r_0016[m] + 1.72533e-05 prot_P25605 => (S)-2-acetyl-2-hydroxybutanoate[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 32.2 0.1 YEP glucose YPL061W,YHR208W -3-Methyl-1-Butanol r_0016No2 2-aceto-2-hydroxybutanoate synthase (No2) pmet_r_0016[m] => (S)-2-acetyl-2-hydroxybutanoate[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 32.2 -3-Methyl-1-Butanol r_0097No1 acetolactate synthase (No1) 3.45066e-05 prot_P25605 + pmet_r_0097[m] => 2-acetyllactic acid[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 16.1 -3-Methyl-1-Butanol r_0097No2 acetolactate synthase (No2) pmet_r_0097[m] => 2-acetyllactic acid[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 16.1 -3-Methyl-1-Butanol r_0352No1 dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylbutanoate) (No1) (R)-2,3-dihydroxy-3-methylbutanoate[m] => 3-methyl-2-oxobutanoate[m] + H2O[m] YJR016C 0 0 1000 P39522 50 -3-Methyl-1-Butanol r_0353No1 dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylpentanoate) (No1) (2R,3R)-2,3-dihydroxy-3-methylpentanoate[m] => (S)-3-methyl-2-oxopentanoate[m] + H2O[m] YJR016C 0 0 1000 P39522 50 -3-Methyl-1-Butanol r_0096No1 acetohydroxy acid isomeroreductase (No1) 2-acetyllactic acid[m] + H+[m] + NADPH[m] => (R)-2,3-dihydroxy-3-methylbutanoate[m] + NADP(+)[m] YLR355C 0 0 1000 P06168 36.6 -3-Methyl-1-Butanol r_0669No1 ketol-acid reductoisomerase (2-aceto-2-hydroxybutanoate) (No1) (S)-2-acetyl-2-hydroxybutanoate[m] + H+[m] + NADPH[m] => (2R,3R)-2,3-dihydroxy-3-methylpentanoate[m] + NADP(+)[m] YLR355C 0 0 1000 P06168 1.96 -3-Methyl-1-Butanol r_0854No1 phenylpyruvate decarboxylase (No1) H+[c] + keto-phenylpyruvate[c] => carbon dioxide[c] + phenylacetaldehyde[c] YDR380W 0 0 1000 Q06408 1140 -3-Methyl-1-Butanol r_0163No1 alcohol dehydrogenase (ethanol to acetaldehyde) (No1) ethanol[c] + NAD[c] => acetaldehyde[c] + H+[c] + NADH[c] YMR303C 0 0 1000 P00331 286 -3-Methyl-1-Butanol r_0024No1 2-isopropylmalate synthase (No1) pmet_r_0024[c] => 2-isopropylmalate[c] + coenzyme A[c] + H+[c] YNL104C 0 0 1000 P06208 27.58 -3-Methyl-1-Butanol r_0025No1 2-isopropylmalate synthase (No1) 3-methyl-2-oxobutanoate[m] + acetyl-CoA[m] + H2O[m] => 2-isopropylmalate[m] + coenzyme A[m] + H+[m] YNL104C 0 0 1000 P06208 27.58 -3-Methyl-1-Butanol r_1598 1 0 Inf - -Naringenin Naringenin_1 Phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL1 0 0 1000 P35510 1.8 78.726 4.3.1.24 0.2 Min glucose YDR035W,YBR249C,YDR380W,YLR134W,YGR087C -Naringenin Naringenin_2 Cinnamate-4-hydroxylase H+[c] + oxygen[c] + cinnamate[c] + NADPH[c] => H2O[c] + NADP(+)[c] + trans-4-coumarate[c] C4H 0 0 1000 P92994 1.72 57.792 1.14.13.11 -Naringenin Naringenin_3 Chalcone isomerase H+[c] + naringenin chalcone[c] => naringenin[c] CHI1 0 0 1000 Q8VZW3 23.332 5.5.1.6 -Naringenin Naringenin_4 Chalcone synthase 2 H+[c] + 4-coumaroyl-CoA[c] + 3 malonyl-CoA[c] => 4 coenzyme A[c] + 3 carbon dioxide[c] + naringenin chalcone[c] CHS3 0 0 1000 P13114 0.001 43.116 2.3.1.74 -Naringenin Naringenin_5 4-coumarate:CoA ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => diphosphate[c] + AMP[c] + 4-coumaroyl-CoA[c] 4CL3 0 0 1000 Q9S777 0.84 61.311 6.2.1.12 -Naringenin Naringenin_6 tyrosine ammonia-lyase L-tyrosine[c] => ammonium[c] + trans-4-coumarate[c] TAL 0 0 1000 A0A1M4NET9 27.7 55.539 4.3.1.23 -Naringenin Naringenin_7 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4G226S 0 0 1000 P32449ly 7.9 39.7487 2.5.1.54 -Naringenin Naringenin_8 naringenin transport naringenin[c] => naringenin[e] 0 0 1000 -Naringenin Naringenin_9 naringenin exchange naringenin[e] => 1 0 1000 - -Catechin Catechin_1 Phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL2 0 0 1000 P45724 3.2 77.86 4.3.1.24 0.1 Min glucose -Catechin Catechin_2 Cinnamate-4-hydroxylase H+[c] + oxygen[c] + cinnamate[c] + NADPH[c] => H2O[c] + NADP(+)[c] + trans-4-coumarate[c] C4H 0 0 1000 Q84TQ4 1.72 57.937 1.14.13.11 -Catechin Catechin_3 Chalcone isomerase H+[c] + naringenin chalcone[c] => naringenin[c] CHI 0 0 1000 P28012 671000 23.826 5.5.1.6 -Catechin Catechin_4 Chalcone synthase 2 H+[c] + 4-coumaroyl-CoA[c] + 3 malonyl-CoA[c] => 4 coenzyme A[c] + 3 carbon dioxide[c] + naringenin chalcone[c] CHS 0 0 1000 Q9FUB7 0.042 42.713 2.3.1.74 -Catechin Catechin_5 4-coumarate:CoA ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => diphosphate[c] + AMP[c] + 4-coumaroyl-CoA[c] 4CL2 0 0 1000 Q9S725 3 60.842 6.2.1.12 -Catechin Catechin_6 flavonoid-3'-hydroxylase H+[c] + oxygen[c] + naringenin[c] + NADPH[c] => eriodictyol[c] + H2O[c] + NADP(+)[c] F3'H 0 0 1000 Q9SBQ9 17 56.936 1.14.14.82 -Catechin Catechin_7 flavanone-3-hydroxylase eriodictyol[c] + 2-oxoglutarate[c] + oxygen[c] => taxifolin[c] + succinate[c] + carbon dioxide[c] F3H 0 0 1000 Q06942 40.771 1.14.11.9 -Catechin Catechin_8 dihydroflavonol-4-reductase taxifolin[c] + NADPH[c] + H+[c] => leucocyanidin[c] + NADP(+)[c] DFR 0 0 1000 B9GRL5 27.60528667 38.699 1.1.1.219 -Catechin Catechin_9 leucoanthocyanidin reductase leucocyanidin[c] + NADPH[c] + H+[c] => catechin[c] + NADP(+)[c] + H2O[c] LAR 0 0 1000 Q4W2K4 0.065 38.019 1.17.1.3 -Catechin Catechin_10 catechin transport catechin[c] => catechin[e] 0 0 1000 -Catechin Catechin_11 catechin exchange catechin[e] => 1 0 1000 - -Amorphadiene Amorphadiene_1 amorphadiene synthase farnesyl diphosphate[c] => amorphadiene[c] + diphosphate[c] ADS 0 0 1000 Q9AR04 0.518 63.933 4.2.3.24 0.1 Min glucose YBR020W,YBR018C,YBR019C -Amorphadiene Amorphadiene_2 amorphadiene transport amorphadiene[c] => amorphadiene[e] 0 0 1000 -Amorphadiene Amorphadiene_3 amorphadiene exchange amorphadiene[e] => 1 0 1000 -Amorphadiene r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 -Amorphadiene r_0904No1 phosphomevalonate kinase (No1) (R)-5-phosphomevalonic acid[c] + ATP[c] => (R)-5-diphosphomevalonic acid[c] + ADP[c] YMR220W 0 0 1000 P24521 6.8 50.4544 2.7.4.2 -Amorphadiene r_0103No1 acetyl-CoA C-acetyltransferase (No1) 2 acetyl-CoA[c] => acetoacetyl-CoA[c] + coenzyme A[c] YPL028W 0 0 1000 P41338 1800 41.7282 2.3.1.9 -Amorphadiene r_0104No1 acetyl-CoA C-acetyltransferase (No1) 2 acetyl-CoA[m] => acetoacetyl-CoA[m] + coenzyme A[m] YPL028W 0 0 1000 P41338 1800 41.7282 2.3.1.9 -Amorphadiene r_0103_REVNo1 acetyl-CoA C-acetyltransferase (reversible) (No1) acetoacetyl-CoA[c] + coenzyme A[c] => 2 acetyl-CoA[c] YPL028W 0 0 1000 P41338 10000000 41.7282 2.3.1.9 -Amorphadiene r_0104_REVNo1 acetyl-CoA C-acetyltransferase (reversible) (No1) acetoacetyl-CoA[m] + coenzyme A[m] => 2 acetyl-CoA[m] YPL028W 0 0 1000 P41338 10000000 41.7282 2.3.1.9 -Amorphadiene r_0735No1 mevalonate kinase (atp) (No1) (R)-mevalonate[c] + ATP[c] => (R)-5-phosphomevalonic acid[c] + ADP[c] + H+[c] YMR208W 0 0 1000 P07277 43.8001 48.459 2.7.1.36 -Amorphadiene r_0736No1 mevalonate kinase (ctp) (No1) (R)-mevalonate[c] + CTP[c] => (R)-5-phosphomevalonic acid[c] + CDP[c] + H+[c] YMR208W 0 0 1000 P07277 43.8001 48.459 2.7.1.36 -Amorphadiene r_0737No1 mevalonate kinase (gtp) (No1) (R)-mevalonate[c] + GTP[c] => (R)-5-phosphomevalonic acid[c] + GDP[c] + H+[c] YMR208W 0 0 1000 P07277 43.8001 48.459 2.7.1.36 -Amorphadiene r_0738No1 mevalonate kinase (UTP) (No1) (R)-mevalonate[c] + UTP[c] => (R)-5-phosphomevalonic acid[c] + H+[c] + UDP[c] YMR208W 0 0 1000 P07277 43.8001 48.459 2.7.1.36 -Amorphadiene r_0559No1 hydroxymethylglutaryl CoA synthase (No1) acetoacetyl-CoA[c] + acetyl-CoA[c] + H2O[c] => 3-hydroxy-3-methylglutaryl-CoA[c] + coenzyme A[c] + H+[c] YML126C 0 0 1000 P54839 0.83 55.0128 2.3.3.10 -Amorphadiene r_0560No1 hydroxymethylglutaryl CoA synthase (No1) acetoacetyl-CoA[m] + acetyl-CoA[m] + H2O[m] => 3-hydroxy-3-methylglutaryl-CoA[m] + coenzyme A[m] + H+[m] YML126C 0 0 1000 P54839 0.83 55.0128 2.3.3.10 -Amorphadiene r_0739No1 mevalonate pyrophoshate decarboxylase (No1) (R)-5-diphosphomevalonic acid[c] + ATP[c] => ADP[c] + carbon dioxide[c] + isopentenyl diphosphate[c] + phosphate[c] YNR043W 0 0 1000 P32377 9.8 44.1154 4.1.1.33 -Amorphadiene r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -Amorphadiene r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -Amorphadiene r_0667No1 isopentenyl-diphosphate D-isomerase (No1) isopentenyl diphosphate[c] => prenyl diphosphate(3-)[c] YPL117C 0 0 1000 P15496 59800 33.3511 5.3.3.2 -Amorphadiene r_0667_REVNo1 isopentenyl-diphosphate D-isomerase (reversible) (No1) prenyl diphosphate(3-)[c] => isopentenyl diphosphate[c] YPL117C 0 0 1000 P15496 0.1212 33.3511 5.3.3.2 -Amorphadiene r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 -Amorphadiene r_1710_REV 0 0 1 - -Protopanaxadiol Protopanaxadiol_1 dammarenediol-II synthase (S)-2,3-epoxysqualene[c] + H2O[c] => Dammarenediol II[c] DDS 0 0 1000 Q08IT1 88.343 4.2.1.125 0.1 Min glucose -Protopanaxadiol Protopanaxadiol_2 protopanaxadiol synthase H+[c] + oxygen[c] + Dammarenediol II[c] + NADPH[c] => protopanaxadiol[c] + H2O[c] + NADP(+)[c] PPDS 0 0 1000 H2DH16 55.356 1.14.14.120 -Protopanaxadiol Protopanaxadiol_3 protopanaxadiol transport protopanaxadiol[c] => protopanaxadiol[e] 0 0 1000 -Protopanaxadiol Protopanaxadiol_4 protopanaxadiol exchange protopanaxadiol[e] => 1 0 1000 -Protopanaxadiol r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 -Protopanaxadiol r_1010No1 squalene epoxidase (NAD) (No1) H+[er] + NADH[er] + oxygen[er] + squalene[er] => (S)-2,3-epoxysqualene[er] + H2O[er] + NAD[er] YGR175C 0 0 1000 P32476 0.152 55.1254 1.14.14.17 -Protopanaxadiol r_1011No1 squalene epoxidase (NADP) (No1) H+[er] + NADPH[er] + oxygen[er] + squalene[er] => (S)-2,3-epoxysqualene[er] + H2O[er] + NADP(+)[er] YGR175C 0 0 1000 P32476 0.152 55.1254 1.14.14.17 -Protopanaxadiol r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 3.3 51.7193 2.5.1.21 -Protopanaxadiol r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -Protopanaxadiol r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -Protopanaxadiol r_1900_REV 0 0 1 - -Geraniol Geraniol_1 geraniol synthase geranyl diphosphate[c] + H2O[c] => Geraniol[c] + diphosphate[c] GES 0 0 1000 J9PZR5 1 67.728 3.1.7.11 0.31 YEP glucose -Geraniol Geraniol_2 protopanaxadiol transport Geraniol[c] => Geraniol[e] 0 0 1000 -Geraniol Geraniol_3 protopanaxadiol exchange Geraniol[e] => 1 0 1000 -Geraniol r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 -Geraniol r_0667No1 isopentenyl-diphosphate D-isomerase (No1) isopentenyl diphosphate[c] => prenyl diphosphate(3-)[c] YPL117C 0 0 1000 P15496 59800 33.3511 5.3.3.2 -Geraniol r_0667_REVNo1 isopentenyl-diphosphate D-isomerase (reversible) (No1) prenyl diphosphate(3-)[c] => isopentenyl diphosphate[c] YPL117C 0 0 1000 P15496 0.1212 33.3511 5.3.3.2 -Geraniol r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -Geraniol r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 - -Patchoulol Patchoulol_1 patchoulol synthase farnesyl diphosphate[c] + H2O[c] => patchoulol[c] + diphosphate[c] PTS 0 0 1000 Q49SP3 0.00043 64.199 4.2.3.70 0.1 YEP glucose -Patchoulol Patchoulol_2 patchoulol transport patchoulol[c] => patchoulol[e] 0 0 1000 -Patchoulol Patchoulol_3 patchoulol exchange patchoulol[e] => 1 0 1000 -Patchoulol r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 -Patchoulol r_0667No1 isopentenyl-diphosphate D-isomerase (No1) isopentenyl diphosphate[c] => prenyl diphosphate(3-)[c] YPL117C 0 0 1000 P15496 59800 33.3511 5.3.3.2 -Patchoulol r_0667_REVNo1 isopentenyl-diphosphate D-isomerase (reversible) (No1) prenyl diphosphate(3-)[c] => isopentenyl diphosphate[c] YPL117C 0 0 1000 P15496 0.1212 33.3511 5.3.3.2 -Patchoulol r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -Patchoulol r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -Patchoulol r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 - -Lupeol Lupeol_1 lupeol synthase (S)-2,3-epoxysqualene[c] => lupeol[c] LUP 0 0 1000 A0A3B1EU92 86.705 5.4.99.41 0.1 Min glucose -Lupeol Lupeol_2 lupeol transport lupeol[c] => lupeol[e] 0 0 1000 -Lupeol Lupeol_3 lupeol exchange lupeol[e] => 1 0 1000 -Lupeol r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 -Lupeol r_0559No1 hydroxymethylglutaryl CoA synthase (No1) acetoacetyl-CoA[c] + acetyl-CoA[c] + H2O[c] => 3-hydroxy-3-methylglutaryl-CoA[c] + coenzyme A[c] + H+[c] YML126C 0 0 1000 P54839 0.83 55.0128 2.3.3.10 -Lupeol r_0560No1 hydroxymethylglutaryl CoA synthase (No1) acetoacetyl-CoA[m] + acetyl-CoA[m] + H2O[m] => 3-hydroxy-3-methylglutaryl-CoA[m] + coenzyme A[m] + H+[m] YML126C 0 0 1000 P54839 0.83 55.0128 2.3.3.10 -Lupeol r_0698No1 lanosterol synthase (No1) (S)-2,3-epoxysqualene[c] => lanosterol[c] YHR072W 0 0 1000 P38604 2.0382 83.4594 5.4.99.7 -Lupeol r_1710_REV 0 0 1 - -¦Â-Amyrin ¦Â-Amyrin_1 ¦Â-amyrin synthase (S)-2,3-epoxysqualene[c] => ¦Â-Amyrin[c] bAS 0 0 1000 Q9MB42 0.77 87.516 5.4.99.39 0.1 YEP glucose -¦Â-Amyrin ¦Â-Amyrin_2 squalene epoxidase (NAD) (No1) H+[er] + NADH[er] + oxygen[er] + squalene[er] => (S)-2,3-epoxysqualene[er] + H2O[er] + NAD[er] CaERG1 0 0 1000 Q92206 55.298 1.14.14.17 -¦Â-Amyrin ¦Â-Amyrin_3 squalene epoxidase (NADP) (No1) H+[er] + NADPH[er] + oxygen[er] + squalene[er] => (S)-2,3-epoxysqualene[er] + H2O[er] + NADP(+)[er] CaERG1 0 0 1000 Q92206 55.298 1.14.14.17 -¦Â-Amyrin ¦Â-Amyrin_4 pyrophosphate isomerase isopentenyl diphosphate[c] => prenyl diphosphate(3-)[c] EcIDI 0 0 1000 Q46822 20.508 5.3.3.2 -¦Â-Amyrin ¦Â-Amyrin_5 pyrophosphate isomerase prenyl diphosphate(3-)[c] => isopentenyl diphosphate[c] EcIDI 0 0 1000 Q46822 20.508 5.3.3.2 -¦Â-Amyrin ¦Â-Amyrin_6 ¦Â-Amyrin transport ¦Â-Amyrin[c] => ¦Â-Amyrin[e] 0 0 1000 -¦Â-Amyrin ¦Â-Amyrin_7 ¦Â-Amyrin exchange ¦Â-Amyrin[e] => 1 0 1000 -¦Â-Amyrin r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 3.3 51.7193 2.5.1.21 -¦Â-Amyrin r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -¦Â-Amyrin r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 - -Astaxanthin Astaxanthin_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 YEP glucose -Astaxanthin Astaxanthin_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 -Astaxanthin Astaxanthin_3 Phytoene desaturase phytoene[c] => neurosporene[c] crtI 0 0 1000 Q7Z858 0.000314486 65.066 1.3.99.28 -Astaxanthin Astaxanthin_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 -Astaxanthin Astaxanthin_5 Bifunctional lycopene cyclase/phytoene synthase lycopene[c] => ¦Â-carotene[c] crtYB 0 0 1000 Q7Z859 0.4434336 74.736 5.5.1.19 -Astaxanthin Astaxanthin_6 ¦Â-carotene transport ¦Â-carotene[c] => ¦Â-carotene[e] 0 0 1000 -Astaxanthin Astaxanthin_7 ¦Â-carotene exchange ¦Â-carotene[e] => 0 0 1000 -Astaxanthin Astaxanthin_8 ¦Â-carotenoid ketolase ¦Â-carotene[c] + oxygen[c] => echinenone[c] + H2O[c] bkt 0 0 1000 Q39982 35.989 1.14.99.63 0.1 YEP glucose -Astaxanthin Astaxanthin_9 ¦Â-carotenoid ketolase echinenone[c] + oxygen[c] => canthaxanthin[c] + H2O[c] bkt 0 0 1000 Q39982 35.989 1.14.99.63 -Astaxanthin Astaxanthin_10 ¦Â-carotenoid hydroxylase H+[c] + NADH[c] + canthaxanthin[c] + oxygen[c] => H2O[c] + phoenicoxanthin[c] + NAD[c] crtZ 0 0 1000 A0A0K0P8J8 32.017 1.14.15.24 -Astaxanthin Astaxanthin_11 ¦Â-carotenoid hydroxylase H+[c] + NADH[c] + phoenicoxanthin[c] + oxygen[c] => H2O[c] + astaxanthin[c] + NAD[c] crtZ 0 0 1000 A0A0K0P8J8 32.017 1.14.15.24 -Astaxanthin Astaxanthin_12 astaxanthin transport astaxanthin[c] => astaxanthin[e] 0 0 1000 -Astaxanthin Astaxanthin_13 astaxanthin exchange astaxanthin[e] => 1 0 1000 -Astaxanthin r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 - -Farnesene Farnesene_1 farnesene synthase farnesyl diphosphate[c] => alpha-Farnesene[c] + diphosphate[c] AFS 0 0 1000 Q84LB2 0.0613 66.183 4.2.3.46 0.043 Min glucose YDR503C,YDR284C,YOR375C -Farnesene Farnesene_2 farnesene transport alpha-Farnesene[c] => alpha-Farnesene[e] 0 0 1000 -Farnesene Farnesene_3 farnesene exchange alpha-Farnesene[e] => 1 0 1000 -Farnesene Farnesene_4 santalene synthase farnesyl diphosphate[c] => Santalene[c] + diphosphate[c] SAS 0 0 1000 E5LLI1 0.075 63.937 4.2.3.82 -Farnesene Farnesene_5 farnesene transport Santalene[c] => Santalene[e] 0 0 1000 -Farnesene Farnesene_6 farnesene exchange Santalene[e] => 0 0 1000 -Farnesene r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 -Farnesene r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -Farnesene r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -Farnesene r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 -Farnesene r_0470No1 glutamate dehydrogenase (NAD) (No1) H2O[c] + L-glutamate[c] + NAD[c] => 2-oxoglutarate[c] + ammonium[c] + H+[c] + NADH[c] YDL215C 0 0 1000 P33327 47.9999 124.331 1.4.1.2 - -Santalene Santalene_1 farnesene synthase farnesyl diphosphate[c] => alpha-Farnesene[c] + diphosphate[c] AFS 0 0 1000 Q84LB2 0.0613 66.183 4.2.3.46 0.05 Min glucose YDR503C,YDR284C,YOR375C -Santalene Santalene_2 farnesene transport alpha-Farnesene[c] => alpha-Farnesene[e] 0 0 1000 -Santalene Santalene_3 farnesene exchange alpha-Farnesene[e] => 0 0 1000 -Santalene Santalene_4 santalene synthase farnesyl diphosphate[c] => Santalene[c] + diphosphate[c] SAS 0 0 1000 E5LLI1 0.075 63.937 4.2.3.82 -Santalene Santalene_5 farnesene transport Santalene[c] => Santalene[e] 0 0 1000 -Santalene Santalene_6 farnesene exchange Santalene[e] => 1 0 1000 -Santalene r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 -Santalene r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -Santalene r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -Santalene r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 -Santalene r_0470No1 glutamate dehydrogenase (NAD) (No1) H2O[c] + L-glutamate[c] + NAD[c] => 2-oxoglutarate[c] + ammonium[c] + H+[c] + NADH[c] YDL215C 0 0 1000 P33327 47.9999 124.331 1.4.1.2 - -lactase lactase_1 production of lactase 2.01 GTP[c] + 0.6516 L-alanine[c] + 0.2643 L-arginine[c] + 0.5013 L-asparagine[c] + 0.4921 L-aspartate[c] + 0.0547 L-cysteine[c] + 0.4375 L-glutamate[c] + 0.2552 L-glutamine[c] + 0.9114 L-glycine[c] + 0.1276 L-histidine[c] + 0.4466 L-isoleucine[c] + 0.8567 L-leucine[c] + 0.4192 L-lysine[c] + 0.0638 L-methionine[c] + 0.3645 L-phenylalanine[c] + 0.4921 L-proline[c] + 0.8567 L-serine[c] + 0.7109 L-threonine[c] + 0.1823 L-tryptophan[c] + 0.5377 L-tyrosine[c] + 0.5559 L-valine[c] => 2.01 GDP[c] + 2.01 phosphate[c] + lactase[c] 0 0 1000 0.18 YEP glucose -lactase lactase_2 lactase transport lactase[c] => lactase[e] 0 0 1000 -lactase lactase_3 lactase exchange lactase[e] => 1 0 1000 - -L-ornithine L-ornithine _1 Amino-acid acetyltransferase acetyl-CoA[c] + L-glutamate[c] => coenzyme A[c] + N-acetyl-L-glutamate[c] argA 0 0 1000 P0A6C5 109.0489167 49.195 2.3.1.1 0.1 Min glucose YLR438W -L-ornithine L-ornithine _2 Acetylglutamate kinase ATP[c] + N-acetyl-L-glutamate[c] => ADP[c] + N-acetyl-L-gamma-glutamyl phosphate[c] argB 0 0 1000 P0A6C8 0.24444 27.16 2.7.2.8 -L-ornithine L-ornithine _3 N-acetyl-gamma-glutamyl-phosphate reductase N-acetyl-L-gamma-glutamyl phosphate[c] + NADPH[c] + H+[c] => NADP(+)[c] + phosphate[c] + 2-acetamido-5-oxopentanoate[c] argC 0 0 1000 Q59279 35.888 1.2.1.38 -L-ornithine L-ornithine _4 acetylornithine aminotransferase 2-acetamido-5-oxopentanoate[c] + L-glutamate[c] => N(2)-acetyl-L-ornithine[c] + 2-oxoglutarate[c] argD 0 0 1000 Q59282 41.206 2.6.1.11 -L-ornithine L-ornithine _5 glutamate N-acetyltransferase N(2)-acetyl-L-ornithine[c] + L-glutamate[c] => ornithine[c] + N-acetyl-L-glutamate[c] argJ 0 0 1000 Q59280 0.0099285 39.714 2.3.1.35 -L-ornithine r_1237 (update) ornithine transport H+[c] + ornithine[m] => H+[m] + ornithine[c] ORT1 0 0 1000 Q12375 0.1816 31.52 -L-ornithine r_1118 (update) aspartate-glutamate transporter L-aspartate[m] + L-glutamate[c] => L-aspartate[c] + L-glutamate[m] AGC1 0 0 1000 Q12482 0.01318 Identification and metabolic role of the mitochondrial aspartate-glutamate transporter in Saccharomyces cerevisiae 104.304 -L-ornithine r_0471No2 glutamate dehydrogenase (NADP) (No2) pmet_r_0471[c] => H2O[c] + L-glutamate[c] + NADP(+)[c] YOR375C 0 0 1000 P07262 106.66 -L-ornithine r_0816No1 ornithine carbamoyltransferase (No1) carbamoyl phosphate[c] + ornithine[c] => H+[c] + L-citrulline[c] + phosphate[c] YJL088W 0 0 1000 P05150 41 -L-ornithine r_1987 1 0 Inf - -(S)-reticuline (S)-reticuline_1 tyrosine hydroxylase oxygen[c] + 2 L-tyrosine[c] => 2 3,4-Dihydroxy-L-phenylalanine(L-DOPA)[c] CYP76AD1 0 0 1000 I3PFJ5 56.212 1.14.18.1 0.1 YEP glucose -(S)-reticuline (S)-reticuline_2 L-3,4-dihydroxyphenylalanine decarboxylase 3,4-Dihydroxy-L-phenylalanine(L-DOPA)[c] + H+[c] => carbon dioxide[c] + dopamine[c] DODC 0 0 1000 Q88JU5 1.8 51.444 4.1.1.28 -(S)-reticuline (S)-reticuline_3 4-hydroxyphenylpyruvate decarboxylase (update) 3-(4-hydroxyphenyl)pyruvate[c] + H+[c] => carbon dioxide[c] + (4-hydroxyphenyl)acetaldehyde[c] YDR380W 0 0 1000 Q06408 11 71.384 4.1.1.80 -(S)-reticuline (S)-reticuline_4 norcoclaurine synthase dopamine[c] + (4-hydroxyphenyl)acetaldehyde[c] => H2O[c] + (S)-norcoclaurine[c] NCS 0 0 1000 B6E2Z2 5.8 26.001 4.2.1.78 -(S)-reticuline (S)-reticuline_5 6-O-methyltransferase (S)-norcoclaurine[c] + S-adenosyl-L-methionine[c] => S-adenosyl-L-homocysteine[c] + (S)-Coclaurine[c] 6OMT 0 0 1000 Q6WUC1 0.08 38.511 2.1.1.128 -(S)-reticuline (S)-reticuline_6 coclaurine N-methyltransferase (S)-Coclaurine[c] + S-adenosyl-L-methionine[c] => S-adenosyl-L-homocysteine[c] + H+[c] + (S)-N-Methylcoclaurine[c] CNMT 0 0 1000 Q7XB08 0.000478707 41.032 2.1.1.140 -(S)-reticuline (S)-reticuline_7 N-methylcoclaurine hydroxylase (S)-N-Methylcoclaurine[c] + H+[c] + oxygen[c] + NADPH[c] => H2O[c] + NADP(+)[c] + (S)-3'-hydroxy-N-methylcoclaurine[c] CYP80B1 0 0 1000 O64899 54.644 1.14.14.102 -(S)-reticuline (S)-reticuline_8 4¡ä-O-methyltransferase (S)-3'-hydroxy-N-methylcoclaurine[c] + S-adenosyl-L-methionine[c] => S-adenosyl-L-homocysteine[c] + H+[c] + (S)-Reticuline[c] 4'OMT 0 0 1000 Q7XB11 0.071869248 39.402 2.1.1.116 -(S)-reticuline (S)-reticuline_9 (S)-Reticuline transport (S)-Reticuline[c] => (S)-Reticuline[e] 0 0 1000 -(S)-reticuline (S)-reticuline_10 (S)-Reticuline exchange (S)-Reticuline[e] => 1 0 1000 - -¦Â-ionone ¦Â-ionone_1 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 0.106 YEP glucose YDR284C,YDR503C -¦Â-ionone ¦Â-ionone_2 Phytoene desaturase phytoene[c] => neurosporene[c] crtI 0 0 1000 Q7Z858 0.000314486 65.066 1.3.99.28 -¦Â-ionone ¦Â-ionone_3 Phytoene desaturase neurosporene[c] + oxygen[c] => 2 H2O[c] + lycopene[c] crtI 0 0 1000 Q7Z858 0.000314486 65.066 1.3.99.28 -¦Â-ionone ¦Â-ionone_4 Bifunctional lycopene cyclase/phytoene synthase lycopene[c] => ¦Â-carotene[c] crtYB 0 0 1000 Q7Z859 0.4434336 74.736 5.5.1.19 -¦Â-ionone ¦Â-ionone_5 carotenoid cleavage dioxigenase ¦Â-carotene[c] + 2 oxygen[c] => C14-dialdehyde[c] + 2 ¦Â-ionone[c] CCD1 0 0 1000 Q6E4P3 61.311 1.13.11 -¦Â-ionone ¦Â-ionone_6 ¦Â-ionone transport ¦Â-ionone[c] => ¦Â-ionone[e] 0 0 1000 -¦Â-ionone ¦Â-ionone_7 ¦Â-ionone exchange ¦Â-ionone[e] => 1 0 1000 -¦Â-ionone ¦Â-ionone_8 C14-dialdehyde transport C14-dialdehyde[c] => C14-dialdehyde[e] 0 0 1000 -¦Â-ionone ¦Â-ionone_9 C14-dialdehyde exchange => C14-dialdehyde[e] 0 0 1000 -¦Â-ionone r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -¦Â-ionone r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 -¦Â-ionone r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 -¦Â-ionone r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 -¦Â-ionone r_0373No1 farnesyltranstransferase (No1) farnesyl diphosphate[c] + isopentenyl diphosphate[c] => geranylgeranyl diphosphate[c] + diphosphate[c] YPL069C 0 0 1000 Q12051 6.6 - -Xanthone Xanthone_1 benzoic acid exchange => benzoic acid[e] 0 0 1000 0.1 YEP glucose -Xanthone Xanthone_2 benzoic acid transport benzoic acid[e] => benzoic acid[c] 0 0 1000 -Xanthone Xanthone_3 benzoate:CoA ligase benzoic acid[c] + coenzyme A[c] + ATP[c] => diphosphate[c] + AMP[c] + benzoyl-CoA[c] BZL 0 0 1000 Q53005 8 58.93 6.2.1.25 -Xanthone Xanthone_4 benzophenone synthase 3 malonyl-CoA[c] + benzoyl-CoA[c] => 4 coenzyme A[c] + 3 carbon dioxide[c] + 2,4,6-Trihydroxybenzophenone[c] BPS 0 0 1000 A4ZYX5 0.055 43.039 2.3.1.220 -Xanthone Xanthone_5 xanthone synthase 2 H+[c] + 2,4,6-Trihydroxybenzophenone[c] + 2 oxygen[c] + 2 NADPH[c] => 2 H2O[c] + 2 NADP(+)[c] + 1,3,5-trihydroxyxanthone[c] TXS 0 0 1000 A0A161I263 57.849 -Xanthone Xanthone_6 xanthone transport 1,3,5-trihydroxyxanthone[c] => 1,3,5-trihydroxyxanthone[e] 0 0 1000 -Xanthone Xanthone_7 xanthone exchange 1,3,5-trihydroxyxanthone[e] => 1 0 1000 -Xanthone r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 0.55 40.4829 2.5.1.1 -Xanthone r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 0.55 40.4829 2.5.1.1 - -tyrosine tyrosine_1 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.082809792 39.7487 2.5.1.54 0.089 YEP glucose YDR035W,YBR249C,YDR380W,Zwf1 -tyrosine tyrosine_2 tyrosine ammonia-lyase L-tyrosine[c] => ammonium[c] + trans-4-coumarate[c] TAL 0 0 1000 Q3IWB0 0.9 54.914 4.3.1.23 -tyrosine tyrosine_3 cyclohexadienyl dehydrogenase prephenate[c] + NAD[c] => 3-(4-hydroxyphenyl)pyruvate[c] + carbon dioxide[c] + NADH[c] TyrC 0 0 1000 Q04983 32.051 1.3.1.12 - -triacylglycerol triacylglycerol_1 triacylglycerols transport triglyceride backbone[c] => triacylglycerol[e] 0 0 1000 0.1 Min glucose YMR313C,YKR089C,YOR081C,YPL147W -triacylglycerol triacylglycerol_2 triacylglycerols exchange triacylglycerol[e] => 1 0 1000 -triacylglycerol r_0109No1 acetyl-CoA carboxylase, reaction (No1) acetyl-CoA[c] + ATP[c] + bicarbonate[c] + 6.17284e-10 prot_P48445 => ADP[c] + H+[c] + malonyl-CoA[c] + phosphate[c] YNR016C 0 0 1000 Q00955 65.3426 -triacylglycerol r_2344No1 PA phosphatase (1-16:0, 2-16:1), ER membrane (No1) H2O[erm] + phosphatidate (1-16:0, 2-16:1)[erm] => phosphate[erm] + diglyceride (1-16:0, 2-16:1)[erm] YMR165C 0 0 1000 P32567 23.1467 -triacylglycerol r_2345No1 PA phosphatase (1-16:0, 2-18:1), ER membrane (No1) H2O[erm] + phosphatidate (1-16:0, 2-18:1)[erm] => phosphate[erm] + diglyceride (1-16:0, 2-18:1)[erm] YMR165C 0 0 1000 P32567 23.1467 -triacylglycerol r_2346No1 PA phosphatase (1-16:1, 2-16:1), ER membrane (No1) H2O[erm] + phosphatidate (1-16:1, 2-16:1)[erm] => phosphate[erm] + diglyceride (1-16:1, 2-16:1)[erm] YMR165C 0 0 1000 P32567 23.1467 -triacylglycerol r_2347No1 PA phosphatase (1-16:1, 2-18:1), ER membrane (No1) H2O[erm] + phosphatidate (1-16:1, 2-18:1)[erm] => phosphate[erm] + diglyceride (1-16:1, 2-18:1)[erm] YMR165C 0 0 1000 P32567 23.1467 -triacylglycerol r_2348No1 PA phosphatase (1-18:0, 2-16:1), ER membrane (No1) H2O[erm] + phosphatidate (1-18:0, 2-16:1)[erm] => phosphate[erm] + diglyceride (1-18:0, 2-16:1)[erm] YMR165C 0 0 1000 P32567 23.1467 -triacylglycerol r_2349No1 PA phosphatase (1-18:0, 2-18:1), ER membrane (No1) H2O[erm] + phosphatidate (1-18:0, 2-18:1)[erm] => phosphate[erm] + diglyceride (1-18:0, 2-18:1)[erm] YMR165C 0 0 1000 P32567 23.1467 -triacylglycerol r_2350No1 PA phosphatase (1-18:1, 2-16:1), ER membrane (No1) H2O[erm] + phosphatidate (1-18:1, 2-16:1)[erm] => phosphate[erm] + diglyceride (1-18:1, 2-16:1)[erm] YMR165C 0 0 1000 P32567 23.1467 -triacylglycerol r_2351No1 PA phosphatase (1-18:1, 2-18:1), ER membrane (No1) H2O[erm] + phosphatidate (1-18:1, 2-18:1)[erm] => phosphate[erm] + diglyceride (1-18:1, 2-18:1)[erm] YMR165C 0 0 1000 P32567 23.1467 - -ARA ARA_1 Delta9-desaturase H+[erm] + stearoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + oleoyl-CoA[erm] D9D 0 0 1000 D5KSD1 50.809 1.14.19.1 0.1 Min glucose -ARA ARA_2 Delta12-desaturase H+[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + linoleoyl-CoA[erm] D12D 0 0 1000 Q9Y8H5 46.001 1.14.19.6 -ARA ARA_3 Omega-3 desaturase linoleoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (9Z,12Z,15Z)-Octadecatrienoyl-CoA[erm] FAD3 0 0 1000 D5KSD6 47.718 1.14.19.- -ARA ARA_4 Delta6-desaturase linoleoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (6Z,9Z,12Z)-octadecatrienoyl-CoA[erm] D6D 0 0 1000 A0A1Y5I9G7 51.674 1.14.19.3 -ARA ARA_5 Delta6-desaturase (9Z,12Z,15Z)-Octadecatrienoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (6Z,9Z,12Z,15Z)-Octadecatetraenoyl-CoA[erm] D6D 0 0 1000 A0A1Y5I9G7 51.674 1.14.19.3 -ARA ARA_6 Delta6-elongase (6Z,9Z,12Z)-octadecatrienoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (8Z,11Z,14Z)-eicosatrienoyl-CoA[erm] D6E 0 0 1000 D5KSD4 36.746 2.3.1.199 -ARA ARA_7 Delta6-elongase (6Z,9Z,12Z,15Z)-Octadecatetraenoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA[erm] D6E 0 0 1000 D5KSD4 36.746 2.3.1.199 -ARA ARA_8 Delta-5 desaturase (8Z,11Z,14Z)-eicosatrienoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[erm] D5D 0 0 1000 HQ678517 59.89 1.14.19.44 -ARA ARA_9 Delta-5 desaturase (8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] D5D 0 0 1000 HQ678517 59.89 1.14.19.44 -ARA ARA_10 ARA-CoA transport (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[erm] => (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[p] 0 0 1000 -ARA ARA_11 peroxisomal acyl-CoA thioesterase (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (5Z,8Z,11Z,14Z)-eicosatetraenoate (ARA)[p] YJR019C 0 0 1000 P41903 3.1.2.2 -ARA ARA_12 ARA transport (5Z,8Z,11Z,14Z)-eicosatetraenoate (ARA)[p] => ARA[e] 0 0 1000 -ARA ARA_13 ARA exchange ARA[e] => 1 0 1000 -ARA ARA_14 EPA-CoA transport (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] => (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[p] 0 0 1000 -ARA ARA_15 peroxisomal acyl-CoA thioesterase (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate (EPA)[p] YJR019C 0 0 1000 P41903 3.1.2.2 -ARA ARA_16 EPA transport (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate (EPA)[p] => EPA[e] 0 0 1000 -ARA ARA_17 EPA exchange EPA[e] => 0 0 1000 -ARA ARA_18 Delta5-elongase (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA[erm] 0 0 1000 -ARA ARA_19 Delta-4 desaturase (7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[erm] 0 0 1000 -ARA ARA_20 EPA-CoA transport (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[erm] => (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[p] 0 0 1000 -ARA ARA_21 peroxisomal acyl-CoA thioesterase (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate (DHA)[p] YJR019C 0 0 1000 P41903 3.1.2.2 -ARA ARA_22 EPA transport (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate (DHA)[p] => DHA[e] 0 0 1000 -ARA ARA_23 EPA exchange DHA[e] => 0 0 1000 - -EPA EPA_1 Delta9-desaturase H+[erm] + stearoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + oleoyl-CoA[erm] D9D 0 0 1000 D5KSD1 50.809 1.14.19.1 0.1 Min glucose -EPA EPA_2 Delta12-desaturase H+[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + linoleoyl-CoA[erm] D12D 0 0 1000 Q9Y8H5 46.001 1.14.19.6 -EPA EPA_3 Omega-3 desaturase linoleoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (9Z,12Z,15Z)-Octadecatrienoyl-CoA[erm] FAD3 0 0 1000 D5KSD6 47.718 1.14.19.- -EPA EPA_4 Delta6-desaturase linoleoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (6Z,9Z,12Z)-octadecatrienoyl-CoA[erm] D6D 0 0 1000 A0A1Y5I9G7 51.674 1.14.19.3 -EPA EPA_5 Delta6-desaturase (9Z,12Z,15Z)-Octadecatrienoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (6Z,9Z,12Z,15Z)-Octadecatetraenoyl-CoA[erm] D6D 0 0 1000 A0A1Y5I9G7 51.674 1.14.19.3 -EPA EPA_6 Delta6-elongase (6Z,9Z,12Z)-octadecatrienoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (8Z,11Z,14Z)-eicosatrienoyl-CoA[erm] D6E 0 0 1000 D5KSD4 36.746 2.3.1.199 -EPA EPA_7 Delta6-elongase (6Z,9Z,12Z,15Z)-Octadecatetraenoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA[erm] D6E 0 0 1000 D5KSD4 36.746 2.3.1.199 -EPA EPA_8 Delta-5 desaturase (8Z,11Z,14Z)-eicosatrienoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[erm] D5D 0 0 1000 HQ678517 59.89 1.14.19.44 -EPA EPA_9 Delta-5 desaturase (8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] D5D 0 0 1000 HQ678517 59.89 1.14.19.44 -EPA EPA_10 ARA-CoA transport (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[erm] => (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[p] 0 0 1000 -EPA EPA_11 peroxisomal acyl-CoA thioesterase (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (5Z,8Z,11Z,14Z)-eicosatetraenoate (ARA)[p] YJR019C 0 0 1000 P41903 3.1.2.2 -EPA EPA_12 ARA transport (5Z,8Z,11Z,14Z)-eicosatetraenoate (ARA)[p] => ARA[e] 0 0 1000 -EPA EPA_13 ARA exchange ARA[e] => 0 0 1000 -EPA EPA_14 EPA-CoA transport (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] => (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[p] 0 0 1000 -EPA EPA_15 peroxisomal acyl-CoA thioesterase (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate (EPA)[p] YJR019C 0 0 1000 P41903 3.1.2.2 -EPA EPA_16 EPA transport (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate (EPA)[p] => EPA[e] 0 0 1000 -EPA EPA_17 EPA exchange EPA[e] => 1 0 1000 -EPA EPA_18 Delta5-elongase (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA[erm] 0 0 1000 -EPA EPA_19 Delta-4 desaturase (7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[erm] 0 0 1000 -EPA EPA_20 EPA-CoA transport (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[erm] => (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[p] 0 0 1000 -EPA EPA_21 peroxisomal acyl-CoA thioesterase (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate (DHA)[p] YJR019C 0 0 1000 P41903 3.1.2.2 -EPA EPA_22 EPA transport (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate (DHA)[p] => DHA[e] 0 0 1000 -EPA EPA_23 EPA exchange DHA[e] => 0 0 1000 - -DHA DHA_1 Delta9-desaturase H+[erm] + stearoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + oleoyl-CoA[erm] D9D 0 0 1000 D5KSD1 50.809 1.14.19.1 0.1 Min glucose -DHA DHA_2 Delta12-desaturase H+[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + linoleoyl-CoA[erm] D12D 0 0 1000 Q9Y8H5 46.001 1.14.19.6 -DHA DHA_3 Omega-3 desaturase linoleoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (9Z,12Z,15Z)-Octadecatrienoyl-CoA[erm] FAD3 0 0 1000 D5KSD6 47.718 1.14.19.- -DHA DHA_4 Delta6-desaturase linoleoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (6Z,9Z,12Z)-octadecatrienoyl-CoA[erm] D6D 0 0 1000 A0A1Y5I9G7 51.674 1.14.19.3 -DHA DHA_5 Delta6-desaturase (9Z,12Z,15Z)-Octadecatrienoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (6Z,9Z,12Z,15Z)-Octadecatetraenoyl-CoA[erm] D6D 0 0 1000 A0A1Y5I9G7 51.674 1.14.19.3 -DHA DHA_6 Delta6-elongase (6Z,9Z,12Z)-octadecatrienoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (8Z,11Z,14Z)-eicosatrienoyl-CoA[erm] D6E 0 0 1000 D5KSD4 36.746 2.3.1.199 -DHA DHA_7 Delta6-elongase (6Z,9Z,12Z,15Z)-Octadecatetraenoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA[erm] D6E 0 0 1000 D5KSD4 36.746 2.3.1.199 -DHA DHA_8 Delta-5 desaturase (8Z,11Z,14Z)-eicosatrienoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[erm] D5D 0 0 1000 HQ678517 59.89 1.14.19.44 -DHA DHA_9 Delta-5 desaturase (8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] D5D 0 0 1000 HQ678517 59.89 1.14.19.44 -DHA DHA_10 ARA-CoA transport (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[erm] => (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[p] 0 0 1000 -DHA DHA_11 peroxisomal acyl-CoA thioesterase (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (5Z,8Z,11Z,14Z)-eicosatetraenoate (ARA)[p] YJR019C 0 0 1000 P41903 3.1.2.2 -DHA DHA_12 ARA transport (5Z,8Z,11Z,14Z)-eicosatetraenoate (ARA)[p] => ARA[e] 0 0 1000 -DHA DHA_13 ARA exchange ARA[e] => 0 0 1000 -DHA DHA_14 EPA-CoA transport (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] => (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[p] 0 0 1000 -DHA DHA_15 peroxisomal acyl-CoA thioesterase (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate (EPA)[p] YJR019C 0 0 1000 P41903 3.1.2.2 -DHA DHA_16 EPA transport (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate (EPA)[p] => EPA[e] 0 0 1000 -DHA DHA_17 EPA exchange EPA[e] => 0 0 1000 -DHA DHA_18 Delta5-elongase (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA[erm] 0 0 1000 -DHA DHA_19 Delta-4 desaturase (7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[erm] 0 0 1000 -DHA DHA_20 EPA-CoA transport (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[erm] => (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[p] 0 0 1000 -DHA DHA_21 peroxisomal acyl-CoA thioesterase (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate (DHA)[p] YJR019C 0 0 1000 P41903 3.1.2.2 -DHA DHA_22 EPA transport (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate (DHA)[p] => DHA[e] 0 0 1000 -DHA DHA_23 EPA exchange DHA[e] => 1 0 1000 - -n-butanol n-butanol_1 Citramalate synthase pyruvate[m] + acetyl-CoA[m] => (R)-Citramalate[m] cimA 0 0 1000 A0FDH8 18.6 47.186 2.3.1.182 0.1 YEP glucose YOL086C -n-butanol n-butanol_2 citraconate hydratase (R)-Citramalate[m] + H2O[m] => 2-Methylmaleate[m] LEU1m 0 0 1000 P07264ly 18.54 85.794 4.2.1.35 -n-butanol n-butanol_3 2-methylmaleate hydratase 2-Methylmaleate[m] + H2O[m] => D-erythro-3-Methylmalate[m] LEU1m 0 0 1000 P07264ly 18.54 85.794 4.2.1.35 -n-butanol n-butanol_4 3-isopropylmalate dehydrogenase D-erythro-3-Methylmalate[m] + NAD[m] => 2-oxobutanoate[m] + NADH[m] + H+[m] + carbon dioxide[m] LEU2m 0 0 1000 P04173ly 18.1 38.953 1.1.1.85 -n-butanol n-butanol_5 2-ethylmalate synthase 2-oxobutanoate[m] + H2O[m] + acetyl-CoA[m] => coenzyme A[m] + (R)-2-Ethylmalate[m] LEU4m 0 0 1000 P06208ly 27.58 68.409 2.3.3.6 -n-butanol n-butanol_6 NA (R)-2-Ethylmalate[m] => 3-Ethylmalate[m] LEU1m 0 0 1000 P07264ly 18.54 85.794 4.2.1.35 -n-butanol n-butanol_7 NA 3-Ethylmalate[m] + NAD[m] => NADH[m] + H+[m] + 3-ethyl-2-oxosuccinate[m] LEU2m 0 0 1000 P04173ly 18.1 38.953 1.1.1.85 -n-butanol n-butanol_8 NA 3-ethyl-2-oxosuccinate[m] + H+[m] => carbon dioxide[m] + alpha-ketovalerate[m] LEU2m 0 0 1000 P04173ly 18.1 38.953 1.1.1.85 -n-butanol n-butanol_9 2-ethylmalate transport (R)-2-Ethylmalate[m] => (R)-2-Ethylmalate[c] 0 0 1000 -n-butanol n-butanol_10 alpha-ketovalerate transport alpha-ketovalerate[m] => alpha-ketovalerate[c] 0 0 1000 -n-butanol n-butanol_11 NA (R)-2-Ethylmalate[c] => 3-Ethylmalate[c] YGL009C 0 0 1000 P07264 18.54 85.794 4.2.1.35 -n-butanol n-butanol_12 NA 3-Ethylmalate[c] + NAD[c] => NADH[c] + H+[c] + 3-ethyl-2-oxosuccinate[c] YCL018W 0 0 1000 P04173 18.1 38.953 1.1.1.85 -n-butanol n-butanol_13 NA 3-ethyl-2-oxosuccinate[c] + H+[c] => carbon dioxide[c] + alpha-ketovalerate[c] YCL018W 0 0 1000 P04173 18.1 38.953 1.1.1.85 -n-butanol n-butanol_14 keto-acid decarboxylase alpha-ketovalerate[c] => butyraldehyde[c] + carbon dioxide[c] YDR380W 0 0 1000 Q06408 10.4 71.384 4.1.1.43 -n-butanol n-butanol_15 alcohol dehydrogenase butyraldehyde[c] + NADH[c] + H+[c] => NAD[c] + n-butanol[c] YCR105W 0 0 1000 P25377 8.3156 39.348 1.1.1.2 -n-butanol n-butanol_16 n-butanol transport n-butanol[c] => n-butanol[e] 0 0 1000 -n-butanol n-butanol_17 n-butanol exchange n-butanol[e] => 1 0 1000 -n-butanol r_1129 (update) coenzyme A transport coenzyme A[c] => coenzyme A[m] LEU5 0 0 1000 P38702 40.825 2.A.29.12.4 -n-butanol r_4173No1 L-cysteine:sulfur-acceptor sulfurtransferase (No1) (sulfur carrier)-H[m] + L-cysteine[m] => L-alanine[m] + (sulfur carrier)-SH[m] YCL017C 0 0 1000 P25374 1.74 -n-butanol r_4173_REVNo1 L-cysteine:sulfur-acceptor sulfurtransferase (reversible) (No1) L-alanine[m] + (sulfur carrier)-SH[m] => (sulfur carrier)-H[m] + L-cysteine[m] YCL017C 0 0 1000 P25374 274.1995 - -2-phenylethanol 2-phenylethanol_1 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.215305458 39.7487 2.5.1.54 0.1 Min glucose YDR035W,YBR249C,YPR060C,YGL202W -2-phenylethanol 2-phenylethanol_2 chorismate mutase chorismate[c] => prephenate[c] ARO7T226I 0 0 1000 P32178ly 0.0619725 29.7468 5.4.99.5 -2-phenylethanol 2-phenylethanol_3 Shikimate kinase shikimate[c] + ATP[c] => 3-phosphoshikimic acid[c] + H+[c] + ADP[c] aroL 0 0 1000 P0A6E1 130.8651667 19.151 2.7.1.71 -2-phenylethanol r_0279No1 chorismate synthase (No1) 5-O-(1-carboxyvinyl)-3-phosphoshikimic acid[c] => chorismate[c] + phosphate[c] YGL148W 0 0 1000 P28777 1.74 -2-phenylethanol r_0026No4 2-keto-4-methylthiobutyrate transamination (No4) pmet_r_0026[c] => 2-oxoglutarate[c] + L-methionine[c] YHR137W 0 0 1000 P38840 3080 -2-phenylethanol r_2117No1 phenylalanine transaminase (No1) L-phenylalanine[c] + pyruvate[c] => keto-phenylpyruvate[c] + L-alanine[c] YHR137W 0 0 1000 P38840 2400 -2-phenylethanol r_2118No1 tryptophan transaminase (No1) keto-phenylpyruvate[c] + L-tryptophan[c] => indole-3-pyruvate[c] + L-phenylalanine[c] YHR137W 0 0 1000 P38840 699.9998 -2-phenylethanol r_2119No1 tyrosine transaminase (No1) 3-(4-hydroxyphenyl)pyruvate[c] + L-alanine[c] => L-tyrosine[c] + pyruvate[c] YHR137W 0 0 1000 P38840 3080 -2-phenylethanol r_2117_REVNo1 phenylalanine transaminase (reversible) (No1) keto-phenylpyruvate[c] + L-alanine[c] => L-phenylalanine[c] + pyruvate[c] YHR137W 0 0 1000 P38840 3080 -2-phenylethanol r_2119_REVNo1 tyrosine transaminase (reversible) (No1) L-tyrosine[c] + pyruvate[c] => 3-(4-hydroxyphenyl)pyruvate[c] + L-alanine[c] YHR137W 0 0 1000 P38840 999.9992 -2-phenylethanol r_0938No1 prephenate dehydratase (No1) H+[c] + prephenate[c] => carbon dioxide[c] + H2O[c] + keto-phenylpyruvate[c] YNL316C 0 0 1000 P32452 3864 -2-phenylethanol r_1049No2 transketolase 1 (No2) pmet_r_1049[c] => glyceraldehyde 3-phosphate[c] + sedoheptulose 7-phosphate[c] YPR074C 0 0 1000 P23254 138.0002 -2-phenylethanol r_1050No2 transketolase 2 (No2) pmet_r_1050[c] => D-fructose 6-phosphate[c] + glyceraldehyde 3-phosphate[c] YPR074C 0 0 1000 P23254 138.0002 -2-phenylethanol r_1049_REVNo2 transketolase 1 (reversible) (No2) pmet_r_1049_REV[c] => D-xylulose 5-phosphate[c] + ribose-5-phosphate[c] YPR074C 0 0 1000 P23254 138.0002 -2-phenylethanol r_1050_REVNo2 transketolase 2 (reversible) (No2) pmet_r_1050_REV[c] => D-erythrose 4-phosphate[c] + D-xylulose 5-phosphate[c] YPR074C 0 0 1000 P23254 138.0002 -2-phenylethanol r_0962No1 pyruvate kinase (No1) pmet_r_0962[c] => ATP[c] + pyruvate[c] YAL038W 0 0 1000 P00549 115.9998 -2-phenylethanol r_0854No1 phenylpyruvate decarboxylase (No1) H+[c] + keto-phenylpyruvate[c] => carbon dioxide[c] + phenylacetaldehyde[c] YDR380W 0 0 1000 Q06408 2280 -2-phenylethanol r_0939No1 prephenate dehydrogenase (NADP) (No1) NADP(+)[c] + prephenate[c] => 3-(4-hydroxyphenyl)pyruvate[c] + carbon dioxide[c] + NADPH[c] YDR380W 0 0 1000 Q06408 13.15 -2-phenylethanol r_1589 1 0 Inf - -docosanol docosanol_1 Fatty acyl-CoA reductase docosanoyl-CoA[c] + 2 H+[c] + 2 NADPH[c] => docosanol[c] + coenzyme A[c] + 2 NADP(+)[c] FAR1 0 0 1000 Q39152 55.481 1.2.1.84 0.1 Min glucose YCR048W,YOR245C,YNR019W,YNR008W,YGL205W,YLR372W,YBR020W -docosanol docosanol_2 fatty acid synthase acetyl-CoA[c] + 21 H+[c] + 7 malonyl-CoA[c] + 14 NADPH[c] => 7 carbon dioxide[c] + 7 coenzyme A[c] + 7 H2O[c] + 14 NADP(+)[c] + palmitoyl-CoA[c] FAS 0 0 1000 K0V149 2.04404375 327.047 2.3.1.86 -docosanol docosanol_3 fatty acid synthase acetyl-CoA[c] + 24 H+[c] + 8 malonyl-CoA[c] + 16 NADPH[c] => 8 carbon dioxide[c] + 8 coenzyme A[c] + 8 H2O[c] + 16 NADP(+)[c] + stearoyl-CoA[c] FAS 0 0 1000 K0V149 2.04404375 327.047 2.3.1.86 -docosanol docosanol_4 acyl carrier protein synthase coenzyme A[c] + H2O[c] => adenosine 3',5'-bismonophosphate[c] + 2 H+[c] + pantetheine 4'-phosphate[c] Acps 0 0 1000 K0V045 14.161 2.7.8.7 -docosanol docosanol_5 fatty acid elongase malonyl-CoA[c] + palmitoyl-CoA[c] + H+[c] => coenzyme A[c] + stearoyl-CoA[c] + carbon dioxide[c] FAS 0 0 1000 K0V149 2.04404375 327.047 2.3.1.86 -docosanol docosanol_6 fatty acid elongase malonyl-CoA[c] + stearoyl-CoA[c] + H+[c] => coenzyme A[c] + icosanoyl-CoA[c] + carbon dioxide[c] FAS 0 0 1000 K0V149 2.04404375 327.047 2.3.1.86 -docosanol docosanol_7 fatty acid elongase malonyl-CoA[c] + icosanoyl-CoA[c] + H+[c] => coenzyme A[c] + docosanoyl-CoA[c] + carbon dioxide[c] FAS 0 0 1000 K0V149 2.04404375 327.047 2.3.1.86 -docosanol docosanol_8 docosanol transport docosanol[c] => docosanol[e] 0 0 1000 -docosanol docosanol_9 docosanol exchange docosanol[e] => 1 0 1000 -docosanol r_2154No1 elongase I (3-oxotetradecanoyl-CoA) (No1) lauroyl-CoA[erm] + malonyl-CoA[erm] + H+[erm] => carbon dioxide[erm] + coenzyme A[erm] + 3-oxotetradecanoyl-CoA[erm] YJL196C 0 0 1000 P39540 5.4 -docosanol r_2155No1 elongase I (3-oxopalmitoyl-CoA) (No1) malonyl-CoA[erm] + H+[erm] + myristoyl-CoA[erm] => carbon dioxide[erm] + coenzyme A[erm] + 3-oxopalmitoyl-CoA[erm] YJL196C 0 0 1000 P39540 27.6 -docosanol r_2156No1 elongase II (3-oxooctadecanoyl-CoA) (No1) malonyl-CoA[erm] + H+[erm] + palmitoyl-CoA[erm] => carbon dioxide[erm] + coenzyme A[erm] + 3-oxooctadecanoyl-CoA[erm] YCR034W 0 0 1000 P25358 5.4 -docosanol r_2157No1 elongase II or III (3-oxoicosanoyl-CoA) (No1) pmet_r_2157[erm] => carbon dioxide[erm] + coenzyme A[erm] + 3-oxoicosanoyl-CoA[erm] YCR034W 0 0 1000 P25358 5.4 -docosanol r_2158No1 elongase II or III (3-oxodocosanoyl-CoA) (No1) pmet_r_2158[erm] => carbon dioxide[erm] + coenzyme A[erm] + 3-oxodocosanoyl-CoA[erm] YCR034W 0 0 1000 P25358 5.4 -docosanol r_2159No1 elongase II or III (3-oxotetracosanoyl-CoA) (No1) pmet_r_2159[erm] => carbon dioxide[erm] + coenzyme A[erm] + 3-oxotetracosanoyl-CoA[erm] YCR034W 0 0 1000 P25358 5.4 -docosanol r_0109No1 acetyl-CoA carboxylase, reaction (No1) acetyl-CoA[c] + ATP[c] + bicarbonate[c] + 6.17284e-10 prot_P48445 => ADP[c] + H+[c] + malonyl-CoA[c] + phosphate[c] YNR016C 0 0 1000 Q00955 65.3426 - -Itaconic acid Itaconic acid_1 cis-aconitic acid decarboxylase cis-aconitate[c] + H+[c] => carbon dioxide[c] + Itaconic acid[c] CAD 0 0 1000 B3IUN8 0.242756323 52.754 4.1.1.6 0.1 YEP glucose YJR078W,YJR019C -Itaconic acid Itaconic acid_2 itaconic acid transport Itaconic acid[c] => Itaconic acid[e] 0 0 1000 -Itaconic acid Itaconic acid_3 itaconic acid exchange Itaconic acid[e] => 1 0 1000 - -Glutathione Glutathione_1 gamma-glutamylcysteine synthetase ATP[c] + L-cysteine[c] + L-glutamate[c] => ADP[c] + H+[c] + L-gamma-glutamyl-L-cysteine[c] + phosphate[c] GshF 0 0 1000 D4N892 1167.652667 85.438 6.3.2.2 0.1 YEP glucose -Glutathione Glutathione_2 glutathione synthetase (No1) ATP[c] + L-gamma-glutamyl-L-cysteine[c] + L-glycine[c] => ADP[c] + glutathione[c] + H+[c] + phosphate[c] GshF 0 0 1000 D4N892 1103.574167 85.438 6.3.2.3 -Glutathione Glutathione_3 glutathione synthetase (No1) ATP[c] + L-gamma-glutamyl-L-cysteine[c] + L-glycine[c] => ADP[c] + glutathione[c] + H+[c] + phosphate[c] gshB 0 0 1000 P04425 151 35.561 6.3.2.3 -Glutathione Glutathione_4 glutathione transport glutathione[c] => glutathione[e] 0 0 1000 -Glutathione r_0460No1 gamma-glutamylcysteine synthetase (No1) ATP[c] + L-cysteine[c] + L-glutamate[c] => ADP[c] + H+[c] + L-gamma-glutamyl-L-cysteine[c] + phosphate[c] YJL101C 0 0 1000 P32477 20380 -Glutathione r_0485No1 glutathione synthetase (No1) ATP[c] + L-gamma-glutamyl-L-cysteine[c] + L-glycine[c] => ADP[c] + glutathione[c] + H+[c] + phosphate[c] YOL049W 0 0 1000 Q08220 26 -Glutathione r_0468No1 glutamate 5-kinase (No1) ATP[c] + L-glutamate[c] => ADP[c] + L-gamma-glutamyl phosphate[c] YDR300C 0 0 1000 P32264 23.03 -Glutathione r_1807 1 0 Inf - -Ethylene Ethylene_1 ethylene forming enzyme 2-oxoglutarate[c] + 2 H+[c] + oxygen[c] => H2O[c] + 3 carbon dioxide[c] + Ethylene[c] efe 0 0 1000 Q9Z3T0 0.5 38.064 1.13.12.19 0.24 Min glucose -Ethylene Ethylene_2 ethylene transport Ethylene[c] => Ethylene[e] 0 0 1000 -Ethylene Ethylene_3 ethylene exchange Ethylene[e] => 1 0 1000 -Ethylene r_1889_REV 0 0 1 - -Human Serum Albumin (HSA) Human Serum Albumin (HSA)_1 production of HAS 0.8928 L-alanine[c] + 0.4032 L-arginine[c] + 0.2448 L-asparagine[c] + 0.5184 L-aspartate[c] + 0.504 L-cysteine[c] + 0.288 L-glutamate[c] + 0.8928 L-glutamine[c] + 0.1872 L-glycine[c] + 0.2304 L-histidine[c] + 0.1296 L-isoleucine[c] + 0.9216 L-leucine[c] + 0.864 L-lysine[c] + 0.1008 L-methionine[c] + 0.504 L-phenylalanine[c] + 0.3456 L-proline[c] + 0.4032 L-serine[c] + 0.4176 L-threonine[c] + 0.0288 L-tryptophan[c] + 0.2736 L-tyrosine[c] + 0.6192 L-valine[c] + 1.22 GTP[c] => HAS[c] + 1.22 GDP[c] + 1.22 phosphate[c] 0 0 1000 0.22 4.6 Min glucose -Human Serum Albumin (HSA) Human Serum Albumin (HSA)_2 HSA transport HAS[c] => HAS[e] 0 0 1000 -Human Serum Albumin (HSA) Human Serum Albumin (HSA)_3 HSA exchange HAS[e] => 1 0 1000 - -¦Á-Amylase ¦Á-Amylase_1 production of ¦Á-Amylase 0.7663 L-alanine[c] + 0.1825 L-arginine[c] + 0.4744 L-asparagine[c] + 0.7663 L-aspartate[c] + 0.1642 L-cysteine[c] + 0.2189 L-glutamate[c] + 0.3649 L-glutamine[c] + 0.7846 L-glycine[c] + 0.1277 L-histidine[c] + 0.5109 L-isoleucine[c] + 0.6751 L-leucine[c] + 0.3649 L-lysine[c] + 0.2007 L-methionine[c] + 0.2737 L-phenylalanine[c] + 0.4014 L-proline[c] + 0.6751 L-serine[c] + 0.7298 L-threonine[c] + 0.2189 L-tryptophan[c] + 0.6386 L-tyrosine[c] + 0.5656 L-valine[c] + GTP[c] => ¦Á-Amylase[c] + GDP[c] + phosphate[c] 0 0 1000 0.2 Min glucose -¦Á-Amylase ¦Á-Amylase_2 ¦Á-Amylase transport ¦Á-Amylase[c] => ¦Á-Amylase[e] 0 0 1000 -¦Á-Amylase ¦Á-Amylase_3 ¦Á-Amylase exchange ¦Á-Amylase[e] => 1 0 1000 - -Hemoglobin Hemoglobin_1 heme o transport heme o[m] => heme o[c] 0 0 1000 0.25 Min glucose -Hemoglobin Hemoglobin_2 production of globin 1.1532 L-alanine[c] + 0.1922 L-arginine[c] + 0.3203 L-asparagine[c] + 0.4805 L-aspartate[c] + 0.0961 L-cysteine[c] + 0.3844 L-glutamate[c] + 0.1281 L-glutamine[c] + 0.6407 L-glycine[c] + 0.6087 L-histidine[c] + 1.1532 L-leucine[c] + 0.7048 L-lysine[c] + 0.1602 L-methionine[c] + 0.4805 L-phenylalanine[c] + 0.4485 L-proline[c] + 0.5125 L-serine[c] + 0.5125 L-threonine[c] + 0.0961 L-tryptophan[c] + 0.1922 L-tyrosine[c] + 0.9931 L-valine[c] + 1.16 GTP[c] => globin[c] + 1.16 GDP[c] + 1.16 phosphate[c] 0 0 1000 -Hemoglobin Hemoglobin_3 production of hemoglobin globin[c] + 4 heme o[c] => hemoglobin[c] 0 0 1000 -Hemoglobin Hemoglobin_4 hemoglobin transport hemoglobin[c] => hemoglobin[e] 0 0 1000 -Hemoglobin Hemoglobin_5 hemoglobin exchange hemoglobin[e] => 1 0 1000 -Hemoglobin r_0557No1 hydroxymethylbilane synthase (No1) H2O[c] + 4 porphobilinogen[c] => 4 ammonium[c] + preuroporphyrinogen[c] YDL205C 0 0 1000 P28789 0.125 - -Glucagon Glucagon_1 production of glucagon 0.6223 L-alanine[c] + 0.7659 L-arginine[c] + 0.3829 L-asparagine[c] + 0.7659 L-aspartate[c] + 0.6223 L-glutamate[c] + 0.4787 L-glutamine[c] + 0.4308 L-glycine[c] + 0.1915 L-histidine[c] + 0.3829 L-isoleucine[c] + 0.5744 L-leucine[c] + 0.4787 L-lysine[c] + 0.2393 L-methionine[c] + 0.5265 L-phenylalanine[c] + 0.1436 L-proline[c] + 0.8137 L-serine[c] + 0.4308 L-threonine[c] + 0.1915 L-tryptophan[c] + 0.1915 L-tyrosine[c] + 0.3829 L-valine[c] + 0.36 GTP[c] => glucagon[c] + 0.36 GDP[c] + 0.36 phosphate[c] 0 0 1000 0.1 YEP glucose -Glucagon Glucagon_2 glucagon transport glucagon[c] => glucagon[e] 0 0 1000 -Glucagon Glucagon_3 glucagon exchange glucagon[e] => 1 0 1000 - -Glycolate Glycolate_1 glycolate transport glycolate[c] => glycolate[e] 0 0 1000 0.1 Min glucose -Glycolate Glycolate_2 glycolate exchange glycolate[e] => 1 0 1000 - -L-phenylacetylcarbinol L-phenylacetylcarbinol_1 benzaldehyde exchange => benzaldehyde[e] 0 0 1 0.13 2 1 YEP glucose -L-phenylacetylcarbinol L-phenylacetylcarbinol_2 benzaldehyde transport benzaldehyde[e] => benzaldehyde[c] 0 0 1000 -L-phenylacetylcarbinol L-phenylacetylcarbinol_3 pyruvate decarboxylase (arm) pyruvate[c] + benzaldehyde[c] => pmet_r_3[c] 0 0 1000 -L-phenylacetylcarbinol L-phenylacetylcarbinol_4 pyruvate decarboxylase (No1) pmet_r_3[c] => L-phenylacetylcarbinol[c] + carbon dioxide[c] YGR087C 0 0 1000 P26263 62 -L-phenylacetylcarbinol L-phenylacetylcarbinol_5 pyruvate decarboxylase (No2) pmet_r_3[c] => L-phenylacetylcarbinol[c] + carbon dioxide[c] YLR044C 0 0 1000 P06169 144.9999 -L-phenylacetylcarbinol L-phenylacetylcarbinol_6 pyruvate decarboxylase (No3) pmet_r_3[c] => L-phenylacetylcarbinol[c] + carbon dioxide[c] YLR134W 0 0 1000 P16467 62 -L-phenylacetylcarbinol L-phenylacetylcarbinol_7 L-PAC transport L-phenylacetylcarbinol[c] => L-phenylacetylcarbinol[e] 0 0 1000 -L-phenylacetylcarbinol L-phenylacetylcarbinol_8 L-PAC exchange L-phenylacetylcarbinol[e] => 1 0 1000 -L-phenylacetylcarbinol L-phenylacetylcarbinol_9 Alcohol dehydrogenase 1 benzaldehyde[c] + NADH[c] => benzylalcohol[c] + NAD[c] YOL086C 0 0 1000 P00330 -L-phenylacetylcarbinol L-phenylacetylcarbinol_10 benzylalcohol transport benzylalcohol[c] => benzylalcohol[e] 0 0 1000 -L-phenylacetylcarbinol L-phenylacetylcarbinol_11 benzylalcohol exchange benzylalcohol[e] => 0 0 1000 -L-phenylacetylcarbinol L-phenylacetylcarbinol_12 Benzaldehyde oxidase benzaldehyde[c] + oxygen[c] => Benzoic Acid[c] 0 0 1000 -L-phenylacetylcarbinol L-phenylacetylcarbinol_13 Benzoic Acid transport Benzoic Acid[c] => Benzoic Acid[e] 0 0 1000 -L-phenylacetylcarbinol L-phenylacetylcarbinol_14 Benzoic Acid exchange Benzoic Acid[e] => 0 0 1000 - -3-hydroxypropanoate-malcoa 3-hydroxypropanoate-malcoa_1 Malonyl-CoA reductase 2 H+[c] + malonyl-CoA[c] + 2 NADPH[c] => coenzyme A[c] + 2 NADP(+)[c] + 3-hydroxypropanoate[c] MCRca 0 0 1000 Q6QQP7 50 300 1.2.1.75 0.1 Min glucose -3-hydroxypropanoate-malcoa 3-hydroxypropanoate-malcoa_2 3-hydroxypropionate transport 3-hydroxypropanoate[c] => 3-hydroxypropanoate[e] 0 0 1000 -3-hydroxypropanoate-malcoa 3-hydroxypropanoate-malcoa_3 3-hydroxypropionate exchange 3-hydroxypropanoate[e] => 1 0 1000 - -3-hydroxypropanoate-asp 3-hydroxypropanoate-asp_1 3-hydroxypropionate dehydrogenase H+[c] + NADPH[c] + 3-oxopropanoate[c] => NADP(+)[c] + 3-hydroxypropanoate[c] fdyG 0 0 1000 P39831 115 27.249 1.1.1.298 0.1 Min glucose -3-hydroxypropanoate-malcoa 3-hydroxypropanoate-asp_2 3-hydroxypropionate transport 3-hydroxypropanoate[c] => 3-hydroxypropanoate[e] 0 0 1000 -4-hydroxypropanoate-asp 3-hydroxypropanoate-asp_3 3-hydroxypropionate exchange 3-hydroxypropanoate[e] => 1 0 1000 -4-hydroxypropanoate-malcoa 3-hydroxypropanoate-asp_4 beta-alanine-pyruvate aminotransferase beta-alanine[c] + pyruvate[c] => L-alanine[c] + 3-oxopropanoate[c] bcere0029_32090 0 0 1000 -5-hydroxypropanoate-asp 3-hydroxypropanoate-asp_5 aspartate 1-decarboxylase H+[c] + L-aspartate[c] => beta-alanine[c] + carbon dioxide[c] A7U8C7 0 0 1000 A7U8C7 7.03 61.24 4.1.1.11 -5-hydroxypropanoate-malcoa r_4572 beta-alanine:2-oxoglutarate aminotransferase 2-oxoglutarate[c] + beta-alanine[c] => L-glutamate[c] + 3-oxopropanoate[c] YGR019Wly 0 0 1000 P17649ly 0.1324 52.946 2.6.1.19 - -FFA FFA_1 FFAs Biosyntheis decanoate[e] + laurate[e] + myristate[e] + palmitate[e] + palmitoleate[e] + stearate[e] + oleate[e] => Free fatty acid[e] 0 0 1000 0.03 Min glucose YGL205W,YOR317W,YMR246W,YMR110C,YDL078C -FFA FFA_2 FFAs exchange Free fatty acid[e] => 1 0 1000 -FFA FFA_3 malic enzyme (S)-malate[m] + NAD[m] => carbon dioxide[m] + NADH[m] + pyruvate[m] ME 0 0 1000 1.1.1.38 -FFA FFA_4 ATP:citrate lyase ATP[c] + citrate[c] + coenzyme A[c] => acetyl-CoA[c] + ADP[c] + oxaloacetate[c] + phosphate[c] ACL 0 0 1000 Q91V92 27.1383 120 2.3.3.8 -FFA FFA_5 fatty acid synthase (C16:0) acetyl-CoA[c] + 21 H+[c] + 7 malonyl-CoA[c] + 14 NADPH[c] => 7 carbon dioxide[c] + 7 coenzyme A[c] + 7 H2O[c] + 14 NADP(+)[c] + palmitoyl-CoA[c] FAS1,FAS2 0 0 1000 A0A2Z6EZ44,A0A2Z6EYW1 4.16 318.115,137.582 -FFA FFA_6 fatty acid synthase (C18:0) acetyl-CoA[c] + 24 H+[c] + 8 malonyl-CoA[c] + 16 NADPH[c] => 8 carbon dioxide[c] + 8 coenzyme A[c] + 8 H2O[c] + 16 NADP(+)[c] + stearoyl-CoA[c] FAS1,FAS2 0 0 1000 A0A2Z6EZ44,A0A2Z6EYW1 4.16 318.115,137.582 -FFA FFA_7 fatty acid synthase (C14:0) acetyl-CoA[c] + 18 H+[c] + 6 malonyl-CoA[c] + 12 NADPH[c] => 6 carbon dioxide[c] + 6 coenzyme A[c] + 6 H2O[c] + 12 NADP(+)[c] + myristoyl-CoA[c] FAS1,FAS2 0 0 1000 A0A2Z6EZ44,A0A2Z6EYW1 4.16 318.115,137.582 -FFA FFA_8 fatty acid synthase (C12:0) acetyl-CoA[c] + 15 H+[c] + 5 malonyl-CoA[c] + 10 NADPH[c] => 5 carbon dioxide[c] + 5 coenzyme A[c] + 5 H2O[c] + 10 NADP(+)[c] + lauroyl-CoA[c] FAS1,FAS2 0 0 1000 A0A2Z6EZ44,A0A2Z6EYW1 4.16 318.115,137.582 -FFA FFA_9 fatty acid synthase (C10:0) acetyl-CoA[c] + 12 H+[c] + 4 malonyl-CoA[c] + 8 NADPH[c] => 4 carbon dioxide[c] + 4 coenzyme A[c] + 4 H2O[c] + 8 NADP(+)[c] + decanoyl-CoA[c] FAS1,FAS2 0 0 1000 A0A2Z6EZ44,A0A2Z6EYW1 4.16 318.115,137.582 -FFA FFA_10 thioesterase (C16:0) palmitoyl-CoA[c] + H2O[c] => coenzyme A[c] + palmitate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 -FFA FFA_11 thioesterase (C18:0) stearoyl-CoA[c] + H2O[c] => coenzyme A[c] + stearate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 -FFA FFA_12 thioesterase (C18:1) oleoyl-CoA[c] + H2O[c] => coenzyme A[c] + oleate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 -FFA FFA_13 thioesterase (C10:0) decanoyl-CoA[c] + H2O[c] => coenzyme A[c] + decanoate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 -FFA FFA_14 thioesterase (C12:0) lauroyl-CoA[c] + H2O[c] => coenzyme A[c] + laurate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 -FFA FFA_15 thioesterase (C14:0) myristoyl-CoA[c] + H2O[c] => coenzyme A[c] + myristate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 -FFA FFA_16 thioesterase (C16:1) palmitoleoyl-CoA(4-)[c] + H2O[c] => coenzyme A[c] + palmitoleate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 - -Succinic acid Succinic acid_1 Fumarate hydratase fumarate[c] + H2O[c] => (S)-malate[c] FumC 0 0 1000 A0A024L3D9 1150 50.489 4.2.1.2 0.25 Min glucose YLR044C,YLR134W,YGR087C,YPL262W,YER065C,YNL117W -Succinic acid Succinic acid_2 Fumarate hydratase (S)-malate[c] => fumarate[c] + H2O[c] FumC 0 0 1000 A0A024L3D9 11.2 50.489 4.2.1.2 -Succinic acid r_1671_REV 0 0 1 -Succinic acid r_2056 1 0 Inf - -Nicotianamine Nicotianamine_1 5,10-methylenetetrahydrofolate reductase (NADPH) 5,10-methylenetetrahydrofolate[c] + 2 H+[c] + NADPH[c] => 5-methyltetrahydrofolate[c] + NADP(+)[c] MTHFR1 0 0 1000 Q9SE60 0.0353536 66.288 1.5.1.20 0.1 YEP glucose YGL125W -Nicotianamine Nicotianamine_2 5,10-methylenetetrahydrofolate reductase (NADPH) 5,10-methylenetetrahydrofolate[c] + 2 H+[c] + NADH[c] => 5-methyltetrahydrofolate[c] + NAD[c] MTHFR1 0 0 1000 Q9SE60 0.0364584 66.288 1.5.1.20 -Nicotianamine Nicotianamine_3 Nicotianamine synthase 3 S-adenosyl-L-methionine[c] => 3 H+[c] + Nicotianamine[c] + 3 5'-S-methyl-5'-thioadenosine [c] NAS2 0 0 1000 Q9FKT9 35.679 2.5.1.43 -Nicotianamine Nicotianamine_4 nicotianamine transport Nicotianamine[c] => Nicotianamine[e] 0 0 1000 -Nicotianamine Nicotianamine_5 nicotianamine exchaneg Nicotianamine[e] => 1 0 1000 -Nicotianamine r_1810_REV 0 0 1 -Nicotianamine r_1793_REV 0 0 1 -Nicotianamine r_0080No2 0 0 0 - -Psilocybin Psilocybin_1 tryptophan decarboxylase L-tryptophan[c] => tryptamine[c] + carbon dioxide[c] CrTdc 0 0 1000 A0A3S7SKS7 3.33 56.221 4.1.1.105 0.1 Min glucose YBR249C -Psilocybin Psilocybin_2 Tryptamine 4-monooxygenase tryptamine[c] + oxygen[c] => 4-hydroxytryptamine[c] + H2O[c] PcpsiH 0 0 1000 P0DPA7 57.515 1.14.99.59 -Psilocybin Psilocybin_3 4-hydroxytryptamine kinase 4-hydroxytryptamine[c] + ATP[c] => norbaeocystin[c] + ADP[c] + H+[c] PcPsiK 0 0 1000 P0DPA8 40.442 2.7.1.222 -Psilocybin Psilocybin_4 N-methyltransferase norbaeocystin[c] + 2 S-adenosyl-L-methionine[c] => 2 H+[c] + psilocybin[c] + 2 S-adenosyl-L-homocysteine[c] PcPsiM 0 0 1000 P0DPA9 34.434 2.1.1.345 -Psilocybin Psilocybin_5 spontaneous reaction psilocybin[c] => psilocin[c] 0 0 1000 -Psilocybin Psilocybin_6 4-hydroxytryptamine kinase ATP[c] + psilocin[c] => ADP[c] + psilocybin[c] PcPsiK 0 0 1000 P0DPA8 40.442 2.7.1.222 -Psilocybin r_0997No1 shikimate dehydrogenase ATP[c] + shikimate[c] => 3-phosphoshikimic acid[c] + ADP[c] + H+[c] YDR127W 0 0 1000 P08566 120 174.753 -Psilocybin r_0279No1 chorismate synthase (No1) 5-O-(1-carboxyvinyl)-3-phosphoshikimic acid[c] => chorismate[c] + phosphate[c] YGL148W 0 0 1000 P28777 1.74 -Psilocybin Psilocybin_7 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.082809792 39.7487 2.5.1.54 -Psilocybin Psilocybin_8 Psilocybin transport psilocybin[c] => psilocybin[e] 0 0 1000 -Psilocybin Psilocybin_9 Psilocybin exchange psilocybin[e] => 1 0 1000 - -vanillin-¦Â-glucoside vanillin-¦Â-glucoside_1 dehydroshikimate dehydratase 3-dehydroshikimate[c] => 3,4-Dihydroxybenzoate[c] + H2O[c] 3DSD 0 0 1000 Q86ZM4 125.055 41.685 4.2.1.118 0.3 Min glucose YMR318C,YLR300W Regulatory control circuits for stabilizing long-term anabolic product formation in yeast -vanillin-¦Â-glucoside vanillin-¦Â-glucoside_2 O-methyltransferase 3,4-Dihydroxybenzoate[c] + 5-methyltetrahydrofolate[c] => THF[c] + Vanillate[c] OMT 0 0 1000 P21964 4.605673333 30.037 2.1.1.341 -vanillin-¦Â-glucoside vanillin-¦Â-glucoside_3 aromatic carboxylic acid reductase 3,4-Dihydroxybenzoate[c] + NADPH[c] + ATP[c] + H+[c] => protocatechuic aldehyde[c] + AMP[c] + diphosphate[c] + NADP(+)[c] ACAR 0 0 1000 Q6RKB1 4.49211 128.346 1.2.1.30 -vanillin-¦Â-glucoside vanillin-¦Â-glucoside_4 aromatic carboxylic acid reductase Vanillate[c] + NADH[c] + H+[c] => NAD[c] + H2O[c] + vanillin[c] ACAR 0 0 1000 Q6RKB1 4.49211 128.346 1.2.1.30 -vanillin-¦Â-glucoside vanillin-¦Â-glucoside_5 O-methyltransferase protocatechuic aldehyde[c] + 5-methyltetrahydrofolate[c] => THF[c] + vanillin[c] OMT 0 0 1000 P21964 4.605673333 30.037 2.1.1.341 -vanillin-¦Â-glucoside vanillin-¦Â-glucoside_6 UDP-glycosyltransferase UDP-D-glucose[c] + vanillin[c] => UDP[c] + H+[c] + vanillin-¦Â-glucoside[c] UGT 0 0 1000 Q9LVR1 52.992 -vanillin-¦Â-glucoside vanillin-¦Â-glucoside_7 draw_prot_Q86ZM4 vanillin-¦Â-glucoside[c] => vanillin-¦Â-glucoside[e] 0 0 1000 -vanillin-¦Â-glucoside vanillin-¦Â-glucoside_8 draw_prot_P21964 vanillin-¦Â-glucoside[e] => 1 0 1000 - -Betaxanthin Betaxanthin_1 tyrosine hydroxylase oxygen[c] + 2 L-tyrosine[c] => 2 3,4-Dihydroxy-L-phenylalanine(L-DOPA)[c] CYP76AD5 0 0 1000 I3PFJ5 56.212 1.14.18.1 0.1 YEP raffinose YBR249C -Betaxanthin Betaxanthin_2 L-Dopa dioxygenase 3,4-Dihydroxy-L-phenylalanine(L-DOPA)[c] + oxygen[c] => 4-(L-Alanin-3-yl)-2-hydroxy-cis,cis-muconate 6-semialdehyde[c] + H+[c] DOD 0 0 1000 B6F0W8 0.030171 30.171 1.13.11.29 -Betaxanthin Betaxanthin_3 spontaneous reaction 4-(L-Alanin-3-yl)-2-hydroxy-cis,cis-muconate 6-semialdehyde[c] + H+[c] => betalamic acid[c] + H2O[c] 0 0 1000 -Betaxanthin Betaxanthin_4 spontaneous reaction betalamic acid[c] + L-tyrosine[c] => betaxanthin[c] + H2O[c] 0 0 1000 -Betaxanthin Betaxanthin_5 Betaxanthin transport betaxanthin[c] => betaxanthin[e] 0 0 1000 -Betaxanthin Betaxanthin_6 Betaxanthin exchange betaxanthin[e] => 1 0 1000 -Betaxanthin Betaxanthin_7 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.082809792 39.7487 2.5.1.54 - -Ergosterol 0.1 Min glucose -Glycine 0.1 Min glucose -Alanine 0.1 Min glucose -Arginine 0.1 Min glucose -Asparagine 0.1 Min glucose -Aspartate 0.1 Min glucose -Cysteine 0.1 Min glucose -Glutamate 0.1 Min glucose -Glutamine 0.1 Min glucose -Histidine 0.1 Min glucose -Isoleucine 0.1 Min glucose -Leucine 0.1 Min glucose -Lysine 0.1 Min glucose -Methionine 0.1 Min glucose -Phenylalanine 0.1 Min glucose -Proline 0.1 Min glucose -Serine 0.1 Min glucose -Threonine 0.1 Min glucose -Tryptophan 0.1 Min glucose -Valine 0.1 Min glucose -Xanthine 0.1 Min glucose -Urea 0.1 Min glucose -Thymidine 0.1 Min glucose -Putrescine 0.1 Min glucose -Hypoxanthine 0.1 Min glucose -Hexanoate 0.1 Min glucose -Homoserine 0.1 Min glucose -Guanine 0.1 Min glucose -Glycerol 0.1 Min glucose -Citrate 0.1 Min glucose -Oxoglutarate 0.1 Min glucose -Acetaldehyde 0.1 Min glucose -Acetate 0.1 Min glucose -R,R-2,3-butanediol 0.1 Min glucose -Citrulline 0.1 Min glucose -Oleate 0.1 Min glucose -Spermine 0.1 Min glucose -Palmitoleate 0.1 Min glucose -Laurate 0.1 Min glucose -Choline 0.1 Min glucose +Chemicals rxns rxnNames formulas grRules c lb ub proteins kcats MWs EC_number ¦Ì qO2 ATP Medium Carbon source deletion +Lactic acid Lactic acid_1 L-lactate dehydrogenase pyruvate[c] + NADH[c] + H+[c] => (S)-lactate[c] + NAD[c] LDHA 0 0 1000 P19858 7.0146 36.598 1.1.1.27 0.29 YEP glucose "YDL022W,YML054C,YLR044C,YOL086C,YPL061W" +Lactic acid Lactic acid_2 acetaldehyde dehydrogenase acetaldehyde[c] + coenzyme A[c] + NAD[c] => acetyl-CoA[c] + NADH[c] + H+[c] EutE 0 0 1000 P77445 15.7 49.022 1.2.1.10 +Lactic acid Lactic acid_3 L-lactate transport (S)-lactate[c] => (S)-lactate[e] 0 0 1000 +Lactic acid Lactic acid_4 L-lactate exchange (S)-lactate[e] => 1 0 1000 + +Malate r_0958No1 pyruvate carboxylase (No1) pmet_r_0958[c] => ADP[c] + H+[c] + oxaloacetate[c] + phosphate[c] YBR218C 0 0 1000 P32327 0.52 130.166 0.1 Min glucose "YLR044C,YLR134W,YGR087C,YDL078C" +Malate r_0958No2 pyruvate carboxylase (No2) pmet_r_0958[c] => ADP[c] + H+[c] + oxaloacetate[c] + phosphate[c] YGL062W 0 0 1000 P11154 0.52 130.098 +Malate r_0714_REVNo1 "malate dehydrogenase, cytoplasmic (reversible) (No1)" H+[c] + NADH[c] + oxaloacetate[c] => (S)-malate[c] + NAD[c] YOL126C 0 0 1000 P22133 20.70467083 40.7305 +Malate r_1901_REV L-malate transport (reversible) (S)-malate[c] => (S)-malate[e] mae1 0 0 1000 P50537 49.304 2.A.16.2.1 + +"cis,cis-muconic acid" "cis,cis-muconic acid_1" dehydroshikimate dehydratase "3-dehydroshikimate[c] => 3,4-Dihydroxybenzoate[c] + H2O[c]" Pa_5_5120 0 0 1000 3DSD 121.44 40.48 4.2.1.118 0.1 YEP glucose "YDR035W,YBR249C,YNL241C" +"cis,cis-muconic acid" "cis,cis-muconic acid_2" protocatechuic acid decarboxylase "3,4-Dihydroxybenzoate[c] + H+[c] => carbon dioxide[c] + Catechol[c]" ECL_01944 0 0 1000 A0A0H3CJN8 90 53.541 4.1.1.63 +"cis,cis-muconic acid" "cis,cis-muconic acid_3" "catechol 1,2-dioxygenase" "Catechol[c] + oxygen[c] => 2 H+[c] + cis,cis-muconate[c]" HQD2 0 0 1000 P86029 157.7333333 33.8 1.13.11.1 +"cis,cis-muconic acid" "cis,cis-muconic acid_4" 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.082809792 39.7487 2.5.1.54 +"cis,cis-muconic acid" "cis,cis-muconic acid_5" "cis,cis-muconic acid transport" "cis,cis-muconate[c] => cis,cis-muconate[e]" 0 0 1000 +"cis,cis-muconic acid" "cis,cis-muconic acid_6" "cis,cis-muconic acid exchange" "cis,cis-muconate[e] =>" 1 0 1000 + +Resveratrol Resveratrol_1 tyrosine ammonia-lyase L-tyrosine[c] => ammonium[c] + trans-4-coumarate[c] Haur_4629 0 0 1000 A9B0P2 0.076 56.397 4.3.1.23 0.15 Min glucose +Resveratrol Resveratrol_2 4-coumaryl-CoA ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => AMP[c] + diphosphate[c] + 4-coumaroyl-CoA[c] 4CL1 0 0 1000 Q42524 12.719375 61.053 6.2.1.12 +Resveratrol Resveratrol_3 resveratrol synthase 3 H+[c] + 4-coumaroyl-CoA[c] + 3 malonyl-CoA[c] => 4 coenzyme A[c] + 4 carbon dioxide[c] + resveratrol[c] VST1 0 0 1000 P28343 0.003 42.84 2.3.1.95 +Resveratrol Resveratrol_4 resveratrol transport resveratrol[c] => resveratrol[e] 0 0 1000 +Resveratrol Resveratrol_5 resveratrol exchange resveratrol[e] => 1 0 1000 + +Genistein Genistein_1 Phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL 0 0 1000 P45730 22 77.919 4.3.1.24 0.1 YEP glucose +Genistein Genistein_2 Cinnamate-4-hydroxylase H+[c] + oxygen[c] + cinnamate[c] + NADPH[c] => H2O[c] + NADP(+)[c] + trans-4-coumarate[c] C4H 0 0 1000 C0LUU6 161.8 58.011 1.14.13.11 +Genistein Genistein_3 4-coumarate:CoA ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => diphosphate[c] + AMP[c] + 4-coumaroyl-CoA[c] 4CL 0 0 1000 C0LUU7 0.101656667 60.994 6.2.1.12 +Genistein Genistein_4 Isoflavone synthase naringenin[c] => 3 H+[c] + genistein[c] IFS 0 0 Inf Q9M6D6 58.93 1.14.14.87 +Genistein Genistein_5 Chalcone synthase 2 H+[c] + 4-coumaroyl-CoA[c] + 3 malonyl-CoA[c] => 4 coenzyme A[c] + 3 carbon dioxide[c] + naringenin chalcone[c] CHS 0 0 1000 Q6X0M9 0.006019133 42.488 2.3.1.74 +Genistein Genistein_6 Chalcone isomerase H+[c] + naringenin chalcone[c] => naringenin[c] CHI 0 0 1000 C0LUV0 139.8476667 24.679 5.5.1.6 +Genistein Genistein_7 Flavanone 3-hydroxylase naringenin[c] + oxygen[c] + 2-oxoglutarate[c] => carbon dioxide[c] + succinate[c] + dihydrokaempferol[c] F3H 0 0 0 Q53B69 42.673 1.14.11.9 +Genistein Genistein_8 Flavonoid 3'-hydroxylase H+[c] + oxygen[c] + NADPH[c] + dihydrokaempferol[c] => dihydroquercetin[c] + H2O[c] + NADP(+)[c] F3'H 0 0 0 Q8W3Y5 12.5 56.982 1.14.13.21 +Genistein Genistein_9 Flavonol synthase dihydrokaempferol[c] + 2-oxoglutarate[c] + oxygen[c] => H+[c] + carbon dioxide[c] + H2O[c] + succinate[c] + kaempferol[c] FLS 0 0 0 C0LUV3 6.6 40.041 1.14.11.23 +Genistein Genistein_10 Flavonol synthase dihydroquercetin[c] + 2-oxoglutarate[c] + oxygen[c] => H+[c] + carbon dioxide[c] + H2O[c] + succinate[c] + quercetin[c] FLS 0 0 0 C0LUV3 3.9 40.041 1.14.11.23 +Genistein Genistein_11 quercetin transport quercetin[c] => quercetin[e] 0 0 1000 +Genistein Genistein_12 quercetin exchange quercetin[e] => 0 0 1000 +Genistein Genistein_13 kaempferol transport kaempferol[c] => kaempferol[e] 0 0 1000 +Genistein Genistein_14 kaempferol exchange kaempferol[e] => 0 0 1000 +Genistein Genistein_15 genisteinl transport genistein[c] => genistein[e] 0 0 1000 +Genistein Genistein_16 genistein exchange genistein[e] => 1 0 1000 + +Kaempferol Kaempferol_1 Phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL 0 0 1000 P45730 22 77.919 4.3.1.24 0.1 YEP glucose +Kaempferol Kaempferol_2 Cinnamate-4-hydroxylase H+[c] + oxygen[c] + cinnamate[c] + NADPH[c] => H2O[c] + NADP(+)[c] + trans-4-coumarate[c] C4H 0 0 1000 C0LUU6 161.8 58.011 1.14.13.11 +Kaempferol Kaempferol_3 4-coumarate:CoA ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => diphosphate[c] + AMP[c] + 4-coumaroyl-CoA[c] 4CL 0 0 1000 C0LUU7 0.101656667 60.994 6.2.1.12 +Kaempferol Kaempferol_4 Isoflavone synthase naringenin[c] => 3 H+[c] + genistein[c] IFS 0 0 0 Q9M6D6 58.93 1.14.14.87 +Kaempferol Kaempferol_5 Chalcone synthase 2 H+[c] + 4-coumaroyl-CoA[c] + 3 malonyl-CoA[c] => 4 coenzyme A[c] + 3 carbon dioxide[c] + naringenin chalcone[c] CHS 0 0 1000 Q6X0M9 0.006019133 42.488 2.3.1.74 +Kaempferol Kaempferol_6 Chalcone isomerase H+[c] + naringenin chalcone[c] => naringenin[c] CHI 0 0 1000 C0LUV0 139.8476667 24.679 5.5.1.6 +Kaempferol Kaempferol_7 Flavanone 3-hydroxylase naringenin[c] + oxygen[c] + 2-oxoglutarate[c] => carbon dioxide[c] + succinate[c] + dihydrokaempferol[c] F3H 0 0 1000 Q53B69 42.673 1.14.11.9 +Kaempferol Kaempferol_8 Flavonoid 3'-hydroxylase H+[c] + oxygen[c] + NADPH[c] + dihydrokaempferol[c] => dihydroquercetin[c] + H2O[c] + NADP(+)[c] F3'H 0 0 1000 Q8W3Y5 12.5 56.982 1.14.13.21 +Kaempferol Kaempferol_9 Flavonol synthase dihydrokaempferol[c] + 2-oxoglutarate[c] + oxygen[c] => H+[c] + carbon dioxide[c] + H2O[c] + succinate[c] + kaempferol[c] FLS 0 0 Inf C0LUV3 6.6 40.041 1.14.11.23 +Kaempferol Kaempferol_10 Flavonol synthase dihydroquercetin[c] + 2-oxoglutarate[c] + oxygen[c] => H+[c] + carbon dioxide[c] + H2O[c] + succinate[c] + quercetin[c] FLS 0 0 0 C0LUV3 3.9 40.041 1.14.11.23 +Kaempferol Kaempferol_11 quercetin transport quercetin[c] => quercetin[e] 0 0 1000 +Kaempferol Kaempferol_12 quercetin exchange quercetin[e] => 0 0 1000 +Kaempferol Kaempferol_13 kaempferol transport kaempferol[c] => kaempferol[e] 0 0 1000 +Kaempferol Kaempferol_14 kaempferol exchange kaempferol[e] => 1 0 1000 +Kaempferol Kaempferol_15 genisteinl transport genistein[c] => genistein[e] 0 0 1000 +Kaempferol Kaempferol_16 genistein exchange genistein[e] => 0 0 1000 + +Quercetin Quercetin_1 Phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL 0 0 1000 P45730 22 77.919 4.3.1.24 0.1 YEP glucose +Quercetin Quercetin_2 Cinnamate-4-hydroxylase H+[c] + oxygen[c] + cinnamate[c] + NADPH[c] => H2O[c] + NADP(+)[c] + trans-4-coumarate[c] C4H 0 0 1000 C0LUU6 161.8 58.011 1.14.13.11 +Quercetin Quercetin_3 4-coumarate:CoA ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => diphosphate[c] + AMP[c] + 4-coumaroyl-CoA[c] 4CL 0 0 1000 C0LUU7 0.101656667 60.994 6.2.1.12 +Quercetin Quercetin_4 Isoflavone synthase naringenin[c] => 3 H+[c] + genistein[c] IFS 0 0 0 Q9M6D6 58.93 1.14.14.87 +Quercetin Quercetin_5 Chalcone synthase 2 H+[c] + 4-coumaroyl-CoA[c] + 3 malonyl-CoA[c] => 4 coenzyme A[c] + 3 carbon dioxide[c] + naringenin chalcone[c] CHS 0 0 1000 Q6X0M9 0.006019133 42.488 2.3.1.74 +Quercetin Quercetin_6 Chalcone isomerase H+[c] + naringenin chalcone[c] => naringenin[c] CHI 0 0 1000 C0LUV0 139.8476667 24.679 5.5.1.6 +Quercetin Quercetin_7 Flavanone 3-hydroxylase naringenin[c] + oxygen[c] + 2-oxoglutarate[c] => carbon dioxide[c] + succinate[c] + dihydrokaempferol[c] F3H 0 0 1000 Q53B69 42.673 1.14.11.9 +Quercetin Quercetin_8 Flavonoid 3'-hydroxylase H+[c] + oxygen[c] + NADPH[c] + dihydrokaempferol[c] => dihydroquercetin[c] + H2O[c] + NADP(+)[c] F3'H 0 0 1000 Q8W3Y5 12.5 56.982 1.14.13.21 +Quercetin Quercetin_9 Flavonol synthase dihydrokaempferol[c] + 2-oxoglutarate[c] + oxygen[c] => H+[c] + carbon dioxide[c] + H2O[c] + succinate[c] + kaempferol[c] FLS 0 0 0 C0LUV3 6.6 40.041 1.14.11.23 +Quercetin Quercetin_10 Flavonol synthase dihydroquercetin[c] + 2-oxoglutarate[c] + oxygen[c] => H+[c] + carbon dioxide[c] + H2O[c] + succinate[c] + quercetin[c] FLS 0 0 1000 C0LUV3 3.9 40.041 1.14.11.23 +Quercetin Quercetin_11 quercetin transport quercetin[c] => quercetin[e] 0 0 1000 +Quercetin Quercetin_12 quercetin exchange quercetin[e] => 1 0 1000 +Quercetin Quercetin_13 kaempferol transport kaempferol[c] => kaempferol[e] 0 0 1000 +Quercetin Quercetin_14 kaempferol exchange kaempferol[e] => 0 0 1000 +Quercetin Quercetin_15 genisteinl transport genistein[c] => genistein[e] 0 0 1000 +Quercetin Quercetin_16 genistein exchange genistein[e] => 0 0 1000 + +Trans-cinnamate Trans-cinnamate_1 phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL 0 0 1000 P11544 25.7 76.88 4.3.1.24 0.1 YEP glucose +Trans-cinnamate Trans-cinnamate_2 cinnamate transport cinnamate[c] => cinnamate[e] 0 0 1000 +Trans-cinnamate Trans-cinnamate_3 cinnamate exchange cinnamate[e] => 1 0 1000 + +p-coumaric acid p-coumaric acid_1 tyrosine ammonia-lyase L-tyrosine[c] => ammonium[c] + p-coumaric acid[c] TAL 0 0 1000 A5FKY3 0.023 56.649 4.3.1.23 0.1 YEP glucose "YBR249C,YPR060C,YDR380W,YLR134W" +p-coumaric acid p-coumaric acid_2 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.215305458 39.7487 2.5.1.54 +p-coumaric acid p-coumaric acid_3 chorismate mutase chorismate[c] => prephenate[c] ARO7G141S 0 0 1000 P32178ly 0.1338606 29.7468 5.4.99.5 +p-coumaric acid p-coumaric acid_4 shikimate kinase ATP[c] + shikimate[c] => 3-phosphoshikimic acid[c] + ADP[c] + H+[c] aroL 0 0 1000 P0A6E1 31.91833333 19.151 2.7.1.71 +p-coumaric acid p-coumaric acid_5 p-coumaric acid transport p-coumaric acid[c] => p-coumaric acid[e] 0 0 1000 +p-coumaric acid p-coumaric acid_6 p-coumaric acid exchange p-coumaric acid[e] => 1 0 1000 + +p-coumaric acid p-coumaric acid_1 tyrosine ammonia-lyase L-tyrosine[c] => ammonium[c] + p-coumaric acid[c] TAL 0 0 1000 A5FKY3 0.023 56.649 4.3.1.23 0.11 Min xylose "YBR249C,YPR060C,YDR380W,YLR134W" +p-coumaric acid p-coumaric acid_2 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.215305458 39.7487 2.5.1.54 +p-coumaric acid p-coumaric acid_3 chorismate mutase chorismate[c] => prephenate[c] ARO7G141S 0 0 1000 P32178ly 0.1338606 29.7468 5.4.99.5 +p-coumaric acid p-coumaric acid_4 shikimate kinase ATP[c] + shikimate[c] => 3-phosphoshikimic acid[c] + ADP[c] + H+[c] aroL 0 0 1000 P0A6E1 31.91833333 19.151 2.7.1.71 +p-coumaric acid p-coumaric acid_5 p-coumaric acid transport p-coumaric acid[c] => p-coumaric acid[e] 0 0 1000 +p-coumaric acid p-coumaric acid_6 p-coumaric acid exchange p-coumaric acid[e] => 1 0 1000 +p-coumaric acid p-coumaric acid_7 xylose reductase D-xylose[c] + H+[c] + NADH[c] => xylitol[c] + NAD[c] 0 0 1000 P31867 27.5 35.923 1.1.1.307 +p-coumaric acid p-coumaric acid_8 xylose reductase D-xylose[c] + H+[c] + NADPH[c] => xylitol[c] + NADP(+)[c] 0 0 1000 P31867 27.5 35.923 1.1.1.307 +p-coumaric acid p-coumaric acid_9 xylulose reductase xylitol[c] + NAD[c] => D-xylulose[c] + H+[c] + NADH[c] 0 0 1000 P22144 30.33 38.521 1.1.1.9 +p-coumaric acid p-coumaric acid_10 xylulokinase ATP[c] + D-xylulose[c] => ADP[c] + D-xylulose 5-phosphate[c] + H+[c] 0 0 1000 Q9P938 1.144819177 69.397 2.7.1.17 + +Artemisinic acid Artemisinic acid_1 amorphadiene synthase "farnesyl diphosphate[c] => diphosphate[c] + amorpha-4,11-diene[c]" ADS 0 0 1000 Q9AR04 0.186 63.933 4.2.3.24 0.1 YEP glucose +Artemisinic acid Artemisinic acid_2 "Amorpha-4,11-diene 12-monooxygenase" "2 H+[c] + amorpha-4,11-diene[c] + 3 oxygen[c] + 3 NADPH[c] => 4 H2O[c] + 3 NADP(+)[c] + artemisinic acid[c]" CYP71AV1 0 0 1000 Q1PS23 7.74 55.725 1.14.14.114 +Artemisinic acid Artemisinic acid_3 artemisinic acid transport artemisinic acid[c] => artemisinic acid[e] 0 0 1000 +Artemisinic acid Artemisinic acid_4 artemisinic acid exchange artemisinic acid[e] => 1 0 1000 +Artemisinic acid r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 +Artemisinic acid r_0558No2 hydroxymethylglutaryl CoA reductase (No2) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YML075C 0 0 1000 P12683 92.4996 115.624 1.1.1.34 +Artemisinic acid r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 + +¦Â-Carotene ¦Â-Carotene_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 YEP glucose +¦Â-Carotene ¦Â-Carotene_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 +¦Â-Carotene ¦Â-Carotene_3 Phytoene desaturase phytoene[c] => neurosporene[c] crtI 0 0 1000 Q7Z858 0.000314486 65.066 1.3.99.28 +¦Â-Carotene ¦Â-Carotene_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 +¦Â-Carotene ¦Â-Carotene_5 Bifunctional lycopene cyclase/phytoene synthase lycopene[c] => ¦Â-carotene[c] crtYB 0 0 1000 Q7Z859 0.4434336 74.736 5.5.1.19 +¦Â-Carotene ¦Â-Carotene_6 ¦Â-carotene transport ¦Â-carotene[c] => ¦Â-carotene[e] 0 0 1000 +¦Â-Carotene ¦Â-Carotene_7 ¦Â-carotene exchange ¦Â-carotene[e] => 1 0 1000 +¦Â-Carotene r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 + +Linalool Linalool_1 monoterpene synthase geranyl diphosphate[c] + H2O[c] => diphosphate[c] + linalool[c] NES1 0 0 1000 H9M5U5 0.044 65.381 4.2.3.25 0.09 Min glucose +Linalool Linalool_2 Limonene synthase geranyl diphosphate[c] => diphosphate[c] + Limonene[c] ClLIS1 0 0 1000 Q8L5K3 0.186 70.348 4.2.3.20 +Linalool Linalool_3 linalool transport linalool[c] => linalool[e] 0 0 1000 +Linalool Linalool_4 linalool exchange linalool[e] => 1 0 1000 +Linalool Linalool_5 limonene transport Limonene[c] => Limonene[e] 0 0 1000 +Linalool Linalool_6 limonene exchange Limonene[e] => 0 0 1000 +Linalool r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 0.55 40.4829 + +Limonene Limonene_1 monoterpene synthase geranyl diphosphate[c] + H2O[c] => diphosphate[c] + linalool[c] NES1 0 0 1000 H9M5U5 0.044 65.381 4.2.3.25 0.1 Min glucose +Limonene Limonene_2 Limonene synthase geranyl diphosphate[c] => diphosphate[c] + Limonene[c] ClLIS1 0 0 1000 Q8L5K3 0.186 70.348 4.2.3.20 +Limonene Limonene_3 linalool transport linalool[c] => linalool[e] 0 0 1000 +Limonene Limonene_4 linalool exchange linalool[e] => 0 0 1000 +Limonene Limonene_5 limonene transport Limonene[c] => Limonene[e] 0 0 1000 +Limonene Limonene_6 limonene exchange Limonene[e] => 1 0 1000 +Limonene r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 0.55 40.4829 + +4-hydroxymandelic 4-hydroxymandelic_1 hydroxymandelate synthase 3-(4-hydroxyphenyl)pyruvate[c] + oxygen[c] => carbon dioxide[c] + 4-hydroxymandelic[c] hmaS 0 0 1000 Q5J1Q8 3.7 36.597 1.13.11.46 0.1 Min glucose "YNL316C,YER090W,YDR380W,YLR134W,YGL202W,YBR249C" +4-hydroxymandelic 4-hydroxymandelic_2 hydroxymandelate synthase keto-phenylpyruvate[c] + oxygen[c] => carbon dioxide[c] + mandelic[c] + H+[c] hmaS 0 0 1000 Q5J1Q8 0.88 36.597 1.13.11.46 +4-hydroxymandelic 4-hydroxymandelic_3 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.215305458 39.7487 2.5.1.54 +4-hydroxymandelic 4-hydroxymandelic_4 4-hydroxymandelic transport 4-hydroxymandelic[c] => 4-hydroxymandelic[e] 0 0 1000 +4-hydroxymandelic 4-hydroxymandelic_5 4-hydroxymandelic exchange 4-hydroxymandelic[e] => 1 0 1000 +4-hydroxymandelic 4-hydroxymandelic_6 mandelic transport mandelic[c] => mandelic[e] 0 0 1000 +4-hydroxymandelic 4-hydroxymandelic_7 mandelic exchange mandelic[e] => 0 0 1000 +4-hydroxymandelic 4-hydroxymandelic_8 anthranilate transport anthranilate[e] => anthranilate[c] 0 0 1000 +4-hydroxymandelic 4-hydroxymandelic_9 anthranilate exchange => anthranilate[e] 0 0 1 +4-hydroxymandelic r_0997No1 shikimate dehydrogenase ATP[c] + shikimate[c] => 3-phosphoshikimic acid[c] + ADP[c] + H+[c] YDR127W 0 0 1000 P08566 120 174.753 +4-hydroxymandelic r_1903_REV 0 0 1 + +mandelic mandelic_1 hydroxymandelate synthase 3-(4-hydroxyphenyl)pyruvate[c] + oxygen[c] => carbon dioxide[c] + 4-hydroxymandelic[c] hmaS 0 0 1000 Q5J1Q8 3.7 36.597 1.13.11.46 0.1 Min glucose "YBR166C,YER090W,YDR380W,YLR134W,YGL202W,YBR249C" +mandelic mandelic_2 hydroxymandelate synthase keto-phenylpyruvate[c] + oxygen[c] => carbon dioxide[c] + mandelic[c] + H+[c] hmaS 0 0 1000 Q5J1Q8 0.88 36.597 1.13.11.46 +mandelic mandelic_3 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.215305458 39.7487 2.5.1.54 +mandelic mandelic_4 4-hydroxymandelic transport 4-hydroxymandelic[c] => 4-hydroxymandelic[e] 0 0 1000 +mandelic mandelic_5 4-hydroxymandelic exchange 4-hydroxymandelic[e] => 0 0 1000 +mandelic mandelic_6 mandelic transport mandelic[c] => mandelic[e] 0 0 1000 +mandelic mandelic_7 mandelic exchange mandelic[e] => 1 0 1000 +mandelic mandelic_8 anthranilate transport anthranilate[e] => anthranilate[c] 0 0 1000 +mandelic mandelic_9 anthranilate exchange => anthranilate[e] 0 0 1 +mandelic r_0997No1 shikimate dehydrogenase ATP[c] + shikimate[c] => 3-phosphoshikimic acid[c] + ADP[c] + H+[c] YDR127W 0 0 1000 P08566 120 174.753 +mandelic r_1913_REV 0 0 1 + +Oleanolic acid Oleanolic acid_1 Beta-amyrin synthase "(S)-2,3-epoxysqualene[c] => ¦Â-amyrin[c]" GgbAS1 0 0 1000 Q9MB42 0.77 87.516 5.4.99.39 0.1 YEP glucose YBR020W +Oleanolic acid Oleanolic acid_2 Beta-amyrin 28-monooxygenase 2 H+[c] + ¦Â-amyrin[c] + 3 oxygen[c] + 3 NADPH[c] => 4 H2O[c] + Oleanolic acid[c] + 3 NADP(+)[c] CYP716A12 0 0 1000 Q2MJ20 54.713 1.14.13.201 +Oleanolic acid Oleanolic acid_3 oleanolic acid transport Oleanolic acid[c] => Oleanolic acid[e] 0 0 1000 +Oleanolic acid Oleanolic acid_4 oleanolic acid exchange Oleanolic acid[e] => 1 0 1000 +Oleanolic acid r_0558No2 hydroxymethylglutaryl CoA reductase (No2) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YML075C 0 0 1000 P12683 92.4996 +Oleanolic acid r_1010No1 squalene epoxidase (NAD) (No1) "H+[er] + NADH[er] + oxygen[er] + squalene[er] => (S)-2,3-epoxysqualene[er] + H2O[er] + NAD[er]" YGR175C 0 0 1000 P32476 0.152 +Oleanolic acid r_1011No1 squalene epoxidase (NADP) (No1) "H+[er] + NADPH[er] + oxygen[er] + squalene[er] => (S)-2,3-epoxysqualene[er] + H2O[er] + NADP(+)[er]" YGR175C 0 0 1000 P32476 0.152 +Oleanolic acid r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 3.3 + +Fumaric acid Fumaric acid_1 malate dehydrogenase H+[c] + NADH[c] + oxaloacetate[c] => (S)-malate[c] + NAD[c] RoMDH 0 0 1000 D6R7B7 24.026625 35.595 1.1.1.37 0.1 Min glucose block r_0714_REVNo1 (Mdh2p is known to be subject to glucose catabolite inactivation) +Fumaric acid r_0958No1 pyruvate carboxylase (No1) pmet_r_0958[c] => ADP[c] + H+[c] + oxaloacetate[c] + phosphate[c] YBR218C 0 0 1000 P32327 72.48055072 130.166 +Fumaric acid r_0958No2 pyruvate carboxylase (No2) pmet_r_0958[c] => ADP[c] + H+[c] + oxaloacetate[c] + phosphate[c] YGL062W 0 0 1000 P11154 72.48041459 130.098 +Fumaric acid r_1798 1 0 Inf +Fumaric acid r_0714_REVNo1 0 0 0 + +Pyruvate Pyruvate_1 NADH oxidase oxygen[c] + 3 H+[c] + NADH[c] => 2 H2O[c] + NAD[c] noxE 0 0 1000 A2RIB7 57.4246 48.872 1.6.99.3 0.2 YEP glucose "YLR044C,YLR134W,YGR087C" +Pyruvate Pyruvate_2 transhydrogenase NADP(+)[c] + NADH[c] => NADPH[c] + NAD[c] udhA 0 0 1000 P27306 167.9 51.56 1.6.1.1 +Pyruvate Pyruvate_2_REV transhydrogenase NADPH[c] + NAD[c] => NADP(+)[c] + NADH[c] udhA 0 0 1000 P27306 9.1304 51.56 1.6.1.1 +Pyruvate r_2033 1 0 Inf + +Adipic acid Adipic acid_1 dehydroshikimate dehydratase "3-dehydroshikimate[c] => 3,4-Dihydroxybenzoate[c] + H2O[c]" Pa_5_5120 0 0 1000 3DSD 121.44 40.48 4.2.1.118 0.1 YEP glucose "YDR035W,YBR249C,YNL241C" +Adipic acid Adipic acid_2 protocatechuic acid decarboxylase "3,4-Dihydroxybenzoate[c] + H+[c] => carbon dioxide[c] + Catechol[c]" ECL_01944 0 0 1000 A0A0H3CJN8 90 53.541 4.1.1.63 +Adipic acid Adipic acid_3 "catechol 1,2-dioxygenase" "Catechol[c] + oxygen[c] => 2 H+[c] + cis,cis-muconate[c]" HQD2 0 0 1000 P86029 157.7333333 33.8 1.13.11.1 +Adipic acid Adipic acid_4 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.082809792 39.7487 2.5.1.54 +Adipic acid Adipic acid_5 "cis,cis-muconic acid transport" "cis,cis-muconate[c] => cis,cis-muconate[e]" 0 0 1000 +Adipic acid Adipic acid_6 "cis,cis-muconic acid exchange" "cis,cis-muconate[e] =>" 0 0 1000 +Adipic acid Adipic acid_7 enoate reductase "cis,cis-muconate[c] + NADH[c] + 3 H+[c] => Adipic acid[c] + NAD[c]" ERBC 0 0 1000 G2TQU6 8.376025 72.835 1.3.1.31 0.1 +Adipic acid Adipic acid_8 adipic acid transport Adipic acid[c] => Adipic acid[e] 0 0 1000 +Adipic acid Adipic acid_9 adipic acid exchange Adipic acid[e] => 1 0 1000 +Adipic acid r_2189_REV 0 0 1 +Adipic acid r_1757_REV 0 0 1 +Adipic acid r_2038_REV 0 0 1 +Adipic acid r_1807_REV 0 0 1 + +Isobutanol r_0016No1 2-aceto-2-hydroxybutanoate synthase (No1) pmet_r_0016[m] => (S)-2-acetyl-2-hydroxybutanoate[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 32.2 0.1 YEP glucose "YPL061W,YHR208W" +Isobutanol r_0016No2 2-aceto-2-hydroxybutanoate synthase (No2) pmet_r_0016[m] => (S)-2-acetyl-2-hydroxybutanoate[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 32.2 +Isobutanol r_0097No1 acetolactate synthase (No1) pmet_r_0097[m] => 2-acetyllactic acid[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 16.1 +Isobutanol r_0097No2 acetolactate synthase (No2) pmet_r_0097[m] => 2-acetyllactic acid[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 16.1 +Isobutanol r_0352No1 "dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylbutanoate) (No1)" "(R)-2,3-dihydroxy-3-methylbutanoate[m] => 3-methyl-2-oxobutanoate[m] + H2O[m]" YJR016C 0 0 1000 P39522 50 +Isobutanol r_0353No1 "dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylpentanoate) (No1)" "(2R,3R)-2,3-dihydroxy-3-methylpentanoate[m] => (S)-3-methyl-2-oxopentanoate[m] + H2O[m]" YJR016C 0 0 1000 P39522 50 +Isobutanol r_0096No1 acetohydroxy acid isomeroreductase (No1) "2-acetyllactic acid[m] + H+[m] + NADPH[m] => (R)-2,3-dihydroxy-3-methylbutanoate[m] + NADP(+)[m]" YLR355C 0 0 1000 P06168 36.6 +Isobutanol r_0669No1 ketol-acid reductoisomerase (2-aceto-2-hydroxybutanoate) (No1) "(S)-2-acetyl-2-hydroxybutanoate[m] + H+[m] + NADPH[m] => (2R,3R)-2,3-dihydroxy-3-methylpentanoate[m] + NADP(+)[m]" YLR355C 0 0 1000 P06168 1.96 +Isobutanol r_0854No1 phenylpyruvate decarboxylase (No1) H+[c] + keto-phenylpyruvate[c] => carbon dioxide[c] + phenylacetaldehyde[c] YDR380W 0 0 1000 Q06408 1140 +Isobutanol r_0163No1 alcohol dehydrogenase (ethanol to acetaldehyde) (No1) ethanol[c] + NAD[c] => acetaldehyde[c] + H+[c] + NADH[c] YMR303C 0 0 1000 P00331 286 +Isobutanol r_1866 1 0 Inf + +3-Methyl-1-Butanol r_0016No1 2-aceto-2-hydroxybutanoate synthase (No1) pmet_r_0016[m] => (S)-2-acetyl-2-hydroxybutanoate[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 32.2 0.1 YEP glucose "YPL061W,YHR208W" +3-Methyl-1-Butanol r_0016No2 2-aceto-2-hydroxybutanoate synthase (No2) pmet_r_0016[m] => (S)-2-acetyl-2-hydroxybutanoate[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 32.2 +3-Methyl-1-Butanol r_0097No1 acetolactate synthase (No1) pmet_r_0097[m] => 2-acetyllactic acid[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 16.1 +3-Methyl-1-Butanol r_0097No2 acetolactate synthase (No2) pmet_r_0097[m] => 2-acetyllactic acid[m] + carbon dioxide[m] YMR108W 0 0 1000 P07342 16.1 +3-Methyl-1-Butanol r_0352No1 "dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylbutanoate) (No1)" "(R)-2,3-dihydroxy-3-methylbutanoate[m] => 3-methyl-2-oxobutanoate[m] + H2O[m]" YJR016C 0 0 1000 P39522 50 +3-Methyl-1-Butanol r_0353No1 "dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylpentanoate) (No1)" "(2R,3R)-2,3-dihydroxy-3-methylpentanoate[m] => (S)-3-methyl-2-oxopentanoate[m] + H2O[m]" YJR016C 0 0 1000 P39522 50 +3-Methyl-1-Butanol r_0096No1 acetohydroxy acid isomeroreductase (No1) "2-acetyllactic acid[m] + H+[m] + NADPH[m] => (R)-2,3-dihydroxy-3-methylbutanoate[m] + NADP(+)[m]" YLR355C 0 0 1000 P06168 36.6 +3-Methyl-1-Butanol r_0669No1 ketol-acid reductoisomerase (2-aceto-2-hydroxybutanoate) (No1) "(S)-2-acetyl-2-hydroxybutanoate[m] + H+[m] + NADPH[m] => (2R,3R)-2,3-dihydroxy-3-methylpentanoate[m] + NADP(+)[m]" YLR355C 0 0 1000 P06168 1.96 +3-Methyl-1-Butanol r_0854No1 phenylpyruvate decarboxylase (No1) H+[c] + keto-phenylpyruvate[c] => carbon dioxide[c] + phenylacetaldehyde[c] YDR380W 0 0 1000 Q06408 1140 +3-Methyl-1-Butanol r_0163No1 alcohol dehydrogenase (ethanol to acetaldehyde) (No1) ethanol[c] + NAD[c] => acetaldehyde[c] + H+[c] + NADH[c] YMR303C 0 0 1000 P00331 286 +3-Methyl-1-Butanol r_0024No1 2-isopropylmalate synthase (No1) pmet_r_0024[c] => 2-isopropylmalate[c] + coenzyme A[c] + H+[c] YNL104C 0 0 1000 P06208 27.58 +3-Methyl-1-Butanol r_0025No1 2-isopropylmalate synthase (No1) 3-methyl-2-oxobutanoate[m] + acetyl-CoA[m] + H2O[m] => 2-isopropylmalate[m] + coenzyme A[m] + H+[m] YNL104C 0 0 1000 P06208 27.58 +3-Methyl-1-Butanol r_1598 1 0 Inf + +Naringenin Naringenin_1 Phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL1 0 0 1000 P35510 1.8 78.726 4.3.1.24 0.2 Min glucose "YDR035W,YBR249C,YDR380W,YLR134W,YGR087C" +Naringenin Naringenin_2 Cinnamate-4-hydroxylase H+[c] + oxygen[c] + cinnamate[c] + NADPH[c] => H2O[c] + NADP(+)[c] + trans-4-coumarate[c] C4H 0 0 1000 P92994 1.72 57.792 1.14.13.11 +Naringenin Naringenin_3 Chalcone isomerase H+[c] + naringenin chalcone[c] => naringenin[c] CHI1 0 0 1000 Q8VZW3 23.332 5.5.1.6 +Naringenin Naringenin_4 Chalcone synthase 2 H+[c] + 4-coumaroyl-CoA[c] + 3 malonyl-CoA[c] => 4 coenzyme A[c] + 3 carbon dioxide[c] + naringenin chalcone[c] CHS3 0 0 1000 P13114 0.001 43.116 2.3.1.74 +Naringenin Naringenin_5 4-coumarate:CoA ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => diphosphate[c] + AMP[c] + 4-coumaroyl-CoA[c] 4CL3 0 0 1000 Q9S777 0.84 61.311 6.2.1.12 +Naringenin Naringenin_6 tyrosine ammonia-lyase L-tyrosine[c] => ammonium[c] + trans-4-coumarate[c] TAL 0 0 1000 A0A1M4NET9 27.7 55.539 4.3.1.23 +Naringenin Naringenin_7 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4G226S 0 0 1000 P32449ly 7.9 39.7487 2.5.1.54 +Naringenin Naringenin_8 naringenin transport naringenin[c] => naringenin[e] 0 0 1000 +Naringenin Naringenin_9 naringenin exchange naringenin[e] => 1 0 1000 + +Catechin Catechin_1 Phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL2 0 0 1000 P45724 3.2 77.86 4.3.1.24 0.1 Min glucose +Catechin Catechin_2 Cinnamate-4-hydroxylase H+[c] + oxygen[c] + cinnamate[c] + NADPH[c] => H2O[c] + NADP(+)[c] + trans-4-coumarate[c] C4H 0 0 1000 Q84TQ4 1.72 57.937 1.14.13.11 +Catechin Catechin_3 Chalcone isomerase H+[c] + naringenin chalcone[c] => naringenin[c] CHI 0 0 1000 P28012 671000 23.826 5.5.1.6 +Catechin Catechin_4 Chalcone synthase 2 H+[c] + 4-coumaroyl-CoA[c] + 3 malonyl-CoA[c] => 4 coenzyme A[c] + 3 carbon dioxide[c] + naringenin chalcone[c] CHS 0 0 1000 Q9FUB7 0.042 42.713 2.3.1.74 +Catechin Catechin_5 4-coumarate:CoA ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => diphosphate[c] + AMP[c] + 4-coumaroyl-CoA[c] 4CL2 0 0 1000 Q9S725 3 60.842 6.2.1.12 +Catechin Catechin_6 flavonoid-3'-hydroxylase H+[c] + oxygen[c] + naringenin[c] + NADPH[c] => eriodictyol[c] + H2O[c] + NADP(+)[c] F3'H 0 0 1000 Q9SBQ9 17 56.936 1.14.14.82 +Catechin Catechin_7 flavanone-3-hydroxylase eriodictyol[c] + 2-oxoglutarate[c] + oxygen[c] => taxifolin[c] + succinate[c] + carbon dioxide[c] F3H 0 0 1000 Q06942 40.771 1.14.11.9 +Catechin Catechin_8 dihydroflavonol-4-reductase taxifolin[c] + NADPH[c] + H+[c] => leucocyanidin[c] + NADP(+)[c] DFR 0 0 1000 B9GRL5 27.60528667 38.699 1.1.1.219 +Catechin Catechin_9 leucoanthocyanidin reductase leucocyanidin[c] + NADPH[c] + H+[c] => catechin[c] + NADP(+)[c] + H2O[c] LAR 0 0 1000 Q4W2K4 0.065 38.019 1.17.1.3 +Catechin Catechin_10 catechin transport catechin[c] => catechin[e] 0 0 1000 +Catechin Catechin_11 catechin exchange catechin[e] => 1 0 1000 + +Amorphadiene Amorphadiene_1 amorphadiene synthase farnesyl diphosphate[c] => amorphadiene[c] + diphosphate[c] ADS 0 0 1000 Q9AR04 0.518 63.933 4.2.3.24 0.1 Min glucose "YBR020W,YBR018C,YBR019C" +Amorphadiene Amorphadiene_2 amorphadiene transport amorphadiene[c] => amorphadiene[e] 0 0 1000 +Amorphadiene Amorphadiene_3 amorphadiene exchange amorphadiene[e] => 1 0 1000 +Amorphadiene r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 +Amorphadiene r_0904No1 phosphomevalonate kinase (No1) (R)-5-phosphomevalonic acid[c] + ATP[c] => (R)-5-diphosphomevalonic acid[c] + ADP[c] YMR220W 0 0 1000 P24521 6.8 50.4544 2.7.4.2 +Amorphadiene r_0103No1 acetyl-CoA C-acetyltransferase (No1) 2 acetyl-CoA[c] => acetoacetyl-CoA[c] + coenzyme A[c] YPL028W 0 0 1000 P41338 1800 41.7282 2.3.1.9 +Amorphadiene r_0104No1 acetyl-CoA C-acetyltransferase (No1) 2 acetyl-CoA[m] => acetoacetyl-CoA[m] + coenzyme A[m] YPL028W 0 0 1000 P41338 1800 41.7282 2.3.1.9 +Amorphadiene r_0103_REVNo1 acetyl-CoA C-acetyltransferase (reversible) (No1) acetoacetyl-CoA[c] + coenzyme A[c] => 2 acetyl-CoA[c] YPL028W 0 0 1000 P41338 10000000 41.7282 2.3.1.9 +Amorphadiene r_0104_REVNo1 acetyl-CoA C-acetyltransferase (reversible) (No1) acetoacetyl-CoA[m] + coenzyme A[m] => 2 acetyl-CoA[m] YPL028W 0 0 1000 P41338 10000000 41.7282 2.3.1.9 +Amorphadiene r_0735No1 mevalonate kinase (atp) (No1) (R)-mevalonate[c] + ATP[c] => (R)-5-phosphomevalonic acid[c] + ADP[c] + H+[c] YMR208W 0 0 1000 P07277 43.8001 48.459 2.7.1.36 +Amorphadiene r_0736No1 mevalonate kinase (ctp) (No1) (R)-mevalonate[c] + CTP[c] => (R)-5-phosphomevalonic acid[c] + CDP[c] + H+[c] YMR208W 0 0 1000 P07277 43.8001 48.459 2.7.1.36 +Amorphadiene r_0737No1 mevalonate kinase (gtp) (No1) (R)-mevalonate[c] + GTP[c] => (R)-5-phosphomevalonic acid[c] + GDP[c] + H+[c] YMR208W 0 0 1000 P07277 43.8001 48.459 2.7.1.36 +Amorphadiene r_0738No1 mevalonate kinase (UTP) (No1) (R)-mevalonate[c] + UTP[c] => (R)-5-phosphomevalonic acid[c] + H+[c] + UDP[c] YMR208W 0 0 1000 P07277 43.8001 48.459 2.7.1.36 +Amorphadiene r_0559No1 hydroxymethylglutaryl CoA synthase (No1) acetoacetyl-CoA[c] + acetyl-CoA[c] + H2O[c] => 3-hydroxy-3-methylglutaryl-CoA[c] + coenzyme A[c] + H+[c] YML126C 0 0 1000 P54839 0.83 55.0128 2.3.3.10 +Amorphadiene r_0560No1 hydroxymethylglutaryl CoA synthase (No1) acetoacetyl-CoA[m] + acetyl-CoA[m] + H2O[m] => 3-hydroxy-3-methylglutaryl-CoA[m] + coenzyme A[m] + H+[m] YML126C 0 0 1000 P54839 0.83 55.0128 2.3.3.10 +Amorphadiene r_0739No1 mevalonate pyrophoshate decarboxylase (No1) (R)-5-diphosphomevalonic acid[c] + ATP[c] => ADP[c] + carbon dioxide[c] + isopentenyl diphosphate[c] + phosphate[c] YNR043W 0 0 1000 P32377 9.8 44.1154 4.1.1.33 +Amorphadiene r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Amorphadiene r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Amorphadiene r_0667No1 isopentenyl-diphosphate D-isomerase (No1) isopentenyl diphosphate[c] => prenyl diphosphate(3-)[c] YPL117C 0 0 1000 P15496 59800 33.3511 5.3.3.2 +Amorphadiene r_0667_REVNo1 isopentenyl-diphosphate D-isomerase (reversible) (No1) prenyl diphosphate(3-)[c] => isopentenyl diphosphate[c] YPL117C 0 0 1000 P15496 0.1212 33.3511 5.3.3.2 +Amorphadiene r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 +Amorphadiene r_1710_REV 0 0 1 + +Protopanaxadiol Protopanaxadiol_1 dammarenediol-II synthase "(S)-2,3-epoxysqualene[c] + H2O[c] => Dammarenediol II[c]" DDS 0 0 1000 Q08IT1 88.343 4.2.1.125 0.1 Min glucose +Protopanaxadiol Protopanaxadiol_2 protopanaxadiol synthase H+[c] + oxygen[c] + Dammarenediol II[c] + NADPH[c] => protopanaxadiol[c] + H2O[c] + NADP(+)[c] PPDS 0 0 1000 H2DH16 55.356 1.14.14.120 +Protopanaxadiol Protopanaxadiol_3 protopanaxadiol transport protopanaxadiol[c] => protopanaxadiol[e] 0 0 1000 +Protopanaxadiol Protopanaxadiol_4 protopanaxadiol exchange protopanaxadiol[e] => 1 0 1000 +Protopanaxadiol r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 +Protopanaxadiol r_1010No1 squalene epoxidase (NAD) (No1) "H+[er] + NADH[er] + oxygen[er] + squalene[er] => (S)-2,3-epoxysqualene[er] + H2O[er] + NAD[er]" YGR175C 0 0 1000 P32476 0.152 55.1254 1.14.14.17 +Protopanaxadiol r_1011No1 squalene epoxidase (NADP) (No1) "H+[er] + NADPH[er] + oxygen[er] + squalene[er] => (S)-2,3-epoxysqualene[er] + H2O[er] + NADP(+)[er]" YGR175C 0 0 1000 P32476 0.152 55.1254 1.14.14.17 +Protopanaxadiol r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 3.3 51.7193 2.5.1.21 +Protopanaxadiol r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Protopanaxadiol r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Protopanaxadiol r_1900_REV 0 0 1 + +Geraniol Geraniol_1 geraniol synthase geranyl diphosphate[c] + H2O[c] => Geraniol[c] + diphosphate[c] GES 0 0 1000 J9PZR5 1 67.728 3.1.7.11 0.31 YEP glucose +Geraniol Geraniol_2 protopanaxadiol transport Geraniol[c] => Geraniol[e] 0 0 1000 +Geraniol Geraniol_3 protopanaxadiol exchange Geraniol[e] => 1 0 1000 +Geraniol r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 +Geraniol r_0667No1 isopentenyl-diphosphate D-isomerase (No1) isopentenyl diphosphate[c] => prenyl diphosphate(3-)[c] YPL117C 0 0 1000 P15496 59800 33.3511 5.3.3.2 +Geraniol r_0667_REVNo1 isopentenyl-diphosphate D-isomerase (reversible) (No1) prenyl diphosphate(3-)[c] => isopentenyl diphosphate[c] YPL117C 0 0 1000 P15496 0.1212 33.3511 5.3.3.2 +Geraniol r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Geraniol r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 + +Patchoulol Patchoulol_1 patchoulol synthase farnesyl diphosphate[c] + H2O[c] => patchoulol[c] + diphosphate[c] PTS 0 0 1000 Q49SP3 0.00043 64.199 4.2.3.70 0.1 YEP glucose +Patchoulol Patchoulol_2 patchoulol transport patchoulol[c] => patchoulol[e] 0 0 1000 +Patchoulol Patchoulol_3 patchoulol exchange patchoulol[e] => 1 0 1000 +Patchoulol r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 +Patchoulol r_0667No1 isopentenyl-diphosphate D-isomerase (No1) isopentenyl diphosphate[c] => prenyl diphosphate(3-)[c] YPL117C 0 0 1000 P15496 59800 33.3511 5.3.3.2 +Patchoulol r_0667_REVNo1 isopentenyl-diphosphate D-isomerase (reversible) (No1) prenyl diphosphate(3-)[c] => isopentenyl diphosphate[c] YPL117C 0 0 1000 P15496 0.1212 33.3511 5.3.3.2 +Patchoulol r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Patchoulol r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Patchoulol r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 + +Lupeol Lupeol_1 lupeol synthase "(S)-2,3-epoxysqualene[c] => lupeol[c]" LUP 0 0 1000 A0A3B1EU92 86.705 5.4.99.41 0.1 Min glucose +Lupeol Lupeol_2 lupeol transport lupeol[c] => lupeol[e] 0 0 1000 +Lupeol Lupeol_3 lupeol exchange lupeol[e] => 1 0 1000 +Lupeol r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 +Lupeol r_0559No1 hydroxymethylglutaryl CoA synthase (No1) acetoacetyl-CoA[c] + acetyl-CoA[c] + H2O[c] => 3-hydroxy-3-methylglutaryl-CoA[c] + coenzyme A[c] + H+[c] YML126C 0 0 1000 P54839 0.83 55.0128 2.3.3.10 +Lupeol r_0560No1 hydroxymethylglutaryl CoA synthase (No1) acetoacetyl-CoA[m] + acetyl-CoA[m] + H2O[m] => 3-hydroxy-3-methylglutaryl-CoA[m] + coenzyme A[m] + H+[m] YML126C 0 0 1000 P54839 0.83 55.0128 2.3.3.10 +Lupeol r_0698No1 lanosterol synthase (No1) "(S)-2,3-epoxysqualene[c] => lanosterol[c]" YHR072W 0 0 1000 P38604 2.0382 83.4594 5.4.99.7 +Lupeol r_1710_REV 0 0 1 + +¦Â-Amyrin ¦Â-Amyrin_1 ¦Â-amyrin synthase "(S)-2,3-epoxysqualene[c] => ¦Â-Amyrin[c]" bAS 0 0 1000 Q9MB42 0.77 87.516 5.4.99.39 0.1 YEP glucose +¦Â-Amyrin ¦Â-Amyrin_2 squalene epoxidase (NAD) (No1) "H+[er] + NADH[er] + oxygen[er] + squalene[er] => (S)-2,3-epoxysqualene[er] + H2O[er] + NAD[er]" CaERG1 0 0 1000 Q92206 55.298 1.14.14.17 +¦Â-Amyrin ¦Â-Amyrin_3 squalene epoxidase (NADP) (No1) "H+[er] + NADPH[er] + oxygen[er] + squalene[er] => (S)-2,3-epoxysqualene[er] + H2O[er] + NADP(+)[er]" CaERG1 0 0 1000 Q92206 55.298 1.14.14.17 +¦Â-Amyrin ¦Â-Amyrin_4 pyrophosphate isomerase isopentenyl diphosphate[c] => prenyl diphosphate(3-)[c] EcIDI 0 0 1000 Q46822 20.508 5.3.3.2 +¦Â-Amyrin ¦Â-Amyrin_5 pyrophosphate isomerase prenyl diphosphate(3-)[c] => isopentenyl diphosphate[c] EcIDI 0 0 1000 Q46822 20.508 5.3.3.2 +¦Â-Amyrin ¦Â-Amyrin_6 ¦Â-Amyrin transport ¦Â-Amyrin[c] => ¦Â-Amyrin[e] 0 0 1000 +¦Â-Amyrin ¦Â-Amyrin_7 ¦Â-Amyrin exchange ¦Â-Amyrin[e] => 1 0 1000 +¦Â-Amyrin r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 3.3 51.7193 2.5.1.21 +¦Â-Amyrin r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +¦Â-Amyrin r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 + +Astaxanthin Astaxanthin_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 YEP glucose +Astaxanthin Astaxanthin_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 +Astaxanthin Astaxanthin_3 Phytoene desaturase phytoene[c] => neurosporene[c] crtI 0 0 1000 Q7Z858 0.000314486 65.066 1.3.99.28 +Astaxanthin Astaxanthin_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 +Astaxanthin Astaxanthin_5 Bifunctional lycopene cyclase/phytoene synthase lycopene[c] => ¦Â-carotene[c] crtYB 0 0 1000 Q7Z859 0.4434336 74.736 5.5.1.19 +Astaxanthin Astaxanthin_6 ¦Â-carotene transport ¦Â-carotene[c] => ¦Â-carotene[e] 0 0 1000 +Astaxanthin Astaxanthin_7 ¦Â-carotene exchange ¦Â-carotene[e] => 0 0 1000 +Astaxanthin Astaxanthin_8 ¦Â-carotenoid ketolase ¦Â-carotene[c] + oxygen[c] => echinenone[c] + H2O[c] bkt 0 0 1000 Q39982 35.989 1.14.99.63 0.1 +Astaxanthin Astaxanthin_9 ¦Â-carotenoid ketolase echinenone[c] + oxygen[c] => canthaxanthin[c] + H2O[c] bkt 0 0 1000 Q39982 35.989 1.14.99.63 +Astaxanthin Astaxanthin_10 ¦Â-carotenoid hydroxylase H+[c] + NADH[c] + canthaxanthin[c] + oxygen[c] => H2O[c] + phoenicoxanthin[c] + NAD[c] crtZ 0 0 1000 A0A0K0P8J8 32.017 1.14.15.24 +Astaxanthin Astaxanthin_11 ¦Â-carotenoid hydroxylase H+[c] + NADH[c] + phoenicoxanthin[c] + oxygen[c] => H2O[c] + astaxanthin[c] + NAD[c] crtZ 0 0 1000 A0A0K0P8J8 32.017 1.14.15.24 +Astaxanthin Astaxanthin_12 astaxanthin transport astaxanthin[c] => astaxanthin[e] 0 0 1000 +Astaxanthin Astaxanthin_13 astaxanthin exchange astaxanthin[e] => 1 0 1000 +Astaxanthin r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 + +Farnesene Farnesene_1 farnesene synthase farnesyl diphosphate[c] => alpha-Farnesene[c] + diphosphate[c] AFS 0 0 1000 Q84LB2 0.0613 66.183 4.2.3.46 0.043 Min glucose "YDR503C,YDR284C,YOR375C" +Farnesene Farnesene_2 farnesene transport alpha-Farnesene[c] => alpha-Farnesene[e] 0 0 1000 +Farnesene Farnesene_3 farnesene exchange alpha-Farnesene[e] => 1 0 1000 +Farnesene Farnesene_4 santalene synthase farnesyl diphosphate[c] => Santalene[c] + diphosphate[c] SAS 0 0 1000 E5LLI1 0.075 63.937 4.2.3.82 +Farnesene Farnesene_5 farnesene transport Santalene[c] => Santalene[e] 0 0 1000 +Farnesene Farnesene_6 farnesene exchange Santalene[e] => 0 0 1000 +Farnesene r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 +Farnesene r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Farnesene r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Farnesene r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 +Farnesene r_0470No1 glutamate dehydrogenase (NAD) (No1) H2O[c] + L-glutamate[c] + NAD[c] => 2-oxoglutarate[c] + ammonium[c] + H+[c] + NADH[c] YDL215C 0 0 1000 P33327 47.9999 124.331 1.4.1.2 + +Santalene Santalene_1 farnesene synthase farnesyl diphosphate[c] => alpha-Farnesene[c] + diphosphate[c] AFS 0 0 1000 Q84LB2 0.0613 66.183 4.2.3.46 0.05 Min glucose "YDR503C,YDR284C,YOR375C" +Santalene Santalene_2 farnesene transport alpha-Farnesene[c] => alpha-Farnesene[e] 0 0 1000 +Santalene Santalene_3 farnesene exchange alpha-Farnesene[e] => 0 0 1000 +Santalene Santalene_4 santalene synthase farnesyl diphosphate[c] => Santalene[c] + diphosphate[c] SAS 0 0 1000 E5LLI1 0.075 63.937 4.2.3.82 +Santalene Santalene_5 farnesene transport Santalene[c] => Santalene[e] 0 0 1000 +Santalene Santalene_6 farnesene exchange Santalene[e] => 1 0 1000 +Santalene r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 +Santalene r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Santalene r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Santalene r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 +Santalene r_0470No1 glutamate dehydrogenase (NAD) (No1) H2O[c] + L-glutamate[c] + NAD[c] => 2-oxoglutarate[c] + ammonium[c] + H+[c] + NADH[c] YDL215C 0 0 1000 P33327 47.9999 124.331 1.4.1.2 + +lactase lactase_1 production of lactase 2.01 GTP[c] + 0.6516 Ala-tRNA(Ala)[c] + 0.2643 Arg-tRNA(Arg)[c] + 0.5013 Asn-tRNA(Asn)[c] + 0.4921 Asp-tRNA(Asp)[c] + 0.0547 Cys-tRNA(Cys)[c] + 0.4375 Glu-tRNA(Glu)[c] + 0.2552 Gln-tRNA(Gln)[c] + 0.9114 Gly-tRNA(Gly)[c] + 0.1276 His-tRNA(His)[c] + 0.4466 Ile-tRNA(Ile)[c] + 0.8567 Leu-tRNA(Leu)[c] + 0.4192 Lys-tRNA(Lys)[c] + 0.0638 Met-tRNA(Met)[c] + 0.3645 Phe-tRNA(Phe)[c] + 0.4921 Pro-tRNA(Pro)[c] + 0.8567 Ser-tRNA(Ser)[c] + 0.7109 Thr-tRNA(Thr)[c] + 0.1823 Trp-tRNA(Trp)[c] + 0.5377 Tyr-tRNA(Tyr)[c] + 0.5559 Val-tRNA(Val)[c] => 2.01 GDP[c] + 2.01 phosphate[c] + lactase[c] + 0.6516 tRNA(Ala)[c] + 0.2643 tRNA(Arg)[c] + 0.5013 tRNA(Asn)[c] + 0.4921 tRNA(Asp)[c] + 0.0547 tRNA(Cys)[c] + 0.4375 tRNA(Glu)[c] + 0.2552 tRNA(Gln)[c] + 0.9114 tRNA(Gly)[c] + 0.1276 tRNA(His)[c] + 0.4466 tRNA(Ile)[c] + 0.8567 tRNA(Leu)[c] + 0.4192 tRNA(Lys)[c] + 0.0638 tRNA(Met)[c] + 0.3645 tRNA(Phe)[c] + 0.4921 tRNA(Pro)[c] + 0.8567 tRNA(Ser)[c] + 0.7109 tRNA(Thr)[c] + 0.1823 tRNA(Trp)[c] + 0.5377 tRNA(Tyr)[c] + 0.5559 tRNA(Val)[c] 0 0 1000 0.18 YEP glucose +lactase lactase_2 lactase transport lactase[c] => lactase[e] 0 0 1000 +lactase lactase_3 lactase exchange lactase[e] => 1 0 1000 + +L-ornithine L-ornithine _1 Amino-acid acetyltransferase acetyl-CoA[c] + L-glutamate[c] => coenzyme A[c] + N-acetyl-L-glutamate[c] argA 0 0 1000 P0A6C5 109.0489167 49.195 2.3.1.1 0.1 Min glucose YLR438W +L-ornithine L-ornithine _2 Acetylglutamate kinase ATP[c] + N-acetyl-L-glutamate[c] => ADP[c] + N-acetyl-L-gamma-glutamyl phosphate[c] argB 0 0 1000 P0A6C8 0.24444 27.16 2.7.2.8 +L-ornithine L-ornithine _3 N-acetyl-gamma-glutamyl-phosphate reductase N-acetyl-L-gamma-glutamyl phosphate[c] + NADPH[c] + H+[c] => NADP(+)[c] + phosphate[c] + 2-acetamido-5-oxopentanoate[c] argC 0 0 1000 Q59279 35.888 1.2.1.38 +L-ornithine L-ornithine _4 acetylornithine aminotransferase 2-acetamido-5-oxopentanoate[c] + L-glutamate[c] => N(2)-acetyl-L-ornithine[c] + 2-oxoglutarate[c] argD 0 0 1000 Q59282 41.206 2.6.1.11 +L-ornithine L-ornithine _5 glutamate N-acetyltransferase N(2)-acetyl-L-ornithine[c] + L-glutamate[c] => ornithine[c] + N-acetyl-L-glutamate[c] argJ 0 0 1000 Q59280 0.0099285 39.714 2.3.1.35 +L-ornithine r_1237 (update) ornithine transport H+[c] + ornithine[m] => H+[m] + ornithine[c] ORT1 0 0 1000 Q12375 0.1816 31.52 +L-ornithine r_1118 (update) aspartate-glutamate transporter L-aspartate[m] + L-glutamate[c] => L-aspartate[c] + L-glutamate[m] AGC1 0 0 1000 Q12482 0.01318 Identification and metabolic role of the mitochondrial aspartate-glutamate transporter in Saccharomyces cerevisiae 104.304 +L-ornithine r_0471No2 glutamate dehydrogenase (NADP) (No2) pmet_r_0471[c] => H2O[c] + L-glutamate[c] + NADP(+)[c] YOR375C 0 0 1000 P07262 106.66 +L-ornithine r_0816No1 ornithine carbamoyltransferase (No1) carbamoyl phosphate[c] + ornithine[c] => H+[c] + L-citrulline[c] + phosphate[c] YJL088W 0 0 1000 P05150 41 +L-ornithine r_1987 1 0 Inf + +(S)-reticuline (S)-reticuline_1 tyrosine hydroxylase "oxygen[c] + 2 L-tyrosine[c] => 2 3,4-Dihydroxy-L-phenylalanine(L-DOPA)[c]" CYP76AD1 0 0 1000 I3PFJ5 56.212 1.14.18.1 0.1 YEP glucose +(S)-reticuline (S)-reticuline_2 "L-3,4-dihydroxyphenylalanine decarboxylase" "3,4-Dihydroxy-L-phenylalanine(L-DOPA)[c] + H+[c] => carbon dioxide[c] + dopamine[c]" DODC 0 0 1000 Q88JU5 1.8 51.444 4.1.1.28 +(S)-reticuline (S)-reticuline_3 4-hydroxyphenylpyruvate decarboxylase (update) 3-(4-hydroxyphenyl)pyruvate[c] + H+[c] => carbon dioxide[c] + (4-hydroxyphenyl)acetaldehyde[c] YDR380W 0 0 1000 Q06408 11 71.384 4.1.1.80 +(S)-reticuline (S)-reticuline_4 norcoclaurine synthase dopamine[c] + (4-hydroxyphenyl)acetaldehyde[c] => H2O[c] + (S)-norcoclaurine[c] NCS 0 0 1000 B6E2Z2 5.8 26.001 4.2.1.78 +(S)-reticuline (S)-reticuline_5 6-O-methyltransferase (S)-norcoclaurine[c] + S-adenosyl-L-methionine[c] => S-adenosyl-L-homocysteine[c] + (S)-Coclaurine[c] 6OMT 0 0 1000 Q6WUC1 0.08 38.511 2.1.1.128 +(S)-reticuline (S)-reticuline_6 coclaurine N-methyltransferase (S)-Coclaurine[c] + S-adenosyl-L-methionine[c] => S-adenosyl-L-homocysteine[c] + H+[c] + (S)-N-Methylcoclaurine[c] CNMT 0 0 1000 Q7XB08 0.000478707 41.032 2.1.1.140 +(S)-reticuline (S)-reticuline_7 N-methylcoclaurine hydroxylase (S)-N-Methylcoclaurine[c] + H+[c] + oxygen[c] + NADPH[c] => H2O[c] + NADP(+)[c] + (S)-3'-hydroxy-N-methylcoclaurine[c] CYP80B1 0 0 1000 O64899 54.644 1.14.14.102 +(S)-reticuline (S)-reticuline_8 4¡ä-O-methyltransferase (S)-3'-hydroxy-N-methylcoclaurine[c] + S-adenosyl-L-methionine[c] => S-adenosyl-L-homocysteine[c] + H+[c] + (S)-Reticuline[c] 4'OMT 0 0 1000 Q7XB11 0.071869248 39.402 2.1.1.116 +(S)-reticuline (S)-reticuline_9 (S)-Reticuline transport (S)-Reticuline[c] => (S)-Reticuline[e] 0 0 1000 +(S)-reticuline (S)-reticuline_10 (S)-Reticuline exchange (S)-Reticuline[e] => 1 0 1000 + +¦Â-ionone ¦Â-ionone_1 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 0.106 YEP glucose "YDR284C,YDR503C" +¦Â-ionone ¦Â-ionone_2 Phytoene desaturase phytoene[c] => neurosporene[c] crtI 0 0 1000 Q7Z858 0.000314486 65.066 1.3.99.28 +¦Â-ionone ¦Â-ionone_3 Phytoene desaturase neurosporene[c] + oxygen[c] => 2 H2O[c] + lycopene[c] crtI 0 0 1000 Q7Z858 0.000314486 65.066 1.3.99.28 +¦Â-ionone ¦Â-ionone_4 Bifunctional lycopene cyclase/phytoene synthase lycopene[c] => ¦Â-carotene[c] crtYB 0 0 1000 Q7Z859 0.4434336 74.736 5.5.1.19 +¦Â-ionone ¦Â-ionone_5 carotenoid cleavage dioxigenase ¦Â-carotene[c] + 2 oxygen[c] => C14-dialdehyde[c] + 2 ¦Â-ionone[c] CCD1 0 0 1000 Q6E4P3 61.311 1.13.11 +¦Â-ionone ¦Â-ionone_6 ¦Â-ionone transport ¦Â-ionone[c] => ¦Â-ionone[e] 0 0 1000 +¦Â-ionone ¦Â-ionone_7 ¦Â-ionone exchange ¦Â-ionone[e] => 1 0 1000 +¦Â-ionone ¦Â-ionone_8 C14-dialdehyde transport C14-dialdehyde[c] => C14-dialdehyde[e] 0 0 1000 +¦Â-ionone ¦Â-ionone_9 C14-dialdehyde exchange => C14-dialdehyde[e] 0 0 1000 +¦Â-ionone r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +¦Â-ionone r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +¦Â-ionone r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 +¦Â-ionone r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 +¦Â-ionone r_0373No1 farnesyltranstransferase (No1) farnesyl diphosphate[c] + isopentenyl diphosphate[c] => geranylgeranyl diphosphate[c] + diphosphate[c] YPL069C 0 0 1000 Q12051 6.6 38.6511 2.5.1.29 + +Xanthone Xanthone_1 benzoic acid exchange => benzoic acid[e] 0 0 1000 0.1 YEP glucose +Xanthone Xanthone_2 benzoic acid transport benzoic acid[e] => benzoic acid[c] 0 0 1000 +Xanthone Xanthone_3 benzoate:CoA ligase benzoic acid[c] + coenzyme A[c] + ATP[c] => diphosphate[c] + AMP[c] + benzoyl-CoA[c] BZL 0 0 1000 Q53005 8 58.93 6.2.1.25 +Xanthone Xanthone_4 benzophenone synthase "3 malonyl-CoA[c] + benzoyl-CoA[c] => 4 coenzyme A[c] + 3 carbon dioxide[c] + 2,4,6-Trihydroxybenzophenone[c]" BPS 0 0 1000 A4ZYX5 0.055 43.039 2.3.1.220 +Xanthone Xanthone_5 xanthone synthase "2 H+[c] + 2,4,6-Trihydroxybenzophenone[c] + 2 oxygen[c] + 2 NADPH[c] => 2 H2O[c] + 2 NADP(+)[c] + 1,3,5-trihydroxyxanthone[c]" TXS 0 0 1000 A0A161I263 57.849 +Xanthone Xanthone_6 xanthone transport "1,3,5-trihydroxyxanthone[c] => 1,3,5-trihydroxyxanthone[e]" 0 0 1000 +Xanthone Xanthone_7 xanthone exchange "1,3,5-trihydroxyxanthone[e] =>" 1 0 1000 +Xanthone r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 0.55 40.4829 2.5.1.1 +Xanthone r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 0.55 40.4829 2.5.1.1 + +tyrosine tyrosine_1 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.082809792 39.7487 2.5.1.54 0.089 YEP glucose "YDR035W,YBR249C,YDR380W,Zwf1" +tyrosine tyrosine_2 tyrosine ammonia-lyase L-tyrosine[c] => ammonium[c] + trans-4-coumarate[c] TAL 0 0 1000 Q3IWB0 0.9 54.914 4.3.1.23 +tyrosine tyrosine_3 cyclohexadienyl dehydrogenase prephenate[c] + NAD[c] => 3-(4-hydroxyphenyl)pyruvate[c] + carbon dioxide[c] + NADH[c] TyrC 0 0 1000 Q04983 32.051 1.3.1.12 + +triacylglycerol triacylglycerol_1 triacylglycerols transport triglyceride backbone[c] => triacylglycerol[e] 0 0 1000 0.1 Min glucose "YMR313C,YKR089C,YOR081C,YPL147W" +triacylglycerol triacylglycerol_2 triacylglycerols exchange triacylglycerol[e] => 1 0 1000 +triacylglycerol r_0109No1 "acetyl-CoA carboxylase, reaction (No1)" acetyl-CoA[c] + ATP[c] + bicarbonate[c] => ADP[c] + H+[c] + malonyl-CoA[c] + phosphate[c] YNR016C 0 0 1000 Q00955 65.3426 +triacylglycerol r_2344No1 "PA phosphatase (1-16:0, 2-16:1), ER membrane (No1)" "H2O[erm] + phosphatidate (1-16:0, 2-16:1)[erm] => phosphate[erm] + diglyceride (1-16:0, 2-16:1)[erm]" YMR165C 0 0 1000 P32567 23.1467 +triacylglycerol r_2345No1 "PA phosphatase (1-16:0, 2-18:1), ER membrane (No1)" "H2O[erm] + phosphatidate (1-16:0, 2-18:1)[erm] => phosphate[erm] + diglyceride (1-16:0, 2-18:1)[erm]" YMR165C 0 0 1000 P32567 23.1467 +triacylglycerol r_2346No1 "PA phosphatase (1-16:1, 2-16:1), ER membrane (No1)" "H2O[erm] + phosphatidate (1-16:1, 2-16:1)[erm] => phosphate[erm] + diglyceride (1-16:1, 2-16:1)[erm]" YMR165C 0 0 1000 P32567 23.1467 +triacylglycerol r_2347No1 "PA phosphatase (1-16:1, 2-18:1), ER membrane (No1)" "H2O[erm] + phosphatidate (1-16:1, 2-18:1)[erm] => phosphate[erm] + diglyceride (1-16:1, 2-18:1)[erm]" YMR165C 0 0 1000 P32567 23.1467 +triacylglycerol r_2348No1 "PA phosphatase (1-18:0, 2-16:1), ER membrane (No1)" "H2O[erm] + phosphatidate (1-18:0, 2-16:1)[erm] => phosphate[erm] + diglyceride (1-18:0, 2-16:1)[erm]" YMR165C 0 0 1000 P32567 23.1467 +triacylglycerol r_2349No1 "PA phosphatase (1-18:0, 2-18:1), ER membrane (No1)" "H2O[erm] + phosphatidate (1-18:0, 2-18:1)[erm] => phosphate[erm] + diglyceride (1-18:0, 2-18:1)[erm]" YMR165C 0 0 1000 P32567 23.1467 +triacylglycerol r_2350No1 "PA phosphatase (1-18:1, 2-16:1), ER membrane (No1)" "H2O[erm] + phosphatidate (1-18:1, 2-16:1)[erm] => phosphate[erm] + diglyceride (1-18:1, 2-16:1)[erm]" YMR165C 0 0 1000 P32567 23.1467 +triacylglycerol r_2351No1 "PA phosphatase (1-18:1, 2-18:1), ER membrane (No1)" "H2O[erm] + phosphatidate (1-18:1, 2-18:1)[erm] => phosphate[erm] + diglyceride (1-18:1, 2-18:1)[erm]" YMR165C 0 0 1000 P32567 23.1467 + +ARA ARA_1 Delta9-desaturase H+[erm] + stearoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + oleoyl-CoA[erm] D9D 0 0 1000 D5KSD1 50.809 1.14.19.1 0.1 Min glucose +ARA ARA_2 Delta12-desaturase H+[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + linoleoyl-CoA[erm] D12D 0 0 1000 Q9Y8H5 46.001 1.14.19.6 +ARA ARA_3 Omega-3 desaturase "linoleoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (9Z,12Z,15Z)-Octadecatrienoyl-CoA[erm]" FAD3 0 0 1000 D5KSD6 47.718 1.14.19.- +ARA ARA_4 Delta6-desaturase "linoleoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (6Z,9Z,12Z)-octadecatrienoyl-CoA[erm]" D6D 0 0 1000 A0A1Y5I9G7 51.674 1.14.19.3 +ARA ARA_5 Delta6-desaturase "(9Z,12Z,15Z)-Octadecatrienoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (6Z,9Z,12Z,15Z)-Octadecatetraenoyl-CoA[erm]" D6D 0 0 1000 A0A1Y5I9G7 51.674 1.14.19.3 +ARA ARA_6 Delta6-elongase "(6Z,9Z,12Z)-octadecatrienoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (8Z,11Z,14Z)-eicosatrienoyl-CoA[erm]" D6E 0 0 1000 D5KSD4 36.746 2.3.1.199 +ARA ARA_7 Delta6-elongase "(6Z,9Z,12Z,15Z)-Octadecatetraenoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA[erm]" D6E 0 0 1000 D5KSD4 36.746 2.3.1.199 +ARA ARA_8 Delta-5 desaturase "(8Z,11Z,14Z)-eicosatrienoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[erm]" D5D 0 0 1000 HQ678517 59.89 1.14.19.44 +ARA ARA_9 Delta-5 desaturase "(8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm]" D5D 0 0 1000 HQ678517 59.89 1.14.19.44 +ARA ARA_10 ARA-CoA transport "(5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[erm] => (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[p]" 0 0 1000 +ARA ARA_11 peroxisomal acyl-CoA thioesterase "(5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (5Z,8Z,11Z,14Z)-eicosatetraenoate (ARA)[p]" YJR019C 0 0 1000 P41903 3.1.2.2 +ARA ARA_12 ARA transport "(5Z,8Z,11Z,14Z)-eicosatetraenoate (ARA)[p] => ARA[e]" 0 0 1000 +ARA ARA_13 ARA exchange ARA[e] => 1 0 1000 +ARA ARA_14 EPA-CoA transport "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] => (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[p]" 0 0 1000 +ARA ARA_15 peroxisomal acyl-CoA thioesterase "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate (EPA)[p]" YJR019C 0 0 1000 P41903 3.1.2.2 +ARA ARA_16 EPA transport "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate (EPA)[p] => EPA[e]" 0 0 1000 +ARA ARA_17 EPA exchange EPA[e] => 0 0 1000 +ARA ARA_18 Delta5-elongase "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA[erm]" 0 0 1000 +ARA ARA_19 Delta-4 desaturase "(7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[erm]" 0 0 1000 +ARA ARA_20 EPA-CoA transport "(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[erm] => (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[p]" 0 0 1000 +ARA ARA_21 peroxisomal acyl-CoA thioesterase "(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate (DHA)[p]" YJR019C 0 0 1000 P41903 3.1.2.2 +ARA ARA_22 EPA transport "(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate (DHA)[p] => DHA[e]" 0 0 1000 +ARA ARA_23 EPA exchange DHA[e] => 0 0 1000 + +EPA EPA_1 Delta9-desaturase H+[erm] + stearoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + oleoyl-CoA[erm] D9D 0 0 1000 D5KSD1 50.809 1.14.19.1 0.1 Min glucose +EPA EPA_2 Delta12-desaturase H+[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + linoleoyl-CoA[erm] D12D 0 0 1000 Q9Y8H5 46.001 1.14.19.6 +EPA EPA_3 Omega-3 desaturase "linoleoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (9Z,12Z,15Z)-Octadecatrienoyl-CoA[erm]" FAD3 0 0 1000 D5KSD6 47.718 1.14.19.- +EPA EPA_4 Delta6-desaturase "linoleoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (6Z,9Z,12Z)-octadecatrienoyl-CoA[erm]" D6D 0 0 1000 A0A1Y5I9G7 51.674 1.14.19.3 +EPA EPA_5 Delta6-desaturase "(9Z,12Z,15Z)-Octadecatrienoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (6Z,9Z,12Z,15Z)-Octadecatetraenoyl-CoA[erm]" D6D 0 0 1000 A0A1Y5I9G7 51.674 1.14.19.3 +EPA EPA_6 Delta6-elongase "(6Z,9Z,12Z)-octadecatrienoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (8Z,11Z,14Z)-eicosatrienoyl-CoA[erm]" D6E 0 0 1000 D5KSD4 36.746 2.3.1.199 +EPA EPA_7 Delta6-elongase "(6Z,9Z,12Z,15Z)-Octadecatetraenoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA[erm]" D6E 0 0 1000 D5KSD4 36.746 2.3.1.199 +EPA EPA_8 Delta-5 desaturase "(8Z,11Z,14Z)-eicosatrienoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[erm]" D5D 0 0 1000 HQ678517 59.89 1.14.19.44 +EPA EPA_9 Delta-5 desaturase "(8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm]" D5D 0 0 1000 HQ678517 59.89 1.14.19.44 +EPA EPA_10 ARA-CoA transport "(5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[erm] => (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[p]" 0 0 1000 +EPA EPA_11 peroxisomal acyl-CoA thioesterase "(5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (5Z,8Z,11Z,14Z)-eicosatetraenoate (ARA)[p]" YJR019C 0 0 1000 P41903 3.1.2.2 +EPA EPA_12 ARA transport "(5Z,8Z,11Z,14Z)-eicosatetraenoate (ARA)[p] => ARA[e]" 0 0 1000 +EPA EPA_13 ARA exchange ARA[e] => 0 0 1000 +EPA EPA_14 EPA-CoA transport "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] => (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[p]" 0 0 1000 +EPA EPA_15 peroxisomal acyl-CoA thioesterase "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate (EPA)[p]" YJR019C 0 0 1000 P41903 3.1.2.2 +EPA EPA_16 EPA transport "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate (EPA)[p] => EPA[e]" 0 0 1000 +EPA EPA_17 EPA exchange EPA[e] => 1 0 1000 +EPA EPA_18 Delta5-elongase "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA[erm]" 0 0 1000 +EPA EPA_19 Delta-4 desaturase "(7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[erm]" 0 0 1000 +EPA EPA_20 EPA-CoA transport "(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[erm] => (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[p]" 0 0 1000 +EPA EPA_21 peroxisomal acyl-CoA thioesterase "(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate (DHA)[p]" YJR019C 0 0 1000 P41903 3.1.2.2 +EPA EPA_22 EPA transport "(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate (DHA)[p] => DHA[e]" 0 0 1000 +EPA EPA_23 EPA exchange DHA[e] => 0 0 1000 + +DHA DHA_1 Delta9-desaturase H+[erm] + stearoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + oleoyl-CoA[erm] D9D 0 0 1000 D5KSD1 50.809 1.14.19.1 0.1 Min glucose +DHA DHA_2 Delta12-desaturase H+[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + linoleoyl-CoA[erm] D12D 0 0 1000 Q9Y8H5 46.001 1.14.19.6 +DHA DHA_3 Omega-3 desaturase "linoleoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (9Z,12Z,15Z)-Octadecatrienoyl-CoA[erm]" FAD3 0 0 1000 D5KSD6 47.718 1.14.19.- +DHA DHA_4 Delta6-desaturase "linoleoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (6Z,9Z,12Z)-octadecatrienoyl-CoA[erm]" D6D 0 0 1000 A0A1Y5I9G7 51.674 1.14.19.3 +DHA DHA_5 Delta6-desaturase "(9Z,12Z,15Z)-Octadecatrienoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (6Z,9Z,12Z,15Z)-Octadecatetraenoyl-CoA[erm]" D6D 0 0 1000 A0A1Y5I9G7 51.674 1.14.19.3 +DHA DHA_6 Delta6-elongase "(6Z,9Z,12Z)-octadecatrienoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (8Z,11Z,14Z)-eicosatrienoyl-CoA[erm]" D6E 0 0 1000 D5KSD4 36.746 2.3.1.199 +DHA DHA_7 Delta6-elongase "(6Z,9Z,12Z,15Z)-Octadecatetraenoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA[erm]" D6E 0 0 1000 D5KSD4 36.746 2.3.1.199 +DHA DHA_8 Delta-5 desaturase "(8Z,11Z,14Z)-eicosatrienoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[erm]" D5D 0 0 1000 HQ678517 59.89 1.14.19.44 +DHA DHA_9 Delta-5 desaturase "(8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm]" D5D 0 0 1000 HQ678517 59.89 1.14.19.44 +DHA DHA_10 ARA-CoA transport "(5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[erm] => (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[p]" 0 0 1000 +DHA DHA_11 peroxisomal acyl-CoA thioesterase "(5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (5Z,8Z,11Z,14Z)-eicosatetraenoate (ARA)[p]" YJR019C 0 0 1000 P41903 3.1.2.2 +DHA DHA_12 ARA transport "(5Z,8Z,11Z,14Z)-eicosatetraenoate (ARA)[p] => ARA[e]" 0 0 1000 +DHA DHA_13 ARA exchange ARA[e] => 0 0 1000 +DHA DHA_14 EPA-CoA transport "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] => (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[p]" 0 0 1000 +DHA DHA_15 peroxisomal acyl-CoA thioesterase "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate (EPA)[p]" YJR019C 0 0 1000 P41903 3.1.2.2 +DHA DHA_16 EPA transport "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate (EPA)[p] => EPA[e]" 0 0 1000 +DHA DHA_17 EPA exchange EPA[e] => 0 0 1000 +DHA DHA_18 Delta5-elongase "(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA[erm] + 2 NADPH[erm] + malonyl-CoA[erm] + 3 H+[erm] => coenzyme A[erm] + carbon dioxide[erm] + H2O[erm] + NADP(+)[erm] + (7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA[erm]" 0 0 1000 +DHA DHA_19 Delta-4 desaturase "(7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA[erm] + oleoyl-CoA[erm] + oxygen[erm] + NADH[erm] => 2 H2O[erm] + NAD[erm] + (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[erm]" 0 0 1000 +DHA DHA_20 EPA-CoA transport "(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[erm] => (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[p]" 0 0 1000 +DHA DHA_21 peroxisomal acyl-CoA thioesterase "(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA[p] + H2O[p] => H+[p] + coenzyme A[p] + (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate (DHA)[p]" YJR019C 0 0 1000 P41903 3.1.2.2 +DHA DHA_22 EPA transport "(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate (DHA)[p] => DHA[e]" 0 0 1000 +DHA DHA_23 EPA exchange DHA[e] => 1 0 1000 + +n-butanol n-butanol_1 Citramalate synthase pyruvate[m] + acetyl-CoA[m] => (R)-Citramalate[m] cimA 0 0 1000 A0FDH8 18.6 47.186 2.3.1.182 0.1 YEP glucose YOL086C +n-butanol n-butanol_2 citraconate hydratase (R)-Citramalate[m] + H2O[m] => 2-Methylmaleate[m] LEU1m 0 0 1000 P07264ly 18.54 85.794 4.2.1.35 +n-butanol n-butanol_3 2-methylmaleate hydratase 2-Methylmaleate[m] + H2O[m] => D-erythro-3-Methylmalate[m] LEU1m 0 0 1000 P07264ly 18.54 85.794 4.2.1.35 +n-butanol n-butanol_4 3-isopropylmalate dehydrogenase D-erythro-3-Methylmalate[m] + NAD[m] => 2-oxobutanoate[m] + NADH[m] + H+[m] + carbon dioxide[m] LEU2m 0 0 1000 P04173ly 18.1 38.953 1.1.1.85 +n-butanol n-butanol_5 2-ethylmalate synthase 2-oxobutanoate[m] + H2O[m] + acetyl-CoA[m] => coenzyme A[m] + (R)-2-Ethylmalate[m] LEU4m 0 0 1000 P06208ly 27.58 68.409 2.3.3.6 +n-butanol n-butanol_6 NA (R)-2-Ethylmalate[m] => 3-Ethylmalate[m] LEU1m 0 0 1000 P07264ly 18.54 85.794 4.2.1.35 +n-butanol n-butanol_7 NA 3-Ethylmalate[m] + NAD[m] => NADH[m] + H+[m] + 3-ethyl-2-oxosuccinate[m] LEU2m 0 0 1000 P04173ly 18.1 38.953 1.1.1.85 +n-butanol n-butanol_8 NA 3-ethyl-2-oxosuccinate[m] + H+[m] => carbon dioxide[m] + alpha-ketovalerate[m] LEU2m 0 0 1000 P04173ly 18.1 38.953 1.1.1.85 +n-butanol n-butanol_9 2-ethylmalate transport (R)-2-Ethylmalate[m] => (R)-2-Ethylmalate[c] 0 0 1000 +n-butanol n-butanol_10 alpha-ketovalerate transport alpha-ketovalerate[m] => alpha-ketovalerate[c] 0 0 1000 +n-butanol n-butanol_11 NA (R)-2-Ethylmalate[c] => 3-Ethylmalate[c] YGL009C 0 0 1000 P07264 18.54 85.794 4.2.1.35 +n-butanol n-butanol_12 NA 3-Ethylmalate[c] + NAD[c] => NADH[c] + H+[c] + 3-ethyl-2-oxosuccinate[c] YCL018W 0 0 1000 P04173 18.1 38.953 1.1.1.85 +n-butanol n-butanol_13 NA 3-ethyl-2-oxosuccinate[c] + H+[c] => carbon dioxide[c] + alpha-ketovalerate[c] YCL018W 0 0 1000 P04173 18.1 38.953 1.1.1.85 +n-butanol n-butanol_14 keto-acid decarboxylase alpha-ketovalerate[c] => butyraldehyde[c] + carbon dioxide[c] YDR380W 0 0 1000 Q06408 10.4 71.384 4.1.1.43 +n-butanol n-butanol_15 alcohol dehydrogenase butyraldehyde[c] + NADH[c] + H+[c] => NAD[c] + n-butanol[c] YCR105W 0 0 1000 P25377 8.3156 39.348 1.1.1.2 +n-butanol n-butanol_16 n-butanol transport n-butanol[c] => n-butanol[e] 0 0 1000 +n-butanol n-butanol_17 n-butanol exchange n-butanol[e] => 1 0 1000 +n-butanol r_1129 (update) coenzyme A transport coenzyme A[c] => coenzyme A[m] LEU5 0 0 1000 P38702 40.825 2.A.29.12.4 +n-butanol r_4173No1 L-cysteine:sulfur-acceptor sulfurtransferase (No1) (sulfur carrier)-H[m] + L-cysteine[m] => L-alanine[m] + (sulfur carrier)-SH[m] YCL017C 0 0 1000 P25374 1.74 +n-butanol r_4173_REVNo1 L-cysteine:sulfur-acceptor sulfurtransferase (reversible) (No1) L-alanine[m] + (sulfur carrier)-SH[m] => (sulfur carrier)-H[m] + L-cysteine[m] YCL017C 0 0 1000 P25374 274.1995 + +2-phenylethanol 2-phenylethanol_1 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.215305458 39.7487 2.5.1.54 0.1 Min glucose "YDR035W,YBR249C,YPR060C,YGL202W" +2-phenylethanol 2-phenylethanol_2 chorismate mutase chorismate[c] => prephenate[c] ARO7T226I 0 0 1000 P32178ly 0.0619725 29.7468 5.4.99.5 +2-phenylethanol 2-phenylethanol_3 Shikimate kinase shikimate[c] + ATP[c] => 3-phosphoshikimic acid[c] + H+[c] + ADP[c] aroL 0 0 1000 P0A6E1 130.8651667 19.151 2.7.1.71 +2-phenylethanol r_0279No1 chorismate synthase (No1) 5-O-(1-carboxyvinyl)-3-phosphoshikimic acid[c] => chorismate[c] + phosphate[c] YGL148W 0 0 1000 P28777 1.74 +2-phenylethanol r_0026No4 2-keto-4-methylthiobutyrate transamination (No4) pmet_r_0026[c] => 2-oxoglutarate[c] + L-methionine[c] YHR137W 0 0 1000 P38840 3080 +2-phenylethanol r_2117No1 phenylalanine transaminase (No1) L-phenylalanine[c] + pyruvate[c] => keto-phenylpyruvate[c] + L-alanine[c] YHR137W 0 0 1000 P38840 2400 +2-phenylethanol r_2118No1 tryptophan transaminase (No1) keto-phenylpyruvate[c] + L-tryptophan[c] => indole-3-pyruvate[c] + L-phenylalanine[c] YHR137W 0 0 1000 P38840 699.9998 +2-phenylethanol r_2119No1 tyrosine transaminase (No1) 3-(4-hydroxyphenyl)pyruvate[c] + L-alanine[c] => L-tyrosine[c] + pyruvate[c] YHR137W 0 0 1000 P38840 3080 +2-phenylethanol r_2117_REVNo1 phenylalanine transaminase (reversible) (No1) keto-phenylpyruvate[c] + L-alanine[c] => L-phenylalanine[c] + pyruvate[c] YHR137W 0 0 1000 P38840 3080 +2-phenylethanol r_2119_REVNo1 tyrosine transaminase (reversible) (No1) L-tyrosine[c] + pyruvate[c] => 3-(4-hydroxyphenyl)pyruvate[c] + L-alanine[c] YHR137W 0 0 1000 P38840 999.9992 +2-phenylethanol r_0938No1 prephenate dehydratase (No1) H+[c] + prephenate[c] => carbon dioxide[c] + H2O[c] + keto-phenylpyruvate[c] YNL316C 0 0 1000 P32452 3864 +2-phenylethanol r_1049No2 transketolase 1 (No2) pmet_r_1049[c] => glyceraldehyde 3-phosphate[c] + sedoheptulose 7-phosphate[c] YPR074C 0 0 1000 P23254 138.0002 +2-phenylethanol r_1050No2 transketolase 2 (No2) pmet_r_1050[c] => D-fructose 6-phosphate[c] + glyceraldehyde 3-phosphate[c] YPR074C 0 0 1000 P23254 138.0002 +2-phenylethanol r_1049_REVNo2 transketolase 1 (reversible) (No2) pmet_r_1049_REV[c] => D-xylulose 5-phosphate[c] + ribose-5-phosphate[c] YPR074C 0 0 1000 P23254 138.0002 +2-phenylethanol r_1050_REVNo2 transketolase 2 (reversible) (No2) pmet_r_1050_REV[c] => D-erythrose 4-phosphate[c] + D-xylulose 5-phosphate[c] YPR074C 0 0 1000 P23254 138.0002 +2-phenylethanol r_0962No1 pyruvate kinase (No1) pmet_r_0962[c] => ATP[c] + pyruvate[c] YAL038W 0 0 1000 P00549 115.9998 +2-phenylethanol r_0854No1 phenylpyruvate decarboxylase (No1) H+[c] + keto-phenylpyruvate[c] => carbon dioxide[c] + phenylacetaldehyde[c] YDR380W 0 0 1000 Q06408 2280 +2-phenylethanol r_0939No1 prephenate dehydrogenase (NADP) (No1) NADP(+)[c] + prephenate[c] => 3-(4-hydroxyphenyl)pyruvate[c] + carbon dioxide[c] + NADPH[c] YDR380W 0 0 1000 Q06408 13.15 +2-phenylethanol r_1589 1 0 Inf + +docosanol docosanol_1 Fatty acyl-CoA reductase docosanoyl-CoA[c] + 2 H+[c] + 2 NADPH[c] => docosanol[c] + coenzyme A[c] + 2 NADP(+)[c] FAR1 0 0 1000 Q39152 55.481 1.2.1.84 0.1 Min glucose "YCR048W,YOR245C,YNR019W,YNR008W,YGL205W,YLR372W,YBR020W" +docosanol docosanol_2 fatty acid synthase acetyl-CoA[c] + 21 H+[c] + 7 malonyl-CoA[c] + 14 NADPH[c] => 7 carbon dioxide[c] + 7 coenzyme A[c] + 7 H2O[c] + 14 NADP(+)[c] + palmitoyl-CoA[c] FAS 0 0 1000 K0V149 2.04404375 327.047 2.3.1.86 +docosanol docosanol_3 fatty acid synthase acetyl-CoA[c] + 24 H+[c] + 8 malonyl-CoA[c] + 16 NADPH[c] => 8 carbon dioxide[c] + 8 coenzyme A[c] + 8 H2O[c] + 16 NADP(+)[c] + stearoyl-CoA[c] FAS 0 0 1000 K0V149 2.04404375 327.047 2.3.1.86 +docosanol docosanol_4 acyl carrier protein synthase "coenzyme A[c] + H2O[c] => adenosine 3',5'-bismonophosphate[c] + 2 H+[c] + pantetheine 4'-phosphate[c]" Acps 0 0 1000 K0V045 14.161 2.7.8.7 +docosanol docosanol_5 fatty acid elongase malonyl-CoA[c] + palmitoyl-CoA[c] + H+[c] => coenzyme A[c] + stearoyl-CoA[c] + carbon dioxide[c] FAS 0 0 1000 K0V149 2.04404375 327.047 2.3.1.86 +docosanol docosanol_6 fatty acid elongase malonyl-CoA[c] + stearoyl-CoA[c] + H+[c] => coenzyme A[c] + icosanoyl-CoA[c] + carbon dioxide[c] FAS 0 0 1000 K0V149 2.04404375 327.047 2.3.1.86 +docosanol docosanol_7 fatty acid elongase malonyl-CoA[c] + icosanoyl-CoA[c] + H+[c] => coenzyme A[c] + docosanoyl-CoA[c] + carbon dioxide[c] FAS 0 0 1000 K0V149 2.04404375 327.047 2.3.1.86 +docosanol docosanol_8 docosanol transport docosanol[c] => docosanol[e] 0 0 1000 +docosanol docosanol_9 docosanol exchange docosanol[e] => 1 0 1000 +docosanol r_2154No1 elongase I (3-oxotetradecanoyl-CoA) (No1) lauroyl-CoA[erm] + malonyl-CoA[erm] + H+[erm] => carbon dioxide[erm] + coenzyme A[erm] + 3-oxotetradecanoyl-CoA[erm] YJL196C 0 0 1000 P39540 5.4 +docosanol r_2155No1 elongase I (3-oxopalmitoyl-CoA) (No1) malonyl-CoA[erm] + H+[erm] + myristoyl-CoA[erm] => carbon dioxide[erm] + coenzyme A[erm] + 3-oxopalmitoyl-CoA[erm] YJL196C 0 0 1000 P39540 27.6 +docosanol r_2156No1 elongase II (3-oxooctadecanoyl-CoA) (No1) malonyl-CoA[erm] + H+[erm] + palmitoyl-CoA[erm] => carbon dioxide[erm] + coenzyme A[erm] + 3-oxooctadecanoyl-CoA[erm] YCR034W 0 0 1000 P25358 5.4 +docosanol r_2157No1 elongase II or III (3-oxoicosanoyl-CoA) (No1) pmet_r_2157[erm] => carbon dioxide[erm] + coenzyme A[erm] + 3-oxoicosanoyl-CoA[erm] YCR034W 0 0 1000 P25358 5.4 +docosanol r_2158No1 elongase II or III (3-oxodocosanoyl-CoA) (No1) pmet_r_2158[erm] => carbon dioxide[erm] + coenzyme A[erm] + 3-oxodocosanoyl-CoA[erm] YCR034W 0 0 1000 P25358 5.4 +docosanol r_2159No1 elongase II or III (3-oxotetracosanoyl-CoA) (No1) pmet_r_2159[erm] => carbon dioxide[erm] + coenzyme A[erm] + 3-oxotetracosanoyl-CoA[erm] YCR034W 0 0 1000 P25358 5.4 +docosanol r_0109No1 "acetyl-CoA carboxylase, reaction (No1)" acetyl-CoA[c] + ATP[c] + bicarbonate[c] => ADP[c] + H+[c] + malonyl-CoA[c] + phosphate[c] YNR016C 0 0 1000 Q00955 65.3426 + +Itaconic acid Itaconic acid_1 cis-aconitic acid decarboxylase cis-aconitate[c] + H+[c] => carbon dioxide[c] + Itaconic acid[c] CAD 0 0 1000 B3IUN8 0.242756323 52.754 4.1.1.6 0.1 YEP glucose "YJR078W,YJR019C" +Itaconic acid Itaconic acid_2 itaconic acid transport Itaconic acid[c] => Itaconic acid[e] 0 0 1000 +Itaconic acid Itaconic acid_3 itaconic acid exchange Itaconic acid[e] => 1 0 1000 + +Glutathione Glutathione_1 gamma-glutamylcysteine synthetase ATP[c] + L-cysteine[c] + L-glutamate[c] => ADP[c] + H+[c] + L-gamma-glutamyl-L-cysteine[c] + phosphate[c] GshF 0 0 1000 D4N892 1167.652667 85.438 6.3.2.2 0.1 YEP glucose +Glutathione Glutathione_2 glutathione synthetase (No1) ATP[c] + L-gamma-glutamyl-L-cysteine[c] + L-glycine[c] => ADP[c] + glutathione[c] + H+[c] + phosphate[c] GshF 0 0 1000 D4N892 1103.574167 85.438 6.3.2.3 +Glutathione Glutathione_3 glutathione synthetase (No1) ATP[c] + L-gamma-glutamyl-L-cysteine[c] + L-glycine[c] => ADP[c] + glutathione[c] + H+[c] + phosphate[c] gshB 0 0 1000 P04425 151 35.561 6.3.2.3 +Glutathione Glutathione_4 glutathione transport glutathione[c] => glutathione[e] 0 0 1000 +Glutathione r_0460No1 gamma-glutamylcysteine synthetase (No1) ATP[c] + L-cysteine[c] + L-glutamate[c] => ADP[c] + H+[c] + L-gamma-glutamyl-L-cysteine[c] + phosphate[c] YJL101C 0 0 1000 P32477 20380 +Glutathione r_0485No1 glutathione synthetase (No1) ATP[c] + L-gamma-glutamyl-L-cysteine[c] + L-glycine[c] => ADP[c] + glutathione[c] + H+[c] + phosphate[c] YOL049W 0 0 1000 Q08220 26 +Glutathione r_0468No1 glutamate 5-kinase (No1) ATP[c] + L-glutamate[c] => ADP[c] + L-gamma-glutamyl phosphate[c] YDR300C 0 0 1000 P32264 23.03 +Glutathione r_1807 1 0 Inf + +Ethylene Ethylene_1 ethylene forming enzyme 2-oxoglutarate[c] + 2 H+[c] + oxygen[c] => H2O[c] + 3 carbon dioxide[c] + Ethylene[c] efe 0 0 1000 Q9Z3T0 0.5 38.064 1.13.12.19 0.24 Min glucose +Ethylene Ethylene_2 ethylene transport Ethylene[c] => Ethylene[e] 0 0 1000 +Ethylene Ethylene_3 ethylene exchange Ethylene[e] => 1 0 1000 +Ethylene r_1889_REV 0 0 1 + +Human Serum Albumin (HSA) Human Serum Albumin (HSA)_1 production of HAS "0.8928 Ala-tRNA(Ala)[c] + 0.4032 Arg-tRNA(Arg)[c] + 0.2448 Asn-tRNA(Asn)[c] + 0.5184 Asp-tRNA(Asp)[c] + 0.504 Cys-tRNA(Cys)[c] + 0.288 Glu-tRNA(Glu)[c] + 0.8928 Gln-tRNA(Gln)[c] + +0.1872 Gly-tRNA(Gly)[c] + 0.2304 His-tRNA(His)[c] + 0.1296 Ile-tRNA(Ile)[c] + 0.9216 Leu-tRNA(Leu)[c] + 0.864 Lys-tRNA(Lys)[c] + 0.1008 Met-tRNA(Met)[c] + 0.504 Phe-tRNA(Phe)[c] + +0.3456 Pro-tRNA(Pro)[c] + 0.4032 Ser-tRNA(Ser)[c] + 0.4176 Thr-tRNA(Thr)[c] + 0.0288 Trp-tRNA(Trp)[c] + 0.2736 Tyr-tRNA(Tyr)[c] + 0.6192 Val-tRNA(Val)[c] + 1.22 GTP[c] => HAS[c] ++ 1.22 GDP[c] + 1.22 phosphate[c] + 0.8928 tRNA(Ala)[c] + 0.4032 tRNA(Arg)[c] + 0.2448 tRNA(Asn)[c] + 0.5184 tRNA(Asp)[c] + 0.504 tRNA(Cys)[c] + 0.288 tRNA(Glu)[c] + 0.8928 tRNA(Gln)[c] + 0.1872 tRNA(Gly)[c] + 0.2304 tRNA(His)[c] + 0.1296 tRNA(Ile)[c] + 0.9216 tRNA(Leu)[c] + 0.864 tRNA(Lys)[c] + 0.1008 tRNA(Met)[c] + 0.504 tRNA(Phe)[c] + +0.3456 tRNA(Pro)[c] + 0.4032 tRNA(Ser)[c] + 0.4176 tRNA(Thr)[c] + 0.0288 tRNA(Trp)[c] + 0.2736 tRNA(Tyr)[c] + 0.6192 tRNA(Val)[c]" 0 0 1000 0.22 4.6 Min glucose +Human Serum Albumin (HSA) Human Serum Albumin (HSA)_2 HSA transport HAS[c] => HAS[e] 0 0 1000 +Human Serum Albumin (HSA) Human Serum Albumin (HSA)_3 HSA exchange HAS[e] => 1 0 1000 + +¦Á-Amylase ¦Á-Amylase_1 production of ¦Á-Amylase "0.7663 Ala-tRNA(Ala)[c] + 0.1825 Arg-tRNA(Arg)[c] + 0.4744 Asn-tRNA(Asn)[c] + 0.7663 Asp-tRNA(Asp)[c] + 0.1642 Cys-tRNA(Cys)[c] + 0.2189 Glu-tRNA(Glu)[c] + 0.3649 Gln-tRNA(Gln)[c] + +0.7846 Gly-tRNA(Gly)[c] + 0.1277 His-tRNA(His)[c] + 0.5109 Ile-tRNA(Ile)[c] + 0.6751 Leu-tRNA(Leu)[c] + 0.3649 Lys-tRNA(Lys)[c] + 0.2007 Met-tRNA(Met)[c] + 0.2737 Phe-tRNA(Phe)[c] + +0.4014 Pro-tRNA(Pro)[c] + 0.6751 Ser-tRNA(Ser)[c] + 0.7298 Thr-tRNA(Thr)[c] + 0.2189 Trp-tRNA(Trp)[c] + 0.6386 Tyr-tRNA(Tyr)[c] + 0.5656 Val-tRNA(Val)[c] + GTP[c] => ¦Á-Amylase[c] ++ GDP[c] + phosphate[c] + 0.7663 tRNA(Ala)[c] + 0.1825 tRNA(Arg)[c] + 0.4744 tRNA(Asn)[c] + 0.7663 tRNA(Asp)[c] + 0.1642 tRNA(Cys)[c] + 0.2189 tRNA(Glu)[c] + 0.3649 tRNA(Gln)[c] + +0.7846 tRNA(Gly)[c] + 0.1277 tRNA(His)[c] + 0.5109 tRNA(Ile)[c] + 0.6751 tRNA(Leu)[c] + 0.3649 tRNA(Lys)[c] + 0.2007 tRNA(Met)[c] + 0.2737 tRNA(Phe)[c] + +0.4014 tRNA(Pro)[c] + 0.6751 tRNA(Ser)[c] + 0.7298 tRNA(Thr)[c] + 0.2189 tRNA(Trp)[c] + 0.6386 tRNA(Tyr)[c] + 0.5656 tRNA(Val)[c]" 0 0 1000 0.2 Min glucose +¦Á-Amylase ¦Á-Amylase_2 ¦Á-Amylase transport ¦Á-Amylase[c] => ¦Á-Amylase[e] 0 0 1000 +¦Á-Amylase ¦Á-Amylase_3 ¦Á-Amylase exchange ¦Á-Amylase[e] => 1 0 1000 + +Hemoglobin Hemoglobin_1 heme o transport heme o[m] => heme o[c] 0 0 1000 0.25 Min glucose +Hemoglobin Hemoglobin_2 production of globin "1.1532 Ala-tRNA(Ala)[c] + 0.1922 Arg-tRNA(Arg)[c] + 0.3203 Asn-tRNA(Asn)[c] + 0.4805 Asp-tRNA(Asp)[c] + 0.0961 Cys-tRNA(Cys)[c] + 0.3844 Glu-tRNA(Glu)[c] + 0.1281 Gln-tRNA(Gln)[c] + +0.6407 Gly-tRNA(Gly)[c] + 0.6087 His-tRNA(His)[c] + 1.1532 Leu-tRNA(Leu)[c] + 0.7048 Lys-tRNA(Lys)[c] + 0.1602 Met-tRNA(Met)[c] + 0.4805 Phe-tRNA(Phe)[c] + +0.4485 Pro-tRNA(Pro)[c] + 0.5125 Ser-tRNA(Ser)[c] + 0.5125 Thr-tRNA(Thr)[c] + 0.0961 Trp-tRNA(Trp)[c] + 0.1922 Tyr-tRNA(Tyr)[c] + 0.9931 Val-tRNA(Val)[c] + 1.16 GTP[c] => globin[c] ++ 1.16 GDP[c] + 1.16 phosphate[c] + 1.1532 tRNA(Ala)[c] + 0.1922 tRNA(Arg)[c] + 0.3203 tRNA(Asn)[c] + 0.4805 tRNA(Asp)[c] + 0.0961 tRNA(Cys)[c] + 0.3844 tRNA(Glu)[c] + 0.1281 tRNA(Gln)[c] + 0.6407 tRNA(Gly)[c] + 0.6087 tRNA(His)[c] + 1.1532 tRNA(Leu)[c] + 0.7048 tRNA(Lys)[c] + 0.1602 tRNA(Met)[c] + 0.4805 tRNA(Phe)[c] + +0.4485 tRNA(Pro)[c] + 0.5125 tRNA(Ser)[c] + 0.5125 tRNA(Thr)[c] + 0.0961 tRNA(Trp)[c] + 0.1922 tRNA(Tyr)[c] + 0.9931 tRNA(Val)[c]" 0 0 1000 +Hemoglobin Hemoglobin_3 production of hemoglobin globin[c] + 4 heme o[c] => hemoglobin[c] 0 0 1000 +Hemoglobin Hemoglobin_4 hemoglobin transport hemoglobin[c] => hemoglobin[e] 0 0 1000 +Hemoglobin Hemoglobin_5 hemoglobin exchange hemoglobin[e] => 1 0 1000 +Hemoglobin r_0557No1 hydroxymethylbilane synthase (No1) H2O[c] + 4 porphobilinogen[c] => 4 ammonium[c] + preuroporphyrinogen[c] YDL205C 0 0 1000 P28789 0.125 + +Glucagon Glucagon_1 production of glucagon "0.6223 Ala-tRNA(Ala)[c] + 0.7659 Arg-tRNA(Arg)[c] + 0.3829 Asn-tRNA(Asn)[c] + 0.7659 Asp-tRNA(Asp)[c] + 0.6223 Glu-tRNA(Glu)[c] + 0.4787 Gln-tRNA(Gln)[c] + +0.4308 Gly-tRNA(Gly)[c] + 0.1915 His-tRNA(His)[c] + 0.3829 Ile-tRNA(Ile)[c] + 0.5744 Leu-tRNA(Leu)[c] + 0.4787 Lys-tRNA(Lys)[c] + 0.2393 Met-tRNA(Met)[c] + 0.5265 Phe-tRNA(Phe)[c] + +0.1436 Pro-tRNA(Pro)[c] + 0.8137 Ser-tRNA(Ser)[c] + 0.4308 Thr-tRNA(Thr)[c] + 0.1915 Trp-tRNA(Trp)[c] + 0.1915 Tyr-tRNA(Tyr)[c] + 0.3829 Val-tRNA(Val)[c] + 0.36 GTP[c] => glucagon[c] ++ 0.36 GDP[c] + 0.36 phosphate[c] + 0.6223 tRNA(Ala)[c] + 0.7659 tRNA(Arg)[c] + 0.3829 tRNA(Asn)[c] + 0.7659 tRNA(Asp)[c] + 0.6223 tRNA(Glu)[c] + 0.4787 tRNA(Gln)[c] + +0.4308 tRNA(Gly)[c] + 0.1915 tRNA(His)[c] + 0.3829 tRNA(Ile)[c] + 0.5744 tRNA(Leu)[c] + 0.4787 tRNA(Lys)[c] + 0.2393 tRNA(Met)[c] + 0.5265 tRNA(Phe)[c] + +0.1436 tRNA(Pro)[c] + 0.8137 tRNA(Ser)[c] + 0.4308 tRNA(Thr)[c] + 0.1915 tRNA(Trp)[c] + 0.1915 tRNA(Tyr)[c] + 0.3829 tRNA(Val)[c]" 0 0 1000 0.1 YEP glucose +Glucagon Glucagon_2 glucagon transport glucagon[c] => glucagon[e] 0 0 1000 +Glucagon Glucagon_3 glucagon exchange glucagon[e] => 1 0 1000 + +Glycolate Glycolate_1 glycolate transport glycolate[c] => glycolate[e] 0 0 1000 0.1 Min glucose +Glycolate Glycolate_2 glycolate exchange glycolate[e] => 1 0 1000 + +L-phenylacetylcarbinol L-phenylacetylcarbinol_1 benzaldehyde exchange => benzaldehyde[e] 0 0 1 0.13 2 1 YEP glucose +L-phenylacetylcarbinol L-phenylacetylcarbinol_2 benzaldehyde transport benzaldehyde[e] => benzaldehyde[c] 0 0 1000 +L-phenylacetylcarbinol L-phenylacetylcarbinol_3 pyruvate decarboxylase (arm) pyruvate[c] + benzaldehyde[c] => pmet_r_3[c] 0 0 1000 +L-phenylacetylcarbinol L-phenylacetylcarbinol_4 pyruvate decarboxylase (No1) pmet_r_3[c] => L-phenylacetylcarbinol[c] + carbon dioxide[c] YGR087C 0 0 1000 P26263 62 +L-phenylacetylcarbinol L-phenylacetylcarbinol_5 pyruvate decarboxylase (No2) pmet_r_3[c] => L-phenylacetylcarbinol[c] + carbon dioxide[c] YLR044C 0 0 1000 P06169 144.9999 +L-phenylacetylcarbinol L-phenylacetylcarbinol_6 pyruvate decarboxylase (No3) pmet_r_3[c] => L-phenylacetylcarbinol[c] + carbon dioxide[c] YLR134W 0 0 1000 P16467 62 +L-phenylacetylcarbinol L-phenylacetylcarbinol_7 L-PAC transport L-phenylacetylcarbinol[c] => L-phenylacetylcarbinol[e] 0 0 1000 +L-phenylacetylcarbinol L-phenylacetylcarbinol_8 L-PAC exchange L-phenylacetylcarbinol[e] => 1 0 1000 +L-phenylacetylcarbinol L-phenylacetylcarbinol_9 Alcohol dehydrogenase 1 benzaldehyde[c] + NADH[c] => benzylalcohol[c] + NAD[c] YOL086C 0 0 1000 P00330 +L-phenylacetylcarbinol L-phenylacetylcarbinol_10 benzylalcohol transport benzylalcohol[c] => benzylalcohol[e] 0 0 1000 +L-phenylacetylcarbinol L-phenylacetylcarbinol_11 benzylalcohol exchange benzylalcohol[e] => 0 0 1000 +L-phenylacetylcarbinol L-phenylacetylcarbinol_12 Benzaldehyde oxidase benzaldehyde[c] + oxygen[c] => Benzoic Acid[c] 0 0 1000 +L-phenylacetylcarbinol L-phenylacetylcarbinol_13 Benzoic Acid transport Benzoic Acid[c] => Benzoic Acid[e] 0 0 1000 +L-phenylacetylcarbinol L-phenylacetylcarbinol_14 Benzoic Acid exchange Benzoic Acid[e] => 0 0 1000 + +3-hydroxypropanoate-malcoa 3-hydroxypropanoate-malcoa_1 Malonyl-CoA reductase 2 H+[c] + malonyl-CoA[c] + 2 NADPH[c] => coenzyme A[c] + 2 NADP(+)[c] + 3-hydroxypropanoate[c] MCRca 0 0 1000 Q6QQP7 50 300 1.2.1.75 0.1 Min glucose +3-hydroxypropanoate-malcoa 3-hydroxypropanoate-malcoa_2 3-hydroxypropionate transport 3-hydroxypropanoate[c] => 3-hydroxypropanoate[e] 0 0 1000 +3-hydroxypropanoate-malcoa 3-hydroxypropanoate-malcoa_3 3-hydroxypropionate exchange 3-hydroxypropanoate[e] => 1 0 1000 + +3-hydroxypropanoate-asp 3-hydroxypropanoate-asp_1 3-hydroxypropionate dehydrogenase H+[c] + NADPH[c] + 3-oxopropanoate[c] => NADP(+)[c] + 3-hydroxypropanoate[c] fdyG 0 0 1000 P39831 115 27.249 1.1.1.298 0.1 Min glucose +3-hydroxypropanoate-malcoa 3-hydroxypropanoate-asp_2 3-hydroxypropionate transport 3-hydroxypropanoate[c] => 3-hydroxypropanoate[e] 0 0 1000 +4-hydroxypropanoate-asp 3-hydroxypropanoate-asp_3 3-hydroxypropionate exchange 3-hydroxypropanoate[e] => 1 0 1000 +4-hydroxypropanoate-malcoa 3-hydroxypropanoate-asp_4 beta-alanine-pyruvate aminotransferase beta-alanine[c] + pyruvate[c] => L-alanine[c] + 3-oxopropanoate[c] bcere0029_32090 0 0 1000 +5-hydroxypropanoate-asp 3-hydroxypropanoate-asp_5 aspartate 1-decarboxylase H+[c] + L-aspartate[c] => beta-alanine[c] + carbon dioxide[c] A7U8C7 0 0 1000 A7U8C7 7.03 61.24 4.1.1.11 +5-hydroxypropanoate-malcoa r_4572 beta-alanine:2-oxoglutarate aminotransferase 2-oxoglutarate[c] + beta-alanine[c] => L-glutamate[c] + 3-oxopropanoate[c] YGR019Wly 0 0 1000 P17649ly 0.1324 52.946 2.6.1.19 + +FFA FFA_1 FFAs Biosyntheis decanoate[e] + laurate[e] + myristate[e] + palmitate[e] + palmitoleate[e] + stearate[e] + oleate[e] => Free fatty acid[e] 0 0 1000 0.03 Min glucose "YGL205W,YOR317W,YMR246W,YMR110C,YDL078C" +FFA FFA_2 FFAs exchange Free fatty acid[e] => 1 0 1000 +FFA FFA_3 malic enzyme (S)-malate[m] + NAD[m] => carbon dioxide[m] + NADH[m] + pyruvate[m] ME 0 0 1000 1.1.1.38 +FFA FFA_4 ATP:citrate lyase ATP[c] + citrate[c] + coenzyme A[c] => acetyl-CoA[c] + ADP[c] + oxaloacetate[c] + phosphate[c] ACL 0 0 1000 Q91V92 27.1383 120 2.3.3.8 +FFA FFA_5 fatty acid synthase (C16:0) acetyl-CoA[c] + 21 H+[c] + 7 malonyl-CoA[c] + 14 NADPH[c] => 7 carbon dioxide[c] + 7 coenzyme A[c] + 7 H2O[c] + 14 NADP(+)[c] + palmitoyl-CoA[c] "FAS1,FAS2" 0 0 1000 "A0A2Z6EZ44,A0A2Z6EYW1" 4.16 "318.115,137.582" +FFA FFA_6 fatty acid synthase (C18:0) acetyl-CoA[c] + 24 H+[c] + 8 malonyl-CoA[c] + 16 NADPH[c] => 8 carbon dioxide[c] + 8 coenzyme A[c] + 8 H2O[c] + 16 NADP(+)[c] + stearoyl-CoA[c] "FAS1,FAS2" 0 0 1000 "A0A2Z6EZ44,A0A2Z6EYW1" 4.16 "318.115,137.582" +FFA FFA_7 fatty acid synthase (C14:0) acetyl-CoA[c] + 18 H+[c] + 6 malonyl-CoA[c] + 12 NADPH[c] => 6 carbon dioxide[c] + 6 coenzyme A[c] + 6 H2O[c] + 12 NADP(+)[c] + myristoyl-CoA[c] "FAS1,FAS2" 0 0 1000 "A0A2Z6EZ44,A0A2Z6EYW1" 4.16 "318.115,137.582" +FFA FFA_8 fatty acid synthase (C12:0) acetyl-CoA[c] + 15 H+[c] + 5 malonyl-CoA[c] + 10 NADPH[c] => 5 carbon dioxide[c] + 5 coenzyme A[c] + 5 H2O[c] + 10 NADP(+)[c] + lauroyl-CoA[c] "FAS1,FAS2" 0 0 1000 "A0A2Z6EZ44,A0A2Z6EYW1" 4.16 "318.115,137.582" +FFA FFA_9 fatty acid synthase (C10:0) acetyl-CoA[c] + 12 H+[c] + 4 malonyl-CoA[c] + 8 NADPH[c] => 4 carbon dioxide[c] + 4 coenzyme A[c] + 4 H2O[c] + 8 NADP(+)[c] + decanoyl-CoA[c] "FAS1,FAS2" 0 0 1000 "A0A2Z6EZ44,A0A2Z6EYW1" 4.16 "318.115,137.582" +FFA FFA_10 thioesterase (C16:0) palmitoyl-CoA[c] + H2O[c] => coenzyme A[c] + palmitate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 +FFA FFA_11 thioesterase (C18:0) stearoyl-CoA[c] + H2O[c] => coenzyme A[c] + stearate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 +FFA FFA_12 thioesterase (C18:1) oleoyl-CoA[c] + H2O[c] => coenzyme A[c] + oleate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 +FFA FFA_13 thioesterase (C10:0) decanoyl-CoA[c] + H2O[c] => coenzyme A[c] + decanoate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 +FFA FFA_14 thioesterase (C12:0) lauroyl-CoA[c] + H2O[c] => coenzyme A[c] + laurate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 +FFA FFA_15 thioesterase (C14:0) myristoyl-CoA[c] + H2O[c] => coenzyme A[c] + myristate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 +FFA FFA_16 thioesterase (C16:1) palmitoleoyl-CoA(4-)[c] + H2O[c] => coenzyme A[c] + palmitoleate[c] + H+[c] tesA 0 0 1000 P0ADA1 10.13 23.622 3.1.2.2 + +Succinic acid Succinic acid_1 Fumarate hydratase fumarate[c] + H2O[c] => (S)-malate[c] FumC 0 0 1000 A0A024L3D9 1150 50.489 4.2.1.2 0.25 Min glucose "YLR044C,YLR134W,YGR087C,YPL262W,YER065C,YNL117W" +Succinic acid Succinic acid_2 Fumarate hydratase (S)-malate[c] => fumarate[c] + H2O[c] FumC 0 0 1000 A0A024L3D9 11.2 50.489 4.2.1.2 +Succinic acid r_1671_REV 0 0 1 +Succinic acid r_2056 1 0 Inf + +Nicotianamine Nicotianamine_1 "5,10-methylenetetrahydrofolate reductase (NADPH)" "5,10-methylenetetrahydrofolate[c] + 2 H+[c] + NADPH[c] => 5-methyltetrahydrofolate[c] + NADP(+)[c]" MTHFR1 0 0 1000 Q9SE60 0.0353536 66.288 1.5.1.20 0.1 YEP glucose YGL125W +Nicotianamine Nicotianamine_2 "5,10-methylenetetrahydrofolate reductase (NADPH)" "5,10-methylenetetrahydrofolate[c] + 2 H+[c] + NADH[c] => 5-methyltetrahydrofolate[c] + NAD[c]" MTHFR1 0 0 1000 Q9SE60 0.0364584 66.288 1.5.1.20 +Nicotianamine Nicotianamine_3 Nicotianamine synthase 3 S-adenosyl-L-methionine[c] => 3 H+[c] + Nicotianamine[c] + 3 5'-S-methyl-5'-thioadenosine [c] NAS2 0 0 1000 Q9FKT9 35.679 2.5.1.43 +Nicotianamine Nicotianamine_4 nicotianamine transport Nicotianamine[c] => Nicotianamine[e] 0 0 1000 +Nicotianamine Nicotianamine_5 nicotianamine exchaneg Nicotianamine[e] => 1 0 1000 +Nicotianamine r_1810_REV 0 0 1 +Nicotianamine r_1793_REV 0 0 1 +Nicotianamine r_0080No2 0 0 0 + +Psilocybin Psilocybin_1 tryptophan decarboxylase L-tryptophan[c] => tryptamine[c] + carbon dioxide[c] CrTdc 0 0 1000 A0A3S7SKS7 3.33 56.221 4.1.1.105 0.1 Min glucose YBR249C +Psilocybin Psilocybin_2 Tryptamine 4-monooxygenase tryptamine[c] + oxygen[c] => 4-hydroxytryptamine[c] + H2O[c] PcpsiH 0 0 1000 P0DPA7 57.515 1.14.99.59 +Psilocybin Psilocybin_3 4-hydroxytryptamine kinase 4-hydroxytryptamine[c] + ATP[c] => norbaeocystin[c] + ADP[c] + H+[c] PcPsiK 0 0 1000 P0DPA8 40.442 2.7.1.222 +Psilocybin Psilocybin_4 N-methyltransferase norbaeocystin[c] + 2 S-adenosyl-L-methionine[c] => 2 H+[c] + psilocybin[c] + 2 S-adenosyl-L-homocysteine[c] PcPsiM 0 0 1000 P0DPA9 34.434 2.1.1.345 +Psilocybin Psilocybin_5 spontaneous reaction psilocybin[c] => psilocin[c] 0 0 1000 +Psilocybin Psilocybin_6 4-hydroxytryptamine kinase ATP[c] + psilocin[c] => ADP[c] + psilocybin[c] PcPsiK 0 0 1000 P0DPA8 40.442 2.7.1.222 +Psilocybin r_0997No1 shikimate dehydrogenase ATP[c] + shikimate[c] => 3-phosphoshikimic acid[c] + ADP[c] + H+[c] YDR127W 0 0 1000 P08566 120 174.753 +Psilocybin r_0279No1 chorismate synthase (No1) 5-O-(1-carboxyvinyl)-3-phosphoshikimic acid[c] => chorismate[c] + phosphate[c] YGL148W 0 0 1000 P28777 1.74 +Psilocybin Psilocybin_7 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.082809792 39.7487 2.5.1.54 +Psilocybin Psilocybin_8 Psilocybin transport psilocybin[c] => psilocybin[e] 0 0 1000 +Psilocybin Psilocybin_9 Psilocybin exchange psilocybin[e] => 1 0 1000 + +vanillin-¦Â-glucoside vanillin-¦Â-glucoside_1 dehydroshikimate dehydratase "3-dehydroshikimate[c] => 3,4-Dihydroxybenzoate[c] + H2O[c]" 3DSD 0 0 1000 Q86ZM4 125.055 41.685 4.2.1.118 0.3 Min glucose "YMR318C,YLR300W" +vanillin-¦Â-glucoside vanillin-¦Â-glucoside_2 O-methyltransferase "3,4-Dihydroxybenzoate[c] + 5-methyltetrahydrofolate[c] => THF[c] + Vanillate[c]" OMT 0 0 1000 P21964 4.605673333 30.037 2.1.1.341 +vanillin-¦Â-glucoside vanillin-¦Â-glucoside_3 aromatic carboxylic acid reductase "3,4-Dihydroxybenzoate[c] + NADPH[c] + ATP[c] + H+[c] => protocatechuic aldehyde[c] + AMP[c] + diphosphate[c] + NADP(+)[c]" ACAR 0 0 1000 Q6RKB1 4.49211 128.346 1.2.1.30 +vanillin-¦Â-glucoside vanillin-¦Â-glucoside_4 aromatic carboxylic acid reductase Vanillate[c] + NADH[c] + H+[c] => NAD[c] + H2O[c] + vanillin[c] ACAR 0 0 1000 Q6RKB1 4.49211 128.346 1.2.1.30 +vanillin-¦Â-glucoside vanillin-¦Â-glucoside_5 O-methyltransferase protocatechuic aldehyde[c] + 5-methyltetrahydrofolate[c] => THF[c] + vanillin[c] OMT 0 0 1000 P21964 4.605673333 30.037 2.1.1.341 +vanillin-¦Â-glucoside vanillin-¦Â-glucoside_6 UDP-glycosyltransferase UDP-D-glucose[c] + vanillin[c] => UDP[c] + H+[c] + vanillin-¦Â-glucoside[c] UGT 0 0 1000 Q9LVR1 52.992 +vanillin-¦Â-glucoside vanillin-¦Â-glucoside_7 draw_prot_Q86ZM4 vanillin-¦Â-glucoside[c] => vanillin-¦Â-glucoside[e] 0 0 1000 +vanillin-¦Â-glucoside vanillin-¦Â-glucoside_8 draw_prot_P21964 vanillin-¦Â-glucoside[e] => 1 0 1000 + +Betaxanthin Betaxanthin_1 tyrosine hydroxylase "oxygen[c] + 2 L-tyrosine[c] => 2 3,4-Dihydroxy-L-phenylalanine(L-DOPA)[c]" CYP76AD5 0 0 1000 I3PFJ5 56.212 1.14.18.1 0.1 YEP raffinose YBR249C +Betaxanthin Betaxanthin_2 L-Dopa dioxygenase "3,4-Dihydroxy-L-phenylalanine(L-DOPA)[c] + oxygen[c] => 4-(L-Alanin-3-yl)-2-hydroxy-cis,cis-muconate 6-semialdehyde[c] + H+[c]" DOD 0 0 1000 B6F0W8 0.030171 30.171 1.13.11.29 +Betaxanthin Betaxanthin_3 spontaneous reaction "4-(L-Alanin-3-yl)-2-hydroxy-cis,cis-muconate 6-semialdehyde[c] + H+[c] => betalamic acid[c] + H2O[c]" 0 0 1000 +Betaxanthin Betaxanthin_4 spontaneous reaction betalamic acid[c] + L-tyrosine[c] => betaxanthin[c] + H2O[c] 0 0 1000 +Betaxanthin Betaxanthin_5 Betaxanthin transport betaxanthin[c] => betaxanthin[e] 0 0 1000 +Betaxanthin Betaxanthin_6 Betaxanthin exchange betaxanthin[e] => 1 0 1000 +Betaxanthin Betaxanthin_7 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.082809792 39.7487 2.5.1.54 + +Rosmarinic acid Rosmarinic acid_1 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.215305458 39.7487 2.5.1.54 0.1 Min glucose "YBR249C,YPR060C,YDR380W,YLR134W" +Rosmarinic acid Rosmarinic acid_2 chorismate mutase chorismate[c] => prephenate[c] ARO7G141S 0 0 1000 P32178ly 0.1338606 29.7468 5.4.99.5 +Rosmarinic acid Rosmarinic acid_3 shikimate kinase ATP[c] + shikimate[c] => 3-phosphoshikimic acid[c] + ADP[c] + H+[c] aroL 0 0 1000 P0A6E1 31.91833333 19.151 2.7.1.71 +Rosmarinic acid Rosmarinic acid_4 tyrosine ammonia-lyase L-tyrosine[c] => ammonium[c] + p-coumaric acid[c] TAL 0 0 1000 A5FKY3 0.023 56.649 4.3.1.23 +Rosmarinic acid Rosmarinic acid_5 tyrosine transaminase (No1) 3-(4-hydroxyphenyl)pyruvate[c] + L-glutamate[c] => 2-oxoglutarate[c] + L-tyrosine[c] TAT 0 0 1000 Q8GUE9 45.179 2.6.1.5 +Rosmarinic acid Rosmarinic acid_6 tyrosine transaminase (reversible) (No1) 2-oxoglutarate[c] + L-tyrosine[c] => 3-(4-hydroxyphenyl)pyruvate[c] + L-glutamate[c] TAT 0 0 1000 Q8GUE9 45.179 2.6.1.5 +Rosmarinic acid Rosmarinic acid_7 4-hydroxyphenylacetate 3-hydroxylase complex B and C p-coumaric acid[c] => caffeic acid[c] hpaBC 0 0 1000 "Q57160,Q57501" 4.3843 "58.848,18.522" 1.14.14.9 +Rosmarinic acid Rosmarinic acid_8 Hydroxyphenylpyruvate reductase 3-(4-hydroxyphenyl)pyruvate[c] + NADPH[c] + H+[c] => 4-hydroxyphenyllactate[c] + NADP(+)[c] HPPR 0 0 1000 Q65CJ7 2.570976 34.128 1.1.1.237 +Rosmarinic acid Rosmarinic acid_9 4-hydroxyphenylacetate 3-hydroxylase complex B and C "4-hydroxyphenyllactate[c] + oxygen[c] + NADH[c] + H+[c] => NAD[c] + H2O[c] + 3,4-dihydroxyphenyllactate[c]" hpaBC 0 0 1000 "Q57160,Q57501" 4.3843 "58.848,18.522" 1.14.14.9 +Rosmarinic acid Rosmarinic acid_10 4-coumaryl-CoA?ligase trans-4-coumarate[c] + ATP[c] + coenzyme A[c] => AMP[c] + diphosphate[c] + 4-coumaroyl-CoA[c] 4CL1 0 0 1000 Q42524 12.719375 61.053 6.2.1.12 +Rosmarinic acid Rosmarinic acid_11 4-coumaryl-CoA?ligase caffeic acid[c] + ATP[c] + coenzyme A[c] => AMP[c] + diphosphate[c] + caffeoyl-CoA[c] 4CL1 0 0 1000 Q42524 12.719375 61.053 6.2.1.12 +Rosmarinic acid Rosmarinic acid_12 Rosmarinate synthase "3,4-dihydroxyphenyllactate[c] + caffeoyl-CoA[c] => rosmarinate[c] + coenzyme A[c]" RAS 0 0 1000 G0LD36 5.737921667 47.161 2.3.1.140 +Rosmarinic acid Rosmarinic acid_13 Rosmarinate synthase 4-hydroxyphenyllactate[c] + 4-coumaroyl-CoA[c] => 4-coumaroyl-4'-hydroxyphenyllactic acid[c] + coenzyme A[c] RAS 0 0 1000 G0LD36 5.737921667 47.161 2.3.1.140 +Rosmarinic acid Rosmarinic acid_14 hydroxycinnamoyl-hydroxyphenyllactate 3- and 3¡ä-hydroxylases 4-coumaroyl-4'-hydroxyphenyllactic acid[c] + 2 NADH[c] => 2 NAD[c] + 2 H+[c] + rosmarinate[c] CYP98A14 0 0 1000 +Rosmarinic acid Rosmarinic acid_15 Rosmarinate transport rosmarinate[c] => rosmarinate[e] 0 0 1000 +Rosmarinic acid Rosmarinic acid_16 Rosmarinate exchange rosmarinate[e] => 1 0 1000 + +Tyrosol Tyrosol_1 tyrosine decarboxylase L-tyrosine[c] + oxygen[c] + H2O[c] => 4-Hydroxyphenylacetaldehyde[c] + carbon dioxide[c] + Ammonia[c] + hydrogen peroxide[c] AAS 0 0 1000 Q06086 57.45 4.1.1.108 0.1 YEP glucose "YNL316C,YLR044C,YKL211C" +Tyrosol Tyrosol_2 chorismate mutase/prephenate dehydrogenase prephenate[c] + NAD[c] => 3-(4-hydroxyphenyl)pyruvate[c] + carbon dioxide[c] + NADH[c] + H+[c] TyrAM53I/A354V 0 0 1000 P07023 6.628779667 42.043 1.3.1.12 +Tyrosol Tyrosol_3 phosphoketolase D-fructose 6-phosphate[c] + phosphate[c] => acetyl phosphate[c] + D-erythrose 4-phosphate[c] + H2O[c] xfp 0 0 1000 A0A0L0LT01 10.00945833 92.395 4.1.2.22 +Tyrosol Tyrosol_4 alcohol dehydrogenase 4-Hydroxyphenylacetaldehyde[c] + NADH[c] + H+[c] => Tyrosol[c] + NAD[c] ADH 0 0 1000 P0A9Q7 96.127 1.1.1.90 +Tyrosol Tyrosol_5 UDP©\glycosyltransferase Tyrosol[c] + UDP-D-glucose[c] => UDP[c] + Salidroside[c] UGT85A1 0 0 1000 Q9SK82 55.01 2.4.1.- +Tyrosol Tyrosol_6 Tyrosol transport Tyrosol[c] => Tyrosol[e] 0 0 1000 +Tyrosol Tyrosol_7 Tyrosol exchange Tyrosol[e] => 1 0 1000 +Tyrosol Tyrosol_8 Salidroside transport Salidroside[c] => Salidroside[e] 0 0 1000 +Tyrosol Tyrosol_9 Salidroside exchange Salidroside[e] => 0 0 1000 +Tyrosol Tyrosol_10 Ammonia transport Ammonia[c] => Ammonia[e] 0 0 1000 +Tyrosol Tyrosol_11 Ammonia exchange Ammonia[e] => 0 0 1000 +Tyrosol Tyrosol_12 acetyl phosphate transport acetyl phosphate[c] => acetyl phosphate[e] 0 0 1000 +Tyrosol Tyrosol_13 acetyl phosphate exchange acetyl phosphate[e] => 0 0 1000 + +Salidroside Salidroside_1 tyrosine decarboxylase L-tyrosine[c] + oxygen[c] + H2O[c] => 4-Hydroxyphenylacetaldehyde[c] + carbon dioxide[c] + Ammonia[c] + hydrogen peroxide[c] AAS 0 0 1000 Q06086 57.45 4.1.1.108 0.1 YEP glucose "YNL316C,YLR044C,YKL211C" +Salidroside Salidroside_2 chorismate mutase/prephenate dehydrogenase prephenate[c] + NAD[c] => 3-(4-hydroxyphenyl)pyruvate[c] + carbon dioxide[c] + NADH[c] + H+[c] TyrAM53I/A354V 0 0 1000 P07023 6.628779667 42.043 1.3.1.12 +Salidroside Salidroside_3 phosphoketolase D-fructose 6-phosphate[c] + phosphate[c] => acetyl phosphate[c] + D-erythrose 4-phosphate[c] + H2O[c] xfp 0 0 1000 A0A0L0LT01 10.00945833 92.395 4.1.2.22 +Salidroside Salidroside_4 alcohol dehydrogenase 4-Hydroxyphenylacetaldehyde[c] + NADH[c] + H+[c] => Tyrosol[c] + NAD[c] ADH 0 0 1000 P0A9Q7 96.127 1.1.1.90 +Salidroside Salidroside_5 UDP©\glycosyltransferase Tyrosol[c] + UDP-D-glucose[c] => UDP[c] + Salidroside[c] UGT85A1 0 0 1000 Q9SK82 55.01 2.4.1.- +Salidroside Salidroside_6 Tyrosol transport Tyrosol[c] => Tyrosol[e] 0 0 1000 +Salidroside Salidroside_7 Tyrosol exchange Tyrosol[e] => 0 0 1000 +Salidroside Salidroside_8 Salidroside transport Salidroside[c] => Salidroside[e] 0 0 1000 +Salidroside Salidroside_9 Salidroside exchange Salidroside[e] => 1 0 1000 +Salidroside Salidroside_10 Ammonia transport Ammonia[c] => Ammonia[e] 0 0 1000 +Salidroside Salidroside_11 Ammonia exchange Ammonia[e] => 0 0 1000 +Salidroside Salidroside_12 acetyl phosphate transport acetyl phosphate[c] => acetyl phosphate[e] 0 0 1000 +Salidroside Salidroside_13 acetyl phosphate exchange acetyl phosphate[e] => 0 0 1000 + +Miltiradiene r_0373No1 farnesyltranstransferase (No1) farnesyl diphosphate[c] + isopentenyl diphosphate[c] => geranylgeranyl diphosphate[c] + diphosphate[c] YPL069C 0 0 1000 Q12051 6.6 38.6511 2.5.1.29 0.1 YEP glucose +Miltiradiene r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Miltiradiene r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Miltiradiene r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 +Miltiradiene Miltiradiene_1 labdadienyl/copalyl diphosphate synthase geranylgeranyl diphosphate[c] => Copalyl diphosphate[c] CPS 0 0 1000 B8PQ84 90.483 5.5.1.12 +Miltiradiene Miltiradiene_2 kaurene synthase Copalyl diphosphate[c] => diphosphate[c] + Miltiradiene[c] KSL 0 0 1000 C8XPS0 68.37 4.2.3.131 +Miltiradiene Miltiradiene_3 Miltiradiene transport Miltiradiene[c] => Miltiradiene[e] 0 0 1000 +Miltiradiene Miltiradiene_4 Miltiradiene exchange Miltiradiene[e] => 1 0 1000 + +Caffeic acid Caffeic acid_1 coumarate 3-hydroxylase p-coumaric acid[c] => caffeic acid[c] C3H 0 0 1000 O22203 57.927 1.14.13.- 0.1 YEP glucose "YDR380W,YLR134W" +Caffeic acid Caffeic acid_2 tyrosine ammonia-lyase L-tyrosine[c] => ammonium[c] + p-coumaric acid[c] TAL 0 0 1000 A0A1M4NET9 27.7 55.539 4.3.1.23 +Caffeic acid Caffeic acid_3 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase D-erythrose 4-phosphate[c] + H2O[c] + phosphoenolpyruvate[c] => 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid[c] + phosphate[c] ARO4K229L 0 0 1000 P32449ly 0.082809792 39.7487 2.5.1.54 +Caffeic acid Caffeic acid_4 chorismate mutase chorismate[c] => prephenate[c] ARO7G141S 0 0 1000 P32178ly 0.1338606 29.7468 5.4.99.5 +Caffeic acid Caffeic acid_5 caffeic acid transpory caffeic acid[c] => caffeic acid[e] +Caffeic acid Caffeic acid_6 caffeic acid exchange caffeic acid[e] => + +Valencene Valencene_1 valencene synthase farnesyl diphosphate[c] => valencene[c] + diphosphate[c] VS 0 0 1000 S4SC87 0.0032 69.219 4.2.3.73 0.1 YEP glucose "YPL069C,YDR284C,YDR503C" +Valencene Valencene_2 valencene transport valencene[c] => valencene[e] 0 0 1000 +Valencene Valencene_3 valencene exchange valencene[e] => 1 0 1000 +Valencene r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] YLR450W 0 0 1000 P12684 92.5526 115.691 1.1.1.34 +Valencene r_0904No1 phosphomevalonate kinase (No1) (R)-5-phosphomevalonic acid[c] + ATP[c] => (R)-5-diphosphomevalonic acid[c] + ADP[c] YMR220W 0 0 1000 P24521 6.8 50.4544 2.7.4.2 +Valencene r_0103No1 acetyl-CoA C-acetyltransferase (No1) 2 acetyl-CoA[c] => acetoacetyl-CoA[c] + coenzyme A[c] YPL028W 0 0 1000 P41338 1800 41.7282 2.3.1.9 +Valencene r_0104No1 acetyl-CoA C-acetyltransferase (No1) 2 acetyl-CoA[m] => acetoacetyl-CoA[m] + coenzyme A[m] YPL028W 0 0 1000 P41338 1800 41.7282 2.3.1.9 +Valencene r_0103_REVNo1 acetyl-CoA C-acetyltransferase (reversible) (No1) acetoacetyl-CoA[c] + coenzyme A[c] => 2 acetyl-CoA[c] YPL028W 0 0 1000 P41338 10000000 41.7282 2.3.1.9 +Valencene r_0104_REVNo1 acetyl-CoA C-acetyltransferase (reversible) (No1) acetoacetyl-CoA[m] + coenzyme A[m] => 2 acetyl-CoA[m] YPL028W 0 0 1000 P41338 10000000 41.7282 2.3.1.9 +Valencene r_0735No1 mevalonate kinase (atp) (No1) (R)-mevalonate[c] + ATP[c] => (R)-5-phosphomevalonic acid[c] + ADP[c] + H+[c] YMR208W 0 0 1000 P07277 43.8001 48.459 2.7.1.36 +Valencene r_0736No1 mevalonate kinase (ctp) (No1) (R)-mevalonate[c] + CTP[c] => (R)-5-phosphomevalonic acid[c] + CDP[c] + H+[c] YMR208W 0 0 1000 P07277 43.8001 48.459 2.7.1.36 +Valencene r_0737No1 mevalonate kinase (gtp) (No1) (R)-mevalonate[c] + GTP[c] => (R)-5-phosphomevalonic acid[c] + GDP[c] + H+[c] YMR208W 0 0 1000 P07277 43.8001 48.459 2.7.1.36 +Valencene r_0738No1 mevalonate kinase (UTP) (No1) (R)-mevalonate[c] + UTP[c] => (R)-5-phosphomevalonic acid[c] + H+[c] + UDP[c] YMR208W 0 0 1000 P07277 43.8001 48.459 2.7.1.36 +Valencene r_0559No1 hydroxymethylglutaryl CoA synthase (No1) acetoacetyl-CoA[c] + acetyl-CoA[c] + H2O[c] => 3-hydroxy-3-methylglutaryl-CoA[c] + coenzyme A[c] + H+[c] YML126C 0 0 1000 P54839 0.83 55.0128 2.3.3.10 +Valencene r_0560No1 hydroxymethylglutaryl CoA synthase (No1) acetoacetyl-CoA[m] + acetyl-CoA[m] + H2O[m] => 3-hydroxy-3-methylglutaryl-CoA[m] + coenzyme A[m] + H+[m] YML126C 0 0 1000 P54839 0.83 55.0128 2.3.3.10 +Valencene r_0739No1 mevalonate pyrophoshate decarboxylase (No1) (R)-5-diphosphomevalonic acid[c] + ATP[c] => ADP[c] + carbon dioxide[c] + isopentenyl diphosphate[c] + phosphate[c] YNR043W 0 0 1000 P32377 9.8 44.1154 4.1.1.33 +Valencene r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Valencene r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] YJL167W 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Valencene r_0667No1 isopentenyl-diphosphate D-isomerase (No1) isopentenyl diphosphate[c] => prenyl diphosphate(3-)[c] YPL117C 0 0 1000 P15496 59800 33.3511 5.3.3.2 +Valencene r_0667_REVNo1 isopentenyl-diphosphate D-isomerase (reversible) (No1) prenyl diphosphate(3-)[c] => isopentenyl diphosphate[c] YPL117C 0 0 1000 P15496 0.1212 33.3511 5.3.3.2 +Valencene r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] YHR190W 0 0 1000 P29704 0.825 51.7193 2.5.1.21 + +Glycyrrhetinic acid Glycyrrhetinic acid_1 ¦Â-amyrin synthase "(S)-2,3-epoxysqualene[c] => ¦Â-Amyrin[c]" bAS 0 0 1000 Q9MB42 0.77 87.516 5.4.99.39 0.1 YEP glucose +Glycyrrhetinic acid Glycyrrhetinic acid_2 Beta-amyrin 11-oxidase ¦Â-Amyrin[c] + 2 oxygen[c] => 11-Oxo-beta-amyrin[c] + 3 H2O[c] uni25647 0 0 1000 A0A218KSA8 56.456 1.14.14.152 +Glycyrrhetinic acid Glycyrrhetinic acid_3 11-oxo-beta-amyrin 30-oxidase 11-Oxo-beta-amyrin[c] + 3 oxygen[c] => Glycyrrhetinic acid[c] + 4 H2O[c] CYP72A63 0 0 1000 H1A981 59.454 1.14.14.115 +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] => ¦Â-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" ¦Â-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 + +nootkatone nootkatone_1 valencene synthase farnesyl diphosphate[c] => valencene[c] + diphosphate[c] VS 0 0 1000 S4SC87 0.0032 69.219 4.2.3.73 0.1 YEP glucose +nootkatone r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +nootkatone r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +nootkatone r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558 => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] 0 0 1000 P12684 92.5526 115.691 1.1.1.34 +nootkatone r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] 0 0 1000 P29704 0.825 51.7193 2.5.1.21 +nootkatone nootkatone_2 Premnaspirodiene oxygenase valencene[c] + 2 oxygen[c] => 3 H2O[c] + ¦Â-nootkatone[c] HPO 0 0 1000 A6YIH8 15.9 56.788 1.14.14.151 +nootkatone nootkatone_3 Zerumbone synthase ¦Â-nootkatone[c] => (+)-nootkatone[c] ZSD1 0 0 1000 F1SWA0 4.4 28.67 1.1.1.326 +nootkatone nootkatone_4 (+)-nootkatone transport (+)-nootkatone[c] => (+)-nootkatone[e] 0 0 1000 +nootkatone nootkatone_5 (+)-nootkatone exchange (+)-nootkatone[e] => 1 0 1000 +nootkatone r_1710_REV 0 0 1 + +Squalene r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558 => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] 0 0 1000 P12684 92.5526 115.691 1.1.1.34 0.1 YEP ethanol +Squalene r_0355No1 dimethylallyltranstransferase (No1) isopentenyl diphosphate[c] + prenyl diphosphate(3-)[c] => diphosphate[c] + geranyl diphosphate[c] 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Squalene r_0462No1 geranyltranstransferase (No1) geranyl diphosphate[c] + isopentenyl diphosphate[c] => farnesyl diphosphate[c] + diphosphate[c] 0 0 1000 P08524 2.2 40.4829 2.5.1.1 +Squalene r_1012No1 squalene synthase (No1) 2 farnesyl diphosphate[c] + H+[c] + NADPH[c] => 2 diphosphate[c] + NADP(+)[c] + squalene[c] 0 0 1000 P29704 3.3 +Squalene r_0904No1 phosphomevalonate kinase (No1) (R)-5-phosphomevalonic acid[c] + ATP[c] => (R)-5-diphosphomevalonic acid[c] + ADP[c] 0 0 1000 P24521 6.8 50.4544 2.7.4.2 +Squalene r_0103No1 acetyl-CoA C-acetyltransferase (No1) 2 acetyl-CoA[c] => acetoacetyl-CoA[c] + coenzyme A[c] 0 0 1000 P41338 1800 41.7282 2.3.1.9 +Squalene r_0104No1 acetyl-CoA C-acetyltransferase (No1) 2 acetyl-CoA[m] => acetoacetyl-CoA[m] + coenzyme A[m] 0 0 1000 P41338 1800 41.7282 2.3.1.9 +Squalene r_0103_REVNo1 acetyl-CoA C-acetyltransferase (reversible) (No1) acetoacetyl-CoA[c] + coenzyme A[c] => 2 acetyl-CoA[c] 0 0 1000 pP41338 10000000 41.7282 2.3.1.9 +Squalene r_0104_REVNo1 acetyl-CoA C-acetyltransferase (reversible) (No1) acetoacetyl-CoA[m] + coenzyme A[m] => 2 acetyl-CoA[m] 0 0 1000 pP41338 10000000 41.7282 2.3.1.9 +Squalene r_0735No1 mevalonate kinase (atp) (No1) (R)-mevalonate[c] + ATP[c] => (R)-5-phosphomevalonic acid[c] + ADP[c] + H+[c] 0 0 1000 P07277 43.8001 48.459 2.7.1.36 +Squalene r_0736No1 mevalonate kinase (ctp) (No1) (R)-mevalonate[c] + CTP[c] => (R)-5-phosphomevalonic acid[c] + CDP[c] + H+[c] 0 0 1000 P07278 43.8001 48.459 2.7.1.36 +Squalene r_0737No1 mevalonate kinase (gtp) (No1) (R)-mevalonate[c] + GTP[c] => (R)-5-phosphomevalonic acid[c] + GDP[c] + H+[c] 0 0 1000 P07279 43.8001 48.459 2.7.1.36 +Squalene r_0738No1 mevalonate kinase (UTP) (No1) (R)-mevalonate[c] + UTP[c] => (R)-5-phosphomevalonic acid[c] + H+[c] + UDP[c] 0 0 1000 P07280 43.8001 48.459 2.7.1.36 +Squalene r_0559No1 hydroxymethylglutaryl CoA synthase (No1) acetoacetyl-CoA[c] + acetyl-CoA[c] + H2O[c] => 3-hydroxy-3-methylglutaryl-CoA[c] + coenzyme A[c] + H+[c] 0 0 1000 P54839 0.83 55.0128 2.3.3.10 +Squalene r_0560No1 hydroxymethylglutaryl CoA synthase (No1) acetoacetyl-CoA[m] + acetyl-CoA[m] + H2O[m] => 3-hydroxy-3-methylglutaryl-CoA[m] + coenzyme A[m] + H+[m] 0 0 1000 P54839 0.83 55.0128 2.3.3.10 +Squalene 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 P32377 9.8 44.1154 4.1.1.33 +Squalene Squalene_1 3-hydroxy-3-methylglutaryl coenzyme A reductase 3-hydroxy-3-methylglutaryl-CoA[c] + 2 NADH[c] + 2 H+[c] => (R)-mevalonate[c] + coenzyme A[c] + 2 NAD[c] mvaA 0 0 1000 Q5LL64 NA 45.41 1.1.1.88 +Squalene r_0163No1 alcohol dehydrogenase (ethanol to acetaldehyde) (No1) ethanol[c] + NAD[c] => acetaldehyde[c] + H+[c] + NADH[c] 0 0 1000 P00331 286 +Squalene Squalene_2 Acetaldehyde dehydrogenase acetaldehyde[c] + NAD[c] + coenzyme A[c] => acetoacetyl-CoA[c] + H+[c] + NADH[c] ADA 0 0 1000 A0A0A8FFU5 NA 33.168 1.2.1.10 +Squalene Squalene_3 Squalene transport squalene[c] => Squalene[e] 0 0 1000 +Squalene Squalene_4 Squalene exchange Squalene[e] => 1 0 1000 + +Tropane alkaloids (cinnamoyltropine) r_0817No1 ornithine decarboxylase (No1) H+[c] + ornithine[c] => carbon dioxide[c] + putrescine[c] 0 0 1000 P08432 8.4 52.2847 4.1.1.17 0.1 YEP glucose "YMR170C,YMR169C,YOR374W,YER073W,YMR110C,YLR017W" +Tropane alkaloids (cinnamoyltropine) r_0206No1 arginase (No1) H2O[c] + L-arginine[c] => ornithine[c] + urea[c] 0 0 1000 P00812 0.54 35.6616 3.5.3.1 +Tropane alkaloids (cinnamoyltropine) r_0761No1 N-acteylglutamate synthase (No1) pmet_r_0761 => coenzyme A[m] + H+[m] + N-acetyl-L-glutamate[m] 0 0 1000 P40360 0.44 65.6095 2.3.1.1 +Tropane alkaloids (cinnamoyltropine) r_0761_REVNo1 N-acteylglutamate synthase (reversible) (No1) pmet_r_0761_REV => acetyl-CoA[m] + L-glutamate[m] 0 0 1000 P40360 1.56 65.6095 2.3.1.1 +Tropane alkaloids (cinnamoyltropine) r_0929No1 polyamine oxidase (No1) H2O[c] + N(1)-acetylspermidine[c] + oxygen[c] => 3-aminopropanal[c] + hydrogen peroxide[c] + N-acetylputrescine[c] 0 0 1000 P50264 78 57.8051 1.5.3.17 +Tropane alkaloids (cinnamoyltropine) r_0936No1 poylamine oxidase (No1) H2O[c] + N(1)-acetylspermine[c] + oxygen[c] => 3-aminopropanal[c] + hydrogen peroxide[c] + N(1)-acetylspermidine[c] 0 0 1000 P50264 78 57.8051 1.5.3.17 +Tropane alkaloids (cinnamoyltropine) r_0937No1 poylamine oxidase (No1) H2O[c] + oxygen[c] + spermine[c] => 3-aminopropanal[c] + hydrogen peroxide[c] + spermidine[c] 0 0 1000 P50264 78 57.8051 1.5.3.17 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_1 Arginine decarboxylase L-arginine[c] + H+[c] => Agmatine[c] + carbon dioxide[c] ADC 0 0 1000 P22220 9.9 66.706 4.1.1.19 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_2 Agmatinase Agmatine[c] + H2O[c] => putrescine[c] + urea[c] speB 0 0 1000 P60651 NA 33.557 3.5.3.11 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_3 Putrescine N-methyltransferase putrescine[c] + S-adenosyl-L-methionine[c] => S-adenosyl-L-homocysteine[c] + N-Methylputrescine[c] AtPMT1 + DsPMT1 0 0 1000 Q9S7W8 + Q70EW6 NA + 5.14 36.976 + 37.727 2.1.1.53 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_4 Putative N-methyltransferase oxidase N-Methylputrescine[c] + oxygen[c] + H2O[c] => hydrogen peroxide[c] + Ammonia[c] + 4-Methylaminobutanal[c] MPO1 0 0 1000 Psmolke NA NA 1.4.3.21 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_5 Spontaneous reaction 4-Methylaminobutanal[c] => 1-Methylpyrrolinium[c] + H2O[c] 0 0 1000 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_6 Pyrrolidine ketide synthase 1-Methylpyrrolinium[c] => 4-(1-methyl-2-pyrrodinyl)-3-oxobutanoic acid[c] PYKS 0 0 1000 A0A3G4RHW3 NA 43.267 2.3.1.74 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_7 Tropinone synthase 4-(1-methyl-2-pyrrodinyl)-3-oxobutanoic acid[c] => Tropinone[c] CYP82M3 0 0 1000 A0A3G4RHY7 NA 59.479 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_8 Tropinone reductase I Tropinone[c] + NADPH[c] + H+[c] => Tropine[c] + NADP(+)[c] TR1 0 0 1000 P50162 25.6 29.617 1.1.1.206 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_9 Phenylalanine ammonia-lyase L-phenylalanine[c] => ammonium[c] + cinnamate[c] PAL1 0 0 1000 P35510 1.8 78.726 4.3.1.24 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_10 4-coumarate:CoA ligase cinnamate[c] + ATP[c] + coenzyme A[c] => diphosphate[c] + AMP[c] + Cinnamoyl-CoA[c] 4CL5 0 0 1000 Q9LU36 5.880546 62.559 6.2.1.12 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_11 Cocaine synthase Tropine[c] + Cinnamoyl-CoA[c] => cinnamoyltropine[c] CS 0 0 1000 A0A059Q4T4 NA 48.753 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_12 cinnamoyltropine trasport cinnamoyltropine[c] => cinnamoyltropine[e] 0 0 1000 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_13 cinnamoyltropine exchange cinnamoyltropine[e] => 1 0 1000 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_14 Ammonia transport Ammonia[c] => Ammonia[e] 0 0 1000 +Tropane alkaloids (cinnamoyltropine) cinnamoyltropine_15 Ammonia exchange Ammonia[e] => 0 0 1000 + +L-(+)-Ergothioneine Ergothioneine_1 Ergothioneine biosynthesis protein L-histidine[c] + 3 S-adenosyl-L-methionine[c] => 3 H+[c] + hercynine[c] + 3 S-adenosyl-L-homocysteine[c] Egt1 0 0 1000 Q7RX33 0.071628083 99.025 2.1.1.44 0.1 Min glucose +L-(+)-Ergothioneine Ergothioneine_2 Ergothioneine biosynthesis protein hercynine[c] + L-cysteine[c] + oxygen[c] => H2O[c] + S-(hercyn-2-yl)-L-cysteine S-oxide[c] Egt1 0 0 1000 Q7RX33 0.071628083 99.025 1.4.99.51 +L-(+)-Ergothioneine Ergothioneine_3 ¦Â-lyase S-(hercyn-2-yl)-L-cysteine S-oxide[c] => ergothioneine[c] + pyruvate[c] + Ammonia[c] Egt2 0 0 1000 A0R5M7 NA 39.033 4.4.1.36 +L-(+)-Ergothioneine Ergothioneine_4 Ergothioneine transport ergothioneine[c] => ergothioneine[e] 0 0 1000 +L-(+)-Ergothioneine Ergothioneine_5 Ergothioneine exchange ergothioneine[e] => 1 0 1000 +L-(+)-Ergothioneine Ergothioneine_6 Ammonia transport Ammonia[c] => Ammonia[e] 0 0 1000 +L-(+)-Ergothioneine Ergothioneine_7 Ammonia exchange Ammonia[e] => 0 0 1000 +L-(+)-Ergothioneine r_1879_REV 0 0 1 +L-(+)-Ergothioneine r_1893_REV 0 0 1 +L-(+)-Ergothioneine r_1902_REV 0 0 1 +L-(+)-Ergothioneine r_2028_REV 0 0 1 + +S-adenosyl-L-methionine r_0726No1 methionine adenosyltransferase (No1) pmet_r_0726 => diphosphate[c] + phosphate[c] + S-adenosyl-L-methionine[c] 0 0 1 P19358 1.7660e-04 (Kcat*2) 42.2555 2.5.1.6 0.159 YEP glucose YOL052C +S-adenosyl-L-methionine S-adenosyl-L-methionine_1 S-adenosyl-L-methionine transport S-adenosyl-L-methionine[c] => S-adenosyl-L-methionine[e] 0 0 1 +S-adenosyl-L-methionine r_2043 1 0 Inf + +2'-Fucosyllactose 2'-Fucosyllactose_1 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 0.1 YEP xylose + lactose "YDL236W,YPL061W" +2'-Fucosyllactose 2'-Fucosyllactose_2 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 +2'-Fucosyllactose 2'-Fucosyllactose_3 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 +2'-Fucosyllactose 2'-Fucosyllactose_4 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 +2'-Fucosyllactose 2'-Fucosyllactose_5 "GDP-mannose 4,6-dehydratase" GDP-alpha-D-mannose[c] => H2O[c] + GDP-4-dehydro-6-deoxy-D-mannose[c] Gmd 0 0 1000 O85339 5 41.674 4.2.1.47 +2'-Fucosyllactose 2'-Fucosyllactose_6 GDP-L-fucose synthase GDP-4-dehydro-6-deoxy-D-mannose[c] + NADPH[c] + H+[c] => NADP(+)[c] + GDP-L-fucose[c] WcaG 0 0 1000 P32055 1.5 36.141 1.1.1.271 +2'-Fucosyllactose 2'-Fucosyllactose_7 fucosyltransferase GDP-L-fucose[c] + lactose[c] => GDP[c] + 2'-fucosyllactose[c] WbgL 0 0 1000 A6M9C2 3.96 34.942 +2'-Fucosyllactose 2'-Fucosyllactose_8 2¡ä-Fucosyllactose transport 2'-fucosyllactose[c] => 2'-fucosyllactose[e] 0 0 1000 +2'-Fucosyllactose 2'-Fucosyllactose_9 3¡ä-Fucosyllactose exchange 2'-fucosyllactose[e] => 1 0 1000 +2'-Fucosyllactose 2'-Fucosyllactose_10 lactose exchange => lactose[e] 0 0 1 +2'-Fucosyllactose 2'-Fucosyllactose_11 lactose transport lactose[e] => lactose[c] Lac12 0 0 1000 P07921 65.383 + +lycopene r_0558No1 hydroxymethylglutaryl CoA reductase (No1) pmet_r_0558 => (R)-mevalonate[c] + coenzyme A[c] + 2 NADP(+)[c] P12684 92.5526 115.691 1.1.1.34 0.1 YEP glucose "YBR020W,YBR018C,YBR019C,YLR300W" +lycopene lycopene_1 geranylgeranyl diphosphate synthase farnesyl diphosphate[c] + isopentenyl diphosphate[c] => diphosphate[c] + geranylgeranyl diphosphate[c] crtE Q9ZPM3 3.3 42.572 2.5.1.29 +lycopene lycopene_2 Bifunctional lycopene cyclase/phytoene synthase 2 geranylgeranyl diphosphate[c] => 2 diphosphate[c] + phytoene[c] crtB D5KXJ0 NA 32.786 2.5.1.32 +lycopene lycopene_3 Phytoene desaturase phytoene[c] => neurosporene[c] crtI Q5BTY7 NA 66.46 1.3.99.28 +lycopene lycopene_4 Phytoene desaturase neurosporene[c] + oxygen[c] => 2 H2O[c] + lycopene[c] crtI Q5BTY7 NA 66.46 1.3.99.28 +lycopene r_0163No1 alcohol dehydrogenase (ethanol to acetaldehyde) (No1) ethanol[c] + NAD[c] => acetaldehyde[c] + H+[c] + NADH[c] P00331 286 +lycopene r_0173No1 "aldehyde dehydrogenase (acetaldehyde, NADP) (No1)" acetaldehyde[c] + H2O[c] + NADP(+)[c] => acetate[c] + 2 H+[c] + NADPH[c] P54115 43.9999 54.4134 +lycopene r_0177No1 "aldehyde dehydrogenase (indole-3-acetaldehyde, NADP) (No1)" H2O[c] + indol-3-ylacetaldehyde[c] + NADP(+)[c] => 2 H+[c] + indole-3-acetate[c] + NADPH[c] P54115 43.9999 54.4134 +lycopene lycopene_5 acetyl-CoA synthetase acetate[c] + ATP[c] + coenzyme A[c] => acetyl-CoA[c] + AMP[c] + diphosphate[c] ACS Q8ZKF6 9400 72.153 6.2.1.1 +lycopene r_0766No3 NAD kinase (No3) pmet_r_0766 => ADP[m] + H+[m] + NADP(+)[m] Q06892 1.68 46.2464 +lycopene r_0772No3 NADH kinase mitochondrial (No3) pmet_r_0772 => ADP[m] + H+[m] + NADPH[m] Q06892 32.2 46.2464 +lycopene r_2344No1 "PA phosphatase (1-16:0, 2-16:1), ER membrane (No1)" "H2O[er membrane] + phosphatidate (1-16:0, 2-16:1)[er membrane]=> phosphate[er membrane] + diglyceride (1-16:0, 2-16:1)[er membrane] " P32567 23.1467 95.03 +lycopene r_2345No1 "PA phosphatase (1-16:0, 2-18:1), ER membrane (No1)" "H2O[er membrane] + phosphatidate (1-16:0, 2-18:1)[er membrane] => phosphate[er membrane] + diglyceride (1-16:0, 2-18:1)[er membrane] " P32567 23.1467 95.03 +lycopene r_2346No1 "PA phosphatase (1-16:1, 2-16:1), ER membrane (No1)" "H2O[er membrane] + phosphatidate (1-16:1, 2-16:1)[er membrane] => phosphate[er membrane] + diglyceride (1-16:1, 2-16:1)[er membrane] " P32567 23.1467 95.03 +lycopene r_2347No1 "PA phosphatase (1-16:1, 2-18:1), ER membrane (No1)" "H2O[er membrane] + phosphatidate (1-16:1, 2-18:1)[er membrane] => phosphate[er membrane] + diglyceride (1-16:1, 2-18:1)[er membrane] " P32567 23.1467 95.03 +lycopene r_2348No1 "PA phosphatase (1-18:0, 2-16:1), ER membrane (No1)" "H2O[er membrane] + phosphatidate (1-18:0, 2-16:1)[er membrane] => phosphate[er membrane] + diglyceride (1-18:0, 2-16:1)[er membrane] " P32567 23.1467 95.03 +lycopene r_2349No1 "PA phosphatase (1-18:0, 2-18:1), ER membrane (No1)" "H2O[er membrane] + phosphatidate (1-18:0, 2-18:1)[er membrane] => phosphate[er membrane] + diglyceride (1-18:0, 2-18:1)[er membrane] " P32567 23.1467 95.03 +lycopene r_2350No1 "PA phosphatase (1-18:1, 2-16:1), ER membrane (No1)" "H2O[er membrane] + phosphatidate (1-18:1, 2-16:1)[er membrane] => phosphate[er membrane] + diglyceride (1-18:1, 2-16:1)[er membrane] " P32567 23.1467 95.03 +lycopene r_2351No1 "PA phosphatase (1-18:1, 2-18:1), ER membrane (No1)" "H2O[er membrane] + phosphatidate (1-18:1, 2-18:1)[er membrane] => phosphate[er membrane] + diglyceride (1-18:1, 2-18:1)[er membrane] " P32567 23.1467 95.03 +lycopene r_0109No1 "acetyl-CoA carboxylase, reaction (No1)" acetyl-CoA[c] + ATP[c] + bicarbonate[c] => ADP[c] + H+[c] + malonyl-CoA[c] + phosphate[c] Q00955 65.3426 +lycopene r_2182No1 "palmitoyl-CoA desaturase (n-C16:0CoA -> n-C16:1CoA), ER membrane (No1)" H+[er membrane] + palmitoyl-CoA[er membrane] + oxygen[er membrane] + NADH[er membrane] => 2 H2O[er membrane] + palmitoleoyl-CoA(4-)[er membrane] + NAD[er membrane] P21147 1 58.4023 +lycopene r_2183No1 "stearoyl-CoA desaturase (n-C18:0CoA -> n-C18:1CoA), ER membrane (No1)" H+[er membrane] + stearoyl-CoA[er membrane] + oxygen[er membrane] + NADH[er membrane] => 2 H2O[er membrane] + NAD[er membrane] + oleoyl-CoA[er membrane] P21147 0.7 58.4023 +lycopene lycopene_6 lycopene transport lycopene[c] => lycopene[e] +lycopene lycopene_7 lycopene exchange lycopene[e] => + +Ergosterol 0.1 Min glucose +Glycine 0.1 Min glucose +Alanine 0.1 Min glucose +Arginine 0.1 Min glucose +Asparagine 0.1 Min glucose +Aspartate 0.1 Min glucose +Cysteine 0.1 Min glucose +Glutamate 0.1 Min glucose +Glutamine 0.1 Min glucose +Histidine 0.1 Min glucose +Isoleucine 0.1 Min glucose +Leucine 0.1 Min 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a/strain_design_ecYeast/Model_construction_others.asv +++ b/strain_design_ecYeast/Model_construction_others.asv @@ -1322,8 +1322,8 @@ Kcat20=0.5377; Kcat21=0.5559; model = addReaction(model,'newRxn2','metaboliteList',{'s_4285','s_4286'},'stoichCoeffList',[-1 1],'reversible',false); model = addReaction(model,'newRxn3','metaboliteList',{'s_4286'},'stoichCoeffList',[-1],'reversible',false); -model = addReaction(model,'newRxn1','metaboliteList',{'s_0955','s_0965','s_0969','s_0973','s_0981','s_0991','s_0999','s_1003','s_1006','s_1016','s_1021','s_1025',... - 's_1029','s_1032','s_1035','s_1039','s_1045','s_1048','s_1051','s_1056','s_0785','s_4285','s_0739','s_1322'},'stoichCoeffList',[-Kcat2 -Kcat3 -Kcat4 -Kcat5 -Kcat6... +model = addReaction(model,'newRxn1','metaboliteList',{'s_0404','s_0428','s_0430','s_0432','s_0542','s_0748','s_0747','s_0757','s_0832','s_0847','s_1077',... + 's_1099','s_1148','s_1314','s_1379','s_1428','s_1491','s_1527','s_1533','s_1561','s_0785','s_4285','s_0739','s_1322','+ 0.6516 s_1582 + 0.2643 s_1583 + 0.5013 s_1585 + 0.4921 s_1587 + 0.0547 s_1589 + 0.4375 s_1591 + 0.2552 s_1590 + 0.9114 s_1593 + 0.1276 s_1594 + 0.4466 s_1596 + 0.8567 s_1598 + 0.4192 s_1600 + 0.0638 s_1602 + 0.3645 s_1604 + 0.4921 s_1606 + 0.8567 s_1607 + 0.7109 s_1608 + 0.1823 s_1610 + 0.5377 s_1612 + 0.5559 s_1614'},'stoichCoeffList',[-Kcat2 -Kcat3 -Kcat4 -Kcat5 -Kcat6... -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -Kcat20 -Kcat21 -2.01 1 2.01 2.01],'reversible',false); model.metComps(4147)=1; model.metComps(4148)=3; @@ -2166,9 +2166,11 @@ Kcat17=0.4176; Kcat18=0.0288; Kcat19=0.2736; Kcat20=0.6192; -model = addReaction(model,'newRxn1','metaboliteList',{'s_0955','s_0965','s_0969','s_0973','s_0981','s_0991','s_0999','s_1003','s_1006','s_1016','s_1021','s_1025',... - 's_1029','s_1032','s_1035','s_1039','s_1045','s_1048','s_1051','s_1056','s_0785','s_4353','s_0739','s_1322'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... - -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -Kcat20 -1.22 1 1.22 1.22],'reversible',false); +model = addReaction(model,'newRxn1','metaboliteList',{'s_0404','s_0428','s_0430','s_0432','s_0542','s_0748','s_0747','s_0757','s_0832','s_0847','s_1077','s_1099',... + 's_1148','s_1314','s_1379','s_1428','s_1491','s_1527','s_1533','s_1561','s_0785','s_4353','s_0739','s_1322','s_1582','s_1583','s_1585','s_1587','s_1589','s_1591',... + 's_1590','s_1593','s_1594','s_1596','s_1598','s_1600','s_1602','s_1604','s_1606','s_1607','s_1608','s_1610','s_1612','s_1614'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... + -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -Kcat20 -1.22 1 1.22 1.22 Kcat1 Kcat2 Kcat3 Kcat4 Kcat5... + Kcat6 Kcat7 Kcat8 Kcat9 Kcat10 Kcat11 Kcat12 Kcat13 Kcat14 Kcat15 Kcat16 Kcat17 Kcat18 Kcat19 Kcat20],'reversible',false); model = addReaction(model,'newRxn2','metaboliteList',{'s_4353','s_4354'},'stoichCoeffList',[-1 1],'reversible',false); model = addReaction(model,'newRxn3','metaboliteList',{'s_4354'},'stoichCoeffList',[-1],'reversible',false); model.metComps(4147)=1; @@ -2205,9 +2207,11 @@ Kcat17=0.7298; Kcat18=0.2189; Kcat19=0.6386; Kcat20=0.5656; -model = addReaction(model,'newRxn1','metaboliteList',{'s_0955','s_0965','s_0969','s_0973','s_0981','s_0991','s_0999','s_1003','s_1006','s_1016','s_1021','s_1025',... - 's_1029','s_1032','s_1035','s_1039','s_1045','s_1048','s_1051','s_1056','s_0785','s_4287','s_0739','s_1322'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... - -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -Kcat20 -1 1 1 1],'reversible',false); +model = addReaction(model,'newRxn1','metaboliteList',{'s_0404','s_0428','s_0430','s_0432','s_0542','s_0748','s_0747','s_0757','s_0832','s_0847','s_1077','s_1099',... + 's_1148','s_1314','s_1379','s_1428','s_1491','s_1527','s_1533','s_1561','s_0785','s_4287','s_0739','s_1322','s_1582','s_1583','s_1585','s_1587','s_1589','s_1591',... + 's_1590','s_1593','s_1594','s_1596','s_1598','s_1600','s_1602','s_1604','s_1606','s_1607','s_1608','s_1610','s_1612','s_1614'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... + -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -Kcat20 -1 1 1 1 Kcat1 Kcat2 Kcat3 Kcat4 Kcat5... + Kcat6 Kcat7 Kcat8 Kcat9 Kcat10 Kcat11 Kcat12 Kcat13 Kcat14 Kcat15 Kcat16 Kcat17 Kcat18 Kcat19 Kcat20],'reversible',false); model = addReaction(model,'newRxn2','metaboliteList',{'s_4287','s_4355'},'stoichCoeffList',[-1 1],'reversible',false); model = addReaction(model,'newRxn3','metaboliteList',{'s_4355'},'stoichCoeffList',[-1],'reversible',false); model.metComps(4147)=1; @@ -2244,9 +2248,11 @@ Kcat18=0.1922; Kcat19=0.9931; Kcat20=0.125*3600; model = addReaction(model,'newRxn1','metaboliteList',{'s_0812','s_4356'},'stoichCoeffList',[-1 1],'reversible',false); -model = addReaction(model,'newRxn2','metaboliteList',{'s_0955','s_0965','s_0969','s_0973','s_0981','s_0991','s_0999','s_1003','s_1006','s_1021','s_1025',... - 's_1029','s_1032','s_1035','s_1039','s_1045','s_1048','s_1051','s_1056','s_0785','s_4357','s_0739','s_1322'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... - -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -1.16 1 1.16 1.16],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0404','s_0428','s_0430','s_0432','s_0542','s_0748','s_0747','s_0757','s_0832','s_1077','s_1099',... + 's_1148','s_1314','s_1379','s_1428','s_1491','s_1527','s_1533','s_1561','s_0785','s_4357','s_0739','s_1322','s_1582','s_1583','s_1585','s_1587','s_1589',... + 's_1591','s_1590','s_1593','s_1594','s_1598','s_1600','s_1602','s_1604','s_1606','s_1607','s_1608','s_1610','s_1612','s_1614'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... + -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -1.16 1 1.16 1.16 Kcat1 Kcat2 Kcat3 Kcat4 Kcat5... + Kcat6 Kcat7 Kcat8 Kcat9 Kcat10 Kcat11 Kcat12 Kcat13 Kcat14 Kcat15 Kcat16 Kcat17 Kcat18 Kcat19],'reversible',false); model = addReaction(model,'newRxn3','metaboliteList',{'s_4357','s_4356','s_4358'},'stoichCoeffList',[-1 -4 1],'reversible',false); model = addReaction(model,'newRxn4','metaboliteList',{'s_4358','s_4359'},'stoichCoeffList',[-1 1],'reversible',false); model = addReaction(model,'newRxn5','metaboliteList',{'s_4359'},'stoichCoeffList',[-1],'reversible',false); @@ -2285,9 +2291,11 @@ Kcat16=0.4308; Kcat17=0.1915; Kcat18=0.1915; Kcat19=0.3829; -model = addReaction(model,'newRxn1','metaboliteList',{'s_0955','s_0965','s_0969','s_0973','s_0991','s_0999','s_1003','s_1006','s_1016','s_1021','s_1025',... - 's_1029','s_1032','s_1035','s_1039','s_1045','s_1048','s_1051','s_1056','s_0785','s_4360','s_0739','s_1322'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... - -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -0.36 1 0.36 0.36],'reversible',false); +model = addReaction(model,'newRxn1','metaboliteList',{'s_0404','s_0428','s_0430','s_0432','s_0748','s_0747','s_0757','s_0832','s_0847','s_1077','s_1099',... + 's_1148','s_1314','s_1379','s_1428','s_1491','s_1527','s_1533','s_1561','s_0785','s_4360','s_0739','s_1322','s_1582','s_1583','s_1585','s_1587','s_1591',... + 's_1590','s_1593','s_1594','s_1596','s_1598','s_1600','s_1602','s_1604','s_1606','s_1607','s_1608','s_1610','s_1612','s_1614'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... + -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -0.36 1 0.36 0.36 Kcat1 Kcat2 Kcat3 Kcat4 Kcat5... + Kcat6 Kcat7 Kcat8 Kcat9 Kcat10 Kcat11 Kcat12 Kcat13 Kcat14 Kcat15 Kcat16 Kcat17 Kcat18 Kcat19],'reversible',false); model = addReaction(model,'newRxn2','metaboliteList',{'s_4360','s_4361'},'stoichCoeffList',[-1 1],'reversible',false); model = addReaction(model,'newRxn3','metaboliteList',{'s_4361'},'stoichCoeffList',[-1],'reversible',false); model.metComps(4147)=1; @@ -2542,18 +2550,128 @@ model = removeGenes(model,'YBR249C'); model=changeGeneAssociation(model,'newRxn1','CYP76AD5'); model=changeGeneAssociation(model,'newRxn2','DOD'); model=changeGeneAssociation(model,'newRxn7','ARO4K229L'); -model.geneShortNames(1126)={'3DSD'}; -model.geneShortNames(1127)={'OMT'}; -model.geneShortNames(1128)={'ACAR'}; -model.geneShortNames(1129)={'UGT'}; -model.enzymes(964)={'Q86ZM4'}; -model.enzymes(965)={'P21964'}; -model.enzymes(966)={'Q6RKB1'}; -model.enzymes(967)={'Q9LVR1'}; -model.enzGenes(964)={'3DSD'}; -model.enzGenes(965)={'OMT'}; -model.enzGenes(966)={'ACAR'}; -model.enzGenes(967)={'UGT'}; +model.geneShortNames(1127)={'CYP76AD5'}; +model.geneShortNames(1128)={'DOD'}; +model.geneShortNames(1129)={'ARO4K229L'}; +model.enzymes(964)={'I3PFJ5'}; +model.enzymes(965)={'B6F0W8'}; +model.enzymes(966)={'P32449ly'}; +model.enzGenes(964)={'CYP76AD5'}; +model.enzGenes(965)={'DOD'}; +model.enzGenes(966)={'ARO4K229L'}; +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(4154)=1; +cd ../../strain_design_ecYeast +c_sourceID = 'raffinose exchange (reversible)'; +model = lychangeMedia_batch(model,c_sourceID,'YEP'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn6'); +FBAsolution=optimizeCbModel(model) +cd ../result_ecYeast/ecModels +save ecBetaxanthin.mat model + +% Rosmarinic acid +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.2153*3600; +MW1=39.7487; +Kcat2=0.1339*3600; +MW2=29.7468; +Kcat3=31.9183*3600; +MW3=19.151; +Kcat4=0.023*3600; +MW4=56.649; +MW5=45.179; +Kcat6=4.3843*3600; +MW61=58.848; +MW62=18.522; +Kcat7=2.571*3600; +MW7=34.128; +Kcat8=12.7194*3600; +MW8=61.053; +Kcat9=5.7379*3600; +MW9=47.161; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0551','s_0803','s_1360','prot_P32449ly','s_0349','s_1322'},'stoichCoeffList',[-1 -1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0515','prot_P32178ly','s_1377'},'stoichCoeffList',[-1 -1/Kcat2 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_1429','s_0434','prot_P0A6E1','s_0261','s_0794','s_0394'},'stoichCoeffList',[-1 -1 -1/Kcat3 1 1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_1051','prot_A5FKY3','s_0419','s_4231'},'stoichCoeffList',[-1 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_0204','s_0991','prot_Q8GUE9','s_0180','s_1051'},'stoichCoeffList',[-1 -1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_0180','s_1051','prot_Q8GUE9','s_0204','s_0991'},'stoichCoeffList',[-1 -1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'s_4231','prot_Q57160','prot_Q57501','s_4387'},'stoichCoeffList',[-1 -1/Kcat6 -1/Kcat6 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'s_0204','s_1212','s_0794','prot_Q65CJ7','s_4388','s_1207'},'stoichCoeffList',[-1 -1 -1 -1/Kcat7 1 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_4388','s_1275','s_1203','s_0794','prot_Q57160','prot_Q57501','s_1198','s_0803','s_4389'},'stoichCoeffList',[-1 -1 -1 -1 -1/Kcat6 -1/Kcat6 1 1 1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'s_4215','s_0434','s_0529','prot_Q42524','s_0423','s_0633','s_4216'},'stoichCoeffList',[-1 -1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'s_4387','s_0434','s_0529','prot_Q42524','s_0423','s_0633','s_4390'},'stoichCoeffList',[-1 -1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'newRxn12','metaboliteList',{'s_4389','s_4390','prot_G0LD36','s_4391','s_0529'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1],'reversible',false); +model = addReaction(model,'newRxn13','metaboliteList',{'s_4388','s_4216','prot_G0LD36','s_4392','s_0529'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1],'reversible',false); +model = addReaction(model,'newRxn14','metaboliteList',{'s_4392','s_1203','s_1198','s_0794','s_4391'},'stoichCoeffList',[-1 -2 2 2 1],'reversible',false); +model = addReaction(model,'newRxn15','metaboliteList',{'prot_pool','prot_A5FKY3'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn16','metaboliteList',{'prot_pool','prot_P32449ly'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn17','metaboliteList',{'prot_pool','prot_P32178ly'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn18','metaboliteList',{'prot_pool','prot_P0A6E1'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn19','metaboliteList',{'prot_pool','prot_Q8GUE9'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'newRxn20','metaboliteList',{'prot_pool','prot_Q57160'},'stoichCoeffList',[-MW61 1],'reversible',false); +model = addReaction(model,'newRxn21','metaboliteList',{'prot_pool','prot_Q57501'},'stoichCoeffList',[-MW62 1],'reversible',false); +model = addReaction(model,'newRxn22','metaboliteList',{'prot_pool','prot_Q65CJ7'},'stoichCoeffList',[-MW7 1],'reversible',false); +model = addReaction(model,'newRxn23','metaboliteList',{'prot_pool','prot_Q42524'},'stoichCoeffList',[-MW8 1],'reversible',false); +model = addReaction(model,'newRxn24','metaboliteList',{'prot_pool','prot_G0LD36'},'stoichCoeffList',[-MW9 1],'reversible',false); +model = addReaction(model,'newRxn25','metaboliteList',{'s_4391','s_4393'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn26','metaboliteList',{'s_4393'},'stoichCoeffList',[-1],'reversible',false); +model = removeGenes(model,'YBR249C'); % delete ARO4 +model = removeGenes(model,'YPR060C'); % delete ARO7 +model = removeGenes(model,'YDR380W'); % delete ARO10 +model = removeGenes(model,'YLR134W'); % delete PDC5 +model=changeGeneAssociation(model,'newRxn1','ARO4K229L'); +model=changeGeneAssociation(model,'newRxn2','ARO7G141S'); +model=changeGeneAssociation(model,'newRxn3','aroL'); +model=changeGeneAssociation(model,'newRxn4','TAL'); +model=changeGeneAssociation(model,'newRxn5','TAT'); +model=changeGeneAssociation(model,'newRxn6','TAT'); +model=changeGeneAssociation(model,'newRxn7','hpaBC'); +model=changeGeneAssociation(model,'newRxn8','HPPR'); +model=changeGeneAssociation(model,'newRxn9','hpaBC'); +model=changeGeneAssociation(model,'newRxn10','4CL1'); +model=changeGeneAssociation(model,'newRxn11','4CL1'); +model=changeGeneAssociation(model,'newRxn12','RAS'); +model=changeGeneAssociation(model,'newRxn13','RAS'); +model=changeGeneAssociation(model,'newRxn14','CYP98A14'); +model.geneShortNames(1124)={'ARO4K229L'}; +model.geneShortNames(1125)={'ARO7G141S'}; +model.geneShortNames(1126)={'aroL'}; +model.geneShortNames(1127)={'TAL'}; +model.geneShortNames(1128)={'TAT'}; +model.geneShortNames(1129)={'hpaBC'}; +model.geneShortNames(1130)={'HPPR'}; +model.geneShortNames(1131)={'4CL1'}; +model.geneShortNames(1132)={'RAS'}; +model.geneShortNames(1133)={'CYP98A14'}; +model.enzymes(964)={'P32449ly'}; +model.enzymes(965)={'P32178ly'}; +model.enzymes(966)={'P0A6E1'}; +model.enzymes(967)={'A5FKY3'}; +model.enzymes(968)={'Q8GUE9'}; +model.enzymes(969)={'Q57160'}; +model.enzymes(970)={'Q57501'}; +model.enzymes(971)={'Q65CJ7'}; +model.enzymes(972)={'Q42524'}; +model.enzymes(973)={'G0LD36'}; +model.enzGenes(964)={'ARO4K229L'}; +model.enzGenes(965)={'ARO7G141S'}; +model.enzGenes(966)={'aroL'}; +model.enzGenes(967)={'TAL'}; +model.enzGenes(968)={'TAT'}; +model.enzGenes(969)={'hpaBC'}; +model.enzGenes(970)={'HPPR'}; +model.enzGenes(971)={'4CL1'}; +model.enzGenes(972)={'RAS'}; +model.enzGenes(973)={'CYP98A14'}; model.metComps(4147)=1; model.metComps(4148)=1; model.metComps(4149)=1; @@ -2563,21 +2681,1065 @@ model.metComps(4152)=1; model.metComps(4153)=1; model.metComps(4154)=1; model.metComps(4155)=1; -model.metComps(4156)=3; +model.metComps(4156)=1; +model.metComps(4157)=1; +model.metComps(4158)=1; +model.metComps(4159)=1; +model.metComps(4160)=1; +model.metComps(4161)=1; +model.metComps(4162)=1; +model.metComps(4163)=1; +model.metComps(4164)=1; +model.metComps(4165)=1; +model.metComps(4166)=3; +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn26'); +FBAsolution=optimizeCbModel(model) +cd ../../result_ecYeast/ecModels +save ecRosmarinic_acid.mat model +% p-coumaric acid (xylose as carbon source) +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.023*3600; +MW1=56.649; +Kcat2=0.2153*3600; +MW2=39.7487; +Kcat3=0.1339*3600; +MW3=29.7468; +Kcat4=31.9183*3600; +MW4=19.151; +Kcat5=27.5*3600; +MW5=35.923; +Kcat6=30.33*3600; +MW6=38.521; +Kcat7=1.1448*3600; +MW7=69.397; +model = addReaction(model,'newRxn1','metaboliteList',{'s_1051','prot_A5FKY3','s_0419','s_4231'},'stoichCoeffList',[-1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0551','s_0803','s_1360','prot_P32449ly','s_0349','s_1322'},'stoichCoeffList',[-1 -1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_0515','prot_P32178ly','s_1377'},'stoichCoeffList',[-1 -1/Kcat3 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_0434','s_1429','prot_P0A6E1','s_0261','s_0394','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat4 1 1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'prot_pool','prot_A5FKY3'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'prot_pool','prot_P32449ly'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'prot_pool','prot_P32178ly'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'prot_pool','prot_P0A6E1'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_4231','s_4232'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'s_4232'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'s_0578','s_0794','s_1203','prot_P31867','s_1566','s_1198'},'stoichCoeffList',[-1 -1 -1 -1/Kcat5 1 1],'reversible',false); +model = addReaction(model,'newRxn12','metaboliteList',{'s_0578','s_0794','s_1212','prot_P31867','s_1566','s_1207'},'stoichCoeffList',[-1 -1 -1 -1/Kcat5 1 1],'reversible',false); +model = addReaction(model,'newRxn13','metaboliteList',{'s_1566','s_1198','prot_P22144','s_0580','s_0794','s_1203'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1 1],'reversible',false); +model = addReaction(model,'newRxn14','metaboliteList',{'s_0434','s_0580','prot_Q9P938','s_0394','s_0581','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'newRxn15','metaboliteList',{'prot_pool','prot_P31867'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'newRxn16','metaboliteList',{'prot_pool','prot_P22144'},'stoichCoeffList',[-MW6 1],'reversible',false); +model = addReaction(model,'newRxn17','metaboliteList',{'prot_pool','prot_Q9P938'},'stoichCoeffList',[-MW7 1],'reversible',false); +model = removeGenes(model,'YDR380W'); % delete ARO10 +model = removeGenes(model,'YLR134W'); % delete PDC5 +model=changeGeneAssociation(model,'newRxn1','TAL'); +model=changeGeneAssociation(model,'newRxn2','ARO4K229L'); +model=changeGeneAssociation(model,'newRxn3','ARO7G141S'); +model=changeGeneAssociation(model,'newRxn4','aroL'); +model=changeGeneAssociation(model,'newRxn11','XYL1'); +model=changeGeneAssociation(model,'newRxn12','XYL1'); +model=changeGeneAssociation(model,'newRxn13','XYL2'); +model=changeGeneAssociation(model,'newRxn14','XYL3'); +model.geneShortNames(1126)={'TAL'}; +model.geneShortNames(1127)={'ARO4K229L'}; +model.geneShortNames(1128)={'ARO7G141S'}; +model.geneShortNames(1129)={'aroL'}; +model.geneShortNames(1130)={'XYL1'}; +model.geneShortNames(1131)={'XYL2'}; +model.geneShortNames(1132)={'XYL3'}; +model.enzymes(964)={'A5FKY3'}; +model.enzymes(965)={'P32449ly'}; +model.enzymes(966)={'P32178ly'}; +model.enzymes(967)={'P0A6E1'}; +model.enzymes(968)={'P31867'}; +model.enzymes(969)={'P22144'}; +model.enzymes(970)={'Q9P938'}; +model.enzGenes(964)={'TAL'}; +model.enzGenes(965)={'ARO4K229L'}; +model.enzGenes(966)={'ARO7G141S'}; +model.enzGenes(967)={'aroL'}; +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)=3; +model.metComps(4153)=1; +model.metComps(4154)=1; +model.metComps(4155)=1; +model=changeRxnBounds(model,'r_1714_REV',0,'u'); +model=changeRxnBounds(model,'r_1718_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.11,'l'); +model=changeObjective(model,'newRxn10'); +FBAsolution=optimizeCbModel(model) +cd ../../result_ecYeast/ecModels +save ecCoumaric_acid_xylose.mat model +% Tyrosol + Salidroside +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +MW1=57.45; +Kcat2=6.6288*3600; +MW2=42.043; +Kcat3=10.0095*3600; +MW3=92.395; +MW4=96.127; +MW5=55.01; +model = addReaction(model,'newRxn1','metaboliteList',{'s_1051','s_1275','s_0803','prot_Q06086','s_4394','s_0456','s_4395','s_0837'},'stoichCoeffList',[-1 -1 -1 -1 1 1 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_1377','s_1198','prot_P07023','s_0204','s_0456','s_1203','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_0557','s_1322','prot_A0A0L0LT01','s_4396','s_0551','s_0803'},'stoichCoeffList',[-1 -1 -1/Kcat3 1 1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4394','s_1203','s_0794','prot_P0A9Q7','s_4397','s_1198'},'stoichCoeffList',[-1 -1 -1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_4397','s_1543','prot_Q9SK82','s_1538','s_4398'},'stoichCoeffList',[-1 -1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_4397','s_4399'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'s_4399'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'s_4398','s_4400'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_4400'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'prot_pool','prot_Q06086'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'prot_pool','prot_P07023'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn12','metaboliteList',{'prot_pool','prot_A0A0L0LT01'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn13','metaboliteList',{'prot_pool','prot_P0A9Q7'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn14','metaboliteList',{'prot_pool','prot_Q9SK82'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'newRxn15','metaboliteList',{'s_4395','s_4401'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn16','metaboliteList',{'s_4399'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn17','metaboliteList',{'s_4396','s_4402'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn18','metaboliteList',{'s_4402'},'stoichCoeffList',[-1],'reversible',false) +model = removeGenes(model,'YNL316C'); % delete PHA2 +model = removeGenes(model,'YLR044C'); % delete PDC1 +model = removeGenes(model,'YKL211C'); % delete TRP3 +model=changeGeneAssociation(model,'newRxn1','AAS'); +model=changeGeneAssociation(model,'newRxn2','TyrAM53I/A354V'); +model=changeGeneAssociation(model,'newRxn3','xfp'); +model=changeGeneAssociation(model,'newRxn4','ADH'); +model=changeGeneAssociation(model,'newRxn5','UGT85A1'); +model.geneShortNames(1125)={'AAS'}; +model.geneShortNames(1126)={'TyrAM53I/A354V'}; +model.geneShortNames(1127)={'xfp'}; +model.geneShortNames(1128)={'ADH'}; +model.geneShortNames(1129)={'UGT85A1'}; +model.enzymes(964)={'Q06086'}; +model.enzymes(965)={'P07023'}; +model.enzymes(966)={'A0A0L0LT01'}; +model.enzymes(967)={'P0A9Q7'}; +model.enzymes(968)={'Q9SK82'}; +model.enzGenes(964)={'AAS'}; +model.enzGenes(965)={'TyrAM53I/A354V'}; +model.enzGenes(966)={'xfp'}; +model.enzGenes(967)={'ADH'}; +model.enzGenes(968)={'UGT85A1'}; +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)=3; +model.metComps(4158)=3; +model.metComps(4159)=3; +model.metComps(4160)=3; +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn7'); % For tyrosol production +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 ecTyrosol.mat model +model=changeObjective(model,'newRxn9'); % For salidroside production +FBAsolution=optimizeCbModel(model) +save ecSalidroside.mat model +% Miltiradiene +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +MW1=90.483; +MW2=68.37; +Kcat1=6.6*3600; +Kcat2=2.2*3600; +Kcat3=92.5526*3600; +model = addReaction(model,'r_0373No1','metaboliteList',{'s_0190','s_0943','prot_Q12051','s_0633','s_0189'},'stoichCoeffList',[-1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'r_0355No1','metaboliteList',{'s_0943','s_1376','prot_P08524','s_0633','s_0745'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'r_0462No1','metaboliteList',{'s_0745','s_0943','prot_P08524','s_0190','s_0633'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'r_0558No1','metaboliteList',{'pmet_r_0558','prot_P12684','s_0028','s_0529','s_1207'},'stoichCoeffList',[-1 -1/Kcat3 1 1 2],'reversible',false); +model = addReaction(model,'newRxn1','metaboliteList',{'s_0189','prot_B8PQ84','s_4403'},'stoichCoeffList',[-1 -1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_4403','prot_C8XPS0','s_0633','s_4404'},'stoichCoeffList',[-1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_4404','s_4405'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4405'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'prot_pool','prot_B8PQ84'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'prot_pool','prot_C8XPS0'},'stoichCoeffList',[-MW2 1],'reversible',false); +model=changeGeneAssociation(model,'newRxn1','CPS'); +model=changeGeneAssociation(model,'newRxn2','KSL'); +model.geneShortNames(1128)={'CPS'}; +model.geneShortNames(1129)={'KSL'}; +model.enzymes(964)={'B8PQ84'}; +model.enzymes(965)={'C8XPS0'}; +model.enzGenes(964)={'CPS'}; +model.enzGenes(965)={'KSL'}; +model.metComps(4147)=1; +model.metComps(4148)=1; +model.metComps(4149)=1; +model.metComps(4150)=1; +model.metComps(4151)=3; +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn4'); +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 ecMiltiradiene.mat model +% Caffeic acid +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +MW1=57.927; +MW2=55.539; +MW3=39.7487; +MW4=29.7468; +Kcat2=27.7*3600; +Kcat3=0.0828*3600; +Kcat4=0.1339*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_4231','prot_O22203','s_4387'},'stoichCoeffList',[-1 -1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_1051','prot_A0A1M4NET9','s_0419','s_4231'},'stoichCoeffList',[-1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_0551','s_0803','s_1360','prot_P32449ly','s_0349','s_1322'},'stoichCoeffList',[-1 -1 -1 -1/Kcat3 1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_0515','prot_P32178ly','s_1377'},'stoichCoeffList',[-1 -1/Kcat4 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'prot_pool','prot_O22203'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'prot_pool','prot_A0A1M4NET9'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'prot_pool','prot_P32449ly'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'prot_pool','prot_P32178ly'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_4387','s_4406'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'s_4406'},'stoichCoeffList',[-1],'reversible',false); +model = removeGenes(model,'YDR380W'); % delete ARO10 +model = removeGenes(model,'YLR134W'); % delete PDC5 +model=changeGeneAssociation(model,'newRxn1','C3H'); +model=changeGeneAssociation(model,'newRxn2','TAL'); +model=changeGeneAssociation(model,'newRxn3','ARO4K229L'); +model=changeGeneAssociation(model,'newRxn4','ARO7G141S'); +model.geneShortNames(1126)={'C3H'}; +model.geneShortNames(1127)={'TAL'}; +model.geneShortNames(1128)={'ARO4K229L'}; +model.geneShortNames(1129)={'ARO7G141S'}; +model.enzymes(964)={'O22203'}; +model.enzymes(965)={'A0A1M4NET9'}; +model.enzymes(966)={'P32449ly'}; +model.enzymes(967)={'P32178ly'}; +model.enzGenes(964)={'C3H'}; +model.enzGenes(965)={'TAL'}; +model.enzGenes(966)={'ARO4K229L'}; +model.enzGenes(967)={'ARO7G141S'}; +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=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn10'); +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 ecCaffeic_acid.mat model + +% Valencene +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.0032*3600; +MW1=69.219; +Kcat2=92.5526*3600; +Kcat3=6.8*3600; +Kcat4=1800*3600; +Kcat5=10000000*3600; +Kcat6=43.8001*3600; +Kcat7=0.83*3600; +Kcat8=9.8*3600; +Kcat9=2.2*3600; +Kcat10=59800*3600; +Kcat11=0.1212*3600; +Kcat12=0.825*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0190','prot_S4SC87','s_4407','s_0633'},'stoichCoeffList',[-1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'r_0558No1','metaboliteList',{'pmet_r_0558','prot_P12684','s_0028','s_0529','s_1207'},'stoichCoeffList',[-1 -1/Kcat2 1 1 2],'reversible',false); +model = addReaction(model,'r_0904No1','metaboliteList',{'s_0019','s_0434','prot_P24521','s_0018','s_0394'},'stoichCoeffList',[-1 -1 -1/Kcat3 1 1],'reversible',false); +model = addReaction(model,'r_0103No1','metaboliteList',{'s_0373','prot_P41338','s_0367','s_0529'},'stoichCoeffList',[-2 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'r_0104No1','metaboliteList',{'s_0376','prot_P41338','s_0370','s_0532'},'stoichCoeffList',[-2 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'r_0103_REVNo1','metaboliteList',{'s_0367','s_0529','prot_P41338','s_0373'},'stoichCoeffList',[-1 -1 -1/Kcat5 2],'reversible',false); +model = addReaction(model,'r_0104_REVNo1','metaboliteList',{'s_0370','s_0532','prot_P41338','s_0376'},'stoichCoeffList',[-1 -1 -1/Kcat5 2],'reversible',false); +model = addReaction(model,'r_0735No1','metaboliteList',{'s_0028','s_0434','prot_P07277','s_0019','s_0394','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1 1],'reversible',false); +model = addReaction(model,'r_0736No1','metaboliteList',{'s_0028','s_0539','prot_P07277','s_0019','s_0467','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1 1],'reversible',false); +model = addReaction(model,'r_0737No1','metaboliteList',{'s_0028','s_0785','prot_P07277','s_0019','s_0739','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1 1],'reversible',false); +model = addReaction(model,'r_0738No1','metaboliteList',{'s_0028','s_1559','prot_P07277','s_0019','s_1538','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1 1],'reversible',false); +model = addReaction(model,'r_0559No1','metaboliteList',{'s_0367','s_0373','s_0803','prot_P54839','s_0218','s_0529','s_0794'},'stoichCoeffList',[-1 -1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0560No1','metaboliteList',{'s_0370','s_0376','s_0807','prot_P54839','s_0221','s_0532','s_0799'},'stoichCoeffList',[-1 -1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0739No1','metaboliteList',{'s_0018','s_0434','prot_P32377','s_0394','s_0456','s_0943','s_1322'},'stoichCoeffList',[-1 -1 -1/Kcat8 1 1 1 1],'reversible',false); +model = addReaction(model,'r_0355No1','metaboliteList',{'s_0943','s_1376','prot_P08524','s_0633','s_0745'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1],'reversible',false); +model = addReaction(model,'r_0462No1','metaboliteList',{'s_0745','s_0943','prot_P08524','s_0190','s_0633'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1],'reversible',false); +model = addReaction(model,'r_0667No1','metaboliteList',{'s_0943','prot_P15496','s_1376'},'stoichCoeffList',[-1 -1/Kcat10 1],'reversible',false); +model = addReaction(model,'r_0667_REVNo1','metaboliteList',{'s_1376','prot_P15496','s_0943'},'stoichCoeffList',[-1 -1/Kcat11 1],'reversible',false); +model = addReaction(model,'r_1012No1','metaboliteList',{'s_0190','s_0794','s_1212','prot_P29704','s_0633','s_1207','s_1447'},'stoichCoeffList',[-2 -1 -1 -1/Kcat12 2 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_4407','s_4408'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_4408'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'prot_pool','prot_S4SC87'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = removeGenes(model,'YPL069C'); % delete BTS1 +model = removeGenes(model,'YDR284C'); % delete DPP1 +model = removeGenes(model,'YDR503C'); % delete LPP1 +model=changeGeneAssociation(model,'newRxn1','VS'); +model.geneShortNames(1125)={'VS'}; +model.enzymes(964)={'S4SC87'}; +model.enzGenes(964)={'VS'}; +model.metComps(4147)=1; +model.metComps(4148)=1; +model.metComps(4149)=3; +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn3'); +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 ecValencene.mat model +% Glycyrrhetinic acid +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.77*3600; +MW1=87.516; +MW2=56.456; +MW3=59.454; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0037','prot_Q9MB42','s_4272'},'stoichCoeffList',[-1 -1/Kcat1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_4272','s_1275','prot_A0A218KSA8','s_4409','s_0803'},'stoichCoeffList',[-1 -2 -1 1 3],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_4409','s_1275','prot_H1A981','s_4410','s_0803'},'stoichCoeffList',[-1 -3 -1 1 4],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4410','s_4411'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_4411'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'prot_pool','prot_Q9MB42'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'prot_pool','prot_A0A218KSA8'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'prot_pool','prot_H1A981'},'stoichCoeffList',[-MW3 1],'reversible',false); +model=changeGeneAssociation(model,'newRxn1','bAS'); +model=changeGeneAssociation(model,'newRxn2','uni25647'); +model=changeGeneAssociation(model,'newRxn3','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.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=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn5'); +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 ecGlycyrrhetinic_acid.mat model +% Paclitaxel precursor +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.16*3600; +MW1=97.962; +Kcat2=8.4*3600; +MW2=42.153; +MW3=86.497; +Kcat4=7.03*3600; +MW4=42.151; +MW5=56.558; +Kcat6=29.59*3600; +MW6=49.08; +Kcat7=6.8*3600; +Kcat8=43.8001*3600; +Kcat9=9.8*3600; +Kcat10=2.2*3600; +Kcat11=59800*3600; +Kcat12=0.1212*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0189','prot_Q2PRN4','s_0633','s_4412'},'stoichCoeffList',[-1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'r_0904No1','metaboliteList',{'s_0019','s_0434','prot_P24521','s_0018','s_0394'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1],'reversible',false); +model = addReaction(model,'r_0735No1','metaboliteList',{'s_0028','s_0434','prot_P07277','s_0019','s_0394','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'r_0736No1','metaboliteList',{'s_0028','s_0539','prot_P07277','s_0019','s_0467','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'r_0737No1','metaboliteList',{'s_0028','s_0785','prot_P07277','s_0019','s_0739','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'r_0738No1','metaboliteList',{'s_0028','s_1559','prot_P07277','s_0019','s_1538','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'r_0739No1','metaboliteList',{'s_0018','s_0434','prot_P32377','s_0394','s_0456','s_0943','s_1322'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1 1 1],'reversible',false); +model = addReaction(model,'r_0355No1','metaboliteList',{'s_0943','s_1376','prot_P08524','s_0633','s_0745'},'stoichCoeffList',[-1 -1 -1/Kcat10 1 1],'reversible',false); +model = addReaction(model,'r_0462No1','metaboliteList',{'s_0745','s_0943','prot_P08524','s_0190','s_0633'},'stoichCoeffList',[-1 -1 -1/Kcat10 1 1],'reversible',false); +model = addReaction(model,'r_0667No1','metaboliteList',{'s_0943','prot_P15496','s_1376'},'stoichCoeffList',[-1 -1/Kcat11 1],'reversible',false); +model = addReaction(model,'r_0667_REVNo1','metaboliteList',{'s_1376','prot_P15496','s_0943'},'stoichCoeffList',[-1 -1/Kcat12 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0190','s_0943','prot_Q1L6K3','s_0633','s_0189'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_0373','prot_Q9FD70','s_0529','s_0367'},'stoichCoeffList',[-1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_0373','s_0367','s_0803','prot_Q9FD71','s_0218','s_0529'},'stoichCoeffList',[-1 -1 -1 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_4412','s_1275','prot_Q6WG30','s_4413','s_0803'},'stoichCoeffList',[-1 -1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_4413','s_0373','prot_Q9M6F0','s_4414','s_0529'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'s_4414','s_4415'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'s_4415'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'prot_pool','prot_Q2PRN4'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'prot_pool','prot_Q1L6K3'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'prot_pool','prot_Q9FD70'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn12','metaboliteList',{'prot_pool','prot_Q9FD71'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn13','metaboliteList',{'prot_pool','prot_Q6WG30'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'newRxn14','metaboliteList',{'prot_pool','prot_Q9M6F0'},'stoichCoeffList',[-MW6 1],'reversible',false); +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,'newRxn6','TAT'); +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)=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)={'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 +% nootkatone +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.0032*3600; +MW1=69.219; +Kcat2=15.9*3600; +MW2=56.788; +Kcat3=4.4*3600; +MW3=28.67; +Kcat4=2.2*3600; +Kcat5=92.5526*3600; +Kcat6=0.825*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0190','prot_S4SC87','s_4407','s_0633'},'stoichCoeffList',[-1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_4407','s_1275','prot_A6YIH8','s_0803','s_4420'},'stoichCoeffList',[-1 -2 -1/Kcat2 3 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_4420','prot_F1SWA0','s_4421'},'stoichCoeffList',[-1 -1/Kcat3 1],'reversible',false); +model = addReaction(model,'r_0355No1','metaboliteList',{'s_0943','s_1376','prot_P08524','s_0633','s_0745'},'stoichCoeffList',[-1 -1 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'r_0462No1','metaboliteList',{'s_0745','s_0943','prot_P08524','s_0190','s_0633'},'stoichCoeffList',[-1 -1 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'r_1012No1','metaboliteList',{'s_0190','s_0794','s_1212','prot_P29704','s_0633','s_1207','s_1447'},'stoichCoeffList',[-2 -1 -1 -1/Kcat6 2 1 1],'reversible',false); +model = addReaction(model,'r_0558No1','metaboliteList',{'pmet_r_0558','prot_P12684','s_0028','s_0529','s_1207'},'stoichCoeffList',[-1 -1/Kcat5 1 1 2],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4421','s_4422'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_4422'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'prot_pool','prot_S4SC87'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'prot_pool','prot_A6YIH8'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'prot_pool','prot_F1SWA0'},'stoichCoeffList',[-MW3 1],'reversible',false); +model=changeGeneAssociation(model,'newRxn1','VS'); +model=changeGeneAssociation(model,'newRxn2','HPO'); +model=changeGeneAssociation(model,'newRxn3','ZSD1'); +model.geneShortNames(1128)={'VS'}; +model.geneShortNames(1129)={'HPO'}; +model.geneShortNames(1130)={'ZSD1'}; +model.enzymes(964)={'S4SC87'}; +model.enzymes(965)={'A6YIH8'}; +model.enzymes(966)={'F1SWA0'}; +model.enzGenes(964)={'VS'}; +model.enzGenes(965)={'HPO'}; +model.enzGenes(966)={'ZSD1'}; +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=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn5'); +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 ecNootkatone.mat model +% Squalene +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +MW1=45.41; +MW2=33.168; +Kcat1=92.5526*3600; +Kcat2=2.2*3600; +Kcat3=3.3*3600; +Kcat4=6.8*3600; +Kcat5=1800*3600; +Kcat6=10000000*3600; +Kcat7=43.8001*3600; +Kcat8=0.83*3600; +Kcat9=9.8*3600; +Kcat10=286*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0218','s_1203','s_0794','prot_Q5LL64','s_0028','s_0529','s_1198'},'stoichCoeffList',[-1 -2 -2 -1 1 1 2],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0359','s_1198','s_0529','prot_A0A0A8FFU5','s_0367','s_0794','s_1203'},'stoichCoeffList',[-1 -1 -1 -1 1 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'prot_pool','prot_Q5LL64'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'prot_pool','prot_A0A0A8FFU5'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'r_0558No1','metaboliteList',{'pmet_r_0558','prot_P12684','s_0028','s_0529','s_1207'},'stoichCoeffList',[-1 -1/Kcat1 1 1 2],'reversible',false); +model = addReaction(model,'r_0904No1','metaboliteList',{'s_0019','s_0434','prot_P24521','s_0018','s_0394'},'stoichCoeffList',[-1 -1 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'r_0103No1','metaboliteList',{'s_0373','prot_P41338','s_0367','s_0529'},'stoichCoeffList',[-2 -1/Kcat5 1 1],'reversible',false); +model = addReaction(model,'r_0104No1','metaboliteList',{'s_0376','prot_P41338','s_0370','s_0532'},'stoichCoeffList',[-2 -1/Kcat5 1 1],'reversible',false); +model = addReaction(model,'r_0103_REVNo1','metaboliteList',{'s_0367','s_0529','prot_P41338','s_0373'},'stoichCoeffList',[-1 -1 -1/Kcat6 2],'reversible',false); +model = addReaction(model,'r_0104_REVNo1','metaboliteList',{'s_0370','s_0532','prot_P41338','s_0376'},'stoichCoeffList',[-1 -1 -1/Kcat6 2],'reversible',false); +model = addReaction(model,'r_0735No1','metaboliteList',{'s_0028','s_0434','prot_P07277','s_0019','s_0394','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0736No1','metaboliteList',{'s_0028','s_0539','prot_P07277','s_0019','s_0467','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0737No1','metaboliteList',{'s_0028','s_0785','prot_P07277','s_0019','s_0739','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0738No1','metaboliteList',{'s_0028','s_1559','prot_P07277','s_0019','s_1538','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0559No1','metaboliteList',{'s_0367','s_0373','s_0803','prot_P54839','s_0218','s_0529','s_0794'},'stoichCoeffList',[-1 -1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'r_0560No1','metaboliteList',{'s_0370','s_0376','s_0807','prot_P54839','s_0221','s_0532','s_0799'},'stoichCoeffList',[-1 -1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'r_0739No1','metaboliteList',{'s_0018','s_0434','prot_P32377','s_0394','s_0456','s_0943','s_1322'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1 1 1],'reversible',false); +model = addReaction(model,'r_0355No1','metaboliteList',{'s_0943','s_1376','prot_P08524','s_0633','s_0745'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'r_0462No1','metaboliteList',{'s_0745','s_0943','prot_P08524','s_0190','s_0633'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'r_1012No1','metaboliteList',{'s_0190','s_0794','s_1212','prot_P29704','s_0633','s_1207','s_1447'},'stoichCoeffList',[-2 -1 -1 -1/Kcat3 2 1 1],'reversible',false); +model = addReaction(model,'r_0163No1','metaboliteList',{'s_0680','s_1198','prot_P00331','s_0359','s_0794','s_1203'},'stoichCoeffList',[-1 -1 -1/Kcat10 1 1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_1447','s_4433'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_4433'},'stoichCoeffList',[-1],'reversible',false); +model=changeGeneAssociation(model,'newRxn1','mvaA'); +model=changeGeneAssociation(model,'newRxn2','ADA'); +model.geneShortNames(1128)={'mvaA'}; +model.geneShortNames(1129)={'ADA'}; +model.enzymes(964)={'Q5LL64'}; +model.enzymes(965)={'A0A0A8FFU5'}; +model.enzGenes(964)={'mvaA'}; +model.enzGenes(965)={'ADA'}; +model.metComps(4147)=1; +model.metComps(4148)=1; +model.metComps(4149)=3; +cd ../../strain_design_ecYeast +c_sourceID = 'D-glucose exchange (reversible)'; +model = lychangeMedia_batch(model,c_sourceID,'YEP'); +model=changeRxnBounds(model,'r_1714_REV',0,'u'); +model=changeRxnBounds(model,'r_1761_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn6'); +FBAsolution=optimizeCbModel(model) +cd ../result_ecYeast/ecModels +save ecSqualene.mat model +% Tropane alkaloids (cinnamoyltropine) +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +MW1=66.706; +MW2=33.557; +MW3=36.976; +MW4=37.727; +MW5=43.267; +MW6=59.479; +MW7=29.617; +MW8=78.726; +MW9=62.559; +MW10=48.753; +Kcat1=9.9*3600; +Kcat4=5.14*3600; +Kcat7=25.6*3600; +Kcat8=1.8*3600; +Kcat9=5.8805*3600; +Kcat11=8.4*3600; +Kcat12=0.54*3600; +Kcat13=0.44*3600; +Kcat14=1.56*3600; +Kcat15=78*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0965','s_0794','prot_P22220','s_4423','s_0456'},'stoichCoeffList',[-1 -1 -1/Kcat1 1 1 ],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_4423','s_0803','prot_P60651','s_1389','s_1552'},'stoichCoeffList',[-1 -1 -1 1 1 ],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_1389','s_1416','prot_Q9S7W8','prot_Q70EW6','s_1413','s_4424'},'stoichCoeffList',[-1 -1 -1 -1/Kcat4 1 1 ],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4424','s_1275','s_0803','s_0837','s_4395','s_4425'},'stoichCoeffList',[-1 -1 -1 1 1 1 ],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_4425','s_4426','s_0803'},'stoichCoeffList',[-1 1 1 ],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_4426','prot_A0A3G4RHW3','s_4427'},'stoichCoeffList',[-1 -1 1 ],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'s_4427','prot_A0A3G4RHY7','s_4428'},'stoichCoeffList',[-1 -1 1 ],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'s_4428','s_1212','s_0794','prot_P50162','s_4429','s_1207'},'stoichCoeffList',[-1 -1 -1 -1/Kcat7 1 1 ],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_1032','prot_P35510','s_0419','s_4219'},'stoichCoeffList',[-1 -1/Kcat8 1 1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'s_4219','s_0434','s_0529','prot_Q9LU36','s_0633','s_0423','s_4430'},'stoichCoeffList',[-1 -1 -1 -1/Kcat9 1 1 1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'s_4429','s_4430','prot_A0A059Q4T4','s_4431'},'stoichCoeffList',[-1 -1 -1 1],'reversible',false); +model = addReaction(model,'newRxn12','metaboliteList',{'s_4431','s_4432'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn13','metaboliteList',{'s_4432'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn14','metaboliteList',{'prot_pool','prot_P22220'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn15','metaboliteList',{'prot_pool','prot_P60651'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn16','metaboliteList',{'prot_pool','prot_Q9S7W8'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn17','metaboliteList',{'prot_pool','prot_Q70EW6'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn18','metaboliteList',{'prot_pool','prot_A0A3G4RHW3'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'newRxn19','metaboliteList',{'prot_pool','prot_A0A3G4RHY7'},'stoichCoeffList',[-MW6 1],'reversible',false); +model = addReaction(model,'newRxn20','metaboliteList',{'prot_pool','prot_P50162'},'stoichCoeffList',[-MW7 1],'reversible',false); +model = addReaction(model,'newRxn21','metaboliteList',{'prot_pool','prot_P35510'},'stoichCoeffList',[-MW8 1],'reversible',false); +model = addReaction(model,'newRxn22','metaboliteList',{'prot_pool','prot_Q9LU36'},'stoichCoeffList',[-MW9 1],'reversible',false); +model = addReaction(model,'newRxn23','metaboliteList',{'prot_pool','prot_A0A059Q4T4'},'stoichCoeffList',[-MW10 1],'reversible',false); +model = addReaction(model,'r_0817No1','metaboliteList',{'s_0794','s_1266','prot_P08432','s_0456','s_1389'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_0206No1','metaboliteList',{'s_0803','s_0965','prot_P00812','s_1266','s_1552'},'stoichCoeffList',[-1 -1 -1/Kcat12 1 1],'reversible',false); +model = addReaction(model,'r_0761No1','metaboliteList',{'pmet_r_0761','prot_P40360','s_0532','s_0799','s_1192'},'stoichCoeffList',[-1 -1/Kcat13 1 1 1],'reversible',false); +model = addReaction(model,'r_0761_REVNo1','metaboliteList',{'prot_P40360','pmet_r_0761_REV','s_0376','s_0993'},'stoichCoeffList',[-1/Kcat14 -1 1 1],'reversible',false); +model = addReaction(model,'r_0929No1','metaboliteList',{'s_0803','s_1180','s_1275','prot_P50264','s_0208','s_0837','s_1193'},'stoichCoeffList',[-1 -1 -1 -1/Kcat15 1 1 1],'reversible',false); +model = addReaction(model,'r_0936No1','metaboliteList',{'s_0803','s_1181','s_1275','prot_P50264','s_0208','s_0837','s_1180'},'stoichCoeffList',[-1 -1 -1 -1/Kcat15 1 1 1],'reversible',false); +model = addReaction(model,'r_0937No1','metaboliteList',{'s_0803','s_1442','s_1275','prot_P50264','s_0208','s_0837','s_1439'},'stoichCoeffList',[-1 -1 -1 -1/Kcat15 1 1 1],'reversible',false); +model = addReaction(model,'newRxn24','metaboliteList',{'s_4395','s_4401'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn25','metaboliteList',{'s_4401'},'stoichCoeffList',[-1],'reversible',false); +model=changeGeneAssociation(model,'newRxn1','ADC'); +model=changeGeneAssociation(model,'newRxn2','speB'); +model=changeGeneAssociation(model,'newRxn3','AtPMT1'); +model=changeGeneAssociation(model,'newRxn3','DsPMT1'); +model=changeGeneAssociation(model,'newRxn4','MPO1'); +model=changeGeneAssociation(model,'newRxn6','PYKS'); +model=changeGeneAssociation(model,'newRxn7','CYP82M3'); +model=changeGeneAssociation(model,'newRxn8','TR1'); +model=changeGeneAssociation(model,'newRxn9','PAL1'); +model=changeGeneAssociation(model,'newRxn10','4CL5'); +model=changeGeneAssociation(model,'newRxn11','CS'); +model.geneShortNames(1128)={'ADC'}; +model.geneShortNames(1129)={'speB'}; +model.geneShortNames(1130)={'AtPMT1'}; +model.geneShortNames(1131)={'DsPMT1'}; +model.geneShortNames(1132)={'MPO1'}; +model.geneShortNames(1133)={'PYKS'}; +model.geneShortNames(1134)={'CYP82M3'}; +model.geneShortNames(1135)={'TR1'}; +model.geneShortNames(1136)={'PAL1'}; +model.geneShortNames(1137)={'4CL5'}; +model.geneShortNames(1138)={'CS'}; +model.enzymes(964)={'P22220'}; +model.enzymes(965)={'P60651'}; +model.enzymes(966)={'Q9S7W8'}; +model.enzymes(967)={'Q70EW6'}; +model.enzymes(968)={'A0A3G4RHW3'}; +model.enzymes(969)={'A0A3G4RHY7'}; +model.enzymes(970)={'P50162'}; +model.enzymes(971)={'P35510'}; +model.enzymes(972)={'Q9LU36'}; +model.enzymes(973)={'A0A059Q4T4'}; +model.enzGenes(964)={'ADC'}; +model.enzGenes(965)={'speB'}; +model.enzGenes(966)={'AtPMT1'}; +model.enzGenes(967)={'DsPMT1'}; +model.enzGenes(968)={'PYKS'}; +model.enzGenes(969)={'CYP82M3'}; +model.enzGenes(970)={'TR1'}; +model.enzGenes(971)={'PAL1'}; +model.enzGenes(972)={'4CL5'}; +model.enzGenes(973)={'CS'}; +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)=1; +model.metComps(4162)=1; +model.metComps(4163)=1; +model.metComps(4164)=1; +model.metComps(4165)=1; +model.metComps(4166)=1; +model.metComps(4167)=1; +model.metComps(4168)=1; +model.metComps(4169)=3; +model.metComps(4170)=3; +cd ../../strain_design_ecYeast +c_sourceID = 'D-glucose exchange (reversible)'; +model = lychangeMedia_batch(model,c_sourceID,'YEP'); +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn13'); +model = removeGenes(model,'YMR170C'); % delete ALD2 +model = removeGenes(model,'YMR169C'); % delete ALD3 +model = removeGenes(model,'YOR374W'); % delete ALD4 +model = removeGenes(model,'YER073W'); % delete ALD5 +model = removeGenes(model,'YMR110C'); % delete HFD1 +model = removeGenes(model,'YLR017W'); % delete MEU1 +FBAsolution=optimizeCbModel(model) +cd ../result_ecYeast/ecModels +save ecCinnamoyltropine.mat model +% L-(+)-Ergothioneine +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.0716*3600; +MW1=99.025; +MW2=39.033; +model = addReaction(model,'newRxn1','metaboliteList',{'s_1006','s_1416','prot_Q7RX33','s_0794','s_4434','s_1413'},'stoichCoeffList',[-1 -3 -1/Kcat1 3 1 3],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_4434','s_0981','s_1275','prot_Q7RX33','s_0803','s_4435'},'stoichCoeffList',[-1 -1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_4435','prot_A0R5M7','s_4436','s_1399','s_4395'},'stoichCoeffList',[-1 -1 1 1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4436','s_4437'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_4437'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'prot_pool','prot_Q7RX33'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'prot_pool','prot_A0R5M7'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'s_4395','s_4401'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_4401'},'stoichCoeffList',[-1],'reversible',false); +model=changeGeneAssociation(model,'newRxn1','Egt1'); +model=changeGeneAssociation(model,'newRxn2','Egt1'); +model=changeGeneAssociation(model,'newRxn3','Egr2'); +model.geneShortNames(1128)={'Egt1'}; +model.geneShortNames(1129)={'Egt2'}; +model.enzymes(964)={'Q7RX33'}; +model.enzymes(965)={'A0R5M7'}; +model.enzGenes(964)={'Egt1'}; +model.enzGenes(965)={'Egt2'}; +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(4154)=3; +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn5'); +model=changeRxnBounds(model,'r_1879_REV',1,'u'); % add arginine +model=changeRxnBounds(model,'r_1893_REV',1,'u'); % add histidine +model=changeRxnBounds(model,'r_1902_REV',1,'u'); % add methionine +model=changeRxnBounds(model,'r_2028_REV',1,'u'); % add pyridoxine +FBAsolution=optimizeCbModel(model) +cd ../../result_ecYeast/ecModels +save ecErgothioneine.mat model +% S-adenosyl-L-methionine +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=1.7660e-04*3600; +model = addReaction(model,'r_0726No1','metaboliteList',{'pmet_r_0726','prot_P19358','s_0633','s_1322','s_1416'},'stoichCoeffList',[-1 -1/Kcat1 1 1 1],'reversible',false); +model = addReaction(model,'newRxn1','metaboliteList',{'s_1416','s_1418'},'stoichCoeffList',[-1 1],'reversible',false); +model = removeGenes(model,'YOL052C'); % delete SPE2 +cd ../../strain_design_ecYeast +c_sourceID = 'D-glucose exchange (reversible)'; +model = lychangeMedia_batch(model,c_sourceID,'YEP'); +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.159,'l'); +model=changeObjective(model,'r_2043'); +FBAsolution=optimizeCbModel(model) +cd ../result_ecYeast/ecModels +save ecS-adenosyl-L-methionine.mat model +% 2'-Fucosyllactose +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=27.5*3600; +MW1=35.923; +Kcat2=30.33*3600; +MW2=38.521; +Kcat3=1.1448*3600; +MW3=69.397; +Kcat4=5*3600; +MW4=41.674; +Kcat5=1.5*3600; +MW5=36.141; +Kcat6=3.96*3600; +MW6=34.942; +MW7=65.383; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0578','s_0794','s_1203','prot_P31867','s_1566','s_1198'},'stoichCoeffList',[-1 -1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0578','s_0794','s_1212','prot_P31867','s_1566','s_1207'},'stoichCoeffList',[-1 -1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_1566','s_1198','prot_P22144','s_0580','s_0794','s_1203'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_0434','s_0580','prot_Q9P938','s_0394','s_0581','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat3 1 1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_0743','prot_O85339','s_0803','s_4438'},'stoichCoeffList',[-1 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_4438','s_1212','s_0794','prot_P32055','s_1207','s_4439'},'stoichCoeffList',[-1 -1 -1 -1/Kcat5 1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'s_4439','s_4444','prot_A6M9C2','s_0739','s_4440'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'s_4440','s_4441'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_4441'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'prot_pool','prot_P31867'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'prot_pool','prot_P22144'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn12','metaboliteList',{'prot_pool','prot_Q9P938'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn13','metaboliteList',{'prot_pool','prot_O85339'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn14','metaboliteList',{'prot_pool','prot_P32055'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'newRxn15','metaboliteList',{'prot_pool','prot_A6M9C2'},'stoichCoeffList',[-MW6 1],'reversible',false); +model = addReaction(model,'newRxn16','metaboliteList',{'s_4443'},'stoichCoeffList',[1],'reversible',false); +model = addReaction(model,'newRxn17','metaboliteList',{'s_4443','prot_P07921','s_4444'},'stoichCoeffList',[-1 -1 1],'reversible',false); +model = addReaction(model,'newRxn18','metaboliteList',{'prot_pool','prot_P07921'},'stoichCoeffList',[-MW7 1],'reversible',false); +model = removeGenes(model,'YDL236W'); % delete PHO13 +model = removeGenes(model,'YPL061W'); % delete ALD6 +model=changeGeneAssociation(model,'newRxn1','XYL1'); +model=changeGeneAssociation(model,'newRxn2','XYL1'); +model=changeGeneAssociation(model,'newRxn3','XYL2'); +model=changeGeneAssociation(model,'newRxn4','XYL3'); +model=changeGeneAssociation(model,'newRxn5','Gmd'); +model=changeGeneAssociation(model,'newRxn6','WcaG'); +model=changeGeneAssociation(model,'newRxn7','WbgL'); +model=changeGeneAssociation(model,'newRxn8','Lac12'); +model.geneShortNames(1126)={'XYL1'}; +model.geneShortNames(1127)={'XYL2'}; +model.geneShortNames(1128)={'XYL3'}; +model.geneShortNames(1129)={'Gmd'}; +model.geneShortNames(1130)={'WcaG'}; +model.geneShortNames(1131)={'WbgL'}; +model.geneShortNames(1132)={'Lac12'}; +model.enzymes(964)={'P31867'}; +model.enzymes(965)={'P22144'}; +model.enzymes(966)={'Q9P938'}; +model.enzymes(967)={'O85339'}; +model.enzymes(968)={'P32055'}; +model.enzymes(969)={'A6M9C2'}; +model.enzymes(970)={'P07921'}; +model.enzGenes(964)={'XYL1'}; +model.enzGenes(965)={'XYL2'}; +model.enzGenes(966)={'XYL3'}; +model.enzGenes(967)={'Gmd'}; +model.enzGenes(968)={'WcaG'}; +model.enzGenes(969)={'WbgL'}; +model.enzGenes(970)={'Lac12'}; +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)=3; +model.metComps(4158)=3; +model.metComps(4159)=1; +cd ../../strain_design_ecYeast +c_sourceID = 'D-xylose exchange (reversible)'; +model = lychangeMedia_batch(model,c_sourceID,'YEP'); +model=changeRxnBounds(model,'newRxn16',1,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn9'); +FBAsolution=optimizeCbModel(model) +cd ../result_ecYeast/ecModels +save ec2_Fucosyllactose.mat model +% lycopene +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=3.3*3600; +MW1=42.572; +MW2=32.786; +MW3=66.46; +Kcat5=9400*3600; +MW5=72.153; +Kcat6=92.5526*3600; +Kcat7=286*3600; +Kcat8=43.9999*3600; +Kcat9=1.68*3600; +Kcat10=32.2*3600; +Kcat11=23.1467*3600; +Kcat12=65.3426*3600; +Kcat13=1*3600; +Kcat14=0.7*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0190','s_0943','prot_Q9ZPM3','s_0633','s_0189'},'stoichCoeffList',[-1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0189','prot_D5KXJ0','s_0633','s_4236'},'stoichCoeffList',[-2 -1 2 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_4236','prot_Q5BTY7','s_4237'},'stoichCoeffList',[-1 -1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4237','s_1275','prot_Q5BTY7','s_0803','s_4238'},'stoichCoeffList',[-1 -1 -1 2 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_0362','s_0434','s_0529','prot_Q8ZKF6','s_0373','s_0423','s_0633'},'stoichCoeffList',[-1 -1 -1 -1/Kcat5 1 1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_4238','s_4442'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'s_4442'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'prot_pool','prot_Q9ZPM3'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'prot_pool','prot_D5KXJ0'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'prot_pool','prot_Q5BTY7'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'prot_pool','prot_Q8ZKF6'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'r_0558No1','metaboliteList',{'pmet_r_0558','prot_P12684','s_0028','s_0529','s_1207'},'stoichCoeffList',[-1 -1/Kcat6 1 1 2],'reversible',false); +model = addReaction(model,'r_0163No1','metaboliteList',{'s_0680','s_1198','prot_P00331','s_0359','s_0794','s_1203'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0173No1','metaboliteList',{'s_0359','s_0803','s_1207','prot_P54115','s_0362','s_0794','s_1212'},'stoichCoeffList',[-1 -1 -1 -1/Kcat8 1 2 1],'reversible',false); +model = addReaction(model,'r_0177No1','metaboliteList',{'s_0803','s_0850','s_1207','prot_P54115','s_0853','s_0794','s_1212'},'stoichCoeffList',[-1 -1 -1 -1/Kcat8 1 2 1],'reversible',false); +model = addReaction(model,'r_0766No3','metaboliteList',{'pmet_r_0766','prot_Q06892','s_0397','s_0799','s_1210'},'stoichCoeffList',[-1 -1/Kcat9 1 1 1],'reversible',false); +model = addReaction(model,'r_0772No3','metaboliteList',{'prot_Q06892','pmet_r_0772','s_0397','s_0799','s_1214'},'stoichCoeffList',[-1/Kcat10 -1 1 1 1],'reversible',false); +model = addReaction(model,'r_2344No1','metaboliteList',{'s_2808','s_2954','prot_P32567','s_2966','s_2967'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2345No1','metaboliteList',{'s_2808','s_2955','prot_P32567','s_2966','s_2968'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2346No1','metaboliteList',{'s_2808','s_2956','prot_P32567','s_2966','s_2969'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2347No1','metaboliteList',{'s_2808','s_2957','prot_P32567','s_2966','s_2970'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2348No1','metaboliteList',{'s_2808','s_2958','prot_P32567','s_2966','s_2971'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2349No1','metaboliteList',{'s_2808','s_2959','prot_P32567','s_2966','s_2972'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2350No1','metaboliteList',{'s_2808','s_2960','prot_P32567','s_2966','s_2973'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2351No1','metaboliteList',{'s_2808','s_2961','prot_P32567','s_2966','s_2974'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_0109No1','metaboliteList',{'s_0373','s_0434','s_0445','prot_P48445','prot_Q00955','s_0394','s_0794','s_1101','s_1322'},'stoichCoeffList',[-1 -1 -1 -1/450000/3600 -1/Kcat12 1 1 1 1],'reversible',false); +model = addReaction(model,'r_2182No1','metaboliteList',{'s_2783','s_2789','s_2817','s_2818','prot_P21147','s_2808','s_2819','s_2820'},'stoichCoeffList',[-1 -1 -1 -1 -1/Kcat13 2 1 1],'reversible',false); +model = addReaction(model,'r_2183No1','metaboliteList',{'s_2783','s_2791','s_2817','s_2818','prot_P21147','s_2808','s_2821','s_2820'},'stoichCoeffList',[-1 -1 -1 -1 -1/Kcat14 2 1 1],'reversible',false); +model = removeGenes(model,'YBR020W'); % delete GAL1 +model = removeGenes(model,'YBR018C'); % delete GAL7 +model = removeGenes(model,'YBR019C'); % delete GAL10 +model = removeGenes(model,'YLR300W'); % delete EXG1 +model=changeGeneAssociation(model,'newRxn1','crtE'); +model=changeGeneAssociation(model,'newRxn2','crtB'); +model=changeGeneAssociation(model,'newRxn3','crtI'); +model=changeGeneAssociation(model,'newRxn4','crtI'); +model=changeGeneAssociation(model,'newRxn5','ACS'); +model.geneShortNames(1124)={'crtE'}; +model.geneShortNames(1125)={'crtB'}; +model.geneShortNames(1126)={'crtI'}; +model.geneShortNames(1127)={'ACS'}; +model.enzymes(964)={'Q9ZPM3'}; +model.enzymes(965)={'D5KXJ0'}; +model.enzymes(966)={'Q5BTY7'}; +model.enzymes(967)={'Q8ZKF6'}; +model.enzGenes(964)={'crtE'}; +model.enzGenes(965)={'crtB'}; +model.enzGenes(966)={'crtI'}; +model.enzGenes(967)={'ACS'}; +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)=3; +cd ../../strain_design_ecYeast +c_sourceID = 'D-glucose exchange (reversible)'; +model = lychangeMedia_batch(model,c_sourceID,'YEP'); +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn7'); +FBAsolution=optimizeCbModel(model) +cd ../result_ecYeast/ecModels +save ecLycopene.mat model diff --git a/strain_design_ecYeast/Model_construction_others.m b/strain_design_ecYeast/Model_construction_others.m index 9d2a1ca..1491358 100644 --- a/strain_design_ecYeast/Model_construction_others.m +++ b/strain_design_ecYeast/Model_construction_others.m @@ -1322,9 +1322,11 @@ Kcat21=0.5559; model = addReaction(model,'newRxn2','metaboliteList',{'s_4285','s_4286'},'stoichCoeffList',[-1 1],'reversible',false); model = addReaction(model,'newRxn3','metaboliteList',{'s_4286'},'stoichCoeffList',[-1],'reversible',false); -model = addReaction(model,'newRxn1','metaboliteList',{'s_0955','s_0965','s_0969','s_0973','s_0981','s_0991','s_0999','s_1003','s_1006','s_1016','s_1021','s_1025',... - 's_1029','s_1032','s_1035','s_1039','s_1045','s_1048','s_1051','s_1056','s_0785','s_4285','s_0739','s_1322'},'stoichCoeffList',[-Kcat2 -Kcat3 -Kcat4 -Kcat5 -Kcat6... - -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -Kcat20 -Kcat21 -2.01 1 2.01 2.01],'reversible',false); +model = addReaction(model,'newRxn1','metaboliteList',{'s_0404','s_0428','s_0430','s_0432','s_0542','s_0748','s_0747','s_0757','s_0832','s_0847','s_1077',... + 's_1099','s_1148','s_1314','s_1379','s_1428','s_1491','s_1527','s_1533','s_1561','s_0785','s_4285','s_0739','s_1322','s_1582','s_1583','s_1585','s_1587',... + 's_1589','s_1591','s_1590','s_1593','s_1594','s_1596','s_1598','s_1600','s_1602','s_1604','s_1606','s_1607','s_1608','s_1610','s_1612','s_1614'},'stoichCoeffList',[-Kcat2 -Kcat3 -Kcat4 -Kcat5 -Kcat6... + -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -Kcat20 -Kcat21 -2.01 1 2.01 2.01 Kcat2 Kcat3 Kcat4 Kcat5 Kcat6... + Kcat7 Kcat8 Kcat9 Kcat10 Kcat11 Kcat12 Kcat13 Kcat14 Kcat15 Kcat16 Kcat17 Kcat18 Kcat19 Kcat20 Kcat21],'reversible',false); model.metComps(4147)=1; model.metComps(4148)=3; model=changeRxnBounds(model,'r_1714_REV',1000,'u'); @@ -2166,9 +2168,11 @@ save ec(S)-reticuline.mat model Kcat18=0.0288; Kcat19=0.2736; Kcat20=0.6192; -model = addReaction(model,'newRxn1','metaboliteList',{'s_0955','s_0965','s_0969','s_0973','s_0981','s_0991','s_0999','s_1003','s_1006','s_1016','s_1021','s_1025',... - 's_1029','s_1032','s_1035','s_1039','s_1045','s_1048','s_1051','s_1056','s_0785','s_4353','s_0739','s_1322'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... - -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -Kcat20 -1.22 1 1.22 1.22],'reversible',false); +model = addReaction(model,'newRxn1','metaboliteList',{'s_0404','s_0428','s_0430','s_0432','s_0542','s_0748','s_0747','s_0757','s_0832','s_0847','s_1077','s_1099',... + 's_1148','s_1314','s_1379','s_1428','s_1491','s_1527','s_1533','s_1561','s_0785','s_4353','s_0739','s_1322','s_1582','s_1583','s_1585','s_1587','s_1589','s_1591',... + 's_1590','s_1593','s_1594','s_1596','s_1598','s_1600','s_1602','s_1604','s_1606','s_1607','s_1608','s_1610','s_1612','s_1614'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... + -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -Kcat20 -1.22 1 1.22 1.22 Kcat1 Kcat2 Kcat3 Kcat4 Kcat5... + Kcat6 Kcat7 Kcat8 Kcat9 Kcat10 Kcat11 Kcat12 Kcat13 Kcat14 Kcat15 Kcat16 Kcat17 Kcat18 Kcat19 Kcat20],'reversible',false); model = addReaction(model,'newRxn2','metaboliteList',{'s_4353','s_4354'},'stoichCoeffList',[-1 1],'reversible',false); model = addReaction(model,'newRxn3','metaboliteList',{'s_4354'},'stoichCoeffList',[-1],'reversible',false); model.metComps(4147)=1; @@ -2205,9 +2209,11 @@ save ec(S)-reticuline.mat model Kcat18=0.2189; Kcat19=0.6386; Kcat20=0.5656; -model = addReaction(model,'newRxn1','metaboliteList',{'s_0955','s_0965','s_0969','s_0973','s_0981','s_0991','s_0999','s_1003','s_1006','s_1016','s_1021','s_1025',... - 's_1029','s_1032','s_1035','s_1039','s_1045','s_1048','s_1051','s_1056','s_0785','s_4287','s_0739','s_1322'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... - -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -Kcat20 -1 1 1 1],'reversible',false); +model = addReaction(model,'newRxn1','metaboliteList',{'s_0404','s_0428','s_0430','s_0432','s_0542','s_0748','s_0747','s_0757','s_0832','s_0847','s_1077','s_1099',... + 's_1148','s_1314','s_1379','s_1428','s_1491','s_1527','s_1533','s_1561','s_0785','s_4287','s_0739','s_1322','s_1582','s_1583','s_1585','s_1587','s_1589','s_1591',... + 's_1590','s_1593','s_1594','s_1596','s_1598','s_1600','s_1602','s_1604','s_1606','s_1607','s_1608','s_1610','s_1612','s_1614'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... + -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -Kcat20 -1 1 1 1 Kcat1 Kcat2 Kcat3 Kcat4 Kcat5... + Kcat6 Kcat7 Kcat8 Kcat9 Kcat10 Kcat11 Kcat12 Kcat13 Kcat14 Kcat15 Kcat16 Kcat17 Kcat18 Kcat19 Kcat20],'reversible',false); model = addReaction(model,'newRxn2','metaboliteList',{'s_4287','s_4355'},'stoichCoeffList',[-1 1],'reversible',false); model = addReaction(model,'newRxn3','metaboliteList',{'s_4355'},'stoichCoeffList',[-1],'reversible',false); model.metComps(4147)=1; @@ -2244,9 +2250,11 @@ save ec(S)-reticuline.mat model Kcat19=0.9931; Kcat20=0.125*3600; model = addReaction(model,'newRxn1','metaboliteList',{'s_0812','s_4356'},'stoichCoeffList',[-1 1],'reversible',false); -model = addReaction(model,'newRxn2','metaboliteList',{'s_0955','s_0965','s_0969','s_0973','s_0981','s_0991','s_0999','s_1003','s_1006','s_1021','s_1025',... - 's_1029','s_1032','s_1035','s_1039','s_1045','s_1048','s_1051','s_1056','s_0785','s_4357','s_0739','s_1322'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... - -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -1.16 1 1.16 1.16],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0404','s_0428','s_0430','s_0432','s_0542','s_0748','s_0747','s_0757','s_0832','s_1077','s_1099',... + 's_1148','s_1314','s_1379','s_1428','s_1491','s_1527','s_1533','s_1561','s_0785','s_4357','s_0739','s_1322','s_1582','s_1583','s_1585','s_1587','s_1589',... + 's_1591','s_1590','s_1593','s_1594','s_1598','s_1600','s_1602','s_1604','s_1606','s_1607','s_1608','s_1610','s_1612','s_1614'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... + -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -1.16 1 1.16 1.16 Kcat1 Kcat2 Kcat3 Kcat4 Kcat5... + Kcat6 Kcat7 Kcat8 Kcat9 Kcat10 Kcat11 Kcat12 Kcat13 Kcat14 Kcat15 Kcat16 Kcat17 Kcat18 Kcat19],'reversible',false); model = addReaction(model,'newRxn3','metaboliteList',{'s_4357','s_4356','s_4358'},'stoichCoeffList',[-1 -4 1],'reversible',false); model = addReaction(model,'newRxn4','metaboliteList',{'s_4358','s_4359'},'stoichCoeffList',[-1 1],'reversible',false); model = addReaction(model,'newRxn5','metaboliteList',{'s_4359'},'stoichCoeffList',[-1],'reversible',false); @@ -2285,9 +2293,11 @@ save ec(S)-reticuline.mat model Kcat17=0.1915; Kcat18=0.1915; Kcat19=0.3829; -model = addReaction(model,'newRxn1','metaboliteList',{'s_0955','s_0965','s_0969','s_0973','s_0991','s_0999','s_1003','s_1006','s_1016','s_1021','s_1025',... - 's_1029','s_1032','s_1035','s_1039','s_1045','s_1048','s_1051','s_1056','s_0785','s_4360','s_0739','s_1322'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... - -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -0.36 1 0.36 0.36],'reversible',false); +model = addReaction(model,'newRxn1','metaboliteList',{'s_0404','s_0428','s_0430','s_0432','s_0748','s_0747','s_0757','s_0832','s_0847','s_1077','s_1099',... + 's_1148','s_1314','s_1379','s_1428','s_1491','s_1527','s_1533','s_1561','s_0785','s_4360','s_0739','s_1322','s_1582','s_1583','s_1585','s_1587','s_1591',... + 's_1590','s_1593','s_1594','s_1596','s_1598','s_1600','s_1602','s_1604','s_1606','s_1607','s_1608','s_1610','s_1612','s_1614'},'stoichCoeffList',[-Kcat1 -Kcat2 -Kcat3 -Kcat4 -Kcat5... + -Kcat6 -Kcat7 -Kcat8 -Kcat9 -Kcat10 -Kcat11 -Kcat12 -Kcat13 -Kcat14 -Kcat15 -Kcat16 -Kcat17 -Kcat18 -Kcat19 -0.36 1 0.36 0.36 Kcat1 Kcat2 Kcat3 Kcat4 Kcat5... + Kcat6 Kcat7 Kcat8 Kcat9 Kcat10 Kcat11 Kcat12 Kcat13 Kcat14 Kcat15 Kcat16 Kcat17 Kcat18 Kcat19],'reversible',false); model = addReaction(model,'newRxn2','metaboliteList',{'s_4360','s_4361'},'stoichCoeffList',[-1 1],'reversible',false); model = addReaction(model,'newRxn3','metaboliteList',{'s_4361'},'stoichCoeffList',[-1],'reversible',false); model.metComps(4147)=1; @@ -2568,19 +2578,1169 @@ save ec(S)-reticuline.mat model cd ../result_ecYeast/ecModels save ecBetaxanthin.mat model +% Rosmarinic acid +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.2153*3600; +MW1=39.7487; +Kcat2=0.1339*3600; +MW2=29.7468; +Kcat3=31.9183*3600; +MW3=19.151; +Kcat4=0.023*3600; +MW4=56.649; +MW5=45.179; +Kcat6=4.3843*3600; +MW61=58.848; +MW62=18.522; +Kcat7=2.571*3600; +MW7=34.128; +Kcat8=12.7194*3600; +MW8=61.053; +Kcat9=5.7379*3600; +MW9=47.161; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0551','s_0803','s_1360','prot_P32449ly','s_0349','s_1322'},'stoichCoeffList',[-1 -1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0515','prot_P32178ly','s_1377'},'stoichCoeffList',[-1 -1/Kcat2 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_1429','s_0434','prot_P0A6E1','s_0261','s_0794','s_0394'},'stoichCoeffList',[-1 -1 -1/Kcat3 1 1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_1051','prot_A5FKY3','s_0419','s_4231'},'stoichCoeffList',[-1 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_0204','s_0991','prot_Q8GUE9','s_0180','s_1051'},'stoichCoeffList',[-1 -1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_0180','s_1051','prot_Q8GUE9','s_0204','s_0991'},'stoichCoeffList',[-1 -1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'s_4231','prot_Q57160','prot_Q57501','s_4387'},'stoichCoeffList',[-1 -1/Kcat6 -1/Kcat6 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'s_0204','s_1212','s_0794','prot_Q65CJ7','s_4388','s_1207'},'stoichCoeffList',[-1 -1 -1 -1/Kcat7 1 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_4388','s_1275','s_1203','s_0794','prot_Q57160','prot_Q57501','s_1198','s_0803','s_4389'},'stoichCoeffList',[-1 -1 -1 -1 -1/Kcat6 -1/Kcat6 1 1 1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'s_4215','s_0434','s_0529','prot_Q42524','s_0423','s_0633','s_4216'},'stoichCoeffList',[-1 -1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'s_4387','s_0434','s_0529','prot_Q42524','s_0423','s_0633','s_4390'},'stoichCoeffList',[-1 -1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'newRxn12','metaboliteList',{'s_4389','s_4390','prot_G0LD36','s_4391','s_0529'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1],'reversible',false); +model = addReaction(model,'newRxn13','metaboliteList',{'s_4388','s_4216','prot_G0LD36','s_4392','s_0529'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1],'reversible',false); +model = addReaction(model,'newRxn14','metaboliteList',{'s_4392','s_1203','s_1198','s_0794','s_4391'},'stoichCoeffList',[-1 -2 2 2 1],'reversible',false); +model = addReaction(model,'newRxn15','metaboliteList',{'prot_pool','prot_A5FKY3'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn16','metaboliteList',{'prot_pool','prot_P32449ly'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn17','metaboliteList',{'prot_pool','prot_P32178ly'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn18','metaboliteList',{'prot_pool','prot_P0A6E1'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn19','metaboliteList',{'prot_pool','prot_Q8GUE9'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'newRxn20','metaboliteList',{'prot_pool','prot_Q57160'},'stoichCoeffList',[-MW61 1],'reversible',false); +model = addReaction(model,'newRxn21','metaboliteList',{'prot_pool','prot_Q57501'},'stoichCoeffList',[-MW62 1],'reversible',false); +model = addReaction(model,'newRxn22','metaboliteList',{'prot_pool','prot_Q65CJ7'},'stoichCoeffList',[-MW7 1],'reversible',false); +model = addReaction(model,'newRxn23','metaboliteList',{'prot_pool','prot_Q42524'},'stoichCoeffList',[-MW8 1],'reversible',false); +model = addReaction(model,'newRxn24','metaboliteList',{'prot_pool','prot_G0LD36'},'stoichCoeffList',[-MW9 1],'reversible',false); +model = addReaction(model,'newRxn25','metaboliteList',{'s_4391','s_4393'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn26','metaboliteList',{'s_4393'},'stoichCoeffList',[-1],'reversible',false); +model = removeGenes(model,'YBR249C'); % delete ARO4 +model = removeGenes(model,'YPR060C'); % delete ARO7 +model = removeGenes(model,'YDR380W'); % delete ARO10 +model = removeGenes(model,'YLR134W'); % delete PDC5 +model=changeGeneAssociation(model,'newRxn1','ARO4K229L'); +model=changeGeneAssociation(model,'newRxn2','ARO7G141S'); +model=changeGeneAssociation(model,'newRxn3','aroL'); +model=changeGeneAssociation(model,'newRxn4','TAL'); +model=changeGeneAssociation(model,'newRxn5','TAT'); +model=changeGeneAssociation(model,'newRxn6','TAT'); +model=changeGeneAssociation(model,'newRxn7','hpaBC'); +model=changeGeneAssociation(model,'newRxn8','HPPR'); +model=changeGeneAssociation(model,'newRxn9','hpaBC'); +model=changeGeneAssociation(model,'newRxn10','4CL1'); +model=changeGeneAssociation(model,'newRxn11','4CL1'); +model=changeGeneAssociation(model,'newRxn12','RAS'); +model=changeGeneAssociation(model,'newRxn13','RAS'); +model=changeGeneAssociation(model,'newRxn14','CYP98A14'); +model.geneShortNames(1124)={'ARO4K229L'}; +model.geneShortNames(1125)={'ARO7G141S'}; +model.geneShortNames(1126)={'aroL'}; +model.geneShortNames(1127)={'TAL'}; +model.geneShortNames(1128)={'TAT'}; +model.geneShortNames(1129)={'hpaBC'}; +model.geneShortNames(1130)={'HPPR'}; +model.geneShortNames(1131)={'4CL1'}; +model.geneShortNames(1132)={'RAS'}; +model.geneShortNames(1133)={'CYP98A14'}; +model.enzymes(964)={'P32449ly'}; +model.enzymes(965)={'P32178ly'}; +model.enzymes(966)={'P0A6E1'}; +model.enzymes(967)={'A5FKY3'}; +model.enzymes(968)={'Q8GUE9'}; +model.enzymes(969)={'Q57160'}; +model.enzymes(970)={'Q57501'}; +model.enzymes(971)={'Q65CJ7'}; +model.enzymes(972)={'Q42524'}; +model.enzymes(973)={'G0LD36'}; +model.enzGenes(964)={'ARO4K229L'}; +model.enzGenes(965)={'ARO7G141S'}; +model.enzGenes(966)={'aroL'}; +model.enzGenes(967)={'TAL'}; +model.enzGenes(968)={'TAT'}; +model.enzGenes(969)={'hpaBC'}; +model.enzGenes(970)={'HPPR'}; +model.enzGenes(971)={'4CL1'}; +model.enzGenes(972)={'RAS'}; +model.enzGenes(973)={'CYP98A14'}; +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)=1; +model.metComps(4162)=1; +model.metComps(4163)=1; +model.metComps(4164)=1; +model.metComps(4165)=1; +model.metComps(4166)=3; +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn26'); +FBAsolution=optimizeCbModel(model) +cd ../../result_ecYeast/ecModels +save ecRosmarinic_acid.mat model +% p-coumaric acid (xylose as carbon source) +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.023*3600; +MW1=56.649; +Kcat2=0.2153*3600; +MW2=39.7487; +Kcat3=0.1339*3600; +MW3=29.7468; +Kcat4=31.9183*3600; +MW4=19.151; +Kcat5=27.5*3600; +MW5=35.923; +Kcat6=30.33*3600; +MW6=38.521; +Kcat7=1.1448*3600; +MW7=69.397; +model = addReaction(model,'newRxn1','metaboliteList',{'s_1051','prot_A5FKY3','s_0419','s_4231'},'stoichCoeffList',[-1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0551','s_0803','s_1360','prot_P32449ly','s_0349','s_1322'},'stoichCoeffList',[-1 -1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_0515','prot_P32178ly','s_1377'},'stoichCoeffList',[-1 -1/Kcat3 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_0434','s_1429','prot_P0A6E1','s_0261','s_0394','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat4 1 1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'prot_pool','prot_A5FKY3'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'prot_pool','prot_P32449ly'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'prot_pool','prot_P32178ly'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'prot_pool','prot_P0A6E1'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_4231','s_4232'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'s_4232'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'s_0578','s_0794','s_1203','prot_P31867','s_1566','s_1198'},'stoichCoeffList',[-1 -1 -1 -1/Kcat5 1 1],'reversible',false); +model = addReaction(model,'newRxn12','metaboliteList',{'s_0578','s_0794','s_1212','prot_P31867','s_1566','s_1207'},'stoichCoeffList',[-1 -1 -1 -1/Kcat5 1 1],'reversible',false); +model = addReaction(model,'newRxn13','metaboliteList',{'s_1566','s_1198','prot_P22144','s_0580','s_0794','s_1203'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1 1],'reversible',false); +model = addReaction(model,'newRxn14','metaboliteList',{'s_0434','s_0580','prot_Q9P938','s_0394','s_0581','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'newRxn15','metaboliteList',{'prot_pool','prot_P31867'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'newRxn16','metaboliteList',{'prot_pool','prot_P22144'},'stoichCoeffList',[-MW6 1],'reversible',false); +model = addReaction(model,'newRxn17','metaboliteList',{'prot_pool','prot_Q9P938'},'stoichCoeffList',[-MW7 1],'reversible',false); +model = removeGenes(model,'YDR380W'); % delete ARO10 +model = removeGenes(model,'YLR134W'); % delete PDC5 +model=changeGeneAssociation(model,'newRxn1','TAL'); +model=changeGeneAssociation(model,'newRxn2','ARO4K229L'); +model=changeGeneAssociation(model,'newRxn3','ARO7G141S'); +model=changeGeneAssociation(model,'newRxn4','aroL'); +model=changeGeneAssociation(model,'newRxn11','XYL1'); +model=changeGeneAssociation(model,'newRxn12','XYL1'); +model=changeGeneAssociation(model,'newRxn13','XYL2'); +model=changeGeneAssociation(model,'newRxn14','XYL3'); +model.geneShortNames(1126)={'TAL'}; +model.geneShortNames(1127)={'ARO4K229L'}; +model.geneShortNames(1128)={'ARO7G141S'}; +model.geneShortNames(1129)={'aroL'}; +model.geneShortNames(1130)={'XYL1'}; +model.geneShortNames(1131)={'XYL2'}; +model.geneShortNames(1132)={'XYL3'}; +model.enzymes(964)={'A5FKY3'}; +model.enzymes(965)={'P32449ly'}; +model.enzymes(966)={'P32178ly'}; +model.enzymes(967)={'P0A6E1'}; +model.enzymes(968)={'P31867'}; +model.enzymes(969)={'P22144'}; +model.enzymes(970)={'Q9P938'}; +model.enzGenes(964)={'TAL'}; +model.enzGenes(965)={'ARO4K229L'}; +model.enzGenes(966)={'ARO7G141S'}; +model.enzGenes(967)={'aroL'}; +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)=3; +model.metComps(4153)=1; +model.metComps(4154)=1; +model.metComps(4155)=1; +model=changeRxnBounds(model,'r_1714_REV',0,'u'); +model=changeRxnBounds(model,'r_1718_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.11,'l'); +model=changeObjective(model,'newRxn10'); +FBAsolution=optimizeCbModel(model) +cd ../../result_ecYeast/ecModels +save ecCoumaric_acid_xylose.mat model +% Tyrosol + Salidroside +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +MW1=57.45; +Kcat2=6.6288*3600; +MW2=42.043; +Kcat3=10.0095*3600; +MW3=92.395; +MW4=96.127; +MW5=55.01; +model = addReaction(model,'newRxn1','metaboliteList',{'s_1051','s_1275','s_0803','prot_Q06086','s_4394','s_0456','s_4395','s_0837'},'stoichCoeffList',[-1 -1 -1 -1 1 1 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_1377','s_1198','prot_P07023','s_0204','s_0456','s_1203','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_0557','s_1322','prot_A0A0L0LT01','s_4396','s_0551','s_0803'},'stoichCoeffList',[-1 -1 -1/Kcat3 1 1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4394','s_1203','s_0794','prot_P0A9Q7','s_4397','s_1198'},'stoichCoeffList',[-1 -1 -1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_4397','s_1543','prot_Q9SK82','s_1538','s_4398'},'stoichCoeffList',[-1 -1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_4397','s_4399'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'s_4399'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'s_4398','s_4400'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_4400'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'prot_pool','prot_Q06086'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'prot_pool','prot_P07023'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn12','metaboliteList',{'prot_pool','prot_A0A0L0LT01'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn13','metaboliteList',{'prot_pool','prot_P0A9Q7'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn14','metaboliteList',{'prot_pool','prot_Q9SK82'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'newRxn15','metaboliteList',{'s_4395','s_4401'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn16','metaboliteList',{'s_4399'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn17','metaboliteList',{'s_4396','s_4402'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn18','metaboliteList',{'s_4402'},'stoichCoeffList',[-1],'reversible',false) +model = removeGenes(model,'YNL316C'); % delete PHA2 +model = removeGenes(model,'YLR044C'); % delete PDC1 +model = removeGenes(model,'YKL211C'); % delete TRP3 +model=changeGeneAssociation(model,'newRxn1','AAS'); +model=changeGeneAssociation(model,'newRxn2','TyrAM53I/A354V'); +model=changeGeneAssociation(model,'newRxn3','xfp'); +model=changeGeneAssociation(model,'newRxn4','ADH'); +model=changeGeneAssociation(model,'newRxn5','UGT85A1'); +model.geneShortNames(1125)={'AAS'}; +model.geneShortNames(1126)={'TyrAM53I/A354V'}; +model.geneShortNames(1127)={'xfp'}; +model.geneShortNames(1128)={'ADH'}; +model.geneShortNames(1129)={'UGT85A1'}; +model.enzymes(964)={'Q06086'}; +model.enzymes(965)={'P07023'}; +model.enzymes(966)={'A0A0L0LT01'}; +model.enzymes(967)={'P0A9Q7'}; +model.enzymes(968)={'Q9SK82'}; +model.enzGenes(964)={'AAS'}; +model.enzGenes(965)={'TyrAM53I/A354V'}; +model.enzGenes(966)={'xfp'}; +model.enzGenes(967)={'ADH'}; +model.enzGenes(968)={'UGT85A1'}; +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)=3; +model.metComps(4158)=3; +model.metComps(4159)=3; +model.metComps(4160)=3; +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn7'); % For tyrosol production +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 ecTyrosol.mat model +model=changeObjective(model,'newRxn9'); % For salidroside production +FBAsolution=optimizeCbModel(model) +save ecSalidroside.mat model +% Miltiradiene +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +MW1=90.483; +MW2=68.37; +Kcat1=6.6*3600; +Kcat2=2.2*3600; +Kcat3=92.5526*3600; +model = addReaction(model,'r_0373No1','metaboliteList',{'s_0190','s_0943','prot_Q12051','s_0633','s_0189'},'stoichCoeffList',[-1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'r_0355No1','metaboliteList',{'s_0943','s_1376','prot_P08524','s_0633','s_0745'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'r_0462No1','metaboliteList',{'s_0745','s_0943','prot_P08524','s_0190','s_0633'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'r_0558No1','metaboliteList',{'pmet_r_0558','prot_P12684','s_0028','s_0529','s_1207'},'stoichCoeffList',[-1 -1/Kcat3 1 1 2],'reversible',false); +model = addReaction(model,'newRxn1','metaboliteList',{'s_0189','prot_B8PQ84','s_4403'},'stoichCoeffList',[-1 -1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_4403','prot_C8XPS0','s_0633','s_4404'},'stoichCoeffList',[-1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_4404','s_4405'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4405'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'prot_pool','prot_B8PQ84'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'prot_pool','prot_C8XPS0'},'stoichCoeffList',[-MW2 1],'reversible',false); +model=changeGeneAssociation(model,'newRxn1','CPS'); +model=changeGeneAssociation(model,'newRxn2','KSL'); +model.geneShortNames(1128)={'CPS'}; +model.geneShortNames(1129)={'KSL'}; +model.enzymes(964)={'B8PQ84'}; +model.enzymes(965)={'C8XPS0'}; +model.enzGenes(964)={'CPS'}; +model.enzGenes(965)={'KSL'}; +model.metComps(4147)=1; +model.metComps(4148)=1; +model.metComps(4149)=1; +model.metComps(4150)=1; +model.metComps(4151)=3; +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn4'); +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 ecMiltiradiene.mat model +% Caffeic acid +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +MW1=57.927; +MW2=55.539; +MW3=39.7487; +MW4=29.7468; +Kcat2=27.7*3600; +Kcat3=0.0828*3600; +Kcat4=0.1339*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_4231','prot_O22203','s_4387'},'stoichCoeffList',[-1 -1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_1051','prot_A0A1M4NET9','s_0419','s_4231'},'stoichCoeffList',[-1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_0551','s_0803','s_1360','prot_P32449ly','s_0349','s_1322'},'stoichCoeffList',[-1 -1 -1 -1/Kcat3 1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_0515','prot_P32178ly','s_1377'},'stoichCoeffList',[-1 -1/Kcat4 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'prot_pool','prot_O22203'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'prot_pool','prot_A0A1M4NET9'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'prot_pool','prot_P32449ly'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'prot_pool','prot_P32178ly'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_4387','s_4406'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'s_4406'},'stoichCoeffList',[-1],'reversible',false); +model = removeGenes(model,'YDR380W'); % delete ARO10 +model = removeGenes(model,'YLR134W'); % delete PDC5 +model=changeGeneAssociation(model,'newRxn1','C3H'); +model=changeGeneAssociation(model,'newRxn2','TAL'); +model=changeGeneAssociation(model,'newRxn3','ARO4K229L'); +model=changeGeneAssociation(model,'newRxn4','ARO7G141S'); +model.geneShortNames(1126)={'C3H'}; +model.geneShortNames(1127)={'TAL'}; +model.geneShortNames(1128)={'ARO4K229L'}; +model.geneShortNames(1129)={'ARO7G141S'}; +model.enzymes(964)={'O22203'}; +model.enzymes(965)={'A0A1M4NET9'}; +model.enzymes(966)={'P32449ly'}; +model.enzymes(967)={'P32178ly'}; +model.enzGenes(964)={'C3H'}; +model.enzGenes(965)={'TAL'}; +model.enzGenes(966)={'ARO4K229L'}; +model.enzGenes(967)={'ARO7G141S'}; +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=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn10'); +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 ecCaffeic_acid.mat model + +% Valencene +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.0032*3600; +MW1=69.219; +Kcat2=92.5526*3600; +Kcat3=6.8*3600; +Kcat4=1800*3600; +Kcat5=10000000*3600; +Kcat6=43.8001*3600; +Kcat7=0.83*3600; +Kcat8=9.8*3600; +Kcat9=2.2*3600; +Kcat10=59800*3600; +Kcat11=0.1212*3600; +Kcat12=0.825*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0190','prot_S4SC87','s_4407','s_0633'},'stoichCoeffList',[-1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'r_0558No1','metaboliteList',{'pmet_r_0558','prot_P12684','s_0028','s_0529','s_1207'},'stoichCoeffList',[-1 -1/Kcat2 1 1 2],'reversible',false); +model = addReaction(model,'r_0904No1','metaboliteList',{'s_0019','s_0434','prot_P24521','s_0018','s_0394'},'stoichCoeffList',[-1 -1 -1/Kcat3 1 1],'reversible',false); +model = addReaction(model,'r_0103No1','metaboliteList',{'s_0373','prot_P41338','s_0367','s_0529'},'stoichCoeffList',[-2 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'r_0104No1','metaboliteList',{'s_0376','prot_P41338','s_0370','s_0532'},'stoichCoeffList',[-2 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'r_0103_REVNo1','metaboliteList',{'s_0367','s_0529','prot_P41338','s_0373'},'stoichCoeffList',[-1 -1 -1/Kcat5 2],'reversible',false); +model = addReaction(model,'r_0104_REVNo1','metaboliteList',{'s_0370','s_0532','prot_P41338','s_0376'},'stoichCoeffList',[-1 -1 -1/Kcat5 2],'reversible',false); +model = addReaction(model,'r_0735No1','metaboliteList',{'s_0028','s_0434','prot_P07277','s_0019','s_0394','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1 1],'reversible',false); +model = addReaction(model,'r_0736No1','metaboliteList',{'s_0028','s_0539','prot_P07277','s_0019','s_0467','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1 1],'reversible',false); +model = addReaction(model,'r_0737No1','metaboliteList',{'s_0028','s_0785','prot_P07277','s_0019','s_0739','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1 1],'reversible',false); +model = addReaction(model,'r_0738No1','metaboliteList',{'s_0028','s_1559','prot_P07277','s_0019','s_1538','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1 1],'reversible',false); +model = addReaction(model,'r_0559No1','metaboliteList',{'s_0367','s_0373','s_0803','prot_P54839','s_0218','s_0529','s_0794'},'stoichCoeffList',[-1 -1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0560No1','metaboliteList',{'s_0370','s_0376','s_0807','prot_P54839','s_0221','s_0532','s_0799'},'stoichCoeffList',[-1 -1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0739No1','metaboliteList',{'s_0018','s_0434','prot_P32377','s_0394','s_0456','s_0943','s_1322'},'stoichCoeffList',[-1 -1 -1/Kcat8 1 1 1 1],'reversible',false); +model = addReaction(model,'r_0355No1','metaboliteList',{'s_0943','s_1376','prot_P08524','s_0633','s_0745'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1],'reversible',false); +model = addReaction(model,'r_0462No1','metaboliteList',{'s_0745','s_0943','prot_P08524','s_0190','s_0633'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1],'reversible',false); +model = addReaction(model,'r_0667No1','metaboliteList',{'s_0943','prot_P15496','s_1376'},'stoichCoeffList',[-1 -1/Kcat10 1],'reversible',false); +model = addReaction(model,'r_0667_REVNo1','metaboliteList',{'s_1376','prot_P15496','s_0943'},'stoichCoeffList',[-1 -1/Kcat11 1],'reversible',false); +model = addReaction(model,'r_1012No1','metaboliteList',{'s_0190','s_0794','s_1212','prot_P29704','s_0633','s_1207','s_1447'},'stoichCoeffList',[-2 -1 -1 -1/Kcat12 2 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_4407','s_4408'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_4408'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'prot_pool','prot_S4SC87'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = removeGenes(model,'YPL069C'); % delete BTS1 +model = removeGenes(model,'YDR284C'); % delete DPP1 +model = removeGenes(model,'YDR503C'); % delete LPP1 +model=changeGeneAssociation(model,'newRxn1','VS'); +model.geneShortNames(1125)={'VS'}; +model.enzymes(964)={'S4SC87'}; +model.enzGenes(964)={'VS'}; +model.metComps(4147)=1; +model.metComps(4148)=1; +model.metComps(4149)=3; +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn3'); +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 ecValencene.mat model + +% Glycyrrhetinic acid +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.77*3600; +MW1=87.516; +MW2=56.456; +MW3=59.454; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0037','prot_Q9MB42','s_4272'},'stoichCoeffList',[-1 -1/Kcat1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_4272','s_1275','prot_A0A218KSA8','s_4409','s_0803'},'stoichCoeffList',[-1 -2 -1 1 3],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_4409','s_1275','prot_H1A981','s_4410','s_0803'},'stoichCoeffList',[-1 -3 -1 1 4],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4410','s_4411'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_4411'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'prot_pool','prot_Q9MB42'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'prot_pool','prot_A0A218KSA8'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'prot_pool','prot_H1A981'},'stoichCoeffList',[-MW3 1],'reversible',false); +model=changeGeneAssociation(model,'newRxn1','bAS'); +model=changeGeneAssociation(model,'newRxn2','uni25647'); +model=changeGeneAssociation(model,'newRxn3','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.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=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn5'); +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 ecGlycyrrhetinic_acid.mat model +% Paclitaxel precursor +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.16*3600; +MW1=97.962; +Kcat2=8.4*3600; +MW2=42.153; +MW3=86.497; +Kcat4=7.03*3600; +MW4=42.151; +MW5=56.558; +Kcat6=29.59*3600; +MW6=49.08; +Kcat7=6.8*3600; +Kcat8=43.8001*3600; +Kcat9=9.8*3600; +Kcat10=2.2*3600; +Kcat11=59800*3600; +Kcat12=0.1212*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0189','prot_Q2PRN4','s_0633','s_4412'},'stoichCoeffList',[-1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'r_0904No1','metaboliteList',{'s_0019','s_0434','prot_P24521','s_0018','s_0394'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1],'reversible',false); +model = addReaction(model,'r_0735No1','metaboliteList',{'s_0028','s_0434','prot_P07277','s_0019','s_0394','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'r_0736No1','metaboliteList',{'s_0028','s_0539','prot_P07277','s_0019','s_0467','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'r_0737No1','metaboliteList',{'s_0028','s_0785','prot_P07277','s_0019','s_0739','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'r_0738No1','metaboliteList',{'s_0028','s_1559','prot_P07277','s_0019','s_1538','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'r_0739No1','metaboliteList',{'s_0018','s_0434','prot_P32377','s_0394','s_0456','s_0943','s_1322'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1 1 1],'reversible',false); +model = addReaction(model,'r_0355No1','metaboliteList',{'s_0943','s_1376','prot_P08524','s_0633','s_0745'},'stoichCoeffList',[-1 -1 -1/Kcat10 1 1],'reversible',false); +model = addReaction(model,'r_0462No1','metaboliteList',{'s_0745','s_0943','prot_P08524','s_0190','s_0633'},'stoichCoeffList',[-1 -1 -1/Kcat10 1 1],'reversible',false); +model = addReaction(model,'r_0667No1','metaboliteList',{'s_0943','prot_P15496','s_1376'},'stoichCoeffList',[-1 -1/Kcat11 1],'reversible',false); +model = addReaction(model,'r_0667_REVNo1','metaboliteList',{'s_1376','prot_P15496','s_0943'},'stoichCoeffList',[-1 -1/Kcat12 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0190','s_0943','prot_Q1L6K3','s_0633','s_0189'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_0373','prot_Q9FD70','s_0529','s_0367'},'stoichCoeffList',[-1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_0373','s_0367','s_0803','prot_Q9FD71','s_0218','s_0529'},'stoichCoeffList',[-1 -1 -1 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_4412','s_1275','prot_Q6WG30','s_4413','s_0803'},'stoichCoeffList',[-1 -1 -1 1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_4413','s_0373','prot_Q9M6F0','s_4414','s_0529'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'s_4414','s_4415'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'s_4415'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'prot_pool','prot_Q2PRN4'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'prot_pool','prot_Q1L6K3'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'prot_pool','prot_Q9FD70'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn12','metaboliteList',{'prot_pool','prot_Q9FD71'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn13','metaboliteList',{'prot_pool','prot_Q6WG30'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'newRxn14','metaboliteList',{'prot_pool','prot_Q9M6F0'},'stoichCoeffList',[-MW6 1],'reversible',false); +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,'newRxn6','TAT'); +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)=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)={'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 +% nootkatone +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.0032*3600; +MW1=69.219; +Kcat2=15.9*3600; +MW2=56.788; +Kcat3=4.4*3600; +MW3=28.67; +Kcat4=2.2*3600; +Kcat5=92.5526*3600; +Kcat6=0.825*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0190','prot_S4SC87','s_4407','s_0633'},'stoichCoeffList',[-1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_4407','s_1275','prot_A6YIH8','s_0803','s_4420'},'stoichCoeffList',[-1 -2 -1/Kcat2 3 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_4420','prot_F1SWA0','s_4421'},'stoichCoeffList',[-1 -1/Kcat3 1],'reversible',false); +model = addReaction(model,'r_0355No1','metaboliteList',{'s_0943','s_1376','prot_P08524','s_0633','s_0745'},'stoichCoeffList',[-1 -1 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'r_0462No1','metaboliteList',{'s_0745','s_0943','prot_P08524','s_0190','s_0633'},'stoichCoeffList',[-1 -1 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'r_1012No1','metaboliteList',{'s_0190','s_0794','s_1212','prot_P29704','s_0633','s_1207','s_1447'},'stoichCoeffList',[-2 -1 -1 -1/Kcat6 2 1 1],'reversible',false); +model = addReaction(model,'r_0558No1','metaboliteList',{'pmet_r_0558','prot_P12684','s_0028','s_0529','s_1207'},'stoichCoeffList',[-1 -1/Kcat5 1 1 2],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4421','s_4422'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_4422'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'prot_pool','prot_S4SC87'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'prot_pool','prot_A6YIH8'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'prot_pool','prot_F1SWA0'},'stoichCoeffList',[-MW3 1],'reversible',false); +model=changeGeneAssociation(model,'newRxn1','VS'); +model=changeGeneAssociation(model,'newRxn2','HPO'); +model=changeGeneAssociation(model,'newRxn3','ZSD1'); +model.geneShortNames(1128)={'VS'}; +model.geneShortNames(1129)={'HPO'}; +model.geneShortNames(1130)={'ZSD1'}; +model.enzymes(964)={'S4SC87'}; +model.enzymes(965)={'A6YIH8'}; +model.enzymes(966)={'F1SWA0'}; +model.enzGenes(964)={'VS'}; +model.enzGenes(965)={'HPO'}; +model.enzGenes(966)={'ZSD1'}; +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=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn5'); +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 ecNootkatone.mat model +% Squalene +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +MW1=45.41; +MW2=33.168; +Kcat1=92.5526*3600; +Kcat2=2.2*3600; +Kcat3=3.3*3600; +Kcat4=6.8*3600; +Kcat5=1800*3600; +Kcat6=10000000*3600; +Kcat7=43.8001*3600; +Kcat8=0.83*3600; +Kcat9=9.8*3600; +Kcat10=286*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0218','s_1203','s_0794','prot_Q5LL64','s_0028','s_0529','s_1198'},'stoichCoeffList',[-1 -2 -2 -1 1 1 2],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0359','s_1198','s_0529','prot_A0A0A8FFU5','s_0367','s_0794','s_1203'},'stoichCoeffList',[-1 -1 -1 -1 1 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'prot_pool','prot_Q5LL64'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'prot_pool','prot_A0A0A8FFU5'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'r_0558No1','metaboliteList',{'pmet_r_0558','prot_P12684','s_0028','s_0529','s_1207'},'stoichCoeffList',[-1 -1/Kcat1 1 1 2],'reversible',false); +model = addReaction(model,'r_0904No1','metaboliteList',{'s_0019','s_0434','prot_P24521','s_0018','s_0394'},'stoichCoeffList',[-1 -1 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'r_0103No1','metaboliteList',{'s_0373','prot_P41338','s_0367','s_0529'},'stoichCoeffList',[-2 -1/Kcat5 1 1],'reversible',false); +model = addReaction(model,'r_0104No1','metaboliteList',{'s_0376','prot_P41338','s_0370','s_0532'},'stoichCoeffList',[-2 -1/Kcat5 1 1],'reversible',false); +model = addReaction(model,'r_0103_REVNo1','metaboliteList',{'s_0367','s_0529','prot_P41338','s_0373'},'stoichCoeffList',[-1 -1 -1/Kcat6 2],'reversible',false); +model = addReaction(model,'r_0104_REVNo1','metaboliteList',{'s_0370','s_0532','prot_P41338','s_0376'},'stoichCoeffList',[-1 -1 -1/Kcat6 2],'reversible',false); +model = addReaction(model,'r_0735No1','metaboliteList',{'s_0028','s_0434','prot_P07277','s_0019','s_0394','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0736No1','metaboliteList',{'s_0028','s_0539','prot_P07277','s_0019','s_0467','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0737No1','metaboliteList',{'s_0028','s_0785','prot_P07277','s_0019','s_0739','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0738No1','metaboliteList',{'s_0028','s_1559','prot_P07277','s_0019','s_1538','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0559No1','metaboliteList',{'s_0367','s_0373','s_0803','prot_P54839','s_0218','s_0529','s_0794'},'stoichCoeffList',[-1 -1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'r_0560No1','metaboliteList',{'s_0370','s_0376','s_0807','prot_P54839','s_0221','s_0532','s_0799'},'stoichCoeffList',[-1 -1 -1 -1/Kcat8 1 1 1],'reversible',false); +model = addReaction(model,'r_0739No1','metaboliteList',{'s_0018','s_0434','prot_P32377','s_0394','s_0456','s_0943','s_1322'},'stoichCoeffList',[-1 -1 -1/Kcat9 1 1 1 1],'reversible',false); +model = addReaction(model,'r_0355No1','metaboliteList',{'s_0943','s_1376','prot_P08524','s_0633','s_0745'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'r_0462No1','metaboliteList',{'s_0745','s_0943','prot_P08524','s_0190','s_0633'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'r_1012No1','metaboliteList',{'s_0190','s_0794','s_1212','prot_P29704','s_0633','s_1207','s_1447'},'stoichCoeffList',[-2 -1 -1 -1/Kcat3 2 1 1],'reversible',false); +model = addReaction(model,'r_0163No1','metaboliteList',{'s_0680','s_1198','prot_P00331','s_0359','s_0794','s_1203'},'stoichCoeffList',[-1 -1 -1/Kcat10 1 1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_1447','s_4433'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_4433'},'stoichCoeffList',[-1],'reversible',false); +model=changeGeneAssociation(model,'newRxn1','mvaA'); +model=changeGeneAssociation(model,'newRxn2','ADA'); +model.geneShortNames(1128)={'mvaA'}; +model.geneShortNames(1129)={'ADA'}; +model.enzymes(964)={'Q5LL64'}; +model.enzymes(965)={'A0A0A8FFU5'}; +model.enzGenes(964)={'mvaA'}; +model.enzGenes(965)={'ADA'}; +model.metComps(4147)=1; +model.metComps(4148)=1; +model.metComps(4149)=3; +cd ../../strain_design_ecYeast +c_sourceID = 'D-glucose exchange (reversible)'; +model = lychangeMedia_batch(model,c_sourceID,'YEP'); +model=changeRxnBounds(model,'r_1714_REV',0,'u'); +model=changeRxnBounds(model,'r_1761_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn6'); +FBAsolution=optimizeCbModel(model) +cd ../result_ecYeast/ecModels +save ecSqualene.mat model +% Tropane alkaloids (cinnamoyltropine) +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +MW1=66.706; +MW2=33.557; +MW3=36.976; +MW4=37.727; +MW5=43.267; +MW6=59.479; +MW7=29.617; +MW8=78.726; +MW9=62.559; +MW10=48.753; +Kcat1=9.9*3600; +Kcat4=5.14*3600; +Kcat7=25.6*3600; +Kcat8=1.8*3600; +Kcat9=5.8805*3600; +Kcat11=8.4*3600; +Kcat12=0.54*3600; +Kcat13=0.44*3600; +Kcat14=1.56*3600; +Kcat15=78*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0965','s_0794','prot_P22220','s_4423','s_0456'},'stoichCoeffList',[-1 -1 -1/Kcat1 1 1 ],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_4423','s_0803','prot_P60651','s_1389','s_1552'},'stoichCoeffList',[-1 -1 -1 1 1 ],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_1389','s_1416','prot_Q9S7W8','prot_Q70EW6','s_1413','s_4424'},'stoichCoeffList',[-1 -1 -1 -1/Kcat4 1 1 ],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4424','s_1275','s_0803','s_0837','s_4395','s_4425'},'stoichCoeffList',[-1 -1 -1 1 1 1 ],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_4425','s_4426','s_0803'},'stoichCoeffList',[-1 1 1 ],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_4426','prot_A0A3G4RHW3','s_4427'},'stoichCoeffList',[-1 -1 1 ],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'s_4427','prot_A0A3G4RHY7','s_4428'},'stoichCoeffList',[-1 -1 1 ],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'s_4428','s_1212','s_0794','prot_P50162','s_4429','s_1207'},'stoichCoeffList',[-1 -1 -1 -1/Kcat7 1 1 ],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_1032','prot_P35510','s_0419','s_4219'},'stoichCoeffList',[-1 -1/Kcat8 1 1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'s_4219','s_0434','s_0529','prot_Q9LU36','s_0633','s_0423','s_4430'},'stoichCoeffList',[-1 -1 -1 -1/Kcat9 1 1 1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'s_4429','s_4430','prot_A0A059Q4T4','s_4431'},'stoichCoeffList',[-1 -1 -1 1],'reversible',false); +model = addReaction(model,'newRxn12','metaboliteList',{'s_4431','s_4432'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn13','metaboliteList',{'s_4432'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn14','metaboliteList',{'prot_pool','prot_P22220'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn15','metaboliteList',{'prot_pool','prot_P60651'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn16','metaboliteList',{'prot_pool','prot_Q9S7W8'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn17','metaboliteList',{'prot_pool','prot_Q70EW6'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn18','metaboliteList',{'prot_pool','prot_A0A3G4RHW3'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'newRxn19','metaboliteList',{'prot_pool','prot_A0A3G4RHY7'},'stoichCoeffList',[-MW6 1],'reversible',false); +model = addReaction(model,'newRxn20','metaboliteList',{'prot_pool','prot_P50162'},'stoichCoeffList',[-MW7 1],'reversible',false); +model = addReaction(model,'newRxn21','metaboliteList',{'prot_pool','prot_P35510'},'stoichCoeffList',[-MW8 1],'reversible',false); +model = addReaction(model,'newRxn22','metaboliteList',{'prot_pool','prot_Q9LU36'},'stoichCoeffList',[-MW9 1],'reversible',false); +model = addReaction(model,'newRxn23','metaboliteList',{'prot_pool','prot_A0A059Q4T4'},'stoichCoeffList',[-MW10 1],'reversible',false); +model = addReaction(model,'r_0817No1','metaboliteList',{'s_0794','s_1266','prot_P08432','s_0456','s_1389'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_0206No1','metaboliteList',{'s_0803','s_0965','prot_P00812','s_1266','s_1552'},'stoichCoeffList',[-1 -1 -1/Kcat12 1 1],'reversible',false); +model = addReaction(model,'r_0761No1','metaboliteList',{'pmet_r_0761','prot_P40360','s_0532','s_0799','s_1192'},'stoichCoeffList',[-1 -1/Kcat13 1 1 1],'reversible',false); +model = addReaction(model,'r_0761_REVNo1','metaboliteList',{'prot_P40360','pmet_r_0761_REV','s_0376','s_0993'},'stoichCoeffList',[-1/Kcat14 -1 1 1],'reversible',false); +model = addReaction(model,'r_0929No1','metaboliteList',{'s_0803','s_1180','s_1275','prot_P50264','s_0208','s_0837','s_1193'},'stoichCoeffList',[-1 -1 -1 -1/Kcat15 1 1 1],'reversible',false); +model = addReaction(model,'r_0936No1','metaboliteList',{'s_0803','s_1181','s_1275','prot_P50264','s_0208','s_0837','s_1180'},'stoichCoeffList',[-1 -1 -1 -1/Kcat15 1 1 1],'reversible',false); +model = addReaction(model,'r_0937No1','metaboliteList',{'s_0803','s_1442','s_1275','prot_P50264','s_0208','s_0837','s_1439'},'stoichCoeffList',[-1 -1 -1 -1/Kcat15 1 1 1],'reversible',false); +model = addReaction(model,'newRxn24','metaboliteList',{'s_4395','s_4401'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn25','metaboliteList',{'s_4401'},'stoichCoeffList',[-1],'reversible',false); +model=changeGeneAssociation(model,'newRxn1','ADC'); +model=changeGeneAssociation(model,'newRxn2','speB'); +model=changeGeneAssociation(model,'newRxn3','AtPMT1'); +model=changeGeneAssociation(model,'newRxn3','DsPMT1'); +model=changeGeneAssociation(model,'newRxn4','MPO1'); +model=changeGeneAssociation(model,'newRxn6','PYKS'); +model=changeGeneAssociation(model,'newRxn7','CYP82M3'); +model=changeGeneAssociation(model,'newRxn8','TR1'); +model=changeGeneAssociation(model,'newRxn9','PAL1'); +model=changeGeneAssociation(model,'newRxn10','4CL5'); +model=changeGeneAssociation(model,'newRxn11','CS'); +model.geneShortNames(1128)={'ADC'}; +model.geneShortNames(1129)={'speB'}; +model.geneShortNames(1130)={'AtPMT1'}; +model.geneShortNames(1131)={'DsPMT1'}; +model.geneShortNames(1132)={'MPO1'}; +model.geneShortNames(1133)={'PYKS'}; +model.geneShortNames(1134)={'CYP82M3'}; +model.geneShortNames(1135)={'TR1'}; +model.geneShortNames(1136)={'PAL1'}; +model.geneShortNames(1137)={'4CL5'}; +model.geneShortNames(1138)={'CS'}; +model.enzymes(964)={'P22220'}; +model.enzymes(965)={'P60651'}; +model.enzymes(966)={'Q9S7W8'}; +model.enzymes(967)={'Q70EW6'}; +model.enzymes(968)={'A0A3G4RHW3'}; +model.enzymes(969)={'A0A3G4RHY7'}; +model.enzymes(970)={'P50162'}; +model.enzymes(971)={'P35510'}; +model.enzymes(972)={'Q9LU36'}; +model.enzymes(973)={'A0A059Q4T4'}; +model.enzGenes(964)={'ADC'}; +model.enzGenes(965)={'speB'}; +model.enzGenes(966)={'AtPMT1'}; +model.enzGenes(967)={'DsPMT1'}; +model.enzGenes(968)={'PYKS'}; +model.enzGenes(969)={'CYP82M3'}; +model.enzGenes(970)={'TR1'}; +model.enzGenes(971)={'PAL1'}; +model.enzGenes(972)={'4CL5'}; +model.enzGenes(973)={'CS'}; +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)=1; +model.metComps(4162)=1; +model.metComps(4163)=1; +model.metComps(4164)=1; +model.metComps(4165)=1; +model.metComps(4166)=1; +model.metComps(4167)=1; +model.metComps(4168)=3; +model.metComps(4169)=3; +cd ../../strain_design_ecYeast +c_sourceID = 'D-glucose exchange (reversible)'; +model = lychangeMedia_batch(model,c_sourceID,'YEP'); +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn13'); +model = removeGenes(model,'YMR170C'); % delete ALD2 +model = removeGenes(model,'YMR169C'); % delete ALD3 +model = removeGenes(model,'YOR374W'); % delete ALD4 +model = removeGenes(model,'YER073W'); % delete ALD5 +model = removeGenes(model,'YMR110C'); % delete HFD1 +model = removeGenes(model,'YLR017W'); % delete MEU1 +FBAsolution=optimizeCbModel(model) +cd ../result_ecYeast/ecModels +save ecCinnamoyltropine.mat model +% L-(+)-Ergothioneine +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=0.0716*3600; +MW1=99.025; +MW2=39.033; +model = addReaction(model,'newRxn1','metaboliteList',{'s_1006','s_1416','prot_Q7RX33','s_0794','s_4434','s_1413'},'stoichCoeffList',[-1 -3 -1/Kcat1 3 1 3],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_4434','s_0981','s_1275','prot_Q7RX33','s_0803','s_4435'},'stoichCoeffList',[-1 -1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_4435','prot_A0R5M7','s_4436','s_1399','s_4395'},'stoichCoeffList',[-1 -1 1 1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4436','s_4437'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_4437'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'prot_pool','prot_Q7RX33'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'prot_pool','prot_A0R5M7'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'s_4395','s_4401'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_4401'},'stoichCoeffList',[-1],'reversible',false); +model=changeGeneAssociation(model,'newRxn1','Egt1'); +model=changeGeneAssociation(model,'newRxn2','Egt1'); +model=changeGeneAssociation(model,'newRxn3','Egr2'); +model.geneShortNames(1128)={'Egt1'}; +model.geneShortNames(1129)={'Egt2'}; +model.enzymes(964)={'Q7RX33'}; +model.enzymes(965)={'A0R5M7'}; +model.enzGenes(964)={'Egt1'}; +model.enzGenes(965)={'Egt2'}; +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(4154)=3; +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn5'); +model=changeRxnBounds(model,'r_1879_REV',1,'u'); % add arginine +model=changeRxnBounds(model,'r_1893_REV',1,'u'); % add histidine +model=changeRxnBounds(model,'r_1902_REV',1,'u'); % add methionine +model=changeRxnBounds(model,'r_2028_REV',1,'u'); % add pyridoxine +FBAsolution=optimizeCbModel(model) +cd ../../result_ecYeast/ecModels +save ecErgothioneine.mat model +% S-adenosyl-L-methionine +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=1.7660e-04*3600; +model = addReaction(model,'r_0726No1','metaboliteList',{'pmet_r_0726','prot_P19358','s_0633','s_1322','s_1416'},'stoichCoeffList',[-1 -1/Kcat1 1 1 1],'reversible',false); +model = addReaction(model,'newRxn1','metaboliteList',{'s_1416','s_1418'},'stoichCoeffList',[-1 1],'reversible',false); +model = removeGenes(model,'YOL052C'); % delete SPE2 +cd ../../strain_design_ecYeast +c_sourceID = 'D-glucose exchange (reversible)'; +model = lychangeMedia_batch(model,c_sourceID,'YEP'); +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.159,'l'); +model=changeObjective(model,'r_2043'); +FBAsolution=optimizeCbModel(model) +cd ../result_ecYeast/ecModels +save ecS-adenosyl-L-methionine.mat model +% 2'-Fucosyllactose +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=27.5*3600; +MW1=35.923; +Kcat2=30.33*3600; +MW2=38.521; +Kcat3=1.1448*3600; +MW3=69.397; +Kcat4=5*3600; +MW4=41.674; +Kcat5=1.5*3600; +MW5=36.141; +Kcat6=3.96*3600; +MW6=34.942; +MW7=65.383; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0578','s_0794','s_1203','prot_P31867','s_1566','s_1198'},'stoichCoeffList',[-1 -1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0578','s_0794','s_1212','prot_P31867','s_1566','s_1207'},'stoichCoeffList',[-1 -1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_1566','s_1198','prot_P22144','s_0580','s_0794','s_1203'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_0434','s_0580','prot_Q9P938','s_0394','s_0581','s_0794'},'stoichCoeffList',[-1 -1 -1/Kcat3 1 1 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_0743','prot_O85339','s_0803','s_4438'},'stoichCoeffList',[-1 -1/Kcat4 1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_4438','s_1212','s_0794','prot_P32055','s_1207','s_4439'},'stoichCoeffList',[-1 -1 -1 -1/Kcat5 1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'s_4439','s_4444','prot_A6M9C2','s_0739','s_4440'},'stoichCoeffList',[-1 -1 -1/Kcat6 1 1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'s_4440','s_4441'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'s_4441'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'prot_pool','prot_P31867'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'prot_pool','prot_P22144'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn12','metaboliteList',{'prot_pool','prot_Q9P938'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn13','metaboliteList',{'prot_pool','prot_O85339'},'stoichCoeffList',[-MW4 1],'reversible',false); +model = addReaction(model,'newRxn14','metaboliteList',{'prot_pool','prot_P32055'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'newRxn15','metaboliteList',{'prot_pool','prot_A6M9C2'},'stoichCoeffList',[-MW6 1],'reversible',false); +model = addReaction(model,'newRxn16','metaboliteList',{'s_4443'},'stoichCoeffList',[1],'reversible',false); +model = addReaction(model,'newRxn17','metaboliteList',{'s_4443','prot_P07921','s_4444'},'stoichCoeffList',[-1 -1 1],'reversible',false); +model = addReaction(model,'newRxn18','metaboliteList',{'prot_pool','prot_P07921'},'stoichCoeffList',[-MW7 1],'reversible',false); +model = removeGenes(model,'YDL236W'); % delete PHO13 +model = removeGenes(model,'YPL061W'); % delete ALD6 +model=changeGeneAssociation(model,'newRxn1','XYL1'); +model=changeGeneAssociation(model,'newRxn2','XYL1'); +model=changeGeneAssociation(model,'newRxn3','XYL2'); +model=changeGeneAssociation(model,'newRxn4','XYL3'); +model=changeGeneAssociation(model,'newRxn5','Gmd'); +model=changeGeneAssociation(model,'newRxn6','WcaG'); +model=changeGeneAssociation(model,'newRxn7','WbgL'); +model=changeGeneAssociation(model,'newRxn8','Lac12'); +model.geneShortNames(1126)={'XYL1'}; +model.geneShortNames(1127)={'XYL2'}; +model.geneShortNames(1128)={'XYL3'}; +model.geneShortNames(1129)={'Gmd'}; +model.geneShortNames(1130)={'WcaG'}; +model.geneShortNames(1131)={'WbgL'}; +model.geneShortNames(1132)={'Lac12'}; +model.enzymes(964)={'P31867'}; +model.enzymes(965)={'P22144'}; +model.enzymes(966)={'Q9P938'}; +model.enzymes(967)={'O85339'}; +model.enzymes(968)={'P32055'}; +model.enzymes(969)={'A6M9C2'}; +model.enzymes(970)={'P07921'}; +model.enzGenes(964)={'XYL1'}; +model.enzGenes(965)={'XYL2'}; +model.enzGenes(966)={'XYL3'}; +model.enzGenes(967)={'Gmd'}; +model.enzGenes(968)={'WcaG'}; +model.enzGenes(969)={'WbgL'}; +model.enzGenes(970)={'Lac12'}; +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)=3; +model.metComps(4158)=3; +model.metComps(4159)=1; +cd ../../strain_design_ecYeast +c_sourceID = 'D-xylose exchange (reversible)'; +model = lychangeMedia_batch(model,c_sourceID,'YEP'); +model=changeRxnBounds(model,'newRxn16',1,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn9'); +FBAsolution=optimizeCbModel(model) +cd ../result_ecYeast/ecModels +save ec2_Fucosyllactose.mat model +% lycopene +cd ../../../ModelFiles/mat +load('ecYeastGEM_batch.mat'); +model = ecModel_batch; +Kcat1=3.3*3600; +MW1=42.572; +MW2=32.786; +MW3=66.46; +Kcat5=9400*3600; +MW5=72.153; +Kcat6=92.5526*3600; +Kcat7=286*3600; +Kcat8=43.9999*3600; +Kcat9=1.68*3600; +Kcat10=32.2*3600; +Kcat11=23.1467*3600; +Kcat12=65.3426*3600; +Kcat13=1*3600; +Kcat14=0.7*3600; +model = addReaction(model,'newRxn1','metaboliteList',{'s_0190','s_0943','prot_Q9ZPM3','s_0633','s_0189'},'stoichCoeffList',[-1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'newRxn2','metaboliteList',{'s_0189','prot_D5KXJ0','s_0633','s_4236'},'stoichCoeffList',[-2 -1 2 1],'reversible',false); +model = addReaction(model,'newRxn3','metaboliteList',{'s_4236','prot_Q5BTY7','s_4237'},'stoichCoeffList',[-1 -1 1],'reversible',false); +model = addReaction(model,'newRxn4','metaboliteList',{'s_4237','s_1275','prot_Q5BTY7','s_0803','s_4238'},'stoichCoeffList',[-1 -1 -1 2 1],'reversible',false); +model = addReaction(model,'newRxn5','metaboliteList',{'s_0362','s_0434','s_0529','prot_Q8ZKF6','s_0373','s_0423','s_0633'},'stoichCoeffList',[-1 -1 -1 -1/Kcat5 1 1 1],'reversible',false); +model = addReaction(model,'newRxn6','metaboliteList',{'s_4238','s_4442'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'newRxn7','metaboliteList',{'s_4442'},'stoichCoeffList',[-1],'reversible',false); +model = addReaction(model,'newRxn8','metaboliteList',{'prot_pool','prot_Q9ZPM3'},'stoichCoeffList',[-MW1 1],'reversible',false); +model = addReaction(model,'newRxn9','metaboliteList',{'prot_pool','prot_D5KXJ0'},'stoichCoeffList',[-MW2 1],'reversible',false); +model = addReaction(model,'newRxn10','metaboliteList',{'prot_pool','prot_Q5BTY7'},'stoichCoeffList',[-MW3 1],'reversible',false); +model = addReaction(model,'newRxn11','metaboliteList',{'prot_pool','prot_Q8ZKF6'},'stoichCoeffList',[-MW5 1],'reversible',false); +model = addReaction(model,'r_0558No1','metaboliteList',{'pmet_r_0558','prot_P12684','s_0028','s_0529','s_1207'},'stoichCoeffList',[-1 -1/Kcat6 1 1 2],'reversible',false); +model = addReaction(model,'r_0163No1','metaboliteList',{'s_0680','s_1198','prot_P00331','s_0359','s_0794','s_1203'},'stoichCoeffList',[-1 -1 -1/Kcat7 1 1 1],'reversible',false); +model = addReaction(model,'r_0173No1','metaboliteList',{'s_0359','s_0803','s_1207','prot_P54115','s_0362','s_0794','s_1212'},'stoichCoeffList',[-1 -1 -1 -1/Kcat8 1 2 1],'reversible',false); +model = addReaction(model,'r_0177No1','metaboliteList',{'s_0803','s_0850','s_1207','prot_P54115','s_0853','s_0794','s_1212'},'stoichCoeffList',[-1 -1 -1 -1/Kcat8 1 2 1],'reversible',false); +model = addReaction(model,'r_0766No3','metaboliteList',{'pmet_r_0766','prot_Q06892','s_0397','s_0799','s_1210'},'stoichCoeffList',[-1 -1/Kcat9 1 1 1],'reversible',false); +model = addReaction(model,'r_0772No3','metaboliteList',{'prot_Q06892','pmet_r_0772','s_0397','s_0799','s_1214'},'stoichCoeffList',[-1/Kcat10 -1 1 1 1],'reversible',false); +model = addReaction(model,'r_2344No1','metaboliteList',{'s_2808','s_2954','prot_P32567','s_2966','s_2967'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2345No1','metaboliteList',{'s_2808','s_2955','prot_P32567','s_2966','s_2968'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2346No1','metaboliteList',{'s_2808','s_2956','prot_P32567','s_2966','s_2969'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2347No1','metaboliteList',{'s_2808','s_2957','prot_P32567','s_2966','s_2970'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2348No1','metaboliteList',{'s_2808','s_2958','prot_P32567','s_2966','s_2971'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2349No1','metaboliteList',{'s_2808','s_2959','prot_P32567','s_2966','s_2972'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2350No1','metaboliteList',{'s_2808','s_2960','prot_P32567','s_2966','s_2973'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_2351No1','metaboliteList',{'s_2808','s_2961','prot_P32567','s_2966','s_2974'},'stoichCoeffList',[-1 -1 -1/Kcat11 1 1],'reversible',false); +model = addReaction(model,'r_0109No1','metaboliteList',{'s_0373','s_0434','s_0445','prot_P48445','prot_Q00955','s_0394','s_0794','s_1101','s_1322'},'stoichCoeffList',[-1 -1 -1 -1/450000/3600 -1/Kcat12 1 1 1 1],'reversible',false); +model = addReaction(model,'r_2182No1','metaboliteList',{'s_2783','s_2789','s_2817','s_2818','prot_P21147','s_2808','s_2819','s_2820'},'stoichCoeffList',[-1 -1 -1 -1 -1/Kcat13 2 1 1],'reversible',false); +model = addReaction(model,'r_2183No1','metaboliteList',{'s_2783','s_2791','s_2817','s_2818','prot_P21147','s_2808','s_2821','s_2820'},'stoichCoeffList',[-1 -1 -1 -1 -1/Kcat14 2 1 1],'reversible',false); +model = removeGenes(model,'YBR020W'); % delete GAL1 +model = removeGenes(model,'YBR018C'); % delete GAL7 +model = removeGenes(model,'YBR019C'); % delete GAL10 +model = removeGenes(model,'YLR300W'); % delete EXG1 +model=changeGeneAssociation(model,'newRxn1','crtE'); +model=changeGeneAssociation(model,'newRxn2','crtB'); +model=changeGeneAssociation(model,'newRxn3','crtI'); +model=changeGeneAssociation(model,'newRxn4','crtI'); +model=changeGeneAssociation(model,'newRxn5','ACS'); +model.geneShortNames(1124)={'crtE'}; +model.geneShortNames(1125)={'crtB'}; +model.geneShortNames(1126)={'crtI'}; +model.geneShortNames(1127)={'ACS'}; +model.enzymes(964)={'Q9ZPM3'}; +model.enzymes(965)={'D5KXJ0'}; +model.enzymes(966)={'Q5BTY7'}; +model.enzymes(967)={'Q8ZKF6'}; +model.enzGenes(964)={'crtE'}; +model.enzGenes(965)={'crtB'}; +model.enzGenes(966)={'crtI'}; +model.enzGenes(967)={'ACS'}; +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)=3; +cd ../../strain_design_ecYeast +c_sourceID = 'D-glucose exchange (reversible)'; +model = lychangeMedia_batch(model,c_sourceID,'YEP'); +model=changeRxnBounds(model,'r_1714_REV',1000,'u'); +model=changeRxnBounds(model,'r_2111',0.1,'l'); +model=changeObjective(model,'newRxn7'); +FBAsolution=optimizeCbModel(model) +cd ../result_ecYeast/ecModels +save ecLycopene.mat model diff --git a/strain_design_ecYeast/Strain_design_Amor.m b/strain_design_ecYeast/Strain_design_Amor.m new file mode 100644 index 0000000..61fc44b --- /dev/null +++ b/strain_design_ecYeast/Strain_design_Amor.m @@ -0,0 +1,152 @@ +% Pathway construction of Amorphadiene (Amor) in yeastGEM model + +% Add new reactions to the model +cd ../ComplementaryScripts +model = loadYeastModel; + +% Load stoichiometry data: +fid = fopen('../ComplementaryData/Amorphadiene_GEM/newpathway_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 properties data: +fid = fopen('../ComplementaryData/Amorphadiene_GEM/newpathway_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.GPR = rev{3}; +newrxn.rxnNames = rev{4}; +newrxn.rxnECNumbers = rev{5}; +newrxn.rxnKEGGID = rev{6}; +newrxn.rxnNotes = rev{7}; +newrxn.rxnMetaNetXID = newrxn.ID; +for i = 1:length(newrxn.rxnMetaNetXID) + if ~startsWith(newrxn.rxnMetaNetXID{i},'MNXR') + newrxn.rxnMetaNetXID{i} = ''; + end +end +newrxn.rxnMetaNetXID = regexprep(newrxn.rxnMetaNetXID,'_cv',''); +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/Amorphadiene_GEM/newpathway_newRxnMetAnnotation.tsv'); +newmet_annot = textscan(fid,'%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} = 'NOTES: added after the heterologous update'; + 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) + cd ../otherChanges + 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),... + 'geneRule',newrxn.GPR{i},... + 'checkDuplicate',1); + cd ../modelexpansion/ + [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) = 1; %reactions without gene but needed for modelling + model.rxnNotes{rxnIndex} = ['NOTES: heterologous pathway; ',newrxn.rxnNotes{i}]; +end + +% Set constraints of pathway +model=changeRxnBounds(model,'r_1714',-1000,'l'); % minimal glucose uptake rate +model=changeRxnBounds(model,'r_2111',0.1,'l'); % maximum growth rate +model=changeObjective(model,'r_4603'); % RxnID of new product's exchange reaction +model=changeRxnBounds(model,'r_0458',0,'u'); % delete GAL1 +model=changeRxnBounds(model,'r_0459',0,'u'); % delete GAL7 +model=changeRxnBounds(model,'r_1071',0,'l'); % delete GAL7 +model=changeRxnBounds(model,'r_1071',0,'u'); % delete GAL7 +model=changeRxnBounds(model,'r_1070',0,'u'); % delete GAL10 +model=changeRxnBounds(model,'r_1070',0,'l'); % delete GAL10 + +% Save model: +cd ../../result_ecYeast/ecModels +save Amor_GEM.mat model diff --git a/strain_design_ecYeast/Strain_design_FFAs.m b/strain_design_ecYeast/Strain_design_FFAs.m index 6ba11ac..55d8772 100644 --- a/strain_design_ecYeast/Strain_design_FFAs.m +++ b/strain_design_ecYeast/Strain_design_FFAs.m @@ -149,7 +149,7 @@ % Pathway construction of FFAs in ecYeast model -% Add new reactions of asp pathway to the model +% Add new reactions of FFA pathway to the model cd ../../../ModelFiles/mat load('ecYeastGEM_batch.mat'); model = ecModel_batch; diff --git a/strain_design_ecYeast/Untitled2.m b/strain_design_ecYeast/Untitled2.m new file mode 100644 index 0000000..0c00083 --- /dev/null +++ b/strain_design_ecYeast/Untitled2.m @@ -0,0 +1,45 @@ +Kcat1=115*3600; +MW1=27.249; +model = addReaction(model,'3HP_newRxn1','metaboliteList',{'s_0794','s_1212','s_4184','prot_P39831','s_1207','s_4207'},'stoichCoeffList',[-1 -1 -1 -1/Kcat1 1 1],'reversible',false); +model = addReaction(model,'3HP_newRxn7','metaboliteList',{'prot_pool','prot_P39831'},'stoichCoeffList',[-MW1 1],'reversible',false); +% Add rxns of gene bcere0029_32090 +model = addReaction(model,'3HP_newRxn4','metaboliteList',{'s_0441','s_1399','s_0955','s_4184'},'stoichCoeffList',[-1 -1 1 1],'reversible',false); +% Add rxns of gene A7U8C7 +Kcat2=7.03*3600; +MW2=61.24; +model = addReaction(model,'3HP_newRxn5','metaboliteList',{'s_0794','s_0973','prot_A7U8C7','s_0441','s_0456'},'stoichCoeffList',[-1 -1 -1/Kcat2 1 1],'reversible',false); +model = addReaction(model,'3HP_newRxn8','metaboliteList',{'prot_pool','prot_A7U8C7'},'stoichCoeffList',[-MW2 1],'reversible',false); +% Add rxns of gene YGR019Wly +Kcat3=0.1324*3600; +MW3=52.946; +model = addReaction(model,'3HP_newRxn6','metaboliteList',{'s_0180','s_0441','prot_P17649ly','s_0991','s_4184'},'stoichCoeffList',[-1 -1 -1/Kcat3 1 1],'reversible',false); +model = addReaction(model,'3HP_newRxn9','metaboliteList',{'prot_pool','prot_P17649ly'},'stoichCoeffList',[-MW3 1],'reversible',false); +% Add transport and exchange rxns of 3HP +model = addReaction(model,'3HP_newRxn2','metaboliteList',{'s_4207','s_4208'},'stoichCoeffList',[-1 1],'reversible',false); +model = addReaction(model,'3HP_newRxn3','metaboliteList',{'s_4208'},'stoichCoeffList',[-1],'reversible',false); + +% Add gene rules to the reaction +model=changeGeneAssociation(model,'3HP_newRxn1','fdyG'); +model=changeGeneAssociation(model,'3HP_newRxn4','bcere0029_32090'); +model=changeGeneAssociation(model,'3HP_newRxn5','A7U8C7'); +model=changeGeneAssociation(model,'3HP_newRxn6','YGR019Wly'); + +% Normalization of geneShortNames, metComps, enzymes, and enzGenes +model.geneShortNames(1128)={'fdyG'}; +model.geneShortNames(1129)={'bcere0029_32090'}; +model.geneShortNames(1130)={'A7U8C7'}; +model.geneShortNames(1131)={'YGR019Wly'}; + +model.metComps(4147)=1; +model.metComps(4148)=1; +model.metComps(4149)=1; +model.metComps(4150)=1; +model.metComps(4151)=3; + +model.enzymes(964)={'P39831'}; +model.enzymes(965)={'A7U8C7'}; +model.enzymes(966)={'P17649ly'}; + +model.enzGenes(964)={'fdyG'}; +model.enzGenes(965)={'A7U8C7'}; +model.enzGenes(966)={'YGR019Wly'}; diff --git a/strain_design_ecYeast/scripts_metEngFinders/lymetEng_TargetsFinder.m b/strain_design_ecYeast/scripts_metEngFinders/lymetEng_TargetsFinder.m index b9bc584..7b6d993 100644 --- a/strain_design_ecYeast/scripts_metEngFinders/lymetEng_TargetsFinder.m +++ b/strain_design_ecYeast/scripts_metEngFinders/lymetEng_TargetsFinder.m @@ -100,7 +100,7 @@ metList = [metList,'Growth']; Rows = ['WT_yields';model.genes]; ResultsTable = cell2table(resultsMat,'VariableNames',metList,'RowNames',Rows); -writetable(ResultsTable,['../../result_ecYeast/' filename],'WriteVariableNames',true,'WriteRowNames',true,'Delimiter','\t') +writetable(ResultsTable,['../../result_ecYeast/results_Findtargets' filename],'WriteVariableNames',true,'WriteRowNames',true,'Delimiter','\t') end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%