Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| γ-resorcylate degradation I Accession ID: BioCyc:META_PWY-7773 |
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Yoshida M, Oikawa T, Obata H, Abe K, Mihara H, Esaki N. Biochemical and genetic analysis of the gamma-resorcylate (2,6-dihydroxybenzoate) catabolic pathway in Rhizobium sp. strain MTP-10005: identification and functional analysis of its gene cluster. J Bacteriol. 2007 Mar;189(5):1573–81. PMID: 17158677; PMCID: PMC1855702.; Chapman PJ, Ribbons DW. Metabolism of resorcinylic compounds by bacteria: alternative pathways for resorcinol catabolism in Pseudomonas putida. J Bacteriol. 1976 Mar;125(3):985–98. doi: 10.1128/jb.125.3.985-998.1976. |
| L-threonine degradation III (to methylglyoxal) Accession ID: BioCyc:META_THRDLCTCAT-PWY |
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Epperly BR, Dekker EE. Inactivation of Escherichia coli L-threonine dehydrogenase by 2,3-butanedione. Evidence for a catalytically essential arginine residue. J Biol Chem. 1989 Nov 05;264(31):18296–301. PMID: 2681195.; Boylan SA, Dekker EE. L-threonine dehydrogenase. Purification and properties of the homogeneous enzyme from Escherichia coli K-12. Journal of Biological Chemistry. 1981 Feb;256(4):1809–15. doi: 10.1016/s0021-9258(19)69880-7.; Komatsubara S, Murata K, Kisumi M, Chibata I. Threonine degradation by Serratia marcescens. J Bacteriol. 1978 Aug;135(2):318–23. doi: 10.1128/jb.135.2.318-323.1978.; Higgins IJ, Turner JM, Willetts AJ. Enzyme mechanism of aminoacetone metabolism by micro-organisms. Nature. 1967 Aug 19;215(5103):887–8. doi: 10.1038/215887a0. PMID: 4292865. |
| urate conversion to allantoin I Accession ID: BioCyc:META_PWY-5691 |
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Raychaudhuri A, Tipton PA. Cloning and expression of the gene for soybean hydroxyisourate hydrolase. Localization and implications for function and mechanism. Plant Physiol. 2002 Dec;130(4):2061–8. PMID: 12481089; PMCID: PMC166717. |
| superpathway of ergosterol biosynthesis II Accession ID: BioCyc:META_PWY-7156 |
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Miller MB, Haubrich BA, Wang Q, Snell WJ, Nes WD. Evolutionarily conserved Delta(25(27))-olefin ergosterol biosynthesis pathway in the alga Chlamydomonas reinhardtii. J Lipid Res. 2012 Aug;53(8):1636–45. PMID: 22591742; PMCID: PMC3540834.; Schwender J, Gemünden C, Lichtenthaler HK. Chlorophyta exclusively use the 1-deoxyxylulose 5-phosphate/2-C-methylerythritol 4-phosphate pathway for the biosynthesis of isoprenoids. Planta. 2001 Feb;212(3):416–23. doi: 10.1007/s004250000409. PMID: 11289606. |
| urate conversion to allantoin II Accession ID: BioCyc:META_PWY-7394 |
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Michiel M, Perchat N, Perret A, Tricot S, Papeil A, Besnard M, de Berardinis V, Salanoubat M, Fischer C. Microbial urate catabolism: characterization of |
| L-isoleucine degradation I Accession ID: BioCyc:META_ILEUDEG-PWY |
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Søvik O. Mitochondrial 2-methylacetoacetyl-CoA thiolase deficiency: an inborn error of isoleucine and ketone body metabolism. J Inherit Metab Dis. 1993;16(1):46–54. doi: 10.1007/bf00711314. PMID: 8487503.; Conrad RS, Massey LK, Sokatch JR. |
| zymosterol biosynthesis Accession ID: BioCyc:META_PWY-6074 |
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Mo C, Valachovic M, Randall SK, Nickels JT, Bard M. Protein-protein interactions among C-4 demethylation enzymes involved in yeast sterol biosynthesis. Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):9739–44. PMID: 12119386; PMCID: PMC124998.; Parks LW, Casey WM. Physiological implications of sterol biosynthesis in yeast. Annu Rev Microbiol. 1995;49():95–116. doi: 10.1146/annurev.mi.49.100195.000523. PMID: 8561481. |
| icosapentaenoate biosynthesis IV (bacteria) Accession ID: BioCyc:META_PWY-7050 |
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Metz JG, Roessler P, Facciotti D, Levering C, Dittrich F, Lassner M, Valentine R, Lardizabal K, Domergue F, Yamada A, Yazawa K, Knauf V, Browse J. Production of polyunsaturated fatty acids by polyketide synthases in both prokaryotes and eukaryotes. Science. 2001 Jul 13;293(5528):290–3. doi: 10.1126/science.1059593. PMID: 11452122. |
| icosapentaenoate biosynthesis V (8-desaturase, lower eukaryotes) Accession ID: BioCyc:META_PWY-7602 |
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Wallis JG, Browse J. The Delta8-desaturase of Euglena gracilis: an alternate pathway for synthesis of 20-carbon polyunsaturated fatty acids. Arch Biochem Biophys. 1999 May 15;365(2):307–16. doi: 10.1006/abbi.1999.1167. PMID: 10328826. |
| protocatechuate degradation III (para-cleavage pathway) Accession ID: BioCyc:META_PWY-6336 |
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Marín M, Plumeier I, Pieper DH. Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway. J Bacteriol. 2012 Aug;194(15):3851–60. PMID: 22609919; PMCID: PMC3416551.; Kasai D, Fujinami T, Abe T, Mase K, Katayama Y, Fukuda M, Masai E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J Bacteriol. 2009 Nov;191(21):6758–68. PMID: 19717587; PMCID: PMC2795304.; Takenaka S, Sato T, Koshiya J, Murakami S, Aoki K. Gene cloning and characterization of a deaminase from the 4-amino-3-hydroxybenzoate-assimilating Bordetella sp. strain 10d. FEMS Microbiol Lett. 2009 Sep;298(1):93–8. doi: 10.1111/j.1574-6968.2009.01699.x. PMID: 19594622.; Crawford RL, Bromley JW, Perkins-Olson PE. Catabolism of protocatechuate by Bacillus macerans. Appl Environ Microbiol. 1979 Mar;37(3):614–8. doi: 10.1128/aem.37.3.614-618.1979. |
| adlupulone and adhumulone biosynthesis Accession ID: BioCyc:META_PWY-7857 |
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Li H, Ban Z, Qin H, Ma L, King AJ, Wang G. A heteromeric membrane-bound prenyltransferase complex from hop catalyzes three sequential aromatic prenylations in the bitter acid pathway. Plant Physiol. 2015 Mar;167(3):650–9. PMID: 25564559; PMCID: PMC4348772.; Paniego NB, Zuurbier KWM, Fung S, van der Heijden R, Scheffer JJC, Verpoorte R. Phlorisovalerophenone synthase, a novel polyketide synthase from hop (Humulus lupulus L.) cones. European Journal of Biochemistry. 1999 Jun;262(2):612–6. doi: 10.1046/j.1432-1327.1999.00444.x. |
| glyoxylate assimilation Accession ID: BioCyc:META_PWY-5744 |
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Zarzycki J, Brecht V, Müller M, Fuchs G. Identifying the missing steps of the autotrophic 3-hydroxypropionate CO 2 fixation cycle in Chloroflexus aurantiacus. Proc. Natl. Acad. Sci. U.S.A. 2009 Dec 15;106(50):21317–22. doi: 10.1073/pnas.0908356106.; Friedmann S, Alber BE, Fuchs G. Properties of Succinyl-Coenzyme A: |
| carbon disulfide oxidation I (anaerobic) Accession ID: BioCyc:META_PWY-1164 |
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Smeulders MJ, Barends TR, Pol A, Scherer A, Zandvoort MH, Udvarhelyi A, Khadem AF, Menzel A, Hermans J, Shoeman RL, Wessels HJ, van den Heuvel LP, Russ L, Schlichting I, Jetten MS, Op den Camp HJ. Evolution of a new enzyme for carbon disulphide conversion by an acidothermophilic archaeon. Nature. 2011 Oct 19;478(7369):412–6. doi: 10.1038/nature10464. PMID: 22012399. |
| β-alanine degradation I Accession ID: BioCyc:META_BETA-ALA-DEGRADATION-I-PWY |
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Kontani Y, Sakata SF, Matsuda K, Ohyama T, Sano K, Tamaki N. The mature size of rat 4-aminobutyrate aminotransferase is different in liver and brain. European Journal of Biochemistry. 1999 Aug 15;264(1):218–22. doi: 10.1046/j.1432-1327.1999.00612.x.; Harris RA, Popov KM, Kedishvili NY, Zhao Y, Shimomura Y, Robbins B, Crabb DW. Molecular cloning of the branched-chain alpha-keto acid dehydrogenase kinase and the CoA-dependent methylmalonate semialdehyde dehydrogenase. Adv Enzyme Regul. 1993;33():255–65. doi: 10.1016/0065-2571(93)90022-6. PMID: 8356911.; Goodwin GW, Rougraff PM, Davis EJ, Harris RA. Purification and characterization of methylmalonate-semialdehyde dehydrogenase from rat liver. Identity to malonate-semialdehyde dehydrogenase. J Biol Chem. 1989 Sep 05;264(25):14965–71. PMID: 2768248.; Fujimoto S, Mizutani N, Mizota C, Tamaki N. The level of ß-alanine aminotransferase activity in regenerating and differentiating rat liver. Biochimica et Biophysica Acta (BBA) - General Subjects. 1986 Jun;882(1):106–12. doi: 10.1016/0304-4165(86)90061-9.; Griffith OW. Beta-amino acids: mammalian metabolism and utility as alpha-amino acid analogues. Annu Rev Biochem. 1986;55():855–78. doi: 10.1146/annurev.bi.55.070186.004231. PMID: 3090932.; Stinson RA, Spencer MS. ß-Alanine aminotransferase(s) from a plant source. Biochemical and Biophysical Research Communications. 1969 Jan;34(1):120–7. doi: 10.1016/0006-291x(69)90537-3. |
| coelimycin P1 biosynthesis Accession ID: BioCyc:META_PWY-7880 |
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| catechol degradation to 2-hydroxypentadienoate II Accession ID: BioCyc:META_PWY-5419 |
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Marín M, Plumeier I, Pieper DH. Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway. J Bacteriol. 2012 Aug;194(15):3851–60. PMID: 22609919; PMCID: PMC3416551.; Sala-Trepat JM, Evans WC. The meta cleavage of catechol by Azotobacter species. 4-Oxalocrotonate pathway. Eur J Biochem. 1971 Jun 11;20(3):400–13. doi: 10.1111/j.1432-1033.1971.tb01406.x. PMID: 4325686. |
| L-ascorbate degradation I (bacterial, anaerobic) Accession ID: BioCyc:META_PWY0-301 |
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Zhang Z, Aboulwafa M, Smith MH, Saier, MH. The Ascorbate Transporter of Escherichia coli. J Bacteriol. 2003 Apr;185(7):2243–50. doi: 10.1128/jb.185.7.2243-2250.2003.; Yew WS, Gerlt JA. Utilization of |
| catechol degradation II (meta-cleavage pathway) Accession ID: BioCyc:META_PWY-5420 |
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Marín M, Plumeier I, Pieper DH. Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway. J Bacteriol. 2012 Aug;194(15):3851–60. PMID: 22609919; PMCID: PMC3416551.; Sala-Trepat JM, Evans WC. The meta cleavage of catechol by Azotobacter species. 4-Oxalocrotonate pathway. Eur J Biochem. 1971 Jun 11;20(3):400–13. doi: 10.1111/j.1432-1033.1971.tb01406.x. PMID: 4325686. |
| plumbagin biosynthesis Accession ID: BioCyc:META_PWY-6314 |
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Springob K, Samappito S, Jindaprasert A, Schmidt J, Page JE, De-Eknamkul W, Kutchan TM. A polyketide synthase of Plumbago indica that catalyzes the formation of hexaketide pyrones. The FEBS Journal. 2006 Dec 06;274(2):406–17. doi: 10.1111/j.1742-4658.2006.05588.x. |
| bacteriochlorophyll d biosynthesis Accession ID: BioCyc:META_PWY-7758 |
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Harada J, Teramura M, Mizoguchi T, Tsukatani Y, Yamamoto K, Tamiaki H. Stereochemical conversion of |