Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| ketogenesis Accession ID: BioCyc:HUMAN_PWY66-367 |
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Fukao T, Lopaschuk GD, Mitchell GA. Pathways and control of ketone body metabolism: on the fringe of lipid biochemistry. Prostaglandins Leukot Essent Fatty Acids. 2004 Mar;70(3):243–51. doi: 10.1016/j.plefa.2003.11.001. PMID: 14769483. |
| glutaryl-CoA degradation Accession ID: BioCyc:HUMAN_PWY-5177 |
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KOCH J, EISENREICH W, BACHER A, FUCHS G. Products of enzymatic reduction of benzoyl-CoA, a key reaction in anaerobic aromatic metabolism. European Journal of Biochemistry. 1993 Feb;211(3):649–61. doi: 10.1111/j.1432-1033.1993.tb17593.x. |
| tryptophan degradation Accession ID: BioCyc:HUMAN_TRYPTOPHAN-DEGRADATION-1 |
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| superpathway of tryptophan utilization Accession ID: BioCyc:HUMAN_PWY66-401 |
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| pyruvate fermentation to acetate I Accession ID: BioCyc:META_P142-PWY |
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Boynton ZL, Bennett GN, Rudolph FB. Cloning, sequencing, and expression of genes encoding phosphotransacetylase and acetate kinase from Clostridium acetobutylicum ATCC 824. Appl Environ Microbiol. 1996 Aug;62(8):2758–66. doi: 10.1128/aem.62.8.2758-2766.1996. |
| L-glutamate degradation V (via hydroxyglutarate) Accession ID: BioCyc:META_P162-PWY |
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Thorpe C, Kim JP. Structure and mechanism of action of the Acyl-CoA dehydrogenases 1. The FASEB Journal. 1995 Jun;9(9):718–25. doi: 10.1096/fasebj.9.9.7601336.; Schweiger G, Dutscho R, Buckel W. Purification of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. An iron-sulfur protein. Eur J Biochem. 1987 Dec 01;169(2):441–8. doi: 10.1111/j.1432-1033.1987.tb13631.x. PMID: 3691501.; Buckel W, Barker HA. Two Pathways of Glutamate Fermentation by Anaerobic Bacteria. J Bacteriol. 1974 Mar;117(3):1248–60. doi: 10.1128/jb.117.3.1248-1260.1974.; Hauge JG, Crane FL, Beinert H. ON THE MECHANISM OF DEHYDROGENATION OF FATTY ACYL DERIVATIVES OF COENZYME A. Journal of Biological Chemistry. 1956 Apr;219(2):727–33. doi: 10.1016/s0021-9258(18)65732-1.; Green DE, Mii S, Mahler HR, Bock RM. STUDIES ON THE FATTY ACID OXIDIZING SYSTEM OF ANIMAL TISSUES. Journal of Biological Chemistry. 1954 Jan;206(1):1–12. doi: 10.1016/s0021-9258(18)71290-8.; MAHLER HR. Studies on the fatty acid oxidizing system of animal tissues. IV. The prosthetic group of butyryl coenzyme A dehydrogenase. J Biol Chem. 1954 Jan;206(1):13–26. PMID: 13130522. |
| L-lysine fermentation to acetate and butanoate Accession ID: BioCyc:META_P163-PWY |
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Tang KH, Harms A, Frey PA. Identification of a novel pyridoxal 5'-phosphate binding site in adenosylcobalamin-dependent lysine 5,6-aminomutase from Porphyromonas gingivalis. Biochemistry. 2002 Jul 09;41(27):8767–76. doi: 10.1021/bi020255k. PMID: 12093296.; Mechichi T, Fardeau ML, Labat M, Garcia JL, Verhé F, Patel BK. Clostridium peptidivorans sp. nov., a peptide-fermenting bacterium from an olive mill wastewater treatment digester. Int J Syst Evol Microbiol. 2000 May;50 Pt 3():1259–64. doi: 10.1099/00207713-50-3-1259. PMID: 10843071.; Ruzicka FJ, Lieder KW, Frey PA. Lysine 2,3-Aminomutase from Clostridium subterminale SB4: Mass Spectral Characterization of Cyanogen Bromide-Treated Peptides and Cloning, Sequencing, and Expression of the Gene kamA in Escherichia coli. J Bacteriol. 2000 Jan 15;182(2):469–76. doi: 10.1128/jb.182.2.469-476.2000.; Thorpe C, Kim JP. Structure and mechanism of action of the Acyl-CoA dehydrogenases 1. The FASEB Journal. 1995 Jun;9(9):718–25. doi: 10.1096/fasebj.9.9.7601336.; Barker HA, Kahn JM, Hedrick L. Pathway of lysine degradation in Fusobacterium nucleatum. J Bacteriol. 1982 Oct;152(1):201–7. doi: 10.1128/jb.152.1.201-207.1982.; Baker JJ, van der Drift C, Stadtman TC. Purification and properties of -lysine mutase, a pyridoxal phosphate and B 12 coenzyme dependent enzyme. Biochemistry. 1973 Mar 13;12(6):1054–63. doi: 10.1021/bi00730a006. PMID: 4540127.; Chirpich TP, Zappia V, Costilow RN, Barker HA. Lysine 2,3-aminomutase. Purification and properties of a pyridoxal phosphate and S-adenosylmethionine-activated enzyme. J Biol Chem. 1970 Apr 10;245(7):1778–89. PMID: 5438361.; Rimerman EA, Barker HA. Formation and Identification of 3-Keto-5-aminohexanoic Acid, a Probable Intermediate in Lysine Fermentation. Journal of Biological Chemistry. 1968 Dec;243(23):6151–60. doi: 10.1016/s0021-9258(18)94472-8.; Costilow RN, Rochovansky OM, Barker HA. Isolation and Identification of ß-Lysine as an Intermediate in Lysine Fermentation. Journal of Biological Chemistry. 1966 Apr;241(7):1573–80. doi: 10.1016/s0021-9258(18)96751-7.; Hauge JG, Crane FL, Beinert H. ON THE MECHANISM OF DEHYDROGENATION OF FATTY ACYL DERIVATIVES OF COENZYME A. Journal of Biological Chemistry. 1956 Apr;219(2):727–33. doi: 10.1016/s0021-9258(18)65732-1.; Green DE, Mii S, Mahler HR, Bock RM. STUDIES ON THE FATTY ACID OXIDIZING SYSTEM OF ANIMAL TISSUES. Journal of Biological Chemistry. 1954 Jan;206(1):1–12. doi: 10.1016/s0021-9258(18)71290-8.; MAHLER HR. Studies on the fatty acid oxidizing system of animal tissues. IV. The prosthetic group of butyryl coenzyme A dehydrogenase. J Biol Chem. 1954 Jan;206(1):13–26. PMID: 13130522. |
| anaerobic energy metabolism (invertebrates, mitochondrial) Accession ID: BioCyc:META_PWY-7384 |
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Müller M, Mentel M, van Hellemond JJ, Henze K, Woehle C, Gould SB, Yu R, van der Giezen M, Tielens AGM, Martin WF. Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes. Microbiol Mol Biol Rev. 2012 Jun;76(2):444–95. doi: 10.1128/mmbr.05024-11.; Tielens AG, Rotte C, van Hellemond JJ, Martin W. Mitochondria as we don't know them. Trends Biochem Sci. 2002 Nov;27(11):564–72. doi: 10.1016/s0968-0004(02)02193-x. PMID: 12417132.; Van Hellemond JJ, Klockiewicz M, Gaasenbeek CPH, Roos MH, Tielens AGM. Rhodoquinone and Complex II of the Electron Transport Chain in Anaerobically Functioning Eukaryotes. Journal of Biological Chemistry. 1995 Dec;270(52):31065–70. doi: 10.1074/jbc.270.52.31065.; Grieshaber MK, Hardewig I, Kreutzer U, Pörtner HO. Physiological and metabolic responses to hypoxia in invertebrates. Rev Physiol Biochem Pharmacol. 1994;125():43–147. doi: 10.1007/bfb0030909. PMID: 7984874.; Campbell T, Rubin N, Komuniecki R. Succinate-dependent energy generation in Ascaris suum mitochondria. Molecular and Biochemical Parasitology. 1989 Feb;33(1):1–12. doi: 10.1016/0166-6851(89)90036-4.; Saz HJ, Pietrzak SM. Phosphorylation associated with succinate decarboxylation to propionate in Ascaris mitochondria. Archives of Biochemistry and Biophysics. 1980 Jul;202(2):388–95. doi: 10.1016/0003-9861(80)90442-7. |
| N10-formyl-tetrahydrofolate biosynthesis Accession ID: BioCyc:META_1CMET2-PWY |
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| folate transformations I Accession ID: BioCyc:META_PWY-2201 |
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| mevalonate pathway I Accession ID: BioCyc:META_PWY-922 |
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Zhong JJ, Yue CJ. Plant cells: secondary metabolite heterogeneity and its manipulation. Adv Biochem Eng Biotechnol. 2005;100():53–88. doi: 10.1007/b136412. PMID: 16270656.; KUZUYAMA T. Mevalonate and Nonmevalonate Pathways for the Biosynthesis of Isoprene Units. Bioscience, Biotechnology, and Biochemistry. 2002 Jan 01;66(8):1619–27. doi: 10.1271/bbb.66.1619.; Daum G, Lees ND, Bard M, Dickson R. Biochemistry, cell biology and molecular biology of lipids of Saccharomyces cerevisiae. Yeast. 1998 Dec;14(16):1471–510. doi: 10.1002/(sici)1097-0061(199812)14:16<1471::aid-yea353>3.0.co;2-y. PMID: 9885152. |
| superpathway of chorismate metabolism Accession ID: BioCyc:META_ALL-CHORISMATE-PWY |
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Keating TA, Marshall CG, Walsh CT. Reconstitution and characterization of the Vibrio cholerae vibriobactin synthetase from VibB, VibE, VibF, and VibH. Biochemistry. 2000 Dec 19;39(50):15522–30. doi: 10.1021/bi0016523. PMID: 11112538. |
| aspartate superpathway Accession ID: BioCyc:META_PWY0-781 |
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Devenish SR, Blunt JW, Gerrard JA. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J Med Chem. 2010 Jun 24;53(12):4808–12. doi: 10.1021/jm100349s. PMID: 20503968.; 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.; Begley TP, Kinsland C, Mehl RA, Osterman A, Dorrestein P. The biosynthesis of nicotinamide adenine dinucleotides in bacteria. Vitam Horm. 2001;61():103–19. doi: 10.1016/s0083-6729(01)61003-3. PMID: 11153263.; Soda K. Microbial sulfur amino acids: an overview. Methods Enzymol. 1987;143():453–9. doi: 10.1016/0076-6879(87)43080-2. PMID: 3309561.; POWELL JT, MORRISON JF. The Purification and Properties of the Aspartate Aminotransferase and Aromatic-Amino-Acid Aminotransferase from Escherichia coli. European Journal of Biochemistry. 1978 Jun;87(2):391–400. doi: 10.1111/j.1432-1033.1978.tb12388.x.; Farkas W, Gilvarg C. The Reduction Step in Diaminopimelic Acid Biosynthesis. Journal of Biological Chemistry. 1965 Dec;240(12):4717–22. doi: 10.1016/s0021-9258(18)97014-6.; Kindler SH, Gilvarg C. N-Succinyl-l-a, e-diaminopimelic Acid Deacylase. Journal of Biological Chemistry. 1960 Dec;235(12):3532–5. doi: 10.1016/s0021-9258(18)64502-8.; Cohen GN, Hirsch M. THREONINE SYNTHASE, A SYSTEM SYNTHESIZING |
| superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis Accession ID: BioCyc:META_PWY-7211 |
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Zrenner R, Stitt M, Sonnewald U, Boldt R. Pyrimidine and purine biosynthesis and degradation in plants. Annu Rev Plant Biol. 2006;57():805–36. doi: 10.1146/annurev.arplant.57.032905.105421. PMID: 16669783. |
| superpathway of tetrahydrofolate biosynthesis Accession ID: BioCyc:ECO_PWY-6612 |
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| pyrimidine deoxyribonucleotides de novo biosynthesis II Accession ID: BioCyc:ECO_PWY-7187 |
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| NAD/NADP-NADH/NADPH mitochondrial interconversion (yeast) Accession ID: BioCyc:YEAST_PWY-7269 |
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| superpathway of cholesterol biosynthesis Accession ID: BioCyc:HUMAN_PWY66-5 |
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| superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) Accession ID: BioCyc:HUMAN_PWY-5910 |
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| NAD/NADP-NADH/NADPH cytosolic interconversion (yeast) Accession ID: BioCyc:META_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. |