Pathways Knowlegdes
Necessitatibus eius consequatur ex aliquid fuga eum quidem sint consectetur velit
| Pathway | DOIs | Note |
|---|---|---|
| superpathway of tryptophan utilization Accession ID: BioCyc:HUMAN_PWY66-401 |
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| superpathway of melatonin degradation Accession ID: BioCyc:HUMAN_PWY-6402 |
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| methanol oxidation to formaldehyde IV Accession ID: BioCyc:META_PWY-5506 |
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Sakai Y, Tani Y. Cloning and sequencing of the alcohol oxidase-encoding gene (AOD1) from the formaldehyde-producing asporogeneous methylotrophic yeast, Candida boidinii S2. Gene. 1992 May 01;114(1):67–73. doi: 10.1016/0378-1119(92)90708-w. PMID: 1587486. |
| methanol oxidation to formaldehyde III Accession ID: BioCyc:META_PWY-6509 |
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Vonck J, Arfman N, De Vries GE, Van Beeumen J, Van Bruggen EF, Dijkhuizen L. Electron microscopic analysis and biochemical characterization of a novel methanol dehydrogenase from the thermotolerant Bacillus sp. C1. Journal of Biological Chemistry. 1991 Feb;266(6):3949–54. doi: 10.1016/s0021-9258(19)67885-3. |
| methanol oxidation to formaldehyde II Accession ID: BioCyc:META_PWY-6510 |
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Arfman N, Hektor HJ, Bystrykh LV, Govorukhina NI, Dijkhuizen L, Frank J. Properties of an NAD(H)-Containing Methanol Dehydrogenase and its Activator Protein from Bacillus methanolicus. European Journal of Biochemistry. 1997 Mar;244(2):426–33. doi: 10.1111/j.1432-1033.1997.00426.x. |
| paerucumarin biosynthesis Accession ID: BioCyc:META_PWY-7955 |
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Lin Y, Yan Y. Biosynthesis of caffeic acid in Escherichia coli using its endogenous hydroxylase complex. Microbial Cell Factories. 2012 Apr 04;11(1):42. doi: 10.1186/1475-2859-11-42.; Drake EJ, Gulick AM. Three-dimensional Structures of Pseudomonas aeruginosa PvcA and PvcB, Two Proteins Involved in the Synthesis of 2-Isocyano-6,7-dihydroxycoumarin. Journal of Molecular Biology. 2008 Dec;384(1):193–205. doi: 10.1016/j.jmb.2008.09.027. |
| proline betaine degradation Accession ID: BioCyc:META_P561-PWY |
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Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE. Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. mBio. 2014 Feb 11;5(1):e00933–13. PMID: 24520058; PMCID: PMC3950512.; Daughtry KD, Xiao Y, Stoner-Ma D, Cho E, Orville AM, Liu P, Allen KN. Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase. J Am Chem Soc. 2012 Feb 08;134(5):2823–34. PMID: 22224443; PMCID: PMC5718839.; Burnet MW, Goldmann A, Message B, Drong R, El Amrani A, Loreau O, Slightom J, Tepfer D. The stachydrine catabolism region in Sinorhizobium meliloti encodes a multi-enzyme complex similar to the xenobiotic degrading systems in other bacteria. Gene. 2000 Feb 22;244(1-2):151–61. doi: 10.1016/s0378-1119(99)00554-5. PMID: 10689197. |
| 4-hydroxycoumarin and dicoumarol biosynthesis Accession ID: BioCyc:META_PWY-6418 |
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Liu B, Raeth T, Beuerle T, Beerhues L. A novel 4-hydroxycoumarin biosynthetic pathway. Plant Mol Biol. 2010 Jan;72(1-2):17–25. doi: 10.1007/s11103-009-9548-0. PMID: 19757094. |
| 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. |
| formaldehyde assimilation III (dihydroxyacetone cycle) Accession ID: BioCyc:META_P185-PWY |
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| dimethyl sulfide degradation II (oxidation) Accession ID: BioCyc:META_PWY-6059 |
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Wicht DK. The reduced flavin-dependent monooxygenase SfnG converts dimethylsulfone to methanesulfinate. Archives of Biochemistry and Biophysics. 2016 Aug;604():159–66. doi: 10.1016/j.abb.2016.07.001.; de Marco P, Moradas-Ferreira P, Higgins TP, McDonald I, Kenna EM, Murrell JC. Molecular Analysis of a Novel Methanesulfonic Acid Monooxygenase from the Methylotroph Methylosulfonomonas methylovora. J Bacteriol. 1999 Apr;181(7):2244–51. doi: 10.1128/jb.181.7.2244-2251.1999.; Higgins TP, Davey M, Trickett J, Kelly DP, Murrell JC. Metabolism of methanesulfonic acid involves a multicomponent monooxygenase enzyme. Microbiology (Reading). 1996 Feb;142 ( Pt 2)():251–60. doi: 10.1099/13500872-142-2-251. PMID: 8932698. |
| formaldehyde oxidation II (glutathione-dependent) Accession ID: BioCyc:META_PWY-1801 |
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Gonzalez CF, Proudfoot M, Brown G, Korniyenko Y, Mori H, Savchenko AV, Yakunin AF. Molecular basis of formaldehyde detoxification. Characterization of two S-formylglutathione hydrolases from Escherichia coli, FrmB and YeiG. J Biol Chem. 2006 May 19;281(20):14514–22. doi: 10.1074/jbc.m600996200. PMID: 16567800.; Gutheil WG, Holmquist B, Vallee BL. Purification, characterization, and partial sequence of the glutathione-dependent formaldehyde dehydrogenase from Escherichia coli: a class III alcohol dehydrogenase. Biochemistry. 1992 Jan 21;31(2):475–81. doi: 10.1021/bi00117a025. PMID: 1731906. |
| formaldehyde oxidation V (bacillithiol-dependent) Accession ID: BioCyc:META_PWY-7908 |
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Müller JEN, Meyer F, Litsanov B, Kiefer P, Vorholt JA. Core pathways operating during methylotrophy of |
| creatinine degradation I Accession ID: BioCyc:META_CRNFORCAT-PWY |
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Wyss M, Kaddurah-Daouk R. Creatine and Creatinine Metabolism. Physiological Reviews. 2000 Jul 01;80(3):1107–213. doi: 10.1152/physrev.2000.80.3.1107.; Nishiya Y, Toda A, Imanaka T. Gene cluster for creatinine degradation in Arthrobacter sp. TE1826. Molecular Genetics and Genomics. 1998 Mar;257(5):581–6. doi: 10.1007/s004380050685. |
| indole glucosinolate activation (herbivore attack) Accession ID: BioCyc:META_PWYQT-4476 |
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Kim JH, Lee BW, Schroeder FC, Jander G. Identification of indole glucosinolate breakdown products with antifeedant effects on Myzus persicae (green peach aphid). The Plant Journal. 2008 Mar 12;54(6):1015–26. doi: 10.1111/j.1365-313x.2008.03476.x. |
| colchicine biosynthesis Accession ID: BioCyc:META_PWY-5846 |
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| formaldehyde oxidation II (glutathione-dependent) Accession ID: BioCyc:ARA_PWY-1801 |
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van Vugt R, van Leeuwen HJ, Tjan DHT, Reusen-Bijsmans EM, van Zanten ARH, Kroeze J. Unexpected tracheal compression detected after immediate extubation failure. European Journal of Anaesthesiology. 2007 Mar;24(3):296–7. doi: 10.1017/s0265021506001438.; Kordic S, Cummins I, Edwards R. Cloning and Characterization of an S-Formylglutathione Hydrolase from Arabidopsis thaliana. Archives of Biochemistry and Biophysics. 2002 Mar;399(2):232–8. doi: 10.1006/abbi.2002.2772.; Martínez MC, Achkor H, Persson B, Fernández MR, Shafqat J, Farrés J, Jörnvall H, Parés X. Arabidopsis formaldehyde dehydrogenase. Molecular properties of plant class III alcohol dehydrogenase provide further insights into the origins, structure and function of plant class p and liver class I alcohol dehydrogenases. Eur J Biochem. 1996 Nov 01;241(3):849–57. doi: 10.1111/j.1432-1033.1996.00849.x. PMID: 8944774. |
| formaldehyde assimilation II (RuMP Cycle) Accession ID: BioCyc:TRYPANO_PWY-1861 |
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| formaldehyde assimilation II (RuMP Cycle) Accession ID: BioCyc:PLASMO_PWY-1861 |
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| formaldehyde oxidation I Accession ID: BioCyc:PLASMO_RUMP-PWY |
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