Pathways Knowlegdes
Necessitatibus eius consequatur ex aliquid fuga eum quidem sint consectetur velit
| Pathway | DOIs | Note |
|---|---|---|
| aromatic biogenic amine degradation (bacteria) Accession ID: BioCyc:META_PWY-7431 |
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Arcos M, Olivera ER, Arias S, Naharro G, Luengo JM. The 3,4-dihydroxyphenylacetic acid catabolon, a catabolic unit for degradation of biogenic amines tyramine and dopamine in Pseudomonas putida U. Environmental Microbiology. 2010 Jun;12(6):1684–704. doi: 10.1111/j.1462-2920.2010.02233.x.; Díaz E, Ferrández A, Prieto MA, García JL. Biodegradation of aromatic compounds by Escherichia coli. Microbiol Mol Biol Rev. 2001 Dec;65(4):523–69, table of contents. PMID: 11729263; PMCID: PMC99040.; Roh JH, Suzuki H, Azakami H, Yamashita M, Murooka Y, Kumagai H. Purification, Characterization, and Crystallization of Monoamine Oxidase fromEscherichia coliK-12. Bioscience, Biotechnology, and Biochemistry. 1994 Jan;58(9):1652–6. doi: 10.1271/bbb.58.1652.; Cuskey SM, Olsen RH. Catabolism of aromatic biogenic amines by Pseudomonas aeruginosa PAO1 via meta cleavage of homoprotocatechuic acid. J Bacteriol. 1988 Jan;170(1):393–9. doi: 10.1128/jb.170.1.393-399.1988.; Cuskey SM, Peccoraro V, Olsen RH. Initial catabolism of aromatic biogenic amines by Pseudomonas aeruginosa PAO: pathway description, mapping of mutations, and cloning of essential genes. J Bacteriol. 1987 Jun;169(6):2398–404. doi: 10.1128/jb.169.6.2398-2404.1987.; Kutty RK, Devi NA, Veeraswamy M, Ramesh S, Rao PV. Degradation of (+/-)-synephrine by Arthrobacter synephrinum. Oxidation of 3,4-dihydroxyphenylacetate to 2-hydroxy-5-carboxymethyl-muconate semialdehyde. Biochem J. 1977 Oct 01;167(1):163–70. PMID: 588248; PMCID: PMC1183633. |
| noradrenaline and adrenaline degradation Accession ID: BioCyc:META_PWY-6342 |
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Goldstein DS, Eisenhofer G, Kopin IJ. Clinical Catecholamine Neurochemistry: A Legacy of Julius Axelrod. Cellular and Molecular Neurobiology. 2006 Jul 27;26(4-6):693–700. doi: 10.1007/s10571-006-9041-0.; Eisenhofer G, Kopin IJ, Goldstein DS. Catecholamine metabolism: a contemporary view with implications for physiology and medicine. Pharmacol Rev. 2004 Sep;56(3):331–49. doi: 10.1124/pr.56.3.1. PMID: 15317907.; Goldstein DS, Eisenhofer G, Kopin IJ. Sources and Significance of Plasma Levels of Catechols and Their Metabolites in Humans. The Journal of Pharmacology and Experimental Therapeutics. 2003 Jun;305(3):800–11. doi: 10.1124/jpet.103.049270.; Kopin IJ, Axelrod J, Gordon E. The Metabolic Fate of H3-Epinephrine and C14-Metanephrine in the Rat. Journal of Biological Chemistry. 1961 Jul;236(7):2109–13. doi: 10.1016/s0021-9258(18)64137-7. |
| nicotine degradation II (pyrrolidine pathway) Accession ID: BioCyc:META_PWY-6993 |
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Tang H, Wang L, Meng X, Ma L, Wang S, He X, Wu G, Xu P. Novel nicotine oxidoreductase-encoding gene involved in nicotine degradation by Pseudomonas putida strain S16. Appl Environ Microbiol. 2009 Feb;75(3):772–8. PMID: 19060159; PMCID: PMC2632140.; Tang H, Wang S, Ma L, Meng X, Deng Z, Zhang D, Ma C, Xu P. A novel gene, encoding 6-hydroxy-3-succinoylpyridine hydroxylase, involved in nicotine degradation by Pseudomonas putida strain S16. Appl Environ Microbiol. 2008 Mar;74(5):1567–74. PMID: 18203859; PMCID: PMC2258644. |
| nicotine degradation IV Accession ID: BioCyc:META_PWY66-201 |
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Hukkanen J, Jacob P, Benowitz NL. Metabolism and disposition kinetics of nicotine. Pharmacol Rev. 2005 Mar;57(1):79–115. doi: 10.1124/pr.57.1.3. PMID: 15734728.; Meger M, Meger-Kossien I, Schuler-Metz A, Janket D, Scherer G. Simultaneous determination of nicotine and eight nicotine metabolites in urine of smokers using liquid chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2002 Oct 05;778(1-2):251–61. doi: 10.1016/s0378-4347(01)00451-0. PMID: 12376133.; Pankow JF. A consideration of the role of gas/particle partitioning in the deposition of nicotine and other tobacco smoke compounds in the respiratory tract. Chem Res Toxicol. 2001 Nov;14(11):1465–81. doi: 10.1021/tx0100901. PMID: 11712903.; Hecht SS, Hochalter JB, Villalta PW, Murphy SE. 2'-Hydroxylation of nicotine by cytochrome P450 2A6 and human liver microsomes: Formation of a lung carcinogen precursor. Proc. Natl. Acad. Sci. U.S.A. 2000 Oct 24;97(23):12493–7. doi: 10.1073/pnas.220207697.; Hecht SS, Carmella SG, Murphy SE. Effects of watercress consumption on urinary metabolites of nicotine in smokers. Cancer Epidemiol Biomarkers Prev. 1999 Oct;8(10):907–13. PMID: 10548320.; Rose JE, Behm FM, Westman EC, Coleman RE. Arterial nicotine kinetics during cigarette smoking and intravenous nicotine administration: implications for addiction. Drug Alcohol Depend. 1999 Sep 01;56(2):99–107. doi: 10.1016/s0376-8716(99)00025-3. PMID: 10482401.; Perry DC, Dávila-Garci´a MI, Stockmeier CA, Kellar KJ. Increased Nicotinic Receptors in Brains from Smokers: Membrane Binding and Autoradiography Studies. The Journal of Pharmacology and Experimental Therapeutics. 1999 Jun;289(3):1545–52. doi: 10.1016/s0022-3565(24)38304-1.; Jacob P, Yu L, Shulgin AT, Benowitz NL. Minor tobacco alkaloids as biomarkers for tobacco use: comparison of users of cigarettes, smokeless tobacco, cigars, and pipes. Am J Public Health. 1999 May;89(5):731–6. PMID: 10224986; PMCID: PMC1508721.; Hecht SS, Hatsukami DK, Bonilla LE, Hochalter JB. Quantitation of 4-oxo-4-(3-pyridyl)butanoic acid and enantiomers of 4-hydroxy-4-(3-pyridyl)butanoic acid in human urine: A substantial pathway of nicotine metabolism. Chem Res Toxicol. 1999 Feb;12(2):172–9. doi: 10.1021/tx980214i. PMID: 10027795.; Eldirdiri N, Ulgen M, Jacob P, Gorrod JW. The in vitro metabolism of norcotinine and related biotransformation products by microsomal preparations. European Journal of Drug Metabolism and Pharmacokinetics. 1997 Dec;22(4):385–90. doi: 10.1007/bf03190974.; Zevin S, Jacob P, Benowitz N. Cotinine effects on nicotine metabolism. Clinical Pharmacology & Therapeutics. 1997 Jun 19;61(6):649–54. doi: 10.1016/s0009-9236(97)90099-0.; Lunell E, Bergström M, Antoni G, Långström B, Nordberg A. Nicotine deposition and body distribution from a nicotine inhaler and a cigarette studied with positron emission tomography. Clinical Pharmacology & Therapeutics. 1996 May 20;59(5):593–4. doi: 10.1016/s0009-9236(96)90188-5.; Benowitz NL. Pharmacology of nicotine: addiction and therapeutics. Annu Rev Pharmacol Toxicol. 1996;36():597–613. doi: 10.1146/annurev.pa.36.040196.003121. PMID: 8725403.; Benowitz NL, Jacob P. Metabolism of nicotine to cotinine studied by a dual stable isotope method. Clinical Pharmacology & Therapeutics. 1994 Nov 09;56(5):483–93. doi: 10.1038/clpt.1994.169.; Benowitz NL, Jacob P, Fong I, Gupta S. Nicotine metabolic profile in man: comparison of cigarette smoking and transdermal nicotine. The Journal of Pharmacology and Experimental Therapeutics. 1994 Jan;268(1):296–303. doi: 10.1016/s0022-3565(25)38479-x.; Henningfield JE, Keenan RM. Nicotine delivery kinetics and abuse liability. Journal of Consulting and Clinical Psychology. 1993;61(5):743–50. doi: 10.1037//0022-006x.61.5.743.; Cashman JR, Park SB, Yang ZC, Wrighton SA, Jacob P, Benowitz NL. Metabolism of nicotine by human liver microsomes: stereoselective formation of trans-nicotine N'-oxide. Chem Res Toxicol. 1992 Sep;5(5):639–46. doi: 10.1021/tx00029a008. PMID: 1446003.; Byrd GD, Chang KM, Greene JM, deBethizy JD. Evidence for urinary excretion of glucuronide conjugates of nicotine, cotinine, and trans-3'-hydroxycotinine in smokers. Drug Metabolism and Disposition. 1992 Mar;20(2):192–7. doi: 10.1016/s0090-9556(25)08565-4.; Dwoskin LP, Leibee LL, Jewell AL, Fang ZX, Crooks PA. Inhibition of [3H]dopamine uptake into rat striatal slices by quaternary N-methylated nicotine metabolites. Life Sci. 1992;50(25):PL233–7. doi: 10.1016/0024-3205(92)90533-u. PMID: 1593921.; Kyerematen GA, Morgan ML, Chattopadhyay B, deBethizy JD, Vesell ES. Disposition of nicotine and eight metabolites in smokers and nonsmokers: identification in smokers of two metabolites that are longer lived than cotinine. Clin Pharmacol Ther. 1990 Dec;48(6):641–51. doi: 10.1038/clpt.1990.208. PMID: 2249376.; Benowitz NL. Drug therapy. Pharmacologic aspects of cigarette smoking and nicotine addiction. N Engl J Med. 1988 Nov 17;319(20):1318–30. doi: 10.1056/nejm198811173192005. PMID: 3054551.; Benowitz NL, Porchet H, Sheiner L, Jacob P. Nicotine absorption and cardiovascular effects with smokeless tobacco use: Comparison with cigarettes and nicotine gum. Clinical Pharmacology & Therapeutics. 1988 Jul 28;44(1):23–8. doi: 10.1038/clpt.1988.107.; Crooks PA, Godin CS. N-methylation of nicotine enantiomers by human liver cytosol. J Pharm Pharmacol. 1988 Feb;40(2):153–4. doi: 10.1111/j.2042-7158.1988.tb05207.x. PMID: 2897456.; Peterson LA, Trevor A, Castagnoli N. Stereochemical studies on the cytochrome P-450 catalyzed oxidation of (S)-nicotine to the (S)-nicotine delta 1'(5')-iminium species. J Med Chem. 1987 Feb;30(2):249–54. doi: 10.1021/jm00385a004. PMID: 3806608.; Neurath GB, Dünger M, Orth D, Pein FG. Trans-3'-hydroxycotinine as a main metabolite in urine of smokers. International Archives of Occupational and Environmental Health. 1987 Feb;59(2):199–201. doi: 10.1007/bf00378497.; Benowitz NL, Jacob P. Daily intake of nicotine during cigarette smoking. Clinical Pharmacology & Therapeutics. 1984 Apr 14;35(4):499–504. doi: 10.1038/clpt.1984.67.; Hibberd AR, Gorrod JW. Nicotine delta 1 '(5)' iminium ion: a reactive intermediate in nicotine metabolism. Adv Exp Med Biol. 1981;136 Pt B():1121–31. PMID: 6896399.; Nguyen TL, Gruenke LD, Castagnoli N. Metabolic oxidation of nicotine to chemically reactive intermediates. J Med Chem. 1979 Mar;22(3):259–63. doi: 10.1021/jm00189a008. PMID: 423207.; Murphy PJ. Enzymatic oxidation of nicotine to nicotine 1'(5') iminium ion. A newly discovered intermediate in the metabolism of nicotine. J Biol Chem. 1973 Apr 25;248(8):2796–800. PMID: 4144545.; Beckett AH, Gorrod JW, Jenner P. Absorption of (-)-nicotine-l-N-oxide in man and its reduction in the gastrointestinal tract. J Pharm Pharmacol. 1970 Sep;22(9):722–3. doi: 10.1111/j.2042-7158.1970.tb12767.x. PMID: 4394772.; McKennis H, Schwartz SL, Bowman ER. Alternate Routes in the Metabolic Degradation of the Pyrrolidine Ring of Nicotine. Journal of Biological Chemistry. 1964 Nov;239(11):3990–6. doi: 10.1016/s0021-9258(18)91232-9.; PAPADOPOULOS NM. FORMATION OF NORNICOTINE AND OTHER METABOLITES FROM NICOTINE IN VITRO AND IN VIVO. Can J Biochem. 1964 Apr;42():435–42. doi: 10.1139/o64-051. PMID: 14166990.; McKennis H, Turnbull LB, Bowman ER. N-Methylation of Nicotine and Cotinine in Vivo. Journal of Biological Chemistry. 1963 Feb;238(2):719–23. doi: 10.1016/s0021-9258(18)81325-4.; Bowman ER, McKennis H. STUDIES ON THE METABOLISM OF (-)-COTININE IN THE HUMAN. The Journal of Pharmacology and Experimental Therapeutics. 1962 Mar;135(3):306–11. doi: 10.1016/s0022-3565(25)26236-x.; WADA E, BOWMAN ER, TURNBULL LB, McKENNIS H. Norcotinine (desmethylcotinine) as a urinary metabolite of nornicotine. J Med Pharm Chem. 1961 Jul 01;4():21–30. doi: 10.1021/jm50017a002. PMID: 14004224. |
| glycine cleavage Accession ID: BioCyc:META_GLYCLEAV-PWY |
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Douce R, Bourguignon J, Neuburger M, Rébeillé F. The glycine decarboxylase system: a fascinating complex. Trends Plant Sci. 2001 Apr;6(4):167–76. doi: 10.1016/s1360-1385(01)01892-1. PMID: 11286922.; Perham RN. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu Rev Biochem. 2000;69():961–1004. doi: 10.1146/annurev.biochem.69.1.961. PMID: 10966480.; Fujiwara K, Okamura-Ikeda K, Motokawa Y. Mechanism of the glycine cleavage reaction. Further characterization of the intermediate attached to H-protein and of the reaction catalyzed by T-protein. Journal of Biological Chemistry. 1984 Sep;259(17):10664–8. doi: 10.1016/s0021-9258(18)90562-4.; Hiraga K, Kochi H, Hayasaka K, Kikuchi G, Nyhan WL. Defective glycine cleavage system in nonketotic hyperglycinemia. Occurrence of a less active glycine decarboxylase and an abnormal aminomethyl carrier protein. J Clin Invest. 1981 Aug;68(2):525–34. PMID: 6790577; PMCID: PMC370827.; MASSEY V, GIBSON QH, VEEGER C. Intermediates in the catalytic action of lipoyl dehydrogenase (diaphorase). Biochem J. 1960 Nov;77():341–51. PMID: 13767908; PMCID: PMC1204990.; SAVAGE N. Preparation and properties of highly purified diaphorase. Biochem J. 1957 Sep;67(1):146–55. PMID: 13471525; PMCID: PMC1200122.; Straub FB. Isolation and properties of a flavoprotein from heart muscle tissue. Biochem J. 1939 May;33(5):787–92. PMID: 16746974; PMCID: PMC1264446. |
| methanogenesis from dimethylamine Accession ID: BioCyc:META_PWY-5248 |
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Ferguson DJ, Gorlatova N, Grahame DA, Krzycki JA. Reconstitution of Dimethylamine:Coenzyme M Methyl Transfer with a Discrete Corrinoid Protein and Two Methyltransferases Purified fromMethanosarcina barkeri. Journal of Biological Chemistry. 2000 Sep;275(37):29053–60. doi: 10.1074/jbc.m910218199. |
| noradrenaline and adrenaline degradation Accession ID: BioCyc:THAPS_PWY-6342 |
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| glycine biosynthesis II Accession ID: BioCyc:META_GLYCINE-SYN2-PWY |
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Maaheimo H, Fiaux J, Çakar ZP, Bailey JE, Sauer U, Szyperski T. Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional 13C labeling of common amino acids. European Journal of Biochemistry. 2001 Apr 15;268(8):2464–79. doi: 10.1046/j.1432-1327.2001.02126.x.; Perham RN. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu Rev Biochem. 2000;69():961–1004. doi: 10.1146/annurev.biochem.69.1.961. PMID: 10966480.; Pasternack LB, Laude DA, Appling DR. 13C NMR detection of folate-mediated serine and glycine synthesis in vivo in Saccharomyces cerevisiae. Biochemistry. 1992 Sep 22;31(37):8713–9. doi: 10.1021/bi00152a005. PMID: 1390656.; Motokawa Y, Kikuchi G. Glycine metabolism by rat liver mitochondria. Isolation and some properties of the protein-bound intermediate of the reversible glycine cleavage reaction. Arch Biochem Biophys. 1974 Oct;164(2):634–40. doi: 10.1016/0003-9861(74)90075-7. PMID: 4460883.; Hiraga K, Kochi H, Motokawa Y, Kikuchi G. Enzyme complex nature of the reversible glycine cleavage system of cock liver mitochondria. J Biochem. 1972 Nov;72(5):1285–9. doi: 10.1093/oxfordjournals.jbchem.a130020. PMID: 4648867.; MASSEY V, GIBSON QH, VEEGER C. Intermediates in the catalytic action of lipoyl dehydrogenase (diaphorase). Biochem J. 1960 Nov;77():341–51. PMID: 13767908; PMCID: PMC1204990.; SAVAGE N. Preparation and properties of highly purified diaphorase. Biochem J. 1957 Sep;67(1):146–55. PMID: 13471525; PMCID: PMC1200122.; Straub FB. Isolation and properties of a flavoprotein from heart muscle tissue. Biochem J. 1939 May;33(5):787–92. PMID: 16746974; PMCID: PMC1264446. |
| superpathway of trimethylamine degradation Accession ID: BioCyc:META_PWY-6962 |
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Chen Y, Scanlan J, Song L, Crombie A, Rahman MT, Schäfer H, Murrell JC. {gamma}-Glutamylmethylamide is an essential intermediate in the metabolism of methylamine by Methylocella silvestris. Appl Environ Microbiol. 2010 Jul;76(13):4530–7. PMID: 20472738; PMCID: PMC2897447.; Large PJ. Non-oxidative demethylation of trimethylamine N-oxide by Pseudomonas aminovorans. FEBS Lett. 1971 Nov 01;18(2):297–300. doi: 10.1016/0014-5793(71)80470-2. PMID: 11946146. |
| trimethylamine degradation Accession ID: BioCyc:META_PWY-6968 |
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Chen Y, Patel NA, Crombie A, Scrivens JH, Murrell JC. Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase. Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17791–6. PMID: 22006322; PMCID: PMC3203794.; Large PJ. Non-oxidative demethylation of trimethylamine N-oxide by Pseudomonas aminovorans. FEBS Lett. 1971 Nov 01;18(2):297–300. doi: 10.1016/0014-5793(71)80470-2. PMID: 11946146. |
| N-methylpyrrolidone degradation Accession ID: BioCyc:META_PWY-7978 |
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Solís-González CJ, Domínguez-Malfavón L, Vargas-Suárez M, Gaytán I, Cevallos MÁ, Lozano L, Cruz-Gómez MJ, Loza-Tavera H. Novel Metabolic Pathway for N-Methylpyrrolidone Degradation in Alicycliphilus sp. Strain BQ1. Appl Environ Microbiol. 2018 Jan 01;84(1). PMID: 29030443; PMCID: PMC5734037. |
| creatinine degradation III Accession ID: BioCyc:META_PWY-4741 |
- | Eyk HG, van, Vermaat RJ, Leijnse-Ybema HJ, Leijnse B. The conversion of creatinine by creatininase of bacterial origin. Enzymologia. 1968 Mar;34(3):198–202. PMID: 5652018. |
| aromatic biogenic amine degradation (bacteria) Accession ID: BioCyc:ANTHRA_PWY-7431 |
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| methanol and methylamine oxidation to formaldehyde Accession ID: BioCyc:SCO_PWY-1701 |
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| superpathway of C1 compounds oxidation to CO2 Accession ID: BioCyc:MOB3B_PWY-1882 |
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Hanson RS, Hanson TE. Methanotrophic bacteria. Microbiol Rev. 1996 Jun;60(2):439–71. doi: 10.1128/mr.60.2.439-471.1996. |
| nicotine degradation III (VPP pathway) Accession ID: BioCyc:META_PWY-7128 |
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Yu H, Tang H, Zhu X, Li Y, Xu P. Molecular Mechanism of Nicotine Degradation by a Newly Isolated Strain, Ochrobactrum sp. Strain SJY1. Appl Environ Microbiol. 2015 Jan;81(1):272–81. doi: 10.1128/aem.02265-14.; Wang S, Huang H, Xie K, Xu P. Identification of nicotine biotransformation intermediates by Agrobacterium tumefaciens strain S33 suggests a novel nicotine degradation pathway. Applied Microbiology and Biotechnology. 2012 Apr 01;95(6):1567–78. doi: 10.1007/s00253-012-4007-2. |
| nicotine degradation I (pyridine pathway) Accession ID: BioCyc:META_P181-PWY |
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Cobzaru C, Ganas P, Mihasan M, Schleberger P, Brandsch R. Homologous gene clusters of nicotine catabolism, including a new ?-amidase for a-ketoglutaramate, in species of three genera of Gram-positive bacteria. Res Microbiol. 2011 Apr;162(3):285–91. doi: 10.1016/j.resmic.2011.01.001. PMID: 21288482.; Mihasan M, Chiribau C, Friedrich T, Artenie V, Brandsch R. An NAD(P)H-Nicotine Blue Oxidoreductase Is Part of the Nicotine Regulon and May Protect Arthrobacter nicotinovorans from Oxidative Stress during Nicotine Catabolism. Appl Environ Microbiol. 2007 Apr 15;73(8):2479–85. doi: 10.1128/aem.02668-06.; Gherna RL, Richardson SH, Rittenberg SC. The bacterial oxidation of nicotine. VI. The metabolism of 2,6-dihydroxypseudooxynicotine. J Biol Chem. 1965 Sep;240(9):3669–74. PMID: 5835946. |
| methylamine degradation II Accession ID: BioCyc:META_PWY-6965 |
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Chen Y, Scanlan J, Song L, Crombie A, Rahman MT, Schäfer H, Murrell JC. {gamma}-Glutamylmethylamide is an essential intermediate in the metabolism of methylamine by Methylocella silvestris. Appl Environ Microbiol. 2010 Jul;76(13):4530–7. PMID: 20472738; PMCID: PMC2897447. |
| methylamine degradation I Accession ID: BioCyc:META_PWY-6967 |
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Hanson RS, Hanson TE. Methanotrophic bacteria. Microbiol Rev. 1996 Jun;60(2):439–71. doi: 10.1128/mr.60.2.439-471.1996. |
| superpathway of C1 compounds oxidation to CO2 Accession ID: BioCyc:SCO_PWY-1882 |
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