Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| trehalose biosynthesis I Accession ID: BioCyc:META_TRESYN-PWY |
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Argüelles JC. Physiological roles of trehalose in bacteria and yeasts: a comparative analysis. Arch Microbiol. 2000 Oct;174(4):217–24. doi: 10.1007/s002030000192. PMID: 11081789. |
| tetrapyrrole biosynthesis I (from glutamate) Accession ID: BioCyc:META_PWY-5188 |
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Warren MJ, Scott AI. Tetrapyrrole assembly and modification into the ligands of biologically functional cofactors. Trends Biochem Sci. 1990 Dec;15(12):486–91. doi: 10.1016/0968-0004(90)90304-t. PMID: 2077690. |
| superpathway of L-isoleucine biosynthesis I Accession ID: BioCyc:META_PWY-3001 |
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UMBARGER HE, BROWN B. Threonine deamination in Escherichia coli. I. D- and L-threonine deaminase activities of cell-free extracts. J Bacteriol. 1956 Apr;71(4):443–9. PMID: 13319259; PMCID: PMC357824. |
| methanogenesis from acetate Accession ID: BioCyc:META_METH-ACETATE-PWY |
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Deppenmeier U. The unique biochemistry of methanogenesis. Prog Nucleic Acid Res Mol Biol. 2002;71():223–83. doi: 10.1016/s0079-6603(02)71045-3. PMID: 12102556. |
| superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis Accession ID: BioCyc:ECO_PWY-7211 |
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| L-homoserine biosynthesis Accession ID: BioCyc:ECO_HOMOSERSYN-PWY |
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Chassagnole C, Raïs B, Quentin E, Fell DA, Mazat JP. An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem J. 2001 Jun 01;356(Pt 2):415–23. PMID: 11368768; PMCID: PMC1221852. |
| superpathway of chorismate metabolism Accession ID: BioCyc:ECO_ALL-CHORISMATE-PWY |
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| aspartate superpathway Accession ID: BioCyc:ECO_PWY0-781 |
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| superpathway of L-homoserine and L-methionine biosynthesis Accession ID: BioCyc:ECO_METSYN-PWY |
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| NAD/NADP-NADH/NADPH cytosolic interconversion Accession ID: BioCyc:YEAST_PWY-7268 |
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Gossmann TI, Ziegler M, Puntervoll P, de Figueiredo LF, Schuster S, Heiland I. NAD+ biosynthesis and salvage – a phylogenetic perspective. The FEBS Journal. 2012 Apr 04;279(18):3355–63. doi: 10.1111/j.1742-4658.2012.08559.x.; Lu S, Lin S. Phosphate-responsive Signaling Pathway Is a Novel Component of NAD+ Metabolism in Saccharomyces cerevisiae. Journal of Biological Chemistry. 2011 Apr;286(16):14271–81. doi: 10.1074/jbc.m110.217885.; Koch-Nolte F, Haag F, Guse AH, Lund F, Ziegler M. Emerging Roles of NAD + and Its Metabolites in Cell SignalingA report on the NAD2008 symposium, Hamburg, Germany, 14 to 17 September 2008. Sci. Signal. 2009 Feb 10;2(57). doi: 10.1126/scisignal.257mr1.; Bieganowski P, Seidle HF, Wojcik M, Brenner C. Synthetic Lethal and Biochemical Analyses of NAD and NADH Kinases in Saccharomyces cerevisiae Establish Separation of Cellular Functions. Journal of Biological Chemistry. 2006 Aug;281(32):22439–45. doi: 10.1074/jbc.m513919200.; Minard KI, McAlister-Henn L. Sources of NADPH in Yeast Vary with Carbon Source. Journal of Biological Chemistry. 2005 Dec;280(48):39890–6. doi: 10.1074/jbc.m509461200.; Shi F, Kawai S, Mori S, Kono E, Murata K. Identification of ATP-NADH kinase isozymes and their contribution to supply of NADP(H) in Saccharomyces cerevisiae. The FEBS Journal. 2005 Jun 24;272(13):3337–49. doi: 10.1111/j.1742-4658.2005.04749.x.; Contreras-Shannon V, Lin A, McCammon MT, McAlister-Henn L. Kinetic Properties and Metabolic Contributions of Yeast Mitochondrial and Cytosolic NADP+-specific Isocitrate Dehydrogenases. Journal of Biological Chemistry. 2005 Feb;280(6):4469–75. doi: 10.1074/jbc.m410140200.; Grabowska D, Chelstowska A. The ALD6 Gene Product Is Indispensable for Providing NADPH in Yeast Cells Lacking Glucose-6-phosphate Dehydrogenase Activity. Journal of Biological Chemistry. 2003 Apr;278(16):13984–8. doi: 10.1074/jbc.m210076200.; Minard KI, McAlister-Henn L. Antioxidant function of cytosolic sources of NADPH in yeast. Free Radic Biol Med. 2001 Sep 15;31(6):832–43. doi: 10.1016/s0891-5849(01)00666-9. PMID: 11557322.; Kawai S, Suzuki S, Mori S, Murata K. Molecular cloning and identification of UTR1 of a yeast Saccharomyces cerevisiae as a gene encoding an NAD kinase. FEMS Microbiol Lett. 2001 Jun 25;200(2):181–4. doi: 10.1111/j.1574-6968.2001.tb10712.x. PMID: 11425472.; Wang X, Mann CJ, Bai Y, Ni L, Weiner H. Molecular Cloning, Characterization, and Potential Roles of Cytosolic and Mitochondrial Aldehyde Dehydrogenases in Ethanol Metabolism in Saccharomyces cerevisiae. J Bacteriol. 1998 Feb 15;180(4):822–30. doi: 10.1128/jb.180.4.822-830.1998.; Meaden PG, Dickinson FM, Mifsud A, Tessier W, Westwater J, Bussey H, Midgley M. The ALD6 gene of Saccharomyces cerevisiae encodes a cytosolic, Mg(2+)-activated acetaldehyde dehydrogenase. Yeast. 1997 Nov;13(14):1319–27. doi: 10.1002/(sici)1097-0061(199711)13:14<1319::aid-yea183>3.0.co;2-t. PMID: 9392076.; Loftus TM, Hall LV, Anderson SL, McAlister-Henn L. Isolation, characterization, and disruption of the yeast gene encoding cytosolic NADP-specific isocitrate dehydrogenase. Biochemistry. 1994 Aug 16;33(32):9661–7. doi: 10.1021/bi00198a035. PMID: 8068643.; MARRES CAM, de VRIES S, GRIVELL LA. Isolation and inactivation of the nuclear gene encoding the rotenone-insensitive internal NADH: ubiquinone oxidoreductase of mitochondria from Saccharomyces cerevisiae. European Journal of Biochemistry. 1991 Feb;195(3):857–62. doi: 10.1111/j.1432-1033.1991.tb15775.x.; Nogae I, Johnston M. Isolation and characterization of the ZWF1 gene of Saccharomyces cerevisiae, encoding glucose-6-phosphate dehydrogenase. Gene. 1990 Dec 15;96(2):161–9. doi: 10.1016/0378-1119(90)90248-p. PMID: 2269430.; Bruinenberg PM. The NADP(H) redox couple in yeast metabolism. Antonie Van Leeuwenhoek. 1986;52(5):411–29. doi: 10.1007/bf00393469. PMID: 3789705. |
| Biosynthesis of Siderophore Group Nonribosomal Peptides Accession ID: PathBank:SMP0000783 |
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| D-Glutamine and D-Glutamate Metabolism Accession ID: PathBank:SMP0000792 |
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| Inner Membrane Transport Accession ID: PathBank:SMP0000808 |
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| L-Glutamate Metabolism Accession ID: PathBank:SMP0000811 |
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| Glycine Biosynthesis Accession ID: PathBank:SMP0000828 |
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| Isoleucine Biosynthesis Accession ID: PathBank:SMP0000838 |
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| Galactose Metabolism Accession ID: PathBank:SMP0000841 |
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| Glutathione Metabolism Accession ID: PathBank:SMP0000853 |
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| Peptidoglycan Biosynthesis I Accession ID: PathBank:SMP0000924 |
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| Porphyrin Metabolism Accession ID: PathBank:SMP0000953 |
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