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Genome Scale Metabolic model

Genome Scale Metabolic model
NameYeast8 v8.5.0
URLhttps://github.com/SysBioChalmers/yeast-GEM/releases/tag/v8.5.0
Associated publication
TitleA consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism.
JournalNat Commun
AuthorsLu H, Li F, Sánchez BJ, Zhu Z, Li G, Domenzain I, Marcišauskas S, Anton PM, Lappa D, Lieven C, Beber ME, Sonnenschein N, Kerkhoven EJ, Nielsen J
Date2019 Aug 8
Pubmedhttps://pubmed.ncbi.nlm.nih.gov/31395883/

 



Available media
Detailed description of each indicated media: "Synthetic Minimal medium" includes glucose and ammonia as sources of carbon and nitrogen, respectively, other essential elements and high oxygen availability; "Glucose-rich SC medium", SC standing for Synthetic Complete, includes glucose and ammonia as sources of carbon and nitrogen, respectively, all amino acids, other essential elements and low oxygen availability; RPMI stands for Roswell Park Memorial Institute 1640 medium, designed to mimic human serum composition. For each metabolite that could be added to the simulated growth medium, an exchange reaction code and name is provided, followed by the rate of metabolite uptake into the cell.
Note: The YEASTRACT+ team is available to include additional media options upon request by the users.
Reaction Name Uptake rate
Synthetic Minimal medium Glucose rich SC medium
r_1542 (1->3)-beta-D-glucan exchange 0.000 0.000
r_1545 (R)-carnitine exchange 0.000 0.000
r_1546 (R)-lactate exchange 0.000 0.000
r_1547 (R)-mevalonate exchange 0.000 0.000
r_1548 (R)-pantothenate exchange 0.000 -0.780
r_1549 (R,R)-2,3-butanediol exchange 0.000 0.000
r_1550 (S)-3-methyl-2-oxopentanoate exchange 0.000 0.000
r_1551 (S)-lactate exchange 0.000 0.000
r_1552 (S)-malate exchange 0.000 0.000
r_1553 1-(sn-glycero-3-phospho)-1D-myo-inositol exchange 0.000 0.000
r_1554 1-acylglycerophosphocholine exchange 0.000 0.000
r_1563 2'-deoxyadenosine exchange 0.000 0.000
r_1564 2'-deoxyguanosine exchange 0.000 0.000
r_1565 2'-deoxyinosine exchange 0.000 0.000
r_1566 2'-deoxyuridine exchange 0.000 0.000
r_1572 2-isopropylmalate exchange 0.000 0.000
r_1577 2-methylbutanal exchange 0.000 0.000
r_1580 2-methylbutanol exchange 0.000 0.000
r_1581 2-methylbutyl acetate exchange 0.000 0.000
r_1586 2-oxoglutarate exchange 0.000 0.000
r_1589 2-phenylethanol exchange 0.000 0.000
r_1598 3-methylbutanal exchange 0.000 0.000
r_1604 4-aminobenzoate exchange 0.000 -0.780
r_1621 5-aminolevulinate exchange 0.000 0.000
r_1625 5-formyltetrahydrofolic acid exchange 0.000 0.000
r_1627 7,8-diaminononanoate exchange 0.000 0.000
r_1629 8-amino-7-oxononanoate exchange 0.000 0.000
r_1630 9H-xanthine exchange 0.000 0.000
r_1631 acetaldehyde exchange 0.000 0.000
r_1634 acetate exchange 0.000 0.000
r_1639 adenine exchange 0.000 -0.780
r_1641 adenosine 3',5'-bismonophosphate exchange 0.000 0.000
r_1643 adenosine exchange 0.000 0.000
r_1648 allantoate exchange 0.000 0.000
r_1649 allantoin exchange 0.000 0.000
r_1650 trehalose exchange 0.000 0.000
r_1651 alpha-D-glucosamine 6-phosphate exchange 0.000 0.000
r_1654 ammonium exchange -1000.000 -1000.000
r_1663 bicarbonate exchange 0.000 0.000
r_1671 biotin exchange 0.000 -0.780
r_1672 carbon dioxide exchange 0.000 0.000
r_1683 choline exchange 0.000 0.000
r_1687 citrate exchange 0.000 -0.780
r_1702 cytidine exchange 0.000 0.000
r_1705 cytosine exchange 0.000 0.000
r_1706 D-arabinose exchange 0.000 0.000
r_1709 D-fructose exchange 0.000 0.000
r_1710 D-galactose exchange 0.000 0.000
r_1711 D-galacturonate exchange 0.000 0.000
r_1712 D-glucitol exchange 0.000 0.000
r_1714 D-glucose exchange -1.000 -80.000
r_1715 D-mannose exchange 0.000 0.000
r_1716 D-ribose exchange 0.000 0.000
r_1718 D-xylose exchange 0.000 0.000
r_1727 decanoate exchange 0.000 0.000
r_1730 deoxycytidine exchange 0.000 0.000
r_1749 dTTP exchange 0.000 0.000
r_1753 episterol exchange 0.000 0.000
r_1757 ergosterol exchange 0.000 0.000
r_1761 ethanol exchange 0.000 0.000
r_1764 ethanolamine exchange 0.000 0.000
r_1765 ethyl acetate exchange 0.000 0.000
r_1788 fecosterol exchange 0.000 0.000
r_1791 FMN exchange 0.000 0.000
r_1792 folic acid exchange 0.000 0.000
r_1793 formate exchange 0.000 0.000
r_1798 fumarate exchange 0.000 0.000
r_1800 gamma-aminobutyrate exchange 0.000 0.000
r_1806 glutathione disulfide exchange 0.000 0.000
r_1807 glutathione exchange 0.000 0.000
r_1808 glycerol exchange 0.000 0.000
r_1810 L-glycine exchange 0.000 -0.780
r_1814 glycolaldehyde exchange 0.000 0.000
r_1815 glyoxylate exchange 0.000 0.000
r_1818 guanine exchange 0.000 0.000
r_1820 guanosine exchange 0.000 0.000
r_1832 H+ exchange -1000.000 -1000.000
r_1834 hexadecanal exchange 0.000 0.000
r_1841 hypoxanthine exchange 0.000 0.000
r_1843 indol-3-ylacetaldehyde exchange 0.000 0.000
r_1847 inosine exchange 0.000 0.000
r_1861 iron(2+) exchange -1000.000 -1000.000
r_1862 isoamyl acetate exchange 0.000 0.000
r_1865 isoamylol exchange 0.000 0.000
r_1866 isobutanol exchange 0.000 0.000
r_1867 isobutyl acetate exchange 0.000 0.000
r_1870 isobutyraldehyde exchange 0.000 0.000
r_1873 L-alanine exchange 0.000 -0.100
r_1875 L-arabinitol exchange 0.000 0.000
r_1878 L-arabinose exchange 0.000 0.000
r_1879 L-arginine exchange 0.000 -0.310
r_1880 L-asparagine exchange 0.000 -0.360
r_1881 L-aspartate exchange 0.000 -0.720
r_1883 L-cysteine exchange 0.000 -0.780
r_1886 L-glucitol exchange 0.000 0.000
r_1889 L-glutamate exchange 0.000 -0.600
r_1891 L-glutamine exchange 0.000 -0.230
r_1893 L-histidine exchange 0.000 0.000
r_1896 L-homoserine exchange 0.000 0.000
r_1897 L-isoleucine exchange 0.000 -0.780
r_1899 L-leucine exchange 0.000 -0.780
r_1900 L-lysine exchange 0.000 -0.780
r_1902 L-methionine exchange 0.000 -0.780
r_1903 L-phenylalanine exchange 0.000 -0.780
r_1904 L-proline exchange 0.000 -0.780
r_1906 L-serine exchange 0.000 -0.470
r_1909 L-sorbose exchange 0.000 0.000
r_1911 L-threonine exchange 0.000 -0.780
r_1912 L-tryptophan exchange 0.000 -0.780
r_1913 L-tyrosine exchange 0.000 -0.130
r_1914 L-valine exchange 0.000 -0.780
r_1915 lanosterol exchange 0.000 0.000
r_1916 laurate exchange 0.000 0.000
r_1931 maltose exchange 0.000 0.000
r_1947 myo-inositol exchange 0.000 -0.780
r_1952 N,N'-diformyldityrosine exchange 0.000 0.000
r_1967 nicotinate exchange 0.000 -0.780
r_1968 NMN exchange 0.000 0.000
r_1984 octanoate exchange 0.000 0.000
r_1987 ornithine exchange 0.000 0.000
r_1989 oxaloacetate(2-) exchange 0.000 0.000
r_1992 oxygen exchange -1000.000 -2.000
r_1993 palmitate exchange 0.000 0.000
r_1994 palmitoleate exchange 0.000 0.000
r_1999 pectin exchange 0.000 0.000
r_2000 phenethyl acetate exchange 0.000 0.000
r_2001 phenylacetaldehyde exchange 0.000 0.000
r_2005 phosphate exchange -1000.000 -1000.000
r_2020 potassium exchange -1000.000 -1000.000
r_2024 putrescine exchange 0.000 0.000
r_2028 pyridoxine exchange 0.000 -0.780
r_2033 pyruvate exchange 0.000 0.000
r_2038 riboflavin exchange 0.000 -0.780
r_2043 S-adenosyl-L-methionine exchange 0.000 0.000
r_2044 S-methyl-L-methionine exchange 0.000 0.000
r_2046 sn-glycero-3-phosphocholine exchange 0.000 0.000
r_2049 sodium exchange -1000.000 -1000.000
r_2051 spermidine exchange 0.000 0.000
r_2052 spermine exchange 0.000 0.000
r_2055 stearate exchange 0.000 0.000
r_2056 succinate exchange 0.000 0.000
r_2058 sucrose exchange 0.000 0.000
r_2060 sulphate exchange -1000.000 -1000.000
r_2061 sulphite exchange 0.000 0.000
r_2062 taurine exchange 0.000 0.000
r_2066 thiamine(1+) diphosphate(1-) exchange 0.000 0.000
r_2067 thiamine(1+) exchange 0.000 0.000
r_2068 thiamine(1+) monophosphate exchange 0.000 0.000
r_2073 thymidine exchange 0.000 0.000
r_2083 tryptophol exchange 0.000 0.000
r_2090 uracil exchange 0.000 -0.780
r_2091 urea exchange 0.000 0.000
r_2092 uridine exchange 0.000 0.000
r_2100 water exchange -1000.000 -1000.000
r_2102 xanthosine exchange 0.000 0.000
r_2104 xylitol exchange 0.000 0.000
r_2106 zymosterol exchange 0.000 0.000
r_2111 growth 0.000 0.000
r_2134 14-demethyllanosterol exchange 0.000 0.000
r_2137 ergosta-5,7,22,24(28)-tetraen-3beta-ol exchange 0.000 0.000
r_2187 butyrate exchange 0.000 0.000
r_2188 hexanoate exchange 0.000 0.000
r_2189 oleate exchange 0.000 0.000
r_2193 myristate exchange 0.000 0.000
r_4043 raffinose exchange 0.000 0.000
r_4044 melibiose exchange 0.000 0.000
r_4062 lipid backbone exchange 0.000 0.000
r_4064 lipid chain exchange 0.000 0.000
r_4442 cysteamine exchange 0.000 0.000
r_4494 methanol exchange 0.000 0.000
r_4496 Ala-Gly exchange 0.000 0.000
r_4497 3-oxalomalate(3-) exchange 0.000 0.000
r_4498 6-O-alpha-D-glucopyranosyl-D-fructofuranose exchange 0.000 0.000
r_4499 5-dehydro-D-gluconate exchange 0.000 0.000
r_4500 D-tagatose exchange 0.000 0.000
r_4501 turanose exchange 0.000 0.000
r_4502 D-glucose 6-phosphate exchange 0.000 0.000
r_4503 alpha-maltotriose exchange 0.000 0.000
r_4504 D-glucose 1-phosphate exchange 0.000 0.000
r_4505 methyl alpha-D-glucopyranoside exchange 0.000 0.000
r_4506 D-Glucosamine exchange 0.000 0.000
r_4507 glycerone exchange 0.000 0.000
r_4508 Ala-Gln exchange 0.000 0.000
r_4509 Ala-Leu exchange 0.000 0.000
r_4510 Gly-Gln exchange 0.000 0.000
r_4511 Ala-His exchange 0.000 0.000
r_4512 Gly-Asn exchange 0.000 0.000
r_4513 Ala-Glu exchange 0.000 0.000
r_4514 Gly-Met exchange 0.000 0.000
r_4515 Ala-Asp exchange 0.000 0.000
r_4516 Gly-Glu exchange 0.000 0.000
r_4517 Ala-Thr exchange 0.000 0.000
r_4518 Met-Ala exchange 0.000 0.000
r_4519 L-citrulline exchange 0.000 0.000
r_4520 2-aminobutanoate exchange 0.000 0.000
r_4521 choline phosphate exchange 0.000 0.000
r_4522 glycerol 1-phosphate exchange 0.000 0.000
r_4523 2-phospho-D-glyceric acid exchange 0.000 0.000
r_4524 GMP exchange 0.000 0.000
r_4525 3-phospho-serine exchange 0.000 0.000
r_4526 O-phosphonatooxy-D-serine(2-) exchange 0.000 0.000
r_4527 diphosphate exchange 0.000 0.000
r_4528 triphosphate exchange 0.000 0.000
r_4529 phosphoenolpyruvate exchange 0.000 0.000
r_4530 N(omega)-phospho-L-arginine exchange 0.000 0.000
r_4531 carbamoyl phosphate exchange 0.000 0.000
r_4532 O-phosphoethanolamine exchange 0.000 0.000
r_4533 cysteamine S-phosphate exchange 0.000 0.000
r_4534 guanosine 2'-monophosphate exchange 0.000 0.000
r_4535 glycerol 2-phosphate(2-) exchange 0.000 0.000
r_4536 3'-GMP exchange 0.000 0.000
r_4537 2-phosphoglycolate exchange 0.000 0.000
r_4538 6-phospho-D-gluconate exchange 0.000 0.000
r_4539 D-mannose 6-phosphate exchange 0.000 0.000
r_4540 2',3'-cyclic GMP exchange 0.000 0.000
r_4541 O(4)-phospho-L-tyrosine exchange 0.000 0.000
r_4542 O-phospho-L-threonine exchange 0.000 0.000
r_4543 3-phosphonato-D-glycerate(3-) exchange 0.000 0.000
r_4544 adenosine 2'-phosphate exchange 0.000 0.000
r_4545 3'-AMP exchange 0.000 0.000
r_4546 2',3'-cyclic AMP exchange 0.000 0.000
r_4547 D-mannose 1-phosphate exchange 0.000 0.000
r_4548 AMP exchange 0.000 0.000
r_4549 N(alpha)-acetyl-L-methionine exchange 0.000 0.000
r_4550 L-Methionine S-oxide exchange 0.000 0.000
r_4551 3-sulfino-L-alanine exchange 0.000 0.000
r_4552 N-acetyl-L-cysteine exchange 0.000 0.000
r_4553 L-cysteate exchange 0.000 0.000
r_4554 2-hydroxyethane-1-sulfonate exchange 0.000 0.000
r_4555 acetoacetate exchange 0.000 0.000
r_4556 N-acetyl-L-glutamate exchange 0.000 0.000
r_4557 UMP exchange 0.000 0.000
r_4558 CMP exchange 0.000 0.000
r_4559 thymidine 5'-monophosphate exchange 0.000 0.000
r_4560 thymidine 3'-monophosphate exchange 0.000 0.000
r_4561 cytidine 2'-phosphate exchange 0.000 0.000
r_4562 uridine 2'-phosphate exchange 0.000 0.000
r_4563 3'-UMP exchange 0.000 0.000
r_4564 2',3'-cyclic CMP exchange 0.000 0.000
r_4565 2',3'-cyclic UMP exchange 0.000 0.000
r_4593 chloride exchange -1000.000 -1000.000
r_4594 Cu2(+) exchange -1000.000 -1000.000
r_4595 Mn(2+) exchange -1000.000 -1000.000
r_4596 Zn(2+) exchange -1000.000 -1000.000
r_4597 Mg(2+) exchange -1000.000 -1000.000
r_4600 Ca(2+) exchange -1000.000 -1000.000
r_4644 ethyl hexanoate exchange 0.000 0.000
r_4645 ethyl octanoate exchange 0.000 0.000
r_4646 ethyl butanoate exchange 0.000 0.000
r_4647 hexyl acetate exchange 0.000 0.000
r_4648 ethyl decanoate exchange 0.000 0.000
r_4658 propanal exchange 0.000 0.000
r_4659 propanol exchange 0.000 0.000
r_4667 methional exchange 0.000 0.000
r_4668 methionol exchange 0.000 0.000
r_4676 (4-hydroxyphenyl)acetaldehyde exchange 0.000 0.000
r_4677 tyrosol exchange 0.000 0.000
r_4689 tyrosyl acetate exchange 0.000 0.000
r_4692 methionyl acetate exchange 0.000 0.000
r_4695 propyl acetate exchange 0.000 0.000
r_4699 ethyl propionate exchange 0.000 0.000
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