Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| pentose phosphate pathway (oxidative branch) Accession ID: BioCyc:HUMAN_OXIDATIVEPENT-PWY |
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| 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. |
| thymine degradation Accession ID: BioCyc:HUMAN_PWY-6430 |
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Tsai CS, Axelrod B. Catabolism of Pyrimidines in Rape Seedlings. Plant Physiol. 1965 Jan;40(1):39–44. PMID: 16656066; PMCID: PMC550236.; Evans WR, Axelrod B. Pyrimidine metabolism in germinating seedlings. Plant Physiol. 1961 Jan;36(1):9–13. PMID: 16655478; PMCID: PMC406080. |
| 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. |
| inosine-5'-phosphate biosynthesis Accession ID: BioCyc:HUMAN_PWY-6124 |
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Zhao H, French JB, Fang Y, Benkovic SJ. The purinosome, a multi-protein complex involved in the de novo biosynthesis of purines in humans. Chem Commun (Camb). 2013 May 18;49(40):4444–52. PMID: 23575936; PMCID: PMC3877848. |
| eumelanin biosynthesis Accession ID: BioCyc:HUMAN_PWY-6498 |
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Munoz-Munoz JL, García-Molina F, Varón R, Tudela J, García-Cánovas F, Rodríguez-López JN. Generation of hydrogen peroxide in the melanin biosynthesis pathway. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 2009 Jul;1794(7):1017–29. doi: 10.1016/j.bbapap.2009.04.002.; Jiménez-Cervantes C, Solano F, Kobayashi T, Urabe K, Hearing VJ, Lozano JA, García-Borrón JC. A new enzymatic function in the melanogenic pathway. The 5,6-dihydroxyindole-2-carboxylic acid oxidase activity of tyrosinase-related protein-1 (TRP1). Journal of Biological Chemistry. 1994 Jul;269(27):17993–8000. doi: 10.1016/s0021-9258(17)32408-0. |
| isoleucine degradation Accession ID: BioCyc:HUMAN_ILEUDEG-PWY |
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Conrad RS, Massey LK, Sokatch JR. |
| lysine degradation II (pipecolate pathway) Accession ID: BioCyc:HUMAN_PWY66-425 |
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Struys EA, Jansen EEW, Salomons GS. Human pyrroline-5-carboxylate reductase (PYCR1) acts on ?1-piperideine-6-carboxylate generating L-pipecolic acid. J of Inher Metab Disea. 2014 Jan 16;37(3):327–32. doi: 10.1007/s10545-013-9673-4.; Hallen A, Jamie JF, Cooper AJL. Lysine metabolism in mammalian brain: an update on the importance of recent discoveries. Amino Acids. 2013 Sep 17;45(6):1249–72. doi: 10.1007/s00726-013-1590-1.; FUJII T, MUKAIHARA M, AGEMATU H, TSUNEKAWA H. Biotransformation of |
| tryptophan degradation Accession ID: BioCyc:HUMAN_TRYPTOPHAN-DEGRADATION-1 |
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| tryptophan degradation via tryptamine Accession ID: BioCyc:HUMAN_PWY-6307 |
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Yu A, Granvil CP, Haining RL, Krausz KW, Corchero J, Küpfer A, Idle JR, Gonzalez FJ. The Relative Contribution of Monoamine Oxidase and Cytochrome P450 Isozymes to the Metabolic Deamination of the Trace Amine Tryptamine. The Journal of Pharmacology and Experimental Therapeutics. 2003 Feb;304(2):539–46. doi: 10.1124/jpet.102.043786.; Mousseau DD. Tryptamine: a metabolite of tryptophan implicated in various neuropsychiatric disorders. Metab Brain Dis. 1993 Mar;8(1):1–44. doi: 10.1007/bf01000528. PMID: 8098507.; Susilo R, Höfle G, Rommelspacher H. Degradation of tryptamine in pig brain: Identification of a new condensation product. Biochemical and Biophysical Research Communications. 1987 Nov;148(3):1045–52. doi: 10.1016/s0006-291x(87)80237-1.; Yamada J, Sugimoto Y, Horisaka K. Determination of endogeneous indoleacetic acid and tryptophol in mouse brain by high performance liquid chromatography with fluorometric detection. Life Sci. 1983 Nov 14;33(20):2043–7. doi: 10.1016/0024-3205(83)90744-0. PMID: 6645790.; Jaeger CB, Teitelman G, Joh TH, Albert VR, Park DH, Reis DJ. Some neurons of the rat central nervous system contain aromatic-L-amino-acid decarboxylase but not monoamines. Science. 1983 Mar 11;219(4589):1233–5. doi: 10.1126/science.6131537. PMID: 6131537.; Young SN, Davis BA, Gauthier S. Precursors and metabolites of phenylethylamine, m and p-tyramine and tryptamine in human lumbar and cisternal cerebrospinal fluid. Journal of Neurology, Neurosurgery & Psychiatry. 1982 Jul 01;45(7):633–9. doi: 10.1136/jnnp.45.7.633.; Young SN, Gauthier S, Anderson GM, Purdy WC. Tryptophan, 5-hydroxyindoleacetic acid and indoleacetic acid in human cerebrospinal fluid: interrelationships and the influence of age, sex, epilepsy and anticonvulsant drugs. Journal of Neurology, Neurosurgery & Psychiatry. 1980 May 01;43(5):438–45. doi: 10.1136/jnnp.43.5.438. |
| superpathway of tryptophan utilization Accession ID: BioCyc:HUMAN_PWY66-401 |
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| arachidonate biosynthesis III (metazoa) Accession ID: BioCyc:HUMAN_PWY-7592 |
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| 7-(3-amino-3-carboxypropyl)-wyosine biosynthesis Accession ID: BioCyc:HUMAN_PWY-7286 |
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| spermidine biosynthesis Accession ID: BioCyc:HUMAN_BSUBPOLYAMSYN-PWY |
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Xiong H, Pegg AE. Mechanistic studies of the processing of human S-adenosylmethionine decarboxylase proenzyme. Isolation of an ester intermediate. J Biol Chem. 1999 Dec 03;274(49):35059–66. doi: 10.1074/jbc.274.49.35059. PMID: 10574985.; Kajander EO, Kauppinen LI, Pajula RL, Karkola K, Eloranta TO. Purification and partial characterization of human polyamine synthases. Biochem J. 1989 May 01;259(3):879–86. PMID: 2730590; PMCID: PMC1138598. |
| superpathway of methionine degradation Accession ID: BioCyc:HUMAN_PWY-5328 |
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| docosahexaenoate biosynthesis III (mammals) Accession ID: BioCyc:HUMAN_PWY-7606 |
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| UMP biosynthesis Accession ID: BioCyc:HUMAN_PWY-5686 |
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| secologanin and strictosidine biosynthesis Accession ID: BioCyc:META_PWY-5290 |
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Miettinen K, Dong L, Navrot N, Schneider T, Burlat V, Pollier J, Woittiez L, van der Krol S, Lugan R, Ilc T, Verpoorte R, Oksman-Caldentey K, Martinoia E, Bouwmeester H, Goossens A, Memelink J, Werck-Reichhart D. Erratum: Corrigendum: The seco-iridoid pathway from Catharanthus roseus. Nature Communications. 2014 Jun 24;5(1):4175. doi: 10.1038/ncomms5175.; Geu-Flores F, Sherden NH, Courdavault V, Burlat V, Glenn WS, Wu C, Nims E, Cui Y, O’Connor SE. An alternative route to cyclic terpenes by reductive cyclization in iridoid biosynthesis. Nature. 2012 Nov 21;492(7427):138–42. doi: 10.1038/nature11692. |
| polymethylated quercetin glucoside biosynthesis I - quercetin series (Chrysosplenium) Accession ID: BioCyc:META_PWY-7150 |
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Anzellotti D, Ibrahim RK. Molecular characterization and functional expression of flavonol 6-hydroxylase. BMC Plant Biol. 2004 Dec 13;4():20. PMID: 15596008; PMCID: PMC544895.; Seguin J, Muzac I, Ibrahim RK. Purification and immunological characterization of a recombinant trimethylflavonol 3'-O-methyltransferase. Phytochemistry. 1998 Sep;49(2):319–25. doi: 10.1016/s0031-9422(98)00138-1. PMID: 9747535.; Gauthier A, Gulick PJ, Ibrahim RK. cDNA cloning and characterization of a 3'/5'-O-methyltransferase for partially methylated flavonols from Chrysosplenium americanum. Plant Mol Biol. 1996 Dec;32(6):1163–9. doi: 10.1007/bf00041401. PMID: 9002616.; Latchinian-Sadek L, Ibrahim RK. Flavonol ring B-specific O-glucosyltransferases: Purification, production of polyclonal antibodies, and immunolocalization. Archives of Biochemistry and Biophysics. 1991 Aug;289(1):230–6. doi: 10.1016/0003-9861(91)90466-v.; Khouri HE, De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. III. Purification and kinetic analysis of S-adenosyl-L-methionine:3-methylquercetin 7-O-methyltransferase. Arch Biochem Biophys. 1988 Aug 15;265(1):1–7. doi: 10.1016/0003-9861(88)90364-5. PMID: 3415239.; De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. I. Partial purification and some properties of S-adenosyl-l-methionine: Flavonol 3-, 6-, 7-, and 4'-O-methyltransferases. Archives of Biochemistry and Biophysics. 1985 May;238(2):596–605. doi: 10.1016/0003-9861(85)90205-x.; De Luca V, Ibrahim RK. Enzymatic synthesis of polymethylated flavonols in Chrysosplenium americanum. II. Substrate interaction and product inhibition studies of flavonol 3-, 6-, and 4'-O-methyltransferases. Archives of Biochemistry and Biophysics. 1985 May;238(2):606–18. doi: 10.1016/0003-9861(85)90206-1.; KHOURI H, IBRAHIM RK. Kinetic mechanism of a flavonol-ring-B O-glucosyltransferase from Chrysosplenium americanum. European Journal of Biochemistry. 1984 Aug;142(3):559–64. doi: 10.1111/j.1432-1033.1984.tb08322.x.; Bajaj KL, de Luca V, Khouri H, Ibrahim RK. Purification and Properties of Flavonol-Ring B Glucosyltransferase from Chrysosplenium americanum. Plant Physiol. 1983 Jul 01;72(3):891–6. doi: 10.1104/pp.72.3.891. |
| nicotine biosynthesis Accession ID: BioCyc:META_PWY-5316 |
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Siminszky B, Gavilano L, Bowen SW, Dewey RE. Conversion of nicotine to nornicotine in Nicotiana tabacum is mediated by CYP82E4, a cytochrome P450 monooxygenase. Proc. Natl. Acad. Sci. U.S.A. 2005 Sep 28;102(41):14919–24. doi: 10.1073/pnas.0506581102.; Heim WG, Jelesko JG. Association of diamine oxidase and S-adenosylhomocysteine hydrolase in Nicotiana tabacum extracts. Plant Mol Biol. 2004 Sep;56(2):299–308. doi: 10.1007/s11103-004-3352-7. PMID: 15604745. |