Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| ethanol degradation III Accession ID: BioCyc:META_PWY66-161 |
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Coon MJ, Koop DR. Alcohol-inducible cytochrome P-450 (P-450ALC). Arch Toxicol. 1987;60(1-3):16–21. doi: 10.1007/bf00296940. PMID: 3304205. |
| ethanol degradation IV Accession ID: BioCyc:META_PWY66-162 |
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| preQ0 biosynthesis Accession ID: BioCyc:META_PWY-6703 |
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McCarty RM, Somogyi Á, Lin G, Jacobsen NE, Bandarian V. The Deazapurine Biosynthetic Pathway Revealed: In Vitro Enzymatic Synthesis of PreQ0 from Guanosine 5'-Triphosphate in Four Steps. Biochemistry. 2009 Apr 17;48(18):3847–52. doi: 10.1021/bi900400e. |
| 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. |
| coenzyme M biosynthesis II Accession ID: BioCyc:META_PWY-6643 |
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Graham DE, Taylor SM, Wolf RZ, Namboori SC. Convergent evolution of coenzyme M biosynthesis in the Methanosarcinales: cysteate synthase evolved from an ancestral threonine synthase. Biochem J. 2009 Dec 10;424(3):467–78. doi: 10.1042/bj20090999. PMID: 19761441. |
| triethylamine degradation Accession ID: BioCyc:META_PWY-7085 |
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Cai T, Chen L, Ren Q, Cai S, Zhang J. The biodegradation pathway of triethylamine and its biodegradation by immobilized Arthrobacter protophormiae cells. J Hazard Mater. 2011 Feb 15;186(1):59–66. doi: 10.1016/j.jhazmat.2010.10.007. PMID: 21134717. |
| L-lysine degradation VII Accession ID: BioCyc:META_PWY-5311 |
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Lukasheva EV, Berezov TT. L-Lysine alpha-oxidase: physicochemical and biological properties. Biochemistry (Mosc). 2002 Oct;67(10):1152–8. doi: 10.1023/a:1020967408229. PMID: 12460113.; Kusakabe H, Kodama K, Kuninaka A, Yoshino H, Misono H, Soda K. A new antitumor enzyme, L-lysine alpha-oxidase from Trichoderma viride. Purification and enzymological properties. Journal of Biological Chemistry. 1980 Feb;255(3):976–81. doi: 10.1016/s0021-9258(19)86128-8. |
| γ-butyrobetaine degradation Accession ID: BioCyc:META_PWY-3621 |
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Lindstedt G, Lindstedt S, Midtvedt T, Tofft M. Inducible ?-Butyrobetaine-Degrading Enzymes in Pseudomonas Species AK 1. J Bacteriol. 1970 Mar;101(3):1094–5. doi: 10.1128/jb.101.3.1094-1095.1970. |
| abscisic acid biosynthesis Accession ID: BioCyc:META_PWY-695 |
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Schwartz SH, Qin X, Zeevaart JA. Elucidation of the indirect pathway of abscisic acid biosynthesis by mutants, genes, and enzymes. Plant Physiol. 2003 Apr;131(4):1591–601. PMID: 12692318; PMCID: PMC1540303.; Milborrow BV. The pathway of biosynthesis of abscisic acid in vascular plants: a review of the present state of knowledge of ABA biosynthesis. 2001 Jun 01;52(359):1145–64. doi: 10.1093/jexbot/52.359.1145. |
| dopamine degradation Accession ID: BioCyc:META_PWY6666-2 |
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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. |
| 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. |
| L-lysine degradation XI (mammalian) Accession ID: BioCyc:META_LYSINE-DEG1-PWY |
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Broquist HP. Lysine-pipecolic acid metabolic relationships in microbes and mammals. Annu Rev Nutr. 1991;11():435–48. doi: 10.1146/annurev.nu.11.070191.002251. PMID: 1909881. |
| L-lysine degradation I Accession ID: BioCyc:META_PWY0-461 |
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Takatsuka Y, Yamaguchi Y, Ono M, Kamio Y. Gene Cloning and Molecular Characterization of Lysine Decarboxylase from Selenomonas ruminantium Delineate Its Evolutionary Relationship to Ornithine Decarboxylases from Eukaryotes. J Bacteriol. 2000 Dec;182(23):6732–41. doi: 10.1128/jb.182.23.6732-6741.2000. |
| L-tyrosine degradation I Accession ID: BioCyc:META_TYRFUMCAT-PWY |
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Moran GR. 4-Hydroxyphenylpyruvate dioxygenase. Archives of Biochemistry and Biophysics. 2005 Jan;433(1):117–28. doi: 10.1016/j.abb.2004.08.015.; Arias-Barrau E, Olivera ER, Luengo JM, Ferna´ndez C, Gala´n B, Garci´a JL, Di´az E, Min~ambres B. The Homogentisate Pathway: a Central Catabolic Pathway Involved in the Degradation of |
| pyruvate fermentation to hexanol (engineered) Accession ID: BioCyc:META_PWY-6863 |
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Dekishima Y, Lan EI, Shen CR, Cho KM, Liao JC. Extending carbon chain length of 1-butanol pathway for 1-hexanol synthesis from glucose by engineered Escherichia coli. J Am Chem Soc. 2011 Aug 03;133(30):11399–401. doi: 10.1021/ja203814d. PMID: 21707101.; Inui H, Miyatake K, Nakano Y, Kitaoka S. Purification and some properties of short chain-length specific trans-2-enoyl-CoA reductase in mitochondria of Euglena gracilis. J Biochem. 1986 Oct;100(4):995–1000. doi: 10.1093/oxfordjournals.jbchem.a121813. PMID: 3102464. |
| valencene and 7-epi-α-selinene biosynthesis Accession ID: BioCyc:META_PWY-6291 |
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Lücker J, Bowen P, Bohlmann J. Vitis vinifera terpenoid cyclases: functional identification of two sesquiterpene synthase cDNAs encoding (+)-valencene synthase and (-)-germacrene D synthase and expression of mono- and sesquiterpene synthases in grapevine flowers and berries. Phytochemistry. 2004 Oct;65(19):2649–59. doi: 10.1016/j.phytochem.2004.08.017. PMID: 15464152. |
| limonene degradation I (D-limonene) Accession ID: BioCyc:META_PWY-5923 |
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van der Werf MJ, Swarts HJ, de Bont JAM. Rhodococcus erythropolis DCL14 Contains a Novel Degradation Pathway for Limonene. Appl Environ Microbiol. 1999 May;65(5):2092–102. doi: 10.1128/aem.65.5.2092-2102.1999. |
| limonene degradation II (L-limonene) Accession ID: BioCyc:META_PWY-5924 |
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van der Werf MJ, Swarts HJ, de Bont JAM. Rhodococcus erythropolis DCL14 Contains a Novel Degradation Pathway for Limonene. Appl Environ Microbiol. 1999 May;65(5):2092–102. doi: 10.1128/aem.65.5.2092-2102.1999. |
| L-tyrosine degradation IV (to 4-methylphenol) Accession ID: BioCyc:META_PWY-7514 |
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Blakley ER. The catabolism of |
| nivalenol biosynthesis Accession ID: BioCyc:META_PWY-7713 |
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Escrivá L, Font G, Manyes L. In vivo toxicity studies of fusarium mycotoxins in the last decade: a review. Food Chem Toxicol. 2015 Apr;78():185–206. doi: 10.1016/j.fct.2015.02.005. PMID: 25680507.; Wisecaver JH, Rokas A. Fungal metabolic gene clusters—caravans traveling across genomes and environments. Front. Microbiol. 2015 Mar 03;6(). doi: 10.3389/fmicb.2015.00161.; Shank RA, Foroud NA, Hazendonk P, Eudes F, Blackwell BA. Current and future experimental strategies for structural analysis of trichothecene mycotoxins--a prospectus. Toxins (Basel). 2011 Dec;3(12):1518–53. PMID: 22295175; PMCID: PMC3268455.; McCormick SP, Stanley AM, Stover NA, Alexander NJ. Trichothecenes: from simple to complex mycotoxins. Toxins (Basel). 2011 Jul;3(7):802–14. PMID: 22069741; PMCID: PMC3202860.; Alexander NJ, McCormick SP, Waalwijk C, van der Lee T, Proctor RH. The genetic basis for 3-ADON and 15-ADON trichothecene chemotypes in Fusarium. Fungal Genet Biol. 2011 May;48(5):485–95. doi: 10.1016/j.fgb.2011.01.003. PMID: 21216300.; Zhang H, Zhang Z, van der Lee T, Chen WQ, Xu J, Xu JS, Yang L, Yu D, Waalwijk C, Feng J. Population genetic analyses of Fusarium asiaticum populations from barley suggest a recent shift favoring 3ADON producers in southern China. Phytopathology. 2010 Apr;100(4):328–36. doi: 10.1094/phyto-100-4-0328. PMID: 20205536.; Proctor RH, McCormick SP, Alexander NJ, Desjardins AE. Evidence that a secondary metabolic biosynthetic gene cluster has grown by gene relocation during evolution of the filamentous fungus Fusarium. Molecular Microbiology. 2009 Nov 20;74(5):1128–42. doi: 10.1111/j.1365-2958.2009.06927.x.; Xu X, Nicholson P. Community Ecology of Fungal Pathogens Causing Wheat Head Blight. Annu. Rev. Phytopathol. 2009 Sep 01;47(1):83–103. doi: 10.1146/annurev-phyto-080508-081737.; Burlakoti RR, Ali S, Secor GA, Neate SM, McMullen MP, Adhikari TB. Comparative mycotoxin profiles of Gibberella zeae populations from barley, wheat, potatoes, and sugar beets. Appl Environ Microbiol. 2008 Nov;74(21):6513–20. PMID: 18791024; PMCID: PMC2576685.; Ward TJ, Clear RM, Rooney AP, O'Donnell K, Gaba D, Patrick S, Starkey DE, Gilbert J, Geiser DM, Nowicki TW. An adaptive evolutionary shift in Fusarium head blight pathogen populations is driving the rapid spread of more toxigenic Fusarium graminearum in North America. Fungal Genet Biol. 2008 Apr;45(4):473–84. doi: 10.1016/j.fgb.2007.10.003. PMID: 18035565.; Starkey DE, Ward TJ, Aoki T, Gale LR, Kistler HC, Geiser DM, Suga H, Tóth B, Varga J, O'Donnell K. Global molecular surveillance reveals novel Fusarium head blight species and trichothecene toxin diversity. Fungal Genet Biol. 2007 Nov;44(11):1191–204. doi: 10.1016/j.fgb.2007.03.001. PMID: 17451976.; McCormick SP, Alexander NJ, Proctor RH. Heterologous expression of two trichothecene P450 genes in Fusarium verticillioides. Can J Microbiol. 2006 Mar;52(3):220–6. doi: 10.1139/w05-124. PMID: 16604118.; Pestka JJ, Smolinski AT. Deoxynivalenol: Toxicology and Potential Effects on Humans. Journal of Toxicology and Environmental Health, Part B. 2005 Dec 14;8(1):39–69. doi: 10.1080/10937400590889458.; McCormick SP, Harris LJ, Alexander NJ, Ouellet T, Saparno A, Allard S, Desjardins AE. Tri1 in Fusarium graminearum Encodes a P450 Oxygenase. Appl Environ Microbiol. 2004 Apr;70(4):2044–51. doi: 10.1128/aem.70.4.2044-2051.2004.; Brown DW, Dyer RB, McCormick SP, Kendra DF, Plattner RD. Functional demarcation of the Fusarium core trichothecene gene cluster. Fungal Genet Biol. 2004 Apr;41(4):454–62. doi: 10.1016/j.fgb.2003.12.002. PMID: 14998528.; Kimura M, Tokai T, O'Donnell K, Ward TJ, Fujimura M, Hamamoto H, Shibata T, Yamaguchi I. The trichothecene biosynthesis gene cluster of Fusarium graminearum F15 contains a limited number of essential pathway genes and expressed non-essential genes. FEBS Lett. 2003 Mar 27;539(1-3):105–10. doi: 10.1016/s0014-5793(03)00208-4. PMID: 12650935.; Brown DW, McCormick SP, Alexander NJ, Proctor RH, Desjardins AE. Inactivation of a cytochrome P-450 is a determinant of trichothecene diversity in Fusarium species. Fungal Genet Biol. 2002 Aug;36(3):224–33. doi: 10.1016/s1087-1845(02)00021-x. PMID: 12135578.; Ward TJ, Bielawski JP, Kistler HC, Sullivan E, O'Donnell K. Ancestral polymorphism and adaptive evolution in the trichothecene mycotoxin gene cluster of phytopathogenic Fusarium. Proc. Natl. Acad. Sci. U.S.A. 2002 Jun 21;99(14):9278–83. doi: 10.1073/pnas.142307199.; Lee T, Han Y, Kim K, Yun S, Lee Y. Tri13 and Tri7 Determine Deoxynivalenol- and Nivalenol-Producing Chemotypes of Gibberella zeae. Appl Environ Microbiol. 2002 May;68(5):2148–54. doi: 10.1128/aem.68.5.2148-2154.2002.; Lee T, Oh D, Kim H, Lee J, Kim Y, Yun S, Lee Y. Identification of Deoxynivalenol- and Nivalenol-Producing Chemotypes of Gibberella zeae by Using PCR. Appl Environ Microbiol. 2001 Jul;67(7):2966–72. doi: 10.1128/aem.67.7.2966-2972.2001.; Brown DW, McCormick SP, Alexander NJ, Proctor RH, Desjardins AE. A genetic and biochemical approach to study trichothecene diversity in Fusarium sporotrichioides and Fusarium graminearum. Fungal Genet Biol. 2001 Mar;32(2):121–33. doi: 10.1006/fgbi.2001.1256. PMID: 11352533.; Windels CE. Economic and social impacts of fusarium head blight: changing farms and rural communities in the northern great plains. Phytopathology. 2000 Jan;90(1):17–21. doi: 10.1094/phyto.2000.90.1.17. PMID: 18944567.; Seo JA, Kim JC, Lee DH, Lee YW. Variation in 8-ketotrichothecenes and zearalenone production by Fusarium graminearum isolates from corn and barley in Korea. Mycopathologia. 1996 Apr;134(1):31–7. doi: 10.1007/bf00437050. PMID: 20882466.; Desjardins AE, Hohn TM, McCormick SP. Trichothecene biosynthesis in Fusarium species: chemistry, genetics, and significance. Microbiol Rev. 1993 Sep;57(3):595–604. doi: 10.1128/mr.57.3.595-604.1993.; Ryu JC, Ohtsubo K, Izumiyama N, Nakamura K, Tanaka T, Yamamura H, Ueno Y. The acute and chronic toxicities of nivalenol in mice. Fundam Appl Toxicol. 1988 Jul;11(1):38–47. doi: 10.1016/0272-0590(88)90268-0. PMID: 3209016.; Ueno Y, Hsieh DPH. The Toxicology of Mycotoxins. CRC Critical Reviews in Toxicology. 1985 Jan;14(2):99–132. doi: 10.3109/10408448509089851.; Grove JF, Mortimer PH. The cytotoxicity of some transformation products of diacetoxyscirpenol. Biochem Pharmacol. 1969 Jun;18(6):1473–8. doi: 10.1016/0006-2952(69)90261-5. PMID: 5816375. |