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Yeast Cell Factory: Large-scale in silico strain design for enhanced production of +100 chemicals in S. cerevisiae

  • Brief Model Description:

This repository contains the data and scripts necessary for in silico strain design for enhanced production of +100 chemicals using an enzyme-constrained model of S. cerevisiae's metabolism.

  • KeyWords:

Category: Constraint-based methods; Utilisation: predictive simulation, in silico strain design; Field: cell factory in silico design; Metabolic engineering Model Source: yeast-GEM,ecYeastGEM; Taxonomy: Saccharomyces cerevisiae; Metabolic System: General Metabolism; enzyme constraints.

  • Last update: 2021-04-21

Product list:

Name Formula KEGG ID CHEBI ID Group class Gene target
(R,R)-2,3-butanediol C4H10O2 C03044 16982 native alcohol Link
2-phenylethanol C8H10O C05853 49000 native alcohol Link
glycerol C3H8O3 C00116 17754 native alcohol Link
isoamylol C5H12O C07328 15837 native alcohol Link
isobutanol C4H10O C14710 46645 native alcohol Link
choline C5H14NO C00114 15354 native alkaloid Link
hypoxanthine C5H4N4O C00262 17368 native alkaloid Link
xanthine C5H4N4O2 C00385 17712 native alkaloid Link
glutathione C10H17N3O6S C00051 16856 native amino acid Link
L-alanine C3H7NO2 C00041 16977 native amino acid Link
L-arginine C6H14N4O2 C00062 16467 native amino acid Link
L-asparagine C4H8N2O3 C00152 17196 native amino acid Link
L-aspartate C4H7NO4 C00049 17053 native amino acid Link
L-citrulline C6H13N3O3 C00327 16349 native amino acid Link
L-cysteine C3H7NO2S C00097 17561 native amino acid Link
L-glutamate C5H8NO4 C00025 29985 native amino acid Link
L-glutamine C5H10N2O3 C00064 18050 native amino acid Link
L-glycine C2H5NO2 C00037 15428 native amino acid Link
L-histidine C6H9N3O2 C00135 15971 native amino acid Link
L-homoserine C4H9NO3 C00263 15699 native amino acid Link
L-isoleucine C6H13NO2 C00407 17191 native amino acid Link
L-leucine C6H13NO2 C00123 15603 native amino acid Link
L-lysine C6H15N2O2 C00047 32551 native amino acid Link
L-methionine C5H11NO2S C00073 16643 native amino acid Link
L-phenylalanine C9H11NO2 C00079 17295 native amino acid Link
L-proline C5H9NO2 C00148 17203 native amino acid Link
L-serine C3H7NO3 C00065 17115 native amino acid Link
L-threonine C4H9NO3 C00188 16857 native amino acid Link
L-tryptophan C11H12N2O2 C00078 16828 native amino acid Link
L-tyrosine C9H11NO3 C00082 17895 native amino acid Link
L-valine C5H11NO2 C00183 16414 native amino acid Link
ornithine C5H13N2O2 C01602 46912 native amino acid Link
putrescine C4H14N2 C00134 326268 native bioamine Link
spermine C10H30N4 C00750 45725 native bioamine Link
Free fatty acids nan nan nan native fatty acids and lipids Link
laurate C12H23O2 C02679 18262 native fatty acids and lipids Link
oleate C18H34O2 C00712 16196 native fatty acids and lipids Link
palmitoleate C16H29O2 C08362 32372 native fatty acids and lipids Link
succinate C4H4O4 C00042 30031 native fatty acids and lipids Link
triacylglycerol C6H5O6R3 C00422 17855 native fatty acids and lipids Link
guanine C5H5N5O C00242 16235 native nucleic acid Link
thymidine C10H14N2O5 C00214 17748 native nucleic acid Link
(S)-lactate C3H6O3 C00186 16651 native organic acid Link
(S)-malate C4H6O5 C00149 15589 native organic acid Link
2-oxoglutarate C5H6O5 C00026 16810 native organic acid Link
acetate C2H4O2 C00033 15366 native organic acid Link
citrate C6H8O7 C00158 16947 native organic acid Link
fumarate C4H4O4 C00122 18012 native organic acid Link
glycolate C2H4O3 C00160 17497 native organic acid Link
hexanoate C6H12O2 C01585 17120 native organic acid Link
pyruvate C3H3O3 C00022 15361 native organic acid Link
acetaldehyde C2H4O C00084 15343 native other Link
urea CH4N2O C00086 16199 native other Link
ergosterol C28H44O C01694 16933 native other Link
L-phenylacetylcarbinol C9H10O2 nan nan heterologous alcohol Link
n-butanol C4H10O C06142 28885 heterologous alcohol Link
(S)-Reticuline C19H23NO4 C02105 16718 heterologous alkaloid Link
psilocybin C12H17N2O4P C07576 8614 heterologous alkaloid Link
Nicotianamine C12H21N3O6 C05324 17721 heterologous amino acid Link
4-hydroxymandelic C8H8O4 C11527 16388 heterologous aromatic Link
cinnamate C9H8O2 C00423 15669  heterologous aromatic Link
mandelic C8H8O3 C01984 17756 heterologous aromatic Link
p-coumaric acid C9H8O3 C00811 32374 heterologous aromatic Link
rosmarinate C18H16O8 C01850 50371 heterologous aromatic Link
Salidroside C14H20O7 C06046 9009 heterologous aromatic Link
Tyrosol C8H10O2 C06044 1879 heterologous aromatic Link
vanillinbetaglucoside nan nan nan heterologous aromatic Link
ARA C20H32O2 C00219  15843 heterologous fatty acids and lipids Link
DHA C22H32O2 C06429 28125 heterologous fatty acids and lipids Link
EPA C20H30O2 C06428 28364 heterologous fatty acids and lipids Link
docosanol C22H46O D03884 31000 heterologous alcohol Link
catechin C15H14O6 C06562 15600 heterologous flavonoid Link
genistein C15H10O5 C06563 28088 heterologous flavonoid Link
kaempferol C15H10O6 C05903 28499 heterologous flavonoid Link
naringenin C15H12O5 C00509 17846 heterologous flavonoid Link
quercetin C15H10O7 C00389 16243 heterologous flavonoid Link
astaxanthin C40H52O4 C08580 40968 heterologous terpene Link
betaxanthin C18H18N2O7 C08565 8341 heterologous terpene Link
_-carotene C40H56 C02094 17579 heterologous terpene Link
artemisinic acid C15H22O2 C20309 63749 heterologous terpene Link
3-hydroxypropanoate C3H6O3 C01013 16510 heterologous organic acid Link
3-hydroxypropanoate C3H6O3 C01013 16510 heterologous organic acid Link
Adipic acid C6H10O4 D08839  30832 heterologous organic acid Link
cis,cis-muconate C6H6O4 C02480 16508 heterologous organic acid Link
Itaconic acid C5H6O4 C00490 17240 heterologous organic acid Link
Ethylene C2H4 C06547 18153 heterologous other Link
1,3,5-trihydroxyxanthone C13H8O5 C10094 514 heterologous other Link
glucagon C153H225N43O49S C01501 5391 heterologous protein Link
Human Serum Albumin nan nan nan heterologous protein Link
hemoglobin nan C01708  5656 heterologous protein Link
lactase nan EC 3.2.1.23 nan heterologous protein Link
_-Amylase - EC 3.2.1.1 - heterologous protein Link
resveratrol C14H12O3 C03582 27881 heterologous other Link
alpha-Farnesene C15H24 C09665 10280 heterologous terpene Link
amorphadiene C15H24 C16028 52026 heterologous terpene Link
Geraniol C10H18O C01500 17447 heterologous terpene Link
Limonene C10H16 C06078 15384 heterologous terpene Link
linalool C10H18O C03985 17580 heterologous terpene Link
lupeol C30H50O C08628 6570 heterologous terpene Link
Oleanolic acid C30H48O3 C17148 37659 heterologous terpene Link
patchoulol C15H26O C19755 7940 heterologous terpene Link
protopanaxadiol C30H52O3 C20715  75950 heterologous terpene Link
Santalene C15H24 C19736 nan heterologous terpene Link
_-Amyrin C30H50O C08616 10352 heterologous terpene Link
_-ionone C13H20O C12287 32325 heterologous terpene Link

Installation

Required Software:

Dependencies - Recommended Software:

Installation Instructions

  • For users: Clone it from master in the Github repo, or just download the latest release.
  • For contributors: Fork it to your Github account, and create a new branch from devel.

Contributing

Contributions are always welcome! Please read the contributions guideline to get started.

Contributors